dataesr/scientific-paragraphs-categorization huggingface dataset:
75%) for visualization and validation. Target bands were cut out and purified using the QIAquick gel extraction kit (QIAGEN, Switzerland). The subsequent second PCR, library preparation and sequencing on an Illumina MiSeq sequencing system using the 2×250 bp Reagent Kit v2 (Illumina, San Diego, CA, USA), was performed at the Genome Quebec Innovation Center (Montreal, Canada) according to the amplicon guidelines provided by Illumina. The FastQC  45  and MultiQC 46 tools were used to assess quality of the sequencing data. Forward and reverse sequences were merged (overlap up to 250 base pairs) using Flash  47. Operational taxonomic unit (OTU) clustering on 97% similarity was performed using UPARSE  48  and taxonomic annotation of OTUs was performed within MGX  49. The raw sequences are openly deposited at the European Nucleotide Archive under the accession number PRJEB33546.
Statistical analyses. Hereafter, forage-N uptake and NO 3 -leaching are defined as "N-cycling processes" while NH 4 + , NO 3 -+ NO 2 , and DON content are defined as "N-related soil indicators". The term "N-related microbial indicators" is composed of the abundance, diversity and composition of proteolytic microbial communities as well as the extracellular enzymatic activity potential degrading organic N rich substrates (NAG + LAP). Treatment effects on N-cycling processes as well as N-related soil and microbial indicators were first assessed using linear mixed effect models and then integrated and linked in a hypothetical causal network using structural equation modeling (SEM). Proteolytic microbial community analyses. In order to assess variations in proteolytic microbial community composition, apr OTU abundances were subjected to a Hellinger transformation using the 'decostand' function implemented in the vegan package  50.
Both ordinations were computed using the vegan package  50. OTUs being most important in differentiating between treatments were assessed with the 'simper. pretty' and 'kruskal. pretty' function  51  using false discovery rate corrections. Only OTUs significantly differing between treatments were selected for biplotting in the ordinations. All analyses were run on R 3. 4. 1  52. Alpha-diversity was assessed based on richness, evenness and Shannon index calculated using UPARSE  48. Coordinates of the ordinations (NMDS and db-RDA) were extracted and used in the following statistical analyses as proxy of the proteolytic microbial community composition. Coordinates extracted from the NMDS were used as indicator of the overall variation while coordinates from db-RDA were used as indicators of the sub-part of microbial community composition under the influence of treatments (constrained composition).
Rain regime and management effects (mixed effects models). Effects of rain regime and management on N-cycling processes and on N-related soil and microbial indicators were assessed using mixed effect models with rain regime and management as fixed factors, country and plot as random factors. Plot was nested in management and together they were nested in country to take into account the nested design of the experiment  53. Data were transformed using log, square-root or inverse functions to satisfy the assumption of normal distribution and variance homogeneity of model residuals when necessary. Post-hoc comparisons were done using Tukey's honest significant difference test. Mixed effect models and post-hoc comparisons were run under R. 3. 5. 1  52  using the nlme  54  and lsmeans  55  packages.
2A ). PERMANOVA showed management effects but no rain regime effect (Table  3 , country specific results can be found in SI Table  2 ). Next, a db-RDA ordination conditioning for countries was used to depict proteolytic (apr) microbial community composition only under the influence of management (Fig. 2B ). ANOVA on the capscale object of the db-RDA confirmed the significant management effect (Table  3 , p= 0. 002). Using the simper. pretty function, a total of 18 single apr OTUs being most important in discriminating between countries could be identified (Fig. 2A ) but could not get assigned to sequences yet known/described. Since significant apr OTUs were found specifically for each country it is assumed that no bias, such as chimeric products, was present but rather that databases are still not complete/deep enough to assign functional gene sequences to taxa.
When analyzing proteolytic microbial community composition in detail, we found apr OTUs discriminating between countries, whereas across all countries no apr OTUs significantly discriminating between managements could be found. Overall, only one third of apr OTUs could be assigned to known sequences/database entries, calling for future research to identify hidden functional players in the proteolytic gene pool. The annotated sequences were dominated by Pseudomonas, which is in line with the current literature  36, 71. However, annotation also revealed sequences to be associated to organisms outside the prokaryotes. In general, results of amplicon sequencing targeting functional genes should be interpreted cautiously due to some limitations  72. Even though highly degenerated, primers might miss certain sequences and thus diversity and composition might be under-or overestimated.
Acknowledgements This work was funded by the  ECO- SERVE  project through the  2013-2014 BiodivERsA/FACCE-JPI joint call for research proposals , with the national funders  ANR, NWO, FCT  ( BiodivERsA/001/2014 ),  MINECO ,  FORMAS  and  SNF. Eduardo Nascimento  was supported by  CNPq -Brazil  ( CNPq Fellowship Holder -Brazil ). The authors would like to thank to  Filipe Carvalho  for helping in the maintenance of the mesocosm experiment. Thanks to  Cindy Arnoldi  for help with chemical and enzymatic analyses. We are greatly indebted to the owners of the different farms from where the TMEs were collected. Thank goes to the  Genome Quebec Innovation Center (Montreal, Canada)  for excellent support and execution of Illumina sequencing. The DOK trial from which the Swiss TMEs were extracted is funded by the  Swiss Federal Office of Agriculture.
We tried to merge both domains by deleting the CS38-40 region (SI Appendix, Fig. S2A ), which contains three CTCF binding sites as well as the CS39 limb enhancer and the transcription start site (TSS) of the Hog and Tog long noncoding RNA (lncRNAs)  (22, 26) , which coincides with a CpG island. We performed circular chromosome conformation capture sequencing (4C-seq) experiments in E9. 5 mutant forelimb buds using several viewpoints distributed both along T-DOM and inside the HoxD cluster (Fig. 2  and SI Appendix, Fig. S2B ). We then compiled all data from the different viewpoints into a virtual Hi-C matrix using the 4Cin software  (30) , which we adapted to plot the relative distances in a linear manner according to the real genomic coordinates. Because the 4Cin processing has an inherent variability that leads to the generation of different models, we assessed the correlation between 20 iterations and clustered them, thus displaying a merged average (Materials and Methods).
All other alleles were generated by electroporation of one-cell embryos with transcribed RNAs. The gRNAs and genotyping primers are listed in SI Appendix, Table  S2. All break points were validated through Sanger sequencing, and this information was used to generate the artificial mutant genomes, which can be found in https://zenodo. org/record/3826913#. X6QqXS9h2L4 and a diagram in SI Appendix, Fig. S8. 4C-Seq. The 4C-seq experiments were carried out as described in ref. 22. Samples were microdissected from E12. 5 or E9. 5 forelimbs and placed in 10% fetal bovine serum (FBS)/phosphate-buffered saline (PBS) and incubated with collagenase at 37 °C for 40 or 15 min, respectively. Cell suspensions were then strained and fixed in 2% formaldehyde (FBS/PBS) for 10 min. For E12. 5 experiments, between 10 and 12 pairs of distal or proximal forelimbs were used while between 90 and 150 pairs of forelimbs were dissected for the E9.
For example, for the inv(CS38-40) allele, only cluster 1 was considered as a bona fide representation, encompassing 17 models, while the other three independent clusters were considered as outliers. In order to display the linear distances of the matrices, the virtual Hi-C output text file was converted to a cool file using a custom python script (https:// github. com/lldelisle/scriptsForRodriguezCarballoEtAl2020). The track profiles were obtained using pygenometracks  (52). The replicates and viewpoints used for each set of 4Cin are listed in SI Appendix, Table  S4. The quantification of the distances for each sub-TAD (sub-TAD1, chr2:74768600-75133816; sub-TAD2, chr2:75153815-75604841) and between them shown in Figs. 2  and  3 and SI Appendix, Fig. S4  was performed using a custom python script.
All samples were processed following the RNeasy Microkit (Qiagen). RNA-seq libraries (one replicate per time point) were generated from 100 ng of total RNA following the TruSeq Stranded mRNA protocol and sequenced on a HiSeq 2500 machine (100-bp single read). The gtf file used for STAR was based on Ensembl version 92 annotations (https://zenodo. org/record/3827120 -. X6Q2qC9h2L5). Adapters were removed using cutadapt (v1. 16; options -a GATCGGAAGAGC-ACACGTCTGAACTCCAGTCAC -m 15 -q 30) and aligned on mm10 using STAR version 2. 6. 0b-1 (54) with ENCODE parameters. Only uniquely mapped reads were kept, and coverage on each strand was obtained with bedtools genomecov v2. 27. 0. The track profiles were obtained using pygenometracks  (52) , and they show uniquely mapped reads normalized to the total number of uniquely mapped reads.
For qRT-PCR (quantitative reverse transcription-PCR), RNA was retrotranscribed using the Promega GoScript Reverse Transcriptase (Promega). Custom SYBR probes were used for qRT-PCR in a QuantStudio5 384-well block machine. All primers were described in refs. 26 and 55. RNA-seq processing was done in a local instance of galaxy (galaxyproject. org) (56). For E9 samples, all values are relative to the average of the respective wild-type littermates. The number of replicates is mentioned in the figure legends. qRT-PCR results were plotted using Graphpad Prism8. ChIP. Limb tissues were dissected and fixed in 1% formaldehyde/PBS for 10 min at room temperature, and then incubated 3 min with Stop Solution from the ChIP-IT High Sensitivity Kit (Active Motif) and washed three times with PBS before being frozen at -80 °C until further use.
S2A and S5A while pygenometracks  (52)  was used for all of the ChIP tracks in other figures. In all figures, the orientations of the CTCF sites were obtained using the CTCFBSDB 2. 0 database (insulatordb. uthsc. edu) based on the E9 CTCF ChIP data. Whole-Mount In Situ Hybridization and LacZ Transgenes. WISH was performed as in ref. 59  with the following modifications. E10. 5 and E12. 5 embryos were bleached in a 3% H 2 O 2 /PBS solution. After rehydration, embryos were digested in a proteinase K solution (20 μg/mL, 10 to 12 min, for E12. 5 embryos; 10 μg/mL, 5 min, for E10. 5 embryos; and 5 μg/mL, 4 to 5 min, for E9. 5 embryos). Digestion of E9. 5 embryos was arrested by three quick washes in a 2-mg/mL glycine solution while E10. 5 and E12. 5 proteinase K digestions were stopped with a 10-min incubation in an acetic anhydride/triethanolamine solution.
ACKNOWLEDGMENTS. We thank  Thi Hanh Nguyen Huynh ,  Marie-Laure Gadolini , and  Julien Codourey  for their help with mice breeding, genotyping, and transgenesis; as well as  Mylène Docquier ,  Didier Chollet ,  Brice Petit , and  Christelle Barraclough  ( Genomics Platform, University of Geneva ). We also thank  Ibai Irastorza-Azcarate  and  Asier Ullate-Agote  for their help in implementing the 4Cin pipeline. We thank  Aurélie Hintermann  and other members of the D. D. laboratories for helpful discussions and suggestions.
26), and then correcting intensities using ComBat package  45  with extraction day as the known batch (Figure  S1 ). Differential expression analysis between mutant and wildtype samples was performed using Limma package. 46 For probes showing statistically significant differential expression (adj. P value < 0. 05), annotations of corresponding genes were retrieved from the EnsEMBL database using BiomaRt package. 47 For the qRT-PCR analysis of anillin and atoh7, total RNA from five pulled pairs of frozen eyes, corresponding to either lakritz or wildtype embryos, was used. After Turbo DNase treatment (Thermo scientific-Ambion), according to the manufacturer instructions, the RNA concentrations were measured with a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies Inc). The RNA integrity was verified by loading the samples on 1% agarose gel that was run at 100 Volts in TBE 1X.
| Weighted gene co-expression network analysis The pipeline proposed by Langfelder and collaborators  52  in their CRAN package was followed to infer gene co-expression networks and identify network modules within R 3. 6. 3 statistical environment. Networks were inferred using the TOMsimilarityFromExpr function with "cor" as gene coexpression measure. The soft-threshold parameter was optimized with the function pickSoftThreshold and the best threshold (α = 16) selected by visual inspection to follow a scale-free topology model, as suggested by the WGCNA pipeline. Correlations between modules eigengenes, status, and library batch were computed. Modules with the highest correlation for status and significant P value (α ≤ 0. 05) were selected for further analysis. Within the selected modules, highly connected structure of submodules were identified using the leading eigenvector community detection method  53  implemented in the igraph package (v1.
P value <. 05) (Figure  2A ) corresponding to 137 genes annotated onto EnsEMBL database (Figure  2B  and Table  S1 ). Among these, we confirmed downregulation of atoh7 in the lakritz, consistent with its known role as self-activator. 37 Also consistent with the presence of bona fide Atoh7-regulated targets in the 137 cohort is the presence of additional seven genes, which have been previously reported to contain a well-characterized Ath5 consensus binding site. 37, 38 Among the eight Atoh7-direct targets, besides atoh7 itself, the thyrotroph embryonic factor tefa  56  and the atypical cadherin receptor 1 celsr1a (CELSR1)  57  were downregulated in the lakritz, suggesting their positive regulation by Atoh7. Conversely, the retina and anterior neural fold homeobox transcription factor rx1 (RAX),  58  the Wnt signaling pathway regulator notum,  59  the transmembrane protein tmem165,  60  and the F-actin binding protein and cytokinesis regulator anillin (ANLN)  61  were upregulated in the lakritz, suggesting that they are negatively modulated by Atoh7.
| Functional category enrichment reveals neural retina, cell cycle and Wnt pathways regulated downstream of Atoh7 Functional enrichment analysis in Metascape using default parameters reveals "neural retina development" (GO:0003407) as the most highly significantly enriched GO Biological Process category, consistent with the role of Atoh7 as regulator of retinal development (Figure  3  and Table  S2 ). To further increase stringency, ruling out sampling or biological bias in the analysis, the background was restricted to the list of expressed genes as detected by the arrays  49  using both Metascape and Kobas 3. 0, which incorporates knowledge from five pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome, and Panther) and five human disease databases (OMIM, KEGG DISEASE, FunDO, GAD, and NHGRI GWAS Catalog).
Analysis revealed a coexpression module with a cluster of genes tightly interconnected to Atoh7 To explore global changes of gene expression in the lakritz mutant, a weight gene co-expression network analysis (WGCNA)  52  was performed. Notwithstanding the small number of array samples, we identified 16 recurrent functional modules based on co-expression pattern analysis on the full transcriptome dataset. To identify co-expression modules significantly affected by the lakritz mutation, we tested their association with available covariates, including batch and mutation status. Out of the 16 modules found, two of them showed a high correlation with the mutation condition.
This analysis therefore further confirms tight functional interaction between neural retinal development and Wnt pathway genes from our gene differential expression data. Lastly, our knowledge-based analysis of the M13 members by STRING database further extended these finding by revealing the existence of a network of interactions between atoh7-and rx1-dependent "retina layer formation," "eye morphogenesis" pathways, Wnt signaling pathway components (eg, tcf7l1b, fzd7a, and mmp14a), and two new gene networks previously found to be dysregulated in light responsive, circadian rhythm processes  56, 135  (Figure  S3 ). 7] [138] [139] [140]  This study further supports this evidence, by showing that Atoh7-dependent regulatory networks integrates such circadian clock genes. In sum, this Atoh7 targets analysis extends data from other studies focusing on transcription factors cascades enhancing RGC differentiation.
Interaction network downstream of Atoh7. Known interactions between downstream targets of Atoh7 from the STRING database visualized with Cytoscape (genes without known interactions are not represented). Node colours represent the log2 fold-change of gene expression in lakritz vs wild-type eyes. Node borders are coloured by gene ontology annotation: "neural retina development" (green), "cell cycle process" (yellow), "Wnt signaling pathway" (pink), and "chromatin remodeling" (orange) [Color figure can be viewed at wileyonlinelibrary. com] F I G U R E 5 Dysregulation of Ctnnb1 localization by anillin knockdown and anillin expression dynamics. A, Ctnnb1 staining in control (ctrlMO, n = 3 embryos) versus anillin knockdown (anlnMO, n = 3 embryos) in morpholino injected embryos at 30hpf. Arrows show apical location, arrowheads show apical-to-basal location.
ACKNOWLEDGMENTS We are grateful to  WA Harris  for supporting this study at  Cambridge University and Karen Vranizan (University of California ) for technical assistance. We also thank  I. Pradel  and  F. Zolessi  ( University of Cambridge ) for technical assistance and  F. Zolessi  for discussion. We acknowledge  S. Sel  ( University of Heidelberg ) for material support. We thank the fish facility management group for fish maintenance and technical assistance. This work was supported by the  Wellcome Trust , the  Deutsche Forschungsgemeinschaft Research  Grant  PO 1440/1-1  to  L. Poggi , the  Landesgraduiertenförderung (Funding program of the State of Baden Württemberg, Germany)  to  A-L. Duchemin  and the  Australian Research Council   Discovery Project Grants   DP140101067  and  DP190102771  to  M.
F I G U R E 4 4 Interaction network downstream of Atoh7. Known interactions between downstream targets of Atoh7 from the STRING database visualized with Cytoscape (genes without known interactions are not represented). Node colours represent the log2 fold-change of gene expression in lakritz vs wild-type eyes. Node borders are coloured by gene ontology annotation: "neural retina development" (green), "cell cycle process" (yellow), "Wnt signaling pathway" (pink), and "chromatin remodeling" (orange) [Color figure can be viewed at wileyonlinelibrary. com] F I G U R E 5 Dysregulation of Ctnnb1 localization by anillin knockdown and anillin expression dynamics. A, Ctnnb1 staining in control (ctrlMO, n = 3 embryos) versus anillin knockdown (anlnMO, n = 3 embryos) in morpholino injected embryos at 30hpf.
7 years (supplemental figure  S1 ). As a design feature of the case-cohort study the final eligible subcohort included 583 participants with incident type 2 diabetes. For the analysis of different biomarkers, the sample size varied according to the number of missing data for the biomarkers or covariates, and the final sample size for each biomarker analysis is presented. All participants gave written informed consent and the study was approved by the local ethics committee in the participating centres, and the internal review board of the International Agency for Research on Cancer. ascertainment and verification of cases of type 2 diabetes Ascertainment of cases of incident type 2 diabetes up until 31 December 2007 involved a review of selfreported data, linkage to primary and secondary care registers, use of medication (drug registers), hospital admissions, and mortality data, which we have described in detail previously.
In sensitivity analyses, we imputed missing values of covariates using multiple imputation with chained equations,  29  to assess the effect of missing data on the biomarker-disease associations; we performed analysis in each of 10 imputed datasets and combined the estimates using Rubin's rules. The imputation model included all covariates from the analysis model, the event variable, and the Nelson-Aalen estimate of cumulative hazard. 29 To examine the influence of each individual biomarker on the composite biomarker score results, we amended the composite biomarker score by excluding one biomarker at a time, and then examined its association with type 2 diabetes. We also assessed robustness of the results from model 2 to take account of other potential confounders, including mutual adjustment for the other individual nutritional biomarkers (vitamin C and six individual carotenoids), use of vitamin supplements, season of blood draw, family history of diabetes, baseline prevalence of stroke, coronary heart diseases or cancers (excluding non-melanoma skin cancer), hormone use and menopausal status in women, genetic risk score for body mass index and for insulin resistance, and a diet quality score (Mediterranean diet score).
Ethical approval: All included studies were approved by local review boards, and all participants gave written informed consent to participate in the study. Data sharing: EPIC-InterAct Study data cannot be deposited publicly as these collaborative data originate from multiple research institutions across eight European countries with different legal frameworks. The authors confirm that researchers seeking the analysis dataset for this work can submit a data request to the EPIC-InterAct study central contact point by emailing interact@mrc-epid. cam. ac. uk. The corresponding author affirms that the manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted; and that any discrepancies from the study as planned (and, if relevant, registered) have been explained.
• Coherence: Establish coherence and complementary among biodiversity directives and other directives such as the WFD. Several directives such as the WFD and HD generate extensive, spatially distributed datasets on aquatic biodiversity, however coherence and complementarity between these needs to be established and the data made available digitally, free of charge. Link with EU Biodiversity strategy: Target 1-protect species and habitats; Target 2-maintain and restore ecosystems; Target 6-help stop the loss of global biodiversity.
Acknowledgments: We warmly thank  Maurice Hoffmann  ( INBO ) and  ALTER-Net  for initiating the request that led to the process,  Anne-Gerdien Prins  ( PBL ) for her involvement in the beginning of the scientific task force process,  Thibault Datry  ( INRAE Lyon ) for his participation at the beginning of the editorial team before his  H2020  project did not allow him to attend our meetings, other participants to the Peyresq initial meeting:  Gregor Kalinkat  ( IGB Berlin ),  Amy McDougall  (JNCC),  Carlos Romao (EEA) ,  Janine van Vessem (INBO) ,  Marie Dolores Lopez Rodriguez (CAESCG) ,  Philip Roche  ( INRAE Aix-en-Provence ),  Martin Sharman ,  Stefano Targetti  ( INRAE Avignon ), the online survey participants and the participants to ALTER-Net & EKLIPSE Ghent conference. We also thank three reviewers for their useful insights on a previous version of this manuscript.