cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t1g1jwt1v
title: Correcting parentage relationships in the endangered California condor: Improving mean kinship estimates for conservation management

description: Maintaining the existing biodiversity of endangered species is a goal of
 conservation management programs, and a major component of many
 collaborative efforts undertaken by zoos, field biologists, and
 conservation scientists. Over the past three decades, the San Diego Zoo
 has performed long-term genetic studies in support of the recovery program
 for the critically endangered California condor (Gymnogyps californianus).
 This work has included sex determination of hatchlings and parentage
 confirmation using microsatellite genotyping. This paper describes the
 genetic work associated with the California condor recovery program, which
 aims to provide a highly accurate pedigree for making informed captive
 pairing and release recommendations. Initial genotyping began after
 reintroduced California condors started reproducing, and the focus was on
 birds hatched from their wild-laid eggs. However, genetic analysis showed
 discrepancies relative to behavioral observations of wild birds, and led
 to the species-wide testing of all available samples. This genetic study
 has resolved instances of individual misidentifications and parental
 misassignments, verified the first cases of extra-pair paternity in this
 species, identified parentage where chicks were observed being raised by
 trios, and found two apparent de novo mutations in the captive condor
 population. Correcting the California condor pedigree according to genetic
 parental analysis has produced more accurate estimates of mean kinship
 values among living birds, ranking potential breeders according to their
 actual breeding value and helping managers to make informed decisions
 about captive pairing and release of condors in the wild.
DOI: 10.15468/dl.sz34mn
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Euphorbia antiquorum"
 ]
}

 The dataset includes 87 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002794-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dv41ns1xf
title: Association of aortic stiffness with biomarkers of neuroinflammation, synaptic dysfunction, and neurodegeneration

description: Objectives: To test the hypothesis that increased aortic stiffening is
 associated with greater cerebrospinal fluid (CSF) evidence of core
 Alzheimer’s disease pathology (Ab, phosphorylated tau (p-tau)),
 neurodegeneration (total tau (t-tau)), synaptic dysfunction (neurogranin),
 neuroaxonal injury (neurofilament light (NFL)), and neuroinflammation
 (YKL-40, sTREM2), we analyzed pulse wave velocity (PWV) data and CSF data
 among older adults. Methods: Participants free of stroke and dementia from
 the Vanderbilt Memory and Aging Project, an observational community-based
 study, underwent cardiac magnetic resonance to assess aortic pulse wave
 velocity (PWV, m/sec) and lumbar puncture to obtain CSF. Linear
 regressions related aortic PWV to CSF Ab, p-tau, t-tau, neurogranin, NFL,
 YKL-40, and sTREM2 concentrations adjusting for age, race/ethnicity,
 education, apolipoprotein (APOE) e4 status, Framingham Stroke Risk
 Profile, and cognitive diagnosis. Models were repeated testing PWV
 interactions with age, diagnosis, APOE-e4, and hypertension on each
 biomarker. Results: 146 participants were examined (72±6 years). Aortic
 PWV interacted with age on p-tau (b=0.31, p=0.04), t-tau, (b=2.67,
 p=0.05), neurogranin (b=0.94, p=0.04), and sTREM2 (b=20.4, p=0.05). Among
 participants over age 73 years, higher aortic PWV related to higher p-tau
 (b=2.4, p=0.03), t-tau (b=19.3, p=0.05), neurogranin (b=8.4, p=0.01), and
 YKL-40 concentrations (b=7880, p=0.005). Aortic PWV had modest
 interactions with diagnosis on neurogranin (b=-10.76, p=0.03) and
 hypertension status on YKL-40 (b=-18020, p&lt;0.001). Conclusions:
 Among our oldest participants, age 74 years and older, greater aortic
 stiffening is associated with in vivo biomarker evidence of
 neuroinflammation, tau phosphorylation, synaptic dysfunction, and
 neurodegeneration, but not amyloidosis. Central arterial stiffening may
 lead to cumulative cerebral microcirculatory damage and blood flow
 delivery to tissue, resulting in neuroinflammation and neurodegeneration
 in more advanced age.
DOI: 10.25338/b80d10
title: Total Cost of Ownership of Plug-in Electric Vehicles Calculations Data sheet

description: Total cost of ownership (TCO) studies are generally used as a tool to
 understand how and when the plug-in electric vehicle (PEV) technology will
 reach cost parity with conventional fuel vehicles. Post cost-parity, the
 PEV market should be able to sustain without government intervention. We
 present here a detailed analysis of vehicle manufacturing costs and
 market-level TCO accounting for technology uncertainties, behavioral
 heterogeneity, and key decision parameters of automakers. Using the
 estimates of the vehicle manufacturing costs, we estimate the cost of
 electrification of California’s LDV fleet to achieve the state’s net-zero
 emission goal by 2045. The results suggest that PEVs may not be
 cost-competitive even in 2030 without stronger policy support and
 automakers' initiative. Moreover, TCO is not a single number and the
 cost of electrification will vary across the population based on the cost
 of vehicles available in the market, their charging capabilities at home
 and public, and energy costs. The TCO estimates and the cost of fleet
 electrification analysis not only has important implications for
 policymakers but can also offer a foundation for understanding the effect
 of market dynamics on the cost-competitiveness of the PEV technology.
description: The data for Total cost of ownership was collected from academic
 research on the topic, technical reports from the industry, and data on
 vehicle technology maintained by the Environmental Protection Agency (EPA)
 and the Alternative Fuel Data Center. The
 household-level data used for market segmentation is obtained from the
 2019 California Vehicle Survey hosted by NREL.
DOI: 10.5061/dryad.547d7wm7p
title: The impact of methanol on behaviour: Dataset from zebrafish (Danio rerio) behavioural research

description: In many pharmacological and toxicological studies solvents are used as
 vehicles for the compound of interest.  The solvents themselves
 may have effects on their own, therefore, it is important to test the
 impact of the solvent on the preparation prior to conducting the
 study.  Methanol, (CH3OH), is a solvent used in many studies, and
 one we have used as a vehicle for benzo[a]pyrene. This data contains raw
 videos of zebrafish after exposure to 0, 0.25%, or 2.5% vol/vol, for 30
 minutes prior to behavioral testing.  Immediately after exposure,
 the individual zebrafish were moved to an open field test to quantify
 movement and location preference and were recorded for 10
 minutes.  Following the open field trial, a novel object was
 placed into the center of the arena to examine the exploratory response
 (boldness) of the fish for a second 10 minute trial. 
 Motion-tracking software (EthoVision XT) was used to quantify the
 dependent variables (distance moved, time in outer 'thigmotaxis'
 zone, 'inner' zone, and 'transition' zone). There were
 no significant differences between groups for any of the variables in
 either the open field or novel object approach tests.  This data
 suggests that 0.25% and 2.5% methanol does not alter locomotion or
 location preference in these two tests.
description: This dataset contains videos recorded from a Basler  monochrome
 camera that was positioned 1m above the arena and utilized a 4-8 mm F1:1.4
 manual iris and focus lens (Computar). Adult wild-type zebrafish
 (<em>Danio rerio</em>) were gently netted and place into the
 center of the arena and recording was tested immediately. The data was
 analyzed using motion tracking software EthoVision XT (version 10, Noldus,
 VA, USA) which quanitified the time spent in the thigmotaxis, transition,
 and center zones, as well as the total distance travelled during
 the trial. The three zones were drawn and mapped onto the arena within the
 EthoVision XT software. 
description: These are raw video files (10 minutes each).
DOI: 10.5061/dryad.4b8gthtbw
title: Photos of a rare warbler hybrid, Yellow Warbler x Black-throated Blue Warbler (Setophaga petechia x Setophaga caerulescens)

description: Hybridization can have profound effects on biological diversity; however,
 predictable inheritance of plumage traits remains poorly understood,
 especially for rare hybrids that are infrequently documented. We reviewed
 the literature and compiled a comprehensive list of hybrids from the wood
 warbler family Parulidae, a diverse radiation of songbirds with divergent
 plumage traits. We used our compilation to analyze modes of inheritance in
 wing bar patterns and carotenoid coloration. Finally, we described an
 unusual hybrid from the University of New Mexico in Albuquerque, New
 Mexico. We identified evidence of hybridization in 44 of 47 (93%) North
 American parulid species, with highest rates of hybridization in the genus
 Setophaga. We found predictable inheritance of plumage patterns between
 hybrid offspring and parental forms in our two focal traits, which
 supports the identification of our hybrid as a Yellow Warbler x
 Black-throated Blue Warbler (S. petechia x S. caerulescens). We based our
 identification on the extent and pattern of white in the tail, a prominent
 white wing flag, and our ability to confidently rule out all other
 alternative parentals. Our results suggest that some hybrid pairings can
 be confidently identified from phenotype alone, and that phenotypes of
 rare hybrid warblers likely have some degree of predictability.
description: Photos were taken by Michael J. Andersen and Kristen M. Oliver
 during an extended observation session of this exceptional hybrid warbler
 pairing, which enabled us to use prior knowledge of hybrid phenotypes to
 identify this unlikely hybrid.
description: You are free to use photos posted here, but we would appreciate
 if you credit the photographer of a given image if used (see README and
 associated zip directories) and cite the article if applicable:
 Williamson, J. L., Gyllenhaal, E. F., Oliver, K. D., Brady, S.
 S., Johnson, A. B., Michelsohn, M. J., & Andersen, M. J. (n.d.).
 Predictable outcomes of warbler hybridization: Synthesis and an
 exceptional Yellow × Black-throated Blue Warbler (Setophaga petechia × S.
 caerulescens) pairing. The Wilson Journal of Ornithology.
 https://doi.org/10.1676/21-00031
DOI: 10.5061/dryad.j6q573nd2
title: Pleiotropic opposing dominance within a color gene block contributes to a nascent species boundary via its influence on hybrid male territorial behavior

description: The divergence of plumage color genes contributes to songbird radiation.
 However, the mechanisms by which color gene divergence counteracts gene
 flow to maintain reproductive isolation during the formation of new
 species boundaries remain elusive. The hybrid zone between Setophaga
 occidentalis (SOCC) and S. townsendi (STOW) in the Cascade Range provides
 a natural observatory to investigate potential behavioral mechanisms
 underlying divergent selection on color genes. Recently, we found that
 selection within a single gene block associated with plumage color
 variation has maintained a stable and narrow hybrid zone. Here, we
 investigated the potential role of plumage signals in moderating a
 behavioral mechanism of selection. Specifically, we assessed whether two
 plumage traits are associated with body size among breeding males and if
 trait mismatch predicted aggressive behavior within hybrid and parental
 individuals in response to simulated territorial intrusion. The two
 plumage signals, cheek and flank coloration, though associated with the
 same gene block, reflect opposing dominance of SOCC and STOW alleles. We
 found that both plumage traits significantly predict the body size in the
 territorial sex (i.e. males). The opposing dominance of the single color
 gene block resulted in plumage signal discordance in heterozygotes, which
 in turn was associated with reduced hybrid territorial performance, an
 important proxy of fitness in this system. Taken together, these
 observations point to a single-locus-two-alleles mechanism of
 incompatibility in shaping a natural species boundary in the early stage
 of speciation.
DOI: 10.5061/dryad.np5hqbzsd
title: Data from: Virulent disease epidemics can increase host density by depressing foraging of hosts

description: All else equal, parasites that harm host fitness should depress densities
 of their hosts. However, parasites that alter host traits may increase
 host density via indirect ecological interactions. Here, we show how
 depression of foraging rate of infected hosts can produce such a hydra
 effect. Using a foraging assay, we quantified reduced foraging rates of a
 zooplankton host infected with a virulent fungal parasite. We then
 parameterized a dynamical model of hosts, parasites, and resources with
 this foraging function, showing how foraging depression can create a hydra
 effect. Mathematically, the hydra arose when increased resource
 productivity exceeded any increase in resource consumption per host.
 Therefore, the foraging-mediated hydra effect more likely emerged (1) for
 hosts that strongly control logistic-like resources and (2) during larger
 epidemics of moderately virulent parasites. We then analyzed epidemics
 from 13 fungal epidemics in nature. We found evidence for a
 foraging-mediated hydra effect: large outbreaks depressed foraging rate
 and correlated with increased densities of both algal resources and
 Daphnia hosts. Therefore, depression of foraging rate of infected hosts
 can produce higher host densities even during epidemics of parasites that
 increase host mortality. Such hydras might prevent collapse of host
 populations but also could produce higher densities of infected hosts.
description: This dataset contains data and code (MATLAB and R) for producing
 figures 1, 3, 4, 6, A1, and A3. Details of data collection can be found in
 the online supplementary materials published with this article
 in <em>American Naturalist</em>.
description: A README text file can be found in the .zip folder associated
 with each figure. Figures 3, A3, 4, and 6 are plotted in MATLAB. To make
 Figures 1 and A1, foraging functions are fit to feeding rate data in
 MATLAB, and then plots are created in R.
DOI: 10.5061/dryad.rxwdbrv7n
title: Modulation of a protein-folding landscape revealed by AFM-based force spectroscopy notwithstanding instrumental limitations

description: Single-molecule force spectroscopy is a powerful tool for studying protein
 folding. Over the last decade, a key question has emerged: how are changes
 in intrinsic biomolecular dynamics altered by attachment to micron-scale
 force probes via flexible linkers? Here, we studied the folding/unfolding
 of α3D using AFM-based force spectroscopy. α3D offers an unusual
 opportunity as a prior smFRET study showed α3D’s molecular diffusion
 constant within the context of Kramers theory varies with pH. The
 resulting pH-dependence provides a test for AFM-based force spectroscopy’s
 ability to track intrinsic changes in protein-folding dynamics.
 Experimentally, however, α3D is challenging. It unfolds at low force
 (&lt;15 pN) and exhibits fast-folding kinetics. We, therefore, used
 focused-ion-beam modified cantilevers that combine exceptional force
 precision, stability, and temporal resolution to detect state occupancies
 as brief as 1 ms. Notably, equilibrium and non-equilibrium
 force-spectroscopy data recapitulated the pH dependence measured using
 smFRET, despite differences in the mechanism of destabilization. We
 reconstructed a 1D free-energy landscape from dynamic data via an inverse
 Weierstrass transform. At both neutral and low pH, the resulting
 constant-force landscapes showed minimal differences (~0.2–0.5 kBT) in the
 transition state height. These landscapes were essentially equal to the
 predicted entropic barrier and symmetric. In contrast, force-dependent
 rates showed that the distance to the unfolding transition state increased
 as pH was decreased and thereby contributed significantly to the
 accelerated kinetics at low pH. More broadly, this precise
 characterization of a fast-folding, mechanically labile protein opens the
 door to future AFM-based studies of subtle transitions in
 mechanoresponsive proteins.
description: Focused-ion beam modification of cantilevers.<br> AFM-based
 single-molecule force spectroscopy (SMFS).<br> Force-dependent
 folding rate map analysis.<br> Hidden-Markov model
 analysis.
description: Original data from each
 figure in the manuscript and supporting information is provided in text
 files with .dat extensions. Each figure is provided in a separate folder.
 In general, the data in each panel is separated into folders as well.
 However, in some cases more than one panel is grouped into one folder if
 identical or nearly identical data is plotted in each panel. The readme
 file contains a detailed breakdown of the data files and traces for each
 figure, including units.
DOI: 10.25338/b8vk7r
title: Preliminary studies on the effects of Taiwanese ritual smoke on Aedes aegypti (Linnaeus, 1762) (Diptera: Culicidae)

description: In Chinese folk religion and Taoism as practiced in Taiwan, Asiatic
 wormwood leaves, agarwood incense sticks, and joss paper (“ghost money”)
 are often burned or carried to pray for health or at festivals that
 overlap with peak mosquito seasons. The possibility exists that some of
 these rituals became popular due to repellent effects of the smoke
 reducing the impact of insect-vectored pathogens. The effects of these
 smokes on the Dengue-vectoring mosquito Aedes aegypti Linnaeus, 1762
 (Diptera: Culicidae) was measured following the World Health Organization
 guidelines for spatial repellency testing. The chemical constituents of
 the smoke were identified using a solid-phase microextraction fiber for
 extraction followed by gas chromatography–mass spectrometry. Samples are
 identified by the NIST library search, and checked against published
 Kovats Index values for a final ID. Ret. Time = Retention time. Area % -
 Area percentage. KI= Kovats Index.
description: To identify compounds in the smoke, a small amount
 (0.01g <i>Artemesia</i>, 2 cm of incense stick weighting 0.07
 g, or 1 cm<sup>2</sup> joss paper weighting &lt;0.005g)
 was lit to smoulder in a 10 L glass vessel covered with a layer of plastic
 wrap. Extraction was done using a 50/30µm
 divinylbenzene-carboxen-polydimethylsiloxane (DVB/CAR/PDMS) solid phase
 microextraction (SPME) fiber (Supelco®, Bellefonte, PA, USA) inserted into
 the plastic wrap to absorb the smoke for 20 minutes. The glass vessel was
 thoroughly washed and rinsed with methanol and acetone between repetitions
 and when changing test substances. The samples were analyzed
 using an Agilent Technologies 7890A-5975C gas chromatography mass
 spectrometer (GC-MS). The GC was equipped with a DB-5MSUI fused silica
 capillary column (30 m, 0.25 mm i.d., 0.25 μm film thickness, Agilent
 Technologies Inc., CA, USA). Helium was used as the carrier gas with the
 constant flow rate of 1.0 mL/min. The injector temperature was set at
 250°C. After exposure to the smoke, the fiber was desorbed in the injector
 for 3 min. The GC oven settings were as follows: the initial temperature
 was held at 30°C for 2 min and then heated to 300°C at 10°C/min. Mass
 spectra were scanned in full scan mode from 50 to 500 m/z. Kovats indices
 were calculated based on the retention time in relation to a serious of
 <i>n</i>-alkane mixture (C7-C30) under the same analyzing
 conditions. The MS library identifications produced by the NIST library
 search were compared to published Kovats retention indices for these
 compounds to find matches for the Kovats indices produced by the
 GC.
DOI: 10.5061/dryad.zw3r2287h
title: Data from: Rapid evolution of a floral trait following acquisition of novel pollinators

description: 1. Changes in the pollinator assemblage visiting a plant can have
 consequences for reproductive success and floral evolution. We studied a
 recent plant trans-continental range expansion to test whether the
 acquisition of new pollinator functional groups can lead to rapid adaptive
 evolution of flowers. 2. In Digitalis purpurea, we compared flower
 visitors, floral traits and natural selection between native European
 populations and those in two Neotropical regions, naturalised after
 independent introductions. Bumblebees are the main pollinators in native
 populations, while both bumblebees and hummingbirds are important visitors
 in the new range. We confirmed that the birds are effective pollinators
 and deposit more pollen grains on stigmas than bumblebees. 3. We found
 convergent changes in the two new regions towards larger proximal corolla
 tubes, a floral trait that restricts access to nectar to visitors with
 long mouthparts. There was strong positive linear selection for this trait
 in the introduced populations, particularly on the length of the proximal
 corolla tube, consistent with the addition of hummingbirds as pollinators.
 4. Synthesis.  The addition of new pollinators is likely to
 happen often as humans influence the ranges of plants and pollinators, but
 it is also a common feature in the long-term evolution of the angiosperms.
 We show how novel selection followed by very rapid evolutionary change can
 be an important force behind the extraordinary diversity of flowers.
description: The Excel file includes four tabs as follows; see legends for
 variable names in each tab within the file:
 <b>Hand pollination</b>: Seed numbers in fruits after
 controlled hand pollinations <b>Floral
 traits:</b> Measures of flowers collected for each plant. Original
 measures and geometric means <b>Nectar and
 vegetation traits:</b> Non-floral morphological measurements and
 measurements of the nectar, for each plant
 <b>Pollinator censuses:</b> 3-minute census data for
 pollination visits to flowers in the field
 <b>Seed Set:</b> Seeds per fruits, number of flowers
 and total seed production for each plant
 <b>Pollen deposition:</b> Number of pollen grains
 deposited onto a virgin stigma for different pollinators, after a single
 visit