dataesr/scientific-paragraphs-categorization huggingface dataset:
Introduction Industrial fishing of albacore tuna (Thunnus alalunga) in the North Atlantic started after the Second World War. Since albacore is a highly migratory species inhabiting both international waters and various exclusive economic zones (EEZs), its management is conducted through international organizations, like the International Commission for the Conservation of Atlantic Tunas (ICCAT: http://www. iccat. org) for the Atlantic Ocean. Stock assessment studies conducted by these management bodies have tried to reconstruct the past history of the stock, based on biological knowledge and the use of fishing data (catch, effort and size frequency of catch), to ac-count for fishing mortality and to statistically fit the stock assessment models. These standard stock assessment studies focused on temporal dynamics of the stock and the computation of fishing mortality.
However, the spatial resolution used here is too coarse to resolve mesoscale features and coastal upwelling regions. The fishing data (catch, fishing effort and size frequencies of catch) of Atlantic tunas by gear, region and flag declared to ICCAT are available on its web site (http://www. iccat. es/en/accesingdb. htm). These raw data were checked and processed to prepare a fishing data set by fishery for SEAPODYM albacore application. This data set (ASCII) is provided together with estimated gridded albacore tuna density by life stage (NetCDF) on PANGAEA (see section Source Data References).
Total reported landings for the North Atlantic generally began to decline after the 1960s, due to a reduction of fishing effort by the traditional surface (troll and baitboat) fisheries, and since 1986 in the case of longline (IC-CAT, 2010). New surface fisheries (drift net and mid-water pair pelagic trawl) developed in the 1990s. ICCAT also maintains a database with monthly tuna catch and effort provided with geographical coordinates at monthly spatial resolution of 1 • or 5 • squares. These data were extracted to be used for the optimization of the model SEAPODYM. Given the broad spatial resolution available for Spanish fleets, additional files at higher resolution were provided by AZTI Tecnalia. Geo-referenced catch effort data exist in the ICCAT database for the most important fisheries, but there is a lack of information in the early years, and for less important fisheries  (ICCAT, 2013a).
The catch effort data available with positional information in the database can represent a fraction or the entire total catch for a given fleet. Over the period 1960-2007, spatially disaggregated data represented on average ∼ 25 % of the total catch, with low percentages in the 1960s (2. 8-24. 8 %) but higher values in the following decades, in the range of 10. 8-46. 9 % (Table  1 ; Fig. 1 ). While the data set was sufficient to optimize the habitats and movements and population dynamics parameters  (Dragon et al. , 2014) , the fishing mortality in the simulation was consequently underestimated, though there are potential compensatory mechanisms at play in the optimization that can partly account for the total fishing effect as expressed in the data even if none of the catch is included (see Discussion).
As indicated above, the level of coverage for spatially disaggregated fishing data was much lower than the total catch, though it was highly variable from one fishery to another. Figure  3  compares these two data sets for the six main fisheries (> 98 % of total catch declared to ICCAT). Japanese and Taiwanese longline fleets appear complete, while other longline fleets (the Republic of Korea; USA) were partially covered (Fig. 3 ). Indeed, it is very likely that complete coverage of spatially geo-referenced catch and effort were due to extrapolation from geo-referenced catch and effort samples before submission to ICCAT, but this extrapolation was not produced for the other fleets. Though the size of actual samples would be useful information, it may be difficult to recover it for all the historical fishing period.
For surface gears, the coverage from geo-referenced catch and effort is 7. 3 % of total catch available for the Spanish fleets and 23 % for the French ones. Part of these gaps is due to the coarse resolution of the model grid that cannot include coastal zones where significant catch by Spanish fleets occurred. The catch for the Canary Islands in one single cell was also not included due to the lack of effort data. Finally, the southern boundary of Units are those of ICCAT database. For SEAPODYM simulation catch have been converted in tonne or in number of fish. the North Atlantic stock for ICCAT was 5 • N, while it was the Equator for the SEAPODYM domain. This explains the higher catch level of Chinese Taipei longline fishery used in SEAPODYM after 1987 compared to the ICCAT total catch series.
Size frequency of catch Length frequencies of catch for North Atlantic albacore were also available from the ICCAT database. They were extracted according to the definition of fisheries for the period 1956-2010, with a quarterly temporal resolution and spatial resolutions varying from 1 • × 1 • to 10 • × 20 • (Fig. 4 ). The resolution used to measure the fish also varied with size bins of 1, 2 or 5 cm (fork length -FL). The screening of data allowed for inconsistencies to be detected with a relatively large number of samples larger than 150 cm, while all studies on the growth of albacore suggest that fish rarely grow to over 130 cm. Given that SEAPODYM uses a single average size-at-age value by cohort and does not yet allow for growth variability around this value to be included, a threshold value of 130 cm has been arbitrarily fixed and all length frequency data above this value removed from the original data set.
In addition, since the presence of fish larger than 130 cm in a given sample may indicate a problem in species identification by the observer, a precautionary approach was followed with a data filter to remove the whole sample (i. e. , all size data collected from the same boat, date and area). The number of remaining samples in ICCAT dataset was well distributed over the entire fishing ground and increased in the second half of the fishing period (Fig. 4 ). 3 North Atlantic albacore population dynamics.
e. , roughly the first year of life. The integrated growth study from  Santiago and Arrizabalaga (2005)  was first used to Figure  3. Time series of annual catch data with geographical coordinates used in the simulation with SEAPODYM and total annual catch declared to ICCAT for the main North Atlantic albacore tuna fisheries over the historical fishing period. When data were declared in number of fish, a conversion factor has been used, i. e. , 16 kg fish -1 for Japanese, Chinese Taipei and US longline, and 8 kg fish -1 for French and Spanish surface fisheries. parameterize the age structure, but produced inconsistencies between the value of L ∞ = 122 cm FL and the length frequency samples. Despite the threshold value being set to 130 cm (cf. above), there were still a very large proportion of fish larger than L ∞.
In this study, the best spatially explicit distribution of catch, effort and size frequency of catch data was prepared from publicly available sources for North Atlantic albacore. However, despite that ICCAT developed a substantial effort to collect data of all tuna fisheries in the Atlantic Ocean, this geo-referenced data set only partially covers the total catch for this tuna stock. Though the level of coverage has increased in the more recent decades, it has always remained below 50 % of the total declared catch. Now that ecosystem and spatially explicit models of population dynamics have been developed, priority should be given in the coming years to the preservation of existing data sets to increase this level of coverage as far as possible. Thereafter,  a second geo-referenced data set should be built with all the necessary expertise and precautions to raise the catch data with positional information to the level of total catch.
structure and biomass of North Atlantic albacore Tuna (Thunnus alalunga) in the NorthAtlantic between  1975-1984 (ICCAT-B14), Collecte Localisation Satellites, doi:10. 1594/PANGAEA. 828238, 2014. Lehodey, P. , Senina, I. , Dragon, A. -C. , and Arrizabalaga, H. : Compilation of Thunnus alalunga (North Atlantic Albacore) fork length frequencies in 1 centimeter intervals from catches in the North Atlantic between 1956-2010, Collecte Localisation Satellites, doi:10. 1594/PANGAEA. 828171, 2014. Lehodey, P. , Senina, I. , Dragon, A. -C. , and Arrizabalaga, H. : Compilation of Thunnus alalunga (North Atlantic Albacore) fork length frequencies in 2 centimeter intervals from catches in the North Atlantic between 1956-2010, Collecte Localisation Satellites, doi:10. 1594/PANGAEA. 828170, 2014. Lehodey, P.
Acknowledgements. We are grateful to ICCAT for the access to its public fishing database and particularly to  Carlos Palma  for his helpful advice on these data. This work was modified from a first analysis presented in 2013 to the ICCAT working group on the stock assessment of Atlantic albacore (reference  SCRS/2013/125 ) and we are grateful to all the group members who provided useful comments that helped in the revision of this study. The authors also wish to thank  Alain Fonteneau  for his suggestions and helpful comments on a first version of the manuscript. The research leading to these results was supported by the  European Commission   FP7 EURO-BASIN (European Basin-Scale Analysis , Synthesis, and  Integration ; grant agreement no. 264 933 ) and the  Space Oceanography Division of CLS, France.
hooks) -1 4495 5 T10 France TROL 1967-2009 no. (no. sets) -1 6289 1 T11 France MWTD 1989-2007 a kg (no. sets) -1 605 1 B12 Spain TROL 1987-2005 a no. (no. sets) -1 2856 1 B13 Spain BB 1987-2005 a no. (no. sets) -1 1644 1 B14 Spain-Canary b BB 1975-2010 kg (day at sea) -1 110 1 a Catch and effort data from recent years not yet available from the ICCAT database. b Not used.
, 2011; Figures 1D, 1E, and S1C). Thus, although reprogramming of Polycomb organization is not observed evolutionarily, it occurs throughout Drosophila's life cycle. In conclusion, nonduplicated and nondeleted Polycomb domains in the embryonic stage conserved their H3K27me3 association to near completeness despite substantial underlying sequence divergence. S1  and S2. PRC1-Binding Sites Are Conserved amidst Dynamic Sequence Evolution We expanded our ChIP-seq data set to study the evolution of PRC1-binding sites (via its core components Polyhomeotic [PH] and Polycomb [PC]). We also generated H3K4me3 ChIP-seq profiles to map transcription start sites (TSSs) in four Drosophila species. Using our previously constructed Drosophila Hi-C maps  (Sexton et al. , 2012) , we identified Polycomb topological domains and studied the different localization of PRC1, H3K27me3, and H3K4me3 distributions around PH peaks within these Polycomb domains, classing sites according to their proximity to a TSS (defining TSS versus non-TSS sites; Figure  2A ).
ChIP Experiments ChIP experiments on whole Drosophila embryos 4-12 hr after egg laying were performed essentially as described in  Schuettengruber et al. (2009). Antibodies were diluted 1:100 for IP. For qChIP, after immunoprecipitation and DNA purification, enrichment of specific DNA fragments was analyzed by real-time PCR using Roche Light Cycler equipment and accessories as described in  Comet et al. (2006). Data are expressed as the percentage of input chromatin precipitated for each region examined. As a negative control, Rp49 was included in the PCR experiments. For primer sequences, see Table  S2. For ChIP-seq, 20 ng of the ChIP reaction and input DNA were used for the library preparation. ChIP-seq was performed by the Montpellier GenomiX facility (MGX, http://www. mgx. cnrs. fr/index.
Sorting of PH Mutant Flies Ph del mutant flies  (Feng et al. , 2011)  were crossed to a balancer line expressing GFP from the Kru ¨ppel promoter. Homozygous Ph del /Ph del embryos were collected from the heterozygous stock by selecting for GFP-negative embryos using an embryo sorter (COPAS SELECT; Union Biometrica). ChIP on WT and Ph del/del embryos was performed as described above. The PHO antibodies used are described in  Schuettengruber et al. (2009). Note that this antibody gives essentially the same ChIP-seq profiles as the PHO antibody used in the species ChIP-seq  (Klymenko et al. , 2006) , but seems to have reduced affinity in some non-melanogaster strains (data not shown).
ACKNOWLEDGMENTS We are grateful to  Jurg Mu  ¨ller and  Judy Kassis  for providing PHO antibodies, and  D. Locker  for providing DSP1 antibodies. We thank  Mythily Ganapathi  for helpful discussions. Research at G. C. 's lab was supported by grants from the  European Research Council  ( ERC-2008-AdG No 232947 ), the  CNRS , the  INSERM , the  European Network of Excellence EpiGeneSys , the  Agence Nationale de la Recherche , and the  Association pour la Recherche sur le Cancer. Research at A. T. 's lab was supported by the  European Research Council , the  European Network of Excellence EpiGeneSys , and the  Israel Science Foundation.
Research on intimate partner violence (IPV) using national samples is important to guide prevention efforts. However, the latest prevalence estimates for Belgium date from more than ten years ago. Therefore, this study used population-based cross-sectional data (N = 1,472) to assess to what extent adult women and men in Belgium experienced psychological, physical or sexual violence from their current partner in the last year. Next to assessing the association with individual health correlates, we explored the association between IPV and relationship quality. The annual prevalence of physical IPV in a current relationship was 1. 3%. Only women experienced sexual IPV (0. 3%). Fourteen percent of the respondents reported psychological violence and no differences were noted between women and men.
Participants and Procedure This study made use of a subsample of a population-based cross-sectional survey on interpersonal violence in Belgium, entitled 'Emotional, physical and sexual abuse -the experiences of women and men'  (Pieters, Italiano, Offermans, & Hellemans, 2010). This survey contained information on violence in the public sphere, family violence, intimate partner violence and sexual violence. Data were collected between April and July 2009. Our study samples were a priori stratified based on language (i. e. , Dutch, French), region (i. e. , Flanders, Wallonia, Brussels), gender (i. e. , women and men), and age (i. e. , between 18 and 75 years of age) to make them representative of the Belgian population. A sample of 5037 individuals was recruited through WDM Belgium, a marketing service provider specialized in gathering data and database management service 2.
Of the total sample, 613 persons were excluded because of death (n = 4), illness (n = 85), language issues (n = 120), age (n = 203), long term absence (e. g. , abroad for a long period; n = 39), or a wrong number or relocation (n = 162). This resulted in 4424 eligible interviews. There were 2351 active and passive (i. e. , unable to contact after five phone attempts) refusals. A full survey was completed by 2073 individuals (response rate: 47. 03% of the eligible respondents). After cleaning the data for missing values, the final dataset consisted of 2014 respondents (94. 5% Belgian nationality; 1211 Flemish and 803 French speakers). After data collection, the data were weighted by age. Comparisons with the adult Belgian population, provided by the Directorate-General for  Statistics and Economic Information Statbel (2008) , indicated no meaningful differences between the study sample and the Belgian population on the gender of the respondents (women: 49.
3% sample , 51. 1% popu- lation ; men: 50. 7% sample , 48. 9% population ) and region (Flanders: 60. 8% sample , 57. 9% popula- tion ; Wallonia: 32. 0% sample , 32. 6% population , and Brussels: 7. 3% sample , 9. 5% population ). Because this study reports on respondents' experiences with IPV in their current relationship we used data from 1472 respondents who were in a relationship at the time of the survey (45. 8% women and 54. 2% men). The mean age of the women was 42. 26 years (SD = 14. 41, Range: 18-75). The mean age of the men was 47. 46 years (SD = 14. 85, Range: 18-75). More than two-thirds (68. 3%) were married, 15. 4% were single, 11. 4% were cohabiting, 3. 9% were divorced and 1. 1% were widowed. Most of the respondents (76. 3%) had one or more children. Among the respondents, 4.
Analyses Analyses were run in SPSS 20. 0. We used a weighting variable based on the variable age because respondents in the older age category (i. e. , 65 to 75 years) were overrepresented and respondents in the younger age categories (i. e. , 18 to 34 years) were underrepresented in our study than would be expected by coincidence. By using a weighing variable, the answers of younger people weigh more in the statistical analyses and the answers of older people weigh less such that the results are in line of what could be expected based on the general population. Bivariate statistics (Pearson chi-square test and independent sample t-tests) were calculated to explore the link between the previously mentioned sociodemographic characteristics and IPV experiences. A series of multiple regression analyses were performed to determine the role of psychological IPV in predicting victims' individual and relational well-being.
Because of the low numbers of respondents reporting sexual and physical IPV, cautiousness regarding the interpretation of these findings is warranted and generalization is limited. Therefore, in the further analyses, we only included data of respondents who have exclusively experienced psychological IPV in the past 12 months from their current partner (n = 189; 14. 0% of the women and 12. 3% of the men). Sociodemographic characteristics of IPV. When examining the sociodemographic characteristics of respondents reporting psychological IPV (see Table  3 ), results revealed no significant effect of education level, area of residence, and age. An effect was found for civil state: Both single (22. 3% vs. 14. 1%) as well as divorced respondents (6. 9% vs. 3. 4%) were much more likely to report psychological IPV, compared to the other groups.
Fourth, a limitation of our population research on IPV was that the data were very skewed towards zero, which has implications for the power of our statistical analyses. Although this sample design provides us authentic descriptive IPV information and generates findings that are applicable to the overall population, it limited us to test individual and relational correlates for physical and sexual IPV because of the small cell accounts. When examining the health correlates of IPV in depth, future studies would benefit from using specific victims samples rather than representative samples. Fifth, this study design unfortunately put restrictions on the number of items that could be included in the survey. Therefore, only single items were used to measure individual health correlates. Standardized measures of these constructs would have been more methodologically sound to capture the mental health status of the respondents.
Notes 1 See the UN Secretary-General's database on violence against women for an overview of country studies: http://sgdatabase. unwomen. org/country. action. 2 WDM Belgium is now active under the name 'Bisnode'. For a detailed overview how Bisnode gathers and manages data, we refer the reader to www. bisnode. be 3 Note. No Cronbach alpha was calculated for the sexual IPV scale as only two items were included.
Investigating the structure -function relationships of LEAPs is thus of primary interest, but remains challenging because experimental evidence is difficult to obtain. A database called LEAPdb (http://forge. info. univ-angers. fr/,gh/Leadb/index. php) dedicated to this purpose is available  [8]  and LEAPs have been classified in 12 non-overlapping classes. A large number of physico-chemical properties of the LEAP classes have been computed and statistically analyzed  [26]. Since LEAPs were early recognized as highly hydrophilic proteins, this led Garay-Arroyo et al. [27]  to propose they were members of a more widespread group of proteins, which they coined hydrophilin, characterized by a high glycine content and high average hydrophilicity. Interestingly, in yeast and Escherichia coli, hydrophilins expression appeared well correlated with osmotic stress  [27] ,  [28]  and the yeast hydrophilin STF2p was found to be essential for dehydration tolerance  [29].
Hydrophilins and HSP12 dataset Hydrophilins were initially characterized by a Gly content. 6%, GRAVY,21 and a mean hydrophilicity. 1  [27] ,  [30]. To take in account the overlap with LEAPs, three pools of proteins were built (Figure  1B ). Pool 1 -« hydrophilins-like LEAPs »: only 24 LEAPs are characterized by %Gly. 6%, GRAVY,21 and mean hydrophilicity. 1 (pool 1). They belong to LEAP classes 1, 2, 3 and 5 (and correspond to 2, 14, 7 and 1 LEAPs, respectively). Pool 2 -« control LEAPs »: it contains 47 LEAPs with values opposite to those characterizing hydrophilins (i. e. , %Gly ,6%, GRAVY. 21 and mean hydrophilicity,1). It contains LEAPs from LEAP classes 6, 7, 9 and 10 (24, 11, 11 and 1 LEAPs, respectively). It must be noticed that only one LEAP has no Gly (LEAP Class 7 -Acc#ACJ83952 from Medicago truncatula).
Pool 3 -hydrophilins: Their sequences were retrieved from the public database NCBI, using hydrophilin-linked keywords and literature sources  [27] [28] [29] [30] ,  [45] ,  [46]. Blasting sequences previously obtained retrieved additional sequences. 159 sequences were thus obtained. Among them, 35 sequences were rejected because they have a %Gly, 6% and/or a GRAVY. 21 and 86 sequences were rejected because they were redundant. It must be noticed that most of sequences are very poorly or even not annotated and that the hydrophilin-like superfamily clan (CL0385) includes PF00477 (i. e. , LEAP class 5  [8] ). Finally, 31 sequences were retained as true hydrophilins. Sequences accession numbers of the three pools are listed in Table  S1. It has been shown that HSP12 from yeast is a hydrophilin  [27].
IDP dataset Sequences corresponding to GRAS proteins (gibberellic acid insensitive (GAI), repressor of GAI, Scarecrow) were collected  [48]. Plant IDPs were searched using DisProt  [49]  and « Entrez » (NCBI). We also searched archetypal IDP or IDR such as p53, abscisic stress ripening protein, CREB-binding protein, proteins related to DNA binding or processing, transcription regulation (cyclin-dependent kinase inhibitor, histone) and specific plants proteins (glutenin, Calvin cycle enzymes). Additional sequences were obtained by BLAST: only sequences having more than 50% identity with the query sequence were kept. Among the results, only fully annotated files corresponding to full-length sequences were retained. Finally, to ensure their IDP character, we retained only 72 sequences with FoldIndex#0.
Characteristics of hydrophilins and LEAPs datasets The distribution of the three pools plus all remaining LEAPs from LEAPdb was plotted as a function of their %Gly and their mean hydrophilicity (Figure  1B ). 622 LEAPs have %Gly. 6% (with a maximum at 34,1%). LEAP pool with %Gly. 6% and hydrophilicity. 1 belong to class 1 and 2. An interesting point is the diversity of organisms from which hydrophilins were retrieved (Table  S1 ): 13 organisms are Fungi (Ascomycota; Saccharomycetales) and 1 organism is a nematode (Caenorhabditis remanei; Metazoa; Nematoda)]. 16 LEAP class 8 sequences contain a second WHy domain with an internal domain separating the two WHy domains whose length ranges from 35 to 70 amino acids (Figure  2B ). The consensus sequence of the second WHy domain is very similar to the first one.