cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/8fbffd791b09ddb746066ce5899fb477
title: Continuous precipitation and stream chemistry data, Hubbard Brook Ecosystem Study, 1963 – present.

description: The Hubbard Brook Ecosystem Study officially began on 1 June 1963. This archive contains HBWatER, the results of &gt;50 years of collection and analysis of weekly stream water and precipitation samples obtained from 1 June 1963 to the most recently approved water year. Stream chemistry is reported for nine gauged watersheds and the mainstem of Hubbard Brook. Precipitation chemistry is reported for rain collectors on both the north facing and south facing slopes of the Hubbard Brook valley. All solute data are reported as concentrations in (mg/l). HBWatER originated with the idea of applying the small watershed approach to study element flux and cycling through intact ecosystems. These chemical data have been used in conjunction with continuous streamflow and precipitation records to estimate watershed biogeochemical inputs and outputs. Such records have been instrumental in: identifying the existence and the impact of acid rain and then documenting its decline and legacy impacts on forested watersheds; documenting the effects of deforestation and natural forest disturbance on ecosystem nutrient exports; and in constructing element budgets for ecosystems over succession. Hundreds of published papers have taken advantage of HBWatER to understand how elements cycle through ecosystems. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
DOI: 10.5281/zenodo.4095913
title: Plasticity of GABA Inhibition in the Early Visual Cortex of Human Adults: Exp1 dataset

description: Dataset from Exp1 in "Proulx, Sébastien, Sheynin, Yasha, Hess, Robert, & Farivar, Reza. (2020). Plasticity of GABA Inhibition in the Early Visual Cortex of Human Adults (in preparation). Metadata included in the 'data' variable of the exp1Data.mat file.
DOI: 10.5281/zenodo.4095912
title: Plasticity of GABA Inhibition in the Early Visual Cortex of Human Adults: Exp1 dataset

description: Dataset from Exp1 in "Proulx, Sébastien, Sheynin, Yasha, Hess, Robert, & Farivar, Reza. (2020). Plasticity of GABA Inhibition in the Early Visual Cortex of Human Adults (in preparation). Metadata included in the 'data' variable of the exp1Data.mat file.
DOI: 10.5281/zenodo.4140080
title: Transcriptome analysis of WT versus H2A.J-KO MEFs for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences

description: Abstract for overall study: The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence. Specific description for this dataset: We further tested a role for H2A.J in Interferon-Stimulated Gene expression by analyzing the transcriptome of WT and H2A.J MEFs induced into senescence by etoposide. TruSeq stranded DNA libraries were prepared from polyA-selected RNA and sequenced as 43 bp paired-end reads. The fastq sequences were mapped to Gencode.vM24.transcripts.fa.gz (GRCm38 transcriptome) with salmon. Read counts were then aggregated to the gene level with tximeta, and differential gene expression was analysed with DESeq2, edgeR, and limma-voom. Gene set enrichment analysis was performed with camera. The transciptomes of senescent WT and H2AFJ-KO showed strong separation from proliferating MEFs, and a weaker separation distinguished WT and H2A.J-KO MEFs. Strikingly, gene set enrichment analysis indicated highly significant defects in Interferon Response Gene Expression in the H2A.J-KO MEFs in senescence with significant down-regulation in senescent H2A.J-KO cells of a series of oligoadenylate synthase genes (Oas1g, Oas1a, Oasl1, Oas2, Oasl2) and several ISGs. Thus, H2A.J also contributes to ISG expression in the heterologous context of senescent MEFs.
description: BioRxiv preprint: doi: https://doi.org/10.1101/2020.10.29.361204
description: {"references": ["BioRxiv preprint: doi: https://doi.org/10.1101/2020.10.29.361204"]}
DOI: 10.5281/zenodo.4140079
title: Transcriptome analysis of WT versus H2A.J-KO MEFs for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences

description: Abstract for overall study: The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence. Specific description for this dataset: We further tested a role for H2A.J in Interferon-Stimulated Gene expression by analyzing the transcriptome of WT and H2A.J MEFs induced into senescence by etoposide. TruSeq stranded DNA libraries were prepared from polyA-selected RNA and sequenced as 43 bp paired-end reads. The fastq sequences were mapped to Gencode.vM24.transcripts.fa.gz (GRCm38 transcriptome) with salmon. Read counts were then aggregated to the gene level with tximeta, and differential gene expression was analysed with DESeq2, edgeR, and limma-voom. Gene set enrichment analysis was performed with camera. The transciptomes of senescent WT and H2AFJ-KO showed strong separation from proliferating MEFs, and a weaker separation distinguished WT and H2A.J-KO MEFs. Strikingly, gene set enrichment analysis indicated highly significant defects in Interferon Response Gene Expression in the H2A.J-KO MEFs in senescence with significant down-regulation in senescent H2A.J-KO cells of a series of oligoadenylate synthase genes (Oas1g, Oas1a, Oasl1, Oas2, Oasl2) and several ISGs. Thus, H2A.J also contributes to ISG expression in the heterologous context of senescent MEFs.
description: BioRxiv preprint: doi: https://doi.org/10.1101/2020.10.29.361204
description: {"references": ["BioRxiv preprint: doi: https://doi.org/10.1101/2020.10.29.361204"]}
DOI: 10.17632/3phhnsd3t7.1
title: Data for: Spatial Variation in Socio-ecological Vulnerability to Covid-19 in the Contiguous United States

description: The data are primarily from U.S. government sources ( U.S. Census, NOAA, CDC, U.S. DOT, Homeland Security and U.S. BLS), with additional data on air quality and smoking prevalence taken from academic sources. Data were processed so that they all used a 6 digit identifier composed of the state FIPS followed by an underscore, followed by the county FIPS (e.g. "49_013"). These were then linked to a shapefile which used the same county identification system.
DOI: 10.25345/c5x49p
title: MassIVE MSV000086388 - p38g/d hyper-activation alters Ca2+ handling and triggers cardiac hypertrophy and arrhythmias
title: To explore the role of the MKK3/6-p38g/d stress signaling pathway in the control of cardiac hypertrophy and predisposition to stress-induced ventricular arrhythmia. An intensive swim exercise protocol and ex-vivo cardiac b-adrenergic stimulation coupled with electrophysiology assays showed that hypertrophic MKK6-mutant hearts were susceptible to stress-induced malignant arrythmias and sudden death. Co-immunoprecipitation and unbiased heart phosphoproteomics uncovered a central role for p38g/d in regulating a multi-kinase protein module that tunes ryanodine receptor 2 (RyR2)-mediated intracellular calcium handling. Thus, hyperactive p38g/d signaling results in RyR2 hyperphosphorylation leading to ectopic activity and stress-induced arrhythmias in live mice.
DOI: 10.6084/m9.figshare.13168847.v1
title: R0312_20191203a_videos

description: Rat 0312, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.5286/isis.e.rb2010798-2
title: Investigation of Multiple Magnetic Structures of CeRh3Si2 Using Neutron Diffraction Study

description: The orthorhombic CeRh3Si2 has been reported to exhibits multiple magnetic phase transitions. The zero-field heat capacity shows an antiferromagnetic order of the cerium magnetic moments at TN = 4.70 K and spin rearrangement at TSR = 4.48 K. In an applied field between 0.3 and 0.6 T the heat capacity reveals three magnetic phase transitions below 4.8 K. Magnetization isotherms at 1.72 K exhibit multiple metamagnetic transitions for applied fields below 1.5 T in all three crystallographic directions. Furthermore, the single crystal susceptibility exhibits strong anisotropy that has been explained by a giant crystal field splitting. We therefore propose neutron diffraction experiments on CeRh3Si2 (polycrystalline and single crystals) using WISH to investigate its magnetic structures in zero-field and in applied magnetic fields H//b-axis.
DOI: 10.5286/isis.e.rb2010062-2
title: Magnetic structure of non-centrosymmetric metal AgCrSe2

description: The aim of the proposed experiment is to establish the magnetic structure of non-centrosymmetric metallic antiferromagnet AgCrSe2 using both polycrystalline and single crystal samples. For the experiment on single crystal, we propose to use the WISH to collect a large number of reflections to properly refine the wavelength dependent extinction. The large number of reflections measured in the present experiment will allow for a comprehensive symmetry assisted refinement of the magnetic structure, including refinement of possible magnetic domain population.
DOI: 10.6084/m9.figshare.8255726
title: Shanshan Wang-The Wealth State Awareness Effect on Attention Allocation in People from Impoverished and Affluent Groups-2018-2019-Eyelink.zip

description: The data was collected from the study about the childhood poverty effects on the individuals' cognitive skills，this is partial data
DOI: 10.6084/m9.figshare.8255726.v2
title: Shanshan Wang-The Wealth State Awareness Effect on Attention Allocation in People from Impoverished and Affluent Groups-2018-2019-Eyelink.zip

description: The data was collected from the study about the childhood poverty effects on the individuals' cognitive skills，this is partial data
DOI: 10.6084/m9.figshare.8255726.v1
title: Shanshan Wang-Eyemovement data-Childhood poverty impact on cognitive skills-figshare-2018-2019-Eyelink.zip

description: The data was collected from the study about the childhood poverty effects on the individuals' cognitive skills，this is partial data
DOI: 10.5281/zenodo.3932127
title: Preprocessed and Harmonised Transcriptomics Datasets for Psoriasis and Atopic Dermatitis

description: The datasets uploaded within this record contain transcriptomics data of psoriasis and atopic dermatitis patients retrieved from the NCBI Gene Expression Omnibus and EBI ArrayExpress repositories. Overall, we retrieved 39 transcriptomics datasets, produced through both DNA microarrays and RNA-Sequencing technologies, along with relative meta-data tables. After data collection, each dataset was quality checked and preprocessed in order to obtain a harmonised source of data, ready-to-use for the research community. Beside, a thorough quality check was carried out on the retrieved meta-data, and data dictionaries were created (both for DNA microarry and RNA-Seq datasets) in order to homogenise the phenotypic data, enabling the comparability across the datasets.
description: {"references": ["Federico, A., Hautanen, V., Christian, N. et al. Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients. Sci Data 7, 343 (2020). https://doi.org/10.1038/s41597-020-00696-8"]}
DOI: 10.5517/ccdc.csd.cc20kgmp
title: CCDC 1863832: Experimental Crystal Structure Determination

description: Related Article: Mark R. J. Elsegood, Andrew J. Lake, Martin B. Smith, George W. Weaver|2019|Phosphorus,Sulfur,Silicon,Relat.Elem.|194|540|doi:10.1080/10426507.2018.1542397
DOI: 10.5517/ccdc.csd.cc20kgqs
title: CCDC 1863835: Experimental Crystal Structure Determination

description: Related Article: Mark R. J. Elsegood, Andrew J. Lake, Martin B. Smith, George W. Weaver|2019|Phosphorus,Sulfur,Silicon,Relat.Elem.|194|540|doi:10.1080/10426507.2018.1542397
DOI: 10.5517/ccdc.csd.cc21gws6
title: CCDC 1891148: Experimental Crystal Structure Determination

description: Related Article: Grace B. Panetti, Elena J. Varela, Michael R. Gau, Eric J. Schelter, Patrick J. Walsh|2019|Phosphorus,Sulfur,Silicon,Relat.Elem.|194|624|doi:10.1080/10426507.2019.1602773
DOI: 10.5517/ccdc.csd.cc21gwt7
title: CCDC 1891149: Experimental Crystal Structure Determination

description: Related Article: Grace B. Panetti, Elena J. Varela, Michael R. Gau, Eric J. Schelter, Patrick J. Walsh|2019|Phosphorus,Sulfur,Silicon,Relat.Elem.|194|624|doi:10.1080/10426507.2019.1602773
DOI: 10.5281/zenodo.4161269
title: Data set and 3d model from Emendi M, Sturla F, Ghosh RP, Bianchi M, Piatti F, Pluchinotta FR, Giese D, Lombardi M, Redaelli A, Bluestein D. Patient-Specific Bicuspid Aortic Valve Biomechanics: A Magnetic Resonance Imaging Integrated Fluid-Structure Interaction Approach. Ann Biomed Eng. 2020 Aug 17. doi: 10.1007/s10439-020-02571-4. Epub ahead of print. PMID: 32804291.

description: Data set and 3d model from Emendi M, Sturla F, Ghosh RP, Bianchi M, Piatti F, Pluchinotta FR, Giese D, Lombardi M, Redaelli A, Bluestein D. Patient-Specific Bicuspid Aortic Valve Biomechanics: A Magnetic Resonance Imaging Integrated Fluid-Structure Interaction Approach. Ann Biomed Eng. 2020 Aug 17. doi: 10.1007/s10439-020-02571-4. Epub ahead of print. PMID: 32804291. This is the abstract: Congenital bicuspid aortic valve (BAV) consists of two fused cusps and represents a major risk factor for calcific valvular stenosis. Herein, a fully coupled fluid-structure interaction (FSI) BAV model was developed from patient-specific magnetic resonance imaging (MRI) and compared against in vivo 4-dimensional flow MRI (4D Flow). FSI simulation compared well with 4D Flow, confirming direction and magnitude of the flow jet impinging onto the aortic wall as well as location and extension of secondary flows and vortices developing at systole: the systolic flow jet originating from an elliptical 1.6 cm<sup>2</sup> orifice reached a peak velocity of 252.2 cm/s, 0.6% lower than 4D Flow, progressively impinging on the ascending aorta convexity. The FSI model predicted a peak flow rate of 22.4 L/min, 6.7% higher than 4D Flow, and provided BAV leaflets mechanical and flow-induced shear stresses, not directly attainable from MRI. At systole, the ventricular side of the non-fused leaflet revealed the highest wall shear stress (WSS) average magnitude, up to 14.6 Pa along the free margin, with WSS progressively decreasing towards the belly. During diastole, the aortic side of the fused leaflet exhibited the highest diastolic maximum principal stress, up to 322 kPa within the attachment region. Systematic comparison with ground-truth non-invasive MRI can improve the computational model ability to reproduce native BAV hemodynamics and biomechanical response more realistically, and shed light on their role in BAV patients' risk for developing complications; this approach may further contribute to the validation of advanced FSI simulations designed to assess BAV biomechanics.
DOI: 10.5281/zenodo.4161268
title: Data set and 3d model from Emendi M, Sturla F, Ghosh RP, Bianchi M, Piatti F, Pluchinotta FR, Giese D, Lombardi M, Redaelli A, Bluestein D. Patient-Specific Bicuspid Aortic Valve Biomechanics: A Magnetic Resonance Imaging Integrated Fluid-Structure Interaction Approach. Ann Biomed Eng. 2020 Aug 17. doi: 10.1007/s10439-020-02571-4. Epub ahead of print. PMID: 32804291.

description: Data set and 3d model from Emendi M, Sturla F, Ghosh RP, Bianchi M, Piatti F, Pluchinotta FR, Giese D, Lombardi M, Redaelli A, Bluestein D. Patient-Specific Bicuspid Aortic Valve Biomechanics: A Magnetic Resonance Imaging Integrated Fluid-Structure Interaction Approach. Ann Biomed Eng. 2020 Aug 17. doi: 10.1007/s10439-020-02571-4. Epub ahead of print. PMID: 32804291. This is the abstract: Congenital bicuspid aortic valve (BAV) consists of two fused cusps and represents a major risk factor for calcific valvular stenosis. Herein, a fully coupled fluid-structure interaction (FSI) BAV model was developed from patient-specific magnetic resonance imaging (MRI) and compared against in vivo 4-dimensional flow MRI (4D Flow). FSI simulation compared well with 4D Flow, confirming direction and magnitude of the flow jet impinging onto the aortic wall as well as location and extension of secondary flows and vortices developing at systole: the systolic flow jet originating from an elliptical 1.6 cm<sup>2</sup> orifice reached a peak velocity of 252.2 cm/s, 0.6% lower than 4D Flow, progressively impinging on the ascending aorta convexity. The FSI model predicted a peak flow rate of 22.4 L/min, 6.7% higher than 4D Flow, and provided BAV leaflets mechanical and flow-induced shear stresses, not directly attainable from MRI. At systole, the ventricular side of the non-fused leaflet revealed the highest wall shear stress (WSS) average magnitude, up to 14.6 Pa along the free margin, with WSS progressively decreasing towards the belly. During diastole, the aortic side of the fused leaflet exhibited the highest diastolic maximum principal stress, up to 322 kPa within the attachment region. Systematic comparison with ground-truth non-invasive MRI can improve the computational model ability to reproduce native BAV hemodynamics and biomechanical response more realistically, and shed light on their role in BAV patients' risk for developing complications; this approach may further contribute to the validation of advanced FSI simulations designed to assess BAV biomechanics.
DOI: 10.6084/m9.figshare.13169090
title: R0312_20191204a_videos

description: Rat 0312, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13169396
title: Supplementary Data 2: Birds of Mt. Hilong-hilong

description: This data contains all the models from the simple Generalised Linear Model for binary extinction risk for birds of Mt. Hilong-hilong
DOI: 10.6084/m9.figshare.13169396.v1
title: Supplementary Data 2: Birds of Mt. Hilong-hilong

description: This data contains all the models from the simple Generalised Linear Model for binary extinction risk for birds of Mt. Hilong-hilong
DOI: 10.6084/m9.figshare.13169408
title: FFNI

description: Data for FFNI study
DOI: 10.6084/m9.figshare.13169408.v1
title: FFNI

description: Data for FFNI study
DOI: 10.6084/m9.figshare.13168916
title: Supplementary Data 1: Birds of Mt. Hilong-hilong

description: This dataset contains the list of birds recorded from Mt. Hilong-Hilong Key Biodiversity Area in the Philippines.
DOI: 10.6084/m9.figshare.13168916.v1
title: Supplementary Data 1: Birds of Mt. Hilong-hilong

description: This dataset contains the list of birds recorded from Mt. Hilong-Hilong Key Biodiversity Area in the Philippines.
DOI: 10.6084/m9.figshare.13169402
title: ICPW_data_raw.numbers

description: This data set is the collection of a community sample of parents of infants under one year of age for purposes of studying their well-being in relationship to their perception of their infant's crying.
DOI: 10.6084/m9.figshare.13169402.v1
title: ICPW_data_raw.numbers

description: This data set is the collection of a community sample of parents of infants under one year of age for purposes of studying their well-being in relationship to their perception of their infant's crying.
DOI: 10.5281/zenodo.4161418
title: SPAD-FCS data of freely diffusing Alexa 488 AB

description: Confocal laser-scanning microscopy based fluorescence fluctuation spectroscopy (FFS) data set of freely diffusing Alexa 488 linked to an antibody. Excitation at 485 nm, 100x/1.4 Leica objective, detection with a 5x5 pixel SPAD array detector. The file "05_Alexa488AB_20ugmL_P60percP_SPAD.7z" contains a binary data file with the raw data of a 200 s FFS measurement. For each time bin of 500 ns, the fluorescence photon counts in each of the 25 pixels are stored. The text file "05_Alexa488AB_20ugmL_P60percP_SPAD_info.txt" contains the metadata. The file "05_Alexa488AB_20ugmL_P60percP_SPAD_xcorrs.7z" contains all 625 cross-correlations between I_1(t) and I_2(t), with I_1 and I_2 the intensity traces of any of the 25 pixels.
DOI: 10.5281/zenodo.4161417
title: SPAD-FCS data of freely diffusing Alexa 488 AB

description: Confocal laser-scanning microscopy based fluorescence fluctuation spectroscopy (FFS) data set of freely diffusing Alexa 488 linked to an antibody. Excitation at 485 nm, 100x/1.4 Leica objective, detection with a 5x5 pixel SPAD array detector. The file "05_Alexa488AB_20ugmL_P60percP_SPAD.7z" contains a binary data file with the raw data of a 200 s FFS measurement. For each time bin of 500 ns, the fluorescence photon counts in each of the 25 pixels are stored. The text file "05_Alexa488AB_20ugmL_P60percP_SPAD_info.txt" contains the metadata. The file "05_Alexa488AB_20ugmL_P60percP_SPAD_xcorrs.7z" contains all 625 cross-correlations between I_1(t) and I_2(t), with I_1 and I_2 the intensity traces of any of the 25 pixels.
DOI: 10.6084/m9.figshare.12951650
title: Collapsed transcripts using cogent

description: Pooled mRNA of ten rice cultivars from the subspecies aus, indica and japonica were sequenced on the PacBio Sequel I platform and collapsed with the tool cogent.
DOI: 10.6084/m9.figshare.12951650.v1
title: Collapsed transcripts using cogent

description: Pooled mRNA of ten rice cultivars from the subspecies aus, indica and japonica were sequenced on the PacBio Sequel I platform and collapsed with the tool cogent.
DOI: 10.6084/m9.figshare.12951788
title: Collapsed transcripts using cDNA cupcake

description: Pooled mRNA of ten rice cultivars from the subspecies aus, indica and japonica were sequenced on the PacBio Sequel I platform and collapsed with the cDNA cupcake (ToFu) pipeline.
DOI: 10.6084/m9.figshare.12951824
title: Functional annotation of genes from ten rice cultivars using Mercator and Trinnotate

description: Filtered and collapsed transcripts sequenced on the PacBio Sequel I platform were functional characterized using the software Mercator and Trinotate. Results from both tools were merged and displayed per cultivar.
DOI: 10.6084/m9.figshare.12951824.v1
title: Functional annotation of genes from ten rice cultivars using Mercator and Trinnotate

description: Filtered and collapsed transcripts sequenced on the PacBio Sequel I platform were functional characterized using the software Mercator and Trinotate. Results from both tools were merged and displayed per cultivar.