cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6m905qfvp
title: Data from: Evaluating Bayesian stable isotope mixing models of wild animal diet and the effects of trophic discrimination factors and informative priors

description: 1. Ecologists quantify animal diets using direct and indirect methods,
 including analysis of faeces, pellets, prey items and gut contents. For
 stable isotope analyses of diet, Bayesian stable isotope mixing models
 (BSIMMs) are increasingly used to infer the relative importance of food
 sources to consumers. Although a powerful approach, it has been hard to
 test BSIMM performance for wild animals because precise, direct dietary
 data are difficult to collect. 2. We evaluated the performance of BSIMMs
 in quantifying animal diets when using δ13C and δ15N stable isotope ratios
 from the feathers and red blood cells of common buzzard Buteo buteo
 chicks. We analysed mixing model outcomes with various trophic
 discrimination factors (TDFs), with and without informative priors, and
 compared these to direct observations of prey provisioned to chicks by
 adults at nests, using remote cameras.  3. Although BSIMMs with
 different TDFs varied markedly in their performance, the statistical
 package SIDER generated TDFs for both feathers and blood that resulted in
 model outputs that accorded well with direct observations of prey
 provisioning. Using feather TDFs derived from captive peregrines Falco
 peregrinus resulted in estimates of diet composition that were also
 similar to provisioned prey, though blood TDFs from the same study
 performed poorly. The inclusion of informative priors, based on
 conventional analysis of pellet and prey remains, markedly reduced model
 performance. 4. BSIMMs can provide accurate assessments of diet in wild
 animals. TDF estimates from the SIDER package performed well. The
 inclusion of informative priors from conventional methods in Bayesian
 mixing models can transfer biases into model outcomes, leading to
 erroneous results.
DOI: 10.5281/zenodo.18166829
title: Long-History PCA in a Dynamic Factor Model with Weak Loadings

description: To reproduce the results reported in “Long-History PCA in a Dynamic Factor Model with Weak Loadings,” users must download the accompanying data files and place them in the designated directory. Detailed instructions are provided in the ReadMe.txt file available on the journal’s website.
description: We have restricted public access to the dataset and released a revised version (https://doi.org/10.5281/zenodo.18166828) of the repository that contains only code for downloading the data from the authorized source (WRDS), in full compliance with the licensing terms.
DOI: 10.15468/dl.chvbur
title: Occurrence Download

description: A dataset containing 64973 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-73.44 46.36,-47.12 46.36,-47.12 60.71,-73.44 60.71,-73.44 46.36))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi"
 ]
}

 The dataset includes 64973 records from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001873-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g1jwstqmf
title: Individual and synergistic effects of male external genital traits in sexual selection

description: Male genital traits exhibit extraordinary inter-specific phenotypic
 variation. This remarkable and general evolutionary trend is widely
 considered to be the result of sexual selection. However, we still do not
 have a good understanding of whether or how individual genital traits
 function in different competitive arenas (episodes of sexual selection),
 or how different genital traits may interact to influence competitive
 outcomes. Here, we use an experimental approach based on high-precision
 laser phenotypic engineering to address these outstanding questions,
 focusing on three distinct sets of micron-scale external
 (non-intromittent) genital spines in male Drosophila kikkawai Burla
 (Diptera: Drosophilidae). Elimination of the large pair of spines on the
 male secondary claspers sharply reduced male ability to copulate, yet
 elimination of the other sets of spines on the primary and secondary
 claspers had no significant effects on copulation probability.
 Intriguingly, both the large spines on the secondary claspers and the
 cluster of spines on the primary claspers were found to independently
 promote male competitive fertilization success. Moreover, when large and
 small secondary clasper spines were simultaneously shortened in individual
 males, these males suffered greater reductions in fertilization success
 relative to males whose traits were altered individually, providing
 evidence for synergistic effects of external genital traits on
 fertilization success. Overall, the results are significant in
 demonstrating that a given genital trait (the large spines on the
 secondary claspers) can function in different episodes of sexual
 selection, and distinct genital traits may interact in sexual selection.
 The results offer an important contribution to evolutionary biology by
 demonstrating an understudied selective mechanism, operating via subtle
 trait interactions in a post-insemination context, by which genital traits
 may be co-evolving.
DOI: 10.5061/dryad.hh4j1f6
title: Data from: Genomic evidence for panmixia of eastern and western North American migratory monarch butterflies

description: Monarch butterflies are known for their spectacular annual migration in
 eastern North America, with millions of monarchs flying up to 4,500
 kilometers to overwintering sites in central Mexico. Monarchs also live
 west of the Rocky Mountains, where they travel shorter distances to
 overwinter along the Pacific Coast. Monarch numbers have recently
 dwindled, and monarch migration may be on the brink of extinction. It is
 often assumed that eastern and western monarchs form distinct evolutionary
 units that require specific protection, but genomic studies to support
 this notion are lacking. We used a tethered flight mill to show that
 migratory eastern monarchs have greater flight performance than western
 monarchs. However, analyzing more than 20 million SNPs in 43 monarch
 genomes, we found no evidence for genomic differentiation between eastern
 and western monarchs, suggesting the existence of one panmictic migratory
 population. Our genomic analysis also showed identical and low levels of
 genetic diversity, and a lack of singleton alleles, indicating a shared
 history of decline of eastern and western monarchs. Gene expression
 analysis of a subset of candidate genes during active flight revealed
 differential gene expression related to non-muscular motor activity. Our
 results demonstrate that North American monarchs form one panmictic and
 declining population, and that differences in migration distance and
 destination are therefore likely driven by environmentally induced
 differential gene expression. Our study indicates that eastern and western
 monarchs do not form distinct genetic populations, suggesting that
 preservation of eastern monarchs could potentially rescue western
 migration and vice versa.
description: Talla_East_West_North_America_Monarch_Genomics_Flight_And_Wing_Morphology_DataFlight trial and wing morphology dataTalla_East_West_North_America_Monarch_Genomics_Gene_Expression_DataGene expression data
DOI: 10.5061/dryad.12jm63xsp
title: Warming and pollutants interact to modulate octocoral immunity and shape disease outcomes

description: Warming environments can alter the outcome of host-parasite relationships
 with important consequences for biodiversity. Warming often increases
 disease risk, and interactions with other environmental factors can
 intensify impacts by modifying the underlying mechanisms, such as host
 immunity. In coastal ecosystems, metal pollution is a pervasive stressor
 that influences disease and immunity in many organisms. Despite the crisis
 facing coral reefs, which stems in part from warming-associated disease
 outbreaks, the impacts of metal pollutants on scleractinian and octocoral
 disease are largely unknown. We investigated how warming oceans and copper
 pollution affect host immunity and disease risk for two diseases of the
 abundant Caribbean octocoral, the sea fan Gorgonia ventalina. Field
 surveys across a sediment copper concentration gradient in Puerto Rico
 revealed that cellular immunity of sea fans increased by 12.6% at higher
 sediment copper concentrations, while recovery from multifocal purple
 spots disease (MFPS) tended to decrease. MFPS severity in the field
 increased at warmer sites. In a controlled laboratory experiment, sea fans
 were inoculated with live cultures of a labyrinthulid parasite to test the
 interactive effects of temperature and copper on immune activation. As in
 the field, higher copper induced greater immunity, but the factorial
 design of the experiment revealed that copper and temperature interacted
 to modulate the immune response to the parasite: immune cell densities
 increased with elevated temperature at lower copper concentrations, but
 not with high copper concentrations. Tissue damage was also greater in
 treatments with higher copper and warmer temperatures. Field and lab
 evidence confirm that elevated copper hinders sea fan immune defenses
 against damaging parasites. Temperature and copper influenced
 host-pathogen interactions in octocorals by modulating immunity, disease
 severity and disease recovery. This is the first evidence that metal
 pollution affects processes influencing disease in octocorals and
 highlights the importance of immune mechanisms in environmentally-mediated
 disease outbreaks. Although coral conservation efforts must include a
 focus on global factors, such as rapid warming, reducing copper and other
 pollutants that compromise coral health on a local scale may help corals
 fight disease in a warming ocean.
DOI: 10.5061/dryad.15dv41ns8
title: Clustering of the structures by using “snakes-&-dragons” approach, or correlation matrix as a signal

description: Biological, ecological, social, and technological systems are complex
 structures with multiple interacting parts, often represented by networks.
 Correlation matrices describing interdependency of the variables in such
 structures provide key information for comparison and classification of
 such systems. Classification based on correlation matrices could
 supplement or improve classification based on variable values, since the
 former reveals similarities in system structures, while the latter relies
 on the similarities in system states. Importantly, this approach of
 clustering correlation matrices is different from clustering elements of
 the correlation matrices, because our goal is to compare and cluster
 multiple networks – not the nodes within the networks. A novel approach
 for clustering correlation matrices, named “snakes-&-dragons,” is
 introduced and illustrated by examples from neuroscience, human
 microbiome, and macroeconomics.
DOI: 10.5061/dryad.pnvx0k6h3
title: Tolerance of novel toxins through generalized mechanisms: simulating gradual host shifts of butterflies

description: Organisms encounter a wide range of toxic compounds in their environments,
 from chemicals that serve anti-consumption or anti-competition functions,
 to pollutants and pesticides. Although we understand many detoxification
 mechanisms that allow organisms to consume toxins typical of their diet,
 we know little about why organisms vary in their ability to tolerate
 entirely novel toxins. We tested whether variation in generalized stress
 responses, such as antioxidant pathways, may underlie variation in
 reactions to novel toxins, and, if so, their associated costs. We used an
 artificial diet to present cabbage white butterfly caterpillars (Pieris
 rapae) with plant material containing toxins not experienced in their
 evolutionary history. Families that maintained high performance (e.g. high
 survival, fast development time, large body size) on diets containing one
 novel, toxic plant also performed well when exposed to two other novel
 toxic plants, consistent with a generalized response. Variation in
 constitutive (but not induced) expression of genes involved in oxidative
 stress responses was positively related to performance on the novel diets.
 While we did not detect reproductive trade-offs of this generalized
 response, there was a tendency to have less melanin investment in the
 wings, consistent of the role of melanin in oxidative stress responses.
 Taken together, our results support the hypothesis that variation in
 generalized stress responses, such as genes involved in oxidative stress
 responses, may explain the variation in tolerance to entirely novel toxins
 and may facilitate colonization of novel hosts and environments.
description: Please see methods of paper for details. Overview: caterpillars
 were reared on artificial diets containing novel plant material and
 performance and gene expression assessed across 12 family groups. The
 dataset allows tests of predictions that a) performance will be correlated
 across toxic diets, b) variation in constitutive or induced
 expression of genes involved in oxidative stress responses will correlate
 with performance on novel toxic diets, and c) variation in performance on
 novel toxic diets will come with life history trade-offs. Additional data
 are included on consumption rates of each diet, dose-response to
 increasing concentrations of novel plant material for one of the three
 diets, and total egg production of founding mothers for each family group.
 This file is the raw data from all experiments included in the
 paper.
description: Please see methods of paper and "key" tab
DOI: 10.5061/dryad.63xsj3tz2
title: Susceptibility of Eucalyptus hybrid clones to Botryosphaeria canker in Uganda

description: The study assessed susceptibility of the nine commonly grown Eucalyptus
 clones to Neofusicoccum species associated with Botryosphaeria canker in
 Uganda. The inoculation trials indicated that susceptibility of Eucalyptus
 hybrids differed significantly (p=0.000), clones GU609, GU7, GC578, and
 GC796 exhibiting a higher tolerance than GC784, GC550, GU8, GC514 and
 GC540. The results further revealed that N. parvum was more pathogenic
 than N. kwambonambiense. The generated information can be exploited by
 expanding the growing of tolerant hybrids in areas with high
 Botryosphaeria canker disease pressure.
description: This sequence data was generated by Amplification of the Internal
 transcribed spacer (ITS) region. Sequences GN1 to GN5 were generated
 during the current study. The other sequences were obtained from
 NCBI genebank. GN1 - GN3 (Neofusicoccum
 parvum) GN 4 (Neofusicoccum sp). GN5
 (Neofusicoccum kwambonambiense)
description: These are Botryosphaeriace fungal sequences
DOI: 10.34740/kaggle/dsv/14642688
title: Booru.org Top Leaderboard
DOI: 10.5281/zenodo.18393759
title: pre_workshop_responses_aggregated.csv
DOI: 10.5281/zenodo.18393760
title: pre_workshop_responses_aggregated.csv
DOI: 10.5061/dryad.tx95x69sc
title: Fear the reaper: ungulate carcasses may generate an ephemeral landscape of fear for rodents

description: Animal carcasses provide an ephemeral pulse of nutrients for scavengers
 that utilize them. Carcass sites can increase species interactions and/or
 ephemeral, localized landscapes of fear for prey within the vicinity. Few
 studies have applied the landscape of fear to carcasses. Here we use a
 mass die-off of reindeer caused by lightning in Norway to test whether
 rodents avoided larger scavengers (e.g. corvids and fox). We used the
 presence and abundance of faeces as a proxy for carcass use over the
 course of two years and found that rodents showed the strongest avoidance
 towards changes in raven abundance (β = -0.469, SE = 0.231, p-value =
 0.0429), but not fox, presumably due to greater predation risk imposed by
 large droves of raven. Moreover, the emergence of rodent occurrence within
 the carcass area corresponded well with the disappearance of raven during
 the second year of the study. We suggest that carcasses have the potential
 to shape the landscape of fear for prey, but that the overall effects of
 carcasses on individual fitness and populations of species ultimately
 depends on the carcass regime, e.g., carcass size, count, and areal
 extent, frequency, and the scavenger guild. We discuss conservation
 implications and how carcass provisioning and landscapes of fear could be
 potentially used to manage populations and ecosystems, but that there is a
 gap in understanding that must first be bridged.
DOI: 10.5061/dryad.vdncjsxpz
title: Pojected temperature rise for 2040, 2060, 2080 and 2100, considering NOAA's climate model

description: The data provided is the projected temperature rise for 2040, 2060, 2080
 and 2100, considering the climate model from the NOAA’s (National Oceanic
 Atmospheric Administration) Geophysical Fluid Dynamics Laboratory GFDL-CM3
 under three Representative Concentration Pathway (RCP) scenarios, which
 are named for the approximate radiative forcing in year 2100: the lower
 forcing scenario RCP 2.6, a moderate scenario RCP 6.0 and the higher
 forcing scenario RCP 8.5
DOI: 10.5061/dryad.p8cz8w9k3
title: Data from: Flower phenology as a disruptor of the fruiting dynamics in temperate oak species

description: Many perennial plants display masting, i.e., fruiting with strong
 interannual variations, irregular and synchronized between trees within
 the population. Here, we tested the hypothesis that the early flower
 phenology in temperate oak species promotes stochasticity into their
 fruiting dynamics, which could play a major role in tree reproductive
 success. From large field monitoring network, we compared the pollen
 phenology between temperate and Mediterranean oak species. Then, focusing
 on temperate oak species, we explored the influence of the weather around
 the time of bud-burst and flowering on seed production, and simulated with
 a mechanistic model the consequences an evolutionary shifting of flower
 phenology would have on fruiting dynamics. Temperate oak species release
 pollen earlier in the season than Mediterranean oak species. Such early
 flowering in temperate oak species results in pollen being often released
 during unfavorable weather conditions and resulting in frequent
 reproductive failure. If pollen release was delayed due to natural
 selection, fruiting dynamics would exhibit much reduced stochastic
 variation. We propose that early flower phenology might be adaptive by
 making mast-seeding years rare and unpredictable, which would greatly help
 controlling the dynamics of seed consumers.
DOI: 10.5061/dryad.sbcc2fr23
title: Supplemental figures and tables of a European multicenter validation study of the External Genitalia Score

description: Context: Standardized description of external genitalia is needed in the
 assessment of children with atypical genitalia. Objectives: To validate
 the External Genitalia Score (EGS), to present reference values for
 preterm and term babies up to 24 months and correlate obtained scores with
 anogenital distances (AGDs). Design, Setting: A European multicentre (n=8)
 validation study  was conducted from 07/2016 until 07/2018.
 Patients and Methods: EGS is based on the external masculinization score
 but uses a gradual scale from female to male (range 0-12) and terminology
 appropriate for both sexes. The reliability of EGS and AGD’s were
 determined by the interclass correlation coefficient (ICC).
 Cross-sectional data were obtained in 686 term (0-24 months), and 181
 preterm babies and 111 babies with atypical genitalia. Results: ICC of EGS
 in typical and atypical genitalia is excellent and good. Median EGS (10th
 - 90th centile) in males &lt; 28 weeks gestation is 10 (8.6-11.5); in
 males 28-32 weeks 11.5 (9.2-12); in males 33-36 weeks 11.5 (10.5-12) and
 in full-term males 12 (10.5-12). In all female babies, EGS is 0 (0-0). The
 mean (SD) AGDl/u is 0.45 (0.1), with significant difference between AGDl/u
 in males 0.49 (0.1) and females 0.39 (0.1) and in-between values in DSD
 0.43 (0.1). AGDl/u correlates with EGS in males with typical genitalia and
 in  atypical genitalia. Conclusions: EGS is a reliable and valid
 tool to describe external genitalia in premature and term babies up to 24
 months. EGS correlates with AGDl/u in males. It facilitates standardized
 assessment, clinical decision-making and multicenter research.
DOI: 10.7910/dvn/wqpt3d
title: Replication Data for: How Early Morning Classes Change Academic Trajectories: Evidence from a Natural Experiment

description: Data Availability Statement

The data used in this study are not publicly available due to privacy restrictions and data use agreements. The authors accessed restricted administrative data under a data use agreement with Purdue University that prohibits sharing the data with third parties. Researchers interested in accessing the data may apply directly through Institutional Data Analytics + Assessment at Purdue University. Information on the application process is available at https://www.purdue.edu/idata/contact/, and inquiries may be directed to idata@purdue.edu.

Anthony Yim
description: Stata do file is included here.