cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14840583
title: High-Fat High-Sugar Diet-Induced Changes in the Lipid Metabolism Are Associated with Mildly Increased COVID-19 Severity and Delayed Recovery in the Syrian Hamster

description: Pre-existing comorbidities such as obesity or metabolic diseases can adversely affect the clinical outcome of COVID-19. Chronic metabolic disorders are globally on the rise and often a consequence of an unhealthy diet, referred to as a Western Diet. For the first time in the Syrian hamster model, we demonstrate the detrimental impact of a continuous high-fat high-sugar diet on COVID-19 outcome. We observed increased weight loss and lung pathology, such as exudate, vasculitis, hemorrhage, fibrin, and edema, delayed viral clearance and functional lung recovery, and prolonged viral shedding. This was accompanied by an altered, but not significantly different, systemic IL-10 and IL-6 profile, as well as a dysregulated serum lipid response dominated by polyunsaturated fatty acid-containing phosphatidylethanolamine, partially recapitulating cytokine and lipid responses associated with severe human COVID-19. Our data support the hamster model for testing restrictive or targeted diets and immunomodulatory therapies to mediate the adverse effects of metabolic disease on COVID-19.<br>
DOI: 10.6084/m9.figshare.14840583.v1
title: High-Fat High-Sugar Diet-Induced Changes in the Lipid Metabolism Are Associated with Mildly Increased COVID-19 Severity and Delayed Recovery in the Syrian Hamster

description: Pre-existing comorbidities such as obesity or metabolic diseases can adversely affect the clinical outcome of COVID-19. Chronic metabolic disorders are globally on the rise and often a consequence of an unhealthy diet, referred to as a Western Diet. For the first time in the Syrian hamster model, we demonstrate the detrimental impact of a continuous high-fat high-sugar diet on COVID-19 outcome. We observed increased weight loss and lung pathology, such as exudate, vasculitis, hemorrhage, fibrin, and edema, delayed viral clearance and functional lung recovery, and prolonged viral shedding. This was accompanied by an altered, but not significantly different, systemic IL-10 and IL-6 profile, as well as a dysregulated serum lipid response dominated by polyunsaturated fatty acid-containing phosphatidylethanolamine, partially recapitulating cytokine and lipid responses associated with severe human COVID-19. Our data support the hamster model for testing restrictive or targeted diets and immunomodulatory therapies to mediate the adverse effects of metabolic disease on COVID-19.<br>
DOI: 10.6084/m9.figshare.17207255
title: Supporting data and models for cnndockbench

description: Supporting data and models for cnndockbench
DOI: 10.6084/m9.figshare.17207255.v1
title: Supporting data and models for cnndockbench

description: Supporting data and models for cnndockbench
DOI: 10.5258/soton/do384.
title: PhD Dataset

description: This is the data from all of the user studies conducted as part of my PhD projectIt comprises of the following categories of the following files:ELN Market Study - ELNMarketStudy.xlsx - full details of all ELNs detailed in the market researchChemists Software Survey - ChemistsSoftwareSurvey-FullSurvey.pdf - full copy of the survey - ChemistsSoftwareSurvey-SoftwareTools.xlsx - list of tools used in survey - ChemistsSoftwareSurvey-Results - anonymised results of the surveyFocus Groups - FocusGroupTranscriptsAnonymised.pdf - anonymised focus group transcriptsLab Observations - ObservationsWriteupsAnonymised.pdf - anonymised observation writeupsSoftware Evaluation Focus Groups - SoftwareEvaluationTranscriptsAnonymised.pdf - anonymised software evaluation focus group transcriptsData supports: Kanza, Samantha (2018) 'What influence would a cloud based semantic laboratory notebook have on the digitisation and management of scientific research?' University of Southampton, Doctoral Thesis, https://eprints.soton.ac.uk/id/eprint/421045
DOI: 10.18430/m37t35
title: X-ray diffraction data for the crystal Structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC from Klebsiella pneumoniae subsp. pneumoniae (7T35)
DOI: 10.5281/zenodo.5784085
title: Lagrangian Sequestration Efficiency Trajectories and Extracted Particle Metrics – 500m Y1 & Y2

description: A dataset of Lagrangian trajectories used to estimate North Atlantic sequestration efficiency and extracted metrics for the re-entrained and sequestered particles. All variables have long names and units. These files have been used for the analysis in Baker et al. ‘Biological carbon pump sequestration efficiency in the North Atlantic: a leaky or a long-term sink?’ with further information about the methodology available in the paper. Due to the size of the datasets, each DOI only contains two files. This dataset contains the 500m particles releases for the years 1996 (Y1) and 1997 (Y2).
DOI: 10.5281/zenodo.5784084
title: Lagrangian Sequestration Efficiency Trajectories and Extracted Particle Metrics – 500m Y1 & Y2

description: A dataset of Lagrangian trajectories used to estimate North Atlantic sequestration efficiency and extracted metrics for the re-entrained and sequestered particles. All variables have long names and units. These files have been used for the analysis in Baker et al. ‘Biological carbon pump sequestration efficiency in the North Atlantic: a leaky or a long-term sink?’ with further information about the methodology available in the paper. Due to the size of the datasets, each DOI only contains two files. This dataset contains the 500m particles releases for the years 1996 (Y1) and 1997 (Y2).
DOI: 10.5517/ccdc.csd.cc28fhw3
title: CCDC 2098355: Experimental Crystal Structure Determination

description: Related Article: Harin Oh, Hee Won Byun, Kyeongwon Moon, Saegun Kim, Prithwish Ghosh, Won An, Jong Hwan Kwak, Jung Su Park, Neeraj Kumar Mishra, In Su Kim|2021|J.Org.Chem.|86|16349|doi:10.1021/acs.joc.1c01752
DOI: 10.5517/ccdc.csd.cc28wvqr
title: CCDC 2112145: Experimental Crystal Structure Determination

description: Related Article: Diana Becerra, Jaime Portilla, Justo Cobo, Juan-Carlos Castillo, Mario A. Macías|2021|J.Mol.Struct.|1252|132098|doi:10.1016/j.molstruc.2021.132098
DOI: 10.5517/ccdc.csd.cc28wvwx
title: CCDC 2112150: Experimental Crystal Structure Determination

description: Related Article: Diana Becerra, Jaime Portilla, Justo Cobo, Juan-Carlos Castillo, Mario A. Macías|2021|J.Mol.Struct.|1252|132098|doi:10.1016/j.molstruc.2021.132098
DOI: 10.5517/ccdc.csd.cc28wvyz
title: CCDC 2112152: Experimental Crystal Structure Determination

description: Related Article: Diana Becerra, Jaime Portilla, Justo Cobo, Juan-Carlos Castillo, Mario A. Macías|2021|J.Mol.Struct.|1252|132098|doi:10.1016/j.molstruc.2021.132098
DOI: 10.5517/ccdc.csd.cc28wvz0
title: CCDC 2112153: Experimental Crystal Structure Determination

description: Related Article: Diana Becerra, Jaime Portilla, Justo Cobo, Juan-Carlos Castillo, Mario A. Macías|2021|J.Mol.Struct.|1252|132098|doi:10.1016/j.molstruc.2021.132098
DOI: 10.5517/ccdc.csd.cc282kdb
title: CCDC 2087831: Experimental Crystal Structure Determination

description: Related Article: Zeki Kartal, Onur Şahin|2021|J.Mol.Struct.|1252|132088|doi:10.1016/j.molstruc.2021.132088
DOI: 10.5281/zenodo.5784150
title: Spades with Phenix demo

description: Rosetta and phenix tarballs needed for the phenix with spades demo - see README.md on GitHub (https://github.com/barth-lab/phenix_with_spades_demo) for installation and usage guide. The code additions in here will be merged with the main branches of rosetta and phenix respectively.
DOI: 10.5281/zenodo.5784149
title: Spades with Phenix demo

description: Rosetta and phenix tarballs needed for the phenix with spades demo - see README.md on GitHub (https://github.com/barth-lab/phenix_with_spades_demo) for installation and usage guide. The code additions in here will be merged with the main branches of rosetta and phenix respectively.
DOI: 10.5281/zenodo.5784152
title: Cletocamptus dominicanus SPAdes preassembly

description: .
DOI: 10.5281/zenodo.5784151
title: Cletocamptus dominicanus SPAdes preassembly

description: .
DOI: 10.5066/p9j22hse
title: Enhanced Terrain Imagery of the Newark 30 x 60 Minute Quadrangle from Lidar-Derived Elevation Models at 3-Meter Resolution

description: This imagery dataset consists of 3-meter resolution, lidar-derived imagery of the Newark 30 x 60 minute quadrangle. It covers portions of New Jersey and New York, including parts of the Delaware River Basin. The source data used to construct this imagery consist of 1-meter, 2-meter, and 3-meter resolution lidar-derived digital elevation models (DEM). The lidar source data were compiled from different acquisitions published between 2013 and 2021 from various sources. The data were processed using geographic information systems (GIS) software. The data are projected in North America Datum (NAD) UTM Zone 18 North. This representation illustrates the terrain as a hillshade with contrast adjusted to highlight local relief according to a topographic position index (TPI) calculation.
DOI: 10.5281/zenodo.5783920
title: Raw data and code for "Addressing gaps in small-scale fisheries: a low-cost tracking system"

description: This repository contains the raw data and code to reproduce results and plots presented in: "Addressing gaps in small-scale fisheries: a low-cost tracking system". The release contains: ssf_function.R. The R function developed for the analysis ssf_workflow.R. The R scripts to reproduce the analysis and the results. gps_data.csv. Raw data used in the paper
description: The work was developed within the framework of the ARGOS Interreg Italy-Croatia Project (https://www.italy-croatia.eu/web/argos). The code is also available at https://github.com/irbimMAPS/ssf
DOI: 10.5281/zenodo.5783919
title: Raw data and code for "Addressing gaps in small-scale fisheries: a low-cost tracking system"

description: This repository contains the raw data and code to reproduce results and plots presented in: "Addressing gaps in small-scale fisheries: a low-cost tracking system". The release contains: ssf_function.R. The R function developed for the analysis ssf_workflow.R. The R scripts to reproduce the analysis and the results. gps_data.csv. Raw data used in the paper
description: The work was developed within the framework of the ARGOS Interreg Italy-Croatia Project (https://www.italy-croatia.eu/web/argos). The code is also available at https://github.com/irbimMAPS/ssf
DOI: 10.5519/0087358
title: Integrative taxonomy at the nexus of population divergence and speciation in insular speckled rattlesnakes

description: We describe two diminutive species of rattlesnakes (Genus _Crotalus_) from small nearshore islands off the coast of Baja California in the western Gulf of California, Mexico. In order to test the hypothesis that some island populations represent cohesive species entities, we applied linear discriminant analysis and uniform validation procedures to multiple classes of intrinsic trait data. By using previously recognised species to establish a threshold for species recognition, we found that assignment of specimens to both new species was as probable as with other established rattlesnake species within the speckled rattlesnake, _Crotalus mitchellii_, complex. We also found that assignment of specimens from other island populations was not as probable as for the established species, and these populations are referable to _C. pyrrhus_. The species endemic to Piojo Island is most closely related to other island and mainland populations of _C. pyrrhus_ whereas the species endemic to Cabeza de Caballo Island is apparently most closely related to _C. angelensis_, a nearby island endemic of large body size. However, patterns from both mitochondrial and nuclear phylogenies, and phenotypic variation indicate that evolutionary trajectories of both of these species have been influenced by introgression from _C. angelensis_. We speculate that collective evidence based on contrasting patterns of nuclear and mitochondrial evolution supports a hybrid origin of the species from Cabeza de Caballo Island followed by exceptionally rapid mitochondrial evolution. Consistent with small body size, both species show a reduction in various scale counts relative to other species of the _C. mitchellii_ species complex, suggesting that dwarfism is not simply a plastic response to insular conditions.
DOI: 10.5519/0027684
title: Molecular insights into the phylogenetic placement of the poorly known genus Niceforonia Goin and Cochran, 1963 (Anura: Brachycephaloidea)

description: Among New World direct-developing frogs belonging to the clade Brachycephaloidea (= Terraranae), there are several genera with uncertain phylogenetic placements. One notable example is the genus _Niceforonia_ Goin & Cochran 1963, which includes three species that are endemic to Colombia. Three specimens of the species _Niceforonia nana_ were collected and for the first time the genus is included in a molecular phylogenetic analysis of mitochondrial (mtDNA; 12S and 16S) and nuclear (nucDNA; TYR and RAG1) markers. Molecular phylogenetic inference based on concatenated and separate mtDNA and nucDNA analyses recovered _Niceforonia nana_ nested within Hypodactylus Hedges et al. 2008, rendering the latter genus paraphyletic. Consequently, herein we place the genus _Hypodactylus_ in the synonymy of _Niceforonia_ to resolve the paraphyly and place _Niceforonia_ in the subfamily Hypodactylinae. Based on our revised concept of the genus _Niceforonia_ we conducted preliminary morphological comparisons using specimens and literature descriptions. _Niceforonia nana_ is quite divergent from other species of _Niceforonia_ (uncorrected genetic distances of ca. 10% 16S and 7% TYR) suggesting that further taxonomic revision may be warranted.
DOI: 10.5519/0078454
title: Analysis of ultraconserved elements supports African origins of narrow-mouthed frogs

description: Narrow-mouthed frogs (Anura: Microhylidae) are globally distributed and molecular data suggest the rapid evolution of multiple subfamilies shortly after their origin. Despite recent progress, several subfamilial relationships remain unexplored using phylogenomic data. We analysed 1,796 nuclear ultraconserved elements, a total matrix of 400,664 nucleotides, from representatives of most microhylid subfamilies. Summary method species tree and maximum likelihood analyses unambiguously supported Hoplophryninae, as the earliest diverging microhylid and Chaperininae as a junior synonym of Microhylinae. Given the emerging consensus that subfamilies from mainland Africa diverged early, microhylids have likely occupied the continent for more than 66 million years.
DOI: 10.5258/soton/d1960
title: Dataset for Defect-induced nonlinearity in 2D nanoparticles

description: This research dataset should be interpreted and understood in the context of the corresponding manuscript, which has been published in Optics Express with DOI: 10.1364/OE.443977. All relevant information regarding the dataset, how it was obtained and its context is contained in the manuscript. The data correspond to the data shown in the figures of the manuscript.
DOI: 10.5519/0091845
title: Amphibian taxonomy: early 21st century case studies

description: These are data files associated with the editorial for 'Amphibian taxonomy: Early 21st century case studies' in Journal of Natural History (Streicher et al. 2020). In this special issue, eleven new species are described (nine frogs and two salamanders) and several revisionary actions are taken. There are contributions dealing with taxa from Africa (including Tanzania and Madagascar, Greenwood et al. 2020; Rancilhac et al. 2020), Asia (Mahony et al. 2020; Nguyen et al. 2020a; Nguyen et al. 2020b; Stuart et al. 2020), North America (Guyer et al. 2020), and South America (Melo-Sampaio et al. 2020). To create context for methods used in the special issue, we collected and summarised data from five years of new species descriptions (2015-2019).
DOI: 10.5281/zenodo.5784166
title: Lagrangian Sequestration Efficiency Trajectories and Extracted Particle Metrics – 500m Y3 & Y4

description: A dataset of Lagrangian trajectories used to estimate North Atlantic sequestration efficiency and extracted metrics for the re-entrained and sequestered particles. All variables have long names and units. These files have been used for the analysis in Baker et al. ‘Biological carbon pump sequestration efficiency in the North Atlantic: a leaky or a long-term sink?’ with further information about the methodology available in the paper. Due to the size of the datasets, each DOI only contains two files. This dataset contains the 500m particles releases for the years 1998 (Y3) and 1999 (Y4).
DOI: 10.5281/zenodo.5784165
title: Lagrangian Sequestration Efficiency Trajectories and Extracted Particle Metrics – 500m Y3 & Y4

description: A dataset of Lagrangian trajectories used to estimate North Atlantic sequestration efficiency and extracted metrics for the re-entrained and sequestered particles. All variables have long names and units. These files have been used for the analysis in Baker et al. ‘Biological carbon pump sequestration efficiency in the North Atlantic: a leaky or a long-term sink?’ with further information about the methodology available in the paper. Due to the size of the datasets, each DOI only contains two files. This dataset contains the 500m particles releases for the years 1998 (Y3) and 1999 (Y4).
DOI: 10.6084/m9.figshare.17207288
title: Supplementary Tables

description: Supplementary Material for a study addressing the relationship between age at menarche, age-adjusted pubertal development, as well as adrenal and gonadal hormones and depression in adolescent girls.<br>
DOI: 10.6084/m9.figshare.17207288.v1
title: Supplementary Tables

description: Supplementary Material for a study addressing the relationship between age at menarche, age-adjusted pubertal development, as well as adrenal and gonadal hormones and depression in adolescent girls.<br>
DOI: 10.5519/imwpcoku
title: Phylogeny of terraranan frogs based on 2,665 loci and impacts of missing data on phylogenomic analyses

description: Terraranae is a large clade of New World direct-developing frogs that includes 3–5 families and &gt;1,100 described species (∼15% of all named frog species). The relationships among major groups of terraranan frogs have been highly contentious, including conflicts among four recent phylogenomic studies utilizing 95, 220, 389, and 2,214 nuclear loci, respectively. In this paper, we re-evaluate relationships within Terraranae using a novel genomic dataset for 16 ingroup species representing most terraranan families and subfamilies. The preferred data matrix consisted of 2,665 nuclear loci from ultraconserved elements (UCEs), with a total of 743,419 aligned base pairs and 57% missing data. Concatenated likelihood analyses and coalescent-based species-tree analyses recovered strong statistical support for the following relationships among terraranan families: (Brachycephalidae, (Eleutherodactylidae, (Craugastoridae + ‘Strabomantidae’))). This position for Brachycephalidae agrees with two previous phylogenomic studies but conflicts with two others. Our results infer _Strabomantis_ (of the Strabomantidae) to be with (or within) _Craugastor_ (Craugastoridae), rather than with other strabomantid genera. This renders Strabomantidae paraphyletic with respect to Craugastoridae. Our results also suggest that Pristimantinae is paraphyletic with respect to Holoadeninae. We also find that using matrices with less missing data (and concomitantly fewer UCE loci) generally resulted in trees with lower mean branch support and problematic phylogenies (e.g. non-monophyly of terraranans). Overall, our results help resolve controversial relationships within one of the largest clades of frogs, with a dataset including ∼7 times more loci than those used in previous studies focused on this clade.
DOI: 10.5281/zenodo.5784215
title: Mask Detection Application Performance Models

description: The repository includes the source code and the datasets used to build performance models for OSCAR Mask Detection application. The results are included in the AI-SPRINT project deliverable "D2.1 - First release and evaluation of the AI-SPRINT design tools".
DOI: 10.5281/zenodo.5784214
title: Mask Detection Application Performance Models

description: The repository includes the source code and the datasets used to build performance models for OSCAR Mask Detection application. The results are included in the AI-SPRINT project deliverable "D2.1 - First release and evaluation of the AI-SPRINT design tools".
DOI: 10.5519/chnr8l9x
title: Survival of climate warming through niche shifts: Evidence from frogs on tropical islands

description: How will organisms cope when forced into warmer-than-preferred thermal environments? This is a key question facing our ability to monitor and manage biota as average annual temperatures increase, and is of particular concern for range-limited terrestrial species unable to track their preferred climatic envelope. Being ectothermic, desiccation prone, and often spatially restricted, island-inhabiting tropical amphibians exemplify this scenario. Pre-Anthropocene case studies of how insular amphibian populations responded to the enforced occupation of warmer-than-ancestral habitats may add a valuable, but currently lacking, perspective. We studied a population of frogs from the Seychelles endemic family Sooglossidae which, due to historic sea-level rise, have been forced to occupy a significantly warmer island (Praslin) than their ancestors and close living relatives. Evidence from thermal activity patterns, bioacoustics, body size distributions, and ancestral state estimations suggest that this population shifted its thermal niche in response to restricted opportunities for elevational dispersal. Relative to conspecifics, Praslin sooglossids also have divergent nuclear genotypes and call characters, a finding consistent with adaptation causing speciation in a novel thermal environment. Using an evolutionary perspective, our study reveals that some tropical amphibians have survived episodes of historic warming without the aid of dispersal and therefore may have the capacity to adapt to the currently warming climate. However, two otherwise co-distributed sooglossid species are absent from Praslin, and the deep evolutionary divergence between the frogs on Praslin and their closest extant relatives (~8 million years) may have allowed for gradual thermal adaptation and speciation. Thus, local extinction is still a likely outcome for tropical frogs experiencing warming climates in the absence of dispersal corridors to thermal refugia.
DOI: 10.5281/zenodo.5784168
title: Data and R files for the analysis of the innovative capacity and the network position of national manufacturing industries in world production

description: Data and R files for the reproducibility of the results obtained in Kim and Ozaygen, Analysis of the innovative capacity and the network position of national manufacturing industries in world production. It also includes an R/Shiny application which runs at https://awekim.shinyapps.io/Manuf_shiny_R/
DOI: 10.5281/zenodo.3739536
title: Data and R files for the analysis of the innovative capacity and the network position of national manufacturing industries in world production

description: Data and R files for the reproducibility of the results obtained in Kim and Ozaygen, Analysis of the innovative capacity and the network position of national manufacturing industries in world production. It also includes an R/Shiny application which runs at https://awekim.shinyapps.io/Manuf_shiny_R/
DOI: 10.6084/m9.figshare.17207348
title: Modeling estimates of agricultural and natural soil nitrous oxide emissions across the contiguous United States: Annual time-series gridded database during 1900-2019

description: This dataset includes the time-series maps of the model-estimated N<sub>2</sub>O emissions, covering the lower U.S. spanning from 1900 to 2019.