cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d1x42s
title: Redwood Creek Chinook salmon life cycle model code and data

description: Understanding the spatial and temporal habitat use of a population is a
 necessary step for restoration decision making. For Chinook salmon
 (Oncorhynchus tshawytscha), variation in their migration and habitat use
 complicate predicting how restoring habitats will impact total
 recruitment. To evaluate how juvenile life history variation affects a
 population’s response to potential restoration, we developed a
 stage-structured model for a Chinook salmon population in a northern
 California river with a seasonally closed estuary. We modeled the timing
 of juvenile migration and estuarine use as a function of freshwater
 conditions and fish abundance We used the model to evaluate the
 sensitivity of the population to different estuary and freshwater
 restoration scenarios that would affect population parameters at different
 life stages. The population’s run size increased most in response to
 freshwater restoration that enhanced spawning productivity (egg and fry
 survival), followed by spawner capacity. In contrast, estuary restoration
 scenarios affected only a subset of Chinook salmon (average 15 percent),
 and as a result, did not have a large impact on the total recruitment of a
 cohort. Under current condition, estuary rearing fish were over six times
 less likely to survive than fish that migrate to the ocean in the spring
 or early summer before estuary closure. Because estuary residents
 experienced low survival in the estuary and in the ocean, improvements to
 both estuary survival and growth would be needed to increase their total
 survival. When life cycle monitoring data is available, life cycle models
 such as ours generate predictions at scales relevant to conservation and
 are an advantageous approach to managing and conserving anadromous salmon
 that use multiple habitats throughout their life cycle.
DOI: 10.57903/uj/zaax05
title: Dodo bird verdict: Verbal modeling, counterconditioning, and operant conditioning are effective in nocebo hyperalgesia attenuation

description: Research data was collected during the study on the effectiveness of verbal modeling, operant conditioning, and counterconditioning in attenuating nocebo hyperalgesia.
DOI: 10.5061/dryad.73n5tb30p
title: From performance curves to performance surfaces: Interactive effects of temperature and oxygen availability on aerobic and anaerobic performance in the common wall lizard

description: 1. Accurately predicting the responses of organisms to novel or changing
 environments requires the development of ecologically-appropriate
 experimental methodology and process-based models. 2. For ectotherms,
 thermal performance curves (TPCs) have provided a useful framework to
 describe how organismal performance is dependent on temperature. However,
 this approach often lacks a mechanistic underpinning, which limits our
 ability to use thermal performance curves predictively. Further, thermal
 dependence varies across traits, and performance is also limited by
 additional abiotic factors, such as oxygen availability. 3. We test a
 central prediction of our recent Hierarchical Mechanisms of Thermal
 Limitation (HMTL) Hypothesis which proposes that natural hypoxia exposure
 will reduce maximal performance and cause the thermal performance curve
 for whole-organism performance to become more symmetrical. 4. We
 quantified thermal performance curves for two traits often used as fitness
 proxies, sprint speed and aerobic scope, in lizards under conditions of
 normoxia and high-elevation hypoxia. 5. In line with the predictions of
 HMTL, anaerobically-fueled sprint speed was unaffected by acute hypoxia
 while the TPC for aerobic scope became shorter and more symmetrical. This
 change in TPC shape resulted from both the maximum aerobic scope and the
 optimal temperature for aerobic scope being reduced in hypoxia as
 predicted. 6. Following these results, we present a mathematical
 framework, which we call Temperature-Oxygen Performance Surfaces (TOPS),
 to quantify the interactive effects of temperature and oxygen on
 whole-organism performance in line with the HMTL hypothesis. This
 framework is transferrable across traits and levels of organization to
 allow predictions for how ectotherms will respond to novel combinations of
 temperature and other abiotic factors, providing a useful tool in a time
 of rapidly changing environmental conditions.
description: These data are from measures made on adult male common wall
 lizards (Podarcis muralis) at laboratories representing normoxia (low
 elevation, 432 m ASL) and hypoxia (high elevation, 2877 m ASL). Sprint
 performance data were collected using a 1-m racetrack outfitted with
 infrared sensors placed every 25-cm, with the highest speed for a 50-cm
 interval used in analysis. Carbon dioxide production data (resting and
 maximal metabolic rates) were measured with gas analyzers and calculated
 as the lowest average rate of carbon dioxide production in a 10-minute
 interval (mL CO2/min) and highest average rate of carbon dioxide
 production in a 15-second interval (mL CO2/min), respectively, using
 ExpeData software.
DOI: 10.5061/dryad.dr7sqvb1w
title: Glutathione and neodiosmin feedback sustain plant immunity

description: Plants have evolved a two-layer immune system comprising pattern-triggered
 immunity (PTI) and effector-triggered immunity (ETI) that is activated in
 response to pathogen invasion. Microbial patterns and pathogen effectors
 can be recognized by surface-localized pattern-recognition receptors
 (PRRs) and intracellularly localized nucleotide-binding leucine-rich
 repeat receptors (NLRs) to trigger PTI and ETI responses, respectively. At
 present, the metabolites activated by PTI and ETI and their roles and
 signalling pathways in plant immunity are not well understood. In this
 study, metabolomic analysis showed that ETI and PTI induced various
 flavonoids and amino acids and their derivatives in plants. Interestingly,
 both glutathione and neodiosmin content were specifically up-regulated by
 ETI and PTI, respectively, which significantly enhanced plant immunity.
 Further studies showed that glutathione and neodiosmin failed to induce a
 plant immune response in which PRRs/co-receptors were mutated. In
 addition, glutathione-reduced mutant gsh1 analysis showed that GSH1 is
 also required for PTI and ETI. Finally, we propose a model in which
 glutathione and neodiosmin are considered signature metabolites induced in
 the process of ETI and PTI activation in plants and further continuous
 enhancement of plant immunity in which PRRs/co-receptors are needed. This
 model is beneficial for an in-depth understanding of the closed-loop mode
 of the positive feedback regulation of PTI and ETI signals at the
 metabolic level.
DOI: 10.5281/zenodo.18401136
title: Probabilistic Mechanism Graphs for GWAS Gene Prioritization - External Validations

description: This release provides a complete, self-contained reproduction package for "Mechanism‑First Causal Graphs for Noncoding GWAS". It contains the scripts, processed result files, source code, and a step‑by‑step guide needed to reproduce the paper’s quantitative claims from processed data. The package highlights the mechanism‑graph implementation (noisy‑OR aggregation + correlation corrections), calibration and benchmark artifacts, and concise reproduction instructions.

Contents



Reproduction scripts: reproduce_paper_claims.py, helper scripts

Processed results: data/processed/* (locus summaries, calibration metrics, benchmark tables)

Source snapshot: mechanism-graph-source-2026-01-21.zip

Reproduction guide: DATA_REPRODUCTION_GUIDE.md, REPRODUCE.md

Results summary: reproduction_results_summary.json

License & citation: LICENSE, CITATION.cff


Key reproduced results (included in package)



Final calibration: ECE = 0.012 (per‑module ECE < 0.05)

Benchmark recall@20: 0.76 [0.71–0.81] vs L2G 0.58

CRISPR benchmark: AUPRC = 0.71 [0.67–0.75]

eQTL replication: 96.8% (exceeds claimed ≥78%)


Quick reproduction



Create environment: conda env create -f [environment.yml](http://_vscodecontentref_/6) && conda activate mechanism-gwas

Run reproduction: python scripts/reproduce_paper_claims.py

See full instructions: DATA_REPRODUCTION_GUIDE.md


Notes



Large raw/external data (>79 GB) are NOT included; processed inputs required for rapid reproduction are included.
DOI: 10.5281/zenodo.17798898
title: Probabilistic Mechanism Graphs for GWAS Gene Prioritization - External Validations

description: This release provides a complete, self-contained reproduction package for "Mechanism‑First Causal Graphs for Noncoding GWAS". It contains the scripts, processed result files, source code, and a step‑by‑step guide needed to reproduce the paper’s quantitative claims from processed data. The package highlights the mechanism‑graph implementation (noisy‑OR aggregation + correlation corrections), calibration and benchmark artifacts, and concise reproduction instructions.

Contents



Reproduction scripts: reproduce_paper_claims.py, helper scripts

Processed results: data/processed/* (locus summaries, calibration metrics, benchmark tables)

Source snapshot: mechanism-graph-source-2026-01-21.zip

Reproduction guide: DATA_REPRODUCTION_GUIDE.md, REPRODUCE.md

Results summary: reproduction_results_summary.json

License & citation: LICENSE, CITATION.cff


Key reproduced results (included in package)



Final calibration: ECE = 0.012 (per‑module ECE < 0.05)

Benchmark recall@20: 0.76 [0.71–0.81] vs L2G 0.58

CRISPR benchmark: AUPRC = 0.71 [0.67–0.75]

eQTL replication: 96.8% (exceeds claimed ≥78%)


Quick reproduction



Create environment: conda env create -f [environment.yml](http://_vscodecontentref_/6) && conda activate mechanism-gwas

Run reproduction: python scripts/reproduce_paper_claims.py

See full instructions: DATA_REPRODUCTION_GUIDE.md


Notes



Large raw/external data (>79 GB) are NOT included; processed inputs required for rapid reproduction are included.
DOI: 10.5061/dryad.1zcrjdfvh
title: Data from: Bateman gradients reflect variation in sexual selection in a species with dynamic sex roles

description: Bateman gradients, the slope of the regression of reproductive success on
 mating success, are among the most commonly reported measures of sexual
 selection. They are particularly insightful in species with reversed sex
 roles, where females are expected to be under sexual selection. We
 measured Bateman gradients in replicate experimental populations of the
 spermatophore gift-giving bushcricket Kawanaphila nartee (Orthoptera:
 Tettigoniidae). In this species, the operational sex ratio (OSR) and thus
 the sex competing for mates varies depending on the availability of pollen
 food resources: under pollen-limited regimens females are more
 competitive, whereas under pollen-rich regimens males are more
 competitive. We maintained populations in enclosures with either limited
 or supplemented pollen, and calculated Bateman gradients for males and
 females under both conditions. Bateman gradients were significantly
 positive in males, and the slope was steeper in pollen-supplemented
 populations where the OSR was more male-biased. Bateman gradients for
 females were shallow and nonsignificant regardless of pollen availability.
 Our results show that the strength of sexual selection on males can depend
 on environmental context. The lack of significant gradients among females
 may reflect experimental limitations on our ability to estimate Bateman
 gradients in female K. nartee.
description: 'cagesurvival.csv' - for each
 individual animal (id), the sex, cage number, and food treatment are
 recorded - under 'survival,' 1 means the
 animal survived, and 0 means it did not  
 'indboth.csv' - i.e. INDividual
 mating success for BOTH sexes - for each individual
 animal (id), the sex and food treatment are recorded -
 under 'obs,' the number of matings observed in the field is
 recorded - under 'gen,' the number of matings
 detected using microsatellites is recorded  
 'obsdata.csv' - for each cage on
 each night, the number of calling males (callers), matings, male
 rejections of females,   spermatophores present (spmt),
 and operational sex ratio (osr) are recorded - this is
 done at the start (early) and end (late) of nightly observations
 - treatment is also recorded for each cage
   'cagebg22-01-18.csv'
 - for each individual animal (id), the sex, food treatment, and
 cage number are recorded - the number of eggs (egg.no)
 is recorded for each female  - the wing area (w.area)
 and gamete mass (g.mass) are recorded for each male -
 the body mass (b.mass), pronotum width (p.width), ear size (e.size), and
 forelimb tibia length   (l.length) are recorded for
 both sexes - the highest number of mates from the
 indboth.csv file is recorded here - various
 standardised measures are recorded but are not pertinent (columns
 O-W) - starting in column X, standardised values are
 recorded - 'zsms' records z-standardised
 mating success (it's an acronym) -
 'msms' records mean-standardised mating success (also an
 acronym) - 'msrs' records mean-standardised
 reproductive success (you guessed it)
DOI: 10.5061/dryad.pg4f4qrss
title: Call combinations in chimpanzees: a social tool?

description: A growing body of evidence suggests the capacity for animals to combine
 calls into larger communicative structures is more common than previously
 assumed. Despite its cross-taxa prevalence, little is known regarding the
 evolutionary pressures driving such combinatorial abilities. One dominant
 hypothesis posits that social complexity and vocal complexity are linked,
 with changes in social structuring (e.g. group size) driving the emergence
 of ever-more complex vocal abilities, such as call sequencing. In this
 paper, we tested this hypothesis through investigating combinatoriality in
 the vocal system of the highly social chimpanzee. Specifically, we
 predicted combinatoriality to be more common in socially-driven contexts
 and in females and lower-ranked males (socially challenging contexts and
 socially challenged individuals respectively). Firstly, through applying
 methods from computational linguistics (i.e. collocation analyses), we
 built an objective repertoire of combinatorial structures in this species.
 Second, we investigated what potential factors influenced call combination
 production. We show that combinatoriality is predominant in i) social
 contexts vs. non-social contexts, ii) females vs. males and iii)
 negatively correlates with male rank. Together, these results suggest one
 function of combinatoriality in chimpanzees may be to help individuals
 navigate their dynamic social world. More generally, we argue these
 findings provide support for the hypothesised link between social and
 vocal complexity and can provide insight into the evolution of our own
 highly combinatorial communication system, language.
description: Call combinations recorded in the wild. Investigation of
 non-random combinations using collocation analyses. Investigation of
 socio-ecological factors influencing the production of combinations using
 GLMMs. 
description: Extraction of the data: Praat Analyses: R
DOI: 10.5061/dryad.9zw3r22hj
title: Parasitism shapes selection by drastically reducing host fitness and increasing host fitness variation

description: Determining the effects of parasites on host reproduction is key to
 understanding how parasites affect the underpinnings of selection on
 hosts. Although infection is expected to be costly, reducing mean fitness,
 infection could also increase variation in fitness costs among hosts, both
 of which determine the potential for selection on hosts. To test these
 ideas, we used a phylogenetically informed meta-analysis of 118 studies to
 examine how changes in the mean and variance in the outcome of
 reproduction differed between parasitized and non-parasitized hosts. We
 found that parasites had severe negative effects on mean fitness, with
 parasitized hosts suffering reductions in fecundity, viability, and mating
 success. Parasite infection also increased variance in reproduction,
 particularly fecundity and offspring viability. Surprisingly, parasites
 had similar effects on viability when either the male or female was
 parasitized. These results not only provide the first synthetic,
 comparative, and quantitative summary of the strong deleterious effects of
 parasites on host reproductive fitness, but also reveal a consistent role
 for parasites in shaping the opportunity for selection.
DOI: 10.5061/dryad.4j0zpc8fj
title: Anthropogenic noise and light alter temporal but not spatial breeding behavior in a wild frog

description: Increasing urbanization has led to large scale land-use changes, exposing
 persistent populations to drastically altered environments. Sensory
 pollutants, including low-frequency anthropogenic noise and artificial
 light at night (ALAN), are typically associated with urban environments
 and known to impact animal populations in a variety of ways. Both ALAN and
 anthropogenic noise can alter behavioral and physiological processes
 important for survival and reproduction, including communication and
 circadian rhythms. Although noise and light pollution typically co-occur
 in urbanized areas, few studies have addressed their combined impact on
 species’ behavior. Here we assessed how anthropogenic noise and ALAN can
 influence spatial and temporal variation in breeding activity of a wild
 frog population. By exposing artificial breeding sites inside a tropical
 rainforest to multiple sensory environments, we found that both
 anthropogenic noise and ALAN impact breeding behavior of túngara frogs
 (Engystomops pustulosus), albeit in different ways. Males arrived later in
 the night at their breeding sites in response to anthropogenic noise.
 ALAN, on the other hand, led to an increase in calling effort. We found no
 evidence that noise or light pollution either attracted frogs to or
 repelled frogs from breeding sites. Thus, anthropogenic noise may
 negatively affect calling males by shifting the timing of sexual
 signaling. Conversely, ALAN may increase the attractiveness of calling
 males. These changes in breeding behavior highlight the complex ways that
 urban multisensory pollution can influence behavior and suggest that such
 changes may have important ecological implications for the wildlife that
 are becoming increasingly exposed to urban multisensory pollution.
description: Datasets were collected by
 placing aritificial breeding sites within the tropical rainforest around
 Gamboa, Panamá. Using audio and video data, we collected data examining
 the presence/absence of frogs at breeding sites, the timing of breeding
 behavior, and multiple calling characteristics. All raw data was further
 processed in R, using the code provided. Additional information concerning
 methods can be found within the Methods section of our
 manuscript.
DOI: 10.5061/dryad.zgmsbccf7
title: The first records of Sea Star Wasting Disease in Crossaster papposus in Europe

description: Sea Star Wasting Disease (SSWD) refers to a suite of gross pathological
 signs observed in Asteroidea species. It presents to varying degrees as
 abnormal posture, epidermal ulceration, arm autotomy and eversion of
 viscera. We report observations of SSWD in the sunstar Crossaster
 papposus, the first observations of its kind in Europe. While the exact
 cause of SSWD remains unknown, studies have proposed pathogenic and
 environmental-stress pathways for disease outbreaks. Although the present
 observations do not support a precise aetiology, the presence of SSWD in a
 keystone predator may have wide reaching ecological and management
 implications.
description: Specimens of <em>C. papposus</em>
 (<em>n</em> = 12) were collected on an <em>ad
 hoc</em> basis from crab creels from around 20–25 m depth in the
 Irish Sea and returned to holding tanks at Queen's University Belfast
 Marine Laboratory, Portaferry in March 2022. 
 Observations were conducted each day until day 31 after capture.
 Mortality resulting from disease progression was recorded, with survival
 time measured in days since capture. A Kaplan–Meier survival curve
 produced for the month-long observation period based on
 time-to-death. The data was processed using R version
 4.1.2
description: Data was processed using R version 4.1.2
DOI: 10.5061/dryad.qv9s4mwhs
title: Neonate personality affects early-life resource acquisition in a large social mammal

description: This file contains the raw data files and R-scripts used for producing the
 final data sets analyzed in the paper: "Neonate personality affects
 early-life resource acquisition in a large social mammal". A full and
 detailed description of the methods can be found in the manuscript, or at
 request from the author (BA).  The R-scripts can be used to
 follow all the steps taken in producing the final data sets. The findings
 in the paper can be then reproduced by using the code provided in the
 supplementary materials (of the paper).   The file
 contains data taken from &gt;150 newborn fallow deer fawns (Dama
 dama), in two different cohorts. Data were taken at capture and recapture
 of these fawns, during their first weeks of life. During this period,
 fallow deer fawns adopt a hiding-strategy where they hide in the
 vegatation from potential predators. Furthermore, it contains time budget
 data taken at summer, when fawns were 1-2 months old, and at autumn, when
 fawns were 3-6 months old. The final file is a datafile that contains data
 on the days that fawns were spotted in a group of deer for the first time,
 after their hider-phase. We have provided a README.docx file, which
 contains additional descriptions of the raw data set and the variables it
 includes.
description: All data have been recorded during capture and recapture of
 newborn fawns, and during subsequent observations taken in the field in
 the sex months after. The fawns are part of a free-living population of
 fallow deer (Dama dama), living in the largest urban park in Europe,
 namely Phoenix Park in Dublin, Ireland.  Full details
 on the procedures are openly accessible in the paper ("Neonate
 personality affects early-life resource acquisition in a large social
 mammal"), which has led to the time budget part of this dataset. A
 previous paper has already provided details on the capture and recapture
 procedures and can be openly accessed here (https://doi.org/10.1111/1365-2435.13790).  The data were analysed by combinations  of generalized linear models and linear mixed-effect models, in R.
description: The data files can be accessed with any program that can open
 .csv files. Further description of the data set and the variables included
 are given in the README file, which can be opened with any software that
 can access .docx files. The scripts used to produce the final datasets are
 made in R-studio and can be run via R or R-studio. No additional packages
 are required for this particular script.
DOI: 10.5061/dryad.x0k6djhnk
title: Combined alignment fasta file used for the phylogenetic analysis of Micropsalliota

description: A new species of Micropsalliota is described from the tropical region of
 Maharashtra, India. The species is recognized on the basis of
 morphological details and its phylogenetic placement is determined by
 using of nrITS and nrLSU sequence data analyses. Micropsalliota
 pileocystidiata is characterised by its robust basidiomes covered by
 reddish-brown appressed fibrillose squamules, ellipsoid to amygdaliform
 basidiospores, pyriform pileocystidia and clavate, utriform to broadly
 utriform or sometimes ellipsoid cheilo- and pleurocystidia.
description: Sanger sequencing and curated sequences. File is viewable via any
 alignment viewer software like MEGA, Aliview, etc.
description: # Combined alignment fast file
 [https://doi.org/10.5061/dryad.x0k6djhnk](https://doi.org/10.5061/dryad.x0k6djhnk) ## Description of the data and file structure To generate the phylogenetic tree to understand the relationships. ## Access information Data was derived from the following sources: * NCBI