cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4570616
title: Chromosight benchmarks and processed data

description: Input data and scripts required to rerun chromosight's benchmarks and associated figures from the manuscript, as well as output results in text format. The record contains 4 tarballs corresponding to two different benchmarks and various processed files. Each tarball contains the scripts, input and output data of its benchmark: <strong>Performance benchmark:</strong> This benchmark is contained in "20200406_benchmark_chromosight_performance.tar.gz" and compares chromosight running time and RAM use with 2 other softwares. This benchmark is run on a real high resolution human Hi-C matrix with different subsampling values. Benchmark scripts are expected to be run on a regular laptop or desktop. <strong>Results benchmark:</strong> This benchmark is contained in "20200406_benchmark_chromosight_results.tar.gz" and assess chromosight's ability to detect chromatin loop patterns on Hi-C contact maps. Chromosight is compared to 4 other softwares. For each software, precision, recall (=sensitivity) and F1 scores are measured using 2000 small synthetic Hi-C matrices with known loop coordinates. Each software is run with a range of 50-200 parameter combinations for all data. Scripts to run this benchmark are written to run as a job array on a SLURM computing cluster to reduce compute time. <strong>Processed data files</strong> Intermediate and output files used throughout the manuscript. This includes contact matrices in cool format, genomic intervals in BED or BED2D format and loop calls from public data for different softwares. <strong>Simulation input:</strong> The file "simulation_input.tar.gz" contains the inputs used to generate synthetic Hi-C contact maps used in the results benchmark. it consists of a contact map from the chromosome 5 <em>Saccharomyces cerevisiae</em> strain W303 from this project, and a corresponding set of domain border coordinates detected on this contact map as described in the methods of Chromosight's paper. Border coordinates are counted in bins from the start of chromosome 5. Both files can be fed to the "chromo_simul.py" script available on github as follows to generate synthetic contact maps:<br> `python chromo_simul.py matrix.cool chr5 borders.txt out_dir`
DOI: 10.5281/zenodo.3742094
title: Chromosight benchmarks and processed data

description: Input data and scripts required to rerun chromosight's benchmarks and associated figures from the manuscript, as well as output results in text format. The record contains 4 tarballs corresponding to two different benchmarks and various processed files. Each tarball contains the scripts, input and output data of its benchmark: <strong>Performance benchmark:</strong> This benchmark is contained in "20200406_benchmark_chromosight_performance.tar.gz" and compares chromosight running time and RAM use with 2 other softwares. This benchmark is run on a real high resolution human Hi-C matrix with different subsampling values. Benchmark scripts are expected to be run on a regular laptop or desktop. <strong>Results benchmark:</strong> This benchmark is contained in "20200406_benchmark_chromosight_results.tar.gz" and assess chromosight's ability to detect chromatin loop patterns on Hi-C contact maps. Chromosight is compared to 4 other softwares. For each software, precision, recall (=sensitivity) and F1 scores are measured using 2000 small synthetic Hi-C matrices with known loop coordinates. Each software is run with a range of 50-200 parameter combinations for all data. Scripts to run this benchmark are written to run as a job array on a SLURM computing cluster to reduce compute time. <strong>Processed data files</strong> Intermediate and output files used throughout the manuscript. This includes contact matrices in cool format, genomic intervals in BED or BED2D format and loop calls from public data for different softwares. <strong>Simulation input:</strong> The file "simulation_input.tar.gz" contains the inputs used to generate synthetic Hi-C contact maps used in the results benchmark. it consists of a contact map from the chromosome 5 <em>Saccharomyces cerevisiae</em> strain W303 from this project, and a corresponding set of domain border coordinates detected on this contact map as described in the methods of Chromosight's paper. Border coordinates are counted in bins from the start of chromosome 5. Both files can be fed to the "chromo_simul.py" script available on github as follows to generate synthetic contact maps:<br> `python chromo_simul.py matrix.cool chr5 borders.txt out_dir`
DOI: 10.17037/data.00002091
title: Behavioural change towards reduced intensity physical activity is disproportionately prevalent among adults with serious health issues or self-perception of high risk during the UK COVID-19 lockdown.

description: Quantitative data on physical activity and health behaviours during the UK COVID-19 lockdown. The anonymous web-based survey was performed between 6th April and 22 April 2020, approximately mapping to weeks 3-5 of the lockdown in the UK. The main survey included 49 questions which covered a broad range of topics including (1) Demographics, (2) Health and Health Behaviours, (3) Adherence to COVID-19 Control measures, (4) Information sources used to learn about COVID-19, (5) Trust in various information sources, government and government decision-making, (6) Rumours and misinformation, (7) Contact & Communication during COVID-19 and (8) Fear and Isolation. This data set includes 20 variables and 9,190 responses. It relates to medRxiv submission MEDRXIV/2020/098921 - Version 1.
description: The survey was publicised using a ‘daisy-chaining’ approach in which respondents were asked to share and to encourage onward sharing of the survey’s Uniform Resource Locator (URL) among friends & colleagues. The study team directly targeted a number of faith institutions, schools and special interest groups and also used Facebook’s premium “Boost Post” feature. A “boosted” post functions as an advert which can be targeted at specific demographics. We boosted details of the survey and it’s URL to a target audience of 113,280 Facebook users aged 13-65+ years and living in England, Wales, Scotland and Northern Ireland. Participants were also provided with URL links to a set of freely available summary reports and analyses which were periodically updated in near-real time. We used an ODK XForm (https://getodk.github.io/xforms-spec/) deployed on Enketo smart paper (https://enketo.org/) via ODK Aggregate v.2.0.3 (https://github.com/getodk/aggregate). Form level encryption and end-to-end encryption of data transfer were implemented on all submissions.
DOI: 10.5281/zenodo.4570636
title: Raw data related to "Interleukin-9 regulates macrophage activation in the progressive multiple sclerosis brain"

description: Levels of activation markers and cytokine production in human macrophages stimulated with IL-9, analysed by flow cytometry and ELISA, respectively.
DOI: 10.5281/zenodo.4570635
title: Raw data related to "Interleukin-9 regulates macrophage activation in the progressive multiple sclerosis brain"

description: Levels of activation markers and cytokine production in human macrophages stimulated with IL-9, analysed by flow cytometry and ELISA, respectively.
DOI: 10.6084/m9.figshare.14135966
title: Evolutionary coupling of female signals.zip

description: Attached in this .zip files are the raw excel files for each dataset used in this study. Included is an R Studio project file and is accompanied by 4 separate R scripts for ease of reading.
DOI: 10.6084/m9.figshare.14135966.v1
title: Evolutionary coupling of female signals.zip

description: Attached in this .zip files are the raw excel files for each dataset used in this study. Included is an R Studio project file and is accompanied by 4 separate R scripts for ease of reading.
DOI: 10.15468/ka328g
title: The Palaearctic types of Chrysididae (Insecta, Hymenoptera) deposited in the Linsenmaier collection. Part 1. Cleptes Latreille

description: This dataset contains the digitized treatments in Plazi based on the original journal article Rosa, Paolo, Heim, René, Bernasconi, Marco Valerio (2020): The Palaearctic types of Chrysididae (Insecta, Hymenoptera) deposited in the Linsenmaier collection. Part 1. Cleptes Latreille. Zootaxa 4881 (1): 54-72, DOI: https://doi.org/10.11646/zootaxa.4881.1.3
DOI: 10.17037/data.00002015
title: Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK - Quantitative Data

description: An anonymised quantitative dataset that contains results for a survey on public perceptions of the UK government's response during the first wave (April 2020) of the COVID-19 pandemic, with specific focus upon the relationship between trust and transparency. It contains data provided by 9,322 respondents aged 20 or over, who completed an online questionnaire between 6 and 22 April 2020. Responses indicate whether they consider the UK government to have made the correct decision, government priority, and their trust in government. It is accompanied by demographic information on the participant's age category, education level, gender, income level, region, and ethnicity, and the use of acceptable force. The only difference between this version (v2) and the previous (v1) is the addition of the acceptable_force column. Qualitative data for this study have not been made available due to the presence of sensitive and potentially disclosure information. See Methods section for information on data capture and analysis.
description: Anonymous survey data from UK residents were collected online between 2020-04-06 and 2020-04-22 using an Open Data Kit (ODK) XLSForm (https://getodk.github.io/xforms-spec/) deployed on Enketo smart paper (https://enketo.org/) via ODK Aggregate v.2.0.3 (https://github.com/getodk/aggregate). Form level encryption and end-to-end encryption of data transfer were implemented on all submissions. The survey contained 49 questions, which covered topics on (1) Demographics; (2) Health and Health Behaviours; (3) Adherence to COVID-19 Control measures; (4) Information sources used to learn about COVID-19; (5) Trust in various information sources, government and government decision-making; (6) Rumours and misinformation; (7) Contact & Communication during COVID-19; and (8) Fear and Isolation. The survey was distributed using Facebook’s premium “Boost Post” feature, which enables a post to function as an advert that can be targeted at specific demographics. The study team boosted details of the survey and its URL to a target audience of 113,280 Facebook users aged 13-65+ years and living in England, Wales, Scotland and Northern Ireland. The survey was further distributed using a ‘daisy-chaining’ approach in which respondents were asked to share and encourage onward sharing of the survey’s Uniform Resource Locator (URL) among friends & colleagues. A number of faith institutions, schools and special interest groups were also contacted directly for assistance in dissemination of the URL. A mixed methods approach was taken to data analysis, combining statistical analyses, structural topic modelling (STM) and qualitative thematic coding of a sub-set of responses. Missing data were imputed via multiple imputation.
DOI: 10.7284/139574
title: Multiplexed data collected during research cruise NBP1510 using a HOBI HydroDAS instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139570
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise NBP1510 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139566
title: Gravimeter data collected during research cruise NBP1510 using a Bell BGM-3 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139577
title: Gyrocompass data collected during research cruise NBP1510 using a Yokogawa CMZ700B instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139576
title: INS (Inertial Navigation System) data collected during research cruise NBP1510 using a Kongsberg Seapath 330+ instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139568
title: Meteorological Station data collected during research cruise NBP1510 using a USAP RVDAS Metstation instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139567
title: pCO2 (Partial Pressure of Carbon Dioxide) data collected during research cruise NBP1510 using a LDEO pCO2 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139569
title: Radiometer data collected during research cruise NBP1510 using a Biospherical GUV-2511 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139580
title: Singlebeam Echosounder data collected during research cruise NBP1510 using a Knudsen 3260 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139575
title: SSV (Sound Speed Velocimeter) data collected during research cruise NBP1510 using a AML SV2000 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139573
title: Water Temperature data collected during research cruise NBP1510 using a Sea-Bird SBE-38 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139571
title: TSG (Thermosalinograph) data collected during research cruise NBP1510 using a Sea-Bird SBE-45 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139572
title: TSG (Thermosalinograph) data collected during research cruise NBP1510 using a Sea-Bird SBE-45 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139578
title: Winch data collected during research cruise NBP1510 using a Markey DUSH-5 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139579
title: Winch data collected during research cruise NBP1510 using a Markey DUSH-9-11 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139557
title: Multiplexed data collected during research cruise NBP1511 using a HOBI HydroDAS instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139553
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise NBP1511 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139549
title: Gravimeter data collected during research cruise NBP1511 using a Bell BGM-3 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139560
title: Gyrocompass data collected during research cruise NBP1511 using a Yokogawa CMZ700B instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139548
title: INS (Inertial Navigation System) data collected during research cruise NBP1511 using a Kongsberg Seapath 200 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139559
title: INS (Inertial Navigation System) data collected during research cruise NBP1511 using a Kongsberg Seapath 330+ instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139551
title: Meteorological Station data collected during research cruise NBP1511 using a USAP RVDAS Metstation instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139565
title: Multibeam Echosounder data collected during research cruise NBP1511 using a Kongsberg EM122 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139550
title: pCO2 (Partial Pressure of Carbon Dioxide) data collected during research cruise NBP1511 using a LDEO pCO2 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139552
title: Radiometer data collected during research cruise NBP1511 using a Biospherical GUV-2511 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139564
title: Singlebeam Echosounder data collected during research cruise NBP1511 using a Knudsen 3260 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139558
title: SSV (Sound Speed Velocimeter) data collected during research cruise NBP1511 using a AML SV2000 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139556
title: Water Temperature data collected during research cruise NBP1511 using a Sea-Bird SBE-38 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139554
title: TSG (Thermosalinograph) data collected during research cruise NBP1511 using a Sea-Bird SBE-45 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139555
title: TSG (Thermosalinograph) data collected during research cruise NBP1511 using a Sea-Bird SBE-45 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139561
title: Winch data collected during research cruise NBP1511 using a Markey DUSH-5 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139562
title: Winch data collected during research cruise NBP1511 using a Markey DUSH-5-5 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/139563
title: Winch data collected during research cruise NBP1511 using a Markey DUSH-9-11 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17037/data.00001859
title: Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK - Qualitative Data

description: A qualitative dataset that contains free-text responses collected during a survey of public perceptions of the UK government's response during the first wave (April 2020) of the COVID-19 pandemic, with specific focus upon the relationship between trust and transparency. It contains free text responses of approximately 7,600 people, drawn from a total of 9,322 respondents who completed the online questionnaire. Respondents were asked the question "Do you think that the government tells you the whole truth about coronavirus and COVID-19?" with the possible answers "Always","Mostly","Sometimes","Almost never", "Never" and "I don't know". Those who did not answer "Always" were then asked to "Briefly describe what it is that you think the government is not being fully truthful about?"
description: Anonymous survey data from UK residents were collected online between 2020-04-06 and 2020-04-22 using an Open Data Kit (ODK) XLSForm (https://getodk.github.io/xforms-spec/) deployed on Enketo smart paper (https://enketo.org/) via ODK Aggregate v.2.0.3 (https://github.com/getodk/aggregate). Form level encryption and end-to-end encryption of data transfer were implemented on all submissions. The survey contained 49 questions, which covered topics on (1) Demographics; (2) Health and Health Behaviours; (3) Adherence to COVID-19 Control measures; (4) Information sources used to learn about COVID-19; (5) Trust in various information sources, government and government decision-making; (6) Rumours and misinformation; (7) Contact & Communication during COVID-19; and (8) Fear and Isolation. The survey was distributed using Facebook’s premium “Boost Post” feature, which enables a post to function as an advert that can be targeted at specific demographics. The study team boosted details of the survey and its URL to a target audience of 113,280 Facebook users aged 13-65+ years and living in England, Wales, Scotland and Northern Ireland. The survey was further distributed using a ‘daisy-chaining’ approach in which respondents were asked to share and encourage onward sharing of the survey’s Uniform Resource Locator (URL) among friends & colleagues. A number of faith institutions, schools and special interest groups were also contacted directly for assistance in dissemination of the URL. A mixed methods approach was taken to data analysis, combining statistical analyses, structural topic modelling (STM) and qualitative thematic coding of a sub-set of responses. Missing data were imputed via multiple imputation.
DOI: 10.6084/m9.figshare.14135804
title: Dog Brain qPCR data

description: Rq and CQ qPCR data for wildtype and DE50-MD (Muscular dystrophy model) dog brain: assessment of panel of potential reference genes for normalisation<br>Data for manuscript entitled <i>"<b>Identification of quantitative polymerase chain reaction reference genes suitable for normalizing gene expression in the brain of normal and dystrophic mice and dogs"</b></i><b></b>
DOI: 10.6084/m9.figshare.14135804.v2
title: Dog Brain qPCR data

description: Rq and CQ qPCR data for wildtype and DE50-MD (Muscular dystrophy model) dog brain: assessment of panel of potential reference genes for normalisation<br>Data for manuscript entitled <i>"<b>Identification of quantitative polymerase chain reaction reference genes suitable for normalizing gene expression in the brain of normal and dystrophic mice and dogs"</b></i><b></b>
DOI: 10.6084/m9.figshare.14135804.v1
title: Dog brain qPCR data

description: Rq and CQ qPCR data for wildtype and DE50-MD (Muscular dystrophy model) dog brain: assessment of panel of potential reference genes for normalisation<br>Data for manuscript entitled <i>"<b>Identification of quantitative polymerase chain reaction reference genes suitable for normalizing gene expression in the brain of normal and dystrophic mice and dogs"</b></i><b></b>
DOI: 10.6084/m9.figshare.14135660.v1
title: Mouse Brain qPCR Results

description: Cq and RQ data for qPCR analysis of wildtype and mdx mouse brains: assessment of a panel of potential reference genes.<br>Data for manuscript "Identification of quantitative polymerase chain reaction reference genes suitable for normalizing gene expression in the brain of normal and dystrophic mice and dogs"<br>