more integration of transform refactor

4 files changed, 32 insertions, 17 deletions

diff --git a/python/fatcat_tools/transforms/csl.py b/python/fatcat_tools/transforms/csl.py
index f9615b26..c2e90539 100644
--- a/python/fatcat_tools/transforms/csl.py
+++ b/python/fatcat_tools/transforms/csl.py
@@ -115,8 +115,8 @@ def release_to_csl(entity):
         #original-publisher
         #original-publisher-place
         #original-title
-        # XXX: page=entity.pages,
-        page_first=entity.pages.split('-')[0],
+        # TODO: page=entity.pages,
+        page_first=entity.pages and entity.pages.split('-')[0],
         PMCID=entity.pmcid,
         PMID=entity.pmid,
         publisher=(entity.container and entity.container.publisher) or entity.publisher,
diff --git a/python/fatcat_transform.py b/python/fatcat_transform.py
index 8d5c34c5..b11ac461 100755
--- a/python/fatcat_transform.py
+++ b/python/fatcat_transform.py
@@ -21,7 +21,7 @@ from fatcat_tools import uuid2fcid, entity_from_json, entity_to_dict, \
     changelog_to_elasticsearch, public_api, release_to_csl
 
 
-def run_transform_releases(args):
+def run_elasticsearch_releases(args):
     for line in args.json_input:
         line = line.strip()
         if not line:
@@ -30,7 +30,7 @@ def run_transform_releases(args):
         args.json_output.write(
             json.dumps(release_to_elasticsearch(entity)) + '\n')
 
-def run_transform_containers(args):
+def run_elasticsearch_containers(args):
     for line in args.json_input:
         line = line.strip()
         if not line:
@@ -39,7 +39,7 @@ def run_transform_containers(args):
         args.json_output.write(
             json.dumps(container_to_elasticsearch(entity)) + '\n')
 
-def run_transform_changelogs(args):
+def run_elasticsearch_changelogs(args):
     for line in args.json_input:
         line = line.strip()
         if not line:
@@ -95,30 +95,30 @@ def main():
         help="connect to this host/port")
     subparsers = parser.add_subparsers()
 
-    sub_transform_releases = subparsers.add_parser('transform-releases')
-    sub_transform_releases.set_defaults(func=run_transform_releases)
-    sub_transform_releases.add_argument('json_input',
+    sub_elasticsearch_releases = subparsers.add_parser('elasticsearch-releases')
+    sub_elasticsearch_releases.set_defaults(func=run_elasticsearch_releases)
+    sub_elasticsearch_releases.add_argument('json_input',
         help="JSON-per-line of release entities",
         default=sys.stdin, type=argparse.FileType('r'))
-    sub_transform_releases.add_argument('json_output',
+    sub_elasticsearch_releases.add_argument('json_output',
         help="where to send output",
         default=sys.stdout, type=argparse.FileType('w'))
 
-    sub_transform_containers = subparsers.add_parser('transform-containers')
-    sub_transform_containers.set_defaults(func=run_transform_containers)
-    sub_transform_containers.add_argument('json_input',
+    sub_elasticsearch_containers = subparsers.add_parser('elasticsearch-containers')
+    sub_elasticsearch_containers.set_defaults(func=run_elasticsearch_containers)
+    sub_elasticsearch_containers.add_argument('json_input',
         help="JSON-per-line of container entities",
         default=sys.stdin, type=argparse.FileType('r'))
-    sub_transform_containers.add_argument('json_output',
+    sub_elasticsearch_containers.add_argument('json_output',
         help="where to send output",
         default=sys.stdout, type=argparse.FileType('w'))
 
-    sub_transform_changelogs = subparsers.add_parser('transform-changelogs')
-    sub_transform_changelogs.set_defaults(func=run_transform_changelogs)
-    sub_transform_changelogs.add_argument('json_input',
+    sub_elasticsearch_changelogs = subparsers.add_parser('elasticsearch-changelogs')
+    sub_elasticsearch_changelogs.set_defaults(func=run_elasticsearch_changelogs)
+    sub_elasticsearch_changelogs.add_argument('json_input',
         help="JSON-per-line of changelog entries",
         default=sys.stdin, type=argparse.FileType('r'))
-    sub_transform_changelogs.add_argument('json_output',
+    sub_elasticsearch_changelogs.add_argument('json_output',
         help="where to send output",
         default=sys.stdout, type=argparse.FileType('w'))
 
diff --git a/python/tests/cli.sh b/python/tests/cli.sh
index 8d594bce..0005c4ba 100755
--- a/python/tests/cli.sh
+++ b/python/tests/cli.sh
@@ -22,5 +22,10 @@ set -x
 ./fatcat_webface.py -h
 ./fatcat_worker.py -h
 
+./fatcat_util.py fcid2uuid aaaaaaaaaaaaamztaaaaaaaaae
+./fatcat_util.py uuid2fcid 00000000-0000-0000-3333-000000000001
+
+cat tests/files/example_releases_pubmed19n0972.json | ./fatcat_transform.py citeproc-releases - /dev/null
+
 set +x
 echo "Done running CLI examples (SUCCESS)"
diff --git a/python/tests/files/example_releases_pubmed19n0972.json b/python/tests/files/example_releases_pubmed19n0972.json
new file mode 100644
index 00000000..b7f4bd0e
--- /dev/null
+++ b/python/tests/files/example_releases_pubmed19n0972.json
@@ -0,0 +1,10 @@
+{"language": "eng", "refs": null, "release_date": null, "issue": "4", "container": {"name": "Roczniki Panstwowego Zakladu Higieny", "issnl": "0035-7715"}, "doi": "10.32394/rpzh.2018.0046", "volume": "69`", "abstracts": [{"mimetype": "text/plain", "lang": "en", "content": "In the prevention of osteoporosis and its treatment, it is important to prevent bone loss by reducing the occurrence of factors determining human health, which reduce the risk of osteoporosis, such as health behaviors."}, {"mimetype": "text/plain", "lang": "en", "content": "Characteristics of modifiable risk factors predisposing to osteoporosis, such as: low intake of calcium and vitamin D3 in the diet, smoking, coffee and alcohol abuse."}, {"mimetype": "text/plain", "lang": "en", "content": "The study involved 400 women aged 50-74 who are suffering from osteoporosis T-score <-2.5 SD and those who are healthy T-score> -1 SD, living in the Malopolska voivodeship. A questionnaire was used to conduct the study."}, {"mimetype": "text/plain", "lang": "en", "content": "More than half of the respondents with osteoporosis (51%) were drinking coffee several times a day. In the healthy group, the majority of respondents (77.5%) were drinking coffee once a day. None of the healthy subjects drank more than two units of alcohol per day, and in the group of patients 2% of respondents declared consumption of more than two units of alcohol every day. Women with osteoporosis were more likely to smoke cigarettes and declared more frequent intake of calcium-containing products than healthy women. In the group of\n200 examined women suffering from osteoporosis, 26.5% daily consumed milk, and 21.5% included this product three times a week in their diet. Healthy women did not drink milk every day. One-third (30.5%) of women with osteoporosis provided the daily recommended dose of calcium by consuming a slice of cheese. None of the healthy women examined included yellow cheese in daily meals, but only once (22%) or three times (26.5%) a week."}, {"mimetype": "text/plain", "lang": "en", "content": "It is important to introduce a health education in order to increase knowledge about the risk factors of osteoporosis , including the principles of proper nutrition with an emphasis on calcium and vitamin D3 intake."}], "work_id": null, "pmid": 30525331, "contribs": [{"raw_name": "Ewa M\u0119drela-Kuder", "role": "author", "raw_affiliation": "University of Physical Education, Department of Health Protection, al. Jana Paw\u0142a II 78, 31-571 Krakow, Poland"}, {"raw_name": "Karolina Szymura", "role": "author", "raw_affiliation": "University of Physical Education, Department of Health Protection, al. Jana Paw\u0142a II 78, 31-571 Krakow, Poland"}], "release_status": "published", "pages": "397-403", "original_title": null, "release_type": "article-journal", "pmcid": null, "release_year": 2018, "title": "Selected anti-health behaviours among women with osteoporosis", "extra": null}
+{"language": "eng", "refs": null, "release_date": null, "issue": "4", "container": {"name": "Roczniki Panstwowego Zakladu Higieny", "issnl": "0035-7715"}, "doi": "10.32394/rpzh.2018.0047", "volume": "69", "abstracts": [{"mimetype": "text/plain", "lang": "en", "content": "One of the important source of food contamination with elements harmful to human health such as lead or cadmium is migration from the articles intended to come into contact with food. Ceramic and glass articles can also be a source of zinc and copper which compounds are used during the production process of vessels."}, {"mimetype": "text/plain", "lang": "en", "content": "Determination of migration of lead, cadmium, zinc and copper from ceramic and glass wares available on the market in Poland and assessment of consumer exposure to these elements."}, {"mimetype": "text/plain", "lang": "en", "content": "Ceramic and glass articles which were available on the retail market and mainly produced in China were tested for release of lead, cadmium, zinc and copper. Samples for testing were prepared in accordance with European Standards: EN 1388-1 and EN 1388-2 and the migration of elements into a food simulant (4% acetic acid) was measured using flame atomic absorption spectrometry (FAAS). Validated and accredited methods according to EN ISO/ IEC 17025:2005 meeting the criteria set in the legislation were applied. Exposure assessment was performed taking into account actual reference doses introduced by the European Food Safety Authority (EFSA) and the Joint FAO/WHO Expert Committee on Food Additives (JECFA)."}, {"mimetype": "text/plain", "lang": "en", "content": "736 samples of ceramic and glass wares were tested. Among investigated samples for migration of lead 82% of results were below limit of quantification (LOQ = 0.1 mg/L) of the analytical method used. For cadmium zinc and copper results below LOQ were found in 94%, 79% and 100% tested samples, respectively (Cd LOQ = 0.01mg/L; Zn LOQ = 0.05 mg/L; Cu LOQ = 0.03 mg/L). Only one sample release lead in amount higher than limit set in Polish Standard PN-B-13210:1997, it was rim of the glass mug and migration value was 4.81 mg/article. In case of cadmium there were two samples which exceeded permissible migration limit, it was flat ceramic dish and the rim of the glass mug, migration values were: 0.14 mg/dm2 and 0.42 mg/article respectively. The most measurable results (above LOQ) in case of lead and cadmium were for the samples of ceramic and glass drinking vessels. Quantifiable amounts of zinc were found also in other groups of articles tested: flat and deep ceramic dishes. None of the tested articles released copper in amount higher than LOQ value. The risk assessment showed that lead and cadmium exposure for some of the samples far exceed the reference doses. For children, assuming a single use only of these vessels, these doses may be exceeded: in the case of lead, 69 times and in the case of cadmium, 8 times."}, {"mimetype": "text/plain", "lang": "en", "content": "It is the urgent need to introduce requirements into the applicable legislation for the rim area of drinking ceramic and glass vessels to reduce exposure especially by the most vulnerable groups of population such as children."}], "work_id": null, "pmid": 30525332, "contribs": [{"raw_name": "Monika Mania", "role": "author", "raw_affiliation": "National Institute of Public Health-National Institute of Hygiene, Department of Food Safety, Warsaw, Poland"}, {"raw_name": "Tomasz Szynal", "role": "author", "raw_affiliation": "National Institute of Public Health-National Institute of Hygiene, Department of Food Safety, Warsaw, Poland"}, {"raw_name": "Ma\u0142gorzata Rebeniak", "role": "author", "raw_affiliation": "National Institute of Public Health-National Institute of Hygiene, Department of Food Safety, Warsaw, Poland"}, {"raw_name": "Jacek Postupolski", "role": "author", "raw_affiliation": "National Institute of Public Health-National Institute of Hygiene, Department of Food Safety, Warsaw, Poland"}], "release_status": "published", "pages": "405-411", "original_title": null, "release_type": "article-journal", "pmcid": null, "release_year": 2018, "title": "Exposure assessment to lead, cadmium, zinc and copper released from ceramic and glass wares intended to come into contact with food", "extra": null}
+{"language": "eng", "refs": null, "release_date": null, "issue": "4", "container": {"name": "Roczniki Panstwowego Zakladu Higieny", "issnl": "0035-7715"}, "doi": "10.32394/rpzh.2018.0048", "volume": "69", "abstracts": [{"mimetype": "text/plain", "lang": "en", "content": "Consumers may feel confused by receiving conflicting information about health-related aspects of beef. Therefore, it is invariably important to assess how consumers perceive the health benefits of beef."}, {"mimetype": "text/plain", "lang": "en", "content": "The aim of the study was to assess the impact of consumer perception of beef values on consumer behavior towards this type of meat."}, {"mimetype": "text/plain", "lang": "en", "content": "The study consisted of a survey conducted among residents of \u015awi\u0119tokrzyskie voivodeship in the period February 2013 \u2013 September 2014. The research was conducted among 1004 consumers. The questions included in the questionnaire concerned habits associated with consumption of beef, as well as issues related to the process of purchasing decisions, and in particular the place and frequency of purchase of beef."}, {"mimetype": "text/plain", "lang": "en", "content": "It was found that the frequency of buying beef was also significantly dependent on consumer belief in the health attributes of beef. Consumers consuming beef for this reason more often indicated that they consume beef once a week and 2-3 times a month. On the other hand, consumers who did not eat beef because of its impact on health in which they believed, more often pointed to its occasional/ sporadic consumption, that is once a month and less often."}, {"mimetype": "text/plain", "lang": "en", "content": "A significant percentage of consumers in the \u015awi\u0119tokrzyskie voivodship misinterpret dietary recommendations and conclude that it is necessary to increase the consumption of beef due to medical reasons. Medical recommendations indicating the need to reduce meat consumption for a significant percentage of consumers from the \u015awi\u0119tokrzyskie Voivodeship are of little importance and do not contribute to changing their eating behavior. Especially in the case of men, there is often a reluctance to change eating habits if it would involve the need to reduce the consumption of meat. There is a need to verify marketing messages and to carry out general nutrition education so that it is possible to actually reach consumers with information about the need to limit the consumption of meat products."}], "work_id": null, "pmid": 30525333, "contribs": [{"raw_name": "Krystyna Gutkowska", "role": "author", "raw_affiliation": "Department of Organization and Consumption Economics, Faculty of Human Nutrition and Consumer Sciences, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland"}, {"raw_name": "Jacek Czarnecki", "role": "author", "raw_affiliation": "Nestl\u00e9 Polska S.A., Warsaw, Poland"}, {"raw_name": "Dominika G\u0142\u0105bska", "role": "author", "raw_affiliation": "Department of Dietetics, Faculty of Human Nutrition and Consumer Sciences, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland"}, {"raw_name": "Dominika Guzek", "role": "author", "raw_affiliation": "Department of Organization and Consumption Economics, Faculty of Human Nutrition and Consumer Sciences, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland"}, {"raw_name": "Agnieszka Bat\u00f3g", "role": "author", "raw_affiliation": "Department of Organization and Consumption Economics, Faculty of Human Nutrition and Consumer Sciences, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland"}], "release_status": "published", "pages": "413-419", "original_title": null, "release_type": "article-journal", "pmcid": null, "release_year": 2018, "title": "Consumer perception of health properties and of other attributes of beef as determinants of consumption and purchase decisions", "extra": null}
+{"language": "eng", "refs": null, "release_date": "2018-12-10", "issue": "1", "container": {"name": "Journal of psychiatry & neuroscience : JPN", "issnl": "1180-4882"}, "doi": "10.1503/jpn.170220", "volume": "44", "abstracts": [{"mimetype": "text/plain", "lang": "en", "content": "Previous studies have implicated white-matter-related changes in the pathophysiology of bipolar disorder. However, most of what is known is derived from in vivo subcortical white-matter imaging or postmortem studies. In this study, we investigated whole-brain intracortical myelin (ICM) content in people with bipolar disorder type I and controls."}, {"mimetype": "text/plain", "lang": "en", "content": "Between Sept. 1, 2014, and Jan. 31, 2017, we used a 3 T General Electric scanner to collect T1-weighted images in 45 people with bipolar disorder type I and 60 controls aged 17 to 45 years using an optimized sequence that was sensitive to ICM content. We analyzed images using a surfacebased approach. We used general linear models with quadratic age terms to examine the signal trajectory of ICM across the age range."}, {"mimetype": "text/plain", "lang": "en", "content": "In healthy controls, the T1-weighted signal followed an inverted-U trajectory over age; in people with bipolar disorder type I, the association between ICM and age followed a flat trajectory (p < 0.05, Bonferroni corrected). Exploratory analyses showed that ICM signal intensity was associated with duration of illness, age of onset, and anticonvulsant and antipsychotic use in people with bipolar disorder type I (p < 0.05, uncorrected)."}, {"mimetype": "text/plain", "lang": "en", "content": "Because of the cross-sectional nature of the study, we were unable to comment on whether the effects were due to dysmyelination or demyelination in bipolar disorder."}, {"mimetype": "text/plain", "lang": "en", "content": "This foundational study is, to our knowledge, the first to show global age-related deficits in ICM maturation throughout the cortex in bipolar disorder. Considering the impact of myelination on the maintenance of neural synchrony and the integrity of neural connections, this work may help us better understand the cognitive and behavioural deficits seen in bipolar disorder."}], "work_id": null, "pmid": 30525334, "contribs": [{"raw_name": "Manpreet Sehmbi", "role": "author", "raw_affiliation": "From the Graduate Student, MiNDS Neuroscience Graduate Program, McMaster University, Hamilton, ON (Sehmbi, Rowley); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON (Minuzzi, Kapczinski, Frey); the Women\u2019s Health Concerns Clinic, St. Joseph\u2019s Healthcare, Hamilton, ON (Minuzzi, Frey); the Department of Pathology and Molecular Medicine, M. deGroote School of Medicine, McMaster University, Hamilton, ON (Kwiecien); the Department of Psychology, Neuroscience, and Behaviour, McMaster University, Hamilton, ON (Bock); and the Department of Clinical Pathomorphology, Medical University of Lublin, Poland (Kwiecien)."}, {"raw_name": "Christopher D. Rowley", "role": "author", "raw_affiliation": "From the Graduate Student, MiNDS Neuroscience Graduate Program, McMaster University, Hamilton, ON (Sehmbi, Rowley); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON (Minuzzi, Kapczinski, Frey); the Women\u2019s Health Concerns Clinic, St. Joseph\u2019s Healthcare, Hamilton, ON (Minuzzi, Frey); the Department of Pathology and Molecular Medicine, M. deGroote School of Medicine, McMaster University, Hamilton, ON (Kwiecien); the Department of Psychology, Neuroscience, and Behaviour, McMaster University, Hamilton, ON (Bock); and the Department of Clinical Pathomorphology, Medical University of Lublin, Poland (Kwiecien)."}, {"raw_name": "Luciano Minuzzi", "role": "author", "raw_affiliation": "From the Graduate Student, MiNDS Neuroscience Graduate Program, McMaster University, Hamilton, ON (Sehmbi, Rowley); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON (Minuzzi, Kapczinski, Frey); the Women\u2019s Health Concerns Clinic, St. Joseph\u2019s Healthcare, Hamilton, ON (Minuzzi, Frey); the Department of Pathology and Molecular Medicine, M. deGroote School of Medicine, McMaster University, Hamilton, ON (Kwiecien); the Department of Psychology, Neuroscience, and Behaviour, McMaster University, Hamilton, ON (Bock); and the Department of Clinical Pathomorphology, Medical University of Lublin, Poland (Kwiecien)."}, {"raw_name": "Flavio Kapczinski", "role": "author", "raw_affiliation": "From the Graduate Student, MiNDS Neuroscience Graduate Program, McMaster University, Hamilton, ON (Sehmbi, Rowley); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON (Minuzzi, Kapczinski, Frey); the Women\u2019s Health Concerns Clinic, St. Joseph\u2019s Healthcare, Hamilton, ON (Minuzzi, Frey); the Department of Pathology and Molecular Medicine, M. deGroote School of Medicine, McMaster University, Hamilton, ON (Kwiecien); the Department of Psychology, Neuroscience, and Behaviour, McMaster University, Hamilton, ON (Bock); and the Department of Clinical Pathomorphology, Medical University of Lublin, Poland (Kwiecien)."}, {"raw_name": "Jacek M. Kwiecien", "role": "author", "raw_affiliation": "From the Graduate Student, MiNDS Neuroscience Graduate Program, McMaster University, Hamilton, ON (Sehmbi, Rowley); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON (Minuzzi, Kapczinski, Frey); the Women\u2019s Health Concerns Clinic, St. Joseph\u2019s Healthcare, Hamilton, ON (Minuzzi, Frey); the Department of Pathology and Molecular Medicine, M. deGroote School of Medicine, McMaster University, Hamilton, ON (Kwiecien); the Department of Psychology, Neuroscience, and Behaviour, McMaster University, Hamilton, ON (Bock); and the Department of Clinical Pathomorphology, Medical University of Lublin, Poland (Kwiecien)."}, {"raw_name": "Nicholas A. Bock", "role": "author", "raw_affiliation": "From the Graduate Student, MiNDS Neuroscience Graduate Program, McMaster University, Hamilton, ON (Sehmbi, Rowley); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON (Minuzzi, Kapczinski, Frey); the Women\u2019s Health Concerns Clinic, St. Joseph\u2019s Healthcare, Hamilton, ON (Minuzzi, Frey); the Department of Pathology and Molecular Medicine, M. deGroote School of Medicine, McMaster University, Hamilton, ON (Kwiecien); the Department of Psychology, Neuroscience, and Behaviour, McMaster University, Hamilton, ON (Bock); and the Department of Clinical Pathomorphology, Medical University of Lublin, Poland (Kwiecien)."}, {"raw_name": "Benicio N. Frey", "role": "author", "raw_affiliation": "From the Graduate Student, MiNDS Neuroscience Graduate Program, McMaster University, Hamilton, ON (Sehmbi, Rowley); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON (Minuzzi, Kapczinski, Frey); the Women\u2019s Health Concerns Clinic, St. Joseph\u2019s Healthcare, Hamilton, ON (Minuzzi, Frey); the Department of Pathology and Molecular Medicine, M. deGroote School of Medicine, McMaster University, Hamilton, ON (Kwiecien); the Department of Psychology, Neuroscience, and Behaviour, McMaster University, Hamilton, ON (Bock); and the Department of Clinical Pathomorphology, Medical University of Lublin, Poland (Kwiecien)."}], "release_status": "published", "pages": "1-10", "original_title": null, "release_type": "article-journal", "pmcid": null, "release_year": 2018, "title": "Age-related deficits in intracortical myelination in young adults with bipolar disorder type I", "extra": null}
+{"language": "fre", "refs": null, "release_date": null, "issue": "4", "container": {"name": "La Revue du praticien", "issnl": "0035-2640"}, "doi": null, "volume": "67", "abstracts": null, "work_id": null, "pmid": 30525335, "contribs": [{"raw_name": "Alain Tenaillon", "role": "author"}], "release_status": "published", "pages": "351", "original_title": "L\u2019UNAASS : un petit ou un grand pas pour la d\u00e9mocratie en sant\u00e9 ?", "release_type": "editorial", "pmcid": null, "release_year": 2017, "title": "UNAASS: a small or a big step for democracy in health?", "extra": null}
+{"language": "eng", "refs": null, "release_date": "2018-12-05", "issue": null, "container": {"name": "Ecology", "issnl": "0012-9658"}, "doi": "10.1002/ecy.2576", "volume": null, "abstracts": [{"mimetype": "text/plain", "lang": "en", "content": "The abundance and distribution of species across the landscape depend on the interaction between local, spatial and stochastic processes. However, empirical syntheses relating these processes to spatio-temporal patterns of structure in metacommunities remains elusive. One important reason for this lack of synthesis is that the relative importance of the core assembly processes (dispersal, selection and drift) critically depends on the spatial grain and extent over which communities are studied. To illustrate this, we simulated different aspects of community assembly on heterogeneous landscapes, including the strength of response to environmental heterogeneity (inherent to niche theory) versus dispersal and stochastic drift (inherent to neutral theory). We show that increasing spatial extent leads to increasing importance of niche selection, whereas increasing spatial grain leads to decreasing importance of niche selection. The strength of these scaling effects depended on environment configuration, dispersal capacity and niche breadth. By mapping the variation observed from the scaling effects in simulations, we could recreate the entire range of variation observed within and among empirical studies. This means that variation in the relative importance of assembly processes among empirical studies is largely scale dependent and cannot be directly compared. The scaling coefficient of the relative contribution of assembly processes, however, can be interpreted as a scale-integrative estimate to compare assembly processes across different regions and ecosystems. This emphasizes the necessity to consider spatial scaling as an explicit component of studies intended to infer the importance of community assembly processes. This article is protected by copyright. All rights reserved."}], "work_id": null, "pmid": 30516271, "contribs": [{"raw_name": "Duarte S Viana", "role": "author", "raw_affiliation": "German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany."}, {"raw_name": "Jonathan M Chase", "role": "author", "raw_affiliation": "German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany."}], "release_status": "published", "pages": null, "original_title": null, "release_type": "article-journal", "pmcid": null, "release_year": 2018, "title": "Spatial scale modulates the inference of metacommunity assembly processes", "extra": null}
+{"language": "eng", "refs": null, "release_date": "2018-12-05", "issue": null, "container": {"name": "Biometrics", "issnl": "0006-341X"}, "doi": "10.1111/biom.13010", "volume": null, "abstracts": [{"mimetype": "text/plain", "lang": "en", "content": "Several recent methods address the dimension reduction and decomposition of linked high-content data matrices. Typically, these methods consider one dimension, rows or columns, that is shared among the matrices. This shared dimension may represent common features measured for different sample sets (horizontal integration) or a common sample set with features from different platforms (vertical integration). We introduce an approach for simultaneous horizontal and vertical integration, Linked Matrix Factorization (LMF), for the general case where some matrices share rows (e.g., features) and some share columns (e.g., samples). Our motivating application is a cytotoxicity study with accompanying genomic and molecular chemical attribute data. The toxicity matrix (cell lines\u2009\u00d7\u2009chemicals) shares samples with a genotype matrix (cell lines\u2009\u00d7\u2009SNPs) and shares features with a molecular attribute matrix (chemicals\u2009\u00d7\u2009attributes). LMF gives a unified low-rank factorization of these three matrices, which allows for the decomposition of systematic variation that is shared and systematic variation that is specific to each matrix. This allows for efficient dimension reduction, exploratory visualization, and the imputation of missing data even when entire rows or columns are missing. We present theoretical results concerning the uniqueness, identifiability, and minimal parametrization of LMF, and evaluate it with extensive simulation studies. This article is protected by copyright. All rights reserved."}], "work_id": null, "pmid": 30516272, "contribs": [{"raw_name": "Michael J O'Connell", "role": "author", "raw_affiliation": "Department of Statistics, Miami University, Oxford, OH 45056, USA."}, {"raw_name": "Eric F Lock", "role": "author", "raw_affiliation": "Division of Biostatistics, University of Minnesota, Minneapolis, MN 55455, USA."}], "release_status": "published", "pages": null, "original_title": null, "release_type": "article-journal", "pmcid": null, "release_year": 2018, "title": "Linked Matrix Factorization", "extra": null}
+{"language": "eng", "refs": null, "release_date": "2018-12-05", "issue": null, "container": {"name": "Ecology", "issnl": "0012-9658"}, "doi": "10.1002/ecy.2578", "volume": null, "abstracts": [{"mimetype": "text/plain", "lang": "en", "content": "Research on regime shifts has focused primarily on how changes in the intensity and duration of press disturbances precipitate natural systems into undesirable, alternative states. By contrast, the role of recurrent pulse perturbations, such as extreme climatic events, has been largely neglected, hindering our understanding of how historical processes regulate the onset of a regime shift. We performed field manipulations to evaluate whether combinations of extreme events of temperature and sediment deposition that differed in their degree of temporal clustering generated alternative states in rocky intertidal epilithic microphytobenthos (biofilms) on rocky shores. The likelihood of biofilms to shift from a vegetated to a bare state depended on the degree of temporal clustering of events, with biofilm biomass showing both states under a regime of non-clustered (60 days apart) perturbations while collapsing in the clustered (15 days apart) scenario. Our results indicate that time since the last perturbation can be an important predictor of collapse in systems exhibiting alternative states and that consideration of historical effects in studies of regime shifts may largely improve our understanding of ecosystem dynamics under climate change. This article is protected by copyright. All rights reserved."}], "work_id": null, "pmid": 30516273, "contribs": [{"raw_name": "Martina Dal Bello", "role": "author", "raw_affiliation": "Department of Biology, University of Pisa, CoNISMa, Via Derna 1, Pisa, Italy."}, {"raw_name": "Luca Rindi", "role": "author", "raw_affiliation": "Department of Biology, University of Pisa, CoNISMa, Via Derna 1, Pisa, Italy."}, {"raw_name": "Lisandro Benedetti-Cecchi", "role": "author", "raw_affiliation": "Department of Biology, University of Pisa, CoNISMa, Via Derna 1, Pisa, Italy."}], "release_status": "published", "pages": null, "original_title": null, "release_type": "article-journal", "pmcid": null, "release_year": 2018, "title": "Temporal clustering of extreme climate events drives a regime shift in rocky intertidal biofilms", "extra": null}
+{"language": "eng", "refs": null, "release_date": "2018-12-05", "issue": null, "container": {"name": "Ecology", "issnl": "0012-9658"}, "doi": "10.1002/ecy.2573", "volume": null, "abstracts": [{"mimetype": "text/plain", "lang": "en", "content": "The diversity-invasibility hypothesis and ecological theory predict that high-diversity communities should be less easily invaded than species-poor communities, but empirical evidence does not consistently support this prediction. While fine-scale experiments tend to yield the predicted negative association between diversity and invasibility, broad-scale observational surveys generally report a positive correlation. This conflicting pattern between experiments and observational studies is referred to as the invasion paradox, and is thought to arise because different processes control species composition at different spatial scales. Here, we test empirically the extent to which the strength and direction of published diversity-invasibility relationships depend on spatial scale and on the metrics used to measure invasibility. Using a meta-analytic framework, we explicitly separate the two components of spatial scale: grain and extent, by focusing on fine-grain studies that vary in extent. We find evidence of multiple drivers of the paradox. When we consider only fine-grain studies, we still observe conflicting patterns between experiments and observational studies. In contrast, when we examine studies that are conducted at both a fine grain and fine extent, there is broad overlap in effect sizes between experiments and observation, suggesting that comparing studies with similar extents resolves the paradox at local scales. However, we uncover systematic differences in the metrics used to measure invasibility between experiments, which use predominantly invader performance, and observational studies, which use mainly invader richness. When we consider studies with the same metric (i.e., invader performance), the contrasting associations between study types also disappears. It is not possible, at present, to fully disentangle the effect of spatial extent and metric on the paradox because both variables are systematically associated in different directions with study type. There is therefore an urgent need to conduct experiments and observational studies that incorporate the full range of variability in spatial extent and invasibility metric. This article is protected by copyright. All rights reserved."}], "work_id": null, "pmid": 30516274, "contribs": [{"raw_name": "Nicola S Smith", "role": "author", "raw_affiliation": "Earth to Oceans Research Group, Department of Biological Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada."}, {"raw_name": "Isabelle M C\u00f4t\u00e9", "role": "author", "raw_affiliation": "Earth to Oceans Research Group, Department of Biological Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada."}], "release_status": "published", "pages": null, "original_title": null, "release_type": "article-journal", "pmcid": null, "release_year": 2018, "title": "Multiple drivers of contrasting diversity-invasibility relationships at fine spatial grains", "extra": null}
+{"language": "eng", "refs": null, "release_date": "2018-12-05", "issue": null, "container": {"name": "Ecology", "issnl": "0012-9658"}, "doi": "10.1002/ecy.2575", "volume": null, "abstracts": [{"mimetype": "text/plain", "lang": "en", "content": "Most studies consider aboveground plant species richness as a representative biodiversity measure. This approach inevitably assumes that the partitioning of total plant species richness into above- and belowground components is constant or at least consistent within and across vegetation types. However, with studies considering belowground plant richness still scarce and completely absent along vegetation gradients, this assumption lacks experimental support. Novel DNA sequencing techniques allow economical, high-throughput species identification of belowground environmental samples, enabling the measurement of the contributions of both above- and belowground plant components to total plant richness. We investigated above- and belowground plant species richness in four vegetation types (birch forest, heath, low alpine tundra, high alpine tundra) at the scale of herbaceous plant neighborhoods (dm) using 454 sequencing of the chloroplast trnL (UAA) intron to determine the plant species richness of environmental root samples and combined it with aboveground data from vegetation surveys to obtain total plant species richness. We correlated the measured plant species richness components with each other and with their respective plant biomass components within and across vegetation types. Total plant species richness exceeded aboveground richness twice on average and by as much as three times in low alpine tundra, indicating that a significant fraction of belowground plant richness cannot be recorded aboveground. More importantly, no consistent relationship among richness components (above- and belowground) was found within or across vegetation types, indicating that aboveground richness alone cannot predict total plant richness in contrasting vegetation types. Finally, no consistent relationship between plant richness and the corresponding biomass component was found. Our results clearly show that aboveground plant richness alone is a poor estimator of total plant species richness within and across different vegetation types. Consequently, it is crucial to account for belowground plant richness in future plant ecological studies in order to validate currently accepted plant richness patterns, as well as to measure potential changes in plant community composition in a changing environment. This article is protected by copyright. All rights reserved."}], "work_id": null, "pmid": 30516275, "contribs": [{"raw_name": "Sabrina Tr\u00e4ger", "role": "author", "raw_affiliation": "Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, 51005, Tartu, Estonia."}, {"raw_name": "Maarja \u00d6pik", "role": "author", "raw_affiliation": "Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, 51005, Tartu, Estonia."}, {"raw_name": "Martti Vasar", "role": "author", "raw_affiliation": "Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, 51005, Tartu, Estonia."}, {"raw_name": "Scott D Wilson", "role": "author", "raw_affiliation": "Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada."}], "release_status": "published", "pages": null, "original_title": null, "release_type": "article-journal", "pmcid": null, "release_year": 2018, "title": "Belowground plant parts are crucial for comprehensively estimating total plant richness in herbaceous and woody habitats", "extra": null}