cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k3j9kd53k
title: Data from: Long-term dynamics of liana seedlings suggest decelerating increases in liana relative abundance over time

description: Over the past decades, tropical forests have experienced both
 compositional and structural changes. In the Neotropics, researchers at
 multiple sites have observed significant increases in the abundance and
 biomass of lianas (i.e. woody vines) relative to trees. However, the role
 of dynamics at early life stages in contributing to increasing liana
 abundance remains unclear.  We took advantage of a unique dataset
 on seedling dynamics over 16 years in ~20,000 1-m2plots in a tropical
 forest in Panama to examine temporal and spatial trends in liana and tree
 seedling abundance.  We found that the relative abundance of
 liana seedlings increased across the study period, from 0.18 in 2001 to
 0.24 in 2017. However, increases in liana seedling relative abundance
 appear to have leveled off in more recent years. The observed increases in
 liana relative abundance appear to be the result of both higher survival
 and higher recruitment rates of liana seedlings compared to tree
 seedlings. Increasing liana abundance in the seedling layer was not
 explained by annual variation in dry season length, total rainfall, or the
 proportion of area occupied by canopy gaps. In addition, liana seedlings
 did not exhibit a demographic advantage (i.e., higher recruitment or
 survival) over tree seedlings in dry habitats.  Synthesis:Our
 results reveal that seedling communities experienced important
 compositional changes in the past, but liana seedling relative abundance
 may have stabilized in recent years. Longer-term monitoring is needed to
 determine whether tropical forests will continue to experience
 compositional changes that may alter forest structure and ecosystem
 function.
DOI: 10.5061/dryad.f4qrfj6rv
title: Data from: Does vegetation change over 28 years affect habitat use and reproductive success?

description: Individuals should prefer and use habitats that confer high fitness, but
 habitat use is not always adaptive. Vegetation in natural landscapes
 changes gradually and the ability of species to adaptively adjust their
 habitat use to long-term changes is largely unstudied. We studied nest
 patch and territory use over 28 years in Orange-crowned Warblers
 (Oreothlypis celata) in a system that has undergone natural long-term
 changes in vegetation. Abundance of maple (Acer grandidentatum), its
 preferred nesting habitat, has gradually declined from 1987 to 2015. We
 examined whether habitat use and its fitness consequences changed as the
 availability of preferred habitat decreased. We used resource selection
 function models to determine changes over time in the probability of using
 a nest patch given available patches, and the probability of using a
 territory given available territories. We estimated nest survival to
 evaluate changes over time in the fitness consequences of nest patch use.
 We also compared habitat use (nest patch and territory) and fitness (nest
 survival) between areas with naturally reduced abundance of maple and
 experimentally increased abundance of maple (fenced areas). Nest patch use
 depended on maple abundance and did not change drastically across 28
 years, even though the availability of preferred maple patches decreased
 over time. In contrast, nest survival tended to decrease over time. We did
 not see differences in nest patch use and nest survival between unfenced
 and fenced areas, unlike territory use, which increased with the abundance
 of maple in fenced areas and decreased in unfenced areas. Our study
 depicts one example of relatively unchanged habitat use in the face of
 decreased availability of preferred vegetation across years, with a
 resulting decrease in reproductive success. Investigating changes in
 habitat use and fitness consequences for animals exposed to long-term
 habitat change is necessary to understand adaptive behavioral
 responses.
DOI: 10.5061/dryad.q57d4g4
title: Forecasting hourly emergency department arrival using time series analysis

description: Background/aims The stochastic arrival of patients at hospital emergency
 departments complicates their management. More than 50% of a
 hospital's emergency department tends to operate beyond its normal
 capacity and eventually fails to deliver high-quality care. To address
 this concern, much research has been carried out using yearly, monthly and
 weekly time-series forecasting. This article discusses the use of hourly
 time-series forecasting to help improve emergency department management by
 predicting the arrival of future patients. Methods Emergency department
 admission data from January 2014 to August 2017 was retrieved from a
 hospital in Iowa. The auto-regressive integrated moving average (ARIMA),
 Holt–Winters, TBATS, and neural network methods were implemented and
 compared as forecasters of hourly patient arrivals. Results The
 auto-regressive integrated moving average (3,0,0) (2,1,0) was selected as
 the best fit model, with minimum Akaike information criterion and Schwartz
 Bayesian criterion. The model was stationary and qualified under the
 Box–Ljung correlation test and the Jarque–Bera test for normality. The
 mean error and root mean square error were selected as performance
 measures. A mean error of 1.001 and a root mean square error of 1.55 were
 obtained. Conclusions The auto-regressive integrated moving average can be
 used to provide hourly forecasts for emergency department arrivals and can
 be implemented as a decision support system to aid staff when scheduling
 and adjusting emergency department arrivals.
description: The Data is anonymized
 and contains no patient information
DOI: 10.5061/dryad.ft0207r
title: Data from: Effect of information about the benefits and harms of mammography on women's decision making: the InforMa randomised controlled trial

description: Background: In Spain, women invited to breast screening are not usually
 informed about potential harms of screening. The objective of the InforMa
 study is to assess the effect of receiving information about the benefits
 and harms of breast screening on informed choice and other decision making
 outcomes, in women approaching the age of invitation to mammography
 screening. Methods: Two-stage randomised controlled trial. In the first
 stage, 40 elementary territorial units of the public healthcare system
 were selected and randomised to intervention or control. In the second
 stage, women aged 49-50 years were randomly obtained. The target sample
 size was 400 women. Women in the intervention arm received a decision aid
 (DA) with detailed information on the benefits and harms of screening.
 Women in the control arm received a standard leaflet that did not mention
 harms and recommended accepting the invitation to participate in the
 Breast Cancer Screening Program (BCSP). The primary outcome was informed
 choice, defined as adequate knowledge and intentions consistent with
 attitudes. Secondary outcomes included decisional conflict, worry about
 breast cancer, time perspective, opinions about the DA, and participation
 in the BCSP. Results: In the intervention group, 23.2% of 203 women made
 an informed choice compared to only 0.5% of 197 women in the control group
 (p &lt; 0.001). Attitudes and intentions were similar in both study
 groups with a high frequency of women intending to be screened, 82.8% vs
 82.2% (p=0.893). Decisional conflict was significantly lower in the
 intervention group. No differences were observed in confidence in the
 decision, anxiety, and participation in BCSP. Conclusions: Women in Spain
 lack knowledge on the benefits and harms of breast screening. Providing
 quantitative information on benefits and harms has produced a considerable
 increase on knowledge and informed choice, with a high acceptance of the
 informative materials.
description: Datafile of the InforMa
 Study The datafile variables
 correspond to the pre-intervention questionnaire (Q1) and the
 post-intervention questionnaire (Q2) of the InforMa study. Both
 questionnaires can be found in the suplementary material at https://doi.org/10.1371/journal.pone.0214057
DOI: 10.5061/dryad.rn91r08
title: Data from: Elevated synaptic vesicle release probability in synaptophysin/gyrin family quadruple knockouts

description: Synaptophysins 1 and 2 and synaptogyrins 1 and 3 constitute a major family
 of synaptic vesicle membrane proteins. Unlike other widely expressed
 synaptic vesicle proteins such as vSNAREs and synaptotagmins, the primary
 function has not been resolved. Here, we report robust elevation in the
 probability of release of readily releasable vesicles with both high and
 low release probabilities at a variety of synapse types from knockout mice
 missing all four family members. Neither the number of readily releasable
 vesicles, nor the timing of recruitment to the readily releasable pool was
 affected. The results suggest that family members serve as negative
 regulators of neurotransmission, acting directly at the level of
 exocytosis to dampen connection strength selectively when presynaptic
 action potentials fire at low frequency. The widespread expression
 suggests that chemical synapses may play a frequency filtering role in
 biological computation that is more elemental than presently envisioned.
description: <strong>Keys.tar</strong> - This tar archive contains
 the information needed to make sense of the other archives, which contain
 the data. Untar and read the Readme.txt file.
 <strong>Root data directory:</strong>
 
 Data_replace Figure6C
 Hippocampus CalyxofHeld
 Figure6AB_QKO Figure6AB_WT
 Figure6BD_sygyr3plus
 Figure6BD_syp1plus
 Figure6BD_syp1syp2plus
 Figure6BD_syp2sygr3plus
 Figure6B_sygr1sygr3plus
 Figure6B_sygyr1plus
 Figure6B_syp1sygr1plus
 Figure6B_syp1sygr3plus
 Figure6B_syp2plus
 Figure6B_syp2sygr1plus Keys - contains
 information in a Readme.txt file that will explain how to access the
 data.
DOI: 10.5061/dryad.8kprr4xj0
title: Data from: Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

description: Little is known about intraspecific variation within the deacon rockfish
 (Sebastes diaconus), a recently described species found in the northeast
 Pacific Ocean. We investigated population structure among fish sampled
 from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site
 (Stonewall Bank) within a &lt;50 km2 area off the Oregon coast. Fish
 from the three sample sites exhibited small but statistically significant
 differences based on genetic variation at &gt;15,000 neutral loci,
 whether analyzed independently or classified into nearshore and offshore
 groups. Male and females were readily distinguished using genetic data and
 92 outlier loci were associated with sex, potentially indicating
 differential selection between males and females. Morphometric results
 indicated that there was significant secondary sexual dimorphism in
 otolith shape, but further sampling is required to disentangle potential
 confounding influence of age. This study is the first step towards
 understanding intraspecific variation within the deacon rockfish and the
 potential management implications. Since differentiation among the three
 sample sites was small, we consider the results to be suggestive of a
 single stock. However, future studies should evaluate how the stock is
 affected by differences in sex, age, and gene flow between the nearshore
 and offshore environments.
description: Data files for: Sex matters: Otolith shape and genomic variation
 in deacon rockfish (<i>Sebastes diaconus</i>). Spreadsheets
 for the otolith and genetic sampling, and genetic data (vcf, genepop, and
 structure
 genotype files, and the fasta consensus
 file for the 92 outlier loci). <br> <br> Demultiplexed forward
 and reverse DNA sequence reads for the deacon rockfish sequenced in this
 study are openly available on the NCBI sequence read archive (SRA) under:
 PRJNA560239, http://www.ncbi.nlm.nih.gov/bioproject/560239
DOI: 10.5061/dryad.jsxksn052
title: Reliable phylogenetic regressions for multivariate comparative data: illustration with the MANOVA and application to the effect of diet on mandible morphology in Phyllostomid bats

description: Understanding what shapes species phenotypes over macroevolutionary
 timescales from comparative data often requires studying the relationship
 between phenotypes and putative explanatory factors or testing for
 differences in phenotypes across species groups. In phyllostomid bats for
 example, is mandible morphology associated to diet preferences? Performing
 such analyses depends upon reliable phylogenetic regression techniques and
 associated tests (e.g. phylogenetic Generalized Least Squares, pGLS and
 phylogenetic analyses of variance and covariance, pANOVA, pANCOVA). While
 these tools are well established for univariate data, their multivariate
 counterparts are lagging behind. This is particularly true for high
 dimensional phenotypic data, such as morphometric data. Here we implement
 much-needed likelihood-based multivariate pGLS, pMANOVA and pMANCOVA, and
 use a recently developed penalized likelihood framework to extend their
 application to the difficult case when the number of
 traits p approaches or exceeds the number of
 species n. We then focus on the pMANOVA and use intensive
 simulations to assess the performance of the approach
 as p increases, under various levels of phylogenetic
 signal and correlations between the traits, phylogenetic structure in the
 predictors, and under various types of phenotypic differences across
 species groups. We show that our approach outperforms available
 alternatives under all circumstances, with greater power to detect
 phenotypic differences across species group when they exist, and a lower
 risk of improperly detecting nonexistent differences. Finally, we provide
 an empirical illustration of our pMANOVA on a geometric-morphometric
 dataset describing mandible morphology in phyllostomid bats along with
 data on their diet preferences. Overall our results show significant
 differences between ecological groups. Our approach, implemented in the R
 package mvMORPH and illustrated in a tutorial for end-users, provides
 efficient multivariate phylogenetic regression tools for understanding
 what shapes phenotypic differences across species.
DOI: 10.5281/zenodo.18365584
title: Z-Scanner: Geant4 Monte Carlo Dataset for Dual-Parameter Proton Tomography (BL4S 2026)

description:  This dataset contains high-fidelity Geant4 Monte Carlo simulation data generated for the Z-Scanner proposal (CERN Beamline for Schools 2026). The project investigates "Dual-Parameter Proton Tomography via Range–Scattering Correlation," specifically aiming to distinguish materials with identical density but distinct nuclear composition (PVC and Delrin) using Multiple Coulomb Scattering (MCS). The simulation models the CERN PS T9 beamline environment with a 0.7 GeV/c proton beam interacting with a custom PMMA phantom containing inserts of PVC, Delrin, Aluminum, and PMMA (Reference).

(Note: 'Unknown' in the dataset corresponds to particles passing through air or scattering out of the phantom geometry).
description: Dataset StructureThe dataset consists of CSV files generated by the Geant4 simulation:



protonct_runX.csv: Batch files containing event-by-event proton tracking data.

data_calibration.csv: Empty beam runs for alignment.

data_modeA.csv: Combined tracking data.

data_modeB.csv: Combined tracking data (Mode B - if applicable).


Column Definitions: 



Each row represents a single proton event.

EventID: Unique identifier for the event.

Up1_X, Up1_Y, Up1_Z: Entry position at first upstream tracking plane (mm).

Up2_X, Up2_Y, Up2_Z: Entry position at second upstream tracking plane (mm).

Down1_X, Down1_Y, Down1_Z: Exit position at first downstream tracking plane (mm).

Down2_X, Down2_Y, Down2_Z: Exit position at second downstream tracking plane (mm).

ScatterAngle_mrad: True Monte Carlo scattering angle (milliradians).

EntryEnergy_MeV: Kinetic energy of proton before entering phantom.

ExitEnergy_MeV: Kinetic energy of proton after exiting phantom.

WEPL_gcm2: Water Equivalent Path Length (g/cm²).

Material: Ground truth material label (PVC, Delrin, PMMA, PMMAref, Aluminum)

NuclearInteraction: Flag (0 = pure electromagnetic, 1 = nuclear interaction occurred).

PhantomAngle_deg: Rotation angle of the phantom for tomographic reconstruction.


Usage Notes: These files are intended to be processed using Python (Pandas/NumPy) or ROOT. Standard analysis involves filtering NuclearInteraction == 0 to isolate pure MCS events for image reconstruction.
DOI: 10.5061/dryad.9zw3r2299
title: Thoracic adaptations for ventilation during locomotion in humans and other mammals

description: Bipedal humans, like canids and some other cursorial mammals, are thought
 to have been selected for endurance running, which requires the ability to
 sustain aerobic metabolism over long distances by inspiring large volumes
 of air for prolonged periods of time. Here we test the general hypothesis
 that humans and other mammals selected for vigorous endurance activities
 evolved derived thoracic features to increase ventilatory capacity. To do
 so, we investigate whether humans and dogs rely on thoracic motion to
 increase tidal volume during running to a greater extent than goats, a
 species that was not selected for endurance locomotion. We found that
 while all three species use diaphragmatic breathing to increase tidal
 volume with increasing oxygen demand, humans also use both dorsoventral
 and mediolateral expansions of the thorax. Dogs use increased dorsoventral
 expansion of the thorax, representing an intermediate between humans and
 goats. 3D analyses of joint morphology of 10 species across four mammalian
 orders also show that endurance-adapted cursorial species independently
 evolved more concavo-convex costovertebral joint morphologies that allow
 for increased rib mobility for thoracic expansion. Evidence for similarly
 derived concavo-convex costovertebral joints in Homo erectus corresponds
 with other evidence for the evolution of endurance running in the genus
 Homo.
description: Morphological
 Data Morphological
 measurements of the costovertebral joint.   
 Experimental
 Data Spirometry and kinematic
 measurements.
DOI: 10.5061/dryad.m1t32
title: Data from: Phylogenomic analysis of the explosive adaptive radiation of the Espeletia complex (Asteraceae) in the tropical Andes

description: The subtribe Espeletiinae (Asteraceae) is endemic to the high-elevations
 in the Northern Andes. It exhibits an exceptional diversity of species,
 growth-forms and reproductive strategies, including large trees,
 dichotomous trees, shrubs and the extraordinary giant monocarpic or
 polycarpic caulescent rosettes, considered as a classic example of
 adaptation in tropical high-elevation ecosystems. The subtribe has long
 been recognised as a prominent case of adaptive radiation, but the
 understanding of its evolution has been hampered by a lack of phylogenetic
 resolution. Here we produce the first fully resolved phylogeny of all
 morphological groups of Espeletiinae, using whole plastomes and about a
 million nuclear nucleotides obtained with an original de novo assembly
 procedure without reference genome, and analysed with traditional and
 coalescent-based approaches that consider the possible impact of
 incomplete lineage sorting and hybridisation on phylogenetic inference. We
 show that the diversification of Espeletiinae started from a rosette
 ancestor about 2.3 Ma, after the final uplift of the Northern Andes. This
 was followed by two rather independent radiations in the Colombian and
 Venezuelan Andes, with a few trans-cordilleran dispersal events among
 low-elevation tree lineages but none among high-elevation rosettes. We
 demonstrate complex scenarios of morphological change in Espeletiinae,
 usually implying the convergent evolution of growth-forms with frequent
 loss/gains of various traits. For instance, caulescent rosettes evolved
 independently in both countries, likely as convergent adaptations to life
 in tropical high-elevation habitats. Tree growth-forms evolved
 independently three times from the repeated colonisation of lower
 elevations by high-elevation rosette ancestors. The rate of morphological
 diversification increased during the early phase of the radiation, after
 which it decreased steadily towards the present. On the other hand, the
 rate of species diversification in the best-sampled Venezuelan radiation
 was on average very high (3.1 spp/My), with significant rate variation
 among growth-forms (much higher in polycarpic caulescent rosettes). Our
 results point out a scenario where both adaptive morphological evolution
 and geographical isolation due to Pleistocene climatic oscillations
 triggered an exceptionally rapid radiation for a continental plant group.
description: Plastid_datationPlastid sequences of Espeletiinae and some members of the Asteraceae tribes Millerieae, Heliantheae, Anthemidae and Cichorieae used for the divergence time estimationdataset_chloroplastic_datation.nxsNuclear_EspeletiinaeNuclear sequences of Espeletiinae and outgroup taxa used for the phylogenetic inferencedataset_phylo_outgroup_Espeletiinae.nxsPlastid_EspeletiinaePlastid sequences of Espeletiinae and outgroup taxa used for the phylogenetic inferencedataset_phylo_cpDNA_Espeletiinae.nxs
DOI: 10.5061/dryad.931zcrjfn
title: Data from: Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

description: Microbiota inhabiting the gastrointestinal (GI) tract of animals have
 important impacts on many host physiological processes. Although host diet
 is a major factor influencing the composition of the gut microorganismal
 community, few comparative studies have considered how differences in diet
 influence community composition across the length the GI tract. We used
 16S sequencing to compare the microbiota along the length of the GI tract
 in Abert’s (Sciurus aberti) and fox squirrels (S. niger) living in the
 same habitat. While fox squirrels are generalist omnivores, the diet of
 Abert’s squirrels is unusually high in plant fiber, particularly in winter
 when they extensively consume fiber-rich inner bark of ponderosa pine
 (Pinus ponderosa). Consistent with previous studies, microbiota of the
 upper GI tract of both species consisted primarily of facultative
 anaerobes and was less diverse than that of the lower GI tract, which
 included mainly obligate anaerobes. While we found relatively little
 differentiation between the species in the microbiota of the upper GI
 tract, the community composition of the lower GI tract was clearly
 delineated. Notably, the Abert’s squirrel lower GI community was more
 stable in composition and enriched for microbes that play a role in the
 degradation of plant fiber. In contrast, overall microbial diversity was
 higher in fox squirrels. We hypothesize that these disparities reflect
 differences in diet quality and diet breadth between the species.