cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.66t1g1k4t
title: Data from: Protecting great apes from disease: compliance with measures to reduce anthroponotic disease transmission

description: Based on an international sample of past (N=420) and potential future
 visitors (N=569) to wild great ape tourism sites in Africa, we used an
 online questionnaire to characterise visitors’ practices, assess
 expectations (e.g., about proximity to great apes) and identify key
 factors related to potential compliance with disease mitigation measures.
 This was implemented adapting a framework from health literature (the
 Health Belief Model; HBM), particularly focused on reducing COVID-19
 transmission at an early stage of the pandemic.
description: During early stages of the COVID-19 pandemic (data collected from
 the 19th January to 27th February 2021), an online questionnaire was used
 to gather information on potential uptake of disease mitigation measures
 among visitors to wild African great ape tourism sites. Potential
 participants were invited to fill in the questionnaire if they had
 visited, or were interested in visiting, wild great ape tourism
 destinations in Africa and were aged 18 or older. A
 copy of the English version of the final questionnaire is available in
 Appendix I of the published manuscript.
DOI: 10.5061/dryad.dfn2z354x
title: Data for: Habitat functionality: integrating environmental and geographic space in niche modelling for conservation planning

description: Niche modelling is typically used to assess the effects of anthropogenic
 land use and climate change on species distributions and to inform spatial
 conservation planning. These models focus on the suitability of local
 biotic and abiotic conditions for a species in environmental space
 (E-space). Although movements also affect species occurrence, efforts to
 formally integrate geographic space (G-space) into niche modelling have
 been hindered by the lack of comprehensive theoretical
 frameworks.  We propose the 'functional habitat'
 framework to define areas that are simultaneously of high-quality in
 E-space and functionally connected to other suitable habitat in G-space.
 Originating in metapopulation ecology, approaches have been developed to
 assess the amount of suitable connected habitat, based on the proximity
 between pairs of locations. Using network theory, which operates in
 topological space (T-space, defined by a network), we extended these
 metapopulation approaches to integrate movement constraints in G-space
 with niche modelling in E-space.  We demonstrate the functional
 habitat framework using empirical data (GPS-tracking and population
 monitoring) throughout the European wild mountain reindeer (Rangifer t.
 tarandus) distribution range. We show that functional habitat outperforms
 traditional suitability in explaining the species' distribution. This
 approach integrates effects from habitat loss and fragmentation for
 spatial conservation planning and avoids overemphasizing small,
 inaccessible areas with locally suitable habitat. The functional habitat
 framework formally integrates biotic, abiotic, and movement constraints in
 niche modeling using network theory, thus opening a wide range of
 applications in spatial conservation planning.
description: The data and analysis are supporting the paper: 'Habitat
 Functionality: integrating environmental and geographic space in niche
 modelling for conservation planning', see the description
 therein. The repository contains Data and Scripts for
 I. the functional habitat computation and II. the comparison of
 functionality and suitability for reindeer distribution.
 I. Functional habitat computation<br>1) RSF & SSF
 maps (data/rsf_sum.tif & data/ssf_sum.tif)<br>2) The study
 areas (data/reindeer_areas.shp)<br>3) Data preparation in R
 (data_prep.r)<br>4) Habitat functionality computation in Julia
 (functionality_computation.jl) II. Functionality vs.
 suitability comparison<br>1) data frame with data
 (data/rastdf.rda)<br>2) model fitting script
 (model_comparison.r)
DOI: 10.5061/dryad.g4f4qrft2
title: Timescale reverses the relationship between host density and infection risk

description: Host density shapes infection risk through two opposing phenomena. First,
 when infective stages are subdivided among multiple hosts, greater host
 densities decrease infection risk through “safety in numbers”. Hosts,
 however, represent resources for parasites, and greater host availability
 also fuels parasite reproduction. Hence, host density increases infection
 risk through “density-dependent transmission”. Theory proposes that these
 phenomena are not disparate outcomes but occur over different timescales.
 That is, higher host densities may reduce short-term infection risk, but
 because they support parasite reproduction, may increase long-term risk.
 We tested this theory in a zooplankton-disease system with laboratory
 experiments and field observations. Supporting theory, we found that
 negative density-risk relationships (‘safety in numbers’) sometimes
 emerged over short timescales, but these relationships reversed to
 ‘density-dependent transmission’ within two generations. By allowing
 parasite numerical responses to play out, time can shift the consequences
 of host density, from reduced immediate risk to amplified future risk.
description: All methods related to the present
 data can be found in the methods and supplementary materials of Stewart
 Merrill et al. 2022 Proc R Soc B.
description: All files can be opened in Excel and contain a
 "metadata" tab with additional information regarding the column
 headers and notes for interpretation. The files (which follow the order of
 the methods and results in the manuscript) include:
 <strong>master_SIN_lab infection
 prevalence.xlsx:</strong> The dataset containing infection statuses
 of Daphnia to experimentally assess how host density influences infection
 risk over time. <strong>master_SIN_spore
 counts.xlsx: </strong>The dataset containing spore counts following
 Metschnikowia reproduction to assess the parasite's numerical
 response over time.
 <strong>master_SIN_microscopic evaluations.xlsx:
 </strong>The dataset in which individual Daphnia were assessed under
 high magnification to groundtruth assumptions regarding safety in
 numbers. <strong>master_SIN_field density and
 prevalence.xlsx</strong>: The dataset containing field infections
 used to explore safety in numbers and density-dependent transmission in
 the natural environment.
DOI: 10.5061/dryad.ghx3ffbrw
title: Data for: Capturing complex interactions in disease ecology with simplicial sets

description: Here we provide archived code for: Code for Capturing Complex Interactions
 in Disease Ecology with Simplicial Sets. Ecology Letters. The code
 provided can be used to generate the figures used in the manuscript as
 well as to generate appendix 3 in the supplementary materials. In the
 paper, we describe how higher-order network approaches can be applied in
 disease ecology research. We explain what simplicial sets are; why their
 use would be beneficial in different subject areas; where these areas are:
 social, transmission, movement/spatial and ecological networks; and when
 using them would help most in each context. To demonstrate their
 application, we develop a novel approach to identify how pathogens persist
 within a host population (see code for Appendix 3 in this repository). We
 also provide an overview of how to use simplicial sets, highlighting
 specific metrics, generative models and software. Finally, we synthesize
 key research questions simplicial sets will help us answer and highlight
 the methodological developments required.
description: Software code (R, Python, Julia) to generate the figures (1-4)
 and appendix 3 in Capturing Complex Interactions in Disease Ecology with
 Simplicial Sets
DOI: 10.5061/dryad.4f4qrfjft
title: Experimental introgression in Drosophila: Asymmetric postzygotic isolation associated with chromosomal inversions and an incompatibility locus on the X chromosome

description: Interspecific gene flow (introgression) is an important source of new
 genetic variation, but selection against it can reinforce reproductive
 barriers between interbreeding species. We used an experimental approach
 to trace the role of chromosomal inversions and incompatibility genes in
 preventing introgression between two partly sympatric Drosophila virilis
 group species, D. flavomontana and D. montana. We backcrossed F1 hybrid
 females from a cross between D. flavomontana female and D. montana male
 with the males of the parental species for two generations and sequenced
 pools of parental strains and their reciprocal 2nd generation backcross
 (BC2mon and BC2fla) females. Contrasting the observed amount of
 introgression (mean hybrid index, HI) in BC2 female pools along the genome
 to simulations under different scenarios allowed us to identify
 chromosomal regions of restricted and increased introgression. We found no
 deviation from the HI expected under a neutral null model for any
 chromosome for the BC2mon pool, suggesting no evidence for genetic
 incompatibilities in backcrosses towards D. montana. In contrast, the
 BC2fla pool showed high variation in the observed HI between different
 chromosomes, and massive reduction of introgression on the X chromosome
 (large X-effect). We find that this observation is compatible with reduced
 recombination combined with at least one dominant incompatibility locus
 residing within the X inversion(s). Overall, our study suggests that
 genetic incompatibilities arising within chromosomal inversions can play
 an important role in speciation.
DOI: 10.15468/dl.w4yzc5
title: Occurrence Download

description: A dataset containing 604 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lagotis glauca"
 ]
}

 The dataset includes 604 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003170-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bcc2fqzg6
title: Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

description: As phylogenomics focuses on comprehensive taxon sampling at the species
 and population/subspecies levels, incorporating genomic data from
 historical specimens has become increasingly common. While historical
 samples can fill critical gaps in our understanding of the evolutionary
 history of diverse groups, they also introduce additional sources of
 phylogenomic uncertainty, making it difficult to discern novel
 evolutionary relationships from artifacts caused by sample quality issues.
 These problems highlight the need for improved strategies to disentangle
 artifactual patterns from true biological signal as historical specimens
 become more prevalent in phylogenomic datasets. Here, we tested the limits
 of historical specimen-driven phylogenomics to resolve subspecies-level
 relationships within a highly polytypic family, the New World quails
 (Odontophoridae), using thousands of ultraconserved elements (UCEs). We
 found that relationships at and above the species level were well-resolved
 and highly supported across all analyses, with the exception of discordant
 relationships within the two most polytypic genera which included many
 historical specimens. We examined the causes of discordance and found that
 inferring phylogenies from subsets of taxa resolved the disagreements,
 suggesting that analyzing subclades can help remove artifactual causes of
 discordance in datasets that include historical samples. At the
 subspecies-level, we found well-resolved geographic structure within the
 two most polytypic genera, including the most polytypic species in this
 family, Northern Bobwhites (Colinus virginianus), demonstrating that
 variable sites within UCEs are capable of resolving phylogenetic structure
 below the species level. Our results highlight the importance of complete
 taxonomic sampling for resolving relationships among polytypic species,
 often through the inclusion of historical specimens, and we propose an
 integrative strategy for understanding and addressing the uncertainty that
 historical samples sometimes introduce to phylogenetic analyses.
DOI: 10.5061/dryad.3j9kd51n0
title: Data from: Timing and probability of arrival for sea lice dispersing between salmon farms

description: Sea lice are a threat to the health of both wild and farmed salmon and an
 economic burden for salmon farms. With a free-living larval stage, sea
 lice can disperse tens of kilometers in the ocean between salmon farms,
 leading to connected sea lice populations that are difficult to control in
 isolation. In this paper, we develop a simple analytical model for the
 dispersal of sea lice between two salmon farms. From the model we
 calculate the arrival time distribution of sea lice dispersing between
 farms, as well as the level of cross-infection of sea lice. We also use
 numerical flows from a hydrodynamic model, coupled with a particle
 tracking model, to directly calculate the arrival time of sea lice
 dispersing between two farms in the Broughton Archipelago, BC, in order to
 fit our analytical model and find realistic parameter estimates. Using the
 parametrized analytical model we show that there is often an intermediate
 inter-farm spacing that maximizes the level of cross-infection between
 farms, and that increased temperatures will lead to increased levels of
 cross-infection.
description: Sea lice particle tracking data for a simulation of sea lice
 particles released from 20 farms in the Broughton Archipelago, Canada, on
 May 2, 2009. The output files are stored in netCDF format and so software
 that can read netCDF files is required to open the data files (R, MATLAB,
 and others). The associated R code was used to run the analysis in the
 manuscript. See README.txt file for details.
DOI: 10.5061/dryad.rjdfn2zdp
title: Data from: Computational model of the full-length TSH receptor

description: The receptor for thyroid stimulating hormone (TSHR), a GPCR, is of
 particular interest as the primary antigen in autoimmune hyperthyroidism
 (Graves' disease) caused by stimulating TSHR antibodies. To date,
 only one domain of the extracellular region of the TSHR has been
 crystallized. We have run a 1000ns Molecular Dynamic simulation on a model
 of the entire TSHR generated by merging the extracellular region of the
 receptor, obtained using artificial intelligence, with our recent homology
 model of the transmembrane domain, embedded it in a lipid membrane
 solvated it with water and counterions. The simulations showed that the
 structure of the transmembrane and leucine-rich domains were remarkably
 constant while the linking region (LR), known more commonly as the
 "hinge region", showed significant flexibility, forming several
 transient secondary structural elements. Furthermore, the relative
 orientation of the leucine-rich domain with the rest of the receptor was
 also seen to be variable. These data suggest that this linker region is an
 intrinsically disordered protein (IDP). Furthermore, preliminary data
 simulating the full TSHR model complexed with its ligand (TSH) showed that
 (a) there is a strong affinity between the linker region and TSH ligand
 and (b) the association of the linker region and the TSH ligand reduces
 the structural fluctuations in the linker region. This full-length model
 illustrates the importance of the linker region in responding to ligand
 binding and lays the foundation for studies of pathologic TSHR
 autoantibodies complexed with the TSHR to give further insight into their
 interaction with the flexible linker region. The dataset represents the
 coordinates of a model of the Thyroid Stimulating Hormone Recpetor (TSHR)
 built from the AI-based alphafold2 model of the TSHR ectodomain and the MD
 geverated model of the transmembrane domain (TMD) of TSHR.
description: The cooordinates were generated by judiciously chosen translation
 and rotation of the ecodomain model to merge it with the TMD
 model.
description: The file is in the classic PDB format - any molecular graphics
 program (e.g., VMD) can display it.
DOI: 10.5061/dryad.3r2280gjx
title: Elevational range of mammals, birds, and amphibians in the Himalayas

description: The lowest and highest elevations known for each species are used to
 delineate its elevational limits. We assume that species potentially exist
 between their elevational limits. For species that have a single
 elevational distribution record (resulting in an elevational range of
 zero) as well as those with elevational ranges less than 200 m, we
 adjusted their elevation ranges to 200 m. We verified all data for
 accuracy by experts within the region and any dubious outlying records
 were removed. Elevational limits were given for 1,488 species, including
 314 mammals, 1027 birds, and 147 amphibians in the Himalayas.
description: For quantifying the
 elevational range of mammals, birds, and amphibians, we compiled a
 comprehensive dataset from publications, online academic databases, and
 field surveys in the Himalayas (see Appendix S1 for the complete data
 sources). Most of the existing data in the China Himalayas were recorded
 by the Qinghai-Tibet Plateau scientific expedition organized by the
 Chinese Academy of Science in the 1960s. To update and verify these data,
 we conducted systematic field surveys within each subregion of the China
 Himalayas from 2011 to 2018 and collected species distribution data from
 regions where data are relatively sparse. These surveys are under the
 framework of the Second National Survey on Terrestrial Wildlife Resources
 in China and currently represent the most comprehensive survey of
 terrestrial vertebrates in the China Himalayas. Details on the field
 sampling procedures are described in Appendix S2.
 The lowest and highest elevations known for each
 species are used to delineate its elevational limits. We assume that
 species potentially exist between their elevational limits. For species
 that have a single elevational distribution record (resulting in an
 elevational range of zero) as well as those with elevational ranges less
 than 200 m, we adjusted their elevation ranges to 200 m. We verified all
 data for accuracy by experts within the region and any dubious outlying
 records were removed. Elevational limits were given for 1,488 species,
 including 314 mammals and 147 amphibians. Taxonomy of mammals, birds, and amphibians
 follows the International Union for Conservation of Nature Red List of
 Threatened Species Version 2018-2 (http://www.iucnredlist.org), the Handbook of the Birds of the World (BirdLife International Digital Checklist of the Birds of the World Version 2, http://datazone.birdlife.org/species/taxonomy) and the Amphibian Species of the World: An Online Reference version 6 (http://research.amnh.org/herpetology/amphibia/index.html) respectively.
DOI: 10.5061/dryad.d2547d853
title: Phenotypic screening using waveform analysis of synchronized calcium oscillations in primary cortical cultures

description: At present, in vitro phenotypic screening methods are widely used for drug
 discovery. In the field of epilepsy research, measurements of neuronal
 activities have been utilized for predicting efficacy of anti-epileptic
 drugs (AEDs). Fluorescence measurements of calcium oscillations in neurons
 are commonly used for measurement of neuronal activities, and some
 anti-epileptic drugs have been evaluated using this assay technique.
 However, changes in waveforms were not quantified in previous reports.
 Here, we have developed a high-throughput screening system containing a
 new analysis method for quantifying waveforms, and our method has
 successfully enabled simultaneous measurement of calcium oscillations in a
 96-well plate. Features of waveforms were extracted automatically and
 allowed the characterization of some anti-epileptic drugs using principal
 component analysis. Moreover, we have shown that trajectories in
 accordance with the concentrations of compounds in principal component
 analysis plots were unique to the mechanism of anti-epileptic drugs. We
 believe that an approach that focuses on the features of calcium
 oscillations will lead to better understanding of the characteristics of
 existing anti-epileptic drugs and allow prediction of the mechanism of
 action (MoA) of novel drug candidates.
description: <strong>Calcium
 imaging</strong> A vial of Cal-520 (#21130, AAT-Bioquest) was
 resuspended to 2 µM in Tyrode’s buffer (0.1 mM
 Mg<sup>2+</sup>) containing 0.01% Pluronic F-127 (#P3000MP,
 Invitrogen). The cultures were washed three times in Tyrode’s buffer, and
 incubated in 80 µL of Cal-520 per well for 1 hour at 37°C. Culture plates
 were set to an assay stage and stabilized for more than 10 minutes before
 measurement. For calcium imaging, an FDSS/µCell (Hamamatsu
 Photonics) kinetic plate reader was used. After incubation, 20 µL of
 compounds dissolved in Tyrode’s buffer were dispensed using the 96
 dispenser head of the FDSS/µCell and, 5 or more minutes after dispensing,
 calcium signals were measured for 5 minutes using the following settings:
 exposure time 36.5 ms, excitation wavelength 480 nm, emission wavelength
 540 nm, temperature controlled at 37°C.
 <strong>Data
 analysis</strong> Fluorescence
 intensity data were extracted using FDSS/µCell software. Data analysis and
 visualization were processed using the “Wave Finder” in Spotfire (Data
 Visualization & Analytics Software—TIBCO Spotfire, http://spotfire.tibco.com/) and custom code written in R for PCA. PCA features were selected based on correlation of features and visual inspection of each waveform.
DOI: 10.5061/dryad.gxd2547q0
title: Supporting data for: Risk factors common to leading eye health conditions and major non-communicable diseases: A rapid review and commentary

description: Background: To gain an understanding of the intersection of risk factors
 between the most prevalent eye health conditions that are associated with
 vision impairment and non-communicable diseases (NCDs). Methods: A series
 of rapid reviews of reviews reporting on non-modifiable risk factors, age
 and sex, and modifiable risk factors, including social determinants, were
 conducted for five common eye health conditions that are the leading
 causes of vision impairment globally (refractive error including
 uncorrected refractive error, cataract, age-related macular degeneration
 (AMD), glaucoma, and diabetic retinopathy) and five prevalent NCDs
 (cancer, cardiovascular disease, chronic respiratory disease, dementia,
 and depressive disorders). Results: Eye health conditions and NCDs share
 many risk factors. Increased age was found to be the most common shared
 risk factor, associated with increased risks of AMD, cataract, diabetic
 retinopathy, glaucoma, refractive error, cancer, cardiovascular disease,
 chronic obstructive pulmonary disease, and dementia. Other shared risk
 factors included smoking, obesity, alcohol consumption (mixed results),
 and physical activity was protective, though limited evidence was found
 for eye conditions. Social determinants are well documented as risk
 factors for NCDs. Conclusion: There is substantial overlap in common
 established risk factors for the most frequent vision-impairing eye
 conditions and leading NCDs. Increasing efforts should be made to
 integrate preventative and risk reduction interventions to improve health,
 with the greatest shared benefits for initiatives that aim to reduce
 smoking, improve diet, and promote physical activity.