cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jh9w0vtcq
title: 7-O-Galloyltricetifavan: a promising natural radical scavenger

description: This dataset contains data from the calculations described in the paper:
 “Le Trung Hieu, Tran Thi Van Thi, Nguyen Thi Hoa, Adam
 Mechler and Quan V. Vo*. (2021), 7-O-Galloyltricetifavan: a
 promising natural radical scavenger. Royal Society Open Science. 2021.
 7-O-Galloyltricetifavan (7OGT), a natural flavonoid, is isolated from the
 leaves of Pithecellobium clypearia. The compound exhibits a variety of
 biological activities. This study details the evaluation of the HOO·
 antiradical activity of 7OGT by quantum chemistry calculations. The HOO•
 trapping activity of 7OGT in the gas phase (reference state) was
 discovered to follow the formal hydrogen transfer (FHT) mechanism with a
 rate constant of k = 4.58×108 M-1s-1. In physiological environments, 7OGT
 is predicted to be an excellent HOO· radical scavenger with koverall =
 6.01×108 and 1.40×104 M-1s-1 in water and pentyl ethanoate solvents,
 respectively. The HOO• antiradical activity of 7OGT in water at
 physiological pH is approximately 4620 times that of Trolox and
 substantially higher than that of other well-known natural antioxidants
 such as trans-resveratrol or ascorbic acid. Thus, 7OGT is an excellent
 natural antioxidant in polar environments.
description: The dataset was collected during the Gaussian 09 suite of
 programs at The University of Danang - University of Technology and
 Education, Vietnam, and La Trobe University, Australia.
 M06-2X/6-311++G(d,p) model chemistry was used for all calculations. It was
 demonstrated before that the M06-2X functional is one of the most reliable
 methods to study thermodynamics and kinetics of radical reactions,
 particularly in physiological environments. The solvation model density
 (SMD) method was used for including the effects of water and pentyl
 ethanoate in the computations. The kinetic calculations were performed
 following the quantum mechanics-based test for the overall free radical
 scavenging activity (QM-ORSA) protocol, using the conventional transition
 state theory (TST) and 1M standard state at 298.15 K.
description: The readme file contains the calculation methods (Table S3, SI)
 and the Cartesian coordinates of the transition states (Table S2, SI).
 Information on how the calculations were done can also be found in the
 associated manuscript referenced above.
DOI: 10.5061/dryad.6djh9w12p
title: Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats

description: Genotypic data from 1,040 Murciano-Granadina female goats genotyped with
 the Goat SNP50 BeadChip, as well as milk production records of
 817 Murciano-Granadina goats for the traits milk yield
 measured in kilograms at 210 days (MY210), 240 days (MY240) and 305 days
 (MY305), the natural logarithm of the somatic cell count divided by 1,000
 (lnSCC, to convert this value into a somatic cell count please use the
 formula: elnSCC × 103 cells/mL), fat percentage (FP), protein percentage
 (PP) and lactose percentage (LP).
DOI: 10.5061/dryad.gf1vhhmr7
title: Turbulent Mechanisms for the Deep Convective Boundary Layer in the Taklimakan Desert

description: The deep convective boundary layer (CBL) in the Taklimakan Desert plays an
 important role in the climate system in East Asia. Based on the
 observation experiment and large-eddy simulation, turbulent mechanisms for
 its formation were revealed in this study. This explained why the daily
 maximum CBL depth was independent of surface heating. In the late-morning,
 there was a weak temperature inversion and a near-neutral residual layer
 (RL) above the CBL.   With the development of the CBL,
 stronger convection could penetrate the RL and even overshoot the top of
 the RL. The distinctive boundary-layer process entrained free-tropospheric
 air to warm the RL and then promoted the entrainment of the warmed air in
 the RL into the CBL. This extra energy supply effectively contributed to
 the growth of the CBL. With further positive feedback between the CBL and
 RL depths, a deeper CBL would form in consecutive fair-weather conditions.
description: The data were collected in July 2016 at the Tazhong
 meteorological station (39° 00'N, 83° 40'E), situated in the
 hinterland of the TD. The station is surrounded by relatively homogeneous
 shifting sand and dunes. The radiosonde data were collected from the GPS
 radiosonde system developed by the Beijing Institute of Radio Measurement.
 The variations of air density and specific heat capacity at constant
 pressure with height were empirically calculated using radiosondes. The
 turbulence data were obtained by the eddy covariance system (IGRASON,
 Campbell Scientific, Inc., USA) mounted on a mast, at a height of 3 m
 above the sand surface.
DOI: 10.5061/dryad.wm37pvmpj
title: Community patch‐dynamics governs direct and indirect nutrient recycling by aggregated animals across spatial scales

description: Animals can have pervasive effects on ecosystems as they modify their
 biogeochemical and physical environments. In particular, when animals
 occur in high densities these effects can result in dramatic changes in
 the physical environment and biogeochemical hotspots or hot moments. While
 most research to date has focused on the direct role of animals in
 biogeochemical cycles, few have examined how animals indirectly influence
 biogeochemical cycles across scales. Freshwater mussels occur as spatially
 heterogeneous, dense and species-rich aggregations in many river
 ecosystems worldwide. Here we examined how mussel communities (1) directly
 influence the flux of particulate and dissolved nutrients and (2)
 indirectly effect the flux of N2 production, via denitrification, across a
 gradient of mussel biomass and differences in community composition at the
 patch- (0.25 m2) and stream reach-scales (60-80 m). We combined
 measurements of ammonia (N) and soluble reactive phosphorous (P) excretion
 and C, N, and P biodeposition rates for ten species with biomass and
 distribution estimates for seven mixed-species aggregations to quantify
 direct mussel contributions to biogeochemical cycling and the spatial
 heterogeneity of their impact. Additionally, we sampled sediments at a
 fine spatial scale to determine how mussel biomass and richness influence
 potential denitrification (indirect flux) rates at the patch- and
 reach-scales. We predicted that increasing mussel biomass would lead to
 greater direct and indirect fluxes of nutrients, manifesting in
 heterogeneous nutrient redistribution within and among stream reaches. We
 also predicted that variation in community composition would result in
 differential nutrient excretion and egestion stoichiometries. Our results
 indicate that mussel aggregations directly influence soluble and
 particulate nutrient fluxes with community composition, particularly
 phylogenetic tribe composition, controlling the stoichiometry. Mussel
 aggregations also indirectly influenced nutrient fluxes as greater mussel
 biomass and species richness resulted in higher denitrification rates as
 mediated by their interactions with the sediments and enhancement of
 nutrient availability. Our results underscore the importance of patchy
 communities in acting as biogeochemical control points.
DOI: 10.5061/dryad.66t1g1k3g
title: Coffee Berry Borer (Hypothenemus hampei Ferrari) trap catch and associated weather variables on Hawaii Island

description: We sampled flying female CBB adults bi-weekly over a three-year period
 using red funnel traps baited with an alcohol lure at 14 commercial coffee
 farms on Hawaii Island to characterize seasonal phenology and the
 relationship between flight activity and five weather variables. We
 captured almost 5 million scolytid beetles during the sampling period,
 with 81-93% of the trap catch comprised of CBB. Of the captured non-target
 beetles, the majority were tropical nut borer, black twig borer and a
 species of Cryphalus. Two major flight events were consistent across all
 three years: an initial emergence from January-April that coincided with
 early fruit development and a second flight during the harvest season from
 September-December. A generalized additive mixed model (GAMM) revealed
 that mean daily air temperature had a highly significant positive
 correlation with CBB flight; most flight events occurred between 20-26 °C.
 Mean daily solar radiation also had a significant positive relationship
 with flight. Flight was positively correlated with maximum daily relative
 humidity at values below ~94%, and cumulative rainfall up to 100 mm;
 flight was also positively correlated with maximum daily wind speeds up to
 ~2.5 m/s, after which activity declined.
DOI: 10.15468/dl.y7bkp4
title: Occurrence Download

description: A dataset containing 464 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 {
 "and" : [
 "Country is one of (Mexico)",
 "EventDate 2020-01-01-2026-01-27",
 "TaxonKey is one of (Ctenosaura similis [GBIF Backbone Taxonomy])"
 ]
 }
 ]
}

 The dataset includes 464 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003012-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1ns1rn8vr
title: Bottom-up effect of host protective symbionts on parasitoid diversity: Limited evidence from two field experiments

description: 1. Protective symbionts can provide effective and specific protection to
 their hosts. This protection can differ between different symbiont strains
 with each strain providing protection against certain components of the
 parasite and pathogen community their host faces. Protective symbionts are
 especially well known from aphids where, among other functions, they
 provide protection against different parasitoid wasps. However, most of
 the evidence for this protection comes from laboratory experiments. 2. Our
 aim was to understand how consistent protection is across different
 symbiont strains under natural field conditions and whether symbiont
 diversity enhanced the species diversity of colonizing parasitoids, as
 could be expected from the specificity of their protection. 3. We used
 experimental colonies of the black bean aphid, Aphis fabae, to investigate
 symbiont conferred protection under natural field conditions over two
 seasons. Colonies differed only in their symbiont composition, carrying
 either no symbionts, a single strain of the protective symbiont
 Hamiltonella defensa, or a mixture of three H. defensa strains. These
 aphid colonies were exposed to natural parasitoid communities in the
 field. Subsequently, we determined the parasitoids hatched from each aphid
 colony. 4. The evidence for a protective effect of H. defensa was limited
 and inconsistent between years, and aphid colonies harboring multiple
 symbiont strains did not support a more diverse parasitoid community.
 Instead, parasitoid diversity tended to be highest in the absence of H.
 defensa. 5. Symbiont conferred protection, although a strong and
 repeatable effect under laboratory conditions, may not always cause the
 predicted bottom-up effects under natural conditions in the field.
description: We sampled plants which we had planted in the field with aphids
 at the end of each block in 2018 or weekly in 2019 (see paper for
 experimental set up). We measured the length of each plant and counted the
 number of aphids either by counting aphids in groups of roughly five
 individuals (2018) or counting their exact number (2019). We also counted
 the number of mummies, irrespective of whether or not the parasitoid had
 already hatched. Unhatched mummies were collected in insect dishes for
 hatching and subsequent identification. We additionally kept the plants in
 the cellophane bags to be able to catch and determine any parasitoids that
 would hatch from mummies that only formed after collection. Lastly, we
 counted all ants and predators. For predators we recorded which order they
 belonged to and which stage they were in (i.e. egg, larvae, pupae, or
 adult). After they had hatched, we determined parasitoids under a stereo
 microscope. We identified primary parasitoids to the species level and
 secondary parasitoids at least to the genus level.
description: See readme file.
DOI: 10.5061/dryad.g79cnp5r5
title: Are metapopulation species drivers of metacommunity structure in sandstone outcrop communities?

description: Questions The extent to which metacommunities exhibit species with
 metapopulation dynamics is poorly understood. We investigate this issue
 within sandstone glade plant communities scattered across an upland
 hardwood forest. We investigate the life forms of metapopulation species
 and relationships between taxonomic, phylogenetic, and functional
 diversity, composition, and environmental factors. Locations Twenty-three
 sandstone outcrop communities in southern Illinois, USA. Methods Following
 vegetation surveys, species exhibiting metapopulations dynamics were
 identified and compared to all species based on origin, growth form, and
 lifecycle. Cohesion, turnover, and boundary clumping were utilized to
 determine metacommunity structure. Correlations evaluated associations
 between site-based variables, and regressions evaluated associations
 between diversity indices. Multivariate analyses compared sites to
 determine which variables contributed to compositional differences.
 Results Twenty of 130 species exhibited metapopulations dynamics and were
 usually annual or biennial exotics. Metacommunity elements indicated a
 Clementsian metacommunity, where metapopulation species were subordinate
 as opposed to dominant or transient. The largest sites were the most
 regularly shaped, but not the most diverse. Species richness and
 metapopulation species determined phylogenetic and functional diversity,
 but largely non-standardized measures of diversity, indicating
 independence between types of diversity. Multivariate analyses showed that
 diversity metrics explained community composition differences, where more
 species-rich sites with more metapopulation species were also more
 phylogenetically and functional diverse. Conclusions:  Sandstone
 glade communities exhibited diverse plant communities, where phylogenetic
 and functional diversity were driven by both total and metapopulation
 species independently. The metapopulation species were usually short-lived
 and exotic species with their low number likely constrained via dispersal
 limitations. The communities exhibited Clementsian metacommunity structure
 indicating predictable community assemblages. Functional traits indicated
 that these communities include species adapted to xeric, substrate-poor
 conditions.
DOI: 10.5061/dryad.x3ffbg7m5
title: Condition dependent seminal fluid gene expression and intergenerational paternal effects on ejaculate quality

description: 1. There is increasing evidence to show that the environment experienced
 by fathers can have intergenerational paternal effects on the phenotype of
 offspring. Paternal effects can be mediated by ejaculate traits beyond the
 genes carried by sperm, for example through methylation of DNA during
 spermatogenesis, or non-sperm components of the ejaculate such as small
 RNAs or seminal fluid proteins (sfp). 2. Theory suggests that
 ejaculate-mediated paternal effects can have important evolutionary
 consequences, especially if they exhibit condition dependent expression.
 Here we use the nutritional geometry approach to explore condition
 dependence in ejaculate traits and intergenerational paternal effects in
 the cricket Teleogryllus oceanicus. 3. We fed males one of 24 chemically
 defined diets that varied in macronutrient concentration and the ratio of
 protein (P) to carbohydrate (C). We measured paternal expenditure on
 testes and accessory gland growth, and the expression of three seminal
 fluid protein genes that are known to impact sperm viability and the
 survival of embryos to hatching. We also measured the hatching success and
 reproductive phenotypes of adult offspring. 4. We found linear effects of
 P and C on testes and accessory gland mass, and linear and correlated
 effects of P and C on the expression of two sfp genes. Paternal diet had
 no effect on the survival of embryos to hatching. 5. There were
 significant intergenerational effects of paternal diet on the viability of
 sperm produced by sons, but no paternal effects on the expression of sfp
 genes in sons or fecundity in daughters. 6. Our data suggest that
 ejaculate quality can have a significant non-genetic component determined
 by the paternal environment, which holds important implications for the
 evolutionary maintenance of variation in heritable male fitness.
DOI: 10.5061/dryad.tht76hf11
title: Plant collections for conservation and restoration: can they be adapted and adaptable?

description: Plant collections are important for the conservation of threatened
 species, and as a source of material for ecological restoration. Typically
 we want collections to have high genetic diversity so populations founded
 from it are adaptable to future challenges. Sometimes, we have additional
 objectives for collections, such as enrichment for desirable traits
 controlled by adaptive alleles. We used landscape genomic datasets for two
 plants, Westringia fruticosa and Wilkiea huegeliana, to design collections
 that are genetically diverse, and that are adapted to warming climates. We
 characterized temperature adaptation by: (i) using the mean annual
 temperature of the sites of origin of the plants, and (ii) using the
 representation of alleles that are associated with warm temperatures. In
 Westringia fruticosa, there was a negative correlation, or tradeoff
 between designing a collection that was both genetically diverse and
 adapted to warm temperatures. This tradeoff was weaker in Wilkiea
 huegeliana. We hypothesized this was because neutral genetic variation was
 strongly correlated with temperature in Westringia fruticosa, and not in
 Wilkiea huegeliana. Accordingly, when we shuffled the temperature data,
 breaking up the covariance between Westringia fruticosa genetic variation
 and temperature, there was a relaxation of the observed tradeoff. In sum,
 we explore tradeoffs between genetic diversity and environmental
 adaptation in plant collections, and highlight factors that influence the
 strength of these tradeoffs. This represents a useful step towards
 understanding when selection will have a large cost in genetic diversity,
 and when it will be possible to design a collection that is both adapted
 and adaptable.
description: Samples of two species, Westringia fruticosa and Wilkiea
 huegeliana, were collected across their respective ranges. Each sample was
 genotyped using DArTseq, a restriction based method. The resulting
 genotype data and sample meta-data are in this repository. These data were
 analysed using R code, which is archived in this repository.
description: A README file accompanies this archive, and outlines the
 directory structure, and describes the data and code available in those
 directories.
DOI: 10.5061/dryad.pzgmsbcnn
title: Preserving the woody plant tree of life in China under future climate and land-cover changes

description: The tree of life (TOL) is severely threatened by climate and land-cover
 changes. Preserving the TOL is urgent, but has not been included in the
 post-2020 global biodiversity framework. Protected areas (PAs) are
 fundamental for biological conservation. However, we know little about the
 effectiveness of existing PAs in preserving the TOL of plants and how to
 prioritize PA expansion for better TOL preservation under future climate
 and land-cover changes. Here, using high-resolution distribution maps of
 8732 woody species in China and phylogeny-based Zonation, we find that
 current PAs perform poorly in preserving the TOL both at the present and
 in the 2070s. The geographical coverage of TOL branches by current PAs is
 ca. 9%, and &lt; 3% of the identified priority areas for preserving
 the TOL are currently protected. Interestingly, the geographical coverage
 of TOL branches by PAs will be improved from 9% to 52–79% by the
 identified priority areas for PA expansion. Human pressures in the
 identified priority areas are high, leading to high costs for future PA
 expansion. We thus suggest that besides nature reserves and national
 parks, other effective area-based conservation measures should be
 considered. Our study argues for the inclusion of preserving the TOL in
 the post-2020 conservation framework and provides references for
 decision-makers to preserve the Earth’s evolutionary history.
DOI: 10.5061/dryad.qfttdz0jg
title: Patient experience with nursing care and patient satisfaction with overall hospital services

description: Objective: To determine how patient experience with nursing care influence
 patient satisfaction with overall hospital services. Design: This was a
 cross-sectional study. Setting: Inpatients were consecutively recruited at
 the national hospital (with 2000 beds) in Shanghai, China. Participants:
 The inclusion criteria were as follows: (1) hospitalized for 2 days or
 more; (2) able to read and understand Chinese; and (3) aged 18 years old
 or above. Patients with mental health problems were excluded. 756 patient
 surveys distributed among 36 wards were analyzed. The mean age of
 participants in the study was 57.7 (SD=14.5) and ranged from 18-80 years.
 Most participants were male (61.5%) and ever married (94.6%). Primary and
 secondary outcome measures: Patient experience with nursing care,
 meaning the sum of all interactions between patients and nurses, was
 measured using the self-designed questionnaire, which was developed by
 patient interviews, literature analysis and expert consultation. The
 overall patient satisfaction question was measured with a ten-point
 response option ranging from 1-10. Results: A linear relationship between
 the patient experience with nursing care and overall patient satisfaction
 was observed. The patient experience with nursing care was significantly
 associated with overall satisfaction in the crude model and in the
 adjusted models. Even after adjusting for 6 sociodemographic and 3
 disease-related factors, the patient experience with nursing care
 explained 34.9% of the variation in overall patient satisfaction.
 Conclusions: This study showed that patient experience with nursing care
 was an important predictor for overall patient satisfaction.
description: Eligible
 patients were invited to participate in the study. After informed consent
 was given, all data were obtained by trained investigators.
 Characteristics included in the hospital information system, such as
 gender, age, and diagnosis, were collected by checking the information
 system, while characteristics related to family income, literacy level and
 number of hospital admissions were assessed by interviewing patients and
 their family members. The timing of collecting the patients’ feedback may
 affect their response to the questionnaires because some of them may worry
 that negative appraisals about their hospital experience and satisfaction
 would affect the treatment and care they received during hospitalization,
 and thus they might be unwilling to provide negative feedback. To
 encourage the participants to respond frankly, the patient experience with
 nursing care survey and the overall patient satisfaction survey were taken
 on the patients’ discharge day, and the nursing staff did not administer
 the survey.