cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4906727.v9
title: Spitschan_2017_NatureNeuro_fMRIMelanopsin

description: Complete raw dataset for the referenced paper
DOI: 10.6084/m9.figshare.4906376
title: Functional elucidation of hypothetical proteins for their indispensable roles toward drug designing targets from <i>Helicobacter pylori</i> strain HPAG1

description: <i>Helicobacter pylori</i> is a flagellated and slow growing gram-negative bacterium that persistently infects about half of the entire world population. In present study, we examined the proteome of <i>H. pylori</i> strain HPAG1 for identification of key uncharacterized proteins toward their novel regulatory functions. The complete proteome of this strain consists of 1539 proteins, out of which 520 proteins are annotated as hypothetical. Based on the functional motifs in their primary sequences, we were able to classify 254 of these hypothetical proteins into 6 functional categories. Further, KEGG database was used to find the roles of these hypothetical proteins in several pathways and structural prediction was done by homology modeling methods. Thirty-three of these hypothetical proteins were found to have strong association in various pathways including signaling and defense mechanisms. We noted that 27 of these proteins are specific to <i>H. pylori</i> and can be selected for drug designing targets, based on their virulence and regulatory role. We were able to successfully model the 3D structures of three of these proteins: YP_626977.1, YP_626786.1, and YP_628146.1. The stability of these proteins was also validated using molecular dynamics simulations, and their possible role in the regulation of different pathways was explained. These novel annotations may contribute to the understanding of disease mechanism at molecular level and provide novel potential targets for designing new drugs against <i>H. pylori</i> strain HPAG1.
DOI: 10.6084/m9.figshare.4906376.v1
title: Functional elucidation of hypothetical proteins for their indispensable roles toward drug designing targets from <i>Helicobacter pylori</i> strain HPAG1

description: <i>Helicobacter pylori</i> is a flagellated and slow growing gram-negative bacterium that persistently infects about half of the entire world population. In present study, we examined the proteome of <i>H. pylori</i> strain HPAG1 for identification of key uncharacterized proteins toward their novel regulatory functions. The complete proteome of this strain consists of 1539 proteins, out of which 520 proteins are annotated as hypothetical. Based on the functional motifs in their primary sequences, we were able to classify 254 of these hypothetical proteins into 6 functional categories. Further, KEGG database was used to find the roles of these hypothetical proteins in several pathways and structural prediction was done by homology modeling methods. Thirty-three of these hypothetical proteins were found to have strong association in various pathways including signaling and defense mechanisms. We noted that 27 of these proteins are specific to <i>H. pylori</i> and can be selected for drug designing targets, based on their virulence and regulatory role. We were able to successfully model the 3D structures of three of these proteins: YP_626977.1, YP_626786.1, and YP_628146.1. The stability of these proteins was also validated using molecular dynamics simulations, and their possible role in the regulation of different pathways was explained. These novel annotations may contribute to the understanding of disease mechanism at molecular level and provide novel potential targets for designing new drugs against <i>H. pylori</i> strain HPAG1.
DOI: 10.6084/m9.figshare.4906361
title: Table S5 from Common reef-building coral in the Northern Red Sea resistant to elevated temperature and acidification

description: Coral reefs are currently experiencing substantial ecological impoverishment as a result of anthropogenic stressors and the majority of reefs are facing immediate risk. Increasing ocean surface temperatures induce frequent coral mass bleaching events—the breakdown of the nutritional photo-symbiosis with intracellular algae (genus: <i>Symbiodinium</i>). Here, we report that <i>Stylophora pistillata</i> from a highly diverse reef in the Gulf of Aqaba showed no signs of bleaching despite spending 1.5 months at 1–2°C above their long-term summer maximum (amounting to 11 degree heating weeks) and a seawater pH of 7.8. Instead, their symbiotic dinoflagellates exhibited improved photochemistry, higher pigmentation and a doubling in net oxygen production, leading to a 51% increase in primary productivity. Nanoscale secondary ion mass spectrometry imaging revealed subtle cellular-level shifts in carbon and nitrogen metabolism under elevated temperatures, but overall host and symbiont biomass proxies were not significantly affected. Now living well below their thermal threshold in the Gulf of Aqaba, these corals have been evolutionary selected for heat tolerance during their migration through the warm Southern Red Sea after the last ice age. This may allow them to withstand future warming for a longer period of time, provided that successful environmental conservation measures are enacted across national boundaries in the region.
DOI: 10.6084/m9.figshare.4906727.v10
title: Spitschan_2017_NatureNeuro_fMRIMelanopsin

description: Complete raw dataset for the referenced paper
DOI: 10.6084/m9.figshare.4906727.v12
title: Spitschan_2017_PNAS

description: Complete raw dataset for the referenced paper
DOI: 10.6084/m9.figshare.4906727.v11
title: Spitschan_2017_NatureNeuro_fMRIMelanopsin

description: Complete raw dataset for the referenced paper
DOI: 10.6084/m9.figshare.4906328
title: protein_ligand_binding_site_WSRC_codes

description: Identification of Protein-Ligand Binding Sites bySequence Information and Ensemble WeightedSparse Representation Model: Datasets Download link1(ADP, ATP, AMP, GDP, GTP, DNA and HEME): https://figshare.com/s/3f9e005364ea58a5e84a<br><br> Download link2(Ca2+, Mg2+, Fe3+, Mn2+ and Zn2+): https://figshare.com/s/f22e1b2d7a0b443d3f05<br>
DOI: 10.6084/m9.figshare.4906325
title: Dataset for: Early Activation of Deleterious Molecular Pathways in the Kidney in Experimental Heart Failure with Atrial Remodeling

description: Heart failure (HF) is a major health problem with worsening outcomes when renal impairment is present. Therapeutics for early phase HF may be effective for cardiorenal protection, however the detailed characteristics of the kidney in early-stage HF (ES-HF), and therefore treatment for potential renal protection, are poorly defined. We sought to determine the gene and protein expression profiles of specific maladaptive pathways of ES-HF in the kidney and heart. Experimental canine ES-HF, characterized by de-novo HF with atrial remodeling but not ventricular fibrosis, was induced by right ventricular pacing for 10 days. Kidney cortex (KC), medulla (KM), left ventricle (LV), and left atrial (LA) tissues from ES-HF vs normal canines (n=4 of each) were analyzed using RT-PCR microarrays and protein assays to assess genes and proteins related to inflammation, renal injury, apoptosis, and fibrosis. ES-HF was characterized by increased circulating natriuretic peptides and components of the renin-angiotensin-aldosterone system and decreased sodium and water excretion with mild renal injury with up-regulation of CNP and renin genes in the kidney. Compared to normals, widespread genes, especially genes of the inflammatory pathways, were up-regulated in KC similar to increases seen in LA. Protein expressions related to inflammatory cytokines were also augmented in the KC. Gene and protein changes were less prominent in the LV and KM. The ES-HF displayed mild renal injury with widespread gene changes and increased inflammatory cytokines. These changes may provide important clues into the pathophysiology of ES-HF and for therapeutic molecular targets in the kidney of ES-HF.
DOI: 10.6084/m9.figshare.4906325.v1
title: Dataset for: Early Activation of Deleterious Molecular Pathways in the Kidney in Experimental Heart Failure with Atrial Remodeling

description: Heart failure (HF) is a major health problem with worsening outcomes when renal impairment is present. Therapeutics for early phase HF may be effective for cardiorenal protection, however the detailed characteristics of the kidney in early-stage HF (ES-HF), and therefore treatment for potential renal protection, are poorly defined. We sought to determine the gene and protein expression profiles of specific maladaptive pathways of ES-HF in the kidney and heart. Experimental canine ES-HF, characterized by de-novo HF with atrial remodeling but not ventricular fibrosis, was induced by right ventricular pacing for 10 days. Kidney cortex (KC), medulla (KM), left ventricle (LV), and left atrial (LA) tissues from ES-HF vs normal canines (n=4 of each) were analyzed using RT-PCR microarrays and protein assays to assess genes and proteins related to inflammation, renal injury, apoptosis, and fibrosis. ES-HF was characterized by increased circulating natriuretic peptides and components of the renin-angiotensin-aldosterone system and decreased sodium and water excretion with mild renal injury with up-regulation of CNP and renin genes in the kidney. Compared to normals, widespread genes, especially genes of the inflammatory pathways, were up-regulated in KC similar to increases seen in LA. Protein expressions related to inflammatory cytokines were also augmented in the KC. Gene and protein changes were less prominent in the LV and KM. The ES-HF displayed mild renal injury with widespread gene changes and increased inflammatory cytokines. These changes may provide important clues into the pathophysiology of ES-HF and for therapeutic molecular targets in the kidney of ES-HF.
DOI: 10.6084/m9.figshare.4906328.v2
title: protein_ligand_binding_site_WSRC_codes

description: Identification of Protein-Ligand Binding Sites bySequence Information and Ensemble WeightedSparse Representation Model: Datasets Download link1(ADP, ATP, AMP, GDP, GTP, DNA and HEME): https://figshare.com/s/3f9e005364ea58a5e84a<br><br> Download link2(Ca2+, Mg2+, Fe3+, Mn2+ and Zn2+): https://figshare.com/s/f22e1b2d7a0b443d3f05<br>
DOI: 10.6084/m9.figshare.4906328.v1
title: protein_ligand_binding_site_WSRC_codes

description: Download link (Identi cation of Protein-Ligand Binding Sites bySequence Information and Ensemble WeightedSparse Representation Model)
DOI: 10.5281/zenodo.3934122
title: Wrong-way migrations of benthic species driven by ocean warming and larval transport: Data

description: All data used to generate figures, tables, and other results in the publication cited below. All data are derived from publicly available data archives as indicated in the publication's Data Availability Statement. Archived data may change over time, and results in the paper are only relevant to data as originally downloaded. These condensed data were used in the analyses and are provided to ensure that analyses are replicable. If using any code or data, please cite the following publication:<br> Heidi L. Fuchs, Robert J. Chant, Elias J. Hunter, Enrique N. Curchitser, Gregory P. Gerbi, and Emily A. Chen. 2020. Wrong-way migrations of benthic species driven by ocean warming and larval transport. Nature Climate Change. DOI: 10.1038/s41558-020-0894-x The paper is available at: https://www.nature.com/articles/s41558-020-0894-x
description: Funding was provided by the National Science Foundation (OCE-1756646)
DOI: 10.5281/zenodo.3934121
title: Wrong-way migrations of benthic species driven by ocean warming and larval transport: Data

description: All data used to generate figures, tables, and other results in the publication cited below. All data are derived from publicly available data archives as indicated in the publication's Data Availability Statement. Archived data may change over time, and results in the paper are only relevant to data as originally downloaded. These condensed data were used in the analyses and are provided to ensure that analyses are replicable. If using any code or data, please cite the following publication:<br> Heidi L. Fuchs, Robert J. Chant, Elias J. Hunter, Enrique N. Curchitser, Gregory P. Gerbi, and Emily A. Chen. 2020. Wrong-way migrations of benthic species driven by ocean warming and larval transport. Nature Climate Change. DOI: 10.1038/s41558-020-0894-x The paper is available at: https://www.nature.com/articles/s41558-020-0894-x
description: Funding was provided by the National Science Foundation (OCE-1756646)
DOI: 10.6084/m9.figshare.4905755
title: Sample ND49 Dataset

description: This is a sample of 14-day, hourly surface O3 and speciated PM2.5 data at 2x2.5 deg resolution produced via GEOS-Chem.
DOI: 10.6084/m9.figshare.4905677
title: Separating Slow and Fast Sleep Spindles

description: This Matlab code demonstrates how to implement slow and fast sigma peak detection based on generalized eigendecomposition, as described in the following paper:<br>R Cox, AC Schapiro, DS Manoach, R Stickgold, <i>Front. Hum. Neurosci.</i> <b>11</b> (2017), doi:10.3389/fnhum.2017.00433. <i><br></i><b>exampleSigmaPeakGED.m</b> is the main script<br><br><b>*.set files</b> hold multichannel EEG sleep records in EEGlab format of three subjects (N2 and N3 separate)<br><b>vline.m</b> is a helper file for drawing vertical lines
DOI: 10.6084/m9.figshare.4905755.v2
title: Sample ND49 Dataset

description: This is a sample of 14-day, hourly surface O3 and speciated PM2.5 data at 2x2.5 deg resolution produced via GEOS-Chem.
DOI: 10.6084/m9.figshare.4905755.v1
title: Sample ND49 Dataset

description: This is a sample of 14-day, hourly surface O3 and speciated PM2.5 data at 2x2.5 deg resolution produced via GEOS-Chem.
DOI: 10.6084/m9.figshare.4905686.v1
title: electronic supplementary material file 2.xlsx

description: Sequence ID used in the studyLikelihood ratio tests for genes.
DOI: 10.6084/m9.figshare.4905506
title: Datafile 4 for Cael Bisson Follows 2017 Limnology & Oceanography Letters

description: NOAA OISST reanalysis as retrieved 8 August 2016; see associated metadata file for full description
DOI: 10.6084/m9.figshare.4905503
title: Datafile 3 for Cael Bisson Follows 2017 Limnology & Oceanography Letters

description: VGPM & CbPMv2 NPP climatologies as retrieved 2 August 2016; see associated metadata file for full description
DOI: 10.6084/m9.figshare.4905506.v1
title: Datafile 4 for Cael Bisson Follows 2017 Limnology & Oceanography Letters

description: NOAA OISST reanalysis as retrieved 8 August 2016; see associated metadata file for full description
DOI: 10.6084/m9.figshare.4905494
title: Datafile 2 for Cael Bisson Follows 2017 Limnology & Oceanography Letters

description: NCEP ESRL COBE SST reanalysis as retrieved 2 August 2016; see associated metadata file for full description
DOI: 10.6084/m9.figshare.4905503.v1
title: Datafile 3 for Cael Bisson Follows 2017 Limnology & Oceanography Letters

description: VGPM & CbPMv2 NPP climatologies as retrieved 2 August 2016; see associated metadata file for full description
DOI: 10.6084/m9.figshare.4905491
title: Datafile 1 for Cael Bisson Follows 2017 Limnology & Oceanography Letters

description: ERA Interim SST reanalysis as retrieved 5 August 2016; see associated metadata file for full description
DOI: 10.6084/m9.figshare.4903964
title: MeshCleaner

description: Source Code and Sample testing data for the submitted paper "<b>MeshCleaner: A Generic and Straightforward Algorithm for Cleaning Finite Element Meshes</b>"<br>
DOI: 10.6084/m9.figshare.4905491.v1
title: Datafile 1 for Cael Bisson Follows 2017 Limnology & Oceanography Letters

description: ERA Interim SST reanalysis as retrieved 5 August 2016; see associated metadata file for full description
DOI: 10.6084/m9.figshare.4905494.v1
title: Datafile 2 for Cael Bisson Follows 2017 Limnology & Oceanography Letters

description: NCEP ESRL COBE SST reanalysis as retrieved 2 August 2016; see associated metadata file for full description
DOI: 10.6084/m9.figshare.4903937
title: The weighted priors approach for combining expert opinions in logistic regression experiments

description: When modeling the reliability of a system or component, it is not uncommon for more than one expert to provide very different prior estimates of the expected reliability as a function of an explanatory variable such as age or temperature. Our goal is to incorporate all information from the experts when choosing a design about which units to test. Bayesian design of experiments has been shown to be very successful for generalized linear models, including logistic regression models. We use this approach to develop methodology for the case where there are several potentially non-overlapping priors under consideration. While multiple priors have been used for analysis in the past, they have never been used in a design context. The Weighted Priors method performs well for a broad range of true underlying model parameter choices and is more robust when compared to other reasonable design choices. We illustrate the method through multiple scenarios and a motivating example. Additional figures for this article are available in the online supplementary information.
DOI: 10.6084/m9.figshare.4903931
title: Dataset for: One-week glucose control via zero-order release kinetics from an injectable depot of glucagon-like peptide-1 fused to a thermosensitive biopolymer

description: Data from manuscript, titled "One-week glucose control via zero-order release kinetics from an injectable depot of glucagon-like peptide-1 fused to a thermosensitive biopolymer", published in Nature Biomedical Engineering. <br>For other inquiries, please contact Ashutosh Chilkoti (chilkoti@duke.edu)
DOI: 10.6084/m9.figshare.4903937.v2
title: The weighted priors approach for combining expert opinions in logistic regression experiments

description: When modeling the reliability of a system or component, it is not uncommon for more than one expert to provide very different prior estimates of the expected reliability as a function of an explanatory variable such as age or temperature. Our goal is to incorporate all information from the experts when choosing a design about which units to test. Bayesian design of experiments has been shown to be very successful for generalized linear models, including logistic regression models. We use this approach to develop methodology for the case where there are several potentially non-overlapping priors under consideration. While multiple priors have been used for analysis in the past, they have never been used in a design context. The Weighted Priors method performs well for a broad range of true underlying model parameter choices and is more robust when compared to other reasonable design choices. We illustrate the method through multiple scenarios and a motivating example. Additional figures for this article are available in the online supplementary information.
DOI: 10.6084/m9.figshare.4903964.v1
title: MeshCleaner

description: Source Code and Sample testing data for the submitted paper "<b>MeshCleaner: A Generic and Straightforward Algorithm for Cleaning Finite Element Meshes</b>"<br>
DOI: 10.6084/m9.figshare.4903874
title: On Moments of Folded and Truncated Multivariate Normal Distributions

description: Recurrence relations for integrals that involve the density of multivariate normal distributions are developed. These recursions allow fast computation of the moments of folded and truncated multivariate normal distributions. Besides being numerically efficient, the proposed recursions also allow us to obtain explicit expressions of low-order moments of folded and truncated multivariate normal distributions. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.4903931.v1
title: Dataset for: One-week glucose control via zero-order release kinetics from an injectable depot of glucagon-like peptide-1 fused to a thermosensitive biopolymer

description: Data from manuscript, titled "One-week glucose control via zero-order release kinetics from an injectable depot of glucagon-like peptide-1 fused to a thermosensitive biopolymer", published in Nature Biomedical Engineering. <br>For other inquiries, please contact Ashutosh Chilkoti (chilkoti@duke.edu)
DOI: 10.6084/m9.figshare.4903937.v1
title: The Weighted Priors Approach for Combining Expert Opinions in Logistic Regression Experiments

description: When modeling the reliability of a system or component, it is not uncommon for more than one expert to provide very different prior estimates of the expected reliability as a function of an explanatory variable such as age or temperature. Our goal is to incorporate all information from the experts when choosing a design about which units to test. Bayesian design of experiments has been shown to be very successful for generalized linear models, including logistic regression models. We use this approach to develop methodology for the case where there are several potentially non-overlapping priors under consideration. While multiple priors have been used for analysis in the past, they have never been used in a design context. The Weighted Priors method performs well for a broad range of true underlying model parameter choices and is more robust when compared to other reasonable design choices. We illustrate the method through multiple scenarios and a motivating example. Additional figures for this article are available as Supplementary Materials.
DOI: 10.17028/rd.lboro.4903841
title: Rail complaints lodged by disabled travellers

description: This is a list of issues raised by travellers using the FixMyTransport platform developed by mySociety. The problems were submitted by travellers between mid 2011 and early 2015.The problem descriptions provide a good overview of the issues faced by rail travellers with disability.
DOI: 10.6084/m9.figshare.4903814
title: Brugada Syndrome data for rare variant association analysis

description: The directory contains data described by Le Scouarnec et al. (2015) for the rare variant association analysis of Brugada syndrome (BrS). The quality control of this processed data is further detailed in the publication.<br>The directory contains:<br>-files named .txt. These files are genotype files with each row corresponding to a SNV and each column corresponding to an individual. SNV identifiers are indicated in the first column CHROM_POS_REF_ALT. Positions are according to the GRCh37/hg19 assembly. Other column names are the individual identifiers. Genotypes are coded 0, 1 or 2 according to the number of alternative alleles.<br>- a file named "phenotypes_BrS.txt". This file contains two columns: the individual identifier and the phenotype (affected: 1, unaffected: 0).<br>