cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12593865
title: The data for the work of 'Using non-adiabatic excitation transfer for signal transmission between molecular logic gates'

description: There are input and output data for calculation of non-adiabatic transfer rates which was performed using the NATRC program. It was calculated rates for transfer and relaxation of an exciton in the molecule of 3H-thioxanthene-TTF-dibenzo-BODIPY.  The study was carried out using three isomers of this molecule: 'Chain', 'Line' and 'S-line'
DOI: 10.15482/usda.adc/24712827
title: Data from: Expansion of Proteome-wide <i>Coxiella burnetii </i>Comparative T-cell Epitope Prediction to Include Small Ruminant Hosts

description: T-cell epitopes represent sampled environmental- and self-peptides loaded into major histocompatibility complex (MHC) proteins. Bioinformatic tools have been produced to predict these interactions for many species, providing peptides of interest in vaccine development studies.Prior work by the researchers (DOI: 10.1186/s12859-021-04181-w) assessed the ability of <i>Coxiella burnetii </i>proteins to interact with MHC alleles in human, mouse, and cattle species, the data from which is available on the Open Science Framework repository with accession number RN6QA (DOI: 10.17605/OSF.IO/RN6QA).Presently, bioinformatic programs NetBoLAIIpan 1.0 and NetMHCpan 4.1 were employed to predict T-cell epitopes within the <i>C. burnetii </i>proteome for the small ruminant species and to expand cattle predictions. The new datasets available herein provide the species, amino acid sequence, position within the protein, GenBank ID, allele name, and the predicted binding strength for each tested peptide.
DOI: 10.15482/usda.adc/24712827.v1
title: Data from: Expansion of Proteome-wide <i>Coxiella burnetii </i>Comparative T-cell Epitope Prediction to Include Small Ruminant Hosts

description: T-cell epitopes represent sampled environmental- and self-peptides loaded into major histocompatibility complex (MHC) proteins. Bioinformatic tools have been produced to predict these interactions for many species, providing peptides of interest in vaccine development studies.Prior work by the researchers (DOI: 10.1186/s12859-021-04181-w) assessed the ability of <i>Coxiella burnetii </i>proteins to interact with MHC alleles in human, mouse, and cattle species, the data from which is available on the Open Science Framework repository with accession number RN6QA (DOI: 10.17605/OSF.IO/RN6QA).Presently, bioinformatic programs NetBoLAIIpan 1.0 and NetMHCpan 4.1 were employed to predict T-cell epitopes within the <i>C. burnetii </i>proteome for the small ruminant species and to expand cattle predictions. The new datasets available herein provide the species, amino acid sequence, position within the protein, GenBank ID, allele name, and the predicted binding strength for each tested peptide.
DOI: 10.15468/dl.sb37tu
title: Occurrence Download

description: A dataset containing 5137 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Anaxyrus punctatus (Baird & Girard, 1852)"
 ]
}

 The dataset includes 5137 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018484-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26030/rxc2-1v61
title: Simulated Galactic Cosmic Ray Exposure Activates Dose-Dependent DNA Repair Response and Downregulates Glucosinolate Pathway in Arabidopsis Seedlings

description: This study's objective was to develop an understanding of the biological effects of space radiation on plants with the goal of producing fresh food during long duration space missions to support astronauts' nutritional and psychological needs.10-day-old Arabidopsis seedlings were exposed to simulated Galactic Cosmic Rays (GCR) and assessed for transcriptomic changes. The simulated GCR irradiation was carried out in the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Lab (BNL). The exposures were conducted acutely for two dose points at 40 cGy or 80 cGy, with sequential delivery of proton, helium, oxygen, silicon, and iron ions. Control and irradiated seedlings were then harvested and stabilized in RNAlater at 3 hrs. post irradiation. Total RNA was isolated for transcriptomic analyses using RNAseq. The data revealed that the transcriptomic responses were dose-dependent, with significant upregulation of DNA repair pathways and downregulation of glucosinolate biosynthetic pathways. Glucosinolates are important for plant pathogen defense and for the taste of a plant, which are both relevant to growing plants for spaceflight. These findings fill in knowledge gaps of how plants respond to radiation in beyond-Earth environments.
DOI: 10.5281/zenodo.12695127
title: Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction

description: Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map eQTLs in Saccharomyces cerevisiae by single-cell RNA sequencing (scRNA-seq) and applied it to over 100,000 single cells from three crosses. We used scRNA-seq data to genotype each cell, measure gene expression, and classify the cells by cell-cycle stage. We mapped thousands of local and distant eQTLs and identified interactions between eQTL effects and cell-cycle stages. We took advantage of single-cell expression information to identify hundreds of genes with allele-specific effects on expression noise. We used cell-cycle stage classification to map 20 loci that influence cell-cycle progression. One of these loci influenced the expression of genes involved in the mating response. We showed that the effects of this locus arise from a common variant (W82R) in the gene GPA1, which encodes a signaling protein that negatively regulates the mating pathway. The 82R allele increases mating efficiency at the cost of slower cell-cycle progression and is associated with a higher rate of outcrossing in nature. Our results provide a more granular picture of the effects of genetic variants on gene expression and downstream traits.
DOI: 10.5281/zenodo.12695128
title: Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction

description: Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map eQTLs in Saccharomyces cerevisiae by single-cell RNA sequencing (scRNA-seq) and applied it to over 100,000 single cells from three crosses. We used scRNA-seq data to genotype each cell, measure gene expression, and classify the cells by cell-cycle stage. We mapped thousands of local and distant eQTLs and identified interactions between eQTL effects and cell-cycle stages. We took advantage of single-cell expression information to identify hundreds of genes with allele-specific effects on expression noise. We used cell-cycle stage classification to map 20 loci that influence cell-cycle progression. One of these loci influenced the expression of genes involved in the mating response. We showed that the effects of this locus arise from a common variant (W82R) in the gene GPA1, which encodes a signaling protein that negatively regulates the mating pathway. The 82R allele increases mating efficiency at the cost of slower cell-cycle progression and is associated with a higher rate of outcrossing in nature. Our results provide a more granular picture of the effects of genetic variants on gene expression and downstream traits.
DOI: 10.15468/dl.dbpp63
title: Occurrence Download

description: A dataset containing 32092 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Actualización de la base de datos del Atlas Mastozoológico de México"
 ]
}

 The dataset includes 32092 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018486-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12701467
title: Association between Dysregulated Expression of Ca2+ and ROS-Related Gene Pairs and Breast Cancer Patient Survival

description: This document contains an SPSS file with data from the BRCA-TCGA database, specifically detailing gene expression for each patient. It includes categorizations into high and low expression groups, as well as quartiles of gene expression.
DOI: 10.5281/zenodo.12701468
title: Association between Dysregulated Expression of Ca2+ and ROS-Related Gene Pairs and Breast Cancer Patient Survival

description: This document contains an SPSS file with data from the BRCA-TCGA database, specifically detailing gene expression for each patient. It includes categorizations into high and low expression groups, as well as quartiles of gene expression.
DOI: 10.5281/zenodo.12701762
title: Massive Compression for High Data Rate Macromolecular Crystallography: Impact on Diffraction Data and Subsequent Structural Analysis

description: This is a dataset containing raw "uncompressed" diffraction data from  test sample.

Data are collected on a lysozyme sample at 7.5 keV for a S-SAD experiment at the AMX beamline using an EIGEr 9M detector.

The compression used, to generate the cbf files can be derived from the filenames: 

BINx: pixel binning by a factor x

SUMx: frame summing by a factor x 

J2Kx: JPEG2000 compression used with a factor of x

HCOMPx: Hcompress used with a scale factor x 

For example: lyso_BIN2_SUM2_HCOMP4 was compressed using 2x pixel binning + 2x frame summing + Hcompress with scale of 4. 

More information will be included after publication, in the meantime, please contact author if details about processing are required.

All zstd tar directories contain the cbf files, ready to be processed. 

All data were collected at the AMX beamline at the NSLS-II using a DECTRIS EIGER X 9 M detector. 

 

See more details from the related work (xds.inpo files included)
DOI: 10.5281/zenodo.12701763
title: Massive Compression for High Data Rate Macromolecular Crystallography: Impact on Diffraction Data and Subsequent Structural Analysis

description: This is a dataset containing raw "uncompressed" diffraction data from  test sample.

Data are collected on a lysozyme sample at 7.5 keV for a S-SAD experiment at the AMX beamline using an EIGEr 9M detector.

The compression used, to generate the cbf files can be derived from the filenames: 

BINx: pixel binning by a factor x

SUMx: frame summing by a factor x 

J2Kx: JPEG2000 compression used with a factor of x

HCOMPx: Hcompress used with a scale factor x 

For example: lyso_BIN2_SUM2_HCOMP4 was compressed using 2x pixel binning + 2x frame summing + Hcompress with scale of 4. 

More information will be included after publication, in the meantime, please contact author if details about processing are required.

All zstd tar directories contain the cbf files, ready to be processed. 

All data were collected at the AMX beamline at the NSLS-II using a DECTRIS EIGER X 9 M detector. 

 

See more details from the related work (xds.inpo files included)
DOI: 10.26030/k1ez-4x16
title: Influence of gonadectomy on muscle health in micro- and partial-gravity environments in rats (Estrous Cycle Monitoring)

description: Gonadal hormones, such as testosterone and estradiol, modulate muscle size and strength in males and females. However, the influence of sex hormones on muscle strength in micro- and partial-gravity environments (e.g., the Moon or Mars) is not fully understood. The purpose of this study was to determine the influence of gonadectomy (castration/ovariectomy) on progression of muscle atrophy in both micro- and partial-gravity environments in male and female rats. Male and female Fischer rats (n equals 120) underwent castration/ovariectomy (CAST/OVX) or sham surgery (SHAM) at 11 weeks of age. After 2 weeks of recovery, rats were exposed to hindlimb unloading (0g), partial weight bearing at 40% of normal loading (0.4g, Martian gravity), or normal loading (1.0g) for 28 days. In males, CAST did not exacerbate body weight loss or other metrics of musculoskeletal health. In females, OVX animals tended to have greater body weight loss and greater gastrocnemius loss. Within 7 days of exposure to either microgravity or partial gravity, females had detectable changes to estrous cycle, with greater time spent in low-estradiol phases diestrus and metestrus (∼47% in 1g vs. 58% in 0g and 72% in 0.4g animals, P equals 0.005). We conclude that in males testosterone deficiency at the initiation of unloading has little effect on the trajectory of muscle loss. In females, initial low estradiol status may result in greater musculoskeletal losses. This study derives results from Estrous Cycle Monitoring (Cytology).
DOI: 10.5281/zenodo.12628226
title: Supplemental Data Files for Advances in Organ-Specific Dosimetry Models for Radionuclides and Radiopharmaceuticals at Their Macro And Micro Scales

description: Data sets for Aims 1 and 2 of my dissertation. Both aims contain three excel spreadsheets for a total of 6 files with the computed specific absorbed fractions and S-values.
DOI: 10.5281/zenodo.12628227
title: Supplemental Data Files for Advances in Organ-Specific Dosimetry Models for Radionuclides and Radiopharmaceuticals at Their Macro And Micro Scales

description: Data sets for Aims 1 and 2 of my dissertation. Both aims contain three excel spreadsheets for a total of 6 files with the computed specific absorbed fractions and S-values.
DOI: 10.15468/dl.f5yx6n
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Colombia Rang, 1835, Aetanthus colombianus A.C.Sm.)"
 ]
}

 The dataset includes 86 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018489-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12701874
title: cyanomitra_cyanolaema_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.12701875
title: cyanomitra_cyanolaema_spades_01.fasta.gz

description: .
DOI: 10.15468/dl.2yzq6z
title: Occurrence Download

description: A dataset listing the 140 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-3.47739 43.46044,-3.45137 43.46044,-3.45137 43.46823,-3.47739 43.46823,-3.47739 43.46044))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 140 records were derived from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018460-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.23589747
title: <strong>Norepinephrine release in the cerebellum contributes to aversive learning</strong>

description: These excel sheets contain raw data required to produce the data in Stanley et al. 2023 "<strong>Norepinephrine release in the cerebellum contributes to aversive learning</strong>".
DOI: 10.6084/m9.figshare.23589747.v1
title: GrabNE Fear Conditioning and Foot-shock Photometry Data

description: These excel sheets contain raw data required to produce the data in Stanley et al. 2023 "<strong>Norepinephrine release in the cerebellum contributes to aversive learning</strong>".
DOI: 10.57745/i1dktn
title: maps_2020_2021_2022_48H.prj

description: Spatial files entitled "maps_2020_2021_2022_48H" are the simulations outputs for the 48-hour dispersion scenario. They return the weekly probability of long-distance dispersal to any destination in mainland Europe. Any destination is defined by an ID and its spatial definition (polygon) at resolution 0.5°. Weekly probabilities were calculated from Week 11 (mid March) to week 46 (mid of November). The probability output corresponds to the average probability across 2020, 2021 and 2022 simulations.
DOI: 10.57745/qc0mgs
title: start_points.prj

description: File that sets the start points from which the atmospheric simulations were initiated. All points are located in the southwest of Sardinia Island (source area)
DOI: 10.57745/33cflz
title: maps_2020_2021_2022_24H.shx

description: Spatial files entitled "maps_2020_2021_2022_24H" are the simulations outputs for the 24-hour dispersion scenario. They return the weekly probability of long-distance dispersal to any destination in mainland Europe. Any destination is defined by an ID and its spatial definition (polygon) at resolution 0.5°. Weekly probabilities were calculated from Week 11 (mid March) to week 46 (mid of November). The probability output corresponds to the average probability across 2020, 2021 and 2022 simulations.
DOI: 10.57745/ginsml
title: maps_2020_2021_2022_48H.shx

description: Spatial files entitled "maps_2020_2021_2022_48H" are the simulations outputs for the 48-hour dispersion scenario. They return the weekly probability of long-distance dispersal to any destination in mainland Europe. Any destination is defined by an ID and its spatial definition (polygon) at resolution 0.5°. Weekly probabilities were calculated from Week 11 (mid March) to week 46 (mid of November). The probability output corresponds to the average probability across 2020, 2021 and 2022 simulations.
DOI: 10.57745/igyr0b
title: maps_2020_2021_2022_48H.dbf

description: Spatial files entitled "maps_2020_2021_2022_48H" are the simulations outputs for the 48-hour dispersion scenario. They return the weekly probability of long-distance dispersal to any destination in mainland Europe. Any destination is defined by an ID and its spatial definition (polygon) at resolution 0.5°. Weekly probabilities were calculated from Week 11 (mid March) to week 46 (mid of November). The probability output corresponds to the average probability across 2020, 2021 and 2022 simulations.
DOI: 10.57745/nc22p0
title: maps_2020_2021_2022_24H.dbf

description: Spatial files entitled "maps_2020_2021_2022_24H" are the simulations outputs for the 24-hour dispersion scenario. They return the weekly probability of long-distance dispersal to any destination in mainland Europe. Any destination is defined by an ID and its spatial definition (polygon) at resolution 0.5°. Weekly probabilities were calculated from Week 11 (mid March) to week 46 (mid of November). The probability output corresponds to the average probability across 2020, 2021 and 2022 simulations.
DOI: 10.57745/oaonyr
title: maps_2020_2021_2022_24H.prj

description: Spatial files entitled "maps_2020_2021_2022_24H" are the simulations outputs for the 24-hour dispersion scenario. They return the weekly probability of long-distance dispersal to any destination in mainland Europe. Any destination is defined by an ID and its spatial definition (polygon) at resolution 0.5°. Weekly probabilities were calculated from Week 11 (mid March) to week 46 (mid of November). The probability output corresponds to the average probability across 2020, 2021 and 2022 simulations.
DOI: 10.57745/9be6wt
title: README.txt

description: :unav
DOI: 10.57745/djocoi
title: start_points.shx

description: File that sets the start points from which the atmospheric simulations were initiated. All points are located in the southwest of Sardinia Island (source area)
DOI: 10.57745/moweia
title: start_points.dbf

description: File that sets the start points from which the atmospheric simulations were initiated. All points are located in the southwest of Sardinia Island (source area)
DOI: 10.57745/oh7o1h
title: start_points.shp

description: File that sets the start points from which the atmospheric simulations were initiated. All points are located in the southwest of Sardinia Island (source area)
DOI: 10.57745/qhclcv
title: maps_2020_2021_2022_48H.shp

description: Spatial files entitled "maps_2020_2021_2022_48H" are the simulations outputs for the 48-hour dispersion scenario. They return the weekly probability of long-distance dispersal to any destination in mainland Europe. Any destination is defined by an ID and its spatial definition (polygon) at resolution 0.5°. Weekly probabilities were calculated from Week 11 (mid March) to week 46 (mid of November). The probability output corresponds to the average probability across 2020, 2021 and 2022 simulations.
DOI: 10.57745/qjx0ux
title: maps_2020_2021_2022_24H.shp

description: Spatial files entitled "maps_2020_2021_2022_24H" are the simulations outputs for the 24-hour dispersion scenario. They return the weekly probability of long-distance dispersal to any destination in mainland Europe. Any destination is defined by an ID and its spatial definition (polygon) at resolution 0.5°. Weekly probabilities were calculated from Week 11 (mid March) to week 46 (mid of November). The probability output corresponds to the average probability across 2020, 2021 and 2022 simulations.
DOI: 10.15468/dl.d9q4pe
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zanthoxylum gentryi Reynel"
 ]
}

 The dataset includes 57 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018492-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wh8vc3
title: Occurrence Download

description: A dataset containing 202548 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Occurrence evidence, Specimen)",
 "Country is United States of America",
 "OccurrenceStatus is Present",
 "TaxonKey is Apis mellifera Linnaeus, 1758"
 ]
}

 The dataset includes 202548 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018455-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26030/8k7j-dn29
title: Combined space stressors induce independent behavioral deficits predicted by early peripheral blood monocytes (flow cytometry)

description: Interplanetary space travel poses many hazards to the human body. To protect astronaut health and performance on critical missions, there is first a need to understand the effects of deep space hazards, including ionizing radiation, confinement, and altered gravity. Previous studies of rodents exposed to a single such stressor document significant deficits, but our study is the first to investigate possible cumulative and synergistic impacts of simultaneous ionizing radiation, confinement, and altered gravity on behavior and cognition. Our cohort was divided between 6‐month‐old female and male mice in group, social isolation, or hindlimb unloading housing, exposed to 0 or 50 cGy of 5 ion simplified simulated galactic cosmic radiation (GCRsim). We report interactions and independent effects of GCRsim exposure and housing conditions on behavioral and cognitive performance. Exposure to GCRsim drove changes in immune cell populations in peripheral blood collected early after irradiation, while housing conditions drove changes in blood collected at a later point. Female mice were largely resilient to deficits observed in male mice. Finally, we used principal component analysis to represent total deficits as principal component scores, which were predicted by general linear models using GCR exposure, housing condition, and early blood biomarkers. This dataset derives results from the flow cytometry assay using blood samples from same source animals used for behavioral studies in OSD-618.