cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8252465.v1
title: Additional file 3: of Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development

description: Metabolic model functionalities. (XLSX 66 kb)
DOI: 10.6084/m9.figshare.8252471.v1
title: Additional file 5: of Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development

description: Metabolites, reactions and enzymes present in OvoFol Recon 1. (XLSX 307 kb)
DOI: 10.6084/m9.figshare.8252459.v1
title: Additional file 2: of Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development

description: Metabolites, reactions and enzymes present in Mice Recon 2. (XLSX 452 kb)
DOI: 10.6084/m9.figshare.8252462
title: Additional file 10: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations

description: Table S5. Details of the 771 samples from TCGA used for DNA methylation analysis. (XLSX 85 kb)
DOI: 10.6084/m9.figshare.8252462.v1
title: Additional file 10: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations

description: Table S5. Details of the 771 samples from TCGA used for DNA methylation analysis. (XLSX 85 kb)
DOI: 10.6084/m9.figshare.8252447
title: Additional file 4: of The genome profiling method can be applied for species identification of biological materials collected at crime scenes

description: PaSS values (average of SP-1-3). (CSV 25 kb)
DOI: 10.6084/m9.figshare.8252447.v1
title: Additional file 4: of The genome profiling method can be applied for species identification of biological materials collected at crime scenes

description: PaSS values (average of SP-1-3). (CSV 25 kb)
DOI: 10.6084/m9.figshare.8252441
title: Additional file 3: of The genome profiling method can be applied for species identification of biological materials collected at crime scenes

description: PaSS values (SP-3). (CSV 18 kb)
DOI: 10.6084/m9.figshare.8252432
title: Additional file 2: of The genome profiling method can be applied for species identification of biological materials collected at crime scenes

description: PaSS values (SP-2). (CSV 16 kb)
DOI: 10.6084/m9.figshare.8252441.v1
title: Additional file 3: of The genome profiling method can be applied for species identification of biological materials collected at crime scenes

description: PaSS values (SP-3). (CSV 18 kb)
DOI: 10.6084/m9.figshare.8252429
title: Additional file 1: of The genome profiling method can be applied for species identification of biological materials collected at crime scenes

description: PaSS values (SP-1). (CSV 18 kb)
DOI: 10.6084/m9.figshare.8252432.v1
title: Additional file 2: of The genome profiling method can be applied for species identification of biological materials collected at crime scenes

description: PaSS values (SP-2). (CSV 16 kb)
DOI: 10.6084/m9.figshare.8252429.v1
title: Additional file 1: of The genome profiling method can be applied for species identification of biological materials collected at crime scenes

description: PaSS values (SP-1). (CSV 18 kb)
DOI: 10.6084/m9.figshare.8252396
title: Additional file 1: of Smoking-associated AHRR demethylation in cord blood DNA: impact of CD235a+ nucleated red blood cells

description: Supplemental Tables S1-S6. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.8252396.v1
title: Additional file 1: of Smoking-associated AHRR demethylation in cord blood DNA: impact of CD235a+ nucleated red blood cells

description: Supplemental Tables S1-S6. (XLSX 59 kb)
DOI: 10.25345/c5b17m
title: MassIVE MSV000086023 - 08-17-2020-only-run-benz-for-plate-81-82-52-53
title: we only run samples treated with benznidazole for plate 81 82 52 53.
DOI: 10.6084/m9.figshare.8252252
title: Additional file 4: of Plasma microRNA miR-26b as a potential diagnostic biomarker of degenerative myelopathy in Pembroke welsh corgis

description: Table S4. Demographic, raw Ct value and relative plasma level of candidate miRNAs. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8252252.v1
title: Additional file 4: of Plasma microRNA miR-26b as a potential diagnostic biomarker of degenerative myelopathy in Pembroke welsh corgis

description: Table S4. Demographic, raw Ct value and relative plasma level of candidate miRNAs. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8252243
title: Additional file 3: of Plasma microRNA miR-26b as a potential diagnostic biomarker of degenerative myelopathy in Pembroke welsh corgis

description: Table S3. The putative mRNA targets of dysregulated miRNAs by using the TargetScan database. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.8252243.v1
title: Additional file 3: of Plasma microRNA miR-26b as a potential diagnostic biomarker of degenerative myelopathy in Pembroke welsh corgis

description: Table S3. The putative mRNA targets of dysregulated miRNAs by using the TargetScan database. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.8252234
title: Additional file 2: of Plasma microRNA miR-26b as a potential diagnostic biomarker of degenerative myelopathy in Pembroke welsh corgis

description: Table S2. Relative plasma level of miRNA using RT-qPCR array in DM-affected PWCs. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.8252234.v1
title: Additional file 2: of Plasma microRNA miR-26b as a potential diagnostic biomarker of degenerative myelopathy in Pembroke welsh corgis

description: Table S2. Relative plasma level of miRNA using RT-qPCR array in DM-affected PWCs. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.8252228
title: Additional file 1: of Plasma microRNA miR-26b as a potential diagnostic biomarker of degenerative myelopathy in Pembroke welsh corgis

description: Table S1. Raw Ct value of PCR array. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.8252228.v1
title: Additional file 1: of Plasma microRNA miR-26b as a potential diagnostic biomarker of degenerative myelopathy in Pembroke welsh corgis

description: Table S1. Raw Ct value of PCR array. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.8252201
title: Additional file 4: of Microbiomes of stony and soft deep-sea corals share rare core bacteria

description: Filtered ASV table. List of ASVs organized by sample and coral host, after the removal of unclassified sequences. Includes ASV abundance per sample, reference sequence for each ASV, and the taxonomy. (XLSX 1270â kb)
DOI: 10.6084/m9.figshare.8252195
title: Additional file 3: of Microbiomes of stony and soft deep-sea corals share rare core bacteria

description: Non-rarefied OTU table. List of OTUs organized by sample and coral host. Includes OTU abundance per sample, reference sequence for each OTU, and the taxonomy. (XLSX 985â kb)
DOI: 10.6084/m9.figshare.8252201.v1
title: Additional file 4: of Microbiomes of stony and soft deep-sea corals share rare core bacteria

description: Filtered ASV table. List of ASVs organized by sample and coral host, after the removal of unclassified sequences. Includes ASV abundance per sample, reference sequence for each ASV, and the taxonomy. (XLSX 1270â kb)
DOI: 10.6084/m9.figshare.8252186
title: Additional file 2: of Microbiomes of stony and soft deep-sea corals share rare core bacteria

description: Workflow with commented scripts and parameters. System information, scripts, and comments for each step in the QIIME analysis to produce OTUs and the DADA2 analysis to produce ASVs. (TXT 52â kb)
DOI: 10.6084/m9.figshare.8252186.v1
title: Additional file 2: of Microbiomes of stony and soft deep-sea corals share rare core bacteria

description: Workflow with commented scripts and parameters. System information, scripts, and comments for each step in the QIIME analysis to produce OTUs and the DADA2 analysis to produce ASVs. (TXT 52â kb)
DOI: 10.6084/m9.figshare.8252099
title: Additional file 4: of West Nile virus infection and interferon alpha treatment alter the spectrum and the levels of coding and noncoding host RNAs secreted in extracellular vesicles

description: Table S1. EV miRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to WNV infection comparing to mock EVs. Table S2. EV miRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to IFN-alpha treatment comparing to mock EVs. Table S3. EV sncRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to WNV infection comparing to mock EVs. Table S4. EV sncRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to IFN-alpha treatment comparing to mock EVs. Table S5. EV mRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to WNV infection comparing to mock EVs. Table S6. EV mRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to IFN-alpha treatment comparing to mock EVs. Table S7. GO terms associated with mRNAs exhibiting decreased levels in EVs secreted by WNV infected A549 cells. Table S8. GO terms associated with mRNAs exhibiting decreased levels in EVs secreted by IFN-alpha treated A549 cell. Table S9. PCR primers used in the study. (XLSX 349 kb)
DOI: 10.6084/m9.figshare.8252099.v1
title: Additional file 4: of West Nile virus infection and interferon alpha treatment alter the spectrum and the levels of coding and noncoding host RNAs secreted in extracellular vesicles

description: Table S1. EV miRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to WNV infection comparing to mock EVs. Table S2. EV miRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to IFN-alpha treatment comparing to mock EVs. Table S3. EV sncRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to WNV infection comparing to mock EVs. Table S4. EV sncRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to IFN-alpha treatment comparing to mock EVs. Table S5. EV mRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to WNV infection comparing to mock EVs. Table S6. EV mRNAs significantly (FDR&lt;0.05, logFC&gt;1) altered in response to IFN-alpha treatment comparing to mock EVs. Table S7. GO terms associated with mRNAs exhibiting decreased levels in EVs secreted by WNV infected A549 cells. Table S8. GO terms associated with mRNAs exhibiting decreased levels in EVs secreted by IFN-alpha treated A549 cell. Table S9. PCR primers used in the study. (XLSX 349 kb)
DOI: 10.6084/m9.figshare.8252054
title: Additional file 2: of On trends and patterns in macroevolution: Williston’s law and the branchiostegal series of extant and extinct osteichthyans

description: Data and scripts used in the subsampling analyses. This consists of 4 files (a,b,c,d). Data files include the branchiostegal count and stratigraphic information collected for extant and extinct species (bst_analysis.csv, tabular data), and the time-scaled trees (trees.tre, Newick format) used in the analyses. The 2 R script files also included were used for running the jackniffing analyses that subsample extinct (fossil_subsampling_1.R) or extant species (extant_subsampling_1.R). The “species” column in the CSV file contains the species in the tree to which the data were mapped. The “old_label” column contains the names of the taxa as they appeared in our original sources. An anonymous referee kindly noted that our data had an erroneous value of 1 branchiostegal ray for Lepidosiren paradoxa, which does not have any branchiostegals in reality. We did not rerun our analyses because they are very time-consuming, and this small correction is unlikely to have any significant effect. However, we amended the CVS file that we provide here, so that the error does not propagate to any possible future uses of the data by other researchers. (ZIP 162 kb)
DOI: 10.6084/m9.figshare.8252054.v1
title: Additional file 2: of On trends and patterns in macroevolution: Williston’s law and the branchiostegal series of extant and extinct osteichthyans

description: Data and scripts used in the subsampling analyses. This consists of 4 files (a,b,c,d). Data files include the branchiostegal count and stratigraphic information collected for extant and extinct species (bst_analysis.csv, tabular data), and the time-scaled trees (trees.tre, Newick format) used in the analyses. The 2 R script files also included were used for running the jackniffing analyses that subsample extinct (fossil_subsampling_1.R) or extant species (extant_subsampling_1.R). The “species” column in the CSV file contains the species in the tree to which the data were mapped. The “old_label” column contains the names of the taxa as they appeared in our original sources. An anonymous referee kindly noted that our data had an erroneous value of 1 branchiostegal ray for Lepidosiren paradoxa, which does not have any branchiostegals in reality. We did not rerun our analyses because they are very time-consuming, and this small correction is unlikely to have any significant effect. However, we amended the CVS file that we provide here, so that the error does not propagate to any possible future uses of the data by other researchers. (ZIP 162 kb)
DOI: 10.6084/m9.figshare.8252009
title: Additional file 1: of Polygenic prediction of breast cancer: comparison of genetic predictors and implications for risk stratification

description: Table S1. Cohort characteristics of UK Biobank and Estonian Biobank. Table S2. Associations of breast cancer and standardized GRSs in the UK Biobank (with and without adjustment of family history) and in Estonian Biobank without family history. Table S3. Associations between GRSs and risk factors of breast cancer in Estonian Biobank. Table S4. Associations between GRSs and risk factors of breast cancer in UK Biobank. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.8252009.v1
title: Additional file 1: of Polygenic prediction of breast cancer: comparison of genetic predictors and implications for risk stratification

description: Table S1. Cohort characteristics of UK Biobank and Estonian Biobank. Table S2. Associations of breast cancer and standardized GRSs in the UK Biobank (with and without adjustment of family history) and in Estonian Biobank without family history. Table S3. Associations between GRSs and risk factors of breast cancer in Estonian Biobank. Table S4. Associations between GRSs and risk factors of breast cancer in UK Biobank. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.8251751
title: Supplement to manuscript

description: Supporting data to manuscript: Maternal transfer of persistent organic pollutants to sea turtle eggs: addressing knowledge and data gaps toward an improved synthesis of research outputs<br>Note: Bibliographic detalis of references cited in the tables can be found in the reference list of the original paper.<br> Table A1: Data extraction and conversions for the individual studies included in the systematic search. Table A2: Overview of mean (± standard error, SE) concentrations of OCPs reported in the current study that were extracted and converted from the literature (when available) into ng/g wet mass in either yolk or whole eggs. Details include sampling year (Samp. Date), species (<i>Chelonia mydas</i>, Cm; <i>Caretta caretta</i>, Cc; <i>Dermochelys coriacea</i>, Dc and <i>Eretmochelys imbricata</i> Ei), locations (F.W.I.: French West Indies, Yuc: Yucatan State, Q. Roo: Quintana Roo State), tissue sampled (whole egg: yolk + albumen) and number of eggs sampled (when unclear, a the estimated minimum number of eggs was taken, as this value was used to convert standard deviations into SE). Fig A3: Trends in mean concentrations of ƩPCB and individual PCB congeners (± standard error in red dotted line) extracted and converted from the literature (when available) into ng/g wet mass in either yolk (triangles) or whole eggs (circles) for <i>Caretta caretta </i>(black), <i>Chelonia mydas </i>(green), <i>Demorchelys coriacea</i> (blue) and <i>Eretmochelys imbricata</i> (red). Table A4: Overview of mean (± standard error, SE) concentrations of ƩPCB and individual PCB congeners (when available), extracted and converted from the literature into ng/g wet mass in either yolk or whole eggs. sampling year (Samp. Date), species (<i>Chelonia mydas</i>, Cm; <i>Caretta caretta</i>, Cc; <i>Dermochelys coriacea</i>, Dc and <i>Eretmochelys imbricata</i> Ei), locations (FWI: French West Indies, Yuc: Yucatan State, Q. Roo: Quintana Roo State) and tissue sampled (whole egg: yolk + albumen). Concentrations for coeluted compounds are repeated for each of the individual congeners that coeluted. No measure of sample variance (e.g. standard deviation or standard error) were available for the studies of Guirlet et al. 2010 and De Andres et al. 2016.
DOI: 10.6084/m9.figshare.8251865
title: Effects of protected area establishment and cash crop price dynamics on land use transitions 1990–2017 in north-eastern Madagascar

description: We applied a participatory mapping approach supported by very high-resolution satellite imagery to reconstruct spatially explicit, year-to-year land use transitions in two highly biodiverse, data-scarce forest frontier landscapes in north-eastern Madagascar. We explored these transitions in the light of major continuous trends and discrete events highlighted by local farmers as influencing their land use decisions. Our results suggest that the process of establishing protected areas first reinforced ongoing deforestation, but later led to a significant reduction of forest loss rates. Recent cash crop booms appear to have induced agricultural intensification processes in our study landscapes, while also putting additional pressure on forests, as people may be encouraged to clear forest for cash crop cultivation. These findings are crucial to understanding rapid land use change processes in forest frontier contexts in the humid tropics, and especially to informing natural resource governance and development initiatives in complex mosaic landscapes.
DOI: 10.6084/m9.figshare.8251751.v1
title: Supplement to manuscript

description: Supporting data to manuscript: Maternal transfer of persistent organic pollutants to sea turtle eggs: addressing knowledge and data gaps toward an improved synthesis of research outputs<br>Note: Bibliographic detalis of references cited in the tables can be found in the reference list of the original paper.<br> Table A1: Data extraction and conversions for the individual studies included in the systematic search. Table A2: Overview of mean (± standard error, SE) concentrations of OCPs reported in the current study that were extracted and converted from the literature (when available) into ng/g wet mass in either yolk or whole eggs. Details include sampling year (Samp. Date), species (<i>Chelonia mydas</i>, Cm; <i>Caretta caretta</i>, Cc; <i>Dermochelys coriacea</i>, Dc and <i>Eretmochelys imbricata</i> Ei), locations (F.W.I.: French West Indies, Yuc: Yucatan State, Q. Roo: Quintana Roo State), tissue sampled (whole egg: yolk + albumen) and number of eggs sampled (when unclear, a the estimated minimum number of eggs was taken, as this value was used to convert standard deviations into SE). Fig A3: Trends in mean concentrations of ƩPCB and individual PCB congeners (± standard error in red dotted line) extracted and converted from the literature (when available) into ng/g wet mass in either yolk (triangles) or whole eggs (circles) for <i>Caretta caretta </i>(black), <i>Chelonia mydas </i>(green), <i>Demorchelys coriacea</i> (blue) and <i>Eretmochelys imbricata</i> (red). Table A4: Overview of mean (± standard error, SE) concentrations of ƩPCB and individual PCB congeners (when available), extracted and converted from the literature into ng/g wet mass in either yolk or whole eggs. sampling year (Samp. Date), species (<i>Chelonia mydas</i>, Cm; <i>Caretta caretta</i>, Cc; <i>Dermochelys coriacea</i>, Dc and <i>Eretmochelys imbricata</i> Ei), locations (FWI: French West Indies, Yuc: Yucatan State, Q. Roo: Quintana Roo State) and tissue sampled (whole egg: yolk + albumen). Concentrations for coeluted compounds are repeated for each of the individual congeners that coeluted. No measure of sample variance (e.g. standard deviation or standard error) were available for the studies of Guirlet et al. 2010 and De Andres et al. 2016.
DOI: 10.6084/m9.figshare.8251865.v1
title: Effects of protected area establishment and cash crop price dynamics on land use transitions 1990–2017 in north-eastern Madagascar

description: We applied a participatory mapping approach supported by very high-resolution satellite imagery to reconstruct spatially explicit, year-to-year land use transitions in two highly biodiverse, data-scarce forest frontier landscapes in north-eastern Madagascar. We explored these transitions in the light of major continuous trends and discrete events highlighted by local farmers as influencing their land use decisions. Our results suggest that the process of establishing protected areas first reinforced ongoing deforestation, but later led to a significant reduction of forest loss rates. Recent cash crop booms appear to have induced agricultural intensification processes in our study landscapes, while also putting additional pressure on forests, as people may be encouraged to clear forest for cash crop cultivation. These findings are crucial to understanding rapid land use change processes in forest frontier contexts in the humid tropics, and especially to informing natural resource governance and development initiatives in complex mosaic landscapes.
DOI: 10.6084/m9.figshare.8251637
title: Game theory based multi-task scheduling in cloud manufacturing using an extended biogeography-based optimization algorithm

description: This is the experimental data of the manuscript entitled "Game theory based multi-task scheduling in cloud manufacturing using an extended biogeography-based optimization algorithm". All data are generated through computer simulation and saved in the file with csv format. The data are the simulation of the real-world case. There are forty-seven instances for these experiments, which cover multiple scales. Three attributes including time, cost, and reliability of servies for achieving corresponding subtasks are shown in datasets.
DOI: 10.6084/m9.figshare.8251637.v1
title: Game theory based multi-task scheduling in cloud manufacturing using an extended biogeography-based optimization algorithm

description: This is the experimental data of the manuscript entitled "Game theory based multi-task scheduling in cloud manufacturing using an extended biogeography-based optimization algorithm". All data are generated through computer simulation and saved in the file with csv format. The data are the simulation of the real-world case. There are forty-seven instances for these experiments, which cover multiple scales. Three attributes including time, cost, and reliability of servies for achieving corresponding subtasks are shown in datasets.
DOI: 10.6084/m9.figshare.8251613
title: Coding strategies in the otolith system differ for translational head motion vs. static orientation relative to gravity

description: Figure source data for manuscript titled "Coding strategies in the otolith system differ for translational head motion vs. static orientation relative to gravity" for review in eLife.
DOI: 10.6084/m9.figshare.8251583
title: Replication Package 170 FSE2019

description: Thank you for coming to our replication package page! In the zip folder, we include documents, scripts, and data to replicate our study.
DOI: 10.17608/k6.auckland.8251574
title: BIOMD0000000498_url.omex

description: COMBINE archive containing a working SBML model with semantic annotation in a separate RDF file.
DOI: 10.25345/c56b5q
title: MassIVE MSV000086024 - Baylor-NHP-serum-samples-08-03-2020
title: baylor NHP serum samples experiment date is 08 03 2020.
DOI: 10.6084/m9.figshare.8251541
title: Alignments of 18S rDNA sequences used in Wetherbee et al. 2019

description: Three sequence alignments are provided:<br>Alignment 1 contains only long sequences (&gt;600 nt) downloaded from Genbank. <br>Alignment 2 contains sequences from the Ocean Sampling Day (OSD)<br>Alignment 3 contains sequences form the Tara Oceans expedition.<br>
DOI: 10.17608/k6.auckland.8251574.v2
title: BIOMD0000000498_url.omex

description: COMBINE archive containing a working SBML model with semantic annotation in a separate RDF file.