cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5068/d17w9m
title: Data from: Tropical tree size-frequency distributions from airborne lidar

description: Tropical rainforest canopies, where stems and crowns reside, are hotspots
 of biological diversity, mediate the global biochemical processes and are
 the interface between organic nature and the atmosphere. Ecosystem
 functions such as growth, competition and mortality, depend on the spatial
 arrangement of tree crowns that varies significantly across forest types
 and disturbance gradients. The exact nature and function of tropical tree
 canopies are not well known. Field inventories often focus on measuring
 the horizontal component of the canopy (tree diameter and species
 identification) and rarely measure tree height or crown size. Remote
 sensing airborne lidar (light detection and ranging) is considered a
 complementary method to circumvent the difficulty of field techniques in
 measuring forest canopies, with recognized ability to estimate canopy
 height and vegetation vertical profiles. A recent lidar-based method
 (adaptive mean shift, AMS3D) shown improved capabilities to deal with the
 complexity of tropical forest and to provide spatial explicit measurements
 of crown morphology and packing by modeling individual trees. Here, we
 report tree-level forest inventory (field and LiDAR) over nine 1 ha forest
 plots in the La Selva Biological Station, Costa Rica. The field inventory
 includes stem location (tree height &gt; 10m), tree diameter, tree
 height and wood density. Crown radii measurements for a tree subsample
 (n=285) were used to derive local tree allometry. The lidar forest
 inventory includes the point clouds measurements over the 1 ha plots with
 an additional attribute to cluster the individual points into tree crowns.
 The lidar tree crowns were modeled to estimate tree location, tree height,
 crown depth, crown area, crown volume and crown surface. Additionally, we
 provide tree-level LiDAR forest inventory for 45360 plots (1 ha)
 distributed over old-growth, selectively-logged, secondary and swamp
 forests. The field inventories have been compared and show good agreement
 in terms of stem number density, size-frequency distributions (stem
 diameter, tree height), basal area and aboveground biomass.
         
description: The methods used to derive the field and lidar forest
 inventory are described in  Clark DB, Ferraz A, Clark
 DA, Kellner JR, Letcher SG, Saatchi S (2019) Diversity, distribution and
 dynamics of large trees across an old-growth lowland tropical rain forest
 landscape. PLoS ONE 14(11): e0224896.
 https://doi.org/10.1371/journal.pone.0224896
 and  Ferraz A, Saatchi S, Longo M, Clark DB
 (2020) Tropical tree size-frequency distributions from airborne lidar.
 Ecological Applications  respectively.
DOI: 10.15468/dl.h8bmpy
title: Occurrence Download

description: A dataset containing 205494 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((133 6.3,135 6.3,135 8.6,133 8.6,133 6.3))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 205494 records from 222 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002264-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.573n5tb4d
title: Data from: Phylogeographic estimation and simulation of global diffusive dispersal

description: The analysis of time-resolved phylogenies (timetrees) and geographic
 location data allows estimation of dispersal rates, for example for
 invasive species and infectious diseases. Many estimation methods are
 based on the Brownian Motion model for diffusive dispersal on a
 2-dimensional plane, however the accuracy of these methods deteriorates
 substantially when dispersal occurs at global scales because Spherical
 Brownian Motion (SBM) differs from planar Brownian Motion. No statistical
 method exists for estimating SBM diffusion coefficients from a given
 timetree and tip coordinates, and no method exists for simulating SBM
 along a given timetree. Here I present new methods for simulating SBM
 along a given timetree, and for estimating SBM diffusivity from a given
 timetree and tip coordinates using a modification of Felsenstein's
 independent contrasts and maximum-likelihood. My simulation and fitting
 methods can accommodate arbitrary time-dependent diffusivities and scale
 efficiently to trees with millions of tips, thus enabling new analyses
 even in cases where planar BM would be a sufficient approximation. I
 demonstrate these methods using a timetree of marine and terrestrial
 Cyanobacterial genomes, as well as timetrees of two globally circulating
 Influenza B clades. My methods are implemented in the R package
 "castor."
DOI: 10.5061/dryad.0p2ngf1x0
title: Molecular assays of pollen use consistently reflect pollinator visitation patterns in a system of flowering plants

description: Determining how pollinators visit plants versus how they carry and
 transfer pollen is an ongoing project in pollination ecology. The current
 tools for identifying the pollens that bees carry have different strengths
 and weaknesses when used for ecological inference. In this study we use
 three methods to better understand a system of congeneric, co-flowering
 plants in the genus Clarkia and their bee pollinators: observations of
 plant-pollinator contact in the field, and two different molecular methods
 to estimate the relative abundance of each Clarkia pollen in samples
 collected from pollinators. We use these methods to investigate if
 observations of plant-pollinator contact in the field correspond to the
 pollen bees carry; if individual bees carry Clarkia pollens in predictable
 ways, based on previous knowledge of their foraging behaviors; and how the
 three approaches differ for understanding plant-pollinator interactions.
 We find that observations of plant-pollinator contact are generally
 predictive of the pollens that bees carry while foraging, and network
 topologies using the three different methods are statistically
 indistinguishable from each other. Results from molecular pollen analysis
 also show that while bees can carry multiple species of Clarkia at the
 same time, they often carry one species of pollen. Our work contributes to
 the growing body of literature aimed at resolving how pollinators use
 floral resources. We suggest our novel relative amplicon quantification
 method as another tool in the developing molecular ecology and pollination
 biology toolbox.
DOI: 10.5061/dryad.k3j9kd54m
title: Data from: Colonize, radiate, decline: unraveling the dynamics of island community assembly with Fijian trap-jaw ants

description: The study of island community assembly has been fertile ground for
 developing and testing theoretical ideas in ecology and
 evolution.  The eco-evolutionary trajectory of lineages after
 colonization has been a particular interest, as this is a key component of
 understanding community assembly.  In this system, existing ideas
 such as the taxon cycle posit that lineages pass through a regular
 sequence of eco-evolutionary changes after colonization, with lineages
 shifting toward reduced dispersal ability, increased ecological
 specialization, and declines in abundance. However, these predictions have
 historically been difficult to test. Here, we integrate phylogenomics,
 population genomics, and x-ray microtomography/3D morphometrics, to test
 hypotheses for whether the ecomorphological diversity of trap-jaw ants
 (Strumigenys) in the Fijian archipelago is assembled primarily through
 colonization or post-colonization radiation, and whether species show
 ecological shifts toward niche specialization, toward upland habitats, and
 decline in abundance after colonization. We infer that most Fijian endemic
 Strumigenys evolved in situ from a single colonization and have
 diversified to fill a large fraction of global morphospace occupied by the
 genus. Within this adaptive radiation, lineages trend to different degrees
 toward high elevation, reduced dispersal ability, and demographic decline,
 and we find no evidence of repeated colonization that displaces the
 initial radiation.  Overall these results are only partially
 consistent with taxon cycle and associated ideas, while highlighting the
 potential role of priority effects in assembling island communities.
description: We provide three datasets that have been used in the
 paper: 1. Phylogenimics data. All phylogenies and the
 original PHYLIP file generated by ipyrad assembly. 2.
 VCF data. Filtered vcf files that used for all the population genomics
 analyses. The vcf files were generated by ipyrad. 3. 3D
 geometric morphometrics data. 3D surface models of Fijian Strumigenys and
 R script for 3D geometric morphometrics analysis.
description: There are three folders: 1. Phylogeny:
 including the Ml tree infered by IQtree
 ("Fijian_Strumigenys_IQtree.tre"), the date-calibrated tree
 inferred by BEAST ("Fijian_Strumigenys_Beast.tre"), and the SNP
 tree inferred by Tetrad ("Fijian_Strumigenys_Tetrad.tre"). In
 addition, this folder also include the original supermatrix
 ("Fijian_Strumigenys.phy") for all the phylogeneic
 analysis. 2 Vcf: All the filtered vcf files.
 3. 3D morphometrics. including all the 3d surface data generated
 by microCT, and the 3D geometric morphometrics analyzing code
 ("Landmark_Analysis.html")
DOI: 10.5061/dryad.2280gb5p4
title: Data from: Evaluation of a pharmacist-led actionable audit and feedback intervention for improving medication safety in primary care: an interrupted time series analysis

description: Background. We evaluated the impact of a pharmacist-led Safety Medication
 dASHboard (SMASH) intervention on medication safety in primary care.
 Methods and findings. SMASH comprised: (1) training of clinical
 pharmacists to deliver the intervention; (2) a web-based dashboard
 providing actionable, patient-level feedback; and (3) pharmacists
 reviewing individual at-risk patients, and initiating remedial actions or
 advising general practitioners on doing so. It was implemented in
 forty-three general practices covering a population of 235,595 people in
 Salford (Greater Manchester), UK. All practices started receiving the
 intervention between 18 April 2016 and 26 September 2017. We used an
 interrupted time series analysis of rates of potentially hazardous
 prescribing and inadequate blood-test monitoring, comparing observed rates
 post-intervention to extrapolations from a 24-month pre-intervention
 trend. The number of people registered to participating practices and
 having one or more risk factors for being exposed to hazardous prescribing
 or inadequate blood-test monitoring at the start of the intervention was
 47,413 (males: 23,073 [48.7%]; mean age: 60 [standard deviation: 21]). At
 baseline, 95% of practices had rates of potentially hazardous prescribing
 (composite of 10 indicators) between 0.88% and 6.19%. The prevalence of
 potentially hazardous prescribing reduced by 27.9% (95% confidence
 interval [CI], 20.3% to 36.8%) at 24 weeks and by 40.7% (95% CI, 29.1% to
 54.2%) at twelve months after introduction of SMASH. The rate of
 inadequate blood-test monitoring (composite of 2 indicators) reduced by
 22.0% (95% CI, 0.2% to 50.7%) at 24 weeks and by 23.5% (95% CI, -4.5% to
 61.6%) at 12 months. After 12 months, 95% of practices had rates of
 potentially hazardous prescribing between 0.74% and 3.02%. We did not
 randomise practices but enrolled them in a naturalistic fashion. All our
 measurements were based on routinely kept electronic health records.
 Conclusions. The SMASH intervention was associated with reduced rates of
 potentially hazardous prescribing and inadequate blood-test monitoring in
 general practices. This reduction was sustained over 12 months after start
 of the intervention for prescribing but not for monitoring of medication.
 There was a marked reduction in the variation in rates of high-risk
 prescribing between practices.
description: The dataset contains prevalence rates for 13 medication safety
 indicators and various composites thereof (column
 <strong>measures</strong>), collected across 43 general
 practices (column <strong>practice_id</strong>) and 39 periods
 of 4 weeks (3 years in total; column <strong>week</strong>).
 Prevalence rates are described by numerator (column
 <strong>num</strong>), denominator (column
 <strong>denom</strong>), and percentage (column
 <strong>perc</strong>). For further details, see
 manuscript.
DOI: 10.5281/zenodo.18395216
title: THE IMPACT OF DIGITAL TECHNOLOGIES ON MODERN LANGUAGE LEARNING.

description: In today’s interconnected and competitive world, learning foreign languages has become one of the key elements for personal, academic, and professional success. This article explores the digitalization of education and its effectiveness. As digital tools become increasingly integrated into everyday life, their influence on language learning has grown rapidly. Modern technologies such as mobile applications, artificial intelligence, interactive platforms, and multimedia resources have transformed traditional learning methods by making education more accessible, personalized, and engaging for learners of all ages.
DOI: 10.5281/zenodo.18395217
title: THE IMPACT OF DIGITAL TECHNOLOGIES ON MODERN LANGUAGE LEARNING.

description: In today’s interconnected and competitive world, learning foreign languages has become one of the key elements for personal, academic, and professional success. This article explores the digitalization of education and its effectiveness. As digital tools become increasingly integrated into everyday life, their influence on language learning has grown rapidly. Modern technologies such as mobile applications, artificial intelligence, interactive platforms, and multimedia resources have transformed traditional learning methods by making education more accessible, personalized, and engaging for learners of all ages.
DOI: 10.15468/dl.7836kk
title: Occurrence Download

description: A dataset containing 3171 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Moroteuthopsis ingens",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 3171 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002321-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6078/d1b12g
title: Toxic Y-chromosome in D. miranda

description: Large portions of eukaryotic genomes consist
 of transposable elements (TEs), and the
 establishment of transcription-repressing heterochromatin during early
 development safeguards genome integrity. Repeat-rich Y
 chromosomes can act as reservoirs for TEs (toxic Y effect),
 and TEs may exploit vulnerabilities associated with
 incomplete genomic defenses during early development. Here,
 we contrast the dynamics of early TE activation
 in two Drosophila species with vastly different Y
 chromosomes of different age. Zygotic TE
 expression is elevated in male embryos relative to females in
 both species, mostly due to expression of Y-linked
 TEs. Interestingly, male-biased
 TE misexpression diminishes across
 development in D. pseudoobscura, but remains elevated
 in D. miranda, the species with the younger and
 larger neo-Y
 chromosome. In D. miranda, misexpression of TEs is associated with incomplete heterochromatin formation on the neo-Y and results in more de novo insertions of repeats in males compared to females.  We find that because the neo-Y of D. miranda still contains many actively transcribed genes embedded in TEs, the formation of silencing heterochromatin is compromised, causing elevated TE expression and mobilization. This lends support to the idea that the ‘toxic Y chromosome’ can create a mutational burden in males when genome-wide defense mechanisms are compromised, and reveals a previously unappreciated epigenetic conflict on evolving Y chromosomes between transcription of essential genes and silencing of selfish DNA. 
description: RNA-seq: Read counts at TEs are normalized
 by the median read counts at autosomal genes then averaged across
 replicate libraries. Read counts at genes are inferred using featureCounts
 in the Subread package. Libraries are generated by Lott et al
 2014.   ChIP-seq: Sex-specific
 H3K9me3 enrichment across the genome in 25kb windows. Enrichment is
 normalized using quantiles of spike-ins. Enrichment is averaged between
 libraries of the same sex and developmental stages. 
 de novo TE insertions: Genomic regions with
 paired-end reads that span unique sequences and TEs are provided.
 Insertions with both the 5' and 3' junctions found are deemd
 true de novo insertions.
DOI: 10.6086/d16h37
title: Data from: Estimating egg mass-body mass relationships in birds

description: The mass of a bird’s egg is a critical attribute of the species’ life
 history and represents a fundamental component of reproductive
 effort.  Indeed, the trade-off between the number of eggs in a
 clutch and clutch mass lies at the heart of understanding how
 environmental attributes such as nest predation or adult mortality
 influence reproductive investment.  However, egg masses have not
 been reported for the majority of avian species.  We capitalized
 on the strong allometric relationship between avian body mass and egg mass
 to produce egg mass estimates for over 5,500 species previously lacking
 such information.  These estimates are accompanied by measures of
 the robustness of the regressions used to produce them (e.g., sample size,
 root mean square error of estimation, coefficient of determination, degree
 of extrapolation), thus allowing independent evaluation of the suitability
 of any estimate to address a particular research question relating to
 avian life history.  Most estimates (~5,000) were based on family
 level egg mass-body mass regressions, with the remainder derived from
 other relationships such as ordinal regressions.  We compared
 estimating regressions based on adult vs. female body masses, and after
 finding little difference between the two based our final estimates on
 adult masses as those were more numerous in the literature.  What
 small differences between adult- and female-based regressions that did
 occur were not related to sexual size dimorphism across
 families.  These new estimates, coupled with ~5,000 egg masses
 reported in the literature, provide a foundation of over 10,000 species
 for wider investigations assessing variation in reproductive effort in
 birds over a broad array of ecological and evolutionary
 contexts. 
description: Avian egg mass and body mass data downloaded from various
 published sources as indicated in Methods.  For the large majority of
 species for which egg masses had not been reported we estimated them based
 on the ordinary least squares regression relationship derived from other
 species with known values in the same family.
description: See ReadMe file for contents of each dataset.
DOI: 10.5061/dryad.9kd51c5dc
title: Data from: Phylogenomics reveals ancient gene tree discordance in the amphibian Tree of Life

description: Molecular phylogenies have yielded strong support for many parts of the
 amphibian Tree of Life, but poor support for the resolution of deeper
 nodes, including relationships among families and orders. To clarify these
 relationships, we provide a phylogenomic perspective on amphibian
 relationships by developing a taxon-specific Anchored Hybrid Enrichment
 protocol targeting hundreds of conserved exons which are effective across
 the class. After obtaining data from 220 loci for 286 species
 (representing 94% of the families and 44% of the genera), we estimate a
 phylogeny for extant amphibians and identify gene tree–species tree
 conflict across the deepest branches of the amphibian phylogeny. We
 perform locus-by-locus genealogical interrogation of alternative
 topological hypotheses for amphibian monophyly, focusing on interordinal
 relationships. We find that phylogenetic signal deep in the amphibian
 phylogeny varies greatly across loci in a manner that is consistent with
 incomplete lineage sorting in the ancestral lineage of extant amphibians.
 Our results overwhelmingly support amphibian monophyly and a sister
 relationship between frogs and salamanders, consistent with the Batrachia
 hypothesis. Species tree analyses converge on a small set of topological
 hypotheses for the relationships among extant amphibian families. These
 results clarify several contentious portions of the amphibian Tree of
 Life, which in conjunction with a set of vetted fossil calibrations,
 support a surprisingly younger timescale for crown and ordinal amphibian
 diversification than previously reported. More broadly, our study provides
 insight into the sources, magnitudes, and heterogeneity of support across
 loci in phylogenomic data sets.
DOI: 10.5061/dryad.rfj6q5778
title: Data from: Copulatory function and development shape modular architecture of genitalia differently in males and females

description: Genitalia are multitasking structures whose development is mediated by
 numerous regulatory pathways. This multi-factorial nature provides an
 avenue for multiple sources of selection. As a result, genitalia tend to
 evolve as modular systems comprising semi-independent subsets of
 structures, yet the processes that give rise to those patterns are still
 poorly understood. Here, we ask what are the relative roles of development
 and function in shaping modular patterns of genitalia within populations
 and across species of stink-bugs. We found that male genitalia are less
 integrated, more modular, and primarily shaped by functional demands. In
 contrast, females show higher integration, lower modularity, and a
 predominant role of developmental processes. Further, interactions among
 parts of each sex are more determinant to modularity than those between
 the sexes, and patterns of modularity are equivalent between and within
 species. Our results strongly indicate that genitalia have been subjected
 to sex-specific selection, although male and female genitalia are
 homologous and functionally associated. Moreover, modular patterns are
 seemingly constant in the evolutionary history of stink-bugs, suggesting a
 scenario of multivariate stabilizing selection within each sex. Our study
 demonstrates that interactions among genital parts of the same sex may be
 more fundamental to genital evolution than previously thought.
description: We collected genital data using geometric morphometrics and
 converted landmarks to Jacobian matrices, which were used in the tests of
 modularity and integration. Here we provide the Jacobian data along with R
 codes, the phylogenetic trees and all other necessary files for analyses
 of intra- and interspecific levels and for males and females. Please see
 the "read.me" file for a complete description of the files, and
 the paper for detailed methodological procedures.