cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/kjym3w4g36.1
title: Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex

description: Nuclear pore proteins (Nups) physically interact with hundreds of chromosomal sites, impacting transcription. In yeast, transcription factors mediate interactions between Nups and enhancers and promoters. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC). This mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 and Nups co-occupy enhancers and Crm1 inhibition blocks interaction of the nuclear pore protein Nup2 with the genome. In vivo, Crm1 interacts stably with the NPC. In vitro, Crm1 binds both Gcn4 and Nup2 directly. Importantly, the interaction between Crm1 and Gcn4 requires neither Ran-GTP nor the nuclear export sequence binding site. Finally, Crm1 and Ran-GTP stimulate DNA binding by Gcn4, suggesting that allosteric coupling between Crm1-Ran-GTP binding and DNA binding facilitates docking of transcription factor-bound enhancers at the NPC.

This dataset contains processed aligned reads (.bam files) from four main questions we addressed in our paper:
1) Where do Crm1, Nups, and RNA Pol II bind in the genome? [ChEC-seq2]
2) What is the relationship between Crm1 and Nup2? Are they interdependent or does the binding of one factor depend on the other? [ChEC-seq2]
3) Does loss of Crm1 or Nups (Nup1/Nup2) affect nascent transcription? If so, how? [SLAM-seq]
4) How does Leptomycin B (LMB, inhibitor of Crm1) affect binding of Crm1 and transcription factor Gcn4 to the genome? [ChEC-seq2]

ChEC-seq2 data was obtained and processed as described in VanBelzen et al. 2024, with reads trimmed with Trimmomatic and mapped to the Saccharomyces cerevisiae genome (sacCer3) using Bowtie2. For peak calling analyses, we processed the bam files by trimming them to the first base pair and called peaks using DoubleChEC (VanBelzen et al. 2024). SLAM-seq was performed as described in Herzog et al. 2017 and Alalam et al., 2022, using 0.2 mM 4-thiouracil (4sU) for 6 min at 30°C prior to harvesting, and processed using SLAM-DUNK (Herzog et al. 2017), which generated the read counts (.tsv files). Differential expression was analyzed using DESeq2 (Love et al., 2014). All sample information (BioProject, Biosample, SRA, GEO) is included in the Sample information spreadsheet.
DOI: 10.17632/pnrbbbfc6f.1
title: Dados sobre publicações decoloniais indexadas nas bases Scopus, Web of Science e OpenAlex

description: Este conjunto de dados foi gerado em 30/01/2025 a partir de buscas realizadas nas bases Scopus, Web of Science, Lens e OpenAlex. A pesquisa considerou publicações do ano de 2024 que contêm o termo "decolonial" nos títulos. Os dados foram processados para a elaboração do artigo correspondente. Os arquivos disponíveis neste repositório são: 1) vilker.pessin(decolonialScopus).csv – Dados extraídos da base Scopus; 2) vilker.pessin(decolonialWoS).xlsx – Dados extraídos da base Web of Science; 3) vilker.pessin(decolonialOAlex).csv – Dados extraídos da base OpenAlex; Esses dados podem ser utilizados para análises adicionais sobre a produção acadêmica relacionada à perspectiva decolonial em 2024.
Este conjunto de dados foi utilizado para contextualizar a produção científica sobre o tema decolonial, analisando como esse campo do conhecimento está indexado em diferentes bases de dados acadêmicas. A pesquisa teve como objetivo comparar a indexação das publicações que contêm o termo "decolonial" nos títulos, identificando padrões e discrepâncias entre as bases Scopus, Web of Science e OpenAlex. Além disso, a análise buscou compreender o predomínio do idioma inglês na disseminação internacional da produção acadêmica sobre o tema, verificando a proporção de publicações em diferentes idiomas e como elas são representadas nas bases indexadoras. Os dados coletados e processados permitiram uma reflexão sobre a visibilidade e acessibilidade do conhecimento "decolonial" no cenário global.
DOI: 10.17632/kmphv3fzdh.1
title: LINF_050014200

description: surface antigen-like protein; Leishmania infantum
DOI: 10.17632/kmphv3fzdh.2
title: LINF_050014200

description: Surface antigen-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.26208/d06c-rx45
title: Influence functions for the Delaware Oil and Gas Basin Tower Network

description: This data consists of influence functions created for the Delaware tower network for the purpose of calculating methane enhancements in the region. Two different footprint models were used. The Lagrangian Particle Dispersion model (LPDM, Uliasz 1993) was run from March 2020-May 2023. The model uses in-house WRF simulations for the meteorological transport as described in Barkley et al., (2023). Nine hundred (900) particles were released during each hourly period and are traced back 72 hours backwards in time. A static binning height of 110 m AGL was used to calculate surface influence. After May 2023, the LPDM simulations were phased out and replaced with influence functions created using HYSPLIT under the STILT configuration (Lin et al., 2003). The STILT influence functions use HRRR for the meteorological transport (Dowell et al., 2022). Nine hundred (900) particles were released during each hourly period and are traced back 72 hours backwards in time. A binning height of half the boundary layer height was used to calculate surface influence. Footprints are currently available from Sept 2020-December 2024 and will be updated periodically as more are generated in time. No STILT influence functions were created for tower site Maljimar, which was decommissioned in March 2022.

Lat/Lon grid information for the LPDM influence functions is contained in lpdm-lat-lon-grid.nc. STILT grid information is contained within the influence functions themselves. Tower coordinates and heights can be found in tower-info.csv
DOI: 10.17632/5gc7hwydwg.1
title: Disease Dataset of Wheat: Original, Augmented, and Balanced for Deep Learning

description: The dataset originated from a wheat crop field in Bangladesh where five separate wheat leaf image categories exist. The dataset contains 1,603 original images with 1920 × 1080 pixels resolution and is separated into five different disease categories consisting of Black Point (303 images), Fusarium Foot Rot (250 images), Healthy Leaf (250 images), Leaf Blight (400 images), and Wheat Blast (400 images).

The application of data augmentation techniques produced 1,000 additional images per class to balance the dataset before creating the augmented dataset. After data augmentation, the total number of images across the 5,000 dataset represents an equal distribution of disease categories.

The machine learning model needs training, so the augmented dataset split into training (70%) and testing (20%) and validation (10%) portions to help evaluation. The structured splitting technique enables effective generalization of models while ensuring the best results in multiple experimental testing conditions.

The dataset follows a system of three main directories:
1) Original Dataset: Contains raw images captured directly from the field.
2) Augmented Dataset: A separate section in the database features synthetic images that aid distribution balance.
3) Split Dataset: The Split Dataset holds pre-processed divisions of training data, testing data, and validation data that stem from the augmented dataset.

The wheat disease dataset provides researchers with essential resources to conduct investigations about wheat disease categorization as well as agricultural AI development and deep learning-based plant disease identification studies.
DOI: 10.17632/ftgdmhh2mj.1
title: LINF_050015100

description: 3-mercaptopyruvate sulfurtransferase; Leishmania infantum
DOI: 10.15468/dl.a5p39f
title: Occurrence Download

description: A dataset containing 30835371 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 30835371 records from 2853 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006290-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.td8z4e
title: Occurrence Download

description: A dataset containing 867 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus ilex L.)",
 "Country is one of (Spain)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 867 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003727-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10844444
title: Top Spotify Songs in 73 Countries (Daily Updated)
DOI: 10.6084/m9.figshare.28477316
title: Project: Illiterate adolescents

description: Youth-Friendly Health Services (YFHS) centers in Rwanda were established to bridge the gap in information and services related to reproductive health. However, limited research has explored the challenges faced by illiterate adolescents in accessing sexual and reproductive health services. This study examined the accessibility and utilization of adolescent sexual and reproductive health (ASRH) services within YFHS among illiterate adolescents in Rwanda. A total of 150 illiterate adolescents were selected through convenience sampling. Additionally, a checklist was utilized to assess 16 YFHS centers.
DOI: 10.25919/tmcb-1r47
title: Parkes observations for project P1338 semester 2024OCTS_47

description: Fast radio bursts (FRBs) are millisecond-duration radio bursts of extragalactic origin. Since the discovery of the first FRB in the archival Parkes/Murriyang multibeam data, a broad dichotomy in population has emerged. Some FRBs have been seen to be repeating, while others are not, despite a significant amount of follow-up using different radio telescopes. The repeating FRB 20240114A was recently discovered by CHIME/FRB, which has been seen to have an exceptionally high burst activity. Such extreme burst activity has not been seen in any other source. The repeating FRBs, such as FRB 20240114A, provide an unparalleled window into their circumburst environment due to their repeating nature, which can be used to constrain possible progenitor models and test underlying emission mechanisms. The previous Parkes/Murriyang source follow-up has also revealed intriguing spectro-polarimetric properties, such as frequency-dependent evolution of burst central frequency or chromaticity, a possible activity window, significantly large circular polarisation (CP), and frequency-dependent CP. These properties hold the key towards understanding the circumburst environment of the FRBs, and test possible progenitor models. A large bandwidth instrument with reliable polarimetry has been critical in uncovering these properties. The ultra-wideband low (UWL) receiver on Parkes/Murriyang is ideally suited to explore the source's wideband spectro-temporal and polarimetric behaviour. We propose a campaign to regularly follow up FRB 20240114A to ascertain its long-term evolution of spectro-temporal properties.
DOI: 10.25919/x9zs-rw02
title: Parkes observations for project P595 semester 2024OCTS_13

description: We propose to continue the PULSE@Parkes project in which high school students from Australia and around the World use the Parkes radio telescope in a remote observing model to observe and analyse pulsar data. The data from some PULSE@Parkes observations are used to support the space missions, other observations supplement the P456 Pulsar Timing Array project and the remainder were chosen in order to make a detailed analysis of pulsar timing irregularities and intermittency.
DOI: 10.15468/dl.azvf4e
title: Occurrence Download

description: A dataset containing 77 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is one of (United States of America, Canada)",
 "Geometry POLYGON((-127.27722 34.55057,-112.98295 34.55057,-112.98295 50.56252,-127.27722 50.56252,-127.27722 34.55057))",
 "HasGeospatialIssue is false",
 "StateProvince is one of (Oregon, Washington (State), CALIFORNIA USA.)",
 "TaxonKey is one of (Strix occidentalis (Xántus de Vésey, 1860), Strix occidentalis occidentalis, Strix occidentalis caurina (Merriam, 1898))"
 ]
}

 The dataset includes 77 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003728-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22003/xfel.eu-data-900456-00
title: SPB/SFX MHz Microscopy Commissioning
DOI: 10.22003/xfel.eu-data-900463-00
title: SPB/SFX commissioning
DOI: 10.22003/xfel.eu-data-008236-00
title: Bring-Up Days HED
DOI: 10.22003/xfel.eu-data-006827-00
title: SFX Consortium Block Allocation Group (BAG) at the European XFEL
DOI: 10.22003/xfel.eu-data-006937-00
title: Understanding Fast Phenomena of Fluid Transport in Porous Media using MHz X-ray Microscopy (combined with 6961)
DOI: 10.22003/xfel.eu-data-007944-00
title: Water's glass transition at the nanosecond timescale
DOI: 10.22003/xfel.eu-data-007955-00
title: Structural dynamics and mechanism of covalent bond formation.
DOI: 10.15468/dl.cc7u9s
title: Occurrence Download

description: A dataset containing 7721 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "TaxonKey is Bombus nevadensis Cresson, 1874",
 "Year 2008-2025"
 ]
}

 The dataset includes 7721 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003731-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zzr6cj
title: Occurrence Download

description: A dataset containing 796 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "PublishingOrg is 939ed180-aa7b-11db-8edf-b8a03c50a862",
 "TaxonKey is Agelaius phoeniceus (Linnaeus, 1766)"
 ]
}

 The dataset includes 796 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003730-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y6cevg
title: Occurrence Download

description: A dataset containing 7721 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "TaxonKey is Bombus nevadensis Cresson, 1874",
 "Year 2008-2025"
 ]
}

 The dataset includes 7721 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003729-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aux8a8
title: Occurrence Download

description: A dataset containing 19780 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Eulachon migration bottom trawl surveys"
 ]
}

 The dataset includes 19780 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003733-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uhxew3
title: Occurrence Download

description: A dataset containing 61910 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.87744 5.8999,-75.8325 5.82498,-75.68674 5.74885,-75.63451 5.7851,-75.59078 5.86969,-75.60414 5.95548,-75.6588 6.01829,-75.77784 6.03762,-75.82643 5.99051,-75.87744 5.8999))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 61910 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003732-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14681092
title: Heart interbeat interval (IBI) time series segmented by Berg Balance Scale (BBS) activities

description: The corresponding article is Messaoud, I. B., & Thamsuwan, O. (2025). Heart Rate Variability-Based Stress Detection and Fall Risk Monitoring During Daily Activities: A Machine Learning Approach. Computers, 14(2), 45. https://doi.org/10.3390/computers14020045.
DOI: 10.5281/zenodo.14681093
title: Heart interbeat interval (IBI) time series segmented by Berg Balance Scale (BBS) activities

description: The corresponding article is Messaoud, I. B., & Thamsuwan, O. (2025). Heart Rate Variability-Based Stress Detection and Fall Risk Monitoring During Daily Activities: A Machine Learning Approach. Computers, 14(2), 45. https://doi.org/10.3390/computers14020045.
DOI: 10.15468/dl.acd87u
title: Occurrence Download

description: A dataset containing 1808 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "PublishingOrg is b554c320-0560-11d8-b851-b8a03c50a862",
 "TaxonKey is Agelaius phoeniceus (Linnaeus, 1766)"
 ]
}

 The dataset includes 1808 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003734-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60520/ieda/113692
title: Geochemical and isotope analysis of rhyolites from Peak Ranges, Central Queensland, Australia

description: The dataset comprises: 1. Supplementary Figures, 2. Petrographic, geochemical and Sr -Nd isotope data tables, 3. Mineral chemistry data tables, and, 4 MELTS modelling methods and results, for volcanic rocks of the Peak Ranges, Central Queensland. The analyses were conducted in dedicated geochemical laboratories at The University of Adelaide, Australia and at Bureau Veritas geochemical laboratories (Vancouver and Adelaide), using well characterised standards and methodologies.
DOI: 10.5281/zenodo.14919285
title: Ibex BCR Deep Encoders

description: Ibex

This is a series of 72 Keras3-based amino acid encoders for Heavy and Light chains of the B cell Receptor (BCR). These are the individual trained models for larger Ibex package that will be available after review from BioConductor. The package itself has the functionality to employ these models and interact with single-cell data, but due to the size of the trained models, the keras objects are stored here.Sequence inputs 



Human Heavy: 10000000

Human Light: 5000000

Human Heavy-Expanded: 5000000

Human Light-Expanded: 2500000

Mouse Heavy: 5000000

Mouse Heavy-Expanded: 5000000


Model details



Architecture: 512-256-128-256-512

Parameters: 



Batch Size = 128

Latent Dimensions = 128

Epochs = 128

Loss = Mean Squared Error (CNN) & KL Divergence (VAE)

Activation = ReLU

Learning rate = 1e-6

Optimizers: Adam



Early stopping was set to patients of 10 for minimal validation loss and restoration of best weights

CNN autoencoders have batch normalization layers between the dense layers. 


More information available at the GitHub Repo
DOI: 10.5281/zenodo.14919286
title: Ibex BCR Deep Encoders

description: Ibex

This is a series of 72 Keras3-based amino acid encoders for Heavy and Light chains of the B cell Receptor (BCR). These are the individual trained models for larger Ibex package that will be available after review from BioConductor. The package itself has the functionality to employ these models and interact with single-cell data, but due to the size of the trained models, the keras objects are stored here.Sequence inputs 



Human Heavy: 10000000

Human Light: 5000000

Human Heavy-Expanded: 5000000

Human Light-Expanded: 2500000

Mouse Heavy: 5000000

Mouse Heavy-Expanded: 5000000


Model details



Architecture: 512-256-128-256-512

Parameters: 



Batch Size = 128

Latent Dimensions = 128

Epochs = 128

Loss = Mean Squared Error (CNN) & KL Divergence (VAE)

Activation = ReLU

Learning rate = 1e-6

Optimizers: Adam



Early stopping was set to patients of 10 for minimal validation loss and restoration of best weights

CNN autoencoders have batch normalization layers between the dense layers. 


More information available at the GitHub Repo
DOI: 10.15468/dl.q5vuva
title: Occurrence Download

description: A dataset containing 486 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pangshura tecta (Gray, 1831)"
 ]
}

 The dataset includes 486 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003735-250221090833381/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.28477355
title: News articles for RASIM Ukrain study

description: Raw news articles for the RASIM study.
DOI: 10.6084/m9.figshare.28477355.v1
title: News articles for RASIM Ukrain study

description: Raw news articles for the RASIM study.
DOI: 10.15468/dl.edc9j9
title: Occurrence Download

description: A dataset containing 791 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is one of (United States of America, Canada)",
 "Geometry POLYGON((-128.46002 36.12649,-116.30655 36.12649,-116.30655 50.90713,-128.46002 50.90713,-128.46002 36.12649))",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Strix occidentalis (Xántus de Vésey, 1860), Strix occidentalis occidentalis, Strix occidentalis lucida (Nelson, 1903))"
 ]
}

 The dataset includes 791 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003736-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11211933
title: Data from: Handheld lidar sensors can accurately measure herbaceous biomass

description: Data and code used in Handheld lidar sensors can accurately measure herbaceous biomass. Lidar data is provided for MLS and iPad sensors in las_files.zip. Las files are named by site, plot and subplot (e.g., FP-1-5). Data for response and predictors are avilable in data.zip. R code is provided for predictor creation, modeling, and figure creation in Rcode.zip.
DOI: 10.5281/zenodo.11211934
title: Data from: Handheld lidar sensors can accurately measure herbaceous biomass

description: Data and code used in Handheld lidar sensors can accurately measure herbaceous biomass. Lidar data is provided for MLS and iPad sensors in las_files.zip. Las files are named by site, plot and subplot (e.g., FP-1-5). Data for response and predictors are avilable in data.zip. R code is provided for predictor creation, modeling, and figure creation in Rcode.zip.
DOI: 10.5281/zenodo.14920245
title: Data from: Handheld lidar sensors can accurately measure herbaceous biomass

description: Data and code used in Handheld lidar sensors can accurately measure herbaceous biomass. Lidar data is provided for MLS and iPad sensors in las_files.zip. Las files are named by site, plot and subplot (e.g., FP-1-5). Data for response and predictors are avilable in data.zip. R code is provided for predictor creation, modeling, and figure creation in Rcode.zip.
DOI: 10.5281/zenodo.14880098
title: rMD-autoencoder for reinforced molecular dynamics simulations

description: Reinforced molecular dynamics: Physics-infused generative machine learning model simulates protein motion