cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g63c748
title: Data from: Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus Amanita

description: Fungi are evolutionary shape shifters and adapt quickly to new
 environments. Ectomycorrhizal (EM) symbioses are mutualistic associations
 between fungi and plants and have evolved repeatedly and independently
 across the fungal tree of life, suggesting lineages frequently reconfigure
 genome content to take advantage of open ecological niches. To date
 analyses of genomic mechanisms facilitating EM symbioses have involved
 comparisons of distantly related species, but here, we use the genomes of
 three EM and two asymbiotic (AS) fungi from the genus Amanita as well as
 an AS outgroup to study genome evolution following a single origin of
 symbiosis. Our aim was to identify the defining features of EM genomes,
 but our analyses suggest no clear differentiation of genome size, gene
 repertoire size or transposable element content between EM and AS species.
 Phylogenetic inference of gene gains and losses suggests the transition to
 symbiosis was dominated by the loss of plant cell wall decomposition
 genes, a confirmation of previous findings. However, the same dynamic
 defines the AS species A. inopinata, suggesting loss is not strictly
 associated with origin of symbiosis. Gene expansions in the common
 ancestor of EM Amanita were modest, but lineage specific and large gene
 family expansions are found in two of the three EM extant species. Even
 closely related EM genomes appear to share few common features. The
 genetic toolkit required for symbiosis appears already encoded in the
 genomes of saprotrophic species, and this dynamic may explain the
 pervasive, recurrent evolution of ectomycorrhizal associations.
description: READMEPhylogenomic_analysisAnnotations
DOI: 10.5281/zenodo.18389020
title: Integrated proteomics and metabolomics profiling reveal mechanisms for the improvement of hoof health, liver function, and oxidative stress in lactating dairy cows fed rumen-protected biotin
DOI: 10.6084/m9.figshare.28776703
title: Tracking the norms: A regression-based approach to trail making test performance in the Turkish population

description: <b>Objective:</b> The Trail Making Test (TMT) is a widely used neuropsychological tool for assessing executive functions. This study aimed to establish regression-based normative data for TMT performance in a Turkish population aged 18–80, accounting for the effects of age, education, and sex on both basic (TMT A and TMT B) and derived scores (TMT B-A and TMT B/A). <b>Method:</b> A total of 462 participants were recruited, with 409 included in the final analysis after applying exclusion criteria. Participants completed the international version of the TMT. Pearson correlation analyses and multiple linear regression models assessed relationships between TMT scores and demographic variables. Education was treated as a continuous variable, and regression-based norms were developed for all TMT scores. <b>Results:</b> Age and education were significant predictors of TMT performance. Age primarily affected TMT A scores, while education was the strongest predictor for TMT B, TMT B-A, and TMT B/A scores. The regression models explained 36–38% of the variance in basic scores and 6–24% in derived scores. Women performed better than men on the TMT B/A ratio score, but overall, sex had a less pronounced effect than age and education. <b>Conclusions:</b> This study provides the first regression-based normative data for the TMT in a Turkish population. These norms are crucial for improving the accuracy of neuropsychological assessments in Turkey and facilitating cross-cultural comparisons in cognitive research. The findings emphasize the importance of adjusting for demographic factors in clinical and research settings to ensure precise evaluations of cognitive functioning.
DOI: 10.6084/m9.figshare.28776703.v1
title: Tracking the norms: A regression-based approach to trail making test performance in the Turkish population

description: <b>Objective:</b> The Trail Making Test (TMT) is a widely used neuropsychological tool for assessing executive functions. This study aimed to establish regression-based normative data for TMT performance in a Turkish population aged 18–80, accounting for the effects of age, education, and sex on both basic (TMT A and TMT B) and derived scores (TMT B-A and TMT B/A). <b>Method:</b> A total of 462 participants were recruited, with 409 included in the final analysis after applying exclusion criteria. Participants completed the international version of the TMT. Pearson correlation analyses and multiple linear regression models assessed relationships between TMT scores and demographic variables. Education was treated as a continuous variable, and regression-based norms were developed for all TMT scores. <b>Results:</b> Age and education were significant predictors of TMT performance. Age primarily affected TMT A scores, while education was the strongest predictor for TMT B, TMT B-A, and TMT B/A scores. The regression models explained 36–38% of the variance in basic scores and 6–24% in derived scores. Women performed better than men on the TMT B/A ratio score, but overall, sex had a less pronounced effect than age and education. <b>Conclusions:</b> This study provides the first regression-based normative data for the TMT in a Turkish population. These norms are crucial for improving the accuracy of neuropsychological assessments in Turkey and facilitating cross-cultural comparisons in cognitive research. The findings emphasize the importance of adjusting for demographic factors in clinical and research settings to ensure precise evaluations of cognitive functioning.
DOI: 10.5281/zenodo.17163319
title: Integrated proteomics and metabolomics profiling reveal mechanisms for the improvement of hoof health, liver function, and oxidative stress in lactating dairy cows fed rumen-protected biotin
DOI: 10.5061/dryad.7g0f132
title: Data from: Impact of solar and wind development on conservation values in the Mojave Desert

description: In 2010, The Nature Conservancy completed the Mojave Desert Ecoregional
 Assessment, which characterizes conservation values across nearly 130,000
 km2 of the desert Southwest. Since this assessment was completed, several
 renewable energy facilities have been built in the Mojave Desert, thereby
 changing the conservation value of these lands. We have completed a new
 analysis of land use to reassess the conservation value of lands in two
 locations in the Mojave Desert where renewable energy development has been
 most intense: Ivanpah Valley, and the Western Mojave. We found that 99 of
 our 2.59-km2 planning units were impacted by development such that they
 would now be categorized as having lower conservation value, and most of
 these downgrades in conservation value were due to solar and wind
 development. Solar development alone was responsible for a direct
 development footprint 86.79 km2: 25.81 km2 of this was primarily high
 conservation value Bureau of Land Management lands in the Ivanpah Valley,
 and 60.99 km2 was privately owned lands, mostly of lower conservation
 value, in the Western Mojave. Our analyses allow us to understand patterns
 in renewable energy development in the mostly rapidly changing regions of
 the Mojave Desert. Our analyses also provide a baseline that will allow us
 to assess the effectiveness of the Desert Renewable Energy Conservation
 Plan in preventing development on lands of high conservation value over
 the coming decades.
description: Mojave Desert
 Ecoregional Assessment 2010 Original and 2017 UpdateThis dataset
 characterizes the Mojave Desert Ecoregion into 4 classes: Ecologically
 Core: Land with high landscape integrity which support conservation
 targets and whose protection is critical for the long-term conservation of
 the ecoregion's biological diversity. Ecologically Intact: Land which
 has high landscape integrity or support conservation targets and which
 requires a level of protection that will enable it to continue to support
 ecological processes and provide connectivity. Moderately Degraded: Lands
 fragmented by roads, off-road-vehicle trails or in close proximity to
 urban, agricultural and other developments. Highly Converted: Land in
 urban and agricultural areas that is fragmented and most impacted by human
 uses. This dataset contains both the original conservation values and
 updated 2017 conservation values.
DOI: 10.5061/dryad.k0h70b0
title: Data from: Patterns of authorship in ecology and evolution: first, last and corresponding authorship vary with gender and geography

description: The position of an author on the byline of a paper affects the inferences
 readers make about their contributions to the research. We examine gender
 differences in authorship in the ecology literature using two datasets:
 submissions to six journals between 2010 and 2015 (regardless of whether
 they were accepted), and manuscripts published by 151 journals between
 2009 and 2015. Women were less likely to be last (i.e., ‘senior’) authors
 (averaging ~23% across journals, years and datasets) and sole authors
 (~24%), but more likely to be first author (~38%), relative to their
 overall frequency of authorship (~31%). However, the proportion of women
 in all authorship roles, except sole authorship, has increased
 year-on-year. Women were less likely to be authors on papers with male
 last authors, and all-male papers were more abundant than expected given
 the overall gender ratio. Women were equally-well represented on papers
 published in higher versus lower impact factor journals at all authorship
 positions. Female first authors were less likely to serve as corresponding
 author of their papers; this difference increased with the degree of
 gender inequality in the author’s home country, but did not depend on the
 gender of the last author. First authors from non-English speaking
 countries were less likely to serve as corresponding author of their
 papers, especially if the last author was from an English-speaking
 country. That women more often delegate corresponding authorship to one of
 their coauthors may increase the likelihood that readers undervalue their
 role in the research by shifting credit for their contributions to
 coauthors. We suggest that author contribution statements be more
 universally adopted and that these statements declare how and/or why the
 corresponding author was selected for this role.
description: Authorship of submitted
 papers_anonymizedThe submitted papers
 dataset used for analyses in Fox et al. The dataset has been anonymized by
 removing author country identifiers (and associated country data),
 inclusion of which could allow some authors to be identified; the dataset
 only includes higher level geographic locations.Data for
 Dryad_anonymized.xlsx
DOI: 10.5281/zenodo.17762845
title: INRIM_Brand1_25F_2_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 25F SC sample 2 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.73q5474
title: Data from: The Bogert effect revisited: salamander regulatory behaviors are differently constrained by time and space

description: The use of behavior to buffer extreme environmental variation is expected
 to enable species to a) extend the breadth of environments they inhabit
 beyond that predicted from climatic data, and b) diminish the negative
 effects of broad-scale and chronic disturbances such as climate change.
 The term Bogert effect refers to behavioral compensation entailing
 microhabitat selection to maintain performance across a gradient of
 environmental conditions resulting in evolutionary inertia of
 physiological traits. Here we compare microhabitats used by plethodontid
 salamanders distributed along an elevational gradient to determine whether
 there is behavioral compensation that buffers them from deleterious
 temperatures and moisture levels. Overall, salamanders preferred cooler
 and more mesic environments and occupied microhabitats that maintained
 constant moisture conditions at both high and low elevation sites. Our
 results suggest that salamanders use microhabitats to regulate temperature
 and moisture levels, which is consistent with the Bogert effect.
 Maintenance of more moist conditions may help buffer these species from
 rising temperatures, but only in suitable high-elevation environments that
 are likely to disappear over the next century. We conclude that behavioral
 regulation of temperature and moisture is a potential mechanism for the
 Bogert effect in plethodontid salamanders.
description: Microhabitat_UseThis file contains data used to determine what microhabitats salamanders used and when they used them. The data file includes detailed comments on the column headers that explain each of the variables and attempt to clarify any part of the data that might be confusing.Microhabitat_VariationThis file contains data used to test part of our hypothesis that microhabitats differ in their moisture and temperature characteristics across elevation. The analysis also includes variation across time. The data file includes detailed comments on the column headers that explain each of the variables and attempt to clarify any part of the data that might be confusing.Pairwise_ComparisionsThis file contains data used to test whether salamanders will preferentially utilize microhabitats that permit them to maintain consistent moisture and temperature levels. This was a paired analysis with each survey being broken into microhabitats where salamanders were found and where they were not found. For example, if during one survey salamanders were found under rocks and under woody debris, but not found under moss, leaf litter, above ground, or in trees. Then we include mean temperature and water loss value for under rocks and woody debris for the presence pair and mean values for under moss, leaf litter, above ground, or in trees for the absence pair. The data file includes detailed comments on the column headers that explain each of the variables and attempt to clarify any part of the data that might be confusing.
DOI: 10.5281/zenodo.17762844
title: INRIM_Brand1_25F_2_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 25F SC sample 2 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.ds6p94f
title: Data from: Heterogeneous and efficient transesterification of Jatropha curcas L. seed oil to produce biodiesel catalyzed by nano-sized SO42-/TiO2

description: Developing high-efficiency hetero-catalysts for transesterification
 reaction is of great importance in the production of biodiesel from
 Jatropha curcas L. seed oil (JO). Here, we synthesized a series of
 sulfated TiO2 by treating with varying H2SO4 concentration (xSO42-/TiO2)
 and TiO2 catalysts and applied to the transesterification of JO.
 Furthermore, these heterostructures were characterized by many
 characterization methods including XRD, FT–IR, N2–adsorption, SEM, TEM,
 TG, py-IR and NH3-TPD, and their catalytic performance were investigated
 under various operating conditions. The results reveal that both the
 Brønsted and Lewis acid sites are presented in the xSO42-/TiO2 catalysts,
 while only Lewis-type sites are observed in the TiO2 catalyst. And the
 acid intensity, surface area and mesoporous volume of catalysts are
 improved obviously after treating with sulfuric acid of TiO2. Then the
 xSO42-/TiO2 catalysts exhibit much higher catalytic activity than TiO2
 catalyst, which is attributed to the larger surface area and mesoporous
 volume and stronger acidity. Furthermore, the reusability behavior of
 1.5SO42-/TiO2 catalyst in transesterification of JO was also studied.
description: Date-Heterogeneous and
 efficient transesterification of Jatropha curcas L. seed
 oil
DOI: 10.5061/dryad.4b3j2bj
title: Data from: Full Bayesian comparative phylogeography from genomic data

description: A challenge to understanding biological diversification is accounting for
 community-scale processes that cause multiple, co-distributed lineages to
 co-speciate. Such processes predict non-independent, temporally clustered
 divergences across taxa. Approximate-likelihood Bayesian computation (ABC)
 approaches to inferring such patterns from comparative genetic data are
 very sensitive to prior assumptions and often biased toward estimating
 shared divergences. We introduce a full-likelihood Bayesian approach,
 ecoevolity, which takes full advantage of information in genomic data. By
 analytically integrating over gene trees, we are able to directly
 calculate the likelihood of the population history from genomic data, and
 efficiently sample the model-averaged posterior via Markov chain Monte
 Carlo algorithms. Using simulations, we find that the new method is much
 more accurate and precise at estimating the number and timing of
 divergence events across pairs of populations than existing
 approximate-likelihood methods. Our full Bayesian approach also requires
 several orders of magnitude less computational time than existing ABC
 approaches. We find that despite assuming unlinked characters (e.g.,
 unlinked single-nucleotide polymorphisms), the new method performs better
 if this assumption is violated in order to retain the constant characters
 of whole linked loci. In fact, retaining constant characters allows the
 new method to robustly estimate the correct number of divergence events
 with high posterior probability in the face of character-acquisition
 biases, which commonly plague loci assembled from reduced-representation
 genomic libraries. We apply our method to genomic data from four pairs of
 insular populations of Gekko lizards from the Philippines that are not
 expected to have co-diverged. Despite all four pairs diverging very
 recently, our method strongly supports that they diverged independently,
 and these results are robust to very disparate prior assumptions.
description: Supplemental
 figuresThe supplemental figures
 referred to in the paper (Figures S1-S40).supporting-information.pdfEcoevolity source codeAn archive of the version of the ecoevolity source code that was used in the paper.Pycoevolity source codeAn archive of the version of the pycoevolity source code that was used in the paper.NCBI BioProjectThis NCBI BioProject includes the raw (demultiplexed) sequence reads that were used in the paper.Gecko sample dataA tab-delimited text file containing the data for all the geckos that were analyzed in the paper. The field numbers in the table correspond to the data in the NCBI BioProject PRJNA486413.comparison-samples.txtProject repositoryAn archived version of the project git repository. The archive is in Zenodo; the original repository is hosted on GitHub.
DOI: 10.15468/dl.7duuud
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Kazakhstan",
 "TaxonKey is Ferula teterrima"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001553-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x283bb
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dioscorea tubuliflora"
 ]
}

 The dataset includes 13 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001554-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d0s2gm0
title: Data from: Effect of Ghost pepper on cell proliferation, apoptosis, senescence and global proteomic profile in human renal adenocarcinoma cells

description: Chili peppers are an important constituent of many foods and contain
 medicinally valuable compounds, such as capsaicin and dihydrocapsaicin. As
 various dietary botanicals have anticancer properties, this study was
 aimed to examine the effect of Ghost pepper (Bhut Jolokia), one of the
 hottest chili peppers in the world, on cell proliferation, apoptosis,
 senescence and the global proteomic profile in human renal cell
 adenocarcinoma in vitro. 769-P human renal adenocarcinoma cells were
 cultured on RPMI-1640 media supplemented with fetal bovine serum (10%) and
 antibiotic-antimycotic solution (1%). Treatment stock solutions were
 prepared in ethanol. Cell proliferation was tested with phenol red-free
 media with capsaicin (0–400 μM), dihydrocapsaicin (0–400 μM), capsaicin +
 dihydrocapsaicin (5:1), and dry Ghost peppers (0–3 g L-1) for 24, 48 and
 72 h. Polycaspase and senescence associated-beta-galactosidase
 (SA-beta-gal) activities were tested with capsaicin (400 μM),
 dihydrocapsaicin (400 μM), capsaicin (400 μM) + dihydrocapsaicin (80 μM),
 and ghost pepper (3 g L-1) treatments. Global proteomic profile of cells
 in control and ghost pepper treatment (3 g L-1) was analyzed after 6 h by
 a shotgun proteomic approach using tandem mass spectrometry. At 24 h after
 treatment (24 HAT), relative to control, cell proportion with capsaicin
 (400 μM), dihydrocapsaicin (400 μM), capsaicin (400 μM) + dihydrocapsaicin
 (80 μM), and ghost pepper (3 g L-1) treatments was reduced to 36%, 18%,
 33% and 20%, respectively, and further reduced at 48 and 72 HAT. All
 treatments triggered an early polycaspase response. SA-beta-gal activity
 was normal or suppressed with all treatments. About 68,220 protein
 isoforms were identified by shotgun proteomic approach. Among these, about
 8.2% were significantly affected by ghost pepper. Ghost pepper regulated
 various proteins involved in intrinsic and extrinsic apoptotic pathways,
 Ras, Rb/E2F, p53, TGF-beta, WNT-beta catenin, and calcium induced cell
 death pathways. Ghost pepper also induced changes in proteins related to
 methylation, acetylation, genome stability, cell cycle check points,
 carbohydrate, protein and other metabolism and cellular mechanisms. Ghost
 pepper exhibited antiproliferation activity by inducing apoptosis through
 a complex network of proteins in human renal cell adenocarcinoma in vitro.
description: Additional file 1-Perla
 et alSupplementary data Perla
 et al