dataesr/scientific-paragraphs-categorization huggingface dataset:
Samples, genotypes, datasets DNA was extracted from blood samples (see Additional file 1: Table  S1 ) and used for genotyping on the Illumina Ovine 50 K SNP bead array as described previously  [22, 25]. We used the Plink 1. 9 program (http://www. coggenom ics. org/plink 2) for data management and quality checks. Samples and markers with more than 10% missing genotypes were removed. The resulting data were combined with published genotypes for other breeds (see Additional file 1: Table  S1 ). We used the Splitstree v4. 14. 6 software (https ://softw are-ab. infor matik. uni-tuebi ngen. de/downl oad/split stree 4/welco me. html  [48] ) to construct Neighbour-Joining trees on the basis of allele-sharing distances (ASD) between individuals. We detected seven duplicate samples, whereas deviations from the expected clustering per breed in both novel and published data identified 16 outliers, i.
e. samples for which the pure breed origin is questionable, presumably due to recent crossbreeding (AFS26, ALT15-18, BIE42, CAS03, IST38, LBA759571, LEC1, LEC2, LEC33, OJA10, SAM24, SAM49 and ZEL759420, all breed abbreviations are explained in the legend of Fig. 1 ). These samples together with those of declared F1 animals were discarded. In order to balance the composition of the dataset, we retained only the Australian Merino and the Spanish Estremadura populations from the available Merino samples. For most analyses, we used 25 or less individuals per breed. We retained 21,960 SNPs after linkage disequilibrium (LD)-pruning (Plink-indep-pairwise 50 50 0. 03), which alleviates the ascertainment bias  [49]. Additional file 2: Table  S2  shows how datasets were tailored to the mode of analysis.
From the dataset of  [46] , we retrieved genotypes from European mouflons sampled in Corsica, Sardinia and Hungary. For supervised admixture (v1. 3. 0) analysis  [50] , we assembled, based on the ASD NJ tree topology, a representive metapopulation (mEMF), consisting of 42 European mouflons sampled in Spain (2), Corsica (2), Hungary  (8)  and Sardinia (22 SMF-1 and 8 SMF-2 animals), respectively.
Diversity and differentiation of breeds Observed heterozygosities averaged per breed (H o ) were calculated via Plink. Runs of homozygosity (ROH) longer than 1 Mb and containing more than 30 SNPs with an average density of more than one SNP/100 kb, a maximum gap between consecutive SNPs of 250 kb, and at most one missing and one heterozygous SNP, were calculated by using Plink as described previously  [51]. We analyzed the differentiation of the Pramenka populations by means of the ASD Neighbour-Joining tree as described in the previous section. For the same purpose, data were filtered and phased haplotypes were inferred using the Shapeit v2. r900 software  [52]. Shared haplotypes were identified by the program Chromopainter v2 and posterior distribution of clusters were visualized via the associated fineStructure v2 tree-building algorithm  [53].
Detection of clines Principal component analysis (PCA) was performed with Plink, using a balanced dataset of less than six samples per breed for detection of genetic clines. To prevent bias arising from the large genetic distances between the most inbred sheep (East-Friesian Brown, Karakachanska and Valais Black-Nose) or the mouflons (AMF, EMF and SMF) and the other samples, we used the Plink option to calculate PCs for a subset of the individuals that are to be plotted, in this case all sheep except the EFB, KCH,VBS, AMF, EMF and SMF outliers. We refer to this procedure as supervised PCA (svPCA). For the detection of geographic clines, we carried out a 'geographic svPCA' by calculating the PC only for the breeds living at the geographic extremes in the north (Norway, Finland), southwest (Spain) and southeast (southwest Asia, Egypt).
Ancestry and introgression Model-based clustering using genome-wide SNPs was performed as implemented in the software Admixture v. 1. 22  [50]. Admixture was further analyzed by three methods: model-based clustering with ancestry-informative markers (AIM  [55] ); calculation of f 4 statistics; and TreeMix tree constructions. The first two methods were used for detecting the influence of AMF, EMF and Merino, respectively. For this purpose, we assembled four metapopulations: • mEMF, consisting of 42 mouflons that were less inbred than our Spanish EMF sample (2 Corsican, 8 Hungarian and 30 Sardinian mouflons  [46]  and 2 Spanish mouflons (EMF) with similar degree of inbreeding); The use of panels of AIM for model-based clustering as implemented in Structure  [56]  has been demonstrated in  [35]  for fat-tailed sheep and is denoted here as breedspecific admixture analysis (BSAA).
Coordination analysis In Fig. 2b , the svPC values have been averaged over the breeds. In this plot, svPC1 shows an east-west cline that is particularly strong for the Greek breeds. SvPC2 values show a cline from the Balkan region along the Mediterranean coast and as well as a cline south to north. SvPC3 emphasizes the contrast of northern and southwest Europe (see Additional file 9: Figure  S5 ). Spatial PCA (sPCA) combines genetic and geographic information in order to optimize the detection of geographical trends  [54] , with a choice of three methods of triangulation to calculate spatial distances between breeds. However, with our dataset, the three methods of triangulation in sPCA (see Additional file 10: Figure  S6 ) generated essentially the same pattern as PCA (see Additional file 8: Figure  S4  right panels).
The TreeMix program offers a sophisticated and currently favored approach to combine phylogenetic trees with identification of admixture events  [58]. The tree generated without assuming migrations (m = 0) (see Additional file 15: Figure  S10 ) agrees with the Neighbornet graph (see Additional file 14: Figure  S9 ), but joins the feral EMF and SMF mouflons to the Nordic and Dutch-German Heath breeds as in Additional file 14: Figures  S9D  and S9E. Several but not all gene flows indicated by the colored line in the m = 6, 10 or 20 patterns are consistent with the admixtures found by BSAA and f4 analysis. A more extensive description of theTreeMix pattern is in Additional file 15: Figure  S10.
Scope of this study In order to identify historic and prehistoric gene flows and admixture events, we analyzed genotypes of several Balkan sheep breeds together with those from southwest-Asian, Mediterranean, central-European and north-European populations. Our samples cover the area through which sheep were originally introduced into Europe, and initiated their dispersal all over the continent. We have tested several variants of existing modes of analysis, which may have a more general applicability. A geographically supervised PCA appeared to be more effective to detect genetic clines than the spatial In this analysis, the dataset has been supplemented with additional mouflon samples  [46]. For the selection of SNPs for BSAA, see Methods. Regions and countries have been indicated below the plots; in this plot 'Balkan' does not include Greek breeds PCA  [54] , while the admixtures identified consistently by breed-specific admixture analysis and f 4 analysis could be only partially reproduced by the TreeMix algorithm.
This has generated several clusters of related breeds. Greek breeds are intermediate between fat-tailed Asian and European sheep. The several incompletely differentiated Zackel breeds, most of which were kept in the former Ottoman Empire, form one of the coherent breed clusters. In agreement with a history of mixed German ('Zaupel')-Hungarian origin, Cikta is intermediate between the Zackel and central European sheep. Similarly, Delle Langhe of north Italy is not closely related to other north Italian breeds (see Additional file 13: Figure  S8 ) and may have been influenced by breeds not included in our dataset. Correlation of genetic distances of breeds or clusters with corresponding geographic distances indicate genetic clines. Plausibly, the clines detected by svPCA (Fig. 2b, c ) correspond to the expansion of wool sheep, which may have overruled the earlier clines formed during the introduction of farming along the Mediterranean and Danubian routes  [9] [10] [11] [12] [13].
Acknowledgements We thank  Dr. Dag Vage  ( Ås, Norway ),  Dr. Andrés Legarra  ( Castanel-Tolosan ) for sending SNP datasets,  Dr. Michael W. Bruford  ( Cardiff  ) for sending samples and  Dr. Oliver Hardy  ( Bruxelles ) for helping with computations. The Sheephapmap dataset has been generated by the  International Sheep Genomic Consortium.
TEER measurements Transepithelial electrical resistance (TEER) was evaluated at ALI-35 using an EVOM2 resistance meter with an STX2 electrode (World Precision Instruments Hitchin) at room temperature. The electrode was equilibrated in PnC-ALI during 1 h at room temperature before measurement. One mL PnC-ALI was added to the apical compartment and triplicate measurements were performed per sample. Data were corrected for blank values and area. Average resistance was subtracted from the measured value of every well according to data acquired on cell-free permeable supports and results are presented as resistance per surface (V x cm2).
Immunofluorescent staining and analyses Immunohistochemistry was performed on formalin-fixed paraffin-embedded (FFPE) lung tissues distant from the tumour as previously described  [50]  and frozen tissues. Five 5 mm sections were processed for H&E staining and observed on microscope (x20) to confirm the presence of bronchi. Bronchial epithelium was analysed on the entire slide including 2 to 7 bronchi per patient. FFPE lung tissues sections slides were deparaffinised and blocked with 10% BSA in PBS for 30 min at room temperature. Tissue sections were then incubated with the following primary antibodies for one night at 4 °C in 3% BSA in PBS: rabbit anti-Arl13b (17711À1-ap, ProteinTech, 1:200); mouse anti-Muc5ac (NBP2-15196, Novus Biologicals, 1:100); rabbit anti-Muc5B (E-AB-15988, Elabscience, 1:100); mouse anti-Acetylateda-tubulin (T6793, Sigma Aldrich, 1:1000); goat anti-P63 (AF1916, R&D systems, 1:100); rabbit anti-Gli1 (HPA065172, Sigma Aldrich, 1 mg/mL); rabbit anti-Gli2 (HPA074275, Sigma Aldrich, 0,4 mg/mL); rabbit anti-Gli3 (HPA005534, Sigma, 0,6 mg/mL); goat anti-Shh (AF464, R&D Systems); rabbit anti-Smoothened (E-AB-12925, Elabscience, 1:50) and rabbit anti-Patched1 (E-AB-10571, Elabscience, 1:100).
Sections were washed with PBS and incubated with the appropriate secondary antibodies in 3% BSA in PBS for 1 h at room temperature. DNA was stained with DAPI during incubation with the secondary antibodies. Micrographs were acquired by AxioImageur Zeiss (20x Ph) with ZEN software (8. 1, 2012) and processed with ImageJ (National Institutes of Health) for analysis. For each patient, five random fields per section containing bronchi were taken to evaluate the localization of Gli2 and Smo on epithelial cells. Total epithelium length was measured by ImageJ and the presence of the protein of interest was assessed in 5 sub-compartments: cilia, sub-cilia, cytoplasm, cytoplasmic membrane, and nuclei.
Whole-mount immunofluorescent immunostaining Methanol fixed AEC from ALI cultures were rehydrated by decreasing methanol concentration before a post fixation with acetone. Cells were then blocked with 10% BSA in PBS for 2 h at room temperature and incubated with previous primary antibodies for one night at 4 °C in 3% BSA in PBS. Cells were washed with PBS and incubated with the appropriate secondary antibodies in PBS for 2 h at room temperature. DNA was stained with DAPI during incubation with the secondary antibodies. Clarification of cells was achieving by a glycerol gradient (25%/50%/75%) before mounting the slides. Micrographs were acquired by Confocal Zeiss LSM710 microscope (20X/0. 8) with ZEN software  (8. 1, 2012)  and processed with ImageJ for max-intensity z-stack projections.
Immunoblot analyses AEC were lysed on ice in RIPA (Radioimmunoprecipitation assay) buffer (50 mM Tris pH 7,4, 150 mM NaCl, 1% (v/v) Igepal, 1% (w/v) sodium deoxycholate, 5 mM iodoacetamide and 0,1% (v/v) SDS) supplemented with protease inhibitor cocktail inhibitor (Roche diagnostics), then lysates were clarified by centrifugation (13,000 £ g for 10 min at 4 °C). Ten mg of total proteins quantified by Biorad DC protein Assay Reagent Package (Biorad) were submitted to electrophoresis. Subcellular Protein Fractionation Kit (Thermo Scientific) was used to resolve proteins according to their subcellular localizations following the manufacturer's instructions. Primary antibodies were antiÀGli1 (AF3455, R&D Systems), anti-Gli2 (HPA074275, Sigma Aldrich), anti-Gli3 (HPA005534, Sigma Aldrich), anti-Patched1 (E-AB-10571, Elabscience), anti-Smoothened (NBP2-24543, Novus Biologicals), anti-Ck5 (AB24647, Abcam, Cambridge), anti-GAPDH (clone 6C5, Chemicon, Millipore), anti-Foxj1 (14À9965À82, Ebioscience, ThermoFisher Scientific).
Transcriptomic analysis of Lgr5 + CBC cells reveals a cancer-related and pro-inflammatory basal state under Ubc9 haploinsufficiency Taking advantage of Lgr5-driven expression of EGFP in Lgr5-IRES-EGFP-Cre ERT2 mice, we obtained fluorescenceactivated cell sorting (FACS)-purified Lgr5-EGFP + cells derived from normal (Apc +/+ ) intestines from both Ubc9 +/+ and Ubc9 +/-mice and performed a comparative analysis of their transcriptomic profiles (Fig. S4a ). We found 205 DEGs (|log2FC| > log2(1. 5) and adj. p value (FDR) < 0. 05) in Ubc9 +/-Lgr5-EGFP + cells, when compared to Ubc9 +/+ Lgr5-EGFP + cells, of which 92 and 113 were up-and downregulated, respectively (Fig. 4 , Table  S3 ). Interrogation of curated gene expression databases, using as template up-and downregulated genes separately, now revealed a group of DEGs that have been associated with different types of cancers.
Of note, this is consistent with findings in human colon adenocarcinomas that also exhibit elevated Ubc9 protein expression  [34]  and almost twofold increases in median transcript levels in tumors (n = 275) compared to non-tumor (n = 349) tissues (GEPIA database, http://gepia. cancer-pku. cn/index. html, queried for UBE2I (Ubc9))  [35].
Transcriptome profiling RNA profiling was performed using GeneChip MoGene 2. 0 ST Array (Applied Biosystems) and normalized and analyzed using open-source Bioconductor packages on R  [53, 54]. Differentially-expressed genes (adj. p value (FDR) < 0. 05 and |log2FC| > 1. 5) were used to challenge curated databases  [55] [56] [57] [58] [59] [60] [61]. For GSEA analysis, all differentially and non-differentially-expressed genes in FACS-purified EGF-P high CBC cells were queried against a previously published intestinal stem cell signature  [30]. See Supplementary Information for details.
Statistics Cell-based experiments were carried out with at least three biological replicates. Experiments involving mice were performed in at least six animals per group. Statistical analysis was performed with GraphPad Prism 8 software. See Supplementary Information for details. Ethical approval Mice were bred at the Pasteur Institute animal facility in specific-pathogen-free conditions and studies were conducted in accordance with institutional guidelines and French and European law (Institut Pasteur animal experimentation ethics committee approval number 2016-0025). Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Open Access This article is licensed under a Creative Commons Attribution 4. 0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Acknowledgements This work was supported by grants from  INCa ,  LNCC (Equipe labellisée), Odyssey ,  ANR  and  ERC-AdG  " SUMOS-TRESS" and "SUMiDENTITY " to AD, and by the  Josef Steiner Cancer Foundation  and  ERC-CoG "Cancer Recurrence " to JvR. IL was supported by  Fondation ARC  ( PDF20170505624 ). We thank  Dr. Giulia Nigro  and the  Institut Pasteur UTechS facility  for technical input and  Drs. Bob Weinberg ,  Maria Jasin , and  Sérgio F. de Almeida  for providing reagents.
Acknowledgements: The authors wish to thank  Dr S. L. Berger, PhD  for the gift of  GST-HAP4  ( 330-554 ) plasmid,  Pr Jasper Rine  and  Pr Jerry Kaplan  for the gift of the plasmid HMG2-LacZ,  Corinne Blancard  and  Jim Dompierre  for technical help in microscopy experiments. This work was supported by the  Ligue contre le Cancer , the  Agence Nationale de la Recherche  and the  CNRS  ( Conseil National de la Recherche Scientifique ).
Systematic literature review To identify all reported IEM patients treated with D,L-3-HB and their health-care providers, a comprehensive search strategy for relevant publications before 21 December 2016 was performed in PubMed and EMBASE public databases. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed as accurately as possible. The detailed search strategy, a protocol of the screening process and data extraction, a flowchart, and the PRISMA-P 2015 checklist are presented in Supplementary Data 1. Articles were included based on the presence of detailed patient data concerning D,L-3-HB-or KB treatment, as well as a confirmed diagnosis by biochemical (acylcarnitine or urinary organic acid profile), DNA, or enzymatic analysis. Exclusion criteria were (1) no detailed patient data described, (2) lack of accessibility of the abstracts or articles, and (3) no availability in English or Dutch language.
10, 11 Patients with genetic defects of RFVT (i. e. , SLC52A1, SLC52A2, SLC52A3 [alias C20orf54]) and FAD metabolism (i. e. , SLC25A32, FLAD1) were, therefore, included in this study in addition to those with ETF or ETF dehydrogenase defects. MADD(-like) patients were eligible for enrollment in case of a diagnosis confirmed by biochemical, DNA, or enzymatic analysis, performed conforming to local protocols. Outcome parameters included data on clinical presentation, laboratory and molecular parameters, D,L-3-HB treatment method, and (long-term) outcome. Data was collected via an anonymous questionnaire in Microsoft Word to be completed by health-care providers involved. Data inclusion was concluded in December 2018, after which data from all completed questionnaires were summarized. The STROBE checklist for reporting observational studies is presented in Supplementary Data 2.
Statistical analysis Data analysis was performed using Microsoft Excel and GraphPad Prism, version 5. 0 (GraphPad Software, La Jolla, CA). Descriptive statistics were used to summarize the data. Categorical and continuous variables are presented as numbers (percentages) or median (interquartile range [IQR]), respectively. Kaplan-Meier plots were used to estimate the survival and visualize the data on time until first reported clinical improvement and D,L-3-HB treatment duration. The survival of MADD(-like) patients treated with D,L-3-HB was compared with survival data from historical controls who were not reported to have been treated with D, L-3-HB, as collected in a previous meta-analysis. 12 ann-Whitney U test was used to analyze the significance of differences between groups. If data were missing, the analysis was performed on data from the remaining patients.
ACKNOWLEDGEMENTS The authors thank  Katinka A. M. Mulder , legal advisor-research contracts, for her contribution to the realization of the consortium agreement. Pharmaceutical industries did not play any role in this study. The MD/PhD scholarships of W. J. v. R. and E. A. J. are funded by the  Junior Scientific Masterclass  from the  University of Groningen, University Medical Center Groningen  (MD/PhD 15-30, MD/PhD 18-55, respectively). J. V. is supported in part by  National Institutes of Health (NIH)  grant  R01-DK78755. The sources of funding had no involvement in the study design; data collection, analysis, and interpretation; reporting of the results; or in the decision to submit the paper for publication.
1° for epinephrine and 158. 5° for norepinephrine; median values; Figure  4C ). Altogether, these data show that epinephrine and norepinephrine can partially restore the posterior axis geometry of scospondin icm15/icm15 mutants, suggesting that monoamines can rescue the Reissner fiber-dependent signal required for a straight embryonic body axis. Next, we analyzed the effect of epinephrine and norepinephrine on urp1 and urp2 gene expression using qRT-PCR. In control siblings, urp1 expression remains comparable after vehicle, epinephrine or norepinephrine exposure (Figure  4D ). Consistently with our previous results, urp1 expression is not significantly modified in curled-down scospondin icm15/icm15 embryos compared to their control siblings receiving the same treatment (1. 01 +/-0. 17 fold change; mean ± SEM; Figure  4D ).
, 2020; Rose et al. , 2020; Troutwine et al. , 2019; Zhang et al. , 2018). Our work will pave the way for future investigations to identify the potential of the interplay between CSF-cNs and the adrenergic system to modulate the Reissner fiberdependent morphogenesis of the spine in the juvenile. Poor quality sequences was trimmed or removed using Trimmomatic software  (Bolger et al. , 2014)  to retain only good quality paired reads. Star v2. 5. 3a  (Dobin et al. , 2013)  was used to align reads on GRCz11 reference genome using standard options. Quantification of gene and isoform abundances was achived using with Rsem 1. 2. 28, prior to normalization with the edgeR bioconductor package  (Robinson et al. , 2009). Finally, differential analysis was conducted with the GLM framework likelihood ratio test from edgeR.
Statistics All values are represented as boxplots (median ± interquartile range) or mean ± SEM (stated for each in the figure legend). All statistics were performed using MATLAB and Excel. In the figure panels, asterisks denote the statistical significance calculated using the appropriate test (stated for each test in the legends): *, p<0. 05; **, p<0. 01; ***, p<0. 001; ns, p>0. 05. After filtering for low expression, we kept a list of genes that were differentially expressed in null scospondin icm13/icm13 and hypomorphic scospondin icm15/icm15 mutant embryos at 48 hpf. The table shows the average fold changes in the two alleles and their mean. Genes are ranked based on their p-value that compare the reproducibility of the change inside and between the two alleles using a GLM framework. We adjusted the false discovery rate due to multiple comparisons using the Benjamini-Hochberg procedure (see Material and Methods for details).
Embryos were imaged 20 to 60 minutes after hindbrain ventricle injections. Calcium imaging was performed at 4 Hz using a spinning disk confocal microscope (Intelligent Imaging Systems, Denver) for 4 minutes. Imaging was restricted to the region of the spinal cord located above the yolk extension. Regions of interest were manually selected based on an average projection of the time-lapse and according to the dorso-ventral position of the cells. The integrals of normalized ΔF/F signals were calculated using a custom script on MATLAB (see full description in (Sternberg et al. , 2018) ). The MATLAB codes used for data analysis are available at Github https://github. com/wyartlab/Cantaut-Belarif-et-al. -2020. In vivo patch clamp recordingWhole-cell recordings were performed in aCSF on 30 hpf double transgenic Tg(pkd2l1:GAL4;UAS:mCherry) embryos carrying the scospondin icm15 mutation and their respective control siblings.