cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fttdz08pt
title: Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae

description: Angiosperms have become the dominant terrestrial plant group by
 diversifying for ~145 million years into a broad range of environments.
 During the course of evolution, numerous morphological innovations arose,
 often preceded by whole genome duplications (WGD). The mustard family
 (Brassicaceae), a successful angiosperm clade with ~4000 species, has been
 diversifying into many evolutionary lineages for more than 30 million
 years. Here we develop a species inventory, analyze morphological
 variation, and present a maternal, plastome-based genus-level phylogeny.
 We show that increased morphological disparity, despite an apparent
 absence of clade-specific morphological innovations, is found in tribes
 with WGDs or diversification rate shifts. Both are important processes in
 Brassicaceae, resulting in an overall high net diversification rate.
 Character states show frequent and independent gain and loss, and form
 varying combinations. Therefore, Brassicaceae pave the way to concepts of
 phylogenetic genome-wide association studies to analyze the evolution of
 morphological form and function.
description: The dataset comprises a detailed SupplementaryDataset1 providing
 all accession details and corresponding data sources. A Dataset2 provides
 a Brassicaceae species checklist. Datasets 3 and 4 provide the
 morphological datamatrices on genus and tribal level, respectively.
 Dataset 5 provided the plastome alignment including data partioning.
 Dataset 6 provides the nrDNA operon alignment. Dataset 7 provides the
 results of the BEAST analaysis of plsatome data in *.tre file
 format.
DOI: 10.5061/dryad.0gb5mkkxt
title: Data from: Artificial refuges to combat habitat loss for an endangered marsupial predator: how do they measure up?

description: One technique used to combat the growing global species extinction crisis
 has been to create artificial refuges—human-made replacements for natural
 refuges destroyed during habitat modification. However, there is
 limited knowledge of how closely artificial
 refuges replicate the natural refuges they seek to
 replace. Mining threatens many species worldwide through large-scale
 habitat modification, and artificial refuges have been proposed as a
 method to offset the resulting habitat loss. Here, we examined the
 microclimatic, physical, and biotic characteristics of natural dens
 occupied by the northern quoll (Dasyurus hallucatus)—an endangered
 marsupial threatened by habitat loss—and compared these to 1)
 superficially similar unoccupied crevices, and 2) artificial dens created
 by mining companies for northern quolls. Northern quolls occupied natural
 dens that were cooer and deeper than unoccupied crevices, likely
 to avoid lethal air temperatures as well
 as predators. Artificial dens provided similar thermal properties
 to occupied dens, but lacked
 key characteristics in having shallower den cavities, less complex surrounding habitat, increased feral cat visitation, and less small mammal prey compared to occupied dens. This study highlights the need to consider multiple facets when constructing artificial refuges, in order to avoid perverse outcomes, such as inadequate shelter, increased predation and food shortages.
description: <strong>Raw Records</strong> This
 dataset includes the data and code used in study analysis. Including
 temperature data, humidity data, den characteristic and site data, as well
 as quoll, predator, and prey visitation and activity data. This also
 includes all code used in the study.
DOI: 10.5061/dryad.gxd2547h9
title: Data from: Osteosarcopenia in reproductive-aged women with polycystic ovary syndrome: a multicenter case-control study

description: Context: Osteosarcopenia (loss of skeletal muscle and bone mass and/or
 function usually associated with aging) shares pathophysiological
 mechanisms with polycystic ovary syndrome (PCOS). However, the
 relationship between osteosarcopenia and PCOS remains unclear. Objective:
 We evaluated skeletal muscle index% (SMI%=[appendicular muscle mass/weight
 {kg}]×100) and bone mineral density (BMD) in PCOS
 (hyperandrogenism+oligoamenorrhea), and contrasted these musculoskeletal
 markers against 3 reproductive phenotypes: (1) HA
 (hyperandrogenism+eumenorrhea); (2) OA (normoandrogenic+oligoamenorrhea)
 and, (3) controls (normoandrogenic+eumenorrhea). Endocrine predictors of
 SMI% and BMD were evaluated across groups. Design, Setting, Participants:
 Multicenter case-control study of 203 women (18–48y) in New York
 State.  Results: PCOS group exhibited reduced SMI% (mean [95%CI];
 26.2% [25.1,27.3] vs. 28.8% [27.7,29.8]), lower-extremity SMI% (57.6%
 [56.7,60.0] vs. 62.5% [60.3,64.6]), and BMD (1.11 [1.08,1.14] vs. 1.17
 [1.14,1.20] g/cm2) compared to controls. PCOS group also had decreased
 upper (0.72 [0.70,0.74] vs. 0.73 [0.71,0.76] g/cm2) and lower (1.13
 [1.10,1.16] vs. 1.15 [1.12,1.18] g/cm2) limb BMD compared to HA. Matsuda
 index was lower in PCOS vs. controls and positively associated with SMI%
 in all groups (All:P≤0.05). Only controls showed associations between
 insulin-like-growth-factor-1 (IGF-1) and upper (r=0.84) and lower (r=0.72)
 limb BMD (All:P&lt;0.01). Unlike in PCOS, IGF binding-protein-2 was
 associated with SMI% in controls (r=0.45) and HA (r=0.67), and with upper
 limb BMD (r=0.98) in HA (All:P&lt;0.05). Conclusions: Women with PCOS
 exhibit early signs of osteosarcopenia compared to controls likely
 attributed to disrupted insulin function. Understanding the degree of
 musculoskeletal deterioration in PCOS is critical for implementing
 targeted interventions that prevent and delay osteosarcopenia in this
 clinical population.
DOI: 10.5061/dryad.w3r2280mr
title: Paternally inherited P-element copy number affects the magnitude of hybrid dysgenesis in Drosophila simulans and D. melanogaster

description: Transposable elements (TEs) are repetitive regions of DNA that are able to
 self-replicate and reinsert themselves throughout host genomes. Since the
 discovery of TEs, a prevalent question has been whether increasing TE copy
 number has an effect on the fitness of their hosts. P-elements (PEs) in
 Drosophila are a well-studied TE that has strong phenotypic effects. When
 a female without PEs (M) is crossed to a male with them (P), the resulting
 females are often sterile, a phenomenon called hybrid dysgenesis (HD).
 Here, we used short and long-read sequenced to infer the number of PEs in
 the genomes of dozens of isofemale lines from two Drosophila species and
 measured whether the magnitude of HD was correlated with the number of PEs
 in the paternal genome. Consistent with previous reports, we find evidence
 for a positive correlation between the paternal PE copy number and the
 magnitude of HD in progeny from ♀M ´ ♂ P crosses for both species. Other
 crosses are not affected by the number of PE copies. We also find that the
 correlation between the strength of HD and PE copy number differs between
 species which suggest there are genetic differences that might make some
 genomes more resilient to the potentially deleterious effects of TEs. Our
 results suggest that PE copy number interacts with other factors in the
 genome and the environment to cause HD and that the importance of these
 interactions is species-specific.
DOI: 10.5061/dryad.pnvx0k6j8
title: The novel ciliogenesis regulator DYRK2 governs Hedgehog signaling during mouse embryogenesis

description: Mammalian Hedgehog (Hh) signaling plays key roles in embryogenesis and
 uniquely requires primary cilia. Functional analyses of several
 ciliogenesis-related genes led to the discovery of the developmental
 diseases known as ciliopathies. Hence, identification of mammalian factors
 that regulate ciliogenesis can provide insight into the molecular
 mechanisms of embryogenesis and ciliopathy. Here, we demonstrate that
 DYRK2 acts as a novel mammalian ciliogenesis-related protein kinase. Loss
 of Dyrk2 in mice causes suppression of Hh signaling and results in
 skeletal abnormalities during in vivo embryogenesis. Deletion of Dyrk2
 induces abnormal ciliary morphology and trafficking of Hh pathway
 components. Mechanistically, transcriptome analyses demonstrate
 down-regulation of AurkA and other disassembly genes following Dyrk2
 deletion. Taken together, the present study demonstrates for the first
 time that DYRK2 controls ciliogenesis and is necessary for Hh signaling
 during mammalian development.
DOI: 10.5061/dryad.t4b8gthzh
title: Hummingbird torpor in context: duration, more than temperature, is the key to nighttime energy savings

description: Torpor is an important energy saving strategy in some small birds, but it
 has rarely been studied in natural field conditions. We compared torpor
 use across 43 wild-caught individuals of eight hummingbird species across
 sites with different natural temperature regimes. Most laboratory studies
 focus on the relationship between metabolic rate and temperature, but our
 aim was to evaluate what environmental factors most influence hummingbird
 nighttime energy management under natural conditions. We found that the
 probability of an individual entering torpor was weakly correlated with
 mass but unrelated to nighttime temperature and that hummingbirds at both
 warm, tropical and cooler, temperate sites used torpor. Energy savings in
 torpor were maximized as ambient temperatures approached a species’
 minimum body temperature, consistent with laboratory studies; energy
 savings ranged between 65-92% of energy per hour in torpor compared to
 normothermy. However, regardless of the degree of energy savings in
 torpor, variation in total nighttime energy expenditure was most
 significantly influenced by torpor bout duration. Lab studies largely
 assess the effect of temperature on torpor use, but our findings indicate
 that other environmental conditions are more important in determining
 hummingbirds’ total nighttime energy expenditure under natural temperature
 cycles. Our results show that a small endotherm’s nighttime energy
 management in its natural habitat is more affected by torpor bout
 duration, which is linked to photoperiod, than by temperature. This result
 suggests that in their natural environments hummingbirds are able to save
 energy in torpor across a range of nighttime temperatures, indicating that
 they may have sufficient physiological flexibility to tolerate climatic
 variation.
description: Energy expenditure data collected via open-flow respirometry, in
 the field in Arizona and Ecuador. 
description: See metadata document for file descriptions, including column
 identifiers and keys.
DOI: 10.3886/e241296
title: Multi-view Deep Learning Improves Detection of Major Cardiac Conditions from Echocardiography

description: This dataset provides a minimal, fully de-identified example of the multiview echocardiography inputs used in “Multi-view Deep Learning Improves Detection of Major Cardiac Conditions from Echocardiography.” It contains 30 echocardiography studies, each with three standard non-Doppler views (apical four-chamber, apical two-chamber, and parasternal long-axis) along with a CSV file specifying file paths and study-level labels for ventricular abnormality. Videos were preprocessed exactly as described in the manuscript, including cropping to the echo cone, removing burned-in text, resizing to 224×224 pixels, and selecting the first 64 frames.
This small dataset is intended only to illustrate the multiview data format and support reproducibility of model-loading and training code. It is not suitable for clinical modeling. All clips are fully de-identified and contain no protected health information.
DOI: 10.5061/dryad.bk3j9kd7n
title: Spatial drivers of composition and connectivity across endangered tropical dry forests

description: 1. Tropical dry forests are among the most threatened ecosystems in the
 world. Rapid loss, degradation, and fragmentation of these native
 ecosystems in a changing climate have driven a time-sensitive need to
 improve our understanding and management of remaining dry forests. 2. We
 used advanced remote sensing technologies, combined with extensive field
 data and machine learning, to better understand how spatial drivers (e.g.,
 climate, fire, human) of canopy species composition vary in importance and
 correlate with forest cover (total, native and non-native), within an
 endangered Hawaiian tropical dry forest. 3. Past introductions of
 non-native, drought-tolerant tree species into this Hawaiian dry forest
 have created a new forest canopy composition and a loss of native forest
 biodiversity and connectivity at the landscape scale. 4. Synthesis and
 application. Our findings help to spatially visualize the loss and
 transition of native Hawaiian forests and provide a new conservation
 planning tool. Conservation and restoration efforts can now be informed by
 spatial maps of canopy composition, connectivity, and determinants of
 forest cover for the region. For example, our models identified a climatic
 transition zone between 800-1000 m where native forests exist in high
 densities, and non-native forests are not yet dominant. This area may be
 optimal for cost-effective conservation and targeted management.
description: The raw data contains
 information from multiple sources. Most of the data was originally
 downloaded from the Hawaii GIS portal (https://planning.hawaii.gov/gis/) and is freely available. Hyperspectral data to create the forest cover map was obtained from the Global Airborne Observatory (https://gdcs.asu.edu/programs/global-airborne-observatory ). A more in-depth description of the data can be found in the associated paper.
DOI: 10.3886/e241296v2
title: Multi-view Deep Learning Improves Detection of Major Cardiac Conditions from Echocardiography

description: This dataset provides a minimal, fully de-identified example of the multiview echocardiography inputs used in “Multi-view Deep Learning Improves Detection of Major Cardiac Conditions from Echocardiography.” It contains 30 echocardiography studies, each with three standard non-Doppler views (apical four-chamber, apical two-chamber, and parasternal long-axis) along with a CSV file specifying file paths and study-level labels for ventricular abnormality. Videos were preprocessed exactly as described in the manuscript, including cropping to the echo cone, removing burned-in text, resizing to 224×224 pixels, and selecting the first 64 frames.
This small dataset is intended only to illustrate the multiview data format and support reproducibility of model-loading and training code. It is not suitable for clinical modeling. All clips are fully de-identified and contain no protected health information.
DOI: 10.5061/dryad.fn2z34tqv
title: Data from: Climate and soil nutrients differentially drive multidimensional fine root traits in ectomycorrhizal‐dominated alpine coniferous forests

description: Fine root traits vary greatly with environmental changes, but the
 understanding of root-trait variation and its drivers is limited over
 broad geographical scales, especially for ectomycorrhizal (ECM)-dominated
 conifers in alpine forests. Herein, the covariation patterns of and
 environmental controls for fine root traits among ECM-dominated conifers
 were examined to test whether and how climate and soil nutrients
 differentially affect fine root trait variations. Eight traits of first-
 and second-order roots were measured, i.e., root diameter (RD), specific
 root length (SRL), branching intensity (BRI), root tissue density (RTD),
 mycorrhizal colonization rate (MCR), and concentrations of carbon (C),
 nitrogen (N) and phosphorus (P), across 76 alpine coniferous populations
 on the eastern Tibetan Plateau, China. Our results showed that variations
 of the fine root traits fell into two major dimensions: the first
 dimension (32.39% of the total variance) was mainly represented by RD and
 SRL, potentially conveying a tradeoff between root lifespan and efficiency
 of resource foraging; the second dimension (23.70% of the variance)
 represented coordinated variation for root nutrients (i.e., N and P) and
 RTD, which depicts the conservation-acquisition tradeoff in resource
 uptake, i.e., root economic spectrum (RES). Variations in RD and SRL were
 mainly driven by climatic variables, characterized by a significant
 increase in RD and a decrease in SRL with increasing mean annual
 precipitation. In contrast, variations in fine root nutrients (i.e., N and
 P) and RTD were primarily driven by soil fertility, showing a significant
 increase in root N and P concentrations but a decrease in RTD with
 increasing soil resource levels. Synthesis. Our study clearly shows two
 distinct dimensions of the variation of fine root traits in ECM-dominated
 alpine coniferous forests, providing further evidence of the inherent
 multidimensionality of root traits. Moreover, our findings highlight
 different roles of climatic and soil variables in driving the variation of
 fine root traits, potentially leading to the multidimensionality of root
 traits. This study provides new insights for understanding and predicting
 shifts in plant belowground strategies in climate-sensitive alpine forests
 worldwide.
DOI: 10.5061/dryad.1zcrjdfph
title: The beak and unfeathered skin as heat radiators in the Southern Ground-hornbill

description: The avian beak is increasingly recognised as an important organ for
 thermoregulation, particularly in disproportionately large-beaked taxa
 such as toucans and hornbills. We used infrared thermography to test the
 prediction that Southern Ground-hornbills (Bucorvus leadbeateri)
 physiologically regulate the surface temperature of their beak (Tbeak), as
 well as that of their facial (Tfacial) and gular skin (Tgular) in such a
 way that these surfaces provide avenues for non-evaporative heat
 dissipation in warm weather. Our data, collected over air temperatures
 (Ta) ranging from 11 °C to 36 °C, supported these predictions. At Ta
 &lt; 20 °C, Tbeak tracked Ta, but rapidly increased to values 6-12 °C
 above Ta at Ta = 20-22 °C. The Tbeak-Ta gradient was maintained at
 approximately 7 °C between Ta = 22 °C and 28 °C, before decreasing
 linearly with Ta &gt; 28 °C. We also found evidence for active
 regulation of Tfacial and Tgular, with both surfaces regulated at
 approximately constant increments above Ta up to inflection Ta values of
 22 °C and 29 °C, respectively. The presence of inflection Ta values
 corresponding with abrupt changes in physiological regulation of these
 surface areas suggests a high degree of physiological control. Estimates
 of heat exchange suggest that SGH may be able to dissipate up to 75 % of
 basal metabolic rate via these surfaces, confiming the beak and areas of
 unfeather skin play an important thermoregulatory role in these large,
 distinctive and threatened birds.
DOI: 10.5061/dryad.h9w0vt4fm
title: Cortinarius brunneocarpus var. microsporus, an interesting variety with Eurasian distribution

description: Cortinarius brunneocarpus var. microsporus is described and illustrated
 from coniferous forests of District Swat, Pakistan based on morphological
 characters and phylogenetic analyses of the nuclear rDNA internal
 transcribed spacer (ITS) region. It is morphologically well-supported by
 significantly smaller basidiospores which are moderately to densely
 verrucose and with a suprahilar depression  The new variety has
 Eurasian distribution and is being reported from Pakistan, Norway and
 Estonia. Differences between the new variety and similar taxa are briefly
 discussed.
DOI: 10.5061/dryad.m0cfxpp0v
title: Data from: Research culture: a survey of travel behaviour among scientists in Germany and the potential for change

description: Awareness of the environmental impact of conferences is growing within the
 scientific community. Here we report the results of a survey in which
 scientists in Germany were asked about their attendance at conferences,
 their reasons for attending, and their willingness to explore new
 approaches that would reduce the impact of conferences on the environment.
 A majority of respondents were keen to reduce their own carbon footprint
 and were willing to explore alternatives to the traditional conference.
description: Scientists travel across the globe to attend scientific
 conferences in their specialized research areas, for presentation of novel
 data, career development and networking. Concomitantly, scientists have
 the opportunity to drive societal change by taking a leading role in
 confronting climate change and promoting sustainability.   
 Here we report the results of a survey of international
 scientists from all academic career stages with regard to their travels to
 scientific conferences in 2019 as well as their disposition for changing
 their traveling behaviour for sustainability reasons. The majority of
 surveyed scientists travel in a sustainable fashion, are willing to reduce
 their conferences travels for environmental protection and are open to
 alternative web-based conference formats. Changes in institutional
 policies granting sustainable framework conditions combinedwith the
 courage of leading scientists to set examples for innovative conference
 formats are needed to transform the scientific community and drive
 societal change.
DOI: 10.5061/dryad.v9s4mw6rt
title: Data from: Fitness consequences of redundant cues of competition in male D. melanogaster

description: Phenotypic plasticity can allow animals to adapt their behaviour, such as
 their mating effort, to their social and sexual environment. However, this
 relies on the individual receiving accurate and reliable cues of the
 environmental conditions. This can be achieved via the receipt of
 multimodal cues, which may provide redundancy and robustness. Male
 Drosophila melanogaster detect presence of rivals via combinations of any
 two or more redundant cue components (sound, smell and touch) and respond
 by extending their subsequent mating duration, which is associated with
 higher reproductive success. Although alternative combinations of cues of
 rival presence have previously been found to elicit equivalent increases
 in mating duration and offspring production, their redundancy in securing
 success under sperm competition has not previously been tested. Here, we
 explicitly test this by exposing male D. melanogaster to alternative
 combinations of rival cues, and examine reproductive success in both the
 presence and absence of sperm competition. The results supported previous
 findings of redundancy of cues in terms of behavioural responses. However,
 there was no evidence of reproductive benefits accrued by extending mating
 duration in response to rivals. The lack of identifiable fitness benefits
 of longer mating under these conditions, both in the presence and absence
 of sperm competition, contrasted with some previous results, but could be
 explained by: 1) damage sustained from aggressive interactions with rivals
 leading to reduced ability to increase ejaculate investment, 2) presence
 of features of the social environment, such as male and female mating
 status, that obscured the fitness benefits of longer mating, 3) decoupling
 of behavioural investment with fitness benefits.
description: Details of collection are given in the read me data tab and
 details of the statistical analyses in the main MS.
description: Read me tab forms the first sheet of the raw data file.