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

description: A dataset containing 170232 records in GBIF matching the query:
SELECT
 '432' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= -88.12157328514692
 AND decimalLongitude &lt;= -77.9229717807129
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 170232 records were derived from 257 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011318-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18218623
title: PyHealer: Agentic Self-Repair for Python Program Execution

description: PyHealer is an LLM-backed, agentic execution error repair pipeline for Python projects. It automatically analyzes execution failures, infers dependencies and Python versions, builds isolated Docker environments, and applies iterative fixes using specialized LLM agents.

The system is intended for research, experimentation, and automated program repair. Key features include:





LLM-driven API extraction




Automatic dependency and Python version inference




Docker-based isolated execution




Agentic feedback loop with specialized agents (Dependency, Code, Python, System)




Meta-Agent for failure classification




Iterative repair attempts




Structured JSON reports and metrics



The pipeline relies on pre-built knowledge artifacts for dependency resolution, Python feature mapping, and system error correction. Users can run PyHealer on target Python projects or benchmark datasets (e.g., Gistable Hg2.9k) to automatically detect and repair execution errors.

Prerequisites: Python 3.8+, Docker, and the Ollama local LLM runtime with the codellama:70b model.

License: (Specify your license here, e.g., MIT, Apache 2.0)

Repository / Files Structure:





PyHealer.py – main script




Example_Project/ – sample target project




Knowledge Data/ – knowledge artifacts for repair agents
DOI: 10.5281/zenodo.18218624
title: PyHealer: Agentic Self-Repair for Python Program Execution

description: PyHealer is an LLM-backed, agentic execution error repair pipeline for Python projects. It automatically analyzes execution failures, infers dependencies and Python versions, builds isolated Docker environments, and applies iterative fixes using specialized LLM agents.

The system is intended for research, experimentation, and automated program repair. Key features include:





LLM-driven API extraction




Automatic dependency and Python version inference




Docker-based isolated execution




Agentic feedback loop with specialized agents (Dependency, Code, Python, System)




Meta-Agent for failure classification




Iterative repair attempts




Structured JSON reports and metrics



The pipeline relies on pre-built knowledge artifacts for dependency resolution, Python feature mapping, and system error correction. Users can run PyHealer on target Python projects or benchmark datasets (e.g., Gistable Hg2.9k) to automatically detect and repair execution errors.

Prerequisites: Python 3.8+, Docker, and the Ollama local LLM runtime with the codellama:70b model.

License: (Specify your license here, e.g., MIT, Apache 2.0)

Repository / Files Structure:





PyHealer.py – main script




Example_Project/ – sample target project




Knowledge Data/ – knowledge artifacts for repair agents
DOI: 10.6084/m9.figshare.31146430
title: Automated Georeferencing Historical Maps

description: These data support the analysis of automatic georeferencing of Sanborn maps.
DOI: 10.6084/m9.figshare.31146430.v1
title: Automated Georeferencing Historical Maps

description: These data support the analysis of automatic georeferencing of Sanborn maps.
DOI: 10.15468/dl.m876ka
title: Occurrence Download

description: A dataset containing 468 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hydrophyllum canadense",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 468 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011326-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.apbs7h
title: Occurrence Download

description: A dataset containing 21299 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eichhornia crassipes"
 ]
}

 The dataset includes 21299 records from 653 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011327-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tb2rbp094
title: High throughput sequence data for association and description of female Calicnemia haksik (Odonata: Platycnemididae)

description: High throughput sequencing is a cost and time effective method for
 associating sexually dimorphic species. Increasing the available taxonomic
 understanding of females is important for biodiversity and conservation
 efforts. Here, we confirm the association of females caught in copulation
 with Calicnemia haksik Wilson and Reeds males in Vietnam using high
 throughput sequencing (92 loci) and provide the description of the female.
description: # High throughput sequence data for association and description of female
 Calicnemia haksik (Odonata: Platycnemididae)
 [https://doi.org/10.5061/dryad.tb2rbp094](https://doi.org/10.5061/dryad.tb2rbp094) ## Description of the data and file structure 1. The zipfile "raw_sequences" contains the raw reads received from LGC-Genomics. There is a textfile "sequence_filenames" which correlates the forward and reverse folders with each taxon used in the study. 2. The concatenated alignment that was used for phylogenetic reconstruction is provided in the file titled "concatenated_smatrix". 3. The file "partition.best_model" is the results of PartitionFinder and ModelFinder. It provides which loci are in each partition and the best model associated with that partition.  4.  The results from IQtree are provided in "tree.contree" (consensus tree) and "tree.treefile" (maximum likelihood). The phylogenetic reconstruction presented in the paper is based on the maximum likelihood reconstruction.
DOI: 10.15468/dl.g4uk5v
title: Occurrence Download

description: A dataset containing 2069 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Telicota colon"
 ]
}

 The dataset includes 2069 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004001-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18112/openneuro.ds007262.v1.0.4
title: Cognitive Workload 8 categories of mental arithmetic
DOI: 10.5061/dryad.t1g1jwt9q
title: Phylogeny and evolution of larval feeding mode in the megadiverse superfamily Sciaroidea (Diptera)

description: The superfamily Sciaroidea is a megadiverse clade within Diptera that
 exhibits diverse larval feeding modes. In this study, we explored the
 phylogenetic relationships and evolution of larval feeding modes within
 Sciaroidea using a fossil-calibrated time tree. We found that filtering
 out potentially fast-evolving sites altered the family-level tree topology
 of Sciaroidea and that species within Sciaroidea incertae sedis might be
 crucial in determining the general tree topology. The most recent common
 ancestor of Sciaroidea was inferred to have originated in the Upper
 Triassic (~230 Ma). A major radiation of families occurred from the
 Uppermost Triassic to the Lowermost Jurassic (190–200 Ma). The
 plesiomorphic larval feeding mode was inferred to be mycophagy. Most
 families retained this feeding mode with only minor transitions occurring
 in some clades; however, Cecidomyiidae and Keroplatidae went through
 notable shifts in larval feeding mode. Cecidomyiidae underwent a
 transition from mycophagy to phytophagy in the Lower Cretaceous, in line
 with angiosperm radiation as suggested in previous studies. The larvae of
 stem Keroplatidae were inferred to be predatory since the Jurassic. A
 transition back to mycophagy occurred within the subfamily Keroplatinae
 during the Paleogene to Uppermost Cretaceous, coinciding with the origin
 and radiation of species-rich mycophagous clades of other Sciaroidea
 families. Our study highlights the importance of taxon sampling and
 sequence filtering in phylogenetic analyses of Sciaroidea. We suggest,
 based on temporal patterns of lineage diversification, that the evolution
 of larval feeding modes within Sciaroidea might be correlated with the
 diversification of mushroom-forming fungi and angiosperms.
description: # Phylogeny and evolution of larval feeding mode in the megadiverse
 superfamily Sciaroidea (Diptera)
 [https://doi.org/10.5061/dryad.t1g1jwt9q](https://doi.org/10.5061/dryad.t1g1jwt9q) The current repository includes alignment fasta files and tree files generated in the associated study. * Concatenated.fasta: Sequence data after alignment, cleaning, and concatenation * Concatenated_valid_tiger_10.fasta: Sequence alignment of 100 species without missing genes filtered by TIGER (masked columns marked with X) * FULL.treefile; Full.runtrees: Tree file of the best tree and trees from 30 independent runs of ALL dataset * TIGER.treefile; TIGER.runtrees: Tree file of the best tree and trees from 30 independent runs of the TIG dataset * TIGER_pruned.treefile; TIGER_pruned.runtrees: Tree file of best tree and trees from 30 independent runs of pruned TIG dataset * BEAST.tree: Fossil-calibrated timetree obtained from BEAST analysis * BEAST_woroot.tree: Fossil-calibrated timetree obtained from BEAST analysis ran without root calibration
DOI: 10.15468/dl.32tp8p
title: Occurrence Download

description: A dataset listing the 130 species recorded in GBIF matching the query:
{
 "and" : [
 "Locality is New York City",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 130 records were derived from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003988-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8w9ghx3vq
title: Data from: A new species of Baorangia (Boletaceae, Boletales) from a sacred grove in India

description: Baorangia albostipitata sp. nov. from India is proposed based on
 morphological and molecular phylogenetic data. The species is
 characterized by a pinkish pileus with a yellowish pileal margin, a
 whitish pileal context that changes to pale blue very slowly on bruising
 or cut, a yellowish hymenophore without any color change on bruising or
 cut, a whitish stipe that changes to bright orange when bruised, and
 subglobose to ellipsoid basidiospores. Detailed descriptions,
 macrophotographs, illustrations, and comparisons with similar species are
 presented.
description: # A new species of Baorangia (Boletaceae, Boletales) from a sacred grove
 in India
 [https://doi.org/10.5061/dryad.8w9ghx3vq](https://doi.org/10.5061/dryad.8w9ghx3vq) Dataset contains ITS and 28S gene sequences. constructed a phylogram based on ITS and 28S sequence data. ## Description of the data and file structure ITS1F and ITS4R were the two primers used for the amplification of the ITS gene region and LROR and LR7 for the 28S gene region. All the sequences generated in this study are deposited in GenBank ([https://www.ncbi.nlm.nih.gov/genbank](https://www.ncbi.nlm.nih.gov/genbank); GenBank accession numbers: OR990613, OR990614). The obtained sequences were compared with the sequences available in GenBank using the BLASTN software. Phylogenetic analysis was carried out using ITS and 28S gene sequences. Sequences generated in this study, obtained from GenBank, and based on a previous published study of Zhang et al. (2021) were used for the analysis. ITS and 28S sequences retrieved from GenBank included the sequences that showed more than 80% similarity in BLAST search.
DOI: 10.5061/dryad.hhmgqnkqc
title: Data from: The biogeochemical boomerang: Site fidelity creates nutritional hotspots that may promote recurrent calving site reuse

description: Animals interact with nutrient cycles by consuming and depositing
 nutrients, interactions that are studied in the separate fields of
 nutritional ecology and zoogeochemistry. Recent theoretical work has begun
 bridging these disciplines, highlighting that animal-driven nutrient
 recycling could be crucial in helping animals meet nutritional needs. When
 animals exhibit site fidelity, they consistently deposit nutrients,
 potentially improving vegetation quality. We investigated this potential
 feedback by analyzing changes in forage nitrogen stocks following
 simulated caribou calving. We found that forage nitrogen stocks increased
 after two weeks and remained elevated after one year, a change due to an
 increase in forage quality but not quantity. We thus highlight a positive
 zoogeochemical feedback whereby caribou deposit nutrients during calving
 that become bioavailable during lactation and provide evidence that site
 fidelity creates a biogeochemical boomerang in which animals deposit
 nutrients that can be reused at a later time.
description: # Data from: The biogeochemical boomerang: Site fidelity creates
 nutritional hotspots that may promote recurrent calving site reuse
 [https://doi.org/10.5061/dryad.hhmgqnkqc](https://doi.org/10.5061/dryad.hhmgqnkqc) Data collected in May/June 2022-2023 to asses the role of caribou calving on nutrient cycles in Newfoundland. Data contains soil properties, environmental data, and %N, %C, and 15N data for plant and soil samples.  ## Description of the data and file structure Data can be found in two files.  Ferraro_BiogeochemicalBoomerang_Data_2024 contains the soil and plant data taken from the experimental calving plots. Ferraro_DistanceSamples_2024 contains the data from the plant samples taken in the transect outward from the calving plots in the second year of sampleing.  Ferraro_BiogeochemicalBoomerang_MetaData_2024.xlsx contains descriptions of the columns found within both data set, with a tab for each one.  Missing data code : NA ## Sharing/Access information Code for processing the data can be found at [https://github.com/kristymferraro/BiogeochemicalBoomerang ](https://github.com/kristymferraro/BiogeochemicalBoomerang) DOI: 10.5281/zenodo.12759695 Note: updated on July 2024 to address minor bug in code and add DOI
DOI: 10.5061/dryad.h44j0zptx
title: Data from: Icing-related injuries in polar bears (Ursus maritimus) at high latitudes

description: Climate change has broad ecological implications for wildlife, especially
 for species that rely on temperature-sensitive habitats. For polar bears
 (Ursus maritimus), loss of Arctic sea ice reduces access to prey and
 lengthens seasonal fasting periods leading to behavioral, nutritional, and
 reproductive impacts that may result in population declines. Secondary
 factors, such as disease and contaminants can exacerbate primary stressors
 and new health-related conditions are likely to emerge.  For
 example, once unusual but now increasingly frequent warming cycles are
 creating unprecedented icing conditions that have demographic consequences
 for cold-adapted mammals. We report on icing-related lesions observed in
 wild polar bears during live-capture research in two high-latitude
 subpopulations, Kane Basin (KB) and East Greenland (EG), between 2012 and
 2022.  We observed ice build-up, hair loss (alopecia), and skin
 ulcerations primarily affecting the feet of adult bears as well as other
 parts of the body. The most severely affected individuals had blocks of
 ice up to 30 cm in diameter adhered to the foot pads, deep, bleeding
 ulcerations of foot pads and exhibited lameness. These injuries have not
 been observed during previous research in these areas or reported in the
 scientific literature, suggesting this may be a new phenomenon. To provide
 context for our observations, we conducted interviews with Indigenous
 polar bear subsistence hunters in West and East Greenland and Nunavut to
 document Indigenous knowledge about the potential causes and frequency of
 these injuries.
description: This video was collected by mobile phone in East Greenland. The
 polar bear in the video is temporarialy sedated for physical capture. The
 video has not been processed. 
description: # Data from: Icing-related injuries in polar bears (Ursus maritimus) at
 high latitudes
  [https://doi.org/10.5061/dryad.h44j0zptx](https://doi.org/10.5061/dryad.h44j0zptx) This is a video taken in East Greenland, April 2022 of severe ice build up on the feet of an adult polar bear. The polar bear is sedated for physical capture during the filming. The video was taken with a mobile phone and has not been processed. Videographer credit: Kristin L. Laidre. Full manuscript is titled: "Icing-related injuries in polar bears (Ursus maritimus) at high latitudes". Laidre and Atkinson, 2024, Ecology. Description of the data and file structure: This is a *.mpeg video file. This supplemental file supports the observational study by Laidre and Atkinson (2024) in The Scientific Naturalist section of Ecology. See the full manuscript for more examples.  Sharing/Access information: Public (CCO) with credit.  Recorded via Samsung S20 mobile phone.
DOI: 10.25983/cbi/3014743
title: Pseudomonas putida produces two distinct populations of membrane vesicles during growth on lignin ProteomeXchange

description: ProteomeXchange version of Pseudomonas putida produces two distinct populations of membrane vesicles during growth on lignin - Proteomics, Targeted Quantitation, and Lipidomics
DOI: 10.5061/dryad.ngf1vhj33
title: Data from: Inference of cross-species gene flow using genomic data depends on the methods: Case study of gene flow in Drosophila

description: Analysis of genomic data in the past two decades has highlighted the
 prevalence of introgression as an important evolutionary force in both
 plants and animals. The genus Drosophila has received much attention
 recently, with an analysis of genomic sequence data detailing widespread
 introgression across the species phylogeny for the genus. However, the
 methods used in the study are based on data summaries for species triplets
 and are unable to infer gene flow between sister lineages or to identify
 the direction of gene flow. Hence, we reanalyze a subset of the data using
 the Bayesian program bpp, which is a full-likelihood implementation of the
 multispecies coalescent (MSC) model and can provide more powerful
 inference of gene flow between species, including its direction, timing,
 and strength. While our analysis supports the presence of gene flow in the
 species group, the results differ from the previous study: we infer gene
 flow between sister lineages undetected previously whereas most gene-flow
 events inferred in the previous study are rejected in our tests. To verify
 our conclusions, we performed simulations to examine the properties of
 Bayesian and summary methods. Bpp was found to have high power to detect
 gene flow, high accuracy in estimated rates of gene flow, and robustness
 under misspecification of the mode of gene flow. In contrast, summary
 methods had low power and produced biased estimates of introgression
 probability. Our results highlight an urgent need for improving the
 statistical properties ofsummary methods and the computational efficiency
 of likelihood methods for inferring gene flow using genomic sequence data.
description: Supplemental Information containing supplemental text, figures,
 and tables.  
description: # Inference of cross-species gene flow using genomic data depends on the
 methods: Case study of gene flow in Drosophila This dataset contains all
 necessary files to reproduce the BPP A00 runs under the MSC-I model using
 two halves of Drosophila sequence data, as conduct in
 [https://doi.org/10.5061/dryad.ngf1vhj33](https://doi.org/10.5061/dryad.ngf1vhj33). ## Description of the data and file structure Files Included: seqfile_half_0.txt: Sequence data file for the first half, containing 1389 loci. seqfile_half_1.txt: Sequence data file for the second half, containing 1388 loci. bpp_half_0.ctl: BPP control file. The seqfile parameter is set to seqfile_half_0.txt. If you want to use the second half of the data, modify this line to seqfile = seqfile_half_1.txt and update the number of loci to 1388 (as the second half contains one fewer loci). Imap.txt: BPP individual map (Imap) file. This file maps individual IDs to their corresponding species IDs for each sequence. The supplemental information includes the following contents. SI text. Bayesian parameter estimation in data simulated using the quartet trees of figure 2 Figures S1-S11 Tables S1-S9
DOI: 10.48366/r1581201
title: Higher Order Thinking Skills in Learning

description: Five research papers elaborate the peculiarities and successsful implementation of Higher Order Thinking skills in Learning.