cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25338/b8nk7w
title: Effects of low-carbon energy adoption on airborne particulate matter concentrations with feedbacks to future climate over California

description: California plans to reduce emissions of long-lived greenhouse gases (GHGs)
 through adoption of new energy systems that will also lower concentrations
 of short-lived absorbing soot contained in airborne particulate matter
 (PM). Here we examine the direct and indirect effects of reduced PM
 concentrationsunder a low-carbon energy (GHG-Step) scenario on radiative
 forcing in California.  Simulations were carried out using the
 source-oriented WRF/Chem (SOWC) model over California with 12 km spatial
 resolutionfor the year 2054. The avoided aerosol emissions due to
 technology advances in the GHG-step scenario reduce ground level PM
 concentrations by ~8.85% over landcompared to the Business as Usual (BAU)
 scenario, but changes to meteorological parameters are more
 modest.  Top of atmospheric forcing predicted by the SOWC model
 increased by 0.15 W m-2, surface temperature warmedby 0.001 K, and
 planetary boundary layer height (PBLH)increased by 2.20 cm in the GHG-Step
 scenario compared to the BAU scenario. PM climate feedbacks are small
 because the significant changes in ground level PM concentrations
 associated with the GHG-Step scenario are limited to the first few hundred
 meters of the atmosphere, with little change for the majority of the
 vertical column above that level.  As an
 order-of-magnitudecomparison, the long-term effects of global reductions
 in GHG emissions (RCP8.5 – RCP4.5) lowered average surface temperature
 over the California study domain by approximately 0.76 K.  The
 effects of long-lived climate pollutants such as CO2are much stronger than
 the effects of short-lived climate pollutants such as PM soot over
 California in the year 2054.
description: <pre> JGR_Repository_Input_Output/Input/BAU has model input emission
 files under BAU scenerio JGR_Repository_Input_Output/Input/GHG-Step has
 model input emission files under GHG-Step scenerio
 JGR_Repository_Input_Output/Output/BAU has model output wrfout files under
 BAU scenerio JGR_Repository_Input_Output/Output/GHG-Step has model output
 wrfout files under GHG-Step scenerio</pre>
DOI: 10.5061/dryad.jh9w0vt89
title: Data from: Local adaptation to herbivory within tropical tree species along a rainfall gradient

description: In tropical forests, insect herbivores exert significant pressure on plant
 populations. Adaptation to such pressure is hypothesized to be a driver of
 high tropical diversity, but direct evidence for local adaptation to
 herbivory in tropical forests is sparse. At the same time, herbivore
 pressure has been hypothesized to increase with rainfall in the tropics,
 which could lead to differences among sites in the degree of local
 adaptation. To assess the presence of local adaptation and its interaction
 with rainfall, we compared herbivore damage on seedlings of local vs
 non-local populations at sites differing in moisture availability in a
 reciprocal transplant experiment spanning a rainfall gradient in Panama.
 For 13 native tree species, seeds collected from multiple populations
 along the rainfall gradient were germinated in a shadehouse and then
 transplanted to experimental sites within the species range. We tracked
 the likelihood of herbivore attack over 1.5 years and quantified the
 percentage of leaf area damaged at the end of the study. Seedlings
 originating from local populations were less likely to be attacked and
 experienced lower amounts of herbivore damage than those from non-local
 populations, but only on the wetter end of the rainfall gradient. However,
 overall herbivore damage was higher at the drier site compared to wetter
 sites, contrary to expectation. Taken together, these findings support the
 idea that herbivory can result in local adaptation within tropical tree
 species; however, the likelihood of local adaptation varies among sites
 due to environmentally-driven differences in investment in defense or
 herbivore specialization or both.
description: Seed from 13 shade-tolerant tree species from Central Panama,
 representing 2-3 populations of each species, was grown to seedling in a
 shadehouse and reciprocally transplanted into the forest understory across
 each species' range. Seedlings were monitored in fenced 1x1 meter
 plots for 1.5 years, where we tracked whether each individual experienced
 herbivory during the experiment, and quantified detailed percent standing
 herbivory at the end of the experiment using photos and corresponding
 image analysis.
description: Please see 'SpeciesCodes.txt' for seedling identity.
 See 'ReadMe.txt' for explanation of variables in
 dataset.
DOI: 10.57931/3012850
title: Data for Unraveling the Drivers of Water Shortage across Spatial Scales and Sectors in Colorado's West Slope River Basins

description: Results from Sunkara et al. submitted to Earth's Future. All code to reproduce the experiment and make the figures can be found here: https://github.com/ssaiveena/Sunkara-etal_2025_WestSlope
For a detailed guide to data in this repository, see the README.txt file.
Shortage output from .xdd files generated by StateMod was compressed into .parquet files in the Uncertain_scenarios folder. Reservoir output from .xre files can be found in the "Reservoir" directory within the Uncertain_scenarios folder. We adopted the CDSS naming convention: 
cm = Upper Colorado River Basin
gm = Gunnison River Basin
ym = Yampa River Basin
wm = White River Basin
sj = Southwest Basin
DOI: 10.5061/dryad.rxwdbrv5m
title: Frontal tau pathology underlies behavioural/dysexecutive presentations of Alzheimer’s disease

description: Objective: To determine the associations between amyloid-PET, tau-PET and
 atrophy with the behavioural/dysexecutive presentation of Alzheimer’s
 disease (AD) and how these differ from amnestic AD. Background: The
 behavioural/dysexecutive variant of AD is a rare clinical syndrome
 presenting with behavioural changes, apathy and/or executive dysfunction,
 similar to frontotemporal dementia. Small autopsy studies provide
 conflicting reports of frontal pathology and recent studies challenge the
 notion of frontal involvement in this condition. We tested the hypothesis
 that patterns of cortical tau pathology differentiate
 behavioural/dysexecutive AD from amnestic AD and correlate to clinical
 symptoms. Methods: We assessed 15 cases of behavioural/dysexecutive AD
 recruited from a tertiary care memory clinic, all of whom had biologically
 defined AD. They were compared with 25 disease severity- and age-matched
 amnestic AD patients and a group of 131 cognitively unimpaired (CU)
 elderly individuals. All subjects were evaluated with amyloid-PET,
 tau-PET, MRI and neuropsychological testing. Results: Voxelwise contrasts
 identified patterns of frontal cortical tau aggregation in
 behavioural/dysexecutive AD, with peaks in medial prefrontal, anterior
 cingulate and frontal insular cortices. No differences were observed in
 the distribution of amyloid-PET. Voxelwise area under the ROC curve
 analyses revealed that tau-PET uptake in the medial prefrontal, anterior
 cingulate and frontal insular cortices were best able to differentiate
 between behavioural/dysexecutive and amnestic AD (AUC=0.87). Voxelwise
 regressions demonstrated relationships between frontal cortical tau load
 and degree of executive dysfunction. Conclusions: Our results provide
 evidence of frontal cortical involvement of tau pathology in
 behavioural/dysexecutive AD and highlight the need for consensus clinical
 criteria in this syndrome.
DOI: 10.5061/dryad.9ghx3fffc
title: Data from: Hidden leks in a migratory songbird: mating advantages for earlier and more attractive males

description: In some socially monogamous birds, territories sometimes occur in
 aggregations. The “hidden lek” hypothesis suggests that territorial
 aggregations might be explained by males establishing territories near
 successful males (“hotshot” model), or by females preferring to mate in
 large clusters (“female preference” model). In both scenarios, clusters
 would provide more opportunities for finding mates and achieving
 extra-pair copulations. Our study tests predictions of these two models in
 the blue-black grassquit (Volatinia jacarina). Males of this species
 migrate to their breeding grounds, establish territories within clusters
 and initiate courtship displays. These displays consist of vertical leaps
 synchronized with vocalizations, or only the latter, without leaps. The
 “hotshot” model predicts that: 1) earlier-arriving males would establish
 territories more centrally within clusters; 2) earlier or centrally
 positioned males would produce more elaborate displays; and 3) these same
 males would achieve higher success via within and extrapair
 fertilizations. The “female preference” model predicts that: 4) pairing
 success and 5) per-capita extrapair fertilizations would increase with
 cluster size. We found that earlier-arriving males executed higher leaps
 and longer songs, but there was no relationship between these traits and
 male position within clusters. We also found earlier-arriving males were
 more likely to obtain extrapair fertilizations. However, we found little
 evidence that cluster size related to overall or per-capita breeding
 success. Considered together, our data provide partial validation of the
 hotshot model of hidden leks, and expand on prior findings in this species
 by showing that females benefit by choosing males leaping higher and
 settling earlier in clusters.
description: See main text in publication.
description: These data files describe male blue-black grassquits’ display
 parameters, spatial position within clusters, territory establishment date
 and breeding success
DOI: 10.5061/dryad.7pvmcvdqn
title: Supporting data for changing climate reallocates the carbon debt of frequent-fire forests

description: Ongoing climate change will likely alter the carbon carrying capacity of
 forests as they adjust to climatic extremes and changing disturbance
 regimes. Increasing drought frequency and severity are already causing
 widespread tree mortality events, which can exacerbate the carbon debt
 that has developed as a result of fire-exclusion. Reducing tree density
 and surface fuels decreases the risk of high-severity wildfire and may
 also limit drought-induced mortality by reducing competition. We utilized
 a long-term thinning and burning experiment in a mixed-conifer forest to
 investigate the effects of the 2012-2015 California drought on forest
 carbon dynamics, including the carbon emissions from a second-entry
 prescribed fire that followed the drought. We assessed differences in
 carbon stability and drought survival across treatments, with the
 expectation that both carbon stability and survival probability would
 increase with increasing treatment intensity (decreasing basal area).
  Additionally, we analyzed the effects of drought- mortality on
 second-entry burn emissions and compared emissions for the first and
 second-entry burns. We did not find a linear relationship between
 treatment intensity and carbon stability, which was in part driven by
 varying relationships between growing space and survival across
 treatments. Drought mortality also increased dead tree and surface fuel
 carbon in all treatments, which contributed to an increase in second-entry
 burn emissions for two of the three burn treatments. Our findings suggest
 that restoration treatments will not serve as a panacea for ongoing
 climate change and that the carbon debt of these forests will increase as
 the carbon carrying capacity adjusts to severe drought events. Managing
 this additional carbon debt with prescribed fire will help reduce the risk
 of additional mortality from wildfire, but at an increasing carbon cost
 for forest management. 
description: This is a full factorial design experiment with three levels of
 thinning (no thin, understory thin, overstory thin) and two levels of
 prescribed burning (no burn, burn).  Treatments were each replicated three
 times in four hectare treatment units.  The thinning treatments were
 conducted in 2000 and 2001.  The first-entry prescribed burn was
 implemented in 2001 and the second-entry prescribed burn in 2017.  Within
 each treatment unit, each tree greater than 5 cm diameter at breast height
 was measured and mapped.  Within each treatment unit surface fuels were
 measured on a 50 m grid, at a total of nine points.  The .csv files are
 the dataframes associated with each analysis that is in the .html
 file.
DOI: 10.5061/dryad.gtht76hj6
title: Does genome size increase with water depth in marine fishes?

description: A growing body of research suggests that genome size in animals can be
 affected by ecological factors. Half a century ago, Ebeling et al. (1971;
 EEA71) proposed that genome size increases with depth in some teleost fish
 groups and discussed a number of biological mechanisms that may explain
 this pattern (e.g., passive accumulation, adaptive acclimation). Using
 phylogenetic comparative approaches, we revisit this hypothesis based on
 genome size and ecological data from up to 708 marine fish species in
 combination with a set of large-scale phylogenies, including a newly
 inferred tree. We also conduct modelling approaches of trait evolution and
 implement a variety of regression analyses to assess the relationship
 between genome size and depth. Our reanalysis of the EEA71 dataset shows a
 weak association between these variables, but the overall pattern in their
 data is driven by a single clade. While analyses based on the new dataset
 resulted in positive correlations, providing some evidence that genome
 size evolves adaptively as a function of depth, only a fraction of
 individual subclade analyses yielded statistically significant results. By
 contrast, negative correlations are rare and largely non-significant. All
 in all, we find modest evidence for an increase in genome size along the
 depth axis in marine fishes. We discuss some mechanistic explanations for
 the observed trends.
DOI: 10.5061/dryad.1rn8pk0r4
title: Data from: Clinical management and mortality among COVID-19 cases in sub-Saharan Africa: a retrospective study from Burkina Faso and simulated case analysis.

description: Absolute numbers of COVID-19 cases and deaths reported to date in the
 sub-Saharan Africa (SSA) region have been relatively low. As a result,
 there has been limited investigation into deceased cases in the region, as
 well as the impacts of different case management strategies. We detail
 demographic, epidemiological, and clinical information derived from
 publicly available information on deceased cases in SSA and, for cases in
 Burkina Faso, from aggregate records at the Center Hospitalier
 Universitaire de Tengandogo. Logistic regression was conducted on a
 synthetic case population to evaluate the adjusted odds of survival for
 patients receiving oxygen therapy or convalescent plasma, based on
 therapeutic effectiveness observed for other respiratory illnesses. Across
 SSA, deceased cases have been predominantly male and over 50 years of age.
 After adjustment for sex, age, and underlying conditions, the odds of
 mortality among cases in the synthetic population not receiving oxygen
 therapy was significantly higher than those receiving oxygen (OR: 2.07;
 95%CI: 1.56-2.75). Cases receiving convalescent plasma had 50% reduced
 odds of mortality (95%CI: 0.24-0.93). Investment in sustainable oxygen
 therapy could reduce COVID-19 deaths in SSA. Ongoing investigation into
 convalescent plasma is warranted, as data on its effectiveness
 specifically in treating COVID-19 becomes available.
description: Data were collected from COVID-19 hospitalized patients,
 curated, binned by age and gender to be made publique or shared with
 collaborators. Line-list data  from Sub-Saharan 
 African Countries are public data available from the internet (Ministry of
 health websites ect..)  Simulated data are simulated
 using appropriate statisctical method to create individuals based data
 based on hospital setting's binned data.
DOI: 10.5061/dryad.bnzs7h47q
title: Modifiable cardiovascular risk factors in patients with sporadic cerebral cavernous malformations: obesity matters

description: Objective To assess the influence of modifiable cardiovascular risk
 factors on hemorrhage risk of sporadic cerebral cavernous malformations
 (CCMs). Methods From 1219 consecutive CCM patients (2003-2018), adult
 subjects with sporadic CCM and complete MRI were included. We evaluated
 presence of intracerebral hemorrhage (ICH) as mode of presentation,
 occurrence of ICH during follow-up and risk factors arterial hypertension,
 diabetes mellitus, hyperlipidemia, nicotine abuse, and obesity
 (BMI&gt;30kg/m²). Impact of risk factors on ICH at presentation was
 calculated using univariate and multivariate logistic regression with age-
 and sex-adjustment. We performed Kaplan Meier and Cox regression to
 analyze cumulative 5-year-risk for (re-)bleeding.  Results We
 included 682 CCM patients. The univariate logistic regression showed a
 significant relationship (OR=1.938, 95% CI: (1.120–3.353), p=0.018)
 between obesity and ICH as mode of presentation. Multivariate adjusted
 logistic regression confirmed significant correlation with OR=1.902 (95%
 CI: 1.024–3.532, p=0.042). Cox regression did not identify predictors for
 occurrence of (re-)hemorrhage (p&gt;0.05; Hazard ratios: arterial
 hypertension 1.112 (95% CI: 0.622–1.990), diabetes 0.850 (95% CI:
 0.208–3.482), hyperlipidemia 0.719 (95% CI: 0.261–1.981), nicotine abuse
 1.123 (95% CI: 0.591–2.134), and obesity 0.928 (95% CI:
 0.416–2.070)).  Conclusions This study provides evidence that
 obesity may be a risk factor for CCM hemorrhage. It was significantly
 associated with ICH as mode of presentation. Other risk factors (arterial
 hypertension, diabetes mellitus, hyperlipidemia and current nicotine
 abuse) showed no such effect. None of the factors showed to be independent
 predictors for cumulative 5-year-risk of
 (re-)bleeding.
DOI: 10.5061/dryad.xwdbrv1bh
title: Most cultural importance indices do not predict species cultural keystone status

description: The use of quantitative indices to quantify the importance of a plant
 species to human societies is widespread. While quantifi- cation may yield
 support for standardized methodologies and facilitate generalizations, it
 is important to examine the potential limitations of these indices.
 Moreover, because these indices are calculated at the species level,
 failure to control for phylogenetic relatedness in predictive models may
 yield misleading conclusions. We test if commonly used cultural importance
 indices predict species cultural keystone status among the Shipibo-Konibo
 community of Paoyhan in the Peruvian Amazon. Eleven of the 12 indices were
 correlated with each other indicating most cultural importance indices are
 redundant. Most indices did not predict species cultural keystone status.
 Phylogenetic control improved our models indicating a significant part of
 the predictive power of even the best index was explained by species
 shared evolutionary history. Our findings highlight the need for the
 cautious use of cultural importance indices to infer species cultural
 keystone status. Newly developed indices should be tested for correlation
 with existing indices to avoid redundancy.
description: Data was collected via ethnobotanical methods decribed in detail
 in our manuscript entitled "Most cultural importance indices do not
 predict species cultural keystone status."
description: All predictor variables were estimated via cultural importance
 indices cited in our manuscript entitled "Most cultural importance
 indices do not predict species cultural keystone status." The
 response variable was estimated via PCA using a correlation  matrix.
  Details are provided in the data analysis section of our manuscript. All
 analysis were conducted in R.
DOI: 10.5061/dryad.98sf7m0g1
title: Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi (Notiomystis cincta)

description: To predict if a threatened species can adapt to changing selective
 pressures, it is crucial to understand the genetic basis of adaptive
 traits, especially in species historically affected by severe bottlenecks.
 We estimated the heritability of three hihi (Notiomystis cincta)
 morphological traits known to be under selection: nestling tarsus length,
 body mass and head-bill length, using 523 individuals and 39,699 single
 nucleotide polymorphisms (SNPs) from a 50K Affymetrix SNP chip. We then
 examined the genetic architecture of the traits via chromosome
 partitioning analyses and genome-wide association scans (GWAS).
 Heritabilities estimated using pedigree relatedness or genomic relatedness
 were low. For tarsus length, the proportion of genetic variance explained
 by each chromosome was positively correlated with its size, and more than
 one chromosome explained significant variation for body mass and head-bill
 length. Finally, GWAS analyses suggested many loci of small effect
 contributing to trait variation for all three traits, although one locus
 (a SNP within an intron of the transcription factor HEY2) was tentatively
 associated with tarsus length. Our findings suggest a polygenic nature for
 the morphological traits, with many small effect size loci contributing to
 the majority of the variation, similar to results from many other wild
 populations. However, the small effective population size, polygenic
 architecture and already low heritabilities suggest that both the total
 response and rate of response to selection are likely to be limited in
 hihi.
description: Information on data collection and processing can be found in the
 <em>Methods </em>section of the article.
description: <strong>.phen</strong> Phenotypic
 data in<strong> </strong><em>RepeatABEL
 </em>format for the individuals used in the
 article. More info in
 the README.txt file. <b>.tfam</b>
 Family data in a standard <em>PLINK </em>format for
 the individuals used in the article.
 More info in the
 README.txt file. <b>.tped</b>
 Genotype data in a standard <em>PLINK </em>format for
 the individuals used in the
 article. More info in
 the README.txt file.
 <strong>.R</strong> R scipt with main settings used
 to retrieve heritability from <em>MCMCglmm
 </em>output (including partitioning among chromosomes) and full R
 code to perform a GWAS in <em>RepeatABEL</em>, including the
 model.