cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3623192_d2
title: Additional file 1 of Computational modeling of phagocyte transmigration for foreign body responses to subcutaneous biomaterial implants in mice

description: List of histamine, P selectin, PMN and M ÎŚ measurement data named. (XLS 31 kb)
DOI: 10.6084/m9.figshare.c.3623231_d5
title: MOESM4 of â  Gap huntingâ   to characterize clustered probe signals in Illumina methylation array data

description: Additional file 4: Table S2. Breakdown of all C/G and SBE site measured polymorphism scenarios. We isolated specifics scenarios in which the following conditions were met: a probe contained a measured SNP that mapped to the C, G, or SBE sites of a probe, and it also did not contain any other form of mapping SNP. This table contains a list of all SNP C, G and SBE site scenarios herein and their corresponding Figure #. Also included is the number of probes analyzed for each scenario, along with the count and proportion of those probes that were classified as gap signals. Most probes in SEED that overlapped with measured SNPs were not classified as gap signals (though ~80% of gap signals did overlap with SNPs, see Additional file 7).
DOI: 10.15468/dl.m4a3sy
title: Occurrence Download

description: A dataset containing 571 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Colombia, Ecuador, Peru, Bolivia (Plurinational State of), Venezuela (Bolivarian Republic of))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Juglans neotropica Diels",
 "Year 2020-2024"
 ]
}

 The dataset includes 571 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033933-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3623417_d1
title: Additional file 1: of Systems toxicology identifies mechanistic impacts of 2-amino-4,6-dinitrotoluene (2A-DNT) exposure in Northern Bobwhite

description: Supplemental tables. (XLSX 1436 kb)
DOI: 10.6084/m9.figshare.c.3623423_d1
title: Additional file 2:  of Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp. tritici)

description: Top 100 Pst -sRNA sequences sorted by abundance. Each Pst-sRNA was uniquely named based on the treatment in which it was found, length, and rank abundance in that treatment. Fungal reads in sRNA libraries from two infected cultivars. IP = Infected Penawawa; IL = Infected Louise. Counts represent the sum of three replicates. (CSV 5 kb)
DOI: 10.6084/m9.figshare.c.3623411_d3
title: Additional file 4: of Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera)

description: GenBank accession numbers. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.c.3623387_d12
title: Additional file 4: of Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling

description: GEO dataset references of microarray data repository and number of samples selected in each of the two meta-analysis steps: (i) the hierarchical clustering analysis with 264 microarray samples (SET 264); and (ii) the differential expression resampling protocol with 119 microarray samples (SET 119). (XLSX 57 kb)
DOI: 10.6084/m9.figshare.c.3623387_d13
title: Additional file 14: of Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling

description: Cytoscape file (produced with Cytoscape version 3.1.0) that includes a gene coexpression network derived from the expression values of the 489 genes along the exon arrays in 15 samples of the different cell types studied. The coexpression was calculated using a Pearson correlation with a stringent cutoff to select the pairs with correlation coefficient r ≥ 0.95. The file includes only the gene pairs that passed the cutoff threshold, incorporating 447 genes and 9969 interactions. Several views of the network are included and various clusters of genes were produced as subnetworks. Biological information and annotation for individual genes is also provided. (CYS 781 kb)
DOI: 10.6084/m9.figshare.c.3623393_d9
title: MOESM5 of What evidence exists for the effectiveness of on-farm conservation land management strategies for preserving ecosystem services in developing countries? A systematic map

description: Additional file 5. Coding tool for systematic map.
DOI: 10.6084/m9.figshare.c.3623468_d1
title: Additional file 11: Table S10. of Characterization of the cytokinin-responsive transcriptome in rice

description: Primers used in the NanoString analysis. (XLSX 44Â kb)
DOI: 10.5281/zenodo.14174468
title: Digital appendix: Microbial communities as sentinels of environmental changes in Svalbard (MicroSIOS)
title: Appendix A, Table A1. Study of microbial diversity in Svalbard environments
title: Appendix A, Table A2. Pattern of bacterial antibiotic susceptibility/resistance of bacterial isolates from svalbard environments

description: This is supplementary material for chapter 6 (MicroSIOS) in the State of Environmental Science in Svalbard (SESS) report 2024 (https://sios-svalbard.org/SESS_Issue7)”
DOI: 10.5281/zenodo.14174469
title: Appendix A, Microbial communitieS as sentInels of envirOnmental changes in Svalbard MicroSIOS_SIOS SESS REPORT 2024
title: Appendix A, Table A1. Study of microbial diversity in Svalbard environments
title: Appendix A, Table A2. Pattern of bacterial antibiotic susceptibility/resistance of bacterial isolates from svalbard environments
DOI: 10.5281/zenodo.14455795
title: Digital appendix: Microbial communities as sentinels of environmental changes in Svalbard (MicroSIOS)
title: Appendix A, Table A1. Study of microbial diversity in Svalbard environments
title: Appendix A, Table A2. Pattern of bacterial antibiotic susceptibility/resistance of bacterial isolates from svalbard environments

description: This is supplementary material for chapter 6 (MicroSIOS) in the State of Environmental Science in Svalbard (SESS) report 2024 (https://sios-svalbard.org/SESS_Issue7)”
DOI: 10.6084/m9.figshare.c.3623684_d1
title: Additional file 3: of The effectiveness bundling of zinc with Oral Rehydration Salts (ORS) for improving adherence to acute watery diarrhea treatment in Ethiopia: cluster randomised controlled trial

description: The code book for the dataset supporting the conclusions of the article. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3623699_d1
title: Additional file 4: of The role of socio-demographic factors in premature cervical cancer mortality in Colombia

description: Results of the final model using imputed data including the interaction between age and type of health insurance (.xls format). Description of the file: This file contains the estimates of the final model using imputed data that assessed the association between with type of health insurance and CC mortality adjusting by rural or urban residence, region of residence, and age. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3623684_d3
title: Additional file 2: of The effectiveness bundling of zinc with Oral Rehydration Salts (ORS) for improving adherence to acute watery diarrhea treatment in Ethiopia: cluster randomised controlled trial

description: The dataset supporting the conclusions of the article. (XLS 481 kb)
DOI: 10.6084/m9.figshare.c.3623699_d2
title: Additional file 2: of The role of socio-demographic factors in premature cervical cancer mortality in Colombia

description: Results of the final model using complete data including the interaction between age and type of health insurance (.xls format). Description of the file: This file contains the estimates of the final model using complete data that assessed the association between with type of health insurance and CC mortality adjusting by rural or urban residence, region of residence, and age. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3623702_d2
title: Additional file 4: Table S3. of Time-course microarray analysis for identifying candidate genes involved in obesity-associated pathological changes in the mouse colon

description: Genes affected by high-fat diet at different time points in the colon tissue of C57BL/6N mice. Log2 fold change of ≥1 or ≤−1 corresponds to a fold change of ≥2 or ≤−2, respectively, based on a comparison between high-fat diet- and normal diet-fed mice at each time point (P
DOI: 10.6084/m9.figshare.c.3623699_d3
title: Additional file 1: of The role of socio-demographic factors in premature cervical cancer mortality in Colombia

description: Results of the final model using complete data including the interaction between age and educational level (.xls format). Description of the file: This file contains the estimates of the final model using complete data that assessed the association between educational level and CC mortality adjusting by rural or urban residence, region of residence, and age. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3623699_d4
title: Additional file 3: of The role of socio-demographic factors in premature cervical cancer mortality in Colombia

description: Results of the final model using imputed data including the interaction between age and educational level (.xls format). Description of the file: This file contains the estimates of the final model using imputed data that assessed the association between with educational level and CC mortality adjusting by rural or urban residence, region of residence, and age. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3623708_d1
title: Additional file 3: Figure S1. of RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior

description: Comparison of relative mRNA expression from biological replicate r1 and r2 using quantitative RT-PCR (qRT-PCR) and RNA-Seq of various genes show that both methods yield similar results in most cases. Note that all graphs have different scaling and show relative expression levels for qRT-PCR and RPKM values for RNA-Seq data. A. Comparison of quantitative RT-PCR and RNAseq data of DEGs involved in iron metabolism. The two biological replicates are shown in RPKM values (RNAseq) and relative expression levels (qRT-PCR). The middle column shows the obtained corrected RPKM values from both replicates. B. Comparison of quantitative RT-PCR and RNAseq data of DEGs from the Hexadehydroastechrome (HAS) cluster. Columns as mentioned in A. C. Comparison of quantitative RT-PCR and RNAseq data of some DEGs discussed on different paragraphs in the text. Columns as mentioned in A. All mRNA levels were measured by qRT-PCR with primers specific for the corresponding gene (Additional file 5: Table S4), and normalization with akuA primers were carried out. The delta CT method including efficiencies was used for quantification. (ZIP 940Â kb)
DOI: 10.6084/m9.figshare.c.3623702_d4
title: Additional file 5: Table S4. of Time-course microarray analysis for identifying candidate genes involved in obesity-associated pathological changes in the mouse colon

description: Biological processes associated with high-fat diet-responsive genes at different time points in the colon tissue of C57BL/6N mice.
DOI: 10.34740/kaggle/dsv/10192841
title: IPCC Scenarios
DOI: 10.6084/m9.figshare.c.3623984_d2
title: Additional file 5: Table S4. of Stress granules and RNA processing bodies are novel autoantibody targets in systemic sclerosis

description: Processing body and stress granule proteins identified in this analysis. *Proteins with multiple subunits. Data indicate non-redundant peptide hits. (ODS 20 kb)
DOI: 10.6084/m9.figshare.c.3623984_d3
title: Additional file 2: Table S2. of Stress granules and RNA processing bodies are novel autoantibody targets in systemic sclerosis

description: Gene lists used in these analyses. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3623984_d4
title: Additional file 1: Table S1. of Stress granules and RNA processing bodies are novel autoantibody targets in systemic sclerosis

description: Complete list of peptides identified in this analysis. TP number of total peptides mapping to a protein, UP number of unique peptides mapping to a protein, UM number of non-redundant peptides mapping exclusively to a protein, MW molecular weight, Length protein length in amino acids. (XLS 639 kb)
DOI: 10.6084/m9.figshare.c.3623984_d5
title: Additional file 3: Table S3. of Stress granules and RNA processing bodies are novel autoantibody targets in systemic sclerosis

description: Systemic sclerosis (SSc)-specific enrichment of processes and components. Proteins differentially detected in SSc were analyzed using gProfiler. Statistically significant processes and components are shown. A) Peptides detected at any level across all four groups. B) Peptides identified in all SSc groups, but absent in controls. C) Analysis of 137 proteins differentially detected in SSc. BP biological process, CC cellular component, MF molecular function, ke KEGG pathway, re REACTOME pathway. (ODS 70 kb)
DOI: 10.6084/m9.figshare.c.3624002_d1
title: Additional file 2: Table S1. of The genome-wide role of HSF-1 in the regulation of gene expression in Caenorhabditis elegans

description: Significantly altered transcripts from each experimental condition compared to the hsf-1(+);-HS control. (XLSX 600Â kb)
DOI: 10.6084/m9.figshare.c.3624017_d6
title: Additional file 8: of Modeling hormonal and inflammatory contributions to preterm and term labor using uterine temporal transcriptomics

description: Canonical pathways enrichment calculated by Ingenuity Pathway Analysis. A total of 46 pathways were detected as significantly enriched with genes differentially expressed in the pairwise comparisons indicated in the first row of the table (Pâ
DOI: 10.6084/m9.figshare.c.3624002_d7
title: AdditionalÂ file 7: Table S6.

description: Aging-related genes regulated by HSF-1 in a HS-independent manner. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3624122_d15
title: Additional file 3: of Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets

description: Annotation and amino acid sequences for predicted effectors based on RNA-seq and bioinformatics analyses. Also includes a list of previously identified putative effectors and corresponding sequences identified in this study (sheet 2). (XLSX 351 kb)
DOI: 10.6084/m9.figshare.c.3624182_d4
title: Additional file 3: of Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

description: Summary of the Anchored Phylogenomics assembly results. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3624194_d1
title: MOESM1 of Screening for potential endocrine disruptors in fish: evidence from structural alerts and in vitro and in vivo toxicological assays

description: Additional file 1. Estrogenic and androgenic endocrine activities in vitro.
DOI: 10.6084/m9.figshare.c.3624212_d3
title: Additional file 3: of Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

description: Complete list of gene products with an alternative function to that previously described by Brown et al. (XLSX 101 kb)
DOI: 10.6084/m9.figshare.c.3624239_d6
title: Additional file 7: of Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins

description: Metagenomic datasets used for evaluation of performance. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3624239_d7
title: Additional file 10: of Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins

description: Instructions for running the stand-alone version of HyPe on the Linux PC. (TXT 845 bytes)
DOI: 10.6084/m9.figshare.c.3624680_d1
title: Additional file 1: of Availability and affordability of essential medicines for children in the Western part of Ethiopia: implication for access

description: Medicine Price Data Collection Form. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3624728_d3
title: Additional file 8: of Differential responses of the gut transcriptome to plant protein diets in farmed Atlantic salmon

description: List of common and unique Gene Ontology (GO) terms for biological processes that were significantly altered ( P -value
DOI: 10.6084/m9.figshare.c.3624743_d1
title: Additional file 1: of Knowledge and use of unauthorized HIV self-test kits among men who have sex with men in Spain, following approval of an over-the-counter self-test in the U.S: a cross-sectional study

description: Contains the data used in the analysis. (XLSX 9721 kb)
DOI: 10.6084/m9.figshare.c.3624932_d6
title: Additional file 4 of A semi-automated, KNIME-based workflow for biofilm assays

description: Plate-reading method for Tecanâ  s Magellan software. See section Robotised biofilm quantification for details. (MTH 15.6 kb)
DOI: 10.6084/m9.figshare.c.3624965_d2
title: Additional file 2: of Leveraging genetically simple traits to identify small-effect variants for complex phenotypes

description: ChiSqTests. This spreadsheet contains chi-squared tests to determine if there is greater overlap than expected by chance between QTL for milk production traits and QTL for milk composition traits. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3625004_d2
title: MOESM1 of Temporally and spatially dynamic germ cell niches in Botryllus schlosseri revealed by expression of a TGF-beta family ligand and vasa

description: Additional file 1: Data S1. Species origins and GenBank or NCBI Reference IDs for protein sequences used in phylogenetic analyses. Column A contains the label given to the sequence in the phylogenetic trees. Column B contains the GenBank or NCBI Reference ID for the sequence used in the phylogenetic analysis. Column C contains the name of the species from which the protein sequence is derived.
DOI: 10.6084/m9.figshare.c.3624998_d3
title: Additional file 8: Table S8. of Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

description: Distribution of EPIC probes across the regulatory regions of individual cell types defined using ENCODE DNAse hypersensitivity data. (XLS 46 kb)
DOI: 10.6084/m9.figshare.c.3625196_d4
title: MOESM8 of Age-associated hydroxymethylation in human bone-marrow mesenchymal stem cells

description: Additional file 8: Table S8. Gene ontology analyisis of both hyper5hmC and hypo5mC CpG sites during aging. RR: relative risk is a measure of effect size describing the change of proportions between our selected set of genes and a given term; Q value is the result from the adjustment of P values in order to control the false discovery rate (FDR) using the Benjamini-Hochberg method.
DOI: 10.25345/c52f7k352
title: MassIVE MSV000096662 - GNPS - Daphnia dentifera - Metschnikowia bicuspidata host-pathogen system
title: The unexplained variation in susceptibility in several Daphnia species to multiple pathogens indicates that much remains to be learned about the Daphnia immune system. The goal of this experiment is to identify potentially important metabolites that contribute to the susceptibility or resistance of the host Daphnia dentifera to the fungal pathogen Metschnikowia bicuspidata. Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA). Data acquired in positive mode.
DOI: 10.5281/zenodo.14455862
title: 1KGP Trios ImmunoTyper2 output
DOI: 10.5281/zenodo.14455863
title: 1KGP Trios ImmunoTyper2 output
DOI: 10.6084/m9.figshare.c.3625196_d5
title: MOESM1 of Age-associated hydroxymethylation in human bone-marrow mesenchymal stem cells

description: Additional file 1: Table S1. Information on the human mesenchymal stem cells included in the study.
DOI: 10.6084/m9.figshare.c.3625196_d6
title: MOESM2 of Age-associated hydroxymethylation in human bone-marrow mesenchymal stem cells

description: Additional file 2: Table S2. Primers used for pyrosequencing validations.
DOI: 10.6084/m9.figshare.c.3625196_d7
title: MOESM4 of Age-associated hydroxymethylation in human bone-marrow mesenchymal stem cells

description: Additional file 4: Table S4. List of CpG sites hyperhydroxymethylated in MSCs during aging.
DOI: 10.6084/m9.figshare.c.3625196_d8
title: MOESM5 of Age-associated hydroxymethylation in human bone-marrow mesenchymal stem cells

description: Additional file 5: Table S5. List of CpG sites hypohydroxymethylated in MSCs during aging.
DOI: 10.6084/m9.figshare.c.3625265_d5
title: Additional file 4: of Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes

description: TABLE (.XLS) including the data and IDs of the 17,437 human protein-coding genes included in each of the eight evolutionary stages. (XLSX 1432 kb)
DOI: 10.6084/m9.figshare.c.3625487_d2
title: MOESM1 of Engineering Aspergillus niger for galactaric acid production: elimination of galactaric acid catabolism by using RNA sequencing and CRISPR/Cas9

description: Additional file 1: Table S1. RNA sequencing data of A. niger wild type strain pre-cultivated on YP-medium (0 hour) and cultivated to galactaric acid medium (5 and 18 hours). Transcript levels are presented as fragments per kilobase of exon per million fragments mapped (FPKM).
DOI: 10.6084/m9.figshare.c.3625499_d1
title: Additional file 1: of A common monitoring framework for ending preventable maternal mortality, 2015â  2030: phase I of a multi-step process

description: Summary of feedback from stakeholders on proposed EPMM Phase 1 indicators. (XLSX 69Â kb)
DOI: 10.6084/m9.figshare.c.3625517_d1
title: Additional file 2: Table S3. of Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea

description: Annotations for candidate genes within QTLs. (XLSX 44Â kb)
DOI: 10.6084/m9.figshare.c.3625508_d3
title: MOESM4 of What evidence exists on the local impacts of energy systems on marine ecosystem services: a systematic map

description: Additional file 4. Reference included in systematic map database.
DOI: 10.6084/m9.figshare.c.3625577_d1
title: Additional file 3 of iRDA: a new filter towards predictive, stable, and enriched candidate genes

description: Table S3. Parsimonious gene sets of AUC performance. The file provides all the gene sets of four filters over eleven datasets based on AUC measurement from Tables 4 and 7. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3625724_d1
title: Additional file 2: of Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice

description: Functional enrichment analysis using the DAVID bioinformatics resources. The whole mouse genome was used as background with default parameter settings. Full results, including p-values after correcting for multiple hypotheses testing, are shown. Statistically significant enriched categories amongst overexpressed genes related to the two broad categories of ‘ribosomes/rRNA binding and translation’ and ‘mitochondria/electron transport chain’. Amongst the down-regulated genes no statistically significant categories were found. (XLSX 166 kb)
DOI: 10.6084/m9.figshare.c.3625700_d5
title: Additional file 5: File S3. of Gender differences in murine pulmonary responses elicited by cellulose nanocrystals

description: The list of key transcriptional factors which regulated the expression of the upregulated differentially expressed genes in males and females upon exposure to CNC. The prediction of transcription factors was performed using ChEA (ChIP Enrichment Analysis) software tool. A P value cutoff of ≤ 0.05 was considered significant in each case. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3625724_d2
title: Additional file 1: of Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice

description: RNAseq list of gene expression changes in hypothalamus samples from Gnasxl m+/p- mice versus WT littermates. Genes are listed by their log2(fold change) from most up-regulated to most down-regulated. (XLSX 5507 kb)