cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.x7pfpd
title: Occurrence Download

description: A dataset containing 29773 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Prionace glauca",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 29773 records from 139 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009945-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ummq6c
title: Occurrence Download

description: A dataset containing 895 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Patella ferruginea",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 895 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009948-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.he44m7
title: Occurrence Download

description: A dataset containing 134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hermbstaedtia glauca",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 134 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009949-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6arr2
title: Occurrence Download

description: A dataset containing 22830 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Equus quagga"
 ]
}

 The dataset includes 22830 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009947-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8fhgqp
title: Occurrence Download

description: A dataset containing 66 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-12.0",
 "Country is Mongolia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ursus arctos"
 ]
}

 The dataset includes 66 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009950-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18472176
title: Biophysical Modeling of Enzyme-Kinetic Calcium-Dependent Stochastic Synaptic Plasticity: Integrating STDP, Metabolic Constraints, Bayesian Inference, Sensitivity Analysis, and Validation with Allen Institute Data

description: This paper introduces a novel framework for modeling enzyme-kinetic calcium-dependent stochastic synaptic plasticity in neural networks, grounded in biophysical principles. We extend the Hodgkin-Huxley model to incorporate intracellular calcium dynamics linked to NMDA receptor activation, driving synaptic weight changes through a stochastic plasticity rule based on competitive enzyme kinetics between CaMKII and calcineurin, enhanced by trace-based spike-timing-dependent plasticity (STDP) as a modulator of calcium influx. The framework integrates nonlinear dynamics, stochastic differential equations with colored noise, dynamic metabolic energy constraints via evolving ATP levels affecting calcium extrusion, Bayesian inference, global sensitivity analysis (including STDP time constants), uncertainty quantification, weight bounding for stability, homeostatic plasticity with a sliding threshold, and empirical validation using the Allen Institute Synaptic Physiology Dataset. Mathematical derivations, reproducible Python simulations with network scaling and stationary state analysis, quantitative statistics (sample sizes, confidence intervals, Kullback-Leibler divergence), Bayesian evidence, falsifiability criteria, and visualizations (time-course curves for calcium, enzyme activation, weight stability, parameter heatmaps) demonstrate model fidelity to observed synaptic strengths, kinetics, and short-term plasticity. Parameter sweeps over 100 values, comparative plots overlaying predictions with empirical data, and a roadmap for neuromorphic hardware implementation highlight applications in neuromodulation for neurological disorders.
DOI: 10.5281/zenodo.18469798
title: Debris Flow - Praia Preta, São Sebastião, SP, Brazil - UAV photos for SfM-MVS

description: Data for SfM-MVS modelling of a debris flow area in São Sebastião, southeastern Brazil.  Raw photos captured with a DJI Phantom4Pro drone. Data provided by FAPESP grants 2019/26568-0 and 2023/1119-1.
DOI: 10.5281/zenodo.18469797
title: Debris Flow - Praia Preta, São Sebastião, SP, Brazil - UAV photos for SfM-MVS

description: Data for SfM-MVS modelling of a debris flow area in São Sebastião, southeastern Brazil.  Raw photos captured with a DJI Phantom4Pro drone. Data provided by FAPESP grants 2019/26568-0 and 2023/1119-1.
DOI: 10.57745/tdulxv
title: Data and scripts for the manuscript "Weak but consistent genomic signals of intragenerational selection during estuarine migration in the European eel (Anguilla anguilla)"

description: This directory contains most of the datasets and scripts used in the article: Genetic differentiation between two locations along an ocean/river gradient captures the signature of intragenerational selection in the European eel (Anguilla anguilla) by Stellia Sebihi, Aurélie Manicki, Sylvie Oddou-Muratorio, M. Gautier, Christophe Klopp.
DOI: 10.15468/dl.x6bvkc
title: Occurrence Download

description: A dataset listing the 133 species recorded in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((-94.12647 18.11988,-93.91397 18.11988,-93.91397 18.24655,-94.12647 18.24655,-94.12647 18.11988))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 133 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009927-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17856819
title: The Distribution of Power and Inclusiveness across Deep Time, Feinman et al. Science Advances - R Scripts and Dataset

description: This is the digital archive for the paper: 

Gary M. Feinman, David Stasavage, David M. Carballo, Sarah B. Barber, Adam Green, Jacob Holland-Lulewicz, Dan Lawrence, Jessica Munson, Linda M. Nicholas, Francesca Fulminante, Sarah Klassen, Keith W. Kintigh,John Douglass, The Distribution of Power and Inclusiveness across Deep Time. Science Advances

The dataset provides information on a series of proxies for governance (concentration of power and citizen inclusiveness), population size, hierarchical complexity, geographic region, modes of fiscal financing, bureaucratic structure, ritual practices, and socioeconomic inequality for 40 case observations across 31 polities. Proxy values were assigned by regional experts (the co-authors) based on archaeological and textual data.

This digital archive also provides reproducible analyses and figure construction related to the paper as a script written in R statistical computing language. Coding was undertaken by Dan Lawrence and Adam Green. 

Funding for this research was provided by the Coalition for Archaeological Synthesis, the Amerind Foundation, and the Field Museum of Natural History and the Amerind Foundation in Dragoon, Arizona.
DOI: 10.5281/zenodo.17856818
title: The Distribution of Power and Inclusiveness across Deep Time, Feinman et al. Science Advances - R Scripts and Dataset

description: This is the digital archive for the paper: 

Gary M. Feinman, David Stasavage, David M. Carballo, Sarah B. Barber, Adam Green, Jacob Holland-Lulewicz, Dan Lawrence, Jessica Munson, Linda M. Nicholas, Francesca Fulminante, Sarah Klassen, Keith W. Kintigh,John Douglass, The Distribution of Power and Inclusiveness across Deep Time. Science Advances

The dataset provides information on a series of proxies for governance (concentration of power and citizen inclusiveness), population size, hierarchical complexity, geographic region, modes of fiscal financing, bureaucratic structure, ritual practices, and socioeconomic inequality for 40 case observations across 31 polities. Proxy values were assigned by regional experts (the co-authors) based on archaeological and textual data.

This digital archive also provides reproducible analyses and figure construction related to the paper as a script written in R statistical computing language. Coding was undertaken by Dan Lawrence and Adam Green. 

Funding for this research was provided by the Coalition for Archaeological Synthesis, the Amerind Foundation, and the Field Museum of Natural History and the Amerind Foundation in Dragoon, Arizona.
DOI: 10.15468/dl.z9csxw
title: Occurrence Download

description: A dataset containing 14538 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is North America",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "StateProvince is Texas",
 "TaxonKey is Procyon lotor",
 "Year 2020-2026"
 ]
}

 The dataset includes 14538 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009951-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uv86sz
title: Occurrence Download

description: A dataset containing 8151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Centaurium erythraea, Centaurium erythraea)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 8151 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009952-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18472187
title: TUPROQ ORQALI YUQADIGAN INFEKTSIYALAR EPIDEMIYOLOGIYASI

description: Tuproq orqali yuqadigan infektsiyalar inson salomatligi uchun global miqyosda dolzarb bo‘lgan epidemiologik muammolardan biridir. Tuproq tabiiy rezervuar sifatida ko‘plab patogen mikroorganizmlar, parazitlar va gelmintlarning yashash va saqlanish muhiti hisoblanadi. Ushbu maqolada tuproq orqali yuqadigan infektsiyalarning epidemiologik xususiyatlari, yuqish mexanizmlari, xavf omillari va tarqalish qonuniyatlari tahlil qilinadi. Shuningdek, iqlim, sanitariya-gigiyena holati va ijtimoiy omillarning infektsiyalar tarqalishiga ta’siri ilmiy manbalar asosida yoritiladi.
DOI: 10.5281/zenodo.18472188
title: TUPROQ ORQALI YUQADIGAN INFEKTSIYALAR EPIDEMIYOLOGIYASI

description: Tuproq orqali yuqadigan infektsiyalar inson salomatligi uchun global miqyosda dolzarb bo‘lgan epidemiologik muammolardan biridir. Tuproq tabiiy rezervuar sifatida ko‘plab patogen mikroorganizmlar, parazitlar va gelmintlarning yashash va saqlanish muhiti hisoblanadi. Ushbu maqolada tuproq orqali yuqadigan infektsiyalarning epidemiologik xususiyatlari, yuqish mexanizmlari, xavf omillari va tarqalish qonuniyatlari tahlil qilinadi. Shuningdek, iqlim, sanitariya-gigiyena holati va ijtimoiy omillarning infektsiyalar tarqalishiga ta’siri ilmiy manbalar asosida yoritiladi.
DOI: 10.5281/zenodo.17379050
title: Origins and breadth of pairwise epistasis in an α-helix of β-lactamase TEM-1, data processing

description: The effect of mutations in a protein may depend on the presence of others—a phenomenon known as epistasis. Epistasis plays a key role in protein evolution and complicates predictions of mutational effects, as effects can be context-dependent. Yet, despite its importance, the mechanistic basis of epistasis remains poorly understood. To better characterize epistasis, we focused on an 11-residue α-helix in TEM-1 β-lactamase and constructed a comprehensive library of over 15,000 double mutants. Fitness and minimum inhibitory concentration assays, two contrasted measure of protein efficiency, revealed consistent widespread epistasis. A non-linear two-state protein stability model in which inactivating, destabilizing, neutral, or stabilizing mutations contribute additively to the stability phenotype, largely explained the data. Most epistatic effects were consequently predictable from single-mutation effects. However, systematic deviations from the model occurred when both mutated residues directly interacted in the 3D structure—a fold conserved across distant TEM-1 homologues. We therefore investigated the predictive power of statistical models trained on distant homologous sequences and found that they could partially recover the observed epistatic interactions. Our results, built on a short structural element of a protein, shed light on multiple determinants of the epistatic landscape that have shaped the evolutionary trajectory of β-lactamase proteins over long timescales.

 

Here are all the files required for preocessing the raw data to the figure and table production.
DOI: 10.5281/zenodo.18457561
title: Origins and breadth of pairwise epistasis in an α-helix of β-lactamase TEM-1, data processing

description: The effect of mutations in a protein may depend on the presence of others—a phenomenon known as epistasis. Epistasis plays a key role in protein evolution and complicates predictions of mutational effects, as effects can be context-dependent. Yet, despite its importance, the mechanistic basis of epistasis remains poorly understood. To better characterize epistasis, we focused on an 11-residue α-helix in TEM-1 β-lactamase and constructed a comprehensive library of over 15,000 double mutants. Fitness and minimum inhibitory concentration assays, two contrasted measure of protein efficiency, revealed consistent widespread epistasis. A non-linear two-state protein stability model in which inactivating, destabilizing, neutral, or stabilizing mutations contribute additively to the stability phenotype, largely explained the data. Most epistatic effects were consequently predictable from single-mutation effects. However, systematic deviations from the model occurred when both mutated residues directly interacted in the 3D structure—a fold conserved across distant TEM-1 homologues. We therefore investigated the predictive power of statistical models trained on distant homologous sequences and found that they could partially recover the observed epistatic interactions. Our results, built on a short structural element of a protein, shed light on multiple determinants of the epistatic landscape that have shaped the evolutionary trajectory of β-lactamase proteins over long timescales.

 

Here are all the files required for preocessing the raw data to the figure and table production.
DOI: 10.5281/zenodo.18471015
title: Dataset for "Further insights into hydrotalcite (Mg-Al layered double hydroxide) in cements"

description: This dataset is a part of article entitled "Further insights into hydrotalcite (Mg-Al layered double hydroxide) in cements" authored by Hoang Nguyen, Ellina Bernard, Mina Esmailzade, Daniel Rentsch, Nikolajs Toropovs, and Paivo Kinnunen.
DOI: 10.5281/zenodo.18471014
title: Dataset for "Further insights into hydrotalcite (Mg-Al layered double hydroxide) in cements"

description: This dataset is a part of article entitled "Further insights into hydrotalcite (Mg-Al layered double hydroxide) in cements" authored by Hoang Nguyen, Ellina Bernard, Mina Esmailzade, Daniel Rentsch, Nikolajs Toropovs, and Paivo Kinnunen.
DOI: 10.15468/dl.99eayb
title: Occurrence Download

description: A dataset containing 1149 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Diphasiastrum alpinum, Lycopodium alpinum, Diphasium alpinum)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 1149 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009953-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6gsgam
title: Occurrence Download

description: A dataset containing 173 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cardamine fulcrata"
 ]
}

 The dataset includes 173 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080324-251120083545085/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/14427454
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.13145/bacdive171162.20240510.9
title: Pasteurella bettyae

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive171162.20251217.10
title: Pasteurella bettyae

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive171163.20240510.9
title: Pasteurella bettyae

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.57702/uasleu3u
title: CamCAN dataset

description: CamCAN dataset consists of data obtained from the CamCAN repository.
DOI: 10.13145/bacdive171163.20251217.10
title: Pasteurella bettyae

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive171164.20241212.9.2
title: Leptospira biflexa

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive171164.20251217.10
title: Leptospira biflexa

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive171165.20241212.9.2
title: Leptospira biflexa

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive171165.20251217.10
title: Leptospira biflexa

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.57702/x4dt0k1p
title: ConvBench

description: ConvBench is a comprehensive benchmark for evaluating and comparing convolution algorithms. It assesses 9243 convolution operations derived from 1097 real-world deep learning models.
DOI: 10.13145/bacdive171166.20241212.9.2
title: Leptospira biflexa

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive171166.20251217.10
title: Leptospira biflexa

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.57702/v1seadoj
title: GoogleNews

description: The dataset used in this paper is a collection of news articles from Google News.
DOI: 10.13145/bacdive171167.20241212.9.2
title: Leptospira biflexa

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive171167.20251217.10
title: Leptospira biflexa

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.5281/zenodo.17041226
title: Automated Segmentation of Hepatic Vessels and Lobules in Whole-Slide Images Using U-Net Models

description: The repository contains curated datasets and trained models developed for the automated analysis of liver histopathology whole slide images (WSIs), specifically focused on the detection and segmentation of liver lobules and vascular structures. The dataset includes six ZIP files containing patch-level training and testing data for each task. Each dataset is organized into training/ and testing/ folders, with corresponding images/ and masks/ subdirectories. The masks provide pixel-level annotations for supervised segmentation. Additionally, the "Training WSIs" and "Testing WSIs" folders contain original WSIs used for generating training and testing samples. A separate Zip file archive includes the PyTorch .pth model files trained on these datasets, enabling reproducibility and further experimentation. An additional ZIP file titled "completeStitchedOverlays" provides complete segmented whole slide liver images used to qualitatively evaluate model performance on unseen data.
DOI: 10.5281/zenodo.17151860
title: Automated Segmentation of Hepatic Vessels and Lobules in Whole-Slide Images Using U-Net Models

description: The repository contains curated datasets and trained models developed for the automated analysis of liver histopathology whole slide images (WSIs), specifically focused on the detection and segmentation of liver lobules and vascular structures. The dataset includes six ZIP files containing patch-level training and testing data for each task. Each dataset is organized into training/ and testing/ folders, with corresponding images/ and masks/ subdirectories. The masks provide pixel-level annotations for supervised segmentation. Additionally, the "Training WSIs" and "Testing WSIs" folders contain original WSIs used for generating training and testing samples. A separate Zip file archive includes the PyTorch .pth model files trained on these datasets, enabling reproducibility and further experimentation. An additional ZIP file titled "completeStitchedOverlays" provides complete segmented whole slide liver images used to qualitatively evaluate model performance on unseen data.
DOI: 10.13145/bacdive171168.20241212.9.2
title: Leptospira biflexa

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive171168.20251217.10
title: Leptospira biflexa

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.