cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2070022
title: Dress in the Workplace

description: A study of how variation in clothing influences perceptions
DOI: 10.6084/m9.figshare.2070031.v1
title: 23 March 2015 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.2951263.v497
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2070013
title: kitchingroup-59

description: Zhongnan Xu and John R. Kitchin. <i>Tuning Oxide Activity through Modification of the Crystal and Electronic Structure: From Strain to Potential Polymorphs</i>, Accepted in PCCP, Sept 28, 2015. http://dx.doi.org/10.1039/C5CP04840K.
DOI: 10.6084/m9.figshare.2070007
title: Complete fMRI dataset of one awake dog during visual stimulation.

description: <br>Data corresponding to article:"Our Faces in the Dog's Brain: Functional imaging reveals temporal cortex activation during perception of human faces".PLoS ONE 2016.10.1371/journal.pone.0149431<br><br><br>Includes: anatomic image, fMRI images (5 runs) and vector files. <br>F1-F5 indicate run number.V1-V3 indicate corresponding stimulation paradigm (txt files)<br>All image files are in Nifti format. For any question or more data lconcha@unam.mx
DOI: 10.6084/m9.figshare.2070022.v2
title: Dress in the Workplace

description: A study of how variation in clothing influences perceptions
DOI: 10.6084/m9.figshare.2951263.v498
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2070022.v1
title: Dress in the Workplace

description: A study of how variation in clothing influences perceptions
DOI: 10.6084/m9.figshare.2070004
title: swissmodel_glyco_E_zika with compounds docked.zip

description: <b>supplemental data for preprint Open Drug Discovery for the Zika Virus<br><br>SDF file<br></b>
DOI: 10.6084/m9.figshare.2070013.v2
title: kitchingroup-59

description: Zhongnan Xu and John R. Kitchin. <i>Tuning Oxide Activity through Modification of the Crystal and Electronic Structure: From Strain to Potential Polymorphs</i>, Accepted in PCCP, Sept 28, 2015. http://dx.doi.org/10.1039/C5CP04840K.
DOI: 10.6084/m9.figshare.2951263.v499
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2070004.v1
title: swissmodel_glyco_E_zika with compounds docked.zip

description: <b>supplemental data for preprint Open Drug Discovery for the Zika Virus<br><br>SDF file<br></b>
DOI: 10.6084/m9.figshare.2070007.v1
title: Complete dataset of one dog

description: Includes: anatomic image, fMRI images (5 runs) without manual segmetation and vector files. All files are in Nifti format. For any question or more data lconcha@unam.mx
DOI: 10.6084/m9.figshare.2070013.v1
title: kitchingroup-59

description: Zhongnan Xu and John R. Kitchin. <i>Tuning Oxide Activity through Modification of the Crystal and Electronic Structure: From Strain to Potential Polymorphs</i>, Accepted in PCCP, Sept 28, 2015. http://dx.doi.org/10.1039/C5CP04840K.
DOI: 10.6084/m9.figshare.2070001
title: Homology model for Zika virus glycoprotein E

description: <b>Open Drug Discovery for the Zika Virus - supplemental data<br><br>Model created with Swiss Model<br></b>
DOI: 10.6084/m9.figshare.2951263.v500
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2070001.v2
title: Homology model for Zika virus glycoprotein E

description: <b>Open Drug Discovery for the Zika Virus - supplemental data<br><br>Model created with Swiss Model<br></b>
DOI: 10.6084/m9.figshare.2070001.v1
title: swissmodel_glyco_E_zika for docking.pdb

description: <b>Open Drug Discovery for the Zika Virus - supplemental data<br></b>
DOI: 10.6084/m9.figshare.2069989
title: Treseder et al 2016 Global Change Biol: Suppl information

description: Authors' supplementary figures and data for publication:Treseder, K. K., Y. Marusenko, A. L. Romero-Olivares, and M. R. Maltz. 2016. Experimental warming alters potential function of the fungal community in boreal forest. Global Change Biology, DOI: 10.1111/gcb.13238
DOI: 10.6084/m9.figshare.2069992
title: Compounds tested against Dengue and may be useful for Zika virus

description: Some compounds from papers on Dengue - this file will be expanded in future..<br><br>Suplemental data for Open Drug Discovery for the Zika virus<br>
DOI: 10.6084/m9.figshare.2951263.v501
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2951263.v503
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2951263.v502
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2069962
title: Novel insights into human respiratory syncytial virus-host factor interactions through integrated proteomics and transcriptomics analysis

description: The lack of vaccine and limited antiviral options against respiratory syncytial virus (RSV) highlights the need for novel therapeutic strategies. One alternative is to develop drugs that target host factors required for viral replication. Several microarray and proteomics studies had been published to identify possible host factors that are affected during RSV replication. In order to obtain a comprehensive understanding of RSV-host interaction, we integrated available proteome and transcriptome datasets and used it to construct a virus-host interaction network. Then, we interrogated the network to identify host factors that are targeted by the virus and we searched for drugs from the DrugBank database that interact with these host factors, which may have potential applications in repositioning for future treatment options of RSV infection.
DOI: 10.6084/m9.figshare.2069962.v1
title: Novel insights into human respiratory syncytial virus-host factor interactions through integrated proteomics and transcriptomics analysis

description: The lack of vaccine and limited antiviral options against respiratory syncytial virus (RSV) highlights the need for novel therapeutic strategies. One alternative is to develop drugs that target host factors required for viral replication. Several microarray and proteomics studies had been published to identify possible host factors that are affected during RSV replication. In order to obtain a comprehensive understanding of RSV-host interaction, we integrated available proteome and transcriptome datasets and used it to construct a virus-host interaction network. Then, we interrogated the network to identify host factors that are targeted by the virus and we searched for drugs from the DrugBank database that interact with these host factors, which may have potential applications in repositioning for future treatment options of RSV infection.
DOI: 10.6084/m9.figshare.2069881.v1
title: Plasmodium ashfordi GRW2 preliminary unfiltered transcriptome assembly

description: The transcriptome assembly has been through an initial filtering round to remove the vast majority of contigs originating from the host and contamination, but a few host transcripts remain.
DOI: 10.6084/m9.figshare.2069743
title: Feasibility of quantifying arterial cerebral blood volume using multiphase alternate ascending/descending directional navigation (ALADDIN)

description: Raw data of the Figures and Tables in the paper.
DOI: 10.6084/m9.figshare.2069743.v2
title: Feasibility of quantifying arterial cerebral blood volume using multiphase alternate ascending/descending directional navigation (ALADDIN)

description: Raw data of the Figures and Tables in the paper.
DOI: 10.6084/m9.figshare.2069743.v1
title: Feasibility of quantifying arterial cerebral blood volume using multiphase alternate ascending/descending directional navigation (ALADDIN)

description: Raw data of the Figures and Tables in the paper.
DOI: 10.6084/m9.figshare.2069722
title: Star Classification System for Age Models

description: This is the supplementary information for paper Flantua, Blaauw and Hooghiemstra, 2016. Clim.Past 12, 387-414, 2016. <br><br>Here we present the outcomes of this paper in terms of recalibrated age models and their corresponding descriptions. Furthermore in the README file there are instructions and a test-folder on how to do age model running using Clam that will produce a star classification. <br>Please open first the README file for more details.
DOI: 10.6084/m9.figshare.2069719
title: Semiparametric Spatial Autoregressive Models With Endogenous Regressors: With an Application to Crime Data

description: This study considers semiparametric spatial autoregressive models that allow for endogenous regressors, as well as the heterogenous effects of these regressors across spatial units. For the model estimation, we propose a semiparametric series generalized method of moments estimator. We establish that the proposed estimator is both consistent and asymptotically normal. As an empirical illustration, we apply the proposed model and method to Tokyo crime data to estimate how the existence of a neighborhood police substation (NPS) affects the household burglary rate. The results indicate that the presence of an NPS helps reduce household burglaries, and that the effects of some variables are heterogenous with respect to residential distribution patterns. Furthermore, we show that using a model that does not adjust for the endogeneity of NPS does not allow us to observe the significant relationship between NPS and the household burglary rate. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2069718
title: Robust and Defensible Mark–Recapture Methodologies for Salmonid Escapement: Modernizing the Use of Data and Resources

description: Estimates of population size, required for most ecological investigations, are often achieved by mark–recapture experiments, frequently by applying pooled or stratified Petersen estimators. Unfortunately, the closure assumption required by Petersen estimators is frequently violated in the estimation of salmonid escapement, even though the consequences of this violation have been known for decades. We illustrate how biologists and analysts can and should make better use of statistical, mathematical, and computational advances in their analysis of mark–recapture data. Modern, easily applied approaches address and minimize the effects of violations to the model assumptions on which abundance estimators are based. Using examples from research estimating the numbers of Chinook Salmon <i>Oncorhynchus tshawytscha</i> escaping fisheries to spawn, this study demonstrates and provides evidence in support of the use of a robust and defensible approach to salmonid escapement estimation based on the analysis of individual encounter histories. The main attributes of the approach include (1) testing for demographic closure, (2) allowing different hypotheses about the demographic attributes and capture history of the studied population to be expressed within a model selection framework, encompassing suites of open- or closed-population approaches, and (3) optimizing the use of information by embracing the opportunities that mark–recapture experiments generate to increase our knowledge of salmonid ecology and hence improve both future study designs and management decisions. This study also demonstrates that discrepancies (positive) in abundance estimates produced with the Petersen estimator relative to those produced by the “best models” from robust estimators are inversely proportional to sampling rates. Received May 20, 2015; accepted October 22, 2015
DOI: 10.6084/m9.figshare.2069717
title: G1 cyclin driven DNA replication

description: The mitotic cell cycle is driven by Cyclin-Dependent Kinases (CDK). CDK activation requires the binding of activatory subunits termed cyclins. Different waves of cyclins are expressed during the cell cycle, enabling CDKs to trigger phase specific events. For instance, S phase cyclins promote the initiation of DNA replication but not chromosome segregation. There are at least 2 explanations for how such regulation is achieved. According to one of the visions, cyclins confer intrinsic substrate specificity to the CDK catalytic subunit. Alternatively a quantitative model has been proposed, according to which ever-increasing CDK activity is required to trigger cell cycle events from G1 to M. If a quantitative control prevails, then an early cyclin should trigger later cycle events if accumulated at high enough levels at the right time and place. We show here that a G1 phase cyclin bears the potential to trigger DNA replication and promote S and G2 phase specific transcription.
DOI: 10.6084/m9.figshare.2069718.v1
title: Robust and Defensible Mark–Recapture Methodologies for Salmonid Escapement: Modernizing the Use of Data and Resources

description: Estimates of population size, required for most ecological investigations, are often achieved by mark–recapture experiments, frequently by applying pooled or stratified Petersen estimators. Unfortunately, the closure assumption required by Petersen estimators is frequently violated in the estimation of salmonid escapement, even though the consequences of this violation have been known for decades. We illustrate how biologists and analysts can and should make better use of statistical, mathematical, and computational advances in their analysis of mark–recapture data. Modern, easily applied approaches address and minimize the effects of violations to the model assumptions on which abundance estimators are based. Using examples from research estimating the numbers of Chinook Salmon <i>Oncorhynchus tshawytscha</i> escaping fisheries to spawn, this study demonstrates and provides evidence in support of the use of a robust and defensible approach to salmonid escapement estimation based on the analysis of individual encounter histories. The main attributes of the approach include (1) testing for demographic closure, (2) allowing different hypotheses about the demographic attributes and capture history of the studied population to be expressed within a model selection framework, encompassing suites of open- or closed-population approaches, and (3) optimizing the use of information by embracing the opportunities that mark–recapture experiments generate to increase our knowledge of salmonid ecology and hence improve both future study designs and management decisions. This study also demonstrates that discrepancies (positive) in abundance estimates produced with the Petersen estimator relative to those produced by the “best models” from robust estimators are inversely proportional to sampling rates. Received May 20, 2015; accepted October 22, 2015
DOI: 10.6084/m9.figshare.2069722.v1
title: Star Classification System for Age Models

description: This is the supplementary information for paper Flantua, Blaauw and Hooghiemstra, 2016. Clim.Past 12, 387-414, 2016. <br><br>Here we present the outcomes of this paper in terms of recalibrated age models and their corresponding descriptions. Furthermore in the README file there are instructions and a test-folder on how to do age model running using Clam that will produce a star classification. <br>Please open first the README file for more details.
DOI: 10.6084/m9.figshare.2069716
title: Cell cycle-dependent changes in H3K56ac in human cells

description: The incorporation of histone H3 with an acetylated lysine 56 (H3K56ac) into the nucleosome is important for chromatin remodeling and serves as a marker of new nucleosomes during DNA replication and repair in yeast. However, in human cells, the level of H3K56ac is greatly reduced, and its role during the cell cycle is controversial. Our aim was to determine the potential of H3K56ac to regulate cell cycle progression in different human cell lines. A significant increase in the number of H3K56ac foci, but not in H3K56ac protein levels, was observed during the S and G2 phases in cancer cell lines, but was not observed in embryonic stem cell lines. Despite this increase, the H3K56ac signal was not present in late replication chromatin, and H3K56ac protein levels did not decrease after the inhibition of DNA replication. H3K56ac was not tightly associated with the chromatin and was primarily localized to active chromatin regions. Our results support the role of H3K56ac in transcriptionally active chromatin areas but do not confirm H3K56ac as a marker of newly synthetized nucleosomes in DNA replication.
DOI: 10.6084/m9.figshare.2069717.v1
title: G1 cyclin driven DNA replication

description: The mitotic cell cycle is driven by Cyclin-Dependent Kinases (CDK). CDK activation requires the binding of activatory subunits termed cyclins. Different waves of cyclins are expressed during the cell cycle, enabling CDKs to trigger phase specific events. For instance, S phase cyclins promote the initiation of DNA replication but not chromosome segregation. There are at least 2 explanations for how such regulation is achieved. According to one of the visions, cyclins confer intrinsic substrate specificity to the CDK catalytic subunit. Alternatively a quantitative model has been proposed, according to which ever-increasing CDK activity is required to trigger cell cycle events from G1 to M. If a quantitative control prevails, then an early cyclin should trigger later cycle events if accumulated at high enough levels at the right time and place. We show here that a G1 phase cyclin bears the potential to trigger DNA replication and promote S and G2 phase specific transcription.
DOI: 10.6084/m9.figshare.2069714
title: Biomarker Benchmark - GSE30784

description: <br><b>[NOTICE: This data set has been deprecated. Please see our new version of the data (and additional data sets) here: https://osf.io/mhk93 ]</b><br><br>"OSCC is associated with substantial mortality and morbidity. To identify potential biomarkers for the early detection of invasive OSCC, we compared the gene expressions of OSCC, oral dysplasia, and normal<br>oral tissue from patients without oral cancer or preneoplastic oral lesions (controls). Results provided models of gene expression to distinguish OSCC from controls."<br><br>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30784<br><br>We have included gene-expression data, the outcome (class) being predicted, and any clinical covariates. When gene-expression data were processed in multiple batches, we have provided batch information. Each data set is organized into a file set, where each contains all pertinent files for an individual dataset. The gene expression files have been normalized using both the SCAN and UPC methods using the SCAN.UPC package in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). We summarized the data at the gene level using the BrainArray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp). We used Ensembl identifiers. The class, clinical, and batch data were hand curated to ensure consistency ("tidy data" formatting). In addition, the data files have been formatted to be imported easily into the ML-Flex machine learning package (http://mlflex.sourceforge.net/).
DOI: 10.6084/m9.figshare.2069719.v1
title: Semiparametric Spatial Autoregressive Models with Endogenous Regressors: With an Application to Crime Data

description: This study considers semiparametric spatial autoregressive models that allow for endogenous regressors, as well as the heterogeneous effects of these regressors across spatial units. For the model estimation, we propose a semiparametric series generalized method of moments estimator. We establish that the proposed estimator is both consistent and asymptotically normal. As an empirical illustration, we apply the proposed model and method to Tokyo crime data in order to estimate how the existence of a neighborhood police substation (NPS) affects the household burglary rate. The results indicate that the presence of an NPS helps reduce household burglaries, and that the effects of some variables are heterogeneous with respect to residential distribution patterns. Furthermore, we show that using a model that does not adjust for the endogeneity of NPS does not allow us to observe the significant relationship between NPS and the household burglary rate. A supplementary material for this article is available online.