cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17041397
title: Rapid adjustments in thermal tolerance and the metabolome to daily environmental changes – a field study on the Arctic seed bug Nysius groenlandicus

description: Laboratory investigations on terrestrial model-species, typically of temperate origin, have demonstrated that terrestrial ectotherms can cope with daily temperature variations by rapid heat or cold hardening. However, few studies have investigated this ability and its physiological basis in the field. This is even more true in the polar regions, where temporal and spatial temperature variations can be extreme, e.g. during the arctic summer. We examined adjustments in heat and cold tolerance in the Greenlandic seed bug <i>Nysius groenlandicus</i> to daily changes in microhabitat temperatures by collecting individuals for thermal assessment at different time points within and across days. Secondly, we assessed underlying metabolomic fingerprints using GC-MS metabolomics in a subset of individuals collected during days with either low or high temperature variation. We found a significant correlation between observed heat or cold tolerance and the ambient microhabitat temperatures at the time of capture, indicating that <i>N. groenlandicus </i>continuously and within short time-windows respond physiologically to thermal changes in their microhabitats. Concentrations of some metabolites varied significantly with time of collection and temperature. For instance, we detected elevated sugar levels in animals caught at the lowest daily field temperatures. Polyol concentrations were lower in individuals collected at the time points with the coldest temperatures and higher at the warmest temperatures. Additionally, changes in concentrations of metabolites associated with energetic metabolism was observed across collection times. Our findings suggest that hardening responses under natural conditions are marked and likely play a crucial role for coping with microhabitat temperature variation on a daily scale, and that metabolite levels are actively altered on a daily basis. Such results provide interesting new knowledge on the thermal biology of a common insect from the Arctic region, and contribute to our understanding of responses and robustness of arthropods to environmental changes in fragile and thermally variable ecosystems.
DOI: 10.6084/m9.figshare.17041397.v1
title: Rapid adjustments in thermal tolerance and the metabolome to daily environmental changes – a field study on the Arctic seed bug Nysius groenlandicus

description: Laboratory investigations on terrestrial model-species, typically of temperate origin, have demonstrated that terrestrial ectotherms can cope with daily temperature variations by rapid heat or cold hardening. However, few studies have investigated this ability and its physiological basis in the field. This is even more true in the polar regions, where temporal and spatial temperature variations can be extreme, e.g. during the arctic summer. We examined adjustments in heat and cold tolerance in the Greenlandic seed bug <i>Nysius groenlandicus</i> to daily changes in microhabitat temperatures by collecting individuals for thermal assessment at different time points within and across days. Secondly, we assessed underlying metabolomic fingerprints using GC-MS metabolomics in a subset of individuals collected during days with either low or high temperature variation. We found a significant correlation between observed heat or cold tolerance and the ambient microhabitat temperatures at the time of capture, indicating that <i>N. groenlandicus </i>continuously and within short time-windows respond physiologically to thermal changes in their microhabitats. Concentrations of some metabolites varied significantly with time of collection and temperature. For instance, we detected elevated sugar levels in animals caught at the lowest daily field temperatures. Polyol concentrations were lower in individuals collected at the time points with the coldest temperatures and higher at the warmest temperatures. Additionally, changes in concentrations of metabolites associated with energetic metabolism was observed across collection times. Our findings suggest that hardening responses under natural conditions are marked and likely play a crucial role for coping with microhabitat temperature variation on a daily scale, and that metabolite levels are actively altered on a daily basis. Such results provide interesting new knowledge on the thermal biology of a common insect from the Arctic region, and contribute to our understanding of responses and robustness of arthropods to environmental changes in fragile and thermally variable ecosystems.
DOI: 10.6084/m9.figshare.19379885
title: Wearing & Scott 2022 - CD1 Telemetry Supplementary Datasheet

description: This dataset contains source data for our manuscript titled 'Effects of chronic hypoxia on routine cardiovascular function and metabolism'
DOI: 10.6084/m9.figshare.19379885.v1
title: Wearing & Scott 2022 - CD1 Telemetry Supplementary Datasheet

description: This dataset contains source data for our manuscript titled 'Effects of chronic hypoxia on routine cardiovascular function and metabolism'
DOI: 10.6084/m9.figshare.19615761
title: Wearing and Scott 2022 - Deer Mouse Telemetry Supplementary Datasheet

description: This dataset contains source data for our manuscript titled 'Evolved reductions in body temperature and the metabolic costs of thermoregulation in deer mice native to high altitude'
DOI: 10.6084/m9.figshare.19615761.v1
title: Wearing and Scott 2022 - Deer Mouse Telemetry Supplementary Datasheet

description: This dataset contains source data for our manuscript titled 'Evolved reductions in body temperature and the metabolic costs of thermoregulation in deer mice native to high altitude'
DOI: 10.6084/m9.figshare.20713345
title: RawData_ProvenceCoast2019.zip

description: <strong>Abstract: </strong> Mesophotic marine ecosystems are characterized by lower light penetration supporting specialized fish fauna. Due to their depths (-30 to -150 m), accessibility is challenging, and the structure of mesophotic fish assemblages is generally less known than either shallow reefs or deep zones with soft bottoms which are generally trawled. Environmental DNA metabarcoding from seawater filtered <em>in situ</em> could improve our ability to monitor the diversity of mesophotic ecosystems. Here, we developed and tested a submersible standalone pumping device allowing targeted marine water filtering to explore the biodiversity of two mesophotic ecosystems, one temperate along the Provence coast in the North-Western Mediterranean Sea and one tropical at the seamount La Pérouse in the Western Indian Ocean. We filtered water samples from depths ranging between 0 and 200 m in the Mediterranean Sea and between 60 and 140 m in the Indian Ocean and applied a metabarcoding protocol using the teleo primer pair targeting the 12S mitochondrial rDNA (Actinopterygii and Chondrichthyes). For both study regions, our eDNA survey was able to recover highly diverse fish assemblages and the compositional analysis of eDNA samples showed both a marked signal of fish compositional turnover and overlapping taxa between depth zones. Further, we observed that a substantial number of species were found in samples collected in depths beyond their reported depth range suggesting an underestimation of species’ depth tolerances. eDNA metabarcoding should thus complement existing knowledge of species' geographic distributions across space and depth. Overall, our results demonstrate the potential of eDNA metabarcoding for future mesophotic surveys as it allows fast and broad biodiversity assessment. <br> <strong>Data set:</strong> These data sets include the raw data of the Provence coast of the Environmental DNA article "Environmental DNA highlights fish biodiversity in mesophotic ecosystems".
DOI: 10.6084/m9.figshare.20714404
title: Selection for promoter CpG content_DATA.csv

description: Data for CpG content of genes for different vertebrate species and thier associated life history traits.
DOI: 10.6084/m9.figshare.20714404.v1
title: Selection for promoter CpG content_DATA.csv

description: Data for CpG content of genes for different vertebrate species and thier associated life history traits.
DOI: 10.5281/zenodo.7032167
title: A Parcellation Scheme of Mouse Isocortex Based on Reversals in Connectivity Gradients

description: This dataset contains a parcellation of mouse isocortex into a hierarchy of subregions. The parcellation is based on the detection of gradient reversals in voxelized connectivity, as described in our latest preprint manuscript. The connectivity dataset used for this purpose was the voxelized mouse connectome published by the Allen Institute for Brain Science, available at connectivity.brain-map.org (data) and github.com/AllenInstitute (code) Region id annotations are provided in .nrrd format. Refer to the NRRD documentation for details. The hierarchy is provided in the accompanying json file. For each region, an entry "structure_id_path" is provided that lists the ids of regions on the path from the root (i.e. isocortex) to the region in question. For more information, please read the accompanying manuscript. We will provide the link here, once it is online.
DOI: 10.6084/m9.figshare.20666349
title: Uncertainty modulates visual maps during non-instrumental information demand

description: Raw data associated with manuscipt "<strong>Uncertainty modulates visual maps during non-instrumental information demand"</strong>
DOI: 10.6084/m9.figshare.20666349.v1
title: Uncertainty modulates visual maps during non-instrumental information demand

description: Raw data associated with manuscipt "<strong>Uncertainty modulates visual maps during non-instrumental information demand"</strong>
DOI: 10.5281/zenodo.7029888
title: The ORACLES database

description: This experimental database gives access to both the processed and the raw<br> (instantaneous) velocity data measured by 2-component laser Doppler velocimetry on the<br> ORACLES test facility. It contains more than 55000 files. The access to the raw data<br> gives the opportunity to the end-user to re-process them according to his needs.<br> The processed files are cast in a Tecplot compatible format. The files headers are<br> meaningful so that these files can also be read by other means (text editor, specific<br> routines…).<br> All the necessary technical information regarding these data can be found in the<br> directory “Documents” where are present: 1) the related paper (authors’ version)<br> published in 2009 in Flow Turbulence and Combustion (82:155-183), 2) the PhD<br> thesis of Phuc-Danh Nguyen (in French) and 3) the complete layout of the database.<br> Numerous “ReadMeFirst” files are also provided in the sub-directories to explain wherever needed<br> the content of the related files.<br>
description: Part of this work has been supported by the FP5 European Project MOLECULES with Contract No. G4RD-CT-2000-00402 and by the Région Poitou-Charentes (France).
DOI: 10.5281/zenodo.7029887
title: The ORACLES database

description: This experimental database gives access to both the processed and the raw<br> (instantaneous) velocity data measured by 2-component laser Doppler velocimetry on the<br> ORACLES test facility. It contains more than 55000 files. The access to the raw data<br> gives the opportunity to the end-user to re-process them according to his needs.<br> The processed files are cast in a Tecplot compatible format. The files headers are<br> meaningful so that these files can also be read by other means (text editor, specific<br> routines…).<br> All the necessary technical information regarding these data can be found in the<br> directory “Documents” where are present: 1) the related paper (authors’ version)<br> published in 2009 in Flow Turbulence and Combustion (82:155-183), 2) the PhD<br> thesis of Phuc-Danh Nguyen (in French) and 3) the complete layout of the database.<br> Numerous “ReadMeFirst” files are also provided in the sub-directories to explain wherever needed<br> the content of the related files.<br>
description: Part of this work has been supported by the FP5 European Project MOLECULES with Contract No. G4RD-CT-2000-00402 and by the Région Poitou-Charentes (France).
DOI: 10.6084/m9.figshare.20685118
title: Microarray data_BJC-A3340621

description: Total cellular RNA from myofibroblasts isolated from Normal (N; n = 4) and Colonic Adenocarcinoma (CA; n = 5) tissues, was extracted using RNAqueous (Ambion, Austin, TX, USA) according to the manufacturer’s recommendations. Total RNA extracted from the samples was processed using the RNA labeling protocol described by Ambion (MessageAmp aRNA Kit Instruction Manual) and hybridized to Affymetrix Gene Chips (HGU133 Plus 2.0 arrays). <br>
DOI: 10.6084/m9.figshare.20685118.v1
title: Microarray data_BJC-A3340621

description: Total cellular RNA from myofibroblasts isolated from Normal (N; n = 4) and Colonic Adenocarcinoma (CA; n = 5) tissues, was extracted using RNAqueous (Ambion, Austin, TX, USA) according to the manufacturer’s recommendations. Total RNA extracted from the samples was processed using the RNA labeling protocol described by Ambion (MessageAmp aRNA Kit Instruction Manual) and hybridized to Affymetrix Gene Chips (HGU133 Plus 2.0 arrays). <br>
DOI: 10.6084/m9.figshare.20685118.v2
title: Microarray data_BJC-A3340621

description: Total cellular RNA from myofibroblasts isolated from Normal (N; n = 4) and Colonic Adenocarcinoma (CA; n = 5) tissues, was extracted using RNAqueous (Ambion, Austin, TX, USA) according to the manufacturer’s recommendations. Total RNA extracted from the samples was processed using the RNA labeling protocol described by Ambion (MessageAmp aRNA Kit Instruction Manual) and hybridized to Affymetrix Gene Chips (HGU133 Plus 2.0 arrays). <br>
DOI: 10.5281/zenodo.7032262
title: Malignant pleural effusion LADC immunity 700 gene dataset

description: MPE cytologic cell blocks of 83 LADC patients were analysed for the mRNA expression of 770 cancer-immune genes by the NanoString nCounter platform.
DOI: 10.5281/zenodo.7032261
title: Malignant pleural effusion LADC immunity 700 gene dataset

description: MPE cytologic cell blocks of 83 LADC patients were analysed for the mRNA expression of 770 cancer-immune genes by the NanoString nCounter platform.
DOI: 10.5281/zenodo.7032267
title: Data from: The Effects of Multi-Level Identity Dynamics in New Venture Creation

description: Anonymized interview data from SNF project<strong> The Effects of Multi-Level Identity Dynamics in New Venture Creation </strong>(in the context of collective entrepreneurial ventures) that has been used for publications (as stated in Data Management Plan). Additional data available upon request.
DOI: 10.5281/zenodo.7032268
title: Data from: The Effects of Multi-Level Identity Dynamics in New Venture Creation

description: Anonymized interview data from SNF project<strong> The Effects of Multi-Level Identity Dynamics in New Venture Creation </strong>(in the context of collective entrepreneurial ventures) that has been used for publications (as stated in Data Management Plan). Additional data available upon request.
DOI: 10.17188/mpcontribs/1883597
title: Data for the MOF Explorer on the Materials Project

description: This is the data backend for the MOF Explorer application on the Materials Project and is built around the QMOF Database.
DOI: 10.5281/zenodo.7031396
title: mofdscribe data - QMOF

description: Dataset used by the mofdscribe software. Contains a subset of the original data, additional GCMC and process data as well as hashes and features. <em>Not intended for direct use. </em>
DOI: 10.5281/zenodo.7031397
title: mofdscribe data - QMOF

description: Dataset used by the mofdscribe software. Contains a subset of the original data, additional GCMC and process data as well as hashes and features. <em>Not intended for direct use. </em>
DOI: 10.6084/m9.figshare.20439810
title: RNA structure-altering mutations underlying positive selection on Spike protein reveal novel putative signatures to trace crossing host-species barriers in Betacoronavirus

description: Similar to other RNA viruses, the emergence of Betacoronavirus relies on cross-species viral transmission, which requires careful health surveillance monitoring of protein-coding information as well as genome-wide analysis. Although the evolutionary jump from natural reservoirs to humans may be mainly traced-back by studying the effect that hotspot mutations have on viral proteins, it is largely unexplored if other impacts might emerge on the structured RNA genome of Betacoronavirus. In this survey, the protein-coding and viral genome architecture were simultaneously studied to uncover novel insights into cross-species horizontal transmission events. We analysed 1,252,952 viral genomes of SARS-CoV, MERS-CoV, and SARS-CoV-2 distributed across the world in bats, intermediate animals, and humans to build a new landscape of changes in the RNA viral genome. Phylogenetic analyses suggest that bat viruses are the most closely related to the time of most recent common ancestor of​ Betacoronavirus, and missense mutations in viral proteins, mainly in the S protein S1 subunit: SARS-CoV (G &gt; T; A577S); MERS-CoV (C &gt; T; S746R and C &gt; T; N762A); and SARS-CoV-2 (A &gt; G; D614G) appear to have driven viral diversification. We also found that codon sites under positive selection on S protein overlap with non-compensatory mutations that disrupt secondary RNA structures in the RNA genome complement. These findings provide pivotal factors that might be underlying the eventual jumping the species barrier from bats to intermediate hosts. Lastly, we discovered that nearly half of the Betacoronavirus genomes carry highly conserved RNA structures, and more than 90% of these RNA structures show negative selection signals, suggesting essential functions in the biology of Betacoronavirus that have not been investigated to date. Further research is needed on negatively selected RNA structures to scan for emerging functions like the potential of coding virus-derived small RNAs and to develop new candidate antiviral therapeutic strategies.
DOI: 10.6084/m9.figshare.20439810.v1
title: RNA structure-altering mutations underlying positive selection on Spike protein reveal novel putative signatures to trace crossing host-species barriers in Betacoronavirus

description: Similar to other RNA viruses, the emergence of Betacoronavirus relies on cross-species viral transmission, which requires careful health surveillance monitoring of protein-coding information as well as genome-wide analysis. Although the evolutionary jump from natural reservoirs to humans may be mainly traced-back by studying the effect that hotspot mutations have on viral proteins, it is largely unexplored if other impacts might emerge on the structured RNA genome of Betacoronavirus. In this survey, the protein-coding and viral genome architecture were simultaneously studied to uncover novel insights into cross-species horizontal transmission events. We analysed 1,252,952 viral genomes of SARS-CoV, MERS-CoV, and SARS-CoV-2 distributed across the world in bats, intermediate animals, and humans to build a new landscape of changes in the RNA viral genome. Phylogenetic analyses suggest that bat viruses are the most closely related to the time of most recent common ancestor of​ Betacoronavirus, and missense mutations in viral proteins, mainly in the S protein S1 subunit: SARS-CoV (G &gt; T; A577S); MERS-CoV (C &gt; T; S746R and C &gt; T; N762A); and SARS-CoV-2 (A &gt; G; D614G) appear to have driven viral diversification. We also found that codon sites under positive selection on S protein overlap with non-compensatory mutations that disrupt secondary RNA structures in the RNA genome complement. These findings provide pivotal factors that might be underlying the eventual jumping the species barrier from bats to intermediate hosts. Lastly, we discovered that nearly half of the Betacoronavirus genomes carry highly conserved RNA structures, and more than 90% of these RNA structures show negative selection signals, suggesting essential functions in the biology of Betacoronavirus that have not been investigated to date. Further research is needed on negatively selected RNA structures to scan for emerging functions like the potential of coding virus-derived small RNAs and to develop new candidate antiviral therapeutic strategies.
DOI: 10.5281/zenodo.6985376
title: WS22 database: combining Wigner Sampling and geometry interpolation towards configurationally diverse molecular datasets

description: This database provides a collection of molecular datasets that explores a broad configurational space of flexible organic molecules. It includes several chemical properties calculated with a quantum chemical method. Details about the methodology, content, and structure of the datasets are provided in the README file included in this repository.
DOI: 10.5281/zenodo.6985377
title: WS22 database: combining Wigner Sampling and geometry interpolation towards configurationally diverse molecular datasets

description: This database provides a collection of molecular datasets that explores a broad configurational space of flexible organic molecules. It includes several chemical properties calculated with a quantum chemical method. Details about the methodology, content, and structure of the datasets are provided in the README file included in this repository.
DOI: 10.6084/m9.figshare.20714392
title: Supplementary Table S3-S5 new manuscript

description: This datasheet contains the Supplementary Tables listed below, which are separate sheets of a single excel file named Supplementary Table S3-S5 new manuscript to complement the data and analyses of the manuscript entitled: Multiple approaches define the bacterial ancestry of mitochondria. <br> <strong>Supplementary Table S3.</strong> Tabulation of 20 aerobic traits (Box1) and their cumulative score in 15 alphaproteobacterial lineages plus 20 aerobic mitochondria from eukaryotes. The rightmost column shows the sum values for the 2-oxoacid:ferredoxin oxidoreductases (OFORs) considered as traits of anaerobic metabolism. <strong>Supplementary Table S3B.</strong> Statistical results of the T test on the lineage-specific scores of aerobic traits listed in Table S3. Lineages displaying high levels of P values (&gt;0.1) indicating no significant difference with respect to aerobic mitochondria are highlighted in pale purple. <strong>Supplementary Table S4. </strong>Distribution of <em>spt</em> (the gene for serine-palmitoyl transferases) and allied genes for ceramide biosynthesis, as well as of <em>kynU</em> (gene for kynureninase) and allied genes of the kynurenine pathway among 15 lineages of alphaproteobacteria. When the <em>kynA</em> gene for tryptophan di-oxygenase gene lies in the same genomic region of <em>kynU</em> it is annotated as 1. <strong>Supplementary Table S5</strong>. Distribution of four enzymes for cardiolipin metabolism along the alphaproteobacterial lineages, cf. Fig. 3E. Taxa with both types of cardiolipin synthase are highlighted in pale green. <br> We add to the above Tables the separate MEGAX file named Contig829 with the DNA sequence of the re-assembled metagenomic DNA sequence for Alphaproteobacteria J134 from Ward et al (2019) DOI: 10.1264/jsme2.ME19017 . <br> <br>