cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mv711kb
title: Data from: Field observations of turbulence, sand suspension and cross-shore transport under spilling and plunging breakers

description: Measurements of wave orbital velocity, near-bed turbulence levels and
 sediment suspension were obtained under plunging and spilling breakers in
 the outer surf zone on the beach at Vejers, Denmark. For the same range of
 relative wave heights and indicators of wave nonlinearity, we observed
 significantly larger suspended sediment concentrations and
 onshore-directed rates of suspended sediment transport under (long-period)
 plunging breakers, compared to (short-period) spilling breakers. This is
 consistent with the long-held understanding that, for a given beach slope,
 onshore transport and beach accretion is associated with longer-period
 waves and offshore transport and erosion is associated with shorter-period
 waves. An intra-wave analysis of hydrodynamics and sediment suspension
 revealed that the main reason for the larger suspended sediment transport
 rates under plunging waves was i) larger time-averaged suspended sediment
 loads under plunging waves, and ii) a larger difference in cumulated
 sediment load under the wave crest phase compared to the wave trough phase
 for plunging breakers. This latter difference was due to an earlier
 arrival at the seabed of higher levels of turbulent kinetic energy (TKE)
 under plunging waves compared to spilling waves. Hence, both magnitude and
 timing within the wave cycle of TKE production is important in a
 quantification of sediment transport under breaking waves. For
 ensemble-averaged intense suspension events, contributing roughly 50% of
 the total sediment suspension during individual records, we found that
 instantaneous near-bed sediment load was linearly related to instantaneous
 levels of Froude-scaled TKE.
description: Sediment suspension
 under breaking wavesThe file consists of six
 data records of cross-shore, longshore and vertical velocity, water depth
 and sediment concentrations at six elevations. The records were obtained
 under plunging (PL) and spilling (SP) wave breaking conditions at Vejers
 Beach, Denmark, in the fall of 2007.all_runs.dat
DOI: 10.5061/dryad.9b21271
title: Data from: A fast-evolving X-linked duplicate of importin-α2 is overexpressed in sex-ratio drive in Drosophila neotestacea

description: Selfish genetic elements that manipulate gametogenesis to achieve a
 transmission advantage are known as meiotic drivers. Sex-ratio
 X-chromosomes (SR) are meiotic drivers that prevent the maturation of
 Y-bearing sperm in male carriers to result in the production of mainly
 female progeny. The spread of an SR chromosome can affect host genetic
 diversity and genome evolution, and can even cause host extinction if it
 reaches sufficiently high prevalence. Meiotic drivers have evolved
 independently many times, though only in a few cases is the underlying
 genetic mechanism known. In this study we use a combination of
 transcriptomics and population genetics to identify widespread expression
 differences between the standard (ST) and sex-ratio (SR) X-chromosomes of
 the fly Drosophila neotestacea. We found the X-chromosome is enriched for
 differentially expressed transcripts, and that many of these X-linked
 differentially expressed transcripts had elevated Ka/Ks values between ST
 and SR, indicative of potential functional differences. We identified a
 set of candidate transcripts, including a testis-specific, X-linked
 duplicate of the nuclear transport gene importin-2 that is overexpressed
 in SR. We find suggestions of positive selection in the lineage leading to
 the duplicate and that its molecular evolutionary patterns are consistent
 with relaxed purifying selection in ST. As these patterns are consistent
 with involvement in the mechanism of drive in this species, this duplicate
 is a strong candidate worthy of further functional investigation. Nuclear
 transport may be a common target for genetic conflict, as the mechanism of
 the autosomal Segregation Distorter drive system in D. melanogaster
 involves the same pathway.
description: D. neotestacea sex ratio
 transcriptome and pop gen sequenceTranscriptome and
 population genetic DNA sequences from Pieper, Unckless and Dyer 2018.
 Please see the readme file for a full description of the
 data.dryad_data.zip
DOI: 10.5281/zenodo.18389788
title: HimalHydro - database of run-of-the-river projects in the Himalayan region

description: HimalHydro is a spatially distributed database of run-of-the-river projects (and other hydropower schemes) in the Himalayan region.
DOI: 10.5281/zenodo.18389787
title: HimalHydro - database of run-of-the-river projects in the Himalayan region

description: HimalHydro is a spatially distributed database of run-of-the-river projects (and other hydropower schemes) in the Himalayan region.
DOI: 10.5061/dryad.97r9289
title: Data from: One and two year visual outcomes from the Moorfields age-related macular degeneration database: a retrospective cohort study and an open science resource

description: Objectives: To analyse treatment outcomes and share clinical data from a
 large, single-center, well-curated database (8174 eyes / 6664 patients
 with 120,756 single entries) of patients with neovascular age related
 macular degeneration (AMD) treated with anti-vascular endothelial growth
 factor (VEGF). By making our depersonalised raw data openly available, we
 aim to stimulate further research in AMD, as well as setting a precedent
 for future work in this area. Setting: Retrospective, comparative,
 non-randomised electronic medical record (EMR) database cohort study of
 the UK Moorfields AMD database with data extracted between 2008 and 2018.
 Participants: Including one eye per patient, 3357 eyes/patients (61%
 female). Extraction criteria were ≥ 1 ranibizumab or aflibercept
 injection, entry of “AMD” in the diagnosis field of the EMR, and a minimum
 of one year of follow-up. Exclusion criteria were unknown date of first
 injection and treatment outside of routine clinical care at Moorfields
 before the first recorded injection in the database. Main outcome
 measures: Primary outcome measure was change in VA at one and two years
 from baseline as measured in Early Treatment Diabetic Retinopathy Study
 (ETDRS) letters. Secondary outcomes were the number of injections and
 predictive factors for VA gain. Results: Mean VA gain at one-year and two
 years were +5.5 (95%CI:5.0,6.0) and +4.9 (95%CI:4.2,5.6) letters
 respectively. Fifty-four percent of eyes gained ≥5 letters at two years,
 63% had stable VA (±≤14 letters), forty-four percent of eyes maintained
 good VA (≥70 letters). Patients received a mean of 7.7 (95%CI:7.6,7.8)
 injections during year one and 13.0 (95%CI:12.8,13.2) injections over two
 years. Younger age, lower baseline VA, and more injections were associated
 with higher VA gain at two years. Conclusion: This study benchmarks high
 quality EMR study results of real life AMD treatment and promotes open
 science in clinical AMD research by making the underlying data publicly
 available.
description: Moorfields_AMD_Database_1
DOI: 10.5061/dryad.gh4p57r
title: Data from: An exceptionally preserved association of complete dinosaur skeletons reveals the oldest long-necked sauropodomorphs

description: The rise of sauropodomorphs is still poorly understood due to the scarcity
 of well-preserved fossils in early Norian rocks. Here, we present an
 association of complete and exceptionally well-preserved dinosaur
 skeletons that helps filling that gap. They represent a new species, which
 is recovered as member of a clade solely composed of Gondwanan Triassic
 taxa. The new species allows defining a set of anatomical changes that
 shaped sauropodomorph evolution along a period from 233–225 Ma, as
 recorded in the well dated Late Triassic beds of Brazil. In that time
 span, apart from achieving a more herbivorous diet, sauropodomorph
 dinosaurs increased their size in a ratio of 230% and their typical long
 neck was also established, becoming proportionally twice longer than those
 of basal taxa. Indeed, the new dinosaur is the oldest-known sauropodomorph
 with such an elongated neck, suggesting that the ability to feed on high
 vegetation was a key trait achieved along the early Norian. Finally, the
 clustered preservation mode of the skeletons represents the oldest
 evidence of gregarious behaviour among sauropodomorphs.
description: Supplementary
 information for "An exceptionally preserved association of complete
 dinosaur skeletons reveals the oldest long-necked
 sauropodomorphs"Outline of contents (a)
 Supplementary figure 1 (b) Supplementary figure 2 (c) Comparison between
 Macrocollum itaquii and Unaysaurus tolentinoi (d) Details of the
 phylogenetic analysis (e) List of characters (f) Data matrix (g)
 References for supplementary informationSupplementary
 information.docx
DOI: 10.5061/dryad.75mg6b1
title: Data from: Environmentally-induced noise dampens and reddens with increasing trophic level in a complex food web

description: Stochastic variability of key abiotic factors including temperature,
 precipitation and the availability of light and nutrients greatly
 influences species’ ecological function and evolutionary fate. Despite
 such influence, ecologists have typically ignored the effect of abiotic
 stochasticity on the structure and dynamics of ecological networks. Here
 we help to fill that gap by advancing the theory of how abiotic
 stochasticity, in the form of environmental noise, affects the population
 dynamics of species within food webs. We do this by analysing an
 allometric trophic network model of Lake Constance subjected to positive
 (red), negative (blue), and non-autocorrelated (white) abiotic temporal
 variability (noise) introduced into the carrying capacity of basal
 species. We found that, irrespective of the colour of the introduced
 noise, the temporal variability of the species biomass within the network
 both reddens (i.e. its positive autocorrelation increases) and dampens
 (i.e. the magnitude of variation decreases) as the environmental noise is
 propagated through the food web by its feeding interactions from the
 bottom to the top. The reddening reflects a buffering of the noise-induced
 population variability by complex food web dynamics such that
 non-autocorrelated oscillations of noise-free deterministic dynamics
 become positively autocorrelated. Our research helps explain frequently
 observed red variability of natural populations by suggesting that
 ecological processing of environmental noise through food webs with a
 range of species’ body sizes reddens population variability in nature.
description: NoiseLCMatlab code for the simulation model. Output of simulations. R code to produce figures and analyses.
DOI: 10.5061/dryad.1v2k8b1
title: Data from: Persistence at the final stage of volcanic island ontogeny: abiotic predictors explain native plant species richness on 111 remote Pacific atolls

description: Aim: The final island ontogeny of the General Dynamic Model (GDM) (i.e.
 before island submergence) in tropical oceans corresponds to the coral
 atoll stage. Here, we examined whether the species richness of native
 vascular plants (indigenous and endemic species) on atolls is controlled
 by spatial and/or physical processes. We also predicted that atolls
 strongly affected by anthropogenic disturbance would have lower native
 species richness than predicted by spatial and physical processes.
 Location: Marshall Islands, Kiribati Islands, Nauru, Niue, Johnston, Cook
 Islands, French Polynesia and Pitcairn Islands (Pacific Ocean). Taxon:
 Native vascular plants Methods: We used stepwise regression to test the
 relative influence of five biogeographic variables on native species
 richness. Relationships were assessed for the full set of 111 Pacific
 coral atolls, as well as for atoll subsets ranging from 9 to 45 atolls. An
 index of human impact was then estimated, and residuals in the regression
 model predicting species richness from biogeographic variables were
 compared with the level of human impact. Results: A regression model
 including atoll area, highest atoll elevation, the stepping stone
 distances from the nearest raised atoll and volcanic island explained
 native species richness on the 111 Pacific coral atolls. Regression models
 for different archipelagos and atoll subsets were also significant.
 Endemic species richness was significantly linked with highest atoll
 elevation and the stepping stone distances from the nearest raised atoll.
 Residuals in the biogeographic regression model were barely related to
 human impact across the 111 atolls but were significantly related to human
 impact in the Kiribati atolls. Main conclusions: Native species richness
 on atolls is mainly controlled by physical and spatial characteristics.
 However, anthropogenic disturbances have altered the predicted pattern of
 native species richness leading to a lower model fit in some atoll
 subsets.
description: Physical and spatial
 data (n=111 atolls)The data contains
 physical and spatial measurements, the number of endemic and indigenous
 species per atoll, and some criteria used to estimate the level of human
 impact.Data_paper
 2018.xls
DOI: 10.5061/dryad.8g1nn0j
title: Data from: Distinct mesoderm migration phenotypes in extra-embryonic and embryonic regions of the early mouse embryo

description: In the gastrulation mouse embryo, epiblast cells delaminate at the
 primitive streak to form mesoderm and definitive endoderm, through an
 epithelial-mesenchymal transition. Mosaic expression of a membrane
 reporter in nascent mesoderm enabled recording cell shape and trajectory
 through live imaging. Upon leaving the streak, cells changed shape and
 extended protrusions of distinct size and abundance depending on the
 neighboring germ layer, as well as the region of the embryo. Embryonic
 trajectories were meandrous but directional, while extra-embryonic
 mesoderm cells showed little net displacement. Embryonic and
 extra-embryonic mesoderm transcriptomes highlighted distinct guidance,
 cytoskeleton, adhesion, and extracellular matrix signatures. Specifically,
 intermediate filaments were highly expressed in extra-embryonic mesoderm,
 while live imaging for F-actin showed abundance of actin filaments in
 embryonic mesoderm only. Accordingly, RhoA or Rac1 conditional deletion in
 mesoderm inhibited embryonic, but not extra-embryonic mesoderm migration.
 Overall, this indicates separate cytoskeleton regulation coordinating the
 morphology and migration of mesoderm subpopulations.
description: RNASeq_mouse embryo
 mesodermThis file contains the
 following excel files: Sample list, Expression levels, Ranked list of
 differential expressionZip1.zip
DOI: 10.5061/dryad.71f1s18
title: Data from: Identification of reactive intermediate formation and bioactivation pathways in Abemaciclib metabolism by LC–MS/MS: in vitro metabolic investigation

description: Abemaciclib (Verzenio®) is approved as tyrosine kinase inhibitor (TKI) for
 breast cancer treatment. In this study, in vitro phase I metabolic
 profiling of Abemaciclib (ABC) was done using rat liver microsomes (RLMs).
 We checked the formation of reactive intermediates in ABC metabolism using
 (RLMs) in the presence of potassium cyanide (KCN) that was used as
 capturing agent for iminium reactive intermediates forming a stable
 complex that can be characterized by LC-MS/MS. Nine in vitro phase I
 metabolites and three cyano adducts were identified. The metabolic
 reactions involved in formation of these metabolites and adducts are
 reduction, oxidation, hydroxylation and cyanide addition. The
 bioactivation pathway was also proposed. Knowing the electrodeficient
 bioactive centre in ABC structure helped in making targeted modifications
 to improve its safty and retain its efficacy. Blocking or isosteric
 replacement of α carbon to the tertiary nitrogen atoms of piperazine ring
 can aid in reducing toxic side effects of ABC. No previous articles were
 found about in vitro metabolic profiling for ABC or structural
 identification of the formed reactive metabolites for ABC.
description: ESM
 fileDataset
 fileESM
 File.rarREAD
 MERead me
 file
DOI: 10.5061/dryad.kg593qs
title: Data from: Asynchrony between ant seed dispersal activity and fruit dehiscence of myrmecochorous plants

description: Phenological mismatch has received attention in plant-pollinator
 interactions, but less so in seed dispersal mutualisms. We investigated
 whether the seasonal availability of myrmecochorous seeds is well matched
 to the seasonal activity patterns of seed-dispersing ants. Methods We
 compared seasonal timing of seed removal by a keystone seed-dispersing
 ant, Aphaenogaster rudis, and fruit dehiscence of several species of
 plants whose seeds it disperses in a deciduous forest in southern Ontario,
 Canada. We examined the timing of elaiosome ‘robbing’ by the non-native
 slug, Arion subfuscus, and tested whether seed removal by ants declines in
 response to supplementation with additional elaiosome-bearing seeds (ant
 “satiation”). Key Results Seed removal from experimental depots peaked
 early in the season for all plant species, and that seed removal
 correlated with temperature. In contrast, elaiosome robbing by slugs
 increased late in the season and thus may disproportionately affect plants
 with late-dehiscing fruits. Ant colonies removed seeds at similar rates
 regardless of seed supplementation, indicating that satiation likely does
 not impact seasonal patterns of seed dispersal in this system. Fruits of
 the five myrmecochorous plant species in our study dehisced at discrete
 intervals throughout the season, with minimal overlap among species. Peak
 dehiscence did not overlap with peak seed removal for any plant species.
 Conclusions Fruit dehiscence of myrmecochorous plants and peak ant seed
 dispersal activity occur asynchronously. Whether future climate warming
 will shift ant and plant phenologies in ways that have consequences for
 seed dispersal remains an open question. In compliance with data
 protection regulations, please contact the publication office if you would
 like to have your personal information removed from the database.
description: Satiation
 ExperimentDataset for the
 satiation experiment.Phenology of Seed and
 Elaiosome Removal, and DehiscenceDataset containing
 observations of fruit dehiscence timing as well as seed and elaiosome
 removal from seed depots.Phenology of Seed:Elaiosome
 Removal and Dehiscence.txtTemperature
 DataDataset containing
 temperature observations. Please note that small time increments are
 missing due to inclement weather.Read
 MeThis file explains all
 of the variables in each of the datasets that accompany: Gordon SCC,
 Meadley-Dunphy SA, Prior KM, Frederickson ME, 2018ms. Asynchrony between
 ant seed dispersal activity and fruit dehiscence of myrmecochorous
 plants.READ
 ME.rtf
DOI: 10.5061/dryad.7f9q2cd
title: Data from: High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans) populations

description: Range expansion is a widespread biological process, with well described
 theoretical expectations for the genomic outcomes accompanying the
 colonization of novel ranges. However, comparatively few empirical studies
 address the genome-wide consequences associated with the range expansion
 process, particularly in recent or on-going expansions. Here, we assess
 two recent and distinct eastward expansion fronts of a highly mobile
 carnivore, the coyote (Canis latrans), to investigate patterns of genomic
 diversity and identify variants that may have been under selection during
 range expansion. Using a restriction enzyme assisted sequencing approach
 (RADseq), we genotyped 394 coyotes at 22,935 SNPs and found that overall
 population structure corresponded to their 19th century historical range
 and two distinct populations that expanded during the 20th century.
 Counter to theoretical expectations for populations to bottleneck during
 range expansions, we observed minimal evidence for decreased genomic
 diversity across coyotes sampled along either expansion front, which is
 likely due to hybridization with other Canis species. Furthermore, we
 identified 12 SNPs, located either within genes or putative regulatory
 regions, that were consistently associated with range expansion. Of these
 12 genes, three (CACNA1C, ALK, and EPHA6) have putative functions related
 to dispersal, including habituation to novel environments and spatial
 learning, consistent with the expectations for traits under selection
 during range expansion. Although coyote colonization of eastern North
 America is well-publicized, this study provides novel insights by
 identifying genes associated with dispersal capabilities in coyotes on the
 two eastern expansion fronts.
description: Genotype data for 394
 coyotes at 22,935 SNPsPlink format (map &
 ped) genotype files along with sample meta data.Heppenheimer_et_al_Ecol_Evol_2018.zip
DOI: 10.5061/dryad.7k2g187
title: Data from: Partitioning drivers of spatial genetic variation for a continuously-distributed population of boreal caribou: implications for management unit delineation

description: Isolation-by-distance (IBD) is a natural pattern not readily incorporated
 into theoretical models nor traditional metrics for differentiating
 populations, although clinal genetic differentiation can be characteristic
 of many wildlife species. Landscape features can also drive population
 structure additive to baseline IBD resulting in differentiation through
 isolation-by-resistance (IBR). We assessed the population genetic
 structure of boreal caribou across western Canada using non-spatial
 (STRUCTURE) and spatial (MEMGENE) clustering methods and investigated the
 relative contribution of IBD and IBR on genetic variation of 1221 boreal
 caribou multilocus genotypes across western Canada. We further introduced
 a novel approach to compare the partitioning of individuals into
 management units (MU) and assessed levels of genetic connectivity under
 different MU scenarios. STRUCTURE delineated five genetic clusters while
 MEMGENE identified finer-scale differentiation across the study area. IBD
 was significant and did not differ for males and females both across and
 among detected genetic clusters. MEMGENE landscape analysis further
 quantified the proportion of genetic variation contributed by IBD and IBR
 patterns, allowing for the relative importance of spatial drivers,
 including roads, water bodies and wildfires, to be assessed and
 incorporated into the characterization of population structure for the
 delineation of MUs. Local population units, as currently delineated in the
 boreal caribou recovery strategy, do not capture the genetic variation and
 connectivity of the ecotype across the study area. Here, we provide the
 tools to assess fine-scale spatial patterns of genetic variation,
 partition drivers of genetic variation and evaluate the best management
 options for maintaining genetic connectivity. Our approach is highly
 relevant to vagile wildlife species that are of management and
 conservation concern and demonstrate varying degrees of IBD and IBR with
 clinal spatial genetic structure that challenges the delineation of
 discrete population boundaries.
description: Priadka_etal_2018_genotypesGenotypes for 1221 boreal caribou at 9 microsatellite loci. Missing data is indicated by "-99". Coordinates for sampling locations have not been included because boreal caribou are listed as Threatened under Canada's Species At Risk Act.Priadka_etal_2018_Landscape_rastersRaster .asc files of landscape resistance models. Univariate models include resistance costs of 10, 50 and 100. Optimized models for Cluster 1 and Cluster 2 reflect the optimized resistance costs for roads and water bodies (land1), roads and forestry (land2), water bodies and forestry (land3) and roads, water bodies and forestry (land4). Raster cell size is 250m in planar projection.