dataesr/scientific-paragraphs-categorization huggingface dataset:
DCL1 is one of the genes involved in ta-siRNA-mediated RdDM  50. Figure  5. Relative expression assays of some genes related to homologous recombination in bud samples. Red asterisks mark the genes that are overexpressed more than two-fold in all of the mutants compared with the wild type. Orange asterisks mark the genes that are overexpressed 1. 5-to 2. 0-fold. We found increased levels of mRNAs from genes involved in chromatin structure maintenance, which could be due to the direct or indirect action of miRNAs on these mRNAs. A recent analysis of 338 mature Arabidopsis miRNAs from the Plant microRNA Database (PMRD; http://bioinformatics. cau. edu. cn/PMRD)  38 identified 2,862 potential targets  51. These targets include several genes encoding proteins involved in histone modification, DNA methylation and chromatin remodeling, including SMC6A, TOPII and SWI1, whose mRNAs we found accumulated in the mutants studied here.
Acknowledgements This work was supported by the  Ministerio de Economía, Industria y Competitividad of Spain  (grants  AGL2012-38852  and  AGL2015-67349-P  to JLS, and  BIO2014-56889-R  to MRP), the  European Union   Framework Program 7 (Meiosys- KBBE-2009-222883  to JLS) and the  Generalitat Valenciana  ( PROMETEOII/2014/006  to MRP). We are very grateful to  Prof. José Luis Micol  and  Prof. Héctor Candela  for comments on the manuscript, and  Dr. Enrique Sánchez Molano  and  Diego Bersabé  for their help with the statistical analyses.
A growing interest is devoted to global-scale approaches in ecology and evolution that examine patterns and determinants of species diversity and the threats resulting from global change. These analyses obviously require global datasets of species distribution. Freshwater systems house a disproportionately high fraction of the global fish diversity considering the small proportion of the earth's surface that they occupy, and are one of the most threatened habitats on Earth. Here we provide complete species lists for 3119 drainage basins covering more than 80% of the Earth surface using 14953 fish species inhabiting permanently or occasionally freshwater systems. The database results from an extensive survey of native and non-native freshwater fish species distribution based on 1436 published papers, books, grey literature and web-based sources.
Describing global scale freshwater fish diversity patterns, understanding the environmental drivers and evolutionary processes shaping such diversity and revealing the major human-related threats were the major goals that motivated the compilation of the present database. Indeed, global scale datasets allowing for biogeographical, macroecological, macroevolutionary and conservation studies were available for only a few well-documented animal taxa such as birds, mammals and amphibians  [13] [14] [15]. The present database increases this list of taxa by providing occurrence data by drainage basin worldwide for the most diverse group of vertebrates (i. e. fishes), with more than 33500 species described to date (FishBase; http://www. fishbase. org), from which c. 40% inhabit permanently freshwater systems.
We conducted an extensive survey of freshwater fish species distribution based on 1436 published papers, books, grey literature, databases and web-based sources, resulting in species lists for 3119 drainage basins covering more than 80% of the Earth surface (Fig. 1 ). Two important survey efforts were conducted, respectively completed in 2008 (ref. 16) and 2013 (ref. 17). To date, these databases have been used in several studies that have increased our understanding of freshwater fish species distributions. These studies allowed to accurately map global patterns of native  18  , endemic  19  and non-native  20  freshwater fish species richness and to reveal their environmental and human-related determinants. The databases were also used to evaluate non-native species influence on native communities structure  21  , to forecast climate change effects on species extinction processes  11  and to analyse effects of current and future scenarios of species introductions on fish faunas homogenization processes  [22] [23] [24] [25].
Recent studies also focused on analysing the influence of past river connections on the present distribution of native fish species  17  , on analysing geographical and trait-based differences in diversification rates and origin of actinopterygian fish families  5  , and on evaluating human-related extinction drivers  12. Although the database has already provided a lot of insightful knowledge, it still represents a valuable source of information for further studies on freshwater macroecology, macroevolution, biogeography and conservation. For instance, the present dataset could serve to identify diversity hotspots and to generate a global map of ichthyogeographic regions by combining data on the distributions and phylogenetic relationships of species, allowing in fine the identification of geographic areas harbouring distinct evolutionary histories.
Furthermore, in association with data on the time and place of origin of species or on species functional traits, the global occurrence dataset could provide new insights on the macroevolution of freshwater fishes or approach the functional characteristics of communities. Those   27. The 3119 drainage basins cover more than 80% of the Earth surface (excluding deserts), ranging from 70% for the Indo-Malay region to over 90% for the Afrotropical region. forthcoming approaches would surely help designing large scale conservation priorities for freshwater fishes. The database is organised in three sub-datasets and one shapefile. The first dataset contains the species occurrence records by drainage basin along with their native or non-native status and the corresponding FishBase species code and valid name.
The second dataset, which is simply the export of the shapefile attributes table, contains geographic information on the drainage basins (e. g. geographic coordinates, surface area). The third dataset contains the list of references that were used to build the species lists for each of the drainage basins. This reference list is obviously not definitive and updates of the database will be performed regularly to include new occurrence records, the distribution of newly described species, species lists of new drainage basins and nomenclature changes in the always moving taxonomy.
Information sources This global database of freshwater fish species distribution results from a joint collaboration between three French research institutes, i. e. the University Paul Sabatier in Toulouse (UPS), the National Museum of Natural History (MNHN) and the Research Institute for Development (IRD). The financial support necessary to build this database mainly came from two projects: the 'Freshwater Fish Diversity' (National Agency for Research: ANR-06-BDIV-010) and 'BioFresh' (7th Framework European program, Contract N°226874) projects. Starting in 2003, we conducted an extensive survey of literature published from 1960 to 2014 on native and non-native freshwater fish species at the drainage basin grain. This survey was complemented with web-based sources from national and international biodiversity inventory initiatives compiling either or both collection and field sampling data.
Our efforts were mainly devoted to find information sources providing complete fish species lists of a given drainage basin, except for some large basins (e. g. the Amazon basin) where we cumulated subdrainage basin species lists and point sampling locations to obtain the most complete possible coverage of the entire drainage basin. We also used local or regional check lists such as local inventories of stream reaches or inventories based solely on a given family or genus to complement our species lists and for cross-checking available information at the drainage basin scale. The resulting database was gathered from 1436 sources including published papers, books, grey literature and web-based sources that included museum collections, national or regional initiatives compiling monitoring data (mainly for developed countries), continental scale atlases of species distribution and international biodiversity initiatives.
Species, taxonomy and status Sub-species were not considered due to limited data availability and all occurrences not identified to species level were discarded (i. e. occurrences giving only genus names commonly abbreviated to sp. , species affinis commonly abbreviated to: sp. aff. , aff. , or affin. or species confer abbreviated to cf. ). Species migrating between both marine and freshwater environments where systematically included in the database. Concerning marine and estuarine species occasionally occurring in freshwaters, these species may be reported in the database but their distribution information should not be considered as exhaustive in any case, as these systems are not the focus of the database. All species scientific names are reported in the database as given in each information source.
These species names were then carefully checked for typing errors and misspellings. Because taxonomy is a 'moving target', species names were standardized based on valid species names and their synonyms reported in FishBase using the 'rfishbase' package  26  from the R environment (http://www. R-project. org). For those species names that did not match with any synonym or valid name from FishBase, a manual search was applied in the Catalogue of Fishes (http://researcharchive. calacademy. org/research/ ichthyology/catalog/fishcatmain. asp). This last step allowed finding valid species names and species recently described that are still not included in FishBase. For recently described species not yet validated by FishBase or species only considered valid by the Catalogue of Fishes, a temporary code was created starting by 'x' (0.
04% of all valid species). The remaining species names were considered as invalid and excluded from the database (only 0. 6% of all species names). The final standardized species list has 14953 valid names avoiding biases due to synonyms and uncertain identifications (see 'Technical Validation'). According to FishBase, from this list of 14953 valid names our database contains the distribution of 13721 species inhabiting fresh or brackish waters, the remaining being marine species also entering fresh or brackish waters, but not recorded as such by FishBase. As a whole, the database harbours 101779 occurrence records (i. e. single species-drainage basin couples). A native or exotic status was assigned to each species occurrence record based on the information provided by the sources and further checked (see 'Technical Validation').
An exotic species is defined as a directly or indirectly (e. g. via artificial channels) introduced species that established in the considered drainage basin. Exotic species included in the database are supposed to complete all their life cycle in the considered basins and to present self-sustaining populations in those basins. When an exotic species occurrence was acknowledged to be unsuccessful (i. e. failure of establishment of that species in the drainage basin) or needing regular release of new individuals to maintain the presence of the introduced species (i. e. stocking), the species was not included in the basin's species list. Species that might be globally extinct or extirpated from a drainage basin were considered as native in the database because the inventory of freshwater fish diversity loss was not targeted (see for instance Dias et al.
Some drainage basins from oceanic islands have no HydroSheds code simply because not considered in the HydroSheds shapefile. Maps and geographic information available in the compiled literature and web-based sources were used to locate, name and improve our drainage basins layer, complemented by country and continental scale geographic data (e. g. Faunafri project for the African continent; http://www. poissons-afrique. ird. fr/faunafri/) and local topographic maps. This new geographic referential is provided as a shapefile to facilitate future uses of the database.
Updates and limitations Species are continuously being discovered and freshwater fishes are no exception, even in well-know regions  29. Rivers are also continuously being explored and re-explored by freshwater scientists. The database is obviously not complete and definitive, and we aim to support the database with regular updates, ideally with bi-annual steps, depending on the resources and funding. Three main factors will be considered in future updates: (1) new or previously non available data sources with species lists or records for additional drainage basins or drainage basins already present in the database; (2) distribution of newly described species; and (3) nomenclature changes in the taxonomic classification. The technical validation procedures described below will also be applied to any new information included in the database.
Researchers having access to new data that want this information to be included in the database can send the references or data to the corresponding author PAT. This information will be included, after validation, in the next update release. The resulting new versions of the database will be released through Figshare and also through the more specialized Freshwater Biodiversity Data Portal (http://data. freshwaterbiodiversity. eu/) to ensure the long-term availability of the database. All biogeographic realms are well represented in terms of surface coverage (Fig. 1 ). There are however some regional gaps that will be gradually filled in the next updates of the database. For instance, Indonesian islands, coastal rivers of Peru and Northeast Brazil are regions where only few drainage basins are informed in the database.
Data Records The database is organised in three datasets and one shapefile: the species occurrence records, the drainage basins and the information sources table. The three tables are in csv format (columns separated by comas) and the shapefile in ArcGis shp format (Data Citation 1). The drainage basins table is given in. csv and shapefile formats. Both formats can be linked to the species occurrence table using the unique drainage basin names to visualize and analyse species distribution using any adapted software (e. g. R or QGIS, http://qgis. osgeo. org). A. The species occurrence records table has six columns: (1) the name of the drainage basin, (2) the scientific name of the fish species according to the information source, (3) the native or exotic status of the occurrence records, (4) the taxonomic serial number (TSN) from the Integrated Taxonomic Information System (ITIS, https://www.
itis. gov/) when available, (5) the FishBase code when available, (6) the FishBase or Catalogue of Fishes valid scientific name at the time of releasing the database, (7) the occurrence status which can be either 'valid' or 'questionable' (see Technical Validation). B. The geographic information on drainage basins is organised in nine columns given in table and shapefile formats: (1) the unique drainage basin name, (2) the main country where it belongs, (3) the corresponding biogeographic region, (4) the endorheic or exorheic status, (  5 ) and (  6 ) the longitude and latitude coordinates of the drainage basin outlet to the sea (only for exorheic drainages), (  7 ) and (  8 ) the centroid longitude and latitude coordinates of the drainage basin, (9) the surface area of the drainage basin.
Species distribution and status validation Occurrence records were carefully reviewed by the database' contributors. When several information sources were used to compile the species list of a given drainage basin, particular attention was given to cross check the occurrence records and ensure a good spatial representation of the drainage basin to avoid (or at least minimize) incomplete species lists. Because occurrence data available in FishBase is often incomplete, FishBase was only used as a secondary source to collect species distribution data and to check that the resulting species distributions from our database corresponded to the broad information given in FishBase. Because only a few (mostly migratory) freshwater species can occur in more than one biogeographic realm, the distribution of every species occurring in more than one realm was carefully verified.
Acknowledgements The construction of this database was mainly supported by the  National Agency for Research (ANR) Freshwater Fish Diversity  ( ANR-06-BDIV-010 ) and by the  EU   BIOFRESH  project (7th  Framework European program , Contract  N°226874 ). EDB laboratory was also supported by  'Investissement d'Avenir ' grants ( CEBA ,  ANR-10-LABX-0025 ;  TULIP ,  ANR-10-LABX-41 ). BOREA laboratory was also supported by the  National Agency for Research (ANR)   FISHLOSS  project ( ANR-09-PEXT-008 ). We are grateful to the  AMAZONFISH  project (ERANet-LAC:  ELAC2014/DCC-0210 ; www. amazon-fish. com)for validating our list of fish species for the Amazon River basin. M. S. D. received a PhD grant from the  Brazilian government (Science without Borders program ,  CNPq /GDE n°201167/2012-3).
(A) Relative gene expression of Chrebp, Chrebpb, Lpk, Scd1, and Fgf21 was determined by qPCR. Data are expressed as means ± SEM (n = 6 individual mice per group). Significance is based on two-way ANOVA followed by Bonferroni post hoc test (fasting or glucose versus fed; #p % 0. 05; ##p % 0. 01; ###p % 0. 001). Significance of the effect of genotype is based two-way ANOVA followed by Bonferroni post hoc test (Ppara hepÀ/À versus Ppara hep +/+ ; *p % 0. 05; **p % 0. 01; ***p % 0. 001). (B) ELISA quantification of FGF21 in plasma. Data are expressed as means ± SEM from n = 6 individual mice per group. Significance of the effect of fasting or glucose challenge is based on two-way ANOVA followed by post hoc test (fasting or glucose versus fed; #p % 0. 05; ##p % 0. 01; ###p % 0. 001). Significance of the effect of genotype is based on two-way ANOVA followed by Bonferroni post hoc test (Ppara hepÀ/À versus Ppara hep +/+ ; *p % 0.
05; **p % 0. 01; ***p % 0. 001). (C) Fgf21 promoter sequence from the transcription start site to À184 bp. The PPARa binding site (PPRE) is indicated in gray. The ChREBP binding site (ChoRE) is indicated in yellow. Primers used for ChIP analysis are indicated on the sequence. (D) ChIP analysis followed by qPCR of whole mouse liver tissue. Immunoprecipitation (IP) was conducted with PPARa, ChREBP, H3K9ac, and RNA Pol II antibodies. The DNA region of the Fgf21 promoter was amplified using the primers indicated in (C). (E) ChIP analysis followed by qPCR of whole mouse liver tissue. IP were conducted with ChREBP and RNA Pol II antibodies. Data are expressed as means ± SEM from n = 3 individual mice per group. Significance is based on two-way ANOVA followed by Bonferroni post hoc test (**p % 0.
Gene Expression Analysis Total cellular RNA was extracted using the SV total RNA isolation system (Promega). For qPCR analysis, total RNA samples (2 mg) were reverse transcribed using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems). Primers for SYBR green assays are presented in Tables  S2  and S3. Primers used to measure Chrebp expression were designed to detect the Chrebpa and Chrebpb isoforms. A specific primer to detect only the b isoform was also used. Primers for Vnn1, Cyp4a10, and Cyp4a14 were previously described  (Montagner et al. , 2016). Amplifications were performed on an ABI Prism 7300 Real Time PCR System (Applied Biosystems). qPCR data were normalized by TATA-box binding protein (TBP) mRNA levels or 18S ribosomal (18S) for human samples and analyzed with LinRegPCR.
22. Transcriptomic profiles were obtained using Agilent SurePrint G3 Mouse V2 GE 8x60K (Design 074809) following the manufacturer's instructions. Data were analyzed with R (http://www. r-project. org) using Bioconductor packages (http://www. bioconductor. org, v 2. 12;  Gentleman et al. , 2004)  as described in GEO: GSE26728. A model was fitted using the limma lmFit function  (Wettenhall and Smyth, 2004). Correction for multiple testing was applied using a false discovery rate  (Benjamini and Hochberg, 1995). Probes with adjusted p % 0. 05 were considered differentially expressed (n = 6). Hierarchical clustering was applied and the differentially expressed probes using 1 À Pearson correlation coefficient as distance and Ward's criterion for agglomeration. The resulting dendrogram were illustrated as a heatmap.
ACKNOWLEDGMENTS We would like to thank  Dr. B. Staels  and  Dr. P. Lefebvre  ( Inserm U1011, Lille ),  Dr. N. Venteclef  ( Inserm UMR_S1138, Paris ), and  Dr. D. Langin  ( Inserm UMR 1048, Toulouse ) for scientific discussion. We also thank  Dr. A. Kayali  and  Dr. T. Issad  ( Institut Cochin, Inserm U1016 ) for critical reading of the manuscript. We thank  L. Francese ,  S. Topcu  ( Institut Cochin, Inserm U1016 ),  C. Naylies  ( GeT-TRiX, INRA ToxAlim ), and  G. Michel  for providing excellent technical assistance. We thank the animal facility staff ( EZOP, INRA ToxAlim ) for their excellent work. H. Guillou 's lab (TIM, ToxAlim) is supported by grants from  Region Occitanie. W. W. was supported by a start-up grant from  Lee Kong Chian School of Medicine, Nanyang Technological University.
C. Postic's lab ( U1016-Institut Cochin ) is supported by grants from  ChroME Network (Marie Curie Sklodowska Action   H2020-MSCA-ITN-2015-675610 ), the  Foundation for the Medical Research (FRM)  ( DEQ20150331744 ), and the  European Foundation for the Study of Diabetes (EFSD) Novonordisk. H. Guillou 's and  C. Postic 's labs are also supported by grants from the  National Agency for Research (ANR)  ( ANR-12BSV1-0025-ObeLiP  and  ANR-15-CE14-0026-Hepatokind ). R. Dentin 's lab ( U1016-Institut Cochin ) is supported by the  European Research.
In the last decade, treatment with BP has become more often at the University Hospital Zurich. Here we have analysed retrospectively the data from the clinical practice. Well-documented female patients aged above 18 years, with a single pregnancy, undergoing tocolysis between 01. 01. 2009 and 31. 12. 2014 were included in the present analysis (n = 216). Data was extracted from the hospital and department databases, completed when necessary by consulting the clinical history, encrypted and analysed using IBM® SPSS® 22. Patients were 33 ± 5. 2 years old, had a gestational age of 29 weeks at admission and received state-of-the-art tocolytic treatment. BP was prescribed to 134 of the 216 patients (62%) as an add-on therapy. Time to delivery was longer among patients treated with BP than among the remaining ones (16 ± 19.
This transdisciplinary educational activity takes place on a monthly basis at the headquarters of MOF. With a two-hour duration, the "Dialogue" comprises two stages: the first, lasting thirty minutes, consists of a theoretical explanation based on scientific literature searched in database such as PubMed, SCIELO or WEB OF SCIENCE. During the second step, a dialogue among participants is conducted and encouraged, in order to facilitate knowledge and experience exchange. Until October 2016, 24 events have been held with an attendance of about over 1,000 people. Since the october of year 2015, events have also been broadcast through the Internet, in real time, reaching viewers in several Brazilian states and even those from other countries like USA, Canada, Japan and Germany.
Methods We designed a cross-sectional study, and inquiried the student from five classes in Beijing University of Chinese Medicine. We having collected the basic information, performance in college, and communication comprehension degrees, we designed questionnaire including gender, whether the only-child, growth environment, average grades, credits grades. Then we used Personal Report of Communication Apprehension (PRCA -24) to evaluate the degrees of communication apprehension. We distributed PRCA -24 scale and self-designed questionnaires to students. We applied EpiData3. 1 software to establish database and data entry control procedures, and used SPSS 22. 0 software for statistical analysis.