cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gtht76hk2
title: Data from: Early maternal loss affects diurnal cortisol slopes in immature but not mature wild chimpanzees

description: Biological embedding of stress experienced early in life is a mechanism
 proposed to explain the fitness costs of maternal loss in mammals. This
 embedding is expected to lead to long-term alterations of the hypothalamic
 pituitary adrenal (HPA) axis activity. This idea has, however, rarely been
 tested in wild long-lived animals. We assessed whether, as in humans,
 maternal loss had short and long-term impacts on orphan wild chimpanzee
 urinary cortisol levels and diurnal urinary cortisol slopes, both
 indicative of the HPA axis functioning. Immature orphan chimpanzees who
 experienced early maternal loss had diurnal cortisol slopes indicative of
 high activation of the HPA axis and recently orphaned immatures had
 elevated cortisol levels. However, unlike in humans, the cortisol profiles
 did not differ between orphan and non-orphan adult male chimpanzees. Our
 study highlights that long-term alteration of stress physiology related to
 early life adversity may not be viable in some wild animal populations.
DOI: 10.5061/dryad.g79cnp5nw
title: Effect of B-site co-substitution on the structure and magnetic properties of nanocrystalline neodymium orthoferrite synthesized by auto-combustion

description: Samples of cobalt-doped neodymium orthoferrite compounds, NdCoxFe1-xO3
 (0.0 ≤ x ≤ 0.5) were synthesized via glycine auto-combustion between 250 –
 300 °C and calcined at 500 °C for two hours. X-ray diffraction showed that
 all compounds had an orthorhombic perovskite structure with space group
 Pbnm. Increasing cobalt doping gradually reduced the lattice parameters
 and contracted the unit cell volume. Both X-ray diffraction and Scanning
 Electron Microscopy showed that the particles were spherical and in the
 nano-sized range (19 – 52 nm) with pores between grains. Vibrating sample
 magnetometry at room temperature indicated that NdFeO3 has high coercive
 field (1950 Oe) and cobalt substitution for iron led to a decrease in the
 coercive field, saturation and remanent magnetization which was as a
 result of decreased magnetic moments in the crystal and reduced canting of
 the FeO6 octahedra. The increase in magnetization and coercive fields with
 increase Co was connected to the microstructure (bond lengths and angles,
 defects, pores, grain boundaries) and crystallite size. The compounds
 NdCoxFe1-xO3 show antiferromagnetism with weak ferromagnetism due to
 uncompensated noncollinear moments. These compounds could serve as
 prototypes for tuning the properties of magnetic materials (ferromagnetic
 and antiferromagnetic) with potential applications in data storage, logic
 gates, switches and sensors.
DOI: 10.5061/dryad.tx95x69w8
title: Microbial communities developing within bulk sediments under fish carcasses on a tidal flat

description: Animal carcasses are often brought into tidal flats where they are at the
 boundary between terrestrial and marine ecosystems. Since these carcasses
 act as microhabitats with large amounts of energy and nutrients, they
 likely develop unique bacterial assemblages in the ambient sediment, which
 in turn may stimulate colonization of other organisms such as protozoans.
 However, little is known about the microbial assemblages colonized in
 sediment around animal carcasses in the tidal zone. Herein we examined the
 bacterial and ciliophoran assemblages developed in association with fish
 carcasses by incubating the carcasses in the Higashiyachi tidal flat
 (Sendai, Japan). We collected sediment samples at 2, 9, and 42 days of
 incubation and analyzed the bacterial and ciliophoran assemblages by 16S
 and 18S rRNA gene amplicon sequencing. We observed significant differences
 in the composition and relative abundance of bacterial and ciliophoran
 operational taxonomic units (OTUs) between the sediments with and without
 the carcasses. Our analyses suggest that these unique assemblages were
 created through the direct effects of the carcass and indirect effects
 through interactions between bacteria and ciliophorans. These results also
 suggest that animal carcasses developed a temporally unique microbial food
 web in the sediments close to the carcasses, although it disappeared for
 several weeks.
DOI: 10.5061/dryad.73n5tb2vx
title: High resolution lidar data of the Khumbu glacier

description: This Dryad repository contains an airborne lidar dataset of the Khumbu
 Glacier from the base of the Lhotse Face in the Western Cwm to the
 trekking village of Dugla at the toe of the glacier. The data were
 collected by helicopter borne lidar on 27 May 2019 to 28 May 2019. The
 data were collected as part of the National Geographic and
 Rolex Perpetual Planet Everest Expedition. This research was
 conducted in partnership with National Geographic Society, Rolex,
 Tribhuvan University, and the Nepal Survey Department, with approval from
 all relevant agencies of the Government of Nepal.
description: Acquisition of helicopter-based lidar data was accomplished with
 a Riegl VQ480II device. Due to the cold temperatures, a specially
 constructed externally front-mounted sensor pod with heaters and
 insulation was designed and deployed. The lidar sensor was configured to
 provide a maximum measurement range of 1,000 m, and an operating flight
 altitude of up to 530 m above ground level, at up to 6,400m
 elevation The raw lidar data (output to .LAS 1.2 or 1.4
 format) and IMU trajectories were post-processed using Riegl RiProcess and
 Applanix POSPac Mobile Mapping Suite, respectively. RiProcess is
 proprietary Riegl software for processing raw lidar data into a .LAS 1.4
 output file. The first step creates a trajectory from the IMU and GPS/GNSS
 data using the Applanix POSPac software into an SBET file, which is then
 combined with the .RPX files from the Riegl VQ480II lidar scanner. Ground
 control points were brought into the processing workflow during the
 alignment of the .RPX and SBET files to provide additional accuracy beyond
 that achieved with the on board GPS/GNSS. Further alignment of each
 individual scan line is processed through a combination of the Riegl
 RiPrecision software extension and BayesMap StripAlign.
description: Note that there is sparser point density in some of the snow and
 ice areas of the glacier, higher density in rock and rubble covered areas.
 The data are provided for scientific use and should credit the National
 Geographic and Rolex’s Perpetual Planet Everest Expedition and National
 Geographic Society.
DOI: 10.5061/dryad.jwstqjq7j
title: Nicotiana benthamiana as a transient expression host to produce auxin analogues: Pisum sativum seed transcriptomic data

description: Plant secondary metabolites have applications for the food, biofuel, and
 pharmaceutical industries. Recent advances in pathway elucidation and host
 expression systems now allow metabolic engineering of plant metabolic
 pathways to produce “new-to-nature” derivatives with novel biological
 activities, thereby amplifying the range of industrial uses for plant
 metabolites. Here we use a transient expression system in the model plant
 Nicotiana benthamiana to reconstitute the two-step plant-derived
 biosynthetic pathway for auxin (indole acetic acid) to achieve
 accumulation up to 500 ng/g fresh mass (FM). By expressing these
 plant-derived enzymes in combination with either bacterial halogenases and
 alternative substrates, we can produce both natural and new-to-nature
 halogenated auxin derivatives up to 990 ng/g FM. Proteins from the auxin
 synthesis pathway, tryptophan aminotransferases (TARs) and
 flavin-dependent monooxygenases (YUCs), could be transiently expressed in
 combination with four separate bacterial halogenases to generate
 halogenated auxin derivatives. Brominated auxin derivatives could also be
 observed after infiltration of the transfected N. benthamiana with
 potassium bromide and the halogenases. Finally, the production of
 additional auxin derivatives could also be achieved by co-infiltration of
 TAR and YUC genes with various tryptophan analogues. Given the emerging
 importance of transient expression in N. benthamiana for industrial scale
 protein and product expression, this work provides insight into the
 capacity of N. benthamiana to interface bacterial genes and synthetic
 substrates to produce novel halogenated metabolites.
description: <i>P. sativum</i>
 seeds (cultivar Cameor) were obtained from the Germplasm Resources Unit at
 the John Innes Centre UK and were grown in a glasshouse at 24/16 °C
 day/night temperature with a 14‐h photoperiod and at 70% relative
 humidity. The developing seeds were collected between 7 and 21 days after
 floral anthesis and the RNA was extracted using a RNeasy Plant mini kit
 (Qiagen). RNA sequencing was performed at the Earlham Institute (UK).
 Briefly, Illumina barcoded TruSeq RNA library were prepared and sequenced
 using Illumina HiSeq 2000/2500 in High-Output mode using 100 bp paired-end
 reads to generate at least 100 million pairs of reads per lane. FASTQC
 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used on
 the reads to assess the quality. Trinity software<sup>41</sup>
 was used to assembly a <i>de novo</i> transcriptome from the
 paired-end reads with the default parameters after removal of low-quality
 reads and trimming. <i>PsYUC</i> genes were identified by
 blasting the <i>AtYUC6</i> sequence into the assembled
 transcriptome and retrieving the closest homologues.
description: Assembled transcriptomic dataset.
DOI: 10.5061/dryad.bnzs7h48s
title: Sex‐specific effects of predation risk on parental care in a sexually dichromatic Neotropical songbird

description: Predation risk affects a broad range of bird behaviours, especially
 parental care. The adaptive behavioural changes presented by both parents,
 however, may differ according to different levels of predation risk
 suffered by each sex. This is especially prominent in sexually dichromatic
 species, where one of the sexes is more visually conspicuous and hence
 vulnerable to increased nest predation risk during nest visits. Here, we
 experimentally investigated how predation risk affects the parental
 behaviour of a sexually dichromatic Neotropical passerine, the blue-black
 grassquit (Volatinia jacarina). We used playbacks of known predators and
 non-predatorial control sympatric species near nesting pairs in the field.
 Results show that grassquits modify their behaviour according to predation
 risk and that this behavioural response is sexdependent. Males decrease
 their nest visit times, become more discreet when moving towards the nest,
 and stop performing sexual displays after leaving the nest. In contrast,
 females tend to decrease latency to visit the nest and increase the
 duration of brooding bouts. These different sex responses reduce nest
 visual and acoustic detectability, since conspicuous males are readily
 spotted on nests and cryptic females camouflage nestlings and suppress
 begging calls. Although these behavioural changes might reduce predation
 risk, there might be a cost of reduced food load to nestlings and
 increased brood starvation risk. These changes in nesting activities
 illustrate the behavioural adaptability of passerines to ensure offspring
 survival in tropical high predation risk environments.
description: This dataset was collected through video analysis of blue-black
 grassquit nest and parental behavior during experimental conditions that
 simulated high and low predation risk through the broadcast
 of vocalizations of known predator and control species. The R script used
 for analysis is also available.
description: Metadata is available in a secondary sheet in this file.
DOI: 10.5061/dryad.ncjsxkssv
title: Contrasting effects of Miocene and Anthropocene levels of atmospheric CO2 on silicon accumulation in a model grass

description: Grasses are hyper-accumulators of silicon (Si) which they acquire from the
 soil and deposit in tissues to resist environmental stresses. Moreover,
 given the high metabolic costs of herbivore defensive chemicals and
 structural constituents (e.g. cellulose), grasses may substitute Si for
 these components when carbon (C) is limited. Indeed, high Si uptake
 grasses evolved in the Miocene when atmospheric CO2 concentration was much
 lower than present levels. It is; however, unknown how pre-industrial CO2
 concentrations affect Si accumulation in grasses. Using Brachypodium
 distachyon, we hydroponically manipulated Si-supply (0.0, 0.5, 1, 1.5, 2
 mM) and grew plants under Miocene (200 ppm) and Anthropocene levels of CO2
 comprising ambient (410 ppm) and elevated (640 ppm) CO2 concentrations. We
 showed that regardless of Si-treatments, the Miocene CO2 levels increased
 foliar Si concentrations by 47% and 56% relative to plants grown under
 ambient and elevated CO2, respectively. This is due to higher accumulation
 overall, but also the reallocation of Si from the roots into the shoots.
 Our results suggest that grasses may accumulate high Si concentrations in
 foliage when carbon is less available (i.e. pre-industrial CO2 levels) but
 this is likely to decline under future climate change scenarios,
 potentially leaving grasses more susceptible to environmental stresses
description: Plant biomass, silicon, carbon and nitrogen data
 All data (Plant biomass and chemistry) support the role of higher
 silicon accumulation in grass. Data columns include descriptive titles for
 clarity. Supplementary material data.xlsx
DOI: 10.15468/dl.aubztg
title: Occurrence Download

description: A dataset containing 1536 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cicer arietinum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1536 records from 140 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002631-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ksn02v72s
title: Cerebral small vessel disease and functional outcome prediction after intracerebral haemorrhage

description: Background.  It is unknown whether adding cerebral small vessel
 disease (SVD) biomarkers can improve the performance of intracerebral
 hemorrhage (ICH) outcome predictive scores. Purpose. To determine whether:
 (1) CT-based SVD biomarkers are associated with 6-month functional outcome
 after ICH and (2) whether these biomarkers improve the performance of
 pre-existing ICH score.  Methods. We included 864 patients with
 acute ICH from a multicentre, hospital-based prospective cohort study. We
 evaluated CT-based SVD biomarkers (white matter hypodensities [WMH];
 lacunes; brain atrophy; and a composite SVD burden score) and their
 associations with poor 6-month functional outcome (modified Rankin Scale
 [mRS] score &gt;2). The area under the receiver operating
 characteristic curve (AUROC) and Hosmer-Lemeshow test were used to assess
 discrimination and calibration of the ICH score with and without SVD
 biomarkers. Results. In multivariable models (adjusted for ICH score
 components), WMH presence (OR 1.52, 95%CI 1.12-2.06), cortical atrophy
 presence (OR 1.80, 95%CI 1.19-2.73), deep atrophy presence (OR 1.66, 95%CI
 1.17-2.34), and severe atrophy (either deep or cortical) (OR 1.94, 95%CI
 1.36-2.74) were independently associated with poor functional outcome. For
 the ICH score, the AUROC was 0.71 (95%CI 0.68-0.74). Adding SVD markers
 did not significantly improve ICH score discrimination; for the best model
 (adding severe atrophy) the AUROC was 0.73 (95%CI 0.69-0.76). These
 results were confirmed when considering lobar and non-lobar ICH,
 separately. Conclusions. The ICH score has acceptable discrimination for
 predicting 6-month functional outcome after ICH. CT biomarkers of SVD are
 associated with functional outcome but adding them does not significantly
 improve ICH score discrimination.
DOI: 10.5061/dryad.p8cz8w9nq
title: Stacking microscopy images of the pteropod Limacina bulimoides

description: Pteropods, a group of holoplanktonic gastropods, are regarded as
 bioindicators of the effects of ocean acidification on open ocean
 ecosystems, because their thin aragonitic shells are susceptible to
 dissolution. While there have been recent efforts to address their
 capacity for physiological acclimation, it is also important to gain
 predictive understanding of their ability to adapt to future ocean
 conditions. However, little is known about the levels of genetic variation
 and large scale population structuring of pteropods, key characteristics
 enabling local adaptation. We examined the spatial distribution of genetic
 diversity in the mitochondrial cytochrome c oxidase I (COI) and nuclear
 28S gene fragments, as well as shell shape variation, across a latitudinal
 transect in the Atlantic Ocean (35°N-36°S) for the pteropod Limacina
 bulimoides. We observed high levels of genetic variability (COI π = 0.034,
 28S π = 0.0021) and strong spatial structuring (COI ΦST = 0.230, 28S ΦST =
 0.255) across this transect. Based on the congruence of mitochondrial and
 nuclear differentiation, as well as differences in shell shape, we
 identified a primary dispersal barrier in the southern Atlantic
 subtropical gyre (15-18°S). This barrier is maintained despite the
 presence of expatriates, a gyral current system, and in the absence of any
 distinct oceanographic gradients in this region, suggesting that
 reproductive isolation between these populations must be strong. A
 secondary dispersal barrier supported only by 28S pairwise ΦST comparisons
 was identified in the equatorial upwelling region (between 15°N-4°S),
 which is concordant with barriers observed in other zooplankton species.
 Both oceanic dispersal barriers were congruent with regions of low
 abundance reported for a similar basin-scale transect that was sampled two
 years later. Our finding supports the hypothesis that low abundance
 indicates areas of suboptimal habitat that result in barriers to gene flow
 in widely-distributed zooplankton species. Such species may in fact
 consist of several populations or (sub)species that are adapted to local
 environmental conditions, limiting their potential for adaptive responses
 to ocean changes. Future analyses of genome-wide diversity in pteropods
 could provide further insight into the strength, formation and maintenance
 of oceanic dispersal barriers.
description: This dataset contains stacking mircoscropy images of the
 following: 136 undamaged adult shells of
 <em>Limcina bulimoides</em> specimens. 30
 invidual <em>Limcina bulimoides </em>specimens. Each
 individual was photographed and digitised twice. 
 Specimens were photographed in standardised apertural orientation
 using a Zeiss V20 stacking stereomicroscope with Axiovision
 software.
description: These images can be used for geometric morphometrics analyses of
 shell shape.
DOI: 10.5061/dryad.95x69p8j6
title: Supporting data from: The distribution of leaf form among indigenous woody angiosperms in New Zealand

description: New Zealand’s woody indigenous eudicot flora comprises a variety of leaf
 shapes and features and occupies environments extending from subtropical
 to cold temperate climates. We used a dataset of over 300,000 occurrences
 of 557 indigenous woody eudicot species to investigate patterns and trends
 in the occurrence of six leaf features (leaf pubescence, leaf margin
 teeth, leaf size, leaf apex and base shape, and leaf length to width
 ratio) along critical climate gradients. Major climate variables examined
 included temperature, precipitation, moisture deficit and solar radiation.
 Our results reveal strong latitudinal gradients in toothed leaves and leaf
 area with both declining at higher latitudes. Leaf base and leaf apex
 angle are also aligned latitudinally, both declining in northern areas. In
 contrast, the occurrence of pubescent leaves and leaf length to width
 ratio are independent of other leaf features and latitudinal gradients.
 Larger leaves are positively associated with warmer climates while
 serrated margins are more common in warmer and wetter zones. The
 occurrence of pubescent leaves is greatest in seasonally dry environments
 with low annual precipitation. Long thin leaves (high length to width
 ratio) were more common in areas with a high rainfall to potential
 evapotranspiration ratio. Leaf apex angle is negatively correlated with
 temperature while leaf base angle distribution in relation to climate was
 highly variable. Overall, results confirm global patterns for leaf size
 and climate, highlighting the importance of small leaves limiting heat
 loss in cool climates. The positive correlation between leaf teeth and
 warmer climates has not been found elsewhere. High occurrence of pubescent
 leaves in low rainfall and highly moisture deficient environments in New
 Zealand suggests that the trait is associated with water retention in dry
 climates.
description: Dataset includes: - Table S1: New Zealand
 species leaf morphological data derived from descriptions referenced in
 the dataset. - Table S2: Geodetic coordinates of plot
 centroids in New Zealand with associated leaf trait variables, derived
 from species descriptions in Table S1 and species occurrences
 from https://doi.org/10.15468/bxxmis, https://doi.org/10.15468/ab3s5x
 and https://doi.org/10.15468/uzxpbn - Table S3:
 Geodetic coordinates of plot centroids in New Zealand with associated
 climate variables derived from Leathwick, J. R., Morgan, F., Wilson, G.
 J., Rutlegde, D., McLeod, M., & Johnston, K. (2002). <i>Land
 Environments of New Zealand: A technical guide. Ministry for the
 Environment, Auckland, New Zealand.</i>
DOI: 10.5061/dryad.7h44j0zsj
title: Living and fossil Ginkgo leaves

description: The data presented here are a collection of images of living and
 fossil Ginkgo leaves. Mature and fully expanded
 leaves were harvested from a reproductively immature Ginkgo biloba tree
 growing in partial shade as a specimen on the campus of The Open
 University, UK. The specimen was ascended using a ladder and seven
 branches growing towards the West at approximately halfway up the specimen
 were removed from the trunk using a saw. Every leaf growing on each branch
 was plucked from the base of the petiole and dried in a plant press. A
 total of 468 leaves from a mixture of short-shoots and long-shoots were
 collected from the specimen. Each of these leaves was photographed next to
 a scale bar using a digital camera positioned 20cm above a light box.
 Twenty-two fossil leaves produced by evolutionary relatives of living
 Ginkgo biloba were extracted from the collections of the Natural History
 Museum in London, and two fossil leaves were extracted from the geology
 collections of the School of Environment, Earth and Ecosystem Sciences,
 The Open University. Each fossil leaf was photographed next to a scale bar
 using a digital camera and the outline of each fossil was traced using
 Adobe Illustrator to create a digital outline of each leaf.