cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.bh29h4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Asquamiceps caeruleus Markle, 1980",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((8.6827 2.71,8.9648 2.8113,8.9648 10.8496,-0.0352 10.8496,-0.0352 5.0957,0.3816 5.278,1.1532 5.3393,1.5603 5.6976,3.8925 5.9309,4.2618 5.8773,4.5416 5.6356,5.1549 4.4105,5.7546 3.8683,6.2396 3.7859,8.2757 4.0386,7.9361 3.4903,8.1439 2.8795,8.6827 2.71))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011602-250525065834625/datasets/export for details.
DOI: 10.15468/dl.n2zu5g
title: Occurrence Download

description: A dataset containing 529 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Danthonia californica Bol.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 529 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011604-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15561429
title: Source Code and Dataset for ASE 2025 #207

description: This repository implements the C3 framework, which integrates centralized auction-based collaboration and decentralized communication-aware competition to overcome the collaboration degeneration problem in multi-agent LLM systems, particularly in complex software development tasks.

In C3 folder:

auction.py contains the  AuctionCoordinator class used to evaluate and score agent proposals based on novelty, executability, and diversity. Also responsible for generating peer feedback.

agent.py defines the base Agent class and specialized roles (e.g., Architect, Engineer). Each agent can generate and refine proposals using OpenAI's Chat API. Includes utility computation based on LLM-assessed quality.

proposal_pool.py provides Proposal and ProposalPool classes to manage agent submissions and evaluation metadata. Used in scoring and refinement cycles.

sop_templates.py contains standardized SOP (Standard Operating Procedure) templates that define role-specific proposal formats and evaluation criteria.

metrics.py implements offline quantitative metrics such as Task Ownership Entropy (TOE), Adaptation Responsiveness Rate (ARR), and Feedback Utilization Score (FUS) for evaluating inter-agent dynamics.

dcc.py implements the Decentralized Communication-aware Competition (DCC) mechanism. Agents iteratively observe and refine proposals until convergence. 

cab.py implements a multi-stage pipeline across Product Manager, Architect, Engineer, and QA Engineer agents. Proposals are generated, refined, and passed between roles in a structured pipeline. 

naive_isolated.py implements naive competition, where all agents generate proposals independently, followed by a centralized auction-style winner selection. No refinement or communication is involved and solated competition, where agents generate proposals in complete isolation without visibility, feedback, or scoring. Serves as a baseline for collaboration-free behavior.

dataset: 70 tasks extended from SoftwareDev since it is not fully open-source.
DOI: 10.5281/zenodo.15561430
title: Source Code and Dataset for ASE 2025 #207

description: This repository implements the C3 framework, which integrates centralized auction-based collaboration and decentralized communication-aware competition to overcome the collaboration degeneration problem in multi-agent LLM systems, particularly in complex software development tasks.

In C3 folder:

auction.py contains the  AuctionCoordinator class used to evaluate and score agent proposals based on novelty, executability, and diversity. Also responsible for generating peer feedback.

agent.py defines the base Agent class and specialized roles (e.g., Architect, Engineer). Each agent can generate and refine proposals using OpenAI's Chat API. Includes utility computation based on LLM-assessed quality.

proposal_pool.py provides Proposal and ProposalPool classes to manage agent submissions and evaluation metadata. Used in scoring and refinement cycles.

sop_templates.py contains standardized SOP (Standard Operating Procedure) templates that define role-specific proposal formats and evaluation criteria.

metrics.py implements offline quantitative metrics such as Task Ownership Entropy (TOE), Adaptation Responsiveness Rate (ARR), and Feedback Utilization Score (FUS) for evaluating inter-agent dynamics.

dcc.py implements the Decentralized Communication-aware Competition (DCC) mechanism. Agents iteratively observe and refine proposals until convergence. 

cab.py implements a multi-stage pipeline across Product Manager, Architect, Engineer, and QA Engineer agents. Proposals are generated, refined, and passed between roles in a structured pipeline. 

naive_isolated.py implements naive competition, where all agents generate proposals independently, followed by a centralized auction-style winner selection. No refinement or communication is involved and solated competition, where agents generate proposals in complete isolation without visibility, feedback, or scoring. Serves as a baseline for collaboration-free behavior.

dataset: 70 tasks extended from SoftwareDev since it is not fully open-source.
DOI: 10.5281/zenodo.15561431
title: Dataset for the occurrence and correlation of urinary mycotoxin levels with food consumption patters

description: These datasets were generated within the PRISMA project (Marie Skłodowska-Curie Grant Agreement No. 101110615) for the correlation of urinary mycotoxin levels with food consumption patterns.

The files contain:



comparisons of low versus high consumption of cereals, tubers, fruits, vegetables, legumes, and dairy;

Spearman correlations of food group consumption (cereals, nuts, etc.) with urinary mycotoxin levels;

Spearman correlaitons of food items consumption (i.e., cofffee, bread, etc.) with urinary mycotoxin levels.
DOI: 10.15468/dl.4zqvaw
title: Occurrence Download

description: A dataset containing 46271 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Prunus persica (L.) Stokes"
 ]
}

 The dataset includes 46271 records from 803 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011603-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ynq8rr
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pimelodella australis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 78 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025394-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f9z384
title: Occurrence Download

description: A dataset listing the 3587 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Slovenia",
 "OccurrenceStatus is Present",
 "Year is 2021"
 ]
}

 The dataset's 3587 records were derived from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025389-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7u4kab
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Desmodium rensonii (J.H.Painter ex Renson) Choussy",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Occurrence evidence)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010005-250525065834625/datasets/export for details.
DOI: 10.15468/dl.dwqgdf
title: Occurrence Download

description: A dataset containing 36448 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Streptomyces Waksman & Henrici, 1943"
 ]
}

 The dataset includes 36448 records from 425 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016213-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7916/d8ms3s3j
title: Institutions Don't Rule: Direct Effects of Geography on Per Capita Income

description: Data on the direct effects of geography on per capita income, available as xls, do, and dta files.
DOI: 10.5061/dryad.f1vhhmgzf
title: Phenotypic and genotypic divergence of plant-herbivore interactions along an urbanization gradient

description: Urban environments provide challenging conditions for species survival,
 including increased temperatures, drought, and pollution. Species can deal
 with these conditions through evolution across generations or the
 immediate expression of phenotypic plasticity. The resulting phenotypic
 changes are key to the performance of species and their interactions with
 other species in the community. We here document patterns of herbivory in
 Arabidopsis thaliana along a rural-urban gradient, and tested the genetic
 background and ecological consequences of traits related to herbivore
 resistance. Aphid densities increased with urbanization levels along the
 gradient while plant size did not change. Offspring of urban mothers,
 raised under common garden conditions, were larger and had a decreased
 trichome density and seed set but a higher caterpillar (Pieris brassicae)
 tolerance. In contrast, no urban evolution was detected for defenses
 against aphids (Myzus persicae). Aphids reduced seed set more strongly in
 urban offspring, but this effect disappeared in second-generation plants.
 In general, urban adaptations as expressed in size and caterpillar
 tolerance were found, but these adaptations were associated with smaller
 inflorescences. The maternal effect on the response of seed set to aphid
 feeding demonstrates the relevance of intergenerational plasticity as a
 direct ecological consequence of herbivory. Our study demonstrates that
 the urban environment interacts with the plant's genotype and the
 extended phenotype as determined by ecological interactions.
DOI: 10.5061/dryad.2z34tmpnx
title: What can be learned from fishers’ perceptions for fishery management planning? Case study insights from Sainte-Marie, Madagascar

description: Local support is critical to the success and longevity of fishery
 management initiatives. Previous research suggests that how resource users
 perceive ecological changes, explain them, and cope with them, influences
 local support. The objectives of this study were two-fold. First, we
 collated local fishers’ knowledge to characterize the long-term
 socio-ecological dynamics of the small-scale fishery of Sainte-Marie
 Island, in Madagascar. Second, we empirically assessed the individual- and
 site-level factors influencing support for fishery restrictions. Our
 results indicate that fishers observed a decline in fish abundance and
 catch sizes, especially in nearshore areas; many also perceived a
 reduction in fish sizes and the local disappearance of species. To
 maintain their catches, most fishers adapted by fishing harder and further
 offshore. Accordingly, fishers identified increased fishing effort (number
 of fishers and gear evolution) as the main cause of fishery changes.
 Collectively, our results highlight that the transition from a subsistence
 to commercial fishery, and resulting changes in the relationship between
 people and the fisheries, was an underlying driver of fishery changes.
 Additionally, we found that gender, membership to local associations,
 coping mechanisms, and perceptions of ecological health, were all
 interlinked and significantly associated with conservation-oriented
 attitudes. Conservation-oriented attitudes, however, were not associated
 with fishers’ willingness to decrease fishing. In the short-term,
 area-based restrictions could contribute to building support for
 conservation. In the long-term, addressing the underlying causes of the
 decline will necessitate collaborations among the various groups involved
 to progressively build livelihood flexibility. Collectively, our study
 provides additional insights on the individual- and site-level factors
 influencing support for fishery restrictions. It also highlights the
 importance of dialoguing with fishers to ensure that fishery management
 plans are adapted to the local context.
description: Catches.txt includes recollected catch volume for a number of
 species, along with year, fishers ID, and fishing gear used. It was used
 to run GAMs.  Dist.txt includes recollected fishing
 site distance, along with year, fishers ID, and fishing gear used. It was
 used to run GLMs.  SM_MFA.txt includes site- and
 individual-level characteristics. It was used to run the MFA.
DOI: 10.5061/dryad.sf7m0cg7n
title: Fish resist temptation from junk food: State-dependent diet choice in reproductive Atlantic cod (Gadus morhua) facing seasonal fluxes of lipid-rich prey

description: In ecological sciences, animal diets are often simplified to “resources”
 or “caloric quantities”. However, in the present study, we investigated
 the optimal foraging strategy of Atlantic cod (Gadus morhua) when both
 macro- and micro-nutritional requirements are accounted for. Proteins
 cannot be synthesized from fatty acids, so the proteins for gonad
 development must come from other dietary sources. In addition,
 micronutrients are required in smaller quantities. For example, for cod,
 arachidonic acid (ARA) acts as a micronutrient precursor for
 prostaglandins, which is important for reproduction. We formulated a
 dynamic state-dependent model to make predictions about optimal diet
 choice and foraging behavior. We applied the model to a case study in the
 strait between Denmark and Sweden. The model predicted that energy
 acquired from dietary protein should be twice that acquired from lipids,
 with a small increase in the lipid requirements when gonads are growing.
 The model also predicted that the “energy sparing effect of lipids” made
 it beneficial to engage in risky foraging activity to supplement a lean
 diet with a little bit of fat. When we re-constructing the model to also
 optimize ARA uptake, the cod consumed relatively more ARA-rich crabs in
 the months prior to spawning, despite the otherwise poor energetic value
 of this prey. In support of the model predictions, field observations
 indicated that lipid stores reached a peak shortly after the arrival of
 the lipid-rich migrating herring and the fatty acid signal of these
 herring were evident in the liver of nearly all cod. Three month later,
 only half of the cod contained the herring-derived fatty acid signal,
 supporting the predicted shift in prey type prior to spawning. From these
 model predictions and field observations, we conclude that, also in the
 wild, nutritional requirements can be at least as important as pure energy
 acquisition.
DOI: 10.5061/dryad.bg79cnpc4
title: Data from: Different evolutionary pathways lead to incomplete convergence of elongate body shapes in carnivoran mammals

description: Although convergence is often recognized as a ubiquitous feature across
 the Tree of Life, whether the underlying traits also exhibit similar
 evolutionary pathways towards convergent forms puzzles biologists. In
 carnivoran mammals, “elongate,” “slender,” and “long” are often used to
 describe and even to categorize mustelids (martens, polecats, and
 weasels), herpestids (mongooses), viverrids (civets and genets), and other
 carnivorans together. But just how similar these carnivorans are and
 whether there is convergence in the morphological component that
 contribute to elongation has never been assessed. Here, I found that these
 qualitatively-described elongate carnivorans exhibited incomplete
 convergence towards elongate bodies compared to other terrestrial
 carnivorans. In contrast, the morphological components underlying body
 shape variation do not exhibit convergence despite evidence that these
 components are more elongate in elongate carnivorans compared to
 non-elongate carnivorans. Furthermore, these components also exhibited
 shorter but different phylogenetic half-lives towards more elongate
 adaptive peaks, indicating that different selective pressures can create
 multiple pathways to elongation. Incorporating the fossil record will
 facilitate further investigation of whether body elongation evolved
 adaptively or if it is simply a retained ancestral trait.
description: Supplementary Methods Tables S1-S9
DOI: 10.5061/dryad.p2ngf1vs0
title: Relative forelimb-hindlimb investment is associated with flight style, foraging strategy, and nestling period, but not nest type

description: We investigated Dial’s 2003 hypothesis that birds that rely more heavily
 upon flight as their primary mode of locomotion and thus invest more in
 their forelimbs than hindlimbs will experience selection for smaller body
 sizes, greater altriciality, and more complex nests. To test this
 hypothesis, we examined the skeletons of over 2,000 individuals from 313
 species representing the majority of avian families and all major branches
 of the avian tree. We used the lengths of the sternal keel and long bones
 of the wing relative to the lengths of the leg long bones as an index of
 relative locomotor investment. We found that locomotor investment was
 predicted by flight style, foraging method, and length of nestling period,
 supporting Dial’s hypothesis. Soaring birds and birds with more acrobatic
 flight styles, birds whose foraging methods were heavily reliant upon
 flight, and whose young spent more time in the nest tended to invest more
 in their forelimbs relative to hindlimbs. Nest type and body size were not
 significant predictors of relative forelimb-hindlimb investment, however,
 suggesting that the relationships among flight style, locomotor
 investment, and life history are not as tightly intertwined as Dial
 originally hypothesized.
description: This dataset includes measurements of over 2,000 museum bird
 skeletal specimens, including the lengths of the sternal keel, humerus,
 ulna, carpometacarpus, femur, tibiotarsus, and tarsometatarsus. It also
 includes life-history traits for over 300 bird species. Skeletal
 measurements were taken from scaled photographs using ImageJ (see methods
 in Kotnour et al. 2021, Relative forelimb-hindlimb investment is
 associated with flight style, foraging strategy, and nestling period, but
 not nest type, Ornithology, for more details). Included is R code to run
 all analyses and create all figures from the article.
DOI: 10.5061/dryad.1zcrjdftd
title: No link between population isolation and speciation rate in squamate reptiles

description: Rates of species formation vary widely across the tree of life and
 contribute to massive disparities in species richness among clades. This
 variation can emerge from differences in metapopulation-level processes
 that affect the rates at which lineages diverge, persist, and evolve
 reproductive barriers and ecological differentiation. For example,
 populations that evolve reproductive barriers quickly should form new
 species at faster rates than populations that acquire reproductive
 barriers more slowly. This expectation implicitly links microevolutionary
 processes (the evolution of populations) and macroevolutionary patterns
 (the profound disparity in speciation rate across taxa). Here, leveraging
 extensive field sampling from the Neotropical Cerrado biome in a
 biogeographically-controlled natural experiment, we test the role of an
 important microevolutionary process – the propensity for population
 isolation – as a control on speciation rate in lizards and snakes. By
 quantifying population genomic structure across a set of co-distributed
 taxa with extensive and phylogenetically independent variation in
 speciation rate, we show that broad-scale patterns of species formation
 are decoupled from demographic and genetic processes that promote the
 formation of population isolates. Population isolation is likely a
 critical stage of speciation for many taxa, but our results suggest that
 interspecific variability in the propensity for isolation has little
 influence on speciation rates. These results suggest that other stages of
 speciation – including the rate at which reproductive barriers evolve and
 the extent to which newly formed populations persist – are likely to play
 a larger role than population isolation in controlling speciation rate
 variation in squamates.
description: These are variant call formats (VCFs) for species included in our
 study.
DOI: 10.25338/b88s7j
title: An approach to quantifying the key greenhouse gas emissions in California concrete production

description: The objective of this study is to develop a cohesive, unified dataset of
 life cycle inventories - needed to quantify the effects of material,
 energy, waste, and emission flows on the environmental impacts of
 concrete. The models developed will consider GHG emissions, namely CO2,
 CH4, and N2O emissions, for the key components of cement and concrete
 production in California. The structure of the data will allow for the
 tailoring of inputs to capture variations in different regions around the
 world. This allows the user to adapt for production in other regions or
 for importing material from other regions.
description: Data are based on the academic and grey literature. References
 and methods for determining inputs are in the attached files.
description: Data are limited to values found by the authors and are not
 necessarily representative of consistent or specific spatial or temporal
 attributes.