cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/hkn2tbcp67.1
title: Low-Cost VOC MOx Sensor Data for Estimating Individual and Groups of VOCs, Colorado, Summer 2014

description: Included are data and code to reproduce analysis in which the ability of low-cost VOC sensors to estimate ambient levels of individual and groups of VOCs is explored. This data was collected in Colorado at the Platteville Atmospheric Observatory during the FRAPPE/DISCOVER-AQ Campaigns (Summer 2014). More details regarding this analysis are available in the paper: "Understanding the ability of low-cost MOx sensors to quantify ambient VOCs ", Collier-Oxandale et al., 2019. A README is included for more detailed information regarding the data and its organization. Any questions should be addressed to the main contributor of this dataset and listed contact for the associated journal article.
DOI: 10.18112/openneuro.ds004148.v1.0.1
title: A test-retest resting and cognitive state EEG dataset
DOI: 10.18739/a2b853h78
title: Temperature and salinity profiles adjacent to a tidewater glacier in Sarqardleq Fjord, West Greenland, collected during July 2013
DOI: 10.5281/zenodo.2386816
title: GTEX BioBombe Results - Randomly Permuted Data

description: BioBombe analysis applied to <strong>randomly permuted </strong>gene expression data from The Genotype-Tissue Expression (GTEx) project. Method and results described in https://github.com/greenelab/BioBombe
DOI: 10.5522/04/20769637.v1
title: COG-UK hospital-onset COVID-19 infection study dataset

description: These files comprise the publicly available data for the COG-UK hospital-onset COVID-19 infection study. The individual CSV files provided are: - HOCI_public_dataset: Anonymized version of main study dataset, with one row per HOCI case included in the final analysis - HOCI_public_varlist: Variable descriptions for main study dataset - epi_data_combined: Weekly data on total SARS-CoV-2 +ve (cov_pos_epi) and -ve (cov_neg_epi) inpatients at each study site -community_incidence_summary: Weekly local community incidence data for each study site, per 100,000 people per week, obtained from UK government testing dashboard and weighted according to outer postcodes of inpatients at each site. <br> Notes on anonymisation: HOCI_public_dataset is an anonymised version of the main HOCI study database. In order to fully anonymise individuals, and because the focus of the study was on infection control actions rather than patient outcomes, all individual-level patient demographic and clinical characteristics have been removed. Site and ward names have been changed to anonymized codes, and all free text fields have been removed as some of these contained unblinded details of hospitals and wards. All date fields have been removed, with study week of SARS-CoV-2 +ve test result for each HOCI case provided. <br> Notes on acronyms: In ‘HOCI_public_varlist’, the following acronyms are used: AGP, aerosol-generating procedure CR, contact restrictions CT, contact tracing DIPC, Director of IPC HCAI, healthcare-associated infection HCW, healthcare worker IPC, infection prevention and control SR, sequence report SRO, sequence report output QM, quality management <br> <br>
DOI: 10.6084/m9.figshare.21079648
title: Supplementary Material for: Carotid Artery Stenosis and Progression of Hemispheric Brain Atrophy: The SMART-MR Study

description: <b><i>Introduction:</i></b> It has been hypothesized that carotid artery stenosis (CAS) may lead to greater atrophy of subserved brain regions; however, prospective studies on the impact of CAS on progression of hemispheric brain atrophy are lacking. We examined the association between CAS and progression of hemispheric brain atrophy. <b><i>Methods:</i></b> We included 654 patients (57 ± 9 years) of the SMART-MR study, a prospective cohort study of patients with manifest arterial disease. Patients had baseline CAS duplex measurements and a 1.5T brain MRI at baseline and after 4 years of follow-up. Mean change in hemispheric brain volumes (% of intracranial volume [ICV]) was estimated between baseline and follow-up for left-sided and right-sided CAS across three degrees of stenosis (mild [≤29%], moderate [30–69%], and severe [≥70%]), adjusting for demographics, cerebrovascular risk factors, and brain infarcts. <b><i>Results:</i></b> Mean decrease in left and right hemispheric brain volumes was 1.15% ICV and 0.82% ICV, respectively, over 4 years of follow-up. Severe right-sided CAS, compared to mild CAS, was associated with a greater decrease in volume of the left hemisphere (B = −0.49% ICV, 95% CI: −0.86 to −0.13) and more profoundly of the right hemisphere (B = −0.90% ICV, 95% CI: −1.27 to −0.54). This pattern was independent of cerebrovascular risk factors, brain infarcts, and white matter hyperintensities on MRI, and was also observed when accounting for the presence of severe bilateral CAS. Increasing degrees of left-sided CAS, however, was not associated with greater volume loss of the left or right hemisphere. <b><i>Conclusions:</i></b> Our data indicate that severe (≥70%) CAS could represent a risk factor for greater ipsilateral brain volume loss, independent of cerebrovascular risk factors, brain infarcts, or white matter hyperintensities on MRI. Further longitudinal studies in other cohorts are warranted to confirm this novel finding.
DOI: 10.6084/m9.figshare.21087634
title: Supplementary Material for: Early Enhancement with Contrast-Enhanced Ultrasonography Relates to the Number of Small-Diameter Neovessels in the Carotid Plaque

description: <b><i>Background and Purpose:</i></b> Intraplaque neovessels (INVs) have been recognized as a major cause of intraplaque hemorrhage and subsequent vulnerability of the carotid plaque. However, the exact mechanisms by which INVs cause intraplaque hemorrhage remain unclear. Various sizes of INVs coexist in carotid plaques pathologically, and we hypothesized that the size of INVs would be associated with carotid plaque histology, particularly in terms of intraplaque hemorrhage. Detection method of INV is important when determining whether carotid plaques are vulnerable, and contrast-enhanced ultrasonography (CEUS) is one of the most useful methods to detect them. The purpose of this study was to examine the relationship between findings from CEUS and vascular pathology obtained by carotid endarterectomy (CEA). We focused on associations between small and large INVs evaluated by CEUS and histologically defined intraplaque hemorrhage. <b><i>Methods:</i></b> Participants comprised 115 patients (mean age, 73.0 ± 7.2 years; 96 men) who underwent preoperative CEUS and underwent CEA. CEUS findings were evaluated as vascular grade at 0 min (Vas-G0) and 10 min (Vas-G10) after contrast injection. Plaques were histologically evaluated quantitatively for the total area of intraplaque hemorrhage, cholesterol, and calcification and the thinnest fibrous cap. Immunohistochemical studies were conducted using anti-CD-34 antibody as a marker for endothelial cells. INVs were divided into two groups depending on diameter: small INVs, &lt;50 μm; and large INVs, ≥50 μm. The numbers of small and large blood vessels in the plaque were quantified histologically. Associations of small and large INVs with CEUS, plaque histology, and clinical findings were assessed by uni- and multivariable analyses. <b><i>Results:</i></b> Multivariable analyses indicated that CEUS Vas-G0 was associated with the 4th quartile of the number of small INVs compared with other quartiles, and Vas-G10 was associated with the 4th quartile of the number of large INVs. Histologically, the presence and area of intraplaque hemorrhage were associated with the number of small INVs, while the increased number of large INVs was associated with infrequent plaque disruption and thicker fibrous cap. <b><i>Conclusions:</i></b> Our study showed that early phase enhancement in the CEUS can help identify plaque vulnerability by predicting a larger number of small INVs. This information can also help determine treatment strategies for carotid plaque.
DOI: 10.5281/zenodo.7041030
title: Demographic information, as well as questionnaire answers

description: Demographic information, as well as questionnaire answers
DOI: 10.6084/m9.figshare.21088495
title: Supplementary Material for: Effects of Direct Oral Anticoagulants’ Nonrecommended Dose in Atrial Fibrillation: A Meta-Analysis

description: <b><i>Background:</i></b> The efficacy and safety profiles of nonrecommended direct oral anticoagulant (DOAC) doses in patients with nonvalvular atrial fibrillation (NVAF) are still undefined. <b><i>Summary:</i></b> We searched for randomized controlled trials and observational studies that compared nonrecommended versus recommended doses of DOACs, published up to December 2021. Primary study outcomes were ischemic stroke/transient ischemic attack/systemic embolism (IS/TIA/SE) and major bleeding (MB). All-cause mortality was a secondary outcome. We determined pooled odds ratios (ORs) between groups of patients with a random-effect model. Twenty-three studies with 175,801 patients were included. Nonrecommended doses were associated with a higher risk of IS/TIA/SE and all-cause mortality, but not of MB as compared to recommended doses of DOACs (OR 1.25 [95% CI: 1.14–1.38], OR 1.69 [95% CI: 1.31–2.18] and OR 1.10 [95% CI: 0.93–1.31], respectively). The nonrecommended low dose was associated with an increased risk of IS/TIA/SE and all-cause death (OR 1.21 [95% CI: 1.05–1.39] and OR 1.66 [95% CI: 1.18–2.35], respectively) but not of MB (OR 1.01 [95% CI: 0.83–1.22] as compared to recommended doses. Subgroup analysis of nonrecommended low doses of DOACs showed a nonsignificant increase in IS/TIA/SE in Asians (OR 1.17 [95% CI: 0.89–1.54] vs. non-Asian (OR 1.21 [95% CI: 1.07–1.36]). <b><i>Key Messages:</i></b> Compared with recommended doses, nonrecommended low doses of DOACs increase the risk of ischemic events without decreasing the risk of bleeding. For Asians, the efficacy of DOACs seemed preserved despite the nonrecommended low-dose prescription. Clinicians should carefully adhere to recommended DOAC prescription advice in managing NVAF patients.
DOI: 10.6084/m9.figshare.7692269
title: High-Load Reovirus Infections Do Not Imply Physiological Impairment in Salmon - Collected and Generated Data

description: Data collected and generated as part of:<br>Zhang Y, Polinski MP, Morrison PR, Brauner CJ, Farrell APand Garver KA (2019) High-Load Reovirus Infections Do Not Imply Physiological Impairment in Salmon. Front. Physiol. 10:114. doi: 10.3389/fphys.2019.00114
DOI: 10.17632/73fpxk7vzb.1
title: Video data of the hydraulic fracturing propagation in two-dimensionally confined gelatin plate

description: This dataset comprises 36 raw and unprocessed video files obtained from the high-speed camera (UI-3360CP-C-HQ, IDS Corp.) during hydraulic fracturing test. The movies are formatted in MP4 format with the frame size of 1920 × 1080 pixels. Conditions for each experiment are indicated by the filename: S for the gelatin stiffness, Q for the fluid injection rate, and CP for the fluid viscosity. The video was recorded from the fluid injection. The bi-wing hydraulic fractures were generated and propagated, and then experiment was terminated by stopping fluid injection.
DOI: 10.23687/ec9e2659-1c29-4ddb-87a2-6aced147a990
title: Species composition, forest properties and land cover types across Canada’s forests at 250m resolution for 2001 and 2011

description: This data publication contains two collections of raster maps of forest attributes across Canada, the first collection for year 2001, and the second for year 2011. The 2001 collection is actually an improved version of an earlier set of maps produced also for year 2001 (Beaudoin et al 2014, DOI: https://doi.org/10.1139/cjfr-2013-0401) that is itself available through the web site “http://nfi-nfis.org”. Each collection contains 93 maps of forest attributes: four land cover classes, 11 continuous stand-level structure variables such as age, volume, biomass and height, and 78 continuous values of percent composition for tree species or genus. The mapping was done at a spatial resolution of 250m along the MODIS grid. Briefly the method uses forest polygon information from the first version of photoplots database from Canada’s National Forest Inventory as reference data, and the non-parametric k-nearest neighbors procedure (kNN) to create the raster maps of forest attributes. The approach uses a set of 20 predictive variables that include MODIS spectral reflectance data, as well as topographic and climate data. Estimates are carried out on target pixels across all Canada treed landmass that are stratified as either forest or non-forest with 25% forest cover used as a threshold. Forest cover information was extracted from the global forest cover product of Hansen et al (2013) (DOI: https://doi.org/10.1126/science.1244693). The mapping methodology and resultant datasets were intended to address the discontinuities across provincial borders created by their large differences in forest inventory standards. Analysis of residuals has failed to reveal residual discontinuities across provincial boundaries in the current raster dataset, meaning that our goal of providing discontinuity-free maps has been reached. The dataset was developed specifically to address strategic issues related to phenomena that span multiple provinces such as fire risk, insect spread and drought. In addition, the use of the kNN approach results in the maintenance of a realistic covariance structure among the different variable maps, an important property when the data are extracted to be used in models of ecosystem processes. For example, within each pixel, the composition values of all tree species add to 100%. A scientific publication is under review, the reference will be provided.
DOI: 10.5281/zenodo.2110752
title: TCGA BioBombe Results

description: BioBombe analysis applied to gene expression data from The Cancer Genome Atlas (TCGA) PanCanAtlas. Method and results described in https://github.com/greenelab/BioBombe
DOI: 10.5281/zenodo.2222463
title: TARGET BioBombe Results

description: BioBombe analysis applied to gene expression data from The Therapeutically Applicable Research To Generate Effective Treatments (TARGET) program. Method and results described in https://github.com/greenelab/BioBombe
DOI: 10.5281/zenodo.2222469
title: TARGET BioBombe Results - Randomly Permuted Data

description: BioBombe analysis applied to <strong>randomly permuted</strong> gene expression data from The Therapeutically Applicable Research To Generate Effective Treatments (TARGET) program. Method and results described in https://github.com/greenelab/BioBombe
DOI: 10.5281/zenodo.2300616
title: GTEX BioBombe Results

description: BioBombe analysis applied to gene expression data from The Genotype-Tissue Expression (GTEx) project. Method and results described in https://github.com/greenelab/BioBombe
DOI: 10.5281/zenodo.5025636
title: TRIPEx-pol level-2 data

description: This dataset was collected during the TRIple-frequency and Polarimetric radar Experiment for improving process observation of winter precipitation (TRIPEx-pol) campaign. During the campaign, three zenith pointing radars were operated at he research core facility Jülich ObservatorY for Cloud Evolution (JOYCE-CF, 50°54′31′′\,N, 6°24′49′′\,E; 111\,m above mean sea level) close to Cologne, Germany. The radars were measuring at X,Ka and W-band frequencies. For a detailed information on the campaign and the radars see von Terzi et al 2021. The dataset here is the LV2 data. That means that the original Doppler Spectra data was regridded to a common time height grid with 4s temporal and 36m spatial resolution. The Doppler spectra were also fitlered (see von Terzi et al 2021 level-0 processing). The moments were calculated directly from the LV0 dataset. The LV2 processing follows Dias-Neto et al. 2019 (https://doi.org/10.5194/essd-11-845-2019 ). In the LV2 processing step, the radar specific offsets were calculated using a forward simulation of rain drop size distribution from a PARSIVEL instrument which is operated at JOYCE-CF. The calibration offsets are stored in the variable rain_offset_{band} (band stands for the radar band, so X,Ka or W). Then gaseous attenuation due to nitrogen, oxygen and water vapour were calculated from temperature, pressure and humidity profiles using the CloudNet product (more detail in von Terzi et al. 2021 lvel-2 processing). The attenuation due to gas is stored in the variable pia_{band}. Furthermore, the attenuation due to liquid or ice hydrometeors with the DWR-calibration described in Dias-Neto et al. 2019. In the DWR-calibration, the X and W-band radars are calibrated with respect to the Ka-band radar in the highest part of the cloud present. In the upper parts of ice clouds, the ice particles present can be assumed to be small enough to be Rayleigh scatterers and their reflectivity should not depend on the radar frequency. The relative radar offset is calculated for each time by looking at the reflectivity differences within a moving time window of 10 minutes. The attenuation due to liquid/ice hydrometeors is stored in the offset_{band} variable. The rain_offset_{band}, pia_{band} and offset_{band} have already been added to the radar reflectivity in the files, to return to the not-offset corrected dataset, simply subtract the named offsets. The variables quality_flag_offset_{band} contains flags indicating how trustworthy the offset correction is.
description: {"references": ["Dias-Neto et al. 2019 https://doi.org/10.5194/essd-11-845-2019"]}
DOI: 10.5281/zenodo.6501535
title: The phenotypic plasticity of an evolving digital organism

description: Data set and R code used in the analysis reported in the manuscript entitled "<em>The phenotypic plasticity of an evolving digital organism</em>", which has been accepted in Proc. R. Open. Sci. for publication.
description: https://gitlab.com/fortunalab/publications/phenotypic-plasticity-of-an-evolving-digital-organism
DOI: 10.17632/ckgb9zv7cg.1
title: Male rock hyraxes that maintain an isochronous song rhythm achieve higher reproductive success

description: Male hyrax reproductive success and categorical song rhythm ratios dataset. The data consists of three data objects: 

CV data: a summary of male annual reproductive success, body weights, social status and calculated coefficient of inter-call interval variance for songs recorded in the given year. 

Singing effort data: summary of male annual reproductive success, body weights, social status and singing effort (singing events/total behavioral events) 

Rhythmic proportions data: summary of male annual reproductive success, body weights, social status and calculated proportions between on-integer and off integer inter-call-interval ratios.
The provided data was used as an input for statistical analysis detailed in the paper and for drafting the corresponding figures. 

Scripts folder: an R script used for calculating Inter-call-interval rations, categorizing and normalizing them. A sample data set is provided
DOI: 10.5281/zenodo.2221216
title: TCGA BioBombe Results - Randomly Permuted Data

description: BioBombe analysis applied to <strong>randomly permuted</strong> gene expression data from The Cancer Genome Atlas (TCGA) PanCanAtlas. Method and results described in https://github.com/greenelab/BioBombe
DOI: 10.5281/zenodo.6579184
title: DEER data

description: Primary DEER data and field sweeps
DOI: 10.6073/pasta/4541694f7928bc7f0d8b604ff9936a81
title: MCR LTER: Coral Reef: Long-term Population and Community Dynamics: Fishes, ongoing since 2005

description: These data describe the species abundance and size distributions of fishes surveyed as part of MCR LTER's annual reef fish monitoring program. This study began in 2005 and the dataset is updated annually. The abundances of all mobile taxa of fishes (Scarids, Labrids, Acanthurids, Serranids, etc.) observed on a five by fifty meter transect which extends from the bottom to the surface of the water column are recorded by a diver using SCUBA. The diver then swims back along a one by fifty meter section of the original transect line and records the abundances of all non-mobile or cryptic taxa of fishes (Pomacentids, Gobiids, Cirrhitids, Holocentrids etc). Surveys are conducted between 0900 and 1600 hours (Moorea time) during late July or early August each year. In 2006, divers also began to estimate the size (length) of each fish observed to the nearest half cm. Four replicate transects are surveyed in each of six locations on the forereef (two on each of Moorea's three sides), six locations on the backreef (two on each of Moorea's three sides) and on six locations on the fringing reef (two on each of Moorea's three sides) for a total of 72 individual transects. Transects are permanently marked using a series of small, stainless steel posts affixed to the reef. Transects on the forereef are located at a depth of approximately 12m, those on the backreef are located at a depth of approximately 1.5m and those on the fringing reef are located at a depth of approximately 10m. In addition to the biotic data collected, divers also record data on the date and time each transect was surveyed, wind speed and sea state, swell height in m, amount of cloud cover in % and horizontal visability in m. This monitoring program is consistent with the protocols adopted by the Global Coral Reef Monitoring Network and the Australian Institute of Marine Science for use with the Great Barrier Reef Long-term Monitoring Program.
DOI: 10.3886/e125761v3
title: 2020 Census Tracking Survey

description: The 2020 Census Integrated Communications Campaign used a research-informed, data-driven approach to maximize the impact and efficiency of communications activities in support of the 2020 Census enumeration. As a part of this research, the Census Bureau and its contractor, Team Y&R, conducted a year-long nationally-representative tracking survey—from September 6, 2019 to September 13, 2020—to understand public opinion about census participation leading up to and during the enumeration period. The tracking survey consisted of two independent data collection methodologies: phone and web. Team Y&R conducted live phone interviews from September 2019 to June 2020 and online web panel surveys from September 2019 to September 13, 2020. Both surveys were fielded in English and Spanish. <br><br>The surveys measured a variety of attitudes, including awareness of the 2020 Census, intent to respond to the 2020 Census, stated response behavior, potential barriers to completing the 2020 Census, recall of census messages, and the mode with which people would prefer to respond to the 2020 Census.<br>