cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5639920
title: Additional file 1: of Dietary energy drives the dynamic response of bovine rumen viral communities

description: VFA concentrations and pH measurements at the time of rumen sampling. VFA concentrations (mmol) were measured for acetate, propionate, isobutyrate, butyrate, isovalerate, and valerate. In addition to VFA concentrations, pH measurements were collected at the time of rumen sampling. (CSV 1Â kb)
DOI: 10.6084/m9.figshare.5639920.v1
title: Additional file 1: of Dietary energy drives the dynamic response of bovine rumen viral communities

description: VFA concentrations and pH measurements at the time of rumen sampling. VFA concentrations (mmol) were measured for acetate, propionate, isobutyrate, butyrate, isovalerate, and valerate. In addition to VFA concentrations, pH measurements were collected at the time of rumen sampling. (CSV 1Â kb)
DOI: 10.6084/m9.figshare.5639911
title: MOESM1 of Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance

description: Additional file 1. Nexus alignment file for the phylogenetic analysis of the core histone protein set.
DOI: 10.6084/m9.figshare.5639911.v1
title: MOESM1 of Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance

description: Additional file 1. Nexus alignment file for the phylogenetic analysis of the core histone protein set.
DOI: 10.6084/m9.figshare.5639902
title: Additional file 7: Table S5. of Quantitative trait locus mapping of Populus bark features and stem diameter

description: The 90th percentile candidate genes within the ninety four QTL detected in Populus Family 52â 124. Physical localization, annotation and expression profile of gene models in the 90th percentile with high expression within LOD peaks for each QTL interval for all traits. (XLSX 78Â kb)
DOI: 10.6084/m9.figshare.5639902.v1
title: Additional file 7: Table S5. of Quantitative trait locus mapping of Populus bark features and stem diameter

description: The 90th percentile candidate genes within the ninety four QTL detected in Populus Family 52â 124. Physical localization, annotation and expression profile of gene models in the 90th percentile with high expression within LOD peaks for each QTL interval for all traits. (XLSX 78Â kb)
DOI: 10.6084/m9.figshare.5639884
title: Additional file 6: Table S4. of Quantitative trait locus mapping of Populus bark features and stem diameter

description: All candidate genes within the ninety four QTL detected in Populus Family 52â 124. Physical localization, annotation and expression profile of gene models within each QTL interval for all traits. (XLS 4640Â kb)
DOI: 10.6084/m9.figshare.5639884.v1
title: Additional file 6: Table S4. of Quantitative trait locus mapping of Populus bark features and stem diameter

description: All candidate genes within the ninety four QTL detected in Populus Family 52â 124. Physical localization, annotation and expression profile of gene models within each QTL interval for all traits. (XLS 4640Â kb)
DOI: 10.6084/m9.figshare.5639878
title: Additional file 2: of Awareness, discussion and non-prescribed use of HIV pre-exposure prophylaxis among persons living with HIV/AIDS in Italy: a Nationwide, cross-sectional study among patients on antiretrovirals and their treating HIV physicians

description: a: PrEPventHIV_patients_1405. Original database (Patients). b: PrEPventHIV_physicians_87. Original database (HIV specialists). (ZIP 177â kb)
DOI: 10.6084/m9.figshare.5639878.v1
title: Additional file 2: of Awareness, discussion and non-prescribed use of HIV pre-exposure prophylaxis among persons living with HIV/AIDS in Italy: a Nationwide, cross-sectional study among patients on antiretrovirals and their treating HIV physicians

description: a: PrEPventHIV_patients_1405. Original database (Patients). b: PrEPventHIV_physicians_87. Original database (HIV specialists). (ZIP 177â kb)
DOI: 10.6084/m9.figshare.5639857
title: Additional file 1: of Awareness, discussion and non-prescribed use of HIV pre-exposure prophylaxis among persons living with HIV/AIDS in Italy: a Nationwide, cross-sectional study among patients on antiretrovirals and their treating HIV physicians

description: a: Questionario per i pazienti: original questionnaire (Italian version) on Pre-Exposure Prophylaxis awareness, discussion and practice for Persons Living With HIV/AIDS; b: English version. c: Questionario per i medici: original questionnaire (Italian version) on Pre-Exposure Prophylaxis awareness, discussion and practice for HIV Specialists caring for Persons Living With HIV/AIDS; 1d: English version. (ZIP 958Â kb)
DOI: 10.6084/m9.figshare.5639857.v1
title: Additional file 1: of Awareness, discussion and non-prescribed use of HIV pre-exposure prophylaxis among persons living with HIV/AIDS in Italy: a Nationwide, cross-sectional study among patients on antiretrovirals and their treating HIV physicians

description: a: Questionario per i pazienti: original questionnaire (Italian version) on Pre-Exposure Prophylaxis awareness, discussion and practice for Persons Living With HIV/AIDS; b: English version. c: Questionario per i medici: original questionnaire (Italian version) on Pre-Exposure Prophylaxis awareness, discussion and practice for HIV Specialists caring for Persons Living With HIV/AIDS; 1d: English version. (ZIP 958Â kb)
DOI: 10.6084/m9.figshare.5639848
title: Additional file 4: Table S2. of Quantitative trait locus mapping of Populus bark features and stem diameter

description: QTL associated with bark texture, diameter and bark thickness identified in Populus Family 52–124 in Oregon and West Virginia. Note: Chr: chromosome; V2: markers anchored on version 2 of the P. trichocarpa genome; V3: version 3 updated physical location; PVE: percent phenotypic variance explained; DD: homozygous for the P. deltoides allele, DT: heterozygous for the P. deltoides and P. trichocarpa alleles. LOD max determined using MQM mapping, value with *: above GW threshold, otherwise above CW threshold. Alternating white or grey shades represent unique QTL found in one or multiple replicates across years and sites. Indexes 1, 2, 3 or m designate: replicate one, two, three or replicates’ mean value for OR samples, whereas for WV samples only one replicate was available; BT: bark texture; D: diameter; BTh: bark thickness; 3y, 4y, 5y or 6y: # years old; OR: Oregon, WV: West Virginia. (Example for population: 1BT3yOR: replicate one, bark texture, 3 year old samples, Oregon site). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.5639848.v1
title: Additional file 4: Table S2. of Quantitative trait locus mapping of Populus bark features and stem diameter

description: QTL associated with bark texture, diameter and bark thickness identified in Populus Family 52–124 in Oregon and West Virginia. Note: Chr: chromosome; V2: markers anchored on version 2 of the P. trichocarpa genome; V3: version 3 updated physical location; PVE: percent phenotypic variance explained; DD: homozygous for the P. deltoides allele, DT: heterozygous for the P. deltoides and P. trichocarpa alleles. LOD max determined using MQM mapping, value with *: above GW threshold, otherwise above CW threshold. Alternating white or grey shades represent unique QTL found in one or multiple replicates across years and sites. Indexes 1, 2, 3 or m designate: replicate one, two, three or replicates’ mean value for OR samples, whereas for WV samples only one replicate was available; BT: bark texture; D: diameter; BTh: bark thickness; 3y, 4y, 5y or 6y: # years old; OR: Oregon, WV: West Virginia. (Example for population: 1BT3yOR: replicate one, bark texture, 3 year old samples, Oregon site). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.5639830
title: Additional file 6: Table S3. of HLA genotyping by next-generation sequencing of complementary DNA

description: Primers for PCR of circularized single-strand DNA. (XLS 34 kb)
DOI: 10.6084/m9.figshare.5639830.v1
title: Additional file 6: Table S3. of HLA genotyping by next-generation sequencing of complementary DNA

description: Primers for PCR of circularized single-strand DNA. (XLS 34 kb)
DOI: 10.6084/m9.figshare.5639812
title: Additional file 7: Table S1 of Phylogenomics of Cas4 family nucleases

description: Worksheet “loci” provides detailed information on all cas4 loci in completely sequenced and draft genomes of archaea and bacteria. Annotation for the proteins encoded in the loci is based on Cas protein and CDD assignments using PSI-BLAST program (see Methods for details). Worksheet “tree order and assignments” provides information of the order of the Cas4 in the tree (Supplementary file 1), Cas4 assignments to distinct groups of CAS-Cas4, solo-Cas4 and others. (TXT 28 kb)
DOI: 10.6084/m9.figshare.5639812.v1
title: Additional file 7: Table S1 of Phylogenomics of Cas4 family nucleases

description: Worksheet “loci” provides detailed information on all cas4 loci in completely sequenced and draft genomes of archaea and bacteria. Annotation for the proteins encoded in the loci is based on Cas protein and CDD assignments using PSI-BLAST program (see Methods for details). Worksheet “tree order and assignments” provides information of the order of the Cas4 in the tree (Supplementary file 1), Cas4 assignments to distinct groups of CAS-Cas4, solo-Cas4 and others. (TXT 28 kb)
DOI: 10.6084/m9.figshare.5639806
title: Additional file 2: Table S1. of Quantitative trait locus mapping of Populus bark features and stem diameter

description: Pair-wise estimates of phenotypic correlations calculated as Pearson correlation coefficients between bark texture (BT), diameter (D) and bark thickness (BTh) phenotypes collected from Populus Family 52–124. Note: Specifically, the analysis was done within and between experimental blocks, across years and across sites. Symbols show p-values, where p ≤ 0.05 = *, p ≤ 0.01 = **, p ≤ 0.001 = ***, and p ≤ 0.0001 = ****. White cells are correlations between the same traits across years and sites; red cells are correlations between diameter and bark texture; green cells are correlations between bark thickness and bark texture; blue cells are correlations between bark thickness and diameter. (XLSX 158 kb)
DOI: 10.6084/m9.figshare.11920128
title: Data for "Sharing for science: High-resolution trophic interactions revealed rapidly by social media"

description: Data associated with:Maritz, R. and Maritz, B. 2020. Sharing for Science: High-resolution trophic interactions revealed rapidly by social media. PeerJ DOI: 10.7717/peerj.9485<br><br><br>Maritz_FacebookDatabase.csv<br>Feeding interactions involving reptiles and amphibians in southern Africa gathered using Facebook (Predation Records - Reptiles and Frogs (Sub-Saharan Africa)). Data retrieved between Aug. 2017 - Dec. 2019.<br>Maritz_LiteratureDatabase.csvSnakes in southern Africa as predators collected using published scientific and grey literature. Data last retrieved from in Dec. 2019<br>Maritz_LitDatabaseRefs.xlsx<br>Full citations for literature sources used in this study including the snake species for which it provided data for.<br>Maritz_iNaturalistDatabase.csvSnakes in southern Africa as predators collected using iNaturalist. Data retrieved in Dec. 2019<br><br>Maritz_GoogleDatabase.csvSnakes in southern Africa as predators collected using Google Images. Four target species used: <i>Boaedon capensis</i>, <i>Python natalensis, Naja nivea, </i>and<i> Dispholidus typus. </i>Data retrieved in Oct. 2019.<br><br>Maritz_PreyRatios.csvRatios of prey for four target species of snakes using Facebook, iNaturalist, and Google Images.<br><br>Associated R code for analyses and figures: 10.6084/m9.figshare.12287714<br>Please notify us if you would like to use these data in a publication (maritzrobin.a@gmail.com) and provide recognition to our efforts by citing our database and publication in your work.
DOI: 10.6084/m9.figshare.11920128.v1
title: Data for "Sharing for Science: High-resolution trophic interactions revealed rapidly by social media"

description: Data associated with:Maritz, R. and Maritz, B. Sharing for Science: High-resolution trophic interactions revealed rapidly by social media.<br><br><br>Maritz_FacebookDatabase.csv<br>Feeding interactions involving reptiles and amphibians in southern Africa gathered using Facebook (Predation Records - Reptiles and Frogs (Sub-Saharan Africa)). Data retrieved between Aug. 2017 - Dec. 2019.<br>Maritz_LiteratureDatabase.csvSnakes in southern Africa as predators collected using published scientific and grey literature. Data last retrieved from in Dec. 2019<br>Maritz_LitDatabaseRefs.xlsx<br>Full citations for literature sources used in this study including the snake species for which it provided data for.<br>Maritz_iNaturalistDatabase.csvSnakes in southern Africa as predators collected using iNaturalist. Data retrieved in Dec. 2019<br><br>Maritz_GoogleDatabase.csvSnakes in southern Africa as predators collected using Google Images. Four target species used: <i>Boaedon capensis</i>, <i>Python natalensis, Naja nivea, </i>and<i> Dispholidus typus. </i>Data retrieved in Oct. 2019.<br><br>Maritz_PreyRatios.csvRatios of prey for four target species of snakes using Facebook, iNaturalist, and Google Images.<br><br>Associated R code for analyses and figures: 10.6084/m9.figshare.12287714
DOI: 10.6084/m9.figshare.5639770
title: Additional file 3: Table S2. of HLA genotyping by next-generation sequencing of complementary DNA

description: Comparison of the performance of automatic HLA typing. (XLS 28 kb)
DOI: 10.6084/m9.figshare.5639770.v1
title: Additional file 3: Table S2. of HLA genotyping by next-generation sequencing of complementary DNA

description: Comparison of the performance of automatic HLA typing. (XLS 28 kb)
DOI: 10.6084/m9.figshare.5639761
title: Additional file 4: Information File S2. of Phylogenomics of Cas4 family nucleases

description: Breakdown of CAS-Cas4 and solo-Cas4 presence in completely sequenced genomes. (XLSX 248Â kb)
DOI: 10.6084/m9.figshare.5639761.v1
title: Additional file 4: Information File S2. of Phylogenomics of Cas4 family nucleases

description: Breakdown of CAS-Cas4 and solo-Cas4 presence in completely sequenced genomes. (XLSX 248Â kb)
DOI: 10.6084/m9.figshare.5639734
title: Additional file 3: Information File S1. of Phylogenomics of Cas4 family nucleases

description: Complete tree for Cas4-like set in Newick format. Cas4 assignments are included in the leaf name. (TXT 463Â kb)
DOI: 10.6084/m9.figshare.5639734.v1
title: Additional file 3: Information File S1. of Phylogenomics of Cas4 family nucleases

description: Complete tree for Cas4-like set in Newick format. Cas4 assignments are included in the leaf name. (TXT 463Â kb)
DOI: 10.6084/m9.figshare.5639725
title: Additional file 1: Table S1. of HLA genotyping by next-generation sequencing of complementary DNA

description: The sequence of the primers for HLA typing system 01. (XLS 30 kb)
DOI: 10.6084/m9.figshare.5639725.v1
title: Additional file 1: Table S1. of HLA genotyping by next-generation sequencing of complementary DNA

description: The sequence of the primers for HLA typing system 01. (XLS 30 kb)
DOI: 10.6084/m9.figshare.5639716
title: Additional file 2: of Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening

description: Supplementary tables. (XLSX 39181 kb)
DOI: 10.6084/m9.figshare.5639716.v1
title: Additional file 2: of Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening

description: Supplementary tables. (XLSX 39181 kb)
DOI: 10.6084/m9.figshare.5639701
title: MOESM2 of Quantitative in vivo phosphoproteomics reveals reversible signaling processes during nitrogen starvation and recovery in the biofuel model organism Chlamydomonas reinhardtii

description: Additional file 2: Table S1. List of the 1227 quantified phosphopeptides in the whole cell for each samples. Phosphopeptides abundance was quantified based on MS1 intensity in Maxquant (see “Methods”). Data were log2 transformed and a Zero-mean normalization was applied. Percentage of coverage and number of unique peptides used for identification and score are indicated. MapMan bins were manually curated. Table S2. List of the 470 phosphopeptides significantly changed in the one-way ANOVA (p-value &lt; 0.05). The mean abundance ± SD for each sampling time are indicated. Table S3. List of the 125 proteins identified in both proteomics and phosphoproteomics approach. For each protein the corresponding phosphopeptide(s) were added (total of 276 phosphopeptides) and coefficients of correlation were calculated. Proteomics data were zero-mean normalized. Table S4. PCA variable loadings of the phosphopeptides dataset. Table S5. Dataset for the Hierarchical clustering, based on the Mapman bin Table S6. sPLS analysis correlations of the integrated dataset employing phosphopeptides as predictive variables and physiological measurements as responsive variables. Table S7. Extraction of the network characteristics from STRING database ( https://string-db.org/ ). Table S8. sPLS analysis correlations of the integrated dataset employing Eukaryotic phosphorylations sites as predictive variables and proteomics [7] data measurements as responsive variables. Table S9. list of protein sequences used for STRING analysis in Fig. 5a.
DOI: 10.6084/m9.figshare.5639701.v1
title: MOESM2 of Quantitative in vivo phosphoproteomics reveals reversible signaling processes during nitrogen starvation and recovery in the biofuel model organism Chlamydomonas reinhardtii

description: Additional file 2: Table S1. List of the 1227 quantified phosphopeptides in the whole cell for each samples. Phosphopeptides abundance was quantified based on MS1 intensity in Maxquant (see “Methods”). Data were log2 transformed and a Zero-mean normalization was applied. Percentage of coverage and number of unique peptides used for identification and score are indicated. MapMan bins were manually curated. Table S2. List of the 470 phosphopeptides significantly changed in the one-way ANOVA (p-value &lt; 0.05). The mean abundance ± SD for each sampling time are indicated. Table S3. List of the 125 proteins identified in both proteomics and phosphoproteomics approach. For each protein the corresponding phosphopeptide(s) were added (total of 276 phosphopeptides) and coefficients of correlation were calculated. Proteomics data were zero-mean normalized. Table S4. PCA variable loadings of the phosphopeptides dataset. Table S5. Dataset for the Hierarchical clustering, based on the Mapman bin Table S6. sPLS analysis correlations of the integrated dataset employing phosphopeptides as predictive variables and physiological measurements as responsive variables. Table S7. Extraction of the network characteristics from STRING database ( https://string-db.org/ ). Table S8. sPLS analysis correlations of the integrated dataset employing Eukaryotic phosphorylations sites as predictive variables and proteomics [7] data measurements as responsive variables. Table S9. list of protein sequences used for STRING analysis in Fig. 5a.
DOI: 10.6084/m9.figshare.5639572
title: Additional file 1: Table S1. of Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines

description: Description of algorithms used in the analyses. Table S2. Concordance rate of different combination of algorithms with dataset without missing data. Table S3. Number of variants and their review statuses for which majority of algorithm assertion was opposite to that in ClinVar. Table S4. Concordance among different combination of algorithms. Note that as MetaSVM and MetaLR are very similar and uses the same training set we omitted combinations that included both of these algorithms. Table S5. Percentage of damaging/tolerant call by each algorithm. Table S6. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and a cutoff estimated from the ROC curve of the indicated datasets. (XLSX 1124 kb)
DOI: 10.6084/m9.figshare.5639572.v1
title: Additional file 1: Table S1. of Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines

description: Description of algorithms used in the analyses. Table S2. Concordance rate of different combination of algorithms with dataset without missing data. Table S3. Number of variants and their review statuses for which majority of algorithm assertion was opposite to that in ClinVar. Table S4. Concordance among different combination of algorithms. Note that as MetaSVM and MetaLR are very similar and uses the same training set we omitted combinations that included both of these algorithms. Table S5. Percentage of damaging/tolerant call by each algorithm. Table S6. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and a cutoff estimated from the ROC curve of the indicated datasets. (XLSX 1124 kb)
DOI: 10.5281/zenodo.3977385
title: Contrasting Collision-induced Far-field Orogenesis Controlled by Thermo–rheological Properties of the Composite Terrane - Dataset

description: This is the dataset for the paper "Contrasting Collision-induced Far-field Orogenesis Controlled by Thermo–rheological Properties of the Composite Terrane" that has been submitted to "Geophysical Research Letters".
DOI: 10.6084/m9.figshare.5639551
title: Additional file 2: of What is the impact of a clinically related readmission measure on the assessment of hospital performance?

description: Codes clinically related to index admissions for all conditions. Codes considered to be clinically related to index admissions for hip replacement. Codes considered to be clinically related to index admissions for knee replacement. Codes considered to be clinically related to index admissions for pneumonia. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.5639551.v1
title: Additional file 2: of What is the impact of a clinically related readmission measure on the assessment of hospital performance?

description: Codes clinically related to index admissions for all conditions. Codes considered to be clinically related to index admissions for hip replacement. Codes considered to be clinically related to index admissions for knee replacement. Codes considered to be clinically related to index admissions for pneumonia. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.5639539
title: MOESM2 of Farmersâ knowledge and perception of enset Xanthomonas wilt in southern Ethiopia

description: Additional file 2. SPSS Data document S1. Datasets.
DOI: 10.6084/m9.figshare.5639539.v1
title: MOESM2 of Farmersâ knowledge and perception of enset Xanthomonas wilt in southern Ethiopia

description: Additional file 2. SPSS Data document S1. Datasets.
DOI: 10.6084/m9.figshare.5639536
title: MOESM2 of Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails

description: Additional file 2. List of insertion sites of all the tested conditions. Raw sequencing reads are available upon request.
DOI: 10.6084/m9.figshare.5639536.v1
title: MOESM2 of Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails

description: Additional file 2. List of insertion sites of all the tested conditions. Raw sequencing reads are available upon request.
DOI: 10.6084/m9.figshare.5639425
title: LSCC.rar

description: 16S rRNA gene sequencing data from swab sample of LSCC and control to investigate microbial signatures of LSCC onset.
DOI: 10.6084/m9.figshare.5639425.v1
title: LSCC.rar

description: 16S rRNA gene sequencing data from swab sample of LSCC and control to investigate microbial signatures of LSCC onset.
DOI: 10.6084/m9.figshare.5639347
title: Metagenomic analysis exploring soil microbial communities associated with Antarctic vascular plants and functional analysis. Supplementary figures & tables

description: Rhizosphere core microbiome and relative abundance eggNOG categories heatmap for all analyzed rhizospheric soil samples from Antarctic vascular plants. Raw reads were trimmed and aligned using DIAMOND agains NR database (NCBI). Taxonomical and functional classification was performed using MEGAN6