cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0zpc866zm
title: A comparative study on the stability of the furfural molecule on the low index Ni, Pd and Pt surfaces

description: We present a comparative density functional theory investigation of the
 furfural (Ff ) molecule on the low index Ni, Pd and Pt surfaces to
 understand its geometrical and electronic properties to gain mechanistic
 insights into the experimentally measured catalytic reactivities of these
 metal catalysts. We show that the number of metal d-states, which
 hybridize with the nearest C and O p-orbitals of the Ff molecule, can be
 used to explain the stability of the Ff molecule on these surfaces. We
 find that the hybridization between atoms with higher electronegativity
 and the metal d-states plays a crucial role in determining the stability
 of these systems. Furthermore, we also find electron transfer from metal
 to the Ff molecule on the Ni and Pd surfaces, with a reverse process
 occurring on the Pt surface.
description: The data contains the optimised geometries of all the models used
 in this study. 
description: The Coordinate folder contains all the relaxed structures of the
 furfural molecule on the low index Ni, Pd and Pt surfaces. There are 9
 folders, which
 includes<br>aNi111<br>bNi110<br>cNi100<br>dPd111<br>ePd110<br>fPd100<br>gPt111<br>hPt110<br>iPt100<br>For any further details please contact Dr. Arunabhiram Chutia (achutia@lincoln.ac.uk)
DOI: 10.5061/dryad.41ns1rnfr
title: Long-term outcomes and prognostic factors in kidney transplant recipients in Jakarta, Indonesia: a cohort study

description: Objectives To determine the long-term survival rates and prognostic
 factors in kidney transplant (KT) recipients in Jakarta, Indonesia. Design
 Retrospective cohort study. Setting A KT centre in Jakarta. Participants
 We enrolled 754 consecutive adult recipients who underwent KT between 2010
 and 2020. Main outcome measures Rates of 10-year patient, all-cause and
 death-censored graft survival and their prognostic factors in KT
 recipients. Results The 10-year patient survival, all-cause survival and
 death-censored graft survival rates of KT recipients were 74%, 68% and
 81%, respectively. The prognostic factors for poor patient survival were a
 pretransplant dialysis duration&gt;24 months (HR 1.64, 95% CI, 1.08 to
 2.49; p=0.02), cardiovascular disease (HR 1.59, 95% CI, 1.11 to 2.31;
 p=0.01), delayed graft function (DGF) (HR 4.94, 95% CI, 2.76 to 8.82;
 p&lt;0.001), post-transplant infection (HR 2.63, 95% CI, 1.56 to 4.43;
 p&lt;0.001) and acute rejection (HR 2.49, 95% CI, 1.20 to 5.15;
 p=0.01). All-cause graft survival was prognosticated by a pretransplant
 dialysis duration&gt;24 months (HR 1.74, 95% CI, 1.15 to 2.47;
 p=0.007), cardiovascular disease (HR 1.65, 95% CI, 1.18 to 2.33; p=0.004),
 DGF (HR 5.39, 95% CI, 3.13 to 9.28; p&lt;0.001), post-transplant
 infection (HR 2.46, 95% CI, 1.05 to 4.02; p&lt;0.001) and acute
 rejection (HR 4.18, 95% CI, 2.23 to 7.84; p&lt;0.001). Factors
 associated with poor death-censored graft survival were a pretransplant
 dialysis duration &gt;24 months (HR 2.19, 95% CI, 1.32 to 3.63;
 p=0.002), cardiovascular disease (HR 1.65, 95% CI, 1.02 to 2.68; p=0.04)
 and acute rejection (HR 5.52, 95% CI, 2.80 to 10.83; p&lt;0.001).
 Conclusions The survival rates of KT recipients are prognosticated by
 pretransplant dialysis duration, cardiovascular disease, DGF,
 post-transplant infection and acute rejection. Stricter eligibility
 criteria for recipients, more sensitive cross-match testing methods and
 better infection management strategies may be beneficial for improving the
 survival rates.
DOI: 10.5061/dryad.5hqbzkh77
title: Data from: Herbivore-induced volatiles induce increases in net photosynthesis and reduce plant susceptibility to oviposition in wild and cultivated plants

description: Despite the growing body of studies demonstrating that herbivore-induced
 plant volatiles (HIPV) induce and prime receiver plant defences, few
 studies have investigated the effect of HIPVs on primary metabolism of
 receiver plants and whether responses to HIPVs are consistent across wild
 and cultivated plant varieties. Here we investigated the effect of HIPVs
 on net photosynthesis, stomatal conductance, volatile emissions, and
 number of eggs laid by female Plutella xylostella on receiver plants in
 two wild and two cultivated Brassica rapa varieties. Plants responded to
 exposure to HIPVs by increasing their net photosynthesis and stomatal
 conductance. Responses were clearest in two varieties i.e., Cordelia and a
 wild Moroccan population, for which exposure to HIPVs also reduced their
 susceptibility to oviposition but did not alter volatile emissions. The
 results constitute an advance to research on plant-plant interactions by
 showing that exposure to HIPVs can promote plant primary metabolism by
 increasing photosynthesis as a probable mechanism to compensate for costs
 of induced defences. The results also suggest that responses to HIPVs is
 maintained across wild and cultivated plants but varies among varieties,
 and that the traits responsible for effective plant-plant interaction
 might not have been affected by breeding.
description: Data were collected between the 14 October 2020 to 30 March 2021
 in laboratories of the Department of Environmental and Biological
 Sciences, University of Eastern Finland, Kuopio FIN-70211,
 Finland.
DOI: 10.5061/dryad.73n5tb2z6
title: Revision of the genus Jethsura Cameron, 1902 (Hymenoptera: Ichneumonidae: Ichneumoninae: Phaeogenini)

description: The genus Jethsura Cameron is revised. Jethsura euthenia sp. nov.,
 Jethsura gondawindua sp. nov., and Jethsura serpentina sp. nov. are newly
 described from Colombia, and Jethsura rubricauda sp. nov. is described
 from Mexico. Jethsura pyriformis (Provancher) from the Nearctic region is
 redescribed. Species images, distribution maps and an illustrated key is
 provided.
description: Material examined data in tab-delimited format collected from
 <em>Jethsura</em> specimens from the Canadian National
 Collection of Insects (CNCI), Entomology Museum of Utah State University
 (EMUS), and the Natural History Museum of the Alexander Humboldt Institute
 (IAVH).
description: For ease of use, GPS coordinates were either added based on
 locality data or, for specimens originating from Colombia, converted from
 degree, minute, second format to decimal degrees.
DOI: 10.5061/dryad.931zcrjmg
title: Data: Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon

description: Chromosomal rearrangements (e.g., inversions, fusions, and translocations)
 have long been associated with environmental variation in wild
 populations. New genomic tools provide the opportunity to examine the role
 of these structural variants in shaping adaptive differences within and
 among wild populations of non-model organisms. In Atlantic Salmon (Salmo
 salar), variations in chromosomal rearrangements exist across the species
 natural range, yet the role and importance of these structural variants in
 maintaining adaptive differences among wild populations remains poorly
 understood. We genotyped Atlantic Salmon (n = 1429) from 26 populations
 within a highly genetically structured region of southern Newfoundland,
 Canada with a 220K SNP array. Multivariate analysis, across two
 independent years, consistently identified variation in a structural
 variant (translocation between chromosomes Ssa01 and Ssa23), previously
 associated with evidence of trans-Atlantic secondary contact, as the
 dominant factor influencing population structure in the region. Redundancy
 analysis suggested that variation in the Ssa01/Ssa23 chromosomal
 translocation is strongly correlated with temperature. Our analyses
 suggest environmentally mediated selection acting on standing genetic
 variation in genomic architecture introduced through secondary contact may
 underpin fine-scale local adaptation in Placentia Bay, Newfoundland,
 Canada, a large and deep embayment, highlighting the importance of
 chromosomal structural variation as a driver of contemporary adaptive
 divergence.
description: Juvenile Atlantic Salmon, young-of-the-year (YOY) and parr (ages
 1 to 2+), were collected by electrofishing during the period July to
 September of 2017 and 2018 from 26 rivers around Placentia Bay,
 Newfoundland, Canada. Individuals were genotyped by Centre for Integrative
 Genetics (CIGENE, Ås, Norway) using a 220K bi-allelic single nucleotide
 polymorphism (SNP) Affymetrix Axiom array developed for Atlantic Salmon as
 described in Barson et al. (2015). SNPs were filtered for a minor allele
 frequency (MAF) cut-off of 0.01, a missingness threshold of 0.05 across
 samples, and non-biallelic loci within each year sampled. SNPs were
 retained only if they passed filtering in both years resulting in a total
 of 139,038 SNPs.
DOI: 10.5061/dryad.j9kd51cdw
title: Host traits and environment interact to drive persistence of bat populations impacted by white-nose syndrome

description: Emerging infectious diseases have resulted in severe population declines
 across diverse taxa. In some instances, despite attributes associated with
 high extinction risk, disease emergence and host declines are followed by
 host stabilization for unknown reasons. While host, pathogen, and the
 environment are recognized as important factors that interact to determine
 host-pathogen coexistence, they are often considered independently. Here,
 we use a translocation experiment to disentangle the role of host traits
 and environmental conditions in driving the persistence of remnant bat
 populations a decade after they declined 70-99% due to white-nose syndrome
 and subsequently stabilized. While survival was significantly higher than
 during the initial epidemic within all sites, protection from severe
 disease only existed within a narrow environmental space, suggesting host
 traits conducive to surviving disease are highly environmentally
 dependent. Ultimately, population persistence following pathogen invasion
 is the product of host-pathogen interactions that vary across a patchwork
 of environments.
DOI: 10.5061/dryad.1rn8pk0vq
title: Systemic application of the TRPV4 antagonist GSK2193874 induces tail vasodilation in a mouse model of thermoregulation

description: In humans, skin is a primary thermoregulatory organ, with vasodilation
 leading to rapid body cooling, whereas in Rodentia the tail performs an
 analogous function. Many thermodetection mechanisms are likely to be
 involved including transient receptor potential vanilloid-type 4 (TRPV4),
 an ion channel with thermosensitive properties. Previous studies have
 shown that TRPV4 is a vasodilator by local action in blood vessels, so
 here we investigated whether constitutive TRPV4 activity effects Mus
 muscularis tail vascular tone and thermoregulation. We measured tail blood
 flow by pressure plethysmography in lightly sedated Mus muscularis
  (CD1 strain) at a range of ambient temperatures, with and
 without intraperitoneal administration of the blood brain barrier crossing
 TRPV4 antagonist GSK2193874. We also measured heart rate and blood
 pressure. As expected for a thermoregulatory organ, we found that tail
 blood flow increased with temperature. However, unexpectedly we found that
 GSK2193874 increased tail blood flow at all temperatures, and we observed
 changes in heart rate variability. Since local TRPV4 activation causes
 vasodilation that would increase tail blood-flow, these data suggest that
 increases in tail blood flow resulting from the TRPV4 antagonist may arise
 from a site other than the blood vessels themselves, perhaps in central
 cardiovascular control centres.
description: CODA Non-invasive tail cuff.
DOI: 10.5061/dryad.bk3j9kddd
title: Multi-regional comparison of scarring and pigmentation patterns in Cuvier’s beaked whales

description: These files represent standardized appearance data from photos of
 individually-identified, known-sex, adult Cuvier's beaked whales
 (Ziphius cavirostris) from three distinct study regions. We provide both
 the original raw datasets and the filtered datasets that were ultimately
 used in analyses of scarring density and pigmentation patterns to
 determine the extent to which they are diagnostic of sex in all three
 regions. The R code used to analyze these files is provided along with
 detailed descriptions of the data in a README file.
description: Please see the associated article for a detailed explanation of
 data collection and processing.
DOI: 10.6078/d11b01
title: Genomes and transposable elements in the Drosophila nasuta species group

description: Transposable element (TE) mobilization is a constant threat to genome
 integrity. Eukaryotic organisms have evolved robust defensive mechanisms
 to suppress their activity, yet TEs can escape suppression and
 proliferate, creating strong selective pressure for host defense to adapt.
 This genomic conflict fuels a never-ending arms race that drives the rapid
 evolution of TEs and recurrent positive selection of genes involved in
 host defense; the latter has been shown to contribute to postzygotic
 hybrid incompatibility. However, how TE proliferation impacts genome and
 regulatory divergence remains poorly understood. Here, we report the
 highly complete and contiguous (N50=33.8Mb - 38.0Mb) genome assemblies of
 seven closely-related Drosophila species that belong to
 the nasuta species group - a poorly studied group of
 flies that radiated in the last 2 million years. We constructed a high
 quality de novo TE library and gathered germline RNA-seq data, which
 allowed us to comprehensively annotate and compare insertion patterns
 between the species, and infer the evolutionary forces controlling their
 spread. We find a strong negative association between TE insertion
 frequency and expression of genes nearby; this likely reflects
 survivor-bias from reduced fitness impact of TE inserting near lowly
 expressed, non-essential genes, with limited TE-induced epigenetic
 silencing. Phylogenetic analyses of insertions of 147 TE families reveal
 that 53% of them show recent amplification in at least one species. The
 most highly amplified TE is an non-autonomous DNA element DINE which has
 gone through multiple bouts of expansions with thousands of full length
 copies littered throughout each genome. Across all TEs, we find that TEs
 expansions are significantly associated with high expression in the
 expanded species consistent with suppression escape. Altogether, our
 results shed light on the heterogenous and context-dependent nature in
 which TEs affect gene regulation and the dynamics of rampant TE
 proliferation amidst a recently radiated species group.
description: genomes.zip: Final genome assemblies for seven Drosophila species
 D. albomicans, D. nasuta, D. kepuluana, D. s. albostrigata, D. s.
 bilimbata, D. s. sulfurigaster, D. pallidifrons.
 Gene_annotations.zip: maker annotations files (transcripts.fa,
 proteins.fa, gff) for the seven species.
 initialTElibrary.zip: First de novo repeat libraries using
 RepeatModeller2 for each species. finalTElibrary.zip:
 Finalized merged and processed repeat library and RepeatMasker
 annotations.
DOI: 10.18150/m9qiqu
title: Nanoplatform based on SW480-derived exosome nanocarriers for efficient doxorubicin hydrochloride drug loading

description: The collection contains raw data generated during the successful isolation of exosomes from the human colon cancer cell line SW480 and their subsequent loading with doxorubicin hydrochloride as a drug-delivery nanoplatform. The size distribution of exosomes was obtained using the nanoparticle tracking assay (NTA). The loading of exosomes with doxorubicin was monitored using fluorescence spectroscopy and the standard addition method. The viability of HBE cells after exosomes loaded with doxorubicin uptake was evaluated using Alamar Blue assay.
DOI: 10.5061/dryad.d7wm37q2r
title: Ecogeographical patterns in owl plumage colouration: climate and vegetation cover predict global colour variation

description: Aim: Ecogeographical rules link animal colours, especially those produced
 by melanin pigments, with variation in environmental conditions over wide
 geographical scales. In particular, Gloger’s rule, coined in two versions
 for endothermic animals, suggests that tegument darkness would increase at
 high temperature, as well as in highly humid environments. On the other
 hand, the thermal melanism hypothesis, predicts that darker colourations
 should be more frequent in colder areas given their thermoregulation
 benefits. Location: Global Time period: Contemporary Major taxa studied:
 Strigiformes Methods: Here, we provide a global comparative test of these
 contrasting expectations in all extant owls (n = 198 species), a group of
 nocturnal birds displaying huge variability in the degree of melanin-based
 plumage colouration and environmental specialization. Combining analyses
 at both species and assemblage level, we assessed the climatic and
 environmental variables explaining variation in plumage lightness and
 redness across broad geographical gradients. Results: Darker and redder
 owl phenotypes are more likely found near the equator. Species and
 assemblage level analyses reveal that owls have more frequently darker and
 redder plumages in warmer regions. In addition, owl species living in more
 vegetated areas are darker, and owl assemblages show darker colours in
 wetter areas. Main conclusions: Global patterns of colour variation in
 owls do not fit expectations from the thermal melanism hypothesis but
 supports Gloger´s rule. Our findings also stresses that several
 alternative selective forces may explain climatic effects on colouration
 over large geographical scales. Experimental work is urged to uncover the
 possible mechanisms behind the detected associations between owl colour
 and environmental variables.
DOI: 10.5061/dryad.6q573n60m
title: Data from: Loss-of-heterozygosity facilitates a fitness valley crossing in experimentally evolved multicellular yeast

description: These data sets are generated to investigate a simple evolutionary
 landscape that arises from underdominance at a single locus where the
 fitness valley consists of only one less-fit genotype. We make use of an
 experimental system previous evolved in the laboratory, the Saccharomyces
 cerevisiae snowflake system. This system was experimentally selected
 resulting in a significant evolutionary shift, the transition from
 uni-to-multicellularity in asexual diploid populations. We carried out the
 phenotypic and fitness characterization of the strains. Additionally, we
 observed a rapid loss of heterozygosity (LOH) events in the heterozygote
 strains. Experimental evolution starting with the heterozygote strains
 suggests that LOH is common both under selection and without
 selection.  LOH event drive adaptation that may enable
 rapid evolution in diploid yeast. 
description: Phenotypic characterization of the ancestral wildtype and
 constructed heterozygous and homozygous recessive strains was conducted in
 a Coulter Counter Multisizer 4 and FlowCam® 3.0. Replicate populations of
 different isolated strains were analyzed to obtain the population
 distributions. Fitness assays were carried out by measuring absorbance
 with Tecan ® infinite 200pro microplate reader, by Colony formation Units
 (CFUs) of single strains, and by means of competition assays by replica
 plating. Cells were also counted under an optic microscope in a Neubauer
 chamber. Populations during the evolution experiment were monitored by
 Colony formation Units and imaged with the FlowCam® at the end of the
 experiment, after 10 cycles of selection.  Data
 collected by: -Beckman Coulter Counter Multisizer
 4. -Flow cytometer (FlowCam® 3.0 Fluid Imaging
 Technologies). -Tecan ® infinite 200pro microplate
 reader growth curves data. -Agar plating Colony
 formation Units (CFUs). -Fitness assays were calculated
 with replica platting.
description: <strong>Phenotyping data : </strong>
 -Raw_data_sizing
 -Raw_data_counts_and_total_cells_under_the_microscope
 <strong>Fitness assays: </strong>
 -Raw_data_TECAN
 -Raw_data_fitness_by_CFUs
 <strong>Experimental Evolution
 data:</strong>
 -Raw_data__Settling_experiment_FlowCam_data_adter_10_passes -Raw_data__Settling_experiment_plates_CFUs
DOI: 10.5061/dryad.6t1g1jx0r
title: Genomic associations with poxvirus across divergent island populations in Berthelot’s pipit

description: Understanding the mechanisms and genes that enable animal populations to
 adapt to pathogens is important from an evolutionary, health and
 conservation perspective. Berthelot’s pipit (Anthus berthelotii)
 experiences extensive and consistent spatial heterogeneity
 in avian pox infection pressure across its range of island
 populations, thus providing an excellent system with which to examine how
 pathogen-mediated selection drives spatial variation in immunogenetic
 diversity. Here we test for evidence of genetic variation associated with
 avian pox at both an individual and population-level. At the individual
 level, we find no evidence that variation in MHC class I and TLR4 (both
 known to be important in recognising viral infection) was associated with
 pox infection within two separate populations. However, using
 genotype-environment association (Bayenv) in conjunction with genome-wide
 (ddRAD-seq) data, we detected strong associations
 between population-level avian pox prevalence and allele
 frequencies of single nucleotide polymorphisms (SNPs) at a number of sites
 across the genome. These sites were located within genes involved
 in cellular stress signalling and immune responses, many of which
 have previously been associated with responses to viral infection in
 humans and other animals. Consequently, our analyses indicates that
 pathogen-mediated selection may play a role in shaping genomic variation
 among relatively recently colonised island bird populations and highlights
 the utility of genotype-environment associations for identifying candidate
 genes potentially involved in host-pathogen interactions.