cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jm63xsjf9
title: Data from: Hidden variable models reveal the effects of infection from changes in host survival

description: The impacts of disease on host vital rates can be demonstrated using
 longitudinal studies, but these studies can be expensive and logistically
 challenging. We examined the utility of hidden variable models to infer
 the individual effects of infectious disease from population-level
 measurements of survival when longitudinal studies are not possible. Our
 approach seeks to explain temporal deviations in population-level survival
 after introducing a disease causative agent when disease prevalence cannot
 be directly measured by coupling survival and epidemiological models. We
 tested this approach using an experimental host system (Drosophila
 melanogaster) with multiple distinct pathogens to validate the ability of
 the hidden variable model to infer per-capita disease rates. We then
 applied the approach to a disease outbreak in harbor seals (Phoca
 vituline) that had data on observed strandings but no epidemiological
 data. We found that our hidden variable modeling approach could
 successfully detect the per-capita effects of disease from monitored
 survival rates in both the experimental and wild populations. Our approach
 may prove useful for detecting epidemics from public health data in
 regions where standard surveillance techniques are not available and in
 the study of epidemics in wildlife populations, where longitudinal studies
 can be especially difficult to implement.
description: Fly survival data was collected from an experimental design that
 monitored daily survival in populations of flies that were challenged with
 the Drosophila C virus (DCV) and Drosophila X virus (DXV).
 Seal stranding data was digitized from an existing report by
 Brasseur, "Stranding and Rehabilitation in Numbers: Population
 development and stranding data on the Dutch coasts 1990-2016". 
 Surveys covered the coastline of the Dutch Wadden Sea and nearby
 areas.
description: JAGS (https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/) and R (https://cran.r-project.org/) need to be installed to reproduce these analyses.
DOI: 10.5061/dryad.fqz612jw9
title: Data for: Multi-omics analysis identifies symbionts and pathogens of blacklegged ticks (Ixodes scapularis) from a Lyme disease hotspot in southeastern Ontario, Canada

description: Ticks in the family Ixodidae are recognized as important vectors of
 zoonoses including Lyme disease (LD), which is caused by spirochete
 bacteria from the Borreliella (Borrelia) burgdorferi sensu lato (Bbsl)
 complex. The blacklegged tick (Ixodes scapulars) continues to expand
 across Canada, creating hotspots of elevated LD risk at the
 leading edge of its expansion range. Current efforts to understand the
 risk of pathogen transmission associated with I. scapularis in Canada
 focus primarily on targeted screens, while variation in the tick
 microbiome remains poorly understood. Using multi-omics consisting of 16S
 metabarcoding and ribosome-depleted, whole-shotgun RNA transcriptome
 sequencing, we examined the microbial communities associated with adult I.
 scapularis (N = 32), sampled from four tissue types (whole tick, salivary
 glands, midgut, and viscera) and three geographical locations within an LD
 hotspot near Kingston, Ontario. The communities consisted of both
 endosymbiotic and known or potentially pathogenic microbes, including RNA
 viruses, bacteria, and a Babesia sp. intracellular parasite. We show that
 β-diversity is significantly higher between individual tick salivary gland
 and midgut bacterial communities, compared to whole ticks; while linear
 discriminant analysis (LDA) effect size (LEfSe) determined that the three
 potentially pathogenic bacteria detected by V4 16S rDNA sequencing were
 also discriminatory for dissected tissues only, including a Borrelia from
 the Bbsl complex, Borrelia miyamotoi, and Anaplasma phagocytophilum.
 Importantly, we find co-infection of I. scapularis by multiple microbes,
 in contrast to diagnostic protocols for LD, which typically focus on
 infection from a single pathogen of interest (B. burgdorferi sensu
 stricto).
description: See methods in paper, supplementary material, and README.md
 file. Latest version of the analysis pipeline available
 on GitHub: https://github.com/damselflywingz/tick_microbiome A Small Read Archive of this sequencing data is available on GenBank under Accession: SRR17194087 - 16S of Ixodes: 2016-2017 A Sequence Read Archive of this sequencing data is available on GenBank under Accession: SRR17194086
description: All code is based on the dada2 pipeline in R, which uses
 text-based files.
DOI: 10.5061/dryad.ht76hdrkc
title: Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity

description: The expansion of DNA trinucleotide repeats (TRs) beyond a threshold often
 results in neurodegenerative diseases in humans. The mechanisms causing
 these expansions remain unknown, although the tendency of TR ssDNA to
 self-associate into hairpins that slip along their length is widely
 presumed to be related. Here we apply single molecule FRET (smFRET)
 experiments and molecular dynamics simulations to determine conformational
 stabilities and slipping dynamics for CAG, CTG, GAC, and GTC hairpins. By
 developing novel analysis approaches for states with closely spaced FRET
 efficiencies along with improved transition detection algorithms, we
 determined the kinetic slipping schemes for these hairpins. Tetraloops are
 favored in CAG (89%), CTG (89%) and GTC (69%) while GAC favors triloops.
 We also determined that TTG interrupts near the loop in the CTG hairpin
 stabilize the hairpin against slipping (as do CAA substitutions in CAG
 hairpins). The different loop stabilities have implications for
 intermediate structures that may form when TR-containing duplex DNA opens.
 Opposing hairpins in the (CAG) ∙ (CTG) duplex would have matched stability
 whereas opposing hairpins in a (GAC) ∙ (GTC) duplex would have unmatched
 stability. This unmatched stability would introduce mechanical stress or
 frustration in the (GAC) ∙ (GTC) opposing hairpins that would be absent in
 (CAG) ∙ (CTG) structures. Given the biological observation that the CAG
 and CTG TR can undergo large, disease-related expansion whereas the GAC
 and GTC sequences do not, the mechanical stability differences we have
 identified can inform and constrain models of the expansion mechanisms of
 TR regions.
description: Single molecule FRET data from total internal reflection
 microscope
DOI: 10.5061/dryad.3j9kd51nq
title: Data from: A rallid ballad: Communal signaling is correlated with year-round territoriality in the most duet-rich family of birds (Gruiformes: Rallidae)

description: Duetting, in which two or more individuals call in coordinated unison, is
 common in birds, yet most research investigating the function of avian
 duets has focused only on oscine passerines. However, we have discovered
 that duetting occurs in 61 species (59%) in the family Rallidae (rails),
 one of the highest known rates in any bird clade, and that rail duets are
 also significantly associated with year-round territoriality and habitat
 type. We applied a comparative approach to study the occurrence of
 duetting relative to socio-ecological traits and call properties in 103
 rail species, with the prediction that duetting rails produce
 low-frequency calls that spread well over short distances in densely
 vegetated habitats. Using a model correcting for phylogenetic signal, we
 found that duetting is the ancestral state in Rallidae, and that duetting
 rails show a trending effect for being sedentary and non-migratory.
 Contrary to our predictions, there was no significant correlation between
 rail duetting and social bond length, breeding system, breeding latitude
 from the equator, or sexual dimorphism, as year-round territoriality and
 forest or heterogeneous habitats were the strongest predictors of duets.
 Despite the prevalence of duetting in Rallidae, few studies have tested
 duet functions such as territory defense in this family, and our
 comparative phylogenetic study lays the groundwork for future research, as
 little remains known about the behavioral ecology and vocal interactions
 of many rails.
description: The data in this dataset include measurements obtained from sound
 recordings downloaded from the Macaulay Library of the Cornell Lab of
 Ornithology (http://macaulaylibrary.org/) and from Xeno-Canto
 (http://xenocanto.org/) that were processed in Raven Pro Version 1.5.1
 (Center for Conservation Bioacoustics 2014). In the related Zenodo
 Software dataset are one NEXUS and one TRE file of 103 species in Rallidae
 that we generated in FigTree Version 1.4.2
 (https://github.com/rambaut/figtree), and three R scripts that we
 generated and processed in R Studio Version 1.4.1 (R Core Team
 2020).
description: R Studio Version 1.4.1 or newer is required to open the R scripts
 in the Zenodo Software dataset, and FigTree Version 1.4.2 is required to
 visualize the NEXUS file (RallidFigTree) and TRE file (RallidTree) from
 Zenodo. Microsoft Excel is sufficient to open the comma-separated (CSV)
 files in the Dryad dataset.
DOI: 10.5061/dryad.rjdfn2zfr
title: Data for: Behavioral differences underlie toxicity and predation variation in blooms of Prymnesium parvum

description: Much of the evolutionary ecology of toxic algal blooms (TABs) remains
 unclear, including the role of algal toxins in the adaptive ‘strategies’
 of TAB-forming species. Most eukaryotic TABs are caused by mixotrophs that
 augment autotrophy with organic nutrient sources, including competing
 algae (intraguild predation). We leverage the standing diversity of TABs
 formed by the toxic, invasive mixotroph Prymnesium parvum to identify
 cell-level behaviors involved in toxin-assisted predation using direct
 observations as well as comparisons between genetically distinct low- and
 high-toxicity isolates. Our results suggest that P. parvum toxins are
 primarily delivered at close range and promote subsequent prey
 capture/consumption. Surprisingly, we find opposite chemotactic
 preferences for organic (prey-derived) and inorganic nutrients between
 differentially toxic isolates, respectively, suggesting behavioral
 integration of toxicity and phagotrophy. Variation in toxicity may
 therefore reflect broader phenotypic integration of key traits that
 ultimately contribute to the remarkable flexibility, diversity, and
 success of invasive populations.
description: All data files are in .CSV format.
DOI: 10.15468/dl.vhrftx
title: Occurrence Download

description: A dataset listing the 485 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((1.64794 44.72586,1.6456 44.72247,1.64287 44.71872,1.64062 44.71167,1.6425 44.69955,1.65086 44.69326,1.66278 44.6911,1.67396 44.69138,1.67791 44.69674,1.68552 44.70585,1.68927 44.7205,1.68946 44.73177,1.69132 44.74208,1.67925 44.74909,1.66076 44.75192,1.64659 44.74625,1.64137 44.73507,1.64794 44.72586))",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 485 records were derived from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003305-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mw6m9060s
title: Data from: Scratch-AID, a deep learning-based system for automatic detection of mouse scratching behavior with high accuracy

description: Mice are the most commonly used model animals for itch research and for
 the development of anti-itch drugs. Most laboratories manually quantify
 mouse scratching behavior to assess itch intensity. This process is
 labor-intensive and limits large-scale genetic or drug screenings. In this
 study, we developed a new system, Scratch-AID (Automatic Itch Detection),
 which could automatically identify and quantify mouse scratching behavior
 with high accuracy. Our system included a custom-designed videotaping box
 to ensure high-quality and replicable mouse behavior recording and a
 convolutional recurrent neural network trained with frame-labeled mouse
 scratching behavior videos, induced by nape injection of chloroquine. The
 best-trained network achieved 97.6% recall and 96.9% precision on
 previously unseen test videos. Remarkably, Scratch-AID could reliably
 identify scratching behavior in other major mouse itch models, including
 the acute cheek model, the histaminergic model, and the chronic itch
 model. Moreover, our system detected significant differences in scratching
 behavior between control and mice treated with an anti-itch drug. Taken
 together, we have established a novel deep learning-based system that
 could replace manual quantification for mouse scratching behavior in
 different itch models and for drug screening. This dataset includes all
 videos for the study to establish a novel deep learning-based system for
 automatic mouse scratching behavior quantification.
description: # Data from: Scratch-AID, a deep learning-based system for automatic
 detection of mouse scratching behavior with high accuracy ## Description
 of the Data and file structure In the videos.zip folder, there are five
 subfolders: 1. Training_test_videos subfolder: This folder includes 40
 videos for training the model, V1-V32 are videos for training, and V33-V40
 are videos for validation and testing. 2. test_videos_SADBE_chronic_itch
 subfolder: This folder includes 9 videos V1-V9 for testing model
 performance in chronic itch. 3. test_videos_histamine_nape subfolder: This
 folder includes 4 videos V1-V4 for testing model performance in
 histamine-induced acute itch in the nape. 4. test_videos_CQ_cheek
 subfolder: This folder includes 7 videos V1-V7 for testing model
 performance in CQ-induced acute itch in the cheek. 5.
 test_videos_anti-itch subfolder: This folder includes two subfolders: In
 the anti-itch subfolder, there are 6 videos V1-V6; and in the control
 subfolder, there are 7 videos V1-V7. These videos are for testing model
 performance in an anti-itch drug screening paradigm.  ## Sharing/Access
 Information NA
DOI: 10.5061/dryad.ksn02v77x
title: Mechanical nanolattices printed using nanocluster-based photoresists

description: Natural materials exhibit emergent mechanical properties due to their
 nanoarchitected, nanocomposite structures with optimized hierarchy,
 anisotropy and nanoporosity. Fabrication of such complex systems is
 currently challenging because high-quality 3D nanoprinting is mostly
 limited to simple, homogenous materials. We report a strategy for the
 rapid nanoprinting of complex structural nanocomposites using metal
 nanoclusters. These ultrasmall, quantum-confined nanoclusters function as
 highly sensitive two-photon activators, and simultaneously serve as
 precursors for mechanical reinforcements and nanoscale porogens.
 Nanocomposites with complex 3D architectures are printed, as well as
 structures with tunable, hierarchical and anisotropic nanoporosity.
 Nanocluster-polymer nanolattices exhibit high specific strength, energy
 absorption, deformability, and recoverability. This framework provides a
 generalizable, versatile approach for the use of photoactive nanomaterials
 in additive manufacturing of complex systems with emergent mechanical
 properties.
DOI: 10.6076/d1m889
title: Data for: Differences in interference processing and frontal brain function with climate trauma from California’s deadliest wildfire

description: As climate change accelerates extreme weather disasters, the mental health
 of the impacted communities is a rising concern. In a recent study of 725
 Californians, we showed that individuals that were directly exposed to
 California’s deadliest wildfire, the Camp Fire of 2018, had significantly
 greater chronic symptoms of post-traumatic stress disorder, anxiety and
 depression than control individuals not exposed to the fires. Here, we
 study a subsample of these individuals: directly exposed (n = 27),
 indirectly exposed (who witnessed the fire but were not directly impacted,
 n = 21), versus age and gender-matched non-exposed controls (n = 27). All
 participants underwent cognitive testing with synchronized
 electroencephalography (EEG) brain recordings. In our sample, 67% of the
 individuals directly exposed to the fire reported having experienced
 recent trauma, while 14% of the indirectly exposed individuals and 0% of
 the non-exposed controls reported recent trauma exposure. Fire-exposed
 individuals showed significant cognitive deficits, particularly on the
 interference processing task and greater stimulus-evoked fronto-parietal
 activity as measured on this task. Across all subjects, we found that
 stimulus-evoked activity in left frontal cortex was associated with
 overall improved interference processing efficiency, suggesting the
 increased activity observed in fire-exposed individuals may reflect a
 compensatory increase in cortical processes associated with cognitive
 control. To the best of our knowledge, this is the first study to examine
 the cognitive and underlying neural impacts of recent climate trauma.
DOI: 10.5061/dryad.02v6wwq6j
title: Vermivora location data

description: Aim: Climate change is affecting the distribution of species and
 subsequent biotic interactions, including hybridization potential. The
 imperiled Golden-winged Warbler (GWWA) competes and hybridizes with
 Blue-winged Warblers (BWWA), which may threaten the persistence of GWWA
 due to introgression. We examined how climate change is likely to alter
 the breeding distributions and potential for hybridization between GWWA
 and BWWA.  Location: North America  Methods: We used
 GWWA and BWWA occurrence data to model climatically suitable conditions
 under historical and future climate scenarios. Models were parameterized
 with 13 bioclimatic variables and 3 topographic variables. Using ensemble
 modeling, we estimated historical and modern distributions, as well as
 projected distribution under six future climate scenarios. We quantified
 breeding distribution area, position of, and amount of overlap
 between GWWA and BWWA distributions under each climate scenario. We
 summarized the top explanatory variables in our model to predict
 environmental parameters of the distributions under future climate
 scenarios relative to historical climate. Results: GWWA and BWWA
 distributions are projected to substantially change under future climate
 scenarios. GWWA are projected to undergo the greatest change; the area of
 climatically suitable breeding season conditions is expected to shift
 north to northwest and range contraction is predicted in five out of six
 future climate scenarios. Climatically suitable conditions for BWWA
 decreased in four of the six future climate scenarios, while the
 distribution is projected to shift east. A reduction in overlapping
 distributions for GWWA and BWWA is projected under all six future climate
 scenarios.  Main Conclusions: Climate change is expected to
 substantially alter the area of climatically suitable conditions for GWWA
 and BWWA, with the southern portion of the current breeding ranges likely
 to become climatically unsuitable. However, interactions between
 BWWA and GWWA are expected to decline with the decrease in overlapping
 habitat, which may reduce the risk of genetic introgression.
DOI: 10.5061/dryad.0cfxpnw69
title: Data from: Optimising the hatching success of artificially incubated eggs for use in a conservation program for the western saw-shelled turtle (Myuchelys bellii)

description: Artificial incubation of eggs and the release of hatchlings into the wild
 is a common conservation intervention designed to augment threatened
 turtle populations. We investigate a range of incubation temperatures to
 establish an optimal temperature for maximum hatching success of western
 saw-shelled turtle (Myuchelys bellii) eggs. We report on the influence of
 incubation temperature on incubation duration and hatching success and
 describe two experimental incubation methods which, for the same
 incubation temperature, resulted in 77% and 97% hatching success,
 respectively. Eggs were incubated at constant temperatures (27°C, 28°C and
 29°C) to determine the influence of temperature on incubation period,
 hatchling morphology and external residual yolk. Incubation duration was
 negatively correlated with incubation temperature. We report on the
 morphology of eggs and hatchlings and show that their dimensions are
 positively correlated with maternal adult size and mass. A constant
 incubation temperature of 27°C produced the highest hatching success and
 smallest external residual yolk on hatching and is therefore recommended
 for incubation of eggs for population reinforcement programs. Our study is
 the first to optimise artificial incubation procedures for M. bellii and
 will be a valuable resource for M. bellii and other threatened freshwater
 turtle conservation initiatives.
description: Methods used for collection/generation of data are described in
 the publication: Streeting LM, Bower DS, Dillon ML,
 Spark P, Gough M, Skidmore A, McDonald PG, Delaney H, Burns A, Watson S,
 Dissanayake DSB, Georges A and McKnight DT (2022). Optimising the hatching
 success of artificially incubated eggs for use in a conservation program
 for the western saw-shelled turtle (<em>Myuchelys
 bellii</em>). Australian Journal of Zoology.
DOI: 10.15468/dl.aet8pn
title: Occurrence Download

description: A dataset containing 689 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Austria",
 "DatasetKey is one of (MVZ Mammal Collection (Arctos), ZOBODAT (Zoological Botanical Database), ZMUO Common vertebrate collection, University of Michigan Museum of Zoology, Division of Mammals, Roadkill, Naturalis Biodiversity Center (NL) - Mammalia, Collection Mammalia SMF, AMNH Mammal Collections, Biodiversitätsdatenbank Salzburg)",
 "OccurrenceStatus is Present",
 "TaxonKey is Mus musculus"
 ]
}

 The dataset includes 689 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003316-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.