cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5522/04/19641279
title: Scanning electron micrographs: lumbar spinal cords

description: <strong>Large area ultrastructural micographs via backscatter scanning electron microscopy associated with </strong><em><strong>Pocratsky et al 2023, Science Translational Medicine</strong></em> <br> Data generated from postnatal day 18 littermate controls (Cdx2::wt;Tor1a-wt/frt) and spinal <em>Tor1a </em>d-cko mice (Cdx2::FlpO;Tor1a-frt/frt) that develop early onset generalised torsional dystonia <br> Images were collected using the sense backscatter detector on a Gemini 300 SEM (Zeiss) <br> <strong>SEM_SpinalCord_metaData.xlsx: </strong>summary spreadsheet of images provided, including codes for genotypes <br> Full methodological details provided in manuscript <br> <br>
DOI: 10.5522/04/19641279.v1
title: Scanning electron micrographs: lumbar spinal cords

description: <strong>Large area ultrastructural micographs via backscatter scanning electron microscopy associated with </strong><em><strong>Pocratsky et al 2023, Science Translational Medicine</strong></em> <br> Data generated from postnatal day 18 littermate controls (Cdx2::wt;Tor1a-wt/frt) and spinal <em>Tor1a </em>d-cko mice (Cdx2::FlpO;Tor1a-frt/frt) that develop early onset generalised torsional dystonia <br> Images were collected using the sense backscatter detector on a Gemini 300 SEM (Zeiss) <br> <strong>SEM_SpinalCord_metaData.xlsx: </strong>summary spreadsheet of images provided, including codes for genotypes <br> Full methodological details provided in manuscript <br> <br>
DOI: 10.21943/auas.22332841.v1
title: Data belonging to study "The relationships between children’s motor competence, physical activity, perceived motor competence, physical fitness and weight status in relation to age"

description: This dataset belongs to our study " The relationships between children’s motor competence, physical activity, perceived motor competence, physical fitness and weight status in relation to age" (10.1371/journal.pone.0278438). This study was done to describe the relations between several factors related to motor skill competence, being physical activity, health related fitness, perceived motor competence and weight status. The published data are the final data used for our analyses. Data was collected in children between 4 and 13 years old. Motor skill competence is measured by the 4 Skills Test and the outcome is ' motor lead' (motor age - calendar age). Perceived Motor Competence is measured with the Pictorial Scale of Perceived Competence (4-8 years old) / Self-Perception Profile for Children (8 - 13 years old). Physical activity is measured as sports participation in minutes per week by use of a questionnaire that is filled in by the parents (4-9 years old) or by children themselves (10-13 years old). Health related fitness is measured by the Eurofit test. A composite score (Fitness_totalscore) is calculated from 8 items (1. Standing long jump 2. Bent arm hang 3. Sit and reach 4. 10x5m shuttle run 5. Plate tapping 6. Sit-ups 7. Handgrip strength 8. Shuttle run test). In 6- and 7-year old children plate tapping and the shuttle run test were not performed. Missings were handled by use of a Full Information Maximum Likelihood, as described in our methods section.
DOI: 10.21943/auas.22332841
title: Data belonging to study "The relationships between children’s motor competence, physical activity, perceived motor competence, physical fitness and weight status in relation to age"

description: This dataset belongs to our study " The relationships between children’s motor competence, physical activity, perceived motor competence, physical fitness and weight status in relation to age" (10.1371/journal.pone.0278438). This study was done to describe the relations between several factors related to motor skill competence, being physical activity, health related fitness, perceived motor competence and weight status. The published data are the final data used for our analyses. Data was collected in children between 4 and 13 years old. Motor skill competence is measured by the 4 Skills Test and the outcome is ' motor lead' (motor age - calendar age). Perceived Motor Competence is measured with the Pictorial Scale of Perceived Competence (4-8 years old) / Self-Perception Profile for Children (8 - 13 years old). Physical activity is measured as sports participation in minutes per week by use of a questionnaire that is filled in by the parents (4-9 years old) or by children themselves (10-13 years old). Health related fitness is measured by the Eurofit test. A composite score (Fitness_totalscore) is calculated from 8 items (1. Standing long jump 2. Bent arm hang 3. Sit and reach 4. 10x5m shuttle run 5. Plate tapping 6. Sit-ups 7. Handgrip strength 8. Shuttle run test). In 6- and 7-year old children plate tapping and the shuttle run test were not performed. Missings were handled by use of a Full Information Maximum Likelihood, as described in our methods section.
DOI: 10.25345/c5bz61j61
title: MassIVE MSV000091556 - The intracellular helical bundle of human glucose transporter GLUT4 is of importance for complex formation with ASPL
title: DSS-based cross-linking MS of the human glucose transporter GLUT4 in interaction with the human TUG homolog Alveolar Soft Part Sarcoma Locus (ASPL) protein.
DOI: 10.5281/zenodo.7772651
title: Multiple Sequence Alignment of a diverse dataset with 1788 Mycobacterium tuberculosis isolates

description: <strong>Multiple Sequence Alignment of a diverse dataset with 1788 <em>Mycobacterium tuberculosis</em> isolates used for ReporTree benchmarking</strong> The dataset comprises whole-genome sequence data published by Walker et al. 2015. For the multiple sequence analysis, we proceeded as follows: Reads were downloaded from ENA BioProject PRJNA282721 (accessed on March 16<sup>th</sup>, 2023) and trimmed using Trimmomatic (Bolger et al., 2014) with INNUca default settings; Quality-processed reads were individually mapped against the H37Rv reference genome (Genbank accession: NC_000962.3) using Snippy v4.5.1 and SNP-calling was performed on variant sites with the following criteria: a minimum proportion of reads differing from the reference of 70%, a minimum mapping quality of 30 and a minimum coverage for SNP calling of 10; A full alignment was extracted using Snippy’s core module (snippy-core), with masking of SNPs falling within known <em>M. tuberculosis</em> genomic regions with high GC content, repetitive elements and resistance-associated positions (corresponding to ~8% of the genome), as previously described for surveillance purposes (Macedo et al., 2019); <em>M. tuberculosis </em>lineages were determined using tb-profiler v4.4.1 (Phelan et al., 2019), with samples from the <em>M. tuberculosis</em> complex other than <em>M. tuberculosis</em>, representing a mix of multiple lineages, or with less than 95% of mapped positions in the reference, being excluded; A filtered alignment comprising the maximum number of informative sites (88,562 nucleotide sites with at least one mutation in a given sequence) was extracted from the full alignment using the alignment_processing.py v1.1.0 (default settings) of ReporTree, and then used as input for the benchmarking. In this repository, we provide two alignment files: Core_MTB_1787_strs.full.aln: this corresponds to the full multiple sequence alignment comprising 1787 samples and the reference (corresponding to the point 4 of the methodology). MTb_original_align_profile.fasta: this corresponds to the multiple sequence alignment comprising 1787 samples and the reference and only presenting the alignment informative sites (corresponding to the point 5 of the methodology)
DOI: 10.5281/zenodo.7772652
title: Multiple Sequence Alignment of a diverse dataset with 1788 Mycobacterium tuberculosis isolates

description: <strong>Multiple Sequence Alignment of a diverse dataset with 1788 <em>Mycobacterium tuberculosis</em> isolates used for ReporTree benchmarking</strong> The dataset comprises whole-genome sequence data published by Walker et al. 2015. For the multiple sequence analysis, we proceeded as follows: Reads were downloaded from ENA BioProject PRJNA282721 (accessed on March 16<sup>th</sup>, 2023) and trimmed using Trimmomatic (Bolger et al., 2014) with INNUca default settings; Quality-processed reads were individually mapped against the H37Rv reference genome (Genbank accession: NC_000962.3) using Snippy v4.5.1 and SNP-calling was performed on variant sites with the following criteria: a minimum proportion of reads differing from the reference of 70%, a minimum mapping quality of 30 and a minimum coverage for SNP calling of 10; A full alignment was extracted using Snippy’s core module (snippy-core), with masking of SNPs falling within known <em>M. tuberculosis</em> genomic regions with high GC content, repetitive elements and resistance-associated positions (corresponding to ~8% of the genome), as previously described for surveillance purposes (Macedo et al., 2019); <em>M. tuberculosis </em>lineages were determined using tb-profiler v4.4.1 (Phelan et al., 2019), with samples from the <em>M. tuberculosis</em> complex other than <em>M. tuberculosis</em>, representing a mix of multiple lineages, or with less than 95% of mapped positions in the reference, being excluded; A filtered alignment comprising the maximum number of informative sites (88,562 nucleotide sites with at least one mutation in a given sequence) was extracted from the full alignment using the alignment_processing.py v1.1.0 (default settings) of ReporTree, and then used as input for the benchmarking. In this repository, we provide two alignment files: Core_MTB_1787_strs.full.aln: this corresponds to the full multiple sequence alignment comprising 1787 samples and the reference (corresponding to the point 4 of the methodology). MTb_original_align_profile.fasta: this corresponds to the multiple sequence alignment comprising 1787 samples and the reference and only presenting the alignment informative sites (corresponding to the point 5 of the methodology)
DOI: 10.5522/04/19426331
title: Postnatal video recordings: training dataset, videos scored by external raters, test results

description: <strong>Files are associated with </strong><em><strong>Pocratsky et al 2023, Science Translational Medicine</strong></em><br> Full contents were deployed to 5 external raters for unbiased review of spinal <em>Tor1a </em>d-cko postnatal phenotype vs littermate controls<br> <strong>ReadMe.pdf</strong> - introduction to external reviewers about objective <br> <strong>TrainingVideos.pptx</strong> - optional videos provided to delineate normal functional milestones of postnatal sensory-motor development <br> <strong>VideosToScore_PPT1.pptx</strong> - videos scored that correspond to data published, part 1<br> <strong>VideosToScore_PPT2.pptx</strong> - videos scored that correspond to data published, part 2 <br> <strong>Deployed_test.pdf</strong> - exported copy of the complete online test taken by external raters <br> <strong>Phenotype_results.xlsx </strong>- data, including test key + rater results, sensitivity and specificity of test, body regions affected in cko's, and individual cko outcomes<br> Full methodological details provided in manuscript <br>
DOI: 10.5522/04/19426331.v1
title: Postnatal video recordings: training dataset, videos scored by external raters, test results

description: <strong>Files are associated with </strong><em><strong>Pocratsky et al 2023, Science Translational Medicine</strong></em><br> Full contents were deployed to 5 external raters for unbiased review of spinal <em>Tor1a </em>d-cko postnatal phenotype vs littermate controls<br> <strong>ReadMe.pdf</strong> - introduction to external reviewers about objective <br> <strong>TrainingVideos.pptx</strong> - optional videos provided to delineate normal functional milestones of postnatal sensory-motor development <br> <strong>VideosToScore_PPT1.pptx</strong> - videos scored that correspond to data published, part 1<br> <strong>VideosToScore_PPT2.pptx</strong> - videos scored that correspond to data published, part 2 <br> <strong>Deployed_test.pdf</strong> - exported copy of the complete online test taken by external raters <br> <strong>Phenotype_results.xlsx </strong>- data, including test key + rater results, sensitivity and specificity of test, body regions affected in cko's, and individual cko outcomes<br> Full methodological details provided in manuscript <br>
DOI: 10.6084/m9.figshare.22284385.v4
title: Development and evaluation of prevention bundle for neonatal healthcare-associated infections

description: Root cause analysis, Observations and survey, testing of the prevention bundles
DOI: 10.5522/04/19650942
title: Extracellular spinal recordings: spontaneous activity and fictive locomotion

description: <em><strong>In vitro</strong></em><strong> extracellular recording dataset of spontaneous activity in normal artificial cerebrospinal fluid (aCSF) and drug-induced fictive locomotion associated with </strong><em><strong>Pocratsky et al 2023, Science Translational Medicine</strong></em> <br> <em><strong>ENG_spontAct_aCSF.xlsx: </strong></em>raw and analysed data from extracellular recordings from lumbar spinal ventral roots of postnatal spinal cords (postnataly day 3-5). Data reflects spontaneous activity observed when cords were perfused with artifical cerebrospinal fluid (aCSF). Groups: Littermate control and spinal Tor1a d-cko mice that develop early onset generalised torsional dystonia <br> <em><strong>ENG_fictiveLocomotion.xlsx:</strong></em> raw and analysed data from extracellular recordings from lumbar spinal ventral roots of postnatal spinal cords (postnatal day 1-5). Data reflects stable rhythmic bursting activity observed when cords were perfused with aCSF mixed with a cocktail of NMDA, 5-HT, and dopamine (for p3-p5 recordings, only). <br> Full methodological details can be found with publication <br> <br>
DOI: 10.5522/04/19650942.v1
title: Extracellular spinal recordings: spontaneous activity and fictive locomotion

description: <em><strong>In vitro</strong></em><strong> extracellular recording dataset of spontaneous activity in normal artificial cerebrospinal fluid (aCSF) and drug-induced fictive locomotion associated with </strong><em><strong>Pocratsky et al 2023, Science Translational Medicine</strong></em> <br> <em><strong>ENG_spontAct_aCSF.xlsx: </strong></em>raw and analysed data from extracellular recordings from lumbar spinal ventral roots of postnatal spinal cords (postnataly day 3-5). Data reflects spontaneous activity observed when cords were perfused with artifical cerebrospinal fluid (aCSF). Groups: Littermate control and spinal Tor1a d-cko mice that develop early onset generalised torsional dystonia <br> <em><strong>ENG_fictiveLocomotion.xlsx:</strong></em> raw and analysed data from extracellular recordings from lumbar spinal ventral roots of postnatal spinal cords (postnatal day 1-5). Data reflects stable rhythmic bursting activity observed when cords were perfused with aCSF mixed with a cocktail of NMDA, 5-HT, and dopamine (for p3-p5 recordings, only). <br> Full methodological details can be found with publication <br> <br>
DOI: 10.17632/v55v6bwnd6.1
title: CIVIL ESTABLISHMENT CODE (ESTACODE), Rules for reservation of vacancies for the Scheduled Castes

description: CIVIL ESTABLISHMENT CODE (ESTACODE), Rules for reservation of vacancies for the Scheduled Castes
DOI: 10.34845/pacs-cs.000005
title: Lattice QCD gauge ensemble: JLDG/PACS-CS/RCNF2+1/RC32x64_B1900Kud01377000Ks01364000C1715

description: Lattice QCD gauge ensemble: JLDG/PACS-CS/RCNF2+1/RC32x64_B1900Kud01377000Ks01364000C1715
DOI: 10.34845/pacs-cs.000002
title: Lattice QCD gauge ensemble: JLDG/PACS-CS/RCNF2+1/RC32x64_B1900Kud01372700Ks01364000C1715

description: Lattice QCD gauge ensemble: JLDG/PACS-CS/RCNF2+1/RC32x64_B1900Kud01372700Ks01364000C1715
DOI: 10.34845/pacs-cs.000004
title: Lattice QCD gauge ensemble: JLDG/PACS-CS/RCNF2+1/RC32x64_B1900Kud01375400Ks01366000C1715

description: Lattice QCD gauge ensemble: JLDG/PACS-CS/RCNF2+1/RC32x64_B1900Kud01375400Ks01366000C1715
DOI: 10.17632/khhhyhhkjz.1
title: Data for Ni-goethite sulfidation to pyrite

description: Including XRD data; solution chemistry; XAS data at Fe K-edges; TGA data; Chemical analyses upon HCl/HNO3 acid treatment.
DOI: 10.34845/pacs-cs.000003
title: Lattice QCD gauge ensemble: JLDG/PACS-CS/RCNF2+1/RC32x64_B1900Kud01375400Ks01364000C1715

description: Lattice QCD gauge ensemble: JLDG/PACS-CS/RCNF2+1/RC32x64_B1900Kud01375400Ks01364000C1715
DOI: 10.17632/5wzyb3x5hx.1
title: Supplemental materials for the manuscript entitled "APOA4 as a novel predictor of prognosis in Stevens-Johnson syndrome/toxic epidermal necrolysis: a proteomics analysis from two prospective cohorts"

description: supplemental materials for APOA4 as a novel predictor of prognosis in Stevens-Johnson syndrome/toxic epidermal necrolysis: a proteomics analysis from two prospective cohorts
DOI: 10.17632/5wzyb3x5hx.2
title: Supplemental materials for the manuscript entitled "APOA4 as a novel predictor of prognosis in Stevens-Johnson syndrome/toxic epidermal necrolysis: a proteomics analysis from two prospective cohorts"

description: Mendeley supplemental figure 1. Participants disposition. Forty-eight patients in cohort 1 were treated with steroids alone and thirty-five patients received steroids plus adalimumab in cohort 2.
Mendeley supplemental figure 2. Representative photos illustrate disease progression in cohort2.
Mendeley supplemental figure 3. Plasma proteomics profiling of SJS/TEN before and after the combination treatment. (A) Comparative Venn diagram of plasma proteins between AP group and RP group. (B) The volcano plot demonstrated the differential encapsulation of plasma proteins between AP and RP. (C) GO analysis of the candidates for differentially expressed proteins in plasma from AP and RP. (D) The candidates for differentially expressed proteins in plasma from RP were analyzed using KEGG software, and the top 20 KEGG pathways were demonstrated in the bubble map.
Mendeley supplemental figure 4. (A) The heat map of hierarchical clustering indicated the candidates for differentially expressed proteins in the AP and RP plasma. (B) ELISA analysis of APOA4 levels in the plasma of HC (n=21) and SJS/TEN patients in AP/RP (n=21). 
Mendeley supplemental figure 5. (A and B) Protein levels of APOA4 were increased in RP compared with AP by western blot analysis.
Mendeley supplemental figure 6. Clinical correlation analysis between TNF-α decline and APOA4 increase.
Mendeley supplemental figure 7. Comparison of plasm cytokine levels before and after the treatment. 
Mendeley supplemental figure 8. NF-κB signaling pathway.
Mendeley supplemental figure 9. TNF signaling pathway.
Mendeley supplemental figure 10. The diagnostic criteria of SJS/TEN by the RegiSCAR study group.
Mendeley supplemental table 1. Demographic and clinical characteristics of the patients in two cohorts.
Mendeley supplemental table 2. Culprit drugs in two cohorts.
Mendeley supplemental table 3. The candidates of differentially expressed proteins in plasma before and after the combination treatment.
Mendeley supplemental table 4. Correlation analysis of APOA4 levels with associated factors of SJS/TEN severity.
Mendeley supplemental table 5. Linear regression analysis of factors associated with ScorTEN in SJS/TEN patients.
Mendeley supplemental table 6. Characteristics in included RCT and case series.
Mendeley supplemental table 7.  The clinical scoring system, “SCORTEN”, for predicting mortality in SJS/TEN.
DOI: 10.17632/5wzyb3x5hx.3
title: Supplemental materials for the manuscript entitled "APOA4 as a novel predictor of prognosis in Stevens-Johnson syndrome/toxic epidermal necrolysis: a proteomics analysis from two prospective cohorts"

description: Mendeley supplemental figure 1. Participants disposition. Forty-eight patients in cohort 1 were treated with steroids alone and thirty-five patients received steroids plus adalimumab in cohort 2.
Mendeley supplemental figure 2. Representative photos illustrate disease progression in cohort2.
Mendeley supplemental figure 3. Plasma proteomics profiling of SJS/TEN before and after the combination treatment. (A) Comparative Venn diagram of plasma proteins between AP group and RP group. (B) The volcano plot demonstrated the differential encapsulation of plasma proteins between AP and RP. (C) GO analysis of the candidates for differentially expressed proteins in plasma from AP and RP. (D) The candidates for differentially expressed proteins in plasma from RP were analyzed using KEGG software, and the top 20 KEGG pathways were demonstrated in the bubble map.
Mendeley supplemental figure 4. (A) The heat map of hierarchical clustering indicated the candidates for differentially expressed proteins in the AP and RP plasma. (B) ELISA analysis of APOA4 levels in the plasma of HC (n=21) and SJS/TEN patients in AP/RP (n=21). 
Mendeley supplemental figure 5. (A and B) Protein levels of APOA4 were increased in RP compared with AP by western blot analysis.
Mendeley supplemental figure 6. Clinical correlation analysis between TNF-α decline and APOA4 increase.
Mendeley supplemental figure 7. Comparison of plasm cytokine levels before and after the treatment. 
Mendeley supplemental figure 8. NF-κB signaling pathway.
Mendeley supplemental figure 9. TNF signaling pathway.
Mendeley supplemental figure 10. The diagnostic criteria of SJS/TEN by the RegiSCAR study group.
Mendeley supplemental table 1. Demographic and clinical characteristics of the patients in two cohorts.
Mendeley supplemental table 2. Culprit drugs in two cohorts.
Mendeley supplemental table 3. The candidates of differentially expressed proteins in plasma before and after the combination treatment.
Mendeley supplemental table 4. Correlation analysis of APOA4 levels with associated factors of SJS/TEN severity.
Mendeley supplemental table 5. Linear regression analysis of factors associated with ScorTEN in SJS/TEN patients.
Mendeley supplemental table 6. Characteristics in included RCT and case series.
Mendeley supplemental table 7.  The clinical scoring system, “SCORTEN”, for predicting mortality in SJS/TEN.
DOI: 10.34845/pacs-cs.000001
title: Lattice QCD gauge ensemble: JLDG/PACS-CS/RCNF2+1/RC32x64_B1900Kud01370000Ks01364000C1715

description: Lattice QCD gauge ensemble: JLDG/PACS-CS/RCNF2+1/RC32x64_B1900Kud01370000Ks01364000C1715
DOI: 10.5522/04/19467233
title: Transmission electron micrographs: lumbar spinal cord

description: <strong>Transmission electron micrographs of spinal neurons generated associated with </strong><em><strong>Pocratsky et al 2023, Science Translational Medicine</strong></em> <br> Images are from postnatal day 18 litterate controls (Cdx2::wt;Tor1a-wt/frt) and spinal <em>Tor1a </em>d-cko mice (Cdx2::FlpO;Tor1a-frt/frt) that develop early onset generalised torsional dystonia <br> Images were collected using a transmission electron microscope (ThermoFisher Tecnai G2 Spirit) and a charge-coupled device camera (Olympus SIS Morada) <br> <strong>TEM_LSc_metaData.xlsx:</strong> summary spreadsheet of raw images provided, including codes for genotypes <br> Full methodological detail provided in manuscript<br>
DOI: 10.5522/04/19467233.v1
title: Transmission electron micrographs: lumbar spinal cord

description: <strong>Transmission electron micrographs of spinal neurons generated associated with </strong><em><strong>Pocratsky et al 2023, Science Translational Medicine</strong></em> <br> Images are from postnatal day 18 litterate controls (Cdx2::wt;Tor1a-wt/frt) and spinal <em>Tor1a </em>d-cko mice (Cdx2::FlpO;Tor1a-frt/frt) that develop early onset generalised torsional dystonia <br> Images were collected using a transmission electron microscope (ThermoFisher Tecnai G2 Spirit) and a charge-coupled device camera (Olympus SIS Morada) <br> <strong>TEM_LSc_metaData.xlsx:</strong> summary spreadsheet of raw images provided, including codes for genotypes <br> Full methodological detail provided in manuscript<br>