cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14802060
title: MetaTIS: A tool to predict eukaryotic translation initiation sites

description: When scanning mRNA sequences, ribosomes start translation typically at an AUG codon flanked by a so-called Kozak region. However, the first AUG of an mRNA is not always effective in initiating translation. In rare cases, also near cognate codon sequences may be recognized as start sites. The ribosome profiling technique, where translation elongation is stalled by chemical agents, is able to identify actively used translation start sites. In the past, various bioinformatics classifiers have been trained on such data to predict putative translation initiation sites from mRNA sequence features. Here, we formulated a stacking approach that can differentiate between false and true translation initiation sites. This was trained on experimental data for translation initiation in HEK293 cells produced by the so-called TISCA protocol. Our classifier gave a good overall performance on its own test set (accuracy 0.93) as well as multiple external validation sets. Moreover, it was able to predict almost quantitatively whether overlapping open-reading frames suppress translation from the main ORF for 11 genes in HeLa cells as validated by experimental luciferase assays. The MetaTIS tool is publicly available as a webserver

 

The FlanksERF, KmersERF, and MetaTIS models with their training data can be found below. For information on how these models are utilized please refer to github. The datasets are composed of 229 columns. Whereby, the first 168 represent the upstream (U) and downstream (D) kmers of sizes 1 till 3. Then comes the start codon used and the normalized Noderer et al. efficiency values based on the flanking region. Next, the 20 upsteam (U) and 20 downstream (D) nucleotides with respect to the initiation site. The final 19 features represent the relative binding scores of the 9 RNA binding proteins (RBPs) considered. Note some RBPs have multiple binding motifs.
DOI: 10.5281/zenodo.14809153
title: MetaTIS: A tool to predict eukaryotic translation initiation sites

description: As the ribosome makes its foray unto a sequence of mRNA, ribosomes typically commence translation at a methionine-encoding AUG codon flanked by a so-called Kozak region, a short nucleic acid motif serving as an initiation site in many eukaryotes. Though, the characteristic AUG start codon of an mRNA is not always effective in initiating translation. In more seldom cases, near-cognate codon sequences may also be recognized as start sites. Ribosome profiling techniques, characterized by the stymieing of mRNA-ribosome complex translation function via chemical treatment, are able to elucidate active translation start sites. Historically, several bioinformatics classifiers have been trained on translation start site data, gleaned from ribosomal profiling, to predict putative translation initiation sites from mRNA sequence features. A stacking approach was formulated for the MetaTIS tool that can differentiate spurious and true translation initiation sites. The tool was trained on experimental data for translation initiation in HEK293 cells produced by the TISCA protocol, a method allowing for accurate translation initiation site identification. Our classifier delivers a notable ROC-AUC of 0.93 while performing on its own test set, as well as multiple external validation sets. Moreover, it was able to almost quantitively predict whether overlapping open-reading frames suppress translation from the main ORF for 11 genes in HeLa cells, as validated by experimental luciferase assays. The MetaTIS tool is publicly available as a webserver

 

The FlanksERF, KmersERF, and MetaTIS models with their training data can be found below. For information on how these models are utilized please refer to github. The datasets are composed of 229 columns. Whereby, the first 168 represent the upstream (U) and downstream (D) kmers of sizes 1 till 3. Then comes the start codon used and the normalized Noderer et al. efficiency values based on the flanking region. Next, 40 columns representing the 20 upsteam (U) and 20 downstream (D) nucleotides with respect to the initiation site. The final 19 features represent the relative binding scores of the 9 RNA binding proteins (RBPs) considered. Note that some RBPs have multiple binding motifs.

 

The FlanksERF and KmersERF are each composed of 40 random forest classifiers which are stored as a dictionary. scikit-learn version 1.5.1 was used to create these models. The DownstreamNegatives and Positives datasets were used to train the KmersERF model, while the UpstreamNegatives and Positives datasets were used to train the FlanksERF model.
DOI: 10.15468/dl.xywbw4
title: Occurrence Download

description: A dataset containing 9143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "MediaType is Image",
 "ScientificName is Solanum dulcamara L."
 ]
}

 The dataset includes 9143 records from 184 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003577-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdmbak
title: Occurrence Download

description: A dataset containing 143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "StateProvince is one of (RIO GRaNdE dO SUL, Rio Grande so Sul)",
 "TaxonKey is Sporophila palustris (Barrows, 1883)"
 ]
}

 The dataset includes 143 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003578-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.keushj
title: Occurrence Download

description: A dataset containing 1311 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "MediaType is Image",
 "ScientificName is Thymus praecox Opiz"
 ]
}

 The dataset includes 1311 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003579-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tgwf7u
title: Occurrence Download

description: A dataset containing 21754 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is The Finnish Nature League's Spring monitoring",
 "TaxonKey is Squamata"
 ]
}

 The dataset includes 21754 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003580-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tg2cfg
title: Occurrence Download

description: A dataset containing 40515 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Lolium rigidum Gaudin"
 ]
}

 The dataset includes 40515 records from 472 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003581-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26023/r6a2-g92q-cf0s
title: NRC Convair 580 Bulk Parameters. Version 0.4

description: Bulk microphysical parameters from the NRC Convair 580 flights conducted during the ICICLE (In-Cloud ICing and Large-drop Experiment) project out of Rockford Illinois. The data are in NetCDF format.
DOI: 10.18739/a20c4sm9d
title: Multi-Commodity, Multi-echelon Stacked Machine Learning Models for Replicating Global Supply Chain Structures with Limited, Publicly Available Information, 2017-2024

description: The ability to replicate global SC (supply chain) structures is important for maintaining and improving the operations of global supply chains. This structure, while known to specific manufacturers and key suppliers, is not generally published and may not be totally transparent to all stakeholders. This paper presents a methodology for replicating the structure of global supply chains with limited, publicly available data.
 The proposed SC replication method decomposes the multi-echelon SC into a set of duo-echelon models, each focused on a single commodity, which are re-constituted for a complete representation of the SC for improved computational efficiency. Flows of raw materials, middle products (product components), and end-products for each duo-echelon model are obtained from a developed stacked machine learning method using only publicly available information. The duo-echelon models are integrated into a final multi-echelon, multi-commodity SC representation.
 The method was applied on a case study of lithium-ion battery production. The findings underscore the model’s capability to capture complex trade relationships and global SC dynamics. Further, the method outperformed numerous other approaches.
 This paper proposes a novel approach to estimating global SC structures, including complexities from its multi-commodity and multi-echelon nature, using publicly available data.
DOI: 10.15468/dl.684cz4
title: Occurrence Download

description: A dataset containing 7261 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Cattleya intermedia, Cattleya intermedia angustifolia, Bombus atratus, Bombus atratus, Bombus brasiliensis, Bombus brasiliensis palliventris, Xylocopa augusti, Xylocopa frontalis, Xylocopa frontalis fabricii)"
 ]
}

 The dataset includes 7261 records from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041834-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wf3qct
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ciliosemina pedunculata",
 "Country is Congo, Democratic Republic of the",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041835-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/ndrfxo
title: UTEP Herpetology Osteology (Arctos)

description: The University of Texas at El Paso Biodiversity Collections (UTEP) - Herpetology Osteology Collection was established to provide a comparative skeletal collection for students and faculty. Some specimens have related elements in the UTEP Herpetology Collection.
DOI: 10.26023/7ewa-ak58-rd09
title: T-PARC: Flight Tracks. Version 1.0

description: KML is a file format used to display geographic data in an Earth browser such as Google Earth. This dataset contains KML files used to display the flight track in real-time during the T-PARC project.
DOI: 10.15468/dl.v4fpqd
title: Occurrence Download

description: A dataset containing 946 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chilomycterus spinosus"
 ]
}

 The dataset includes 946 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041837-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17254125
title: Missing Beats: Dark Matter Silences Short-Period Cepheids in the Galactic Center

description: Reproduction package for the paper "Missing Beats: Dark Matter Silences Short-Period Cepheids in the Galactic Center"
DOI: 10.5281/zenodo.17254126
title: Missing Beats: Dark Matter Silences Short-Period Cepheids in the Galactic Center

description: Reproduction package for the paper "Missing Beats: Dark Matter Silences Short-Period Cepheids in the Galactic Center"
DOI: 10.5281/zenodo.17253891
title: 3D terrain models and configuration files for planetary lava flow simulations

description: This dataset contains 3D terrain models (.obj) and simulation configuration files (.json) used for lava flow simulations with SPlisHSPlasH.



.obj files represent the early (pre-erosion) and current (post-erosion) stages of the J-shaped gully near Hadley Rille.

.json files define the simulation setup, including fluid parameters ("Materials"), terrain geometry ("RigidBodies"), and particle emitter settings ("Emitters"). 


A README file provides instructions for file placement within the SPlisHSPlasH data folder and guidelines for running the simulations.
DOI: 10.5281/zenodo.17253892
title: 3D terrain models and configuration files for planetary lava flow simulations

description: This dataset contains 3D terrain models (.obj) and simulation configuration files (.json) used for lava flow simulations with SPlisHSPlasH.



.obj files represent the early (pre-erosion) and current (post-erosion) stages of the J-shaped gully near Hadley Rille.

.json files define the simulation setup, including fluid parameters ("Materials"), terrain geometry ("RigidBodies"), and particle emitter settings ("Emitters"). 


A README file provides instructions for file placement within the SPlisHSPlasH data folder and guidelines for running the simulations.
DOI: 10.26023/tjkp-rxvh-6107
title: STERAO-A sounding data. Version 1.0

description: Radiosonde data collected during the first Stratospheric-Tropospheric Experiment: Radiation, Aerosols, and Ozone (STERAO). Files beginning in "i" are class interpolated data; filenames beginning in "m" are class raw thermodynamic data; files beginning in "x" are class 10 second data. Data are in ASCII text format, in a single gzipped file.
DOI: 10.15468/dl.sg6c2a
title: Occurrence Download

description: A dataset containing 181 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Massularia acuminata",
 "Country is Congo, Democratic Republic of the",
 "HasCoordinate is true"
 ]
}

 The dataset includes 181 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041838-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/pkbyxy
title: UTEP Herpetology (Arctos)

description: University of Texas at El Paso Biodiversity Collections (UTEP) - Herpetology
DOI: 10.15468/dl.zft5ft
title: Occurrence Download

description: A dataset containing 9902 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is DSMZ Bacteria"
 ]
}

 The dataset includes 9902 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041839-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26023/w4pd-fvek-mj10
title: NRL P-3 Navigation and State Parameter Data. Version 1.0

description: The RAINEX NRL P-3 Navigation and State Parameter Data is one of several datasets archived by the National Center for Atmospheric Research / Earth Observing Laboratory (NCAR/EOL) in support of the Hurricane Rainband and Intensity Change Experiment (RAINEX) 2005. These data were collected aboard the NRL P-3 aircraft during approximately 8 hour flights on selected days.
DOI: 10.15468/dl.5r4tcz
title: Occurrence Download

description: A dataset containing 94517 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vespidae",
 "Year is 2023",
 "Continent is Europe",
 "HasCoordinate is true"
 ]
}

 The dataset includes 94517 records from 182 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041814-250920141307145/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.29222486
title: Domestic dog introgression in Australian dingoes: environmental drivers and evolutionary consequences

description: Hybridization between wild and domestic canids is a widespread phenomenon with important implications for genetic diversity, local adaptation, and conservation management. In Australia, hybridization between dingoes and domestic dogs presents a dual conservation challenge—threatening the genetic integrity of dingoes while allowing potential adaptive introgression. To investigate the genetic and environmental drivers of this process, we analyzed 170,465 SNPs genotyped with a high-density SNP array in 336 dingoes and 396 European and Australian domestic dogs. Principal component analysis and ADMIXTURE revealed clear genetic differentiation between dingoes and domestic dogs, as well as regional structuring among dingo populations. Using local ancestry inference and genome–environment association (GEA) analyses, we found that dingoes from remote areas such as the Big Desert and Western Australia exhibited low levels of dog introgression, while higher levels were observed in eastern and southern populations. These patterns correlated with proximity to human settlements and environmental modifications. Key variables—including maximum temperature of the warmest month, mean temperature of the driest quarter, and the Human Footprint Index—were significant predictors of introgression. We identified genomic regions with overrepresented dog ancestry, including a large introgressed haplotype block on chromosome 27, along with small blocks on chromosomes 13, 14, and 24. Several genes within these regions showed signatures of purifying or positive selection, suggesting adaptive introgression. Together, these results highlight the complex interplay between hybridization, human influence, and local adaptation in dingoes, offering valuable insights for conserving the evolutionary potential of this apex predator in increasingly modified landscapes.
DOI: 10.6084/m9.figshare.29222486.v1
title: Domestic dog introgression in Australian dingoes: environmental drivers and evolutionary consequences

description: Hybridization between wild and domestic canids is a widespread phenomenon with important implications for genetic diversity, local adaptation, and conservation management. In Australia, hybridization between dingoes and domestic dogs presents a dual conservation challenge—threatening the genetic integrity of dingoes while allowing potential adaptive introgression. To investigate the genetic and environmental drivers of this process, we analyzed 170,465 SNPs genotyped with a high-density SNP array in 336 dingoes and 396 European and Australian domestic dogs. Principal component analysis and ADMIXTURE revealed clear genetic differentiation between dingoes and domestic dogs, as well as regional structuring among dingo populations. Using local ancestry inference and genome–environment association (GEA) analyses, we found that dingoes from remote areas such as the Big Desert and Western Australia exhibited low levels of dog introgression, while higher levels were observed in eastern and southern populations. These patterns correlated with proximity to human settlements and environmental modifications. Key variables—including maximum temperature of the warmest month, mean temperature of the driest quarter, and the Human Footprint Index—were significant predictors of introgression. We identified genomic regions with overrepresented dog ancestry, including a large introgressed haplotype block on chromosome 27, along with small blocks on chromosomes 13, 14, and 24. Several genes within these regions showed signatures of purifying or positive selection, suggesting adaptive introgression. Together, these results highlight the complex interplay between hybridization, human influence, and local adaptation in dingoes, offering valuable insights for conserving the evolutionary potential of this apex predator in increasingly modified landscapes.
DOI: 10.15468/dl.pjurbf
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rondeletia purdiei",
 "Country is Congo, Democratic Republic of the",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041840-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26023/gra6-867h-7j0w
title: MethaneAir Chatlogs. Version 1.0

description: This dataset contains the scrubbed chat logs from the MethaneAIR project from 8 November 2019 - 17 August 2021. These chat logs contain conversations between scientists and other project participants collected during the field phase of the MethaneAIR project. The project flight operations occurred in two separate phases. The first phase occurred in October and November 2019 and the second phase occurred in July and August 2021. The project was not continuous between the dates 10/28/2019 and 08/16/2021; however these dates represent the start of the first phase and the end of the second phase. These are the chat logs from the NSF/NCAR GV HIAPER aircraft. There are 2 kinds of files: daq-gv and gv. The daq-gv files are for data acquisition and were chat logs involving instrument testing.
DOI: 10.26023/ahyb-v4a1-f0k
title: OMS CO2 instrument Data. Version 1.0

description: The Observation Middle Stratosphere (OMS) CO2 instrument measured CO2 concentrations in situ aboard the NSF/NCAR GV during HIPPO-3. This dataset contains OMS CO2 data in NASA Ames format collected during HIPPO-3.
DOI: 10.15468/dl.9xnk8f
title: Occurrence Download

description: A dataset containing 1826 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "GadmGid is USA.32_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Crotalus",
 "VerbatimScientificName is Crotalus atrox",
 "Year 1990-2025"
 ]
}

 The dataset includes 1826 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041841-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xut7yg
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Uncaria gambir",
 "Country is Malaysia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 28 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041844-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kchxrd
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Uncaria gambir",
 "Country is Congo, Democratic Republic of the",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041843-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jwevj4
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Uncaria gambir",
 "Country is Singapore",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041845-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.