cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vhhmgqnw5
title: Oxidation of L-leucine amino acid initiated by HO● radical - Are transition metal ions an enhancement factor?

description: Hydroxyl radical (HO●) formation initiated by the Fenton-type reactions of
 Fe and Cu complexes of L-leucine (Leu) amino acid, as well as its
 oxidation reaction by HO● were computationally investigated by
 using the density functional theory (DFT) method at the
 M05-2X/6-311++G(3df,2pd)//M05-2X/6-311++G(d,p) level of theory in the
 aqueous phase. The results showed that dipole-salt is the main form of Leu
 in the physiological condition. Leu exhibits high chelating potential
 towards both Fe(III)/Fe(II) and Cu(II)/Cu(I) ions with the most favorable
 coordinating positions at two oxygen atoms of the –COO functional groups.
 Furthermore, the Leu-ions complexes show a high risk of
 HO● formation via Fenton-like reactions,
 especially when ascorbate anion exists in the environment as a reducing
 agent. Finally, the oxidation reaction of L-leucine by
 HO● demonstrated a relatively high overall apparent reaction rate
 – koverall being 1.18 × 109 M-1s-1, in
 which formal hydrogen transfer (FHT) reactions of the dipole-salt
 form occur as the primary mechanism. Consequently, the Leu oxidation by
 HO● radical can be promoted by the Fenton-reaction enhancement of its
 transition metal complexes.
description: All geometry optimizations and
 vibrational frequency calculations for reactants, transition states,
 pre-reactive complexes, post-reactive complexes and products were
 performed by Gaussian 16 Rev. A.03 package in aqueous phase using M05-2X
 functional and 6-311++G(d,p) basis set. Accuracy of the energy values was
 then improved by single point calculations at M05-2X/6-311++G(3df,2pd)
 level of theory. The standard enthalpies
 (ΔrH0) and Gibbs free energies (ΔrG0) of the reactions forming complexes
 were calculated as the differences between total reactant and total
 product molar enthalpies and Gibbs free energies, respectively. The
 kinetics calculations of the redox reactions as well as the oxidation
 reaction of Leu by  HO<sup style="font-family:Helvetica , sans-serif;">●</sup> radical were determined by using
 conventional transition state theory (TST) in aqueous phase at 298.15 K
 that was employed in KiSThelP program.
description: The readme file contains the Cartesian coordination and
 thermochemistry properties of the Leu in two studied forms (Table SI1),
 optimized structures of five Leu 1:1 metal-to-ligand stoichiometric ratio
 complexes with Fe(III)/Fe(II) ions (Table SI2) and Cu(II)/Cu(I) ions
 (Table SI3); the thermodynamic parameters of the complexation reactions of
 these complexes (Table SI4); and the transition states (TSs) of FHT
 reactions of Leu toward HO● radical (Table SI5). All structures are
 optimized and calculated for thermochemical parameter values in water at
 the M05-2X/6-311++G(3df,2dp)//M05-2X/6-311++G(d,p) level of
 theory.
DOI: 10.5061/dryad.dz08kps09
title: Marbled cats in Southeast Asia: Are diurnal and semi-arboreal felids at greater risk from human disturbances?

description: Southeast Asia supports the greatest diversity of felids globally, but
 this felid diversity is likely to be threatened by the severe forest loss
 and degradation that is occurring in the region. The response of felids to
 disturbances appears to differ depending on their ecology. For example,
 the largely terrestrial and nocturnal leopard cat (Prionailurus
 bengalensis) thrives near forest edges and in oil palm plantations where
 it hunts rodents (Muridae) at night, thereby avoiding human activity
 peaks. Conversely, we hypothesized that the sympatric and similar-sized
 marbled cat (Pardofelis marmorata) would respond negatively to edges and
 relatively open oil palm plantations as they are more arboreal than
 leopard cats, rely on tree connectivity for hunting, and are diurnal so
 have less potential to temporally avoid humans. Using new and previously
 published camera-trapping studies from Southeast Asia to test habitat
 associations at multiple spatial scales using zero-inflated Poission GLMMS
 and hierarchical occupancy modelling, we examined the habitat associated
 and diel behaviour of the marbled cat in relation to human disturbances.
 We found that marbled cats were positively associated with large intact
 forests and, in contrast to leopard cats, negatively associated with oil
 palm plantations. Furthermore we found preliminary evidence suggesting
 marbled cats may adapt their diel behaviour to become more crepuscular in
 degraded forests, likely shifting their activity to avoid humans. These
 findings suggest that the marbled cat's IUCN Red List conservation
 status should be revaluated and potentially upgraded from Near Threatened
 to Vulnerable, matching other forest-dependent felids in the region. We
 posit our findings may be generalizable and that semi-arboreal and diurnal
 felids could face greater threats from habitat degradation than their
 terrestrial and nocturnal relatives.
description: Marbled cat occurrence data was collated through new camera
 trapping in Southeast Asia as well as a literature review to source
 previously published marbled cat occurrence records. This data was used to
 create a marbled cat detection history matrix. The marbled cat detection
 history data was analysed alongside covariate data sourced from GIS
 layers.
DOI: 10.15468/dl.zhccs4
title: Occurrence Download

description: A dataset containing 3862 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Callithamnion corymbosum"
 ]
}

 The dataset includes 3862 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003083-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wm37pvmq2
title: Data from: Long-term cattle grazing shifts the ecological state of forest soils

description: Cattle grazing profoundly affects abiotic and biotic characteristics of
 ecosystems. While most research has been performed on grasslands, the
 effect of large managed ungulates on forest ecosystems has largely been
 neglected. Compared to a baseline semi-natural state, we investigated how
 long-term cattle grazing of birch forest patches affected the abiotic
 state and the ecological community (microbes and invertebrates) of the
 soil subsystem. Grazing strongly modified the soil abiotic environment by
 increasing phosphorus content, pH and bulk density, while reducing the C:N
 ratio. The reduced C:N-ratio was strongly associated with a lower
 microbial biomass, mainly caused by a reduction of fungal biomass. This
 was linked to a decrease in fungivorous nematode abundance and the
 nematode channel index, indicating a relative uplift in the importance of
 the bacterial energy-channel in the nematode assemblages. Cattle grazing
 highly modified invertebrate community composition producing distinct
 assemblages from the semi-natural situation. Richness and abundance of
 microarthropods was consistently reduced by grazing (excepting collembolan
 richness) and grazing-associated changes in soil pH, Olsen P and reduced
 soil pore volume (bulk density) limiting niche space and refuge from
 physical disturbance. Anecic earthworm species predominated in grazed
 patches, but were absent from ungrazed forest, and may benefit from manure
 inputs, while their deep vertical burrowing behaviour protects them from
 physical disturbance. Perturbation of birch forest habitat by long-term
 ungulate grazing profoundly modified soil biodiversity, either directly
 through increased physical disturbance and manure input or indirectly by
 modifying soil abiotic conditions. Comparative analyses revealed the
 ecosystem engineering potential of large ungulate grazers in forest
 systems through major shifts in the composition and structure of microbial
 and invertebrate assemblages, including the potential for reduced energy
 flow through the fungal decomposition pathway. The precise consequences
 for species trophic interactions and biodiversity-ecosystem function
 relationships remains to be established, however.
description: For sampling methods, we refer to
 the publication associated with this dataset All
 R-scripts used for statistical analysis of the raw data are included in
 the dataset. R version 4.1.2 was used.  
description: See readme for short file descriptions All
 data is in excel- or csv format. R-scripts are included. Data was analysed
 with R 4.1.2.
DOI: 10.5061/dryad.9w0vt4bhp
title: Towards an animal economics spectrum for ecosystem research

description: The framework of the plant economics spectrum advanced our understanding
 of plant ecology and proved as a unifying concept across plant taxonomy,
 growth forms and biomes. Similar approaches for animals mostly focus on
 linking life-history and metabolic theory, but not on their application in
 ecosystem research. To fill this gap, we propose the animal economics
 spectrum (AES) based on broadly available traits that describe organismal
 size, biological times and rates. To exemplify the feasibility and general
 usefulness of constructing the AES, we compiled data on adult and
 offspring body mass, life span, age at first reproduction, reproductive
 and metabolic rate of 98 terrestrial taxa from seven selected animal
 classes and mapped these taxa into an exemplary quantitative trait space.
 The AES consists of two principal axes related to reproductive strategies
 and the pace of life; both axes are linked by animal metabolism. The AES
 thus closely mirrors seminal ideas on fundamental life-history strategies
 and more recent discoveries and developments in the fields of life-history
 and metabolic theory. Furthermore, we find associations between the
 positions of animals within the AES and taxonomy, thermoregulation and
 body plan. The AES shows that key dimensions describing different
 ecological strategies of animals can be depicted with functional traits
 that are relatively easily accessible for a broad spectrum of animal taxa.
 We suggest future steps towards an application of the AES in ecosystem
 research aiming at the understanding of ecological processes and ecosystem
 functions. Additionally, we urge for databases that compile comparable
 functional traits for a large proportion of animals but also for further
 groups of organisms with the ultimate goal to map the economics spectrum
 of life. The framework of the AES will be relevant for understanding
 ecological processes across animal taxa at species, community and
 ecosystem level. We further discuss how it can facilitate predictions on
 how the functional composition and diversity of animal communities can be
 affected by global change.
DOI: 10.5061/dryad.7sqv9s4tz
title: Mass cytometry immunophenotyping data of two-week-old mouse pups' spleens depleted of maternal cells

description: The maternal cells transferred into the fetus during gestation persist
 long after birth in the progeny. These maternal cells have been
 hypothesized to promote the maturation of the fetal immune system
 in utero but there are still significant gaps in our knowledge of their
 potential roles after birth. To provide insights into these
 maternal cells' postnatal functional roles, we set up a
 transgenic mouse model to specifically eliminate maternal cells in the
 neonates by diphtheria toxin injection and confirmed significant
 depletion in the spleens. We then performed immunophenotyping of
 the spleens of two-week-old pups by mass cytometry to pinpoint
 the immune profile differences driven by the depletion of maternal cells
 in early postnatal life. We observed a heightened expression of
 markers related to activation and maturation in some natural
 killer and T cell populations. We hypothesize these results
 to indicate a potential postnatal regulation of lymphocytic
 responses by maternal cells. Together, our findings highlight an
 immunological influence of maternal microchimeric
 cells postnatally, possibly protecting against adverse
 hypersensitivity reactions of the neonate at a crucial time of
 new encounters with self and environmental antigens.
description: To compare immune profiles in pups with or without maternal
 cells, B6CF1 control pups from crossing B6 females with Balb/c males (n=6;
 Ref), and DTR(-/-) sample pups from B6 DTR(+/-) females and Balb/c males
 (n=6; MMcDepleted) were injected i.p. every other day from postnatal day 3
 until sacrifice day 15 with diphtheria toxin (8ng/g body weight). The pups
 from each group were obtained from the first litter of the dams and were
 all female. Spleen cell suspensions were prepared by mechanical
 dissociation using 70 μm nylon mesh (Axel), treated with red blood cells
 lysis buffer (Ammonium-Chloride-Potassium) and washed in staining buffer
 (HBSS(-), 2mM EDTA, 1% BSA), frozen at -80°C in Cell Banker 1 Plus, thawed
 and stained on the same day across experimental groups. The cells were
 stained using Maxpar Mouse Sp/LN Phenotyping Panel Kit (Fluidigm)
 containing the following Abs: Ly6G/C (RB6-8C5), CD11c (N418), CD69
 (H1.2F3), CD45 (30-F11), CD11b (M1/70), CD19 (6D5), CD25 (3C7), CD3e
 (145-2C11), Ter-119 (TER119), CD62L (MEL-14), CD8a (53-6.7), TCRβ
 (H57-597), NK1.1 (PK136), CD44 (IM7), CD4 (RM4-5), B220 (RA3-6B2); with
 Cisplatin 198Pt used as a dead cells’ marker. Cells were fixed in 1.6%
 PFA, transported at 4 °C to Fluidigm Tokyo and analyzed on the Helios mass
 cytometry system. Normalization with beads was performed during
 acquisition. 
description: The data files can be opened in R using the package openCyto,
 among others.
DOI: 10.5061/dryad.2280gb5v3
title: The acclimatory response of the mayfly Neocloeon triangulifer to dilute conditions is linked to the plasticity of sodium transport

description: Relative to a growing body of knowledge about the negative consequences of
 freshwater salinization, little is known about how aquatic insects respond
 to progressively ion poor conditions. Here, we examined life-history and
 physiological acclimation in N. triangulifer by rearing larvae from 1 day
 post egg hatch to adulthood across a gradient of decreasing salinities
 (15, 8, 4, 2 and 1 mg L-1 Na). We found no significant changes in
 survival, growth, development time and whole-body Na content across these
 treatments. Radiotracer data revealed that larvae acclimated to their
 dilute exposures by increasing their rates of Na uptake and were able to
 maintain a relatively narrow range of uptake rates (± SEM) of 38.5 ± 4.2
 µg Na g-1 hr-1 across all treatments. In contrast, the Na uptake rates
 observed in naïve larvae were much more concentration dependent. This
 acclimatory response is partially explained by differences in ionocyte
 counts on the gills of larvae reared under different salinities.
 Acclimated larvae were surprisingly less retentive of their sodium
 composition when subjected to deionized water challenge. By contrasting
 our findings with a previous N. triangulifer salinity acclimation study,
 we show a physiological affinity for dilute conditions in this emerging
 mayfly model.
DOI: 10.5061/dryad.6q573n619
title: Data for: Heritability and parental effects in telomere length in a color polymorphic long-lived bird

description: Telomere length, an indicator of senescence, has been shown to be
 heritable but can also be affected by environmental factors, like parental
 effects. Investigating heritability as well as parental effects and
 rearing environment can help us to understand the factors affecting
 offspring telomeres. Moreover, how phenotypic parental traits linked with
 fitness can impact offspring telomere length is still unclear. A
 phenotypic marker closely associated with physiological traits and fitness
 is melanin-based color polymorphism, which in tawny owl (Strix aluco) is
 highly heritable and strongly associated with adult telomere shortening
 and survival.  We studied narrow-sense heritability (h2) of
 telomere length (RTL), as well as the impact of parental age and color
 morph and their interaction on offspring telomere length. Offspring RTL at
 fledging was strongly positively correlated with both mother and father
 RTL at breeding. Offspring RTL was also negatively associated with father
 age, suggesting that older fathers sired offspring with shorter telomeres.
 Parental color morph did not explain offspring telomere length and there
 were no interactive effects of parental morph and age, despite previously
 documented morph-specific senescence patterns. Our results suggest that
 telomere length is highly heritable and affected by paternal age, but not
 related to color polymorphism. This suggests that either morph-specific
 telomere shortening as adult does not result in significantly shorter
 telomeres in their gametes, or that parents compensate morph-specific
 senescence via parental care. Morph-specific patterns of telomere dynamics
 in polymorphic species may thus emerge from different life-history
 strategies adopted in adulthood.
DOI: 10.5061/dryad.08kprr54m
title: Data from: Key innovations and the diversification of Hymenoptera

description: The order Hymenoptera (wasps, ants, sawflies, and bees) represents one of
 the most diverse animal lineages, but whether specific key innovations
 have contributed to its diversification is still unknown. We assembled the
 largest time-calibrated phylogeny of Hymenoptera to date and investigated
 the origin and possible correlation of particular morphological and
 behavioral innovations with diversification in the order: the wasp waist
 of Apocrita; the stinger of Aculeata; parasitoidism, a specialized form of
 carnivory; and secondary phytophagy, a reversal to plant-feeding. Here, we
 show that parasitoidism has been the dominant strategy since the Late
 Triassic in Hymenoptera but was not an immediate driver of
 diversification. Instead, transitions to secondary phytophagy (from
 parasitoidism) had a major influence on diversification rate in
 Hymenoptera. Support for the stinger and the wasp waist as key innovations
 remains equivocal, but these traits may have laid the anatomical and
 behavioral foundations for adaptations more directly associated with
 diversification.
DOI: 10.5063/f1c53jc8
title: Monitoring Animal Diversity along the Qinling Power Transmission Project Using iDNA and eDNA

description: Considering limited coverage range and low efficiency of traditional wildlife monitoring methods in the biodiversity impact assessment of long-distance power transmission projects, the purpose of this study was to explore the monitoring capacity of environmental DNA (eDNA) and insect-derived DNA(iDNA) to terrestrial wildlife surveillance in the complex mountainous environment of the Qinling Mountains.In this study, the Baoji-Hanzhong 750 kV transmission line along the Qinling Mountains was selected as the research area.Infrared cameras were deployed at 15 sampling sites, and air and fly samples were collected at the same sites. After extracting DNA from air and fly samples, PCR amplification was performed using vertebrate specific primers 12SV05, and species identification was performed using high-throughput sequencing technology.The species detection probability, the monitoring effect of animal communities and the influencing factors of the three monitoring methods were compared by using the methods of diversity index, principal coordinate sorting, species accumulation curve and model-based species occupancy.The results showed that 21 species of terrestrial vertebrates were recorded by infrared cameras, and 76 species were monitored by eDNA and iDNA,covering mammals, birds, amphibians and reptiles and including 17 species of national key protected wild animals.The three methods were different in species detection: infrared camera had more advantages for medium and large mammals; eDNA showed higher sensitivity to small birds and nocturnal birds; iDNA was particularly effective in small mammals.The results indicated that eDNA and iDNA technology had the advantages of more convenient sampling method, larger investigation area and more kinds of monitoring animals,especially in the monitoring of small animals, hidden species and rare species.The integration of traditional wildlife monitoring methods and environmental DNA approaches can substantially enhance the comprehensiveness and accuracy of wildlife diversity assessment. This method combination offers a scientific, efficient, and convenient technical solution for the long-term monitoring, assessment, and protection management of ecological and environmental impacts during the planning, construction, and operation of power transmission projects or similar long-distance linear projects.
DOI: 10.5061/dryad.fbg79cnx0
title: Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species

description: Pathogen-mediated selection and sexual selection are important drivers of
 evolution. Both processes are known to target genes of the major
 histocompatibility complex (MHC), a gene family encoding cell-surface
 proteins that display pathogen peptides to the immune system. The MHC is
 also a model for understanding processes such as gene duplication and
 trans-species allele sharing. The class II MHC protein is a heterodimer
 whose peptide-binding groove is encoded by an MHC-IIA gene and an MHC-IIB
 gene. However, our literature review found that class II MHC papers on
 infectious disease or sexual selection included IIA data only 18% and 9%
 of the time, respectively. To assess whether greater emphasis on MHC-IIA
 is warranted, we analyzed MHC-IIA sequence data from 50 species of
 vertebrates (fish, amphibians, birds, mammals) to test for polymorphism
 and positive selection. We found that the number of MHC-IIA alleles within
 a species was often high, and covaried with sample size and number of
 MHC-IIA genes assayed. While MHC-IIA variability tended to be lower than
 that of MHC-IIB, the difference was only ~25%, with ~3 fewer IIA alleles
 than IIB. Furthermore, the unexpectedly high MHC-IIA variability showed
 clear signatures of positive selection in most species, and positive
 selection on MHC-IIA was stronger in fish than in other surveyed
 vertebrate groups. Our findings underscore that MHC-IIA can be an
 important target of selection. Future work should therefore expand the
 characterization of MHC-IIA at both allelic and genomic scales, and
 incorporate MHC-IIA into models of fitness consequences of MHC variation.