cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5114551
title: Time-of-day variation in sustained attentional control

description: Sustained attention is a fundamental cognitive function underlying many activities in daily life including workplace safety, but its natural variation throughout the day is incompletely characterized. To examine time-of-day variation, we collected a large online data set (<i>N</i> = 6,363) with participation throughout the day and around the world on the gradual-onset continuous performance task, a sensitive measure of sustained attention. This allowed us to examine accuracy, attentional stability, and strategy. Results show that both accuracy and attentional stability peak between 9:00 and 11:00 a.m. and progressively decline throughout the day, whereas strategy is more stable.
DOI: 10.6084/m9.figshare.5114518
title: Silhouettes of animal scavengers

description: Silhouettes of a raccoon dog, a weasel, a crow, and a burying beetle.
DOI: 10.6084/m9.figshare.5114551.v1
title: Time-of-day variation in sustained attentional control

description: Sustained attention is a fundamental cognitive function underlying many activities in daily life including workplace safety, but its natural variation throughout the day is incompletely characterized. To examine time-of-day variation, we collected a large online data set (<i>N</i> = 6,363) with participation throughout the day and around the world on the gradual-onset continuous performance task, a sensitive measure of sustained attention. This allowed us to examine accuracy, attentional stability, and strategy. Results show that both accuracy and attentional stability peak between 9:00 and 11:00 a.m. and progressively decline throughout the day, whereas strategy is more stable.
DOI: 10.6084/m9.figshare.5114494
title: Figure 12. Material decomposition results for the phantom simulation experiment.

description: Supplementary data for: Figure 12. Material decomposition results for the phantom simulation experiment.<br>(A) Expected material decomposition<br>(C) PCD Only material decomposition<br>(D) Hybrid material decomposition
DOI: 10.6084/m9.figshare.5114503
title: Figure 13. Hybrid, spectral CT reconstruction in an in vivo mouse model of soft tissue sarcoma.

description: Supplementary data for: Figure 13. Hybrid, spectral CT reconstruction in an in vivo mouse model of soft tissue sarcoma.<br>(B) PCD Only, final reconstruction<br>(D) Hybrid, X final reconstruction<br>
DOI: 10.6084/m9.figshare.5114503.v1
title: Figure 13. Hybrid, spectral CT reconstruction in an in vivo mouse model of soft tissue sarcoma.

description: Supplementary data for: Figure 13. Hybrid, spectral CT reconstruction in an in vivo mouse model of soft tissue sarcoma.<br>(B) PCD Only, final reconstruction<br>(D) Hybrid, X final reconstruction<br>
DOI: 10.6084/m9.figshare.5114494.v1
title: Figure 12. Material decomposition results for the phantom simulation experiment.

description: Supplementary data for: Figure 12. Material decomposition results for the phantom simulation experiment.<br>(A) Expected material decomposition<br>(C) PCD Only material decomposition<br>(D) Hybrid material decomposition
DOI: 10.6084/m9.figshare.5114416
title: Figure 11. Comparison of hybrid and PCD only reconstruction results using identical PCD projection data.

description: Supplemental data for: Figure 11. Comparison of hybrid and PCD only reconstruction results using identical PCD projection data.<br>(A) Expected reconstruction results(B) PCD Only reconstruction results<br>(D) Hybrid reconstruction results<br>
DOI: 10.6084/m9.figshare.5114320
title: Data used in 'results' section from Rensching cats and dogs: feeding ecology and fecundity trends explain variation in the allometry of sexual size dimorphism

description: Data used for the results in this ms
DOI: 10.6084/m9.figshare.5114416.v1
title: Figure 11. Comparison of hybrid and PCD only reconstruction results using identical PCD projection data.

description: Supplemental data for: Figure 11. Comparison of hybrid and PCD only reconstruction results using identical PCD projection data.<br>(A) Expected reconstruction results(B) PCD Only reconstruction results<br>(D) Hybrid reconstruction results<br>
DOI: 10.6084/m9.figshare.5114320.v1
title: Data used in 'results' section from Rensching cats and dogs: feeding ecology and fecundity trends explain variation in the allometry of sexual size dimorphism

description: Data used for the results in this ms
DOI: 10.6084/m9.figshare.5114275
title: A guide to robust statistical methods in neuroscience

description: This package provides data, code and notebooks to reproduce the analyses and figures in:<br>Wilcox, R.R. & Rousselet, G.A. (2018) <b>A Guide to Robust Statistical Methods in Neuroscience</b> <i>Curr Protoc Neurosci</i>, 82.<br>https://doi.org/10.1002/cpns.41<br><br>The general goal was to describe and illustrate some of the many improved methods for comparing groups and studying associations. General suggestions are made about which methods perform relatively well. Installing the required R functions is described in our paper. Code is provided to reproduce all the figures in the paper. All the figures are also included in pdf format. We also include notebooks describing extra simulations on power and type I error in different situations.<br><br><br>
DOI: 10.6084/m9.figshare.5114272
title: Data for article "D-cycloserine improves synaptic transmission in an animal model of Rett syndrome"

description: These are tables with all the raw data used to generate figures and and run statistics in the article "D-cycloserine improves synaptic transmission in an animal model of Rett syndrome"
DOI: 10.6084/m9.figshare.5114272.v1
title: Figure 4 Data.xlsx

description: These are tables with all the raw data used to generate figures and and run statistics in the article "D-cycloserine improves synaptic transmission in an animal model of Rett syndrome"
DOI: 10.6084/m9.figshare.5114245
title: Association between alcohol consumption trajectories and clinical profiles among women and men living with HIV

description: <i>Background</i>: Alcohol use is common among persons living with HIV (PLWH). It is unclear how alcohol consumption changes over time and if these changes are associated with clinical profiles. <i>Objective</i>: We aimed to describe the association between longitudinal patterns of alcohol consumption and the clinical profiles of PLWH. <i>Methods</i>: Data from the Women’s Interagency HIV Study (<i>n</i> = 1123 women) and Multicenter AIDS Cohort Study (<i>n</i> = 597 men) from 2004 to 2013 were utilized. Group-based trajectory models were used to assess alcohol consumption patterns across 10 years. Generalized estimating equations were used to identify associations between clinical factors and alcohol consumption. All analyses were stratified by sex. <i>Results</i>: Four trajectories of alcohol use were identified in women and men (women: abstinent 38%, low: 25%, moderate: 30%, heavy: 7%; men: abstinent 16%, low: 69%, moderate: 9%, heavy: 5%). The Framingham Risk Score (women: adjusted odds ratio [AOR] 1.07, 95% confidence interval [CI] 1.04–1.09), years on ART (women: AOR 1.02, CI 1.00–1.05; men: AOR 1.05, CI 1.01–1.09), suboptimal ART adherence (men: AOR 1.23, CI 1.07–1.42), and unsuppressed viral load (women: AOR 1.82, CI 1.56–2.13; men: AOR 1.36, CI 1.17–1.58) were associated with increased odds for moderate drinking. The Framingham Risk Score (women: AOR 1.10, CI 1.07–1.14; men: AOR 1.12, CI 1.06–1.20), suboptimal adherence (women: AOR 1.25, CI 1.04–1.51), and unsuppressed viral load (women: AOR 1.78, CI 1.42–2.24) were associated with increased odds for heavy drinking. <i>Conclusions</i>: Clinicians should consider screening patients for alcohol consumption, particularly if patients have comorbid medical conditions, suboptimal antiretroviral adherence, and/or detectable viral load.
DOI: 10.6084/m9.figshare.5114248
title: Tethering of Lsh at the <i>Oct4</i> locus promotes gene repression associated with epigenetic changes

description: Lsh is a chromatin remodeling factor that regulates DNA methylation and chromatin function in mammals. The dynamics of these chromatin changes and whether they are directly controlled by Lsh remain unclear. To understand the molecular mechanisms of Lsh chromatin controlled regulation of gene expression, we established a tethering system that recruits a Gal4-Lsh fusion protein to an engineered <i>Oct4</i> locus through Gal4 binding sites in murine embryonic stem (ES) cells. We examined the molecular epigenetic events induced by Lsh binding including: histone modification, DNA methylation and chromatin accessibility to determine nucleosome occupancy before and after embryonic stem cell differentiation. Our results indicate that Lsh assists gene repression upon binding to the <i>Oct4</i> promoter region. Furthermore, we detected less chromatin accessibility and reduced active histone modifications at the tethered site in undifferentiated ES, while GFP reporter gene expression and DNA methylation patterns remained unchanged at this stage. Upon differentiation, association of Lsh promotes transcriptional repression of the reporter gene accompanied by the increase of repressive histone marks and a gain of DNA methylation at distal and proximal <i>Oct4</i> enhancer sites. Taken together, this approach allowed us to examine Lsh mediated epigenetic regulation as a dynamic process and revealed chromatin accessibility changes as the primary consequence of Lsh function.
DOI: 10.6084/m9.figshare.5114245.v1
title: Association between alcohol consumption trajectories and clinical profiles among women and men living with HIV

description: <i>Background</i>: Alcohol use is common among persons living with HIV (PLWH). It is unclear how alcohol consumption changes over time and if these changes are associated with clinical profiles. <i>Objective</i>: We aimed to describe the association between longitudinal patterns of alcohol consumption and the clinical profiles of PLWH. <i>Methods</i>: Data from the Women’s Interagency HIV Study (<i>n</i> = 1123 women) and Multicenter AIDS Cohort Study (<i>n</i> = 597 men) from 2004 to 2013 were utilized. Group-based trajectory models were used to assess alcohol consumption patterns across 10 years. Generalized estimating equations were used to identify associations between clinical factors and alcohol consumption. All analyses were stratified by sex. <i>Results</i>: Four trajectories of alcohol use were identified in women and men (women: abstinent 38%, low: 25%, moderate: 30%, heavy: 7%; men: abstinent 16%, low: 69%, moderate: 9%, heavy: 5%). The Framingham Risk Score (women: adjusted odds ratio [AOR] 1.07, 95% confidence interval [CI] 1.04–1.09), years on ART (women: AOR 1.02, CI 1.00–1.05; men: AOR 1.05, CI 1.01–1.09), suboptimal ART adherence (men: AOR 1.23, CI 1.07–1.42), and unsuppressed viral load (women: AOR 1.82, CI 1.56–2.13; men: AOR 1.36, CI 1.17–1.58) were associated with increased odds for moderate drinking. The Framingham Risk Score (women: AOR 1.10, CI 1.07–1.14; men: AOR 1.12, CI 1.06–1.20), suboptimal adherence (women: AOR 1.25, CI 1.04–1.51), and unsuppressed viral load (women: AOR 1.78, CI 1.42–2.24) were associated with increased odds for heavy drinking. <i>Conclusions</i>: Clinicians should consider screening patients for alcohol consumption, particularly if patients have comorbid medical conditions, suboptimal antiretroviral adherence, and/or detectable viral load.
DOI: 10.6084/m9.figshare.5114248.v2
title: Tethering of Lsh at the <i>Oct4</i> locus promotes gene repression associated with epigenetic changes

description: Lsh is a chromatin remodeling factor that regulates DNA methylation and chromatin function in mammals. The dynamics of these chromatin changes and whether they are directly controlled by Lsh remain unclear. To understand the molecular mechanisms of Lsh chromatin controlled regulation of gene expression, we established a tethering system that recruits a Gal4-Lsh fusion protein to an engineered <i>Oct4</i> locus through Gal4 binding sites in murine embryonic stem (ES) cells. We examined the molecular epigenetic events induced by Lsh binding including: histone modification, DNA methylation and chromatin accessibility to determine nucleosome occupancy before and after embryonic stem cell differentiation. Our results indicate that Lsh assists gene repression upon binding to the <i>Oct4</i> promoter region. Furthermore, we detected less chromatin accessibility and reduced active histone modifications at the tethered site in undifferentiated ES, while GFP reporter gene expression and DNA methylation patterns remained unchanged at this stage. Upon differentiation, association of Lsh promotes transcriptional repression of the reporter gene accompanied by the increase of repressive histone marks and a gain of DNA methylation at distal and proximal <i>Oct4</i> enhancer sites. Taken together, this approach allowed us to examine Lsh mediated epigenetic regulation as a dynamic process and revealed chromatin accessibility changes as the primary consequence of Lsh function.
DOI: 10.6084/m9.figshare.5114236
title: Computational analysis GeCKO v2 library (human)

description: <b>Table 1 - Non-specific sgRNAs GeCKO v2 (human). </b>This table represents the total of 5,664 sgRNAs within the entire GeCKO v2 library (half-libraries A and B combined) that recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. For the analysis, sgRNA target sites were aligned against the human reference genome (GRCh38/hg19 - primary assembly) using BLAT (v36) after optimisation of the algorithm for short length queries (-tileSize=6, -stepSize=3). The resulting alignments were further filtered to only include perfect matches and unique targets (exclusion of hits on alternative assemblies). Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.<br><b>Table 2 - Flagged genes GeCKO v2 (human).</b> This table represents the total of 775 genes for which more than half the corresponding sgRNAs within the entire human GeCKO v2 library (half-libraries A and B combined) are non-specific, i.e. recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. A threshold of &gt;50% non-specific sgRNAs per gene (e.g. 4 out of 6 for protein coding genes; 3 out of 4 for miRNA genes) was set in order to flag a group of sgRNAs. Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.
DOI: 10.6084/m9.figshare.5114248.v1
title: Tethering of Lsh at the Oct4 locus promotes gene repression associated with epigenetic changes

description: Lsh is a chromatin remodeling factor that regulates DNA methylation and chromatin function in mammals. The dynamics of these chromatin changes and whether they are directly controlled by Lsh remain unclear. To understand the molecular mechanisms of Lsh chromatin controlled regulation of gene expression, we established a tethering system that recruits a Gal4-Lsh fusion protein to an engineered <i>Oct4</i> locus through Gal4 binding sites in murine embryonic stem (ES) cells. We examined the molecular epigenetic events induced by Lsh binding including: histone modification, DNA methylation and chromatin accessibility to determine nucleosome occupancy before and after embryonic stem cell differentiation. Our results indicate that Lsh assists gene repression upon binding to the <i>Oct4</i> promoter region. Furthermore, we detected less chromatin accessibility and reduced active histone modifications at the tethered site in undifferentiated ES, while GFP reporter gene expression and DNA methylation patterns remained unchanged at this stage. Upon differentiation, association of Lsh promotes transcriptional repression of the reporter gene accompanied by the increase of repressive histone marks and a gain of DNA methylation at distal and proximal <i>Oct4</i> enhancer sites. Taken together, this approach allowed us to examine Lsh mediated epigenetic regulation as a dynamic process and revealed chromatin accessibility changes as the primary consequence of Lsh function.
DOI: 10.6084/m9.figshare.5114149
title: datasets and scripts for article Measuring behavioral thermal tolerance to address hot topics in ecology, evolution, and conservation

description: datasets and scripts that allow reproducing the article with that name<br>
DOI: 10.6084/m9.figshare.5114122
title: Sorbus aria chorology

description: Distribution map of common whitebeam (<i>Sorbus aria</i>)<br><br>These maps were produced by combining numerous and heterogeneous data collected from atlas monographs providing complete species distribution maps, from national to regional atlases, occurrence geo-databases, scientific and grey literature.<br>The maps were created using ESRI shapefiles (*.shp, *.shx, *.dbf, *.prj files) archived in the ZIP file. Species range is mapped with polygon features (name suffix "plg"), which define continuous areas of occupancy of the species, and with point features (name suffix "pnt"), which identify more fragmented and isolated populations. If synanthropic occurrences are reported outside the species natural range, additional point and/or polygon shapefiles are also present (suffix "syn"). <br>Polygon borders delimiting species ranges are generalized across the mainland and sea boundaries. This offers the possibility to mask sea areas or to clip and extract the terrestrial range parts using GIS data layers of the users' choice. An additional version of polygon ranges are clipped with a coastline (name suffix "clip"), which have been derived from Natural Earth dataset "Admin 0 - Countries" 1:50M version 4.1.0 (https://www.naturalearthdata.com). <br><br>Please cite as:<br>Caudullo, G., Welk, E., San-Miguel-Ayanz, J., 2017. Chorological maps for the main European woody species. Data in Brief 12, 662-666. DOI: doi.org/10.1016/j.dib.2017.05.007 <br><br>Additional information and used references are on 'supplementary materials' document:<br>https://doi.org/10.6084/m9.figshare.5091901<br><br>Chorological maps are part of the "European Atlas of Forest Tree Species" project:<br>https://w3id.org/mtv/FISE-Comm/v01
DOI: 10.6084/m9.figshare.5114149.v2
title: datasets and scripts for article Measuring behavioral thermal tolerance to address hot topics in ecology, evolution, and conservation

description: datasets and scripts that allow reproducing the article with that name<br>
DOI: 10.6084/m9.figshare.5114134
title: Sorbus domestica chorology

description: Distribution map of service tree (<i>Sorbus domestica</i>)<br><br>These maps were produced by combining numerous and heterogeneous data collected from atlas monographs providing complete species distribution maps, from national to regional atlases, occurrence geo-databases, scientific and grey literature.<br>The maps were created using ESRI shapefiles (*.shp, *.shx, *.dbf, *.prj files) archived in the ZIP file. Species range is mapped with polygon features (name suffix "plg"), which define continuous areas of occupancy of the species, and with point features (name suffix "pnt"), which identify more fragmented and isolated populations. If synanthropic occurrences are reported outside the species natural range, additional point and/or polygon shapefiles are also present (suffix "syn"). <br>Polygon borders delimiting species ranges are generalized across the mainland and sea boundaries. This offers the possibility to mask sea areas or to clip and extract the terrestrial range parts using GIS data layers of the users' choice. An additional version of polygon ranges are clipped with a coastline (name suffix "clip"), which have been derived from Natural Earth dataset "Admin 0 - Countries" 1:50M version 4.1.0 (https://www.naturalearthdata.com). <br><br>Please cite as:<br>Caudullo, G., Welk, E., San-Miguel-Ayanz, J., 2017. Chorological maps for the main European woody species. Data in Brief 12, 662-666. DOI: doi.org/10.1016/j.dib.2017.05.007 <br><br>Additional information and used references are on 'supplementary materials' document:<br>https://doi.org/10.6084/m9.figshare.5091901<br><br>Chorological maps are part of the "European Atlas of Forest Tree Species" project:<br>https://w3id.org/mtv/FISE-Comm/v01
DOI: 10.6084/m9.figshare.5114149.v1
title: datasets and scripts for article Measuring behavioral thermal tolerance to address hot topics in ecology, evolution, and conservation

description: datasets and scripts that allow reproducing the article with that name<br>
DOI: 10.6084/m9.figshare.5114116
title: Sambucus nigra chorology

description: Distribution map of black elderberry (<i>Sambucus nigra</i>)<br><br>These maps were produced by combining numerous and heterogeneous data collected from atlas monographs providing complete species distribution maps, from national to regional atlases, occurrence geo-databases, scientific and grey literature.<br>The maps were created using ESRI shapefiles (*.shp, *.shx, *.dbf, *.prj files) archived in the ZIP file. Species range is mapped with polygon features (name suffix "plg"), which define continuous areas of occupancy of the species, and with point features (name suffix "pnt"), which identify more fragmented and isolated populations. If synanthropic occurrences are reported outside the species natural range, additional point and/or polygon shapefiles are also present (suffix "syn"). <br>Polygon borders delimiting species ranges are generalized across the mainland and sea boundaries. This offers the possibility to mask sea areas or to clip and extract the terrestrial range parts using GIS data layers of the users' choice. An additional version of polygon ranges are clipped with a coastline (name suffix "clip"), which have been derived from Natural Earth dataset "Admin 0 - Countries" 1:50M version 4.1.0 (https://www.naturalearthdata.com). <br><br>Please cite as:<br>Caudullo, G., Welk, E., San-Miguel-Ayanz, J., 2017. Chorological maps for the main European woody species. Data in Brief 12, 662-666. DOI: doi.org/10.1016/j.dib.2017.05.007 <br><br>Additional information and used references are on 'supplementary materials' document:<br>https://doi.org/10.6084/m9.figshare.5091901<br><br>Chorological maps are part of the "European Atlas of Forest Tree Species" project:<br>https://w3id.org/mtv/FISE-Comm/v01
DOI: 10.6084/m9.figshare.5114125
title: Sorbus aucuparia chorology

description: Distribution map of rowan (<i>Sorbus aucuparia</i>)<br><br>These maps were produced by combining numerous and heterogeneous data collected from atlas monographs providing complete species distribution maps, from national to regional atlases, occurrence geo-databases, scientific and grey literature.<br>The maps were created using ESRI shapefiles (*.shp, *.shx, *.dbf, *.prj files) archived in the ZIP file. Species range is mapped with polygon features (name suffix "plg"), which define continuous areas of occupancy of the species, and with point features (name suffix "pnt"), which identify more fragmented and isolated populations. If synanthropic occurrences are reported outside the species natural range, additional point and/or polygon shapefiles are also present (suffix "syn"). <br>Polygon borders delimiting species ranges are generalized across the mainland and sea boundaries. This offers the possibility to mask sea areas or to clip and extract the terrestrial range parts using GIS data layers of the users' choice. An additional version of polygon ranges are clipped with a coastline (name suffix "clip"), which have been derived from Natural Earth dataset "Admin 0 - Countries" 1:50M version 4.1.0 (https://www.naturalearthdata.com). <br><br>Please cite as:<br>Caudullo, G., Welk, E., San-Miguel-Ayanz, J., 2017. Chorological maps for the main European woody species. Data in Brief 12, 662-666. DOI: doi.org/10.1016/j.dib.2017.05.007 <br><br>Additional information and used references are on 'supplementary materials' document:<br>https://doi.org/10.6084/m9.figshare.5091901<br><br>Chorological maps are part of the "European Atlas of Forest Tree Species" project:<br>https://w3id.org/mtv/FISE-Comm/v01