cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17901609
title: Enhanced Suite of Probabilistic Models for Benchmarking Agentic Debugging Frameworks in Probabilistic Inference

description: This paper presents an extension to the foundational Reactive Oxygen Species (ROS) stochastic differential equation (SDE) model through four probabilistic models implemented in PyMC v5.25.0+. These models provide a robust empirical framework for evaluating agentic debugging methods in probabilistic programming. The models increase in inferential complexity based on stochastic processes relevant to biological aging: a Gaussian Process (GP) regression with hyperparameter optimization for non-parametric covariance estimation, accounting for biological variability [riihimaki2010]; a Hidden Markov Model (HMM) for sequential latent state inference under regime shifts, representative of cellular transitions [munoz2023]; a non-linear SDE for telomere attrition incorporating regime-switching multiplicative noise to capture stochastic shortening variability, improving on prior linear models [wattis2020]; and a Bayesian hierarchical model for epigenetic age acceleration, modeling senescence thresholds through latent methylation transitions [lu2019].Each model includes reproducible data generation procedures, PyMC implementations using the No-U-Turn Sampler (NUTS) for Hamiltonian Monte Carlo (HMC) inference, and protocols for obtaining high-fidelity reference posteriors via extensive sampling ( N=10^6  draws, effective sample sizes ESS  >10^5 , Gelman-Rubin  \hat{R} < 1.001 ). The derivations are original and grounded in aging biology to ensure independence from AI training data contamination, confirming novelty—no prior combinations of GP-HMM-SDE-epigenetic models for telomere-senescence benchmarking in agentic settings exist, as verified by an exhaustive arXiv search [riihimaki2010, munoz2023, olofsson1999, lu2019]. Diagnostics from  N=500  draws per chain (after 500 tuning steps) show strong convergence (ESS  \gtrsim 400 ;  \hat{R} \lesssim 1.005 ), supported by simulation-based calibration (SBC) rank histograms uniform over 1000 replications ( p -values  \in [0.05, 0.95] ) and prior sensitivity analyses with  <3%  shifts in posterior means.The suite includes detailed mathematical derivations, Stan implementations for validation, diagnostic plots using PGFPlots, model comparisons, and computational profiles (e.g., inference times  <25  s on AMD EPYC 7543 for  N=500 , scalable to  N=10^6  with Dask). This benchmark evaluates agentic performance in non-conjugate, high-dimensional inference. Calibration against longitudinal telomere and epigenetic datasets [aviv2018, horvath2013] ensures biological relevance, while SBC-validated posteriors minimize inferential biases, making the framework robust to methodological scrutiny
DOI: 10.15472/od8jpn
title: Lista de taxones asociados a Páramos de Colombia

description: El presente recurso contiene 8978 registros principalmente de especies y algunas, subespecies, variedades y géneros de Animales y Plantas asociados a páramos de Colombia. Los datos han sido recopilados principalmente de las Colecciones en línea del Instituto de Ciencias Naturales de la Universidad Nacional de Colombia, el IPT del Institute for Biodiversity and Ecosystem Dynamics de la Universidad de Amsterdam, el Instituto Alexander von Humboldt y de diferentes entidades que publican información a través del SiB Colombia. 

La obtención de cada nombre científico se realizó principalmente buscando la palabra "páramo" tanto en los metadatos de cada recurso consultado como en el campo 'localidad' de cada registro biológico. Este recurso se encuentra en constante actualización y pretende ser una guía de consulta de las especies presentes en páramos en el país, una vez se logren acuerdos con los expertos de cada grupo biológico.
DOI: 10.15472/6kpxyu
title: Lista de taxones asociados a Humedales de Colombia

description: El presente recurso contiene 2742 registros principalmente de especies y algunas, subespecies, variedades y géneros de Animales y Plantas asociados a humedales de Colombia. Los datos han sido recopilados principalmente de las Colecciones en línea del Instituto de Ciencias Naturales de la Universidad Nacional de Colombia, el IPT del Institute for Biodiversity and Ecosystem Dynamics de la Universidad de Amsterdam, el Instituto Alexander von Humboldt y de diferentes entidades que publican información a través del SiB Colombia. 

La obtención de cada nombre científico se realizó principalmente buscando la palabra "humedal" tanto en los metadatos de cada recurso consultado como en el campo 'localidad' de cada registro biológico. Se amplió la recuperación de registros asociados a humedales a partir de los sinónimos “ciénagas”, “lagos”, “lagunas”, “sabanas estacionales”, “sabanas inundables”, “planos de inundación”, “represas” y “manglares”. Este recurso se encuentra en constante actualización y pretende ser una guía de consulta de las especies presentes en humedales en el país, una vez se logren acuerdos con los expertos de cada grupo biológico.
DOI: 10.5281/zenodo.17436903
title: Data and code for "Seasonality of Vibrio parahaemolyticus in the Eastern Oyster, Crassostrea virginica, Along the Coast of Maine, USA"

description: Data and code to accompany the paper "Seasonality of Vibrio parahaemolyticus in the eastern oyster, Crassostrea virginica, along the coast of Maine, USA"  (Lurgio, A. (2025). Seasonality of Vibrio parahaemolyticus in the Eastern Oyster, Crassostrea virginica, along the Coast of Maine, USA. DigitalCommons@UMaine.). PCR results are found in the cq_ct_november exel file, water temperate and salinity values from each oyster lease site are labeled Maquoit_corr, Dam_corr, and Scarb_corr csv files, the R code used to evaulate the data using generalized additive models is Aidan_model_input, and the R code used to generate figures in the manuscrip is labeled Lurgiofinalfigures. All statistical analyses were performed in R 4.4.1 (R Core Team., 2023).

Oysters from the Scarborough River, Maquoit Bay, and the Damariscotta River in Maine were tested for the presence of Vibrio parahaemolyticus (Vp) genes. The TLH gene represents all strains of this bacteria and the TDH/TRH genes represent potentially pathogenic strains. The oysters were processed in accordance to the FDA approved MPN-RealTime PCR for Pathogenic Vp and Kinsey et al., (2015). Raw PCR data was analysed using LinRegPCR/RDML guidelines (Lefever et al., 2009 and Untergasser et al., 2021). "Cq" values determined from LinRegPCR anaylsis were used for model input, instead of raw "Ct" values from the 7500 ab fast PCR machine. This paper focused on modeling the pathogenic genes found in oysters and their seasonal relation to site, water temperature, and salinity.
DOI: 10.5281/zenodo.17436902
title: Data and code for "Seasonality of Vibrio parahaemolyticus in the Eastern Oyster, Crassostrea virginica, Along the Coast of Maine, USA"

description: Data and code to accompany the paper "Seasonality of Vibrio parahaemolyticus in the eastern oyster, Crassostrea virginica, along the coast of Maine, USA"  (Lurgio, A. (2025). Seasonality of Vibrio parahaemolyticus in the Eastern Oyster, Crassostrea virginica, along the Coast of Maine, USA. DigitalCommons@UMaine.). PCR results are found in the cq_ct_november exel file, water temperate and salinity values from each oyster lease site are labeled Maquoit_corr, Dam_corr, and Scarb_corr csv files, the R code used to evaulate the data using generalized additive models is Aidan_model_input, and the R code used to generate figures in the manuscrip is labeled Lurgiofinalfigures. All statistical analyses were performed in R 4.4.1 (R Core Team., 2023).

Oysters from the Scarborough River, Maquoit Bay, and the Damariscotta River in Maine were tested for the presence of Vibrio parahaemolyticus (Vp) genes. The TLH gene represents all strains of this bacteria and the TDH/TRH genes represent potentially pathogenic strains. The oysters were processed in accordance to the FDA approved MPN-RealTime PCR for Pathogenic Vp and Kinsey et al., (2015). Raw PCR data was analysed using LinRegPCR/RDML guidelines (Lefever et al., 2009 and Untergasser et al., 2021). "Cq" values determined from LinRegPCR anaylsis were used for model input, instead of raw "Ct" values from the 7500 ab fast PCR machine. This paper focused on modeling the pathogenic genes found in oysters and their seasonal relation to site, water temperature, and salinity.
DOI: 10.15468/dl.y2bnup
title: Occurrence Download

description: A dataset containing 1330 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Solanum lanceolatum"
 ]
}

 The dataset includes 1330 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047578-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ck6p9q
title: Occurrence Download

description: A dataset containing 487 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Salvia protracta"
 ]
}

 The dataset includes 487 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047577-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kmufjk
title: Occurrence Download

description: A dataset containing 481 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Solanum lycopersicum"
 ]
}

 The dataset includes 481 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047579-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6mp93q
title: Occurrence Download

description: A dataset containing 252 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Salvia pubescens"
 ]
}

 The dataset includes 252 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047580-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5zvez6
title: Occurrence Download

description: A dataset containing 3185 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is FSFN: Forest Soil Fauna Network: Sphaeroceridae, Flanders Belgium"
 ]
}

 The dataset includes 3185 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047582-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p2aq2e
title: Occurrence Download

description: A dataset containing 19108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Butterfly distribution records for the UK from Butterfly Conservation, up to 2019",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 1959",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 19108 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047583-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/cxzrld
title: PAN-00160962 - terra sigillata cup type Drag. 27

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00160962&lt;/p&gt;
description: Modified: 2025-11-10T12:58:14+01:00
DOI: 10.5281/zenodo.17878231
title: Dataset and source code for article "In-sensor computing with halide perovskite-based optoelectronic reservoir networks"

description: This replication package contains raw data, including I-V sweeps, pulsed measurements, SEM images, and Python scripts used for analysis and network training, as well as source code to replicate the figures for the article "In-sensor computing with halide perovskite-based optoelectronic reservoir networks" published in Device by Cell Press under https://doi.org/10.1016/j.device.2025.101000.
DOI: 10.5281/zenodo.17878230
title: Dataset and source code for article "In-sensor computing with halide perovskite-based optoelectronic reservoir networks"

description: This replication package contains raw data, including I-V sweeps, pulsed measurements, SEM images, and Python scripts used for analysis and network training, as well as source code to replicate the figures for the article "In-sensor computing with halide perovskite-based optoelectronic reservoir networks" published in Device by Cell Press under https://doi.org/10.1016/j.device.2025.101000.
DOI: 10.5281/zenodo.17433852
title: The Value of Effective Pull Request Description
DOI: 10.5281/zenodo.17901312
title: The Value of Effective Pull Request Description
DOI: 10.26008/1912/bco-dmo.989777.1
title: Compound-specific nitrogen stable isotopes of amino acids in planktic foraminifera from Santa Barbara Basin sediment traps from 2018 to 2021

description: We measured carbon and nitrogen compound-specific stable isotopes of amino acids (CSI-AA) in the shells the three most abundant species of planktic foraminifera from Santa Barbara Basin sediment traps from 2018 to 2021: Globigerina bulloides (d’Orbigny, 1826), Neogloboquadrina incompta (Cifelli, 1961), and Turborotalita quinqueloba (Natland, 1938). Multiple sediment trap collections were combined to constitute representative samples. The N. incompta sample included individuals from sediment trap collections from May 2019 to October 2021 (n=4082). The T. quinqueloba sample included individuals from December 2018 to October 2021 (n=4964). G. bulloides was sufficiently abundant to split into seasonal samples: spring/summer from February 2019 to July 2019 (n=5081) and fall/winter from October to January in years 2018-2019, 2019-2020, 2020-2021 (n=3132). The collection of these data were supported by NSF OCE. This dataset includes only the nitrogen CSI-AA data. Carbon data are available in a related dataset.
DOI: 10.15468/dl.rwzs8j
title: Occurrence Download

description: A dataset containing 885 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Phlebotomus neglectus"
 ]
}

 The dataset includes 885 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047584-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qjjzgt
title: Occurrence Download

description: A dataset containing 1261 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Phlebotomus longicuspis"
 ]
}

 The dataset includes 1261 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047585-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e458br
title: Occurrence Download

description: A dataset containing 539 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Phlebotomus mascittii"
 ]
}

 The dataset includes 539 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047586-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7488/ds/8057
title: Codes and supplemental data for 'Phloem evolution in ferns was shaped by phylogeny and records a trend of decreasing conductivity through geological time'

description: The phloem, the sugar-transporting tissue in vascular plants, is one of the most important but least well characterised plant tissues from an evolutionary perspective. Here we substantially extend the evidence for phloem evolution using ferns as a case study due to their long evolutionary history and famed vascular diversity. We carried out a comparative histological investigation of the conducting cells of the phloem, termed sieve elements, in 26 extant species, spanning 21 families and making over 18,000 measurements. We found that sieve element radius correlates with vascular bundle radius and leaf area, but that these correlations alone didn’t account for the observed diversity in sieve element radii. Instead, sieve element radius preserves a strong phylogenetic signal and is similar in closely related taxa despite differences in leaf and vascular characteristics. Next, by combining evidence from extinct and extant species, we recognised a trend of decreasing sieve element radius and total conducting area through geological time. We predict that this decrease resulted in reduced phloem conductivity especially in the eupolypod ferns that diversified into angiosperm-dominated ecosystems. Our findings demonstrate that phloem structure has changed over the long evolutionary history of ferns and that this likely had an important functional impact.
description: R scripts and source data used to produce the result figures. Images used to collect data on sieve element radius, sieve element numbers, leaf and vascular traits. Image files are named with the initial two letters of the genus name and the initial two letters of the specific epithet. For example, Ceratopteris richardii is abbreviated to CeRi for the image files.
DOI: 10.15468/dl.4yja2g
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Solanum mammosum"
 ]
}

 The dataset includes 69 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047588-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/bqc9jo
title: Replication Data for: Personal Narratives Reduce Negative Attitudes toward Immigrant Outgroups: Evidence from Kenya

description: Replication files for: Personal Narratives Reduce Negative Attitudes toward Immigrant Outgroups: Evidence from Kenya
DOI: 10.15468/dl.cmhjkg
title: Occurrence Download

description: A dataset containing 1117 species occurrences available in GBIF matching the query:
{
 "and" : [
 "MediaType is Image",
 "PublishingOrg is b4640710-8e03-11d8-b956-b8a03c50a862",
 "TaxonKey is Arachnida"
 ]
}

 The dataset includes 1117 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047589-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eagnu3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((116.25 -0.969817, 116.179727 -0.975383, 116.111183 -0.991945, 116.046056 -1.019094, 115.985949 -1.056163, 115.932341 -1.102238, 115.886552 -1.156187, 115.849709 -1.21668, 115.82272 -1.28223, 115.80625 -1.351221, 115.800705 -1.421956, 115.806223 -1.492693, 115.822668 -1.561691, 115.849638 -1.62725, 115.886468 -1.687755, 115.932253 -1.741717, 115.985866 -1.787806, 116.045986 -1.824886, 116.111132 -1.852045, 116.1797 -1.868613, 116.25 -1.874181, 116.3203 -1.868613, 116.388868 -1.852045, 116.454014 -1.824886, 116.514134 -1.787806, 116.567747 -1.741717, 116.613532 -1.687755, 116.650362 -1.62725, 116.677332 -1.561691, 116.693777 -1.492693, 116.699295 -1.421956, 116.69375 -1.351221, 116.67728 -1.28223, 116.650291 -1.21668, 116.613448 -1.156187, 116.567659 -1.102238, 116.514051 -1.056163, 116.453944 -1.019094, 116.388817 -0.991945, 116.320273 -0.975383, 116.25 -0.969817))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047590-251120083545085/datasets/export for details.
DOI: 10.15468/dl.72mhb6
title: Occurrence Download

description: A dataset listing the 352 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.74435 7.99747,-76.73822 7.98305,-76.74971 7.9694,-76.75277 7.94739,-76.75814 7.92539,-76.76886 7.91394,-76.80971 7.90789,-76.88028 7.909,-76.85268 7.87998,-76.74364 7.90212,-76.73604 7.90241,-76.73132 7.94967,-76.72366 7.9785,-76.7206 8.01492,-76.70604 8.04678,-76.71217 8.07939,-76.72596 8.11125,-76.73898 8.12869,-76.75124 8.13628,-76.7612 8.12566,-76.74741 8.10063,-76.74664 8.0885,-76.74894 8.05816,-76.72673 8.06953,-76.72519 8.05285,-76.74818 8.03236,-76.74435 7.99747))",
 "HasGeospatialIssue is false",
 "TaxonKey is Aves"
 ]
}

 The dataset's 352 records were derived from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047564-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17897626
title: Validation of Ionospheric Models at Mid- and High-Latitudes: Climatological Performance of WACCM-X (SD) and TIE-GCM in foF2 (Datasets)

description: The paper dataset contains monthly-averaged foF2, percentage differences, and standard deviations from ionosonde data, as well as WACCM-X, WACCM-X SD, TIE-GCM, and E-CHAIM model runs at Resolute Bay, Canada, and Chilton, UK, between 1950 and 2022, and, where indicated, between 1995 and 2015. Hourly data from TIE-GCM model runs under the Heelis and Weimer configurations is also provided in both locations for the years 2009 and 2013.
DOI: 10.5281/zenodo.17897625
title: Validation of Ionospheric Models at Mid- and High-Latitudes: Climatological Performance of WACCM-X (SD) and TIE-GCM in foF2 (Datasets)

description: The paper dataset contains monthly-averaged foF2, percentage differences, and standard deviations from ionosonde data, as well as WACCM-X, WACCM-X SD, TIE-GCM, and E-CHAIM model runs at Resolute Bay, Canada, and Chilton, UK, between 1950 and 2022, and, where indicated, between 1995 and 2015. Hourly data from TIE-GCM model runs under the Heelis and Weimer configurations is also provided in both locations for the years 2009 and 2013.
DOI: 10.5683/sp3/2vwmn4
title: Replication Data and Code for “Price Caps, Commitment and Innovation”

description: This replication package contains the Python code and documentation used to generate Tables A.1 and A.2 of the article “Price Caps, Commitment and Innovation” by Atallah & Simons.
The tables rely exclusively on equilibrium computations using the linear model described in Appendix A. No external datasets are used.
Running replicate_linear_case.py reproduces all numerical results. See README.pdf for details.