cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7969800
title: Lung CT COVID-19 batch 1

description: This data set is part of the public development data for the 2023 Automated Universal Classification Challenge (AUC23). The data set concerns COVID-19 RT-PCR outcome prediction and prediction of severe COVID-19, defined as death or intubation after one month, from computed tomography (CT). The data set was previously introduced and described by Revel, M. et al (2021). Data was restructured in compliance with the AUC23 challenge format. The STOIC project collected CT images of 10,735 individuals suspected of being infected with SARS-COV-2 during the first wave of the pandemic in France, from March to April 2020. For each patient in the training set, the dataset contains binary labels for COVID-19 presence based on RT-PCR test results, and COVID-19 severity, defined as intubation or death within one month from the acquisition of the CT scan. This data set contains the training sample of the STOIC dataset as used in the STOIC2021 challenge. Images are 3D tensors: 0: 3D CT scan Classification labels: COVID-19: 0: Negative RT-PCR 1: Positive RT-PCR<br> Severe COVID-19: 0: Alive and no intubation after one month 1: Death or intubation after one month imagesTr (root folder with all patients and studies)<br> ├── covid19severity_6_0000.mha (3D CT for study 6)<br> ├── covid19severity_17_0000.mha (3D CT for study 17)<br> ├── ... Please cite the following article if you are using the STOIC2021 training dataset: <pre><code>STOIC2021 Training was accessed on DATE from https://registry.opendata.aws/stoic2021-training. STOIC2021 Training was documented in Thoracic CT in COVID-19: The STOIC Project, Revel, Marie-Pierre, et al. Radiology, 2021, https://doi.org/10.1148/radiol.2021210384.</code></pre> Due to upload size limits, the data set was split into six batches. Batch 2: https://zenodo.org/record/8042589 Batch 3: https://zenodo.org/record/8042817 Batch 4: https://zenodo.org/record/8043089 Batch 5: https://zenodo.org/record/8043216 Batch 6: https://zenodo.org/record/8043218
description: {"references": ["STOIC2021 Training was accessed on DATE from https://registry.opendata.aws/stoic2021-training. STOIC2021 Training was documented in Thoracic CT in COVID-19: The STOIC Project, Revel, Marie-Pierre, et al. Radiology, 2021, https://doi.org/10.1148/radiol.2021210384."]}
DOI: 10.5883/ds-phpcon
title: First detection of invasive Douglas fir needle midges from the genus Contarinia Rondani (Diptera: Cecidomyiidae) in Switzerland

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5281/zenodo.7969799
title: Lung CT COVID-19 batch 1

description: This data set is part of the public development data for the 2023 Automated Universal Classification Challenge (AUC23). The data set concerns COVID-19 RT-PCR outcome prediction and prediction of severe COVID-19, defined as death or intubation after one month, from computed tomography (CT). The data set was previously introduced and described by Revel, M. et al (2021). Data was restructured in compliance with the AUC23 challenge format. The STOIC project collected CT images of 10,735 individuals suspected of being infected with SARS-COV-2 during the first wave of the pandemic in France, from March to April 2020. For each patient in the training set, the dataset contains binary labels for COVID-19 presence based on RT-PCR test results, and COVID-19 severity, defined as intubation or death within one month from the acquisition of the CT scan. This data set contains the training sample of the STOIC dataset as used in the STOIC2021 challenge. Images are 3D tensors: 0: 3D CT scan Classification labels: COVID-19: 0: Negative RT-PCR 1: Positive RT-PCR<br> Severe COVID-19: 0: Alive and no intubation after one month 1: Death or intubation after one month imagesTr (root folder with all patients and studies)<br> ├── covid19severity_6_0000.mha (3D CT for study 6)<br> ├── covid19severity_17_0000.mha (3D CT for study 17)<br> ├── ... Please cite the following article if you are using the STOIC2021 training dataset: <pre><code>STOIC2021 Training was accessed on DATE from https://registry.opendata.aws/stoic2021-training. STOIC2021 Training was documented in Thoracic CT in COVID-19: The STOIC Project, Revel, Marie-Pierre, et al. Radiology, 2021, https://doi.org/10.1148/radiol.2021210384.</code></pre> Due to upload size limits, the data set was split into six batches. Batch 2: https://zenodo.org/record/8042589 Batch 3: https://zenodo.org/record/8042817 Batch 4: https://zenodo.org/record/8043089 Batch 5: https://zenodo.org/record/8043216 Batch 6: https://zenodo.org/record/8043218
description: {"references": ["STOIC2021 Training was accessed on DATE from https://registry.opendata.aws/stoic2021-training. STOIC2021 Training was documented in Thoracic CT in COVID-19: The STOIC Project, Revel, Marie-Pierre, et al. Radiology, 2021, https://doi.org/10.1148/radiol.2021210384."]}
DOI: 10.5883/ds-tepani
title: New Records of Psychodidae for the Dutch Fauna

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/ds-atlasnab
title: The Genetic Atlas of North American Butterflies

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/ds-vgds26
title: Endogean beetles (Coleoptera) of Guatemala: deep soil sampling and illustrated overview

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:adf5834
title: Overview of Barcode Index Number - BOLD:ADF5834

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5066/p94n3ich
title: FUTURES v2: Status Quo Projections of Future Patterns of Urbanization Across the Conterminous United States from 2020 to 2100

description: We simulated future patterns of urban growth using the FUTure Urban-Regional Environment Simulation (FUTURES; Meentemeyer et al., 2013) version 2 framework. FUTURES is an open source urban growth model designed to address the regional-scale ecological and environmental impacts of urbanization; it is one of the few land change models that explicitly captures the spatial structure of development in response to user-specified scenarios. We present probabilistic land change projections that predict urban growth under a Status Quo scenarios of growth. We computed each scenario for 50 stochastic iterations from 2020 through 2100 at annual time steps.
DOI: 10.34740/kaggle/dsv/5931000
title: Robust and Susceptible Litopenaeus vannamei Larvae
DOI: 10.6073/pasta/a3d22413d740799af91924673b8fb556
title: SONGS Mitigation Monitoring: Wetland Process Study - Irrigation, Decompaction, Amendment, Planting and Seeding Experiment Vegetation Cover

description: These data describe estimates of the percent cover of marsh plants in experimental plots designed to evaluate the effectiveness of various soil treatments on increasing vegetation cover at the San Dieguito Wetlands (Del Mar, California). Plots established between 1.61 – 2.1 m MLLW were manipulated to test the effects of irrigation, decompaction, soil amendments, and planting versus seeding, whereas plots between 1.6 – 1.7 m MLLW tested the effects of planting versus seeding alone. Data collection was conducted from 2020 to 2022. During each survey, species of marsh plants were identified and recorded under 98 uniformly spaced points within 4.5 m2 quadrats in each plot.
DOI: 10.6073/pasta/4bf655237e7e71f7e45cd28fe0afcef3
title: UCSB SONGS Mitigation Monitoring: Wetland Process Study - Irrigation, Decompaction, Amendment, Planting and Seeding Experiment Plant Size

description: These data describe estimates of the condition and size of three species of salt marsh plants (Arthrocnemum subterminale, Frankenia salina, and Salicornia virginica) planted in experimental plots designed to evaluate the effectiveness of various soil treatments on increasing vegetation cover at the San Dieguito Wetlands (Del Mar, California). Plots established between 1.61 – 2.1 m MLLW were manipulated to test the effects of irrigation, decompaction, soil amendments, and planting versus seeding, whereas plots between 1.6 – 1.7 m MLLW tested the effects of planting versus seeding alone. Data collection was conducted from 2020 to 2022. During each survey, the length of the longest axis and maximum perpendicular width of each planted individual was measured.
DOI: 10.6073/pasta/07a70b32d7e398b9d95f52aab14f31ae
title: UCSB SONGS Mitigation Monitoring: Wetland Process Study – Soil Properties

description: These data describe physical and chemical properties of soil samples collected as part of the San Onofre Nuclear Generating Station (SONGS) Mitigation Monitoring Program. Data collection began in 2019 at the San Dieguito Wetland in San Diego County, CA. Additional locations at Tijuana Estuary in San Diego County, CA, Carpinteria Salt Marsh is Santa Barbara County, CA, and Mugu Lagoon in Ventura County, CA were added in 2021. Sampling occurred sporadically at various locations in each wetland. All soil samples were characterized for organic matter content and particle size. Additional properties were characterized for select soil samples.
DOI: 10.5066/p9bd5v4b
title: FUTURES v3: Scenarios of Future Patterns of Urbanization in Response to Sea Level Rise and Frequent Flooding Across the Southeast United States from 2020 to 2100

description: Policy-relevant flood risk modeling must capture interactions between physical and social processes to accurately project impacts from scenarios of sea level rise and inland flooding due to climate change. Here we simultaneously model urban growth, flood hazard change, and adaptive response using the FUTure Urban-Regional Environment Simulation (FUTURES) version 3 framework (Sanchez et al., 2023). FUTURES is an open source urban growth model designed to address the regional-scale ecological and environmental impacts of urbanization; it is one of the few land change models that explicitly captures the spatial structure of development in response to user-specified scenarios. We present probabilistic land change projections that predict urban growth while also simulating human migration and other response actions. We simulated two scenarios of urban growth and adaptive response: 1) "Reactive", wherein residents are assumed to adapt to threats as they occur, without incentives or policies in place to affect outcomes; and 2) "Managed Retreat", in which policymakers incentivize converting at-risk developed land to undeveloped land (i.e., abandoned), with residents of all levels of adaptive capacity moving elsewhere. We computed each scenario for 20 stochastic iterations from 2020 through 2100 at annual time steps. Our scenario advances local to national-scale efforts to evaluate tradeoffs between adaptation strategies in response to global anthropogenic change.
DOI: 10.5281/zenodo.7955952
title: Life Cycle Assessment of Power-to-X processes and associated electricity and heat applications in the residential sector

description: This report describes the modelling of life cycle inventories for the provision of heat and electricity for residential purpose, relying on Power-to-X conversion processes. This includes the following energy carriers: hydrogen, synthetic natural gas, and methanol. Several end use technologies are modelled, from boilers to co-generation units and fuel cells. The heat and electricity supply chain specifications and corresponding inventories supplied with this report are available for different LCI databases and software through the datasets included in this repository.
DOI: 10.6084/m9.figshare.22178717
title: Recombination rate variation in Cardiocondyla obscurior

description: Datasets produced to analyze recombination rate variation in <em>C. obscurior</em>. This includes the following files: <br> - <strong>TEislands.w250kb.bed</strong>: bed file with coordinates of TE islands <br> - <strong>final.metrics.in250kbwindows.tsv</strong>: tsv file with various metrics estimated in 250-kb nonoverlapping windows. These metrics include recombination rates, population genomics estimates as well as other sequence parameters (e.g. TE/gene content) <br> - <strong>introgression.250kb.bed</strong>: bed files with coordinates of regions with substantially high Dxy between grandparental haplotypes <br> - <strong>manuallyCurated.markers.forR.txt</strong>: formatted and manually curated MSTmap output <br> - <strong>Cobs3.1.chrom-size.txt</strong>: chromosome length <br> - <strong>manuallyCurated.markers.correctPhase.xlsx</strong>: markers used to produce reference genetic map with the correct phase <br> - <strong>SVs folder</strong>: contains: <br> ---- <strong>sv.bed.filtered.repeat.0.2.txt</strong>: coordinates of SVs with less than 0.2 repeat content <br> ---- <strong>sv.type.recomb.repeat.freq.all.txt</strong>: coordinates and frequencies of all SVs as well as their repeat content (meanperc column) and the corresponding recombination rate
DOI: 10.6084/m9.figshare.22178717.v1
title: Recombination rate variation in Cardiocondyla obscurior

description: Datasets produced to analyze recombination rate variation in <em>C. obscurior</em>. This includes the following files: <br> - <strong>TEislands.w250kb.bed</strong>: bed file with coordinates of TE islands <br> - <strong>final.metrics.in250kbwindows.tsv</strong>: tsv file with various metrics estimated in 250-kb nonoverlapping windows. These metrics include recombination rates, population genomics estimates as well as other sequence parameters (e.g. TE/gene content) <br> - <strong>introgression.250kb.bed</strong>: bed files with coordinates of regions with substantially high Dxy between grandparental haplotypes <br> - <strong>manuallyCurated.markers.forR.txt</strong>: formatted and manually curated MSTmap output <br> - <strong>Cobs3.1.chrom-size.txt</strong>: chromosome length <br> - <strong>manuallyCurated.markers.correctPhase.xlsx</strong>: markers used to produce reference genetic map with the correct phase <br> - <strong>SVs folder</strong>: contains: <br> ---- <strong>sv.bed.filtered.repeat.0.2.txt</strong>: coordinates of SVs with less than 0.2 repeat content <br> ---- <strong>sv.type.recomb.repeat.freq.all.txt</strong>: coordinates and frequencies of all SVs as well as their repeat content (meanperc column) and the corresponding recombination rate
DOI: 10.6084/m9.figshare.22178717.v2
title: Recombination rate variation in Cardiocondyla obscurior

description: Datasets produced to analyze recombination rate variation in <em>C. obscurior</em>. This includes the following files: <br> - <strong>TEislands.w250kb.bed</strong>: bed file with coordinates of TE islands <br> - <strong>final.metrics.in250kbwindows.tsv</strong>: tsv file with various metrics estimated in 250-kb nonoverlapping windows. These metrics include recombination rates, population genomics estimates as well as other sequence parameters (e.g. TE/gene content) <br> - <strong>introgression.250kb.bed</strong>: bed files with coordinates of regions with substantially high Dxy between grandparental haplotypes <br> - <strong>manuallyCurated.markers.forR.txt</strong>: formatted and manually curated MSTmap output <br> - <strong>Cobs3.1.chrom-size.txt</strong>: chromosome length <br> - <strong>manuallyCurated.markers.correctPhase.xlsx</strong>: markers used to produce reference genetic map with the correct phase <br> - <strong>SVs folder</strong>: contains: <br> ---- <strong>sv.bed.filtered.repeat.0.2.txt</strong>: coordinates of SVs with less than 0.2 repeat content <br> ---- <strong>sv.type.recomb.repeat.freq.all.txt</strong>: coordinates and frequencies of all SVs as well as their repeat content (meanperc column) and the corresponding recombination rate
DOI: 10.6084/m9.figshare.22336285
title: Supplementary Material for: Impact of changes in human airway epithelial cellular composition and differentiation on SARS-CoV-2 infection biology

description: The consequences of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can range from asymptomatic to fatal disease. Variations in epithelial susceptibility to SARS-CoV-2 infection depend on the anatomical location from the proximal to distal respiratory tract. However, the cellular biology underlying these variations is not completely understood. Thus, air-liquid interface (ALI) cultures of well-differentiated primary human tracheal and bronchial epithelial cells were employed to study the impact of epithelial cellular composition and differentiation on SARS-CoV-2 infection by transcriptional (RNA sequencing) and immunofluorescent analyses. Changes of cellular composition were investigated by varying time of differentiation or by using specific compounds. We found that SARS-CoV-2 primarily infected ciliated cells but also goblet cells and transient secretory cells. Viral replication was impacted by differences in cellular composition, which depended on culturing time and anatomical origin. A higher percentage of ciliated cells correlated with a higher viral load. However, DAPT-treatment, which increased number of ciliated cells and reduced goblet cells, decreased viral load, indicating the contribution of goblet cells to infection. Cell-entry factors, especially cathepsin L and transmembrane protease serine 2, were also affected by differentiation time. In conclusion, our study demonstrates that viral replication is affected by changes in cellular composition, especially in cells related to the mucociliary system. This could explain in part the variable susceptibility to SARS-CoV-2 infection between individuals and between anatomical locations in the respiratory tract.
DOI: 10.6084/m9.figshare.17868605
title: Exploring sport participation in individuals with spinal cord injury: A qualitative thematic synthesis

description: Individuals with spinal cord injury (SCI) are susceptible to various physical, psychological, and social challenges. Sport is an activity that may holistically address these concerns. No existing research provides an overview of the current landscape of SCI-specific sport participation. To synthesize the findings of qualitative studies exploring the perceptions of people with SCI participating in sport, in relation to physical, psychological, and social health. This thematic synthesis included studies published in APA PsycInfo, CINAHL, Embase, Emcare, Medline, and PubMed. Eligible articles studied adults who had a SCI for ≥12 months and explored experiences following ≥3 months of sport participation using qualitative or mixed-methods. Articles were excluded if participants with SCI composed less than one-third of the study sample. From 8473 unique titles and abstracts screened, 47 articles underwent full-text review and 14 articles were included. The Mixed Methods Appraisal Tool was used to critically appraise the 13 qualitative studies and one mixed-methods study. The overarching theme was that sport facilitates the progression to living an enriching life with SCI. Four sub-themes were identified within this theme: adjusting to SCI, factors influencing sport initiation, outcomes resulting from sport participation, and reshaping views of SCI. Participants detailed many benefits of sport, including improved fitness, independence, confidence, and sense of community. Beyond the participants themselves, sport helped reshape views of SCI by breaking stereotypes and inspiring others. Sport can play a crucial role in facilitating the progression to living an enriching life following SCI.
DOI: 10.6084/m9.figshare.17868605.v1
title: Exploring sport participation in individuals with spinal cord injury: A qualitative thematic synthesis

description: Individuals with spinal cord injury (SCI) are susceptible to various physical, psychological, and social challenges. Sport is an activity that may holistically address these concerns. No existing research provides an overview of the current landscape of SCI-specific sport participation. To synthesize the findings of qualitative studies exploring the perceptions of people with SCI participating in sport, in relation to physical, psychological, and social health. This thematic synthesis included studies published in APA PsycInfo, CINAHL, Embase, Emcare, Medline, and PubMed. Eligible articles studied adults who had a SCI for ≥12 months and explored experiences following ≥3 months of sport participation using qualitative or mixed-methods. Articles were excluded if participants with SCI composed less than one-third of the study sample. From 8473 unique titles and abstracts screened, 47 articles underwent full-text review and 14 articles were included. The Mixed Methods Appraisal Tool was used to critically appraise the 13 qualitative studies and one mixed-methods study. The overarching theme was that sport facilitates the progression to living an enriching life with SCI. Four sub-themes were identified within this theme: adjusting to SCI, factors influencing sport initiation, outcomes resulting from sport participation, and reshaping views of SCI. Participants detailed many benefits of sport, including improved fitness, independence, confidence, and sense of community. Beyond the participants themselves, sport helped reshape views of SCI by breaking stereotypes and inspiring others. Sport can play a crucial role in facilitating the progression to living an enriching life following SCI.
DOI: 10.6084/m9.figshare.19330375
title: Systematic overviews of partnership principles and strategies identified from health research about spinal cord injury and related health conditions: A scoping review

description: Scoping review. To identify and provide systematic overviews of partnership principles and strategies identified from health research about spinal cord injury (SCI) and related health conditions. Four health electronic databases (Medline, Embase, CINAHL, PsycINFO) were searched from inception to March 2019. We included articles that described, reflected, and/or evaluated one or more collaborative research activities in health research about SCI, stroke, multiple sclerosis, Parkinson’s disease, amputation, cerebral palsy, spina bifida, amyotrophic lateral sclerosis, acquired brain injury, or wheelchair-users. Partnership principles (i.e. norms or values) and strategies (i.e. observable actions) were extracted and analyzed using directed qualitative content analysis. We included 39 articles about SCI (n = 13), stroke (n = 15), multiple sclerosis (n = 5), amputation (n = 2), cerebral palsy (n = 2), Parkinson’s disease (n = 1), and wheelchair users (n = 1). We extracted 110 principles and synthesized them into 13 overarching principles. Principles related to building and maintaining relationships between researchers and research users were most frequently reported. We identified 32 strategies that could be applied at various phases of the research process and 26 strategies that were specific to a research phase (planning, conduct, or dissemination). We provided systematic overviews of principles and strategies for research partnerships. These could be used by researchers and research users who want to work in partnership to plan, conduct and/or disseminate their SCI research. The findings informed the development of the new SCI Integrated Knowledge Translation Guiding Principles (www.iktprinciples.com) and will support the implementation of these Principles within the SCI research system.