cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tht76hdv9
title: Thinner bark increases sensitivity of wetter Amazonian tropical forests to fire

description: Understory fires represent an accelerating threat to Amazonian tropical
 forests and can, during drought, affect larger areas than deforestation
 itself. These fires kill trees at rates varying from &lt; 10
 to c. 90% depending on fire intensity, forest disturbance history and tree
 functional traits. Here, we examine variation in bark thickness across the
 Amazon. Bark can protect trees from fires, but it is often assumed to be
 consistently thin across tropical forests. Here, we show that investment
 in bark varies, with thicker bark in dry forests and thinner in wetter
 forests. We also show that thinner bark translated into higher fire‐driven
 tree mortality in wetter forests, with between 0.67 and 5.86 gigatonnes
 CO2 lost in Amazon understory fires between 2001 and 2010.
 Trait‐enabled global vegetation models that explicitly include variation
 in bark thickness are likely to improve the predictions of fire effects on
 carbon cycling in tropical forests.
DOI: 10.15468/dl.9n9z9d
title: Occurrence Download

description: A dataset containing 15974 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aspidosperma quebracho-blanco, Tessaria integrifolia, Celtis ehrenbergiana, Sapium haematospermum, Chloroleucon tenuiflorum, Enterolobium contortisiliquum, Erythrina crista-galli, Geoffroea decorticans, Inga affinis, Neltuma, Pseudalbizzia inundata, Sesbania virgata, Vachellia caven, Nectandra angustifolia, Ocotea acutifolia, Eugenia myrcianthes, Phyllanthus sellowianus, Myrsine laetevirens, Salix humboldtiana, Solanum glaucophyllum, Porlieria microphylla, Schinopsis, Blepharocalyx salicifolius, Lycium vimineum, Jodina rhombifolia, Anadenanthera colubrina, Schoenoplectus, Amaranthus hybridus, Amaranthus standleyanus, Amaranthus deflexus, Chenopodium album, Chenopodium hircinum, Dysphania ambrosioides)",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 15974 records from 113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001938-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8hv6726
title: Data from: Exact distribution of divergence times from fossil ages and tree topologies

description: Being given a phylogenetic tree of both extant and extinct taxa in which
 the fossil ages are the only temporal information (namely, in which
 divergence times are considered unknown), we provide a method to compute
 the probability distribution of any divergence time of the tree with
 regard to any speciation (cladogenesis), extinction and fossilization
 rates under the Fossilized-Birth-Death model. We then use this method to
 obtain a probability distribution for the age of Amniota (the
 synapsid/sauropsid or bird/mammal divergence), one of the most-frequently
 used dating constraint.
description: 100 Cotylosauria
 trees100 equiparsimonious
 trees of Cotylosauria in Newick format (109 taxa)CotylosauriaTree.phyIntervals of fossil ages of CotylosauriaIntervals of fossil ages of Cotylosauria associated to the trees of 'CotylosauriaTree.phy'CotylosauriaAges.csv
DOI: 10.5061/dryad.cvdncjt05
title: Symbiotic moss-cyanobacteria associations as a novel source of biological N2-fixation in temperate grasslands

description: Aims. Terrestrial mosses contribute significantly to nitrogen
 budgets in boreal forests through symbiotic associations with
 N2-fixing cyanobacteria, but few studies have considered these
 interactions in temperate systems. We investigated how N2-fixation by
 moss-cyanobacterial associations contribute spatio-temporally to
 site-level N dynamics in a western North American prairie ecosystem.
 Methods. We first tested for the presence of N2-fixing
 cyanobacteria on six moss species using epi-fluorescence light microscopy.
 We then used an acetylene reduction assay to estimate monthly N2-fixation
 rates in moss-cyanobacteria associations across three prairies located in
 the Puget Sound, Washington State, USA. We evaluated temperature and
 precipitation effects on N2-fixation activity. 
 Results. We confirmed the presence of N2-fixing cyanobacteria on
 three moss species (Pleurozium schreberi (Brid.) Mitt.,
 Racomitrium elongatum Frisvoll, Rhytidiadelphus
 triquetrus (Hedw) Warnst.) and found species, site and seasonal
 variation in N2-fixation
 rates. Racomitrium elongatum exhibited the
 highest N2-fixation rates, with peaks in April and August. We found that
 temperature and precipitation were strongly correlated with N2-fixation
 rates and likelihood of activity.  Conclusions. Our
 results highlight a previously undescribed source of biological
 N2-fixation in temperate grasslands. Changes in the distribution and
 activity of these species due to climate change and management practices
 could impact stand-level nitrogen dynamics.
DOI: 10.6078/d1j68b
title: X-Ray Spectra (Mg, Ge)

description: Here are 4 x-ray emission spectra of the 3p1/2→2s1/2 transition
 in neonlike germanium and 2 x-ray emission spectra of Lyα1 and
 Lyα2 of hydrogenlike magnesium.  These were taken at the
 electron beam ion trap at Lawrence Livermore National
 Laboratory.  Two crystals were used and thus, there are two peaks
 detected for each line.  The experiment was performed
 under the auspices of the U. S. Department of Energy by Lawrence Livermore
 National Laboratory under contract No. DE-AC52-07NA27344.
DOI: 10.15468/dl.7h2ww7
title: Occurrence Download

description: A dataset containing 1205 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-94.0",
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Ficus petiolaris"
 ]
}

 The dataset includes 1205 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001940-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.v6wwpzgqx
title: Consumer mobility predicts impacts of herbivory across a wave stress gradient

description: Environmental stress impedes predation and herbivory by limiting the
 ability of animals to search for and consume prey. We tested the
 contingency of this relationship on consumer traits, and specifically
 hypothesized that herbivore mobility relative to the return time of
 limiting environmental stress would predict consumer effects. We examined
 how wave-induced water motion affects marine communities via herbivory by
 highly mobile (fish) versus slow moving (pencil urchin) consumers at two
 wave-sheltered and two wave-exposed rocky subtidal locations in the
 Galapagos Islands. The exposed locations experienced 99th percentile flow
 speeds that were 2-5 times greater than sheltered locations, with mean
 flow speeds &gt;33 cm/s vs &lt;16 cm/s, 2-7 times higher standing
 macroalgal cover and 2-3 times lower cover of crustose coralline algae
 than the sheltered locations. As predicted by the Environmental Stress
 Hypothesis (ESH), there was a negative relationship between mean flow
 speed and urchin abundance and herbivory rates on Ulva spp. algal feeding
 assays. In contrast, the biomass of surgeonfishes (Acanthuridae) and
 parrotfishes (Labridae- Scarinae) was positively correlated with mean flow
 speed. Ulva assays were consumed at equal rates by fish at exposed and
 sheltered locations, indicating continued herbivory even when flow speeds
 surpassed maximum reported swimming speeds at a rate of 1-2 times per
 minute. Modeled variation in fish species richness revealed minimal
 effects of diversity on herbivory rates at flow speeds &lt;40 cm/s,
 when all species were capable of foraging, and above 120 cm/s, when no
 species could forage, while increasing diversity maximized herbivory rates
 at flow speeds of 40 – 120 cm/s. Two-month herbivore exclusion experiments
 during warm and cool seasons revealed that macroalgal biomass was
 positively correlated with flow speed. Fish limited macroalgal development
 by 65-91% at one exposed location but not the second, and by 70% at the
 two sheltered locations. In contrast, pencil urchins did not affect algal
 communities at either exposed location, but reduced macroalgae by 87%
 relative to controls at both sheltered locations. We propose an extension
 of the ESH that is contingent upon mobility to explain species-specific
 changes in feeding rates and consumer effects on benthic communities
 across environmental gradients.
DOI: 10.25338/b8tg8s
title: Data from: Body shape diversification along the benthic-pelagic axis in marine fishes

description: Colonization of novel habitats can result in marked phenotypic responses
 to the new environment that include changes in body shape and
 opportunities for further morphological diversification. Fishes have
 repeatedly transitioned along the benthic-pelagic axis, with varying
 degrees of association with the substrate. Previous work focusing on
 individual lineages shows that these transitions are accompanied by highly
 predictable changes in body form. Here, we generalize expectations drawn
 from this literature to study the effects of habitat on body shape
 diversification across 3,344 marine teleost fishes. We compare rates and
 patterns of evolution in eight linear measurements of body shape among
 fishes that live in pelagic, demersal, and benthic habitats. While average
 body shape differs between habitats, these differences are subtle compared
 to the high diversity of shapes found within each habitat. Benthic living
 increases the rate of body shape evolution and has led to numerous
 lineages evolving extreme body shapes, including both exceptionally wide
 bodies and highly elongate, eel-like forms. In contrast, we find that
 benthic living is associated with the slowest diversification of
 structures associated with feeding. Though we find that habitat can serve
 as an impetus for predictable trait changes, we also highlight the
 diversity of responses in marine teleosts to opportunities presented by
 major habitats.
DOI: 10.25345/c5707x269
title: MassIVE MSV000100606 - Single-Cell Proteomics Reveals Cytoplasmic Defects in Patl2-Deficient Oocytes Rescued by Spindle Transfer
title: In vivo matured MII oocytes from Patl2-/- and Patl2+/+ female mice were collected for single-cell proteomics and prepared using a one-pot workflow. Data were acquired using a U3000 using a 30-minute trap-and-elute method in-line with a timsTOF Ultra operated in dia-PASEF mode.
DOI: 10.5061/dryad.fj6q573q1
title: No evidence for early fitness penalty in glyphosate-resistant biotypes of Conyza canadensis: common garden experiments in the absence of glyphosate

description: Strong selection from herbicides has led to the rapid evolution of
 herbicide-resistant weeds, greatly complicating weed management efforts
 worldwide.  In particular, overreliance on glyphosate, the active
 ingredient in RoundUp®, has spurred the evolution of resistance to this
 herbicide in ≥40 species.  Previously, we reported that Conyza
 canadensis (horseweed) has evolved extreme resistance to glyphosate,
 surviving at 40x the original 1x effective dosage.  Here, we
 tested for underlying fitness effects of glyphosate resistance to better
 understand whether resistance could persist indefinitely in this
 self-pollinating, annual weed.  We sampled seeds from a single
 maternal plant (“biotype”) at each of 26 horseweed populations in Iowa,
 representing 9 susceptible biotypes (S), 8 with low-level resistance (LR),
 and 9 with extreme resistance (ER).  In 2016 and 2017, we
 compared early growth rates and bolting dates of these biotypes in common
 garden experiments at two sites near Ames, Iowa.  Nested ANOVAs
 showed that, as a group, ER biotypes attained similar or larger rosette
 size after 6 weeks compared to S or LR biotypes, which were similar to
 each other in size.  Also, ER biotypes bolted 1-2 weeks earlier
 than S or LR biotypes.  These fitness-related traits also varied
 among biotypes within the same resistance category, and time to bolting
 was inversely correlated with rosette size across all biotypes. 
 Disease symptoms affected 40% of all plants in 2016 and 78% in 2017, so we
 did not attempt to measure lifetime fecundity.  In both years,
 the frequency of disease symptoms was greatest in S biotypes and similar
 in LR vs. ER biotypes.  Overall, our findings indicate there is
 no early growth penalty and possibly no lifetime fitness penalty
 associated with glyphosate resistance, including extremely strong
 resistance.  We conclude that glyphosate resistance is likely to
 persist in horseweed populations, with or without continued selection
 pressure from exposure to glyphosate.
DOI: 10.15468/dl.hs8wc6
title: Occurrence Download

description: A dataset containing 656 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-98.50879 19.10171,-98.33154 19.10171,-98.33154 19.22256,-98.50879 19.22256,-98.50879 19.10171))",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 656 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001939-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p8ub8z
title: Occurrence Download

description: A dataset containing 1620 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "TaxonKey is Ursus arctos horribilis"
 ]
}

 The dataset includes 1620 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001942-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m63xsj3x6
title: Neural, functional, and aesthetic impacts of spatially heterogeneous flicker: a potential role of natural flicker

description: Spatially heterogeneous flicker, characterized by probabilistic and
 locally independent luminance modulations, abounds in nature. It is
 generated by flames, water surfaces, rustling leaves, and so on, and it is
 pleasant to the senses. It affords spatiotemporal multistability that
 allows sensory activation conforming to the biases of the visual system,
 thereby generating the perception of spontaneous motion and likely
 facilitating the calibration of motion detectors. One may thus hypothesize
 that spatially heterogeneous flicker might potentially provide restoring
 stimuli to the visual system that engage fluent (requiring minimal
 top-down control) and self-calibrating processes. Here, we present some
 converging behavioral and electrophysiological evidence consistent with
 this idea. Spatially heterogeneous (multistable) flicker (relative to
 controls matched in temporal statistics) reduced posterior EEG
 (electroencephalography) beta power implicated in long-range neural
 interactions that impose top-down influences on sensory processing.
 Further, the degree of spatiotemporal multistability, the amount of
 posterior beta-power reduction, and the aesthetic responses to flicker
 were closely associated. These results are consistent with the idea that
 the pleasantness of natural flicker may derive from its spatiotemporal
 multistability that affords fluent and self-calibrating visual processing.
DOI: 10.5061/dryad.qv9s4mw9b
title: Population structure in landrace barley (Hordeum vulgare L.) during the late 19th century crop failures in Fennoscandia

description: Agricultural disasters and the subsequent need for supply of relief seed
 can be expected to influence the genetic composition of crop plant
 populations. The consequences of disasters and seed relief have, however,
 rarely been studied since specimens sampled before the events are seldomly
 available. A series of crop failures struck northern Fennoscandia (Norway,
 Sweden and Finland) during the second half of the 19th century.
 In order to assess population genetic dynamics of landrace barley (Hordeum
 vulgare), and consequences of crop failure and possible seed relief during
 this time period, we genotyped seeds from 16 historical accessions
 originating from two time periods spanning the period of repeated crop
 failure. Reliable identification of genetic structuring is highly
 dependent on sampling regimes and detecting fine-scale geographic or
 temporal differentiation requires large sample sizes. The robustness of
 the results under different sampling regimes was evaluated by analyzing
 subsets of the data and an artificially pooled dataset. The results led to
 the conclusion that six individuals per accession were insufficient for
 reliable detection of the observed genetic structure. We found that
 population structure among the data was best explained by collection year
 of accessions, rather than geographic origin. The correlation with
 collection year indicated a change in genetic composition of landrace
 barley in the area after repeated crop failures, likely a consequence of
 introgression of relief seed in local populations. Identical genotypes
 were found to be shared among some accessions, suggesting founder effects
 and local seed exchange along known routes for trade and cultural
 exchange. 
description: Individual 19th century seeds were genotyped using an Illumina
 Golden Gate assay for the C-384 barley SNP set detailed by Moragues et al.
 (2010). Quality control based on CG10 scores led to the exclusion of 26 low performance samples, including all nine negative controls. Samples with more than 25 % missing data (39 samples), markers with more than 20 % missing data (92 SNPs) and monomorphic SNPs (140 SNPs) were also excluded, in that order.  
description: Heterozygous loci and missing values are given in the data set as
 -9. Genotypes in the dataset are homozygous genotypes.
DOI: 10.5061/dryad.c2fqz6140
title: Data from: Effects of marker type and filtering criteria on QST-FST comparisons

description: Comparative studies of quantitative and neutral genetic differentiation
 (QST-FST tests) provide means to detect adaptive population
 differentiation. However, QST-FST tests can be overly liberal if the
 markers used deflate FST below its expectation, or overly conservative if
 methodological biases lead to inflated FST estimates.
 We investigated how marker type and filtering criteria for marker
 selection influence QST-FST comparisons through their effects on
 FST using simulations and empirical data on over 18 000 in silico
 genotyped microsatellites and 3.8 million SNP loci from 4
 populations of nine-spined sticklebacks (Pungitius pungitius). Empirical
 and simulated data revealed that FST decreased with increasing
 marker variability, and was generally higher with SNPs than with
 microsatellites. The estimated baseline FST levels were also sensitive to
 filtering criteria for SNPs: both minor alleles and linkage
 disequilibrium pruning influenced FST estimation, as did
 marker ascertainment. However, in the case of stickleback data
 used here where QST is high, the choice of marker type, their
 genomic location, ascertainment and filtering made little difference to
 outcomes of QST-FST tests. Nevertheless, we recommend that
 QST-FST tests using microsatellites should discard the most variable loci,
 and those using SNPs should pay attention to marker ascertainment
 and properly account for linkage disequilibrium before filtering
 SNPs. This may be especially important when level of quantitative trait
 differentiation is low and levels of neutral differentiation
 high.
DOI: 10.5061/dryad.hqbzkh1bb
title: An innovative non-invasive technique for subcutaneous tumour measurements

description: In oncological drug development, animal studies continue to play a central
 role in which the volume of subcutaneous tumours is monitored to assess
 the efficacy of new drugs. The tumour volume is estimated by taking the
 volume to be that of a regular spheroid with the same
 dimensions. However, this method is subjective, insufficiently
 traceable, and is subject to error in the accuracy of volume estimates as
 tumours are frequently irregular. This paper reviews the standard
 technique for tumour volume assessment, calliper measurements, by
 conducting a statistical review of a large dataset consisting of 2,500
 tumour volume measurements from 1,600 mice by multiple operators across 6
 mouse strains and 20 tumour models. Additionally, we explore the impact of
 six different tumour morphologies on volume estimation and the detection
 of treatment effects using a computational tumour growth model. Finally,
 we propose an alternative method to callipers for estimating volume –
 BioVolumeTM, a 3D scanning technique. BioVolume simultaneously captures
 both stereo RGB (Red, Green and Blue) images from different light sources
 and infrared thermal images of the tumour in under a second. It then
 detects the tumour region automatically and estimates the tumour volume in
 under a minute. Furthermore, images can be processed in parallel within
 the cloud and so the time required to process multiple images is similar
 to that required for a single image. We present data of a pre-production
 unit test consisting of 297 scans from over 120 mice collected by four
 different operators. This work demonstrates that it is possible to record
 tumour measurements in a rapid minimally invasive, morphology-independent
 way, and with less human-bias compared to callipers, whilst also improving
 data traceability. Furthermore, the images collected by BioVolume may be
 useful, for example, as a source of biomarkers for animal welfare and
 secondary drug toxicity / efficacy.
DOI: 10.5061/dryad.2fqz612jx
title: Hemorrhage from cerebral cavernous malformations: the role of associated developmental venous anomalies

description: Objective To determine the role of associated developmental venous
 malformations (DVA) in intracranial hemorrhage (ICH) caused by cerebral
 cavernous malformations (CCM).   Methods We analyzed patient
 registry data of 1219 patients with cavernous malformations treated in our
 institution between 2003 and 2018. Patients with spinal and familial CCM
 as well as patients without complete MRI data were excluded. Impact of
 various variables on ICH as mode of presentation was assessed using
 multivariate binary logistic regression analysis. Kaplan Meier/Cox
 regression analysis was performed to analyze cumulative 5-year-risk for
 (re-) hemorrhage and identify baseline predictors of this outcome.
   Results Seven-hundred-thirty-one CCM patients were included.
 Multivariate logistic regression confirmed statistically significant
 negative correlation with DVA (Odds ratio (OR) 0.635 (0.459 – 0.878)) and
 positive correlation with brainstem localization (OR 6.277 (95% CI 4.287 –
 9.191)) with ICH as mode of presentation. Among 731 patients, 76
 experienced (re-) hemorrhage during 2338 person-years of follow-up.
 Overall cumulative 5-year risk was 24.1% (21.1%-27.5% 95% CI). Cox
 regression analysis revealed initial presentation with ICH (hazard ratio
 (HR) 8.0 (3.549 – 18.122 95% CI)) and brainstem localization (HR 2.9
 (1.756 – 4.765 95% CI)) as independent baseline predictors of
 (re)-hemorrhage. Presence of DVA added no independent prognostic
 information (HR 1.1 (0.717 – 1.885 95% CI)).   Conclusions CCM
 with associated DVAs are at lower risk to present with ICH. During
 untreated 5-year follow-up they showed equal (re-)hemorrhage risk compared
 to CCM without DVA.