dataesr/scientific-paragraphs-categorization huggingface dataset:
(C) Bone marrow hematopoietic precursors from Vdr À/À and WT mice (BALB/c background) were transduced with retrovirus coding for MLL-ENL, MLL-AF9, or Flt3-ITD. Cell differentiation was evaluated using flow cytometry with CD11b pan-myeloid and F4/80 monocyte markers. Results are presented as mean ± SEM (n R 3 mice per group). (D) Cell morphology (May-Gr€ unwald Giemsa [MGG] staining) from cells generated in (C). (E-G) Vdr and VDR-targeted gene expression correlates with AML prognosis. Overall survival of patients from GEO: GSE12417 series (a pool of AML4 or AML5 subtypes; n = 62) according to Vdr expression. Log rank analysis comparing different groups of patients (separated into tertiles) according to the relative Vdr expression (low Vdr expression [n = 21, black line], medium Vdr expression [n = 20, red line], and high Vdr expression [n = 21, green line]) (E).
ACKNOWLEDGMENTS This work was supported by  Agence Nationale pour la Recherche (ANR ; grants  ANR-10-JCJC-1108 ,  ANR-12-BSV1-0039 , and  ANR-10-BLAN-1109 ),  APHP-CNRS Contrat Hospitalier de Recherche Translationnelle ,  Institut National contre le Cancer (INCA) ,  Canceropôle d'Ile de France, Fondation pour la Recherche Medicale (FRM) ,  Fondation de France ,  Association Laurette Fugain , and  Association pour la Recherche contre le Cancer (ARC). This study was supported by grants from  Laboratory of Excellence GR-Ex  ( ANR-11-LABX-0051 ). The  Imagine Institute  and the  Laboratory of Excellence GR-Ex  are funded by the  program Investissements d'Avenir of the French National Research Agency  ( ANR-10-IAHU-01  and  ANR-11-IDEX-0005-02 , respectively). We are grateful to  S. Nelson  and  J.
(C and D) Limited myeloid differentiation in Vdr À/À transformed cells. (C) Bone marrow hematopoietic precursors from Vdr À/À and WT mice (BALB/c background) were transduced with retrovirus coding for MLL-ENL, MLL-AF9, or Flt3-ITD. Cell differentiation was evaluated using flow cytometry with CD11b pan-myeloid and F4/80 monocyte markers. Results are presented as mean ± SEM (n R 3 mice per group). (D) Cell morphology (May-Gr€ unwald Giemsa [MGG] staining) from cells generated in (C). (E-G) Vdr and VDR-targeted gene expression correlates with AML prognosis. Overall survival of patients from GEO: GSE12417 series (a pool of AML4 or AML5 subtypes; n = 62) according to Vdr expression. Log rank analysis comparing different groups of patients (separated into tertiles) according to the relative Vdr expression (low Vdr expression [n = 21, black line], medium Vdr expression [n = 20, red line], and high Vdr expression [n = 21, green line]) (E).
Lake watershed and geomorphology A portable sonar system, equipped with an internal GPS antenna (Humminbird model 859XD) and mounted on a small Zodiac, was used to map the lake bottom in July 2014 (as in  Bouchard et al. , 2015b). Lake-depth signals were continuously recorded along regularly spaced (20-25 m apart) navigation lines, mainly of SW-NE and SE-NW orientations. Depth data were interpolated between navigation lines using the compatible software (AutoChart) to produce a georeferenced 3-D bathymetric map. The acquired data were also used to calibrate and extrapolate lake-bottom depths inferred from ground-penetrating radar (GPR) mapping conducted the following year. Ground-penetrating radar (GPR) surveying on lake ice cover allows for an accurate description of lake-bottom topography  (Moorman, 2001; Paquette et al.
, 2015; You et al. , 2017). Three GPR survey lines crossing the lake were done in May 2015 (Fig. 2 ) using a sleigh-dragged Sensors and Software PulseEkko GPR and 50 MHz antennas. GPR line processing was performed using Ekko project software https://doi. org/10. 5194/tc-14-2607-2020 The Cryosphere, 14, 2607-2627, 2020  and included dewow, a low-pass temporal filter to diminish background noise and a background average subtraction to remove the overwhelming ice and water boundary signal. The base of the ice cover and lake-bottom depth were manually identified and corresponded well to the dielectric properties of ice and water. Signal travel velocities of 0. 06 and 0. 13 m ns -1 were used for unfrozen and frozen ground, respectively, and GPR vertical signal resolution (no pulse overlap) is approximately 1 m but slightly lower in ice and frozen ground than in water.
Sediment core sampling and logging Sediment cores were collected from the same location (Fig. 2 ) during two consecutive years: (1) a shorter core (54 cm) from a boat during the ice-free season of 2014 (July) and (2) a longer core (109 cm) from the ice cover in spring 2015 (June). The coring site location (> 4 m water depth) was located in 2014 and 2015 using the bathymetric data from the sonar and GPR surveys  (Bouchard et al. , 2015b). Each core was retrieved using a handheld percussion corer equipped with a 7 cm diameter clear polycarbonate tube (Aquatic Research Instruments). Coring was stopped when the tube would not penetrate further into the sediments (coarse sands and gravels). The 2014 core was subsampled in the field immediately after retrieval at 1 cm intervals, and the subsamples were transferred into polyethylene bags and brought back to the laboratory where they were kept in the dark at 4 • C.
Samples were pretreated (HCl, NaOH, HCl) and combusted to CO 2 at the Radiocarbon Dating Laboratory (Université Laval, Québec, QC, Canada) and 14 C dated by accelerator mass spectrometry (AMS) at Keck Carbon Cycle AMS Facility (University of California, Irvine, CA, USA). Radiocarbon dates were reported using Libby's half-life (5568 yr), corrected for natural fractionation (δ 13 C = -25 ‰ PDB), and calibrated with the CALIB 7. 1 online program  (Stuiver et al. , 2019)  using the IntCal13 calibration data set  (Reimer et al. , 2013). Supplementary 14 C dates available for the surrounding frozen peat deposits, some of them not yet published, were also compiled and added to the dataset  (Allard, 1996; Ellis and Rochefort, 2004, 2006; Fortier et al. , 2006; 2020).
(2000) ,  Krammer (2000 Krammer ( , 2002)) ,  Krammer and Lange-Bertalot (1986 , 1988 , 1991a, b) ,  Lavoie et al. (2008)  and  Zimmermann et al. (2010). The complete diatom dataset is available as an open-access dataset  (Pienitz et al. , 2019). Diatom taxa representing at least 1 % (relative abundance) in at least one sample were displayed on abundance diagrams using the C2 software  (Juggins, 2014). Photos of most of these taxa were taken with a Leica DFC490 camera (mounted on the microscope) and were used to prepare plates of the representative taxa (Supplement S2). In the following sections, taxa names are presented as they appeared originally in consulted floras.
Data availability. The following related datasets are available in the Nordicana D collection at Centre d'études nordiques (CEN -Centre for Northern Studies) (http://www. cen. ulaval. ca/ nordicanad/). The complete citations of each dataset appear in the reference list of this article. Fortier et al. (2019): "Ground-penetrating radar (GPR) survey data for a thermokarst lake, Bylot Island, Nunavut, Canada",.
Muster, S. , Roth, K. , Langer, M. , Lange, S. , Cresto Aleina, F. , Bartsch, A. , Morgenstern, A. , Grosse, G. , Jones, B. , Sannel, A. B. K. , Sjöberg, Y. , Günther, F. , Andresen, C. , Veremeeva, A. , Lindgren, P. R. , Bouchard, F. , Lara, M. J. , Fortier, D. , Charbonneau, S. , Virtanen, T. A. , Hugelius, G. , Palmtag, J. , Siewert, M. B. , Riley, W. J. , Koven, C. D. , and Boike, J. : PeRL: a circum-Arctic Permafrost Region Pond and Lake database, Earth Syst. Sci. Data, 9, 317-348, https://doi. org/10. 5194/essd-9-317- 2017, 2017.
Financial support. support This research has been supported by the W. Garfield Weston Foundation (W. Garfield Weston Postdoctoral Fellowship in Northern Research), ArcticNet, the Natural Sciences and Engineering Research Council of Canada (NSERC), the Polar Continental Shelf Program (PCSP) of Natural Resources Canada, the NSERC Discovery Frontiers grant "Arctic Development and Adaptation to Permafrost in Transition" (ADAPT), and the NSERC CREATE program EnviroNorth.
Association mapping Variant data for 330 C. elegans isotypes were downloaded as the 20180527 CeNDR release soft-filtered vcf. We tested for a match between variants in the recombination-mapping interval (X:12,579,122 -X:12,662,632) and rol-1 suppression phenotype in the panel of N2, CB4856, LSJ1, and the seven other tested wild isolates.
Gene model Sequence and annotation data for the Caenorhabditis genus were downloaded from the Caenorhabditis Genomes Project. RNAseq data from young adults of C. elegans wild isolates were downloaded from the NCBI SRA: CB4856 PRJNA437313  (Zamanian et al. 2018) , AB1 and ED3040 PRJNA288824  (Vu et al. 2015). Reads were mapped to a 100 Kb region of the N2 WS220 genome centered on col-182 with bwa mem version 0. 7. 17  (Li and Durbin 2010) , assembled with Trinity version 2. 3. 2 in genome-guided mode  (Grabherr et al. 2011) , and homologous transcripts were extracted by blast version 2. 9  (Altschul et al. 1990 ) against col-182 orthologs across the genus. Coding and protein sequences were aligned with mafft version 7. 3. 10 in L-INS-i mode  (Katoh et al. 2005) , and homology and gene structures were plotted using R packages ape  (Paradis and Schliep 2019) , ggtree  (Yu et al.
Quantitative locomotion analysis We generated quantitative phenotype data in three genetic backgrounds (wild-type, rol-1(sc22), and sqt-3(sc108)), each with the ancestral and derived col-182 allele. Conditions and worm tracking have been described previously  (Noble et al. 2017; Mallard et al. 2019). Lines (N2, COP1834, BE8, BE22, QG2957, QG3070) were each split to duplicate lineages, bleached, and grown under common conditions on HT115 bacteria in 90mm plates at 20°for two generations before assay, with each generation starting from around 500 L1 larvae that had been starvation synchronized in M9 buffer for 18 hr. Young adults were imaged in random order, on food, during day three post-L1, and again on two further generations (treated as above) for a total of six replicate plates per genotype.
In total, 167,187 diallelic SNPs where all four genotype classes were present at a minimum frequency of 10, excluding any uncertain imputations, were tested. To test for col-182-by-genotype interactions we fit nested bivariate linear models for three pairs of partially correlated traits: length and width (forward state, log transformed), the rol-1 and sqt-3 suppression discriminant functions that are linear combinations of five traits (see Quantitative locomotion analysis), and the single traits with the highest loading in each discriminant function, curvature and track circularity (log transformed). Trait values were best linear unbiased predictions (BLUPs) extracted from linear mixed effects models (R package lme4 ) fit to replicate observations, with fixed effects of population replicate.
Gene expression analysis We extracted data for 199 recombinant inbred advanced intercross lines (RIAILs) from  Rockman et al. (2010) , after excluding data from lines with annotation issues  (Zych et al. 2017). We performed structured nonparametric trait mapping as in  Rockman and Kruglyak (2009)  for abundance of 15,617 transcripts whose genes are more than a megabase from col-182 (to exclude local linkages for genes near col-182 that have their own cis-acting variants). We retained traits with genome-and experiment-wide significant linkage peaks (LOD. 4. 3, 5% FDR) within 1 RIAIL-effective cM of col-182 (approximately 400 Kb). The nine significantly linked transcripts were tested for functional enrichment using the WormBase Enrichment Analysis Suite (Angeles-Albores et al. 2018).
Data availability All quantitative data and code to reproduce our analyses and main figures are available from FigShare and https://github. com/lukemn/ cuticle. Strains are available upon request. File S1 details all supplemental files, File S2 contains genotyping data from Figure  1 , Files S3-S9 contain short videos of mutant and suppressed adult hermaphrodites on plates, File S10 contains gene models from Figure  2A , File S11 contains coding sequence alignments for Figure  2B , Files S12 and S13 contain raw and processed Multi-Worm tracker data for Figure  3  with associated R code in File S14. File S15 contains genotypes and phenotypes used for detecting genetic interactions between col-182 and SNPs in the CeMEE (Figure  4 ), with associated R code in File S16. Supplemental material available at figshare: https://doi.
elegans collagens [with col-72, col-75, col-104, and col-113, none of which have known mutant phenotypes;  (Teuscher et al. 2019) ]. To test whether col-182 is the rol-1 suppressor and whether the ancestral allele functions via the predicted isoform, we commissioned a strain that carries the ancestral splicing and reading frame in an otherwise N2 background (see strains). CRISPR-Cas9 conversion removed the 8-bp insertion and altered 16 additional base pairs, each a synonymous third codon position change in the predicted ancestral reading frame. We then confirmed that this ancestral allele col-182 anc suppressed rol-1, both the e91 and sc22 alleles (videos: CB91 rol-1(e91) vs. QG2953 rol-1(e91); col-182 anc , and BE22 rol-1(sc22) vs. QG2957 rol-1(sc22); col-182 anc , Files S3 and S5-S7). We generated quantitative data for the sc22 allele (selected arbitrarily) by tracking young adult hermaphrodites and extracting an array of statistics describing locomotion, size, and shape (see Quantitative locomotion analysis).
col-182 does not have systemic effects on gene expression Several of the alleles that arose during C. elegans domestication have large and systemic effects on C. elegans biology. These include npr-1 (de  Bono and Bargmann 1998; McGrath et al. 2009; Andersen et al. 2014; Zhao et al. 2018), nath-10 (Duveau and Félix 2012) , nurf-1  (Large et al. 2016), and Y17G9B. 8 (Rockman et al. 2010; Burga et al. 2018). We therefore investigated whether col-182 is linked to systemic effects on gene expression in adult hermaphrodites, using a published dataset of gene expression in 199 N2/CB4856 recombinant inbred advanced intercross lines [RIAILs;  (Rockman et al. 2010) ]. The RIAILs provide much higher genotypic replication than a typical pairwise contrast of strains, as each col-182 allele is homozygous in approximately half the RIAILs, but effects that map to col-182 may be due to nearby variants in other genes.
ACKNOWLEDGMENTS This work was supported by the  National Science Foundation  ( DDIG 1210762  to TK), the  National Institutes of Health  ( R01GM121828  to MVR), the  NYU Dean's Undergraduate Research Fund (AM) , and the  European Commission   Sklodowska-Curie Fellowship  ( H2020-MSCA-IF-2017-798083  to LMN). For sharing data and facilities, we thank  Henrique Teotónio. For strains, we thank  Erik Andersen  and the  Caenorhabditis Genetics Center , funded by the  NIH Office of Research Infrastructure Programs  ( P40 OD010440 ). We thank  Jia Shen ,  John Yuen ,  Arielle Martel ,  James Hong , and  Ambika Natesan  for assistance with experiments, and  Zhenhao Guo  and the  Chalfie lab  for helpful comments on the preprint.
Introduction: To investigate the validity and reliability of the 32-item Motor Function Measure (MFM32) in individuals with neuromuscular disorders (NMD), including spinal muscular atrophy (SMA), aged 2-5 years, and in non-ambulant individuals with Types 2 or 3 SMA, aged 2-25 years. Methods: Test-retest reliability (intraclass correlation coefficient [ICC]), internal consistency (Cronbach's alpha [a]), convergent validity (Spearman rank-order correlations), and known-groups validity (analysis of covariance comparing groups defined by the Clinical Global Impression of Severity [CGI-S] scale and Vignos grade) were calculated. The analysis was performed on a dataset provided by Hospices Civils De Lyon, extracted from the multinational MFM32 database. A total of 165 individuals were included in the analyses, of whom 84 were in the NMD group (aged 2-5 years) and 81 were in the SMA group (aged 2-25 years).
This study had two main objectives. The first was to extend the original validation by  Berard et al. (2005)   [4] , by investigating the validity and reliability of the MFM32 in patients with NMDs, including SMA, aged 2-5 years. The second objective was to assess the validity and reliability of the MFM32 in a population representative of the risdiplam SUNFISH Part 2 study population (NCT02908685), in which the MFM32 is the primary endpoint (i. e. in individuals with Type 2 and non-ambulant Type 3 SMA, aged 2-25 years)  [8].
Analysis Population This study was a retrospective analysis using data extracted from the MFM database, a multinational database containing MFM data collected in routine clinical practice. Two populations were studied: (1) patients with NMD (including SMA), aged 2-5 years; (2) patients with Type 2 or non-ambulant Type 3 SMA, aged 2-25 years. As the study population was not prospectively recruited, the analysis dataset reflects a convenience sample of individuals who provided their data to the MFM database. Ambulatory status was defined by the clinician at each visit, based on questions on walking capacities acquired and loss of ambulation (defined as the ability to walk 10 m) or on MFM items 28 (score of 3), 29 (score of 3), and 30 (score of 2 or 3). The earliest visit with complete data, at which patients met the criteria for age (both populations) and ambulatory status (2-to 25-year age group only), was used for each analysis, with the exception of test-retest reliability, for which the two visits closest together (with available data) were used.
Analyses Analyses were conducted on all patients with available data using SAS v9. 4 statistical software (SAS Institute, Cary, NC, USA). Scoring manuals were used to determine appropriate methods for the handling of item-level missing data (e. g. MFM32 missing item data were imputed as 0). Where appropriate, the threshold for statistical significance was P \ 0. 05 (without adjusting for multiplicity), and suggested thresholds of acceptability were used to aid interpretation.
STUDY LIMITATIONS Due to the study design, there are several study limitations to be considered. Although the 2-to 5-years' population included patients with SMA (20%), patients with a range of NMDs were included in the analysis dataset. Investigation of the measurement properties (validity and reliability) of the MFM32 in a larger population of patients with SMA aged \ 6 years would provide further supportive evidence for the use of the MFM32 total score in younger children with SMA. Furthermore, the 2-to 5-years' population contained a greater proportion of older individuals (i. e. few patients aged 2-3 years [15% of sample]). While this is a limitation, it is one that applies to many scales frequently used within NMD populations, where measurement properties are not commonly assessed within narrow age ranges.
All participants/a primary caregiver consented to their data being used for research activities. Ethical approval for the conduct of these analyses was granted by Comited'E ´thique du CHU de Lyon (No. 20-95). Data Availability. The datasets generated during and/or analyzed during the current study are not publicly available due to the data belonging to the MFM database. For access to the MFM database, please direct enquiries to Hospices Civils de Lyon. Open Access. This article is licensed under a Creative Commons Attribution-NonCommercial 4. 0 International License, which permits any non-commercial 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 licence, and indicate if changes were made.
ACKNOWLEDGEMENTS The authors would like to thank all and their families, who their data to the MFM database, as as the site staff involved in collecting the data and the study investigators ( Dalil Hamroun ,  Pascal Rippert ,  Sylvie Ragot-Mandry ,  Manuella Fournier Mehouas ,  Marguerite Munoz ,  Helene Rauscent ,  Susana Quijano-Roy ,  Jean-Paul Gayraud ,  Vincent Tiffreau ,  Aleksandra Nadaj-Pakleza ,  Pascal Bonnet ,  Francois Rivier ,  Jon Andoni Urtizberea ,  Veronique Bourg ,  Anne Renders ,  Sybille Pellieux ,  Laurent Servais , and  Sylviane Peudenier ). The authors would also like to thank  Hannah Staunton ,  Roche , for her review of the draft manuscript. Funding. This study and Rapid Service Fee were funded by  F. Hoffmann-La Roche Ltd. Authorship. All named authors meet the International Committee of Medical Journal Editors (ICMJE) criteria for authorship for this article, take responsibility for the integrity of the work as a whole, and have given their approval for this version to be published.
Native Soils To measure the effect of soil (biological and physico-chemical effects), 10 soil types were sampled in fields from the main potato production areas in France. In each field, soil samples were collected at 10-30 cm below the surface at several sampling points distributed along a diagonal and were pooled to obtain 25 kg of soil. The soils were homogenized and subsequently stored in containers at ambient temperature in the dark. Physical and chemical properties of each soil were determined at the Capinov laboratory of agri-food, agricultural, and environmental analysis (29,800 Landerneau, France; Table  1 ). A principal component analysis (PCA) was performed on the properties of the 10 sampled soils (dudi. pca function, "ade4" package;  Dray and Dufour, 2007 ; fviz_pca_var function, "factoextra" package;  Kassambara and Mundt, 2017)  to explore variations in the dataset according to factors known as some of the main drivers of microbial community diversity in soils.
Sequence Processing Fastq files (read 1 and read 2) were processed with DADA2 package version 1. 10. 1  (Callahan et al. , 2016)  on the R software (R Development Core Team, 2019). The default parameters proposed by the DADA2 workflow were retained except from truncLen argument, which was set at 200. Moreover, only sequences which lengths ranging from 369 to 374 and from 312 to 324, for bacteria and fungi, respectively, were kept. Taxonomy affiliations for the amplicon sequence variants (ASVs) obtained with DADA2 were performed using a naive Bayesian classifier  (Wang et al. , 2007)  on the Silva ver. One hundred thirty-two databases  (Callahan, 2018)  for bacteria and the Silva 18S ver. One hundred twentyeight databases  (Morien and Parfrey, 2018)  for fungi. Unclassified phyla were removed from the dataset.
Then, rarefaction curves were realized using the "ggrare" function of "ranacapa" package  (Kandlikar et al. , 2018)  to verify that the sequence coverage was sufficient to accurately describe the bacterial and fungal composition of each sample. Data were normalized based on sequencing depth using a rarefaction procedure (rarefy_even_depth function, "phyloseq" package) at 12,614 and 14,873 per sample for bacteria and fungi, respectively. At the end of this workflow, output files obtained were an ASV table and a taxonomy table.
Microbial Analyses Alpha Diversity Bacterial and fungal richness and diversities, characterized as number of ASVs found in each sample and the Shannon index (on normalized data), were determined with the diversity function of R "vegan" package  (Oksanen et al. , 2019). For the analysis, richness and diversities were compared between NS and RS using a Wald chi-square test on a Linear Mixed-Effects Model, (lmer function, "lme4" package;  Bates et al. , 2015)  taking into account the soil (A, D, F, and J) and the type of soil (NS and RS), as fixed factors, and the replicate, as random factor. Pairwise comparisons of estimated marginal means (EMMs) were performed (emmeans function, "emmeans" package;  Lenth, 2019) , applying the false discovery rate (FDR) correction for p-values.