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diff --git a/python/tests/files/23b29ea36382680716be08fc71aa81bd226e8a85.xml b/python/tests/files/23b29ea36382680716be08fc71aa81bd226e8a85.xml new file mode 100644 index 0000000..dbc8be5 --- /dev/null +++ b/python/tests/files/23b29ea36382680716be08fc71aa81bd226e8a85.xml @@ -0,0 +1,2004 @@ +<?xml version="1.0" encoding="UTF-8"?> +<TEI xmlns="http://www.tei-c.org/ns/1.0" +xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" +xsi:schemaLocation="http://www.tei-c.org/ns/1.0 /srv/grobid/grobid-0.5.1/grobid-home/schemas/xsd/Grobid.xsd" + xmlns:xlink="http://www.w3.org/1999/xlink"> + <teiHeader xml:lang="en"> + <encodingDesc> + <appInfo> + <application version="0.5.1-SNAPSHOT" ident="GROBID" when="2018-04-02T00:31+0000"> + <ref target="https://github.com/kermitt2/grobid">GROBID - A machine learning software for extracting information from scholarly documents</ref> + </application> + </appInfo> + </encodingDesc> + <fileDesc> + <titleStmt> + <title level="a" type="main">DYNAMICS OF RAILWAY FREIGHT VEHICLES</title> + </titleStmt> + <publicationStmt> + <publisher/> + <availability status="unknown"><licence/></availability> + <date type="published" when="2015">2015</date> + </publicationStmt> + <sourceDesc> + <biblStruct> + <analytic> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">S</forename><surname>Original Citation Iwnicki</surname></persName> + </author> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">S</forename><surname>Stichel</surname></persName> + </author> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">A</forename><surname>Orlova</surname></persName> + </author> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">M</forename><surname>Hecht</surname></persName> + </author> + <author> + <affiliation key="aff0"> + <orgName type="institution">University of Huddersfield Repository</orgName> + </affiliation> + </author> + <title level="a" type="main">DYNAMICS OF RAILWAY FREIGHT VEHICLES</title> + </analytic> + <monogr> + <title level="m">Dynamics of railway freight vehicles. Vehicle System Dynamics. pp. 139. ISSN 00423114</title> + <imprint> + <date type="published" when="2015">2015</date> + </imprint> + </monogr> + <note>Dynamics of railway freight vehicles</note> + </biblStruct> + </sourceDesc> + </fileDesc> + <profileDesc> + <textClass> + <keywords> + <term>Freight wagon</term> + <term>Vehicle dynamics</term> + <term>Computer simulation</term> + <term>Rail Freight</term> + <term>Running Gear Design</term> + <term>Freight Bogies</term> + </keywords> + </textClass> + <abstract> + <p>This paper summarises the historical development of railway freight vehicles and how vehicle designers have tackled the difficult challenges of producing running gear which can accommodate the very high tare to laden mass of typical freight wagons whilst maintaining stable running at the maximum required speed and good curving performance. The most common current freight bogies are described in detail and recent improvements in techniques used to simulate the dynamic behaviour of railway vehicles are summarised and examples of how these have been used to improve freight vehicle dynamic behaviour are included. A number of recent developments and innovative components and sub systems are outlined and finally two new developments are presented in more detail: the LEILA bogie and the SUSTRAIL bogie.</p> + </abstract> + </profileDesc> + </teiHeader> + <text xml:lang="en"> + <body> +<div xmlns="http://www.tei-c.org/ns/1.0"><head>DYNAMICS OF RAILWAY FREIGHT VEHICLES</head><p>Iwnicki S.D. 1 , Stichel S. <ref type="bibr" target="#b1">2</ref> , Orlova A. 3 , Hecht M. <ref type="bibr" target="#b3">4</ref> </p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="1">Introduction</head><p>From their inception railways have been predominant in the carriage of bulk goods and railway wagons have been designed to allow this to be effected efficiently on different types of railway infrastructure. In more recent times with changes in industrial needs and competition from road and air transport railways have carried an ever declining share of freight. Although there is some evidence in some countries that this trend has started to change recently due to road congestion there is still not yet a widespread evidence of a major modal shift from road to rail which politicians have indicated is desirable. For example the European Transport White paper 2011 <ref type="bibr" target="#b0">[1]</ref> sets a target for modal shift of 30% by 2030 and 50% by 2050 from road freight to other modes such as rail or waterborne transport for distances over 300 km.</p><p>The barriers to this increased modal shift from road to rail seem to be largely due to the requirements from modern shippers for shorter end-to-end times but even more the demand is for high reliability of service and for additional features such as tracking and tracing of shipments, security and temperature control. As Hecht <ref type="bibr" target="#b1">[2]</ref> points out the lower speeds for rail freight compared with passenger services are not mainly related to lower vehicle speed capability but are more due to the fact that freight trains often travel on lower speed lines or are held for passenger traffic to pass and due to complex and lengthy shunting and handling operations and motive power and crew changes.</p><p>Nevertheless if freight vehicle speeds and acceleration and braking capabilities could allow them to be fully integrated with passenger traffic this would bring a step change in end to end freight train speeds as well as overall system capacity. A key factor in obtaining this increased speed is to ensure that the dynamic performance of freight vehicles can allow safe and reliable operation on track with different levels of irregularities and support conditions. Running gear has evolved with the experience of operation on different railways and more recently the use of computer simulation tools and several standardised designs are now ubiquitous. Several research projects and teams have recently been trying to advance from this position using innovative designs adapted from passenger vehicles or using other novel techniques. The use of computer simulations is now established for design of running gear and is also becoming accepted as part of the vehicle acceptance processes in many countries.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="2">Early developments of freight wagons</head></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="2.1">Background</head><p>Designers of freight vehicle running gear face many challenges but not least of these is the fact that the ratio of the laden to tare mass of a freight vehicle can be as much as 5:1 compared with a more manageable 1.5:1 for typical passenger vehicles. This effectively means that the suspension system has to be designed for two different vehicles (and every stage in between). A number of clever designs have evolved over the years and the most successful of these are now summarised.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="2.2">UIC double link</head><p>Freight wagons with link type suspensions have existed for more than 100 years, as can be seen in <ref type="figure" target="#fig_0">figure 1</ref>, and the link suspension is probably still the most common suspension type for two axle freight wagons in Europe today. As early as 1890 the principle of the link suspension was defined as a standard. A review of freight wagons with link suspension can be found in <ref type="bibr" target="#b2">[3]</ref>. After World War II the UIC double link suspension was defined as a standard <ref type="bibr" target="#b4">[5]</ref>. In the beginning of the 1980s a number of improvements were made. The axle load was increased to 22.5 tonnes and the parabolic leaf spring was introduced as standard component <ref type="bibr" target="#b5">[6]</ref>, <ref type="bibr" target="#b6">[7]</ref>. The UIC double link suspension in figure 2 mainly consists of three parts: Leaf springs, links and axle guards. The vehicle is connected to the parabolic or leaf spring by double links. The leaf spring rests on the axle box. This arrangement allows the axle box to move in both the longitudinal and lateral direction relative to the wagon body. The axle guard restricts the horizontal motion of the axle box. The principle of the suspension is that of a pendulum. In the longitudinal direction the suspension links are inclined, whereas in the lateral direction they are in a vertical plane when the vehicle body is in nominal position <ref type="bibr" target="#b0">[1]</ref>, <ref type="bibr" target="#b7">[8]</ref>, <ref type="bibr" target="#b8">[9]</ref>, <ref type="bibr" target="#b9">[10]</ref>. The characteristics of the double-link suspension are quite complex. The main components are shown in <ref type="figure">Figure 3</ref>. One of the main advantages of the link running gear is that it is simple, robust and cheap and also takes up little space in both lateral and vertical directions. Both stiffness and damping are provided by one system and are load dependent. The quasistatic curving performance of the single axle running gear with link suspension is good. For a typical two-axle freight wagon with a wheelbase of 9m on dry rails good steering performance down to 300 m curve radius can be achieved <ref type="bibr" target="#b9">[10]</ref>.</p><p>The running behaviour of two-axle freight wagons with link suspension can be rather poor mainly due to vehicle hunting. The amount of damping provided in the horizontal plane is often not sufficient. Additionally the characteristics of the suspension change during the life of the vehicle, due to suspension wear, and with the running conditions <ref type="bibr" target="#b9">[10]</ref>. The link suspension takes quite a lot of longitudinal space and is a poor isolator for sound and vibration.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="2.3">Link suspension bogies</head><p>The leaf spring and link suspension of the single-axle running gear has also been used on bogies since about 1925 <ref type="bibr" target="#b0">[1]</ref>. More recently it has been standardised with for example bogie type 931 (figure 4), developed in the 1950s by Deutsche Bahn with a wheelbase of 2000 mm and a wheel diameter of 1000 mm. This bogie was developed to run at 100 km/h with an axle load of 20 t and was the first bogie standardised by UIC <ref type="bibr" target="#b5">[6]</ref>, <ref type="bibr" target="#b6">[7]</ref>. In the beginning of the 1980s DB bogie type 665 was introduced with new features like parabolic leaf springs, 22.5 t permissible axle load and shorter links as shown in figure 5 <ref type="bibr" target="#b6">[7]</ref>. The bogie frame is a welded steel design but in some places forged components are used. The frame is connected to parabolic or trapezoidal leaf springs, that rest on the axlebox, being connected by swing links. Nominally the suspension links are positioned in a longitudinal vertical plane and inclined in this plane. During vehicle operation the links swing in that plane and also laterally <ref type="bibr" target="#b0">[1]</ref>, <ref type="bibr" target="#b5">[6]</ref>, <ref type="bibr" target="#b6">[7]</ref>, <ref type="bibr" target="#b10">[11]</ref>. A spherical centre-pivot and two side bearers connect the bogie frame and the wagon body. The side bearers can be either rigid or vertically suspended and have three functions:</p><p> to act as static support for the carbody. to act as roll stiffness. to provide friction damping between carbody and bogie The quasistatic curving performance of a bogie with link suspension is generally very good due to:</p><p> the short wheelset distance in the bogie of 1.8 m. the soft longitudinal primary suspension.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="2.4">The Y25 Standard Bogie</head><p>Most railway vehicles have bogies or trucks which allow longer vehicles supported on two bogies while still keeping attack angles between wheels and rail in curves to reasonable levels. This arrangement also allows two stages of suspension with the 'primary' suspension between wheelset and bogie and secondary suspension between bogie and coach or wagon body. The primary suspension can isolate the bogie from short wavelength irregularities while the secondary suspension deals with the longer wavelength, lower frequency excitations.</p><p>As previously mentioned, a specific challenge for designers of freight vehicle running gear is the large difference between tare and laden vehicle mass. In the Y25 bogie progressive damping with vertical load is effected by the use of 'Lenoir links' which take part of the vertical load through an angled link and a pusher onto a vertical friction surface. This gives a level of damping which is broadly proportional to the vehicle mass. The Y25 bogie design originated in France in 1948 and was standardised by the ORE steering committee in 1967. It is shown in <ref type="figure">figure 6</ref>.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head>Figure 6: A Y25 type bogie</head><p>The design has been hugely successful and Y25 type bogies are the most predominant freight bogie in Europe.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="2.5">'three-piece' Freight Bogies</head><p>The three-piece bogies were first developed in 1930s and seemed to originate simultaneously in the USA (Barber bogie) and the Soviet Union (Hanin bogie). Now the three-piece bogie and its more sophisticated descendents are the most common suspension for freight wagons across North and South Americas, CIS countries, China, Africa, India and Australia. Maximum axle loads range between 7 and 36 t. The most common standards for three-piece bogies are AAR <ref type="bibr" target="#b12">[13]</ref> for 1435 mm gauge and GOST <ref type="bibr" target="#b13">[14]</ref> for 1520 mm gauge. A review of three-piece bogies can be found in <ref type="bibr" target="#b14">[15]</ref>.</p><p>The Russian model 18-100 bogie shown in <ref type="figure">figure 7</ref> is a good example of an early type of three-piece bogie. The term 'three-piece' refers to the design of the bogie frame which consists of three interconnected parts: two side frames and one bolster. The frame parts are usually cast.</p><p>The bogie is equipped with central suspension between the side frames and the bolster that consists of a set of springs and wedge friction dampers working in vertical and lateral direction and keeping the frame square. The side frames with their flat surfaces rest on the axle-boxes (or bearing adapters). The size of the opening in the side frame provides clearances in longitudinal and lateral direction within which the axle-box moves resisted by dry friction forces. The car body rests on the flat center bowl, its roll motion relative to the bolster is limited by side bearers which are usually stiff vertical stops including clearance when the wagon body is in the central position. The three-piece bogie is a very robust design with the advantage of being low cost in production, operation and repair. The following items are considered as disadvantages of traditional three-piece bogie and attempts have been made to address these in its further developments <ref type="bibr" target="#b14">[15]</ref>, <ref type="bibr" target="#b15">[16]</ref>, <ref type="bibr" target="#b16">[17]</ref>:</p><p> Limited critical speed of the empty wagon )with sway oscillation of car body being the major loss of stability mode); Wheel flange contact in curves produced by warping between side frames and bolster; Side frames adding to the unsprung mass and thus increasing track impact on short wavelength irregularities; Deterioration of ride performance with wear of friction wedges and other friction surfaces.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3">Computer simulation</head><p>Computer simulation of freight vehicles is not at all as common as for passenger vehicles. Since many of the European freight vehicles are standardized very little new development has been carried out and the manufacturers do in general not perform a simulation analysis of the running behaviour of freight wagon. However, in several research groups at universities and research institutes and at some consulting companies computer simulation of freight vehicles is now performed.</p><p>Since manufacturers do not usually build simulation models of freight vehicles themselves one of the main challenges in modelling a freight wagon is to obtain all the input parameters required. Another aspect is that most suspension elements are strongly non-linear and in many cases even mathematically non-smooth. This makes it very difficult to build up simulation models that provide good results compared to measurement results. Some of the phenomena observed during simulation of freight vehicles will be discussed below.</p><p>Further, as described in Section 3.1, the characteristics of the suspension elements can vary during operation due to wear or environmental effects such as for example surface contamination changing the friction coefficient in sliding surfaces.</p><p>The main purpose of simulation studies of freight vehicles is very often a stability analysis (see Section 3.2) or an investigation of the curving behaviour of the freight wagon (see Section 3.3). Since the axle loads of freight wagons are usually high, the investigation of wheel or rail wear and rolling contact fatigue is often the primary reason for a simulation study in curves.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.1">Suspension components</head><p>The suspension in most freight vehicles relies on friction damping. Friction elements are low cost, require little maintenance and are usually load dependent. This means that the level of friction damping changes with axle load, an important feature in freight wagons due to the high tare to laden ratio already mentioned. Surveys of modelling of friction components in freight wagon can be found for example in <ref type="bibr" target="#b17">[18]</ref>- <ref type="bibr" target="#b21">[22]</ref>. Papers <ref type="bibr" target="#b17">[18]</ref> and <ref type="bibr" target="#b18">[19]</ref> are general reviews of rail vehicle suspension components, while <ref type="bibr" target="#b19">[20]</ref> is focused on freight vehicles and also discusses issues such as stability and curving of freight vehicles. Papers <ref type="bibr" target="#b20">[21]</ref> and <ref type="bibr" target="#b21">[22]</ref> are focussed on modelling friction wedges of three-piece bogies. Also in the proceedings from the Euromech 500 colloquium <ref type="bibr" target="#b22">[23]</ref> many valuable contributions on the topic of non-smooth suspension elements can be found. Various arrangements of suspension elements to simulate vehicle suspensions are documented in <ref type="bibr" target="#b23">[24]</ref>, <ref type="bibr" target="#b24">[25]</ref>.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.1.1">Friction damping</head><p>In most freight vehicle simulation models friction is modelled as dry Coulomb friction, where the friction force is proportional to the normal load. The friction coefficient is assumed to be constant, see force-deflection curve in <ref type="figure">figure 8</ref>, left. The disadvantage of the Coulomb model is that it is non-smooth, i.e. multi-valued and non-differentiable. Another way to model friction is with a linear spring in series with a friction slider as in <ref type="figure" target="#fig_8">figure 9</ref> with the resulting force-displacement characteristic in <ref type="figure">figure 8</ref>, right. Since most friction damper arrangements have a finite flexibility, such models could also be regarded as more realistic. Note, however that the model with a spring in series is still non-smooth. To avoid the difficulties mentioned above regularization methods are often applied, see for example <ref type="bibr" target="#b25">[26]</ref>, <ref type="bibr" target="#b26">[27]</ref> and <ref type="bibr" target="#b27">[28]</ref>. Piotrowski developed a non-smooth rheological model <ref type="bibr" target="#b28">[29]</ref>, <ref type="bibr" target="#b29">[30]</ref>, which employs the notion of the differential succession involving a contingent derivative of the non- smooth, multi-valued characteristics of Coulomb friction. Tan and Rogers <ref type="bibr" target="#b30">[31]</ref> proposed equivalent viscous damping models to avoid the numerical problems of Coulomb friction. They claim that this substitution works very well for cases where sliding motions predominate.</p><p>In many running gear arrangements two-dimensional friction elements are needed, e.g. in the Y25 and in the three-piece bogie. In these designs motions in two directions tangential to the friction surfaces are possible. Two-dimensional Coulomb friction models can be found e.g. in <ref type="bibr" target="#b31">[32]</ref>, <ref type="bibr" target="#b32">[33]</ref>.</p><p>Another phenomenon that is important to take into account is stochastic excitations that smooth the dry friction damping. Also mid frequency excitation generated in the wheel rail contact - often called dither - can smoothen dry friction and therefore have a significant influence on the simulation results, see for example <ref type="bibr" target="#b29">[30]</ref>, <ref type="bibr" target="#b32">[33]</ref>.</p><p>True and Asmund <ref type="bibr" target="#b32">[33]</ref> investigated the effects of dry friction in the suspension of a simple freight vehicle. They used a relatively simple model of dry friction and found that the stable behaviour for the system with friction exhibited a laterally oscillating motion which makes the system sensitive to external periodic forcing. </p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.1.2">Wagons with link suspension</head></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.1.2.1">Basic model of leaf spring and link suspension</head><p>Leaf springs are often used as vertical suspension. In multibody simulation models they are usually regarded as rigid in both the longitudinal and lateral directions. For dynamic displacements around a static equilibrium position leaf springs are characterized by a relatively high stiffness for small displacements and a significantly lower stiffness for larger displacement, (figure 10). Leaf springs are described in the ORE reports <ref type="bibr" target="#b33">[34]</ref>, <ref type="bibr" target="#b34">[35]</ref>. Since link suspensions show very similar characteristics they are often modelled in a similar way to leaf springs, at least for the lateral link behaviour. The initial higher stiffness k 1 in leaf springs is caused by friction, i.e. the leaves of a leaf spring stick together for small displacements and start to slide on each other for larger displacements. In the same way the link rolls in the end bearing as long as there is no sliding in the contact area. The lower stiffness k 2 is the value for sliding in the leaf spring or the so called pendulum stiffness of a link. The force F d determines the amount of damping in the hysteresis. A commonly used model to represent the two different stiffness values with the hysteresis is to use a linear spring and a friction element in series, in parallel with another linear spring, as shown in <ref type="figure" target="#fig_0">figure 11</ref>. It should be taken into account that the characteristics of leaf springs vary due to wear in running or deterioration or lubrication state.</p><p>The three parameters in the model described above can be derived from measurements. This model, however, is simplified since the shape of the hysteresis curve is usually rounded as shown in <ref type="figure" target="#fig_0">figure 10</ref>. Measurement results and more detailed descriptions of link suspensions can be found in <ref type="bibr" target="#b33">[34]</ref>- <ref type="bibr" target="#b47">[48]</ref>. </p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.1.2.2">Advanced simulation models</head><p>For lateral displacements of a double-link all four joints are assumed to start to slide at the same time; therefore the model in <ref type="figure" target="#fig_0">figure 11</ref> is sufficient. In the longitudinal direction, however, it is more likely that the joints start to slide at different displacements as shown e.g. by Piotrowski <ref type="bibr" target="#b28">[29]</ref>. He uses a set of four sliders and spring elements with different breakout forces in parallel to describe these characteristics. Also in a model used by Stiepel several elements in parallel are used <ref type="bibr" target="#b43">[44]</ref>.</p><p>To give a better representation of the rounded shape of the hysteresis curves, Fancher developed a model for truck leaf springs <ref type="bibr" target="#b44">[45]</ref>, <ref type="bibr" target="#b45">[46]</ref> using exponential expressions. Jönsson <ref type="bibr" target="#b41">[42]</ref> used a similar approach, where the total force over the suspension component is separated into piece-wise elastic and friction forces. The model is used for both leaf springs and double-links.</p><p>Another possibility to describe hysteresis with rounded shape for link suspensions is to use rolling contact theory, which has been proposed by <ref type="bibr">Piotrowski [33]</ref>. Based on the slip velocity the creepage in the contact is calculated.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.1.3">Modelling the three-piece bogie</head></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.1.3.1">Models of the central suspension</head><p>Most of the research in modelling three-piece bogies, such as <ref type="bibr" target="#b20">[21]</ref>, <ref type="bibr" target="#b21">[22]</ref>, is focussed on the central suspension element of the three-piece truck that provides damping with friction wedges. Early models of friction wedge suspensions recognized only vertical load-dependent friction force, later models included two-dimensional friction in the vertical and lateral directions <ref type="bibr" target="#b45">[46]</ref>, <ref type="bibr" target="#b49">[50]</ref>.</p><p>The first approach to account for possible angular and longitudinal displacements of bolster relative to the side frames is to introduce warping and longitudinal nonlinear resistance characteristics into the model, as it is done in <ref type="bibr" target="#b14">[15]</ref>, <ref type="bibr" target="#b16">[17]</ref>. In such case the wedges are not modelled as separate bodies, but the equivalent force against displacement characteristics are introduced accounting for wedge parameters, such as inclination angle, width of the vertical surface, width of the inclined surface, friction coefficients on inclined and vertical surfaces, etc.</p><p>The second approach to account for all possible degrees of freedom between side frame and bolster is to introduce multiple contact points mapped along the edges of the wedge with two-dimensional friction force elements in each of them. Such an approach was used by Ballew et al <ref type="bibr" target="#b45">[46]</ref>, it is implemented in simulation tools such as VAMPIRE <ref type="bibr" target="#b51">[52]</ref>, and the Universal Mechanism software <ref type="bibr" target="#b51">[52]</ref>. Numerous contact elements require an efficient numerical simulation algorithm to be implemented into the software that provides fast solution to resulting stiff system of equations, such as the one developed by Pogorelov <ref type="bibr" target="#b56">[57]</ref>. The wedges are treated as massless. Contact type models allow the study of such complicated phenomenon as uneven distribution of contact forces over the wedge surfaces, implementation of resilient pads on wedge surfaces, jamming and wedging <ref type="bibr" target="#b53">[54]</ref>. In paper <ref type="bibr" target="#b55">[56]</ref> the authors included the mass of the wedge into consideration to study its dynamic properties.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.1.3.2">Models of the axle to side frame interaction</head><p>In the first approach similar to friction wedges the axle to side frame interaction can be described by nonlinear equivalent characteristics as in <ref type="bibr" target="#b14">[15]</ref>, <ref type="bibr" target="#b16">[17]</ref>. The dry friction interaction between the axle box crown and the side frame pedestal is modelled by two dimensional dry friction element in parallel with another nonlinear element that describes bumpstops in longitudinal and lateral dimension. A typical characteristic of the bumpstop element is presented in <ref type="figure" target="#fig_0">figure 12</ref>. To improve numerical integration the transition from clearance to bumpstop is often smoothed.</p><p>If the interaction between the crown and pedestal is a flat surface, then its width can result in roll stiffness that is produced by gravity. Such stiffness can be introduced into the model depending on the axle load. The second approach is to introduce multiple contact points on the edges of the crown with two-dimensional friction elements in them. The bumpstops are then also the contact elements between the axle box or adapter and the stops in the side frame jaws. Such approach is used in <ref type="bibr" target="#b56">[57]</ref> as well as in Universal Mechanism software <ref type="bibr" target="#b51">[52]</ref>.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.1.3.3">Models of the centre bowl and side bearers</head><p>The same approaches can be applied to models of the centre bowl to centre plate interaction and at the side bearers.</p><p>In the first approach, see <ref type="bibr" target="#b14">[15]</ref>, <ref type="bibr" target="#b16">[17]</ref>, centre plate to centre bowl interaction works simultaneously as one dimensional yaw friction and nonlinear roll and pitch torque with soft characteristics as shown in <ref type="figure" target="#fig_0">figure 13</ref>. Knowing the clearance in the side bearers the nonlinear roll characteristic can be linearized. The second approach is to introduce multiple contact points on the edges of the centre plate with two-dimensional friction elements in them. The interaction with the centre bowl rim is then also the contact elements. Such an approach is used in <ref type="bibr" target="#b56">[57]</ref> as well as in Universal Mechanism software <ref type="bibr" target="#b51">[52]</ref>.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.2">Stability</head><p>Freight vehicles in most cases operate at much lower speeds than passenger vehicles. Typical running speeds are at around 100 km/h. This suggests that stability investigations are not as important as for faster passenger vehicles. On the other hand freight vehicles often are much less damped than passenger vehicles and stability investigations are therefore necessary. Several of the wagon types introduced above can - in unfavourable running conditions - show significant hunting behaviour at speeds as low as 70 km/h.</p><p>In a bogie vehicle basically three types of hunting motion can arise:</p><p> Wheelset hunting where one wheelset performs the hunting motion.</p><formula xml:id="formula_0"> M 0 M c Mg </formula><p> Bogie hunting where a whole bogie is taking over the hunting motion. Carbody hunting where the carbody performs a yaw motion and the two bogies mainly follow the carbody with lateral motions, i.e. the whole vehicle takes over the hunting motion.</p><p>Carbody hunting is often a type of resonance phenomenon, where the Klingel hunting frequency given mainly by vehicle speed and conicity in the contact coincides with the yaw eigenfrequency of the carbody.</p><p>Hunting motion with a non-zero limit cycle depends on the wheel-rail geometry, the suspension and the masses and inertias of the vehicle. Since the mass and inertia, and in most cases the suspension stiffness and damping of the freight wagon will significantly change with load, the type of hunting motion observed usually differs between an empty and a loaded wagon. Since the stiffness values between axlebox and bogie frame (in a bogie vehicle) are lower in an unloaded vehicle, the risk for wheelset or bogie hunting is higher. In loaded vehicles, vehicle hunting can often be observed. Since the frequency of wheelset hunting is usually low (typically between 1 and 2 Hz) the wheel rail forces induced are relatively low and in most cases below the limit values stipulated in standards. Therefore, the vehicle design in reality allows for the carbody instability to happen in some conditions. Otherwise the suspension needs to be so stiff that the curving performance would suffer, and the amount of wear and RCF would increase significantly. The risk of carbody hunting can vary with the type of load since this can influence the yaw eigenfrequency of the carbody.</p><p>Due to the significant inherent non-linearity and non-smoothness of the suspension elements linearization of the models is usually not realistic. It is therefore necessary to perform time steppig integration with the full non-linear model. The task is in general to find the non-linear critical speed v B of the wagon as can be seen in the generic bifurcation diagram in figure 14.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head>Figure 14: Generic bifurcation diagram</head><p>In complex models it is very difficult to find the exact critical speed, for example with a path following method <ref type="bibr" target="#b57">[58]</ref>. Therefore other engineering methods are used. One possibility that has been suggested e.g. by <ref type="bibr">Polach [59]</ref> is to excite the vehicle with an initial disturbance that can either be deterministic or stochastic. After the initial disturbance the vehicle is run on ideal smooth track. If the oscillation vanishes the vehicle is regarded as stable. The simulations have to be repeated with increasing speed until the oscillations do not disappear. In that case the non-linear critical speed v b ( <ref type="figure" target="#fig_0">figure 15</ref>) is reached. A risk with this method is that the initial disturbance is not high enough to initiate a limit cycle oscillation and that the critical speed detected is higher than the real non-linear critical speed.</p><p>Another method to detect the non-linear critical speed is start the simulations at a very high speed to be sure that the vehicle has reached the non-zero attractor (limit cycle). Then the speed is continuously reduced until the limit cycle behaviour disappears. Polach also describes this method. It has been used for example by Boronenko et al <ref type="bibr" target="#b14">[15]</ref> to tune the suspension of three-piece bogies.</p><p>A similar method, shown in <ref type="figure" target="#fig_0">figure 15</ref>, is suggested in <ref type="bibr" target="#b59">[60]</ref> to determine the so-called non-linear critical speed. The difference to the method introduced above is that the speed is not reduced continuously but in discrete steps as suggested by True <ref type="bibr" target="#b98">[98]</ref>. <ref type="figure" target="#fig_0">Figure 16</ref> shows the bifurcation diagram for a loaded two-axle vehicle calculated with this method. It can be observed that only the stable branches of the bifurcation diagram can be determined, not the unstable part. The zero solution is also possible at least up to a speed of 120 km/h (bold solid line). This was simulated using the procedure above, starting from low speed and increasing the speed stepwise. Hoffman also investigated the stability of a two-axle wagon with link suspension <ref type="bibr" target="#b42">[43]</ref>, <ref type="bibr" target="#b60">[61]</ref>. He uses the link model developed by Piotrowski <ref type="bibr" target="#b28">[29]</ref>. The leaf springs model is based on Fancher et al <ref type="bibr" target="#b45">[46]</ref>. Gialleonardo et al <ref type="bibr" target="#b61">[62]</ref> extended this type of stability analysis for a two-axle wagon with link suspension on curved track. As can be seen in <ref type="figure" target="#fig_0">figure 18</ref>. the leading wheelset (y lw )</p><p>shows much smaller oscillation amplitudes than the trailing wheelset (y tw ) and the carbody. This is because the outer wheel of the leading wheelset experiences flange contact. In general the results show the presence of large periodic oscillations in narrow curves at commercial operating speeds. It is also shown in the paper that the coupling forces between wagon assemblies significantly reduce the oscillation amplitudes. Zhai et al <ref type="bibr" target="#b62">[63]</ref> extended the stability analysis for a freight wagon with three-piece bogies to also include a visoelastic track structure. The stability analysis is performed according to the methodology suggested by Polach, which is explained above. The authors found that a lower critical hunting speed is obtained on elastic track compared with the rigid track case. The difference in the critical hunting speeds between the elastic track base and the rigid track base is 4.4% for the loaded freight car.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.3">Curving</head><p>As indicated above simulations of the running behaviour of freight wagons in curves are often performed to investigate the risk of wheel wear and Rolling Contact Fatigue (RCF).</p><p>For passenger vehicles curving simulations are often performed on ideal track, i.e. the stochastic track irregularities are neglected. Authors are in this case interested in the quasistatic behaviour of the vehicle, i.e. the mean wheelset attack angles or the mean energy dissipation in the contact points. For freight vehicles with non-linear and non- smooth suspension this can lead to significant mistakes as shown in the example from Jönsson <ref type="bibr" target="#b41">[42]</ref>. On ideal track the friction surfaces might stick together and force the wheelset into a more unfavourable position. Track irregularities help to get relative motion in the friction surfaces, which usually leads to better - and more realistic - steering behaviour of the vehicle. As seen in <ref type="figure" target="#fig_0">figure 19</ref>, the energy dissipation as a measure for the amount of wear or RCF, is much lower when simulating running with track irregularities. In one of their numerous studies on three-piece bogies Boronenko et al <ref type="bibr" target="#b14">[15]</ref> investigate the reason for excessive flange wear in some of the Russian wagons. One conclusion is that the main reason for flange wear is the unstable behaviour of the bogies in curves (rutting mode) <ref type="bibr" target="#b15">[16]</ref>, when the bogie is flanging with a two-point contact situation instead of negotiating the curve using the wheel conicity. The flanging is the result of bogie warping, which increases the angle of attack compared to a radial position. In the article a number of different designs are discussed. Among others it is concluded that a bogie design with radial arms significantly reduces the angle of attack and the wear number in curves, see <ref type="figure" target="#fig_1">figure 20</ref>. Berghuvud [64] investigated the curving behaviour of different types of three-piece bogie with and without braking. He concluded that the influence of braking on the curving behaviour is complex. Braking can have a positive effect on the angle of attack of the wheelsets in a curve since it helps to overcome the static friction in the primary suspension. It can also increase the angle of attack if large longitudinal forces push the wheelset longitudinally towards the limit of the play and thus lock the wheelset in an unfavourable position.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.3.1">Vehicle Resistance</head><p>Radially steering bogies do not only reduce flange wear in curves but also reduce the required traction energy. The inner leading wheel is less affected and the trailing wheelset has much smaller values. With radial steering, ( <ref type="figure" target="#fig_1">figure 22</ref>) the leading axle also has very small creepages. This results in lower wear and running resistance. As a result on track with tight curves more than 20% of the overall running resistance can be reduced with similar levels of energy saving <ref type="bibr" target="#b65">[66]</ref>.</p><p>Of course radial steering may affect running stability on straight track. Therefore bogie designs with cross anchors such as the TVP 2007 or the Leila bogie have an advantage over individual radial steering axles as in the swing hanger bogie.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.3.2">Influence of curving on wheel and rail damage phenomena</head><p>As mentioned in the introduction to this section the curving performance of a freight wagon is very important for the level of wheel and rail damage. This means in turn that the vehicle track interaction in curves determines to a large extent the maintenance cost for the whole system. In <ref type="bibr" target="#b65">[66]</ref> Fröhling discusses the influence of, among others, bogie design, bogie maintenance and the wheel/rail interface in heavy haul operation on different damage phenomena on wheels and rails. In a later publication Fergusson et al <ref type="bibr" target="#b67">[67]</ref> present an analysis of wheel wear as a function of the relationship between the lateral and longitudinal primary suspension stiffness and the coefficient of friction at the centre plate between the wagon body and the bolster to minimise the wheel wear rate of a self-steering three-piece bogie without compromising vehicle stability. Simulation results indicate that wheel wear is theoretically the lowest for low lateral and longitudinal primary suspension stiffness and no friction at the centre plate. Casanueva et al <ref type="bibr" target="#b68">[68]</ref> extend the wear prediction methodology for freight wagons to also include switches and crossings. It is concluded that wear on some parts of the wheel profile can only be explained with running through switches.</p><p>Tunna and Urban <ref type="bibr" target="#b69">[69]</ref> carried out a parametric study to quantify the effects of various freight vehicle parameters on the generation of RCF. Three different freight suspensions wer considered: an enhanced three-piece bogie, a rigid-frame bogie with primary suspension, and a two-axle vehicle with leaf springs. Simulations were performed for track curvature ranging from 400 to 10 000 m. To judge the generation of RCF the Tgamma model from Burstow <ref type="bibr" target="#b70">[70]</ref> was used. It is stated that parameters that clearly need to be considered when evaluating rail surface damage are curve distribution, track quality, conicity, vehicle type and loading state of the wagon. Since several parameters are line dependent it is concluded that a route based analysis is necessary.</p><p>In <ref type="bibr" target="#b71">[71]</ref> a simulation model of an iron ore wagon with three-piece bogie is developed to investigate the risk of RCF on the Swedish and Norwegian iron ore line. 43 load cases with various conditions were used as inputs. The risk for RCF was estimated with the so-called shakedown map. The wear number, which is the product of creepages and creep forces, was calculated to estimate where initiated cracks develop or are worn away. In <ref type="figure" target="#fig_1">figure 23</ref> areas on the wheel profile with high risk of RCF can be seen. The area on the wheel tread coincides very well with field observations of RCF but the areas in the flange root and on the flange did not show RCF damage. It can be concluded that the energy dissipation is high enough to wear away initiated cracks. It seems that simulation of the curving behaviour of freight wagons can provide valuable information about the risk of wheel damage for specific operating conditions.</p><p>In <ref type="bibr" target="#b71">[71]</ref> a simulation by Dukkipati and Dong examine the effects of a freight wagon running over a dipped joint. In a very recent paper Wang and Gao investigate the wheel wear of a freight vehicle with three-piece bogie in curves <ref type="bibr" target="#b99">[99]</ref>. It is shown that wear is most severe on the outer leading wheel in the bogie. </p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="3.4">Parameter identification</head><p>The establishment of the correct parameters for use in computer models is clearly of great importance. Some parameters can easily be measured or provided by the manufacturers but others are very difficult to establish. Ren et el <ref type="bibr" target="#b74">[74]</ref> demonstrate the use of a test rig with a sliding plate underneath one wheelset to establish key parameters. The sliding plate is moved with actuators and forces measured to allow the lateral, shear and warp stiffness to be established as well as the friction characteristics of the bogie.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="4">Modern Developments</head></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="4.1">The British Rail HSF Bogies</head><p>Wickens and colleagues at British Rail Research carried out theoretical and practical work aimed at understanding the dynamic performance of two axle freight vehicles <ref type="bibr" target="#b75">[75]</ref>, <ref type="bibr" target="#b76">[76]</ref>. The aim was to increase the operating speed of freight vehicles and reduce the rate of derailments. A series of experimental two axle vehicles were constructed to confirm the results of the analysis. They included coil springs and viscous dampers and longitudinal rods to control yaw motion and were initially tested on a full size roller rig.</p><p>Computer simulations of curving and stability were carried out with various damper configurations and on-track tests of several prototypes were undertaken</p><p>The result of this work was the prototype 'HSFV.4' high speed freight vehicle with viscous damping ( <ref type="figure" target="#fig_1">figure 24)</ref> which was tested at speeds of up to 120 km/h and proved to run without hunting for a wide range of effective conicity values. </p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="4.2">The Unitruck running gear</head><p>The Unitruck single-axle running gear with lateral "swing hangers" was first developed for the American market and in the 1990's adjusted to suit European conditions. Vehicles with Unitruck running gear <ref type="bibr" target="#b76">[76]</ref> are today used both in North America and Europe. They have only one stage suspension, which also includes friction damping. As in the Y25 bogie, the vertical force in the primary suspension is used to preload the different friction components via an inclined surface. <ref type="figure" target="#fig_1">Figure 25</ref> left shows the wedge element, which is in series with one of the coil springs and in contact with the carbody via an inclined friction surface; the vertical surface in contact with the saddle is also a friction surface. Newer designs have substituted the inclined friction surface by a roller (figure 25 left) <ref type="bibr" target="#b77">[77]</ref>, thus enabling the displacement in the longitudinal direction, but reducing longitudinal damping. Also, adding a coupling plate in the centre of the coil springs increases longitudinal stiffness <ref type="figure" target="#fig_1">(Figure 25</ref> right), which improves critical speed compared to the running gear with rollers and classic coil springs. The 'Swing Motion' bogie ( <ref type="figure" target="#fig_1">figure 26</ref>) is a variant of the three-piece freight bogie and was originally developed for heavy haul operations in North America. In the Swing Motion design an additional cross member or transom is included which connects the two side frames together via pivots at the base of the secondary spring pack. The bolster still sits on the top of the spring packs and is damped through friction wedges. A pivot between the axle boxes and the side frames is also included so that the side frames can pivot or swing to accommodate lateral motion of the bolster. The swing motion gives increased lateral stability at speeds up to 176 km/h and is claimed to reduce wheel and rail wear, reduce rolling resistance and forces on track and vehicle body compared with standard three-piece bogies.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="4.4">The 'LTF' bogie</head><p>In the 1980s British Rail Research in the UK developed a novel, track friendly bogie using passenger vehicle technology. The LTF25bogie is shown in <ref type="figure" target="#fig_1">figure 27</ref> and is described in <ref type="bibr" target="#b79">[79]</ref>.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head>Figure 27: The 'LTF25' bogie</head><p>The LTF25 bogie was specifically designed to reduce dynamic track forces and as part of this effort was made to reduce the unsprung mass. Small wheels (813 mm diameter) were used and inside axle boxes giving a 30% reduction in wheelset mass although this necessitated the use of on-board hotbox detectors.</p><p>Primary suspension is through steel coil springs and secondary suspension is through rubber spring elements and hydraulic dampers.</p><p>The high cost of the LTF25 bogie and concerns about axle fatigue with inboard axle boxes militated against its adoption but Powell Duffryn produced a modified version of the bogies known as the TF25 bogie (shown in <ref type="figure" target="#fig_1">figure 28</ref>) which has achieved considerable production success. </p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="4.5">The 'Gigabox' bogie</head><p>The 'Gigabox'bogie uses pedestal units containing progressive rubber springs with integral hydraulic damping as shown in figures 29 and 30). The system was developed by ContiTec and SKF and is claimed not to require maintenance for up to 1million km and to provide good noise and vibration isolation. A reduction of up to 20% in lateral forces is claimed as well as a 2 dB reduction in noise. </p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="4.6">The Double Rubber Ring Spring (DRRS) bogie</head><p>Originally designed by Talbot the DRRS bogie uses double rubber torroidal ring springs with load proportional friction damping as shown in <ref type="figure" target="#fig_0">figure 31</ref>. Container wagons with DRRS bogies entered service with the DB 'Inter Cargo Express- System'. Maximum axle-load ranges from 22.5 t at 100 km/h to 18.375 t at 160 km/h. </p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="4.7">Advances in three-piece bogies</head><p>The major drivers for advances of AAR three-piece bogies were tightening ride performance and track impact standards, such as M-1001 <ref type="bibr" target="#b79">[79]</ref> and M-976 <ref type="bibr" target="#b80">[80]</ref>, since 2000.</p><p>An overview of improvements in the suspensions is given in <ref type="bibr" target="#b82">[81]</ref>. Suspension springs tend to increase the deflection. Using higher control springs under the wedges increases friction under the empty wagon thus providing its better stability, and makes damping less dependent on the wear of wedges themselves. Different height of the inner and outer springs allows having lower lateral stiffness of the suspension under the empty wagon, thus improving its running performance. Using the set of 9 double springs per each side of the bogie increases warping resistance.</p><p>The innovative designs of the wedges are shown in <ref type="figure" target="#fig_1">figure 32</ref>. Both designs aim to increasing the warping resistance of the bogie. The split wedge consists of two symmetric parts inclined towards each other and interacts with the spatial insert in the bolster pocket. In the spatial wedge the surfaces are inclined in the other direction and they are wider than the vertical surface, which gives the same effect. In the interaction between the side frame and the wheelset axle various elastic components are introduced to reduce unsprung mass as well as to reduce resistance to wheelset displacement in plane, thus reducing the lateral track forces. Some of the designs of elastic shear pads are shown in <ref type="figure">figure 33</ref>. The rigid side bearings with clearances have transformed in modern three-piece bogies into constant contact side bearings, incorporating the elastic element compressed by the weight of the car body, <ref type="bibr" target="#b83">[82]</ref>. Examples of the design are shown in <ref type="figure" target="#fig_3">figure 34</ref>. Constant contact side bearings provide yaw damping for the bogies on straight track, as well as additional car body roll resistance for better curving performance. The rollers positioned with a clearance provide rigid bumpstop that limits the elastic element deflection without increasing the yaw resistance. There are several devices used to increase warping stiffness of three-piece bogies, the most common of which is using cross-braces between the side frames shown in <ref type="figure" target="#fig_4">figure 35</ref>.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head>Cap</head></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head>Elastic element</head><p>Cage Wear resistant element</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head>Insert</head></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head>Roller</head></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head>Cap</head></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head>Elastic element</head><p>Cage 1 - top brace; 2 - bottom brace; 3 - bolt; 4 - washer; 5 - nut; 6 - fastening unit; 7 - rings; 8 - locking plate; 9 - washer; 10 - bolt; 11 - elastic pad; 12 - safety wire; 13, 14 - bracket; 15, 16, 17 - plate; 18 - key <ref type="figure" target="#fig_4">Figure 35</ref> Cross-braces between side frames.</p><p>Using the concept of shear and bending stiffness of the bogie Scheffel <ref type="bibr" target="#b84">[83]</ref>, developed several novel designs of three-piece bogies (figure 36). At first the horizontal motion of the frame is decoupled from the wheelsets by horizontally soft primary suspension. Then the axle boxes are interconnected through sub-frames or arms by elastic elements that support their radial position in curves, but resist in-phase yaw <ref type="bibr" target="#b85">[84]</ref>. Scheffel bogies having the axle load of 32 t provide mileage between wheel turning of up to 1.5 million kilometres thus proving the high efficiency of the design to reduce track forces.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="4.8">The Lenoir pusher spring</head><p>Various alternatives to the double Lenoir linkage have been explored with the aim of providing reduced longitudinal stiffness at low cost. One example is the 'Lenoir pusher spring' which consists of a plunger and washer springs mounted opposite the Lenoir pusher ( <ref type="figure" target="#fig_32">figure 37</ref>). This allows more longitudinal motion than the conventional Piotrowski <ref type="bibr" target="#b87">[86]</ref> reports how this arrangement has been shown to give good performance in a prototype vehicle with significant reductions in wheel wear.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="4.9">The RC25NT Bogie</head><p>Eisenbahn Laufwerke Halle (Germany) has developed the RC25NT self-steering three- piece bogie with direct inter-axle linkages which was presented at the Innotrans exhibition in 2010) <ref type="bibr">[87]</ref> ( <ref type="figure" target="#fig_2">figure 38</ref>). The bogie has horizontally soft rubber bushes in the primary suspension and flexicoil dual rate springs with friction damping in the secondary suspension. The bogie is equipped with disk brakes. The aim of the development was to build a bogie capable of stable running up to 120 km/h, keeping low noise criteria and negotiating curves with minimum of wear. The bogie is designed to replace the Y25 type bogie without changes to the wagon body.</p><p>Simulations have shown that the RC25NT provides better stability on straight track than the Y25 (figure 39) and less wheel and rail wear in curves ( <ref type="figure" target="#fig_3">figure 40</ref>). The bogie was tested according to the UIC 518 standard in Sweden in 2010 for speeds up to 160 km/h. The RC25NT demonstrates that direct inter-axle linkages can allow freight car bogies to run at 120 km/h with proper steering and low wear in curves. </p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="4.10">The 'LEILA' Bogie</head><p>The LEILA bogie ('LEIchtes und LärmArmes GüterwagenDrehGestell' with the meaning of light and low noise freight bogie) is a passive radial steering bogie with a maximum axle load of 22.5 t and was developed between 2000 and 2005 during a German and Swiss research project <ref type="bibr" target="#b88">[88]</ref>. The Institute of Rail Vehicles of the Technische Universität Berlin was one of the involved partner. The aim to develop this bogie was:</p><p> to reduce the noise emissions of freight wagons; to reduce the mass of a bogie to be under 4 t and to reduce significantly wear and running resistance.</p><p>In addition:</p><p> the reliability and availability of freight wagons; transparency in the transport chain; the active and passive safety of the freight traffic and; the transport velocity should be similarly increased <ref type="bibr" target="#b89">[89]</ref>. The primary layer consists of rubber springs and the load dependent stiffness characteristics are separated in vertical and horizontal working components. The bogie has passive radial steering technology of the wheelsets. Wheelsets are able to rotate about the vertical axis without any external energy but only by the roll radius difference between the inner and outer wheel. Both wheelsets are connected with cross anchors; mounted on opposite axle boxes. The secondary layer is defined UIC centre of pivot and side bearer (latter guarantees the exchangeability to Y25 bogies). In addition, the centre of pivot has an elastically bearing using a secondary rubber spring. The LEILA bogie prototype was examined during various field tests where it demonstrated its advantages compared to a Y25 bogie. The noise emissions were reduced up to 18 dB(A) compared to a Y25 bogie with cast iron brake blocks and up to 8 dB(A) compared to a Y25 bogie with composite blocks (k- blocks). But the bogie failed at that time to enter the market. During the very good ongoing homologation process the producer of the bogie decided to stop the production of new freight wagons and bogies. Therefore the homologation was stopped and not finished just for commercial reasons. Right now as more and more EMUs are produced with inner bearings it is expected that the acceptability of inner bearing bogies with the advantages less weight and lower forces at the axles in curves will be more acceptable. As with the Leila bogie the cross anchor couples the two axles so that they turn with a phase shift of 180°. This stabilizes the radial steering effect even when the wheel-rail contact is not perfect and the second very important effect is dynamic stabilisation without yaw dampers for high speed straight track running. On curvy track significant flange and running surface wear reduction and also significant reduction of the running resistance occur.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="4.12">The SUSTRAIL Bogie</head><p>The aim of the SUSTRAIL project is to promote modal shift of freight in Europe from road to rail. The SUSTRAIL project intends to provide the approach, structure, and technical content to support this modal shift through improvements in the railway freight system including innovations in rolling stock in track components. The project includes workpackages focused on market research, vehicles, infrastructure and assessment of cost benefits. The work described here is part of workpackage 3: 'The freight vehicle of the future'.</p><p>The main scientific and technological innovations being considered for the SUSTRAIL freight vehicle are:</p><p> The development of advanced vehicle dynamics concepts based on new wheel profiles and improvements in suspension design responding to the needs of a mixed traffic railway; Developments in the traction and braking systems for high speed low impact freight operation; Novel designs and materials for lightweight high performance freight wagon body vehicles and bogie structures; Advanced condition based predictive maintenance tools for critical components of both railway vehicles and the track; Identification of performance based design principles to move towards the zero maintenance ideal for the vehicle/track system.</p><p>Partners in the project have carried out a technology review to identify the potential innovative technologies to meet the above requirements and the results have been ranked and two concept vehicles are being designed. The 'Conventional' vehicle will use optimised existing technology and a demonstrator for this is being built as part of the project. The 'Futuristic' vehicle will utilise technology which has not yet been proven in the railway field but has potential to make greater improvements.</p><p>Simulations have been carried out of the dynamic behaviour of the concept design vehicles running on typical track in tare, part laden and fully laden cases. In line with the target of a 50% reduction in lateral forces on the track and stable running at 140 km/h a suspension using double Lenoir linkages, longitudinal linkages between axle boxes and centre pivot suspension has been selected. Computer simulation has been used to optimise the suspension and to select suitable parameters for the various components. Assessment of the results is based on:</p><p> Stability: stable running on typical European track at the design speed of 140km/h must be ensured and ride quality (vertical lateral and longitudinal accelerations experienced by the goods transported) will be assessed. Reduced track forces: track geometrical deterioration (ballast settlement and horizontal level, alignment and buckling), rail surface damage (wear, rolling contact fatigue -RCF) and track components damage (sleeper cracking, rail pad deterioration, rail fatigue, fastening deterioration) will all be assessed.</p><p>A benchmark vehicle has been selected based on a Y25 bogie and flat bed wagon and has been used to allow quantification of the benefits of the new design.</p><p>A number of radical innovations were considered during the technology review stage of the project but it was decided that the use of double Lenoir link primary suspension as in the Y37 series of bogies (figure 44), would be investigated. The double Lenoir link suspension provides much lower longitudinal primary stiffness while still utilising standard components and methods which are well established within the railway industry. this work A model of the SUSTRAIL vehicle was set up with double Lenoir links using the computer simulation tool Gensys and the influence of variations in the suspension parameters on the critical speed of the wagon was simulated. Straight track was used for this simulation and an initial lateral disturbance was introduced followed by ideal track with no irregularities. Axle load is 22.5 t, wheel profile is S1002 and rail profile UIC60 inclined at 1:40. The wheel rail coefficient of friction is set at 0.35. The wagon speed was reduced from an initial 170 km/h and critical speed assumed to have been reached when the track shifting force (∑ ) drops below 2.5 kN. An example is shown in <ref type="figure" target="#fig_3">figure 46</ref>. Further variations were carried out and the effect of the friction coefficient and stiffness within the suspension on the maximum contact force is shown in <ref type="figure" target="#fig_3">figure 49</ref>. <ref type="figure" target="#fig_3">Figure 49</ref>: The effect of friction coefficient and spring stiffness on the contact force It can be seen that the maximum vertical contact forces tends to increase with the damping and with the spring stiffness. In order to improve the running behavior of the SUSTRAIL vehicle it was decided to assess the benefit of linkages provividing longitudinal stiffness between the axleboxes using a radial arm. A radial arm designed by <ref type="bibr">Scheffel [90]</ref> was studied previously in the Infra-Radial project <ref type="bibr" target="#b91">[91]</ref> which aimed to develop a bogie for heavy haul vehicles (axle loads over 25T) with reduced life cycle costs. Tests using the radial arm with four different primary suspension types showed good results with stable running and radially aligned wheelsets in curves. Wear of the wheels was seen to reduce significantly <ref type="bibr" target="#b91">[91]</ref>. In the work reported here simulation was carried out using MEDYNA for the SUSTRAIL vehicle with double Lenoir links and modified radial arms. Simulations have confirmed that the radial arm should provide lateral stiffness between the wheelsets and optimised parameters have been defined. A prototype of the SUSTRAIL freight vehicle is being constructed by REMARUL engineering. In addition to Vertical coils spring stiffness <ref type="bibr">[%]</ref> the innovative suspension described in this paper the SUSTRAIL vehicle will have disk brakes with an electronic control system. The bogie design is shown in <ref type="figure" target="#fig_4">figure 50</ref>. </p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="5">Longitudinal dynamics</head><p>The longitudinal dynamic behaviour of railway vehicles is often neglected as the link to the vehicle track interaction is generally not significant and it has been common to assume that all vehicles of the same type in a train will behave identically. In heavy haul freight applications however where long trains are common the effect of longitudinal dynamics can become significant. In <ref type="bibr" target="#b71">[71]</ref> for example Qi et al model the longitudinal behaviour of a long train including traction and braking and the coupling between vehicles. Belforte et al <ref type="bibr" target="#b93">[93]</ref> also analyse the effects of severe traction and braking forces on longitudinal dynamics.</p><p>There are several areas where longitudinal dynamics can interact with the general vehicle dynamics. These include:</p><p> Wheel unloading on curves due to lateral components of coupler forces; Wagon body pitch due to coupler impact forces and Bogie pitch due to coupler impact forces Cole <ref type="bibr" target="#b94">[94]</ref> describes how these effects can be assessed in different cases and McClanachan <ref type="bibr" target="#b95">[95]</ref> and El Sibaie <ref type="bibr" target="#b96">[96]</ref> present results of computer simulations including coupler models.</p><p>Freight vehicles have to provide satisfactory performance at low cost in tare and laden condition on varying track quality. This has resulted in several standard designs including the Y25 and the three-piece bogie. These designs use friction damping proportional to the vehicle mass to provide good dynamic performance at all loading conditions. In recent years vehicle designers have tried to improve on the dynamic performance of freight wagons and the use of computer tools have helped to overcome the compromise between good curving performance and stability at higher speeds. This has resulted in a number of innovative designs with demonstrable performance improvements but it is notable that few of these have yet to make significant impact in the worldwide freight train fleets.</p><p>A key reason for this lack of adoption is probably the innately conservative nature of the railway industry. Of course this often has a sound basis in, for example, the benefit of using standard components which allow effective maintenance of widely dispersed fleets of vehicles but in order to allow the benefits of the innovative techniques and designs summarised in this paper it is time to reconsider the design of freight vehicles. This could allow increases in speed with lower impact on track and environment and a resulting step change in performance of the railway system. One encouraging sign is the establishment in some countries of track access charging which benefits the use of vehicles with 'track friendly' suspension. Together with emerging legislation and growing pressures on system capacity it is likely that the demand for freight vehicles with higher dynamic performance will climb rapidly.</p><p>Rail freight only can contribute in mitigating the environmental impacts of transportation if the knowledge and todays experience for innovative products is used. Some basic thoughts can be found here and in <ref type="bibr" target="#b97">[97]</ref>. Optimising performance through the development of innovative products is to be planned and procured carefully. This paper has demonstrated that freight vehicle designers have innovative designs of running gear and computer simulation tools ready for this challenge.</p></div><figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_0"><head>Figure 1 :</head><label>1</label><figDesc>Figure 1: Freight wagon from Kockums Sweden, built in 1882 [4].</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_1"><head>Figure 2 :</head><label>2</label><figDesc>Figure 2: UIC double link suspension.</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_2"><head>Figure 3 : Double link suspension [ 8 ]. Parts of double link (a), assembled double link (b) and mounted double link (c).</head><label>38</label><figDesc>Figure 3: Double link suspension [8]. Parts of double link (a), assembled double link (b) and mounted double link (c).</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_3"><head>Figure 4 :</head><label>4</label><figDesc>Figure 4:. DB bogie Type 931 [7].</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_4"><head>Figure 5 :</head><label>5</label><figDesc>Figure 5: DB bogie Type 665 [7].</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_5"><head>Figure 7 : Model 18- 100 bogie: a - general view, b - central suspension scheme, c - primary 'suspension' scheme ( 1 - wheelset; 2 - side frame; 3 - bolster; 4 - braking leverage; 5 - central pivot; 6 - rigid side bearings; 7 - suspension springs; 8 - friction wedge; 9 -</head><label>7100123456789</label><figDesc>Figure 7: Model 18-100 bogie: a-general view, b-central suspension scheme, cprimary 'suspension' scheme (1-wheelset; 2-side frame; 3-bolster; 4-braking leverage; 5-central pivot; 6-rigid side bearings; 7-suspension springs; 8friction wedge; 9-axle-box)</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_7"><head>Figure 8 : Force-displacement curve of Coulomb friction model (left) and Coulomb model with spring in series as in [ 29 ]</head><label>829</label><figDesc>Figure 8: Force-displacement curve of Coulomb friction model (left) and Coulomb model with spring in series as in [29] (right).</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_8"><head>Figure 9 : Friction element with spring in series.</head><label>9</label><figDesc>Figure 9: Friction element with spring in series.</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_10"><head>Figure 10 : Typical force-displacement diagram of leaf spring/link suspension. Example of curve for small displacements around static equilibrium.</head><label>10</label><figDesc>Figure 10: Typical force-displacement diagram of leaf spring/link suspension. Example of curve for small displacements around static equilibrium.</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_11"><head>Figure 11 : Model for leaf spring or link suspension as used for example by KTH [ 40 ]. See figure 10 for definition of k1 and k2.</head><label>114010</label><figDesc>Figure 11: Model for leaf spring or link suspension as used for example by KTH [40]. See figure 10 for definition of k1 and k2.</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_12"><head>Figure 12 Model for bumpstop element (∆ - clearance, - stiffness of the bumpstop)</head><label>12</label><figDesc>Figure 12 Model for bumpstop element (∆-clearance,-stiffness of the bumpstop)</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_13"><head>Figure 13 Model for center plate element (∆ - distance between center plate edge and car body center of gravity, - roll angle, - weight of the car body per one center plate, - roll torque, - equivalent roll stiffness)</head><label>13</label><figDesc>Figure 13 Model for center plate element (∆-distance between center plate edge and car body center of gravity,-roll angle,-weight of the car body per one center plate,-roll torque,-equivalent roll stiffness)</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_14"><head>Figure 15 : Procedure to find the non-linear critical speed [ 60 ].</head><label>1560</label><figDesc>Figure 15: Procedure to find the non-linear critical speed [60].</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_15"><head>Figure 16 : Bifurcation diagram for a loaded two-axle vehicle with link suspension ( 21 t axle load) Wheel: somewhat worn S1002. Rail: Nominal UIC60 [ 42 ].</head><label>162142</label><figDesc>Figure 16: Bifurcation diagram for a loaded two-axle vehicle with link suspension (21 t axle load) Wheel: somewhat worn S1002. Rail: Nominal UIC60 [42].</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_16"><head>Figure 17 .</head><label>17</label><figDesc>shows attractors for two different types of freight wagons. The results are in principle quite similar to those in figure 16.</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_17"><head>Figure 17 : Attractors for the Hbbills 311 and the G69 freight wagons. The model with the measured characteristics of the UIC links is damping less than the model with the cylindrical characteristics. The hunting attractor exists even for low speeds [61].</head><label>17</label><figDesc>Figure 17: Attractors for the Hbbills 311 and the G69 freight wagons. The model with the measured characteristics of the UIC links is damping less than the model with the cylindrical characteristics. The hunting attractor exists even for low speeds [61].</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_18"><head>Figure 18 Map of lateral oscillation amplitude in single wagon as function of curve radius [62].</head><label>18</label><figDesc>Figure 18 Map of lateral oscillation amplitude in single wagon as function of curve radius [62].</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_19"><head>Figure 19 : Energy dissipation. Comparative simulation with and without track irregularities. Two-axle vehicle with link suspension. 22 . 5 t axle load [ 42 ].</head><label>1922542</label><figDesc>Figure 19: Energy dissipation. Comparative simulation with and without track irregularities. Two-axle vehicle with link suspension. 22.5 t axle load [42].</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_20"><head>Figure 20 : Angle of attack (a) and wear number (b) for wagons in a curve of 200 m radius at 60 km/h with 18- 100 bogies respectively bogies with radial arm upgrade [ 15 ].</head><label>2010015</label><figDesc>Figure 20: Angle of attack (a) and wear number (b) for wagons in a curve of 200 m radius at 60 km/h with 18-100 bogies respectively bogies with radial arm upgrade [15].</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_21"><head>Figure 21 : Y25 bogie running in a 300m curve Wheel slip lateral and longitudinal at all wheel rail contact points, 90 t tank car with a Y25-Bogie in a 300 m curve, speed 80 km/h, lateral acceleration aq= 0, 67 m/s², s1002 Wheel profile, UIC 60E1, 1 Figure 22 : Radially steered bogie running in a 300 m curve Wheel slip lateral and longitudinal at all wheel- rail contact points, 90 t tank car with a Leila-Bogie in a 300 m curve, speed 80 km/h, lateral acceleration aq= 0, 67 m/s², s1002 Wheel profile, UIC 60E1, 1</head><label>21903006712230090300671</label><figDesc>Figure 21: Y25 bogie running in a 300m curve Wheel slip lateral and longitudinal at all wheel rail contact points, 90 t tank car with a Y25-Bogie in a 300 m curve, speed 80 km/h, lateral acceleration aq= 0,67 m/s², s1002 Wheel profile, UIC 60E1, 1:40 rail inclination</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_22"><head>Figure 23 : Calculated RCF positions of the wheel with corresponding average wear number. The far-left line is also reported as the observed approximate location for RCF initiation.</head><label>23</label><figDesc>Figure 23: Calculated RCF positions of the wheel with corresponding average wear number. The far-left line is also reported as the observed approximate location for RCF initiation.</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_23"><head>Figure 24 :</head><label>24</label><figDesc>Figure 24: The HSFV.1 experimental freight wagon</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_24"><head>Figure 25 :</head><label>25</label><figDesc>Figure 25: Unitruck running gear (left) and modifications for improving curving behaviour (right).</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_25"><head>Figure 28 :</head><label>28</label><figDesc>Figure 28: The TF25 bogie</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_26"><head>Figure 29 : The Gigabox bogie Figure 30 :</head><label>2930</label><figDesc>Figure 29: The Gigabox bogie</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_27"><head>Figure 31 : The DRRS bogie and cross section</head><label>31</label><figDesc>Figure 31: The DRRS bogie and cross section</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_28"><head>Figure 32 :</head><label>32</label><figDesc>Figure 32: Split wedge (left) and spatial wedge (right).</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_30"><head>Figure 33 : Adapter Plus ® by Amsted (left) and layered shear pad in Russian 18- 9800 bogie (right).</head><label>339800</label><figDesc>Figure 33: Adapter Plus ® by Amsted (left) and layered shear pad in Russian 189800 bogie (right).</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_31"><head>Figure 34 : Constant contact side bearing with springs (left) and with non-metal element and roller (right).</head><label>34</label><figDesc>Figure 34: Constant contact side bearing with springs (left) and with non-metal element and roller (right).</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_32"><head>Figure 37 :</head><label>37</label><figDesc>Figure 37: The Lenoir pusher spring</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_33"><head>Figure 38 : RC25NT bogie with direct inter-axle linkages Figure 39 : Simulation stability results for RC25NT bogie vs. Y25 bogie (upper figure = high conicity, lower figure = low conicity)Figure 40 : Simulated wear number for RC25NT bogie vs. Y25 bogie</head><label>383940</label><figDesc>Figure 38: RC25NT bogie with direct inter-axle linkages</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_34"><head>Figure 41</head><label>41</label><figDesc>Figure 41 and 42 show the main components of this bogie. Compared to the standard bogies such as Y25, the LEILA bogie has inner bearings. The resulting better force flow lead to a weight reduction of the bogie frame and wheelset resulting in an overall weight reduction of 750 kg per bogie compared to Y25 bogie. At the web of the wheels (diameter: 920 mm), disc brakes are mounted. The primary layer consists of rubber springs and the load dependent stiffness characteristics are separated in vertical and horizontal working components. The bogie has passive radial steering technology of the wheelsets. Wheelsets are able to rotate about the vertical axis without any external energy but only by the roll radius difference between the inner and outer wheel. Both wheelsets are connected with cross anchors; mounted on opposite axle boxes. The secondary layer is defined UIC centre of pivot and side bearer (latter guarantees the exchangeability to Y25 bogies). In addition, the centre of pivot has an elastically bearing using a secondary rubber spring. The LEILA bogie prototype was examined during various field tests where it demonstrated its advantages compared to a Y25 bogie. The noise emissions were reduced up to 18 dB(A) compared to a Y25 bogie with cast iron brake blocks and up to 8 dB(A) compared to a Y25 bogie with composite blocks (kblocks). But the bogie failed at that time to enter the market. During the very good ongoing homologation process the producer of the bogie decided to stop the production of new freight wagons and bogies. Therefore the homologation was stopped and not finished just for commercial reasons. Right now as more and more EMUs are produced with inner bearings it is expected that the acceptability of inner bearing bogies with the advantages less weight and lower forces at the axles in curves will be more acceptable.</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_35"><head>Figure 41 : Main components of LEILA bogie [ 88 ] Figure 42 : Leila Bogie from beneath with the inner bearings, cross anchor and wheel disc brakes clearly visible 4 .</head><label>4188424</label><figDesc>Figure 41: Main components of LEILA bogie [88]</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_36"><head>Figure 43 : TVP2007 bogie by Tatravagónka a.s.</head><label>43</label><figDesc>Figure 43: TVP2007 bogie by Tatravagónka a.s.</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_37"><head>Figure 44 :</head><label>44</label><figDesc>Figure 44: A suspension with double Lenoir links</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_38"><head>Figure 46 : A sample simulation results showing the establishment of the critical speed for the SUSTRAIL vehicle with double Lenoir links</head><label>46</label><figDesc>Figure 46: A sample simulation results showing the establishment of the critical speed for the SUSTRAIL vehicle with double Lenoir links</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_39"><head>Figure 47 :</head><label>47</label><figDesc>Figure 47: The effect of Lenoir link angle, length and friction coefficient on the critical speed of the SUSTRAIL vehicle</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_40"><head>Figure 48 : Maximum vertical force on the rail for the SUSTRAIL vehicle running at 120 km/h</head><label>48</label><figDesc>Figure 48: Maximum vertical force on the rail for the SUSTRAIL vehicle running at 120 km/h</figDesc></figure> +<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_41"><head>Figure 50 :</head><label>50</label><figDesc>Figure 50: The prototype SUSTRAIL freight bogie</figDesc></figure> + + <note place="foot" n="1">-side frame; 2-bolster; 3-wheelset; 4-primary suspension; 5-elastic connection between sub-frames Figure 36: Scheffel HS bogie (left) and bogie retrofitted with Radial Arm design (right).</note> + </body> + <back> + <div type="references"> + + <listBibl> + +<biblStruct xml:id="b0"> + <analytic> + <title level="a" type="main">European freight vehicle running gear: today's position and future demands</title> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="middle">M</forename><surname>Hecht</surname></persName> + </author> + </analytic> + <monogr> + <title level="j">PartF, Journal of Rail and Rapid Transit</title> + <imprint> + <biblScope unit="volume">215</biblScope> + <biblScope unit="page" from="1" to="11" /> + <date type="published" when="2001" /> + </imprint> + </monogr> + <note>Proc. 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padding-top: 1em;"> + +<h3 class="blue-space">D-Lib Magazine</h3> +<p class="blue">May/June 2017<br /> +Volume 23, Number 5/6<br /> +<a href="../05contents.html">Table of Contents</a> +</p> + +<div class="divider-full"> </div> + +<h3 class="blue-space">Transforming Libraries and Archives through Crowdsourcing</h3> + +<p class="blue">Victoria Van Hyning, University of Oxford, Zooniverse<br /> +victoria [at] zooniverse.org<br /><br /> + +Samantha Blickhan, The Adler Planetarium, Zooniverse<br /> +samantha [at] zooniverse.org<br /><br /> + +Laura Trouille, The Adler Planetarium, Zooniverse<br /> +trouille [at] zooniverse.org<br /><br /> + +Chris Lintott, University of Oxford, Zooniverse<br /> +chris [at] zooniverse.org</p> + +<div class="divider-dot"> </div> + +<p><a href="https://doi.org/10.1045/may2017-vanhyning" class="nolinka">https://doi.org/10.1045/may2017-vanhyning</a></p> + +<div class="divider-full"> </div> + <!-- Abstract or TOC goes here --> + +<h3 class="blue">Abstract</h3> + +<p class="blue">This article will showcase the aims and research goals of the project entitled "Transforming Libraries and Archives through Crowdsourcing", recipient of a 2016 Institute for Museum and Library Services grant. This grant will be used to fund the creation of four bespoke text and audio transcription projects which will be hosted on the Zooniverse, the world-leading research crowdsourcing platform. These transcription projects, while supporting the research of four separate institutions, will also function as a means to expand and enhance the Zooniverse platform to better support galleries, libraries, archives and museums (GLAM institutions) in unlocking their data and engaging the public through crowdsourcing.</p> + +<p class="blue">Keywords: Crowdsourcing, Citizen Humanities, GLAM, Transcription, IMLS</p> + +<!-- Article goes next --> + +<div class="divider-full"> </div> +<h3>1 Overview<span style="vertical-align: super;"><a href="#n6">1</a></span></h3> + +<p>As libraries, museums, and other cultural repositories digitize their collections and place them online, the challenges of transforming these materials into useful and searchable sources of information are becoming increasingly apparent. While OCR and handwriting recognition technology have opened up some print and manuscript corpora, and image and voice recognition software are improving daily, there are still many tasks that require human intervention. For these, volunteer crowdsourcing is a viable and vibrant solution.</p> + +<p>The <a href="https://www.zooniverse.org/">Zooniverse</a> is the world-leading research crowdsourcing platform, hosting over 50 active projects and over 100 projects total since its inception in 2007. The projects cover diverse subject areas from astronomy to zoology, engage over 1.5 million registered volunteers, and have produced data used in more than a hundred peer-reviewed articles.<span style="vertical-align: super;"><a href="#n1">2</a></span> The Zooniverse also hosts the <a href="https://www.zooniverse.org/lab">Project Builder</a>, a free platform through which anyone can build their own project. The Zooniverse grew from a single project developed at the University of Oxford in 2007, and is now developed and managed by a team based in Oxford and at the Adler Planetarium in Chicago and the University of Minnesota (see <a href="https://www.zooniverse.org/about/team">Zooniverse Team</a> for a more complete list).</p> + +<p>In late 2016, the Institute for Museum and Library Services awarded a National Leadership Grant titled "Transforming Libraries and Archives through Crowdsourcing (LG-71-16-0028-16)" to the Adler Planetarium and its collaborators to support the work of the Zooniverse. Through this grant-funded effort, the Zooniverse will further expand and enhance its platform to better support galleries, libraries, archives, and museums (GLAM institutions) in unlocking their data and engaging the public through crowdsourcing. </p> + +<div class="divider-dot"> </div> +<h4>1.1 What Can Crowdsourcing Offer GLAMs?</h4> + +<p>In 2010, author and professor Clay Shirky delivered a rousing <a href="https://www.ted.com/talks/clay_shirky_how_cognitive_surplus_will_change_the_world">TED</a> talk in which he used the phrase "cognitive surplus" to describe the one trillion hours of leisure time humans collectively accumulate each year (a great deal of which is spent watching television), which could be harnessed to advance human knowledge through civic engagement. He concluded that: "free cultures get what they celebrate. [...If we] celebrate and support and reward the people trying to use cognitive surplus to create civic value [...] we'll be able to change society".[<a href="#1">1</a>] One way that GLAMs can harness this cognitive surplus is through web-based crowdsourcing. What Shirky was describing was a type of "social machine", which Tim Berners-Lee defined as "new form[s] of social processes" emergent from the Web, and involving both human and machine components.[<a href="#2">2</a>] </p> + +<p>Academic crowdsourcing invites members of the public to work with specialists to conduct research: for example, to transcribe documents or add metadata to a collection of images, video or audio clips. This data is used in real science, social science, or humanities investigations and should, ideally, lead to publication. Crowdsourcing within GLAMs may not always be oriented around a specific research question or publication, but around making collections more accessible for future research and usability. GLAM crowdsourcing can be the seedbed of future scholarly research.</p> + +<p>GLAMs have been engaging volunteers with their collections for well over a century, usually by inviting select individuals into an institution and training them to do work that cannot be done by staff due to time or money constraints. On-site volunteers often build up valuable knowledge and skills and contribute a great deal to their chosen institutions, but training and supervising them also poses challenges. There is a limit to how many volunteers can be trained, supported on site, and indeed attracted and retained in the first place. Online volunteering, enabled by crowdsourcing platforms such as Zooniverse.org, offer an alternative or complementary form of engagement that has many benefits. Online projects can reach a wider range of individuals, including those who are less able-bodied or geographically remote from the institution in which they want to volunteer and/or unable to travel. Such projects require less training and time commitment from volunteers and typically attract a larger number of participants than on-site programs. They also enable GLAMs to open up rare collections to the public without concern for their material safety and security.<span style="vertical-align: super;"><a href="#n2">3</a></span></p> + +<p>While crowdsourcing projects have proliferated in the last decade, few offer easy to use, open source, and free platforms on which GLAM academics and amateur users can rely. The Zooniverse has the infrastructure, community, and technical expertise to intervene at this critical stage. </p> + +<div class="divider-dot"> </div> +<h4>1.2 How Does The Zooniverse Work?</h4> + +<p>All bespoke Zooniverse projects, including those built on the free Project Builder, have a few core components. Each image, audio or video file (data point) in each project is independently assessed by multiple individuals, whose responses are then aggregated using a variety of algorithms to determine what is in a given image. The amount of required responses for a task to be considered "complete" varies, depending on the project. With relatively quick tasks, such as animal identification in Snapshot Serengeti, upwards of 70 people will see each image. In tasks that require more time, such as transcription projects like <a href="https://www.shakespearesworld.org/#!/">Shakespeare's World</a> and <a href="https://anno.tate.org.uk/#!/">AnnoTate</a>, at least three people transcribe each line on each page. If enough people transcribe the same line and our algorithms deem the line to be completed to a good enough standard, these are greyed out, while outstanding lines are available to future site visitors. This approach was designed along the same principles that underpin all other Zooniverse projects, in which it is assumed that volunteers should work independently on tasks, in order that no one individual should have undue influence over others in the crowd. In the current IMLS project, however, we will test whether allowing volunteers to transcribe and work collaboratively ultimately creates better data and/or better user experiences. We will be able to compare datasets from AnnoTate and Shakespeare's World with text transcription datasets from the two new bespoke text transcription projects and, hopefully, with datasets generated at other institutions that have online crowdsourcing projects. Zooniverse is in a unique position in being able to gather these two very different kinds of data and compare them in order to determine the best outcomes. These findings will ultimately drive our design of free tools on the Project Builder. + +<p>In addition to participating in the classification task, users have the opportunity to communicate with other volunteers through an active, object-oriented discussion forum, called "Talk", associated with each project. Here volunteers can ask questions, interact with researchers and fellow volunteers, create their own "collections", and use hashtags to group together posts or images of interest. An example of the latter is <a href="https://talk.sciencegossip.org/#/search?tags%5Bfemale%5D=true">#female</a> from the <a href="https://www.sciencegossip.org/">Science Gossip</a> project, which indicates female authors, illustrators and printers contributing to the main scientific journals in the nineteenth century (visit the <a href="https://talk.sciencegossip.org/#/boards/BSC0000004/discussions/DSC00004s8">Science Gossip Talk</a> board to view the discussion around this tag). These interactions provide a rich set of experiences that allow users to personally experience the community in which they are participating, beyond simply providing classifications. Additionally, the collections allow volunteers to create their own research focal points within existing projects. During the process of transcribing, users can save images that contain content that is pertinent to their research interests by adding them to a public collection. They can then use the Talk forum to publicize their search, allowing other users to add images to that collection as well. In this way, the volunteer base can be mobilized to help other volunteers with minimal effort required.</p> + +<div class="divider-full"> </div> +<h3>2 IMLS Funded Effort: Approach and Focus</h3> + +<p>Through the IMLS grant, the Zooniverse will engage in a research and development program to identify and implement crowdsourcing best practices in the arenas of text and audio transcription for the purposes of unlocking big data currently trapped in GLAM sources that cannot be machine read. Though to date the majority of Zooniverse projects have been based in STEM fields rather than in the humanities, several text transcription projects have already been hosted on the site. For example, the first Zooniverse humanities project was <a href="https://www.ancientlives.org/">Ancient Lives</a>, which invited volunteers to transcribe ancient papyri one letter at a time using a clickable keyboard on their screen: volunteers did not have to be fluent in ancient Greek, they only needed to character match. Over 250,000 volunteers participated in the project, and made more than 1.5 million transcriptions between 2011 and 2014.[<a href="#6">3</a>] Furthermore, the computational pipeline used to convert individual identified letters into consensus-based transcriptions will benefit future classification projects attempting consensus letter or line sequence identifications.[<a href="#7">4</a>]</p> + +<p>By 2018 we will build four bespoke projects, two projects for text transcription and two projects for audio transcription, identified through open calls, in order to test, iterate, and research the efficacy of new and existing approaches (including within current Zooniverse and other projects) in these arenas. We will also develop the foundation for a GLAM-friendly data pipeline to export data from a Zooniverse project into GLAM collections. These functionalities are among those most frequently requested by GLAM institutions. We will work closely with four different GLAM institutions to build these bespoke crowdsourcing projects and functionalities. The text transcription open call closed in February 2017, with thirty-one submissions. The audio transcription open call will occur in fall 2017 (see <a href="http://zooniverse.org/get-involved/call-for-projects">Call for Projects</a>).</p> + +<p>From the lessons learned in building these bespoke projects, we will explore adding new tools and functionality to the Project Builder, which is freely available to any institution or user who wishes to lead a project. It is a flexible, powerful, and easy-to-use resource for building crowdsourcing projects, with a wide range of potential applications for GLAM collections, including text transcription. A basic text transcription tool is currently available, but will be refined through this grant effort. The Zooniverse has previously used this model of building bespoke projects in order to learn which tools are most useful, before implementing these tools in the Project Builder. We recognize that volunteers' time is precious, and are therefore unwilling to waste it with tools that are not proven to extract data in an efficient, high quality, and useful form. We will also draw on lessons learned from previous experiences supporting transcription projects through Zooniverse and other platforms. For example, <a href="https://www.operationwardiary.org/">Operation War Diary</a> which launched in 2014 to commemorate the outbreak of the First World War, is a partnership between the National Archives (UK), the Imperial War Museum, and the Zooniverse, which invites users to tag and transcribe dates, times, places, and names found in British WWI field diaries. Historian Richard Grayson has used the data to penetrate more deeply than ever before into records of soldiers' daily lives on the front.[<a href="#8">5</a>] All of the Operation War Diary metadata will eventually be integrated into the National Archive catalogues. The process of integrating new metadata into an existing catalogue can be complicated, raising an important question for any GLAM specialist seeking to harness crowdsourcing at their institution. For instance, it is essential to ensure, before starting a project, that the current content management system (CMS) supports the storage of additional metadata, such as large amounts of free-text. If not, it then becomes necessary to use an external resource to make available the results from the crowdsourcing project. Zooniverse can and will do more to facilitate GLAMs and research groups to use and store their data.</p> + +<p>Over the course of the IMLS project, we will also address the following research questions:</p> + +<p class="indentLeft">Q1: How can crowdsourcing be deployed in the arenas of text and audio transcription and metadata extraction for the purposes of unlocking big data currently trapped in GLAM sources that cannot be machine read? What methods produce the best data and make for the best user experience?</p> + +<p class="indentLeft">Q2: Does the current Zooniverse methodology of multiple independent transcribers and aggregation render better results than allowing volunteers to see previous transcriptions by others or indeed collaborate to create a single transcription? How does each methodology impact the quality of data, as well as depth of analysis and participation?</p> + +<p class="indentLeft">Q3: How can we extend our crowdsourcing expertise to more GLAM professionals and learn from them, in turn, how to adjust the Zooniverse platform to best meet their research and curatorial needs?</p> + +<div class="divider-dot"> </div> +<h4>2.1 Addressing Q1 (Crowdsourcing for GLAM)</h4> + +<p>Only a platform like the Zooniverse can systematically address a question such as Q1: the community that has developed within the platform is made up of volunteers who move across projects, allowing us to trace the impact of differences between projects on the same volunteers. Zooniverse also has the infrastructure to implement A/B split experiments within a single project. This allows us to develop projects incorporating different practices which are specifically aimed at understanding different methodologies. Through the bespoke text and audio transcription projects, we will expand on the lessons learned through current Zooniverse text transcription projects, including Ancient Lives, AnnoTate, Old Weather, Measuring the ANZACs, Shakespeare's World, Science Gossip, Decoding the Civil War, Orchid Observers and Operation War Diary, as well as from external text transcription projects including <a href="http://blogs.ucl.ac.uk/transcribe-bentham/">Transcribe Bentham</a>, <a href="http://fromthepage.com/">FromthePage</a>, and <a href="http://scripto.org/">Scripto</a>. </p> + +<p>In the bespoke projects created through the IMLS grant, the features optimizing volunteer engagement and retention will include: </p> + +<ul> + <li><i>Volunteer choice:</i> volunteers choose which document to transcribe and can transcribe as little as a single line or as much as an entire document. We have found through AnnoTate and Shakespeare's World that allowing users to transcribe smaller fragments of text (without being required to complete an entire page) mitigates against forced or uncertain readings. We hypothesize and plan to fully test whether allowing microtasking helps to retain volunteers, giving them the chance to build up their skills and not make forced readings. </li> + + <li><i>Keeping the task simple:</i> in Shakespeare's World and AnnoTate, volunteers drop points at the start and end of individual lines of text (not grammatical sentences) and transcribe the text contained between these two points. They do not use XML markup itself, which has proven to be a major repellent to participants in other text transcription crowdsourcing projects.<span style="vertical-align: super;"><a href="#n3">4</a></span> Instead, volunteers highlight words within the transcribed line and choose among different features (e.g., insertion, deletion, expansion, etc.). We propose to use these tagged words in each line to create simple TEI markup on the back-end, for output into commonly used CMSs such as Drupal and Omeka.</li> + + <li><i>Narrowing the content focus to support sense-making:</i> In Shakespeare's World, the first release (or "chapter") consists of recipes and letters, with more genres to follow. This type of structured approach will be applied to the bespoke projects, as this supports creation of narratives within diverse collections, which in turn enables subject experts to more easily foster, and volunteers to contribute to, discussions in Talk.</li> +</ul> + +<p>Features optimizing best practice in regard to data production and management will include:</p> + +<ul> + <li><i>Reliable, Scalable, Open Source Code Infrastructure:</i> The foundation for the Zooniverse platform that includes the Project Builder is an application written in Ruby on Rails which supports a powerful Application Programming Interface (API). The API serves subjects — images, video or audio — for classification by volunteers via a workflow defined by the project, and receives and records these classifications into a database. The frontend Javascript web software presents user interfaces to volunteers and supports the Project Builder. All Zooniverse code is open source and available through <a href="github.com/zooniverse">Github</a>.</li> + + <li><i>Data Ingestion into Zooniverse:</i> In the current Project Builder, research teams can upload batches of 500 to 1000 subjects (images, videos, or audio clips) at a time by simply dragging and dropping the files. For larger collections and for bespoke projects, typically the research team provides a hard drive and the Zooniverse team uploads the subjects to the API. Through the projects proposed here, we will create a system to better support direct ingestion of large subject sets through a user-friendly web interface, adding functionality to the foundation we already have in place within the Project Builder.</li> + + <li><i>Useful Output for Curation:</i> The Smithsonian Transcription Center is regularly cited as being successful in regard to their output being easily ingestible by CMSs.[<a href="#9">6</a>] Current Zooniverse transcription projects are not set up with this functionality. Currently, through our Project Builder for image annotation/marking projects, research teams can download the raw classification results (i.e. all classifications by all volunteers) as well as automatically-generated aggregated results that include confidence measures on consensus. Through this IMLS-funded effort, we will work with Meghan Ferriter of the Smithsonian Transcription Center, who is on our board of advisors, to design data outputs for full text transcription and full audio transcription that are suitable for ingestion into different GLAM CMSs. A key aspect of this effort is to continue exploring best practices and approaches for transcription aggregation and confidence metrics, building on our efforts with AnnoTate, Shakespeare's World, etc.</li> +</ul> + +<div class="divider-dot"> </div> +<h4>2.2 Addressing Research Q2 (Independent vs. Collaborative Transcription)</h4> + +<p>Through the two bespoke text transcription projects, we will investigate the impact on transcription quality and volunteer experience when volunteers transcribe in isolation versus with knowledge of how others have transcribed the same document. </p> + +<p>In terms of measuring impact on transcription quality, we will compare the rate of accuracy for individuals who transcribe in isolation on projects such as AnnoTate and Shakespeare's World versus individuals who see previous transcriptions. We will also compare the rate of accuracy in aggregated results for lines transcribed only by those working in isolation versus for lines in which all but the first transcriber sees previous transcriptions. In order to measure impact on volunteer experience, we will analyze the user behavior statistics we gather, e.g., number of transcriptions completed in a given session, length of session, number of sessions overall, sentiment analysis of discussion forum comments, etc.</p> + +<p>There are numerous open questions in this experiment: Does knowledge of other individuals' or collective transcriptions lead individuals down the wrong path? Is transcription more or less accurate if people work in isolation or with an awareness of other people's work? Does making transcriptions visible increase retention as a result of highlighting that an individual's effort is part of a broader community effort or have the opposite effect? What environment best promotes skills acquisition, i.e. improved paleography?</p> + +<div class="divider-dot"> </div> +<h4>2.3 Addressing Research Q3 (Feedback/Training)</h4> + +<p>We will provide numerous opportunities for input and feedback from and training for the GLAM community, specifically by working closely with our advisory board and four GLAM project partners throughout. In 2018 we will host feedback sessions at GLAM conferences and summer schools targeting GLAM institutions with collections for which text transcription, audio transcription, or image annotation/marking are of interest (we will include image annotation/marking because those tools are already included via the Project Builder). This will allow for input from a broader set of institutions on our decisions and approach for building new functionality into the Project Builder. In 2018—2019 we will host training workshops for GLAM professionals in using the Project Builder to build their own crowdsourcing projects, incorporate the results into their databases and research, and sustain and nurture their online volunteer communities.</p> + +<div class="divider-full"> </div> +<h3>3 Future Steps: Community Engagement, Output & How to Get Involved</h3> + +<p>The IMLS-Funded Project "Transforming Libraries and Archives through Crowdsourcing" is still in its beginning stages. Currently, we are in the process of selecting the first two bespoke crowdsourcing text transcription projects to be built and incorporated into the Zooniverse platform. The detail of our research questions will evolve alongside these new transcription projects, and during the research and development process we will use conference presentations and feedback sessions to gather input which can then guide the overall project design. The open call for the two bespoke audio transcription projects will occur in the fall of 2017. At this point, the bespoke text transcriptions will be in beta review, allowing us to take advantage of lessons learned through that first round of new projects. We believe that this self-reflexive method will simultaneously benefit our ongoing project while offering new tools and ideas to the larger GLAM and academic community.</p> + +<p>We anticipate this proposed effort will produce two peer-reviewed publications. One article will focus on the methodology for creating, processing, and evaluating the data produced by the new projects. The second will focus on the results of our research exploring the impact of individual versus collaborative text transcription. We also note that all Zooniverse <a href="github.com/zooniverse">code</a> is freely available under a liberal open source license which serves as an additional or parallel form of publication.</p> + +<p>GLAM organizations keen to develop their own crowdsourcing projects should explore the available documentation on <a href="https://www.zooniverse.org/lab-how-to">how to build a project</a> and <a href="https://www.zooniverse.org/lab-best-practices/great-project">best practices for the design, launch and long term phases of a project</a>. While building a project is easy and requires relatively little technical support from Zooniverse or your institution, make sure you have the time to work with your resulting data, and time to support your online volunteer commmunity. Advertising the project's existence should be a long-term task, to avoid a plateau or potential drop-off of user participation. For example, Shakespeare's World received a bump in the number of daily classifications after an article was published in The New Yorker in January of 2017, over a year after the project's launch date.[<a href="#10">7</a>] However, it does not suffice to merely advertise the existence of a project; researchers need to engage with their users on a regular basis.<span style="vertical-align: super;"><a href="#n5">5</a></span> Zooniverse's Talk platform, social media such as blogging, Twitter, Instagram, and indeed in-person or on-site events all provide important channels for engaging current or potential volunteers with your collections. We believe that GLAM organizations, with their long history of volunteer engagement, have many of the skills to work effectively with online volunteers, and will benefit in new ways through cooperation with the crowd.</p> + +<p>In conclusion, while this project is specifically focused on text and audio transcription, it is our hope that the results, including the new Project Builder tools and GLAM data pipeline, will ultimately be used across a variety of disciplines and domains. We hope to facilitate future partnerships between GLAM institutions and volunteer communities around the world, thus extending the aims and outcomes of the National Digital Platform funded through this generous IMLS grant into an international digital platform that will benefit many individuals and institutions. </p> + +<div class="divider-full"> </div> +<h3>Notes</h3> + +<table style="width:90%"> + +<tr> +<td style="padding-bottom: 12px; vertical-align: super;"><a id="n6">1</a></td> +<td style="padding-top: .5em;">Part of this article appeared previously as a blog post for CILIP, The Library and Information Association. Material is reproduced by express permission of CILIP.</td> +</tr> + +<tr> +<td style="padding-bottom: 12px; vertical-align: super;"><a id="n1">2</a></td> +<td style="padding-top: .5em;">For a partial list of publications, please visit <a href="https://www.zooniverse.org/about/publications">https://www.zooniverse.org/about/publications</a>. </td> +</tr> +<tr> +<td style="padding-bottom: 12px; vertical-align: super;"><a id="n2">3</a></td> +<td style="padding-top: .5em;">Further discussion of the use of crowdsourcing in GLAM contexts can be found in Melissa Terras, "Crowdsourcing in the Digital Humanities", in <i>A New Companion to Digital Humanities</i>, eds. Susan Schreibman, Ray Siemens, and John Unsworth (John Wiley & Sons, 2016), 420-438, particularly in the section entitled "The Growth of Crowdsourcing in Cultural and Heritage Applications" (pp. 423-28). See also <i>Crowdsourcing Our Cultural Heritage</i>, ed. Mia Ridge (Ashgate, 2014).</td> +</tr> +<tr> +<td style="padding-bottom: 12px; vertical-align: super;"><a id="n3">4</a></td> +<td style="padding-top: .5em;">Causer and Terras, "Many Hands Make Light Work", p. 81: "It would be fair to say that for volunteers, the XML mark-up complicates participation, and it has undoubtedly dissuaded many from participating more fully, or at all." For opinions from the volunteers about the process, the authors additionally refer the reader to Causer and Valerie Wallace, "<a href="http://www.digitalhumanities.org/dhq/vol/6/2/000125/000125.html">Building a Volunteer Community: Results and Findings from Transcribe Bentham</a>", <i>Digital Humanities Quarterly</i> 6.2 (2012).</td> +</tr> + +<tr> +<td style="padding-bottom: 12px; vertical-align: super;"><a id="n5">5</a></td> +<td style="padding-top: .5em;">Or, as Zephyr Frank, <i>et al</i>. put it: "Paid advertising can generate large numbers of clicks on a website. It cannot, however, produce good metadata or newly uploaded material that is relevant to the scholarly questions posed by academic researchers." "<a href="https://github.com/cestastanford/crowdsourcing/raw/master/files/Mellon%20White%20Paper.pdf">Crowdsourcing for Humanities Research</a>" (2016) Project White Paper. </td> +</tr> +</table> + +<div class="divider-white"> </div> +<div class="divider-full"> </div> +<h3>References</h3> + +<table style="width:90%"> +<tr> +<td style="padding-bottom: 12px; vertical-align: top;"><a id="1">[1]</a></td> +<td style="padding-bottom: 12px; vertical-align: top;">Clay Shirky, "<a href="https://www.ted.com/talks/clay_shirky_how_cognitive_surplus_will_change_the_world">How Cognitive Surplus Will Change the World</a>", June 2010.</td> +</tr> +<tr> +<td style="padding-bottom: 12px; vertical-align: top;"><a id="2">[2]</a></td> +<td style="padding-bottom: 12px; vertical-align: top;">Tim Berners-Lee with Mark Fischetti, <i>Weaving the Web: The Original Design and Ultimate Destiny of the World Wide Web by its Inventor</i> (San Francisco: Harper, 1999).</td> +</tr> + +<tr> +<td style="padding-bottom: 12px; vertical-align: top;"><a id="6">[3]</a></td> +<td style="padding-bottom: 12px; vertical-align: top;">"P.Oxy 5156, Plutarch Moralia 660C, 661B-C (Quaestiones Convivales IV PR., 1.2)", in <i>The Oxyrhynchus Papyri</i>, R.-L. Chang <i>et al</i>., eds, vol. 78 (London, Egypt Exploration Society, 2012), 97-98. </td> +</tr> + +<tr> +<td style="padding-bottom: 12px; vertical-align: top;"><a id="7">[4]</a></td> +<td style="padding-bottom: 12px; vertical-align: top;">Alex C. Williams <i>et al.</i>, "A Computational Pipeline for Crowdsourced Transcriptions of Ancient Greek Papyrus Fragments", in <i>IEEE International Conference on Big Data</i>, October 2014. <a href="https://doi.org/10.1109/BigData.2014.7004460">https://doi.org/10.1109/BigData.2014.7004460</a></td> +</tr> + +<tr> +<td style="padding-bottom: 12px; vertical-align: top;"><a id="8">[5]</a></td> +<td style="padding-bottom: 12px; vertical-align: top;">Richard Grayson, "A Life in the Trenches? The Use of Operation War Diary and Crowdsourcing Methods to Provide an Understanding of the British Army's Day-to-Day Life on the Western Front", <i>British Journal for Military History,</i> 2.2 (2016), 160-85.</td> +</tr> + +<tr> +<td style="padding-bottom: 12px; vertical-align: top;"><a id="9">[6]</a></td> +<td style="padding-bottom: 12px; vertical-align: top;">Katie Mika, "<a href="http://library.mcz.harvard.edu/blog/transcription-tools-survey-katie-mika-ndsr-resident">Transcription Tools: a survey by Katie Mika, NDSR Resident</a>", Harvard University, Ernst Mayr Library Blog.</td> +</tr> + +<tr> +<td style="padding-bottom: 12px; vertical-align: top;"><a id="10">[7]</a></td> +<td style="padding-bottom: 12px; vertical-align: top;">Roberta Kwok, "<a href="http://www.newyorker.com/tech/elements/crowdsourcing-for-shakespeare">Crowdsourcing For Shakespeare</a>", <i>The New Yorker</i>, 16 Jan. 2017. </td> +</tr> +</table> + +<div class="divider-white"> </div> +<div class="divider-full"> </div> +<h3>About the Authors</h3> + +<p class="blue"><b>Victoria Van Hyning</b> is a Junior Research Fellow at Pembroke College, and a British Academy Postdoctoral Fellow. Her current project, 'Court to Convent: Early Modern English Catholic Women's Autobiography', will reveal how Catholic women articulated selfhood in the period when it was illegal to practice Catholicism, 1535 to 1829. She is also the Humanities PI of Zooniverse.org, the world leading academic crowdsourcing organization. Her projects include <a href="https://www.sciencegossip.org">Science Gossip</a>, <a href="http://www.shakespearesworld.org">Shakespeare's World</a> and <a href="https://anno.tate.org.uk">AnnoTate</a>.</p> + +<div class="divider-dot"> </div> + +<p class="blue"><b>Samantha Blickhan</b> is the IMLS Postdoctoral Fellow in the Department of Citizen Science at the Adler Planetarium, working on transcription projects for the Zooniverse. She received her Ph.D. in Musicology from Royal Holloway, University of London, with a thesis on the palaeography of British song notation in the 12th and 13th centuries. Her research interests include music and perception, and their relationships with writing systems, technology and pedagogy.</p> + +<div class="divider-dot"> </div> + +<p class="blue"><b>Laura Trouille</b> is co-Investigator for Zooniverse and Director of Citizen Science at the Adler Planetarium where she leads the Zooniverse web development and Teen Programs teams. While earning her Ph.D. in astronomy in 2010 studying galaxy evolution, she also earned the Center for the Integration of Research, Teaching and Learning's Delta certificate for STEM education research. As a CIERA Postdoctoral Fellow at Northwestern University's CIERA Center for Astrophysics, she continued her research on active galaxies as well as co-led the Computational Thinking in STEM project, bringing computational thinking and modeling curricular materials to high school science and math teachers. </p> + +<div class="divider-dot"> </div> + +<p class="blue">Chris Lintott is a professor of astrophysics at the University of Oxford, where he is also a research fellow at New College. He is the principle investigator for Galaxy Zoo and the Zooniverse, and his own research focuses on novel modes of crowdsourcing for anomaly detection.</p> + +<div class="divider-full"> </div> + + <!-- Standard Copyright line here --> + +<div class="center"> +<p class="footer">Copyright ® 2017 Victoria Van Hyning, Samantha Blickhan, Laura Trouille and Chris Lintott</p> +</div> + +<div style="height:1px;background:#2b538e"></div> + +</div> +</form> +</body> +</html>
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+ + + <span class="date"> <time datetime="2019-04-18">Apr 18, 2019</time></span> + </div> + </div> + + +</header> + + + + + + + <div class="wrapper"> + + <div class="contextual-data"> + + <ul class="contextual-data__list" aria-label="The following contains the number of views, citations and annotations in this article"> + + <li class="contextual-data__item"><a href="/articles/44753#metrics">Cited 0</a></li> + <li class="contextual-data__item"><a href="/articles/44753#metrics">Views 807</a></li> + + <li class="contextual-data__item" data-hypothesis-trigger><span class="contextual-data__item__hypothesis_opener">Annotations</span> <button class="speech-bubble speech-bubble--small " + data-behaviour="SpeechBubble HypothesisOpener" + +aria-live="polite"> + <span class="speech-bubble__inner"><span aria-hidden="true"><span data-visible-annotation-count></span></span><span class="visuallyhidden"> Open annotations. 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These RNs in turn extend axons through the neck to the MG. Among this cluster are the six prRNs and eight pr-AMG RNs (<a href="#fig1">Figure 1</a>; (<a href="#bib43">Ryan et al., 2016</a>)). Previous in situ hybridization studies identified VGAT- and VACHT-expressing neurons in the appropriate place in the BV to be RNs (<a href="#bib56">Yoshida et al., 2004</a>). Moreover, these neurons project axons posteriorly to the MG, a defining characteristic of the pBV RNs. BV neurons expressing other major NTs, including glutamate, dopamine, and serotonin, are neither in the correct brain region to be RNs, nor do they project from the BV to the MG ([<a href="#bib20">Horie et al., 2008b</a>; <a href="#bib31">Moret et al., 2005</a>; <a href="#bib39">Pennati et al., 2007</a>], and our observations). By HCR in situ we observed that the pBV RNs cluster in two distinct groups along the anterior/posterior axis, with the anterior cluster expressing VACHT, and the posterior group expressing VGAT (<a href="#fig3">Figure 3a</a>). We observed an average of 16 (±1.6, n = 9 larvae) VGAT-positive neurons and 11 (±1, n = 8 larvae) VACHT-positive neurons.</p> + <div + id="fig3" + class="asset-viewer-inline asset-viewer-inline-- " + data-variant="" + data-behaviour="AssetNavigation AssetViewer ToggleableCaption" + data-selector=".caption-text__body" + data-asset-viewer-group="fig3" + data-asset-viewer-uri="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig3-v2.tif/full/1500,/0/default.jpg" + data-asset-viewer-width="1500" + data-asset-viewer-height="1109" + > + + <div class="asset-viewer-inline__header_panel"> + <div class="asset-viewer-inline__header_text"> + <span class="asset-viewer-inline__header_text__prominent">Figure 3</span> with 1 supplement <a href="/articles/44753/figures#fig3" class="asset-viewer-inline__header_link">see all</a> + </div> + + + <div class="asset-viewer-inline__figure_access"> + <a href="https://elifesciences.org/download/aHR0cHM6Ly9paWlmLmVsaWZlc2NpZW5jZXMub3JnL2xheDo0NDc1MyUyRmVsaWZlLTQ0NzUzLWZpZzMtdjIudGlmL2Z1bGwvZnVsbC8wL2RlZmF1bHQuanBn/elife-44753-fig3-v2.jpg?_hash=poB6zI7Tss9wKOFGYwhd40WSG4X9%2B4%2FgYw9ffJwpELo%3D" class="asset-viewer-inline__download_all_link" download="Download"><span class="visuallyhidden">Download asset</span></a> + <a href="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig3-v2.tif/full/1500,/0/default.jpg" class="asset-viewer-inline__open_link" target="_blank" rel="noopener noreferrer"><span class="visuallyhidden">Open asset</span></a> + </div> + + </div> + + <figure class="captioned-asset"> + + <a href="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig3-v2.tif/full/1500,/0/default.jpg" class="captioned-asset__link" target="_blank" rel="noopener noreferrer"> + <picture class="captioned-asset__picture"> + <source srcset="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig3-v2.tif/full/1234,/0/default.webp 2x, https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig3-v2.tif/full/617,/0/default.webp 1x" + type="image/webp" + > + <source srcset="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig3-v2.tif/full/1234,/0/default.jpg 2x, https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig3-v2.tif/full/617,/0/default.jpg 1x" + type="image/jpeg" + > + <img src="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig3-v2.tif/full/617,/0/default.jpg" + + alt="" + class="captioned-asset__image" + > + </picture> + </a> + + + + + <figcaption class="captioned-asset__caption"> + + <h6 class="caption-text__heading">Neurotransmitter use in the relay neurons.</h6> + + + <div class="caption-text__body"><p class="paragraph">(<b>a</b>) In situ hybridization of VGAT and VACHT to the relay neurons in the brain vesicle. Also visible is the anterior tip of the motor ganglion. Nuclei are shown as spheres. (<b>b</b>) Confusion matrix for relay neuron registration. (<b>c</b>) Confusion matrix for relay neurons grouped by type. (<b>d</b>) Heat map of neurotransmitter predictions from cell registration of relay neurons, with scale showing color by proportion of iterations predicting either VGAT or VACHT. Abbreviations: ant., anterior; post., posterior; dor., dorsal; vent., ventral; MG, motor ganglion; pr-AMG RN, photoreceptor ascending motor ganglion relay neuron; prRN, photoreceptor relay neuron; AntRN, antenna cell relay neuron; PBRN, photoreceptor-bipolar tail neuron relay neuron; PCRN, photoreceptor-coronet relay neuron; PNRN, peripheral relay neuron; VGAT, vesicular GABA transporter; VACHT, vesicular acetylcholine transporter.</p> +</div> + + <span class="doi doi--asset"><a href="https://doi.org/10.7554/eLife.44753.007" class="doi__link">https://doi.org/10.7554/eLife.44753.007</a></span> + + </figcaption> + + + + + </figure> + + + </div> +<p class="paragraph">Unlike the ocellus, the pBV RN cluster does not have obvious anatomical features, although the various classes of RNs are clustered, with, for example, the antenna cell RNs (AntRN) being posterior to the photoreceptor RNs (<a href="/articles/44753/figures#fig3s1">Figure 3—figure supplement 1</a>; <a href="#bib43">Ryan et al., 2016</a>). However, given the diversity of RN types in the pBV it is unlikely that the expression domains of VGAT and VACHT precisely correspond to the clusters of RN classes. In order to make predictions of NT use in the RNs we used the same registration approach as with the photoreceptors (n = 7 VGAT/VACHT double in situ datasets, <a href="/articles/44753/figures#fig3s1">Figure 3—figure supplement 1</a>). The confusion matrix for the RNs shows a lower level of convergence than for the PR-Is, suggesting that the cellular anatomy of the RN cluster is less structured than the ocellus (<a href="#fig3">Figure 3b</a>; <a href="/articles/44753/figures#fig3s1">Figure 3—figure supplement 1</a>). However, the confusion matrix also shows that the RNs are most often confused for other RNs of the same class (white boxes in <a href="#fig3">Figure 3b</a>). This is most evident when the registration is performed not with single cells, but with pooled RNs of each class (<a href="#fig3">Figure 3c</a>), and is presumably a reflection of the clustering of RN classes in the pBV. Thus we can have higher confidence in the NT use by RN class than we can have in individual neuron identities. For example, the connectome shows the AntRNs are clustered at the rear of the BV (<a href="/articles/44753/figures#fig3s1">Figure 3—figure supplement 1</a>; (<a href="#bib43">Ryan et al., 2016</a>)), as are the VGAT expressing neurons (<a href="#fig3">Figure 3a</a>; <a href="/articles/44753/figures#fig3s1">Figure 3—figure supplement 1</a>). Accordingly, the registration predicts that eight of the ten AntRNs are VGAT positive (<a href="#fig3">Figure 3c</a>). For the present study, which focuses on the visuomotor pathway, the registration predicts that five of the eight pr-AMG RNs are VGAT expressing, two are VACHT expressing, and one (pr-AMG RN 157) cannot be resolved (no dual VGAT/VACHT expression was observed in the <i>in situs</i>). On the other hand, the registration predicts that the six prRNs are evenly mixed between VGAT and VACHT expression. These predictions provide starting points for experimental validation detailed below.</p> + + + + + </div> + +</section> +<section + class="article-section " + id="s2-3" + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">The motor ganglion contains a mixture of cholinergic and GABAergic neurons</h3> + </header> + + <div class="article-section__body"> + <p class="paragraph">The MG contains five left/right pairs of motor neurons, as well as several classes of interneurons, including six MGINs, seven AMGs, two ddNs, and two posterior MG interneurons (<a href="#bib43">Ryan et al., 2016</a>). Also described in the MG are two left/right pairs of decussating VGAT-positive neurons (<a href="#bib21">Horie et al., 2009</a>; <a href="#bib35">Nishino et al., 2010</a>). These are likely the same decussating MG neurons as described in the connectome, although the names are slightly different (<i>anterior caudal inhibitory neurons</i> (<a href="#bib21">Horie et al., 2009</a>) versus <i>ascending contralateral inhibitory neurons</i> (<a href="#bib43">Ryan et al., 2016</a>), both abbreviated as ACIN). However, the connectome reports only three ACINs, with the anterior ACIN not paired. It was speculated that this was an anomalous feature of the particular larva used for the ssEM. Supporting this, a second larva being analyzed by ssEM for connectomics shows two pairs of ACINs (K. Ryan, personal communication).</p> +<p class="paragraph">Like the ocellus, the MG has a well-defined anterior-to-posterior and dorsal-to-ventral cellular anatomy (<a href="#fig4">Figure 4a and b</a>; <a href="#bib43">Ryan et al., 2016</a>; <a href="#bib45">Ryan et al., 2018</a>). Neurotransmitter use by some MG neurons is already documented, including the motor neurons, which are cholinergic (<a href="#bib53">Takamura et al., 2010</a>; <a href="#bib52">Takamura et al., 2002</a>), and the ACINs which are glycinergic (<a href="#bib35">Nishino et al., 2010</a>). By HCR in situ hybridization we observed VGAT- and VACHT-positive neurons in the MG (<a href="#fig4">Figure 4b</a>), but no VGLUT- or TH-positive cells (data not shown). These results are consistent with previous studies (<a href="#bib20">Horie et al., 2008b</a>; <a href="#bib31">Moret et al., 2005</a>). Likewise it was reported that no serotonergic cells were present in the MG (<a href="#bib39">Pennati et al., 2007</a>). As with the RNs, the VGAT- and VACHT-expressing neurons in the MG are segregated anatomically. We also found a population of 6–7 cells between the AMGs and the MNs (asterisks in <a href="#fig4">Figure 4a</a>), that were not annotated in the connectome as neurons and that failed to label with any of our NT markers. We hypothesize that these are ependymal cells, which are abundant in the nerve cord immediately caudal to this region.</p> + <div + id="fig4" + class="asset-viewer-inline asset-viewer-inline-- " + data-variant="" + data-behaviour="AssetNavigation AssetViewer ToggleableCaption" + data-selector=".caption-text__body" + data-asset-viewer-group="fig4" + data-asset-viewer-uri="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig4-v2.tif/full/,1500/0/default.jpg" + data-asset-viewer-width="1274" + data-asset-viewer-height="1500" + > + + <div class="asset-viewer-inline__header_panel"> + <div class="asset-viewer-inline__header_text"> + <span class="asset-viewer-inline__header_text__prominent">Figure 4</span> with 1 supplement <a href="/articles/44753/figures#fig4" class="asset-viewer-inline__header_link">see all</a> + </div> + + + <div class="asset-viewer-inline__figure_access"> + <a href="https://elifesciences.org/download/aHR0cHM6Ly9paWlmLmVsaWZlc2NpZW5jZXMub3JnL2xheDo0NDc1MyUyRmVsaWZlLTQ0NzUzLWZpZzQtdjIudGlmL2Z1bGwvZnVsbC8wL2RlZmF1bHQuanBn/elife-44753-fig4-v2.jpg?_hash=ywXgEBLsOzGfI3rEs2OHLvcZSgqwkJ8EhBicEWmfAJ8%3D" class="asset-viewer-inline__download_all_link" download="Download"><span class="visuallyhidden">Download asset</span></a> + <a href="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig4-v2.tif/full/,1500/0/default.jpg" class="asset-viewer-inline__open_link" target="_blank" rel="noopener noreferrer"><span class="visuallyhidden">Open asset</span></a> + </div> + + </div> + + <figure class="captioned-asset"> + + <a href="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig4-v2.tif/full/,1500/0/default.jpg" class="captioned-asset__link" target="_blank" rel="noopener noreferrer"> + <picture class="captioned-asset__picture"> + <source srcset="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig4-v2.tif/full/1234,/0/default.webp 2x, https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig4-v2.tif/full/617,/0/default.webp 1x" + type="image/webp" + > + <source srcset="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig4-v2.tif/full/1234,/0/default.jpg 2x, https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig4-v2.tif/full/617,/0/default.jpg 1x" + type="image/jpeg" + > + <img src="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig4-v2.tif/full/617,/0/default.jpg" + + alt="" + class="captioned-asset__image" + > + </picture> + </a> + + + + + <figcaption class="captioned-asset__caption"> + + <h6 class="caption-text__heading">Neurotransmitter use in the motor ganglion.</h6> + + + <div class="caption-text__body"><p class="paragraph">(<b>a</b> and <b>b</b>) Expression of VGAT and VACHT by in situ hybridization in the motor ganglion, lateral (<b>a</b>) and dorsal (<b>b</b>) views. Asterisks indicate predicted ependymal cells. (<b>c</b>) Lateral view of VGAT expression in the AMGs. (<b>d</b>) shows same view as c, but with VACHT expression. (<b>e</b>) Diagram of neurons in the motor ganglion (derived from Figure 1 of <a href="#bib44">Ryan et al., 2017</a>). Box indicates approximate positions of panels c and d. Lateral view; anterior is to the left. (<b>f</b>) Dorsal view of VGAT expression in the AMGs. Asterisk indicates central non-VGAT expressing cell. (<b>g</b>) Three dimensional surface rendering of VGAT expressing cells in the AMGs. (<b>h</b>) Diagram of a dorsal view of the motor ganglion. AMG cells are numbered. Abbreviations: dor., dorsal; vent., ventral; ant., anterior; post., posterior; AMG, ascending motor ganglion neuron; MGIN, motor ganglion interneuron; ddN, descending decussating neurons; ACIN, ascending contralateral inhibitory neurons; MN, motor neuron; VGAT, vesicular GABA transporter; VACHT, vesicular acetylcholine transporter.</p> +</div> + + <span class="doi doi--asset"><a href="https://doi.org/10.7554/eLife.44753.009" class="doi__link">https://doi.org/10.7554/eLife.44753.009</a></span> + + </figcaption> + + + + + </figure> + + + </div> +<p class="paragraph">Because of the highly structured MG cellular anatomy, we can identify the various MG cell types in the in situ data. The anterior group of VGAT-positive cells is clustered dorsally in the MG, and correspond to AMGs (4 c, d and e; (<a href="#bib44">Ryan et al., 2017</a>)). In a dorsal view of the MG (<a href="#fig4">Figure 4f,g and h</a>) a ring of VGAT-positive cells was observed with a non-VGAT expressing cell in the center (asterisk, <a href="#fig4">Figure 4f and g</a>). The VGAT-expressing cells appear to be AMGs 1, 2, 3, 4, 6, and 7, while the central cell, which is instead positive for VACHT, appears to be AMG5. The connectome shows that AMG5 differs in its connectivity from the other AMGs. Significantly, AMG5 is the principle synaptic input for PNS neurons. It then synapses to the other AMGs, which in turn project their axons to other cells in the MG, including MGINs and MNs, as well as to the pr-AMG RNs in the BV. In the posterior of the MG we observed two pairs of VGAT-positive neurons, as described previously (<a href="#bib21">Horie et al., 2009</a>). Finally, in the ventral MG we observed a continuous block of VACHT expression that encompasses the anterior three pairs of MNs, the ddNs, and the MGINs. Similar in situ patterns were observed in most larvae (<a href="/articles/44753/figures#fig4s1">Figure 4—figure supplement 1</a>), although the positions of the ACINs were offset in several (see larvae 5 and 6 in <a href="/articles/44753/figures#fig4s1">Figure 4—figure supplement 1</a>), and one larva was observed to be missing both one motor neuron and one ACIN (larva 7in <a href="/articles/44753/figures#fig4s1">Figure 4—figure supplement 1</a>), suggesting that MG variants, such as was observed in the animal used in the connectome study, may be relatively common.</p> + + + + + </div> + +</section> +<section + class="article-section " + id="s2-4" + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">Parallel visuomotor circuits</h3> + </header> + + <div class="article-section__body"> + <p class="paragraph">Our results indicate that the PR-Is, with the exception of two cells, are glutamatergic, while the PR-IIs are a mixture of GABAergic and GABA/glutamatergic. The <i>Ciona</i> genome contains a single glutamate AMPA receptor (AMPAR) (<a href="#bib36">Okamura et al., 2005</a>) that is expressed in larvae in the two antenna cells, and in a small cluster of neurons in the pBV (<a href="#bib18">Hirai et al., 2017</a>). Published results show that most of the pBV group of AMPAR-positive neurons are clustered at the ends of Arrestin-labeled photoreceptor axons, and that they extend their axons to the MG, suggesting they are photoreceptor RNs (see Figure 2B" in <a href="#bib18">Hirai et al., 2017</a>). We find that this pBV group is composed of ~6 cells (<a href="/articles/44753/figures#fig5s1">Figure 5—figure supplement 1</a>). To investigate this further, we co-expressed an pAMPAR >GFP construct (<a href="#bib18">Hirai et al., 2017</a>) with pVACHT >CFP and pVGAT >nuclear RFP constructs. We observed coexpression of the AMPAR reporter in a subset of the VACHT-positive RNs, but never in the VGAT-expressing RNs (<a href="#fig5">Figure 5a</a>).</p> + <div + id="fig5" + class="asset-viewer-inline asset-viewer-inline-- " + data-variant="" + data-behaviour="AssetNavigation AssetViewer ToggleableCaption" + data-selector=".caption-text__body" + data-asset-viewer-group="fig5" + data-asset-viewer-uri="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig5-v2.tif/full/,1500/0/default.jpg" + data-asset-viewer-width="1400" + data-asset-viewer-height="1500" + > + + <div class="asset-viewer-inline__header_panel"> + <div class="asset-viewer-inline__header_text"> + <span class="asset-viewer-inline__header_text__prominent">Figure 5</span> with 1 supplement <a href="/articles/44753/figures#fig5" class="asset-viewer-inline__header_link">see all</a> + </div> + + + <div class="asset-viewer-inline__figure_access"> + <a href="https://elifesciences.org/download/aHR0cHM6Ly9paWlmLmVsaWZlc2NpZW5jZXMub3JnL2xheDo0NDc1MyUyRmVsaWZlLTQ0NzUzLWZpZzUtdjIudGlmL2Z1bGwvZnVsbC8wL2RlZmF1bHQuanBn/elife-44753-fig5-v2.jpg?_hash=0aDXVHgnozrp0Q80t8%2FT5K718EzJQmgreXzfYFK9oAQ%3D" class="asset-viewer-inline__download_all_link" download="Download"><span class="visuallyhidden">Download asset</span></a> + <a href="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig5-v2.tif/full/,1500/0/default.jpg" class="asset-viewer-inline__open_link" target="_blank" rel="noopener noreferrer"><span class="visuallyhidden">Open asset</span></a> + </div> + + </div> + + <figure class="captioned-asset"> + + <a href="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig5-v2.tif/full/,1500/0/default.jpg" class="captioned-asset__link" target="_blank" rel="noopener noreferrer"> + <picture class="captioned-asset__picture"> + <source srcset="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig5-v2.tif/full/1234,/0/default.webp 2x, https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig5-v2.tif/full/617,/0/default.webp 1x" + type="image/webp" + > + <source srcset="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig5-v2.tif/full/1234,/0/default.jpg 2x, https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig5-v2.tif/full/617,/0/default.jpg 1x" + type="image/jpeg" + > + <img src="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig5-v2.tif/full/617,/0/default.jpg" + + alt="" + class="captioned-asset__image" + > + </picture> + </a> + + + + + <figcaption class="captioned-asset__caption"> + + <h6 class="caption-text__heading">AMPA receptors in negative phototaxis.</h6> + + + <div class="caption-text__body"><p class="paragraph">(<b>a</b>) Coexpression of an AMPA-receptor and VACHT expression constructs in the relay neurons (white asterisks). The main panel shows the merge while smaller panels at right show single channels. (<b>b</b>) Negative phototaxis assay in control larvae. Yellow arrow indicates direction of 505 nm light. By 60 min (m) the majority of the larvae have swum to the side of the dish away from the light (red arrow). (<b>c</b>) Perampanel-treated larvae do not show negative phototaxis. (<b>d</b>) Quantification of negative phototaxis in control and perampanel-treated larvae. Points indicate the averages from three independent assays, ±standard deviation. Y-axis represents the percentage of larvae found on the side away from the light source (distal third). Abbreviations: VGAT, vesicular GABA transporter; VACHT, vesicular acetylcholine transporter.</p> +</div> + + <span class="doi doi--asset"><a href="https://doi.org/10.7554/eLife.44753.011" class="doi__link">https://doi.org/10.7554/eLife.44753.011</a></span> + + </figcaption> + + + + + </figure> + + + </div> +<p class="paragraph">To assess the function of the AMPAR-positive cells in <i>Ciona</i> visuomotor behaviors we used the non-competitive AMPAR antagonist perampanel (<a href="#bib17">Hanada et al., 2011</a>). For the assay, larvae were treated at 25 hr post fertilization (hpf) with perampanel in sea water and compared to vehicle-treated control larvae for both negative phototaxis and response to light dimming. The negative phototaxis assay consisted of placing the larvae in a 10 cm petri dish of sea water with a 505 nm LED lamp placed to one side (described by us previously <a href="#bib46">Salas et al., 2018</a>). Images were collected at 1 min intervals over 5 hr to assess for taxis (<a href="#video1">Video 1</a>). <a href="#fig5">Figure 5b and c</a> show representative frames from the time-lapse capture at the start and at 60 min for control and perampanel-treated larvae, respectively. In the control sample the larvae at 60 min were observed to cluster at the side of the petri dish away from the light (distal side; red arrows in <a href="#fig5">Figure 5b</a>). By contrast no taxis was observed in the perampanel treated larvae (<a href="#fig5">Figure 5c</a>). Combined results from three independent assays (n = 129–365 larvae per group) are shown in <a href="#fig5">Figure 5d</a> and presented as the percent of larvae found on distal third of the petri dish. For control larvae ~ 70% swam to the distal third within 1 hr, while the perampanel-treated larvae remained evenly distributed across the dish.</p> + <div + id="video1" + class="asset-viewer-inline asset-viewer-inline--video " + data-variant="video" + data-behaviour="AssetNavigation AssetViewer ToggleableCaption" + data-selector=".caption-text__body" + data-asset-viewer-group="video1" + > + + <div class="asset-viewer-inline__header_panel"> + <div class="asset-viewer-inline__header_text"> + <span class="asset-viewer-inline__header_text__prominent">Video 1</span> + </div> + + + <div class="asset-viewer-inline__figure_access"> + <a href="https://elifesciences.org/download/aHR0cHM6Ly9zdGF0aWMtbW92aWUtdXNhLmdsZW5jb2Vzb2Z0d2FyZS5jb20vbXA0LzEwLjc1NTQvODg2Lzc3MWIyN2VkMjZmNzI1MTEwOGJkMzViODQyY2U1OTYzZTYzNDExOTkvZWxpZmUtNDQ3NTMtdmlkZW8xLm1wNA==/elife-44753-video1.mp4?_hash=QotDe4lMfotdXdc%2BUKEblblnp1b0B6bupqA3BcEJbnU%3D" class="asset-viewer-inline__download_all_link" download="Download"><span class="visuallyhidden">Download asset</span></a> + </div> + + </div> + + <figure class="captioned-asset"> + + + + <video controls="controls" poster="https://iiif.elifesciences.org/lax:44753%2Felife-44753-video1.jpg/full/639,/0/default.jpg" preload="metadata"> + + <img src="https://iiif.elifesciences.org/lax:44753%2Felife-44753-video1.jpg/full/639,/0/default.jpg" alt="posterframe for video" /> + + <p>This video cannot be played in place because your browser does support HTML5 video. You may still download the video for offline viewing.</p> + + <source src="https://static-movie-usa.glencoesoftware.com/mp4/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video1.mp4" type='video/mp4; codecs="avc1.42E01E, mp4a.40.2"' class="media-source"/> + + <div> + + + <a class="media-source__fallback_link" href="https://static-movie-usa.glencoesoftware.com/mp4/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video1.mp4">Download as MPEG-4</a> + + </div> + <source src="https://static-movie-usa.glencoesoftware.com/webm/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video1.webm" type='video/webm; codecs="vp8.0, vorbis"' class="media-source"/> + + <div> + + + <a class="media-source__fallback_link" href="https://static-movie-usa.glencoesoftware.com/webm/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video1.webm">Download as WebM</a> + + </div> + <source src="https://static-movie-usa.glencoesoftware.com/ogv/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video1.ogv" type='video/ogg; codecs="theora, vorbis"' class="media-source"/> + + <div> + + + <a class="media-source__fallback_link" href="https://static-movie-usa.glencoesoftware.com/ogv/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video1.ogv">Download as Ogg</a> + + </div> + + </video> + + + <figcaption class="captioned-asset__caption"> + + <h6 class="caption-text__heading">Negative phototaxis of control and perampanel-treated <i>Ciona</i> larvae in 10 cm petri dishes.</h6> + + + <div class="caption-text__body"><p class="paragraph">Directional 505 nm illumination is from the left. Frames were taken at 1 per minute over five hours. In the video the 5 hr is compressed to 15 s (i.e., 1200X normal speed). Black and white tones were inverted to make the larvae more visible.</p> +</div> + + <span class="doi doi--asset"><a href="https://doi.org/10.7554/eLife.44753.014" class="doi__link">https://doi.org/10.7554/eLife.44753.014</a></span> + + </figcaption> + + + + + </figure> + + + </div> +<p class="paragraph">The inability of the perampanel-treated larvae to undergo phototaxis was not the result of an inability to swim, as seen in <a href="#video2">Video 2</a> which was taken at 8.9 fps, with and without perampanel. Moreover, we observed that perampanel treatment had no effect on the light dimming response (<a href="#video3">Video 3</a>). <a href="#fig6">Figure 6a and b</a> show 5 s projection images from <a href="#video3">Video 3</a> immediately before and after dimming. In these images swims appear as lines, and the responses in control and perampanel-treated larvae appear qualitatively similar. To quantitatively compare dimming response, control and perampanel-treated larvae were exposed to a range of dimming intensities from 2 to 60-fold and the percentage of larvae responding was measured and presented as a percentage in <a href="#fig6">Figure 6c</a> (results are from three independent assays, with 46–139 larvae per group). The percentage responding at all intensities was very similar for both groups, and pair-wise comparisons at each fold change failed to show significance. In addition, no differences were measured in the velocity or duration of swims in pair-wise comparisons of control and perampanel-treated larvae at any fold-dimming (data not shown). We conclude that there is no change in sensitivity to dimming caused by perampanel treatment, while phototaxis was completely disrupted. Finally, we also observed that the touch response was not inhibited by perampanel (data not shown), despite the presence of VGLUT-positive epidermal sensory neurons (<a href="#bib20">Horie et al., 2008b</a>). This would appear to agree with the observation that primary RNs for the PNS, the eminens cells and the AMGs do not express the AMPAR (<a href="#bib18">Hirai et al., 2017</a>; and our observations). In addition to the AMPAR, the <i>Ciona</i> genome contains several other glutamate receptors including one kainate and one NMDA (<a href="#bib36">Okamura et al., 2005</a>), although their expression has not been characterized.</p> + <div + id="fig6" + class="asset-viewer-inline asset-viewer-inline-- " + data-variant="" + data-behaviour="AssetNavigation AssetViewer ToggleableCaption" + data-selector=".caption-text__body" + data-asset-viewer-group="fig6" + data-asset-viewer-uri="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig6-v2.tif/full/1500,/0/default.jpg" + data-asset-viewer-width="1500" + data-asset-viewer-height="1124" + > + + <div class="asset-viewer-inline__header_panel"> + <div class="asset-viewer-inline__header_text"> + <span class="asset-viewer-inline__header_text__prominent">Figure 6</span> + </div> + + + <div class="asset-viewer-inline__figure_access"> + <a href="https://elifesciences.org/download/aHR0cHM6Ly9paWlmLmVsaWZlc2NpZW5jZXMub3JnL2xheDo0NDc1MyUyRmVsaWZlLTQ0NzUzLWZpZzYtdjIudGlmL2Z1bGwvZnVsbC8wL2RlZmF1bHQuanBn/elife-44753-fig6-v2.jpg?_hash=v4N145cqneQAaynzcjF%2FnAcen6AeM%2BkieeWEMRTMIFY%3D" class="asset-viewer-inline__download_all_link" download="Download"><span class="visuallyhidden">Download asset</span></a> + <a href="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig6-v2.tif/full/1500,/0/default.jpg" class="asset-viewer-inline__open_link" target="_blank" rel="noopener noreferrer"><span class="visuallyhidden">Open asset</span></a> + </div> + + </div> + + <figure class="captioned-asset"> + + <a href="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig6-v2.tif/full/1500,/0/default.jpg" class="captioned-asset__link" target="_blank" rel="noopener noreferrer"> + <picture class="captioned-asset__picture"> + <source srcset="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig6-v2.tif/full/1234,/0/default.webp 2x, https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig6-v2.tif/full/617,/0/default.webp 1x" + type="image/webp" + > + <source srcset="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig6-v2.tif/full/1234,/0/default.jpg 2x, https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig6-v2.tif/full/617,/0/default.jpg 1x" + type="image/jpeg" + > + <img src="https://iiif.elifesciences.org/lax:44753%2Felife-44753-fig6-v2.tif/full/617,/0/default.jpg" + + alt="" + class="captioned-asset__image" + > + </picture> + </a> + + + + + <figcaption class="captioned-asset__caption"> + + <h6 class="caption-text__heading">Perampanel does not disrupt the light dimming response.</h6> + + + <div class="caption-text__body"><p class="paragraph">(<b>a</b>) Light dimming response in control larvae. Shown are 5 s (s) projections from time-lapse videos in which swims appear as lines. Left panel shows a projection 5 s before dimming, and right panel 5 s after dimming. (<b>b</b>) same as a, but larvae were perampanel-treated. (<b>c</b>) Quantification of light dimming response in control and perampanel treated larvae. Larvae were exposed to dimming of 505 nm light from 2- to 60-fold. Dimming response was scored as percent of larvae responding. Bars show averages of three independent assays ± standard deviation.</p> +</div> + + <span class="doi doi--asset"><a href="https://doi.org/10.7554/eLife.44753.015" class="doi__link">https://doi.org/10.7554/eLife.44753.015</a></span> + + </figcaption> + + + + + </figure> + + + </div> + <div + id="video2" + class="asset-viewer-inline asset-viewer-inline--video " + data-variant="video" + data-behaviour="AssetNavigation AssetViewer ToggleableCaption" + data-selector=".caption-text__body" + data-asset-viewer-group="video2" + > + + <div class="asset-viewer-inline__header_panel"> + <div class="asset-viewer-inline__header_text"> + <span class="asset-viewer-inline__header_text__prominent">Video 2</span> + </div> + + + <div class="asset-viewer-inline__figure_access"> + <a href="https://elifesciences.org/download/aHR0cHM6Ly9zdGF0aWMtbW92aWUtdXNhLmdsZW5jb2Vzb2Z0d2FyZS5jb20vbXA0LzEwLjc1NTQvODg2Lzc3MWIyN2VkMjZmNzI1MTEwOGJkMzViODQyY2U1OTYzZTYzNDExOTkvZWxpZmUtNDQ3NTMtdmlkZW8yLm1wNA==/elife-44753-video2.mp4?_hash=Td7A8NTjXLYjBj4RDkmj2zYo4EbpSS%2FCisGNZPPo1Ws%3D" class="asset-viewer-inline__download_all_link" download="Download"><span class="visuallyhidden">Download asset</span></a> + </div> + + </div> + + <figure class="captioned-asset"> + + + + <video controls="controls" poster="https://iiif.elifesciences.org/lax:44753%2Felife-44753-video2.jpg/full/639,/0/default.jpg" preload="metadata"> + + <img src="https://iiif.elifesciences.org/lax:44753%2Felife-44753-video2.jpg/full/639,/0/default.jpg" alt="posterframe for video" /> + + <p>This video cannot be played in place because your browser does support HTML5 video. 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Black and white tones were inverted to make the larvae more visible. The video plays at 5X normal speed.</p> +</div> + + <span class="doi doi--asset"><a href="https://doi.org/10.7554/eLife.44753.017" class="doi__link">https://doi.org/10.7554/eLife.44753.017</a></span> + + </figcaption> + + + + + </figure> + + + </div> + <div + id="video3" + class="asset-viewer-inline asset-viewer-inline--video " + data-variant="video" + data-behaviour="AssetNavigation AssetViewer ToggleableCaption" + data-selector=".caption-text__body" + data-asset-viewer-group="video3" + > + + <div class="asset-viewer-inline__header_panel"> + <div class="asset-viewer-inline__header_text"> + <span class="asset-viewer-inline__header_text__prominent">Video 3</span> + </div> + + + <div class="asset-viewer-inline__figure_access"> + <a href="https://elifesciences.org/download/aHR0cHM6Ly9zdGF0aWMtbW92aWUtdXNhLmdsZW5jb2Vzb2Z0d2FyZS5jb20vbXA0LzEwLjc1NTQvODg2Lzc3MWIyN2VkMjZmNzI1MTEwOGJkMzViODQyY2U1OTYzZTYzNDExOTkvZWxpZmUtNDQ3NTMtdmlkZW8zLm1wNA==/elife-44753-video3.mp4?_hash=GCjCBk4K%2BjkExSoFO0Wc8pv%2FhPFCkRZ84QpH%2Bavz994%3D" class="asset-viewer-inline__download_all_link" download="Download"><span class="visuallyhidden">Download asset</span></a> + </div> + + </div> + + <figure class="captioned-asset"> + + + + <video controls="controls" poster="https://iiif.elifesciences.org/lax:44753%2Felife-44753-video3.jpg/full/639,/0/default.jpg" preload="metadata"> + + <img src="https://iiif.elifesciences.org/lax:44753%2Felife-44753-video3.jpg/full/639,/0/default.jpg" alt="posterframe for video" /> + + <p>This video cannot be played in place because your browser does support HTML5 video. You may still download the video for offline viewing.</p> + + <source src="https://static-movie-usa.glencoesoftware.com/mp4/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video3.mp4" type='video/mp4; codecs="avc1.42E01E, mp4a.40.2"' class="media-source"/> + + <div> + + + <a class="media-source__fallback_link" href="https://static-movie-usa.glencoesoftware.com/mp4/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video3.mp4">Download as MPEG-4</a> + + </div> + <source src="https://static-movie-usa.glencoesoftware.com/webm/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video3.webm" type='video/webm; codecs="vp8.0, vorbis"' class="media-source"/> + + <div> + + + <a class="media-source__fallback_link" href="https://static-movie-usa.glencoesoftware.com/webm/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video3.webm">Download as WebM</a> + + </div> + <source src="https://static-movie-usa.glencoesoftware.com/ogv/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video3.ogv" type='video/ogg; codecs="theora, vorbis"' class="media-source"/> + + <div> + + + <a class="media-source__fallback_link" href="https://static-movie-usa.glencoesoftware.com/ogv/10.7554/886/771b27ed26f7251108bd35b842ce5963e6341199/elife-44753-video3.ogv">Download as Ogg</a> + + </div> + + </video> + + + <figcaption class="captioned-asset__caption"> + + <h6 class="caption-text__heading">Dimming response of control and perampanel-treated <i>Ciona</i> larvae in 10 cm petri dishes.</h6> + + + <div class="caption-text__body"><p class="paragraph">Larvae were imaged for 70 s at five frames/second, with dimming of 505 nm ambient light at 10 s. Black and white tones were inverted, and thus the dimming appears as a brightening. The video plays at 5X normal speed.</p> +</div> + + <span class="doi doi--asset"><a href="https://doi.org/10.7554/eLife.44753.018" class="doi__link">https://doi.org/10.7554/eLife.44753.018</a></span> + + </figcaption> + + + + + </figure> + + + </div> +<p class="paragraph">In summary, we are able to separate the phototaxis and dimming behaviors pharmacologically. Moreover, we can identify the VACHT/AMPAR-positive RNs as essential for an excitatory PR-I circuit that involves presynaptic glutamatergic PR-Is and postsynaptic cholinergic MGINs. The number and location of the VACHT/AMPAR-positive RNs, the circuit logic, and our behavioral observations are all consistent with these being prRNs.</p> + + + + + </div> + +</section> +<section + class="article-section " + id="s2-5" + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">A disinhibitory circuit</h3> + </header> + + <div class="article-section__body"> + <p class="paragraph">Of equal significance to our observation that navigation is inhibited by perampanel, is our observation that the dimming response, which is mediated by the PR-IIs (<a href="#bib46">Salas et al., 2018</a>), is not inhibited by perampanel (<a href="#fig6">Figure 6</a>). Our expression studies show that the PR-IIs are comprised of a mixture of VGAT- and VGAT/VGLUT-expressing photoreceptors. Although it is formally possible that PR-IIs signal exclusively via glutamate in an excitatory circuit via a non-AMPA glutamate receptor on their RNs, our observations that several of the PR-IIs are VGAT-only, as are the majority of the pr-AMG RNs, suggests an alternative disinhibitory circuitry logic. This circuit would consist of the inhibitory PR-IIs synapsing to the pr-AMG RNs to reduce their inhibition on the cholinergic MGINs.</p> +<p class="paragraph">Implicit in the disinhibitory model is an autonomous level of motor activity in larvae that could be inhibited by the GABAergic pr-AMG RNs, and that this inhibition is released upon stimulation of the GABAergic PR-IIs. We investigated this possibility by two approaches. In the first approach, we inhibited GABAergic receptors with picrotoxin (<a href="#bib37">Olsen, 2014</a>), which should inhibit signals from the GABAergic photoreceptors and the pr-AMG RNs (and most likely the AntRNs), as well as PNS relay neurons, including the eminens cells and the AMGs. The ACINs, which are essential for the central pattern generator (<a href="#bib35">Nishino et al., 2010</a>), are glycinergic and should not be inhibited by picrotoxin. In the second approach, we took advantage of a previously described <i>Ciona</i> mutant, <i>frimousse (frm)</i> (<a href="#bib10">Deschet and Smith, 2004</a>; <a href="#bib16">Hackley et al., 2013</a>). In homozygous <i>frm</i> larvae the anterior BV is transfated to epidermis due to a null mutation in a neurula stage-specific connexin gene (<a href="#bib16">Hackley et al., 2013</a>). <i>Frm</i> larvae thus lack the ocellus pigment cell and photoreceptors, as well as the otolith, although the motor ganglion appears intact (<a href="#bib10">Deschet and Smith, 2004</a>; <a href="#bib16">Hackley et al., 2013</a>).</p> +<section + class="article-section " + id="s2-5-1" +> + + + </div> + +</section> +<section + class="article-section " + id="s4-4" + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">Hybridization chain reaction (HCR) in situ</h3> + <a href="https://bio-protocol.org/eLIFErap44753?item=s4-4" class="article-section__header_link">Request a detailed protocol</a> + </header> + + <div class="article-section__body"> + <p class="paragraph"><i>Ciona intestinalis</i>-type B were used for in situ studies and staged to match the animals used in the connectome study (<a href="#bib43">Ryan et al., 2016</a>). Optimized HCR in situ probes for each target transcript were obtained from Molecular Technologies. For detection of GABAergic/glycinergic cells, probes were made to the vesicular GABA transporter gene; for glutamatergic cells, probes were made to the vesicular glutamate transporter for cholinergic cells, probes were made to the vesicular acetylcholine transporter. The sequences from which the HCR probe sets were chosen were assembled from scaffold reads available through the Aniseed website (aniseed.cnrs.fr), and are shown in <a href="/articles/44753/figures#supp1">Supplementary file 1</a>. The in situ protocol followed the previously published <i>Ciona in situ</i> hybridization protocol (<a href="#bib8">Corbo et al., 1997</a>) until the prehybridization step. At this point, the protocol follows the published HCR protocol (<a href="#bib7">Choi et al., 2018</a>), with the following exception: during the amplification stage, incubation with hairpins is performed for 3 days instead of 12–16 hr.</p> +<p class="paragraph">HCR in situ stained larvae were cleared with Slowfade Gold with DAPI (Invitrogen) and imaged on a Leica SP8 resonant scanning confocal microscope. Imaris v. 9.1 (Bitplane) was used to visualize embryos and assign centroids to nuclei using the ‘add new spots’ function, followed by manual correction when necessary. Nuclei were assigned using the maximum intensity projection, cropped to the area of interest. Volume rendering of in situ patterns was also done using Imaris v. 9.1.</p> + + + + + </div> + +</section> +<section + class="article-section " + id="s4-5" + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">Cell registration</h3> + </header> + + <div class="article-section__body"> + <p class="paragraph">A rotation matrix was calculated based on the 3-dimensional vectors between the anchor cells (ddN and/or antenna cells) and the center of the target cells (photoreceptors or relay neurons) using the HCR in situ (target set) and connectome cell centroids (source set). The source set was then rotated to an approximate orientation to the target set. Next, the Coherent Point Drift Algorithm was used to calculate an affine transformation matrix between the source set and the target set of cells (<a href="#bib32">Myronenko and Song, 2010</a>). This algorithm models the source set as a Gaussian Mixture Model (GMM), and the target set is treated as observations from the GMM. The transformation matrix is calculated to maximize the Maximum A Posteriori estimation that the observed point cloud is drawn from the GMM. A nearest neighbor mapping based on Euclidean distance is then used to find the closest corresponding point in the target cell set for each cell in the transformed source cell set. The implementation used was adapted from the pure Python implementation <a href="https://github.com/siavashk/pycpd">https://github.com/siavashk/pycpd</a>. The maximum number of iterations was set to 1000 and the maximum root mean squared error for convergence was set to 0.001. The code for the registration is available as supplementary material (<a href="/articles/44753/figures#scode1">Source codes 1</a>–<a href="/articles/44753/figures#scode3">3</a>).</p> +<section + class="article-section " + id="s4-5-1" + + +> + + <header class="article-section__header"> + <h4 class="article-section__header_text">Confusion matrix</h4> + <a href="https://bio-protocol.org/eLIFErap44753?item=s4-5-1" class="article-section__header_link">Request a detailed protocol</a> + </header> + + <div class="article-section__body"> + <p class="paragraph">Each dataset containing NT information was registered to every other dataset of the same type using the algorithm detailed above. The EM-registration based cell assignments of each cell in both sets is then compared to each other to see if they agree (<a href="#bib49">Stehman, 1997</a>). The confusion matrix shows the number of times a cell assignment in one dataset corresponds with each other cell assignment in another dataset.</p> + + + + + </div> + +</section> + + + + + </div> + +</section> +<section + class="article-section " + id="s4-6" + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">Behavioral assays</h3> + </header> + + <div class="article-section__body"> + <p class="paragraph">For time-lapse videos the inverted lid of a 60 mm petri dish was first coated with a thin layer of 1% agarose. Larvae were then added to the inverted lid with filtered sea water containing 0.1% BSA with streptomycin and kanamycin each at 20 μg/ml. Finally the dish was covered with a square of glass leaving no air at the top interface. Stock solutions of perampanel were dissolved in methanol and diluted to final concentrations of either 5 μm (Santa Cruz Biotech) or 15 µM (Adooq Bioscience) in filtered sea water/BSA/antibiotics. Picrotoxin (Tocris) was also diluted in methanol and used at a final concentration of 1 mM. Control samples received methanol alone.</p> +<p class="paragraph">Time-lapse images were collected using a Hamamatsu Orca-ER camera fitted on a Navitar 7000 macro zoom lens. Programmable 700 nm and 505 nm LED lamps were used to illuminate the larvae (Mightex). All light intensity readings were taken with an Extech Instruments light meter.</p> +<section + class="article-section " + id="s4-6-1" + + +> + + <header class="article-section__header"> + <h4 class="article-section__header_text">Dimming-response</h4> + <a href="https://bio-protocol.org/eLIFErap44753?item=s4-6-1" class="article-section__header_link">Request a detailed protocol</a> + </header> + + <div class="article-section__body"> + <p class="paragraph">All larvae used were between 25 and 28 hpf (18°C). For image capture, the larvae were illuminated with the 700 nm LED lamp and the camera was fitted with a red filter to block the 505 nm light. The videos were recorded at five fps. In the assays, larvae were first recorded for 10 s with the 505 nm LED light mounted above the dish at 600 lux and then dimmed to specific values while image capture continued for another 3 min. Larvae were allowed to recover for 5 min before being assayed again.</p> + + + + + </div> + +</section> +<section + class="article-section " + id="s4-6-2" + + +> + + <header class="article-section__header"> + <h4 class="article-section__header_text">Phototaxis</h4> + <a href="https://bio-protocol.org/eLIFErap44753?item=s4-6-2" class="article-section__header_link">Request a detailed protocol</a> + </header> + + <div class="article-section__body"> + <p class="paragraph">All larvae used were approximately 25 hpf (18°C). The 505 nm LED light was mounted to one side to the petri dish at approximately 3000 lux. Images were captured at one frame per minute for five hours, with the exception of 30 s capture session at 8.9 fps to assay swimming behavior.</p> + + + + + </div> + +</section> +<section + class="article-section " + id="s4-6-3" + + +> + + <header class="article-section__header"> + <h4 class="article-section__header_text">Spontaneous Swims</h4> + <a href="https://bio-protocol.org/eLIFErap44753?item=s4-6-3" class="article-section__header_link">Request a detailed protocol</a> + </header> + + <div class="article-section__body"> + <p class="paragraph">All larvae used were between 26 and 28 hpf. The plates were illuminated with only a 700 nm LED light in order to record dark conditions. The videos were recorded at about 8.9 fps for one minute.</p> + + + + + </div> + +</section> + + + + + </div> + +</section> +<section + class="article-section " + id="s4-7" + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">Behavioral data analysis</h3> + </header> + + <div class="article-section__body"> + <section + class="article-section " + id="s4-7-1" + + +> + + <header class="article-section__header"> + <h4 class="article-section__header_text">Dim-response criteria</h4> + <a href="https://bio-protocol.org/eLIFErap44753?item=s4-7-1" class="article-section__header_link">Request a detailed protocol</a> + </header> + + <div class="article-section__body"> + <p class="paragraph">Responses to light dimming were counted if: (1) the larva was stationary at the time of the light dimming, and (2) it swam for longer than 3 s. Three seconds was determined by measuring the duration of tail flicks as previously described (<a href="#bib46">Salas et al., 2018</a>). Larvae that bumped or brushed against other larvae or the dish edges were not counted.</p> + + + + + </div> + +</section> +<section + class="article-section " + id="s4-7-2" + + +> + + <header class="article-section__header"> + <h4 class="article-section__header_text">Tracking and quantification</h4> + <a href="https://bio-protocol.org/eLIFErap44753?item=s4-7-2" class="article-section__header_link">Request a detailed protocol</a> + </header> + + <div class="article-section__body"> + <p class="paragraph">Larval swims were tracked using a custom MATLAB script named Estimators of Locomotion Iterations for Animal Experiments (ELIANE). Before uploading to ELIANE, time-lapse images were first processed with Fiji (ImageJ) by subtracting a minimum Z-projection to all the frames and then inverting black and white. ELIANE takes the processed time-lapse images and first creates a background image by averaging the pixels from all the frames. Next, it goes to the initial frame, subtracts the background image, and stores all remaining objects found in the specified region of interest (ROI) as initial objects. Then, analyzing one-by-one the initial objects, it goes frame-by-frame subtracting the background image and analyzing all objects to determine the new position of the object by comparing the Euclidean distances of it to all other objects in that frame. If the object had moved unrealistically fast (>6.5 mm/s), moved outside the ROI, or did not move after a set time (1 min), the object was not analyzed. This MATLAB script can be found in the Supplemental Materials (<a href="/articles/44753/figures#scode4">Source code 4</a>).</p> +<p class="paragraph">The spontaneous swims in the <i>frimousse</i> experiment were quantified manually.</p> + + + + + </div> + +</section> +<section + class="article-section " + id="s4-7-3" + + +> + + <header class="article-section__header"> + <h4 class="article-section__header_text">Sampling</h4> + <a href="https://bio-protocol.org/eLIFErap44753?item=s4-7-3" class="article-section__header_link">Request a detailed protocol</a> + </header> + + <div class="article-section__body"> + <p class="paragraph">Assessment of larval swim parameters were performed using three independent assays. For the spontaneous swims, which were quantified manually, 25 larvae were selected randomly, starting from the center of the plate going outward, only using the ones that could be tracked for the entire minute recording session.</p> + + + + + </div> + +</section> +<section + class="article-section " + id="s4-7-4" + + +> + + <header class="article-section__header"> + <h4 class="article-section__header_text">Tests of significance</h4> + <a href="https://bio-protocol.org/eLIFErap44753?item=s4-7-4" class="article-section__header_link">Request a detailed protocol</a> + </header> + + <div class="article-section__body"> + <p class="paragraph">Dimming response significance and swim frequency were calculated using the Wilcoxon rank-sum test; spontaneous swim time significance was calculated using the Student’s <i>t</i>-test; and the variance of spontaneous swimming significance was calculated using the F-test.</p> + + + + + </div> + +</section> + + + + + </div> + +</section> + + + + + </div> + +</section> + + + + <button class="speech-bubble speech-bubble--has-placeholder" + data-behaviour="SpeechBubble HypothesisOpener" + +aria-live="polite"> + <span class="speech-bubble__inner"><span aria-hidden="true"><span data-visible-annotation-count>“</span></span><span class="visuallyhidden"> Open annotations. The current annotation count on this page is <span data-hypothesis-annotation-count>being calculated</span>.</span></span> +</button> + + + + <section + class="article-section " + id="references" + data-behaviour="ArticleSection" + data-initial-state="closed" +> + + <header class="article-section__header"> + <h2 class="article-section__header_text">References</h2> + </header> + + <div class="article-section__body"> + +<ol class="reference-list"> + <li class="reference-list__item"> + <span class="reference-list__ordinal_number">1</span> + <div class="reference" data-popup-label="See in references" data-popup-contents="bib1" id="bib1"> + + + <a href="https://doi.org/10.1016/j.coisb.2017.12.005" class="reference__title">Fold-change detection in biological systems</a> + + + + + <ol class="reference__authors_list"> + <li class="reference__author"> + <a href="https://scholar.google.com/scholar?q=%22author:M+Adler%22" class="reference__authors_link">M Adler</a></li> + <li 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Scholar</a></li> + + </ul> + </div> + </li> +</ol> + + + + + </div> + +</section> + + + + <section + class="article-section " + id="SA1" + data-behaviour="ArticleSection" + data-initial-state="closed" +> + + <header class="article-section__header"> + <h2 class="article-section__header_text">Decision letter</h2> + </header> + + <div class="article-section__body"> + <div class="decision-letter-header"> + <ol class="listing-list"> + <li class="listing-list__item"> + <div class="profile-snippet"> + <div class="profile-snippet__container clearfix"> + + <div class="profile-snippet__name">Oliver Hobert</div> + <div class="profile-snippet__title">Reviewing Editor; Howard Hughes Medical Institute, Columbia University, United States</div> + </div> + </div> + </li> + <li class="listing-list__item"> + <div class="profile-snippet"> + <div class="profile-snippet__container clearfix"> + + <div class="profile-snippet__name">Ronald L Calabrese</div> + <div class="profile-snippet__title">Senior Editor; Emory University, United States</div> + </div> + </div> + </li> + </ol> + <div class="decision-letter-header__main_text"><p class="paragraph">In the interests of transparency, eLife includes the editorial decision letter and accompanying author responses. A lightly edited version of the letter sent to the authors after peer review is shown, indicating the most substantive concerns; minor comments are not usually included.</p> +</div> +</div> +<p class="paragraph">Thank you for submitting your article "Parallel Visual Circuitry in a Basal Chordate" for consideration by <i>eLife</i>. Your article has been reviewed by Ronald Calabrese as the Senior Editor, a Reviewing Editor, Oliver Hobert, and two reviewers. The reviewers have opted to remain anonymous.</p> +<p class="paragraph">The reviewers have discussed the reviews with one another and the Reviewing Editor has drafted this decision to help you prepare a revised submission.</p> +<p class="paragraph">The reviewers – and the Reviewing Editor – agree that the manuscript reports an interesting, exciting set of findings that provide new insight into how visual systems evolve. However, there is also agreement that the evidence behind the GABA receptors being involved in the behavioral response to dimming is entirely indirect, and would be substantially strengthened by a pharmacological parallel to the Glutamate receptor antagonist data. That is, according to the disinhibition model, acute blockade of GABA(A) receptors with a pharmacological antagonist should produce a "hyperactive" movement phenotype akin to the <i>frm</i> mutant animal, but one that should still be capable of phototaxis (but not a dimming response). Such a result would provide an elegant "double dissociation" that would parallel the findings with the AMPA receptor antagonist.</p> +<p class="paragraph">There is also agreement that the manuscript requires an extensive revision to the Introduction that puts the work in a broader context. At present, the manuscript begins largely with a description of the <i>Ciona</i> connectome, in relation to other complete connectomes, and then plunges directly into a more detailed description of ganglia, cells and synapses. A broader audience could be engaged by the work if the authors identified the key question of interest, and provides some of the background material currently found in the Discussion section, before diving into the pertinent details.</p> +<p class="paragraph"><i>Reviewer #1:</i></p> +<p class="paragraph">How the functional architecture of visual systems has evolved to subserve different behavioral goals is a fundamental question of broad interest. At present, while we have a deep understanding of visual system organization in a few experimental models, such a fundamental question can be enriched through the exploration of evolutionarily divergent organisms. In this context, Smith and colleagues integrate a new description of neurotransmitter expression patterns, ultrastructural connectivity, pharmacology and behavior to derive new insights into the architecture of the Ascidian <i>Ciona</i> visual system.</p> +<p class="paragraph">First, by mapping RNA expression patterns onto neurons spanning the <i>Ciona</i> nervous system using a combination of HCR in situs and image registration, they assign neurotransmitter types to many neurons. Importantly, these studies reveal three classes of ocellus photoreceptors – one that uses glutamate as a transmitter, one that uses GABA, and one that appears to release both. Next, using a glutamate receptor antagonist, they demonstrate that blockade of signaling from glutamatergic photoreceptors blocks phototaxis, but does not affect a second behavior evoked by transient dimming. Finally, consistent with the idea that a subset of photoreceptors could control the dimming response by depolarizing to darkness, and releasing GABA, the authors describe a mutant in which visual input to motor pathways is disrupted, leading to an animal that swims constitutively.</p> +<p class="paragraph">Overall, this manuscript reports an interesting, exciting set of findings that provide new insight into how visual systems evolve. I find the idea that there might be photoreceptors that appear to hyperpolarize to light and release GABA particularly exciting, and it will be fascinating to learn more about how these photoreceptors are related to retinal and pineal photoreceptors in vertebrates. However, I do feel that the evidence behind these receptors being involved in the behavioral response to dimming is entirely indirect, and would be substantially strengthened by a pharmacological parallel to the Glutamate receptor antagonist data. That is, according to the disinhibition model, acute blockade of GABA(A) receptors with a pharmacological antagonist should produce a "hyperactive" movement phenotype akin to the <i>frm</i> mutant animal, but one that should still be capable of phototaxis (but not a dimming response). Such a result would provide an elegant "double dissociation" that would parallel the findings with the AMPA receptor antagonist.</p> +<p class="paragraph"><i>Reviewer #2:</i></p> +<p class="paragraph">The fact that there is a full map of connections in <i>Ciona</i> provides a great opportunity to dissect circuits. Even better, the tools are there to perform some genetic and pharmacological pertubations, and evaluate effects on behavior. This study begins to exploit these features in a study of the <i>Ciona</i> visual system. The authors dug deeper into two circuits that begin with photoreception. They used transgenic reporter animals and in situ hybridization to define the use of two classical neurotransmitters, glutamate and GABA. Surprisingly, one type of photoreceptor uses GABA, an inhibitory neurotransmitter not previously described as used by photoreceptors in any species. From the known connections, they also make a case for how the two circuits are connected, and further suggest that one of the circuits is disinhibitory, perhaps along with other sensory inputs, for oscillatory swimming behavior. Through the use of a specific antagonist for a glutamate receptor they are able to show that one of the photoreceptor circuits is involved with detection of the direction of light (phototaxis), using a behavioral assay. Interestingly, inhibition of phototaxis has no effect on the other circuit, which detects dimming. However, it is likely that there is cross talk between the two photoreceptor circuits, as suggested by the known anatomy.</p> +<p class="paragraph">Overall this study provides a very nice example of photoreceptor directed behavior as controlled by two different circuits. It provides food for though regarding the evolution of different types of visually guided behaviors and the use of different types of photoreceptors. Optogenetic manipulations and calcium imaging (tried by the authors but did not work due to technical limitations) would greatly add to this story, but as it stands it constitutes a very nice addition to our understanding of a sensory circuit and behavior.</p> + + + + + <span class="doi doi--article-section"><a href="https://doi.org/10.7554/eLife.44753.036" class="doi__link">https://doi.org/10.7554/eLife.44753.036</a></span> + </div> + +</section> + + + + <section + class="article-section " + id="SA2" + data-behaviour="ArticleSection" + data-initial-state="closed" +> + + <header class="article-section__header"> + <h2 class="article-section__header_text">Author response</h2> + </header> + + <div class="article-section__body"> + <p class="paragraph"><i>The reviewers – and the reviewing editor – agree that the manuscript reports an interesting, exciting set of findings that provide new insight into how visual systems evolve. […] A broader audience could be engaged by the work if the authors identified the key question of interest, and provides some of the background material currently found in the Discussion section, before diving into the pertinent details.</i></p> +<p class="paragraph">In our revised manuscript we have thoroughly addressed the reviewers concerns and have included extensive new data from behavioral studies using a GABA receptor antagonist (Figure 7 in the revised manuscript, and related text). As you will read in the text, our results with the GABA receptor antagonist (picrotoxin) agree thoroughly with our disinhibition model (and with our observations of the <i>frm</i> mutant). The use of the GABA receptor antagonist was an excellent suggestion, and we feel that the results presented here greatly strengthen our model. As you will see in Figure 7, picrotoxin (like the <i>frm</i> mutant) leads to increased spontaneous swimming. Moreover, picrotoxin also leads to a dramatic reduction in the dimming response. We then show with use of picrotoxin combined with the AMPAR antagonist perampanel that the residual dimming response is due to parallel activation of the excitatory circuit. Finally, we show that picrotoxin-treated larvae are still capable of phototaxis. However, we observed that the phototaxis ability of the picrotoxin-treated larvae was somewhat dampened in comparison to controls, which we attribute to excitotoxicity of prolonged picrotoxin exposure (Movie5 documents the toxicity of prolonged picrotoxin exposure).</p> +<p class="paragraph">We have also extensively rewritten the Introduction along the lines suggested by the reviewer. Additionally, as requested, we have included in the text the number of animals tested using the pOpsin1/VGAT Kaede combination (n=5). Finally, we have collected additional data on neurotransmitter use by cells of the motor ganglion. These additional data are presented in revised versions of Figure 4 and Figure 4-figure supplement 1. Our conclusions regarding the minimal circuit are unchanged by this additional data; however, we are revising our neurotransmitter assignment to the anterior pair of ACINs. This reassignment was undertaken after consultation with Kerrianne Ryan (author of the <i>Ciona</i> connectome manuscript). We also include an approved personal communication from Dr. Ryan in this section.</p> + + + + + <span class="doi doi--article-section"><a href="https://doi.org/10.7554/eLife.44753.037" class="doi__link">https://doi.org/10.7554/eLife.44753.037</a></span> + </div> + +</section> + + + + <section + class="article-section " + id="info" + data-behaviour="ArticleSection" + data-initial-state="closed" +> + + <header class="article-section__header"> + <h2 class="article-section__header_text">Article and author information</h2> + </header> + + <div class="article-section__body"> + <h3 class="authors-details__heading">Author details</h3> +<ol class="authors-details__authors"> + <li class="authors-details__author"><div class="author-details" data-popup-contents="x8d8d9914" id="x8d8d9914"> + + <h4 class="author-details__name">Matthew J Kourakis</h4> + + <section class="author-details__section"> + <span class="author-details__text">Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Contribution</h5> + <span class="author-details__text">Data curation, Formal analysis, Supervision, Investigation, Methodology, Writing—review and editing</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Contributed equally with</h5> + <span class="author-details__text">Cezar Borba</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Competing interests</h5> + <span class="author-details__text">No competing interests declared</span> + </section> + + <section class="author-details__section"> + <span class="orcid"> + <a href="https://orcid.org/0000-0002-1261-3811"> + <picture> + <source srcset="/assets/patterns/img/icons/orcid.b96370b9.svg" type="image/svg+xml"> + <img src="/assets/patterns/img/icons/orcid.10f6112b.png" class="orcid__icon" + alt="ORCID icon"> + </picture> <span class="visuallyhidden">"This ORCID iD identifies the author of this article:"</span> + 0000-0002-1261-3811</a> + </span> + </section> + + +</div> + +</li> + <li class="authors-details__author"><div class="author-details" data-popup-contents="xf3e51472" id="xf3e51472"> + + <h4 class="author-details__name">Cezar Borba</h4> + + <section class="author-details__section"> + <span class="author-details__text">Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Contribution</h5> + <span class="author-details__text">Software, Formal analysis, Investigation, Methodology, Writing—review and editing</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Contributed equally with</h5> + <span class="author-details__text">Matthew J Kourakis</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Competing interests</h5> + <span class="author-details__text">No competing interests declared</span> + </section> + + + +</div> + +</li> + <li class="authors-details__author"><div class="author-details" data-popup-contents="xb536f34f" id="xb536f34f"> + + <h4 class="author-details__name">Angela Zhang</h4> + + <section class="author-details__section"> + <span class="author-details__text">Department of Electrical and Computer Engineering, University of California, Santa Barbara, Santa Barbara, United States</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Contribution</h5> + <span class="author-details__text">Software, Formal analysis, Methodology, Writing—review and editing</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Competing interests</h5> + <span class="author-details__text">No competing interests declared</span> + </section> + + + +</div> + +</li> + <li class="authors-details__author"><div class="author-details" data-popup-contents="x1d85dfc3" id="x1d85dfc3"> + + <h4 class="author-details__name">Erin Newman-Smith</h4> + + <section class="author-details__section"> + <ol class="author-details__list list list--bullet"> + <li class="author-details__text">Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States</li> + <li class="author-details__text">Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States</li> + </ol> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Contribution</h5> + <span class="author-details__text">Conceptualization, Formal analysis, Investigation, Methodology, Writing—review and editing</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Competing interests</h5> + <span class="author-details__text">No competing interests declared</span> + </section> + + + +</div> + +</li> + <li class="authors-details__author"><div class="author-details" data-popup-contents="x6107dd5d" id="x6107dd5d"> + + <h4 class="author-details__name">Priscilla Salas</h4> + + <section class="author-details__section"> + <span class="author-details__text">Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Contribution</h5> + <span class="author-details__text">Investigation, Writing—review and editing</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Competing interests</h5> + <span class="author-details__text">No competing interests declared</span> + </section> + + + +</div> + +</li> + <li class="authors-details__author"><div class="author-details" data-popup-contents="x8b937bbf" id="x8b937bbf"> + + <h4 class="author-details__name">B Manjunath</h4> + + <section class="author-details__section"> + <span class="author-details__text">Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Contribution</h5> + <span class="author-details__text">Conceptualization, Supervision, Funding acquisition, Project administration, Writing—review and editing</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Competing interests</h5> + <span class="author-details__text">No competing interests declared</span> + </section> + + + +</div> + +</li> + <li class="authors-details__author"><div class="author-details" data-popup-contents="xa3814a31" id="xa3814a31"> + + <h4 class="author-details__name">William C Smith</h4> + + <section class="author-details__section"> + <ol class="author-details__list list list--bullet"> + <li class="author-details__text">Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States</li> + <li class="author-details__text">Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States</li> + </ol> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Contribution</h5> + <span class="author-details__text">Conceptualization, Funding acquisition, Writing—original draft, Project administration</span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">For correspondence</h5> + <span class="author-details__text"><a href="mailto:w_smith@ucsb.edu">w_smith@ucsb.edu</a></span> + </section> + <section class="author-details__section"> + <h5 class="author-details__heading">Competing interests</h5> + <span class="author-details__text">No competing interests declared</span> + </section> + + <section class="author-details__section"> + <span class="orcid"> + <a href="https://orcid.org/0000-0002-6257-7695"> + <picture> + <source srcset="/assets/patterns/img/icons/orcid.b96370b9.svg" type="image/svg+xml"> + <img src="/assets/patterns/img/icons/orcid.10f6112b.png" class="orcid__icon" + alt="ORCID icon"> + </picture> <span class="visuallyhidden">"This ORCID iD identifies the author of this article:"</span> + 0000-0002-6257-7695</a> + </span> + </section> + + +</div> + +</li> +</ol> +<section + class="article-section " + + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">Funding</h3> + </header> + + <div class="article-section__body"> + <section + class="article-section " + + + +> + + <header class="article-section__header"> + <h4 class="article-section__header_text">National Institute of Neurological Disorders and Stroke (R01NS103774)</h4> + </header> + + <div class="article-section__body"> + + + <ul class="list list--bullet"> + <li>William C Smith</li> + </ul> + + + + + + </div> + +</section> +<p class="paragraph">The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</p> + + + + + </div> + +</section> +<section + class="article-section " + + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">Acknowledgements</h3> + </header> + + <div class="article-section__body"> + <p class="paragraph">We thank Takeo Horie and Takahiro Kusakabe for the opsin1 promoter construct; Yasunori Sasakura for the stable pVGAT >kaede line and pVACHT >CFP plasmid; Haruo Okado for the pAMPAR >GFP construct. Kerrianne Ryan for her helpful discussion and sharing unpublished data. Chelsea Parlett-Pelleriti for her advice on statistical analysis. We acknowledge the use of the NRI-MCDB Microscopy Facility and the Resonant Scanning Confocal supported by NSF MRI grant 1625770. This work supported by an award from NIH (NS103774) to WCS and BM.</p> + + + + + </div> + +</section> +<section + class="article-section " + + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">Senior Editor</h3> + </header> + + <div class="article-section__body"> + + <ol class="list"> + <li>Ronald L Calabrese, Emory University, United States</li> + </ol> + + + + + + + </div> + +</section> +<section + class="article-section " + + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">Reviewing Editor</h3> + </header> + + <div class="article-section__body"> + + <ol class="list"> + <li>Oliver Hobert, Howard Hughes Medical Institute, Columbia University, United States</li> + </ol> + + + + + + + </div> + +</section> +<section + class="article-section " + + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">Publication history</h3> + </header> + + <div class="article-section__body"> + + <ol class="list list--bullet"> + <li>Received: December 28, 2018</li> + <li>Accepted: April 11, 2019</li> + <li>Accepted Manuscript published: <a href="/articles/44753v1">April 18, 2019 (version 1)</a></li> + <li>Version of Record published: <a href="/articles/44753">May 3, 2019 (version 2)</a></li> + </ol> + + + + + + + </div> + +</section> +<section + class="article-section " + + + +> + + <header class="article-section__header"> + <h3 class="article-section__header_text">Copyright</h3> + </header> + + <div class="article-section__body"> + <p>© 2019, Kourakis et al.</p><p>This article is distributed under the terms of the <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</a>, which permits unrestricted use and redistribution provided that the original author and source are credited.</p> + + + + </div> + +</section> + + + + + </div> + +</section> + + + + <section + class="article-section " + id="metrics" + 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- 643 119398161 CITESEERX-CRAWL-2017-06-20-20170706014800946-00020-00029-wbgrp-svc285/CITESEERX-CRAWL-2017-06-20-20170706014907678-00022-3671~wbgrp-svc285.us.archive.org~8443.warc.gz diff --git a/python/tests/files/example_grobid_metadata.json b/python/tests/files/example_grobid_metadata.json new file mode 100644 index 0000000..a2d18db --- /dev/null +++ b/python/tests/files/example_grobid_metadata.json @@ -0,0 +1,5 @@ +{"abstract": "In this paper an analytical model is presented for the Micro-Cantilever (MC) of Atomic Force Microscopy with Side Wall probe (AFM-SW) in the tapping excitation mode. In this model the couple motion of the MC is taken into account while the torsional motion is considered as an undesirable motion which is coupled with the vertical motion. To this end, the effect of several parameters, namely; probe mass, probe dislocation, sidewall extension length, and tip sample interaction force is investigated on the occurrence probability of torsional and vertical motions. It is found that the probe dislocation is the prerequisite factor of the undesired motion happening. For sake of validation, the analytical results are compared against the previously published results, and an excellent agreement is observed. Abstrak Dalam kertas ini, model analitikal dipersembahkan bagi micro-julur Mikroskop Daya Atom dengan prob dinding-sisi dan dalam mod pengujaan menoreh. Dalam model ini, gerakan pasangan bagi mikro-julur diambil kira manakala gerakan kilasan dianggap sebagai gerakan yang tidak diingini yang digandingkan dengan pergerakan menegak. Untuk tujuan ini , kesan daripada beberapa parameter, iaitu; jisim prob, kehelan prob, panjang lanjutan sisi, dan daya interaksi di antara tip dan sampel disiasat keatas kebarangkalian berlakunya gerakan kilasan dan menegak. Didapati bahawa kehelan prob adalah faktor prasyarat berlakunya gerakan yang tidak diingini. Untuk pengesahan, keputusan analisis ini dibandingkan dengan keputusan yang sebelum ini telah diterbitkan, dan didapati persetujuannya sangat baik. Kata kunci: Mokroskop daya atom, prob dind ing sisi, micro-jalur, getaran, gerakan pasangan", "acknowledgement": "Acknowledgement We are grateful for the UTM scholarship to Author 1. Authors gratefully acknowledge t he Research Institute of Petroleum Industry (RIPI) and the Iran Nanotechnology Laboratory Network (INLN) for their support.", "authors": [{"name": "Farzad Mokhtarinezhad"}, {"name": "Roslan Rahman"}, {"name": "Sina Eftekhar"}, {"name": "Sadegh Hassani"}], "citations": [{"authors": [{"name": "Julie Last"}, {"name": "Paul Russell"}, {"name": "P aul Nealey"}, {"name": "Christopher Murphy"}], "date": "2010", "id": "b0", "index": 0, "issue": null, "journal": "Investigative Ophthalmology & Visual Science", "publisher" : null, "title": "The applications of atomic force microscopy to vision science", "url": null, "volume": "51"}, {"authors": [{"name": "G Binnig"}, {"name": "C Quate"}, {"name": "C Geber"}], "date": "1986", "id": "b1", "index": 1, "issue": null, "journal": "Phys Rev Let", "publisher": null, "title": "Atomic force microscope", "url": null, "vol ume": "56"}, {"authors": [{"name": "C Wright"}, {"name": "Armstrong"}], "date": "2006", "id": "b2", "index": 2, "issue": null, "journal": "Surf Interface Anal", "publisher" : null, "title": "The application of atomic force microscopy force measurements to the characterisation of microbial surfaces", "url": null, "volume": "38"}, {"authors": [{ "name": "John Withers"}, {"name": "D Aston"}], "date": "2006", "id": "b3", "index": 3, "issue": null, "journal": "Advances in Colloid and Interface Science", "publisher": null, "title": "Nanomechanical measurements with AFM in the elastic limit", "url": null, "volume": "120"}, {"authors": [{"name": "Dara Bayat"}, {"name": "Terunobu Akiyama"}, {"name": "F Nicolaas"}, {"name": "Urs De Rooij"}, {"name": "Staufer"}], "date": "2008", "id": "b4", "index": 4, "issue": null, "journal": "Microelectronic Engineering", "p ublisher": null, "title": "Dynamic behavior of the tuning fork AFM probe", "url": null, "volume": "85"}, {"authors": [{"name": "M Kahrobaiyan"}, {"name": "M Ahmadian"}, {"name": "P Haghighi"}, {"name": "A Haghighi"}], "date": "2010", "id": "b5", "index": 5, "issue": null, "journal": "International Journal of Mechanical Sciences", "publisher": null, "title": "Sensitivity and resonant frequency of an AFM with sidewall and top-surface probes for both flexural and torsional modes", "url": null, "volume": "52"}, {"a uthors": [{"name": "Gaoliang Dai"}, {"name": "Helmut Wolff"}, {"name": "Frank Pohlenz"}, {"name": "Hans-Ulrich Danzebrink"}, {"name": "G5Cu00fcnter Wilkening"}], "date": "2006", "id": "b6", "index": 6, "issue": null, "journal": "APPLIED PHYSICS LETTERS", "publisher": null, "title": "Atomic force probe for sidewall scanning of nano-and micro structures", "url": null, "volume": "88"}, {"authors": [{"name": "Gaoliang Dai"}, {"name": "Helmutwolff"}, {"name": "Min Thomasweimann"}, {"name": "Frank Xu"}, {"name": "Ha ns-Ulrich Pohlenz"}, {"name": "Danzebrink"}], "date": "2007", "id": "b7", "index": 7, "issue": null, "journal": "Meas. Sci. Technol", "publisher": null, "title": "Nanoscale surface measurements at sidewalls of nanoand micro-structures", "url": null, "volume": "18"}, {"authors": [{"name": "Win-Jin Chang"}, {"name": "Haw-Long Lee"}, {"name": "T erry Yuan-Fang Chen"}], "date": "2008", "id": "b8", "index": 8, "issue": null, "journal": "Ultramicroscopy", "publisher": null, "title": "Study of the sensitivity of the fi rst four flexural modes of an AFM cantilever with a sidewall probe", "url": null, "volume": "108"}, {"authors": [{"name": "Xiaohui Tang"}, {"name": "Vincent Bayot"}, {"name": "Nicolas Reckinger"}, {"name": "Denis Flandre"}, {"name": "Jean-Pierre Raskin"}, {"name": "Emmanuel Dubois"}, {"name": "Bernard Nysten"}], "date": "2009", "id": "b9", "i ndex": 9, "issue": null, "journal": "IEEE Transactions on Nanotechnogoly", "publisher": null, "title": "A Simple Method for Measuring Si-Fin Sidewall Roughness by AFM", "ur l": null, "volume": "8"}, {"authors": [{"name": "Ali Hossein Nejat Pishkenari"}, {"name": "Meghdari"}], "date": "2011", "id": "b10", "index": 10, "issue": null, "journal": "Ultramicroscopy", "publisher": null, "title": "Influence of the tip mass on the tip-sample interactions in TM-AFM", "url": null, "volume": "111"}, {"authors": [{"name": "S ohrab Eslami"}, {"name": "Naderjalili"}], "date": "2012", "id": "b11", "index": 11, "issue": null, "journal": "Ultramicroscopy", "publisher": null, "title": "A comprehensiv e modeling and vibration analysis of AFM microcantilevers subjected to nonlinear tip-sample interaction forces", "url": null, "volume": "117"}, {"authors": [{"name": "Yaxin Song"}, {"name": "Bharat Bhushan"}], "date": "2006", "id": "b12", "index": 12, "issue": null, "journal": "Journal of Applied Physics", "publisher": null, "title": "Couplin g of cantilever lateral bending and torsion in torsional resonance and lateral excitation modes of atomic force microscopy", "url": null, "volume": "99"}, {"authors": [{"name": "Haw-Long Lee"}, {"name": "Win-Jin Chang"}], "date": "2008", "id": "b13", "index": 13, "issue": null, "journal": "Ultramicroscopy", "publisher": null, "title": "Couple d lateral bending-torsional vibration sensitivity of atomic force microscope cantilever", "url": null, "volume": "108"}, {"authors": [{"name": "Farzad Mokhtarinezhad"}], "d ate": "2015", "id": "b14", "index": 14, "issue": null, "journal": null, "publisher": null, "title": "Jurnal Teknologi (Sciences & Engineering)", "url": null, "volume": "76" }, {"authors": [{"name": "F Mokhtari-Nezhad"}, {"name": "A Saidi"}, {"name": "S Ziaei-Rad"}], "date": "2009", "id": "b15", "index": 15, "issue": null, "journal": "Ultramicr oscopy", "publisher": null, "title": "Influence of the tip mass and position on the AFM cantilever dynamics: Coupling between bending, torsion and flexural modes", "url": null, "volume": "109"}, {"authors": [{"name": "Arvind Raman"}, {"name": "John Melcher"}, {"name": "Ryan Tung"}], "date": "2008", "id": "b16", "index": 16, "issue": null, "jo urnal": "Nanotodays", "publisher": null, "title": "Cantilever dynamics in atomic force microscopy", "url": null, "volume": "3"}, {"authors": [{"name": "Nader Jalili"}, {"name": "Karthik Laxminarayana"}], "date": "2004", "id": "b17", "index": 17, "issue": null, "journal": "Mechatronic", "publisher": null, "title": "A review of atomic force mic roscopy imaging systems: application to molecular metrology and biological sciences", "url": null, "volume": "14"}, {"authors": [{"name": "B Derjaguin"}, {"name": "V Muller "}, {"name": "Y Toporov"}], "date": "1975", "id": "b18", "index": 18, "issue": null, "journal": "J. Colloid Interf. Sci", "publisher": null, "title": "Effect of contact def ormations on the adhesion of particles", "url": null, "volume": "53"}, {"authors": [{"name": "Yaxin Song"}, {"name": "Bharat Bhushan"}], "date": "2006", "id": "b19", "index ": 19, "issue": null, "journal": "Ultramicroscopy", "publisher": null, "title": "Simulation of dynamic modes of atomic force microscopy using a 3D finite element model", "u rl": null, "volume": "106"}, {"authors": [{"name": "K Johnson"}, {"name": "K Kendall"}, {"name": "A Roberts"}], "date": "1971", "id": "b20", "index": 20, "issue": null, "jo urnal": "Proc. R. Soc. London Ser. A", "publisher": null, "title": "Surface energy and the contact of elastic solids", "url": null, "volume": "324"}, {"authors": [{"name": "D Gorman"}], "date": "1975", "id": "b21", "index": 21, "issue": null, "journal": null, "publisher": null, "title": "Free Vibration Analysis of Beams and Shafts", "url": null, "volume": null}, {"authors": [{"name": "M Mahdavi"}, {"name": "A Farshidianfar"}, {"name": "M Tahani"}, {"name": "S Mahdavi"}, {"name": "H Dalir"}], "date": "2008", "id ": "b22", "index": 22, "issue": null, "journal": "Ultramicroscopy", "publisher": null, "title": "A more comprehensive modeling of atomic force microscope cantilever", "url" : null, "volume": "109"}, {"authors": [{"name": "M Reinstadtler"}, {"name": "U Rabe"}, {"name": "V Scherer"}, {"name": "U Hartmann"}, {"name": "A Goldade"}, {"name": "B Bhu shan"}, {"name": "W Arnold"}], "date": "2003", "id": "b23", "index": 23, "issue": null, "journal": "Applied physics letters", "publisher": null, "title": "On the nanoscale measurement of friction using atomic-force microscope cantilever torsional resonances", "url": null, "volume": "82"}, {"authors": [{"name": "M Reinst5Cu00e4dtler"}, {"name": "T Kasai"}, {"name": "U Rabe"}, {"name": "B Bhushan"}, {"name": "W Arnold"}], "date": "2005", "id": "b24", "index": 24, "issue": null, "journal": "Journal of Physics D: Applied Physics", "publisher": null, "title": "Imaging and measurement of elasticity and friction using the TRmode", "url": null, "volume": "38"}], "date": "2015", "doi": null, "journal": {"eissn": null, "issn": null, "issue": null, "name": null, "publisher": null, "volume": "76"}, "title": "Jurnal Teknologi Full Paper INVESTIGATION OF TORSI ONAL DEFLECTION AS AN UNDESIRED MOTION IN ATOMIC FORCE MICROSCOPY WITH SIDEWALL PROBE"} +{"abstract": "Eight months after triple valve replacement with Bjork-Shiley tilting disc valves a patient developed symptoms and signs suggesting malfunction of the prosthesis in the tricuspid position. This was confirmed by echocardiography and angiocardiography, and at operation the di sc of the prosthesis was found to be stuck half-open by fibrin and clot. A further 11 patients with the same type of prosthesis in the tricuspid position were then studied by phonocardiography and echocardiography. In one of these the prosthesis was found to be stuck and this was confirmed by angiocardiography and surgery. These 2 cases are r eported in detail and thefindings in the other 10 are discussed. The implications of this high incidence of malfunction of the Bj6rk-Shiley prosthesis in the tricuspid posi tion are considered. Echocardiography appears to be essential in the follow-up of such patients.", "acknowledgement": null, "authors": [{"name": "P Bourdillon"}, {"name": " G Sharratt"}], "citations": [{"authors": [{"name": "J Assad-Morell"}, {"name": "A Tajik"}, {"name": "M Anderson"}, {"name": "R Tancredi"}, {"name": "R Wallace"}, {"name": " E Giuliani"}], "date": "1974", "id": "b0", "index": 0, "issue": null, "journal": "Mayo Clinic Proceedings", "publisher": null, "title": "Malfunctioning tricuspid valve pros thesis", "url": null, "volume": "49"}, {"authors": [{"name": "R Bache"}, {"name": "A From"}, {"name": "A Castaneda"}, {"name": "C Jorgensen"}, {"name": "Wang"}, {"name": "Y "}], "date": "1972", "id": "b1", "index": 1, "issue": null, "journal": "Chest", "publisher": null, "title": "Late thrombotic obstruction of Starr-Edwards tricuspid valve pr osthesis", "url": null, "volume": null}, {"authors": [{"name": "I Belenkie"}, {"name": "M Carr"}, {"name": "R Schlant"}, {"name": "D Nutter"}, {"name": "P Symbas"}], "date" : "1973", "id": "b2", "index": 2, "issue": null, "journal": "American Heart,Journal", "publisher": null, "title": "Malfunction of a Cutter Smeloff mitral ball valve prosthe sis: diagnosis by phonocardiography and echocardiography", "url": null, "volume": "86"}, {"authors": [{"name": "J Douglas"}, {"name": "Williams"}, {"name": "G"}], "date": " 1974", "id": "b3", "index": 3, "issue": null, "journal": "Circulation", "publisher": null, "title": "Echocardiographic evaluation of the Bjork-Shiley prosthetic valve", "ur l": null, "volume": "50"}, {"authors": [{"name": "J Gimenez"}, {"name": "W Winters"}, {"name": "Jr"}, {"name": "J Davila"}, {"name": "J Connell"}, {"name": "K Klein"}], "da te": "1965", "id": "b4", "index": 4, "issue": null, "journal": "American Journal of the Medical Sciences", "publisher": null, "title": "Dynamics of the StarrEdwards ball va lve prosthesis: a cine-fluorographic and ultrasonic study in humans", "url": null, "volume": "250"}, {"authors": [{"name": "M Johnson"}, {"name": "J Holmes"}, {"name": "Pat on"}, {"name": "B"}], "date": "1973", "id": "b5", "index": 5, "issue": null, "journal": "Circulation", "publisher": null, "title": "Echocardiographic determination of mitra l disc valve excursion", "url": null, "volume": "47"}, {"authors": [{"name": "M Johnson"}, {"name": "B Paton"}, {"name": "J Holmes"}], "date": "1970", "id": "b6", "index": 6, "issue": null, "journal": "Circulation", "publisher": null, "title": "Ultrasonic evaluation of prosthetic valve motion", "url": null, "volume": null}, {"authors": [{"name": "H Miller"}, {"name": "D Gibson"}, {"name": "J Stephens"}], "date": "1973", "id": "b7", "index": 7, "issue": null, "journal": "British Heart Journal", "publisher": null , "title": "Role of echocardiography and phonocardiography in diagnosis of mitral paraprosthetic regurgitation with Starr-Edwards prostheses", "url": null, "volume": "35"}, {"authors": [{"name": "P Oliva"}, {"name": "M Johnson"}, {"name": "M Pomerantz"}, {"name": "Levene"}, {"name": "A"}], "date": "1973", "id": "b8", "index": 8, "issue": null , "journal": "American journal of Cardiology", "publisher": null, "title": "Dysfunction of the Beall mitral prosthesis and its detection by cinefluoroscopy and echocardiogr aphy", "url": null, "volume": null}, {"authors": [{"name": "J Pfeifer"}, {"name": "N Goldschlager"}, {"name": "T Sweatman"}, {"name": "F Gerbode"}, {"name": "A Selzer"}], " date": "1972", "id": "b9", "index": 9, "issue": null, "journal": "American J7ournal of Cardiology", "publisher": null, "title": "Malfunction of mitral ball valve prosthesis due to thrombus: report of 2 cases with notes on early clinical diagnosis", "url": null, "volume": "29"}, {"authors": [{"name": "H Samaan"}, {"name": "R Murali"}], "date": "1970", "id": "b10", "index": 10, "issue": null, "journal": "Thorax", "publisher": null, "title": "Acute tricuspid valve obstruction following the use of tricuspid ball va lve prosthesis", "url": null, "volume": null}, {"authors": [{"name": "S Suwansirikul"}, {"name": "E Glassman"}, {"name": "F Raia"}, {"name": "F Spencer"}], "date": "1974", "id": "b11", "index": 11, "issue": null, "journal": "American J'ournal of Cardiology", "publisher": null, "title": "Late thrombosis of Starr-Edwards tricuspid ball valve pr osthesis", "url": null, "volume": "34"}, {"authors": [{"name": "Vander"}, {"name": "J Veer"}, {"name": "Jr"}, {"name": "G Rhyneer"}, {"name": "R Hodam"}, {"name": "F Kloste r"}], "date": "1971", "id": "b12", "index": 12, "issue": null, "journal": "Circulation", "publisher": null, "title": "Obstruction of tricuspid ball-valve prostheses", "url" : null, "volume": null}, {"authors": [{"name": "W Winters"}, {"name": "Jr"}, {"name": "J Gimenez"}, {"name": "L Soloff"}], "date": "1967", "id": "b13", "index": 13, "issue" : null, "journal": "American journal of Cardiology", "publisher": null, "title": "Clinical application of ultrasound in the analysis of prosthetic ball valve function", "ur l": null, "volume": "19"}, {"authors": [{"name": "P D V Requests For Reprints To Dr"}, {"name": "Western Bourdillon"}, {"name": "Hospital"}, {"name": "Oakley Road"}], "date ": false, "id": "b14", "index": 14, "issue": null, "publisher": null, "title": null, "url": null, "volume": null}], "date": "1976", "doi": null, "journal": {"eissn": null, "issn": null, "issue": null, "name": "British Heart Journal", "publisher": null, "volume": "38"}, "title": "Malfunction of Bjork-Shiley valve prosthesis in tricuspid positi on"} +{"abstract": "The interference is the major factor disrupting the sending of information in wireless networks. To ge t better performance for these networks as well in the conventional case as in cooperative one, all the necessary ways must be used to eliminate network interference. This article deals with the concept of Physical Layer Network Coding (PLNC). It is a way to exploit the operation of Network Coding (NC) that occurs naturally in the superimpose d electromagnetic waves (EM). It is a simple physical effect when several EM waves meet in the same physical space, they are mixed together. This mixture of EM waves is a f orm of NC produced by nature. Hence, the situation will be reversed and the interference will be a beneficial way to help the relay when sending information. This paper foc uses on the Symbol Error Rate (SER) Analysis of PLNC in the case of 16QAM modulator. It will exploit in detail the concept of mapping (modulation/demodulation) and will dem onstrate its contribution compared to NC and Traditional Network (TN).", "acknowledgement": "Conclusion In this paper, we took a brief description of different cases of coo perative networks in the case of TWRC. We describe the Traditional cooperative Networks, then the Network Coding, and finally, the Physical Layer Network Coding. This one a llows us to reduce the number of phases from 4 to 2. Furthermore, this paper illustrates that in PLNC and for the case of 16QAM constellation, the SER is lower than in the standard modulation case. This is verified with the modulation/demodulation study done and for the In-phase and quadrature case of the modulator.", "authors": [{"name": "R Hajji"}, {"name": "N Hamdi"}], "citations": [{"authors": [{"name": "R Hajji"}, {"name": "N Hamdi"}], "date": "2012", "id": "b0", "index": 0, "issue": null, "journal": "IEEE Electrotechnical Conference (MELECON)", "publisher": null, "title": "Optimizing of Power Allocation for Two-Hop DF Relaying Systems", "url": null, "volume": null}, {"autho rs": [{"name": "J Proakis"}], "date": "1989", "id": "b1", "index": 1, "issue": null, "journal": null, "publisher": null, "title": "Digital Communication", "url": null, "vol ume": null}, {"authors": [{"name": "S Tian"}, {"name": "Li Yonghui"}, {"name": "B Vucetic"}], "date": "2011", "id": "b2", "index": 2, "issue": null, "journal": "IEEE ICC", "publisher": null, "title": "A Near Optimal Amplify and Forward Relaying in Two-Way Relay Networks", "url": null, "volume": null}, {"authors": [{"name": "S Zhang"}, {"name" : "S Liew"}, {"name": "P Lam"}], "date": "2006", "id": "b3", "index": 3, "issue": null, "journal": null, "publisher": null, "title": "Physical Layer Network Coding. ACM Mob iCom", "url": null, "volume": null}], "date": "2013", "doi": null, "journal": {"eissn": null, "issn": null, "issue": "3", "name": "AWERProcedia Information Technology & Com puter Science", "publisher": null, "volume": "03"}, "title": "SER Analysis of Two-Hop Physical Layer Network Coding with 16QAM Modulator, AWERProcedia Information Technolog y & Computer Science"} +{"abstract": "Suffix trees are by far the most important data structure in stringology, with myriads of applications in fields like bioinformatics and information retrieval. Classical representations of suffix trees require O(n log n) bits of space, for a string of size n. This is consid erably more than the n log 2 5Cu03c3 bits needed for the string itself, where 5Cu03c3 is the alphabet size. The size of suffix trees has been a barrier to their wider a doption in practice. Recent compressed suffix tree representations require just the space of the compressed string plus 5Cu0398(n) extra bits. This is already spectacular , but still unsatisfactory when 5Cu03c3 is small as in DNA sequences. In this paper we introduce the first compressed suffix tree representation that breaks this linear-s pace barrier. Our representation requires sublinear extra space and supports a large set of navigational operations in logarithmic time. An essential ingredient of our repr esentation is the lowest common ancestor (LCA) query. We reveal important connections between LCA queries and suffix tree navigation.", "acknowledgement": null, "authors": [{"name": "Lu5Cu00eds Russo"}, {"name": "Gonzalo Navarro"}, {"name": "Arlindo Oliveira"}], "citations": [{"authors": [{"name": "A Apostolico"}], "date": "1985", "id": "b0 ", "index": 0, "issue": null, "journal": "Combinatorial Algorithms on Words. NATO ISI Series", "publisher": null, "title": "The myriad virtues of subword trees", "url": null, "volume": null}, {"authors": [{"name": "M Bender"}, {"name": "M Farach-Colton"}], "date": "2000", "id": "b1", "index": 1, "issue": null, "journal": "Proceedings of LATIN ", "publisher": null, "title": "The LCA problem revisited", "url": null, "volume": "1776"}, {"authors": [{"name": "M Bender"}, {"name": "M Farach-Colton"}], "date": "2004", "id": "b2", "index": 2, "issue": "1", "journal": "Theor. Comp. Sci", "publisher": null, "title": "The level ancestor problem simplified", "url": null, "volume": "321"}, {" authors": [{"name": "M Farach"}], "date": "1997", "id": "b3", "index": 3, "issue": null, "journal": "Proceedings of FOCS", "publisher": null, "title": "Optimal suffix tree construction with large alphabets", "url": null, "volume": null}, {"authors": [{"name": "P Ferragina"}, {"name": "G Manzini"}, {"name": "V M5Cu00e4kinen"}, {"name": "G Na varro"}], "date": "2007", "id": "b4", "index": 4, "issue": "2", "journal": "ACM Trans. Algor", "publisher": null, "title": "Compressed representations of sequences and full -text indexes", "url": null, "volume": "3"}, {"authors": [{"name": "J Fischer"}, {"name": "V Heun"}], "date": "2007", "id": "b5", "index": 5, "issue": null, "journal": "Pro ceedings of ESCAPE", "publisher": null, "title": "A new succinct representation of RMQ-information and improvements in the enhanced suffix array", "url": null, "volume": "4 614"}, {"authors": [{"name": "L Foschini"}, {"name": "R Grossi"}, {"name": "A Gupta"}, {"name": "J Vitter"}], "date": "2006", "id": "b6", "index": 6, "issue": "4", "journal ": "ACM Trans. Algor", "publisher": null, "title": "When indexing equals compression: Experiments with compressing suffix arrays and applications", "url": null, "volume": " 2"}, {"authors": [{"name": "R Geary"}, {"name": "R Raman"}, {"name": "V Raman"}], "date": "2004", "id": "b7", "index": 7, "issue": null, "journal": "Proceedings of SODA", " publisher": null, "title": "Succinct ordinal trees with level-ancestor queries", "url": null, "volume": null}, {"authors": [{"name": "R Giegerich"}, {"name": "S Kurtz"}, {"name": "J Stoye"}], "date": "2003", "id": "b8", "index": 8, "issue": "11", "journal": "Softw., Pract. 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{"eissn": "1941-3084", "issn": "1941-3149", "issue": null, "name": "Circulation: Arrhythmia and Electrophysiology", "publisher": "Ovid Technologies (Wolters Kluwer Health)", "volume" : null}, "title": "Fatigue as Presenting Symptom and a High Burden of Premature Ventricular Contractions Are Independently Associated with Increased Ventricular Wall Stress in Patients with Normal Left Ventricular Function"} diff --git a/python/tests/files/first_monday_ojs3_fulltext.html b/python/tests/files/first_monday_ojs3_fulltext.html new file mode 100644 index 0000000..2248aed --- /dev/null +++ b/python/tests/files/first_monday_ojs3_fulltext.html @@ -0,0 +1,441 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" 2012"http://www.w3.org/TR/html4/loose.dtd"> +<html> +<head> + +<meta http-equiv="content-type" content="text/html; charset=utf-8"> +<title>Surveillance, stigma and sociotechnical design for HIV</title> +</head> +<body bgcolor="#ffffff" LINK="#bb7777" VLINK="#7777bb" ALINK="#ffee99" text="#000000"> +<blockquote><img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71629" border="1" alt="First Monday" align="bottom"><br></blockquote> +<hr> +<blockquote> + +<center><a href="#author"><img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71975" alt="Surveillance, stigma and sociotechnical design for HIV by Calvin Liang, Jevan Alexander Hutson, and Os Keyes" border="1"></a></center> + +<br><hr><br> + +<p><img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71627" alt="Abstract"><br>Online dating and hookup platforms have fundamentally changed people’s day-to-day practices of sex and love — but exist in tension with older social and medicolegal norms. This is particularly the case for people with HIV, who are frequently stigmatized, surveilled, ostracized, and incarcerated because of their status. Efforts to make intimate platforms “work” for HIV frequently focus on user-to-user interactions and disclosure of one’s HIV status but elide both the structural forces at work in regulating sex and the involvement of the state in queer lives. In an effort to foreground these forces and this involvement, we analyze the approaches that intimate platforms have taken in designing for HIV disclosure through a content analysis of 50 current platforms. We argue that the implicit reinforcement of stereotypes about who HIV is or is not a concern for, along with the failure to consider state practices when designing for data disclosure, opens up serious risks for HIV-positive and otherwise marginalized people. While we have no panacea for the tension between disclosure and risk, we point to bottom-up, communal, and queer approaches to design as a way of potentially making that tension easier to safely navigate.</p> + +<p><strong>Contents</strong></p> +<p><a href="#p1">Introduction</a><br> +<a href="#p2">Methods</a><br> +<a href="#p3">Findings</a><br> +<a href="#p4">Discussion</a><br> +<a href="#p5">Conclusion</a></p> + +<p> </p><hr><p> </p> +<p><strong><a name="p1"></a>Introduction</strong></p> + +<table width="70%" align="center"><tr><td>“AIDS is essentially a crisis of governance, of what governments do and do not do, to and for their people — we have the drugs to treat HIV infection, we have the tools to confront the risks that drive HIV transmission and prevent infection itself — what we don’t have is national political will necessary to scale-up our response. We have demanded too little from our leaders, excused far too much.”<br>— Gregg Gonsalves, speech at the 2006 Toronto AIDS Conference.</td></tr></table> + +<table width="70%" align="center"><tr><td>“Design is inherently about change — not just in the creation of new material artifacts, but in the ways that new technological objects afford new practices, social habits, and ways of living and interacting.”<br>— Dombrowski, <em>et al.</em> (2016). “Social justice-oriented interaction design: Outlining key design strategies and commitments.”</td></tr></table> + +<p>Living and loving with HIV is a complicated task. HIV status and the stigma attached to it exists within a complex interplay of social norms and medicolegal infrastructures. The medicolegal history of HIV begins the moment that HIV and AIDS emerged, constituting a mix of medically justified legal norms and legally enforced medical requirements. The criminal justice and public health systems of modern states demarcated people living with HIV as a uniquely dangerous population, “one that needed to be sought out, tracked down, tested, reported, listed, tagged, monitored, regulated, and, increasingly, criminalized” <a name="1a"></a>[<a href="#1">1</a>].</p> + +<p>The immediate policy response in the United States imposed significant criminal and civil liability upon people living with HIV (Hoppe, 2018; Harsono, <em>et al.</em>, 2017; Sykes, <em>et al.</em>, 2016; Thrasher, 2015; Galletly, <em>et al.</em>, 2014; Lehman, <em>et al.</em>, 2014; Gagnon, 2012; Pollard, 2006; Gostin, <em>et al.</em>, 1999). Between 1986–2019, HIV-specific criminal laws and sentence enhancements applicable to people living with HIV have been enacted in 34 states and two U.S. territories (Center for HIV Law & Policy, 2019; Lehman, <em>et al.</em>, 2014). Since 1986, these laws have criminalized nondisclosure of HIV and engagement in “risky” behaviors such as sexual activity, exposure to bodily fluids, needle sharing, sex work, blood/organ/semen donation, and, in a variety of instances, behaviors posing little, if any, risk of HIV transmission (Center for Disease Control and Prevention, 2019a; Center for HIV Law & Policy, 2019).</p> + +<p>Despite claiming medical legitimacy for this punitive approach, researchers have long understood that the criminalization of HIV transmission was instead fueled by the associations between HIV and the gay community and communities of color (Hoppe, 2018; Gallo, 2006; Johnson, 1992; Banks, 1989) at a time when consensual sex between same-sex partners was a criminal offense in twenty-two states and over 61 percent of American evangelicals and 50 percent of non-evangelicals agreed with the statement “I sometimes think AIDS is a punishment for the decline in moral standards” (Gallup and Castelli, 1987).</p> + +<p>A significant body of empirical social science work documents the harmful effects HIV laws have had on the lives of people living with HIV (BarréSinoussi, <em>et al.</em>, 2018; Harsono, <em>et al.</em>, 2017; Sweeney, <em>et al.</em>, 2017; Adam, <em>et al.</em>, 2014). HIV criminalization both reinforces and magnifies HIV-related stigma and discrimination, reduces the willingness of persons at risk for HIV to get tested or seek care, and imperils demographic health collection of information (Harsono, <em>et al.</em>, 2017; Burris and Cameron, 2008; Galletly and Pinkerton, 2006; Elliot, 2002). A survey of over 2,000 people living with HIV in the U.S. revealed that at least 25 percent of respondents knew one or more individuals who were afraid to get tested for fear of facing criminalization (Sero Project, 2012). HIV criminalization also ignores the reality that successful antiretroviral therapy can render the level of the virus to undetectable, which, according to the National Institute of Health, means that HIV is then untransmittable (Eisinger, <em>et al.</em>, 2019).</p> + +<p>While HIV transmission was criminalized, other tools of control — in the form of surveillance — arose and were enforced. Early policy responses to HIV centered on overt surveillance and ostracism of those infected and perceived to be at risk (Fortin, 1995). This surveillance generally consists of disease reporting, sexual contact tracing, and data collection of people who have been diagnosed with HIV (Fan, 2012; 2011; Ward and Bell, 2014; Ward, 2005). The Center for Disease Control, for example, collects HIV data based on confidential name-based reporting laws implemented in all 50 states as of April 2008 (Center for Disease Control and Prevention, 2019b).</p> + +<p>HIV surveillance (and sexually transmitted infection surveillance more broadly) centralizes information and power in the state (Fairchild, <em>et al.</em>, 2007; Fan, 2012); because HIV intervention and surveillance is generally concentrated in lower income communities and health settings (McCree and Hogben, 2010), the most socially and economically marginalized communities bear the heaviest burden of HIV surveillance and its downstream consequences (Miller, <em>et al.</em>, 2004; Banks, 1989; Brandt, 1987). There is a long-racialized history of HIV, one that, in combination with the background racism of the United States, has led to the systemic undertreatment and under-consideration of communities of color (Ford, <em>et al.</em>, 2007; Anonymous, 2000; Johnson, 1992).</p> + +<p>This infrastructure of surveillance in turn reinforces the stigma of HIV, which has dramatic consequences for the likelihood of unwanted disclosure, access to care, psychiatric well-being, housing and employment discrimination, and, consequently, quality (or probability) of life (Lazarus, <em>et al.</em>, 2016; Mahajan, <em>et al.</em>, 2008). Coupled with the overarching stigma of HIV and its criminalization in various contexts, HIV surveillance offers a tool through which the state can identify citizens to be punished.</p> + +<p>In the era of “big data” and ubiquitous surveillance capitalism (Zuboff, 2019) — the private monetization of information about reality — HIV surveillance is not just in the hands of the state, but also in the hands of private organizations and individuals. In the context of widespread state surveillance and control and ongoing stigmatization of HIV, this opens yet more possibilities for harm through enabling the selling and redistribution of HIV status information, without the user’s meaningful consent, to parties who may themselves engage in discrimination or direct violence.</p> + +<p>Many online platforms — including, as we trace out below, dating platforms — constitute not just spaces for the purposes outlined in their marketing materials but also tools for the police in tracing HIV status and criminalized behavior. In recent years, police have used technology to conduct Internet-based investigations for a similar purpose (POZ, 2015). Police now go undercover on Web sites and dating apps by creating fake identities online (Semitsu, 2011), and local law enforcement agencies and federal agencies increasingly employ these tactics in online investigations (Lichtblau and Arkin, 2014).</p> + +<p>Legal and public health scholars and advocates continue to call for a paradigm shift in managing HIV that leaves behind historical responses like surveillance, ostracism, and incarceration and accounts for the rise of the Internet and mobile technology and their impact on sexual attitudes and behaviors (Lehman, <em>et al.</em>, 2014; McCallum, 2014; Fan, 2011; Fenton, 2010). Since the criminalization of HIV, intimate platforms have become vital structures through which millions of people access the opportunity to engage in reciprocal romantic and sexual relationships (Hutson, <em>et al.</em>, 2018; Taylor, <em>et al.</em>, 2017; Rosenfeld and Thomas, 2012). By designing infrastructures for intimate affiliation, intimate platforms wield unmatched structural power to shape who meets whom and how within dating and sexual platforms (Hutson, <em>et al.</em>, 2018; Levy and Barocas, 2018; Emens, 2008; Robinson, 2007). These platforms frame the circumstances within which users understand each other as prospective romantic or sexual partners and shape social norms, sexual scripts, and relative advantages among users (Hardy and Lindtner, 2017; Kannabiran, <em>et al.</em>, 2012).</p> + +<p>The design of intimate platforms provides opportunities to explore new ways of managing HIV that reduce the concentration of power and information in the state (Fan, 2012). Through the role that platform design plays in shaping cultural norms, which has been identified as a more effective way of achieving HIV transmission prevention than flexing the punitive and surveillant arms of the state (Sunstein, 1996), intimate platform design provides opportunities to explore new ways of managing HIV (Fan, 2012). Indeed, a meta-analysis of HIV prevention efforts found that strategies that intervene in social meaning by shaping social norms, cultural practices, and individual attitudes were more effective in empowering behavioral change than appeals to fear (Albarracin, <em>et al.</em>, 2015).</p> + +<p>However, designing intimate platforms to account for HIV also presents serious challenges for social computing researchers and human-computer interaction (HCI) designers. As Handel and Shklovski pointed out: “The minutiae of design decisions around profile options deserves particular attention because even the smallest changes can result in substantial differences for user interactions” (Handel and Shklovski, 2012). In addition to concerns around how to best design for HIV, platforms, Grindr in particular, have already come under fire for sharing user HIV information with third parties (Singer, 2018). Moreover, designing intimate platforms to unburden the risks of extant criminal and civil sexual regulations runs the serious risk of re-entrenching the status quo and its incumbent inequalities and power relations (Bardzell, 2010). While designing for HIV presents opportunities to redress stigma and harm, researchers in HCI must understand that “[i]t is not enough to have good intentions ... [we] must ground [our] efforts in clear political commitments and rigorous evaluations of the likely consequences” (Green, 2018).</p> + +<p>From this comes the recognition that social computing designers and researchers seeking to design for disclosure cannot afford to ignore the ways that the lived experiences of people living with HIV are shaped by structural forces and, particularly, the reality of HIV criminalization and the State’s role in conducting STD surveillance. Platforms, after all, do not exist in a separate sphere from material reality: a redesign that eases HIV disclosure from user-to-user might also involve the storing of disclosure data by the platform — data that can then be accessed, requisitioned, and co-opted by arms of the state. In line with Jackson, <em>et al.’s</em> call for the social computing community to address the structural and lived consequences of law and policy that “establish the very terrain on which design and practice can be conceived, articulated, and imagined — and upon which battles of accountability are inevitably waged” <a name="2a"></a>[<a href="#2">2</a>], we wish to undertake a critical investigation of HIV disclosure in dating and hookup platforms. This involves not just investigating the implications of disclosure in a person-to-person sense, but also how platform design is shaped by legal and administrative regulation and how the risks of disclosure might open users up to systems of surveillance, stigma, and criminalization. We do so by using a range of platforms in an effort to gain a wide view, and to practice prefigurative politics — minimizing our assumptions about the “type” of people at risk of HIV infection and/or surveillance.</p> + +<p>To do this, we analyze platform’s consequences for HIV through the lens of user-to-user interactions, exploring the ways that design renders users visible and vulnerable to wider carceral and surveillance infrastructures, and the way that design shapes (and is shaped) by HIV’s legal status. We ground our discussion in a content analysis of 50 popular, mobile dating and hookup platforms, coding for design and policy choices related to HIV disclosure, prevention, destigmatization, surveillance, privacy, and criminalization. Through this, we reveal that many platforms fail to account for HIV, and of those that do, many neglect to attend to the downstream consequences of HIV disclosure and the data produced by it, while exacerbating the social, racial, and class stereotypes associated with the condition.</p> + +<p>As scholars and designers consider how platform design might aid HIV prevention and destigmatization (Hutson, <em>et al.</em>, 2018; Albury, <em>et al.</em>, 2017; Wohlfeiler, <em>et al.</em>, 2013; Rosser, <em>et al.</em>, 2011), we aim to grapple with the structural and ethical implications of designing for HIV, particularly how intimate platform design might aid and abet the decriminalization and surveillance of HIV (Sykes, <em>et al.</em>, 2016; Kazatchkine, <em>et al.</em>, 2015; Perone, 2013; Gagnon, 2012; Jürgens, <em>et al.</em>, 2009). Drawing on principles from social justice-oriented design to investigate controversies and design possibilities in intimate platforms, we attempt to articulate an approach to intimate platform design that not only works to reduce the stigma of user disclosure, but also works to contest historic and present power imbalances and injustices between users, platforms, and the state.</p> + +<p> </p> +<p><img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71630" alt="++++++++++"></p> +<p><strong><a name="p2"></a>Methods</strong></p> + +<p>Using a directed content analysis (Hsieh and Shannon, 2005), we reviewed 50 existing mobile dating and hookup platforms. Content analyses have proven effective in understanding platform design and governance and the ways design practices mediate user-to-user bias and discrimination (Levy and Barocas, 2018; Hutson, <em>et al.</em>, 2018). We set out to capture a landscape of popular platforms and selected the first 50 dating and hook up platforms in the top 200 grossing social networking applications in the United States on the iOS App Store in March of 2019. <a href="#fig1">Figure 1</a> lists the platforms selected in alphabetical order.</p> + +<p> </p> +<a name="fig1"></a> +<table align="center" width="60%" cellpadding="4"> +<tr align="center"><td><img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71623" alt="50 dating and hookup platforms surveyed"></td></tr> +<tr><td> </td></tr> +<tr align="center"><td><strong>Figure 1:</strong> The 50 dating and hookup platforms surveyed.</td></tr> +<tr><td> </td></tr> +</table> +<p> </p> + +<p>Utilizing the walkthrough method (Light, <em>et al.</em>, 2018), we explored each platform’s HIV-related user experience. We examined design features on each of these platforms, systematically documenting design choices, policies, and informational interventions that mediate HIV. Building upon previous work around intimate platforms and HIV, we coded each of the 50 intimate platforms based on the following dimensions:</p> + +<table width="70%" align="center"><tr><td><p>Prevention</p> +<ul><li>Whether the app allows same-sex connections</li> +<li>Whether a user can disclose HIV/sexually transmitted infection (STI) status (Warner, <em>et al.</em>, 2018)</li> +<li>If they can disclose, what are the options? (Warner, <em>et al.</em>, 2018)</li> +<li>Whether a user can search for or filter out users with HIV/STIs? (Hutson, <em>et al.</em>, 2018)</li> +<li>Whether the platforms provide informational interventions with respect to HIV/STI prevention (Wang, <em>et al.</em>, 2019)</li></ul> +<p>Stigma reduction</p> +<ul><li>Whether a user can identify as having HIV/STI (<em>e.g.</em>, “Poz”, etc.)</li> +<li>Whether a user can indicate interest in or acceptance of people living with HIV/STIs (<em>e.g.</em> outward presentation, separate from filtering, not simply via profile text) (Hutson, <em>et al.</em>, 2018)</li></ul> +<p>Policies</p> +<ul><li>Whether the platform engages HIV/STIs in their policies (terms of service, privacy, and community policies, etc.) (Jackson, <em>et al.</em>, 2014)</li></ul></td></tr></table> + +<p>For ethical reasons, we did not interact with other users, only observed features, and deleted our accounts once data were collected when possible (not all platforms allowed for account deletion). The design and policy choices described and discussed below are not intended as an endorsement of any particular design intervention for managing HIV. Rather, we aim to capture the various ways intimate platforms currently manage and mediate HIV among users and how those choices map onto extant legal and surveillant infrastructures. Additionally, we highlight two limitations in how we chose which platforms to analyze. First, it is possible for a hook-up platform to not have an accompanying mobile app, meaning our selection of platforms from the iOS app store will have invariably missed Web site-based platforms. Second, we may have overlooked platforms that are more niche or community-specific, yet not as popular in the broader platform marketplace (<em>i.e.</em>, not within the top grossing platforms).</p> + +<p> </p> +<p><img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71630" alt="++++++++++"></p> +<p><strong><a name="p3"></a>Findings</strong></p> + +<p> </p> +<a name="fig2"></a> +<table align="center" width="60%" cellpadding="4"> +<tr align="center"><td><img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71624" alt="A visualization of our content analysis"></td></tr> +<tr><td> </td></tr> +<tr align="center"><td><strong>Figure 2:</strong> A visualization of our content analysis.</td></tr> +<tr><td> </td></tr> +</table> +<p> </p> + +<p><em><strong>Design features</strong></em></p> + +<p>Out of the 50 intimate platforms we examined, 13 were meant specifically for queer communities (11 specifically targeted at gay and bisexual men and two at lesbian and bisexual women). None of the platforms we reviewed were distinctly designed for trans people. The remaining 34 platforms were for general audiences, catering to heterosexual and homosexual connections, and three platforms were exclusively for heterosexual connections (eHarmony, Uniform Dating, and Waplog). Only queer-specific platforms (six) had explicit HIV disclosure options and allowed for filtering or searching based on HIV status. <a href="#fig3">Figure 3</a> shows the disclosure options for each platform. Growlr, Taimi, and Scruff allowed users to indicate that they were accepting of people living with HIV. Grindr, Hornet, Mr. X, Xtremboy, and Scruff, five platforms all of which are queer-specific, provide informational interventions with respect to HIV/STI prevention (See <a href="#fig4">Figure 4</a> for examples). Eight dating apps mentioned HIV in their policies (five queer-specific, three general). Four dating apps allowed users to identify with an HIV/STI-relevant identity category, often labeled “poz”. Please see <a href="#fig2">Figure 2</a> for a visualization of our content analysis.</p> + +<p> </p> +<a name="fig3"></a> +<table align="center" width="60%" cellpadding="4"> +<tr align="center"><td><img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71625" alt="Disclosure options"></td></tr> +<tr><td> </td></tr> +<tr align="center"><td><strong>Figure 3:</strong> Disclosure options.</td></tr> +<tr><td> </td></tr> +</table> +<p> </p> + +<p> </p> +<a name="fig4"></a> +<table align="center" width="60%" cellpadding="4"> +<tr align="center"><td><img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71626" alt="Examples of HIV/STI prevention features on Grindr (left, middle) and Hornet (right)"></td></tr> +<tr><td> </td></tr> +<tr align="center"><td><strong>Figure 4:</strong> Examples of HIV/STI prevention features on Grindr (left, middle) and Hornet (right).</td></tr> +<tr><td> </td></tr> +</table> +<p> </p> + +<p><em><strong>Policies</strong></em></p> + +<p>None of the 50 intimate platforms we reviewed explicitly mention HIV in their terms of service. Four platforms expressly discuss HIV in their privacy policies (Grindr, Hornet, Scruff, and Mr. X), and four platforms mention HIV in platform safety policies (Planet Romeo, Tinder, BlackPeopleMeet, and Our Time). No platform engaged any of the legal implications of HIV. No platform engaged the public health surveillance of HIV.</p> + +<p>Of the four platforms that expressly engage HIV in their privacy policies (Grindr, Hornet, Mr. X, Scruff), only two (Grindr & Hornet) explicitly prohibit sharing HIV information with third parties. By disclosing one’s HIV status on Mr. X and Scruff, users consent to the platform’s processing of that information. Grindr warns that HIV status disclosure on a user profile is effectively public information, however the platform does not share HIV status information with third party tracking, analytics, and advertising companies or service providers. Of all the platforms reviewed, Grindr’s privacy policy is the only one that devotes an entire section to HIV status, which is not particularly surprising given Grindr’s involvement in multiple controversies around sharing HIV information with third parties (Fitzsimons, 2019; Singer, 2018):</p> + +<table width="70%" align="center"><tr><td>“HIV Status. At the recommendation of HIV prevention experts and the community of Grindr users, we give you the option of publishing your health characteristics, such as your HIV status, in your Grindr community profile. Remember that if you choose to include information in your profile, that information will become public to other users of the Grindr App. As a result, you should carefully consider whether you want to disclose your HIV status. We do not share HIV status with any third-party service advertisers or third-party service providers other than companies that host data on our behalf (<em>e.g.</em>, Amazon Cloud). In addition, we do not use HIV status for advertising purposes and do not share this information with advertisers.”</td></tr></table> + +<p> According to Hornet’s privacy policies, they “[do] not share any HIV status information with third parties unless required to do so by law”. Of the 50 platforms reviewed, Hornet was the only one to enable users to opt into receiving “in-app reminders to undergo HIV tests and receive information on the location of nearby testing centers.” On Hornet, a user’s HIV status “is only searchable by users who have defined themselves as HIV positive.” Scruff’s privacy policy highlights that “there is no requirement to” provide them with “health details and whether part of the POZ (HIV positive) community (for example, in creating or updating your profile),” and that by doing so, users “are explicitly consenting to [Scruff’s] processing of [their] information.” Mr. X’s privacy policy notes that HIV status information “may be considered ‘special’ or ‘sensitive’ in certain jurisdictions,” and that by providing this information, users “consent to [Mr. X’s] processing that information”.</p> + +<p> </p> +<p><img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71630" alt="++++++++++"></p> +<p><strong><a name="p4"></a>Discussion</strong></p> + +<p><em><strong>Prevention</strong></em></p> + +<p>Platforms can act as an interventional tool to improve access to and perceptions of care for people living with HIV. Examples of HIV/STI prevention include a “Last Tested Date” section on a user’s profile and reminders to get tested for HIV/STIs. Some current platforms engage with HIV more critically by acknowledging that HIV is an issue its users should be aware through specific features. Hornet, for instance, provides its users with HIV-relevant educational material and resources for getting tested. Hornet also limits searching based on HIV status to people who themselves have chosen the HIV positive option, thereby limiting the possibility of HIV status-based discrimination. Hornet and Grindr can also provide reminders for users to get tested. Scruff allows users to choose from sex safety practices that include using condoms, using pre-exposure prophylaxis (PrEP), and/or treatment as prevention (Warner, <em>et al.</em>, 2019).</p> + +<p>Due in large part to the history of HIV’s recognition as a medical condition, HIV has been generally classified as a “gay man’s problem” in North America — frequently (albeit almost as frequently unmarked) a white, cisgender gay man’s problem. This classification and framing acted to both separate normative society from the stigma associated with the condition and provide an avenue for activism by associating it with the most “acceptable” queer bodies: masculine, middle class, cisgender and white (Epstein, 1996).</p> + +<p>HIV has disproportionately impacted gay communities specifically, but transmission does not fit a neat pattern of being binarized tidily along sexuality. It is disproportionately prevalent in communities of color, appears in heterosexual relationships and lives, and risk of transmission follows societal vulnerability and marginalization — transgender women, particularly transgender women of color, are particularly overrepresented in diagnosis rates (Clark, <em>et al.</em>, 2017). While the partial normalization of HIV — holding it outside the direct concerns of white, cisgender, heterosexual people, but embodying it in people who look “just like them” — may have aided in assembling efforts to address the condition, the assumptions that it has created in who is at risk and who “counts” have been tremendous. One only has to look at the ethnographic work of Vivianne Namaste, who highlights how Montreal’s history of HIV, its recognition, and efforts at its prevention simultaneously elided the incidence rate amongst the Haitian community (which at one point had 65 percent of reported AIDS cases) and lacked any advice or conception of susceptibility for women, particularly heterosexual or bisexual women (Namaste, 2015).</p> + +<p>Our platform analysis demonstrates that these same assumptions about vulnerability and risk are present in the design of intimate platforms. Generic platforms (<em>i.e.</em>, those that cater to non-queer or broader, more heteronormative audiences) entirely do not consider, engage, or design for HIV while the platforms for queer — and more specifically gay men — do. Even within the group of 13 queer-specific applications, neither of the two queer women-specific apps allowed for HIV disclosure, even though 23 percent of people with HIV in the U.S. are women (Center for Disease Control and Prevention, 2019c). Most, if not all, platforms dedicated to general audiences do nothing when it comes to HIV prevention, contributing to the knowledge gap for general audiences on sexual health, HIV-specific, and more. Because general audiences can go through online dating experiences without encountering HIV materials, platform designers allow these users to falsely believe that their sexual lives are excluded from important matters of sexual health.</p> + +<p>Our intent is not to suggest that HIV should be narrated as a problem for everyone; to ignore sexuality in the impact and risk of HIV transmission is an ahistorical mistake. But treating it <em>solely</em> as a “gay man’s problem” simultaneously elides differences in vulnerability and risk within gay communities and perpetuates the silence around transmission for other populations, particularly trans women of color and/or heterosexual people. In other words, it is not that HIV is not frequently a risk for gay communities, but that drawing a line between sexuality and risk perpetuates the more nuanced disparities in risk and the discourse that HIV transmission is not something anyone else has to think about.</p> + +<p>Platforms can and have implemented prevention efforts through Last Tested Date and Testing Reminders features. Doing so more ubiquitously, rather than solely on gay male-specific platforms, may be helpful in normalizing prevention efforts like getting tested regularly and knowing one’s status. Through opportunities like this, platform designers have the opportunity to promote HIV/STI prevention and care — an opportunity that is valuable precisely for its ability to normalize prevention efforts. This is not to say that such features are not without risks, particularly with regards to state surveillance, intervention and structural forces, which is our next topic of concern and discussion.</p> + +<p><em><strong>Stigma & disclosure</strong></em></p> + +<p>Designing for HIV is not as simple as including disclosure fields and status-based filtering or not. Allowing disclosure and filtering can protect people living with HIV from negative and sometimes harmful interactions, help filter out people who might discriminate against them, fight HIV stigma, and promote much-needed awareness. However, disclosure and filtering can also lead to discriminatory practices (Hutson, <em>et al.</em>, 2018), have potential for privacy unraveling (Warner, <em>et al.</em>, 2018), and contribute to surveillance (Fan, 2012, 2011).</p> + +<p>De-stigmatizing HIV offers designers an opportunity to engage in the structural dimensions of how HIV operates in social life and can possibly allow us to better tap into social norms around the condition that ultimately improve other outcomes. For instance, humanizing people living with HIV could lead to more people getting tested, being open about their status, and being communicative with their sexual partners. Platforms have the power to shift social norms and destigmatize HIV at scale due to their pervasiveness throughout modern connections, but designers need to contest the ethical implications of de-stigmatizing HIV on these platforms, especially through current features such as HIV-status-based filtering and disclosure options.</p> + +<p>Filtering and searching tools based on HIV status can be instrumental for people living with HIV to find others who are either seropositive or otherwise accepting of seropositive people. Additionally, filtering out those who might discriminate against them for their HIV status anyways allows people living with HIV to avoid awkward or even violent interactions with users who harbor problematic beliefs about people living with HIV. Conversely, HIV status-based filtering and searching tools have representational and allocational harms. First, it represents that there are particularly psycho-social characteristics incumbent with HIV status. These stereotypes play out in a variety of different ways such as the framing that people living with HIV engage in “risky” sexual behavior. Second, HIV status-based filtering can be used to structurally exclude HIV positive users from the opportunity to engage in intimate affiliation (Hutson, <em>et al.</em>, 2018). Platforms can and do provide users the ability to screen out other users who identify as “Poz” or disclose their HIV status. Not only do these design features facilitate exclusion, they may disincentivize HIV related disclosures to the extent that such disclosures can be weaponized by other users to exclude them as potential intimate affiliates.</p> + +<p>Disclosure fields as a way to de-stigmatize HIV are similarly complicated in that they can inhibit and benefit people living with HIV. For one, encouraging users to disclose, regardless of their status, can create a healthier culture and discussion around HIV, possibly making talking about one’s status an acceptable and common practice of intimate engagement. On the other hand, disclosure can be used for a variety of problematic ends that harm seropositive users. Other users may discriminate against users who have disclosed their HIV status, choosing to ignore or disengage with them entirely. Disclosure may have unintended consequences and lead to more personal and violent outcomes. Due to laws in particular jurisdictions, failure to disclose one’s status to a partner can lead to prosecution and potentially incarceration. People living with HIV might also face physical and emotional threats for disclosing their status either publicly or privately.</p> + +<p>Due to these complexities, designers of dating platforms must face the question of how can we de-stigmatize HIV without creating additional obstacles for people living with HIV? Platforms need to critically unpack the possible consequences of well-intentioned design choices, including HIV status-based filtering and HIV status disclosure fields. Of the platforms we reviewed, Scruff is the only one to provide for HIV disclosure without using an express “HIV status” field, allowing instead two disclosure options, Poz and Treatment as Prevention. “Poz” constitutes an association and identification with a community (<em>e.g.</em>, “I am a bear, daddy, poz”), while “Treatment as Prevention,” signals antiretroviral therapy (<em>i.e.</em>, use of HIV medicines to treat HIV infection) and constitutes a link to sex safety practices.</p> + +<p><em><strong>Surveillance & criminalization</strong></em></p> + +<p>At the same time, given the questions of structural power and surveillance built into these platforms, we are leery of treating disclosure option design as the site of de-stigmatization and justice. Questions of privacy and stigma go wider than micro-interactions and touch on how HIV is seen and responded to societally and administratively. The dominant responses to HIV/AIDS “center on adjusting the traditional levers of criminal and tort law, and of public health law, with its surveillance and disciplinary regimes that concentrate information and decision-making in the state” <a name="3a"></a>[<a href="#3">3</a>]. Indeed, HIV continues to function as a “vector for the exercise of state power and the invention of novel logics and techniques of government,” whereby “[i]nfection with HIV virtually guarantees that a citizen will need to interact, either beneficently or coercively, with one or more state bureaucracies” <a name="4a"></a>[<a href="#4">4</a>].</p> + +<p>The broader ecosystem of intimate platforms that we observed provided virtually no HIV-specific privacy information or protections for users living with HIV. Overall, both the platforms that account for HIV in their privacy policies and the platforms that enable disclosure but do not account for HIV in their privacy policies continue to place the risks and burden of surveillance, privacy, and disclosure on users with HIV. Grindr’s “HIV Status” policy puts it clearly: “Remember that if you choose to include information in your profile, that information will become public to other users of the Grindr App.” By surfacing this as a risk we do not mean to suggest that users lack agency — merely that the agency to choose between a range of options can be influenced by how those options are bounded and made available in addition to the affordances and norms that platform design provides. That a user makes information public does not mean that “consumable by all” is the framework of disclosure that they have in mind (Wittkower, 2016).</p> + +<p>While some intimate platforms are working towards promoting HIV disclosure, prevention, and de-stigmatization, they are also failing to grapple with privacy implications of HIV and their responsibility in ensuring it. People living with HIV are already vulnerable and bear the weight of HIV disclosure’s downstream consequences. By continuing to offload the burdens and risk on those with HIV, platforms are likely contributing to issues of nondisclosure as well as HIV testing. Research shows that privacy fears can result in the non-disclosure of HIV status information within close personal relationships (Derlega, <em>et al.</em>, 2004; Zea, <em>et al.</em>, 2003; Derlega, <em>et al.</em>, 2002).</p> + +<p>In this context, proposals to design for HIV disclosure that do not consider the wider structural implications of surveillance are concerning. The focus of most research into HIV and online dating in HCI on micro-interactions and enabling trust and certainty between users elides the implications that providing this data to a platform outside user control has and the way that this data can be used to control. This is not an abstract risk; just this year, Grindr (the platform under study) has been the subject of scrutiny by the U.S. government over its Chinese ownership, due to fears that the Chinese government might access and copy Grindr’s data around HIV disclosure for the purpose of domestic policing and control (Fitzsimons, 2019). If we are designing to enable HIV disclosure, are we working to improve stigma associated with disclosure — or are we enabling new forms of control and surveillance?</p> + +<p>In the United States today, intimate platforms operate within 29 states that have HIV criminal laws, which include laws that target sex/nondisclosure of HIV-positive status, sex work, exposure to bodily fluids, needle-sharing, sex work, and blood/organ/semen donation, nine states that have sentencing enhancements applicable to people living with HIV who commit an underlying assault crime, and 24 states that have prosecuted people living with HIV under non-HIV-specific general criminal laws (Center for HIV Law & Policy, 2019). Here, the design of intimate platforms cannot be removed from the reality of laws that criminalize HIV, particularly HIV non-disclosure.</p> + +<p>People living with HIV in the U.S. with HIV-specific criminal laws must disclose their HIV status to sexual partners. Generally, “disclosure and consent” is an affirmative defense <a name="5a"></a>[<a href="#5">5</a>], whereby a person can avoid criminal and civil liability if they disclose their serostatus <a name="6a"></a>[<a href="#6">6</a>] and their sexual partner voluntarily consents to sexual activity with knowledge of that serostatus <a name="7a"></a>[<a href="#7">7</a>]. Many of the laws that criminalize HIV non-disclosure do not provide guidance as to what methods of disclosure and consent are enough to avoid prosecution and conviction (McCallum, 2014). No court or legislature has affirmatively stated whether verbal disclosure and consent are necessary under criminal HIV transmission statutes. Furthermore, non-verbal communication online create uncertainty as to whether there is sufficient disclosure and consent to remove criminal liability for HIV-positive individuals. Both disclosure and consent can be ambiguous or misunderstood, a problem that is complicated by the design and widespread use of mobile dating and hookup platforms.</p> + +<p>It remains unclear what constitutes appropriate disclosure and informed consent in the context of intimate platforms, such as HIV disclosure fields on user profiles or other communication in a profile’s free form text sections (<em>e.g.</em>, “+” “Poz”, “undetectable”). Although some intimate platforms afford HIV-positive users the ability to disclose their serostatus in new ways, no court or legislature in the U.S. has answered whether disclosing HIV status on an intimate platform is enough to achieve informed consent and avoid criminal and civil liability. Yet many people living with HIV also use records of conversations on intimate platforms as a means of protection. For example, people disclose their status and use that record as a way to protect themselves from future allegations of non-disclosure. This ambiguity and incumbent legal risk places significant responsibility and pressure on HIV users. Research shows that fears around rejection, self-blame, criminalization, and privacy can result in the non-disclosure of HIV status information within close personal relationships (Derlega, <em>et al.</em>, 2004; Zea, <em>et al.</em>, 2003; Derlega, <em>et al.</em>, 2002). Privacy concerns around HIV disclosure are often associated with the need to protect one’s self from HIV related stigma (Adam, <em>et al.</em>, 2011; Serovich and Mosack, 2006; Greene, <em>et al.</em>, 2003). As more and more people use platforms to meet intimate partners, the historical failure of HIV criminalization law to understand how disclosure and consent are negotiated in practice becomes all the more apparent.</p> + +<p>It might seem from this that designers and developers are trapped in an impossible situation — disclosure to protect users simultaneously produces the possibility of structural harms for those disclosing. While we urge designers to take both needs seriously, we do not consider it impossible; in fact, there is a range of work within queer theory and technology that not only articulates this tension of privacy, disclosure and the reuse of data but suggests queer forms of resistance to it. Writing more broadly, Brian Schram highlights the way that the increasing possibilities of “big data” and its attendant surveillance structures “constitute an undoing of Queerness as a radical political injection” <a name="8a"></a>[<a href="#8">8</a>], advocating a politics of <em>melancholia</em> that features a haunting of archives: an insertion of the dead weight of our collective memory as Queer persons into the growing catalog of our digital information. In other words, Schram suggests the deliberate incorporation of masses of false data, profiles, and traces into data stores in order to render ambiguous the truth of any presence and provide cover for those queer persons existing within the platform(s) data highlights. What would this look like in the case of dating platforms? What are the possibilities raised by incorporating a deluge of false accounts, <em>doppelgängers</em>, and doubles, not as a deception of the platform or its users, but against state forces examining the database?</p> + +<p>More broadly, we might see possibilities for the future through practices in the past. In how queer communities responded to HIV disclosure and protection protocols during the 1980s and 1990s, David Halperin has articulated the way that gay communities worked to articulate norms that balanced risks, trust, and vulnerability in the absence of structural norms, that “it is gay men themselves who have continued to define, and to redefine, the limits of safety through an ongoing history of sexual experimentation and mutual consultation, and who have thereby produced, over time, workable compromises and pragmatic solutions that balance safety and risk” <a name="9a"></a>[<a href="#9">9</a>]. Rather than taking universalized, top-down approaches to platform design for all, we might instead seek to work up and to create a diverse range of spaces that challenge the ease of surveillance built into large-scale platforms and afford individual users more agency in establishing those compromises and solutions and engaging in that consultation.</p> + +<p> </p> +<p><img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71630" alt="++++++++++"></p> +<p><strong><a name="p5"></a>Conclusion</strong></p> + +<p>As HCI researchers and designers, we continue to push the boundaries of what is technologically possible but doing so requires us to first ask whether platform design is even an appropriate intervention in a given situation (Keyes, <em>et al.</em>, 2019; Baumer and Silberman, 2011; Suchman, 2011). The current model of platform design for HIV cannot continue, as it is too closely tied to the collection and commodification of highly sensitive personal data. However, reimagining intimate platform design provides the social computing community an opportunity to intervene in the social norms around HIV and HIV disclosure in a manner that could unburden the weight of criminalization without centralizing the surveillant arms of the state.</p> + +<p>We envision a future of dating platforms that does not force people living with HIV to sacrifice surveillance for intimate experiences. Because of their entanglements with sex and romance, intimate platforms need to take on more responsibility in the sexual health and data privacy of their users. Drawing from our analysis and our own lived experiences, we recommend platform-level changes, changes in platform, and mechanisms to prevent platforms from knowing their users’ statuses. First, platforms should make explicit to their users the consequences of storing sensitive, personal information like HIV status and their documentation processes. Next, they should also implement policies that manage how data are stored when users delete their accounts and protect these data from third-party consumers. Finally, ownership of user’s data should belong to the users themselves, rather than the platforms. Users should be able to pass along their information to other users without the platforms tracking it.</p> + +<p>HIV is a medical condition, but its eradication requires not just technical, or even sociotechnical, but socio<em>political</em> solutions. Indeed, the ways in which designers and policy-makers frame HIV is an inherently political decision, one that will impose the contours and boundaries of our response. The social computing community cannot do nothing, but it also must resist the desire to do everything. Designing user interfaces and platform policies to account for HIV will require a rigorous analysis of possible outcomes and consequences as well as a bedrock commitment to centering the voices and experiences of those impacted by HIV and the state’s responses to it. Our commitments must account for the ways pathology and power intertwine to subjugate and otherize impacted communities at home and abroad.</p> + +<p>Designing intimate platforms to unburden the risks of extant criminal and civil sexual regulations runs the risk of re-entrenching the status quo and its incumbent inequalities and power relations (Dombrowski, <em>et al.</em>, 2016; Light, 2011; Irani, <em>et al.</em>, 2010; Bardzell, 2010). The social computing community must ground its efforts to design for HIV in clear political commitments to decriminalizing HIV and decentralizing power and information from the state. We must strive to unburden the weight of surveillance and incarceration on vulnerable and marginalized communities and work towards offloading the significant social and legal risks and pressures for people living with HIV. Moreover, our commitment to designing for HIV must not exclude nor obfuscate our capacity for direct action within and outside of the realms of design and research. This means fighting for the rights, dignity, and safety of people living with HIV in the streets and in the halls of local, national, and international political, legislative, and executive bodies.</p> + +<p>Our instinctual response to the failed and violent efforts of HIV criminalization and surveillance should not be “there’s an app for that,” but rather “there’s a zap for that!”. That is, the practice of designing for people with HIV should be a “critical technical practice” (Agre, 1997), undertaken with a mindset that sits uneasily between and is cognizant of both individual and structural power and consequence. Pioneered by the American gay liberation movement, a zap or “zap action” is a political action of direct and persistent public confrontation. Whether shouting down public figures or smashing pies into the faces of evangelicals, zaps aim to disrupt and disturb persons and institutions of authority to effect change (Cohen, 2018). In the words of AIDS Coalition to Unleash Power’s (ACT UP) “New Member Packet”:</p> + +<table width="70%" align="center"><tr><td>“Zaps are a method for ACT UP members to register their disapproval of and anger toward the zap target. Zaps usually have more specific targets than actions. Because of this focus, numerous zapping techniques have been developed. ACT UP zaps individuals or organizations by: sending postcards or letters; invading offices and distributing fact sheets; sending (lots and lots of) faxes; picketing; outraged (and sometimes outrageous) phone calls. The more zappers who zap the zappee the better the zap.”</td></tr></table> + +<p>A critical approach to designing for HIV requires the contesting of histories of incarceration, stigmatization, and surveillance and the ways in which the state exerts power and domination through its medicolegal levers of criminal law and public health surveillance. Intimate platform design should not only work to reduce the prevalence and stigma of HIV, but also to contest historic and present power imbalances and injustices between users, platforms, and the state. <img src="https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729/71628" alt="End of article"></p> + +<p> </p> +<a name="author"></a> +<p><strong>About the authors</strong></p> + +<p><strong>Calvin Liang</strong> is a Ph.D. student in Human-Centered Design and Engineering Department at the University of Washington. His research broadly focuses on technology’s role in and out of queerness, health, and queer health.<br>E-mail: cliang02 [at] uw [dot] edu</p> + +<p><strong>Jevan Alexander Hutson</strong>, living with HIV for four years, is a technology policy advocate, human-computer interaction researcher, and J.D. candidate at the University of Washington School of Law. His research interests center on issues of technology, law, and social life, with a particular focus on intimate/sexual computing.<br>E-mail: jevanh [at] uw [dot] edu</p> + +<p><strong>Os Keyes</strong> is a Ph.D. student in Human-Centered Design and Engineering at the University of Washington, and an inaugural Ada Lovelace Fellow. Their research examines gender, technology and (counter)power, with a particular focus on the ways technologies of measurement shape and define queer communities.<br>E-mail: okeyes [at] uw [dot] edu</p> + +<p> </p> +<p><strong>Acknowledgements</strong></p> + +<p>We dedicate this paper to the radical history of the AIDS Coalition to Unleash Power (ACT UP) and to all of the souls we’ve lost and continue to lose to HIV/AIDS. We would like to thank Mary Fan, Sean Munson, and Julie Kientz for valuable conversations and feedback, and Margret Wander and Margaret Hopkins for their ongoing care and support. This research was partially funded by a Microsoft Ada Lovelace Fellowship.</p> + +<p> </p> +<p><strong>Notes</strong></p> + +<p><a name="1"></a><a href="#1a">1.</a> Halperin and Hoppe, 2017, p. 349.</p> + +<p><a name="2"></a><a href="#2a">2.</a> Jackson, <em>et al.</em>, 2014, p. 596.</p> + +<p><a name="3"></a><a href="#3a">3.</a> Fan, 2011, p. 36.</p> + +<p><a name="4"></a><a href="#4a">4.</a> Halperin and Hoppe, 2017, p. 255.</p> + +<p><a name="5"></a><a href="#5a">5.</a> See FLA. STAT. ANN. § 775.0877 (2017) (“[I]t is an affirmative defense to a charge of violating this section that the person exposed knew that the offender was infected with HIV, knew that the action being taken could result in transmission of the HIV infection, and consented to the action voluntarily with that knowledge.”). See also <a href="http://www.hivlawandpolicy.org/states/florida">http://www.hivlawandpolicy.org/states/florida</a>.</p> + +<p><a name="6"></a><a href="#6a">6.</a> Serostatus is defined as: “The state of either having or not having detectable antibodies against a specific antigen, as measured by a blood test (serologic test). For example, HIV seropositive means that a person has detectable antibodies to HIV; seronegative means that a person does not have detectable HIV antibodies.” U.S. Department of Health & Human Services, Education Materials, AIDSINFO, at <a href="https://aidsinfo.nih.gov/education-materials/glossary/1632/serostatus" target="_blank">https://aidsinfo.nih.gov/education-materials/glossary/1632/serostatus</a>, accessed 30 August 2019.</p> + +<p><a name="7"></a><a href="#7a">7.</a> Lehman, <em>et al.</em>, 2014, p. 1,101.</p> + +<p><a name="8"></a><a href="#8a">8.</a> Schram, 2019, p. 611.</p> + +<p><a name="9"></a><a href="#9a">9.</a> Halperin, 2015, p. 207.</p> + +<p> </p> +<p><strong>References</strong></p> + +<p>Barry D. 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Fisher Raymond, Tom Kennedy, and Willi McFarland, 2013. “How can we improve online HIV and STD prevention for men who have sex with men? Perspectives of hook-up website owners, website users, and HIV/STD directors,” <em>AIDS and Behavior</em>, volume 17, number 9, pp. 3,024–3,033.<br>doi: <a href="https://doi.org/10.1007/s10461-012-0375-y" target="_blank">https://doi.org/10.1007/s10461-012-0375-y</a>, accessed 5 September 2020.</p> + +<p>Mara Cecilia Zea, Carol A. Reisen, Paul J. Poppen, and Rafael M. Daz. 2003. “Asking and telling: communication about HIV status among Latino HIV-positive gay men,” <em>AIDS and Behavior</em>, volume 7, number 2, pp. 143–152.<br>doi: <a href="https://doi.org/10.1023/A:1023994207984" target="_blank">https://doi.org/10.1023/A:1023994207984</a>, accessed 5 September 2020.</p> + +<p>Shoshana Zuboff, 2019. <em>The age of surveillance capitalism: The fight for a human future at the new frontier of power</em>. London: Profile Books.</p> + +<p> </p> +<hr width="300"> + +<p><strong>Editorial history</strong></p> +<p>Received 17 October 2019; revised 12 February 2020; accepted 28 August 2020.</p> + +<hr> + +<p><a href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" src="https://i.creativecommons.org/l/by/4.0/80x15.png"></a><br>This paper is licensed under a <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</p> + +<p>Surveillance, stigma & sociotechnical design for HIV<br>by Calvin Liang, Jevan Alexander Hutson, and Os Keyes.<br><em>First Monday</em>, Volume 25, Number 10 - 5 October 2020<br>https://firstmonday.org/ojs/index.php/fm/article/download/10274/9729<br>doi: <a href="http://dx.doi.org/10.5210/fm.v25i10.10274" target="_blank">http://dx.doi.org/10.5210/fm.v25i10.10274</a></p> +</blockquote> +</body> +</html>
\ No newline at end of file diff --git a/python/tests/files/first_monday_ojs3_landingpage.html b/python/tests/files/first_monday_ojs3_landingpage.html new file mode 100644 index 0000000..2633256 --- /dev/null +++ b/python/tests/files/first_monday_ojs3_landingpage.html @@ -0,0 +1,616 @@ + <!DOCTYPE html> +<html lang="en-US" xml:lang="en-US"> +<head> + <meta charset="utf-8"> + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + <title> + Surveillance, stigma & sociotechnical design for HIV + | First Monday + </title> + + +<meta name="generator" content="Open Journal Systems 3.1.2.0"> +<link rel="icon" href="https://firstmonday.org/ojs/public/journals/3/favicon_en_US.gif"> +<link rel="schema.DC" href="http://purl.org/dc/elements/1.1/" /> +<meta name="DC.Coverage" xml:lang="en" content=""/> +<meta name="DC.Creator.PersonalName" content="Calvin Liang"/> +<meta name="DC.Creator.PersonalName" content="Jevan Alexander Hutson"/> +<meta name="DC.Creator.PersonalName" content="Os Keyes"/> +<meta name="DC.Date.created" scheme="ISO8601" content="2020-09-10"/> +<meta name="DC.Date.dateSubmitted" scheme="ISO8601" content="2019-09-15"/> +<meta name="DC.Date.issued" scheme="ISO8601" content="2020-10-01"/> +<meta name="DC.Date.modified" scheme="ISO8601" content="2020-10-01"/> +<meta name="DC.Description" xml:lang="en" content="Online dating and hookup platforms have fundamentally changed people’s day-to-day practices of sex and love — but exist in tension with older social and medicolegal norms. This is particularly the case for people with HIV, who are frequently stigmatized, surveilled, ostracized, and incarcerated because of their status. Efforts to make intimate platforms “work” for HIV frequently focus on user-to-user interactions and disclosure of one’s HIV status but elide both the structural forces at work in regulating sex and the involvement of the state in queer lives. In an effort to foreground these forces and this involvement, we analyze the approaches that intimate platforms have taken in designing for HIV disclosure through a content analysis of 50 current platforms. We argue that the implicit reinforcement of stereotypes about who HIV is or is not a concern for, along with the failure to consider state practices when designing for data disclosure, opens up serious risks for HIV-positive and otherwise marginalized people. 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href="https://firstmonday.org/ojs/index.php/fm/index"> + Home + </a> + <span class="separator">/</span> + </li> + <li> + <a href="https://firstmonday.org/ojs/index.php/fm/issue/archive"> + Archives + </a> + <span class="separator">/</span> + </li> + <li> + <a href="https://firstmonday.org/ojs/index.php/fm/issue/view/678"> + Volume 25, Number 10 - 5 October 2020 + </a> + <span class="separator">/</span> + </li> + <li class="current"> + Articles + </li> + </ol> +</nav> + + <article class="obj_article_details"> + <h1 class="page_title"> + Surveillance, stigma & sociotechnical design for HIV + </h1> + + + <div class="row"> + <div class="main_entry"> + + <ul class="item authors"> + <li> + <span class="name"> + Calvin Liang + </span> + <span class="affiliation"> + University of Washington, Department of Human Centered Design & Engineering + </span> + <span class="orcid"> + + <a href="https://orcid.org/0000-0002-3795-3441" target="_blank"> + https://orcid.org/0000-0002-3795-3441 + </a> + </span> + </li> + <li> + <span class="name"> + Jevan Alexander Hutson + </span> + <span class="affiliation"> + University of Washington, School of Law + </span> + <span class="orcid"> + + <a href="https://orcid.org/0000-0003-3312-1733" target="_blank"> + https://orcid.org/0000-0003-3312-1733 + </a> + </span> + </li> + <li> + <span class="name"> + Os Keyes + </span> + <span class="affiliation"> + University of Washington, Department of Human Centered Design & Engineering + </span> + <span class="orcid"> + + <a href="https://orcid.org/0000-0001-5196-609X" target="_blank"> + https://orcid.org/0000-0001-5196-609X + </a> + </span> + </li> + </ul> + + <div class="item doi"> + <span class="label"> + DOI: + </span> + <span class="value"> + <a href="https://doi.org/10.5210/fm.v25i10.10274"> + https://doi.org/10.5210/fm.v25i10.10274 + </a> + </span> + </div> + + <div class="item keywords"> + <span class="label"> + Keywords: + </span> + <span class="value"> + HIV, online dating, design, policy, surveillance, intimacy, social computing, social justice </span> + </div> + + <div class="item abstract"> + <h3 class="label">Abstract</h3> + <p>Online dating and hookup platforms have fundamentally changed people’s day-to-day practices of sex and love — but exist in tension with older social and medicolegal norms. This is particularly the case for people with HIV, who are frequently stigmatized, surveilled, ostracized, and incarcerated because of their status. Efforts to make intimate platforms “work” for HIV frequently focus on user-to-user interactions and disclosure of one’s HIV status but elide both the structural forces at work in regulating sex and the involvement of the state in queer lives. In an effort to foreground these forces and this involvement, we analyze the approaches that intimate platforms have taken in designing for HIV disclosure through a content analysis of 50 current platforms. We argue that the implicit reinforcement of stereotypes about who HIV is or is not a concern for, along with the failure to consider state practices when designing for data disclosure, opens up serious risks for HIV-positive and otherwise marginalized people. While we have no panacea for the tension between disclosure and risk, we point to bottom-up, communal, and queer approaches to design as a way of potentially making that tension easier to safely navigate.</p> + </div> + + + + <div class="item author_bios"> + <h3 class="label"> + Author Biographies + </h3> + <div class="sub_item"> + <div class="label"> + Calvin Liang, <span class="affiliation">University of Washington, Department of Human Centered Design & Engineering</span> + </div> + <div class="value"> + <p>Calvin Liang is a PhD student in Human-Centered Design and Engineering at The University of Washington. Their research broadly focuses on technology’s role in and out of queerness, health, and queer health.</p> + </div> + </div> + <div class="sub_item"> + <div class="label"> + Jevan Alexander Hutson, <span class="affiliation">University of Washington, School of Law</span> + </div> + <div class="value"> + Jevan Hutson is a third-year law student and Gregoire Fellow at the University of Washington School of Law. He holds an M.P.S. from the Department of Information Science at Cornell University, and a B.A. from the Department of Art History and Visual Studies at Cornell University. He has been published in venues including the Association for Computing Machinery’s conferences on Computer Human Interaction and Computer Supported Cooperative Work and Social Computing + </div> + </div> + <div class="sub_item"> + <div class="label"> + Os Keyes, <span class="affiliation">University of Washington, Department of Human Centered Design & Engineering</span> + </div> + <div class="value"> + Os Keyes is a PhD student in Human-Centered Design and Engineering at the University of Washington, and an inaugural Ada Lovelace Fellow. Their research examines gender, technology and (counter)power, with a particular focus on the ways technologies of measurement shape and define queer communities. + </div> + </div> + </div> + + + </div><!-- .main_entry --> + + <div class="entry_details"> + + <div class="item cover_image"> + <div class="sub_item"> + <a href="https://firstmonday.org/ojs/index.php/fm/issue/view/678"> + <img src="https://firstmonday.org/ojs/public/journals/3/cover_issue_678_en_US.png" alt="“Frank Moore, Digital Divide, 2001 gouache, oil and mixed media on paper 14 3/4 x 24 1/4 inches (36,4 x 61,6 cm) sheet”"> + </a> + </div> + </div> + + <div class="item galleys"> + <ul class="value galleys_links"> + <li> + + + + +<a class="obj_galley_link file" href="https://firstmonday.org/ojs/index.php/fm/article/view/10274/9729"> + + + HTML + + </a> + </li> + </ul> + </div> + + <div class="item published"> + <div class="label"> + Published + </div> + <div class="value"> + 2020-09-10 + </div> + </div> + + <div class="item citation"> + <div class="sub_item citation_display"> + <div class="label"> + How to Cite + </div> + <div class="value"> + <div id="citationOutput" role="region" aria-live="polite"> + <div class="csl-bib-body"> + <div class="csl-entry">Liang, C., Hutson, J. A., & Keyes, O. (2020). 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A flashlight waits in a bucket by the door, and visitors crawl on hands and knees, one by one, into the pitch-black interior. After savoring a degree of darkness rare in modern life, they direct beams of light up the tapering walls to marvel at the skill of the stonemasons. It is impossible to resist the impulse to clamber into the chambers and crouch where the bones once lay. Green and smooth, Maeshowe, another Orkney cairn, rises enigmatically from the field where it has stood since around 2700 BC. The designation of this monument and the surrounding Neolithic structures as a UNESCO World Heritage Site (WHS) in 1999 significantly increased tourism to the area (Card et al. 429), so while visitors may still enter Cuween unsupervised, access to the much larger Maeshowe now requires a timed ticket, bought in advance. Throughout the year, thousands of visitors, bending uncomfortably low, shuffle through the tunnel-like passage entry, making the physical journey from light to dark and a more psychological journey from present to past. Exploring any of the Neolithic sites in Orkney is to bridge time, to feel kinship with those who built them.</p> + <p>[2] Without doubt, a major reason Maeshowe attracts so many people is its symbiotic relationship with its environment. Most famously, at sundown during the December solstice, the winter sun lines up with the door of the tomb, shines down the passage, and focuses its rays on the stone wall within. Interest in this phenomenon, the moment when the light stabs the darkness, is so high that Historic Scotland provides web-cam coverage, but Maeshowe fascinates others besides tourists and solstice celebrants. Whether they are vacation visitors, archaeologists, anthropologists, or poets, explorers experience the sites differently, applying their own intellectual tools and imagining Neolithic lives from their respective points of view. Leslie Riddoch has written that these are “Stone Age marvels which inspire and astonish,” and Simon W. Hall expresses the experiences of many when he refers to “the profound impact of entering a tomb” (160). They imply that to enter a cairn is to become one with it, to undergo a transformation. Maeshowe, which can now be experienced only under the regimented conditions required by the Historic Scotland guides, clearly retains extraordinary power to inspire. Indeed, this ancient mound has attracted a great deal of literary attention from both noted and obscure writers. Considering these cumulative interpretations, rather than relying solely on the work of archaeologists, opens up a more comprehensive, textured, and, indeed, gendered understanding of ancient history and our commonality with Neolithic peoples.</p> + <p> [3] George Mackay Brown, Kathleen Jamie, Myra Schneider, and Dilys Rose are four of the more prominent authors for whom Maeshowe has proven inspirational. They have experienced the tomb through a doubly imaginative process: first by reading it as they would read a poem and then by expressing that interpretation in writing. While Brown was an Orcadian, living most of his life alongside the Neolithic sites, Jamie, Schneider, and Rose, all of whom have Scottish roots, experience Maeshowe as tourists, drawn across the Pentland Firth to enter the passage and travel into the darkness. Significantly, all three of these more contemporary writers are women. Hall, in his valuable survey, <u>The History of Orkney Literature</u>, contrasts the use of the prehistoric by female Scottish writers with that of their male counterparts, stating that it is less political, that women authors take “the opportunity to reestablish the place—and, significantly, the inner lives of women in the prehistoric or early historical northern landscape” (162-163). I would argue, however, that their work also engages the public world to a greater extent and is more ideological than this statement implies. Jamie’s, Schneider’s, and Rose’s experiences in Maeshowe lead to readings of the monument that build on the archaeological interpretations, allowing us to consider the possibility of ancient gender power struggles and raising our awareness of the deep roots of masculine dominance.</p> + <p>[4] Archaeologist Colin Richards, who has written extensively about The Heart of Neolithic Orkney WHS, describes how visiting cairns must also have affected prehistoric visitors: “the journey will be one of consequence.” Moving from the light of day to the dark mysteries of a tomb’s interior “is a passage from the profane to the sacred.” As such, “it will involve transformation” (“Doorways” 70-71). However, the nature of the transformation is mysterious. Referring to single-chambered structures divided into stalls, he continues, “If the Orkney-Cromarty ‘chambered’ tombs are principally conceived as a series of doorways, the question arises: where are they leading? To what goal?” (71). In discussing the relationship between buildings and the people who used them thousands of years ago, Richards considers the figurative significance of doors. In doing so, he treats the tombs as if they were literary texts with debatable meaning, having previously pointed out that “the architecture of a chambered tomb relied on analogy and metaphor for its understanding and interpretation” (“Doorways” 67). Rather than merely being repositories for bones, the tombs, Richards asserts, were “built to be experienced visually, physically and imaginatively,” an experience which may well result in some kind of “revelation” (“Doorways.” 69, 70, 76). Since he argues that buildings carry metaphoric meaning, open to imaginative interpretation, it is entirely appropriate that, when explaining this, Richards also changes to the historical present tense. His grammatical shift emphasizes that like <u>Beowulf</u>, <u>Hamlet</u>, or <u>Moby Dick</u>, tombs such as Maeshowe transcend time and are open to new readings, whether by trained archaeologists, pilgrims, casual visitors, or writers.</p> + <p>[5] Robert Crawford draws more explicit parallels between Maeshowe itself and literature in his essay, “Maes Howe Sappho.” Noting the continuing appeal of the tomb, how today “people still treasure” the moment that the sun lines up with the passage, he compares the ancient monument to poetry:</p><blockquote>However different we and our family groups, our tribes, have become, we can and do still savor that sense of alignment and attunement and have our own ways of articulating some sort of consonance between ourselves, our intimate groupings, and the universe that surrounds us. Though such patternings may be deconstructed, they seem to emerge from a deep need that recurs across generations, like a persistent internal rhyme, and poetry, this most nuanced way of making with words, is a way in which that need for attunement is repeatedly articulated through language. If prehistoric sites often appear to relate people to the stars and planets, then poems continue that impulse. (61) + </blockquote> + <p>Ancient tombs, then, prompt us to ponder our place in the universe, our identity as humans, and in that also they resemble literature. According to Kenneth Brophy, Neolithic monuments “were and are locations that embodied the biography of the builders, users, spectators, and excavators” (10). It follows that if we think of Maeshowe as a text, Brophy’s assertion that the monument absorbs the “biography” of all who have used it or visited it, positions it as an example of intertextuality. Maeshowe has many constantly changing stories to tell to its different readers, and readers will respond differently to its figurative meanings.</p> + <p>[6] In a 1977 column for <u>The Orcadian</u> newspaper, George Mackay Brown describes how witnessing the midwinter solstice at Maeshowe affects him: “Winter after winter I never cease to wonder at the way primitive man arranged, in hewn stone, such powerful symbolism” (“Maeshowe at Midwinter” 88). Like Richards, Brown is emphasizing the figurative qualities of the structure, which he has further explored in poetry. However, the first of his 1999 “Two Maeshowe Poems” (often printed as a stand-alone) opens not at the tomb, but with an image of the neighboring stone circle, Brodgar. Perhaps surprising to most readers, this would resonate with archaeologists since current scholarship emphasizes that the sites comprising The Heart of Neolithic Orkney are not self-contained but exist and function in relation to one another and to the surrounding landscape (See “Heart of Neolithic Orkney WHS: Setting Project” 5). As such, they should not be interpreted as discrete entities. It is fitting, then, that Brown’s poem moves seamlessly through a series of images that integrate Brodgar’s “light and darkness” with Maeshowe’s “flowers [and] stone” (a reference to the runic graffiti carved by Vikings inside the tomb) and “skulls” (Lines 1, 9, 11). The first word of the poem, “Circle,” is semantically echoed in the initial word of each ensuing stanza, “Ring,” “Wheel,” and “Round,” subtly shifting from the geometrically circular Brodgar to the tumescent mound of Maeshowe and emphasizing the cycle of “life and death” (7). For this is a poem about regeneration, how “Out of those skulls / Breaks the first green shoot, the full ear, then the bread” (11-12). Throughout, juxtaposed images look for the positive to outweigh the negative: “We move in shadows,” but “Brodgar has burned on the moor a dance of sun”; “Ring of quern and plough” (a quern is a stone for grinding grain) are charged to “contain / Our tumults of blood”; “The stars’ chaos is caught in a strict rein”; the word “stone” is enveloped by “flowers,” and “beauty and love”; similarly, “snow” is flanked by “sun” and “seed.” So darkness becomes light, destructive violence is subservient to the raising and grinding of grain for bread, order makes sense of the universe, the beautiful and the warm temper the hard and the cold, and new life will follow death.</p> + <p>[7] Brown’s interpretation of these monuments, his use of the architectural circularity and roundness of the Ring of Brodgar and Maeshowe as metaphors for the lifecycle and the possibility of renewal, is shared by archaeologists, who despite its being a burial site, have also associated Maeshowe and its rituals with the agricultural year. Neolithic people were not nomadic but had gradually become settled farmers, living by the routines and rhythms of the seasons, which, according to Richards, constituted “an analogy with the human life cycle and past generations” (“Doorways” 65). Time’s passage was the organizational framework for survival as well as mortality, and the tombs, he writes, were “a metaphorical extension of daily life” (“Doorways” 76). Trevor Garnham, an architect, develops that idea further: “Burying bones in the earth was perhaps to seek some metaphoric relationship with the planting of seeds. In its maturity and death, the seed containing the essence of its own renewal served as the inspiration for the hope of life’s rebirth in some other form” (87). In pairing skeletal remains with seeds as an expression of hope for the future, Garnham’s analogy is comparable to the positive final image of Brown’s poem, the “skulls” engendering the “green shoots” and the “bread” of life.</p> + <p>[8] Brown had written earlier of Maeshowe in his 1996 poem, “Maeshowe: Midwinter,” choosing then to focus on the solstice. However, the imagery here is not rooted in the agricultural cycle, the earthly world of querns, ploughs, and bread; instead, he connects the pre-Christian tomb to the Christian calendar. The opening phrase, “Equinox to Hallowmass,” immediately integrates the astronomical with the sacred, giving the season of “darkness” both physical and spiritual dimensions (1). The religious imagery continues in the second stanza as it evokes “St Lucy,” whose feast day falls on the shortest day of the year (6). She is portrayed as a weaver whose “shuttle” creates “a dark web” that “fills the loom” (7-9), placing at the centre of the poem a world in which light is completely absent: “The blackness is solid as a / stone that locks a tomb. / No star shines there” (10-12). To be in such a void, with no guiding star, would seem like a moment of psychological despair, yet just as the days begin to lengthen immediately after the solstice, the poem also brightens. The moment when the sun enters the passage is the “true ceremony,” suggesting that perhaps the pagan reverence for nature carries particular authenticity. Then “the last fleeting solstice flame” is “caught up,” leading to an optimistic note as the children—the future—sing with “voices like leaves of light” (19). Again, the poem ends with an image of rebirth, but its tone is less biological and more cosmological.</p> + <p>[9] While Brown’s poems use these dual frames of reference in order to explore the themes of regeneration that Maeshowe expresses, the biological and cosmological are not at odds. Garnham defines the cosmos as “an all-encompassing world of things and phenomena [. . . .] The essential character of this early form of cosmos bound every aspect of a people’s life into reciprocal relationships with the forces that give shape to their world” (9). The central argument of his book places Neolithic Orkney in this context. Similarly, reading Brown’s two Maeshowe poems together reveals that the “green shoot” which produces the “bread” corresponds to the youthful “voices like leaves of light.” In fact, his insertion of “leaves,” with its agrarian connotations, into that final line establishes the connection, recognizes that the complex architectural system of domestic houses, burial chambers, and stone circles symbolizes the idea that the activities for which they were designed—working, eating, loving, sleeping, worshipping, dying, and the possibility of rebirth—are the web of human existence. The physical bread and the metaphysical song are one.</p> + <p>[10] In their respective responses to Maeshowe, Kathleen Jamie, Myra Schneider, and Dilys Rose also address the theme of the cycle of life and death. Jamie’s essay, “Darkness and Light,” describes a quest: she seeks a good, positive darkness because, in the 21st century, it has become impossible “to see the real dark for the metaphorical dark . . .the death-dark.” Enjoyment of the “natural, courteous dark,” she has come to believe, has been squeezed out by the Christian belief in a metaphorical darkness that stands for the opposite of salvation (9-10). However, as she is planning this trip, a friend points out that “Maes Howe is a metaphor,” perhaps exposing a flaw in Jamie’s thinking: possibly the natural and metaphorical darknesses are inseparable (10 emphasis added). Although her visit to Maeshowe takes place a couple of days before the solstice, the artificial lights of a surveyor’s crew assault her eyes, so she rediscovers no “courteous darkness” and witnesses “no resurrecting beam of sunlight” (19). Nevertheless, through Maeshowe, she becomes reconciled to the conventional negative concept of darkness. In terms of “wonder” similar to Brown’s in <u>The Orcadian</u>, she asks, “Were they the first people . . . to articulate this metaphor of light and dark, of life and death?” and reflects upon its significance:</p><blockquote>For five thousand years we have used darkness as the metaphor of our mortality. We were at the mercy of merciless death, which is darkness. When we died, they sent a beam of midwinter light in among our bones. What a tender, potent gesture. In the Christian era, we were laid in our graves to face the rising sun. We’re still mortal, still don’t want to die, don’t want our loved ones to die. (19-20) + </blockquote> + <p>Her rejection of a metaphor that she has considered “[worn] out” and “redundant” (4, 9) turns out to have been less literary and more personally psychological, for Jamie’s visit to the tomb leads to her acceptance of mortality. Whereas previously she has blamed Christianity, she now appreciates that the Christian concept of darkness is part of a continuum of dread traceable back to Neolithic times and forward to our own. The “tender, potent gesture” of the light penetrating the dark of the tomb, therefore, offers consolation, ameliorating our most profound fears (20).</p> + <p>[11] In her poem, “Maeshowe,” Myra Schneider also describes a guided tour of the cairn, during which the speaker uses the second person singular to address a hypothetical visitor, initially giving the sense that to enter the burial place feels like death as the “chill seeps into your body” (14). However, this ominous impression is immediately dismissed because “a stillness that’s other than death inhabits / this place where the undead gather to greet the dead” (15-17). The journey through the passage will take “you” to a place that is not oblivion but, instead, is where the living may consort with their ancestors. Again, the boundary between life and death, which can seem so irrevocable, becomes less absolute and, therefore, less threatening. After the visit is over, its impact will remain, and the speaker imagines her visitor’s memories:</p><blockquote>In midwinter you’ll visualize the sun piercing the dark that swaddles seeds, see it falling on the aligned entrance, its white shine splitting to burnish the passage wall, flood the ground with gold. (22-26) + </blockquote> + <p>These images recall Garnham’s theory: that the burial of bones is connected metaphorically to the planting of seeds. In the speaker’s memory, the dark cradles seeds, the germ of life, rather than bones. Once sunlight enters the tomb, a radiant moment occurs in which the “ground” will turn “gold,” like a field of ripe grain. Schneider’s poem, like Brown’s, affirms the archaeological reading of Maeshowe as a place of renewal, but in this case that renewal goes beyond the promise of the agricultural cycle. An individual will be able to experience, perhaps during times of psychological or spiritual gloom, the moment of glory when the sun is “piercing / the dark.” There is a Romantic quality to these lines: Maeshowe will stay with Schneider’s speaker as those daffodils stay with Wordsworth, “to flash upon the inward eye / That is the bliss of solitude,” to stimulate the imagination (24). Having herself benefited from the tomb’s restorative qualities, the speaker is inspired to spread the word, to share her revelation with “you,” the reader.</p> + <p>[12] Besides the drama of the solstice, another inspirational feature of Maeshowe is the Viking runes carved on the interior walls. Referring to these inscriptions as “The first island poems,” Brown quotes them emphatically in the second of the paired poems: “INGIBIORG IS THE LOVELIEST GIRL / HERMUND WITH A HARD AXE CARVED RUNES” (“Two” 13, 18-19). Many have been struck by the simple humanity of these statements, as well as the paradox inherent in this lusty youthful scrawling being hidden in a tomb. Dilys Rose, in “Maeshowe Nipple,” for instance, lists the prosaic concerns of the Vikings, portraying them as “intrepid” but also homesick, missing “sweethearts and family” (4, 9). At the ends of their respective poems, both Brown and Rose emphasize that Maeshowe was merely a temporary shelter for the Vikings: the “young seamen climbed out of Maeshowe, / Their nostrils wide to the salt wind”; “the dragon boats moved on” (Brown “Two” 23-24; Rose 11). Crawling out of the subterranean tomb and heading for further maritime adventures, the men re-enter the world, extending the overall theme of regeneration. Brown, as we have seen, has already linked the tomb with the life-giving promise of “the first green shoot, the full ear, then the bread” in the first of these paired poems. Rose, in similar terms, also connects the Viking runes with the reassuring knowledge that there will be a crop next year: over the centuries, “their tongue / took root and sprouted from invaded soil / green words for <u>Father</u>, <u>Daughter</u>, <u>Bread</u>” (11-13). Here, in the final lines, the Viking vocabulary is fresh and verdant, a harbinger of new human life and the grain that nourishes it. Since runic characters are “straight-branched” (Rose 4), they resemble rows of rudimentary skeletal stick figures which have been buried in the tomb. The bony runes, therefore, have become metaphorical seeds, and Rose’s speaker, like Garnham, sees hope in the bone/seed analogy.</p> + <p>[13] It is clear, to summarize briefly, that these four creative writers read Maeshowe much as archaeologists and historians of architecture have done, as an expression of hope for the future, particularly in relation to the coming of spring, but also at a more personal level. The texts suggest that to visit these tombs is, as Richards also emphasizes, transformative. Like their ancestors, contemporary visitors are changed, in some manner revitalized, especially if they witness the sun’s midwinter alignment, which Brown describes as a “pledge of renewal, a cry of resurrection” (“Maeshowe in Midwinter” 88). However, in the work of Jamie, Schneider, and Rose, a further, more political restoration is at work, for all three use images equating Maeshowe with the female body.</p> + <p>[14] Kathleen Jamie states early in her essay, “We are conceived and carried in the darkness,” emphasizing the positive, life-giving qualities of the dark, and inviting the reader to see Maeshowe as a uterus (4). The womb/tomb imagery is developed further when she eroticizes the winter solstice as “a complicit kiss,” during which “the beam of the setting sun shines along the passage, and onto the tomb’s back wall” (12). When she goes inside the tomb, she expects “not utter darkness, but perhaps a wombish red”; however, this is denied her because of the lights of the surveyors, one of whom is “folded, foetus-like, into the little cell in the back wall”: a foetus implanted in the very place where the sunbeam strikes (12,13). When Jamie leaves, she describes taking “the smallest and most challenging of journeys, squeezing down a passageway and out into the world of sound and moving air” (17). The tunnel that admits the beam has become a birth canal, so Jamie’s transformation is not only her intellectual reassessment of the metaphorical value of darkness; she visualizes her own rebirth in more literal terms too, with Maeshowe cast as the mother.</p> + <p>[15] Myra Schneider’s “Maeshowe” also hints that to visit the tomb is to return to the womb when the speaker remarks that although “you” are part of a tour group, you will realize that you are “alone” and have “never travelled so far back / so far in” (8-10). This analogy is made more explicit later in the poem when the sun enters the passage: “In that deep chamber / you’ll be bathed in red, not the red spilt in hatred—/the red that’s birth, the heart looming with the blood” (24-28). In the vision that the speaker evokes for the visitor’s memory, therefore, the “dark that swaddles seeds” not only nurtures and protects the grain that will ripen into crops, but also the fertilized ovum (23). With no dazzling and intrusive surveyors’ lights, Schneider suggests that it is possible for us to experience the “wombish red” that was denied Jamie, blood that is the force of life rather than the mark of violence.</p> + <p>[16] Dilys Rose’s poem, “Maeshowe Nipple,” on the other hand, in addressing the Viking use of the tomb, acknowledges that violence has taken place. The title, of course, immediately signals that Maeshowe is female, and the opening lines graphically describe the tomb’s external anatomy: a “breast,” with an “aureola / sandy-rimmed, the nipple leaking a pale trail / to hidden chambers” (1-3). Within, Maeshowe’s chambers have been “invaded” by men who “inscribed their conquests” and “totted up the loot” (12, 4, 6). Even though the poem has initially compared the cairn to a breast rather than a womb, this seems like a rape or an assault by men exercising their power and keeping track of their plunder. As human and homesick as the poem presents the young men, it does not forget that their presence in Maeshowe is as uninvited intruders who leave their runic seeds carved into the chamber walls.</p> + <p>[17] To make sense of this pattern of imagery, it is helpful to turn to an earlier female author, similarly inspired by her visit to a Neolithic site. Naomi Mitchison wrote <u>Early in Orcadia</u> after a friend took her to another of Orkney’s chambered tombs, Isbister, which has no passage entry, because “she knew it would waken something in me” (8). Set in Neolithic times, the novel follows a family and its descendants as they settle on Orkney, establish homes and villages, and erect the monuments in which they practice their religious rituals. Mitchison depicts the cairns predating the stone circles (both Isbister and Maeshowe are, in fact, thought to have been built before Brodgar) and imaginatively describes the changing beliefs prompting these architectural developments. Tradition holds that pregnant women must visit the tomb in order that the ancestral spirit will be passed to their children (132). One woman, Ba, making this journey, reflects that a “few moons” have passed since she became pregnant and stopped menstruating. She also knows that a powerful goddess, “the big bad Moon Woman had once had an honouring place,” had watched over the dead (119). However, the Moon Woman has been supplanted by the sun. The burial place was “pulled apart and scattered by the Sun Man and the bulls. After that came the beginning of their own honouring place where the bones lay and where you must go down on your knees before you could get in” (119). The later passage cairn, then, is a creation of the masculine sun, the same sun that shines down the passageway at midwinter. Accompanied by bulls, also male, the Sun Man has ravaged the Moon Woman’s tomb and designed a new one to suit his own needs. Even so, the burial place is still associated with female fertility. Nervously, Ba enters “on her hands and knees . . . under and between great stones.” Once inside, though, she thinks of the moments before she conceived her child: “She was waiting, almost as she had waited in the soft sand behind that rock in the sun-warmed geo a few moons back” (130). For Ba, the tomb is not frightening. She recalls not a violent rape, but a loving encounter, and the darkness feels as warm as the “geo” (an Orcadian word referring to a deep, narrow fissure in a cliff) where she met her lover. Following her memory of the moment of conception, she is “push[ed] . . . back, back to the way out, back to the square of light, to the way out into the real world on hands and knees as one must” (130). Like Jamie, Ba is compelled to crawl, to battle her way through the passage to be reborn.</p> + <p>[18] By the end of <u>Early in Orcadia</u>, the stone circle, with its emphasis on light rather than dark, is becoming the ultimate manifestation of the transfer of power from the Moon Woman to the Sun Man. Its significance is explained by the “Great Man,” who is “painted with sun circles,” to Moon Woman after he has summoned her to his presence: “The great tall stones . . . were so raised to show the way of the sun, who is our master and our maker” (169). Moon Woman, however, is aware of the injustice of this arrangement: “They said that the moon was the servant of the sun, to do what he wanted, but that, Moon Woman knew, was not right. In her own mind she unsaid it” (170). At first she is jealous and afraid, but the final vision of the novel is hers, and it is, to an extent, a reconciliation of powers:</p><blockquote>If I were to say a few small and easy words to the Great Man, if I were to move myself in a certain way, then we would be sun and moon. Then I would put my fingers onto the colour, onto that knife, onto his eyes, . . . eyes, onto that round, shining sun that hangs over his heart, fingering it so that my fingers would meet his, me going . . . onto all parts of him. He would be mine as the sun is the moon’s. (176) + </blockquote> + <p>She is picturing an intertwining of sun and moon, of masculine and feminine—a consummation. The partnership is not one of complete equality, though, for she also envisions not that the sun will be the master and the moon the servant, but that he will be hers, that the moon will possess the sun, that her status will be restored.</p> + <p>[19] Mitchison’s fictional representation of light/sun/man emerging as the object of worship and awe, assuming the rank previously held by dark/moon/woman, is an idea rooted across cultures: “A fundamental polarity in many creation myths,” according to Trevor Garnham, “contrasts the dark, fecund, harbouring earth with the up-drawing sun.” (145). He points out, for example, that “by the time of the Celtic occupation of Britain, there were well-established beliefs and practices focused on the sun” and that in Norse mythology, “a male hierarchy supplanted older, matriarchal law” (161, 109). Analyzing the archaeological sites within this paradigm, Garnham argues, supports the theory that religious practice fundamentally changed along with the architecture, that “ritual activity associated with burial cairns became transferred to stone circles” (152).</p> + <p>[20] Maeshowe, however, suggests a mid-point in this ritualistic shift because although, like earlier stalled cairns, it is dark and womb-like, its annual climactic moment is when the sun lights up the passage. Garnham sees the Neolithic architecture of Orkney as a progression. The first structures, the houses, were purely domestic; they had a “nurturing role” (66). The houses at the coastal village site, Scara Brae, therefore, “seem to be fundamentally powerful symbols of protection and gathering, echoing that of the pot and the basket” (70). Since the manufacture of both pots and baskets was the work of women, Garnham is reading the houses as essentially feminine. They were vessels, their stone walls embanked by earth. Both Garnham and Richards point out that the houses were models for the tombs: the passage graves are structurally similar to the houses at Scara Brae, and both were covered with turf (Garnham 48; Challands, Muir & Richards 242, 245). Cairns of the Maeshow type, with passage entries, however, were the later forms. The earlier stalled structures, such as Midhowe, on the island of Rousay, did not feature the tunnel entrance.</p> + <p>[21] Archaeologists do not agree on the social significance of passage cairns and sun circles, the extent to which their development reveals a move to a more hierarchical society. Challands, Muir, and Richards state, “In many ways, everything about the architecture of Maeshowe enforces a notion of separation, division, and restriction” (247). Elsewhere, Richards and another co-writer are more guarded. They point out that the tomb resembles House 2 at the nearby Barnhouse settlement, a larger house than any at Scara Brae that was probably “highly restricted on the basis of an individual’s status, probably additionally defined in terms of age and gender.” However, they also warn that there is insufficient archaeological evidence to “leap to conclusions about a patriarchal group of ‘elders’ who used knowledge as a commodity to maintain their power over women and younger men” (Muir & Richards 204). Although cautious, they do acknowledge that “power and authority,” probably based on “cosmological beliefs,” would have been necessary to build the monuments (199). Leaning not only on physical but also anthropological evidence, Garnham’s view, on the other hand, is that the more formal structure <u>does</u> support the idea of hierarchy and that the estimated 100,000 man/hours that would have been necessary to build it point to a more complex social structure that had to extend beyond the local community (128). Furthermore, he writes, the layout of individual chambers “can be read as a metaphor of primogeniture” (74). Like Richards, Garnham interprets the passage as a symbol of privilege because it was hard to get inside. However, citing Eliade’s <u>Patterns in Comparative Religion</u>, he also emphasizes that there is “a close connection between solar theology and the elite” (163). In this context it seems that “allowing access to the sun . . . was more important that [sic] allowing access to members of the tribe” (131-132).</p> + <p>[22] Maeshowe can be seen, then, as expressing a point of tension between earth and sun in which the dark tomb is literally infiltrated by solar rays on one day only. The subsequent building of the Circle of Brodgar elevates the stature of the sun. Fully above ground, the center of its astronomical and religious year occurs not in December, but in June, at the midsummer solstice. Garnham points out that while a smaller circle, the Stones of Stenness, is open to the sun at its “point of maximum power,” Maeshowe allows the sun inside only when it is “at its lowest ebb.” Except at midwinter, “the tomb is dark, cold, and filled with white bones, echoing the whiteness of the moon” (207). Although Stenness actually predates Maeshowe by perhaps 400 years, throwing off the neat chronology of <u>Early in Orcadia</u>, Garnham’s interpretation of Maeshowe and the stone circles parallels Mitchison’s literary response to the Isbister tomb: compared to earlier cairns, Maeshowe is a more patriarchal development, the passageway allowing the masculine sun to displace the feminine “whiteness of the moon,” and yet the bones, the metaphorical seeds, still lie dormant; the presence of Moon Woman endures.</p> + <p>[23] Although <u>Early in Orcadia</u> ends with Moon Woman’s vision of a mingling of sun and moon, of masculine and feminine, there is a note of uncertainty as she asks herself, “Should I, then?” (176). She does not ask “Can I?” but “Should I?” Her question is not whether she is personally capable, but whether it would be wise to challenge the elite power structure in the name of justice. Readers are left without an answer, but since women are still fighting for equality in the institutions of politics and religion, it is reasonable to assume that if Moon Woman did attempt it, she met with a great deal of resistance. It is with this in mind, then, that we can return to the Maeshowe experiences of Jamie, Schneider and Rose. Their visits to the cairn suggest that to see it merely as a symbol of agricultural regeneration or even more broadly of hope, is incomplete. Something more needs to be resurrected, and their use of the female imagery effectively acknowledges and reclaims a feminine narrative for Maeshowe. In Rose’s poem, 12th century Vikings may take up residence inside, but 900 years later, the reader is instructed to “See,” to bear witness to “a green breast in a green field,” the most nurturing part of a woman’s body surrounded by the new growth of spring (1). When Schneider refers to the “red that’s birth” rather than the “red spilt in hatred,” and describes how the sun will “burnish the passage wall, / flood the ground with gold” and, similarly, when Jamie refers to the “complicit kiss,” it is as if Moon Woman’s consummation has finally taken place and justice restored.</p> + <p>[24] Richards asks where the doors of tombs lead, to what “revelation.” Indeed, the creative writing of Jamie, Schneider, and Rose transports readers through Maeshowe’s entryway towards “revelation.” Their collective responses help us to recognize the humanity of Neolithic peoples, to appreciate how common experiences connect us to the past. They ask us to consider the roots of sexual discrimination, the possible marginalization of women 5000 years ago. More universally, they honor the memory of displaced matriarchal societies and, thus, prompt us to reflect on the status of women today. While, as Hall points out, male authors of the mid-twentieth-century Scottish Literary Renaissance had a nationalist political agenda, “looking for Scotland in Scotland’s prehistory” (160), these female writers look to the past for a feminist renewal, both personal and political. As such, their interpretations complement and illuminate those of archaeologists. Naomi Mitchison, acknowledging that she may be “treading on the toes of archaeologists,” points out that their physical “evidence may not always offer a clear interpretation, in fact it very seldom does” (113). For despite their painstaking sifting (both literal and figurative) of physical evidence, archaeologists must, finally, apply their own imaginations.</p> + <p>[25] Archaeologists themselves recognize the uncertainty inherent in drawing conclusions about ancient societies from the surviving fragments of their lives. In reference to the recent discovery of a complex of temples at the Ness of Brodgar, Richards has said, “This was a ceremonial centre, and a vast one at that. But the religious beliefs of its builders remain a mystery" (qtd. in McKie). In fact, the excavation of this temple complex is prompting a reassessment of the entire Heart of Neolithic Orkney. Tom Muir, of the Orkney Museum, goes so far as to assert that "the whole text book of British archaeology for this period will have to be torn up and rewritten from scratch thanks to this place" (qtd. in McKie). Even as archaeologists, using sophisticated technology, scrape away the dust of time from this long-buried site, it remains true that “Insights can only come from interpretation” (Jones and Richards 195). It is in this interpretative arena that science must join forces with the arts and humanities in the search for knowledge, for a fuller understanding.</p> + <p>[26] George Mackay Brown has written, “People in 2000 AD are essentially the same as the stone-breakers [. . .] of 3000 BC” (“Brodgar Poems” lines 10-12). Knowing where we have come from, fleshing out our understanding of the prehistoric world and, therefore, ourselves, takes the skills and multiple perspectives not only of scientists, archaeologists, architects, and anthropologists, but also essayists, poets, and more. The interdisciplinary synergy involved in comparing archaeological, anthropological, and literary interpretations of Maeshowe sheds light on the shadows of the past, raises questions about the more elusive shadows of Neolithic women, and provides historical context for our understanding of gender relations across time. Like crawling through the passage into the dark and out to the light, the empirical and literary journeys into the mysteries of Maeshowe are indeed transformative, exhuming the bones of the past that we may better nurture the seeds of the future.</p> + <p>ACKNOWLEDGEMENTS. Thanks are due to Edward Gale Agran, Stephen Potthoff, and the anonymous reviewers for their time and valued advice. </p> + <p align="center">WORKS CITED</p> + <p>Bevan, Archie, and Brian Murray. Eds. <u>The Collected Poems of George Mackay Brown</u>. London: John Murray, 2005. Print.</p> + <p>Brown, George Mackay. “Brodgar Poems (1992).” In Bevan and Murray.308-312. Print.</p> + <p>---. “Maeshowe: Midwinter.”1996. In Bevan and Murray. 320. Print.</p> + <p>---. “Maeshowe at Midwinter.” 1977. <u>Under Binkie’s Brae</u>. Edinburgh: Gordon Wright Publishing, 1979. 87-88. Print.</p> + <p>---. “Two Maeshowe Poems.” 1999. In Bevan and Murray. 420-421. Print.</p> + <p>Card, Nick, et al. “Bringing a Landscape to Life? Researching and Managing ‘The Heart of Neolithic Orkney’ World Heritage Site.” <u>World Archaeology</u> 39.3 (2007): 417-435. EBSCO <u>Academic Search Complete</u>. Web. 29 Jun. 2011.</p> + <p>Challands, Adrian, Tom Muir, and Colin Richards. “The Great Passage Grave of Maeshowe.” <u>Dwelling Among the Monuments: The Neolithic Village of Barnhouse, Maeshowe Passage Grave and Surrounding Monuments at Stenness, Orkney</u>. Ed. Colin Richards. Cambridge: McDonald Inst. For Archaeological Research, 2005. 229-248. Print.</p> + <p>Crawford, Robert. “Maes Howe Sappho.” <u>Yale Review</u>: 95.1 (2007): 60-65. OhioLINK Electronic Journal Center. Web. 29 Jun. 2011.</p> + <p>Garnham, Trevor. <u>Lines on the Landscape, Circles from the Sky: Monuments of Neolithic Orkney</u>. Stroud, Gloucestershire: Tempus, 2004. Print.</p> + <p>Hall, Simon W. <u>The History of Orkney Literature</u>. Edinburgh: John Donald/Birlinn Ltd., 2010. Print.</p> + <p>“Heart of Neolithic Orkney WHS: Setting Project” Historic Scotland. 2008. EBSCO <u>Academic Search Complete</u>. Web. 30 Jun. 2011.</p> + <p>Jamie, Kathleen. “Darkness and Light.” <u>Findings: Esssays on the Natural and Unnatural World</u>. Ed. Jamie. St. Paul, MN: Graywolf, 2005. 3-22. Print.</p> + <p>McKie, Robin. “Neolithic Discovery: Why Orkney is the Centre of Ancient Britain.</p> + <p><u>The Guardian / The Observer</u>. 6 Oct. 2012. Web. 16 Mar. 2013.</p> + <p>Mitchison, Naomi. <u>Early in Orcadia</u>. Glasgow: Richard Drew, 1987. Print.</p> + <p>Jones, Siân, and Colin Richards. “The Villagers of Barnhouse.” <u>Dwelling Among the Monuments: The Neolithic Village of Barnhouse, Maeshowe Passage Grave and Surrounding Monuments at Stenness, Orkney</u>. Ed. Colin Richards. Cambridge: McDonald Inst. For Archaeological Research, 2005. 195-204. Print.</p> + <p>Richards, Colin. “Doorways into Another World: The Orkney-Cromarty Chambered Tombs.” <u>Vessels for Ancestors: Essays on the Neolithic of Britain and Ireland in Honour of Audrey Henshall</u>. Ed. Niall Sharples and Alison Sheridan. Edinburgh: Edinburgh UP, 1992. 62-76. Print.</p> + <p>Riddoch, Lesley. “Stone Age Marvels Which Inspire and Astonish: Wonders of Scotland.” <u>The Scotsman</u>. 13 Feb. 2006. Web. 30 Jun. 2011.</p> + <p>Rose, Dilys. “Maes Howe Nipple.” <u>Bodywork</u>. Edinburgh. Luath Press, 2007. Print.</p> + <p>Schneider, Myra. “Maeshowe.” <u>Circling the Core</u>. London: Enitharmon Press, 2008. 23-24. Print.</p> + <p>Wordsworth, William. “I wandered lonely as a cloud.” <u>The Norton Anthology of English Literature</u>. Eighth Ed. Ed. Stephen Greenblatt and M.H. Abrams. New York: Norton, 2006. 305-306. Print.</p> +<p><strong>Contributor's Note</strong></p> + <p><strong>CHARLOTTE FAIRLIE</strong> teaches English at Wilmington College, in Wilmington, Ohio. Her published work focuses on Scottish literature and rural life in literature. She is currently co-editing an anthology of poetry relating to scythes and mowing.</p></td> + <td valign="top"><center> + <a href="../index.html"> <img src="../image/btncu.gif" alt="Current Issue" border="0" height="42" width="79"></a><br> + <a href="../download.html" tppabs="http://www.genders.org/download.html"> <img src="../image/btndo.gif" alt="Download" tppabs="http://www.genders.org/image/btndo.gif" align="bottom" border="0" height="42" width="115"></a><br> + <a href="../edit.html" tppabs="http://www.genders.org/edit.html"> <img src="../image/btned.gif" alt="Editorial Board" tppabs="http://www.genders.org/image/btned.gif" align="bottom" border="0" height="50" width="80"></a><br> + <a href="../guide.html" tppabs="http://www.genders.org/guide.html"> <img src="../image/btngu.gif" alt="Contributor Guidelines" tppabs="http://www.genders.org/image/btngu.gif" align="bottom" border="0" height="42" width="90"></a><br> + <a href="../recent.html"> <img src="../image/btnre.gif" alt="Recent Issues" tppabs="http://www.genders.org/image/btnre.gif" align="bottom" border="0" height="41" width="79"></a><br> + <a href="../link.html"> <img src="../image/btnli.gif" alt="Links & Books" border="0" height="46" width="97"></a><br> + </center></td> + </tr> + </tbody> + </table> + <table width="500"> + <tbody> + <tr> + <td><p><a href="../download.html">Copyright</a> 2010 Ann Kibbey. + + All Rights Reserved Worldwide.<br> + </p> + <p> </p> + <center> + <a href="../download.html"><font size="1">Download</font></a><font size="1"> || <a href="../edit.html">Editorial Board</a> || <a href="../guide.html">Submission + + Guidelines</a> || <a href="../index.html">Current Issue</a> || <a href="../recent.html">Recent Issues</a> || <a href="../link.html">Links + + & Books</a></font> + </center></td> + </tr> + </tbody> + </table> + <p></p> + <p align="right"> + + <table width="550"> + <tbody> + <tr> + <td width="361"></td> + <td width="72"><p><img src="../image/algosmlr.gif" alt="Genders" align="bottom" border="0" height="72" width="72"> </p></td> + <td width="101"><b> <font size="1">Genders Journal</font></b> <font size="1"><br> + 226 UCB<br> + University of Colorado<br> + Boulder, CO 80309<br> + http://www.Genders.org</font></td> + </tr> + </tbody> + </table> + </p> + <p align="right"></p></td> + </tr> + </tbody> +</table> +</p> +<p></p> +</body> +</html>
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cleared"></div> + <h1 class="article-item__title serif" itemprop="headline">More than 100 scientific journals have disappeared from the Internet</h1> + + <div class="article-item__teaser-text serif"> + Researchers have identified dozens of open-access journals that went offline between 2000 and 2019, and hundreds more that could be at risk. + </div> + </header> + + <div class="clear cleared"></div> + + <div class="bordered-container clear cleared pull--both"> + <div id="author-affiliations" class="tab-group text14" role="tablist" data-test="author-affiliations" data-tab-group> + <div class="cleared"> + + <div id="author-affiliation-news-0" class="tab-box js-box-wrapper"> + <h3 id="author-affiliation-news-0-head" data-track="click" data-track-label="view author info" class="sans-serif strong tab tab-skin ma0" role="tab" + aria-controls="author-affiliation-news-0-content" data-tooltip="Show author information"> + Diana Kwon + </h3> + <div id="author-affiliation-news-0-content" 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</svg> + </a> + </li> + <li class="mr10"> + <a class="icon--inline inline-block" data-track="click" data-track-action="email" data-track-category="social" data-track-label="10.1038/d41586-020-02610-z" href="mailto:?subject=More than 100 scientific journals have disappeared from the Internet&body=https%3A%2F%2Fwww.nature.com%2Farticles%2Fd41586-020-02610-z"> + <?xml version="1.0" encoding="UTF-8" standalone="no"?> + <svg role="img" focusable="false" viewBox="0 0 30 30" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"> + <title>Share via E-Mail</title> + <desc>Share via E-Mail</desc> + <defs></defs> + <g stroke="none" stroke-width="1" fill="none" fill-rule="evenodd"> + <g> + <g> + <polygon points="0 0 30 0 30 30 0 30"></polygon> + <path d="M15,15.3269887 L10.6248577,11.9177869 C10.4236021,11.7609644 10.1299323,11.7927468 9.96892789,11.988775 C9.80792343,12.1848031 9.84055341,12.4708451 10.041809,12.6276676 L14.7012493,16.2584003 C14.8680779,16.3940555 15.1152493,16.4013884 15.2915244,16.2640313 C15.2939898,16.2622325 15.2963784,16.2603294 15.2987507,16.2584003 L19.958191,12.6276676 C20.1594466,12.4708451 20.1920766,12.1848031 20.0310721,11.988775 C19.8700677,11.7927468 19.5763979,11.7609644 19.3751423,11.9177869 L15,15.3269887 Z M9,10 L21,10 C21.5522847,10 22,10.4477153 22,11 L22,19 C22,19.5522847 21.5522847,20 21,20 L9,20 C8.44771525,20 8,19.5522847 8,19 L8,11 C8,10.4477153 8.44771525,10 9,10 Z"></path> + </g> + </g> + </g> + </svg> + </a> + </li> +</ul> + + </div> + + + + + <div class="align-left"> + + <div class="article__body serif cleared"> + <p>Scholarly journals are supposed to provide a lasting record of science. But over the past two decades, 176 open-access journals — and many of the papers published in them — have disappeared from the Internet, according to an analysis published on 27 August<sup><a href="#ref-CR1" data-track="click" data-action="anchor-link" data-track-label="go to reference" data-track-category="references">1</a></sup>.</p><p>“There shouldn’t really be any decay or loss in scientific publications, particularly those that have been open on the web,” says Mikael Laakso, an information scientist at the Hanken School of Economics in Helsinki, and a co-author of the study, which was posted on the arXiv preprint server. He and his colleagues identified 176 titles whose online presence vanished between 2000 and 2019.</p><p> + <aside class="recommended pull pull--left sans-serif" data-label="Related"> + <a href="https://www.nature.com/news/investigating-journals-the-dark-side-of-publishing-1.12666" data-track="click" data-track-label="recommended article"><img class="recommended__image" alt="" src="//media.nature.com/w400/magazine-assets/d41586-020-02610-z/d41586-020-02610-z_15541288.jpg"><h1 class="recommended__title serif">Investigating journals: The dark side of publishing</h1></a> + </aside></p><p>More than half of these journals were in the social sciences and humanities, although life sciences, health sciences, physical sciences and mathematics were also represented. Eighty-eight of the journals were affiliated with a scholarly society or a research institution. The analysis also identified 900 journals that are still online but seem to have stopped publishing papers, so might be vulnerable to vanishing in the near future.</p><p>The study lays out a "compelling case" for the vulnerability of online journals, says Elizabeth Lightfoot, a librarian at Florida International University in Miami.</p><h2>Vanishing journals</h2><p>Journals can disappear from the Internet for a number of reasons, says Laakso. The publisher might stop paying to keep its publication’s webpage afloat, for example, or journals might be hosted on an online platform that belongs to an academic institution and is left behind when the site or server is updated.</p><p>Journals are supposed to be preserved in digital archives when this happens. Services such as the LOCKSS (Lots of Copies Keep Stuff Safe) Program, which was launched by Stanford Libraries in 1999, aim to ensure that publications remain available even when the publisher is no longer around. LOCKSS works by making multiple copies of content that is stored on the servers of participating libraries, who pay an annual fee to have their collections preserved. Similar initiatives, including CLOCKSS, Portico and the Public Knowledge Project’s Preservation Network (PKP PN), have emerged over the past two decades. These vary in cost and coverage: Some work with libraries, others with publishers — services such as PKP PN are free for journals that sign up. Tens of thousands of titles are currently curated in such preservation schemes. But, Laakso says, there are dozens of journals that fall through the cracks.</p><p> + <aside class="recommended pull pull--left sans-serif" data-label="Related"> + <a href="https://www.nature.com/articles/d41586-018-06178-7" data-track="click" data-track-label="recommended article"><img class="recommended__image" alt="" src="//media.nature.com/w400/magazine-assets/d41586-020-02610-z/d41586-020-02610-z_16099234.jpg"><h1 class="recommended__title serif">Radical open-access plan could spell end to journal subscriptions</h1></a> + </aside></p><p>Pinning down whether a journal is truly unavailable online is a challenge, because there is no single database that tracks the activity of open-access journals, says Lisa Matthias, one of the authors of the study and a PhD student at the Free University of Berlin. Databases such as the Directory of Open Access Journals (DOAJ) don’t keep track of journals that no longer publish — and journals that cease publishing or stop maintaining their presence on the web usually do so silently.</p><p>To find out how many journals had vanished, the team manually collected historical data from several lists of titles, including the DOAJ, Ulrichsweb and Scopus. Then they checked to see if any of the titles they identified were listed on the Keepers Registry, which keeps track of journals that are enrolled into digital preservation schemes. Finally, they went to the Internet Archive’s Wayback Machine to access snapshots of now-offline journals’ websites to see when they had last published, and when the content was last available on the Internet. Journals were considered “vanished” if less than 50% of their content was still freely available online (the researchers acknowledge that some journals could exist in print form or behind a paywall).</p><p>The majority of the 176 vanished journals had disappeared within 5 years of becoming inactive — the point at which they stopped publishing papers. Around one-third of them disappeared within one year of the last publication. The researchers used this ‘life cycle’ to estimate that another 900 inactive open-access journalscould be at risk of vanishing.</p><h2>Preserving the literature</h2><p>Subscription journals were not included in the study, Laakso says, because paywalls mean that they would have had to have used a different method to collect the data. He adds that because of this and other limitations, the study probably underestimates the number of journals that have disappeared. “It’s really hard to pin down when something doesn't absolutely exist, but we tried our best,” Laakso says. “We hope that there will be more refined and automatic ways to detect these in the future.”</p><p> + <aside class="recommended pull pull--left sans-serif" data-label="Related"> + <a href="https://www.nature.com/articles/d41586-019-02038-0" data-track="click" data-track-label="recommended article"><img class="recommended__image" alt="" src="//media.nature.com/w400/magazine-assets/d41586-020-02610-z/d41586-020-02610-z_16870448.jpg"><h1 class="recommended__title serif">India culls hundreds more ‘dubious’ journals from government approved list</h1></a> + </aside></p><p>Thib Guicherd-Callin, the acting manager of the LOCKSS Program, says it’s not surprising that there are journals that aren't captured by existing preservation services. Although many groups have used the open-source LOCKSS software, efforts to launch digital preservation initiatives are still “woefully underfunded”, he adds. “The desire to preserve these at-risk works is there,” he adds, but few institutions are investing the resources necessary to identify these publications and make sure they’re included in a digital preservation scheme.</p><p>Matthias says that the responsibility for ensuring inactive journals don’t disappear should be shared between publishers, authors, librarians and preservation services. Lightfoot agrees that a coordinated and collaborative effort is necessary. However, she adds, “the twin challenges of what that effort might look like and who would fund it make the pathway forward murky at best”.</p> + </div> + + <div class="emphasis">doi: <a href="https://doi.org/10.1038/d41586-020-02610-z">https://doi.org/10.1038/d41586-020-02610-z</a></div> + <div class="anchor-link mt40" data-toggle="anchor-links"></div> + <div id="references" class="references" data-toggle="anchor-links-section" data-label="References" data-concertina="true"> + <section aria-labelledby="Bib1"><div class="serif article-section js-article-section cleared clear" id="Bib1-section"><h2 class="js-section-title section-title strong position-relative tighten-line-height background-gray-light pt20 pb6 pl0 pr20 standard-space-below small-space-above mq640-pt10 mq640-pb10 mq640-pl20 mq640-mt0 mq640-ml-20 mq640-mr-20 extend-left" id="Bib1">References</h2><div class="pl20 mq875-pl0 js-collapsible-section" id="Bib1-content"><div data-container-section="references"><ol class="clean-list ma0 standard-space-below indented-list" data-test="references-list"><li class="small-space-below border-gray-medium border-bottom-1 position-relative js-ref-item" itemprop="citation" itemscope="itemscope" itemtype="http://schema.org/Article" data-test="citation"><span class="indented-counter serif h2 tighten-line-height text-right position-absolute grade-c-hide">1.</span><p class="tiny-space-below" id="ref-CR1">Laakso, M., Matthias, L. & Jahn, N. Preprint at <a href="https://arxiv.org/abs/2008.11933">https://arxiv.org/abs/2008.11933</a> (2020).</p><ul class="js-ref-links clean-list cleared strong sans-serif text13 hide-print small-space-below"><li class="pin-right"><ul class="clean-list ma0"></ul></li></ul></li></ol><p class="hide-print text-right"><a href="/articles/d41586-020-02610-z-references.ris" class="text14 sans-serif strong" data-track="click" data-track-action="download citation references" data-track-label="link">Download references</a></p></div></div></div></section> + </div> + + + + + + + <div class="nature-briefing nature-briefing-box mt0 cleared hide-print" data-component-id="nature-briefing-box" data-track="in-view" data-track-action="in-view" data-track-category="nature briefing" data-track-label="inPage box visible"> + <div class="nature-briefing-box__header pa20"> + <h1 class="h2 strong pb10 extra-tight-line-height">Nature Briefing</h1> + <p class="nature-briefing-box__standfirst mb0 sans-serif tighten-line-height">An essential round-up of science news, opinion and analysis, delivered to your inbox every weekday.</p> + </div> + <form action="/briefing/signup/formfeedback" method="post" class="nature-briefing-box__form pa20" data-location="box" data-track="submit" data-track-action="transmit-form"> + <input id="briefing-box-signup-form-inPage-input-track-originReferralPoint" type="hidden" name="track_originReferralPoint" value="DirectEmailBox-inPage"> + <input id="briefing-box-signup-form-inPage-input-track-formType" type="hidden" name="track_formType" value="DirectEmailBox"> + <label class="nature-briefing-box__input-label block strong" for="box-inPage-EmailAddressInput">Email address</label> + <input class="nature-briefing-box__input-input block border-all-1 equalize-line-height pa10 mb10 box-sizing grid-12" type="email" id="box-inPage-EmailAddressInput" name="email" value="" placeholder="e.g. jo.smith@university.ac.uk" required="true" aria-required="true" data-test-element="briefing-box-email-input"> + + <div class="mb20 position-relative" role="group"> + <input class="nature-briefing-box__checkbox-checkbox" id="gdpr-briefing-box-inPage-checkbox" type="checkbox" name="gdpr" value="1" data-test-element="briefing-box-gdpr-checkbox" required> + <label class="nature-briefing-box__checkbox-label tighten-line-height" for="gdpr-briefing-box-inPage-checkbox">Yes! 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html> +<html lang="en"> + +<head> + <meta charset="utf-8"> + + <title>The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles [PeerJ]</title> + + + <link rel="dns-prefetch" href="https://d2pdyyx74uypu5.cloudfront.net/"> + <link rel="dns-prefetch" href="http://static.peerj.com/"> +<link rel="dns-prefetch" href="https://doi.org"> + + + <meta name="citation_title" content="The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles"><meta name="citation_date" content="2018-02-13"><meta name="citation_doi" content="10.7717/peerj.4375"><meta name="citation_language" content="en"><meta name="citation_pdf_url" content="https://peerj.com/articles/4375.pdf"><meta name="citation_fulltext_html_url" content="https://peerj.com/articles/4375"><meta name="citation_volume" content="6"><meta name="citation_firstpage" content="e4375"><meta name="citation_keywords" content="Open access; Open science; Scientometrics; Publishing; Libraries; Scholarly communication; Bibliometrics; Science policy"><meta name="citation_journal_title" content="PeerJ"><meta name="citation_journal_abbrev" content="PeerJ"><meta name="citation_publisher" content="PeerJ Inc."><meta name="citation_issn" content="2167-8359"><meta name="citation_author" content="Heather Piwowar"><meta name="citation_author_institution" content="Impactstory, Sanford, NC, USA"><meta name="citation_author_email" content="heather@impactstory.org"><meta name="citation_author" content="Jason Priem"><meta name="citation_author_institution" content="Impactstory, Sanford, NC, USA"><meta name="citation_author_email" content="jason@impactstory.org"><meta name="citation_author" content="Vincent Larivière"><meta name="citation_author_institution" content="École de bibliothéconomie et des sciences de l’information, Université de Montréal, Montréal, QC, Canada"><meta name="citation_author_institution" content="Observatoire des Sciences et des Technologies (OST), Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Université du Québec à Montréal, Montréal, QC, Canada"><meta name="citation_author" content="Juan Pablo Alperin"><meta name="citation_author_institution" content="Canadian Institute for Studies in Publishing, Simon Fraser University, Vancouver, BC, Canada"><meta name="citation_author_institution" content="Public Knowledge Project, Canada"><meta name="citation_author" content="Lisa Matthias"><meta name="citation_author_institution" content="Scholarly Communications Lab, Simon Fraser University, Vancouver, Canada"><meta name="citation_author" content="Bree Norlander"><meta name="citation_author_institution" content="Information School, University of Washington, Seattle, USA"><meta name="citation_author_institution" content="FlourishOA, USA"><meta name="citation_author" content="Ashley Farley"><meta name="citation_author_institution" content="Information School, University of Washington, Seattle, USA"><meta name="citation_author_institution" content="FlourishOA, USA"><meta name="citation_author" content="Jevin West"><meta name="citation_author_institution" content="Information School, University of Washington, Seattle, USA"><meta name="citation_author" content="Stefanie Haustein"><meta name="citation_author_institution" content="Observatoire des Sciences et des Technologies (OST), Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Université du Québec à Montréal, Montréal, QC, Canada"><meta name="citation_author_institution" content="School of Information Studies, University of Ottawa, Ottawa, ON, Canada"> + <meta name="description" content="Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles. We use three samples, each of 100,000 articles, to investigate OA in three populations: (1) all journal articles assigned a Crossref DOI, (2) recent journal articles indexed in Web of Science, and (3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI. We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made free-to-read on the publisher website, without an explicit Open license. We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice."> + + + <meta property="og:image" content="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-1-1x.jpg"> + <meta name="twitter:image" content="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-1-1x.jpg"> + + <meta name="twitter:card" content="summary_large_image"> + <meta name="twitter:url" content="https://peerj.com/articles/4375"> + <meta name="twitter:site" content="@thePeerJ"> + <meta name="twitter:title" content="The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles"> + <meta name="twitter:description" content="Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles. We use three samples, each of 100,000 articles, to investigate OA in three populations: (1) all journal articles assigned a Crossref DOI, (2) recent journal articles indexed in Web of Science, and (3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI. We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made free-to-read on the publisher website, without an explicit Open license. We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice."> + + <meta property="og:type" content="article"> + <meta property="og:title" content="The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles"> + <meta property="og:url" content="https://peerj.com/articles/4375"> + <meta property="og:site_name" content="PeerJ"> + + + <link rel="alternate" type="application/pdf" href="/articles/4375.pdf"> + <link rel="alternate" type="application/rdf+xml" href="/articles/4375.rdf"> + <link rel="alternate" type="application/json" href="/articles/4375.json"> + <link rel="alternate" type="application/xml" href="/articles/4375.xml"> + <link rel="alternate" type="application/unixref+xml" href="/articles/4375.unixref"> + <link rel="alternate" type="application/vnd.citationstyles.csl+json" href="/articles/4375.citeproc"> + <link rel="alternate" type="application/bibjson+json" href="/articles/4375.bibjson"> + <link 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Discutimos este artículo de Piwowar y colaboradore…</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/LorenAndreaEP/status/1317614486359072769" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/LorenAndreaEP/status/1317614486359072769" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/LorenAndreaEP/status/1317614486359072769" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1293635358064807937/YCE7J6e-_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=15271321" target="_blank"><strong>Rachel Borchardt</strong> <span class="twitter-handle">@ButternutSquash</span></a> + <span class="item-tweet-date">12 days ago</span> + </div> + <div>@ces43 May I recommend Piwowar and Priem et al's article for that topic? https://t.co/Fnm0vtYtKS</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/ButternutSquash/status/1317104229358645248" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/ButternutSquash/status/1317104229358645248" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/ButternutSquash/status/1317104229358645248" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1210228942415814656/L6yRkSyu_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=1117109826" target="_blank"><strong>Ana M. Aldana</strong> <span class="twitter-handle">@AMAldanaS</span></a> + <span class="item-tweet-date">40 days ago</span> + </div> + <div>También revisamos el tema de la publicación en abierto: tipos y ventajas. Discutimos este artículo de Piwowar y colaboradores de 2018 en donde se evidencia la ventaja de publicar en green open access: . https://t.co/1HAmYlfoBP</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/AMAldanaS/status/1306761873900044290" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/AMAldanaS/status/1306761873900044290" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/AMAldanaS/status/1306761873900044290" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/982225468286840837/BM5R0jJh_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=982223918223130624" target="_blank"><strong>Scicomm</strong> <span class="twitter-handle">@ScicommBot</span></a> + <span class="item-tweet-date">62 days ago</span> + </div> + <div>RT @InandVertebrate: How many articles are published in Open Access every year? +https://t.co/xkUMWA5jbJ +#openaccess #openscience #scicomm</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/ScicommBot/status/1298798812220346368" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/ScicommBot/status/1298798812220346368" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/ScicommBot/status/1298798812220346368" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1264543181099528193/4WTe1NqL_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=1252313225011449856" target="_blank"><strong>OpenSci Talk</strong> <span class="twitter-handle">@OpenSciTalk</span></a> + <span class="item-tweet-date">62 days ago</span> + </div> + <div>RT @InandVertebrate: How many articles are published in Open Access every year? +https://t.co/xkUMWA5jbJ +#openaccess #openscience #scicomm</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OpenSciTalk/status/1298797962437357568" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OpenSciTalk/status/1298797962437357568" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/OpenSciTalk/status/1298797962437357568" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/879796293132050432/ywML6RLZ_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=879783542498217984" target="_blank"><strong>Open Science</strong> <span class="twitter-handle">@_open_science_</span></a> + <span class="item-tweet-date">62 days ago</span> + </div> + <div>RT @InandVertebrate: How many articles are published in Open Access every year? +https://t.co/xkUMWA5jbJ +#openaccess #openscience #scicomm</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/_open_science_/status/1298795865247801345" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/_open_science_/status/1298795865247801345" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/_open_science_/status/1298795865247801345" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1041368086765559808/9wrfnnLk_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=747439693801848832" target="_blank"><strong>In&Vertebrates</strong> <span class="twitter-handle">@InandVertebrate</span></a> + <span class="item-tweet-date">62 days ago</span> + </div> + <div>How many articles are published in Open Access every year? +https://t.co/xkUMWA5jbJ +#openaccess #openscience #scicomm</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/InandVertebrate/status/1298795617167147009" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/InandVertebrate/status/1298795617167147009" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/InandVertebrate/status/1298795617167147009" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/856499301358477312/GLL-DiUg_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=850296415708471297" target="_blank"><strong>Open Pharma</strong> <span class="twitter-handle">@_OpenPharma</span></a> + <span class="item-tweet-date">90 days ago</span> + </div> + <div>RT @InandVertebrate: How many articles are published in Open Access every year? +https://t.co/xkUMWzNIkb +#openaccess #openscience #scicomm</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/_OpenPharma/status/1288751662912462848" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/_OpenPharma/status/1288751662912462848" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/_OpenPharma/status/1288751662912462848" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/879796293132050432/ywML6RLZ_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=879783542498217984" target="_blank"><strong>Open Science</strong> <span class="twitter-handle">@_open_science_</span></a> + <span class="item-tweet-date">90 days ago</span> + </div> + <div>RT @InandVertebrate: How many articles are published in Open Access every year? +https://t.co/xkUMWzNIkb +#openaccess #openscience #scicomm</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/_open_science_/status/1288734888577961984" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/_open_science_/status/1288734888577961984" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/_open_science_/status/1288734888577961984" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1264543181099528193/4WTe1NqL_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=1252313225011449856" target="_blank"><strong>OpenSci Talk</strong> <span class="twitter-handle">@OpenSciTalk</span></a> + <span class="item-tweet-date">90 days ago</span> + </div> + <div>RT @InandVertebrate: How many articles are published in Open Access every year? +https://t.co/xkUMWzNIkb +#openaccess #openscience #scicomm</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OpenSciTalk/status/1288734146982850560" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OpenSciTalk/status/1288734146982850560" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/OpenSciTalk/status/1288734146982850560" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1041368086765559808/9wrfnnLk_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=747439693801848832" target="_blank"><strong>In&Vertebrates</strong> <span class="twitter-handle">@InandVertebrate</span></a> + <span class="item-tweet-date">90 days ago</span> + </div> + <div>How many articles are published in Open Access every year? +https://t.co/xkUMWzNIkb +#openaccess #openscience #scicomm</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/InandVertebrate/status/1288733817323376640" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/InandVertebrate/status/1288733817323376640" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/InandVertebrate/status/1288733817323376640" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/820790537456226304/Tis8dyhv_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=15137538" target="_blank"><strong>Jason Priem</strong> <span class="twitter-handle">@jasonpriem</span></a> + <span class="item-tweet-date">102 days ago</span> + </div> + <div>@Mietmensch @unpaywall Gotcha. It's tough to generalize the answer to that, as it depends a lot on the specific journal and field. We dove into the details more in this paper, though: https://t.co/HRus7k3P0B</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/jasonpriem/status/1284579350273077248" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/jasonpriem/status/1284579350273077248" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/jasonpriem/status/1284579350273077248" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/820790537456226304/Tis8dyhv_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=15137538" target="_blank"><strong>Jason Priem</strong> <span class="twitter-handle">@jasonpriem</span></a> + <span class="item-tweet-date">103 days ago</span> + </div> + <div>@dwhly @unpaywall @hpiwowar historical stats are in here: https://t.co/HRus7k3P0B + +prediction for future is here: https://t.co/ex0vvThc9G</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/jasonpriem/status/1283946401492119552" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/jasonpriem/status/1283946401492119552" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/jasonpriem/status/1283946401492119552" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/456347532637896704/We-tZ-rF_normal.jpeg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=13616592" target="_blank"><strong>Eric Sieverts</strong> <span class="twitter-handle">@sieverts</span></a> + <span class="item-tweet-date">104 days ago</span> + </div> + <div>RT @jasonpriem: @egonwillighagen @unpaywall yes, we do have this for all years. see https://t.co/HRus7k3P0B and the data behind it for valu…</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/sieverts/status/1283676444158308352" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/sieverts/status/1283676444158308352" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/sieverts/status/1283676444158308352" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/633201529575632897/5rB4RNtd_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=163244377" target="_blank"><strong>Hector Keun</strong> <span class="twitter-handle">@hectorkeun</span></a> + <span class="item-tweet-date">104 days ago</span> + </div> + <div>RT @OxonAndrew: A look ‘under the hood’ of open access publishing: + +“The state of OA: a large-scale analysis of the prevalence and impact o…</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/hectorkeun/status/1283670319841116162" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/hectorkeun/status/1283670319841116162" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/hectorkeun/status/1283670319841116162" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1233869298344611840/suKOWJtS_normal.png"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=1024381399447613443" target="_blank"><strong>Asynchrony</strong> <span class="twitter-handle">@temporalization</span></a> + <span class="item-tweet-date">104 days ago</span> + </div> + <div>RT @egonwillighagen: the vast majority of research cannot be accessed if you do not have a big pile of money #openaccess https://t.co/RZ7UJ…</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/temporalization/status/1283659204922875904" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/temporalization/status/1283659204922875904" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/temporalization/status/1283659204922875904" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/447652981291614208/RtR2dZtC_normal.jpeg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=536409536" target="_blank"><strong>Andrew Singer</strong> <span class="twitter-handle">@OxonAndrew</span></a> + <span class="item-tweet-date">104 days ago</span> + </div> + <div>A look ‘under the hood’ of open access publishing: + +“The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles” @thePeerJ https://t.co/yCu96hCzMK</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OxonAndrew/status/1283655402773786625" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OxonAndrew/status/1283655402773786625" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/OxonAndrew/status/1283655402773786625" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/668462090655371264/SBzaDNdf_normal.png"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=22911650" target="_blank"><strong>Egon Willighⓐgen</strong> <span class="twitter-handle">@egonwillighagen</span></a> + <span class="item-tweet-date">104 days ago</span> + </div> + <div>the vast majority of research cannot be accessed if you do not have a big pile of money #openaccess https://t.co/RZ7UJV72Uf https://t.co/DE9MPIKTdZ</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/egonwillighagen/status/1283654069815586817" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/egonwillighagen/status/1283654069815586817" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/egonwillighagen/status/1283654069815586817" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/668462090655371264/SBzaDNdf_normal.png"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=22911650" target="_blank"><strong>Egon Willighⓐgen</strong> <span class="twitter-handle">@egonwillighagen</span></a> + <span class="item-tweet-date">105 days ago</span> + </div> + <div>RT @jasonpriem: @egonwillighagen @unpaywall yes, we do have this for all years. see https://t.co/HRus7k3P0B and the data behind it for valu…</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/egonwillighagen/status/1283497221950976006" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/egonwillighagen/status/1283497221950976006" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/egonwillighagen/status/1283497221950976006" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/820790537456226304/Tis8dyhv_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=15137538" target="_blank"><strong>Jason Priem</strong> <span class="twitter-handle">@jasonpriem</span></a> + <span class="item-tweet-date">105 days ago</span> + </div> + <div>@egonwillighagen @unpaywall yes, we do have this for all years. see https://t.co/HRus7k3P0B and the data behind it for values.</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/jasonpriem/status/1283494738251800576" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/jasonpriem/status/1283494738251800576" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/jasonpriem/status/1283494738251800576" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1220321309411942408/nhm-dSur_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=1215236299344502791" target="_blank"><strong>Open Science Community Maastricht</strong> <span class="twitter-handle">@OSCMaastricht</span></a> + <span class="item-tweet-date">115 days ago</span> + </div> + <div>RT @InandVertebrate: The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles, 2018 +https://t.co/xkUMWA…</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OSCMaastricht/status/1279836423529680897" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OSCMaastricht/status/1279836423529680897" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/OSCMaastricht/status/1279836423529680897" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1264543181099528193/4WTe1NqL_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=1252313225011449856" target="_blank"><strong>OpenSci Talk</strong> <span class="twitter-handle">@OpenSciTalk</span></a> + <span class="item-tweet-date">115 days ago</span> + </div> + <div>RT @InandVertebrate: The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles, 2018 +https://t.co/xkUMWA…</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OpenSciTalk/status/1279749950268563460" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OpenSciTalk/status/1279749950268563460" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/OpenSciTalk/status/1279749950268563460" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1041368086765559808/9wrfnnLk_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=747439693801848832" target="_blank"><strong>In&Vertebrates</strong> <span class="twitter-handle">@InandVertebrate</span></a> + <span class="item-tweet-date">115 days ago</span> + </div> + <div>The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles, 2018 +https://t.co/xkUMWA5jbJ +#openaccess #openscience #scicomm</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/InandVertebrate/status/1279746851051200513" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/InandVertebrate/status/1279746851051200513" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/InandVertebrate/status/1279746851051200513" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1263564961068077059/CKFX9dV2_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=371391064" target="_blank"><strong>Marie E McVeigh</strong> <span class="twitter-handle">@JopieNet</span></a> + <span class="item-tweet-date">121 days ago</span> + </div> + <div>@lisalibrarian @ashleydfarley @andy_nobes Usual def of "bronze" in @our_research is free to read, but does not have CC license. +https://t.co/T34fQja0nN</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/JopieNet/status/1277662956373921792" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/JopieNet/status/1277662956373921792" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/JopieNet/status/1277662956373921792" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + <div class="row-fluid tweet-item"> + <div class="span1 offset1"><img src="https://pbs.twimg.com/profile_images/1264543181099528193/4WTe1NqL_normal.jpg"></div> + <div class="span8"> + <div> + <a class="twitter-profile-url" href="https://twitter.com/intent/user/?user_id=1252313225011449856" target="_blank"><strong>OpenSci Talk</strong> <span class="twitter-handle">@OpenSciTalk</span></a> + <span class="item-tweet-date">146 days ago</span> + </div> + <div>RT @InandVertebrate: How many articles are published in Open Access every year? +https://t.co/xkUMWzNIkb +#openaccess #openscience #scicomm</div> + <div class="item-tweet-cta"> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OpenSciTalk/status/1268621662469017601" target="_blank"><i class="icon-comment-alt"></i> reply</a></span> + <span class="item-tweet-cta-action"><a href="https://twitter.com/OpenSciTalk/status/1268621662469017601" target="_blank"><i class="icon-retweet"></i> retweet</a></span> + <span><a href="https://twitter.com/OpenSciTalk/status/1268621662469017601" target="_blank"><i class="icon-heart-empty"></i> like</a></span> + </div> + </div> + </div> + +<div class="tweet-pagination pagination"> + + <ul> + + <li class="active"><a href="#">1</a></li> + + <li> + <a href="/articles/4375/tweets/?page=2" class="page">2</a> + </li> + + <li> + <a href="/articles/4375/tweets/?page=3" class="page">3</a> + </li> + + <li> + <a href="/articles/4375/tweets/?page=4" class="page">4</a> + </li> + + <li> + <a href="/articles/4375/tweets/?page=5" class="page">5</a> + </li> + + + <li> + <a href="/articles/4375/tweets/?page=2">Next</a> + </li> + </ul> + + <hr> +</div></div> +</div> + <div id="article-main-container"> + <div class="article-section-breadcrumb"> + <span class="icon-angle-left"></span> + <span><a href="/"><em>PeerJ</em></a></span> + </div> + + + <div class="hidden-print"> + + <div id="article-preexisting" class="well peerj-paper-well" > + <i class="icon-pushpin icon-large"></i> Note that a <a href="/preprints/3119/">Preprint of this article</a> also exists, first published August 2, 2017. + </div> + </div> + + <!-- Main article --> + <article itemscope="itemscope" itemtype="http://schema.org/ScholarlyArticle"><header class="article-meta front"><h1 class="article-title" itemprop="name headline">The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles</h1> +<div class="article-authors"> +<span class="contrib" itemscope="itemscope" itemtype="http://schema.org/Person" id="author-1" data-jats-contrib-type="author" data-jats-corresp="yes" data-jats-equal-contrib="yes" itemprop="author"><a href="author-1" rel="author" itemprop="url"><span class="name" itemprop="name"><span class="given-names" itemprop="givenName">Heather</span> <span class="surname" itemprop="familyName">Piwowar</span></span></a><a class="corresp" href="mailto:heather@impactstory.org" target="_blank" title="email the corresponding author" data-toggle="tooltip" itemprop="email"><i class="icon-envelope"></i></a><span class="equal-contribution" title="These authors contributed equally to this work." data-toggle="tooltip"><i class="icon-asterisk"></i></span><sup class="contrib-xref-group"><a class="aff xref" href="#aff-1" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-1">1</a></sup></span>, <span class="contrib" itemscope="itemscope" itemtype="http://schema.org/Person" id="author-2" data-jats-contrib-type="author" data-jats-corresp="yes" data-jats-equal-contrib="yes" itemprop="author"><a href="author-2" rel="author" itemprop="url"><span class="name" itemprop="name"><span class="given-names" itemprop="givenName">Jason</span> <span class="surname" itemprop="familyName">Priem</span></span></a><a class="corresp" href="mailto:jason@impactstory.org" target="_blank" title="email the corresponding author" data-toggle="tooltip" itemprop="email"><i class="icon-envelope"></i></a><span class="equal-contribution" title="These authors contributed equally to this work." data-toggle="tooltip"><i class="icon-asterisk"></i></span><sup class="contrib-xref-group"><a class="aff xref" href="#aff-1" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-1">1</a></sup></span>, <span class="contrib" itemscope="itemscope" itemtype="http://schema.org/Person" id="author-3" data-jats-contrib-type="author" itemprop="author"><a href="author-3" rel="author" itemprop="url"><span class="name" itemprop="name"><span class="given-names" itemprop="givenName">Vincent</span> <span class="surname" itemprop="familyName">Larivière</span></span></a><sup class="contrib-xref-group"><a class="aff xref" href="#aff-2" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-2">2</a>,<a class="aff xref" href="#aff-3" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-3">3</a></sup></span>, <span class="contrib" itemscope="itemscope" itemtype="http://schema.org/Person" id="author-4" data-jats-contrib-type="author" itemprop="author"><a href="author-4" rel="author" itemprop="url"><span class="name" itemprop="name"><span class="given-names" itemprop="givenName">Juan Pablo</span> <span class="surname" itemprop="familyName">Alperin</span></span></a><sup class="contrib-xref-group"><a class="aff xref" href="#aff-4" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-4">4</a>,<a class="aff xref" href="#aff-5" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-5">5</a></sup></span>, <span class="contrib" itemscope="itemscope" itemtype="http://schema.org/Person" id="author-5" data-jats-contrib-type="author" itemprop="author"><a href="author-5" rel="author" itemprop="url"><span class="name" itemprop="name"><span class="given-names" itemprop="givenName">Lisa</span> <span class="surname" itemprop="familyName">Matthias</span></span></a><sup class="contrib-xref-group"><a class="aff xref" href="#aff-6" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-6">6</a></sup></span>, <span class="contrib" itemscope="itemscope" itemtype="http://schema.org/Person" id="author-6" data-jats-contrib-type="author" itemprop="author"><a href="author-6" rel="author" itemprop="url"><span class="name" itemprop="name"><span class="given-names" itemprop="givenName">Bree</span> <span class="surname" itemprop="familyName">Norlander</span></span></a><sup class="contrib-xref-group"><a class="aff xref" href="#aff-7" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-7">7</a>,<a class="aff xref" href="#aff-8" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-8">8</a></sup></span>, <span class="contrib" itemscope="itemscope" itemtype="http://schema.org/Person" id="author-7" data-jats-contrib-type="author" itemprop="author"><a href="author-7" rel="author" itemprop="url"><span class="name" itemprop="name"><span class="given-names" itemprop="givenName">Ashley</span> <span class="surname" itemprop="familyName">Farley</span></span></a><sup class="contrib-xref-group"><a class="aff xref" href="#aff-7" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-7">7</a>,<a class="aff xref" href="#aff-8" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-8">8</a></sup></span>, <span class="contrib" itemscope="itemscope" itemtype="http://schema.org/Person" id="author-8" data-jats-contrib-type="author" itemprop="author"><a href="author-8" rel="author" itemprop="url"><span class="name" itemprop="name"><span class="given-names" itemprop="givenName">Jevin</span> <span class="surname" itemprop="familyName">West</span></span></a><sup class="contrib-xref-group"><a class="aff xref" href="#aff-7" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-7">7</a></sup></span>, <span class="contrib" itemscope="itemscope" itemtype="http://schema.org/Person" id="author-9" data-jats-contrib-type="author" itemprop="author"><a href="author-9" rel="author" itemprop="url"><span class="name" itemprop="name"><span class="given-names" itemprop="givenName">Stefanie</span> <span class="surname" itemprop="familyName">Haustein</span></span></a><sup class="contrib-xref-group"><a class="aff xref" href="#aff-3" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-3">3</a>,<a class="aff xref" href="#aff-9" itemprop="affiliation" itemscope="itemscope" itemtype="http://schema.org/Organization" itemref="aff-9">9</a></sup></span> +</div> +<div id="article-information"> +<div class="article-notes"> +<div itemscope="itemscope" itemtype="http://schema.org/Organization" id="aff-1"> +<span class="article-label-container"><a class="article-label">1</a></span><span itemprop="address"><span class="institution">Impactstory</span>, <span class="city">Sanford</span>, <span class="state">NC</span>, <span class="country">USA</span></span> +</div> +<div itemscope="itemscope" itemtype="http://schema.org/Organization" id="aff-2"> +<span class="article-label-container"><a class="article-label">2</a></span><span itemprop="address"><span class="institution">École de bibliothéconomie et des sciences de l’information, Université de Montréal</span>, <span class="city">Montréal</span>, <span class="state">QC</span>, <span class="country">Canada</span></span> +</div> +<div itemscope="itemscope" itemtype="http://schema.org/Organization" id="aff-3"> +<span class="article-label-container"><a class="article-label">3</a></span><span itemprop="address"><span class="institution">Observatoire des Sciences et des Technologies (OST), Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Université du Québec à Montréal</span>, <span class="city">Montréal</span>, <span class="state">QC</span>, <span class="country">Canada</span></span> +</div> +<div itemscope="itemscope" itemtype="http://schema.org/Organization" id="aff-4"> +<span class="article-label-container"><a class="article-label">4</a></span><span itemprop="address"><span class="institution">Canadian Institute for Studies in Publishing, Simon Fraser University</span>, <span class="city">Vancouver</span>, <span class="state">BC</span>, <span class="country">Canada</span></span> +</div> +<div itemscope="itemscope" itemtype="http://schema.org/Organization" id="aff-5"> +<span class="article-label-container"><a class="article-label">5</a></span><span itemprop="address"><span class="institution">Public Knowledge Project</span>, <span class="country">Canada</span></span> +</div> +<div itemscope="itemscope" itemtype="http://schema.org/Organization" id="aff-6"> +<span class="article-label-container"><a class="article-label">6</a></span><span itemprop="address"><span class="institution">Scholarly Communications Lab, Simon Fraser University</span>, <span class="city">Vancouver</span>, <span class="country">Canada</span></span> +</div> +<div itemscope="itemscope" itemtype="http://schema.org/Organization" id="aff-7"> +<span class="article-label-container"><a class="article-label">7</a></span><span itemprop="address"><span class="institution">Information School, University of Washington</span>, <span class="city">Seattle</span>, <span class="country">USA</span></span> +</div> +<div itemscope="itemscope" itemtype="http://schema.org/Organization" id="aff-8"> +<span class="article-label-container"><a class="article-label">8</a></span><span itemprop="address"><span class="institution">FlourishOA</span>, <span class="country">USA</span></span> +</div> +<div itemscope="itemscope" itemtype="http://schema.org/Organization" id="aff-9"> +<span class="article-label-container"><a class="article-label">9</a></span><span itemprop="address"><span class="institution">School of Information Studies, University of Ottawa</span>, <span class="city">Ottawa</span>, <span class="state">ON</span>, <span class="country">Canada</span></span> +</div> +</div> +<dl class="article-identifiers"> +<dt> DOI</dt> +<dd> +<a href="https://doi.org/10.7717/peerj.4375" itemprop="sameAs">10.7717/peerj.4375</a><meta itemprop="sameAs" content="info:doi/10.7717/peerj.4375"> +</dd> +</dl> +<dl class="article-dates"> +<dt>Published</dt> +<dd><time itemprop="datePublished">2018-02-13</time></dd> +<dt>Accepted</dt> +<dd><time data-itemprop="dateAccepted">2018-01-25</time></dd> +<dt>Received</dt> +<dd><time itemprop="dateCreated">2017-08-09</time></dd> +</dl> +<dl class="article-editors"> +<dt>Academic Editor</dt> +<dd itemprop="editor" itemscope="itemscope" itemtype="http://schema.org/Person"><a itemprop="url" href="editor-1" class="contrib" data-jats-contrib-type="editor"><span class="name" itemprop="name"><span class="given-names" itemprop="givenName">Robert</span> <span class="surname" itemprop="familyName">McDonald</span></span></a></dd> +</dl> +<dl class="article-subjects"> +<dt>Subject Areas</dt> +<dd> +<a class="subject" itemprop="about" href="/subjects/?filter=Legal%20Issues">Legal Issues</a>, <a class="subject" itemprop="about" href="/subjects/?filter=Science%20Policy">Science Policy</a>, <a class="subject" itemprop="about" href="/subjects/?filter=Data%20Science">Data Science</a> +</dd> +<dt>Keywords</dt> +<dd> +<span class="kwd" itemprop="keywords">Open access</span>, <span class="kwd" itemprop="keywords">Open science</span>, <span class="kwd" itemprop="keywords">Scientometrics</span>, <span class="kwd" itemprop="keywords">Publishing</span>, <span class="kwd" itemprop="keywords">Libraries</span>, <span class="kwd" itemprop="keywords">Scholarly communication</span>, <span class="kwd" itemprop="keywords">Bibliometrics</span>, <span class="kwd" itemprop="keywords">Science policy</span> +</dd> +</dl> +<dl class="article-license"> +<dt>Copyright</dt> +<dd>© <span itemprop="copyrightYear">2018</span> <span itemprop="copyrightHolder">Piwowar et al.</span> +</dd> +<dt>Licence</dt> +<dd> + <span class="license-p">This is an open access article distributed under the terms of the <a class="ext-link" href="http://creativecommons.org/licenses/by/4.0/" rel="license" data-jats-ext-link-type="uri">Creative Commons Attribution License</a>, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.</span> + </dd> +</dl> +<dl class="self-citation"> +<dt>Cite this article</dt> +<dd> +<span class="self-citation-authors">Piwowar H, Priem J, Larivière V, Alperin JP, Matthias L, Norlander B, Farley A, West J, Haustein S.</span> <span class="self-citation-year">2018</span>. <span class="self-citation-title">The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles</span>. <span itemprop="isPartOf" itemscope="itemscope" itemtype="http://schema.org/PublicationVolume"><span class="self-citation-journal" itemprop="isPartOf" itemscope="itemscope" itemtype="http://schema.org/Periodical"><span itemprop="name">PeerJ</span></span> <span class="self-citation-volume" itemprop="volumeNumber">6</span></span>:<span class="self-citation-elocation" itemprop="pageStart">e4375</span> <a href="https://doi.org/10.7717/peerj.4375" itemprop="url">https://doi.org/10.7717/peerj.4375</a> +</dd> +</dl> +<div class="alert alert-success view-public-reviews">The authors have chosen to make <a href="/articles/4375/reviews/">the review history of this article</a> public.</div> +</div> +<div> +<h2>Abstract</h2> +<div class="abstract" itemprop="description"> + <p>Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles. We use three samples, each of 100,000 articles, to investigate OA in three populations: (1) all journal articles assigned a Crossref DOI, (2) recent journal articles indexed in Web of Science, and (3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI. We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made free-to-read on the publisher website, without an explicit Open license. We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice.</p> + </div> +</div></header><main><div class="body" lang="en"> + <section class="sec" id="intro"> + <h2 class="heading">Introduction</h2> + <p id="p-1">The movement to provide open access (OA) to all research literature is now over fifteen years old. In the last few years, several developments suggest that after years of work, a sea change is imminent in OA. First, funding institutions are increasingly mandating OA publishing for grantees. In addition to the US National Institutes of Health, which mandated OA in 2008 (<a class="ext-link" href="https://publicaccess.nih.gov/index.htm" data-jats-ext-link-type="uri">https://publicaccess.nih.gov/index.htm</a>), the Bill and Melinda Gates Foundation (<a class="ext-link" href="http://www.gatesfoundation.org/How-We-Work/General-Information/Open-Access-Policy" data-jats-ext-link-type="uri">http://www.gatesfoundation.org/How-We-Work/General-Information/Open-Access-Policy</a>), the European Commission (<a class="ext-link" href="http://ec.europa.eu/research/participants/data/ref/h2020/grants_manual/hi/oa_pilot/h2020-hi-oa-pilot-guide_en.pdf" data-jats-ext-link-type="uri">http://ec.europa.eu/research/participants/data/ref/h2020/grants_manual/hi/oa_pilot/h2020-hi-oa-pilot-guide_en.pdf</a>), the US National Science Foundation (<a class="ext-link" href="https://www.nsf.gov/pubs/2015/nsf15052/nsf15052.pdf" data-jats-ext-link-type="uri">https://www.nsf.gov/pubs/2015/nsf15052/nsf15052.pdf</a>), and the Wellcome Trust (<a class="ext-link" href="https://wellcome.ac.uk/press-release/wellcome-trust-strengthens-its-open-access-policy" data-jats-ext-link-type="uri">https://wellcome.ac.uk/press-release/wellcome-trust-strengthens-its-open-access-policy</a>), among others, have made OA diffusion mandatory for grantees. Second, several tools have sprung up to build value atop the growing OA corpus. These include discovery platforms like ScienceOpen and 1Science, and browser-based extensions like the Open Access Button, Canary Haz, and Unpaywall. Third, Sci-Hub (a website offering pirate access to full text articles) has built an enormous user base, provoking newly intense conversation around the ethics and efficiency of paywall publishing (<a class="xref xref-bibr" href="https://doi.org/10.1126%2Fscience.352.6285.508" title="Who’s downloading pirated papers? Everyone" data-jats-ref-type="bibr" data-jats-rid="ref-13">Bohannon, 2016</a>; <a class="xref xref-bibr" href="https://doi.org/10.12688%2Ff1000research.11366.1" title="Looking into Pandora’s Box: the content of Sci-Hub and its usage [version 1; referees: 2 approved, 2 approved with reservations]" data-jats-ref-type="bibr" data-jats-rid="ref-26">Greshake, 2017</a>). Academic social networks like ResearchGate and Academia.edu now offer authors an increasingly popular but controversial solution to author self-archiving (<a class="xref xref-bibr" href="https://doi.org/10.1016%2Fj.joi.2016.08.002" title="Hybrid open access—a longitudinal study" data-jats-ref-type="bibr" data-jats-rid="ref-8">Björk, 2016a</a>; <a class="xref xref-bibr" href="https://doi.org/10.1002%2Fleap.1021" title="The open access movement at a crossroad: are the big publishers and academic social media taking over?" data-jats-ref-type="bibr" data-jats-rid="ref-9">Björk, 2016b</a>). Finally, the increasing growth in the cost of toll-access subscriptions, particularly via so-called “Big Deals” from publishers, has begun to force libraries and other institutions to initiate large-scale subscription cancellations; recent examples include Caltech, the University of Maryland, University of Konstanz, Université de Montréal, and the national system of Peru (<a class="xref xref-bibr" href="http://www.bib.umontreal.ca/communiques/20170504-DC-annulation-taylor-francis-va.htm" title="UdeM Libraries cancel Big Deal subscription to 2231 periodical titles published by Taylor & Francis Group" data-jats-ref-type="bibr" data-jats-rid="ref-48">Université de Montréal, 2017</a>; <a class="xref xref-bibr" href="https://doi.org/10.1038%2Fnature.2016.21223" title="Scientists in Germany, Peru and Taiwan to lose access to Elsevier journals" data-jats-ref-type="bibr" data-jats-rid="ref-41">Schiermeier & Mega, 2017</a>; <a class="xref xref-bibr" href="https://scholarlykitchen.sspnet.org/2017/05/01/wolf-finally-arrives-big-deal-cancelations-north-american-libraries/" title="When the wolf finally arrives: big deal cancelations in North American Libraries" data-jats-ref-type="bibr" data-jats-rid="ref-1">Anderson, 2017a</a>; <a class="xref xref-bibr" href="https://www.uni-konstanz.de/universitaet/aktuelles-und-medien/aktuelle-meldungen/aktuelles/aktuelles/teurer-als-die-wissenschaft-erlaubt/" title="Teurer als die Wissenschaft erlaubt" data-jats-ref-type="bibr" data-jats-rid="ref-47">Université Konstanz, 2014</a>). As the toll-access status quo becomes increasingly unaffordable, institutions are looking to OA as part of their “Plan B” to maintain access to essential literature (<a class="xref xref-bibr" href="http://www.ala.org/acrl/sites/ala.org.acrl/files/content/conferences/confsandpreconfs/2017/LeveragingtheGrowthofOpenAccess.pdf" title="Leveraging the growth of open access in library collection decision making" data-jats-ref-type="bibr" data-jats-rid="ref-3">Antelman, 2017</a>).</p> + <p id="p-2">Open access is thus provoking a new surge of investment, controversy, and relevance across a wide group of stakeholders. We may be approaching a moment of great importance in the development of OA, and indeed of the scholarly communication system. However, despite the recent flurry of development and conversation around OA, there is a need for large-scale, high-quality data on the growth and composition of the OA literature itself. In particular, there is a need for a data-driven “state of OA” overview that is (a) large-scale, (b) up-to-date, and (c) reproducible. This paper attempts to provide such an overview, using a new open web service called oaDOI that finds links to legally-available OA scholarly articles.<a class="xref xref-fn" href="#fn-1" data-jats-ref-type="fn" data-jats-rid="fn-1"><sup>1</sup></a> Building on data provided by the oaDOI service, we answer the following questions:</p> + <ol class="list" id="list-1" data-jats-list-type="order"> + <li class="list-item"> +<p id="p-4">What percentage of the scholarly literature is OA, and how does this percentage vary according to publisher, discipline, and publication year?</p> + </li> + <li class="list-item"> +<p id="p-5">Are OA papers more highly-cited than their toll-access counterparts?</p> + </li> + </ol> + <p id="p-6">The next section provides a brief review of the background literature for this paper, followed by a description of the datasets and methods used, as well as details on the definition and accuracy of the oaDOI categorization. Results are then presented, in turn, for each research question, and are followed by a general discussion and conclusions.</p> + </section> + <section class="sec"> + <h2 class="heading">Literature Review</h2> + <p id="p-7">Fifteen years of OA research have produced a significant body of literature, a complete review of which falls outside the scope of this paper (for recent, in-depth reviews, see <a class="xref xref-bibr" href="https://doi.org/10.12688%2Ff1000research.8460.3" title="The academic, economic and societal impacts of Open Access: an evidence-based review (version 3; referees: 3 approved, 2 approved with reservations)" data-jats-ref-type="bibr" data-jats-rid="ref-46">Tennant et al. (2016)</a> and <a class="xref xref-bibr" href="https://doi.org/10.7554%2FeLife.16800" title="How open science helps researchers succeed" data-jats-ref-type="bibr" data-jats-rid="ref-36">McKiernan et al. (2016)</a>. Here we instead briefly review three major topics from the OA literature: defining OA and its subtypes, assessing the prevalence of OA, and examining the relative citation impact of OA.</p> + <p id="p-8">Despite the large literature on OA, the term itself remains “somewhat fluid” (Antelman, 2004), making an authoritative definition challenging. The most influential definition of OA comes from the 2002 Budapest Open Access Initiative (BOAI), and defines OA as making content both <i>free to read</i> and <i>free to reuse</i>, requiring the opportunity of OA users to “crawl (articles) for indexing, pass them as data to software, or use them for any other lawful purpose.” In practice, the BOAI definition is roughly equivalent to the popular “CC-BY” Creative Commons license (<a class="xref xref-bibr" href="https://creativecommons.org/licenses/by/4.0/" title="Attribution 4.0 International (CC BY 4.0)" data-jats-ref-type="bibr" data-jats-rid="ref-19">Creative Commons, 2018</a>). However, a number of other sources prefer a less strict definition, requiring only that OA “makes the research literature free to read online” (<a class="xref xref-bibr" href="https://scholar.google.com/scholar_lookup?title=The%20nine%20flavours%20of%20open%20access%20scholarly%20publishing&author=Willinsky&publication_year=2003" title="The nine flavours of open access scholarly publishing" data-jats-ref-type="bibr" data-jats-rid="ref-51">Willinsky, 2003</a>), or that it is “digital, online, [and] free of charge.” (<a class="xref xref-bibr" href="https://scholar.google.com/scholar_lookup?title=Status%20of%20open%20access%20in%20the%20biomedical%20field%20in%202005&author=Matsubayashi&publication_year=2009" title="Status of open access in the biomedical field in 2005" data-jats-ref-type="bibr" data-jats-rid="ref-34">Matsubayashi et al., 2009</a>). Others have suggested it is more valuable to think of OA as a spectrum (<a class="xref xref-bibr" href="https://doi.org/10.1080%2F00987913.2016.1182672" title="Measuring the degrees of openness of scholarly journals with the open access spectrum (OAS) evaluation tool" data-jats-ref-type="bibr" data-jats-rid="ref-17">Chen & Olijhoek, 2016</a>).</p> + <p id="p-9">Researchers have identified a number of subtypes of OA; some of these have near-universal support, while others remain quite controversial. We will not attempt a comprehensive list of these, but instead note several that have particular relevance for the current study.</p> + <ul class="list" id="list-2" data-jats-list-type="bullet"> + <li class="list-item"> +<p id="p-10">Libre OA (<a class="xref xref-bibr" href="https://dash.harvard.edu/handle/1/4322580" title="Gratis and libre open access" data-jats-ref-type="bibr" data-jats-rid="ref-44">Suber, 2008</a>): extends user’s rights to read and also to reuse literature for purposes like automated crawling, archiving, or other purposes. The Libre OA definition is quite similar to the BOAI definition of OA.</p> + </li> + <li class="list-item"> +<p id="p-11">Gratis OA (<a class="xref xref-bibr" href="https://dash.harvard.edu/handle/1/4322580" title="Gratis and libre open access" data-jats-ref-type="bibr" data-jats-rid="ref-44">Suber, 2008</a>): in contrast to Libre, Gratis extends <i>only</i> rights to read articles.</p> + </li> + <li class="list-item"> +<p id="p-12">Gold OA: articles are published in an “OA journal,” a journal in which all articles are open directly on the journal website. In practice, OA journals are most often defined by their inclusion in the Directory of Open Access Journals (DOAJ) (<a class="xref xref-bibr" href="http://science-metrix.com/sites/default/files/science-metrix/publications/d_1.8_sm_ec_dg-rtd_proportion_oa_1996-2013_v11p.pdf" title="Proportion of open access papers published in peer-reviewed journals at the European and world levels–1996–2013" data-jats-ref-type="bibr" data-jats-rid="ref-5">Archambault et al., 2014</a>; <a class="xref xref-bibr" href="http://arxiv.org/abs/1206.3664" title="Green and gold open access percentages and growth, by discipline" data-jats-ref-type="bibr" data-jats-rid="ref-24">Gargouri et al., 2012</a>).</p> + </li> + <li class="list-item"> +<p id="p-13">Green OA: Green articles are published in a toll-access journal, but self-archived in an OA archive. These “OA archives” are either disciplinary repositories like ArXiv, or “institutional repositories (IRs) operated by universities, and the archived articles may be either the published versions, or electronic preprints (<a class="xref xref-bibr" href="https://doi.org/10.1080%2F00987913.2008.10765150" title="The access/impact problem and the green and gold roads to open access: an update" data-jats-ref-type="bibr" data-jats-rid="ref-28">Harnad et al., 2008</a>). Most Green OA articles do not meet the BOAI definition of OA since they do not extend reuse rights (making them Gratis OA).</p> + </li> + <li class="list-item"> +<p id="p-14">Hybrid OA: articles are published in a subscription journal but are immediately free to read under an open license, in exchange for an an article processing charge (APC) paid by authors (<a class="xref xref-bibr" href="https://doi.org/10.1241%2Fjohokanri.41.678" title="Free internet access to traditional journals" data-jats-ref-type="bibr" data-jats-rid="ref-50">Walker & Soichi, 1998</a>; <a class="xref xref-bibr" href="https://doi.org/10.1002%2Fasi.22856" title="Delayed open access: an overlooked high-impact category of openly available scientific literature" data-jats-ref-type="bibr" data-jats-rid="ref-32">Laakso & Björk, 2013</a>).</p> + </li> + <li class="list-item"> +<p id="p-15">Delayed OA: articles are published in a subscription journal, but are made free to read after an embargo period (<a class="xref xref-bibr" href="https://scholar.google.com/scholar_lookup?title=The%20access%20principle:%20the%20case%20for%20open%20access%20to%20research%20and%20scholarship&author=Willinsky&publication_year=2009" title="The access principle: the case for open access to research and scholarship" data-jats-ref-type="bibr" data-jats-rid="ref-52">Willinsky, 2009</a>; <a class="xref xref-bibr" href="https://doi.org/10.1002%2Fasi.22856" title="Delayed open access: an overlooked high-impact category of openly available scientific literature" data-jats-ref-type="bibr" data-jats-rid="ref-32">Laakso & Björk, 2013</a>).</p> + </li> + <li class="list-item"> +<p id="p-16">Academic Social Networks (ASN): Articles are shared by authors using commercial online social networks like ResearchGate and Academia.edu. While some include these in definitions of OA (<a class="xref xref-bibr" href="http://www.science-metrix.com/pdf/SM_EC_OA_Availability_2004-2011.pdf" title="Proportion of open access peer-reviewed papers at the European and world levels–2004–2011" data-jats-ref-type="bibr" data-jats-rid="ref-4">Archambault et al., 2013</a>; <a class="xref xref-bibr" href="https://doi.org/10.1002%2Fleap.1021" title="The open access movement at a crossroad: are the big publishers and academic social media taking over?" data-jats-ref-type="bibr" data-jats-rid="ref-9">Björk, 2016b</a>), others argue that content shared on ASNs is not OA at all. Unlike Green OA repositories, ASNs do not check for copyright compliance, and therefore as much as half their content is illegally posted and hosted (<a class="xref xref-bibr" href="https://doi.org/10.1007%2Fs11192-017-2291-4" title="Copyright compliance and infringement in ResearchGate full-text journal articles" data-jats-ref-type="bibr" data-jats-rid="ref-30">Jamali, 2017</a>). This raises concerns over the persistence of content, since, as was the case in October 2017, publishers can and do issue large-scale takedown notices to ASN ordering the removal of infringing content (<a class="xref xref-bibr" href="http://www.sciencemag.org/news/2017/10/publishers-take-researchgate-court-alleging-massive-copyright-infringement" title="Publishers take ResearchGate to court, alleging massive copyright infringement" data-jats-ref-type="bibr" data-jats-rid="ref-15">Chawla, 2017</a>). Others have raised questions about the sustainability and ethics of ASN services themselves (<a class="xref xref-bibr" href="http://osc.universityofcalifornia.edu/2015/12/a-social-networking-site-is-not-an-open-access-repository/index.html" title="A social networking site is not an open access repository" data-jats-ref-type="bibr" data-jats-rid="ref-22">Fortney & Gonder, 2015</a>). Due to these concerns, and inconsistent support from the literature, we exclude ASN-hosted content from our definition of OA.<a class="xref xref-fn" href="#fn-2" data-jats-ref-type="fn" data-jats-rid="fn-2"><sup>2</sup></a> </p> + </li> + <li class="list-item"> +<p id="p-18">“Black OA”: Articles shared on illegal pirate sites, primarily Sci-Hub and LibGen. Although (<a class="xref xref-bibr" href="https://doi.org/10.1002%2Fleap.1096" title="Gold, green, and black open access" data-jats-ref-type="bibr" data-jats-rid="ref-10">Björk, 2017</a>) labels these articles as a subtype of OA, the literature has nearly no support for including Sci-Hub articles in definitions of OA. Given this, we exclude Sci-Hub and LibGen content from our definition of OA.</p> + </li> + </ul> + <p id="p-19">Based on the consensus (and in some cases, lack of consensus) around these definitions and subtypes, we will use the following definition of OA in the remainder of this paper: <b>OA articles are free to read online, either on the publisher website or in an OA repository.</b></p> + <section class="sec"> + <h3 class="heading">Prevalence of OA</h3> + <p id="p-20">Many studies have estimated what proportion of the literature is available OA, including <a class="xref xref-bibr" href="https://doi.org/10.1371%2Fjournal.pone.0011273" title="Open access to the scientific journal literature: situation 2009" data-jats-ref-type="bibr" data-jats-rid="ref-12">Björk et al. (2010)</a>, <a class="xref xref-bibr" href="https://doi.org/10.1371%2Fjournal.pone.0020961" title="The development of open access journal publishing from 1993 to 2009" data-jats-ref-type="bibr" data-jats-rid="ref-33">Laakso et al. (2011)</a>, <a class="xref xref-bibr" href="https://doi.org/10.1186%2F1741-7015-10-124" title="Anatomy of open access publishing: a study of longitudinal development and internal structure" data-jats-ref-type="bibr" data-jats-rid="ref-31">Laakso & Björk (2012)</a>, <a class="xref xref-bibr" href="http://arxiv.org/abs/1206.3664" title="Green and gold open access percentages and growth, by discipline" data-jats-ref-type="bibr" data-jats-rid="ref-24">Gargouri et al. (2012)</a>, <a class="xref xref-bibr" href="http://www.science-metrix.com/pdf/SM_EC_OA_Availability_2004-2011.pdf" title="Proportion of open access peer-reviewed papers at the European and world levels–2004–2011" data-jats-ref-type="bibr" data-jats-rid="ref-4">Archambault et al. (2013)</a>, <a class="xref xref-bibr" href="http://science-metrix.com/sites/default/files/science-metrix/publications/d_1.8_sm_ec_dg-rtd_proportion_oa_1996-2013_v11p.pdf" title="Proportion of open access papers published in peer-reviewed journals at the European and world levels–1996–2013" data-jats-ref-type="bibr" data-jats-rid="ref-5">Archambault et al. (2014)</a> and <a class="xref xref-bibr" href="https://doi.org/10.1080%2F19322909.2013.795426" title="Journal article retrieval in an age of Open Access: how journal indexes indicate Open Access articles" data-jats-ref-type="bibr" data-jats-rid="ref-16">Chen (2013)</a>. We are not aware of any studies since 2014. The most recent two analyses estimate that more than 50% of papers are now freely available online, when one includes both OA and ASNs. <a class="xref xref-bibr" href="http://science-metrix.com/sites/default/files/science-metrix/publications/d_1.8_sm_ec_dg-rtd_proportion_oa_1996-2013_v11p.pdf" title="Proportion of open access papers published in peer-reviewed journals at the European and world levels–1996–2013" data-jats-ref-type="bibr" data-jats-rid="ref-5">Archambault et al. (2014)</a>, the most comprehensive study to date, estimates that of papers published between 2011 and 2013, 12% of articles could be retrieved from the journal website, 6% from repositories, and 31% by other mechanisms (including ASNs). <a class="xref xref-bibr" href="http://science-metrix.com/sites/default/files/science-metrix/publications/d_1.8_sm_ec_dg-rtd_proportion_oa_1996-2013_v11p.pdf" title="Proportion of open access papers published in peer-reviewed journals at the European and world levels–1996–2013" data-jats-ref-type="bibr" data-jats-rid="ref-5">Archambault et al. (2014)</a> also found that the availability of papers published between 1996 and 2011 increased by 4% between April 2013 and April 2014, noting that “backfilling” is a significant contributor to green OA. Their discipline-level analysis confirmed the findings of other studies, that the proportion of OA is relatively high in biomedical research and math, while notably low in engineering, chemistry, and the humanities.</p> + <p id="p-21">This <a class="xref xref-bibr" href="http://science-metrix.com/sites/default/files/science-metrix/publications/d_1.8_sm_ec_dg-rtd_proportion_oa_1996-2013_v11p.pdf" title="Proportion of open access papers published in peer-reviewed journals at the European and world levels–1996–2013" data-jats-ref-type="bibr" data-jats-rid="ref-5">Archambault et al. (2014)</a> study is of particular interest because it used automated web scraping to find and identify OA content; most earlier efforts have relied on laborious manual checking of the DOAJ, publisher webpages, Google, and/or Google Scholar (though see <a class="xref xref-bibr" href="http://arxiv.org/abs/cs/0606079" title="Ten-year cross-disciplinary comparison of the growth of open access and how it increases research citation impact" data-jats-ref-type="bibr" data-jats-rid="ref-27">Hajjem, Harnad & Gingras (2006)</a> for a notable early exception). By using automated methods, Archambault et al. were able to sample hundreds of thousands of articles, greatly improving statistical power and supporting more nuanced inferences. Moreover, by creating a system that indexes OA content, they address a major concern in the world of OA research; as <a class="xref xref-bibr" href="https://doi.org/10.1371%2Fjournal.pone.0020961" title="The development of open access journal publishing from 1993 to 2009" data-jats-ref-type="bibr" data-jats-rid="ref-33">Laakso et al. (2011)</a> observes: “A major challenge for research...has been the lack of comprehensive indexing for both OA journals and their articles.” The automated system of <a class="xref xref-bibr" href="http://science-metrix.com/sites/default/files/science-metrix/publications/d_1.8_sm_ec_dg-rtd_proportion_oa_1996-2013_v11p.pdf" title="Proportion of open access papers published in peer-reviewed journals at the European and world levels–1996–2013" data-jats-ref-type="bibr" data-jats-rid="ref-5">Archambault et al. (2014)</a> is very accurate—it only misclassifies a paper as OA 1% of the time, and finds about 75% of all OA papers that exist online, as per <a class="xref xref-bibr" href="https://digitalcommons.unl.edu/cgi/viewcontent.cgi?referer=https://www.google.com/&httpsredir=1&article=1028&context=scholcom" title="Research impact of paywalled versus open access papers" data-jats-ref-type="bibr" data-jats-rid="ref-6">Archambault et al. (2016)</a>. However, the algorithm is not able to distinguish Gold from Hybrid OA. More problematically for researchers, the database used in the study is not open online for use in follow-up research. Instead, the data has since been used to build the commercial subscription-access database 1science (<a class="ext-link" href="http://www.1science.com/oanumbr.html" data-jats-ext-link-type="uri">http://www.1science.com/oanumbr.html</a>).</p> + </section> + <section class="sec"> + <h3 class="heading">The open access citation advantage</h3> + <p id="p-22">Several dozen studies have compared the citation counts of OA articles and toll-access articles. Most of these have reported higher citation counts for OA, suggesting a so-called “open access citation advantage” (OACA); several annotated bibliographies have been created to track this literature (<a class="xref xref-bibr" href="http://sparceurope.org/what-we-do/open-access/sparc-europe-open-access-resources/open-access-citation-advantage-service-oaca/oaca-list/" title="The open access citation advantage: list of studies until 2015" data-jats-ref-type="bibr" data-jats-rid="ref-43">SPARC Europe, 2015</a>; <a class="xref xref-bibr" href="https://doi.org/10.5062%2FF4Q81B0W" title="Open access citation advantage: an annotated bibliography" data-jats-ref-type="bibr" data-jats-rid="ref-49">Wagner, 2010</a>; <a class="xref xref-bibr" href="https://www.scienceopen.com/search#%7B%22order%22%3A0%2C%22context%22%3A%7B%22collection%22%3A%7B%22id%22%3A%22996823e0-8104-4490-b26a-f2f733f810fb%22%2C%22kind%22%3A0%7D%2C%22kind%22%3A11%7D%2C%22kind%22%3A77%7D" title="The open access citation advantage" data-jats-ref-type="bibr" data-jats-rid="ref-45">Tennant, 2017</a>). The OACA is not universally supported. Many studies supporting the OACA have been criticised on methodological grounds (<a class="xref xref-bibr" href="https://doi.org/10.3163%2F1536-5050.99.3.008" title="The impact of free access to the scientific literature: a review of recent research" data-jats-ref-type="bibr" data-jats-rid="ref-21">Davis & Walters, 2011</a>), and an investigation using the randomized-control trial method failed to find evidence of an OACA (<a class="xref xref-bibr" href="https://doi.org/10.1096%2Ffj.11-183988" title="Open access, readership, citations: a randomized controlled trial of scientific journal publishing" data-jats-ref-type="bibr" data-jats-rid="ref-20">Davis, 2011</a>). However, recent investigations using robust methods have continued to observe an OACA. For instance, <a class="xref xref-bibr" href="https://doi.org/10.1111%2Fecin.12064" title="Identifying the effect of open access on citations using a panel of science journals" data-jats-ref-type="bibr" data-jats-rid="ref-35">McCabe & Snyder (2014)</a> used a complex statistical model to remove confounding effects of author selection (authors may selectively publish their higher-impact work as OA), reporting a small but meaningful 8% OACA. <a class="xref xref-bibr" href="http://science-metrix.com/sites/default/files/science-metrix/publications/d_1.8_sm_ec_dg-rtd_proportion_oa_1996-2013_v11p.pdf" title="Proportion of open access papers published in peer-reviewed journals at the European and world levels–1996–2013" data-jats-ref-type="bibr" data-jats-rid="ref-5">Archambault et al. (2014)</a> describe a 40% OACA in a massive sample of over one million articles using field-normalized citation rates. <a class="xref xref-bibr" href="https://doi.org/10.1371%2Fjournal.pone.0159614" title="The post-embargo open access citation advantage: it exists (probably), it’s modest (usually), and the rich get richer (of course)" data-jats-ref-type="bibr" data-jats-rid="ref-38">Ottaviani (2016)</a> used a natural experiment as articles (not selected by authors) emerged from embargoes to become OA, and reports a 19% OACA excluding the author self-selection bias for older articles outside their prime citation years.</p> + </section> + </section> + <section class="sec" id="methods"> + <h2 class="heading">Methods</h2> + <section class="sec"> + <h3 class="heading">OA determination</h3> + <section class="sec"> + <h4 class="heading">Classifications</h4> + <p id="p-23">We classify publications into two categories, OA and Closed. As described above, we define OA as <i>free to read online, either on the publisher website or in an OA repository</i>; all articles not meeting this definition were defined as Closed. We further divide the OA literature into one of four exclusive subcategories, resulting in a five-category classification system for articles:</p> + <ul class="list" id="list-3" data-jats-list-type="bullet"> + <li class="list-item"> +<p id="p-24"><b>Gold</b>: Published in an open-access journal that is indexed by the DOAJ.</p> + </li> + <li class="list-item"> +<p id="p-25"><b>Green</b>: Toll-access on the publisher page, but there is a free copy in an OA repository.</p> + </li> + <li class="list-item"> +<p id="p-26"><b>Hybrid</b>: Free under an open license in a toll-access journal.</p> + </li> + <li class="list-item"> +<p id="p-27"><b>Bronze</b>: Free to read on the publisher page, but without an clearly identifiable license.</p> + </li> + <li class="list-item"> +<p id="p-28"><b>Closed</b>: All other articles, including those shared only on an ASN or in Sci-Hub.</p> + </li> + </ul> + <p id="p-29">These categories are largely consistent with their use throughout the OA literature, although a few clarifications are useful. First, we (like many other OA studies) do not include ASN-hosted content as OA. Second, categories are exclusive, and publisher-hosted content takes precedence over self-archived content. This means that if an article is posted in both a Gold journal and an OA repository, we would classify it as Gold, not Green. Put another way, publisher-hosted content can “shadow” archived articles that would otherwise be Green. This definition of Green (“available in a repository but <i>not</i> available from the publisher”) is often used in the OA literature (including by Steven Harnad, the coiner of the Green and Gold terms <a class="xref xref-bibr" href="https://doi.org/10.1080%2F00987913.2008.10765150" title="The access/impact problem and the green and gold roads to open access: an update" data-jats-ref-type="bibr" data-jats-rid="ref-28">Harnad et al., 2008</a>), but this usage is not unanimous. Some studies allow a given article to be <i>both</i> Gold and Green; compared to these, our classification system does undercount Green. Hybrid articles share properties with Gold articles (both are free to read and are licensed for re-use), but differ in the venue of publication (i.e., Hybrid articles are published in journals not considered open access by the DOAJ) and in that Hybrid articles are not necessarily immediately available (i.e., they may only be freely available after an embargo). We also add a novel subcategory, Bronze. Bronze shares attributes of Gold and Hybrid; like both, Bronze OA articles are publisher-hosted. Unlike Gold OA, Bronze articles are not published in journals considered open access in the DOAJ. Unlike Hybrid, Bronze articles carry no license information. Although this lack of identifiable license may not be intentional, without an identifiable license, the articles are free to read but do not allow extended reuse rights beyond reading. It is also not clear if Bronze articles are temporarily or permanently available to read for free.</p> + <p id="p-30">Finally, we should add that, although our categories of choice reflect the OA literature, they do not necessarily reflect the more complex reality of scholarly publishing today. Organizations like SciELO and Redalyc in Latin America have been acting simultaneously as publishers and repositories and many of the articles found on their site do not fall neatly into the above categories (<a class="xref xref-bibr" href="https://scholar.google.com/scholar_lookup?title=The%20SciELO%20open%20access:%20a%20gold%20way%20from%20the%20south&author=Packer&publication_year=2010" title="The SciELO open access: a gold way from the south" data-jats-ref-type="bibr" data-jats-rid="ref-39">Packer, 2010</a>).</p> + </section> + <section class="sec"> + <h4 class="heading">The oaDOI system</h4> + <p id="p-31">We assigned the categories above by calling the oaDOI service with a DOI for each item. The oaDOI returns a link to a legally-available OA version of the article, when one is available (<a class="ext-link" href="https://oadoi.org/" data-jats-ext-link-type="uri">https://oadoi.org/</a>). It contains records for all 88 million Crossref DOIs.<a class="xref xref-fn" href="#fn-3" data-jats-ref-type="fn" data-jats-rid="fn-3"><sup>3</sup></a> The oaDOI service crawls, aggregates, normalizes, and verifies data from many sources including PMC (<a class="ext-link" href="https://www.ncbi.nlm.nih.gov/pmc/" data-jats-ext-link-type="uri">https://www.ncbi.nlm.nih.gov/pmc/</a>), BASE (<a class="ext-link" href="https://www.base-search.net/about/en/" data-jats-ext-link-type="uri">https://www.base-search.net/about/en/</a>), DOAJ (<a class="ext-link" href="https://doaj.org/" data-jats-ext-link-type="uri">https://doaj.org/</a>), and thousands of institutional repositories and publishers. The oaDOI system offers a fast, free API with no rate-limits, allowing it to support a variety of other services and tools. At the time of writing, oaDOI processes approximately 500,000 requests daily–roughly twice the daily uses of Sci-Hub<a class="xref xref-fn" href="#fn-4" data-jats-ref-type="fn" data-jats-rid="fn-4"><sup>4</sup></a> (<a class="xref xref-bibr" href="https://doi.org/10.1126%2Fscience.352.6285.508" title="Who’s downloading pirated papers? Everyone" data-jats-ref-type="bibr" data-jats-rid="ref-13">Bohannon, 2016</a>; <a class="xref xref-bibr" href="https://doi.org/10.7287%2Fpeerj.preprints.3100v1" title="Sci-Hub provides access to nearly all scholarly literature (No. e3100v1)" data-jats-ref-type="bibr" data-jats-rid="ref-29">Himmelstein et al., 2017</a>). The majority of this volume comes from around 700 academic libraries, who use oaDOI to help readers find articles where the library has no subscription access, addressing the discoverability problem (<a class="xref xref-bibr" href="https://doi.org/10.1080%2F19322909.2013.795426" title="Journal article retrieval in an age of Open Access: how journal indexes indicate Open Access articles" data-jats-ref-type="bibr" data-jats-rid="ref-16">Chen, 2013</a>). The oaDOI service also powers the Unpaywall browser extension, which helps readers to find legal OA copies of paywalled articles as they browse; Unpaywall currently has over 80,000 active users. The oaDOI codebase is open source, and the service is free and open via an open API.</p> + </section> + <section class="sec"> + <h4 class="heading">Accuracy of oaDOI</h4> + <p id="p-34">To assess the accuracy of our automated OA determination, a random subsample of 500 articles were chosen from our main “Crossref-DOI” sample, described below. We manually searched the internet for each article in our subsample to determine if the paper was freely available on the publisher’s website, or on another website, such as an institutional repository, an academic social networking site, or on a personal webpage. DOIs were resolved by appending the DOI to “<a class="ext-link" href="https://doi.org/" data-jats-ext-link-type="uri">https://doi.org/</a>”. If the full text was available through that link, articles were marked as being freely available from the publisher’s site. If articles required a subscription, the title of the article was entered into Google Scholar (GS) and into Google to find alternative versions (i.e., preprints or archived copies). If the fulltext was found on any publisher page or OA repository, these were marked as being freely available from an archive. If the only available open copy was hosted on an academic social network (like Academia.edu or ResearchGate), this was noted but for the sake of the study these were <i>not</i> counted as any category of OA, and were instead added to the “Closed” category;</p> + <p id="p-35">The performance of oaDOI is summarized below, compared to these manual accuracy checks. The complete dataset behind this summary is available in supplementary information. Using this data we calculated the recall and precision of the system. “Recall” asks the question, “when an article is open, how often does oaDOI correctly identify it as open?” The recall of the service is 77.0%, meaning that 77% of the truly open articles are correctly identified as open by oaDOI. “Precision” asks the question, “When oaDOI says an article is open, how often is it correct?” The precision of the system is 96.6%, meaning that 96.6% of the time that oaDOI reports an article is open, it really is open.</p> + <p id="p-36">These results can be roughly compared to the recall of 86.4% and precision of 99.1% reported by <a class="xref xref-bibr" href="http://science-metrix.com/sites/default/files/science-metrix/publications/d_1.8_sm_ec_dg-rtd_proportion_oa_1996-2013_v11p.pdf" title="Proportion of open access papers published in peer-reviewed journals at the European and world levels–1996–2013" data-jats-ref-type="bibr" data-jats-rid="ref-5">Archambault et al. (2014)</a> for their automated system. Their accuracy estimate was also calculated based on a sample of 500 data points, giving each estimate a margin of error of ±4.5 percentage points. The Archambault study used a narrower date window for their sample (starting in 1996, versus our Crossref-DOI sample which was not time restricted), resulting in a more homogeneous task, which may partially explain their somewhat better performance.</p> + <p id="p-37">The oaDOI service is optimized for high precision, rather than high recall. The very high precision of oaDOI means that any estimates derived from the database can be considered a <i>conservative</i> estimate of the actual percentage of open access in the literature. That is, we can safely assume that when oaDOI reports a certain percentage of open access, the real percentage is <i>at least</i> that high—and almost certainly higher given that recall was less than perfect. Put another way, oaDOI delivers very few false positives (where it mistakenly calls an article open), but a relatively high number of false negatives (where it mistakenly calls an article closed) (<a class="xref xref-table" href="#table-1" data-jats-ref-type="table" data-jats-rid="table-1">Table 1</a>). Future improvements to the system are planned that will improve recall while keeping precision high.</p> + <figure class="table-wrap" id="table-1"><div class="caption"> +<span class="caption-label">Table 1: </span> + <div class="title">Accuracy of the prototype version of the oaDOI service used in this study.</div> + </div> + + <div class="table-container"><table class="table table-bordered table-condensed table-hover"> + <colgroup> + <col> + <col> + <col> + <col> + </colgroup> + <thead> + <tr> + <th></th> + <th>oaDOI reports Open</th> + <th>oaDOI reports Closed</th> + <th>Manual count Total (ground truth)</th> + </tr> + </thead> + <tbody> + <tr> + <td>Open</td> + <td>144</td> + <td>43</td> + <td>187</td> + </tr> + <tr> + <td>Closed</td> + <td>5</td> + <td>308</td> + <td>313</td> + </tr> + <tr> + <td>Total</td> + <td>149</td> + <td>351</td> + <td style="text-align:left;;">500</td> + </tr> + </tbody> + </table></div> +<div class="object-id article-component-doi">DOI: <a href="https://doi.org/10.7717/peerj.4375/table-1" data-toggle="tooltip" title="Cite this object using this DOI">10.7717/peerj.4375/table-1</a> +</div> + </figure> + </section> + </section> + <section class="sec"> + <h3 class="heading">Study samples</h3> + <p id="p-38">Three samples of DOI-assigned scholarly resources are summarized in <a class="xref xref-table" href="#table-2" data-jats-ref-type="table" data-jats-rid="table-2">Table 2</a> and described further below.</p> + <section class="sec"> + <h4 class="heading">Crossref sample</h4> + <p id="p-39">The first sample, “Crossref-DOIs,” is a random sample of 100,000 journal articles with Crossref DOIs, across all publication years. There are approximately 88 million Crossref DOIs in total as of May 2017. In order to exclude books, datasets, and other non-article content, we sampled only items whose “type” was listed as “journal-article” in the Crossref API metadata; there are 66 million of these. To verify the accuracy of Crossref metadata, we manually checked 150 items assigned to type “journal-article,” and determined that 93% were indeed journal articles; the remaining 7% were mostly journal front-matter such as tables of content or instructions to authors.</p> + <figure class="table-wrap" id="table-2"><div class="caption"> +<span class="caption-label">Table 2: </span> + <div class="title">Summary of samples used in this study.</div> + </div> + + <div class="table-container"><table class="table table-bordered table-condensed table-hover table-text" data-jats-content-type="text"> + <colgroup> + <col> + <col> + <col> + <col> + <col> + </colgroup> + <thead> + <tr> + <th>Sample name</th> + <th>Sample size</th> + <th>Population sampled</th> + <th>Purpose</th> + <th>Population size</th> + </tr> + </thead> + <tbody> + <tr> + <td>Crossref-DOIs</td> + <td>100,000</td> + <td>All journal articles with Crossref DOIs, all years.</td> + <td>Estimate percentage of the literature that is OA.</td> + <td>66,560,153</td> + </tr> + <tr> + <td>WoS-DOIs</td> + <td>100,000</td> + <td>All citable WoS articles with DOIs, 2009–2015.</td> + <td>Estimate citation impact of recent OA papers, and also OA prevalence by discipline.</td> + <td>8,083,613</td> + </tr> + <tr> + <td>Unpaywall-DOIs</td> + <td>100,000</td> + <td>All articles accessed by Unpaywall users over a 1-week period in 2017.</td> + <td>Estimate percentage of OA experienced by users of the Unpaywall extension.</td> + <td>213,323</td> + </tr> + </tbody> + </table></div> +<div class="object-id article-component-doi">DOI: <a href="https://doi.org/10.7717/peerj.4375/table-2" data-toggle="tooltip" title="Cite this object using this DOI">10.7717/peerj.4375/table-2</a> +</div> + </figure> + <p id="p-40">The purpose of this sample is to roughly proxy the scholarly literature as a whole. As such, it has strengths and weaknesses. One weakness is that although Crossref includes information on citation counts and discipline categorization, we found these to be quite incomplete, and therefore not useful for the present study. Another is that researchers in the scientometrics and OA fields have largely relied on other indexes, particularly Scopus and Web of Science (WoS), to represent the literature as a whole; this makes our results more difficult to compare to previous work. Finally, DOIs are known to be less frequently assigned by publishers in certain disciplines (like humanities; <a class="xref xref-bibr" href="https://doi.org/10.1016%2Fj.joi.2015.11.008" title="Availability of digital object identifiers (DOIs) in web of science and scopus" data-jats-ref-type="bibr" data-jats-rid="ref-25">Gorraiz et al., 2016</a>), in certain geographic regions (particularly the developing world), and among older articles (<a class="xref xref-bibr" href="https://doi.org/10.1007%2Fs11192-016-2225-6" title="Availability of digital object identifiers in publications archived by PubMed" data-jats-ref-type="bibr" data-jats-rid="ref-14">Boudry & Chartron, 2017</a>); consequently, these segments will be underrepresented in our sample. This said, Scopus and WoS are also known to underrepresent important segments of the literature (<a class="xref xref-bibr" href="https://doi.org/10.1007%2Fs11192-015-1765-5" title="The journal coverage of Web of Science and Scopus: a comparative analysis" data-jats-ref-type="bibr" data-jats-rid="ref-37">Mongeon & Paul-Hus, 2016</a>), and so this failing is not limited to Crossref. Moreover, the Crossref sample has important advantages of its own over other indexes. While no sample of the scholarly literature will be complete in every regard, the Crossref index is more expansive than other sources: in July 2017 there were 67 million journal articles indexed in Crossref compared to 30 million in Scopus (<a class="ext-link" href="https://www.elsevier.com/solutions/scopus/content" data-jats-ext-link-type="uri">https://www.elsevier.com/solutions/scopus/content</a>). Also, Crossref has the advantage of being entirely free and open to use, while Scopus and WoS are subscription-access databases; this allows the study data to also be free and open, promoting replication and reuse of our results in further research. However, we did turn to the subscription-access WoS in order to answer questions about the discipline and citation counts of OA articles, since Crossref data is lacking in these areas.</p> + </section> + <section class="sec"> + <h4 class="heading">WoS sample</h4> + <p id="p-41">The second sample, “WoS-DOIs”, is a random sample of 100,000 journal articles with DOIs that are indexed by Web of Science. The sample was drawn from a local version of the WoS database at the Observatoire des sciences et des technologies (OST) at the Université du Québec à Montréal. Only articles that WoS defines as “citable items” are included in the sample; this excludes non-peer reviewed content such as editorial material and news items. This sample is restricted to articles published between 2009 and 2015, due to DOI availability constraints. The sample of 100,000 articles is randomly drawn from a population of 8 million articles and reviews with a DOI in WoS published between 2009 and 2015 as of May 2017.</p> + <p id="p-42">Because the WoS sample is restricted to certain publication years, due to availability of DOIs in the WoS database, this sample is unsuitable for estimating the proportion of the total literature that is OA. However, it is more useful than the Crossref sample in some ways: the WoS sample included accurate discipline information for each article (described below), and also citation counts. Therefore we use the WoS sample to assess OA prevalence by discipline and also the citation impact of recent OA papers. We do not encourage comparisons between the OA percentages in the WoS sample and the Crossref sample, because of large differences in the sampling frames.</p> + <p id="p-43">Documents in the WoS-DOIs sample were classified using the National Science Foundation (NSF) journal classification system. This system assigns every journal exactly one “discipline” (a high-level categorization) and exactly one “specialty” (a finer-grained categorization). Because this is a journal-level classification, all articles from a given journal are assigned the same discipline and specialty as the journal. A downside of this approach is that the system classifies multidisciplinary journals (e.g., Nature, PNAS, PLOS ONE) as “biomedical research”, despite their publishing many articles from other fields.<a class="xref xref-fn" href="#fn-5" data-jats-ref-type="fn" data-jats-rid="fn-5"><sup>5</sup></a> In these cases, we used a ground-up, article-by-article classification approach. Each article published in a list of multidisciplinary journals was assigned to the NSF specialty which appeared most frequently in its own reference list. In other words, papers published in multidisciplinary journals were classified at the article level (instead of at the journal level) to the subject area which they cite most frequently.<a class="xref xref-fn" href="#fn-6" data-jats-ref-type="fn" data-jats-rid="fn-6"><sup>6</sup></a> </p> + <p id="p-46">We assess the relative impact of open and closed articles, using citations as an indicator of their scholarly impact. There are several properties of articles, however, that can confound this kind of comparison. Chief among these are the article’s discipline (some fields are much more cited than others) and its age (older articles have had more time to gather citations). In order to address this, we computed a normalized expected number of citations for each article, based on its age and its NSF specialty, by comparing it to the average citations for similar articles.<a class="xref xref-fn" href="#fn-7" data-jats-ref-type="fn" data-jats-rid="fn-7"><sup>7</sup></a> </p> + <p id="p-48">Using this approach, each article receives an average relative citation (ARC). An ARC of 1.0 indicates that a document was cited according to expectations based on documents published in the same year and NSF specialty, while an ARC above or below 1.0 indicates that the citation impact was above or below world average, respectively. Using these field-normalized citation rates, citation impact can be compared across scientific disciplines as well as across years. We can also compute mean ARCs for groups of articles, like “all open articles” or “all closed articles”, allowing us to compare normalized impact between these two groups. Analyzing results on the level of NSF disciplines, data is not shown for the Humanities (<i>n</i> = 1,091) and Arts (<i>n</i> = 164), because they are underrepresented both in the Web of Science and in terms of DOI coverage.</p> + </section> + <section class="sec"> + <h4 class="heading">Unpaywall sample</h4> + <p id="p-49">The third sample, “Unpaywall-DOIs”, is a random sample of 100,000 articles accessed by users of the free, open-source Unpaywall browser extension, gathered over a one-week time window. We collected IP addresses and DOI requests made to the oaDOI service through the Unpaywall browser extension during the week of June 5–June 11, 2017. In that time period there were 374,703 total accesses, 213,323 unique DOIs, and 42,894 unique IP addresses gathered in total, from which 100,000 unique DOIs were randomly sampled.</p> + <p id="p-50">This sample was used to assess the prevalence of OA experienced by users of the Unpaywall extension (since Unpaywall uses oaDOI data to find OA). It is a convenience sample of what articles people are interested in reading, and thereby lets us roughly estimate the percent of this literature that is OA. The sample has serious limitations, however: we don’t know the demographics of Unpaywall users, and we are aware of a bias towards users from the US (as determined by the IP addresses). As such, we cannot accurately generalize the results by education level, discipline, or purpose in reading the scholarly literature.</p> + </section> + </section> + </section> + <section class="sec" id="results"> + <h2 class="heading">Results</h2> + <section class="sec"> + <h3 class="heading">RQ1. What percent of the literature is open access?</h3> + <section class="sec"> + <h4 class="heading">How much of the literature is OA?</h4> + <p id="p-51">We found 27.9% (95% CI [27.6–28.2]) of all DOI-assigned journal articles are OA, using the Crossref-DOI sample. Based on this, we estimate there are 18.6 million OA articles with Crossref DOIs (95% CI [18.4–18.8]). This is the total population of OA articles that can be identified and accessed by oaDOI. Given our finding (described in Methods above) that the oaDOI service finds 77% of OA compared to manual searches, we can further estimate that an additional 3.5 million articles are OA but not detectable by this version of oaDOI.</p> + <p id="p-52">People reading the literature using the Unpaywall browser extension encounter a significantly higher proportion of OA: we found that 47.0% (95% CI [46.7–47.3]) of the Unpaywall-accessed sample is open access. The main reason for this is article age: since this sample is based on the behavior of actual readers, it is disproportionately comprised of recent articles. In fact, half the accessed articles were published in the last 2 years. Recent articles are much more likely to be OA than their older counterparts (see Results ‘How does Open Access vary by year of publication?’ below).</p> + </section> + <section class="sec"> + <h4 class="heading">What types of Open Access are most common?</h4> + <p id="p-53">The proportion of OA by subtype is relatively similar across the samples, as shown in <a class="xref xref-fig" href="#fig-1" data-jats-ref-type="fig" data-jats-rid="fig-1">Fig. 1</a> and <a class="xref xref-table" href="#table-3" data-jats-ref-type="table" data-jats-rid="table-3">Table 3</a>. Green OA represents a relatively small percentage of OA articles in all three samples. This is partly because self-archived articles are only counted as Green where there is no publisher-hosted option available; that is, Green OA is sometimes “shadowed” by Gold, Bronze, or Hybrid articles. Bronze is the most common OA subtype in all the samples, which is particularly interesting given that few studies have highlighted its role. We manually inspected a small sample of Bronze articles in order to understand this subcategory more; we found that while many Bronze articles were Delayed OA from toll-access publishers, nearly half were hosted on journals that published 100% of content as free-to-read but were <i>not</i> listed on the DOAJ and did not formally license content (using CC-BY or any other license). Such journals might be better described as “Dark Gold” or “Hidden Gold” than Bronze. A more complete examination of Bronze falls outside the scope of this study, and therefore further investigation will be undertaken in future work.</p> + <figure class="fig" itemprop="image" itemscope="itemscope" itemtype="https://schema.org/ImageObject" id="fig-1"><div class="image-container"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-1-2x.jpg" title="View the full image" class="fresco" data-fresco-caption="Figure 1: Percent of articles by OA status, Crossref-DOIs sample vs Unpaywall-DOIs sample." data-fresco-group="figure" data-fresco-options="fit: 'width', ui: 'outside', thumbnails: false, loop: true, position: true, overflow: true, preload: false"><img class="graphic" src="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-1-1x.jpg" itemprop="contentUrl" sizes="(min-width: 1200px) 581px, (max-width: 1199px) and (min-width: 980px) 462px, (max-width: 979px) and (min-width: 768px) 347px, (max-width: 767px) calc(100vw - 50px)" srcset="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-1-2x.jpg 1200w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-1-1x.jpg 600w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-1-small.jpg 355w" data-image-id="fig-1" alt="Percent of articles by OA status, Crossref-DOIs sample vs Unpaywall-DOIs sample." data-full="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-1-full.png" data-thumb="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-1-thumb.jpg" data-original="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-1.png" data-image-type="figure" data-jats-mimetype="image" data-jats-mime-subtype="png" width="600" height="230"></a></div> +<figcaption itemprop="description"> + <h5 class="heading"> +<span class="caption-label">Figure 1: </span>Percent of articles by OA status, Crossref-DOIs sample vs Unpaywall-DOIs sample.</h5> + <div class="figcaption-footer"> +<div class="article-image-download"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-1-full.png" class="btn btn-mini" download="peerj-4375-fig-1.png" itemprop="url"><i class="icon-large icon-picture"> </i> Download full-size image</a></div> +<div class="object-id article-component-doi">DOI: <a href="https://doi.org/10.7717/peerj.4375/fig-1" data-toggle="tooltip" title="Cite this object using this DOI">10.7717/peerj.4375/fig-1</a> +</div> +</div></figcaption></figure> + <figure class="table-wrap" id="table-3"><div class="caption"> +<span class="caption-label">Table 3: </span> + <div class="title">Percent of the literature that is OA, by type, in three samples of 100,000 journal articles, with 95% confidence intervals.</div> + </div> + + <div class="table-container"><table class="table table-bordered table-condensed table-hover"> + <colgroup> + <col> + <col> + <col> + <col> + <col> + <col> + <col> + </colgroup> + <thead> + <tr> + <th>Access type</th> + <th style="text-align:center;" colspan="2">Crossref-DOI All journal articles with Crossref DOIs, all years. (“Articles with DOIs” in <a class="xref xref-fig" href="#fig-1" data-jats-ref-type="fig" data-jats-rid="fig-1">Fig. 1</a>)</th> + <th style="text-align:center;" colspan="2">WoS-DOIs All citable WoS articles with DOIs, 2009–2015</th> + <th style="text-align:center;" colspan="2">Unpaywall-DOIs All articles accessed by Unpaywall users over a 1-week period in 2017</th> + </tr> + <tr> + <th></th> + <th>Estimate</th> + <th>95% CI</th> + <th>Estimate</th> + <th>95% CI</th> + <th>Estimate</th> + <th>95% CI</th> + </tr> + </thead> + <tbody> + <tr> + <td>OA (all types)</td> + <td>27.9%</td> + <td>27.6–28.2</td> + <td>36.1%</td> + <td>36.0–36.2</td> + <td>47.0%</td> + <td>46.7–47.3</td> + </tr> + <tr> + <td>Bronze OA</td> + <td>16.2%</td> + <td>16.0–16.5</td> + <td>12.9%</td> + <td>12.6–13.2</td> + <td>15.3%</td> + <td>15.0–15.6</td> + </tr> + <tr> + <td>Hybrid OA</td> + <td>3.6%</td> + <td>3.3–3.9</td> + <td>4.3%</td> + <td>4.0–4.6</td> + <td>8.3%</td> + <td>8.0–8.6</td> + </tr> + <tr> + <td>Gold OA</td> + <td>3.2%</td> + <td>2.9–3.5</td> + <td>7.4%</td> + <td>7.1–7.7</td> + <td>14.3%</td> + <td>14.0–14.6</td> + </tr> + <tr> + <td>Green OA</td> + <td>4.8%</td> + <td>4.5–5.1</td> + <td>11.5%</td> + <td>11.2–11.8</td> + <td>9.1%</td> + <td>8.8–9.4</td> + </tr> + <tr> + <td>Closed</td> + <td>72.0%</td> + <td>71.8–72.4</td> + <td>63.9%</td> + <td>63.8–64.0</td> + <td>53.0%</td> + <td>52.7–53.3</td> + </tr> + </tbody> + </table></div> +<div class="object-id article-component-doi">DOI: <a href="https://doi.org/10.7717/peerj.4375/table-3" data-toggle="tooltip" title="Cite this object using this DOI">10.7717/peerj.4375/table-3</a> +</div> + </figure> + </section> + <section class="sec"> + <h4 class="heading">How does Open Access vary by year of publication?</h4> + <p id="p-54"><a class="xref xref-fig" href="#fig-2" data-jats-ref-type="fig" data-jats-rid="fig-2">Figure 2</a> presents the number (<a class="xref xref-fig" href="#fig-2" data-jats-ref-type="fig" data-jats-rid="fig-2">Fig. 2A</a>) and proportion (<a class="xref xref-fig" href="#fig-2" data-jats-ref-type="fig" data-jats-rid="fig-2">Fig. 2B</a>) of papers by access category and publication date. Articles published in the last 20 years are increasingly OA, and this trend shows no sign of slowing. More recent articles are more likely to be OA, with the most recent year examined also containing the most OA: 44.7% of 2015 articles are OA (95% CI [43.3–46.2%]), including 17.6% Bronze (95% CI [16.2–19.1]), 9.4% Hybrid (95% CI [8.0–10.9]), 11.3% Gold (95% CI [9.9–12.8]), and 6.3% Green (95% CI [4.9–7.8]). Well over one million OA papers were published in 2015. This growth trend has largely been driven by dramatic growth in Gold and Hybrid OA since the year 2000. However, more than 20% of papers published before the digital age are also freely available. The majority of these older OA papers are Bronze, and based on their age they are probably more precisely Delayed OA, although additional investigation will be required to confirm this. Bronze OA remains remarkably constant as a proportion of the literature for all publication years examined.</p> + <figure class="fig" itemprop="image" itemscope="itemscope" itemtype="https://schema.org/ImageObject" id="fig-2"><div class="image-container"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-2-2x.jpg" title="View the full image" class="fresco" data-fresco-caption="Figure 2: Number of articles (A) and proportion of articles (B) with OA copies, estimated based on a random sample of 100,000 articles with Crossref DOIs." data-fresco-group="figure" data-fresco-options="fit: 'width', ui: 'outside', thumbnails: false, loop: true, position: true, overflow: true, preload: false"><img class="graphic" src="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-2-1x.jpg" itemprop="contentUrl" sizes="(min-width: 1200px) 581px, (max-width: 1199px) and (min-width: 980px) 462px, (max-width: 979px) and (min-width: 768px) 347px, (max-width: 767px) calc(100vw - 50px)" srcset="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-2-2x.jpg 1200w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-2-1x.jpg 600w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-2-small.jpg 355w" data-image-id="fig-2" alt="Number of articles (A) and proportion of articles (B) with OA copies, estimated based on a random sample of 100,000 articles with Crossref DOIs." data-full="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-2-full.png" data-thumb="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-2-thumb.jpg" data-original="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-2.png" data-image-type="figure" data-jats-mimetype="image" data-jats-mime-subtype="png" width="600" height="216"></a></div> +<figcaption itemprop="description"> + <h5 class="heading"> +<span class="caption-label">Figure 2: </span>Number of articles (A) and proportion of articles (B) with OA copies, estimated based on a random sample of 100,000 articles with Crossref DOIs.</h5> + <div class="figcaption-footer"> +<div class="article-image-download"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-2-full.png" class="btn btn-mini" download="peerj-4375-fig-2.png" itemprop="url"><i class="icon-large icon-picture"> </i> Download full-size image</a></div> +<div class="object-id article-component-doi">DOI: <a href="https://doi.org/10.7717/peerj.4375/fig-2" data-toggle="tooltip" title="Cite this object using this DOI">10.7717/peerj.4375/fig-2</a> +</div> +</div></figcaption></figure> + <p id="p-55">The number and proportion of Green papers must be interpreted with particular caution, due to several factors. First, unlike publisher-hosted OA (Gold, Bronze, and Hybrid), the date when the Green article <i>became open</i> is generally different from the date the article was <i>first published</i>. Authors often self-archive articles years after (or before, in the case of preprints) their original publication, leading to so-called “backfilling” of Green stocks (<a class="xref xref-bibr" href="http://science-metrix.com/sites/default/files/science-metrix/publications/d_1.8_sm_ec_dg-rtd_proportion_oa_1996-2013_v11p.pdf" title="Proportion of open access papers published in peer-reviewed journals at the European and world levels–1996–2013" data-jats-ref-type="bibr" data-jats-rid="ref-5">Archambault et al., 2014</a>). Consequently, the graph cannot show the growth of Green OA over time; this would require longitudinal analysis over several years, and so is outside the scope of this analysis. Instead it shows the number and proportion of Green OA by publication year of the article. Second, many articles cannot be legally self-archived until a certain number of months after publication; this embargoing likely influences the apparent plateau in Green shown in <a class="xref xref-fig" href="#fig-2" data-jats-ref-type="fig" data-jats-rid="fig-2">Fig. 2</a>. Finally, as noted earlier, many self-archived articles would otherwise be Green except for being “shadowed” by a Gold, Bronze, or Hybrid of the same article elsewhere. For more detail on the growth of shadowed Green OA, see <a class="xref xref-supplementary-material" href="#supp-1" data-jats-ref-type="supplementary-material" data-jats-rid="supp-1">Figs. SA2</a> and <a class="xref xref-supplementary-material" href="#supp-1" data-jats-ref-type="supplementary-material" data-jats-rid="supp-1">SA3</a>.</p> + </section> + <section class="sec"> + <h4 class="heading">How does Open Access vary by publisher?</h4> + <p id="p-56">We analyzed a subset of the Crossref-DOIs sample by publisher (as listed on the Crossref metadata record) to understand how the extent and types of OA are common across publishers for recent publications (between 2009 and 2015). As we can see in <a class="xref xref-fig" href="#fig-3" data-jats-ref-type="fig" data-jats-rid="fig-3">Fig. 3A</a>, the largest publishers by volume publish the most OA articles by volume, led by Elsevier. As a proportion of all articles published (<a class="xref xref-fig" href="#fig-3" data-jats-ref-type="fig" data-jats-rid="fig-3">Fig. 3B</a>), however, PLOS and Hindawi distinguish themselves as being the only publishers in the top 20 with 100% OA. More than half of the papers published by Oxford University Press, Nature Publishing Group, IOP Publishing, and the American Physical Society (APS) are freely available online. In the case of APS this is largely driven by content available through repositories such as arXiv (for more details on repositories, see <a class="xref xref-supplementary-material" href="#supp-1" data-jats-ref-type="supplementary-material" data-jats-rid="supp-1">Fig. SA1</a>).</p> + <figure class="fig" itemprop="image" itemscope="itemscope" itemtype="https://schema.org/ImageObject" id="fig-3"><div class="image-container"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-3-2x.jpg" title="View the full image" class="fresco" data-fresco-caption="Figure 3: Number (A) and proportion (B) of articles with OA copies, by publisher, for the 20 most prolific publishers. Based on sample of 27,894 Crossref DOI-assigned articles published between 2009–2015." data-fresco-group="figure" data-fresco-options="fit: 'width', ui: 'outside', thumbnails: false, loop: true, position: true, overflow: true, preload: false"><img class="graphic" src="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-3-1x.jpg" itemprop="contentUrl" sizes="(min-width: 1200px) 581px, (max-width: 1199px) and (min-width: 980px) 462px, (max-width: 979px) and (min-width: 768px) 347px, (max-width: 767px) calc(100vw - 50px)" srcset="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-3-2x.jpg 1200w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-3-1x.jpg 600w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-3-small.jpg 355w" data-image-id="fig-3" alt="Number (A) and proportion (B) of articles with OA copies, by publisher, for the 20 most prolific publishers. Based on sample of 27,894 Crossref DOI-assigned articles published between 2009–2015." data-full="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-3-full.png" data-thumb="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-3-thumb.jpg" data-original="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-3.png" data-image-type="figure" data-jats-mimetype="image" data-jats-mime-subtype="png" width="600" height="282"></a></div> +<figcaption itemprop="description"> + <h5 class="heading"> +<span class="caption-label">Figure 3: </span>Number (A) and proportion (B) of articles with OA copies, by publisher, for the 20 most prolific publishers. Based on sample of 27,894 Crossref DOI-assigned articles published between 2009–2015.</h5> + <div class="figcaption-footer"> +<div class="article-image-download"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-3-full.png" class="btn btn-mini" download="peerj-4375-fig-3.png" itemprop="url"><i class="icon-large icon-picture"> </i> Download full-size image</a></div> +<div class="object-id article-component-doi">DOI: <a href="https://doi.org/10.7717/peerj.4375/fig-3" data-toggle="tooltip" title="Cite this object using this DOI">10.7717/peerj.4375/fig-3</a> +</div> +</div></figcaption></figure> + </section> + <section class="sec"> + <h4 class="heading">How does Open Access vary across disciplines?</h4> + <p id="p-57">We used the WoS-DOIs sample to examine OA prevalence differences by discipline, because of the easy availability of discipline metadata in the WoS index. <a class="xref xref-fig" href="#fig-4" data-jats-ref-type="fig" data-jats-rid="fig-4">Figure 4</a> displays our results. More than half of the publications are freely available in biomedical research and mathematics, while in chemistry and engineering & technology less than 20% of the papers are freely available. <a class="xref xref-fig" href="#fig-4" data-jats-ref-type="fig" data-jats-rid="fig-4">Figure 4</a> also highlights the popularity of Green OA in disciplines like physics and mathematics, where more than one fifth of papers are available only through online repositories (mainly arXiv). Hybrid articles are particularly prevalent in mathematics (9.4%), biomedical research (8.1%) and clinical medicine (6.3%), while authors in biomedical research (15.3%), health (11.7%), mathematics (11.2%) and clinical medicine (10.3%) often publish in Gold journals.</p> + <figure class="fig" itemprop="image" itemscope="itemscope" itemtype="https://schema.org/ImageObject" id="fig-4"><div class="image-container"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-4-2x.jpg" title="View the full image" class="fresco" data-fresco-caption="Figure 4: Percentage of different access types of a random sample of WoS articles and reviews with a DOI published between 2009 and 2015 per NSF discipline (excluding Arts and Humanities)." data-fresco-group="figure" data-fresco-options="fit: 'width', ui: 'outside', thumbnails: false, loop: true, position: true, overflow: true, preload: false"><img class="graphic" src="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-4-1x.jpg" itemprop="contentUrl" sizes="(min-width: 1200px) 581px, (max-width: 1199px) and (min-width: 980px) 462px, (max-width: 979px) and (min-width: 768px) 347px, (max-width: 767px) calc(100vw - 50px)" srcset="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-4-2x.jpg 1200w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-4-1x.jpg 600w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-4-small.jpg 355w" data-image-id="fig-4" alt="Percentage of different access types of a random sample of WoS articles and reviews with a DOI published between 2009 and 2015 per NSF discipline (excluding Arts and Humanities)." data-full="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-4-full.png" data-thumb="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-4-thumb.jpg" data-original="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-4.png" data-image-type="figure" data-jats-mimetype="image" data-jats-mime-subtype="png" width="600" height="241"></a></div> +<figcaption itemprop="description"> + <h5 class="heading"> +<span class="caption-label">Figure 4: </span>Percentage of different access types of a random sample of WoS articles and reviews with a DOI published between 2009 and 2015 per NSF discipline (excluding Arts and Humanities).</h5> + <div class="figcaption-footer"> +<div class="article-image-download"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-4-full.png" class="btn btn-mini" download="peerj-4375-fig-4.png" itemprop="url"><i class="icon-large icon-picture"> </i> Download full-size image</a></div> +<div class="object-id article-component-doi">DOI: <a href="https://doi.org/10.7717/peerj.4375/fig-4" data-toggle="tooltip" title="Cite this object using this DOI">10.7717/peerj.4375/fig-4</a> +</div> +</div></figcaption></figure> + <p id="p-58">Large variations can also be observed on the more detailed level of NSF specialties (<a class="xref xref-supplementary-material" href="#supp-1" data-jats-ref-type="supplementary-material" data-jats-rid="supp-1">Fig. SA5</a>). At more than 80% of OA articles, astronomy & astrophysics (87%), fertility (86%), tropical medicine (84%), and embryology (83%) were the specialties where access to literature was the most open. At the other end of the spectrum are pharmacy (7%), inorganic & nuclear chemistry (7%), and chemical engineering (9%), where publications were hidden behind a paywall for more than 90% of papers. More detail on these and other NSF specialties can be seen in <a class="xref xref-supplementary-material" href="#supp-1" data-jats-ref-type="supplementary-material" data-jats-rid="supp-1">Fig. SA1</a>.</p> + </section> + </section> + <section class="sec"> + <h3 class="heading">RQ2. What is the scholarly impact of open access?</h3> + <p id="p-59">Comparing the average relative citation impact of different access categories, the OACA is corroborated: Papers hidden behind a paywall were cited 10% below world average (ARC = 0.90), while those that are freely available obtain, on average, 18% more citations than what is expected (ARC = 1.18). However, citation impact differs between the different manners in which papers are made available for free: those that are only available as Green OA (ARC = 1.33) and Hybrid OA papers (ARC = 1.31) are cited the most with an impact of more than 30% above expectations, those available as Bronze are cited 22% above world average, while papers published as Gold OA obtain an ARC of 0.83. This constitutes an average relative citation impact of 17% below world average and 9% below that of articles hidden behind a paywall. <a class="xref xref-fig" href="#fig-5" data-jats-ref-type="fig" data-jats-rid="fig-5">Figure 5</a> below describes these findings.</p> + <figure class="fig" itemprop="image" itemscope="itemscope" itemtype="https://schema.org/ImageObject" id="fig-5"><div class="image-container"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-5-2x.jpg" title="View the full image" class="fresco" data-fresco-caption="Figure 5: Average relative citations of different access types of a random sample of WoS articles and reviews with a DOI published between 2009 and 2015." data-fresco-group="figure" data-fresco-options="fit: 'width', ui: 'outside', thumbnails: false, loop: true, position: true, overflow: true, preload: false"><img class="graphic" src="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-5-1x.jpg" itemprop="contentUrl" sizes="(min-width: 1200px) 581px, (max-width: 1199px) and (min-width: 980px) 462px, (max-width: 979px) and (min-width: 768px) 347px, (max-width: 767px) calc(100vw - 50px)" srcset="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-5-2x.jpg 1200w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-5-1x.jpg 600w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-5-small.jpg 355w" data-image-id="fig-5" alt="Average relative citations of different access types of a random sample of WoS articles and reviews with a DOI published between 2009 and 2015." data-full="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-5-full.png" data-thumb="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-5-thumb.jpg" data-original="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-5.png" data-image-type="figure" data-jats-mimetype="image" data-jats-mime-subtype="png" width="600" height="388"></a></div> +<figcaption itemprop="description"> + <h4 class="heading"> +<span class="caption-label">Figure 5: </span>Average relative citations of different access types of a random sample of WoS articles and reviews with a DOI published between 2009 and 2015.</h4> + <div class="figcaption-footer"> +<div class="article-image-download"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-5-full.png" class="btn btn-mini" download="peerj-4375-fig-5.png" itemprop="url"><i class="icon-large icon-picture"> </i> Download full-size image</a></div> +<div class="object-id article-component-doi">DOI: <a href="https://doi.org/10.7717/peerj.4375/fig-5" data-toggle="tooltip" title="Cite this object using this DOI">10.7717/peerj.4375/fig-5</a> +</div> +</div></figcaption></figure> + <p id="p-60">These trends vary over time, however, as shown in <a class="xref xref-fig" href="#fig-6" data-jats-ref-type="fig" data-jats-rid="fig-6">Fig. 6</a>. While the ARC of closed access papers remains below world average throughout the period studied, it increased from .86 in 2009 to .93 over in 2014 and 2015. Meanwhile, when looking across all open types, the mean citation rate is consistently above the world average, fluctuating between 1.15 and 1.22. This fluctuation is guided by differences between the access types, with the impact of Hybrid OA papers increasing over the time period. While Green OA papers’ mean citation rate remain relatively stable, the highest impact, for 2015, is obtained by Bronze and Hybrid. The only form of open for which mean impact has decreased steadily over time is Gold. The results for more recent years are only based on a short citation window, however, and results might change over the next years as citations accumulate.</p> + <figure class="fig" itemprop="image" itemscope="itemscope" itemtype="https://schema.org/ImageObject" id="fig-6"><div class="image-container"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-6-2x.jpg" title="View the full image" class="fresco" data-fresco-caption="Figure 6: Percentage and impact of different access types of a random sample of WoS articles and reviews with a DOI, by year of publication." data-fresco-group="figure" data-fresco-options="fit: 'width', ui: 'outside', thumbnails: false, loop: true, position: true, overflow: true, preload: false"><img class="graphic" src="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-6-1x.jpg" itemprop="contentUrl" sizes="(min-width: 1200px) 581px, (max-width: 1199px) and (min-width: 980px) 462px, (max-width: 979px) and (min-width: 768px) 347px, (max-width: 767px) calc(100vw - 50px)" srcset="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-6-2x.jpg 1200w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-6-1x.jpg 600w, https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-6-small.jpg 355w" data-image-id="fig-6" alt="Percentage and impact of different access types of a random sample of WoS articles and reviews with a DOI, by year of publication." data-full="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-6-full.png" data-thumb="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-6-thumb.jpg" data-original="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-6.png" data-image-type="figure" data-jats-mimetype="image" data-jats-mime-subtype="png" width="600" height="465"></a></div> +<figcaption itemprop="description"> + <h4 class="heading"> +<span class="caption-label">Figure 6: </span>Percentage and impact of different access types of a random sample of WoS articles and reviews with a DOI, by year of publication.</h4> + <div class="figcaption-footer"> +<div class="article-image-download"><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/fig-6-full.png" class="btn btn-mini" download="peerj-4375-fig-6.png" itemprop="url"><i class="icon-large icon-picture"> </i> Download full-size image</a></div> +<div class="object-id article-component-doi">DOI: <a href="https://doi.org/10.7717/peerj.4375/fig-6" data-toggle="tooltip" title="Cite this object using this DOI">10.7717/peerj.4375/fig-6</a> +</div> +</div></figcaption></figure> + </section> + </section> + <section class="sec"> + <h2 class="heading">Discussion and Conclusion</h2> + <p id="p-61">Access to scholarly literature is at the heart of current debates in the research community. Research funders are increasingly mandating OA dissemination to their grantees while, at the same time, the growth in toll-access subscriptions costs have prompted more and more university libraries to cancel subscriptions. In this context, several tools have been developed to provide access–both legally and illegally–to scholarly literature. Using data from one of these tools (oaDOI), this paper addresses two broad research questions: what percent of the literature is OA and how does it vary by type of OA, and what is the mean scholarly impact of papers diffused through this form. Three large samples were used, to assess different aspects of OA patterns: (1) 100,000 articles that have a Crossref DOIs, which allows us to assess the relative proportion of OA across all existing literature; (2) 100,000 WoS-indexed journals articles that have a DOI, which allows us to assess the scholarly impact of OA and non OA papers; (3) 100,000 articles accessed by users through the Unpaywall browser extension, which lets us assess the proportion of OA papers found by users of this free tool.</p> + <p id="p-62">We found that 28% of all journal articles are freely available online (Crossref-DOI sample). Encouragingly for proponents of OA, this proportion has been growing steadily over the last 20 years, driven particularly by growth in Gold and Hybrid. Articles from 2015, the most recent year examined, had the highest proportion OA (45%), as well as the largest absolute number of OA articles published in a single year. This disproportionate level of OA in recent years, combined with readers’ preference for more recent articles, leads to a felicitous situation for readers: the proportion of OA they <i>experience</i> as they browse and search is better than the overall percentage of OA across the literature as a whole. Users of the Unpaywall browser extension, which gives individual readers access to the oaDOI service, encounter OA articles nearly half (47%) of the time. The effect almost certainly extends beyond Unpaywall users; one may assume readers in general also favor newer articles, and therefore benefit from the growth of Gold, Bronze, and Hybrid OA among recent papers, even without using Unpaywall. More studies of readership data from other sources would be useful to quantify this further.</p> + <p id="p-63">Interestingly, we found that the majority of OA articles are Bronze–hosted on publisher websites, either without a license at all or without an open license. This is surprisingly high given that Bronze is relatively little-discussed in the OA literature, and suggests that this OA category deserves further attention from the OA community. In particular, Bronze OA may be significant in a policy context, since, unlike other publisher-hosted OA, Bronze articles do not extend any reuse rights beyond reading, making them Gratis OA. Much more research is needed into the characteristics of Bronze OA. How many Bronze articles are licensed openly, but do not make their license available? Is Bronze disproportionately non-peer-reviewed content? How much of Bronze OA is also Delayed OA? How much Bronze is Promotional, and how transient is the free-to-read status of this content? How many Bronze articles are published in “hidden gold” journals that are not listed in the DOAJ? Why are these journals not defining an explicit license for their content, and are there effective ways to encourage this? These and other questions are outside the scope of this study but may provide fruitful insights for future OA research and policy.</p> + <p id="p-64">Only about 7% of the literature overall (and 17% of the OA literature) is Green. This is may at first seem disappointing, given years of advocacy focused on Green OA as well as ongoing growth in the number of Green OA mandates (<a class="xref xref-bibr" href="https://scholar.google.com/scholar_lookup?title=Anatomy%20of%20green%20open%20access&author=Bj%C3%B6rk&publication_year=2014" title="Anatomy of green open access" data-jats-ref-type="bibr" data-jats-rid="ref-11">Björk et al., 2014</a>). However, the full context of Green OA provides reasons for optimism. First, many papers are archived in repositories but are not counted as Green in this analysis because they are also available on the publisher site as Hybrid, Gold, or Bronze versions. These “shadowed Green” copies provide a useful safety net that preserves access in cases where publishers rescind it (as could potentially happen with Delayed OA and other Bronze articles). Further research is needed to determine the prevalence of shadowed Green OA in various disciplines. Second, the phenomenon of “backfilling” (authors self-archiving content published across all years, not just the current one) means that although the percentage graph of Green OA does not show the same year-over-year slope as Gold or Hybrid, the line itself may be rising across <i>all</i> years as authors gradually self-archive papers from years or even decades ago. This assumption is supported by results reported by <a class="xref xref-bibr" href="https://digitalcommons.unl.edu/cgi/viewcontent.cgi?referer=https://www.google.com/&httpsredir=1&article=1028&context=scholcom" title="Research impact of paywalled versus open access papers" data-jats-ref-type="bibr" data-jats-rid="ref-6">Archambault et al. (2016)</a>. Finally, the relatively low proportion of green OA encouragingly leaves room for continued growth. While most journals published by major publishers (Elsevier, Wiley, Springer, etc.) allow for self-archiving, research shows that only a small proportion of papers from these publishers actually are self-archived in OA repositories; for example, <a class="xref xref-bibr" href="https://scholar.google.com/scholar_lookup?title=Knowledge%20sharing%20in%20global%20health%20research;%20the%20impact,%20uptake%20and%20cost%20of%20open%20access%20to%20scholarly%20literature&author=Smith&publication_year=" title="Knowledge sharing in global health research; the impact, uptake and cost of open access to scholarly literature" data-jats-ref-type="bibr" data-jats-rid="ref-42">Smith et al. (in press)</a> report using a sample of Global Health Research papers that only 39% of them made use of available self-archiving rights.</p> + <p id="p-65">Our results confirm the Open Access Citation Advantage found by other studies: open articles receive 18% more citations than otherwise expected. While at least some of this boost is likely due to the fact that more access allows more people to read and hence cite articles they otherwise would not, causation is difficult to establish and there are many possible confounders. Most discussed is the so-called “selection bias postulate”, (<a class="xref xref-bibr" href="https://doi.org/10.1016%2Fj.joi.2007.04.001" title="Do open access articles have greater citation impact?" data-jats-ref-type="bibr" data-jats-rid="ref-18">Craig et al., 2007</a>) which suggests that authors choose only their most impactful work to make OA. The current study does not examine the cause or directionality of correlation, but does find that it exists in a very large sample that is relatively representative of the literature as a whole. Funder requirements may also play a role in the observed citation advantage: high-profile funders are more likely to have an OA publishing requirement; at the same time, well funded studies are independently more likely to receive more citations than poorly funded studies (<a class="xref xref-bibr" href="https://loop.nigms.nih.gov/2010/09/measuring-the-scientific-output-and-impact-of-nigms-grants/" title="Measuring the scientific output and impact of NIGMS grants" data-jats-ref-type="bibr" data-jats-rid="ref-7">Berg, 2010</a>). Interestingly, Gold articles are actually cited <i>less</i>, likely due to an increase in the number of newer and smaller OA journals. Some of these journals are from regions of the world not historically indexed by WoS, are published in languages other than English, or might be considered to be less prestigious because they have not had time to become established or accumulate citations (<a class="xref xref-bibr" href="http://www.science-metrix.com/pdf/SM_EC_OA_Availability_2004-2011.pdf" title="Proportion of open access peer-reviewed papers at the European and world levels–2004–2011" data-jats-ref-type="bibr" data-jats-rid="ref-4">Archambault et al., 2013</a>). On the flip side, the citation disadvantage of Gold OA is likely also affected by the continued growth of so-called ‘mega journals’ such as PLOS ONE (<a class="xref xref-bibr" href="http://journals.plos.org/plosone/s/reviewer-guidelines#loc-criteria-for-publication" title="Reviewer guidelines: criteria for publication" data-jats-ref-type="bibr" data-jats-rid="ref-40"> PLOS, 2018</a>). Whatever the reason, the lower impact of Gold means the overall citation advantage is strongly driven by Green, Hybrid, and Bronze content. In sum, while several factors can affect the observed differences in citation rates, and causation remains difficult to establish, the fact remains that scholars are much more likely to read and cite papers to which they have access than those that they cannot obtain. Hopefully the existence of a free, open index of OA content will help support further research into the OACA question.</p> + <p id="p-66">The relatively high percentage of OA found in this study, particularly among readers of the free Unpaywall extension, has important potential implications for academic libraries. Increasingly, these libraries are under pressure to meet growing prices of “Big Deal” subscription packages, and the once-unthinkable outcome of canceling these Big Deals is becoming an increasingly realistic option. In this environment, knowing that around half of the literature of interest is available without any subscription may tip the scales toward cancellation for some institutions–particularly given that this percentage seems to be growing steadily. Indeed, the Université de Montréal’s cancellation of their Taylor & Francis subscription package (<a class="xref xref-bibr" href="http://www.bib.umontreal.ca/communiques/20170504-DC-annulation-taylor-francis-va.htm" title="UdeM Libraries cancel Big Deal subscription to 2231 periodical titles published by Taylor & Francis Group" data-jats-ref-type="bibr" data-jats-rid="ref-48">Université de Montréal, 2017</a>) is particularly interesting, given that their cancellation announcement directly pointed faculty to Unpaywall and other tools to help them access OA content. This may seem a radical suggestion, but cancellation of subscription journals has long been part of the universal OA roadmap (<a class="xref xref-bibr" href="https://scholarlykitchen.sspnet.org/2017/02/21/forbidden-forecast-thinking-open-access-library-subscriptions/" title="The forbidden forecast: thinking about open access and library subscriptions" data-jats-ref-type="bibr" data-jats-rid="ref-2">Anderson, 2017b</a>). Even when the percentage of OA is not enough to support outright cancellation, it may be enough to negotiate better subscription rates by supporting calculation of “OA-adjusted Cost Per Access” (<a class="xref xref-bibr" href="http://www.ala.org/acrl/sites/ala.org.acrl/files/content/conferences/confsandpreconfs/2017/LeveragingtheGrowthofOpenAccess.pdf" title="Leveraging the growth of open access in library collection decision making" data-jats-ref-type="bibr" data-jats-rid="ref-3">Antelman, 2017</a>). However, much more study is needed to see how OA availability varies across journals and Big Deal packages, along with praxis-oriented work building OA analysis tools that help librarians make cancellation choices.</p> + <p id="p-67">This study has several important limitations. Our dataset only includes journal articles with DOIs, which means that disciplines and geographical areas which rely more heavily on conference papers or articles without DOIs are underrepresented. Our Crossref sample includes about 7% journal “front matter” that the journal has assigned a DOI and Crossref labelled “journal article” but is actually a page describing the journal Editorial Board or similar. Our Bronze OA category includes articles published in OA journals which aren’t indexed in DOAJ; future work must identify these OA journals and classify such articles as Gold. As discussed in our definition of OA, when finding open copies we ignored free-to-read articles from academic social networks like ResearchGate and Academia.edu. The oaDOI system has some coverage of articles published on personal web pages, but this is quite limited compared to web-scale indexes like Google. The oaDOI system includes thousands of institutional and subject repositories, but there are some repositories that it misses. Our accuracy checks suggest that oaDOI, and therefore this study, are probably overlooking around 23% of OA otherwise discoverable using web searches, meaning that estimates in reported in this paper undercount OA by approximately 30%. Finally, our approach did not detect <i>when</i> articles were deposited into repositories. Because repositories are often backfilled with content that has been published many years ago, this study does not measure any increase/decrease in prevalence of Green OA over time, but only the proportion of Green OA by article publication date at the moment of data collection.</p> + <p id="p-68">In addition to the empirical results obtained, this paper clearly shows the potential of the oaDOI service for future research. The freely available oaDOI service provides scholars with the basis for assessing and monitoring the development of access to scholarly literature on a large scale, as well as the factors that affect it. For instance, our results show that the percentage of the literature available as OA is growing, and that articles diffused through this form are generally more cited than closed access articles. Several factors are likely to contribute to these trends; however, those remain poorly understood. Combined with other datasets–such as the WoS, Scopus, or Crossref–oaDOI allows one to assess at a large-scale the effects of various mandates on deposit rates, or to track the development of documents’ accessibility to determine, for example, when authors self-archive, or the sustainability of the promotional OA category. Aggregated at the level of journals and publishing platforms, these data can also provide librarians with indicators to help inform subscription cancellations and mitigate their effects. The application of the oaDOI algorithm on a large scale also allows for more complete analysis of the OA citation advantage across fields and time. As in <a class="xref xref-bibr" href="https://doi.org/10.1371%2Fjournal.pone.0013636" title="Self-selected or mandated, open access increases citation impact for higher quality research" data-jats-ref-type="bibr" data-jats-rid="ref-23">Gargouri et al. (2010)</a>, confounding factors could be mitigated by using article-level metadata to identify article pairs published in the same journal issue, on the same topic or published by the same authors at the same time. We hope that other scholars will dig deeper in those data to better understand OA dissemination and the factors that drive it. This is of utmost importance for the future of scholarly communication.</p> + </section> + <section class="sec" id="supplemental-information"> + <h2 class="heading"> Supplemental Information</h2> + <div class="supplementary-material well well-small" id="supp-1" data-jats-mimetype="application" data-jats-mime-subtype="vnd.openxmlformats-officedocument.wordprocessingml.document"> +<h3 class="heading">Additional results</h3> + + <div class="object-id article-component-doi">DOI: <a href="https://doi.org/10.7717/peerj.4375/supp-1" data-toggle="tooltip" title="Cite this object using this DOI">10.7717/peerj.4375/supp-1</a> +</div> +<div><a href="https://dfzljdn9uc3pi.cloudfront.net/2018/4375/1/appendix.docx" class="btn article-supporting-download" data-rel="supplement" download="appendix.docx" data-filename="appendix.docx"><i class="icon-large icon-download-alt"> </i> Download</a></div> +</div> + </section> + </div> +<div id="article-footnotes"> +<div class="fn article-footnote" id="fn-1"><span class="p">In the interest of full disclosure, it should be noted that two of the authors of the paper are the co-founders of Impactstory, the non-profit organization that developed oaDOI.</span></div> +<div class="fn article-footnote" id="fn-2"><span class="p">Repositories that were included are those covered by the Bielefeld Academic Search Engine (BASE) in May 2017. A full listing of repositories can be found on their website at: <a class="ext-link" href="https://www.base-search.net/about/en/about_sources_date.php?menu=2&submenu=1" data-jats-ext-link-type="uri">https://www.base-search.net/about/en/about_sources_date.php?menu=2&submenu=1</a> + </span></div> +<div class="fn article-footnote" id="fn-3"><span class="p">DOIs are short, unique identifiers for scholarly papers. Crossref is a nonprofit that helps a the DOI system, and is by far the largest supplier of academic DOIs in academia.</span></div> +<div class="fn article-footnote" id="fn-4"><span class="p">Based on a Sci-Hub dataset released in 2016 (the most recent data available).</span></div> +<div class="fn article-footnote" id="fn-5"><span class="p">These journals were identified by selecting journals with over a one thousand articles per year from those classified in the general “biomedical research” category. The full list of journals meeting these criteria were: PLOS ONE, Nature, Science, Scientific Reports, PNAS, Nature Communication, PeerJ, and Science Advances.</span></div> +<div class="fn article-footnote" id="fn-6"><span class="p">Ties between frequently cited specialties were resolved randomly; that is, if a paper cites exactly the same amount of papers from two NSF specialties, it was assigned to one of the two at random</span></div> +<div class="fn article-footnote" id="fn-7"><span class="p">Citations were normalized using the population of WoS articles and reviews with a DOI.</span></div> +</div></main><footer class="back"> + <section class="ack" id="acknowledgements"><h2 class="heading">Acknowledgements</h2> + <p>The authors would like to thank Dorothea Salo, Kristin Antelman, and John Sack for extensive and valuable comments on a draft of this article. The author order of JP and HP was determined by coin flip, as is their custom.</p> + </section> + <div class="sec" id="additional-information"> + <h2 class="heading">Additional Information and Declarations</h2> + <div class="fn-group" data-jats-content-type="competing-interests"> + <h3 class="heading">Competing Interests</h3> +<div class="fn" id="conflict-1" data-jats-fn-type="conflict"><p>Heather Piwowar and Jason Priem are founders of Impactstory, a non-profit company which makes Unpaywall, oaDOI, and other tools to improve scholarly communication.</p></div> +</div> + <div class="fn-group" data-jats-content-type="author-contributions"> + <h3 class="heading">Author Contributions</h3> +<div class="fn" id="contribution-1" data-jats-fn-type="con"><p><a class="xref xref-contrib" href="#author-1" data-jats-ref-type="contrib" data-jats-rid="author-1">Heather Piwowar</a>, <a class="xref xref-contrib" href="#author-2" data-jats-ref-type="contrib" data-jats-rid="author-2">Jason Priem</a> and <a class="xref xref-contrib" href="#author-9" data-jats-ref-type="contrib" data-jats-rid="author-9">Stefanie Haustein</a> conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.</p></div> +<div class="fn" id="contribution-2" data-jats-fn-type="con"><p><a class="xref xref-contrib" href="#author-3" data-jats-ref-type="contrib" data-jats-rid="author-3">Vincent Larivière</a> conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.</p></div> +<div class="fn" id="contribution-3" data-jats-fn-type="con"><p><a class="xref xref-contrib" href="#author-4" data-jats-ref-type="contrib" data-jats-rid="author-4">Juan Pablo Alperin</a> conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.</p></div> +<div class="fn" id="contribution-4" data-jats-fn-type="con"><p><a class="xref xref-contrib" href="#author-5" data-jats-ref-type="contrib" data-jats-rid="author-5">Lisa Matthias</a> performed the experiments, analyzed the data, reviewed drafts of the paper.</p></div> +<div class="fn" id="contribution-5" data-jats-fn-type="con"><p><a class="xref xref-contrib" href="#author-6" data-jats-ref-type="contrib" data-jats-rid="author-6">Bree Norlander</a> analyzed the data, wrote the paper, reviewed drafts of the paper.</p></div> +<div class="fn" id="contribution-6" data-jats-fn-type="con"><p><a class="xref xref-contrib" href="#author-7" data-jats-ref-type="contrib" data-jats-rid="author-7">Ashley Farley</a> wrote the paper, reviewed drafts of the paper.</p></div> +<div class="fn" id="contribution-7" data-jats-fn-type="con"><p><a class="xref xref-contrib" href="#author-8" data-jats-ref-type="contrib" data-jats-rid="author-8">Jevin West</a> reviewed drafts of the paper.</p></div> +</div> + <div class="fn-group" data-jats-content-type="other"> + <h3 class="heading">Data Availability</h3> +<div class="fn" id="addinfo-1"> +<p>The following information was supplied regarding data availability:</p> + <p>Zenodo: <a class="ext-link" href="http://doi.org/10.5281/zenodo.837902" data-jats-ext-link-type="uri">http://doi.org/10.5281/zenodo.837902</a>.</p> + <p>The datasets behind the analysis in this paper are openly available at <a class="ext-link" href="http://dx.doi.org/10.5281/zenodo.837902" data-jats-ext-link-type="uri">http://dx.doi.org/10.5281/zenodo.837902</a> and the R statistics code can be found at <a class="ext-link" href="https://github.com/Impactstory/oadoi-paper1" data-jats-ext-link-type="uri">https://github.com/Impactstory/oadoi-paper1</a>. The oaDOI code is open source at <a class="ext-link" href="https://github.com/impactstory/oadoi" data-jats-ext-link-type="uri">https://github.com/impactstory/oadoi</a> and information about accessing the oaDOI API and full dataset is at <a class="ext-link" href="https://oadoi.org/api" data-jats-ext-link-type="uri">https://oadoi.org/api</a>.</p> +</div> +</div> + <h3 class="heading">Funding</h3> +<p>The authors received no funding for this work.</p> +</div> + <section class="ref-list-container" id="references"><h2 class="heading">References</h2> +<ul class="ref-list" data-jats-content-type="authoryear"> +<li class="ref"><div class="citation" itemprop="citation" itemscope="itemscope" id="ref-1"> +<span class="citation-authors-year"><b><span class="name" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="surname" itemprop="familyName">Anderson</span></span>.</b> <b class="year" itemprop="datePublished">2017a</b>.</span> <cite class="article-title"><a 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Therefore, it is extremely important to select REV-free specific-pathogen-free (SPF) chicken embryos. Generally, REV infection is assessed by detecting REV antibodies in SPF chickens. This present study seeks to evaluate REV infection by replacing serum antibody detection with yolk antibody detection. A cohort of 40 nineteen-week-old SPF chickens were artificially inoculated with REV, with 32 SPF chickens raised in another isolation environment served as a blank control. Eggs and serum from 23-week-old chickens were sampled, and yolks were diluted separately to ratios of 1:150, 1:200, 1:300 and 1:400, which were detected together with serum. We found that the yolk antibody detection findings at a dilution of 1:300 had the highest coincidence rate compared with that based on serum antibody measurements. At a dilution ratio of 1:300 for yolk antibody, 72 chickens were continuously observed for 10 weeks from 25- to 34-weeks-old. Our findings were based on serum antibody or yolk antibody detection, and the evaluation results were completely consistent. Therefore, all serum antibody-positive chickens were yolk antibody-positive, and vice versa. Accordingly, vaccine producers can estimate REV cleanliness in a poultry farm by sampling yolk antibody titers." /> + + <meta name="citation_abstract" content="Reticuloendotheliosis virus (REV) is the most frequent exogenous virus that contaminates attenuated vaccines. Therefore, it is extremely important to select REV-free specific-pathogen-free (SPF) chicken embryos. Generally, REV infection is assessed by detecting REV antibodies in SPF chickens. This present study seeks to evaluate REV infection by replacing serum antibody detection with yolk antibody detection. A cohort of 40 nineteen-week-old SPF chickens were artificially inoculated with REV, with 32 SPF chickens raised in another isolation environment served as a blank control. Eggs and serum from 23-week-old chickens were sampled, and yolks were diluted separately to ratios of 1:150, 1:200, 1:300 and 1:400, which were detected together with serum. We found that the yolk antibody detection findings at a dilution of 1:300 had the highest coincidence rate compared with that based on serum antibody measurements. At a dilution ratio of 1:300 for yolk antibody, 72 chickens were continuously observed for 10 weeks from 25- to 34-weeks-old. Our findings were based on serum antibody or yolk antibody detection, and the evaluation results were completely consistent. Therefore, all serum antibody-positive chickens were yolk antibody-positive, and vice versa. Accordingly, vaccine producers can estimate REV cleanliness in a poultry farm by sampling yolk antibody titers."> + + + <meta name="keywords" content="Chickens,Antibodies,Livestock,Attenuated vaccines,Enzyme-linked immunoassays,Poultry,Animal sexual behavior,Vaccines" /> + + +<meta name="citation_doi" content="10.1371/journal.pone.0213978"/> +<meta name="citation_author" content="Yang Li"/> + <meta name="citation_author_institution" content="China Animal Health and Epidemiology Center, Qingdao, China"/> +<meta name="citation_author" content="Tuanjie Wang"/> + <meta name="citation_author_institution" content="China Institute of Veterinary Drug Control, Beijing, China"/> +<meta name="citation_author" content="Lin Wang"/> + <meta name="citation_author_institution" content="China Animal Health and Epidemiology Center, Qingdao, China"/> +<meta name="citation_author" content="Mingjun Sun"/> + <meta name="citation_author_institution" content="China Animal Health and Epidemiology Center, Qingdao, China"/> +<meta name="citation_author" content="Zhizhong Cui"/> + <meta name="citation_author_institution" content="College of Veterinary Medicine, Shandong Agricultural University, Taian, China"/> +<meta name="citation_author" content="Shuang Chang"/> + <meta name="citation_author_institution" content="College of Veterinary Medicine, Shandong Agricultural University, Taian, China"/> +<meta name="citation_author" content="Yongping Wu"/> + <meta name="citation_author_institution" content="College of Animal Sciences and Technology, Zhejiang A&F University, Hangzhou, China"/> +<meta name="citation_author" content="Xiaodong Zhang"/> + <meta name="citation_author_institution" content="College of Animal Sciences and Technology, Zhejiang A&F University, Hangzhou, China"/> +<meta name="citation_author" content="Xiaohui Yu"/> + <meta name="citation_author_institution" content="China Animal Health and Epidemiology Center, Qingdao, China"/> +<meta name="citation_author" content="Tao Sun"/> + <meta name="citation_author_institution" content="Shandong Entry-exit Inspection and Quarantine Bureau, Qingdao, China"/> +<meta name="citation_author" content="Peng Zhao"/> + <meta name="citation_author_institution" content="College of Veterinary Medicine, Shandong Agricultural University, Taian, China"/> + +<meta name="citation_title" content="Assessment on reticuloendotheliosis virus infection in specific-pathogen-free chickens based on detection of yolk antibody"/> +<meta itemprop="name" content="Assessment on reticuloendotheliosis virus infection in specific-pathogen-free chickens based on detection of yolk antibody"/> +<meta name="citation_journal_title" content="PLOS ONE"/> +<meta name="citation_journal_abbrev" content="PLOS ONE"/> +<meta name="citation_date" content="Apr 22, 2019"/> +<meta name="citation_firstpage" content="e0213978"/> +<meta name="citation_issue" content="4"/> +<meta name="citation_volume" content="14"/> +<meta name="citation_issn" content="1932-6203"/> +<meta name="citation_publisher" content="Public Library of Science"/> + + <meta name="citation_pdf_url" content="https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0213978&type=printable"> + + <meta name="citation_article_type" content="Research Article"> + +<meta name="dc.identifier" content="10.1371/journal.pone.0213978" /> + + + <meta name="twitter:card" content="summary" /> + <meta name="twitter:site" content="@plosone"/> + <meta name="twitter:title" content="Assessment on reticuloendotheliosis virus infection in specific-pathogen-free chickens based on detection of yolk antibody" /> + <meta property="twitter:description" content="Reticuloendotheliosis virus (REV) is the most frequent exogenous virus that contaminates attenuated vaccines. Therefore, it is extremely important to select REV-free specific-pathogen-free (SPF) chicken embryos. Generally, REV infection is assessed by detecting REV antibodies in SPF chickens. This present study seeks to evaluate REV infection by replacing serum antibody detection with yolk antibody detection. A cohort of 40 nineteen-week-old SPF chickens were artificially inoculated with REV, with 32 SPF chickens raised in another isolation environment served as a blank control. Eggs and serum from 23-week-old chickens were sampled, and yolks were diluted separately to ratios of 1:150, 1:200, 1:300 and 1:400, which were detected together with serum. We found that the yolk antibody detection findings at a dilution of 1:300 had the highest coincidence rate compared with that based on serum antibody measurements. At a dilution ratio of 1:300 for yolk antibody, 72 chickens were continuously observed for 10 weeks from 25- to 34-weeks-old. Our findings were based on serum antibody or yolk antibody detection, and the evaluation results were completely consistent. Therefore, all serum antibody-positive chickens were yolk antibody-positive, and vice versa. Accordingly, vaccine producers can estimate REV cleanliness in a poultry farm by sampling yolk antibody titers." /> + <meta property="twitter:image" content="https://journals.plos.org/plosone/article/figure/image?id=10.1371/journal.pone.0213978.t003&size=inline" /> + +<meta property="og:type" content="article" /> +<meta property="og:url" content="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0213978"/> +<meta property="og:title" content="Assessment on reticuloendotheliosis virus infection in specific-pathogen-free chickens based on detection of yolk antibody"/> +<meta property="og:description" content="Reticuloendotheliosis virus (REV) is the most frequent exogenous virus that contaminates attenuated vaccines. Therefore, it is extremely important to select REV-free specific-pathogen-free (SPF) chicken embryos. Generally, REV infection is assessed by detecting REV antibodies in SPF chickens. This present study seeks to evaluate REV infection by replacing serum antibody detection with yolk antibody detection. A cohort of 40 nineteen-week-old SPF chickens were artificially inoculated with REV, with 32 SPF chickens raised in another isolation environment served as a blank control. Eggs and serum from 23-week-old chickens were sampled, and yolks were diluted separately to ratios of 1:150, 1:200, 1:300 and 1:400, which were detected together with serum. We found that the yolk antibody detection findings at a dilution of 1:300 had the highest coincidence rate compared with that based on serum antibody measurements. At a dilution ratio of 1:300 for yolk antibody, 72 chickens were continuously observed for 10 weeks from 25- to 34-weeks-old. 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work with: + Yang Li, + Tuanjie Wang + </p> + + <p class="roles" id="authRoles"> + <span class="type">Roles</span> + Methodology, + + Project administration, + + Resources, + + Writing – original draft + </p> + + <p id="authAffiliations-0"><span class="type">Affiliation</span> + China Animal Health and Epidemiology Center, Qingdao, China + </p> + + <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose0"> ⨯ </a> + </div> +</li> + +<li + data-js-tooltip="tooltip_trigger" + +> + <a data-author-id="1" class="author-name" > +Tuanjie Wang <span class="contribute"> </span>,</a> <div id="author-meta-1" class="author-info" data-js-tooltip="tooltip_target"> + + <p> + <span class="contribute"> </span> Contributed equally to this work with: + Yang Li, + Tuanjie Wang + </p> + + <p class="roles" id="authRoles"> + <span class="type">Roles</span> + Project administration + </p> + + <p id="authAffiliations-1"><span class="type">Affiliation</span> + China Institute of Veterinary Drug Control, Beijing, China + </p> + + <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose1"> ⨯ </a> + </div> +</li> + +<li + data-js-tooltip="tooltip_trigger" + +> + <a data-author-id="2" class="author-name" > +Lin Wang,</a> <div id="author-meta-2" class="author-info" data-js-tooltip="tooltip_target"> + + + <p class="roles" id="authRoles"> + <span class="type">Roles</span> + Methodology + </p> + + <p id="authAffiliations-2"><span class="type">Affiliation</span> + China Animal Health and Epidemiology Center, Qingdao, China + </p> + + <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose2"> ⨯ </a> + </div> +</li> + +<li + data-js-tooltip="tooltip_trigger" + +> + <a data-author-id="3" class="author-name" > +Mingjun Sun,</a> <div id="author-meta-3" class="author-info" data-js-tooltip="tooltip_target"> + + + <p class="roles" id="authRoles"> + <span class="type">Roles</span> + Resources + </p> + + <p id="authAffiliations-3"><span class="type">Affiliation</span> + China Animal Health and Epidemiology Center, Qingdao, China + </p> + + <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose3"> ⨯ </a> + </div> +</li> + +<li + data-js-tooltip="tooltip_trigger" + +> + <a data-author-id="4" class="author-name" > +Zhizhong Cui,</a> <div id="author-meta-4" class="author-info" data-js-tooltip="tooltip_target"> + + + <p class="roles" id="authRoles"> + <span class="type">Roles</span> + Supervision + </p> + + <p id="authAffiliations-4"><span class="type">Affiliation</span> + College of Veterinary Medicine, Shandong Agricultural University, Taian, China + </p> + + <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose4"> ⨯ </a> + </div> +</li> + +<li + data-js-tooltip="tooltip_trigger" + +> + <a data-author-id="5" class="author-name" > +Shuang Chang,</a> <div id="author-meta-5" class="author-info" data-js-tooltip="tooltip_target"> + + + <p class="roles" id="authRoles"> + <span class="type">Roles</span> + Methodology + </p> + + <p id="authAffiliations-5"><span class="type">Affiliation</span> + College of Veterinary Medicine, Shandong Agricultural University, Taian, China + </p> + + <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose5"> ⨯ </a> + </div> +</li> + +<li + data-js-tooltip="tooltip_trigger" + +> + <a data-author-id="6" class="author-name" > +Yongping Wu,</a> <div id="author-meta-6" class="author-info" data-js-tooltip="tooltip_target"> + + + <p class="roles" id="authRoles"> + <span class="type">Roles</span> + Methodology + </p> + + <p id="authAffiliations-6"><span class="type">Affiliation</span> + College of Animal Sciences and Technology, Zhejiang A&F University, Hangzhou, China + </p> + + <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose6"> ⨯ </a> + </div> +</li> + +<li + data-js-tooltip="tooltip_trigger" + +> + <a data-author-id="7" class="author-name" > +Xiaodong Zhang,</a> <div id="author-meta-7" class="author-info" data-js-tooltip="tooltip_target"> + + + <p class="roles" id="authRoles"> + <span class="type">Roles</span> + Methodology + </p> + + <p id="authAffiliations-7"><span class="type">Affiliation</span> + College of Animal Sciences and Technology, Zhejiang A&F University, Hangzhou, China + </p> + + <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose7"> ⨯ </a> + </div> +</li> + +<li + data-js-tooltip="tooltip_trigger" + +> + <a data-author-id="8" class="author-name" > +Xiaohui Yu <span class="email"> </span>,</a> <div id="author-meta-8" class="author-info" data-js-tooltip="tooltip_target"> + + + <p class="roles" id="authRoles"> + <span class="type">Roles</span> + Data curation, + + Investigation, + + Writing – review & editing + </p> + <p id="authCorresponding-8"> <span class="email">* E-mail:</span> <a href="mailto:suntaosdciq@163.com">suntaosdciq@163.com</a> (TS); <a href="mailto:619334017@qq.com">619334017@qq.com</a> (PZ); <a href="mailto:yxhui1030@126.com">yxhui1030@126.com</a> (XY)</p> + <p id="authAffiliations-8"><span class="type">Affiliation</span> + China Animal Health and Epidemiology Center, Qingdao, China + </p> + <div> + <p class="orcid" id="authOrcid-8"> + <span> + <a id="connect-orcid-link" href="http://orcid.org/0000-0003-0555-8727" target="_blank" title="ORCID Registry"> + <img id="orcid-id-logo" src="/plosone/resource/img/orcid_16x16.png" width="16" height="16" alt="ORCID logo"/> + </a> + </span> + <a href="http://orcid.org/0000-0003-0555-8727">http://orcid.org/0000-0003-0555-8727</a> + </p> + </div> + + <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose8"> ⨯ </a> + </div> +</li> + +<li + data-js-tooltip="tooltip_trigger" + +> + <a data-author-id="9" class="author-name" > +Tao Sun <span class="email"> </span>,</a> <div id="author-meta-9" class="author-info" data-js-tooltip="tooltip_target"> + + + <p class="roles" id="authRoles"> + <span class="type">Roles</span> + Data curation + </p> + <p id="authCorresponding-9"> <span class="email">* E-mail:</span> <a href="mailto:suntaosdciq@163.com">suntaosdciq@163.com</a> (TS); <a href="mailto:619334017@qq.com">619334017@qq.com</a> (PZ); <a href="mailto:yxhui1030@126.com">yxhui1030@126.com</a> (XY)</p> + <p id="authAffiliations-9"><span class="type">Affiliation</span> + Shandong Entry-exit Inspection and Quarantine Bureau, Qingdao, China + </p> + + <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose9"> ⨯ </a> + </div> +</li> + +<li + data-js-tooltip="tooltip_trigger" + +> + <a data-author-id="10" class="author-name" > +Peng Zhao <span class="email"> </span></a> <div id="author-meta-10" class="author-info" data-js-tooltip="tooltip_target"> + + + <p class="roles" id="authRoles"> + <span class="type">Roles</span> + Supervision, + + Validation + </p> + <p id="authCorresponding-10"> <span class="email">* E-mail:</span> <a href="mailto:suntaosdciq@163.com">suntaosdciq@163.com</a> (TS); <a href="mailto:619334017@qq.com">619334017@qq.com</a> (PZ); <a href="mailto:yxhui1030@126.com">yxhui1030@126.com</a> (XY)</p> + <p id="authAffiliations-10"><span class="type">Affiliation</span> + College of Veterinary Medicine, Shandong Agricultural University, Taian, China + </p> + + <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose10"> ⨯ </a> + </div> +</li> + +</ul> + +</div> + + +<div id="floatTitleTop" data-js-floater="title_author" class="float-title"> + <div class="set-grid"> + <div class="float-title-inner"> + <h1><?xml version="1.0" encoding="UTF-8"?>Assessment on reticuloendotheliosis virus infection in specific-pathogen-free chickens based on detection of yolk antibody</h1> + +<ul id="floatAuthorList" data-js-floater="floated_authors"> + + <li data-float-index="1">Yang Li, + + </li> + <li data-float-index="2">Tuanjie Wang, + + </li> + <li data-float-index="3">Lin Wang, + + </li> + <li data-float-index="4">Mingjun Sun, + + </li> + <li data-float-index="5">Zhizhong Cui, + + </li> + <li data-float-index="6">Shuang Chang, + + </li> + <li data-float-index="7">Yongping Wu, + + </li> + <li data-float-index="8">Xiaodong Zhang, + + </li> + <li data-float-index="9">Xiaohui Yu, + + </li> + <li data-float-index="10">Tao Sun + +</ul> + + + + </div> + <div class="logo-close" id="titleTopCloser"> + <img src="/plosone/resource/img/logo.plos.95.png" alt="PLOS" /> + <div class="close-floater" title="close">x</div> + </div> + </div> +</div> + + <ul class="date-doi"> + <li id="artPubDate">Published: April 22, 2019</li> + <li id="artDoi"> +<a href="https://doi.org/10.1371/journal.pone.0213978">https://doi.org/10.1371/journal.pone.0213978</a> + </li> + </ul> + + </div> + <div> + + </div> +</header> + + <section class="article-body"> + + + +<ul class="article-tabs"> + + <li class="tab-title active" id="tabArticle"> + <a href="/plosone/article?id=10.1371/journal.pone.0213978" class="article-tab-1">Article</a> + </li> + + + <li class="tab-title " id="tabAuthors"> + <a 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class="carousel-wrapper"> + <div class="slider"> + + <div class="carousel-item lightbox-figure" data-doi="10.1371/journal.pone.0213978.t001"> + + <img src="/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0213978.t001" + alt="Table 1" + /> + + </div> + + <div class="carousel-item lightbox-figure" data-doi="10.1371/journal.pone.0213978.t002"> + + <img src="/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0213978.t002" + alt="Table 2" + /> + + </div> + + <div class="carousel-item lightbox-figure" data-doi="10.1371/journal.pone.0213978.t003"> + + <img src="/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0213978.t003" + alt="Table 3" + /> + + </div> + </div> + </div> + + <div class="carousel-control"> + <span class="button previous"></span> + <span class="button next"></span> + </div> + <div class="carousel-page-buttons"> + + </div> + </div> +</div> + + + <div class="article-text" id="artText"> + + + + +<div class="abstract toc-section"><a id="abstract0" name="abstract0" data-toc="abstract0" class="link-target" title="Abstract"></a><h2>Abstract</h2><a id="article1.front1.article-meta1.abstract1.p1" name="article1.front1.article-meta1.abstract1.p1" class="link-target"></a><p>Reticuloendotheliosis virus (REV) is the most frequent exogenous virus that contaminates attenuated vaccines. Therefore, it is extremely important to select REV-free specific-pathogen-free (SPF) chicken embryos. Generally, REV infection is assessed by detecting REV antibodies in SPF chickens. This present study seeks to evaluate REV infection by replacing serum antibody detection with yolk antibody detection. A cohort of 40 nineteen-week-old SPF chickens were artificially inoculated with REV, with 32 SPF chickens raised in another isolation environment served as a blank control. Eggs and serum from 23-week-old chickens were sampled, and yolks were diluted separately to ratios of 1:150, 1:200, 1:300 and 1:400, which were detected together with serum. We found that the yolk antibody detection findings at a dilution of 1:300 had the highest coincidence rate compared with that based on serum antibody measurements. At a dilution ratio of 1:300 for yolk antibody, 72 chickens were continuously observed for 10 weeks from 25- to 34-weeks-old. Our findings were based on serum antibody or yolk antibody detection, and the evaluation results were completely consistent. Therefore, all serum antibody-positive chickens were yolk antibody-positive, and vice versa. Accordingly, vaccine producers can estimate REV cleanliness in a poultry farm by sampling yolk antibody titers.</p> +</div> + + +<div class="articleinfo"><p><strong>Citation: </strong>Li Y, Wang T, Wang L, Sun M, Cui Z, Chang S, et al. (2019) Assessment on reticuloendotheliosis virus infection in specific-pathogen-free chickens based on detection of yolk antibody. PLoS ONE 14(4): + e0213978. + + https://doi.org/10.1371/journal.pone.0213978</p><p><strong>Editor: </strong>Eric HY Lau, The University of Hong Kong, CHINA</p><p><strong>Received: </strong>June 22, 2018; <strong>Accepted: </strong>March 5, 2019; <strong>Published: </strong> April 22, 2019</p><p><strong>Copyright: </strong> © 2019 Li et al. This is an open access article distributed under the terms of the <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</a>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</p><p><strong>Data Availability: </strong>All relevant data are within the manuscript.</p><p><strong>Funding: </strong>The research was supported by the National Quality Infrastructure of China (2017YFF0210200).The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</p><p><strong>Competing interests: </strong> The authors have declared that no competing interests exist.</p></div> + + + + + +<div id="section1" class="section toc-section"><a id="sec001" name="sec001" data-toc="sec001" class="link-target" title="Introduction"></a><h2>Introduction</h2><a id="article1.body1.sec1.p1" name="article1.body1.sec1.p1" class="link-target"></a><p>Avian reticuloendotheliosis virus (REV) is one of the most important pathogens that can cause avian tumors. Recently, epidemiological investigations showed that REV infection is very common in Chinese chickens, particularly in local poultry species [<a href="#pone.0213978.ref001" class="ref-tip">1</a>–<a href="#pone.0213978.ref003" class="ref-tip">3</a>]. As REV can be vertically transmitted through hatching eggs [<a href="#pone.0213978.ref004" class="ref-tip">4</a>], if REV-contaminated eggs are used to produce attenuated vaccines, vaccines can be contaminated by REV, which represents one of the crucial ways to disseminate REV [<a href="#pone.0213978.ref005" class="ref-tip">5</a>–<a href="#pone.0213978.ref007" class="ref-tip">7</a>]. Recently in China, the use of REV-contaminated attenuated vaccines is considered to be an important cause of REV infection [<a href="#pone.0213978.ref008" class="ref-tip">8</a>–<a href="#pone.0213978.ref010" class="ref-tip">10</a>].</p> +<a id="article1.body1.sec1.p2" name="article1.body1.sec1.p2" class="link-target"></a><p>To overcome this problem, as the Ministry of Agriculture of China stipulated, all attenuated poultry vaccines must use SPF chickens as raw materials to produce attenuated vaccines, and all vaccine producers must confirm whether SPF chickens are infected by REV or not using sampled serum antibody detection. However, because of the specificity of housing standards in SPF poultry farms, others cannot freely enter a breeding area for sampling and detection. In this current study, we attempted to replace antibody detection in serum with antibody detection in egg yolks of SPF chickens.</p> +</div> + +<div id="section2" class="section toc-section"><a id="sec002" name="sec002" data-toc="sec002" class="link-target" title="Results"></a><h2>Results</h2> +<div id="section1" class="section toc-section"><a id="sec003" name="sec003" class="link-target" title="Determination of the optimal yolk dilution"></a> +<h3>Determination of the optimal yolk dilution</h3> +<a id="article1.body1.sec2.sec1.p1" name="article1.body1.sec2.sec1.p1" class="link-target"></a><p>Under the same conditions, we measured REV antibody titers in paired yolk and serum samples collected on the same day or one day before or after in 40 SPF chickens during the initial egg-laying stage when the chickens were 23 weeks old. <a href="#pone-0213978-t001">Table 1</a> shows the “goodness of fit” between yolk antibody titers diluted to various concentrations and serum antibody titers at the required concentration. By comparison, we found that REV antibody detection in the yolk at a 1:300 dilution had the highest goodness of fit with serum antibody measurements, and reached 97.5%.</p> +<a class="link-target" id="pone-0213978-t001" name="pone-0213978-t001"></a><div class="figure" data-doi="10.1371/journal.pone.0213978.t001"><div class="img-box"><a title="Click for larger image" href="article/figure/image?size=medium&id=info:doi/10.1371/journal.pone.0213978.t001" data-doi="info:doi/10.1371/journal.pone.0213978" data-uri="info:doi/10.1371/journal.pone.0213978.t001"><img src="article/figure/image?size=inline&id=info:doi/10.1371/journal.pone.0213978.t001" alt="thumbnail" class="thumbnail"></a><div class="expand"></div></div><div class="figure-inline-download"> + Download: + <ul><li><div class="definition-label"><a href="article/figure/powerpoint?id=info:doi/10.1371/journal.pone.0213978.t001"> + PPT + </a></div><a href="article/figure/powerpoint?id=info:doi/10.1371/journal.pone.0213978.t001"> + PowerPoint slide + </a></li><li><div class="definition-label"><a href="article/figure/image?download&size=large&id=info:doi/10.1371/journal.pone.0213978.t001"> + PNG + </a></div><a href="article/figure/image?download&size=large&id=info:doi/10.1371/journal.pone.0213978.t001"> + larger image + </a></li><li><div class="definition-label"><a href="article/figure/image?download&size=original&id=info:doi/10.1371/journal.pone.0213978.t001"> + TIFF + </a></div><a href="article/figure/image?download&size=original&id=info:doi/10.1371/journal.pone.0213978.t001"> + original image + </a></li></ul></div><div class="figcaption"><span>Table 1. </span> Consistent yolk and serum antibody measurements with different dilutions of yolk.</div><p class="caption_target"></p><p class="caption_object"><a href="https://doi.org/10.1371/journal.pone.0213978.t001"> + https://doi.org/10.1371/journal.pone.0213978.t001</a></p></div></div> + +<div id="section2" class="section toc-section"><a id="sec004" name="sec004" class="link-target" title="Comparison of the goodness of fit for ALV-Ab antibody measurements in serum and yolk from SPF chickens of different ages"></a> +<h3>Comparison of the goodness of fit for ALV-Ab antibody measurements in serum and yolk from SPF chickens of different ages</h3> +<a id="article1.body1.sec2.sec2.p1" name="article1.body1.sec2.sec2.p1" class="link-target"></a><p>In 25–34-week-old chickens, serum and hatching eggs were sampled once per week, and a total of 720 serum samples and 720 yolk samples were collected from 40 SPF infected chickens and 32 SPF chickens without virus challenge. <a href="#pone-0213978-t002">Table 2</a> showed that the yolk antibody findings were completely consistent with those based on serum antibody detection within 10 weeks, as the serum antibody-positive chickens were all yolk antibody-positive, and the serum antibody-negative chickens were all yolk antibody-negative. Additionally, 35 of 40 SPF chickens challenged with REV alone were always REV antibody-positive in the serum and yolk, while 4 were always REV antibody-negative. All 32 SPF chickens without virus challenge were always REV antibody-positive in the serum and yolk. The goodness of fit for serum antibody and yolk antibody detection reached 100%.</p> +<a class="link-target" id="pone-0213978-t002" name="pone-0213978-t002"></a><div class="figure" data-doi="10.1371/journal.pone.0213978.t002"><div class="img-box"><a title="Click for larger image" href="article/figure/image?size=medium&id=info:doi/10.1371/journal.pone.0213978.t002" data-doi="info:doi/10.1371/journal.pone.0213978" data-uri="info:doi/10.1371/journal.pone.0213978.t002"><img src="article/figure/image?size=inline&id=info:doi/10.1371/journal.pone.0213978.t002" alt="thumbnail" class="thumbnail"></a><div class="expand"></div></div><div class="figure-inline-download"> + Download: + <ul><li><div class="definition-label"><a href="article/figure/powerpoint?id=info:doi/10.1371/journal.pone.0213978.t002"> + PPT + </a></div><a href="article/figure/powerpoint?id=info:doi/10.1371/journal.pone.0213978.t002"> + PowerPoint slide + </a></li><li><div class="definition-label"><a href="article/figure/image?download&size=large&id=info:doi/10.1371/journal.pone.0213978.t002"> + PNG + </a></div><a href="article/figure/image?download&size=large&id=info:doi/10.1371/journal.pone.0213978.t002"> + larger image + </a></li><li><div class="definition-label"><a href="article/figure/image?download&size=original&id=info:doi/10.1371/journal.pone.0213978.t002"> + TIFF + </a></div><a href="article/figure/image?download&size=original&id=info:doi/10.1371/journal.pone.0213978.t002"> + original image + </a></li></ul></div><div class="figcaption"><span>Table 2. </span> Agreement of yolk and serum antibody measurements with different dilutions of yolk.</div><p class="caption_target"></p><p class="caption_object"><a href="https://doi.org/10.1371/journal.pone.0213978.t002"> + https://doi.org/10.1371/journal.pone.0213978.t002</a></p></div></div> + +<div id="section3" class="section toc-section"><a id="sec005" name="sec005" class="link-target" title="REV antibody detection in serum and yolk from different SPF chicken populations"></a> +<h3>REV antibody detection in serum and yolk from different SPF chicken populations</h3> +<a id="article1.body1.sec2.sec3.p1" name="article1.body1.sec2.sec3.p1" class="link-target"></a><p>A total of 1000 yolk samples and 1000 serum samples from 10 different SPF chicken populations were detected for REV antibody. <a href="#pone-0213978-t003">Table 3</a> showed that all samples tested were negative based on yolk and serum antibody detection. Our evaluation results were consistent and without false positive results, indicating that the test SPF chicken populations were not infected by REV.</p> +<a class="link-target" id="pone-0213978-t003" name="pone-0213978-t003"></a><div class="figure" data-doi="10.1371/journal.pone.0213978.t003"><div class="img-box"><a title="Click for larger image" href="article/figure/image?size=medium&id=info:doi/10.1371/journal.pone.0213978.t003" data-doi="info:doi/10.1371/journal.pone.0213978" data-uri="info:doi/10.1371/journal.pone.0213978.t003"><img src="article/figure/image?size=inline&id=info:doi/10.1371/journal.pone.0213978.t003" alt="thumbnail" class="thumbnail"></a><div class="expand"></div></div><div class="figure-inline-download"> + Download: + <ul><li><div class="definition-label"><a href="article/figure/powerpoint?id=info:doi/10.1371/journal.pone.0213978.t003"> + PPT + </a></div><a href="article/figure/powerpoint?id=info:doi/10.1371/journal.pone.0213978.t003"> + PowerPoint slide + </a></li><li><div class="definition-label"><a href="article/figure/image?download&size=large&id=info:doi/10.1371/journal.pone.0213978.t003"> + PNG + </a></div><a href="article/figure/image?download&size=large&id=info:doi/10.1371/journal.pone.0213978.t003"> + larger image + </a></li><li><div class="definition-label"><a href="article/figure/image?download&size=original&id=info:doi/10.1371/journal.pone.0213978.t003"> + TIFF + </a></div><a href="article/figure/image?download&size=original&id=info:doi/10.1371/journal.pone.0213978.t003"> + original image + </a></li></ul></div><div class="figcaption"><span>Table 3. </span> Detection of REV antibody from 10 SPF chicken flocks in China (random collection).</div><p class="caption_target"></p><p class="caption_object"><a href="https://doi.org/10.1371/journal.pone.0213978.t003"> + https://doi.org/10.1371/journal.pone.0213978.t003</a></p></div></div> +</div> + +<div id="section3" class="section toc-section"><a id="sec006" name="sec006" data-toc="sec006" class="link-target" title="Discussion"></a><h2>Discussion</h2><a id="article1.body1.sec3.p1" name="article1.body1.sec3.p1" class="link-target"></a><p>Recently, epidemiological surveys have shown that different Chinese chicken populations are frequently infected by REV, especially in local Chinese chicken species [<a href="#pone.0213978.ref001" class="ref-tip">1</a>–<a href="#pone.0213978.ref003" class="ref-tip">3</a>]. To control REV infection, many measures have been employed, including the use of attenuated vaccines without REV contamination. In China and other countries, the possibility of REV contamination in attenuated poultry vaccines has been a major concern for many years. Many REV infections are thought to be caused by REV infection in contaminated attenuated vaccines, particularly for the most frequently used fowlpox virus vaccine (FPV) and anti-Marek’s Disease vaccines [<a href="#pone.0213978.ref005" class="ref-tip">5</a>–<a href="#pone.0213978.ref013" class="ref-tip">13</a>]. Additionally, the capability of REV to integrate into the genome of other viruses complicates its diagnosis and prevention [<a href="#pone.0213978.ref014" class="ref-tip">14</a>–<a href="#pone.0213978.ref021" class="ref-tip">21</a>]. Awad <em>et al</em>. detected REV in contaminated FPV vaccine using PCR identification and REV antibody detection for virus isolation and identification in vaccinated SPF chickens[<a href="#pone.0213978.ref007" class="ref-tip">7</a>]. REV contamination in avian attenuated vaccines can lead to serious consequences, such as a significant reduction in antibody levels in vaccine-immunized chicken populations[<a href="#pone.0213978.ref022" class="ref-tip">22</a>].</p> +<a id="article1.body1.sec3.p2" name="article1.body1.sec3.p2" class="link-target"></a><p>The REV contamination in attenuated vaccines may occur during the production process, but the use of REV-contaminated chicken embryos as raw materials is always the main cause. The national standards of China specify that vaccine production enterprises or SPF chicken breeding manufactures must periodically measure REV antibody levels in SPF chicken serum to evaluate the REV cleanliness in specific flocks. Because of differences in SPF chicken breeding environments, other individuals should not be allowed to enter a SPF chicken breeding area for sampling. This current approach causes both stress responses in SPF chickens and introduces the risk of false results for SPF chicken serum tests resulting from the inspection process. Therefore, the Ministry of Agriculture of China asked whether yolk antibody detection in hatching eggs could be used as a substitute for serum antibody detection to evaluate exogenous virus contamination in SPF chicken embryos.</p> +<a id="article1.body1.sec3.p3" name="article1.body1.sec3.p3" class="link-target"></a><p>The yolk dilution has a strong influence on the antibody detection results, as excessive high yolk concentration is prone to yield false negative or false positive results. The results of this present study showed that yolk at a 1:300 dilution gave the best goodness of fit between the antibody-negative or positive results based on yolk or serum antibody detection. To precisely and scientifically reveal the correlation between the yolk and serum antibody detection, we compared REV antibody detection results in the yolk and serum of 72 SPF chickens (40 were inoculated with REV one month prior to egg-laying) for 10 consecutive weeks. We found that for the 72 chickens, serum antibody detection results coincided with yolk antibody results at a rate of 100%. Our findings indicate that it is feasible to replace serum antibody tests with yolk antibody detection to monitor REV infection in SPF chickens.</p> +<a id="article1.body1.sec3.p4" name="article1.body1.sec3.p4" class="link-target"></a><p>At the optimal dilution determined in this study, a total of 1000 yolk samples and 1000 serum samples from 10 separate SPF chicken populations were tested for REV antibodies, and all showed negative results. The results of undetected antibodies showed that these chickens were not infected with REV or that although these chickens were infected with REV, not enough antibodies were detected. In order to avoid the false negative, we consider that chickens repeatedly tested negatively are not infected with REV, which is very important in flock surveillance. Additionally, detection results that used both methods were fully consistent. Importantly, no false positive results were obtained. These robust results indicate that contemporary SPF chicken embryos in China are mostly or fully not contaminated by REV. Our findings suggest that vaccine production enterprises could evaluate the REV cleanliness of SPF chicken farms by detecting antibodies in the yolk of SPF eggs. This process not only reduces the stress responses of SPF chickens during serum sampling and provides convenience for sampling, it also yields more reliable samples. Indeed, compared with serum sample results, hatching egg-based data are less prone to human error.</p> +</div> + +<div id="section4" class="section toc-section"><a id="sec007" name="sec007" data-toc="sec007" class="link-target" title="Materials and methods"></a><h2>Materials and methods</h2> +<div id="section1" class="section toc-section"><a id="sec008" name="sec008" class="link-target" title="REV strain"></a> +<h3>REV strain</h3> +<a id="article1.body1.sec4.sec1.p1" name="article1.body1.sec4.sec1.p1" class="link-target"></a><p>The strain REV-HA9901 was isolated in 1999 and full-length genomic sequencing had been completed (GenBank Accession No. AY842951) [<a href="#pone.0213978.ref023" class="ref-tip">23</a>]. Supernatants of the pre-frozen virus cells at –80°C were used to calculate TCID<sub>50</sub> by the Karber method; 0.1 mL supernatant of CEF cells contained 10 <sup>4.5</sup> TCID<sub>50</sub>.</p> +</div> + +<div id="section2" class="section toc-section"><a id="sec009" name="sec009" class="link-target" title="Rearing and virus challenge of SPF chickens"></a> +<h3>Rearing and virus challenge of SPF chickens</h3> +<a id="article1.body1.sec4.sec2.p1" name="article1.body1.sec4.sec2.p1" class="link-target"></a><p>A total of 40 nineteen-week-old SPF chickens were purchased from SPAFAS Poultry Co., and were reared in HEPA-filtered negative-pressure isolators. At nineteen weeks of age, groups of 13, 14, and 13 chickens were vaccinated with 10<sup>3</sup> TCID<sub>50</sub> HA9901, 10<sup>4</sup> TCID<sub>50</sub> HA9901, and 10<sup>5</sup> TCID<sub>50</sub> of HA9901, respectively. All labeled chickens were separately raised within a single cage in an SPF animal feeding unit so that eggs and serum samples could corresponded 1:1 with chickens. A total of 32 SPF chickens in the same batch were reared in isolation environments as a negative control. All these chickens from each group were sacrificed by intravenous administration of barbiturates. The use of all laboratory animals in this study was approved by the scientific ethical committee of Shandong province.</p> +</div> + +<div id="section3" class="section toc-section"><a id="sec010" name="sec010" class="link-target" title="Determination of the optimal yolk dilution"></a> +<h3>Determination of the optimal yolk dilution</h3> +<a id="article1.body1.sec4.sec3.p1" name="article1.body1.sec4.sec3.p1" class="link-target"></a><p>The 40 inoculated SPF chickens all began laying eggs when 23-weeks-old, and the hatching eggs and serum samples were collected from each chicken. Serum samples were diluted to the optimal concentration in accordance with the instructions of the ELISA test kit for REV antibody (IDEXX Company); and yolk samples were diluted to 1:150, 1:200, 1:300, and 1:400. To minimize the possibility of human errors, paired serum and yolk from each chicken were tested using the same kit by the same laboratory staff in simultaneous ELISA experiments with identical conditions. Each sample was tested twice, and if the two values differed greatly the test was repeated. Based on these results, we determined the optimal dilution of yolk at which the detection was in accordance with that determined based on serum antibody detection.</p> +</div> + +<div id="section4" class="section toc-section"><a id="sec011" name="sec011" class="link-target" title="REV antibody detection in serum and yolk among chickens of different ages"></a> +<h3>REV antibody detection in serum and yolk among chickens of different ages</h3> +<a id="article1.body1.sec4.sec4.p1" name="article1.body1.sec4.sec4.p1" class="link-target"></a><p>Each week, paired egg and serum samples from each chicken were collected from 72 SPF chickens for 10 weeks from the age of 25 to 34 weeks old. If a chicken did not lay eggs on the blood-collecting day, the egg laid one day before or after the blood collection was used. For REV antibody detection, serum samples were diluted according to the manufacturer’s instructions and yolk samples were diluted in accord with the optimal dilution determined in Section 1.3. To minimize the possibility of human errors, paired serum and yolk from each chicken were tested using the same batch of kits by the same laboratory staff in simultaneous ELISA experiments with identical conditions. Each sample was tested twice, and if the two values differed greatly, tests were repeated. Finally, we compared the “goodness of fit” between the yolk antibody sampled during different stages and serum antibody measurements.</p> +</div> + +<div id="section5" class="section toc-section"><a id="sec012" name="sec012" class="link-target" title="REV antibody detection in the serum and yolk of different SPF chicken populations"></a> +<h3>REV antibody detection in the serum and yolk of different SPF chicken populations</h3> +<a id="article1.body1.sec4.sec5.p1" name="article1.body1.sec4.sec5.p1" class="link-target"></a><p>Paired egg and serum samples from each chicken were sampled from 10 distinct Chinese SPF chicken populations. Serum samples were diluted in accordance with the test kit manufacturer’s instructions (IDEXX Company), and yolk samples were diluted in accordance with the optimal dilution that was determined. We separately estimated the REV cleanliness for different SPF chicken populations based on the two previously described examination methods, and compared differences in the actual operation. To minimize the introduction of human errors, paired serum and yolk samples from a chicken were tested using the same batch of kits by the same laboratory staff in simultaneous ELISA experiments with identical conditions. Each sample was tested twice, and if the two values differed greatly the tests were repeated.</p> +</div> +</div> + + + + + +<div class="section toc-section"><a id="ack" name="ack" data-toc="ack" title="Acknowledgments" class="link-target"></a><h2>Acknowledgments</h2> +<a id="article1.back1.ack1.p1" name="article1.back1.ack1.p1" class="link-target"></a><p>The research was supported by the National Quality Infrastructure of China (2017YFF0210200).</p> +</div><div class="toc-section"><a id="references" name="references" class="link-target" data-toc="references" title="References"></a><h2>References</h2><ol class="references"><li id="ref1"><span class="order">1. + </span><a name="pone.0213978.ref001" id="pone.0213978.ref001" class="link-target"></a>Cheng Z., Shi Y., Zhan L., Zhu G., Diao X. and Cui Z. (2007) Occurrence of reticuloendotheliosis in Chinese partridge. 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(Asuncin)]]></abbrev-journal-title> +<issn>1683-9803</issn> +<publisher> +<publisher-name><![CDATA[Sociedad Paraguaya de Pediatra]]></publisher-name> +</publisher> +</journal-meta> +<article-meta> +<article-id>S1683-98032015000200002</article-id> +<article-id pub-id-type="doi">10.18004/ped.2015.agosto.102-107</article-id> +<title-group> +<article-title xml:lang="es"><![CDATA[Prevalencia de desnutricin y hbitos alimentarios en nios menores de 5 aos en las comunidades indgenas de Yby Yau y Azotey, 2011]]></article-title> +<article-title xml:lang="en"><![CDATA[Prevalence of malnutrition and eating habits in children under 5 years of age in indigenous communities in Azote'y and Yby Yau, 2011]]></article-title> +</title-group> +<contrib-group> +<contrib contrib-type="author"> +<name> +<surname><![CDATA[Ruiz Valiente]]></surname> +<given-names><![CDATA[Syntia Carolina]]></given-names> +</name> +<xref ref-type="aff" rid="A01"/> +</contrib> +<contrib contrib-type="author"> +<name> +<surname><![CDATA[Ruiz Caete]]></surname> +<given-names><![CDATA[Manuel]]></given-names> +</name> +<xref ref-type="aff" rid="A02"/> +</contrib> +<contrib contrib-type="author"> +<name> +<surname><![CDATA[Cohene Velazquez]]></surname> +<given-names><![CDATA[Bartola]]></given-names> +</name> +<xref ref-type="aff" rid="A03"/> +</contrib> +</contrib-group> +<aff id="A01"> +<institution><![CDATA[,Hospital General Peditrico Nios Acosta u. Reducto-San Lorenzo, Paraguay ]]></institution> +<addr-line><![CDATA[ ]]></addr-line> +<country>Paraguay</country> +</aff> +<aff id="A02"> +<institution><![CDATA[,Hospital General Peditrico Nios Acosta u. Reducto-San Lorenzo, Paraguay ]]></institution> +<addr-line><![CDATA[ ]]></addr-line> +<country>Paraguay</country> +</aff> +<aff id="A03"> +<institution><![CDATA[,Puesto de Salud de Paso Tuya. Azotey. Paraguay ]]></institution> +<addr-line><![CDATA[ ]]></addr-line> +<country>Paraguay</country> +</aff> +<pub-date pub-type="pub"> +<day>30</day> +<month>08</month> +<year>2015</year> +</pub-date> +<pub-date pub-type="epub"> +<day>30</day> +<month>08</month> +<year>2015</year> +</pub-date> +<volume>42</volume> +<numero>2</numero> +<fpage>102</fpage> +<lpage>107</lpage> +<copyright-statement/> +<copyright-year/> +<self-uri xlink:href="http://scielo.iics.una.py/scielo.php?script=sci_arttext&pid=S1683-98032015000200002&lng=en&nrm=iso"></self-uri><self-uri xlink:href="http://scielo.iics.una.py/scielo.php?script=sci_abstract&pid=S1683-98032015000200002&lng=en&nrm=iso"></self-uri><self-uri xlink:href="http://scielo.iics.una.py/scielo.php?script=sci_pdf&pid=S1683-98032015000200002&lng=en&nrm=iso"></self-uri><abstract abstract-type="short" xml:lang="es"><p><![CDATA[Introduccin: La infancia es una etapa trascendental en el desarrollo evolutivo del hombre, para lo cual es fundamental una adecuada nutricin. La desnutricin infantil no es solo un problema de falta de alimentos, es un conflicto social ms profundo. La prevalencia de desnutricin en menores de 5 aos del pas es de 5,9% segn datos del Instituto Nacional de Alimentacin y Nutricin. Objetivo: Determinar la prevalencia de desnutricin y hbitos alimentarios en nios menores de 5 aos de las comunidades indgenas de Yby Ya y Azotey. Materiales y Mtodos: Estudio descriptivo, transversal, realizado de enero a abril del 2011, que identific la prevalencia de desnutricin infantil en nios indgenas de las etnias Pa'i Tavyter y Mbya Guaran de 11 comunidades indgenas de Yby Yau y Azotey. Fueron examinados 349 menores de 5 aos de edad. Para la evaluacin del estado nutricional se utiliz la curva de crecimiento de la OMS. Los nios/as fueron pesados/as en balanzas mecnicas. Para la medida de la altura, los mayores de dos aos fueron medidos con el tallimetro y los menores de 2 aos con cinta mtrica. Resultados: Se observ desnutricin en 53 nios que equivale al 15% de la muestra. De estos 60,4% padecan de desnutricin moderada y 39,6% desnutricin grave. El mayor porcentaje de desnutricin se encontr en el grupo de edad de 0 a 24 meses con 71,6%. El 77% de los nios tenan desnutricin crnica. Conclusiones: La prevalencia de desnutricin en indgenas en Yby Ya y Azotey es de 15%, lo que sobrepasa los ndices de desnutricin en menores de 5 aos del pas.]]></p></abstract> +<abstract abstract-type="short" xml:lang="en"><p><![CDATA[Introduction: Childhood is a crucial stage in the development of humans, which is why proper nutrition is essential for this stage. Child malnutrition is not just a problem of lack of food, it is rooted in deeper social problems. The prevalence of malnutrition in children under five years of age in Paraguay is 5.9% , according to the Paraguayan National Institute of Food and Nutrition. Objective: Determine the prevalence of malnutrition and the eating habits in children under five years of age in indigenous communities in the towns of Azote'y and Ya Yby. Materials and Methods: This was a descriptive, cross-sectional study conducted from January to April 2011, which identified the prevalence of child malnutrition in indigenous children in 11 ethnic Pa'i Tavyter and Mbya Guarani indigenous communities in Azote'y and Yby Yau. We examined 349 children under 5 years of age. The World Health Organization (WHO) growth charts were used to assess nutritional status. Children were weighed with mechanical scales. To measure height, children two and older were measured with a stadiometer and children younger than two were measured with tape. Results: Malnutrition was observed in 53 children (15% of the sample). Of these, 60.4% were suffering from moderate malnutrition and 39.6% from severe malnutrition. The highest percentage of malnutrition was found in the 0-24 month age group (71.6%). 77% of children had chronic malnutrition. Conclusions: The prevalence of malnutrition in indigenous children in Yby Ya and Azote'y is 15%, which exceeds the national malnutrition rates in children under five years of age.]]></p></abstract> +<kwd-group> +<kwd lng="es"><![CDATA[Desnutricin aguda]]></kwd> +<kwd lng="es"><![CDATA[desnutricin crnica]]></kwd> +<kwd lng="es"><![CDATA[indgenas]]></kwd> +<kwd lng="en"><![CDATA[Acute malnutrition]]></kwd> +<kwd lng="en"><![CDATA[chronic malnutrition]]></kwd> +<kwd lng="en"><![CDATA[indigenous]]></kwd> +</kwd-group> +</article-meta> +</front><body><![CDATA[ <p align="right"><font size="3" face="Verdana"><b>ARTÍCULO ORIGINAL</b></font></p> <p align="left"> </p> <p align="left"><font size="4" face="Verdana"><b>Prevalencia de desnutrición y hábitos alimentarios en niños menores de 5 años en las comunidades indígenas de Yby Yau y Azote’y, 2011</b></font></p> <p align="left"><font size="3" face="Verdana"><b><i>Prevalence of malnutrition and eating habits in children under 5 years of age in indigenous communities in Azote'y and Yby Yau, 2011</i></b></font></p> <p align="center"> </p> <p align="left"><font size="2" face="Verdana"><b>Syntia Carolina Ruiz Valiente<sup>(1)</sup>, Manuel Ruiz Cañete<sup>(2)</sup>, Bartola Cohene Velazquez<sup>(3)</sup></b></font></p> <p align="left"> <font size="2" face="Verdana">1. Hospital General Pediátrico Niños Acosta Ñu. Reducto-San Lorenzo, Paraguay.</font></p> <p align="left"> <font size="2" face="Verdana">2. Centro de Salud de Yby Yau. Paraguay.</font></p> <p align="left"> <font size="2" face="Verdana">3. Puesto de Salud de Paso Tuya. Azote’y. Paraguay.</font></p> <p align="left"> <font size="2" face="Verdana"><b>Correspondencia</b>: Syntia Carolina Ruiz Valiente. E-mail: scrv_py@hotmail.com</font></p> ]]></body> +<body><![CDATA[<p align="left"> <font size="2" face="Verdana">Recibido: 24/01/2015; Aceptado: 10/06/2015.</font></p> <p align="left"> <font size="2" face="Verdana"><i>Los autores declaran que no existen conflictos de interés en el presente estudio.</i></font></p> <p align="left"> </p> <hr size="1" noshade> <p align="left"><font size="2" face="Verdana"><b>RESUMEN</b></font></p> <p align="left"><font size="2" face="Verdana"><b>Introducción: </b>La infancia es una etapa trascendental en el desarrollo evolutivo del hombre, para lo cual es fundamental una adecuada nutrición. La desnutrición infantil no es solo un problema de falta de alimentos, es un conflicto social más profundo. La prevalencia de desnutrición en menores de 5 años del país es de 5,9% según datos del Instituto Nacional de Alimentación y Nutrición. <b>Objetivo</b>: Determinar la prevalencia de desnutrición y hábitos alimentarios en niños menores de 5 años de las comunidades indígenas de Yby Yaú y Azote’y. <b>Materiales y Métodos:</b> Estudio descriptivo, transversal, realizado de enero a abril del 2011, que identificó la prevalencia de desnutrición infantil en niños indígenas de las etnias Pa'i Tavyterã y Mbya Guaraní de 11 comunidades indígenas de Yby Yau y Azote’y. Fueron examinados 349 menores de 5 años de edad. Para la evaluación del estado nutricional se utilizó la curva de crecimiento de la OMS. Los niños/as fueron pesados/as en balanzas mecánicas. Para la medida de la altura, los mayores de dos años fueron medidos con el tallimetro y los menores de 2 años con cinta métrica. <b>Resultados:</b> Se observó desnutrición en 53 niños que equivale al 15% de la muestra. De estos 60,4% padecían de desnutrición moderada y 39,6% desnutrición grave. El mayor porcentaje de desnutrición se encontró en el grupo de edad de 0 a 24 meses con 71,6%. El 77% de los niños tenían desnutrición crónica. <b>Conclusiones:</b> La prevalencia de desnutrición en indígenas en Yby Yaú y Azote’y es de 15%, lo que sobrepasa los índices de desnutrición en menores de 5 años del país.</font></p> <p align="left"><font size="2" face="Verdana"><b>Palabras clave:</b> Desnutrición aguda, desnutrición crónica, indígenas.</font></p> <p align="left"> </p> <p align="left"><font size="2" face="Verdana"><b>ABSTRACT</b></font></p> <p align="left"><font size="2" face="Verdana"><b>Introduction:</b> Childhood is a crucial stage in the development of humans, which is why proper nutrition is essential for this stage. Child malnutrition is not just a problem of lack of food, it is rooted in deeper social problems. The prevalence of malnutrition in children under five years of age in Paraguay is 5.9% , according to the Paraguayan National Institute of Food and Nutrition. <b>Objective</b>: Determine the prevalence of malnutrition and the eating habits in children under five years of age in indigenous communities in the towns of Azote'y and Yaú Yby. <b>Materials and Methods</b>: This was a descriptive, cross-sectional study conducted from January to April 2011, which identified the prevalence of child malnutrition in indigenous children in 11 ethnic Pa'i Tavyterá and Mbya Guarani indigenous communities in Azote'y and Yby Yau. We examined 349 children under 5 years of age. The World Health Organization (WHO) growth charts were used to assess nutritional status. Children were weighed with mechanical scales. To measure height, children two and older were measured with a stadiometer and children younger than two were measured with tape. <b>Results</b>: Malnutrition was observed in 53 children (15% of the sample). Of these, 60.4% were suffering from moderate malnutrition and 39.6% from severe malnutrition. The highest percentage of malnutrition was found in the 0-24 month age group (71.6%). 77% of children had chronic malnutrition. <b>Conclusions</b>: The prevalence of malnutrition in indigenous children in Yby Yaú and Azote'y is 15%, which exceeds the national malnutrition rates in children under five years of age.</font></p> <p align="left"><font size="2" face="Verdana"><b>Keywords</b>: Acute malnutrition, chronic malnutrition, indigenous.</font></p> <hr size="1" noshade> ]]></body> +<body><![CDATA[<p align="justify"> </p> <p align="left"><font size="3" face="Verdana"><b>INTRODUCCIÓN</b></font></p> <p align="left"><font size="2" face="Verdana">La desnutrición es una enfermedad multisistémica, que afecta todos los órganos y sistemas del ser humano, es producida por una disminución drástica, aguda o crónica, en la disponibilidad de nutrimentos, ya sea por ingestión insuficiente, inadecuada absorción, exceso de pérdidas o la conjunción de dos o más de estos factores. Se manifiesta por grados de déficit antropométrico, signos y síntomas clínicos y alteraciones bioquímicas, hematológicas e inmunológicas (1).</font></p> <p align="left"><font size="2" face="Verdana">La población indígena está gravemente afectada por este problema, tal vez por ser un estrato olvidado y descuidado por la población en general y por el estado paraguayo. A pesar de las leyes, y de todos los proyectos que favorecen a esta esfera de la sociedad, aún existe un abismo inimaginable entre lo ideal y lo real. Mientras se elaboran programas que buscan dar mejores condiciones de vida a estas comunidades, que la mayoría de las veces solo quedan plasmados en el papel, los índices de desnutrición son alarmantes. Esto se debe probablemente a que en la sociedad posmoderna, la deforestación, el uso de agrotóxicos, la invasión de los terratenientes despojó a los nativos de sus tierras, obligándolos a vivir en situaciones carenciales, pues estos debido a su cultura esperan que la naturaleza les ofrezca el sustento diario. Las costumbres, la economía y la religión en las etnias Pa Tavyterã y Mby`a Guaraní están íntimamente relacionadas a la producción alimenticia e ingesta.</font></p> <p align="left"><font size="2" face="Verdana">Para el nativo guaraní es muy difícil comprender que el hombre es el que debe producir alimento para su sustento, pero como la sociedad actual obliga a ello, estos por no conseguir adaptarse a los cambios que se produjeron, están más expuestos a las carencias alimentarias. Según datos del gobierno central en el 2008, 41,8% de los niños indígenas menores de 5 años padecían de desnutrición.</font></p> <p align="left"><font size="2" face="Verdana">En un estudio realizado en México, la prevalencia de desnutrición en indígenas fue 39,4%(2). Un 44% presentó uno o más signos clínicos de malnutrición. Según el Instituto Nacional de Encuestas y Censos del Ecuador (2001 y 2006) 40,1% de los niños indígenas menores de 5 años tienen desnutrición crónica (3).</font></p> <p align="left"><font size="2" face="Verdana">En Caracas, se hizo un estudio con la población infantil warao en la comunidad de Yakariyene, estado Delta Amacuro, y ellos obtuvieron el siguiente resultado: El diagnóstico nutricional hallado con mayor frecuencia fue Nutrición normal (55%) seguida por Desnutrición Subclínica (15%) y Desnutrición Leve (12%). En líneas generales, un 55% de la población se encontraba en rangos de nutrición normal, mientras el 45% restante presentaba problema de malnutrición comprendiendo ésta por déficit y por exceso (4).</font></p> <p align="left"><font size="2" face="Verdana">En el Brasil en un estudio realizado para determinar el perfil nutricional de los aborígenes menores de 5 años de Kaingángen Paraná vieron que cuando utilizado los criterios propuestos por la OMS, se registró una alta prevalencia de déficit Estatura/Edad, con uno en cuatro niños (24,8%) que presentaba este diagnóstico. El déficit de Peso/Edad fue diagnosticado en 9,2% de los niños evaluados. Los índices de peso para la altura diagnosticaron solo tres niños (2,1%) como desnutridas agudas (5).</font></p> <p align="left"><font size="2" face="Verdana">En otro estudio realizado también en el Brasil, esta vez en Amazonia, con niños de la etnia Suruí se observó que los porcentajes de los niños con déficit en los índices de estatura para la edad fue 31,4%, peso para la edad 12,4% y peso para la estatura 0% (6).</font></p> <p align="left"><font size="2" face="Verdana">El objetivo del presente estudio es determinar la prevalencia de desnutrición en niños menores de 5 años de las comunidades indígenas de Yby-Yaú y Azote’y y conocer el comportamiento alimentario de los niños/as de las comunidades indígenas estudiadas.</font></p> ]]></body> +<body><![CDATA[<p align="justify"> </p> <p align="left"><font size="3" face="Verdana"><b>MATERIALES Y MÉTODOS</b></font></p> <p align="left"><font size="2" face="Verdana">Estudio transversal, descriptivo realizado en el periodo de enero a abril del año 2011, donde se identificó la prevalencia de desnutrición infantil en niños indígenas de las etnias Paĩ Tavyterã y Mby`a Guaraní en los distritos de Yby-Yaú y Azote’y.</font></p> <p align="left"><font size="2" face="Verdana">El tamaño muestral total fue de 370 niños, determinado a través de censo realizado por el Centro de Salud de Yby-Yaú y el Puesto de Salud de Paso Tuya. Para los fines del estudio fueron identificados 349 niños (94.3%) de niños recién nacidos a menores de 5 años en los distritos de Yby-Yaú y Azote'y.</font></p> <p align="left"><font size="2" face="Verdana">Las etnias que se encuentran dentro del área de estudio está compuesta por los mby`a guaraní y los paĩ tavyterã, distribuidas en las siguientes comunidades indígenas: Vy'apavẽ, Yrapey, Guyrakeha, Guyra Ñe'engatuamba, Sat;, San Juan, Mbery'o Jaguarymi, Ka'aguy Poty Rory, Yvyra'ija, Tukambiju y Takuaritiy.</font></p> <p align="left"><font size="2" face="Verdana">El trabajo se realizó por concentración, en los locales fijados por los líderes de las distintas comunidades. Fue aplicado un cuestionario a las madres, creado para el efecto por medio de entrevista. La edad de los niños fue dada por las madres, pues la mayoría de estas no cuentan con registro de nacimiento, ni siquiera certificado de nacido vivo.</font></p> <p align="left"><font size="2" face="Verdana">Para la evaluación del estado nutricional de los niños se optó por la curva del gráfico de crecimiento de la Organización Mundial de la Salud (OMS) lo cual está contenido en la libreta del niño y la niña. Los niños/as fueron pesados/as en balanzas mecánicas, los que ya conseguían quedarse de pie fueron pesados en balanza de pie y los niños menores de 1 año en balanzas colgantes.</font></p> <p align="left"><font size="2" face="Verdana">Para la medida de la altura, los niños mayores de dos años fueron colocados en posición de pie, bien rectos, y fueron medidos con el tallimetro. La talla de los niños menores de 2 años fue realizada con cinta métrica con el niño/a en decúbito supino en superficie recta.</font></p> <p align="left"><font size="2" face="Verdana">Los datos fueron analizados manualmente, y los gráficos confeccionados con el programa Microsoft Office Excel 2007.</font></p> <p align="justify"> </p> ]]></body> +<body><![CDATA[<p align="left"><font size="3" face="Verdana"><b>RESULTADOS</b></font></p> <p align="left"><font size="2" face="Verdana">Se evaluaron 349 niños, que representan el 94,3% del total de aborígenes menores de 5 años de las comunidades de Yby-Yaú y Azote’y. Del total de 349 niños, 69 % (240) son Pa; Tavyterã y 31% (109) Mby`a Guaraní. </font></p> <p align="left"><font size="2" face="Verdana">La comunidad con el mayor porcentaje de niños fue la de Vy'ãpavẽ (36,4%), y la de menor frecuencia fue la comunidad de Tekoha Kagãtã, que es una comunidad recién formada localizada en Pasiño (<a href="#2a02f1">Figura 1</a>).</font></p> <p align="center"><a name="2a02f1"></a></p> <p align="left"> </p> <p align="center"><img src="../../../../../img/revistas/ped/v42n2/2a02f1.jpg"></p> <p align="left"><font size="2" face="Verdana">Viendo el perfil nutricional de los niños, se pudo observar que 61% de los niños/as no están desnutridos, 24% de los niños/as están en riesgo de desnutrición y 15% están con desnutrición. Aunque se trata de un estrato social desfavorecido también se observa índice de sobrepeso y obesidad, en las comunidades de Vy'ãpavẽ e Yrapey (<a href="#2a02f2">Figura 2</a>).</font></p> <p align="center"><a name="2a02f2"></a></p> <p align="left"> </p> <p align="center"><img src="../../../../../img/revistas/ped/v42n2/2a02f2.jpg"></p> ]]></body> +<body><![CDATA[<p align="left"><font size="2" face="Verdana">Teniendo presente los gráficos de Talla/Edad la prevalencia de desnutrición crónica es bastante elevada, pues 77% de los niños padecen de desnutrición crónica. El mayor índice de desnutrición se encuentran en los primeros 24 meses de vida (<a href="#2a02t1">Tabla 1</a>). De los 53 niños con desnutrición, 60,4% padecen de desnutrición moderada, y el 39,6% desnutrición grave. Siendo que el mayor porcentaje de desnutrición se observa en Vy'ãpavẽ.</font></p> <p align="center"><a name="2a02t1"></a></p> <p align="left"> </p> <p align="center"><img src="../../../../../img/revistas/ped/v42n2/2a02t1.jpg"></p> <p align="left"><font size="2" face="Verdana">Se estudió además el comportamiento alimentario de estos niños, viendo que alimentos preferencialmente hacen parte de su dieta y la edad de introducción de los mismos, la mayoría de las madres introducen algún tipo alimento entre los 6 y 8 meses de edad (<a href="#2a02f3">Figura 3</a>) y los primeros alimentos introducidos dependen del lugar donde estos habitan. El caldo de pescado es uno de los primeros alimentos introducidos en las comunidades que viven cerca de los ríos, entretanto el 60% inician la alimentación con caldo de arroz y caldo de fideo.</font></p> <p align="center"><a name="2a02f3"></a></p> <p align="left"> </p> <p align="center"><img src="../../../../../img/revistas/ped/v42n2/2a02f3.jpg"></p> <p align="left"><font size="2" face="Verdana">Al observar la frecuencia en que se alimentan estos niños, el 64% se alimenta tres veces al día, el 20% menos de 3 veces al día y solo el 16 % más de tres veces al día.</font></p> <p align="left"><font size="2" face="Verdana">El principal nutriente en la dieta son los carbohidratos, el 47% de los niños consumen carbohidratos más de 5 veces por semana, y el 21% menos de 3 veces por semana. El mayor porcentaje de consumo de proteínas se observa en las comunidades que se encuentran cerca de ríos (Guyra Ñe`engatuamba y Mbery'o Jaguarymi), siendo que 70% consume proteínas menos de 3 veces por semana, y solo el 3% más de cinco veces por semana. El consumo de verduras y hortalizas es muy escaso, el 91% consume verduras y hortalizas menos de 3 veces por semana, el 2% más de 5 veces y 7% entre 3 y 5 veces por semana.</font></p> ]]></body> +<body><![CDATA[<p align="justify"> </p> <p align="left"><font size="3" face="Verdana"><b>DISCUSIÓN</b></font></p> <p align="left"><font size="2" face="Verdana">A lo largo de toda la historia de la humanidad, la desnutrición ha sido una patología de las clases sociales menos privilegiadas, son los que no poseen las condiciones necesarias para tener una vida digna, donde la educación, salud, recursos económicos son miserables, donde esta dolencia alcanza su auge (7).</b></font></p> <p align="left"><font size="2" face="Verdana">Según los datos del Censo realizado por la Unidad de Salud Indígena que se encuentra en el Distrito de Yby-Yaú, los Puestos de Salud de Yby- Yaú y Azote’y en el tercer trimestre del Año 2010, se encontraron 328 niños de hasta 60 meses (8). Al realizar los trabajos de campo, este número se elevó a 349 individuos, por lo que se hizo un nuevo censo solo con los niños de este grupo etario. Ese fenómeno tal vez, se deba a la migraciones que se desarrollan normalmente entre los guaraní. Al observar la historia, y también por la experiencia que se adquirió durante el trabajo de campo, se pudo observar la familia lingüística a la cual pertenecen los mby`a y los pa; (la guaraní) son nómadas, es común que migren a otras comunidades, en un mismo Tekoha (9,10).</b></font></p> <p align="left"><font size="2" face="Verdana">La población diana fue de 370 niños menores de 5 años de los cuales se llegó a entrevistar a las madres de 349 y se hizo las mediciones antropométricas posteriormente. En la mayoría de las comunidades indígenas se obtuvo el 100% de participación, son excepciones las comunidades de Yrapey y Takuaritiy.</b></font></p> <p align="left"><font size="2" face="Verdana">Del total de niños/as, la etnia de mayor prevalencia fue la de Pa; Tavyterã. En relación al sexo, las comunidades son bastante equilibradas, con una ligera prevalencia del sexo masculino sobre el femenino.</b></font></p> <p align="left"><font size="2" face="Verdana">Según datos de la UNICEF en Paraguay se observa 3,4% de desnutrición aguda en niños menores de 5 años (11). La prevalencia de desnutrición en los niños paraguayos menores de 5 años en el área rural es de 5,9% y en el área urbana es de 4,5% (12). Existen pocas publicaciones sobre este tema en aborígenes menores de 5 años, siendo que el mayor número de publicaciones fue realizado por el Brasil (12,4%), México (39,4%) y Ecuador.</b></font></p> <p align="left"><font size="2" face="Verdana">La prevalencia de desnutrición en las comunidades indígenas de Yby-Yaú y Azote’y es de 15,2%, observando los gráficos de Peso/edad si de 2 años y Peso/Talla en mayores de 2 años y menores de 5 años. Las comunidades donde la desnutrición son más prevalentes son Guyrakeha e Yvyra'ija; en Sat; y Tekoha Kagatã no se encontró niños desnutridos.</b></font></p> <p align="left"><font size="2" face="Verdana">De 53 niños con desnutrición, 60,4% padecen de desnutrición moderada, y el 39,6% desnutrición grave. El grupo con mayor índice de desnutrición, se encuentra durante los primeros 24 meses, pues es en esta etapa donde el organismo requiere una mayor cantidad de nutrientes por el mayor crecimiento. Además, después de los 6 meses se inicia la introducción de otros alimentos. Estos dos factores, asociados aumentan el índice de desnutrición en este grupo de edad.</b></font></p> <p align="left"><font size="2" face="Verdana">De la población total de los niños estudiados el 23,8% están con riesgo de desnutrición. Según el Instituto Nacional de Alimentación y Nutrición (INAN) en el año 2010, 13,6% de niños menores de 5 años del área urbana y 16,2% del área rural del Paraguay sufren desnutrición crónica. En una encuesta realizada por la Dirección General de Estadística, Encuestas y Censos en el año 2008, 41,8% de los niños/as indígenas menores de cinco años padecen de desnutrición crónica. Observadas las medidas de Talla/Edad el 77% de los niños padecen de desnutrición crónica. Ese dato es alarmante, porque la desnutrición crónica es consecuencia de una carencia prolongada de alimentos o enfermedades sucesivas. En Tukambiju, Mbery'o Jaguarymi, Guyrakeha, Yvyra'ija y Sat; son comunidades con una prevalencia mayor al 80% de niños/as con talla baja para la edad.</b></font></p> ]]></body> +<body><![CDATA[<p align="left"><font size="2" face="Verdana">El índice de desnutrición en indígenas en los distritos de Yby-Yaú y Azote’y, sobrepasa la prevalencia general de desnutrición en menores de 5 años del país, lo cual está alrededor de 5.9% según datos del INAN.</b></font></p> <p align="left"><font size="2" face="Verdana">En las comunidades indígenas se puede observar que un porcentaje razonable introduce alimentos entre los 6 meses y antes de los 9 meses. El porcentaje de los que introducen antes de los 6 meses es de 18,6% y entre los 9 meses y un año es de 27%. Se pudo observar que, ocho niños tuvieron lactancia materna exclusiva por más de 1 año. Todos los niños/as con lactancia materna exclusiva en la fecha de la recolección de datos tenía menos de 6 meses o 6 meses. El caldo de fideo y de arroz ocupa el primer y segundo lugar respectivamente como primer alimento introducido por las madres. Los alimentos que deberían ser introducidos inicialmente como el puré de frutas y verduras ocupan un pequeño porcentaje en la lista. Otros alimentos que se tendrían que introducir después de los 9 meses, de preferencia a los un año, como por ejemplo el caldo de poroto, caldo de pescado, leche de vaca y huevo son los primeros alimentos que se introducen.</b></font></p> <p align="left"><font size="2" face="Verdana">El 64% de los niños se alimentan tres veces al día, el 20,5% menos de tres veces y 15,5% más de tres veces al día.</b></font></p> <p align="left"><font size="2" face="Verdana">El 69,5% de los niños/as de las comunidades indígenas de Yby-Yaú y Azote’y consumen proteínas menos de tres veces por semana; 27,3% consumen de tres a cinco veces por semana los diferentes tipos de proteínas, teniendo predominancia el consumo de pez. Solo 3,2% consume proteínas más de 5 veces. Las comunidades que viven cerca de bosques, ríos o arroyos son los que más consumen proteínas.</b></font></p> <p align="left"><font size="2" face="Verdana">Los carbohidratos son la principal fuente de alimentación de los niños y niñas de las comunidades indígenas de Yby-Yaú y Azote’y. Eso se debe a que son los alimentos de más fácil adquisición y los más accesibles económicamente hablando.</b></font></p> <p align="left"><font size="2" face="Verdana">En las comunidades indígenas el consumo de verduras y hortalizas es escaso. Las comunidades que más consumen verduras y hortalizas son Mberyo Jaguarymi y Takuaritiy.</b></font></p> <p align="left"><font size="2" face="Verdana">Este trabajo refleja la realidad de las comunidades indígenas de los dos distritos observados, no podemos extrapolar estas mismas cifras en el departamento de Concepción, o en todo el país por el tamaño de la muestra, es necesario hacer nuevos estudios con un tamaño muestral mayor para obtener una visión del verdadero estado nutricional de los niños indígenas. El porcentaje de desnutrición es alto, pero se trata de distritos con no muchos recursos económicos, donde la pobreza es una realidad aún en otros estratos sociales.</b></font></p> <p align="left"><font size="2" face="Verdana">La realidad indígena es un problema real, y una manera de reducir estas cifras es enseñándoles a producir su propio alimento. Para ello no debemos luchar con su cultura ni intentar hacerlos ver el mundo a través de nuestra realidad, sino dentro de sus costumbres encontrar formas de que ellos tengan condiciones de un mejor porvenir.</font></p> <p align="justify"> </p> <p align="left"><font size="3" face="Verdana"><b>AGRADECIMIENTOS</b></font></p> ]]></body> +<body><![CDATA[<p align="left"><font size="2" face="Verdana">A las comunidades indígenas que participaron en nuestro estudio, los profesionales de blanco del Centro de Salud de Yby-Yau y Azote’y, a la Comunidad de Hermanas de la Divina Providencia de Yby-Yau, a la Dra. Blanca Villalba y a la Dra. Gloria Martínez.</font></p> <p align="justify"> </p> <p align="left"><font size="3" face="Verdana"><b>REFERENCIAS</b></font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">1. Monteiro CA. Fome, desnutrição e pobreza: além da semântica. Saúde Soc. 2003;12(1):7-11. [ <a href="javascript:void(0);" onclick="javascript: window.open('/scielo.php?script=sci_nlinks&ref=102986&pid=S1683-9803201500020000200001&lng=','','width=640,height=500,resizable=yes,scrollbars=1,menubar=yes,');">Links</a> ]<!-- end-ref --></font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">2. Viñas MR, Frías ML, Verdú JM. Entorno social y desnutrición en niños de 1 a 4 años de comunidades indígenas de México. Rev Esp Nutr Comunitaria. 2005;11(3):128-34. [ <a href="javascript:void(0);" onclick="javascript: window.open('/scielo.php?script=sci_nlinks&ref=102988&pid=S1683-9803201500020000200002&lng=','','width=640,height=500,resizable=yes,scrollbars=1,menubar=yes,');">Links</a> ]<!-- end-ref --></font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">3. INEC. Ecuador: 40,1% de indígenas con desnutrición crónica. Ecuador: Estudio del INEC; 2009. [ <a href="javascript:void(0);" onclick="javascript: window.open('/scielo.php?script=sci_nlinks&ref=102990&pid=S1683-9803201500020000200003&lng=','','width=640,height=500,resizable=yes,scrollbars=1,menubar=yes,');">Links</a> ]<!-- end-ref --></font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">4. Chumpitaz D, Russo A, Del NogaL B, Case C, Lares M. Evaluación nutricional de la población infantil warao en la comunidad de Yakariyene, estado Delta Amacuro, agosto-octubre 2004. AVFT. 2006;25(1):26-31. [ <a href="javascript:void(0);" onclick="javascript: window.open('/scielo.php?script=sci_nlinks&ref=102992&pid=S1683-9803201500020000200004&lng=','','width=640,height=500,resizable=yes,scrollbars=1,menubar=yes,');">Links</a> ]<!-- end-ref --></font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">5. Kuhl AM, Tittoni C, Leite MS, Bastos JL. Perfil Nutricional e fatores associados à ocorrência de desnutrição entre crianças indígenas Kaingáng da Terra Indígena de Mangueirinha, Paraná, Brasil. Cad Saúde Pública. 2009;25(2):409-420. [ <a href="javascript:void(0);" onclick="javascript: window.open('/scielo.php?script=sci_nlinks&ref=102994&pid=S1683-9803201500020000200005&lng=','','width=640,height=500,resizable=yes,scrollbars=1,menubar=yes,');">Links</a> ]<!-- end-ref --></font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">6. Orellana JD, Coimbra Jr. CE, Lourenço AE, Santos RV. Estado nutricional e anemia en crianças Suruí, Amazônia, Brasil. J Pediatr (Rio J). 2006;82(5):383-88. [ <a href="javascript:void(0);" onclick="javascript: window.open('/scielo.php?script=sci_nlinks&ref=102996&pid=S1683-9803201500020000200006&lng=','','width=640,height=500,resizable=yes,scrollbars=1,menubar=yes,');">Links</a> ]<!-- end-ref --></font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">7. Organización de las Naciones Unidas. Foro permanente para las cuestiones indígenas: informe sobre el quinto período de sesiones (15 a 26 de mayo de 2006). Nueva York: Naciones Unidas; 2006. [ <a href="javascript:void(0);" onclick="javascript: window.open('/scielo.php?script=sci_nlinks&ref=102998&pid=S1683-9803201500020000200007&lng=','','width=640,height=500,resizable=yes,scrollbars=1,menubar=yes,');">Links</a> ]<!-- end-ref --></font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">8. Centro de Salud de Yby-Yau. Censo local de las comunidades indígenas. Yby-Yau; 2010. [ <a href="javascript:void(0);" onclick="javascript: window.open('/scielo.php?script=sci_nlinks&ref=103000&pid=S1683-9803201500020000200008&lng=','','width=640,height=500,resizable=yes,scrollbars=1,menubar=yes,');">Links</a> ]<!-- end-ref --></font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">9. Chase-Sardi M, Brun A, Enciso MA. Situación sociocultural, económica, jurídico-político actual de las comunidades indígenas del Paraguay. Asunción: UCA; 1989. [ <a href="javascript:void(0);" onclick="javascript: window.open('/scielo.php?script=sci_nlinks&ref=103002&pid=S1683-9803201500020000200009&lng=','','width=640,height=500,resizable=yes,scrollbars=1,menubar=yes,');">Links</a> ]<!-- end-ref --></font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">10. Meli B, Grunberg G, Grunberg F. Pa -Tavyter: etnografía guaraní del Paraguay contemporáneo. 2da. ed. Asunción: Centro de Estudios Antropólogicos de la Universidad Católica; 2008. [ <a href="javascript:void(0);" onclick="javascript: window.open('/scielo.php?script=sci_nlinks&ref=103004&pid=S1683-9803201500020000200010&lng=','','width=640,height=500,resizable=yes,scrollbars=1,menubar=yes,');">Links</a> ]<!-- end-ref --></font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">11. FAO. Panorama de la seguridad alimentaria y nutricional en América Latina y el Caribe 2013. FAO; 2014. [ <a href="javascript:void(0);" onclick="javascript: window.open('/scielo.php?script=sci_nlinks&ref=103006&pid=S1683-9803201500020000200011&lng=','','width=640,height=500,resizable=yes,scrollbars=1,menubar=yes,');">Links</a> ]<!-- end-ref --> </font></p> <!-- ref --><p align="left"><font size="2" face="Verdana">12. Masi C, Sánchez Bernal S, Dallman D, Rodas A, Morinigo G, Mendoza L. Perfil nutricional de niños menores de 5 años que acuden a servicios públicos de salud en el Paraguay. Asunción: INAN; 2010. 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+<publisher-loc><![CDATA[Asuncin ]]></publisher-loc> +<publisher-name><![CDATA[INAN]]></publisher-name> +</nlm-citation> +</ref> +</ref-list> +</back> +</article> diff --git a/python/tests/files/small.json b/python/tests/files/small.json new file mode 100644 index 0000000..3f84ea4 --- /dev/null +++ b/python/tests/files/small.json @@ -0,0 +1,52 @@ +{ + "title": "Dummy Example File", + "authors": [ + { + "name": "Brewster Kahle", + "given_name": "Brewster", + "surname": "Kahle", + "affiliation": { + "department": "Faculty ofAgricultrial Engineering", + "laboratory": "Plant Physiology Laboratory", + "institution": "Technion-Israel Institute of Technology", + "address": { + "postCode": "32000", + "settlement": "Haifa", + "country": "Israel" + } + } + }, + {"name": "J Doe", "given_name": "J", "surname": "Doe"} + ], + "journal": { + "name": "Dummy Example File. Journal of Fake News. pp. 1-2. ISSN 1234-5678" + }, + "date": "2000", + "citations": [ + { "authors": [{"name": "A Seaperson", "given_name": "A", "surname": "Seaperson"}], + "date": "2001", + "id": "b0", + "index": 0, + "issue": null, + "journal": "Letters in the Alphabet", + "publisher": null, + "title": "Everything is Wonderful", + "url": null, + "volume": "20"}, + { "authors": [], + "date": "2011-03-28", + "id": "b1", + "index": 1, + "issue": null, + "journal": "The Dictionary", + "publisher": null, + "title": "All about Facts", + "url": null, + "volume": "14"} + ], + "abstract": "Everything you ever wanted to know about nothing", + "body": "Introduction \nEverything starts somewhere, as somebody [1] once said. \n\n In Depth \n Meat \nYou know, for kids. \n Potatos \nQED.", + "grobid_timestamp": "2018-04-02T00:31+0000", + "grobid_version": "0.5.1-SNAPSHOT", + "language_code": "en" +} diff --git a/python/tests/files/small.xml b/python/tests/files/small.xml new file mode 100644 index 0000000..4de4059 --- /dev/null +++ b/python/tests/files/small.xml @@ -0,0 +1,120 @@ +<?xml version="1.0" encoding="UTF-8"?> +<TEI xmlns="http://www.tei-c.org/ns/1.0" +xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" +xsi:schemaLocation="http://www.tei-c.org/ns/1.0 /srv/grobid/grobid-0.5.1/grobid-home/schemas/xsd/Grobid.xsd" + xmlns:xlink="http://www.w3.org/1999/xlink"> + <teiHeader xml:lang="en"> + <encodingDesc> + <appInfo> + <application version="0.5.1-SNAPSHOT" ident="GROBID" when="2018-04-02T00:31+0000"> + <ref target="https://github.com/kermitt2/grobid">GROBID - A machine learning software for extracting information from scholarly documents</ref> + </application> + </appInfo> + </encodingDesc> + <fileDesc> + <titleStmt> + <title level="a" type="main">Dummy Example File</title> + </titleStmt> + <publicationStmt> + <publisher/> + <availability status="unknown"><licence/></availability> + <date type="published" when="2000">2000</date> + </publicationStmt> + <sourceDesc> + <biblStruct> + <analytic> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">Brewster</forename><surname>Kahle</surname></persName> + <affiliation key="aff0"> + <orgName type="department">Faculty ofAgricultrial Engineering</orgName> + <orgName type="laboratory">Plant Physiology Laboratory</orgName> + <orgName type="institution">Technion-Israel Institute of Technology</orgName> + <address> + <postCode>32000</postCode> + <settlement>Haifa</settlement> + <country key="IL">Israel</country> + </address> + </affiliation> + </author> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">J</forename><surname>Doe</surname></persName> + </author> + <author> + <affiliation key="aff0"> + <orgName type="institution">Internet Archive</orgName> + </affiliation> + </author> + <title level="a" type="main">Dummy Example File</title> + </analytic> + <monogr> + <title level="m">Dummy Example File. Journal of Fake News. pp. 1-2. ISSN 1234-5678</title> + <imprint> + <date type="published" when="2000">2000</date> + </imprint> + </monogr> + </biblStruct> + </sourceDesc> + </fileDesc> + <profileDesc> + <textClass> + <keywords> + <term>Fake Data</term> + </keywords> + </textClass> + <abstract> + <p>Everything you ever wanted to know about nothing</p> + </abstract> + </profileDesc> + </teiHeader> + <text xml:lang="en"> + <body> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="1">Introduction</head><p> +Everything starts somewhere, as somebody<ref type="bibr" target="#b0">[1]</ref> once said.</p></div> + +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="2">In Depth</head></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="2.1">Meat</head><p> +You know, for kids.</p></div> +<div xmlns="http://www.tei-c.org/ns/1.0"><head n="2.2">Potatos</head><p> +QED.</p></div> + </body> + <back> + <div type="references"> + + <listBibl> + +<biblStruct xml:id="b0"> + <analytic> + <title level="a" type="main">Everything is Wonderful</title> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="middle">A</forename><surname>Seaperson</surname></persName> + </author> + </analytic> + <monogr> + <title level="j">Letters in the Alphabet</title> + <imprint> + <biblScope unit="volume">20</biblScope> + <biblScope unit="page" from="1" to="11" /> + <date type="published" when="2001" /> + </imprint> + </monogr> +</biblStruct> + +<biblStruct xml:id="b1"> + <analytic> + <title level="a" type="main">All about Facts</title> + </analytic> + <monogr> + <title level="j">The Dictionary</title> + <imprint> + <biblScope unit="volume">14</biblScope> + <date type="published" when="2011-03-28" /> + </imprint> + </monogr> + <note>None</note> +</biblStruct> + + </listBibl> + </div> + </back> + </text> +</TEI> diff --git a/python/tests/test_grobid.py b/python/tests/test_grobid.py new file mode 100644 index 0000000..36d90ef --- /dev/null +++ b/python/tests/test_grobid.py @@ -0,0 +1,79 @@ + +import pytest +import struct +import responses + +from sandcrawler import GrobidClient, GrobidWorker, CdxLinePusher, BlackholeSink, WaybackClient +from test_wayback import wayback_client, cdx_client + + +FAKE_PDF_BYTES = b"%PDF SOME JUNK" + struct.pack("!q", 112853843) + +with open('tests/files/23b29ea36382680716be08fc71aa81bd226e8a85.xml', 'rb') as f: + REAL_TEI_XML = f.read() + +@pytest.fixture +def grobid_client(): + client = GrobidClient( + host_url="http://dummy-grobid", + ) + return client + +@responses.activate +def test_grobid_503(grobid_client): + + status = b'{"status": "done broke due to 503"}' + responses.add(responses.POST, + 'http://dummy-grobid/api/processFulltextDocument', status=503, + body=status) + + resp = grobid_client.process_fulltext(FAKE_PDF_BYTES) + + # grobid gets POST 1x times + assert len(responses.calls) == 1 + + assert resp['status_code'] == 503 + assert resp['status'] == "error" + +@responses.activate +def test_grobid_success(grobid_client): + + responses.add(responses.POST, + 'http://dummy-grobid/api/processFulltextDocument', status=200, + body=REAL_TEI_XML, content_type='text/xml') + + resp = grobid_client.process_fulltext(FAKE_PDF_BYTES) + + # grobid gets POST 1x times + assert len(responses.calls) == 1 + + assert resp['status_code'] == 200 + assert resp['status'] == "success" + #print(type(resp['tei_xml'])) + #print(type(REAL_TEI_XML)) + assert resp['tei_xml'] == REAL_TEI_XML.decode('ISO-8859-1') + +@responses.activate +def test_grobid_worker_cdx(grobid_client, wayback_client): + + sink = BlackholeSink() + worker = GrobidWorker(grobid_client, wayback_client, sink=sink) + + responses.add(responses.POST, + 'http://dummy-grobid/api/processFulltextDocument', status=200, + body=REAL_TEI_XML, content_type='text/xml') + + with open('tests/files/example.cdx', 'r') as cdx_file: + pusher = CdxLinePusher( + worker, + cdx_file, + filter_http_statuses=[200, 226], + filter_mimetypes=['application/pdf'], + ) + pusher_counts = pusher.run() + assert pusher_counts['total'] + assert pusher_counts['pushed'] == 7 + assert pusher_counts['pushed'] == worker.counts['total'] + + assert len(responses.calls) == worker.counts['total'] + diff --git a/python/tests/test_grobid2json.py b/python/tests/test_grobid2json.py new file mode 100644 index 0000000..8497b10 --- /dev/null +++ b/python/tests/test_grobid2json.py @@ -0,0 +1,22 @@ + +import xml +import json +import pytest +from grobid2json import * + + +def test_small_xml(): + + with open('tests/files/small.xml', 'r') as f: + tei_xml = f.read() + with open('tests/files/small.json', 'r') as f: + json_form = json.loads(f.read()) + + assert teixml2json(tei_xml) == json_form + +def test_invalid_xml(): + + with pytest.raises(xml.etree.ElementTree.ParseError): + teixml2json("this is not XML") + with pytest.raises(ValueError): + teixml2json("<xml></xml>") diff --git a/python/tests/test_html.py b/python/tests/test_html.py new file mode 100644 index 0000000..9a81852 --- /dev/null +++ b/python/tests/test_html.py @@ -0,0 +1,33 @@ + +import json +import pytest +import responses + +from sandcrawler.html import extract_fulltext_url + +def test_extract_fulltext_url(): + + resp = extract_fulltext_url("asdf", b"asdf") + assert resp == {} + + resp = extract_fulltext_url( + "http://dummy-site/", + b"""<html> + <head> + <meta name="citation_pdf_url" content="http://www.example.com/content/271/20/11761.full.pdf"> + </head> + <body> + <h1>my big article here</h1> + blah + </body> + </html>""" + ) + assert resp['pdf_url'] == "http://www.example.com/content/271/20/11761.full.pdf" + assert resp['technique'] == "citation_pdf_url" + + with open('tests/files/plos_one_article.html', 'rb') as f: + resp = extract_fulltext_url( + "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0213978", + f.read(), + ) + assert resp['pdf_url'] == "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0213978&type=printable" diff --git a/python/tests/test_html_ingest.py b/python/tests/test_html_ingest.py new file mode 100644 index 0000000..e6e48ac --- /dev/null +++ b/python/tests/test_html_ingest.py @@ -0,0 +1,14 @@ + +import datetime +import pytest + +from sandcrawler.html_ingest import * + + +def test_html_extract_ojs3() -> None: + + with open('tests/files/first_monday_ojs3_fulltext.html', 'rb') as f: + ojs3_html = f.read() + + fulltext = html_extract_body_teixml(ojs3_html) + assert fulltext['status'] == 'success' diff --git a/python/tests/test_html_metadata.py b/python/tests/test_html_metadata.py new file mode 100644 index 0000000..bf26a98 --- /dev/null +++ b/python/tests/test_html_metadata.py @@ -0,0 +1,229 @@ + +import datetime +import pytest + +from sandcrawler.html_metadata import * + + +def test_html_metadata_plos() -> None: + + with open('tests/files/plos_one_article.html', 'r') as f: + plos_html = f.read() + + meta = html_extract_biblio("http://example.org", HTMLParser(plos_html)) + assert meta is not None + assert meta.title == "Assessment on reticuloendotheliosis virus infection in specific-pathogen-free chickens based on detection of yolk antibody" + assert meta.doi == "10.1371/journal.pone.0213978" + assert meta.pdf_fulltext_url == "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0213978&type=printable" + assert meta.contrib_names == [ + "Yang Li", + "Tuanjie Wang", + "Lin Wang", + "Mingjun Sun", + "Zhizhong Cui", + "Shuang Chang", + "Yongping Wu", + "Xiaodong Zhang", + "Xiaohui Yu", + "Tao Sun", + "Peng Zhao", + ] + assert meta.container_name == "PLOS ONE" + assert meta.container_abbrev == "PLOS ONE" + # "Apr 22, 2019" + assert meta.release_date == datetime.date(year=2019, month=4, day=22) + assert meta.first_page == "e0213978" + assert meta.issue == "4" + assert meta.volume == "14" + assert meta.container_issn == "1932-6203" + assert meta.publisher == "Public Library of Science" + assert meta.raw_references and "citation_title=Reticuloendotheliosis virus sequences within the genomes of field strains of fowlpox virus display variability;citation_author=P Singh;citation_author=W. M. Schnitzlein;citation_author=D. N. Tripathy;citation_journal_title=J. Virol;citation_volume=77;citation_number=77;citation_first_page=5855;citation_last_page=5862;citation_publication_date=2003;" in meta.raw_references + assert meta.release_type == "article-journal" + assert meta.pdf_fulltext_url == "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0213978&type=printable" + + +def test_html_metadata_elife() -> None: + + with open('tests/files/elife_article.html', 'r') as f: + elife_html = f.read() + + meta = html_extract_biblio("https://elifesciences.org/articles/44753", HTMLParser(elife_html)) + assert meta is not None + assert meta.title == "Parallel visual circuitry in a basal chordate" + assert meta.doi == "10.7554/eLife.44753" + assert meta.contrib_names == [ + "Matthew J Kourakis", + "Cezar Borba", + "Angela Zhang", + "Erin Newman-Smith", + "Priscilla Salas", + "B Manjunath", + "William C Smith", + ] + assert meta.container_name == "eLife" + # 2019-04-18 + assert meta.release_date == datetime.date(year=2019, month=4, day=18) + assert meta.publisher == "eLife Sciences Publications Limited" + assert meta.pdf_fulltext_url == "https://elifesciences.org/download/aHR0cHM6Ly9jZG4uZWxpZmVzY2llbmNlcy5vcmcvYXJ0aWNsZXMvNDQ3NTMvZWxpZmUtNDQ3NTMtdjIucGRm/elife-44753-v2.pdf?_hash=CfyqOqVryCR4OjcMTfcdpeIWAGZznmh9jXksYKYChCw%3D" + + +def test_html_metadata_peerj() -> None: + + with open('tests/files/peerj_oa_article.html', 'r') as f: + peerj_html = f.read() + + meta = html_extract_biblio("http://example.org", HTMLParser(peerj_html)) + assert meta is not None + assert meta.title == "The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles" + assert meta.doi == "10.7717/peerj.4375" + assert meta.contrib_names == [ + "Heather Piwowar", + "Jason Priem", + "Vincent Larivière", + "Juan Pablo Alperin", + "Lisa Matthias", + "Bree Norlander", + "Ashley Farley", + "Jevin West", + "Stefanie Haustein", + ] + assert meta.container_name == "PeerJ" + # "2018-02-13" + assert meta.release_date == datetime.date(year=2018, month=2, day=13) + assert meta.xml_fulltext_url and ".xml" in meta.xml_fulltext_url + + +def test_html_metadata_nature() -> None: + + with open('tests/files/nature_article.html', 'r') as f: + nature_html = f.read() + + meta = html_extract_biblio("http://example.org", HTMLParser(nature_html)) + assert meta is not None + assert meta.title == "More than 100 scientific journals have disappeared from the Internet" + assert meta.doi == "10.1038/d41586-020-02610-z" + assert meta.contrib_names == [ + "Diana Kwon", + ] + assert meta.container_name == "Nature" + # "2020-09-10" + assert meta.release_date == datetime.date(year=2020, month=9, day=10) + assert meta.publisher == "Nature Publishing Group" + # note: some error in dublin code in nature HTML resulting in duplication + assert meta.abstract == "Researchers have identified dozens of open-access journals that went offline between 2000 and 2019, and hundreds more that could be at risk. Researchers have identified dozens of open-access journals that went offline between 2000 and 2019, and hundreds more that could be at risk." + + +def test_html_metadata_ojs3() -> None: + + with open('tests/files/first_monday_ojs3_landingpage.html', 'r') as f: + ojs3_html = f.read() + + meta = html_extract_biblio("http://example.org", HTMLParser(ojs3_html)) + assert meta is not None + assert meta.title == "Surveillance, stigma & sociotechnical design for HIV" + assert meta.doi == "10.5210/fm.v25i10.10274" + assert meta.contrib_names == [ + "Calvin Liang", + "Jevan Alexander Hutson", + "Os Keyes", + ] + assert meta.container_name == "First Monday" + assert meta.container_abbrev == "1" # NOTE: bad source metadata + assert meta.container_issn == "1396-0466" + # "2020/09/10" + assert meta.release_date == datetime.date(year=2020, month=9, day=10) + assert meta.lang == "en" + assert meta.abstract == "Online dating and hookup platforms have fundamentally changed people’s day-to-day practices of sex and love — but exist in tension with older social and medicolegal norms. This is particularly the case for people with HIV, who are frequently stigmatized, surveilled, ostracized, and incarcerated because of their status. Efforts to make intimate platforms “work” for HIV frequently focus on user-to-user interactions and disclosure of one’s HIV status but elide both the structural forces at work in regulating sex and the involvement of the state in queer lives. In an effort to foreground these forces and this involvement, we analyze the approaches that intimate platforms have taken in designing for HIV disclosure through a content analysis of 50 current platforms. We argue that the implicit reinforcement of stereotypes about who HIV is or is not a concern for, along with the failure to consider state practices when designing for data disclosure, opens up serious risks for HIV-positive and otherwise marginalized people. While we have no panacea for the tension between disclosure and risk, we point to bottom-up, communal, and queer approaches to design as a way of potentially making that tension easier to safely navigate." + assert meta.html_fulltext_url == "https://firstmonday.org/ojs/index.php/fm/article/view/10274/9729" + assert meta.release_type == "article-journal" + + +def test_html_metadata_dlib() -> None: + + with open('tests/files/dlib_05vanhyning.html', 'r') as f: + dlib_html = f.read() + + meta = html_extract_biblio("http://example.org", HTMLParser(dlib_html)) + assert meta is not None + assert meta.doi == "10.1045/may2017-vanhyning" + # "2017-05-15" + assert meta.release_date == datetime.date(year=2017, month=5, day=15) + +def test_html_metadata_dc_case() -> None: + """ + This tests that CSS selector <meta name=""> attribute lookups are not case-sensitive. + """ + + snippet = """ + <html> + <head> + <meta name="DC.Citation.Issue" content="123"/> + </head> + <body>Hi.</body> + </html>""" + + meta = html_extract_biblio("http://example.org", HTMLParser(snippet)) + assert meta is not None + assert meta.issue == "123" + +@pytest.fixture +def adblock() -> Any: + return load_adblock_rules() + +def test_html_resources(adblock) -> None: + + with open('tests/files/dlib_05vanhyning.html', 'r') as f: + dlib_html = f.read() + + resources = html_extract_resources( + "http://www.dlib.org/dlib/may17/vanhyning/05vanhyning.html", + HTMLParser(dlib_html), + adblock, + ) + + assert dict(url="http://www.dlib.org/style/style1.css", type="stylesheet") in resources + + # check that adblock working + for r in resources: + assert '/ga.js' not in r['url'] + + with open('tests/files/plos_one_article.html', 'r') as f: + plos_html = f.read() + + resources = html_extract_resources( + "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0213978", + HTMLParser(plos_html), + adblock, + ) + + # check that custom adblock working + for r in resources: + assert 'crossmark-cdn.crossref.org' not in r['url'] + + with open('tests/files/first_monday_ojs3_landingpage.html', 'r') as f: + monday_html = f.read() + + resources = html_extract_resources( + "https://firstmonday.org/blah/", + HTMLParser(monday_html), + adblock, + ) + + with open('tests/files/elife_article.html', 'r') as f: + elife_html = f.read() + + resources = html_extract_resources( + "https://elife.org/blah/", + HTMLParser(elife_html), + adblock, + ) + + with open('tests/files/nature_article.html', 'r') as f: + nature_html = f.read() + + resources = html_extract_resources( + "https://nature.com/blah/", + HTMLParser(nature_html), + adblock, + ) + diff --git a/python/tests/test_ingest.py b/python/tests/test_ingest.py new file mode 100644 index 0000000..b51f721 --- /dev/null +++ b/python/tests/test_ingest.py @@ -0,0 +1,207 @@ + +import json +import pytest +import responses + +from sandcrawler import * +from test_wayback import * +from test_savepagenow import * +from test_grobid import REAL_TEI_XML + + +@pytest.fixture +def ingest_worker(wayback_client, spn_client): + grobid_client = GrobidClient( + host_url="http://dummy-grobid", + ) + worker = IngestFileWorker( + wayback_client=wayback_client, + spn_client=spn_client, + grobid_client=grobid_client, + ) + return worker + +@pytest.fixture +def ingest_worker_pdf(wayback_client_pdf, spn_client): + grobid_client = GrobidClient( + host_url="http://dummy-grobid", + ) + pgrest_client = SandcrawlerPostgrestClient( + api_url="http://dummy-postgrest", + ) + worker = IngestFileWorker( + wayback_client=wayback_client_pdf, + spn_client=spn_client, + grobid_client=grobid_client, + pgrest_client=pgrest_client, + ) + return worker + + +@responses.activate +def test_ingest_success(ingest_worker_pdf): + + with open('tests/files/dummy.pdf', 'rb') as f: + pdf_bytes = f.read() + + request = { + 'ingest_type': 'pdf', + 'base_url': "http://dummy-host/", + } + responses.add(responses.POST, + 'http://dummy-spnv2/save', + status=200, + body=json.dumps({"url": TARGET, "job_id": JOB_ID})) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=200, + body=json.dumps(PENDING_BODY)) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=200, + body=json.dumps(SUCCESS_BODY)) + responses.add(responses.GET, + 'http://dummy-cdx/cdx', + status=200, + body=json.dumps(CDX_SPN_HIT)) + responses.add(responses.GET, + 'https://web.archive.org/web/{}id_/{}'.format("20180326070330", TARGET + "/redirect"), + status=200, + headers={"X-Archive-Src": "liveweb-whatever.warc.gz"}, + body=pdf_bytes) + responses.add(responses.GET, + 'http://dummy-postgrest/grobid?sha1hex=eq.{}'.format("90ffd2359008d82298821d16b21778c5c39aec36"), + status=200, + body=json.dumps([])) + responses.add(responses.GET, + 'http://dummy-postgrest/pdf_meta?sha1hex=eq.{}'.format("90ffd2359008d82298821d16b21778c5c39aec36"), + status=200, + body=json.dumps([])) + responses.add(responses.POST, + 'http://dummy-grobid/api/processFulltextDocument', status=200, + body=REAL_TEI_XML, content_type='text/xml') + + resp = ingest_worker_pdf.process(request) + + print(resp) + assert resp['hit'] == True + assert resp['status'] == "success" + assert resp['request'] == request + assert resp['terminal']['terminal_sha1hex'] == resp['file_meta']['sha1hex'] + assert type(resp['terminal']['terminal_dt']) == str + assert resp['terminal']['terminal_url'] == TARGET + "/redirect" + assert resp['terminal']['terminal_status_code'] + assert type(resp['file_meta']['size_bytes']) == int + assert resp['file_meta']['mimetype'] == "application/pdf" + assert resp['cdx']['url'] == TARGET + "/redirect" + assert 'warc_path' not in resp['cdx'] + assert 'revisit_cdx' not in resp + assert resp['grobid']['status'] == "success" + assert resp['grobid']['status_code'] == 200 + assert resp['grobid']['grobid_version'] + assert 'fatcat_release' in resp['grobid'] + assert 'grobid_version' not in resp['grobid']['metadata'] + assert 'fatcat_release' not in resp['grobid']['metadata'] + assert not 'tei_xml' in resp['grobid'] + assert resp['pdf_meta']['status'] == "success" + assert resp['pdf_meta']['pdf_extra']['page_count'] == 1 + assert resp['pdf_meta'].get('text') is None + +@responses.activate +def test_ingest_landing(ingest_worker): + + request = { + 'ingest_type': 'pdf', + 'base_url': "http://dummy-host/", + } + responses.add(responses.POST, + 'http://dummy-spnv2/save', + status=200, + body=json.dumps({"url": TARGET, "job_id": JOB_ID})) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=200, + body=json.dumps(PENDING_BODY)) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=200, + body=json.dumps(SUCCESS_BODY)) + responses.add(responses.GET, + 'http://dummy-cdx/cdx', + status=200, + body=json.dumps(CDX_SPN_HIT)) + responses.add(responses.GET, + 'https://web.archive.org/web/{}id_/{}'.format("20180326070330", TARGET + "/redirect"), + status=200, + headers={"X-Archive-Src": "liveweb-whatever.warc.gz"}, + body=WARC_BODY) + + # this is for second time around; don't want to fetch same landing page + # HTML again and result in a loop + responses.add(responses.GET, + 'https://web.archive.org/web/{}id_/{}'.format("20180326070330", TARGET + "/redirect"), + status=200, + headers={"X-Archive-Src": "liveweb-whatever.warc.gz"}, + body="<html></html>") + + resp = ingest_worker.process(request) + + print(resp) + assert resp['hit'] == False + assert resp['status'] == "no-pdf-link" + assert resp['request'] == request + assert 'terminal' in resp + assert 'file_meta' not in resp + assert 'cdx' not in resp + assert 'revisit_cdx' not in resp + assert 'grobid' not in resp + +@responses.activate +def test_ingest_blocklist(ingest_worker): + + ingest_worker.base_url_blocklist = [ + '://test.fatcat.wiki/', + ] + request = { + 'ingest_type': 'pdf', + 'base_url': "https://test.fatcat.wiki/asdfasdf.pdf", + } + + resp = ingest_worker.process(request) + + assert resp['hit'] == False + assert resp['status'] == "skip-url-blocklist" + assert resp['request'] == request + + +@responses.activate +def test_ingest_wall_blocklist(ingest_worker): + + ingest_worker.wall_blocklist = [ + '://test.fatcat.wiki/', + ] + request = { + 'ingest_type': 'pdf', + 'base_url': "https://test.fatcat.wiki/asdfasdf.pdf", + } + + resp = ingest_worker.process(request) + + assert resp['hit'] == False + assert resp['status'] == "skip-wall" + assert resp['request'] == request + +@responses.activate +def test_ingest_cookie_blocklist(ingest_worker): + + request = { + 'ingest_type': 'pdf', + 'base_url': "https://test.fatcat.wiki/cookieAbsent", + } + + resp = ingest_worker.process(request) + + assert resp['hit'] == False + assert resp['status'] == "blocked-cookie" + assert resp['request'] == request + diff --git a/python/tests/test_live_wayback.py b/python/tests/test_live_wayback.py new file mode 100644 index 0000000..429c6b0 --- /dev/null +++ b/python/tests/test_live_wayback.py @@ -0,0 +1,167 @@ + +""" +This file contains tests to run against "live" wayback services. They default +to "skip" because you need authentication, and we shouldn't hit these services +automatically in CI. + +Simply uncomment lines to run. +""" + +import json +import pytest + +from sandcrawler import CdxApiClient, CdxApiError, WaybackClient, WaybackError, PetaboxError, SavePageNowClient, SavePageNowError, CdxPartial, gen_file_metadata + + +@pytest.fixture +def cdx_client(): + client = CdxApiClient() + return client + +@pytest.fixture +def wayback_client(): + client = WaybackClient() + return client + +@pytest.fixture +def spn_client(): + client = SavePageNowClient() + return client + +@pytest.mark.skip(reason="hits prod services, requires auth") +def test_cdx_fetch(cdx_client): + + # org,plos,journals)/plosone/article?id=10.1371/journal.pone.0093949 20181105121428 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093949 text/html 200 OJ6FN5AAPU62VMMVJPXZYNBQD5VMYHFV - - 25338 240665973 MEDIACLOUD-20181105115107-crawl851/MEDIACLOUD-20181105115107-09234.warc.gz + + url = "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093949" + datetime = "20181105121428" + resp = cdx_client.fetch(url, datetime) + + assert resp.url == url + assert resp.datetime == datetime + assert resp.sha1b32 == "OJ6FN5AAPU62VMMVJPXZYNBQD5VMYHFV" + assert resp.warc_csize == 25338 + assert resp.warc_offset == 240665973 + assert resp.warc_path == "MEDIACLOUD-20181105115107-crawl851/MEDIACLOUD-20181105115107-09234.warc.gz" + + # bogus datetime; shouldn't match + with pytest.raises(KeyError): + resp = cdx_client.fetch(url, "12345678123456") + +@pytest.mark.skip(reason="hits prod services, requires auth") +def test_cdx_lookup_best(cdx_client): + + url = "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0093949&type=printable" + resp = cdx_client.lookup_best(url, best_mimetype="application/pdf") + + # won't know datetime, hash, etc + assert resp.url in (url, url.replace("https://", "http://")) + assert resp.mimetype == "application/pdf" + assert resp.status_code == 200 + + url = "https://americanarchivist.org/doi/abs/10.17723/aarc.62.2.gu33570g87v71007" + resp = cdx_client.lookup_best(url, best_mimetype="application/pdf") + + assert resp.url in (url, url.replace("https://", "http://")) + assert resp.mimetype == "text/html" + assert resp.status_code == 200 + +@pytest.mark.skip(reason="hits prod services, requires auth") +def test_wayback_fetch(wayback_client): + + resp = wayback_client.fetch_petabox(25683, 2676464871, "archiveteam_archivebot_go_20171205210002/arstechnica.co.uk-inf-20171201-061309-bb65j-00021.warc.gz") + + assert resp.body + +@pytest.mark.skip(reason="hits prod services, requires auth") +def test_lookup_resource_success(wayback_client): + + url = "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0093949&type=printable" + resp = wayback_client.lookup_resource(url) + + assert resp.hit == True + assert resp.status == "success" + assert resp.terminal_url in (url, url.replace("https://", "http://")) + assert resp.cdx.url in (url, url.replace("https://", "http://")) + +@pytest.mark.skip(reason="hits prod services, requires auth") +def test_cdx_fetch_spn2(cdx_client): + + # https://linkinghub.elsevier.com/retrieve/pii/S2590109519300424 20200110210133 + + # com,elsevier,linkinghub)/retrieve/pii/s2590109519300424 20191201203206 https://linkinghub.elsevier.com/retrieve/pii/S2590109519300424 text/html 200 FPXVUJR7RXVGO6RIY5HYB6JVT7OD53SG - - 5026 364192270 liveweb-20191201204645/live-20191201195942-wwwb-app52.us.archive.org.warc.gz + # com,elsevier,linkinghub)/retrieve/pii/s2590109519300424 20200110210044 https://linkinghub.elsevier.com/retrieve/pii/S2590109519300424 text/html 200 OIQ3TKPBQLYYXQDIG7D2ZOK7IJEUEAQ7 - - 5130 710652442 liveweb-20200110204521-wwwb-spn20.us.archive.org-8001.warc.gz + # com,elsevier,linkinghub)/retrieve/pii/s2590109519300424 20200110210133 https://linkinghub.elsevier.com/retrieve/pii/S2590109519300424 text/html 200 G2MSFAYELECMFGKTYEHUN66WWNW4HXKQ - - 5126 544508422 liveweb-20200110205247-wwwb-spn01.us.archive.org-8000.warc.gz + + url = "https://linkinghub.elsevier.com/retrieve/pii/S2590109519300424" + datetime = "20200110210133" + resp = cdx_client.fetch(url, datetime, filter_status_code=200) + + assert resp.url == url + assert resp.datetime == datetime + assert resp.sha1b32 == "G2MSFAYELECMFGKTYEHUN66WWNW4HXKQ" + assert resp.status_code == 200 + + # https://onlinelibrary.wiley.com/doi/pdf/10.1002/lrh2.10209 20200110222410 + + #com,wiley,onlinelibrary)/doi/pdf/10.1002/lrh2.10209 20200110222410 https://onlinelibrary.wiley.com/doi/pdf/10.1002/lrh2.10209 text/html 200 VYW7JXFK6EC2KC537N5B7PHYZC4B6MZL - - 9006 815069841 liveweb-20200110214015-wwwb-spn18.us.archive.org-8002.warc.gz +#com,wiley,onlinelibrary)/doi/pdf/10.1002/lrh2.10209 20200110222410 https://onlinelibrary.wiley.com/doi/pdf/10.1002/lrh2.10209 text/html 302 AFI55BZE23HDTTEERUFKRP6WQVO3LOLS - - 1096 815066572 liveweb-20200110214015-wwwb-spn18.us.archive.org-8002.warc.gz +#com,wiley,onlinelibrary)/doi/pdf/10.1002/lrh2.10209 20200110222422 https://onlinelibrary.wiley.com/doi/pdf/10.1002/lrh2.10209 text/html 302 AFI55BZE23HDTTEERUFKRP6WQVO3LOLS - - 1094 307563475 liveweb-20200110214449-wwwb-spn18.us.archive.org-8003.warc.gz + + url = "https://onlinelibrary.wiley.com/doi/pdf/10.1002/lrh2.10209" + datetime = "20200110222410" + resp = cdx_client.fetch(url, datetime, filter_status_code=200) + + assert resp.url == url + assert resp.datetime == datetime + assert resp.sha1b32 == "VYW7JXFK6EC2KC537N5B7PHYZC4B6MZL" + assert resp.status_code == 200 + +@pytest.mark.skip(reason="hits prod services, requires auth") +def test_lookup_ftp(wayback_client): + # ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/80/23/10.1177_1559827617708562.PMC6236633.pdf + # ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ad/ab/mmr-17-05-6969.PMC5928650.pdf + # ftp://ftp.cs.utexas.edu/pub/qsim/papers/Xu-crv-08.pdf + + # revisit! + url = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ad/ab/mmr-17-05-6969.PMC5928650.pdf" + resp = wayback_client.lookup_resource(url) + + assert resp.hit == True + assert resp.status == "success" + assert resp.terminal_url == url + assert resp.terminal_status_code == 226 + assert resp.cdx.url == url + assert resp.revisit_cdx + assert resp.revisit_cdx.url != url + + file_meta = gen_file_metadata(resp.body) + assert file_meta['sha1hex'] == resp.cdx.sha1hex + + # not revisit? + url = "ftp://ftp.cs.utexas.edu/pub/qsim/papers/Xu-crv-08.pdf" + resp = wayback_client.lookup_resource(url) + + assert resp.hit == True + assert resp.status == "success" + assert resp.terminal_url == url + assert resp.terminal_status_code == 226 + assert resp.cdx.url == url + + file_meta = gen_file_metadata(resp.body) + assert file_meta['sha1hex'] == resp.cdx.sha1hex + +@pytest.mark.skip(reason="hits prod services, requires auth") +def test_crawl_ftp(spn_client, wayback_client): + + url = "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ad/ab/mmr-17-05-6969.PMC5928650.pdf" + resp = spn_client.crawl_resource(url, wayback_client) + + # FTP isn't supported yet! + #assert resp.hit == True + #assert resp.status == "success" + #assert resp.terminal_url == url + #assert resp.cdx.url == url + + assert resp.hit == False + assert resp.status == "spn2-no-ftp" diff --git a/python/tests/test_misc.py b/python/tests/test_misc.py new file mode 100644 index 0000000..29f9e9f --- /dev/null +++ b/python/tests/test_misc.py @@ -0,0 +1,77 @@ + +import pytest + +from sandcrawler import gen_file_metadata, b32_hex, parse_cdx_line, clean_url + +def test_gen_file_metadata(): + + # valid (but very small) PDF file + with open('tests/files/dummy.pdf', 'rb') as f: + file_meta = gen_file_metadata(f.read()) + assert file_meta == { + 'mimetype': 'application/pdf', + 'md5hex': '2942bfabb3d05332b66eb128e0842cff', + 'sha1hex': '90ffd2359008d82298821d16b21778c5c39aec36', + 'sha256hex': '3df79d34abbca99308e79cb94461c1893582604d68329a41fd4bec1885e6adb4', + 'size_bytes': 13264, + } + + # valid HTML + fm = gen_file_metadata( + b"""<html><head><title>dummy</title></head><body>html document</body></html>""") + assert fm['mimetype'] == 'text/html' + + # bogus text + fm = gen_file_metadata(b"asdf1234") + assert fm['mimetype'] == 'text/plain' + assert fm['size_bytes'] == 8 + +def test_b32_hex(): + + # valid b32 + assert b32_hex('sha1:TZCYZ2ULEHYGESS4L3RNH75I23KKFSMC') == '9e458cea8b21f0624a5c5ee2d3ffa8d6d4a2c982' + assert b32_hex('TZCYZ2ULEHYGESS4L3RNH75I23KKFSMC') == '9e458cea8b21f0624a5c5ee2d3ffa8d6d4a2c982' + + # sha1hex pass-through + s = 'bda3c1017d52e826bbd1da51efad877272d300f9' + assert b32_hex(s) == s + + # invalid + with pytest.raises(ValueError): + assert b32_hex('blah') == 'blah' + +def test_parse_cdx_line(): + + raw = "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz" + correct = { + 'sha1b32': "WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G", + 'sha1hex': "b2f65203da9929c2f758e8dd587b5524f904dbe6", + 'mimetype': "application/pdf", + 'surt': "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf", + 'url': "https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf", + 'datetime': "20170828233154", + 'warc_path': "SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz", + 'warc_offset': 931661233, + 'warc_csize': 210251, + 'http_status': 200, + } + + assert parse_cdx_line(raw) == correct + assert parse_cdx_line(raw + "\n") == correct + assert parse_cdx_line(raw + " extra_field") == correct + +def test_invalid_cdx(): + + print("missing warc") + raw = "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 -" + assert parse_cdx_line(raw) == None + + print("bad datetime") + raw = "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 2070828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233i SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz" + assert parse_cdx_line(raw) == None + +def test_clean_url(): + assert clean_url("http://BLAH.COM/file.pdf") == "http://blah.com/file.pdf" + assert clean_url("https://opensky.ucar.edu:/islandora/object/articles%3A10809/datastream/PDF/view") == \ + "https://opensky.ucar.edu/islandora/object/articles%3A10809/datastream/PDF/view" + diff --git a/python/tests/test_pdfextract.py b/python/tests/test_pdfextract.py new file mode 100644 index 0000000..255e3fb --- /dev/null +++ b/python/tests/test_pdfextract.py @@ -0,0 +1,68 @@ + +import pytest +import struct +import responses +import poppler + +from sandcrawler import PdfExtractWorker, PdfExtractBlobWorker, CdxLinePusher, BlackholeSink, WaybackClient +from sandcrawler.pdfextract import process_pdf +from test_wayback import wayback_client, cdx_client + + +FAKE_PDF_BYTES = b"%PDF SOME JUNK" + struct.pack("!q", 112853843) + +def test_process_fake_pdf(): + resp = process_pdf(FAKE_PDF_BYTES) + print(resp) + assert resp.status == "not-pdf" + + with open('tests/files/dummy_zip.zip', 'rb') as f: + pdf_bytes = f.read() + resp = process_pdf(pdf_bytes) + assert resp.status == 'not-pdf' + +@pytest.mark.skipif(poppler.version_string() == '0.71.0', reason="unsupported version of poppler") +def test_process_dummy_pdf(): + with open('tests/files/dummy.pdf', 'rb') as f: + pdf_bytes = f.read() + resp = process_pdf(pdf_bytes) + assert resp.status == 'success' + assert resp.page0_thumbnail is not None + assert len(resp.text) > 10 + assert resp.meta_xml is None + assert resp.file_meta['mimetype'] == 'application/pdf' + print(resp.pdf_info) + print(resp.pdf_extra) + assert resp.pdf_info['Author'] == "Evangelos Vlachogiannis" + # 595 x 842 + assert resp.pdf_extra['page0_height'] == 842 + assert resp.pdf_extra['page0_width'] == 595 + assert resp.pdf_extra['page_count'] == 1 + +def test_pdfextract_worker_cdx(wayback_client): + + sink = BlackholeSink() + worker = PdfExtractWorker(wayback_client, sink=sink, thumbnail_sink=sink) + + with open('tests/files/example.cdx', 'r') as cdx_file: + pusher = CdxLinePusher( + worker, + cdx_file, + filter_http_statuses=[200, 226], + filter_mimetypes=['application/pdf'], + ) + pusher_counts = pusher.run() + assert pusher_counts['total'] + assert pusher_counts['pushed'] == 7 + assert pusher_counts['pushed'] == worker.counts['total'] + +def test_pdfextract_blob_worker(): + + sink = BlackholeSink() + worker = PdfExtractBlobWorker(sink=sink, thumbnail_sink=sink) + + with open('tests/files/dummy.pdf', 'rb') as f: + pdf_bytes = f.read() + + worker.process(pdf_bytes) + diff --git a/python/tests/test_pushers.py b/python/tests/test_pushers.py new file mode 100644 index 0000000..52f26c0 --- /dev/null +++ b/python/tests/test_pushers.py @@ -0,0 +1,28 @@ + +import pytest + +from sandcrawler.workers import CdxLinePusher, BlackholeSink + + +def test_cdx_line_pusher(): + + sink = BlackholeSink() + + # vanilla (only default filters) + with open('tests/files/example.cdx', 'r') as cdx_file: + pusher = CdxLinePusher(sink, cdx_file) + counts = pusher.run() + assert counts['total'] == 20 + assert counts['skip-parse'] == 1 + assert counts['pushed'] == 19 + + # HTTP 200 and application/pdf + with open('tests/files/example.cdx', 'r') as cdx_file: + pusher = CdxLinePusher(sink, cdx_file, + filter_mimetypes=['application/pdf'], filter_http_statuses=[200, 226]) + counts = pusher.run() + assert counts['total'] == 20 + assert counts['skip-parse'] == 1 + assert counts['skip-http_status'] == 10 + assert counts['skip-mimetype'] == 2 + assert counts['pushed'] == 7 diff --git a/python/tests/test_savepagenow.py b/python/tests/test_savepagenow.py new file mode 100644 index 0000000..63dd887 --- /dev/null +++ b/python/tests/test_savepagenow.py @@ -0,0 +1,204 @@ + +import json +import pytest +import responses + +from sandcrawler import SavePageNowClient, SavePageNowError, CdxPartial +from test_wayback import * + + +TARGET = "http://dummy-target.dummy" +JOB_ID = "e70f33c7-9eca-4c88-826d-26930564d7c8" +PENDING_BODY = { + "status": "pending", + "job_id": JOB_ID, + "resources": [ + "https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js", + "https://ajax.googleapis.com/ajax/libs/jqueryui/1.8.21/jquery-ui.min.js", + "https://cdn.onesignal.com/sdks/OneSignalSDK.js", + ] +} +SUCCESS_BODY = { + "status": "success", + "job_id": JOB_ID, + "original_url": TARGET + "/redirect", + "screenshot": "http://web.archive.org/screenshot/http://brewster.kahle.org/", + "timestamp": "20180326070330", + "duration_sec": 6.203, + "resources": [ + TARGET, + TARGET + "/redirect", + "http://brewster.kahle.org/", + "http://brewster.kahle.org/favicon.ico", + "http://brewster.kahle.org/files/2011/07/bkheader-follow.jpg", + "http://brewster.kahle.org/files/2016/12/amazon-unhappy.jpg", + "http://brewster.kahle.org/files/2017/01/computer-1294045_960_720-300x300.png", + "http://brewster.kahle.org/files/2017/11/20thcenturytimemachineimages_0000.jpg", + "http://brewster.kahle.org/files/2018/02/IMG_6041-1-300x225.jpg", + "http://brewster.kahle.org/files/2018/02/IMG_6061-768x1024.jpg", + "http://brewster.kahle.org/files/2018/02/IMG_6103-300x225.jpg", + "http://brewster.kahle.org/files/2018/02/IMG_6132-225x300.jpg", + "http://brewster.kahle.org/files/2018/02/IMG_6138-1-300x225.jpg", + "http://brewster.kahle.org/wp-content/themes/twentyten/images/wordpress.png", + "http://brewster.kahle.org/wp-content/themes/twentyten/style.css", + "http://brewster.kahle.org/wp-includes/js/wp-embed.min.js?ver=4.9.4", + "http://brewster.kahle.org/wp-includes/js/wp-emoji-release.min.js?ver=4.9.4", + "http://platform.twitter.com/widgets.js", + "https://archive-it.org/piwik.js", + "https://platform.twitter.com/jot.html", + "https://platform.twitter.com/js/button.556f0ea0e4da4e66cfdc182016dbd6db.js", + "https://platform.twitter.com/widgets/follow_button.f47a2e0b4471326b6fa0f163bda46011.en.html", + "https://syndication.twitter.com/settings", + "https://www.syndikat.org/en/joint_venture/embed/", + "https://www.syndikat.org/wp-admin/images/w-logo-blue.png", + "https://www.syndikat.org/wp-content/plugins/user-access-manager/css/uamAdmin.css?ver=1.0", + "https://www.syndikat.org/wp-content/plugins/user-access-manager/css/uamLoginForm.css?ver=1.0", + "https://www.syndikat.org/wp-content/plugins/user-access-manager/js/functions.js?ver=4.9.4", + "https://www.syndikat.org/wp-content/plugins/wysija-newsletters/css/validationEngine.jquery.css?ver=2.8.1", + "https://www.syndikat.org/wp-content/uploads/2017/11/s_miete_fr-200x116.png", + "https://www.syndikat.org/wp-includes/js/jquery/jquery-migrate.min.js?ver=1.4.1", + "https://www.syndikat.org/wp-includes/js/jquery/jquery.js?ver=1.12.4", + "https://www.syndikat.org/wp-includes/js/wp-emoji-release.min.js?ver=4.9.4" + ], + "outlinks":{ + "https://archive.org/": "xxxxxx89b-f3ca-48d0-9ea6-1d1225e98695", + "https://other.com": "yyyy89b-f3ca-48d0-9ea6-1d1225e98695" + } +} +ERROR_BODY = { + "status": "error", + "exception": "[Errno -2] Name or service not known", + "status_ext": "error:invalid-host-resolution", + "job_id": JOB_ID, + "message": "Couldn't resolve host for http://example5123.com.", + "resources": [] +} +CDX_SPN_HIT = [ + ["urlkey","timestamp","original","mimetype","statuscode","digest","redirect","robotflags","length","offset","filename"], + ["wiki,fatcat)/", "20180326070330", TARGET + "/redirect", "application/pdf", "200", CDX_BEST_SHA1B32, "-", "-", "8445", "108062304", "liveweb-20200108215212-wwwb-spn04.us.archive.org-kols1pud.warc.gz"], +] + +@pytest.fixture +def spn_client(): + client = SavePageNowClient( + v2endpoint="http://dummy-spnv2/save", + ia_access_key="dummy-access-key", + ia_secret_key="dummy-secret-key", + ) + client.poll_seconds = 0.0 + return client + +@responses.activate +def test_savepagenow_success(spn_client): + + responses.add(responses.POST, + 'http://dummy-spnv2/save', + status=200, + body=json.dumps({"url": TARGET, "job_id": JOB_ID})) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=200, + body=json.dumps(PENDING_BODY)) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=200, + body=json.dumps(PENDING_BODY)) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=200, + body=json.dumps(SUCCESS_BODY)) + + resp = spn_client.save_url_now_v2(TARGET) + + assert len(responses.calls) == 4 + + assert resp.success == True + assert resp.status == "success" + assert resp.request_url == TARGET + assert resp.terminal_url == TARGET + "/redirect" + assert resp.terminal_dt == SUCCESS_BODY['timestamp'] + assert resp.resources == SUCCESS_BODY['resources'] + +@responses.activate +def test_savepagenow_remote_error(spn_client): + + responses.add(responses.POST, + 'http://dummy-spnv2/save', + status=200, + body=json.dumps({"url": TARGET, "job_id": JOB_ID})) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=200, + body=json.dumps(PENDING_BODY)) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=200, + body=json.dumps(ERROR_BODY)) + + resp = spn_client.save_url_now_v2(TARGET) + + assert len(responses.calls) == 3 + + assert resp.success == False + assert resp.status == ERROR_BODY['status_ext'] + assert resp.request_url == TARGET + assert resp.terminal_url == None + assert resp.terminal_dt == None + assert resp.resources == None + +@responses.activate +def test_savepagenow_500(spn_client): + + responses.add(responses.POST, + 'http://dummy-spnv2/save', + status=200, + body=json.dumps({"url": TARGET, "job_id": JOB_ID})) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=500, + body=json.dumps(ERROR_BODY)) + + with pytest.raises(SavePageNowError): + resp = spn_client.save_url_now_v2(TARGET) + + assert len(responses.calls) == 2 + +@responses.activate +def test_crawl_resource(spn_client, wayback_client): + + responses.add(responses.POST, + 'http://dummy-spnv2/save', + status=200, + body=json.dumps({"url": TARGET, "job_id": JOB_ID})) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=200, + body=json.dumps(PENDING_BODY)) + responses.add(responses.GET, + 'http://dummy-spnv2/save/status/' + JOB_ID, + status=200, + body=json.dumps(SUCCESS_BODY)) + responses.add(responses.GET, + 'http://dummy-cdx/cdx', + status=200, + body=json.dumps(CDX_SPN_HIT)) + responses.add(responses.GET, + 'https://web.archive.org/web/{}id_/{}'.format("20180326070330", TARGET + "/redirect"), + status=200, + headers={"X-Archive-Src": "liveweb-whatever.warc.gz"}, + body=WARC_BODY) + + print('https://web.archive.org/web/{}id_/{}'.format("20180326070330", TARGET + "/redirect")) + resp = spn_client.crawl_resource(TARGET, wayback_client) + + assert len(responses.calls) == 5 + + assert resp.hit == True + assert resp.status == "success" + assert resp.body == WARC_BODY + assert resp.cdx.sha1b32 == CDX_BEST_SHA1B32 + + assert type(resp.cdx) == CdxPartial + with pytest.raises(AttributeError): + print(resp.cdx.warc_path) + diff --git a/python/tests/test_wayback.py b/python/tests/test_wayback.py new file mode 100644 index 0000000..6bc1ca4 --- /dev/null +++ b/python/tests/test_wayback.py @@ -0,0 +1,172 @@ + +import json +import pytest +import responses + +from sandcrawler import CdxApiClient, CdxApiError, WaybackClient, WaybackError, PetaboxError + + +CDX_TARGET = "http://fatcat.wiki/" +CDX_DT = "20180812220054" +# cdx -m exact -p output=json -p from=20180812220054 -p to=20180812220054 http://fatcat.wiki/ +CDX_SINGLE_HIT = [ + ["urlkey","timestamp","original","mimetype","statuscode","digest","redirect","robotflags","length","offset","filename"], + ["wiki,fatcat)/", CDX_DT, CDX_TARGET, "text/html", "200", "O5RHV6OQ7SIHDJIEP7ZW53DLRX5NFIJR", "-", "-", "8445", "108062304", "WIDE-20180810142205-crawl802/WIDE-20180812131623-00059.warc.gz"], +] + +CDX_BEST_SHA1B32 = "AAAAAAAAASIHDJIEP7ZW53DLRX5NFIJR" +# cdx -m exact -p output=json -p from=20180812220054 -p to=20180812220054 http://fatcat.wiki/ +CDX_MULTI_HIT = [ + ["urlkey","timestamp","original","mimetype","statuscode","digest","redirect","robotflags","length","offset","filename"], + ["wiki,fatcat)/", CDX_DT, CDX_TARGET, "text/html", "200", "O5RHV6OQ7SIHDJIEP7ZW53DLRX5NFIJR", "-", "-", "8445", "108062304", "WIDE-20180810142205-crawl802/WIDE-20180812131623-00059.warc.gz"], + # sooner, but not right mimetype + ["wiki,fatcat)/", "20180912220054", CDX_TARGET, "text/html", "200", "O5RHV6OQ7SIHDJIEP7ZW53DLRX5NFIJR", "-", "-", "8445", "108062304", "WIDE-20180810142205-crawl802/WIDE-20180812131623-00059.warc.gz"], + # sooner and mimetype, but wrong status code + ["wiki,fatcat)/", "20180912220054", CDX_TARGET, "application/pdf", "400", "O5RHV6OQ7SIHDJIEP7ZW53DLRX5NFIJR", "-", "-", "8445", "108062304", "WIDE-20180810142205-crawl802/WIDE-20180812131623-00059.warc.gz"], + ["wiki,fatcat)/", "20180912220054", CDX_TARGET, "application/pdf", "500", "O5RHV6OQ7SIHDJIEP7ZW53DLRX5NFIJR", "-", "-", "8445", "108062304", "WIDE-20180810142205-crawl802/WIDE-20180812131623-00059.warc.gz"], + ["wiki,fatcat)/", "20180912220054", CDX_TARGET, "application/pdf", "150", "O5RHV6OQ7SIHDJIEP7ZW53DLRX5NFIJR", "-", "-", "8445", "108062304", "WIDE-20180810142205-crawl802/WIDE-20180812131623-00059.warc.gz"], + # "best" + ["wiki,fatcat)/", CDX_DT, CDX_TARGET, "application/pdf", "200", CDX_BEST_SHA1B32, "-", "-", "8445", "108062304", "WIDE-20180810142205-crawl802/WIDE-20180812131623-00059.warc.gz"], + # older + ["wiki,fatcat)/", "20180712220054", CDX_TARGET, "application/pdf", "200", "O5RHV6OQ7SIHDJIEP7ZW53DLRX5NFIJR", "-", "-", "8445", "108062304", "WIDE-20180810142205-crawl802/WIDE-20180812131623-00059.warc.gz"], +] + +@pytest.fixture +def cdx_client(): + client = CdxApiClient( + host_url="http://dummy-cdx/cdx", + cdx_auth_token="dummy-token", + ) + return client + +@responses.activate +def test_cdx_fetch(cdx_client): + + responses.add(responses.GET, + 'http://dummy-cdx/cdx', + status=200, + body=json.dumps(CDX_SINGLE_HIT)) + + resp = cdx_client.fetch(CDX_TARGET, CDX_DT) + + assert len(responses.calls) == 1 + + assert resp.datetime == CDX_DT + assert resp.url == CDX_TARGET + assert resp.sha1b32 == "O5RHV6OQ7SIHDJIEP7ZW53DLRX5NFIJR" + assert resp.warc_csize == 8445 + assert resp.warc_offset == 108062304 + assert resp.warc_path == "WIDE-20180810142205-crawl802/WIDE-20180812131623-00059.warc.gz" + +@responses.activate +def test_cdx_fetch_errors(cdx_client): + + with pytest.raises(ValueError): + resp = cdx_client.fetch(CDX_TARGET, "2019") + + responses.add(responses.GET, + 'http://dummy-cdx/cdx', + status=200, + body=json.dumps(CDX_SINGLE_HIT)) + + with pytest.raises(KeyError): + resp = cdx_client.fetch(CDX_TARGET, "20180812220055") + + with pytest.raises(KeyError): + resp = cdx_client.fetch("http://some-other.com", CDX_DT) + + resp = cdx_client.fetch(CDX_TARGET, CDX_DT) + assert len(responses.calls) == 3 + +@responses.activate +def test_cdx_lookup_best(cdx_client): + + responses.add(responses.GET, + 'http://dummy-cdx/cdx', + status=200, + body=json.dumps(CDX_MULTI_HIT)) + + resp = cdx_client.lookup_best(CDX_TARGET, best_mimetype="application/pdf") + + assert len(responses.calls) == 1 + + assert resp.datetime == CDX_DT + assert resp.url == CDX_TARGET + assert resp.sha1b32 == CDX_BEST_SHA1B32 + assert resp.warc_path == CDX_SINGLE_HIT[1][-1] + +WARC_TARGET = "http://fatcat.wiki/" +WARC_BODY = b""" +<html> + <head> + <meta name="citation_pdf_url" content="http://www.example.com/content/271/20/11761.full.pdf"> + </head> + <body> + <h1>my big article here</h1> + blah + </body> +</html> +""" + +@pytest.fixture +def wayback_client(cdx_client, mocker): + client = WaybackClient( + cdx_client=cdx_client, + petabox_webdata_secret="dummy-petabox-secret", + ) + # mock out the wayback store with mock stuff + client.rstore = mocker.Mock() + resource = mocker.Mock() + client.rstore.load_resource = mocker.MagicMock(return_value=resource) + resource.get_status = mocker.MagicMock(return_value=(200, "Ok")) + resource.is_revisit = mocker.MagicMock(return_value=False) + resource.get_location = mocker.MagicMock(return_value=WARC_TARGET) + body = mocker.Mock() + resource.open_raw_content = mocker.MagicMock(return_value=body) + body.read = mocker.MagicMock(return_value=WARC_BODY) + + return client + +@pytest.fixture +def wayback_client_pdf(cdx_client, mocker): + + with open('tests/files/dummy.pdf', 'rb') as f: + pdf_bytes = f.read() + + client = WaybackClient( + cdx_client=cdx_client, + petabox_webdata_secret="dummy-petabox-secret", + ) + # mock out the wayback store with mock stuff + client.rstore = mocker.Mock() + resource = mocker.Mock() + client.rstore.load_resource = mocker.MagicMock(return_value=resource) + resource.get_status = mocker.MagicMock(return_value=(200, "Ok")) + resource.is_revisit = mocker.MagicMock(return_value=False) + resource.get_location = mocker.MagicMock(return_value=WARC_TARGET) + body = mocker.Mock() + resource.open_raw_content = mocker.MagicMock(return_value=body) + body.read = mocker.MagicMock(return_value=pdf_bytes) + + return client + +@responses.activate +def test_wayback_fetch(wayback_client): + resp = wayback_client.fetch_petabox(123, 456789, "here/there.warc.gz") + assert resp.body == WARC_BODY + assert resp.location == WARC_TARGET + + resp = wayback_client.fetch_petabox_body(123, 456789, "here/there.warc.gz") + assert resp == WARC_BODY + +@responses.activate +def test_lookup_resource_success(wayback_client): + + responses.add(responses.GET, + 'http://dummy-cdx/cdx', + status=200, + body=json.dumps(CDX_MULTI_HIT)) + + resp = wayback_client.lookup_resource(CDX_TARGET) + + assert resp.hit == True diff --git a/python/tests/test_xml.py b/python/tests/test_xml.py new file mode 100644 index 0000000..a996c56 --- /dev/null +++ b/python/tests/test_xml.py @@ -0,0 +1,18 @@ + +import pytest + +from sandcrawler.xml import xml_reserialize + + +def test_xml_reserialize() -> None: + + with open('tests/files/scielo_article.jats.xml', 'rb') as f: + raw_xml = f.read() + + assert b'encoding="ISO-8859-1"' in raw_xml + raw_xml.decode("ISO-8859-1") + with pytest.raises(UnicodeDecodeError): + raw_xml.decode("utf-8") + + str_xml = xml_reserialize(raw_xml) + assert 'encoding="UTF-8"' in str_xml |