cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7871978.v1
title: The anti-cancer drug 5-fluorouracil affects cell cycle regulators and potential regulatory long non-coding RNAs in yeast

description: 5-fluorouracil (5-FU) was isolated as an inhibitor of thymidylate synthase, which is important for DNA synthesis. The drug was later found to also affect the conserved 3ʹ-5ʹ exoribonuclease EXOSC10/Rrp6, a catalytic subunit of the RNA exosome that degrades and processes protein-coding and non-coding transcripts. Work on 5-FU’s cytotoxicity has been focused on mRNAs and non-coding transcripts such as rRNAs, tRNAs and snoRNAs. However, the effect of 5-FU on long non-coding RNAs (lncRNAs), which include regulatory transcripts important for cell growth and differentiation, is poorly understood. RNA profiling of synchronized 5-FU treated yeast cells and protein assays reveal that the drug specifically inhibits a set of cell cycle regulated genes involved in mitotic division, by decreasing levels of the paralogous Swi5 and Ace2 transcriptional activators. We also observe widespread accumulation of different lncRNA types in treated cells, which are typically present at high levels in a strain lacking EXOSC10/Rrp6. 5-FU responsive lncRNAs include potential regulatory antisense transcripts that form double-stranded RNAs (dsRNAs) with overlapping sense mRNAs. Some of these transcripts encode proteins important for cell growth and division, such as the transcription factor Ace2, and the RNA exosome subunit EXOSC6/Mtr3. In addition to revealing a transcriptional effect of 5-FU action via DNA binding regulators involved in cell cycle progression, our results have implications for the function of putative regulatory lncRNAs in 5-FU mediated cytotoxicity. The data raise the intriguing possibility that the drug deregulates lncRNAs/dsRNAs involved in controlling eukaryotic cell division, thereby highlighting a new class of promising therapeutical targets.
DOI: 10.6084/m9.figshare.7871972
title: gVCF_HG00123

description: 1000 Genomes gVCF mapped to hs37d5 for HG00123.
DOI: 10.6084/m9.figshare.7871972.v1
title: gVCF_HG00123

description: 1000 Genomes gVCF mapped to hs37d5 for HG00123.
DOI: 10.6084/m9.figshare.7871912
title: Bi_etal_2019_associatedData

description: Supporting data for main figures 2 and 4, as reported in:Bi et al. (2019) Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. PLoS Genetics, accepted.<br>Raw sequence data have been deposited on the NCBI Sequence Read Archive under BioProject Accession IDs PRJNA312223 (SRA: SRP070198) and PRJNA312234 (SRA: SRP191784). All custom scripts developed for data filtering and population genetic analysis have been deposited in GitHub (https://github.com/tplinderoth/ngsQCdoi: 10.5281/zenodo.2592044, and https://github.com/tplinderoth/ABCutilsdoi: 10.5281/zenodo.2591546).<b></b>
DOI: 10.6084/m9.figshare.7871882
title: Matrix

description: MALDI Mass Spec Expression Matrix and Pheno data
DOI: 10.6084/m9.figshare.7871897
title: Surgically managed giant left atrial appendage clots

description: Surgically managed giant left atrial appendage clots
DOI: 10.6084/m9.figshare.7871912.v1
title: Bi_etal_2019_associatedData

description: Supporting data for main figures 2 and 4, as reported in:Bi et al. (2019) Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. PLoS Genetics, accepted.<br>Raw sequence data have been deposited on the NCBI Sequence Read Archive under BioProject Accession IDs PRJNA312223 (SRA: SRP070198) and PRJNA312234 (SRA: SRP191784). All custom scripts developed for data filtering and population genetic analysis have been deposited in GitHub (https://github.com/tplinderoth/ngsQCdoi: 10.5281/zenodo.2592044, and https://github.com/tplinderoth/ABCutilsdoi: 10.5281/zenodo.2591546).<b></b>
DOI: 10.6084/m9.figshare.7871897.v1
title: Surgically managed giant left atrial appendage clots

description: Surgically managed giant left atrial appendage clots
DOI: 10.6084/m9.figshare.7871882.v1
title: MALDI Mass Spec Expression Matrix and Pheno data

description: MALDI Mass Spec Expression Matrix and Pheno data
DOI: 10.6084/m9.figshare.7871747
title: PM2.5 disease burdens in cities worldwide

description: This dataset includes the results published in Anenberg, S.C., P. Achakulwisut, M. Brauer, D. Moran, J.S. Apte, and D. Henze (2019) Particulate matter, carbon dioxide, and premature mortality in 250 urban areas worldwide. Scientific Reports, in press.<br><br>variable definitions:<br>id=city idcity=name of urban areacluster=cities within each urban arealat=latitudelon=longitudeiso3c=ISO 3 Codecountry=country <br>gbd_region=Global Burden of Disease regiongbd_superregion=Global Burden of Disease super-regionpop.2016=population in 2016popw.pm=population weighted annual average PM2.5 concentration (in ug/m3)pmdeaths=PM2.5-attributable premature deathspct_ihd=percent of PM2.5-attributable premature deaths that are from ischemic heart diseasepct_stroke=percent of PM2.5-attributable premature deaths that are from strokepct_copd=percent of PM2.5-attributable premature deaths that are from chronic obstructive pulmonary diseasepct_lc=percent of PM2.5-attributable premature deaths that are from lung cancerpct_lri=percent of PM2.5-attributable premature deaths that are from lower respiratory infectionspmdeaths_2.5prctl=lower end of the 95% confidence interval for PM2.5-attributable premature deathspmdeaths_97.5prctl=upper end of the 95% confidence interval for PM2.5-attributable premature deaths<br>
DOI: 10.6084/m9.figshare.7871882.v2
title: MALDI Mass Spec Expression Matrix and Pheno data

description: MALDI Mass Spec Expression Matrix and Pheno data
DOI: 10.23645/epacomptox.7871537.v1
title: Chemical and Product Categories (CPCat) database

description: The EPA CPCat (Chemical and Product Categories) database was released in May 2014. It maps &gt;43,000 chemicals to a set of terms categorizing their usage or function. We have compiled a comprehensive list of chemicals with associated categories of chemical and product use by compiling publicly available sources. Sources include, but are not limited to: the Substances in Preparation in Nordic Countries (SPIN) database, information provided by companies, trade associations, and regulatory agencies such as the U.S. Environmental Protection Agency (EPA) and Food and Drug Administration (FDA), the DrugBank database of pharmaceutical products, and information mined from the Aggregated Computational Toxicology Resource (ACToR) database developed by the U.S. EPA. Unique use category taxonomies from each source are mapped onto a single common set of ~800 terms. The user can search for chemicals by chemical name, Chemical Abstracts Registry Number (CASRN), or by CPCat terms (i.e. category names) associated with chemicals. See Dionisio et al., 2014 for a full description of the database, sources used, interpretation of chemical categories, and potential applications. The .zip file available at the "Download" tab of this website provides a full copy of the database, available for free download, which can be freely searched and sorted for data analysis. The .zip file includes a list of all chemicals included in CPCat. A list of all sources included in CPCat is provided in the table below.
DOI: 10.6084/m9.figshare.7870955
title: pmn_300k.rmc6f

description: this file contains a refined atomic configuration for Pb(Mg1/3Nb2/3)O3 in the rmc6f format of the RMCProfile software. www.rmcprofile.org
DOI: 10.6084/m9.figshare.7870955.v1
title: pmn_300k.rmc6f

description: this file contains a refined atomic configuration for Pb(Mg1/3Nb2/3)O3 in the rmc6f format of the RMCProfile software. www.rmcprofile.org
DOI: 10.6084/m9.figshare.7871354
title: External validation of prognostic models for preeclampsia in a Dutch multicenter prospective cohort

description: <b>Objective</b>: To perform an external validation of all published prognostic models for first-trimester prediction of the risk of developing preeclampsia (PE). <b>Methods</b>: Women &lt;14 weeks of pregnancy were recruited in the Netherlands. All systematically identified prognostic models for PE that contained predictors commonly available were eligible for external validation. <b>Results</b>: 3,736 women were included; 87 (2.3%) developed PE. Calibration was poor due to overestimation. Discrimination of 9 models for LO-PE ranged from 0.58 to 0.71 and of 9 models for all PE from 0.55 to 0.75. <b>Conclusion</b>: Only a few easily applicable prognostic models for all PE showed discrimination above 0.70, which is considered an acceptable performance.
DOI: 10.6084/m9.figshare.7871354.v1
title: External validation of prognostic models for preeclampsia in a Dutch multicenter prospective cohort

description: <b>Objective</b>: To perform an external validation of all published prognostic models for first-trimester prediction of the risk of developing preeclampsia (PE). <b>Methods</b>: Women &lt;14 weeks of pregnancy were recruited in the Netherlands. All systematically identified prognostic models for PE that contained predictors commonly available were eligible for external validation. <b>Results</b>: 3,736 women were included; 87 (2.3%) developed PE. Calibration was poor due to overestimation. Discrimination of 9 models for LO-PE ranged from 0.58 to 0.71 and of 9 models for all PE from 0.55 to 0.75. <b>Conclusion</b>: Only a few easily applicable prognostic models for all PE showed discrimination above 0.70, which is considered an acceptable performance.
DOI: 10.6084/m9.figshare.7869413
title: Phenotypic responses of invasive species to removals affect ecosystem functioning and restoration: implications for invasion management

description: Data to the paper Závorka et al. (2020) published in Global Change Biology.
DOI: 10.6084/m9.figshare.7869389
title: Prevalence and dynamics of missed opportunities for vaccination among children in Africa: applying systems thinking in a systematic review and meta-analysis of observational studies

description: <b>Objective</b>: To estimate the prevalence of missed opportunities for vaccination (MOV) among children aged 0–23 months attending health-care facilities in Africa and explore the factors responsible for MOV using systems thinking. <b>Research design and methods</b>: We conducted a systematic review and meta-analysis of studies reporting the proportion MOVs. Five electronic databases were searched. A random effects model was fitted to obtain pooled estimates of MOV and a causal loop diagram (CLD) was constructed to explore the dynamics of the causes of MOV. MOV was defined as any contact with health services in Africa, by an unvaccinated or under-vaccinated child, aged 0–23 months, who is eligible for vaccination and free of any contraindication, which does not result in vaccination. <b>Results</b>: Four hundred and twenty-one publications were found, of which 20 studies from 14 countries were included. The pooled prevalence of MOV was estimated to be 27.26% (95%CI: 18.80–36.62). A CLD with seven reinforcing and two balancing loops were constructed. <b>Conclusion</b>: Our findings suggest that about one in every four children under the age of two years who visited health facilities in 14 African countries missed the vaccination they were eligible to receive. To enable continent-wide estimates, more MOV assessments are required.
DOI: 10.6084/m9.figshare.7869413.v1
title: Phenotypic responses of invasive species to removals affect ecosystem functioning and restoration: implications for invasion management

description: Data to the paper Závorka et al. (2020) published in Global Change Biology.
DOI: 10.6084/m9.figshare.7869383
title: Distractor familiarity reveals the importance of configural information in musical notation

description: data for 2 experiments in submitted paper by Chang & Gauthier
DOI: 10.6084/m9.figshare.7869416.v1
title: GOSH_v4.pdf

description: Poster on "Open Science Hardware in Microbiology" presented on the "Molecular Biology of Plant Pathogens" meeting in 2019 by Alexander Kutschera (19.03.2019).<br>Hardware is a vital part of science: microscopes, sensors, reagents and instruments are all central to experimentation but the current supply chain limits access to many people and impedes creativity and customisation. Open Science Hardware addresses part of this problem through sharing open designs to expand the availability of customisable and often lower cost tools within academic research, citizen science and education. Technologies such as 3D printing and electronics platforms like Arduino and Raspberry Pi are making it ever easier to get started with designing hardware for your experiments. Here we present two projects as examples for Open Science Hardware in Microbiology.We recently developed a low-cost test tube photometer which is capable of performing continuous cell-density measurements [1]. It is based on a simple photodiode with on-board signal amplification which is connected to a microcontroller. The housing consists out of modular 3D-printed parts which can be easily customized to fit different test tube sizes. The accuracy of the device is equal to commercial photometers and can be used to monitor growth dynamics of microbes. In another project we designed a 3D-printable lighting chamber for agar plates and combined it with a single-board computer and camera. It can be used to take time-lapse images and process the content. We used it to monitor bacterial swarming motility and calculate motility dynamics over time.<br>
DOI: 10.6084/m9.figshare.7869389.v2
title: Prevalence and dynamics of missed opportunities for vaccination among children in Africa: applying systems thinking in a systematic review and meta-analysis of observational studies

description: <b>Objective</b>: To estimate the prevalence of missed opportunities for vaccination (MOV) among children aged 0–23 months attending health-care facilities in Africa and explore the factors responsible for MOV using systems thinking. <b>Research design and methods</b>: We conducted a systematic review and meta-analysis of studies reporting the proportion MOVs. Five electronic databases were searched. A random effects model was fitted to obtain pooled estimates of MOV and a causal loop diagram (CLD) was constructed to explore the dynamics of the causes of MOV. MOV was defined as any contact with health services in Africa, by an unvaccinated or under-vaccinated child, aged 0–23 months, who is eligible for vaccination and free of any contraindication, which does not result in vaccination. <b>Results</b>: Four hundred and twenty-one publications were found, of which 20 studies from 14 countries were included. The pooled prevalence of MOV was estimated to be 27.26% (95%CI: 18.80–36.62). A CLD with seven reinforcing and two balancing loops were constructed. <b>Conclusion</b>: Our findings suggest that about one in every four children under the age of two years who visited health facilities in 14 African countries missed the vaccination they were eligible to receive. To enable continent-wide estimates, more MOV assessments are required.
DOI: 10.6084/m9.figshare.7869383.v1
title: Distractor familiarity reveals the importance of configural information in musical notation

description: data for 2 experiments in submitted paper by Chang & Gauthier
DOI: 10.6084/m9.figshare.7869389.v1
title: Prevalence and dynamics of missed opportunities for vaccination among children in Africa: applying systems thinking in a systematic review and meta-analysis of observational studies

description: <b>Objective</b>: To estimate the prevalence of missed opportunities for vaccination (MOV) among children aged 0–23 months attending health-care facilities in Africa and explore the factors responsible for MOV using systems thinking. <b>Research design and methods</b>: We conducted a systematic review and meta-analysis of studies reporting the proportion MOVs. Five electronic databases were searched. A random effects model was fitted to obtain pooled estimates of MOV and a causal loop diagram (CLD) was constructed to explore the dynamics of the causes of MOV. MOV was defined as any contact with health services in Africa, by an unvaccinated or under-vaccinated child, aged 0–23 months, who is eligible for vaccination and free of any contraindication, which does not result in vaccination. <b>Results</b>: Four hundred and twenty-one publications were found, of which 20 studies from 14 countries were included. The pooled prevalence of MOV was estimated to be 27.26% (95%CI: 18.80–36.62). A CLD with seven reinforcing and two balancing loops were constructed. <b>Conclusion</b>: Our findings suggest that about one in every four children under the age of two years who visited health facilities in 14 African countries missed the vaccination they were eligible to receive. To enable continent-wide estimates, more MOV assessments are required.
DOI: 10.6084/m9.figshare.7869365.v1
title: Ensemble Kalman methods for high-dimensional hierarchical dynamic space-time models

description: We propose a new class of filtering and smoothing methods for inference in high-dimensional, nonlinear, non-Gaussian, spatio-temporal state-space models. The main idea is to combine the ensemble Kalman filter and smoother, developed in the geophysics literature, with state-space algorithms from the statistics literature. Our algorithms address a variety of estimation scenarios, including on-line and off-line state and parameter estimation. We take a Bayesian perspective, for which the goal is to generate samples from the joint posterior distribution of states and parameters. The key benefit of our approach is the use of ensemble Kalman methods for dimension reduction, which allows inference for high-dimensional state vectors. We compare our methods to existing ones, including ensemble Kalman filters, particle filters, and particle MCMC. Using a real data example of cloud motion and data simulated under a number of nonlinear and non-Gaussian scenarios, we show that our approaches outperform these existing methods.
DOI: 10.6084/m9.figshare.7869353
title: Data and code to reproduce Evans et al. 2019 - Microclimate and larval habitat density predict adult Aedes albopictus abundance in urban areas

description: This compressed file contains the data and code to reproduce all the analyses and figures in Evans et al. 2019 AJTMH.<br>Analyses are in the code directory, which contains scripts to clean data and create GLMMs. Scripts should be run in numbered order, with the working directory set to the project directory holding the 'code' and 'data' directories. Scripts beginning with xx are not needed for analysis.
DOI: 10.6084/m9.figshare.7869350.v1
title: Simultaneous Variable and Covariance Selection with the Multivariate Spike-and-Slab LASSO

description: We propose a Bayesian procedure for simultaneous variable and covariance selection using continuous spike-and-slab priors in multivariate linear regression models where <i>q</i> possibly correlated responses are regressed onto <i>p</i> predictors. Rather than relying on a stochastic search through the high-dimensional model space, we develop an ECM algorithm similar to the EMVS procedure of Ročková & George (2014) targeting modal estimates of the matrix of regression coefficients and residual precision matrix. Varying the scale of the continuous spike densities facilitates dynamic posterior exploration and allows us to filter out negligible regression coefficients and partial covariances gradually. Our method is seen to substantially outperform regularization competitors on simulated data. We demonstrate our method with a re-examination of data from a recent observational study of the effect of playing high school football on several later-life cognition, psychological, and socio-economic outcomes. An R package, scripts for replicating examples in this article, and results from further simulation studies are provided in the Supplementary materials available online.
DOI: 10.6084/m9.figshare.7869299
title: Coho Data.zip

description: This contains choice experiment data from the 2019 paper by Lewis, Dundas, Kling, Lew, and Hacker on restoring Oregon Coast Coho salmon
DOI: 10.6084/m9.figshare.7869350.v2
title: Simultaneous Variable and Covariance Selection With the Multivariate Spike-and-Slab LASSO

description: We propose a Bayesian procedure for simultaneous variable and covariance selection using continuous spike-and-slab priors in multivariate linear regression models where <i>q</i> possibly correlated responses are regressed onto <i>p</i> predictors. Rather than relying on a stochastic search through the high-dimensional model space, we develop an ECM algorithm similar to the EMVS procedure of Ročková and George targeting modal estimates of the matrix of regression coefficients and residual precision matrix. Varying the scale of the continuous spike densities facilitates dynamic posterior exploration and allows us to filter out negligible regression coefficients and partial covariances gradually. Our method is seen to substantially outperform regularization competitors on simulated data. We demonstrate our method with a re-examination of data from a recent observational study of the effect of playing high school football on several later-life cognition, psychological, and socio-economic outcomes. An R package, scripts for replicating examples in this article, and results from further simulation studies are provided in the supplementary materials available online.
DOI: 10.6084/m9.figshare.7869293
title: An optimization method tracking EMG, ground reactions forces and marker trajectories for musculo-tendon forces estimation in equinus gait

description: A dataset of emulated equinus gait (toe walking) measured on a healthy adult participant (lower limbs kinematics, kinetics, EMG).<br>
DOI: 10.6084/m9.figshare.7869290
title: README-Description_of_files_Coho.docx

description: READ ME file. Describes data and Matlab code to replicate results in 2019 paper by Lewis, Dundas, Kling, Lew, and Hacker on willingness-to-pay for restoring Oregon Coast Coho Salmon
DOI: 10.6084/m9.figshare.7869299.v1
title: Coho Data.zip

description: This contains choice experiment data from the 2019 paper by Lewis, Dundas, Kling, Lew, and Hacker on restoring Oregon Coast Coho salmon
DOI: 10.6084/m9.figshare.7869290.v1
title: README-Description_of_files_Coho.docx

description: READ ME file. Describes data and Matlab code to replicate results in 2019 paper by Lewis, Dundas, Kling, Lew, and Hacker on willingness-to-pay for restoring Oregon Coast Coho Salmon