cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rxwdbrvbm
title: Oral cholestyramine prevents the enrichment of diverse daptomycin-resistance mutations in intestinal Enterococcus faecium populations

description: Background and Objectives: Previously, we showed proof-of-concept in a
 mouse model that oral administration of cholestyramine prevented
 enrichment of daptomycin-resistant Enterococcus faecium in the
 gastrointestinal (GI) tract during daptomycin therapy. Cholestyramine
 binds daptomycin in the gut, which removes daptomycin selection pressure
 and so prevents the enrichment of resistant clones. Here, we investigated
 two open questions related to this approach: 1) can cholestyramine prevent
 the enrichment of diverse daptomycin mutations emerging de novo in the
 gut? 2) how does the timing of cholestyramine administration impact its
 ability to suppress resistance? Methodology: Mice with GI E. faecium were
 treated with daptomycin with or without cholestyramine, and E. faecium was
 cultured from feces to measure changes in daptomycin susceptibility. A
 subset of clones was sequenced to investigate the genomic basis of
 daptomycin resistance. Results: Cholestyramine prevented the enrichment of
 diverse resistance mutations that emerged de novo in daptomycin-treated
 mice. Whole-genome sequencing revealed that resistance emerged through
 multiple genetic pathways, with most candidate resistance mutations
 observed in the clsA gene. Additionally, we observed that cholestyramine
 was most effective when administration started prior to the first dose of
 daptomycin. However, beginning cholestyramine after the first daptomycin
 dose reduced the frequency of resistant E. faecium compared to not using
 cholestyramine at all. Conclusions and Implications: Cholestyramine
 prevented the enrichment of diverse daptomycin-resistance mutations in
 intestinal E. faecium populations during daptomycin treatment, and it is a
 promising tool for managing transmission of daptomycin-resistant E.
 faecium.
DOI: 10.5061/dryad.dbrv15f3g
title: Data from: Widespread amphibian Perkinsea infections associated with Ranidae hosts, cooler months, and Ranavirus co-infection

description: Amphibians suffer from large-scale population declines globally, and
 emerging infectious diseases contribute heavily to these declines.
 Amphibian Perkinsea (Pr) is a worldwide anuran pathogen associated with
 mass mortality events, yet little is known about its epidemiological
 patterns, especially in comparison to the body of literature on amphibian
 chytridiomycosis and ranavirosis.  Here, we establish Pr
 infection patterns in natural anuran populations and identify important
 covariates including climate, host attributes, and co-infection with
 Ranavirus (Rv).  We used quantitative (q)PCR to determine the
 presence and intensity of Pr and Rv across 1234 individuals sampled
 throughout central Florida in 2017-2019. We then implemented random forest
 ensemble learning models to predict infection with both pathogens based on
 physiological and environmental characteristics.  Perkinsea
 infected 32% of all sampled anurans, and Pr prevalence was significantly
 elevated in Ranidae frogs, cooler months, metamorphosed individuals, and
 frogs co-infected with Rv, while Pr intensity was significantly higher in
 ranid frogs and individuals collected dead. Ranavirus prevalence was 17%
 overall and was significantly higher in Ranidae frogs, metamorphosed
 individuals, locations with higher average temperatures, and individuals
 co-infected with Pr. Perkinsea prevalence was significantly higher than Rv
 prevalence across months, regions, life stages, and species. Among
 locations, Pr prevalence was negatively associated with crayfish
 prevalence and positively associated with relative abundance of
 microhylids, but Rv prevalence did not associate with any tested
 co-variates. Co-infections were significantly more common than single
 infections for both pathogens, and we propose that Pr infections may
 propel Rv infections because seasonal Rv infection peaks followed Pr
 infection peaks and random forest models found Pr intensity was a leading
 factor explaining Rv infections.  Our study elucidates
 epidemiological patterns of Pr in Florida and suggests that Pr may be
 under-recognized as a cause of anuran declines, especially in the context
 of pathogen co-infection.
DOI: 10.15468/dl.v7u5u3
title: Occurrence Download

description: A dataset containing 190 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Gleditsia australis"
 ]
}

 The dataset includes 190 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003115-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7d7wm37xk
title: Data from: First application of dental microwear texture analysis to infer theropod feeding ecology

description: Theropods were the dominating apex predators in most Jurassic and
 Cretaceous terrestrial ecosystems. Their feeding ecology has always been
 of great interest, and new computational methods have yielded more
 detailed reconstructions of differences in theropod feedings behaviour.
 Many approaches however rely on well-preserved skulls. Dental microwear
 texture analysis (DMTA) is potentially applicable to isolated teeth, and
 here employed for the first time to investigate dietary ecology of
 theropods. In particular, we test whether tyrannosaurids show DMT
 associated with more hard-object feeding than compared to Allosaurus –
 which would be a sign for higher levels of osteophagy, as has often been
 suggested. We find no significant difference in complexity and roughness
 of enamel surfaces between Herrerasaurus, Allosaurus, and tyrannosaurids,
 which conflicts with inferences of more frequent osteophagic behaviour in
 Tyrannosaurus as compared to other theropods. Orientation of wear features
 reveals a more pronounced bi-directional puncture-and-pull feeding mode in
 Allosaurus than in tyrannosaurids. Our results further indicate
 ontogenetic niche shift in theropods and crocodylians, significantly
 larger height parameters in juvenile theropods might indicate frequent
 scavenging, resulting in more bone-tooth contact during feeding. Overall,
 DMTA is found to be very similar between theropods and extant large,
 broad-snouted crocodylians and shows great similarity in feeding ecology
 of theropod apex predators throughout the Mesozoic.
description: It is recommended to use MountainsMap v.8.0 or higher for data
 inspection and further processing, but the data files can also be accessed
 through open source packages including the following python packages:
 https://github.com/vincenzooo/read_metrology_formats
DOI: 10.5061/dryad.76hdr7t01
title: Data from: Pan-European phylogeography of the European roe deer (Capreolus capreolus)

description: To provide the most comprehensive picture of species phylogeny and
 phylogeography of European roe deer (Capreolus capreolus), we analysed
 mtDNA control region (610 bp) of 1469 samples of roe deer from Central and
 Eastern Europe and included in the analyses an additional 1,541 mtDNA
 sequences from GenBank from other regions of the continent. We detected
 two mtDNA lineages of the species: European and Siberian (an introgression
 of C. pygargus mtDNA into C. capreolus). The Siberian lineage was most
 frequent in the eastern part of the continent and declined towards Central
 Europe. The European lineage contained three clades (Central, Eastern and
 Western) composed of several subclades, many of which were separated in
 space. The Western clade appeared to have a discontinuous range from
 Portugal to Russia. Most of the subclades in the Central and the Eastern
 clades were under expansion during the Weichselian glacial period before
 the Last Glacial Maximum (LGM), while the expansion time of the Western
 clade overlapped with the Eemian interglacial. The high genetic diversity
 of extant roe deer is the result of their survival during the LGM probably
 in a large, contiguous range spanning from the Iberian Peninsula to the
 Caucasus Mts. and in two northern refugia.
DOI: 10.15468/dl.ttue5p
title: Occurrence Download

description: A dataset listing the 4139312 species recorded in GBIF matching the query:
{
 "OccurrenceStatus" : [
 "is Present"
 ]
}

 The dataset's 4139312 records were derived from 88404 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003113-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nzs7h44tq
title: Factors influencing the sustainability of homestead vegetable production intervention in Rufiji, Tanzania: A cross-sectional mixed methods study

description: Background There is growing evidence that home vegetable gardening
 interventions improve food security and nutrition outcomes at the family
 level. This study assessed factors influencing the sustainability of
 homestead vegetable production intervention, one year after the cessation
 of external support. Methods This was a cross-sectional study using both
 quantitative and qualitative data collection methods. A total of 247
 randomly selected households that participated in the homestead vegetable
 intervention were interviewed using a structured questionnaire. The study
 held four focus group discussions with households that participated in the
 intervention, and four In-Depth interviews with two extension workers, one
 community health worker, and one agriculture district officer. Multiple
 logistic regression for quantitative data and thematic analysis for
 qualitative data was conducted. Results About 20.24% (50/247) of
 households sustained homestead vegetable production for one year after the
 intervention phased out. Lack of seeds (adjusted OR=1.26: CI=0.39-0.89)
 and either manure or fertilizers (adjusted OR=1.69: CI =1.08-2.63) were
 significant factors influencing the sustainability of homesteads vegetable
 production. In the Focus Group discussions (FGDs) and In-Depth Interview
 (IDIs), all participating women and extension workers reported high cost
 of water, destruction from free-grazing animals, agriculture pests and
 diseases, poor soil fertility, shortage of seeds, and lack of capital
 affected homestead vegetable production sustainability. Conclusion
 Existing individual, community, and system challenges influence the
 sustainability of external-funded agriculture and nutrition interventions.
 The study findings underscore the importance of community authorities,
 scientists, and policymakers in having a well-thought sustainability plan
 in all promising external-funded interventions.
description: No missing values identified
DOI: 10.5061/dryad.j9kd51cft
title: Patterns of livestock depredation by snow leopards and effects of intervention strategies: lessons from the Nepalese Himalaya

description: Context. Large carnivores are increasingly threatened by anthropogenic
 activities, and their protection is among the main goals of biodiversity
 conservation. The snow leopard (Panthera uncia) inhabits high-mountain
 landscapes where livestock depredation drives it into conflicts with local
 people and poses an obstacle for its conservation. Aims. The aim of this
 study was to identify the livestock groups most vulnerable to depredation,
 target them in implementation of practical interventions, and assess the
 effectiveness of intervention strategies for conflict mitigation. We
 present a novel attempt to evaluate intervention strategies for
 particularly vulnerable species, age groups, time, and seasons. Methods.
 In 2020, we conducted questionnaire surveys in two regions of the
 Annapurna Conservation Area, Nepal (Manang, n = 146 respondents and Upper
 Mustang, n = 183). We applied sample comparison testing, Jacobs’
 selectivity index, and generalised linear models (GLMs) to assess rates
 and spatio-temporal heterogeneity of depredation, reveal vulnerable
 livestock groups, analyse potential effects of applied intervention
 strategies, and identify husbandry factors relevant to depredation. Key
 results. Snow leopard predation was a major cause of livestock mortality
 in both regions (25.4–39.8%), resulting in an estimated annual loss of
 3.2–3.6% of all livestock. The main intervention strategies (e.g. corrals
 during night-time and herding during daytime) were applied inconsistently
 and not associated with decreases in reported livestock losses. In
 contrast, we found some evidence that dogs, deterrents (light, music
 playing, flapping tape, and dung burning), and the use of multiple
 interventions were associated with a reduction in reported night-time
 depredation of yaks. Conclusions and implications. We suggest conducting
 controlled randomised experiments for quantitative assessment of the
 effectiveness of dogs, deterrents, and the use of multiple interventions,
 and widely applying the most effective ones in local communities. This
 would benefit the long-term co-existence of snow leopards and humans in
 the Annapurna region and beyond.
DOI: 10.6084/m9.figshare.31168336
title: Mas-related G Protein-coupled Receptor X2 Expression in Human Dental Pulp

description: Data associated with the manuscript "Mas-related G Protein-coupled Receptor X2 Expression in Human Dental Pulp"
DOI: 10.6084/m9.figshare.31168336.v1
title: Mas-related G Protein-coupled Receptor X2 Expression in Human Dental Pulp

description: Data associated with the manuscript "Mas-related G Protein-coupled Receptor X2 Expression in Human Dental Pulp"
DOI: 10.5061/dryad.ttdz08m1r
title: Data from: Largest-known fossil penguin provides insight into the early evolution of sphenisciform body size and flipper anatomy

description: Recent fossil discoveries from New Zealand have revealed a remarkably
 diverse assemblage of Paleocene stem group penguins. Here, we add to this
 growing record by describing nine new penguin specimens from the late
 Paleocene (upper Teurian local stage; 55.5–59.5Ma) Moeraki Formation of
 the South Island, New Zealand. The largest specimen is assigned to a new
 species, Kumimanu fordycei sp. nov., that may have been
 the largest penguin ever to have lived. Allometric regressions based on
 humerus length and humerus head width of extant penguins yield mean
 estimates of a live body mass in the range of 159.4 kg (95% CI: 143.4
 kg–179.6kg) and 148.7 kg (95% CI: 143.4kg–180.0kg), respectively,
 for Kumimanu fordycei. A second new species, Petradyptes
 stonehousei gen. et sp. nov., is represented by five specimens
 and was slightly larger than the extant emperor
 penguin Aptenodytes forsteri. Two small humeri represent an
 additional smaller unnamed penguin species. Parsimony and Bayesian
 phylogenetic analyses
 recover Kumimanu and Petradyptes crownward of the early Paleocene mainland NZ taxa Waimanu and Muriwaimanu, but stemward of the Chatham Island taxon Kupoupou. These analyses differ, however, in the placement of these two taxa relative to Sequiwaimanu, Crossvallia, and Kaiika. The massive size and placement of Kumimanu fordycei close to the root of the penguin tree provide additional support for a scenario in which penguins reached the upper limit of sphenisciform body size very early in their evolutionary history, while still retaining numerous plesiomorphic features of the flipper.
DOI: 10.5061/dryad.sj3tx9673
title: Sowerby’s beaked whale biosonar and movement strategy indicate deep-sea foraging niche differentiation in mesoplodont whales

description: Closely related species are expected to diverge in foraging strategy,
 reflecting the evolutionary drive to optimize foraging performance. The
 most speciose cetacean genus, Mesoplodon, comprises beaked whales with
 little diversity in external morphology or diet, and overlapping
 distributions. Moreover, the few studied species of beaked whales
 (Ziphiidae) show very similar foraging styles with slow, energy-conserving
 movement during long, deep foraging dives. This raises the question of
 what factors drive their speciation. Using data from animal-attached tags
 and aerial imagery, we tested the hypothesis that two similar-sized
 mesoplodonts, Sowerby’s(Mesoplodon bidens) and Blainville’s (Mesoplodon
 densirostris) beaked whales, exploit a similar low-energy niche. We show
 that, compared with the low-energy strategist Blainville’s beaked whale,
 AQ6 Sowerby’s beaked whale lives in the fast lane. While targeting a
 similar mesopelagic/bathypelagic foraging zone, they consistently swim and
 hunt faster, perform shorter deep dives, and echolocate at a faster rate
 and with higher frequency clicks. Further, extensive nearsurface travel
 between deep dives challenges the interpretation of beaked whale shallow
 inter-foraging dives as a management strategy for decompression sickness.
 The distinctively higher frequency echolocation clicks do not hold
 apparent foraging benefits. Instead, we argue that a high-speed foraging
 style influences dive duration and echolocation behaviour, enabling access
 to a distinct prey population. Our results demonstrate that beaked whales
 exploit a broader diversity of deep-sea foraging and energetic niches than
 hitherto suspected. The marked deviation of Sowerby’s beaked whales from
 the typical ziphiid foraging strategy has potential implications for their
 response to anthropogenic sounds, which appears to be strongly
 behaviourally driven in other ziphiids.
description: Data was collected using Dtags and processed using standard,
 open-access scripts.
DOI: 10.5061/dryad.bcc2fqzfm
title: Data from: Worldwide impacts of landscape anthropization on mosquito abundance and diversity: a meta-analysis

description: In recent decades, the emergence and resurgence of vector-borne diseases
 have been well documented worldwide, especially in tropical
 regions where protection and defence tools for human populations are still
 very limited. In this context, the dynamics of
 pathogens are influenced by landscape anthropization
 (i.e., urbanization, deforestation, and agricultural
 development), and one of the mechanisms through which this occurs
 is a change in the abundance and/or diversity of the
 vectors. An increasing number of empirical
 studies have described heterogeneous effects of
 landscape anthropization on vector communities; therefore, it is difficult
 to have an overall picture of these effects on a global scale. Here, we
 performed a meta-analysis to quantify the impacts of landscape
 anthropization on a global scale on the presence/abundance and diversity
 of mosquitoes, the most important arthropods affecting human health. We
 obtained 338 effect sizes on 132 mosquito species, compiled from 107
 studies in 52 countries that covered almost every part
 of the world. The results of the meta-analysis showed an overall decline
 of mosquito presence/abundance and diversity in response to urbanization,
 deforestation, and agricultural development, except for
 a few mosquito species that have been able to exploit landscape
 anthropization well. Our results highlighted that these few favoured
 mosquito species are those of global concern. They thus
 provide a better understanding of the overall effect of landscape
 anthropization on vector communities and, more importantly,
 suggest a greater risk of emergence and transmission of vector-borne
 diseases in human-modified landscapes.
description: Review of existing litterature on the effects of landscape
 anthropization on mosquito abundance and diversity.
DOI: 10.5061/dryad.tqjq2bw21
title: Optomotor response (eye movment) and avoidance responses (locomotor activity) of crabs Neohelice granulata for LP-lesioned, control lesioned and control crabs

description: When an animal rotates (whether it is an arthropod, a fish, a bird, or a
 human) a drift of the visual panorama occurs over its retina, termed optic
 flow. The image motion is stabilized by compensatory behaviors (driven by
 the movement of the eyes, head or the whole body depending on the animal)
 collectively termed optomotor response (OR). Dipteran lobula plate has
 been consistently linked with optic flow processing and the control of
 optomotor responses. Crabs have a neuropil similarly located and
 interconnected in the optic lobes, therefore referred to as a lobula plate
 also. Here we show that the crab’s lobula plate is required for normal
 optomotor response since the response was lost or severely impaired in
 animals whose lobula plate had been lesioned. The effect was
 behavior-specific, since avoidance responses to approaching visual stimuli
 were not affected. Crabs require simpler optic flow processing than flies
 (because they move slower and in 2D instead of 3D), consequently their
 lobula plates are relatively smaller. Nonetheless, they perform the same
 essential role in the visual control of behavior. Our findings add a
 fundamental piece to the current debate on the evolutionary relationship
 between the lobula plates of insects and crustaceans.
description: The full description of how animals were prepared are described
 in the methods section. OR was video taped (videos not included due to
 large size but could be provided if needed) and tracked. Here we present
 all the individual tracking files (e.g. 1339.csv) for the three
 experimental groups (derived from six different batches of animals,
 collected from their natural environment). For AR we present the
 individual files (up to 4 animals per file because we had 4 behavioral set
 ups running in parallel, e.g. yy023.csv) .  Raw files
 were further processed (e.g. EXPERIMENTO 10.R) to obtain summary
 measurements in each batch (e.g. output experimento 10 RO - todo el
 trial.csv for OR and medidas_resumen_RE_exp15.csv for AR). Finally, these
 were gathered to produce the final statistical analysis and figures using
 R software (Todo junto RE y Correlaciones - Trial total.R and Todo junto
 RO - Exps 10 a 16 - Trial total.R).
DOI: 10.7280/d1z41r
title: Toward a molecular understanding of the surface composition of atmospherically relevant organic particles

description: Many mass spectrometry methods using various ionization sources provide
 bulk composition of airborne particles, but little is known about the
 surface species that play a major role in determining their
 physicochemical properties that impact air quality, climate, and health.
 The present work shows that the composition of surface layers of
 atmospherically relevant submicron organic particles can be probed without
 the use of an external ionization source. Solid dicarboxylic acid
 particles are used as models, with glutaric acid being the most efficient
 at generating ions. Coating with small diacids or products from α-pinene
 ozonolysis demonstrates that ions are ejected from the surface, providing
 surface molecular characterization of organic particles on the fly. This
 unique approach provides a path forward for elucidating the role of the
 surface in determining chemical and physical properties of particles,
 including heterogeneous reactions, particle growth, water uptake, and
 interactions with biological systems.
description: Inlet ionization mass spectra were collected with a triple
 quadrupole mass spectrometer (Waters, Xevo TQ-S) with the ion source
 removed. Direct analysis in real time mass spectra were collected on the
 same mass spectrometer using a DART ion source (IonSense) equipped with
 the Vapur interface. Particle diameter measurements were made with a
 scanning mobility particle sizer (TSI, Inc.) using an electrostatic
 classifier model 3080, long differential mobility analyzer model 3081, and
 a condensation particle counter model 3776). Data were processed with
 MassLynx and Igor Pro (Wavemetrics).
description: Files can be opened with any spreadsheet software or text file
 viewer.