cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10010540
title: Appendix table 2a & 2b.xlsx

description: Appendix Table 2<br>
DOI: 10.6084/m9.figshare.10010537
title: Appendix table 1a & 1b.xlsx

description: Appendix Table 1a and 1b<br>
DOI: 10.6084/m9.figshare.10010555.v2
title: Characteristic remanent directions for Middle Triassic Yanshiping lavas..xlsx

description: Paleomagnetism, Volcanic, Tibet<br>
DOI: 10.6084/m9.figshare.10010555.v1
title: Characteristic remanent directions for Middle Triassic Yanshiping lavas..xlsx

description: <b>Characteristic remanent directions for Middle Triassic Yanshiping lavas.</b>
DOI: 10.6084/m9.figshare.10010492
title: Supplementary Data 7

description: This file contains the FANTOM5 cell groups used for normalisation and averaging of gene expression (as described in Methods: Gene expression data).<br>
DOI: 10.6084/m9.figshare.10010489
title: Supplementary Data 3

description: This file contains performance results for the simulated disease exomes described in the main publication.<br>
DOI: 10.6084/m9.figshare.10010480
title: Supplementary Data 2

description: This file contains variable importances, across all 1,879 HPO Phenotypic Abnormality terms, for the VARPP classifiers described in the main publication.<br>
DOI: 10.6084/m9.figshare.10010474
title: Supplementary Data 1

description: This file contains performance results (auPRC and PP100), across all 1,879 HPO Phenotypic Abnormality terrms, for the VARPP classifiers described in the main publication.<br>
DOI: 10.26180/5dae68bb85221
title: Sex-specific effects of mitochondrial haplotype on metabolic rate in Drosophila melanogaster support predictions of the Mother's Curse hypothesis

description: Electronic supplementary material and raw data for the journal article "sex-specific effects of mitochondrial haplotype on metabolic rate in <i>Drosophila melanogaster</i> support predictions of the Mother's Curse hypothesis" appearing in the special issue 'linking the mitochondrial genotype to phenotype: a complex endeavour' in Philosophical Transactions of the Royal Society B: Biological Sciences.
DOI: 10.6084/m9.figshare.10010327
title: readme.txt

description: Description of files
DOI: 10.6084/m9.figshare.10010327.v1
title: readme.txt

description: Description of files
DOI: 10.6084/m9.figshare.10010321
title: all.common.bim

description: .bim format for PLINK, variant information
DOI: 10.6084/m9.figshare.10010324
title: all.common.fam

description: .fam format for PLINK, individual information<br>
DOI: 10.6084/m9.figshare.10010321.v1
title: all.common.bim

description: .bim format for PLINK, variant information
DOI: 10.6084/m9.figshare.10010324.v1
title: all.common.fam

description: .fam format for PLINK, individual information<br>
DOI: 10.6084/m9.figshare.10010270
title: all.common.bed.gz

description: all variants and all individuals (P1, P2, P3) in PLINK .bed format (gzipped)
DOI: 10.6084/m9.figshare.10010168
title: Provenance trial experiments

description: Data from: "Climate change disrupts local adaptation and favors upslope migration" by Anderson and Wadgymar at Ecology Letters. This folder contains the raw data and the R script needed to analyze the provenance trial experiments. The R script includes code for each of the experimental cohorts. <br>
DOI: 10.6084/m9.figshare.10010141
title: Integral projection models from reciprocal transplant experiments

description: Data from: "Climate change disrupts local adaptation and favors upslope migration" by Anderson and Wadgymar at Ecology Letters. This folder contains the data on experimental rosettes and seeds from the reciprocal transplant experiment, along with the R scripts necessary to estimate lambdas and confidence intervals. The first R script is 01_Vital_rates.R. The bootstrapping of parameters and lambdas is computationally intensive. For the manuscript, I ran the 05_Boostrapping_lambdas.R script on the University of Georgia's computing cluster, and the process was very slow.<br>
DOI: 10.6084/m9.figshare.10010270.v1
title: all.common.bed.gz

description: all variants and all individuals (P1, P2, P3) in PLINK .bed format (gzipped)
DOI: 10.6084/m9.figshare.10010138
title: Integral projection models from natural populations

description: Data from: "Climate change disrupts local adaptation and favors upslope migrationClimate
DOI: 10.6084/m9.figshare.10009970
title: Price data for Mexican agricultural products: case study Queretaro state (Mx)

description: The daily prices of several fruits and vegetables were extracted, from January 2009 to February 2019, from the National System of Market Information.<br>The products' daily prices were extracted using Python's lxml library from the SNIIM's website (http://www.economia-sniim.gob.mx/). This website provides daily information about several fruits and vegetables from many wholesale food markets in Mexico: price, packaging, origin, and quality. <br>
DOI: 10.6084/m9.figshare.10009919
title: Database of geopostioned Middle East Respiratory Syndrome Coronavirus occurrences

description: A database of geopostioned Middle East Respiratory Syndrome Coronavirus occurrences with associated metadata.
DOI: 10.6084/m9.figshare.10009010
title: ApRES data from FRIS

description: ApRES data from the Filchner Ronne Ice Shelf as published in Vaňková et al. Please cite the following paper if using this data:<br><br>Vaňková I., K. W. Nicholls, H. F. J. Corr, K. Makinson, and P. V. Brennan. Observations of tidal melt and vertical strain at the Filchner-Ronne Ice Shelf. JGR-Earth Surface.
DOI: 10.6084/m9.figshare.10009919.v1
title: Database of geopostioned Middle East Respiratory Syndrome Coronavirus occurrences

description: A database of geopostioned Middle East Respiratory Syndrome Coronavirus occurrences with associated metadata.
DOI: 10.6084/m9.figshare.10008974
title: Dataset for "The Pricing of Open Access Journals: Diverse Niches and Sources of Value in Academic Publishing"

description: Enhanced DOAJ data from 12/2018. Walt Crawford Gold Open Access Journals dataset and Scopus data also appended. Additional variables on journal size added.
DOI: 10.6084/m9.figshare.10008929
title: Nagqu_ET_partitioning_data

description: Meteorological and isotope data used in the article entitled "Quantifying the controls on evapotranspiration partitioning in the highest alpine meadow secosystem", which is published in Water Resources Research.
DOI: 10.6084/m9.figshare.10009919.v2
title: Database of geopostioned Middle East Respiratory Syndrome Coronavirus occurrences

description: A database of geopostioned Middle East Respiratory Syndrome Coronavirus occurrences with associated metadata.
DOI: 10.6084/m9.figshare.10008929.v1
title: Nagqu_data

description: nagqu data
DOI: 10.6084/m9.figshare.10008905
title: Treatment with commonly used antiretroviral drugs induces a type I/III interferon signature in the gut in the absence of HIV infection: ddPCR data

description: The purpose of this data set was to measure how the expression of selected genes is affected by use of oral tenofovir disoproxil fumarate/emtricitabine for prevention of HIV infection. RNA were measured by reverse transcription followed by ddPCR from samples taken from several studies during treatment with daily oral tenofovir disoproxil fumarate (TDF) or TDF/emtricitabine as compared to off-treatment samples. <br>The Excel file contains cleaned and summarized data. The TAR file contains the raw data and can be used to produce the Excel file. The code necessary to go from raw to cleaned data is described in the link below.<br>The complete methods and results are described here: https://doi.org/10.1101/701961
DOI: 10.6084/m9.figshare.10008911
title: ET at Nagqu

description: meteorology
DOI: 10.6084/m9.figshare.10008896
title: A late Holocene shift in typhoon dynamics revealed by coastal sedimentary archives

description: Data Set S1(Grian size for YC01 and Zr/Rb for XCL-02<br>) for“A late Holocene shift in typhoon dynamics revealed by coastal sedimentary archives”
DOI: 10.6084/m9.figshare.10008896.v1
title: A late Holocene shift in typhoon dynamics revealed by coastal sedimentary archives

description: Data Set S1(Grian size for YC01 and Zr/Rb for XCL-02<br>) for“A late Holocene shift in typhoon dynamics revealed by coastal sedimentary archives”
DOI: 10.6084/m9.figshare.10008929.v2
title: Nagqu_ET_partition_data

description: Meteorological and isotope data used in the article entitled "Quantifying the controls on evapotranspiration partitioning in the highest alpine meadow secosystem", which is published in Water Resources Research.
DOI: 10.6084/m9.figshare.10008905.v2
title: Treatment with commonly used antiretroviral drugs induces a type I/III interferon signature in the gut in the absence of HIV infection: ddPCR data

description: The purpose of this data set was to measure how the expression of selected genes is affected by use of oral tenofovir disoproxil fumarate/emtricitabine for prevention of HIV infection. RNA were measured by reverse transcription followed by ddPCR from samples taken from several studies during treatment with daily oral tenofovir disoproxil fumarate (TDF) or TDF/emtricitabine as compared to off-treatment samples. <br>The Excel file contains cleaned and summarized data. The TAR file contains the raw data and can be used to produce the Excel file. The code necessary to go from raw to cleaned data is described in the link below.<br>The complete methods and results are described here: https://doi.org/10.1101/701961
DOI: 10.6084/m9.figshare.10008905.v1
title: ddPCR_all_studies

description: The purpose of this data set was to measure how the expression of selected genes is affected by use of oral tenofovir disoproxil fumarate/emtricitabine for prevention of HIV infection. RNA were measured by reverse transcription followed by ddPCR from samples taken from several studies during treatment with daily oral tenofovir disoproxil fumarate (TDF) or TDF/emtricitabine as compared to off-treatment samples. <br>The Excel file contains cleaned and summarized data. The TAR file contains the raw data and can be used to produce the Excel file. The code necessary to go from raw to cleaned data is described in the link below.<br>The complete methods and results are described here: https://www.biorxiv.org/content/10.1101/701961v1
DOI: 10.6084/m9.figshare.10008911.v2
title: ET at Nagqu

description: meteorology
DOI: 10.6084/m9.figshare.10008911.v1
title: Evapotranspiration partitioning data at Nagqu station, central Tibetan Plateau

description: Meteorological and isotopic data used to partition evapotranspiration at Nagqu station, central Tibetan Plateau.
DOI: 10.6084/m9.figshare.10008758
title: NSF Graduate Research Fellowship Proposal (2017)

description: NSF GRFP application submitted Fall of 2017. Unsuccessful.
DOI: 10.6084/m9.figshare.10008764
title: NSF Graduate Research Fellowship Proposal (2018)

description: NSF GRFP application submitted Fall of 2018. Unsuccessful.
DOI: 10.6084/m9.figshare.10008746
title: Dataset Behavior Electrical Stimulation: Evidence for an attentional priority map in inferotemporal cortex

description: This repository contains behavioral data recorded during electrical microstimulation experiments while subjects were performing an attention demanding motion discrimination task. The figure depicts the histogram of the reaction times. The mat-file contains metadata for each stimulation experiment (29) and results for each session.<br>For questions please contact: Heiko Stemmann (stemmann@uni-bremen.de) or Winrich A. Freiwald (wfreiwald@mail.rockefeller.edu)<br>
DOI: 10.6084/m9.figshare.10008758.v1
title: NSF Graduate Research Fellowship Proposal (2017)

description: NSF GRFP application submitted Fall of 2017. Unsuccessful.
DOI: 10.6084/m9.figshare.10008764.v1
title: NSF Graduate Research Fellowship Proposal (2018)

description: NSF GRFP application submitted Fall of 2018. Unsuccessful.
DOI: 10.6084/m9.figshare.10008731
title: Naples Dataset

description: PLINK files for 8 samples from South Italy (Naples). Technical information are included as a separate file.
DOI: 10.6084/m9.figshare.12866633
title: Supplementary Material for: Spectrums and Prognosis of Kidney Disease in Patients with Ankylosing Spondylitis

description: <b><i>Background/Aims:</i></b> Renal involvement was a common extra-articular manifestation of ankylosing spondylitis (AS). Few reports have investigated the pathological characteristics and renal outcomes of AS patients with kidney disease. The aim of this study was to investigate the pathological spectrums and the renal prognosis of AS patients with kidney disease. <b><i>Methods:</i></b> This retrospective and observational study was conducted working on 62 patients (47 males and 15 females) with a diagnosis of AS (ACR, 1984) and renal biopsies between 2008 and 2017. The histopathological findings and associated clinical manifestations were collected, and the renal prognoses of patients with kidney disease were evaluated too. Multivariate binary logistic regression analysis was performed to identify risk factors for the occurrence of IgA nephropathy (IgAN). <b><i>Results:</i></b> Renal biopsy revealed that IgAN accounted for a majority (74.2%) of the kidney disease with AS, while membranous nephropathies, minimal change disease, focal segmental glomerulosclerosis, and other lesions accounted for a small minority. Multivariate analysis revealed that serum immunoglobulin A &gt;3.45 g/L and immunoglobulin G &gt;9.06 g/L were risk factors for the occurrence of IgAN. With a median follow-up time of 24.3 months, 28 patients (50.9%) reached complete remission, 9 patients (16.4%) had partial remission, and 1 patient had an eGFR decline &gt;30%. No difference was found in prognosis between IgAN and non-IgAN. <b><i>Conclusion:</i></b> IgAN occurred in 76.4% of the kidney disease with AS, and higher serum immunoglobulin A and G increased the risk for the occurrence of IgAN. The renal prognosis of kidney disease in AS was good.
DOI: 10.6084/m9.figshare.12866633.v1
title: Supplementary Material for: Spectrums and Prognosis of Kidney Disease in Patients with Ankylosing Spondylitis

description: <b><i>Background/Aims:</i></b> Renal involvement was a common extra-articular manifestation of ankylosing spondylitis (AS). Few reports have investigated the pathological characteristics and renal outcomes of AS patients with kidney disease. The aim of this study was to investigate the pathological spectrums and the renal prognosis of AS patients with kidney disease. <b><i>Methods:</i></b> This retrospective and observational study was conducted working on 62 patients (47 males and 15 females) with a diagnosis of AS (ACR, 1984) and renal biopsies between 2008 and 2017. The histopathological findings and associated clinical manifestations were collected, and the renal prognoses of patients with kidney disease were evaluated too. Multivariate binary logistic regression analysis was performed to identify risk factors for the occurrence of IgA nephropathy (IgAN). <b><i>Results:</i></b> Renal biopsy revealed that IgAN accounted for a majority (74.2%) of the kidney disease with AS, while membranous nephropathies, minimal change disease, focal segmental glomerulosclerosis, and other lesions accounted for a small minority. Multivariate analysis revealed that serum immunoglobulin A &gt;3.45 g/L and immunoglobulin G &gt;9.06 g/L were risk factors for the occurrence of IgAN. With a median follow-up time of 24.3 months, 28 patients (50.9%) reached complete remission, 9 patients (16.4%) had partial remission, and 1 patient had an eGFR decline &gt;30%. No difference was found in prognosis between IgAN and non-IgAN. <b><i>Conclusion:</i></b> IgAN occurred in 76.4% of the kidney disease with AS, and higher serum immunoglobulin A and G increased the risk for the occurrence of IgAN. The renal prognosis of kidney disease in AS was good.
DOI: 10.6084/m9.figshare.10008746.v1
title: Dataset Behavior Electrical Stimulation: Evidence for an attentional priority map in inferotemporal cortex

description: This repository contains behavioral data recorded during electrical microstimulation experiments while subjects were performing an attention demanding motion discrimination task. The figure depicts the histogram of the reaction times. The mat-file contains metadata for each stimulation experiment (29) and results for each session.<br>For questions please contact: Heiko Stemmann (stemmann@uni-bremen.de) or Winrich A. Freiwald (wfreiwald@mail.rockefeller.edu)<br>
DOI: 10.6084/m9.figshare.10008722
title: Wetland data 2013-2015_Seasonal controls of CO2 and CH4 dynamics in a temporarily flooded subtropical wetland

description: Seasonal controls of CO<sub>2</sub> and CH<sub>4</sub> dynamics in a temporarily flooded subtropical wetland <br>Shared data: NEE, GPP, Reco, CH4 flux, water table depth, soil and air temperature, PAR, VPD and Air pressure.<br>
DOI: 10.6084/m9.figshare.10008722.v1
title: Wetland data 2013-2015_Seasonal controls of CO2 and CH4 dynamics in a temporarily flooded subtropical wetland

description: Seasonal controls of CO<sub>2</sub> and CH<sub>4</sub> dynamics in a temporarily flooded subtropical wetland <br>Shared data: NEE, GPP, Reco, CH4 flux, water table depth, soil and air temperature, PAR, VPD and Air pressure.<br>
DOI: 10.6084/m9.figshare.10008689
title: France Dataset

description: PLINK files (bed/bim/fam) for 256 samples from France. Technical information are included as a separate file.<br>
DOI: 10.6084/m9.figshare.10008566
title: Isoflavone-mediated radioprotection involves regulation of early endothelial cell death and inflammatory signaling in Radiation-Induced lung injury

description: <b>Purpose:</b> Vascular damage and inflammation are limiting toxic effects of lung cancer radiotherapy, which lead to pneumonitis and pulmonary fibrosis. We have demonstrated that soy isoflavones (SIF) mitigate these toxic effects at late time points after radiation. However, the process by which SIF impacts the onset of radiation-induced inflammation remains to be elucidated. We have now investigated early events of radiation-induced inflammation and identified cellular and molecular signaling patterns by endothelial cells that could be modified by SIF to control vascular damage and the initiation of lung inflammation. <b>Materials and methods:</b> Histopathological, cellular and molecular studies were performed on mouse lungs from C57Bl/6 mice treated with 10 Gy of thoracic radiation (XRT) in conjunction with daily oral SIF treatment given prior and after radiation. Parallel studies were performed in-vitro using EA.hy926 endothelial cell line with SIF and radiation. Immunohistochemistry, western blots analysis, and flow cytometry were performed on lung tissue or EA.hy926 cells to analyze endothelial cells, their patterns of cell death or survival, and signaling molecules involved in inflammatory events. <b>Results:</b> Histopathological differences in inflammatory infiltrates and vascular injury in lungs, including vascular endothelial cells, were observed with SIF treatment at early time points post-XRT. XRT-induced expression of proinflammatory adhesion molecule ICAM-1 cells was reduced by SIF in-vitro and in-vivo in endothelial cells. Molecular changes in endothelial cells with SIF treatment in conjunction with XRT included increased DNA damage, reduced cell viability and cyclin B1, and inhibition of nuclear translocation of NF-κB. Analysis of cell death showed that SIF treatment promoted apoptotic endothelial cell death and decreased XRT-induced type III cell death. In-vitro molecular studies indicated that SIF + XRT increased apoptotic caspase-9 activation and production of IFNβ while reducing the release of inflammatory HMGB-1 and IL-1α, the cleavage of pyroptotic gasdermin D, and the release of active IL-1β, which are all events associated with type III cell death. <b>Conclusions:</b> SIF + XRT caused changes in patterns of endothelial cell death and survival, proinflammatory molecule release, and adhesion molecule expression at early time points post-XRT associated with early reduction of immune cell recruitment. These findings suggest that SIF could mediate its radioprotective effects in irradiated lungs by limiting excessive immune cell homing via vascular endothelium into damaged lung tissue and curtailing the overall inflammatory response to radiation.
DOI: 10.6084/m9.figshare.10008566.v2
title: Isoflavone-mediated radioprotection involves regulation of early endothelial cell death and inflammatory signaling in Radiation-Induced lung injury

description: <b>Purpose:</b> Vascular damage and inflammation are limiting toxic effects of lung cancer radiotherapy, which lead to pneumonitis and pulmonary fibrosis. We have demonstrated that soy isoflavones (SIF) mitigate these toxic effects at late time points after radiation. However, the process by which SIF impacts the onset of radiation-induced inflammation remains to be elucidated. We have now investigated early events of radiation-induced inflammation and identified cellular and molecular signaling patterns by endothelial cells that could be modified by SIF to control vascular damage and the initiation of lung inflammation. <b>Materials and methods:</b> Histopathological, cellular and molecular studies were performed on mouse lungs from C57Bl/6 mice treated with 10 Gy of thoracic radiation (XRT) in conjunction with daily oral SIF treatment given prior and after radiation. Parallel studies were performed in-vitro using EA.hy926 endothelial cell line with SIF and radiation. Immunohistochemistry, western blots analysis, and flow cytometry were performed on lung tissue or EA.hy926 cells to analyze endothelial cells, their patterns of cell death or survival, and signaling molecules involved in inflammatory events. <b>Results:</b> Histopathological differences in inflammatory infiltrates and vascular injury in lungs, including vascular endothelial cells, were observed with SIF treatment at early time points post-XRT. XRT-induced expression of proinflammatory adhesion molecule ICAM-1 cells was reduced by SIF in-vitro and in-vivo in endothelial cells. Molecular changes in endothelial cells with SIF treatment in conjunction with XRT included increased DNA damage, reduced cell viability and cyclin B1, and inhibition of nuclear translocation of NF-κB. Analysis of cell death showed that SIF treatment promoted apoptotic endothelial cell death and decreased XRT-induced type III cell death. In-vitro molecular studies indicated that SIF + XRT increased apoptotic caspase-9 activation and production of IFNβ while reducing the release of inflammatory HMGB-1 and IL-1α, the cleavage of pyroptotic gasdermin D, and the release of active IL-1β, which are all events associated with type III cell death. <b>Conclusions:</b> SIF + XRT caused changes in patterns of endothelial cell death and survival, proinflammatory molecule release, and adhesion molecule expression at early time points post-XRT associated with early reduction of immune cell recruitment. These findings suggest that SIF could mediate its radioprotective effects in irradiated lungs by limiting excessive immune cell homing via vascular endothelium into damaged lung tissue and curtailing the overall inflammatory response to radiation.