cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48425/rdss0s2s
title: Protocol plant measurements snowbed experiment varanger

description: Protocol for plant measurments in a herbivore exclosure experiment in snowbeds on the Varanger peninsula. This protocol is used for the following datasets: * V_snowbed_vascular_plant_abundance_experimental * V_snowbed_plant_community_composition_experimental * V_snowbed_ground_cover_experimental * V_snowbed_shrub_height_experimental Version 2 of the protocol is used from 2021 onwards. Snowbeds in Komagdalen have been added to this protocol. Version 3 of the protocol is used from 2022 onwards. One snowbed in Komagdalen has been removed from the study design.
DOI: 10.48425/29qhll1c
title: Protocol plant measurements snowbed experiment varanger

description: Protocol for plant measurments in a herbivore exclosure experiment in snowbeds on the Varanger peninsula. This protocol is used for the following datasets: * V_snowbed_vascular_plant_abundance_experimental * V_snowbed_plant_community_composition_experimental * V_snowbed_ground_cover_experimental * V_snowbed_shrub_height_experimental Version 2 of the protocol is used from 2021 onwards. Snowbeds in Komagdalen have been added to this protocol.
DOI: 10.5281/zenodo.7848788
title: Proboscidean Palaeoproteomic Reference Dataset

description: This entry contains the 'Proboscidean Palaeoproteomic Reference Dataset'. We used PaleoProPhyler ( https://github.com/johnpatramanis/Proteomic_Pipeline ) to generate a palaeoproteomic reference dataset of protein sequences from ancient and present-day Proboscidae. Using the first two modules of PaleoProPhyler, we translated more than 35 publicly available whole genomes from extant and extinct species. Details on the processing of the sequences can be found below. Which individuals / species are included? The full list of individuals, the original fastq repository location and the species included in the dataset are contained within the tab seperated file 'METATADATA.txt', that also contains headers. Most individuals of the dataset belong to one of these 3 species: <em>Loxodonta africana</em>,<em> Elephas maximus</em>, <em>Mammuthus primigenius. </em> Which Proteins are included? We compiled a small initial list of 262 proteins that had been indentified in either teeth, bone or items made out of ivory. For each protein, both the canonical and all alternative protein coding isoforms (based on the Loxodonta africana reference proteome of Ensembl) were translated, leading to more than 350 unique protein sequences for each individual in the dataset. The protein list is available in the file 'proteins.txt' Other files included in the zip folder: - ALL_PROT_REFERENCE.fa contains all of the sequences generated as part of the Proboscidean Palaeoproteomic Reference Dataset described above - PER_PROTEIN is a folder containing one fasta file for each protein within the Proboscidean Palaeoproteomic Reference Dataset, each protein fasta file has the sequences of all individuals for that particular protein - PER_SAMPLE is a folder containing one fasta file for each sample/individual within the Proboscidean Palaeoproteomic Reference Dataset, each sample fasta file has the sequences of all proteins for that particular sample.
DOI: 10.5281/zenodo.7848787
title: Proboscidean Palaeoproteomic Reference Dataset

description: This entry contains the 'Proboscidean Palaeoproteomic Reference Dataset'. We used PaleoProPhyler ( https://github.com/johnpatramanis/Proteomic_Pipeline ) to generate a palaeoproteomic reference dataset of protein sequences from ancient and present-day Proboscidae. Using the first two modules of PaleoProPhyler, we translated more than 35 publicly available whole genomes from extant and extinct species. Details on the processing of the sequences can be found below. Which individuals / species are included? The full list of individuals, the original fastq repository location and the species included in the dataset are contained within the tab seperated file 'METATADATA.txt', that also contains headers. Most individuals of the dataset belong to one of these 3 species: <em>Loxodonta africana</em>,<em> Elephas maximus</em>, <em>Mammuthus primigenius. </em> Which Proteins are included? We compiled a small initial list of 262 proteins that had been indentified in either teeth, bone or items made out of ivory. For each protein, both the canonical and all alternative protein coding isoforms (based on the Loxodonta africana reference proteome of Ensembl) were translated, leading to more than 350 unique protein sequences for each individual in the dataset. The protein list is available in the file 'proteins.txt' How were the proteins translated/generated? All genetic data were downloaded from ENA (https://www.ebi.ac.uk/ena/browser/home) as fastq files and mapped onto LoxAfr3, which is the latest annotated African elephant genome in Ensembl. The scripts used for the mapping are available here: https://github.com/johnpatramanis/Mapping_Scripts . We used the resulting bam files as input for PaleoProPhyler's module 1 & 2 , using LoxAfr3 as the reference proteome. Other files included in the zip folder: - ALL_PROT_REFERENCE.fa contains all of the sequences generated as part of the Proboscidean Palaeoproteomic Reference Dataset described above - PER_PROTEIN is a folder containing one fasta file for each protein within the Proboscidean Palaeoproteomic Reference Dataset, each protein fasta file has the sequences of all individuals for that particular protein - PER_SAMPLE is a folder containing one fasta file for each sample/individual within the Proboscidean Palaeoproteomic Reference Dataset, each sample fasta file has the sequences of all proteins for that particular sample.
DOI: 10.5281/zenodo.7870897
title: Proboscidean Palaeoproteomic Reference Dataset

description: This entry contains the 'Proboscidean Palaeoproteomic Reference Dataset'. We used PaleoProPhyler ( https://github.com/johnpatramanis/Proteomic_Pipeline ) to generate a palaeoproteomic reference dataset of protein sequences from ancient and present-day Proboscidae. Using the first two modules of PaleoProPhyler, we translated more than 35 publicly available whole genomes from extant and extinct species. Details on the processing of the sequences can be found below. Which individuals / species are included? The full list of individuals, the original fastq repository location and the species included in the dataset are contained within the tab seperated file 'METATADATA.txt', that also contains headers. Most individuals of the dataset belong to one of these 3 species: <em>Loxodonta africana</em>,<em> Elephas maximus</em>, <em>Mammuthus primigenius. </em> Which Proteins are included? We compiled a small initial list of 262 proteins that had been indentified in either teeth, bone or items made out of ivory. For each protein, both the canonical and all alternative protein coding isoforms (based on the Loxodonta africana reference proteome of Ensembl) were translated, leading to more than 350 unique protein sequences for each individual in the dataset. The protein list is available in the file 'proteins.txt' How were the proteins translated/generated? All genetic data were downloaded from ENA (https://www.ebi.ac.uk/ena/browser/home) as fastq files and mapped onto LoxAfr3, which is the latest annotated African elephant genome in Ensembl. The scripts used for the mapping are available here: https://github.com/johnpatramanis/Mapping_Scripts . We used the resulting bam files as input for PaleoProPhyler's module 1 & 2 , using LoxAfr3 as the reference proteome. Other files included in the zip folder: - ALL_PROT_REFERENCE.fa contains all of the sequences generated as part of the Proboscidean Palaeoproteomic Reference Dataset described above - PER_PROTEIN is a folder containing one fasta file for each protein within the Proboscidean Palaeoproteomic Reference Dataset, each protein fasta file has the sequences of all individuals for that particular protein - PER_SAMPLE is a folder containing one fasta file for each sample/individual within the Proboscidean Palaeoproteomic Reference Dataset, each sample fasta file has the sequences of all proteins for that particular sample.
DOI: 10.5281/zenodo.7868383
title: CHclim25 - sum of precipitation (Prec)

description: Sum of precipitation are derived from daily 1 km resolution gridded dataset from the Swiss federal agency for meteorology and climate (MeteoSwiss) using a bilinear downscaling to 25 m resolution. Monthly and yearly individual and current average (1981-2010) and future average (2020-2049, 2045-2074, and 2070-2099)<strong> </strong>geoTIFF layers can be downloaded from separate zip files. Future layers are based on the transient daily time series of gridded climate scenarios of temperature at 0.02°D (~2.2 km) provided by the CH2018 initiative. Anomalies between monthly sum of precipitation for 1981-2010 and monthly sum of precipitation for the future period at 2.2 km were downscaled at 25 m using bilinear interpolation. Anomalies were then added to 1981-2010 average monthly variables. We calculated future climatic layers for 4 GCMs (HADGEM, ECEARTH, MPIESM, and IPSL), 3 time slices (2020-2049, 2045-2074, and 2070-2099) and 3 representative concentration pathways (RCP 2.6, 4.5 and 8.5) The layer files are stored in compressed GeoTIFF format with the “deflate” algorithm with option “predictor2” from the GDAL. This format has a high compression ratio but allows direct import in most GIS softwares. All the maps are projected in the Swiss coordinate system CH 1903+ LV95 (epsg:2056) with a resolution of 25x25m using the extent of the digital height model DHM25 of the Swiss office for topography (swisstopo).
DOI: 10.5281/zenodo.7868382
title: CHclim25 - sum of precipitation (Prec)

description: Sum of precipitation are derived from daily 1 km resolution gridded dataset from the Swiss federal agency for meteorology and climate (MeteoSwiss) using a bilinear downscaling to 25 m resolution. Monthly and yearly individual and current average (1981-2010) and future average (2020-2049, 2045-2074, and 2070-2099)<strong> </strong>geoTIFF layers can be downloaded from separate zip files. Future layers are based on the transient daily time series of gridded climate scenarios of temperature at 0.02°D (~2.2 km) provided by the CH2018 initiative. Anomalies between monthly sum of precipitation for 1981-2010 and monthly sum of precipitation for the future period at 2.2 km were downscaled at 25 m using bilinear interpolation. Anomalies were then added to 1981-2010 average monthly variables. We calculated future climatic layers for 4 GCMs (HADGEM, ECEARTH, MPIESM, and IPSL), 3 time slices (2020-2049, 2045-2074, and 2070-2099) and 3 representative concentration pathways (RCP 2.6, 4.5 and 8.5) The layer files are stored in compressed GeoTIFF format with the “deflate” algorithm with option “predictor2” from the GDAL. This format has a high compression ratio but allows direct import in most GIS softwares. All the maps are projected in the Swiss coordinate system CH 1903+ LV95 (epsg:2056) with a resolution of 25x25m using the extent of the digital height model DHM25 of the Swiss office for topography (swisstopo).
DOI: 10.5281/zenodo.7870894
title: Evaluation of the pKa's of Quinazoline Derivatives : Usage of Quantum Mechanical Based Descriptors

description: In this study, several quantum mechanical-based computational approaches have been used in order to propose accurate protocols for predicting the p<em>K<sub>a</sub></em>’s of quinazoline derivatives, which constitute a very important class of natural and synthetic compounds in organic, pharmaceutical, agricultural and medicinal chemistry areas. Linear relationships between the experimental p<em>K<sub>a</sub></em>’s and nine different DFT descriptors (atomic charge on nitrogen atoms (<em>Q</em>(N), ionization energy (<em>I</em>), electron affinity (<em>A</em>), chemical potential (m), hardness (h), electrophilicity index (w), fukui functions (<em>f <sup>+</sup></em>, <em>f <sup>-</sup></em>), condensed dual descriptor (D<em>f</em>) and local hypersoftness (s<sup>(2)</sup>)) were considered. Several DFT methods (a combination of five DFT functionals and two basis sets) in conjunction with two different implicit solvent models were tested, and among them, M06L/6-311++G(d,p) level of theory employing the CPCM solvation model was found to give the strongest correlations between the DFT descriptors and the experimental p<em>K<sub>a</sub></em>’s of the quinazoline derivatives. The calculated atomic charge on N<sub>1</sub> atom (<em>Q</em>(N<sub>1</sub>)) was shown to be the best descriptor to reproduce the experimental p<em>K<sub>a</sub></em>’s (R<sup>2</sup>=0.927), whereas strong correlations were also derived for <em>A</em>, w, m, and Δ<em>f</em>. In the last part, the applicability of isodesmic reaction scheme to the p<em>K<sub>a</sub></em> prediction of quinazoline derivatives was tested, and the calculated <em>A</em> was shown to be a well-established method for the classification of molecules, and thus, for the identification of a suitable reference molecule for the calculations. The QM-based protocols presented in this study will enable fast and accurate high-throughput p<em>K<sub>a</sub></em> predictions of quinazoline derivatives and the relationships derived can be effectively used in data generation for successful machine learning models for p<em>K<sub>a</sub></em> predictions.
DOI: 10.5281/zenodo.7870893
title: Evaluation of the pKa's of Quinazoline Derivatives : Usage of Quantum Mechanical Based Descriptors

description: In this study, several quantum mechanical-based computational approaches have been used in order to propose accurate protocols for predicting the p<em>K<sub>a</sub></em>’s of quinazoline derivatives, which constitute a very important class of natural and synthetic compounds in organic, pharmaceutical, agricultural and medicinal chemistry areas. Linear relationships between the experimental p<em>K<sub>a</sub></em>’s and nine different DFT descriptors (atomic charge on nitrogen atoms (<em>Q</em>(N), ionization energy (<em>I</em>), electron affinity (<em>A</em>), chemical potential (m), hardness (h), electrophilicity index (w), fukui functions (<em>f <sup>+</sup></em>, <em>f <sup>-</sup></em>), condensed dual descriptor (D<em>f</em>) and local hypersoftness (s<sup>(2)</sup>)) were considered. Several DFT methods (a combination of five DFT functionals and two basis sets) in conjunction with two different implicit solvent models were tested, and among them, M06L/6-311++G(d,p) level of theory employing the CPCM solvation model was found to give the strongest correlations between the DFT descriptors and the experimental p<em>K<sub>a</sub></em>’s of the quinazoline derivatives. The calculated atomic charge on N<sub>1</sub> atom (<em>Q</em>(N<sub>1</sub>)) was shown to be the best descriptor to reproduce the experimental p<em>K<sub>a</sub></em>’s (R<sup>2</sup>=0.927), whereas strong correlations were also derived for <em>A</em>, w, m, and Δ<em>f</em>. In the last part, the applicability of isodesmic reaction scheme to the p<em>K<sub>a</sub></em> prediction of quinazoline derivatives was tested, and the calculated <em>A</em> was shown to be a well-established method for the classification of molecules, and thus, for the identification of a suitable reference molecule for the calculations. The QM-based protocols presented in this study will enable fast and accurate high-throughput p<em>K<sub>a</sub></em> predictions of quinazoline derivatives and the relationships derived can be effectively used in data generation for successful machine learning models for p<em>K<sub>a</sub></em> predictions.
DOI: 10.5281/zenodo.7870899
title: desmognathus_auriculatus_decontaminated_gx.fasta.gx

description: .
DOI: 10.5281/zenodo.7870898
title: desmognathus_auriculatus_decontaminated_gx.fasta.gx

description: .
DOI: 10.6084/m9.figshare.22704403
title: Comparative transcriptomic analysis of nasopharyngeal swabs from individuals with and without COVID-19

description: This dataset contains the results of a transcriptomic (RNA-seq) analysis of nasopharyngeal swabs collected from 50 individuals with COVID-19 and 13 individuals without COVID-19 based on clinical qPCR testing. COVID-19 positive individuals included 16 outpatients, 16 hospitalized, non-ICU patients, and 18 hospitalized ICU patients. Samples were collected from a clinical cohort in Greater Toronto Area hospitals and outpatient assessment centres between October 2020 and October 2021. Four comparative analyses were performed using DESeq2: all COVID-19 positive individual versus negatives, COVID-19 ICU individuals versus negatives, non-ICU COVID-19 positive individuals versus negatives, and COVID-19 positive outpatients versus negatives. The analysis was performed with DESeq2 v1.30.1 using the Gencode human reference transcriptome v37.<br>
DOI: 10.5281/zenodo.7870903
title: desmognathus_carolinensis_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.7870902
title: desmognathus_carolinensis_decontaminated_gx.fasta.gz

description: .
DOI: 10.6084/m9.figshare.22708948
title: Data for three turtles, analyzed in the paper entitled "Greater physiological resistance to heat may favor the invasive freshwater turtle to outcompete native species in the changing climate"

description: The CTmax of the invasive turtle<em> T. scripta elegans</em> and two native turtle species <em>P. sinensis</em> and <em>M. reevesii, </em>and the relative gene expression levels of mutiple HSPs, TERT and relative telomere length in the liver and muscle of these three turtle species during acute heat stress of 35, 37, 39 and 41<sup>o</sup>C.
DOI: 10.6084/m9.figshare.22708948.v1
title: Data for three turtles, analyzed in the paper entitled "Greater physiological resistance to heat may favor the invasive freshwater turtle to outcompete native species in the changing climate"

description: The CTmax of the invasive turtle<em> T. scripta elegans</em> and two native turtle species <em>P. sinensis</em> and <em>M. reevesii, </em>and the relative gene expression levels of mutiple HSPs, TERT and relative telomere length in the liver and muscle of these three turtle species during acute heat stress of 35, 37, 39 and 41<sup>o</sup>C.
DOI: 10.5281/zenodo.7870911
title: desmognathus_folkertsi_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.7870910
title: desmognathus_folkertsi_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.7870916
title: Thermal image data sets

description: Thermal image data set captured by an inspection mobile robot
DOI: 10.5281/zenodo.7870915
title: Thermal image data sets

description: Thermal image data set captured by an inspection mobile robot
DOI: 10.48425/kwtbtl7g
title: Protocol snowbed shrub abundance intensive varanger

description: Protocol for recording dwarf shrub abundance in snowbed habitats within the COAT Varanger intensive design.
DOI: 10.6084/m9.figshare.6509870
title: Data for POLS.xlsx

description: All data and the correlativity for all measured parameters of POLS hypothesis in freshwater turtles
DOI: 10.6084/m9.figshare.6509870.v1
title: Data for POLS.xlsx

description: All data and the correlativity for all measured parameters of POLS hypothesis in freshwater turtles
DOI: 10.48425/gzscv34c
title: Protocol_check_exclosures_varanger

description: Protocol for checking exclosures in snowbeds, heath and meadows on the Varanger peninsual. Snowbeds in Komagdalen have been added to version 2 of the protocol.
DOI: 10.5281/zenodo.7870799
title: Spectropolarimetric observations of the solar atmosphere in the Hα 6563 Å line

description: This dataset contains spectropolarimetric measurements obtained in the 6563A Halpha line near the solar limb with the Gregory Coudé Telescope at IRSOL in Locarno. The observations are discussed in the article: Jaume Bestard, J.; Trujillo Bueno, J.; Bianda, M.; Štěpán, J.; Ramelli, R.<br> "Spectropolarimetric observations of the solar atmosphere in the Hα 6563 Å line."<br> 2022A&A...659A.179J<br> DOI: 10.1051/0004-6361/202141834
DOI: 10.5281/zenodo.7870798
title: Spectropolarimetric observations of the solar atmosphere in the Hα 6563 Å line

description: This dataset contains spectropolarimetric measurements obtained in the 6563A Halpha line near the solar limb with the Gregory Coudé Telescope at IRSOL in Locarno. The observations are discussed in the article: Jaume Bestard, J.; Trujillo Bueno, J.; Bianda, M.; Štěpán, J.; Ramelli, R.<br> "Spectropolarimetric observations of the solar atmosphere in the Hα 6563 Å line."<br> 2022A&A...659A.179J<br> DOI: 10.1051/0004-6361/202141834
DOI: 10.6084/m9.figshare.22709098
title: Thesis - Supplementary Table 2.4

description: <strong>Supplementary Table 2.4. Protein sequences used to build the trees in Supplementary Figure 2.7.</strong>
DOI: 10.6084/m9.figshare.22709098.v1
title: Thesis - Supplementary Table 2.4

description: <strong>Supplementary Table 2.4. Protein sequences used to build the trees in Supplementary Figure 2.7.</strong>
DOI: 10.6084/m9.figshare.22709104
title: Thesis - Supplementary Table 2.5

description: <strong>Supplementary Table 1.5. Abundance of defence systems identified with PADLOC in bacteria and archaea. </strong>All genomes from RefSeq v201 Archaea and Bacteria were searched with PADLOC. The values in the table represent, for each genus, the percentage of genomes encoding a system, grouped using GTDB taxonomy.
DOI: 10.6084/m9.figshare.22709104.v1
title: Thesis - Supplementary Table 2.5

description: <strong>Supplementary Table 1.5. Abundance of defence systems identified with PADLOC in bacteria and archaea. </strong>All genomes from RefSeq v201 Archaea and Bacteria were searched with PADLOC. The values in the table represent, for each genus, the percentage of genomes encoding a system, grouped using GTDB taxonomy.
DOI: 10.5281/zenodo.7620900
title: vowel formant representation in human speech cortex

description: Data accompanying the paper publication.
DOI: 10.5281/zenodo.7620899
title: vowel formant representation in human speech cortex

description: Data accompanying the paper publication.
DOI: 10.6084/m9.figshare.22708945
title: Beta Decay and Electron Capture Stellar Rates of Heavy Nuclei.

description: <strong>QRPA rates: </strong>This dataset contains beta decay and electron capture rates which have been computed employing the fully microscopic proton-neutron QRPA (quasi-particle random-phase approximation) within a broad density, ρY<sub>e</sub> = (10 - 10<sup>11</sup>) [g cm<sup>-3</sup>], and temperature, T = (1-30) [GK], grid relevant to the pre-collapse astrophysical environment (from now on referred to as stellar rates). <br> <strong>Class 1 nuclei (Global) rates: </strong>This dataset contains beta decay and electron capture (Global) stellar rates for class 1 nuclei. Class 1 contains nuclides with energy values of the first parent excitation states above 2 MeV calculated by our pn-QRPA model. Our class 1 nuclides belong to the global Brink Axcel (GBA) hypothesis category where the strength distributions of all initial excited states have been replicated only by the ground state GT distribution. <br> <strong>Class 2 nuclei (Local) rates: </strong>This dataset contains beta decay and electron capture (Local) stellar rates for class 2 nuclei. Class 2 contains nuclides, where our (pn-QRPA) model computes only one initial excited state above ground level around 1 MeV energy. In class 2 nuclides, combined GT strength distributions of the parent ground and first excited state have been replaced for all subsequent levels in the parent nucleus. We refer to class 2 as localized Brink Axcel (LBA) hypothesis. <br> <strong>Class 3 nuclei (Local) rates: </strong>This dataset contains beta decay and electron capture (Local) stellar rates for class 3 nuclei. Class 3 contains nuclides, where our (pn-QRPA) model computes several parent excited states with energies up to 1 MeV. In class 3 nuclides, combined GT strength distributions of the parent ground and multiple excited states have been replaced for all subsequent levels in the parent nucleus. We refer to class 3 as localized Brink Axcel (LBA) hypothesis. <br> <br> <br> <br>
DOI: 10.34740/kaggle/dsv/5539555
title: 2021 World Population (updated daily)