cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vb047
title: Data from: Genome-wide analysis of MATE transporters and molecular characterization of aluminum resistance in Populus

description: Ionic aluminum (Al) in acidic soils, comprising approximately 50% of
 arable land globally, is highly toxic to most plant species. Populus grow
 naturally in acidic soils and tolerate high concentrations of Al.
 Multidrug and toxic compound extrusion (MATE) family genes in plants are
 involved in responses to Al tolerance. To date, however, the functional
 roles of the MATE genes in Populus remain unclear. In the present study,
 71 putative MATE transporters were predicted in the genome of Populus
 trichocarpa. The chromosome distribution, phylogenetic relationships, and
 expression level analysis revealed that four candidate MATE genes
 belonging to subgroup IIIc might contribute to high Al tolerance in
 poplar. Further, the expression levels of two subgroup IIIc members,
 PtrMATE1 and PtrMATE2, were induced by Al stress. Transient expression in
 onion epidermal cells showed that PtrMATE1 was localized to the plasma
 membrane. Overexpression of PtrMATE1 increased Al-induced secretion of
 citrate from the root apex of transgenic plants. Al-induced inhibition of
 root growths were alleviated in both PtrMATE1 overexpression lines in
 Populus and in Arabidopsis compared with wild-type plants. In addition,
 PtrMATE1 expression was induced at 12 h after exposure to Al stress
 whereas PtrMATE2 expression was induced at 24 h, indicating that these
 proteins coordinately function in response to Al stress in poplar. Taken
 together, these results provide important insights into the molecular
 mechanisms involved in Al tolerance in poplar.
description: Sequences of all MATE
 proteins described in manuscriptData contains sequences
 of All 101 MATE proteins from populus, arabidpsis, rice and other 13 plant
 species.MATE
 ptoteins.txtFigure
 S1Expression profiles of
 10 PtrMATE genes under Al treatment.Fig.S1.tifFigure S2Multiple sequence alignment of PtrMATE1, PtrMATE2 and AtMATE.Fig.S2.tifFigure S3Time course of PtrMATE2 expression in the roots of Populus in response to Al or La treatment.Fig.S3.tifFigure S4qRT-PCR analysis of transgenic poplar plants.Fig.S4.tifFigure S5PtrMATE1 expression in the roots of poplar under Al treatments with different concentration.Fig.S5.tifFigure S6Overexpression of PtrMATE1 in transgenic AtMATE knockout mutant (ATMATE-KO) and wild-type Arabidopsis confers Al tolerance. (A) Wild-type and transgenic Arabidopsis in MS medium containing 20 μM Al3+ for 10 d. PtrMATE1-OX:overexpression of PtrMATE1 in wild-type Arabidopsis, PtrMATE1-R:overexpression of PtrMATE1 in AtMATE knockout mutant. (B) root growth of these transgenic plants with/without Al treated.Student’s t-test: *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001.Fig.S6.tifTABLE S1Details of MATEs from different species.TABLE. S1.xlsxTABLE S2Primers for qRT-PCR and gene cloning in this study. F and R represented the forward and reverse primers, respectively. In the Excel file, the first column is Primers, the second column is Nucloetide sequence.TABLE. S2.xlsxTABLE S3Motifs of PtrMATE proteins.TABLE. S3.xlsx
DOI: 10.5061/dryad.cs635
title: Data from: Can asexuality confer a short term advantage? Investigating apparent biogeographic success in the apomictic triploid fern Myriopteris gracilis

description: Premise of the study: Although asexual taxa are generally seen as
 evolutionary dead ends, asexuality appears to provide a short-term benefit
 in some taxa, including a wider geographic distribution compared to sexual
 relatives. However, this may be an illusion created by multiple,
 morphologically cryptic, asexual lineages, each occupying a relatively
 small area. In this study we investigate the role of multiple lineages in
 the biogeography of Myriopteris gracilis Fée (Pteridaceae), a North
 American apomictic triploid fern species with a particularly large range.
 Methods: Rangewide asexuality was assessed by counting spores/sporangium
 in 606 M. gracilis specimens from across the species range, and lineage
 structure was assessed with both plastid DNA sequence and Genotyping By
 Sequencing (GBS) SNP datasets. Key Results: Spore counting of &gt;600
 specimens identified no sexual populations, establishing that M. gracilis
 is exclusively asexual. The plastid data estimated the crown age of M.
 gracilis at ca. 2.5 mya and identified two lineages, each largely confined
 to the eastern or western portions of the range. These groups were further
 subdivided by the GBS data, revealing at least seven asexual lineages of
 varying geographic distributions, each occupying a relatively small
 portion of the total range of M. gracilis. Conclusions: Although
 maintained exclusively through asexual reproduction, the broad
 distribution of M. gracilis is a compilation of numerous, independently
 formed asexual lineages. Since no single asexual lineage occupies the full
 extent of the species distribution, recurrent lineage formation should be
 considered when evaluating the short-term benefit of asexuality in this
 taxon and others.
description: Full Grusz 2014 trnGR
 alignmentFull Grusz (2014) trnGR
 alignment used for plastid phylogeny and divergence time
 estimation.full_Grusz_dataset_1.nexTrimmed (1 per species) Grusz (2014) trnGR alignmentTrimmed (1 per species) Grusz (2014) trnGR alignment used for plastid phylogeny and divergence time estimation.1perspecies_2.nexMyriopteris gracilis clade trnGR alignmentMyriopteris gracilis clade trnGR alignment used for plastid phylogeny and divergence time estimation.MGclade_3.nexFinal filtered GBS HapMap fileFinal filtered GBS HapMap file of 17581 SNPs73_taxa_0_missingness_nexusDated maximum clade credibility tree (full Grusz 2014 alignment)Dated maximum clade credibility tree resulting from BEAST analysis of the full Grusz 2014 Myriopteris alignment- Appendix 3 in the manuscript.full_Grusz_dataset_1.trees
DOI: 10.5061/dryad.8h5d8
title: Data from: Fire catalyzed rapid ecological change in lowland coniferous forests of the Pacific Northwest over the past 14,000 years

description: Disturbance can catalyze rapid ecological change by causing widespread
 mortality and initiating successional pathways, and during times of
 climate change, disturbance may contribute to ecosystem state changes by
 initiating a new successional pathway. In the Pacific Northwest of North
 America (PNW), disturbance by wildfires strongly shapes the composition
 and structure of lowland forests, but understanding the role of fire over
 periods of climate change is challenging, because fire-return intervals
 are long (e.g., millennia) and the coniferous trees dominating these
 forests can live for many centuries. We developed stand-scale paleorecords
 of vegetation and fire that span nearly the past 14,000 yr to study how
 fire was associated with state changes and rapid dynamics in forest
 vegetation at the stand scale (1–3 ha). We studied forest history with
 sediment cores from small hollow sites in the Marckworth State Forest,
 located ~1 km apart in the Tsuga heterophylla Zone in the Puget Lowland
 ecoregion of western Washington, USA. The median rate of change in
 pollen/spore assemblages was similar between sites (0.12 and 0.14% per
 year), but at both sites, rates of change increased significantly
 following fire events (ranging up to 1% per year, with a median of 0.28
 and 0.38%, P &lt; 0.003). During times of low climate velocity, forest
 composition was resilient to fires, which initiated successional pathways
 leading back to the dominant vegetation type. In contrast, during times of
 high climate variability and velocity (e.g., the early Holocene) forests
 were not resilient to fires, which triggered large-scale state changes.
 These records provide clear evidence that disturbance, in the form of an
 individual fire event, can be an important catalyst for rapid state
 changes, accelerating vegetation shifts in response to large-scale climate
 change.
description: MW1B_pollen.xlsxPollen data from site MW1B.MW1B charcoal.xlsxCharcoal data from site MW1B.MW13+14_Pollen.xlsPollen data for site MW13+14.MW13+14 charcoal.xlsxCharcoal data for site MW13+14.
DOI: 10.5061/dryad.78v5j
title: Data from: Evolution of mammalian migrations for refuge, breeding, and food

description: Many organisms migrate between distinct habitats, exploiting variable
 resources while profoundly affecting ecosystem services, disease spread,
 and human welfare. However, the very characteristics that make migration
 captivating and significant also make it difficult to study, and we lack a
 comprehensive understanding of which species migrate and why. Here we show
 that, among mammals, migration is concentrated within Cetacea and
 Artiodactyla but also diffusely spread throughout the class (found in 12
 of 27 orders). We synthesize the many ecological drivers of round-trip
 migration into three types of movement—between breeding and foraging
 sites, between breeding and refuge sites, and continuous tracking of
 forage/prey—each associated with different traits (body mass, diet,
 locomotion, and conservation status). Our results provide only partial
 support for the hypothesis that migration occurs without phylogenetic
 constraint. Furthermore, our findings suggest that categorizing migration
 into these three types may aid predictions of migrants’ responses to
 environmental changes.
description: READMEREADME for all
 filesmammals
 dataAll mammal
 classification data.mammals_data.csvreferencesList of references used to classify all mammal species. References are cited by number in the mammals_data.csv file.workspaceR script that loads data (including some sources listed in the manuscript but not contained here, such as phylogenies and Red Listing data) for subsequent analysis.analysesR script to carry out all analyses as described in the manuscript. Note that the script, as it stands currently, assumes that 24 processors are available on your computer - you may want to change this.processingR script to summarise analyses carried out.
DOI: 10.6084/m9.figshare.31157713
title: Sociodemographic Disparities in Cataract-Related Visual Impairment at Initial Presentation: A Sight Outcomes Research Collaborative (SOURCE) Repository Analysis

description: To assess the impact of social determinants of health (SDoH) and clinical factors on visual impairment (VI) at initial presentation to academic centers in cataract patients. Multi-institutional cross-sectional study. We identified patients aged ≥40 years with cataract diagnosis using ICD-9 and ICD-10 codes from the Sight Outcomes Research Collaborative (SOURCE) Ophthalmology Data Repository. Best-recorded vision (BRV) at initial presentation, demographics, Charlson comorbidity index (CCI), cigarette smoking status, and Distressed Community Index (DCI) were recorded. BRV in the better eye was used to categorize VI as none/mild (BRV ≥20/40), moderate (20/40 &lt; BRV &lt; 20/200), and severe (BRV ≤ 20/200). Logistic regression models were used to assess the impact of clinical and sociodemographic factors on moderate and severe VI. Among 137,847 patients with a mean (SD) age of 67.4 (9.1), 58.6% (<i>N</i> = 77,425) were White, 22.5% (<i>N</i> = 29,725) were Black, and 8.8% (<i>N</i> = 11,562) were Hispanic/Latino. Adjusted logistic regression revealed Black patients (OR: 1.16; CI: 1.11–1.22), Native American patients (OR: 1.45; CI: 1.18–1.78), non-English speaking patients (OR: 1.79; CI: 1.69–1.91), and current smokers (OR: 1.29; CI: 1.22–1.37) had higher odds of severe VI. Higher DCI quintiles (more economically distressed) were associated with severe VI compared with the 1st (Prosperous) quintile: 2nd (OR 1.22; 95% CI 1.16–1.27), 3rd (OR 1.45; 95% CI 1.38–1.52), 4th (OR 1.56; 95% CI 1.47–1.64), and 5th (OR 1.36; 95% CI 1.29–1.44) quintiles. This is one of the largest studies examining the impact of DCI on cataract related VI, highlighting the need for interventions to improve access to healthcare and prevent VI in these communities.
DOI: 10.6084/m9.figshare.31157713.v1
title: Sociodemographic Disparities in Cataract-Related Visual Impairment at Initial Presentation: A Sight Outcomes Research Collaborative (SOURCE) Repository Analysis

description: To assess the impact of social determinants of health (SDoH) and clinical factors on visual impairment (VI) at initial presentation to academic centers in cataract patients. Multi-institutional cross-sectional study. We identified patients aged ≥40 years with cataract diagnosis using ICD-9 and ICD-10 codes from the Sight Outcomes Research Collaborative (SOURCE) Ophthalmology Data Repository. Best-recorded vision (BRV) at initial presentation, demographics, Charlson comorbidity index (CCI), cigarette smoking status, and Distressed Community Index (DCI) were recorded. BRV in the better eye was used to categorize VI as none/mild (BRV ≥20/40), moderate (20/40 &lt; BRV &lt; 20/200), and severe (BRV ≤ 20/200). Logistic regression models were used to assess the impact of clinical and sociodemographic factors on moderate and severe VI. Among 137,847 patients with a mean (SD) age of 67.4 (9.1), 58.6% (<i>N</i> = 77,425) were White, 22.5% (<i>N</i> = 29,725) were Black, and 8.8% (<i>N</i> = 11,562) were Hispanic/Latino. Adjusted logistic regression revealed Black patients (OR: 1.16; CI: 1.11–1.22), Native American patients (OR: 1.45; CI: 1.18–1.78), non-English speaking patients (OR: 1.79; CI: 1.69–1.91), and current smokers (OR: 1.29; CI: 1.22–1.37) had higher odds of severe VI. Higher DCI quintiles (more economically distressed) were associated with severe VI compared with the 1st (Prosperous) quintile: 2nd (OR 1.22; 95% CI 1.16–1.27), 3rd (OR 1.45; 95% CI 1.38–1.52), 4th (OR 1.56; 95% CI 1.47–1.64), and 5th (OR 1.36; 95% CI 1.29–1.44) quintiles. This is one of the largest studies examining the impact of DCI on cataract related VI, highlighting the need for interventions to improve access to healthcare and prevent VI in these communities.
DOI: 10.5061/dryad.2h6nf
title: Data from: Distance-dependent pattern blending can camouflage salient aposematic signals

description: The effect of viewing distance on the perception of visual texture is well
 known: spatial frequencies higher than the resolution limit of an
 observer's visual system will be summed and perceived as a single
 combined colour. In animal defensive colour patterns, distance-dependent
 pattern blending may allow aposematic patterns, salient at close range, to
 match the background to distant observers. Indeed, recent research has
 indicated that reducing the distance from which a salient signal can be
 detected can increase survival over camouflage or conspicuous aposematism
 alone. We investigated whether the spatial frequency of conspicuous and
 cryptically coloured stripes affects the rate of avian predation. Our
 results are consistent with pattern blending acting to camouflage salient
 aposematic signals effectively at a distance. Experiments into the
 relative rate of avian predation on edible model caterpillars found that
 increasing spatial frequency (thinner stripes) increased survival.
 Similarly, visual modelling of avian predators showed that pattern
 blending increased the similarity between caterpillar and background.
 These results show how a colour pattern can be tuned to reveal or conceal
 different information at different distances, and produce tangible
 survival benefits.
description: visual_model_dataVisual model output for viewing caterpillar and background colourssurvival_yellowSurvival data (avian predation rate) for yellow-and-black striped caterpillarssurvival_greenSurvival data (avian predation rate) for green-and-black striped caterpillarsdetection_yellowDetection data (supplementary material) for yellow-and-black striped caterpillarsdetection_greenDetection data (supplementary material) for green-and-black striped caterpillars
DOI: 10.17632/2wrkfmb99h
title: Artificial Intelligence–Driven Prediction of Low BMD in Postmenopausal Women Using Cytokine, RANKL/OPG, and Oxidative Stress Biomarker Signatures

description: Cytokine, RNAKL, OPG and Oxidative stress markers in Normal and Low BMD postmenopausal women
DOI: 10.17632/2wrkfmb99h.1
title: Artificial Intelligence–Driven Prediction of Low BMD in Postmenopausal Women Using Cytokine, RANKL/OPG, and Oxidative Stress Biomarker Signatures

description: Cytokine, RNAKL, OPG and Oxidative stress markers in Normal and Low BMD postmenopausal women
DOI: 10.5061/dryad.nj698
title: Data from: Diversification and fruit evolution in eumalvoids (Malvaceae)

description: Morphological innovations associated with more efficient seed dispersal
 have often been considered as drivers for the diversification of
 angiosperm lineages, but studies testing this relationship are relatively
 few and have led to differing results. In this study, we explore the
 evolution of the fruit and its role in the diversification of eumalvoids
 (Malvaceae). Almost two-thirds of the species in this group have
 schizocarps, which exhibit various adaptations to a more efficient
 dispersal compared to capsules. Schizocarp with a high number of carpels
 characterizes Malveae, the most species-rich tribe in the eumalvoid clade.
 We estimated the diversification rates across this clade and tested
 whether the two traits (the schizocarpic fruit and an increased number of
 carpels) were correlated with speciation and net diversification rates in
 the group. The analyses revealed that Malveae diversified at higher rates
 than the remainder of the eumalvoids, with an abrupt acceleration
 occurring between 30 and 40 Mya. The schizocarpic fruit and the high
 number of carpels are correlated with increased speciation rates,
 suggesting that both traits contributed to the success of the eumalvoids
 and especially of Malveae. These traits would have allowed the successful
 exploitation of open, arid ecosystems that accompanied the
 Eocene/Oligocene boundary. The analyses also showed that the transition to
 the schizocarpic condition is irreversible, which also helps to explain
 its predominance in Malvoideae.
description: Combined four-marker DNA
 dataset of MalvoideaeThis file contains the
 concatenated four marker (matK/trnK, ndhF, rpl16 and ITS) dataset in nexus
 format.Areces-Berazain&Ackerman2017Malvoideae
DOI: 10.2908/nrg_stk_h2
title: Stocks level for hydrogen, ammonia and e-fuels
title: Niveaux de stocks d'hydrogène, d'ammoniac et d’e-carburants
title: Bestände von Wasserstoff, Ammoniak und E-Fuels
DOI: 10.2908/nrg_inf_h2stpc
title: Production capacity of hydrogen, ammonia and e-fuels
title: Capacité de production, de stockage et de transport d'hydrogène, d'ammoniac et d’e-carburants
title: Produktions-, Speicher- und Transportkapazitäten von Wasserstoff, Ammoniak und E-Fuels
DOI: 10.2908/nrg_te_h2
title: Exports of hydrogen, ammonia and e-fuels
title: Exportations d'hydrogène, d'ammoniac et d’e-carburants
title: Ausfuhren von Wasserstoff, Ammoniak und E-Fuels
DOI: 10.2908/nrg_ti_h2
title: Imports of hydrogen, ammonia and e-fuels
title: Importations d'hydrogène, d'ammoniac et d’e-carburants
title: Einfuhren von Wasserstoff, Ammoniak und E-Fuels
DOI: 10.5061/dryad.2g343
title: Data from: Factors influencing ocelot occupancy in Brazilian Atlantic Forest reserves

description: Over 80% of Atlantic Forest remnants are &lt;50 ha and protected areas
 are embedded in a matrix dominated by human activities, undermining the
 long-term persistence of carnivores. The ocelot (Leopardus pardalis) is an
 opportunistic species, but little is known about its tolerance to habitat
 alterations and the influence of other species on its occupancy in
 Atlantic Forest remnants. We used camera traps to assess ocelot occupancy
 in protected areas of Atlantic Forest in southeastern Brazil. We found a
 positive correlation between the occupancy of ocelots and top predators
 (jaguars, Panthera onca, and pumas, Puma concolor), and a weaker negative
 effect between the number of domestic dogs (Canis familiaris) detected and
 ocelot occupancy. Ocelot detection was higher at sites with more
 eucalyptus, suggesting that ocelots frequently use these areas.
 Better-protected areas surrounded by permeable matrices may be critical to
 the persistence of ocelots in the fragmented Atlantic Forest.
description: Mammal
 registersRegister of mammals
 sampled with camera traps in six Brazilian Atlantic Forest
 reservesMetadata_Massara_et_al_2017_Biotropica_mammal_registers.xlsxVariables for modeling occupancy and detection of mammalsVariables used to model occupancy and detection of mammals in six reserves of Brazilian Atlantic ForestMetadata_Massara_et_al_2017_variables_Biotropica.xlsx
DOI: 10.2908/nrg_cb_h2
title: Supply, transformation and consumption of hydrogen, ammonia and e-fuels
title: Approvisionnement, transformation et consommation d'hydrogène, d'ammoniac et d’e-carburants
title: Versorgung, Umwandlung und Verbrauch von Wasserstoff, Ammoniak und E-Fuels
DOI: 10.2908/nrg_ind_psth2
title: Production by source and technology of hydrogen, ammonia and e-fuels
title: Production d'hydrogène, d'ammoniac et d’e-carburants, par source et technologie
title: Produktion von Wasserstoff, Ammoniak und E-Fuels nach Quelle und verwendeter Technologie
DOI: 10.5061/dryad.5s3b1
title: Data from: Spatially explicit analysis sheds new light on the Pleistocene megafaunal extinction in North America

description: The late Pleistocene megafaunal extinctions may have been the first
 extinctions directly related to human activity, but in North America the
 close temporal proximity of human arrival and the Younger Dryas climate
 event has hindered efforts to identify the ultimate extinction cause.
 Previous work evaluating the roles of climate change and human activity in
 the North American megafaunal extinction has been stymied by a reliance on
 geographic binning, yielding contradictory results among researchers. We
 used a fine-scale geospatial approach in combination with 95 megafaunal
 last-appearance and 75 human first-appearance radiocarbon dates to
 evaluate the North American megafaunal extinction. We used kriging to
 create interpolated first- and last-appearance surfaces from calibrated
 radiocarbon dates in combination with their geographic autocorrelation. We
 found substantial evidence for overlap between megafaunal and human
 populations in many but not all areas, in some cases exceeding 3000 years
 of predicted overlap. We also found that overlap was highly regional:
 megafauna had last appearances in Alaska before humans first appeared, but
 did not have last appearances in the Great Lakes region until several
 thousand years after the first recorded human appearances. Overlap in the
 Great Lakes region exceeds uncertainty in radiocarbon measurements or
 methodological uncertainty and would be even greater with sampling-derived
 confidence intervals. The kriged maps of last megafaunal occurrence are
 consistent with climate as a primary driver in some areas, but we cannot
 eliminate human influence from all regions. The late Pleistocene
 megafaunal extinction was highly variable in timing and duration of human
 overlap across the continent, and future analyses should take these
 regional trends into account.
description: Table S1 Rejected
 DataData that was available
 to authors through lit review, but discarded for potential inaccuracy or
 age (see methodology).Table S2
 FADsFirst Appearance Data
 (humans) used in paper.Table S3
 LADsLast Appearance Data
 (Megafauna) used in paper.Table S4 Model
 ComparisonsModel statistics as
 output by ArcGIS.Emery-Wetherell_et_al_FigureS1_2colEmery-Wetherell_et_al_FigureS2_2colEmery-Wetherell_et_al_FigureS3_2colEmery-Wetherell_et_al_FigureS4_2col-01Emery-Wetherell et al.gdb