cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5827071
title: Additional file 7: Tables S5 and S6. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

description: Differences in methylation in the spermatozoa between the Untrained, Trained and Detrained state. S5 Table shows results for the FDR 10% cut-off and S6 Table shows results for the FDR 5% cut-off. Regions differentially methylated between, Untrained and Trained as well as Untrained and Detrained. median.p: median P-value in DMR; median.meth.untrained/trained/detrained: median methylation of CpGs in DMR; median.meth.diff: median methylation difference between conditions; annotation: location relative to nearest gene. (ZIP 198Â kb)
DOI: 10.6084/m9.figshare.5827071.v1
title: Additional file 7: Tables S5 and S6. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

description: Differences in methylation in the spermatozoa between the Untrained, Trained and Detrained state. S5 Table shows results for the FDR 10% cut-off and S6 Table shows results for the FDR 5% cut-off. Regions differentially methylated between, Untrained and Trained as well as Untrained and Detrained. median.p: median P-value in DMR; median.meth.untrained/trained/detrained: median methylation of CpGs in DMR; median.meth.diff: median methylation difference between conditions; annotation: location relative to nearest gene. (ZIP 198Â kb)
DOI: 10.6084/m9.figshare.5827065
title: Additional file 3: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with the top nine networks from frameshift and non-frameshift INDELs from the layer and broiler lines combined. QIAGEN’s Ingenuity® Pathway Analysis (IPA®) software ( http://www.ingenuity.com/ ) with default parameters were used to find metabolic pathways of genes with relevant biological functions. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.5827065.v1
title: Additional file 3: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with the top nine networks from frameshift and non-frameshift INDELs from the layer and broiler lines combined. QIAGEN’s Ingenuity® Pathway Analysis (IPA®) software ( http://www.ingenuity.com/ ) with default parameters were used to find metabolic pathways of genes with relevant biological functions. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.5827062
title: Additional file 1: Table S1. of Exploring traditional aus-type rice for metabolites conferring drought tolerance

description: Experimental information and data on metabolite peaks. (XLSX 1006Â kb)
DOI: 10.6084/m9.figshare.5827062.v1
title: Additional file 1: Table S1. of Exploring traditional aus-type rice for metabolites conferring drought tolerance

description: Experimental information and data on metabolite peaks. (XLSX 1006Â kb)
DOI: 10.6084/m9.figshare.5827050
title: Additional file 6: Tables S1 â S4. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

description: Differences in sRNA expression profiles in the spermatozoa between the Untrained, Trained and Detrained state. miRNAs, piRNAs, Repetitive Elements, tRNAs and mRNA fragments differentially expressed between Untrained and Trained, Trained and Detrained, Untrained and Detrained. logFC: Log2 Fold Change; logCPM: Log2 counts per million; LR: Likelihood ratio; feature: sRNA name; FDR: False Discovery Rate. (ZIP 1010Â kb)
DOI: 10.6084/m9.figshare.5827050.v1
title: Additional file 6: Tables S1 â S4. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

description: Differences in sRNA expression profiles in the spermatozoa between the Untrained, Trained and Detrained state. miRNAs, piRNAs, Repetitive Elements, tRNAs and mRNA fragments differentially expressed between Untrained and Trained, Trained and Detrained, Untrained and Detrained. logFC: Log2 Fold Change; logCPM: Log2 counts per million; LR: Likelihood ratio; feature: sRNA name; FDR: False Discovery Rate. (ZIP 1010Â kb)
DOI: 10.6084/m9.figshare.5826978
title: Additional file 9: Table S8. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of differentially transcribed genes. (XLSX 418Â kb)
DOI: 10.6084/m9.figshare.5826978.v1
title: Additional file 9: Table S8. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of differentially transcribed genes. (XLSX 418Â kb)
DOI: 10.6084/m9.figshare.5826951
title: Additional file 7: Table S7. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of operons, sub-operons and monocistrons. (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.5826951.v1
title: Additional file 7: Table S7. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of operons, sub-operons and monocistrons. (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.5826933
title: Additional file 6: Table S6. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of intergenic TSS. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.5826933.v1
title: Additional file 6: Table S6. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of intergenic TSS. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.5826912
title: Additional file 12: Table S10. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

description: Detailled DNA methylation results at Differentially Methylated Regions. Sequencing counts are indicated at each CpG for every participants. (XLSX 149Â kb)
DOI: 10.6084/m9.figshare.5826912.v1
title: Additional file 12: Table S10. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

description: Detailled DNA methylation results at Differentially Methylated Regions. Sequencing counts are indicated at each CpG for every participants. (XLSX 149Â kb)
DOI: 10.6084/m9.figshare.5826909
title: Additional file 5: Table S5. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of corrected CDS start sites. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.5826909.v1
title: Additional file 5: Table S5. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of corrected CDS start sites. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.5826903
title: Additional file 4: Table S4. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of intragenic and antisense TSS. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.5826903.v1
title: Additional file 4: Table S4. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of intragenic and antisense TSS. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.5826894
title: Additional file 11: Table S9. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

description: Overview of sequencing results. Number of reads sequenced, number of reads aligned, mapping rate and number of unique aligned reads for the sRNA and RRBS experiment. (XLSX 52Â kb)
DOI: 10.6084/m9.figshare.5826894.v1
title: Additional file 11: Table S9. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

description: Overview of sequencing results. Number of reads sequenced, number of reads aligned, mapping rate and number of unique aligned reads for the sRNA and RRBS experiment. (XLSX 52Â kb)
DOI: 10.6084/m9.figshare.5826870
title: Additional file 3: Table S3. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of transcription start sites assigned to known CDS. (XLSX 70Â kb)
DOI: 10.6084/m9.figshare.5826870.v1
title: Additional file 3: Table S3. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: List of transcription start sites assigned to known CDS. (XLSX 70Â kb)
DOI: 10.6084/m9.figshare.5826855
title: Additional file 2: Table S2. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: Number of cDNA reads of the cDNA libraries. (XLSX 5Â kb)
DOI: 10.6084/m9.figshare.5826855.v1
title: Additional file 2: Table S2. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: Number of cDNA reads of the cDNA libraries. (XLSX 5Â kb)
DOI: 10.6084/m9.figshare.5826843
title: Additional file 1: Table S1. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: Oligonucleotide sequences. (XLSX 5Â kb)
DOI: 10.6084/m9.figshare.5826843.v1
title: Additional file 1: Table S1. of Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

description: Oligonucleotide sequences. (XLSX 5Â kb)
DOI: 10.6084/m9.figshare.5826807
title: MOESM1 of Optimizing anaerobic growth rate and fermentation kinetics in Saccharomyces cerevisiae strains expressing Calvin-cycle enzymes for improved ethanol yield

description: Additional file 1. Primers used in this study.
DOI: 10.6084/m9.figshare.5826807.v1
title: MOESM1 of Optimizing anaerobic growth rate and fermentation kinetics in Saccharomyces cerevisiae strains expressing Calvin-cycle enzymes for improved ethanol yield

description: Additional file 1. Primers used in this study.
DOI: 10.6084/m9.figshare.5826771
title: Additional file 2: of Data-driven identification of endophenotypes of Alzheimerâ s disease progression: implications for clinical trials and therapeutic interventions

description: List of a priori specified patient-level variables at baseline that were used to define the identified classes distinguishing characteristics (XLSX 40 kb)
DOI: 10.6084/m9.figshare.5826771.v1
title: Additional file 2: of Data-driven identification of endophenotypes of Alzheimerâ s disease progression: implications for clinical trials and therapeutic interventions

description: List of a priori specified patient-level variables at baseline that were used to define the identified classes distinguishing characteristics (XLSX 40 kb)
DOI: 10.6084/m9.figshare.5826750
title: Additional file 1: of Data-driven identification of endophenotypes of Alzheimerâ s disease progression: implications for clinical trials and therapeutic interventions

description: Full list of drug groups and search terms used to evaluate medication use at baseline (XLSX 42 kb)
DOI: 10.6084/m9.figshare.5826750.v1
title: Additional file 1: of Data-driven identification of endophenotypes of Alzheimerâ s disease progression: implications for clinical trials and therapeutic interventions

description: Full list of drug groups and search terms used to evaluate medication use at baseline (XLSX 42 kb)
DOI: 10.6084/m9.figshare.5826543
title: Additional file 1: Table S1. of mRNA export in the apicomplexan parasite Toxoplasma gondii: emerging divergent components of a crucial pathway

description: Proteins involved in nuclear export in the three apicomplexan genomes analyzed. Identification number for proteins involved in nuclear import and export for the apicomplexan genomes, Toxoplasma gondii, Plasmodium falciparum and Cryptosporidium spp. are shown. Gene names for the human homologs are shown, and their corresponding annotation numbers are shown as references. When applicable, the name of the yeast homolog is indicated. Complexes with conserved components are highlighted in color. Statistics (E-value and % identity) are provided for each protein when compared to the human homolog. Conserved proteins are highlighted in bold. (*) indicates that these proteins were previously identified in the respective genomes in another study [77]. The Toxoplasma gondii, Plasmodium falciparum and Cryptosporidium spp. genomes were searched with the following keywords: “nuclear transport receptor”, “nuclear RNA export proteins”, “RNA export”, “importin alpha/beta”, “RNA-binding protein”, “regulator of nonsense transcripts”, “transportin”, “RAs-related nuclear protein/GTP-binding nuclear protein RAN”, “regulator of chromosome condensation”, “major exportin”, “exportins” and “THO complex”. Collected hits were translated into protein sequences, and domains were analyzed using Pfam [91]. To identify human homologs, the collected T. gondii, P. falciparum and Cryptosporidium spp. hits were searched against the Homo sapiens database using the Blastp tool from BLAST, and sequences with the lowest E-value were selected. T. gondii, P. falciparum and Cryptosporidium spp. homologs found were double-checked by searching the T. gondii, P. falciparum and Cryptosporidium spp. genome databases using the human homologs identified in the previous step as queries. Domains identified by Pfam were double-checked using Conserved Domain from BLAST. Using the above strategy, we were able to identify proteins at the protein family level, but the approach was not very accurate for identifying specific homologs. Thus, to identify specific homologs across relevant taxa, we systematically searched mammal, arthropod and apicomplexan databases using the Blastp tool from BLAST. (XLS 52 kb)
DOI: 10.6084/m9.figshare.5826543.v1
title: Additional file 1: Table S1. of mRNA export in the apicomplexan parasite Toxoplasma gondii: emerging divergent components of a crucial pathway

description: Proteins involved in nuclear export in the three apicomplexan genomes analyzed. Identification number for proteins involved in nuclear import and export for the apicomplexan genomes, Toxoplasma gondii, Plasmodium falciparum and Cryptosporidium spp. are shown. Gene names for the human homologs are shown, and their corresponding annotation numbers are shown as references. When applicable, the name of the yeast homolog is indicated. Complexes with conserved components are highlighted in color. Statistics (E-value and % identity) are provided for each protein when compared to the human homolog. Conserved proteins are highlighted in bold. (*) indicates that these proteins were previously identified in the respective genomes in another study [77]. The Toxoplasma gondii, Plasmodium falciparum and Cryptosporidium spp. genomes were searched with the following keywords: “nuclear transport receptor”, “nuclear RNA export proteins”, “RNA export”, “importin alpha/beta”, “RNA-binding protein”, “regulator of nonsense transcripts”, “transportin”, “RAs-related nuclear protein/GTP-binding nuclear protein RAN”, “regulator of chromosome condensation”, “major exportin”, “exportins” and “THO complex”. Collected hits were translated into protein sequences, and domains were analyzed using Pfam [91]. To identify human homologs, the collected T. gondii, P. falciparum and Cryptosporidium spp. hits were searched against the Homo sapiens database using the Blastp tool from BLAST, and sequences with the lowest E-value were selected. T. gondii, P. falciparum and Cryptosporidium spp. homologs found were double-checked by searching the T. gondii, P. falciparum and Cryptosporidium spp. genome databases using the human homologs identified in the previous step as queries. Domains identified by Pfam were double-checked using Conserved Domain from BLAST. Using the above strategy, we were able to identify proteins at the protein family level, but the approach was not very accurate for identifying specific homologs. Thus, to identify specific homologs across relevant taxa, we systematically searched mammal, arthropod and apicomplexan databases using the Blastp tool from BLAST. (XLS 52 kb)
DOI: 10.6084/m9.figshare.5826534
title: Additional file 4: Figure S2. of Disease progression in idiopathic pulmonary fibrosis with mild physiological impairment: analysis from the Australian IPF registry

description: Locally Weighted Scatterplot Smoothing curves for FVC% predicted. a. Mild physiological impairment (FVC ≥ 80%). b. Moderate-severe physiological impairment (FVC
DOI: 10.6084/m9.figshare.5826534.v1
title: Additional file 4: Figure S2. of Disease progression in idiopathic pulmonary fibrosis with mild physiological impairment: analysis from the Australian IPF registry

description: Locally Weighted Scatterplot Smoothing curves for FVC% predicted. a. Mild physiological impairment (FVC ≥ 80%). b. Moderate-severe physiological impairment (FVC
DOI: 10.6084/m9.figshare.5826456
title: Additional file 2: Table S2. of A SNP panel for identification of DNA and RNA specimens

description: Characteristics of 50 selected SNPs. (CSV 15 kb)
DOI: 10.6084/m9.figshare.5826456.v1
title: Additional file 2: Table S2. of A SNP panel for identification of DNA and RNA specimens

description: Characteristics of 50 selected SNPs. (CSV 15 kb)
DOI: 10.6084/m9.figshare.5826294
title: Thermal conductivity dataset_Lu et al 2014.xlsx

description: Soil texture and the related information can be found in Lu et al. (2014) [SSSAJ, 78: 1859-1868]
DOI: 10.6084/m9.figshare.5826276
title: Stress and fat intake

description: Cross-sectional study conducted in a private university in Lima, Peru. Potential participants were those registered in the first three years of the School of Medicine during the first semester of 2015. <br><br><br>
DOI: 10.6084/m9.figshare.5826270
title: Johnson_NEW SPSS version MCAR Combined data.sav

description: SPSS dataset for study entitled "Perfectionism, selective attention and subclinical body dysmorphic disorder in a community sample"
DOI: 10.6084/m9.figshare.5826153
title: Zhu Agricultural Climate Indices

description: See publication for details (https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2017EF000687)<br>File updated on Nov 19, 2019 to fix formatting problems in the conversion to NetCDF. -TJT
DOI: 10.6084/m9.figshare.5825994
title: JARVIS-DFT-Optoelectronics

description: We perform high-throughput density functional theory (DFT) calculation of optoelectronic properties (electronic bandgap and frequency dependent dielectric function) using OptB88vDW (OPT) and Tran-Blaha modified Becke Johnson potential (MBJ) potential. This data is distributed publicly through JARVIS-DFT database. We used this data to evaluate the differences between these two formalisms and quantify their accuracy comparing to experimental data whenever applicable. At present, we have 17,805 OPT and 7,358 MBJ bandgaps and dielectric functions. MBJ is found to predict better bandgaps than OPT, so it can be used to improve the well-known bandgap problem of DFT in a relatively inexpensive way. The peak positions in dielectric function obtained with OPT and MBJ are in comparable agreement with experiments. The data is available at our website: http://www.ctcms.nist.gov/~knc6/JVASP.html .
DOI: 10.6084/m9.figshare.5825943
title: Search Strategies

description: Search estrategy
DOI: 10.6084/m9.figshare.5825943.v1
title: Search Strategies

description: Search estrategy
DOI: 10.6084/m9.figshare.5825940
title: JARVIS-FF(Elastic constants)

description: Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/∼knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery.
DOI: 10.6084/m9.figshare.5825937
title: DatasetS1.xlsx

description: Combined output of the CLfinder-OrthNet analysis for the six crucifer genomes, with RNAseq expression evidence information; Supplementary Dataset S1 of the reference article.<br>
DOI: 10.6084/m9.figshare.5825934
title: Plazas - Equivalence by Exclusion and Blank Comparison Stimulus

description: Fileset include individual data of participants from the study "Formation of Stimulus Equivalence Relations by Exclusion: Evidence from Comparison Stimulus Procedure." Each row corresponde to each trials in the experiment. Each row contains: Phase number; Block number; Trial number; Trial identification name; Trial correct relation; Response by the participant; response correcteness (1/0); latency.
DOI: 10.6084/m9.figshare.5825934.v1
title: Plazas - Equivalence by Exclusion and Blank Comparison Stimulus

description: Fileset include individual data of participants from the study "Formation of Stimulus Equivalence Relations by Exclusion: Evidence from Comparison Stimulus Procedure." Each row corresponde to each trials in the experiment. Each row contains: Phase number; Block number; Trial number; Trial identification name; Trial correct relation; Response by the participant; response correcteness (1/0); latency.