dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We thank  Gordon N Gill  and  Marilyn G Farquhar  ( University of California San Diego [UCSD])  for their critical input during the preparation of the manuscript. We are thankful to  Ying Dunkel ,  Linda Petronella Joosen ,  Katherine Suarez , and  Eileen Lim  for technical support. Funding: This work was supported by  National Institutes for Health (NIH)  grants  DK107585  and  Clinical and Translational Science Award (CTSA)  grant  UL1TR001442  pilot award program (to S Das);  AI141630 ,  CA238042 , and  CA100768  (to P Ghosh); and  R00-CA151673  (to D Sahoo). D Sahoo  was also supported by 2017  Padres Pedal the Cause/Rady Children's Hospital Translational PEDIATRIC Cancer Research Award. S Das  was also supported by a  DiaComp Pilot and Feasibility award  ( Augusta University ) and Padres Pedal the Cause/C3 2019  Moores Cancer Center Clinical and Translational Cancer Research Awards.
Main exclusion criteria are the bilateral or multifactor characters of the lower limb CE, Grade II or greater obesity, any contraindication to MRI, unable or unwilling to provide consent. Until July 2017, all patients enrolled in CHROEDEM study were invited to participate in the survey on patient's pathway at time of enrolment (baseline) visit. Those patients who agreed to participate were asked questions about the management of their disease and on the role of the different healthcare providers in the management of their disease. Those data were collected in an anonymized standardized questionnaire at the time of enrolment visit. For those patients that could not fill in the questionnaire at the time of enrollment visit, a phone interview was scheduled. A questionnaire had been tested beforehand among a sample of 10 patients with PL or SPT to ensure that the questions were clear and unambiguous.
The main following data were collected : demographics (age, sex, weight, height), diagnostic pathway (in case of PL and in case of PTS they were asked where the index DVT had been managed), current therapeutic management pathway (healthcare providers involved, frequency of visit to each and the role of each), treatments and patient's information provided/received. This survey was conducted in agreement with the French legislation on health research. The CHROEDEM study was approved by the ethics committee (Comité Consultatif de Protections des Personnes Sud Méditerranée III) and is referenced on ClinicalTrials. gov (NCT02914808). From a statistical standpoint, our survey sample size was determined by the number of patients enrolled in the CHROEDEM study at time this ancillary study was conducted.
Categorical variables were expressed as frequencies and percentages and continuous variables as means with standard deviation or median with interquartile range. Chi-square or Fisher t tests were used for categorical variables. Wilcoxon and student t tests were used for continuous variables according to their distribution. Two-sided p-values of 0. 05 or less were considered to be statistically significant. Data were anonymously analysed in the Department of Biostatistics using SAS® Enterprise software (SAS Institute Cary, N. C. ).
Objectives: The aim of this study was to describe antibiotic prescribing patterns and antimicrobial resistance rates in hospitalised children with febrile and afebrile urinary tract infections (UTIs). Methods: Antibiotic prescriptions and antibiograms for neonates, infants and older children with UTI admitted to a general district hospital in Central Greece were evaluated. Data covering a 5-year period were collected retrospectively from the Paediatric Department's Electronic Clinical Archive. Patients were included based on clinical and microbiological criteria. Antimicrobial susceptibility was determined by the Kirby-Bauer disk diffusion method. Results: A total of 230 patients were included in the study. Among 459 prescriptions identified, amikacin (31. 2%) was the most common antibiotic prescribed in this population, followed by amoxicillin/clavulanic acid (17.
Data source A retrospective cohort study was performed in Achillopouleion General Hospital of Volos, a general district hospital in Central Greece, from August 2010 to September 2015, including neonates (aged <29 days), infants and toddlers (aged 29 days up to <2 years) and older children (aged 2 to <5 years or !5 years). This paper reports a cross-sectional analysis of the baseline data from the cohort study. Patients' medical notes were retrieved from the Paediatric Department's Electronic Clinical Archive and patients with UTI were identified using a comprehensive approach including ICD-10 codes and free-text information. Demographic data, diagnoses, medical history and antibiograms were extracted from the database. Atypical UTIs were identified according to the UK National Institute for Health and Care Excellence (NICE) guidelines  [13].
Repated washing was followed by revelation using ECL detection reagents (GE Healthcare) and visualized using hyperfilm ECL or ImageQuant LAS 4000. Quantifications were performed with ImageJ software. The antibodies were the following: a mouse monoclonal anti-GAPDH clone 6C5 (1: 10000; Abcam), a mouse monoclonal anti-HuR 3A2 (1:500; Santa Cruz), an anti-mouse IgG HRP (1:10000; Sigma), an anti-rabbit IgG HRP (1:10000; Sigma), an anti-histone 3 (1:1000; Cell Signaling Technologies), a mouse monoclonal anti-phosphorylated p38 (1:2000, clone 28B10; Cell Signaling Technology) and a rabbit polyclonal anti-p38 (1:1000; Cell Signaling Technology).
However, the main side effect observed in patients is the perturbation of iodide uptake by the thyroid. In this context, whether ICM induce intracellular events in the thyroid, identical to those triggered by free iodide (referred to as the Wolff-Chaikoff effect), remains to be determined. As previous imaging data from our group provided indirect evidence that ICM inhibit thyroid iodide uptake through a mechanism different from that of NaI  [16] , the present study was precisely designed to provide strong additional molecular evidence of distinct intracellular events triggered by ICM and NaI in the thyroid using unbiased approaches. To get a general and comparative overview of ICM and NaI effects on thyrocytes protein expression, we applied the so-called TMT quantitative proteomics approach to thyroids from mice that had been treated with ICM or NaI.
Peptide Fractionation and LC-MS/MS Analysis The TMT-labeled samples were analyzed using a LC-MS/MS system consisting of a DIONEX Ultimate 3000 HPLC system and a Q Exactive Plus (Thermo Fischer Scientific, France) equipped with an electrospray source. Sample digests were analyzed with a capillary LC column (Thermo Fischer Scientific, Illkirch, France) PepMap100 C18, 300 µm × 15 cm, 2 µm particle, 100 Å pore size) and a 300 min gradient on the Q Exactive Plus (Thermo Fischer Scientific, Bremen, Germany). Sample digests were labeled with TMT 9-plex reagents at a ratio of 1:1 with a five-hour gradient, analyzed with a data dependent top 15 high-energy collision dissociation (HCD) method on the Q Exactive Plus. The resolution was 70K for full scan and 35K for MS2. The maximum injection time was 250 ms for both full scan and MS2 scan, top 15 HCD was selected with MS2 trigger threshold of 1E5 and dynamic exclusion of 60 s.
Protein Identification and Quantification All MS raw data files were analyzed by Proteome Discoverer software 2. 1. 1. 21 (Thermo Fisher, Illkirch, France) using the Sequest HT search engine against a database of Mus musculus protein sequences (Uniprot 10 090_Mus Musculus taxon 20 September 2018). X corr confidence was held upper to 0. 7 for all parameters. Precursor mass tolerance was set to 10 ppm and fragment ion tolerance was 0. 02 Da with permission of two missed cleavages in the trypsin digests. A decoy database search strategy was also used to estimate the false discovery rate (FDR) to ensure the reliability of the proteins identified: a 1% target FDR as strict criteria and 5% target FDR as relaxed criteria using Percolator. The strict maximum parsimony principle was performed, and only peptide spectra with at least low confidence were considered for protein grouping.
Carbamidomethylation on cysteine (+57. 021 Da) was set as static modifications. TMT6 tags on N termini (+229. 163 Da) and on Lysine were set as static modifications. Two 10-plex technical replicates were acquired for two proteome experiments with the average and standard deviation reported. For relative quantitation, both unique and razor peptides were considered a highly confident identification and used for quantification. Reporter ion abundances were corrected for isotopic impurities based on the manufacturer's data sheets. Signal-to-noise (S/N) values were used to represent the reporter ion abundance with a co-isolation threshold of 75% and an average reporter S/N threshold of 10 and above required for quantitation spectra to be used. The S/N values of peptides, which were summed from the S/N values of the PSMs, were summed to represent the abundance of the proteins.
Bioinformatics Analysis Pathway analyses were performed using Ingenuity Pathway analysis software (Qiagen, v. 48207413, Courtaboeuf, France). Only pathways with p-values under a threshold of 0. 01 were considered significant. Z-scores were also observed as a measure and a predictor for the activation state of the regulator. The activation Z-score makes predictions about potential regulators by using information about the direction of gene regulation. It can be used to infer the activation state of a putative regulator (i. e. , whether the regulator is activated or inhibited). Protein networks were analyzed with STRING (10. 5) (string-db. org) [31].
Altered Pathways To determine the top pathways altered by NaI or ICM, the whole DEPs dataset was analyzed using Ingenuity Pathway analysis (IPA) with the enriched list of proteins (Figure  5 ). Statistically significant canonical pathways for which the p-values < 0. 01 were identified. Nine pathways are common to the two enriched datasets (Table  3 ). They include metabolic pathways and signaling pathways. Only six are exclusive to the NaI versus control enriched dataset (Supplementary Table  S3 ). Finally, 16 pathways are exclusive to the ICM versus control enriched dataset (Supplementary Table  S4 ). Networks of DEPs were created using STRING (Figure  5 ). A higher density of interactions can be observed in the DEP/ICM versus control dataset than in the DEP/NaI versus control dataset.
Commonly Modulated Pathways To for potential common regulation mechanisms in accordance with common reduced NIS expression and reduced iodide uptake, the upstream analysis module of Ingenuity Pathway Analysis was run on the nine total pathways commonly modulated in the two conditions (ICM and NaI). Insulin Receptor (INSR) was identified as a significantly unbiased upstream activator in both treatments: NaI (z-score = 2. 219, p = 1. 63 × 10 -4 ) and ICM (z-score = 2. 433, p = 1. 34 × 10 -4 ) (Figure  6 ) and predictions of activated and inhibited candidates in each treatment are shown (Figure  6C, D ).
This entry results in intracellular events leading to a classical Wolff-Chaikoff effect for which a consequence is a reduction in the expression of the NIS protein  [2]. Measurement of the iodide levels in the thyroids of animals treated with ICM failed to show a significant difference up to 48 h after treatment. Our observation in mice is in agreement with a dataset obtained in humans in which the authors demonstrated that intra-thyroidal iodine was unaffected by ICM (up to 96 h following ICM administration)  [32]. Together with our previous study showing that ICM (and its contaminating free iodide) fails to directly affect thyrocytes uptake in vitro, the present data confirm that ICM induces thyroid stunning independently of free-iodide. To get further insight into the mechanisms involved in thyroid uptake inhibition, we used a quantitative proteomic approach to examine the variations in protein content in thyroids exhibiting maximal radiotracer uptake reduction after NaI or ICM treatment.
Overall, our data demonstrate that ICM induces a dramatic change in the level of many different proteins affecting numerous pathways. In comparison to ICM, administration of NaI leads to a lower level of changes. Only 10 proteins are differentially expressed in thyroids from NaI-treated animals in contrast to 55 in ICM-exposed thyroids, with two proteins being commonly differentially expressed. When pathways are considered, the similarity between the two conditions is much higher: about 30% of total pathways are commonly modulated in the two conditions and these modulated pathways could be the signature of common mechanisms leading to reduced NIS expression and reduced iodide uptake. One of these pathways is the regulation of the eIF4 and p70S6K signaling pathway. The upstream analysis module of Ingenuity Pathway Analysis suggested that the insulin receptor (INSR) was a significantly unbiased upstream activator in both treatments.
A variety of cat breeds have been developed via novelty selection on aesthetic, dermatological traits, such as coat colors and fur types. A recently developed breed, the lykoi (a. k. a. werewolf cat), was bred from cats with a sparse hair coat with roaning, implying full color and all white hairs. The lykoi phenotype is a form of hypotrichia, presenting as a significant reduction in the average numbers of follicles per hair follicle group as compared to domestic shorthair cats, a mild to severe perifollicular to mural lymphocytic infiltration in 77% of observed hair follicle groups, and the follicles are often miniaturized, dilated, and dysplastic. Whole genome sequencing was conducted on a single lykoi cat that was a cross between two independently ascertained lineages. Comparison to the 99 Lives dataset of 194 non-lykoi cats suggested two variants in the cat homolog for Hairless (HR) (HR lysine demethylase and nuclear receptor corepressor) as candidate causal gene variants.
Whole Genome and Variant Calling A single lykoi cat was subjected to whole genome sequencing as previously described  [32]. Illumina paired-end sequencing was conducted to produce approximately 30× coverage. The selected cat was an F1 from the mating of two independently discovered foundation lineages from Virginia and Tennessee. The sequence was included in the 195-cat analysis of the 99 Lives cat genome sequencing project and submitted to the NCBI short read archive under BioProject: PRJNA308208, PRJNA288177; BioSample: SAMN05980355. Moreover, all cats for the 195-cat analysis are publicly available through the NCBI short read archive under the accessions shown in Supplementary File 1. For the 195-cat analysis, reads were mapped to Felis_catus_9. 0  [37]  and assigned to read groups using BWA-MEM from Burrows-Wheeler Aligner version 0.
7. 17  [38]. Duplicate reads were marked using MarkDuplicates from Picard tools version 2. 1. 1 (http://broadinstitute. github. io/picard/), with OPTICAL_DUPLICATE_PIXEL_DISTANCE set at 2500. Genome Analysis Toolkit version 3. 8 (GATK 3. 8) was used to further process the sequence data  [39]. Indel realignment was performed with RealignerTargetCreator and IndelRealigner  [39]  and SNPs, and Indels were called using HaplotypeCaller in gVCF mode (-ERC GVCF)  [40]. The gVCFs were combined into groups of ~20 individuals using CombineGVCFs and were genotyped simultaneously using GenotypeGVCFs. Throughout, Samtools version 1. 7 sort, index, view, and cat functions were used to process BAM files between individual tasks  [41]. Together these processes produced a single VCF comprised of 195-cats for downstream analysis.
Code used to process individual genomes is publicly available on github (https://github. com/mu-feline-genome/github-lewis/blob/master/map_libraries. slurm. sh). DNA variants were viewed, filtered and annotated using VarSeq (Golden Helix, Boseman, MT, USA) with the Ensembl release 98 Felis_catus_9. 0 genome annotation  [42]. VarSeq annotation is similar to Variant Effect Predictor (Ensembl VEP), using the same sequence ontology. Candidate variants were considered to be homozygous or compound heterozygous in the same gene in the lykoi cat and not present in any other cat of the 99 Lives cat database. Only variants that caused high to moderate severity effects (frameshift, nonsense, splice donor-acceptor, splice region, and missense variants) on the protein were considered and variants with high severity and within candidate genes were prioritized.
Lykoi Samples Over 100 cats were ascertained for the lykoi project and were used to develop two pedigrees of the cats segregating for the lykoi phenotype (Supplementary Figures  S1  and S2 ). The relationship of the cats of Pedigree B was confirmed by STRs (data not shown). Sixty-seven cats formed an extended pedigree "A" by crossing three different lineages (Tennessee, Virginia and Texas) (Supplementary Figure  S1 ) and a smaller pedigree "B" was obtained from a French lineage of cats (Supplementary Figure  S2 ). Overall, cats were identified from 16 foundation lines, ascertained from 14 diverse regions in the USA, Canada and France. Two supposed founder lineages were independently ascertained from Florida, California and France, each (Table  1 , Figure  1 ). Vermont Gonzalo Wt/Wt Wt/Wt A/A C/C C/C Wt/Wt hr TX /hr TX North Carolina Wt/Wt G/G T/T C/C Wt/Wt hr NC /hr NC Canada Wt/Wt G/G C/C T/T Wt/Wt hr Ca /hr Ca Florida 1 Wt/Wt G/G C/C T/T Wt/Wt hr Ca /hr Ca Florida 2 † Wt/Wt G/A C/C C/C Wt/Wt Wt/hr TX Protein Change Q420S Splice Splice R748X Q865X S1130R Bolded are the causal variant for each cat.
3389insGACA (chrB1:36051556), which should produce a stop codon at amino acid position 1130 (p. Ser1130Argfs*29) in the Virginia lineage and is designated hr VA allele (Figure  2 ). These two identified frameshift variants were confirmed by direct Sanger sequencing in the cat submitted for WGS and the presented positions are for the newest cat genome assembly Felis_Catus_9. 0 (GCF_000181335. 3/). The lykoi phenotype segregated concordantly with each loss of function variant across the pedigree developed from the Virginia and Tennessee lineages (Supplementary Figure  S1 ). Cats with the lykoi hair coat in these lineages were either homozygous for one of the two loss of function variants or compound heterozygous for both loss of function variants. WGS data also revealed additional HR variants.
HR in the cat is annotated in Ensembl 98  [42]  as ENSFCAG00000012978 B1:36034352-36051895:1. Three transcripts are described containing 17-19 exons, in which exons 17-19 are the variable exons. Three 5 UTRs are recognized, one as part of the 5 portion of exon 1. Two transcripts have short 3 UTRs at the end of exon 18. The variants in this study were annotated with Ensembl 98 transcript HR-202 containing 4227 bp that translate to 1184 amino acids from 18 translated exons. Each of the six variants identified in the lykoi cats either cause termination codons at the variant site or cause downstream terminations after an additional 12 amino acids after the exon 8 c. 2112G>A variant or an additional 100 amino acids after the exon 3 c. 1255_1256dupGT variant, leading to proteins with ~528 -704 + 12 amino acids.
Statistical Analyses A total of 205 R × R, 196 T × T, 34 R × T, and 50 T × R ewe lambs had fleece traits recorded. Greasy fleece weight (n = 484), CFW (n = 476), and LSY (n = 476) as well as A-FD and CV-FD of midside (n = 449), britch (n = 457), and core samples (n = 395) were separately analyzed in the MIXED procedure of SAS (v 9. 4; SAS Institute Inc. , Cary, NC). The model included fixed effects of sire breed, dam breed, birth type (1 or 2+), age of dam (2 to 4+ yr), and birth year and the random effect of sire (nested within sire breed and birth year). All two-way interaction effects were tested and then removed if they were not significant (P > 0. 05). Contrasts were generated using the LSMESTIMATE argument to estimate individual heterosis (H I ) and reciprocal-cross differences (i. e.
Results SnRNA-seq identifies several cell populations in adult skeletal muscles. To characterize the transcriptional profile of myonuclei within myofibers, we developed single nucleus RNA-seq (snRNA-seq) experiments using a droplet-based platform on purified nuclei from different skeletal muscles of adult mice (Fig. 1a  and Supplementary Fig. 1a-d ). By using Seurat software  25  and Uniform Manifold Approximation and Projection (UMAP) clustering we were able to detect a total of 19 different cell populations clusters present in the different muscles (Fig. 1b  and Supplementary Fig. 2b, c ). The origin of the nuclei was identified by specific markers (Fig. 1b  and Supplementary Figs. 1e  and 2a , Supplementary Data 1), with 68% of nuclei originating from myofibers, 19% from FAPs, and around 13% from other cell types, including tenocytes, endothelial and lymphoid cells, smooth muscle cells, and myogenic stem cells (Supplementary Fig.
Briefly, nuclei were transposed using Tn5 transposase and then encapsulated into gel beads emulsion using 10X protocol. After quality assessments and filtering (Supplementary Fig. 4a-c ), 132 966 peaks were identified from 6037 sequenced nuclei. To identify the different populations of nuclei, we classified nuclei from ATAC-seq based on snRNA-seq experiments from Fig. 1b : we used methods for cross-modality integration of snRNA-seq and snATAC-seq data and label transfer from Signac software (Fig. 3a  and Supplementary Fig. 4d, e ). This classification was robust, as shown by the chromatin accessibility of the Myh genes present only in myonuclei (Fig. 3b  and Supplementary Fig. 5a, b ). Using chromVar we characterized the transcription factors (TF) variations in motif accessibility between the different types of myonuclei (Fig.
For e. g. , scale bar: 100 μm. For f, h the graphs show data pooled from three animals and fifteen fibers per animal. Numerical data are presented as mean ± s. e. m. *P < 0. 05, **P < 0. 01, ***P < 0. 001. Source data for f, h are provided in the Source Data file. myogenic stem cells with distinct potential  [45] [46] [47] [48] [49]  could fuse (homotypic fusion  50  ), activating a single Myh gene along the myofiber. Moreover, extracellular signals from surrounding cells may also intervene  51. The de-coordination of myonuclei after denervation observed in our study supports the importance of innervation in the coordination process during development. A better understanding of the matching between motoneuron subtypes and myofiber subtypes that operates during development  52  may help understand how neuromuscular specialization contributes to the onset of coordination.
Nuclei were washed to remove ambient RNAs in 1 ml of cold wash buffer, transferred in a 1. 5 ml Eppendorf tube and centrifuged 5 min at 500 × g at +4 °C. The pellet was resuspended in 250 μl of wash buffer and stained during 15 min in the dark at +4 °C with DAPI (10 μg/ml). Then the nuclei were washed with 1 ml of wash buffer, centrifuged 5 min at 500 × g at +4 °C, resuspended in 300 μl of wash buffer and filtered with 30 μm cell strainers. Nuclei were then FACS sorted to exclude debris with a BD FACSAria III and the BD FACSDIVA software. More than 200,000 nuclei were collected in a tube containing 200 μl of wash buffer. Single-nucleus RNA-seq from skeletal muscle. After FACS sorting, nuclei were centrifuged 5 min at 500 × g at +4 °C, resuspended in 15 μl of wash buffer and counted with a hemocytometer.