dataesr/scientific-paragraphs-categorization huggingface dataset:
Individual refuge use in response to a familiar predatory fish To compare the effect size of exposure to electric shock to an ecologically relevant stress, we analysed data from a previous experiment in which refuge use by G. fossarum from the same population, in response to olfactory cues from brown trout, Salmo trutta, was recorded. The same experimental design was used, except that refuge use was scored every 3 min for 1 h. Refuge use was scored in the absence of olfactory cues from trout (controls), or in water from the tank where trout were maintained at a biomass ratio of 10 g l -1 and fed on live gammarids.
To test for a tendency to increase refuge use with increasing stress level (number of electric shocks), we used the Jonckheere-Terpstra trend test for ordered alternatives (package 'DescTools':  [39] , alternative hypothesis: increasing, 5000 permutations). The number of prey eaten by goldfish was analysed using Wilcoxon's paired signed-rank tests (controlling for individual fish; package 'MASS'  [40] ). All tests were two-sided and used a significance threshold of p < 0. 05, unless specified. Finally, we relied on Cliff's delta as an estimate of the effect size of electric shock on refuge use, activity and vulnerability to predation  [36]. The median and 95% CI of Cliff's delta were calculated using the R-package 'orddom'  [41] , with 10 000 bootstraps. Based on the threshold values for Cliff's delta reported in  [42] , the magnitude of effect sizes was interpreted as negligible (less than 0.
Data accessibility. Data are available from the Dryad Digital Repository: http://dx. doi. org/10. 5061/dryad. 3kj5s [53]. Authors' contributions. M. J. P. -M. and F. C. designed research; M. J. P. -M. , L. B. and F. C. performed research and analysed data; and M. J. P. -M. and F. C. wrote the paper.
17 Two large international registries have been established to collect data for anti-IL-1: the Eurofever physician's registry 31 and the β confident Novartis registry on Canakinumab. 32 enerally, according to expert opinions, patients presenting with the most severe phenotypes, those at risk of severe complications, and patients presenting continuous biological inflammation (elevated CRP and SAA levels) should receive treatment to avoid organ damage and AA amyloidosis. 17 For other patients who do not fulfil these categories, the burden of disease and quality of life should be assessed before a final decision is made. The duration of treatment is theoretically lifelong. Early treatment as soon as the disease is diagnosed may change, at least in part, the natural history, thereby reducing the occurrence of secondary complications.
Egg quality is a complex biological trait and a major determinant of reproductive fitness in all animals. This study delivered the first proteomic portraits of egg quality in zebrafish, a leading biomedical model for early development. Egg batches of good and poor quality, evidenced by embryo survival for 24 h, were sampled immediately after spawning and used to create pooled or replicated sample sets whose protein extracts were subjected to different levels of fractionation before liquid chromatography and tandem mass spectrometry. Obtained spectra were searched against a zebrafish proteome database and detected proteins were annotated, categorized and quantified based on normalized spectral counts. Manually curated and automated enrichment analyses revealed poor quality eggs to be deficient of proteins involved in protein synthesis and energy and lipid metabolism, and of some vitellogenin products and lectins, and to have a surfeit of proteins involved in endo-lysosomal activities, autophagy, and apoptosis, and of some oncogene products, lectins and egg envelope proteins.
Zebrafish are an established biomedical model for research on developmental biology and an emerging model for fertility research  [21]. They are a promising species for investigating proteomic determinants of egg quality because they are small, easily bred in the laboratory with short generation time, and lay large eggs of various quality every few days, with external fertilization of the transparent eggs in which embryonic development is easily observed  [22]. A reference genome sequence is available, providing the needed proteome database for this line of research in zebrafish, which are the only teleost for which any detailed study of the egg proteome has been performed  [23]. The proteome of zebrafish ovary has been characterized and compared to mRNA repertoires and transcript abundances  [15] , and studies have been conducted on proteomics of developing zebrafish embryos  [24, 25, 26, 27].
Proteins up-regulated in good quality eggs were overrepresented in three pathways: Pyruvate metabolism and De novo purine biosynthesis (Pooled Samples Experiment), and 5-hydroxytryptamine degradation (Multiple Samples Experiment). Proteins up-regulated in poor quality eggs were overrepresented in the remaining 11 pathways, 9 of which were significantly enriched in both experiments (S3 Table ). Remarkably, when submitted proteins were individually mapped to all 14 pathways (S4 Fig), it was discovered that only 74 non-redundant proteins could account for all pathway enrichment. Network analysis using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and the zebrafish protein database resolved the 74 'pathway' proteins into a network with a significantly greater number of known and predicted interactions between proteins than would be expected of a list of 74 proteins randomly chosen from the zebrafish database (PPI network enrichment value P.
Survey full scan MS spectra (mass range 400-2000) were acquired in the OrbiTrap section of the instrument with a resolution of r = 60,000 at m/z 400; ion injection times are calculated for each spectrum to allow for accumulation of 10 6 ions in the OrbiTrap. The ten most intense peptide ions in each survey scan with an intensity above 2000 were sequentially isolated and fragmented in the linear ion trap by collision-induced dissociation. For OrbiTrap measurements, an external calibration was used before each injection series ensuring an overall error mass accuracy below 5 ppm for the detected peptides. MS data were saved in RAW file format (Thermo Fisher Scientific) using XCalibur 2. 0. 7 with tune 2. 4. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium  [55]  via the PRIDE  [56]  partner repository under the project name "Proteomic portraits of egg quality in zebrafish (Danio rerio)" with the Pooled Samples Experiment dataset accession number PXD005137 and project DOI number 10.
6019/PXD005137, and the Multiple Samples Experiment dataset accession number PXD005129 and project DOI number 10. 6019/PXD005129. To detect significant differences between egg quality groups in mean N-SC values for differentially expressed proteins from the HMW and LMW fractions (Multiple Samples Experiment) an independent t-test (p<0. 05) followed by Benjamini Hochberg correction for multiple tests (p<0. 1) was used (IBM SPSS Statistics Version 19. 0. 0, Armonk, NY).
A STRING enrichment analysis of these 74 'pathway proteins' included Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways, Protein Families Database (PFAM) Protein Domains, and Interpro Protein Families Database (INTERPRO) Protein Domains and Features (Table 2). Proteins in the good quality egg subnetwork significantly enriched pathways for Pyruvate metabolism, Purine metabolism and Metabolic pathways (KEGG), and also enriched Aldehyde dehydrogenase family domains, IMP dehydrogenase/GMP reductase domain, and Malic enzyme N-terminal and NAD-binding domains (PFAM). Proteins in the poor quality egg subnetwork significantly enriched the pathways Regulation of actin cytoskeleton, Adherins junction, Tight junction, Gap junction, Focal adhesion, Phagosome, and Cell cycle and Oocyte meiosis, among others (KEGG), and also enriched protein domains and features including Actin, Actin and Actin-like conserved site, Actin family, Spectrin repeat, Tubulin GTPase domain and C-terminal domain, 14-3-3 (ywha) protein, conserved site, and domain, Serine/threonine dual specificity protein kinase (e.
This work was supported by: ( OY) Marie Skłodowska-Curie actions  ( MSCA)-FP7-PEOPLE-2013-IEF -626272 , http://cordis. europa. eu/project/rcn/189931_en. html;(OY) Region Bretagne-SAD (2013)-FISHEGG (8210); (JB)  French National Research Agency  ( ANR-13-BSV7-0015 ), http:// www. agence-nationale-recherche. fr/?Project=  ANR-13-BSV7-0015 ; and ( CVS) Carolina Aquagyn. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
ribosylation factor family 3 0. 04 INTERPRO Protein Domains and Features Enriched in Network Pathway ID Domain or feature description Protein count FDR IPR004001 Actin, conserved site 10 1. 18E-20 IPR020902 Actin/actin-like conserved site 10 4. 69E-20 IPR004000 Actin family 10 4. 41E-18 IPR000308 14-3-3 protein 5 1. 75E-08 IPR023409 14-3-3 protein, conserved site 5 1. 75E-08 IPR023410 14-3-3 domain 5 1. 75E-08 IPR002290 Ser/thr/dual spec. protein kinase, cat. domain 7 0. 00219 Results of a STRING enrichment analysis of the protein network shown in Fig 7 for proteins that were differentially regulated in good versus poor quality eggs and were over-represented in specific biological pathways in the PANTHER Pathways enrichment analyses (S3 Table). Shown are KEGG pathways and INTERPRO protein domains represented by !4 or !5 genes, respectively, with a false discovery rate (FDR) <0.
Study design and data This study is part of the International Place of Death (IPoD) study, which is a study of population-level death certificate data. An open call was launched by the principal investigators and candidate partners negotiated a full year's death certificate data for inclusion. An exploration by all candidate partners revealed the most recent available year in all targeted countries was or would be 2008, which was chosen as the reference year. Exceptions were the USA (2007) and Spain (no data were recorded prior to 2010). Fourteen out of the 27 candidate countries obtained permission for data use and their data were integrated into an international database. The principal investigators pooled all data guaranteeing uniform coding throughout the database. Death certification was executed in similar ways in the 14 countries: a physician or a qualified person such as a nurse completes the part of the death certificate indicating cause of death, time, and place of death  37  along with a limited range of demographic information (e.
g. , sex) for the deceased. In some countries another part of the death certificate, containing more socio-demographic information about the deceased, is completed by a civil servant. All information is then processed by trained coders, following strict coding protocols, with the necessary quality checks. The death certificate data were linked across a number of countries with similar population databases such as the Census Data to include more socio-demographic information about the decedents in the database. For this study we used the death certificate data of all 14 countries included in the IPoD study: Belgium, France, Italy, Spain (Andalusia), the Netherlands, The Czech Republic, Hungary, England, Wales, New Zealand, the USA, Canada, Mexico, and Korea. [40].
Data We selected cases where lung cancer (ICD-10 codes C33-C34) or COPD (ICD-10 codes J40-44, J47) was an underlying cause of death. The outcome for our study was the place of death as recorded in the death certificate. The available categories of place of death were: hospital, home, nursing home/residential long-term care, hospice, or others. In Hungary, the death certificate only contains two categories of place of death, hospital and others, whereas hospice (e. g. , palliative care institution) was only available as a category in England, Wales, New Zealand, Canada, and the USA.
Demographic factors included age (categories 0-17, 18-64, 65-85, 85 or above), sex, and marital status (unmarried, married, widowed, or divorced). Relevant confounders and covariates in the models were entered using a forward stepwise selection method with P < 0. 05 set as an entry criterion. All statistical analyses were conducted using IBM-SPSS Statistics version 20 (SPSS Inc. , Chicago, IL, 2010). For all analyses, significance was set at P <. 05 (two-tailed).
ACKNOWLEDGEMENTS The authors thank the IPoD and EURO IMPACT consortium members in giving anonymous suggestions to earlier versions of the manuscript. The  International Place of Death (IPoD)  study is supported by a fund from the  Research Foundation Flanders. This work was supported by  EURO IMPACT  ( FP7/2007-2013 , under grant agreement no [264697]). Joachim Cohen  and  Lieve Van den Block  are supported by a postdoctoral grant from the  Research Foundation-Flanders, Belgium.
Due to availability of genomic sequencing facilities and expansion of bioinformatics tools, the studies from individual gene are switching to whole-genome analysis, which provides a wider view of how the complex of all genes work together  (Wang et al. , 2017). This can lead us to a better understanding of gene function and the probable regulatory matters among networks of genes and generating more easily and faster improved plants. Bioinformatics is the field that makes omics data meaningful and help us to find their powerful ability to discover novel issues. It integrates the data from different omics from genome to phenome  (Edwards and Batley, 2004 ) and allows to mine data across various types of scientific discipline using many bioinformatics tools  (Skuse and Du, 2008). Applications of bioinformatics in Omics studies is an essential part like what the software do in a computer; without the suitable programs no output will be generated.
Bioinformatics During the last years outstanding advances have been achieved in the manner of analyzing omics data, based on several methods frequently using informatics tools. Piecemeal, biologists have taken into advantages of this interdisciplinary field of the biological sciences to inquire deeply on dogma of molecular biology and their complex procedures  (Bayat, 2002). Bioinformatics develops methods and software tools for understanding biological data, allowing that its wide field of action is linked to other sciences, such as: statistics, mathematics, computer, and engineering sciences  (Robinson et al. , 2010). Genomic and proteomic based sequence databases of different organisms with own bioinformatics tools integrated in their platforms are conforming currently an uncountable offer available for biologists and geneticists  (Hamid et al.
Nowadays its utilization has permitted to accelerate the speed of analysis of different genomic and transcriptomic data set. Therefore, it is not astonishing that presently many biological research centers worldwide have commenced to incorporate such bioinformatics type of profiles due to its wide demand by their projects. To all this, the researchers have nominated it like the era of the management, deduction and analysis of genomic and transcriptomic information thank to bioinformatics, which has as last aim of use this information for plant selection. Other tools exist those established by R language program available its bioinformatics version in the website: https://www. bioconductor. org/. Bioconductor, which is a package database, provides tools for the analysis and comprehension of high-throughput genomic data.
They are of genetic approaches of quantitative traits allowing to observe quantitative trait effects and to map phenotype to genotype in the absence of biological context. (Mackay et al. , 2009). SNPs Thanks to high-throughput sequencing (HTS), Single nucleotide polymorphisms (SNPs) have rapidly improved molecular genetics during the recent years due to their abundance in the genomes and their manageability for data processing and compatibility for formats and platforms. Computational bioinformatics approaches are those that overcome SNP discovery methods due to the ever-increasing sequence information that is added to public databases; nevertheless, genome complexity in some plants can make it challengeable in obtaining informative SNPs  (Mammadov et al. , 2012). Thus, other alternative strategies in those crops are probably needed to combine with the undergoing methods.
However, the combination of these methods may result in better conclusion. Actually, GS is deployed to study a population different from the reference population, which possesses the estimated marker effects. There are two types of datasets in GS: a training set and a validation set. The training set is the reference population in which the marker effects are estimated. While marker effects are estimated based on the training set using certain statistical methods to incorporate this information; GBEV of new genotypes are predicted only based on the marker effect. The selection candidates of validation set obtained from the reference population that have been genotyped and selected based on marker effects estimated in the training set. The marker effects of quantitative traits have considerably altered standard practices used in plant breeding.
This preference for GS has been reported in wheat breeding, while the average prediction accuracies for GS was reported 28% greater than MAS and 14% greater than phenotypic selection (PS)  (Heffner et al. , 2011). In order to improve yield in Brassica napus, a study reported that an integration of different methods as GWAS, DEGs and SNPs generate a promising output by which selection of rapeseed accelerates  (Lu et al. , 2017). The authors of this article have shown that candidate gene discovery is more accurate while using various datasets outputted by different methods and approaches and it is possible to determine which genes are key responsible genes involved in yield improvement of rapeseed. In pea, strategies of using SNPs, QTLs and GWAS toward genomic selection seems to be as a proficient approach that can help to generate more efficient peas  (Tayeh et al.
Software implementation and distribution Cantor Digitalis is implemented in Max 14 15. It is distributed under an open-source CeCILL license (a GPLlike license designed by CNRS). Interested readers are able to find all the details of the implementation directly in the software documentation and patches at the following addresses: http://cantordigitalis. limsi. fr or https://github. com/CantorDigitalis/. The code sources are given in Max 6. It is composed of a main Max patch calling Max abstractions. The main Max patch follows the source-filter structure with several sub-patches addressing the rules and parameter mappings. Table  5  presents the list of sub-patches and their references to the corresponding sections of this article. External open-source codes are used, particularly the s2m. wacom and s2m.
wacomtouch Max objects 16 (CeCILL license) allowing to receive the tablet data in Max. Although the continuous surface appears very adapted for Cantor Digitalis, it is possible to plug in any MIDI interface. MIDI piano keyboards with pedal and wheel controls have been tested and allow music to be played that requires fast phrases, which is more difficult with the pen tablet. The robustness of the software implementation has been practically assessed by an important number of downloads to date. The code has already been ported by developers outside our research group to other musical interfaces, such as the Haken Continuum 17  [48] , the Madrona Labs Soundplane 18 , and the ROLI Seaboard  [49]   19.
Acknowledgements This work was supported by the  Agence Nationale de la Recherche ANR , through the  ChaNTeR  project ( ANR-13-CORD-0011 ,  2014-2017 ), the  2PIM - MI3  project ( ANR/06RIAM02 , 2007-2009), and the  Conseil régional d'Ile de France  through the  ORJO  project  ORJO  ( OTP 31226 , 2009( OTP 31226 , -2013)).
Microarray analysis Specific miRNA analysis involved use of Partek Flow v3. 0 (Partek Inc. , St. Louis, MO). CEL files were imported and normalized by Robust Multi-array Averaging (RMA). The miRNA 4. 0 chip contained probes for 490 rat pre-miRNAs and 728 rat mature miRNAs. miRNAs were selected according their average expression levels. miRNAs with nominal p 0. 05 between the two groups of protein diets during gestation were considered differentially expressed. Among these, mature miRNAs showing two-fold variation in expression were retained for further analysis. The complete dataset is available as a Gene Expression Omnibus (GEO) profile in the GEO database (www. ncbi. nih. gov/geo/; accession no. GSE80123). Hierarchical clustering and heatmap analysis involved use of the MeV Package  [13].
cDNA synthesis and real-time qPCR For miRNA expression analysis, total RNA (1 μg) was converted to cDNA by using the qScript microRNA cDNA synthesis kit (Quanta Biosciences, Gaithersburg, MD) as instructed. For gene expression analysis, total RNA (2 μg) was converted to cDNA by using a homemade protocol with M-MLV transcriptase reverse (Invitrogen, Fisher Scientific, Illkirch, France)  [14]. Quantitative PCR involved use of the Light Cycler 480, 96-well apparatus (Roche Diagnostics, Manheim, Germany). Briefly, Perfecta microRNA Assays (Quanta Biosciences) were used to quantify miRNAs, with use of the Light Cycler 480 SYBR Green I Master kit (Roche). Primers for gene expression were chosen by using PRIMER3 software, based on published sequences (Table  1 ). The amplifications were analyzed by the LightCycler software using the three fit points method.
The PCR efficiency was experimentally assessed and was above 90% for all the amplifications. All measurements were performed in duplicate. The results are expressed as Ct values and normalized on the calculated median Ct of each sample (ΔCt). Relative expression was calculated using the comparative Ct method (2 -ΔΔCt ). For miRNA data normalization, miR-10a-3p and miR-124-3p were both used as endogenous controls because they present the least variability across the samples according to Normfinder  [15]. For mRNA data normalization, Glyceraldehyde 3-phosphate dehydrogenase (GADPH) and matrix metalloproteinase 16 (MMP16) were our reference genes as previously used  [16].
Immunohistochemistry Lung tissue sections 4 μm thick were deparaffinized in xylene and rehydrated through graded ethanol concentrations. After antigen retrieval in citrate buffer at pH 6. 0 at 96˚C, slides were processed by using the Polymer novolink kit (Leica, Nanterre, France). Slides were incubated overnight at 4˚C with polyclonal anti-E2F3 antibody (1:800 in phosphate buffered saline-1% bovine serum albumin-0. 1% Triton) and signals were developed with DAB used as a substrate. Signals were analyzed by using ImageJ to quantify the staining within the alveoli under a microscope equipped with a DC 300F camera (digital module R, IM 1000; Leica).
Target gene identification of differentially expressed miRNAs during alveolarization after LPD-induced IUGR We next extracted the predicted and experimentally observed gene targets for the 13 differentially expressed miRNAs from online miRNA databases. From this list of genes, we selected those shown on microarrays to be deregulated during alveolarization after LPDinduced IUGR  [16]. At P10, 17 deregulated genes were predicted targets of our deregulated miRNAs, with 2 experimentally validated targets including CTHRC1 (Table  2  and S2 Table ).