cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bp31rm7
title: Data from: A comprehensive examination of the network position hypothesis across multiple river metacommunities

description: The hierarchical branching nature of river networks can have a strong
 influence on the assembly of freshwater communities. This unique structure
 has spurred the development of the network position hypothesis (NPH),
 which states that the strength of different assembly processes depends on
 the community position in the river network. Specifically, it predicts
 that (1) headwater communities should be exclusively controlled by the
 local environment given that they are more isolated and environmentally
 heterogeneous relative to downstream reaches. In contrast, (2) downstream
 communities should be regulated by both environmental and dispersal
 processes due to increased connectivity given their central position in
 the riverscape. Although intuitive, the NPH has only been evaluated on a
 few catchments and it is not yet clear whether its predictions are
 generalizable. To fill this gap, we tested the NPH on river dwelling
 fishes using an extensive dataset from 28 French watersheds. Stream and
 climatic variables were assembled to characterize environmental conditions
 and graph theory was applied on river networks to create spatial
 variables. We tested both predictions using variation partitioning
 analyses separately for headwater and downstream sites in each catchment.
 Only 10 catchments supported both predictions, 11 failed to support at
 least one of them while in 7 the NPH was partially supported given that
 spatial variables were also significant for headwater communities. We then
 assembled a dataset at the catchment scale (e.g. topography, environmental
 heterogeneity, network connectivity) and applied a classification tree
 analysis (CTA) to determine which regional property could explain these
 results. The CTA showed that the NPH was not supported in watersheds with
 high heterogeneity in connectivity among sites. In more homogeneously
 connected watersheds, the NPH was only supported when headwaters were more
 environmentally heterogeneous than downstream sites. We conclude that the
 NPH is context dependent even for taxa dispersing exclusively within
 streams.
description: Henriques-Silva_et_al_2018.Ecography - downstream datasetHenriques-Silva_et_al_2018.Ecography - Dataset.zip
DOI: 10.5061/dryad.tt481j7
title: Data from: Activation recovery interval imaging of premature ventricular contraction

description: Dispersion of ventricular repolarization due to abnormal activation
 contributes to the susceptibility to cardiac arrhythmias. However, the
 global pattern of repolarization is difficult to assess clinically.
 Activation recovery interval (ARI) has been used to understand the
 properties of ventricular repolarization. In this study, we developed an
 ARI imaging technique to noninvasively reconstruct three-dimensional (3D)
 ARI maps in 10 premature ventricular contraction (PVC) patients and
 evaluated the results with the endocardial ARI maps recorded by a clinical
 navigation system (CARTO). From the analysis results of a total of 100 PVC
 beats in 10 patients, the average correlation coefficient is 0.86±0.05 and
 the average relative error is 0.06±0.03. The average localization error is
 4.5±2.3 mm between the longest ARI sites in 3D ARI maps and those in CARTO
 endocardial ARI maps. The present results suggest that ARI imaging could
 serve as an alternative of evaluating global pattern of ventricular
 repolarization noninvasively and could assist in the future investigation
 of the relationship between global repolarization dispersion and the
 susceptibility to cardiac arrhythmias.
description: BSPM of PVC
 PatientsPublicRepository.zip
DOI: 10.5061/dryad.v51p331
title: Data from: Finish with a sprint: evidence for time‐selected last leg of migration in a long‐distance migratory songbird

description: Under time‐selected migration, birds should choose a strategy for
 outcompeting rivals over securing access to prime resources at the final
 destination. Thus, migration can be viewed as a race among individuals
 where winners are arriving first when conditions are suitable. The sprint
 migration hypothesis predicts that individuals shift from maximum
 sustained speed to a final burst of sprint to shorten the transition from
 migration to breeding (Alerstam, 2006). In this study, we test the
 hypothesis of a final sprint migration in a long‐distance Afro‐Palearctic
 migrant, the collared flycatcher Ficedula albicollis, during autumn and
 spring, and compare migration strategies between the seasons. In both
 seasons, collared flycatchers evidently exhibited sprint migration by
 increasing their overall speed over the last leg of migration after the
 Sahara crossing. This phenomenon was more pronounced in spring,
 contributing to overall faster spring migration and possibly highlighting
 higher importance for early arrival at the breeding grounds. In both
 seasons and particularly in spring, late departing individuals flew at a
 faster rate, partially being able to catch up with their early departing
 conspecifics. Differential fueling strategies may play an important role
 in determining migration speed, especially during the early stages of the
 migration, and might explain the observed differences in migration speeds
 between late and early departing individuals. Our findings suggest
 competition for early arrival at the breeding and at the nonbreeding
 destinations alike. Sprint migration might be an appropriate strategy to
 gain advantage over conspecifics and settle in prime territories as well
 as to cope with the increasingly earlier springs at high latitudes.
description: Data from: Finish with a
 sprint: evidence for time-selected last leg of migration in a
 long-distance migratory songbirdRaw data of geolocator
 recorded suneventsRaw_data_sprint_migration.csv
DOI: 10.5061/dryad.5f82b32
title: Data from: CSF biomarkers of neuroinflammation and cerebrovascular dysfunction in early Alzheimer's disease

description: Objective: To measure cerebrospinal (CSF) levels of biomarkers reflecting
 microglia and astrocytes activation, neuroinflammation and cerebrovascular
 changes and study their associations with the core biomarkers of AD
 pathology (amyloid &[beta] (A&[beta]) and tau), structural
 imaging correlates and clinical disease progression over time. Methods:
 The study included cognitively unimpaired elderly (n=508), patients with
 mild cognitive impairment (MCI, n=256), and AD dementia (n=57) from the
 longitudinal Swedish BioFINDER cohort. CSF samples were analyzed for
 YKL-40, IL-6, IL-7, IL-8, IL-15, IP-10, MCP-1, ICAM-1, VCAM-1, PlGF and
 Flt-1. Magnetic resonance imaging data were available from 677 study
 participants. Longitudinal clinical assessments were conducted in control
 individuals and MCI patients (mean follow-up 3 years, range 1-6 years).
 Results: CSF levels of YKL-40, ICAM-1, VCAM-1, IL-15 and Flt-1 were
 increased during the preclinical, prodromal and dementia stages of AD.
 High levels of these biomarkers were associated with increased CSF levels
 of total-tau, with the associations, especially for YKL-40, being stronger
 in A&[beta]-positive individuals. The results were similar for
 associations between phosphorylated-tau and YKL-40, ICAM-1 and VCAM-1.
 High levels of the biomarkers were also associated with cortical thinning
 (primarily in the precuneus and superior parietal regions) and with
 subsequent cognitive deterioration in non-demented cases as measured with
 MMSE (YKL-40) and CDR-SB (YKL-40, ICAM-1, VCAM-1 and IL-15). Finally,
 higher levels of CSF YKL-40, ICAM-1 and Flt-1 levels increased risk of
 development of AD dementia in non-demented cases. Conclusions:
 Neuroinflammation and cerebrovascular dysfunction are early events
 occurring already at pre-symptomatic stages of AD and contribute to
 disease progression.
description: Supplemental
 DataSupplemental figure 1,
 Supplemental tables 1-5.
DOI: 10.5061/dryad.g9b301f
title: Data from: Taylor's Power Law and its decomposition in urban facilities

description: As one of the few generalities in ecology, Taylor's power law admits
 a power function relationship $V=aM^{b}$ between the variance $V$ and mean
 number $M$ of organisms in a quadrat. We examine the spatial distribution
 data of seven urban service facilities in 37 major cities in China, and
 find that Taylor's law is validated among all types of facilities.
 Moreover, Taylor's law is robust if we shift the observation window
 or vary the size of the quadrats. The exponent $b$ increases linearly with
 the logarithm of the quadrat size, i.e., $b(s) = b_0 + A\log(s)$.
 Furthermore, the ANOVA test indicates that $b$ takes distinct values for
 different facilities in different cities. We decompose $b$ into two
 different factors, a city-specific factor (CSF) and a facility-specific
 factor (FSF). variations in $b$ can be explained to a large extent by the
 differences between cities and types of facilities. Facilities are more
 evenly distributed in larger and more developed cities. Competitive
 interchangeable facilities (e.g. pharmacy), with larger FSFs and smaller
 $b$s, are less aggregated than complimentary services (e.g., restaurants).
description: dataAndsourcecodeIt contains the data and the Matlab source code to process the data.
DOI: 10.5061/dryad.4bp82rc
title: Data from: Effects of mass extinction and recovery dynamics on long-term evolutionary trends: a morphological study of Strophomenida (Brachiopoda) across the Late Ordovician mass extinction

description: Mass extinctions affect the history of life by decimating existing
 diversity and ecological structure and creating new evolutionary and
 ecological pathways. Both the loss of diversity during these events and
 the rebound in diversity following extinction had a profound effect on
 Phanerozoic evolutionary trends. Phylogenetic trees can be used to
 robustly assess the evolutionary implications of extinction and
 origination. We examine both extinction and origination during the Late
 Ordovician mass extinction. This mass extinction was the second largest in
 terms of taxonomic loss but did not appear to radically alter Paleozoic
 marine assemblages. We focus on the brachiopod order Strophomenida, whose
 evolutionary relationships have been recently revised, to explore the
 disconnect between the processes that drive taxonomic loss and those that
 restructure ecological communities. A possible explanation for this
 disconnect is if extinction and origination were random with respect to
 morphology. We define morphospace using principal coordinate analysis
 (PCO) of character data from 61 Ordovician-Devonian taxa and their 45
 ancestral nodes, defined by a most parsimonius reconstruction in Mesquite.
 A bootstrap of the centroid of PCO values indicates that genera were
 randomly removed from morphospace by the Late Ordovician mass extinction,
 and new Silurian genera were clustered within a smaller previously
 unoccupied region of morphospace. Diversification remained morphologically
 constrained throughout the Silurian and into the Devonian. This suggests
 that the recovery from the Late Ordovician mass extinction resulted in a
 long-term shift in strophomenide evolution. More broadly, recovery
 intervals may hold clues to understanding the evolutionary impact of mass
 extinctions.
description: SupplementalThis contains additional graphs that detail morphological change through time and provide results of the analyses excluding ancestral nodesOrdinationDataContains values for each axis in the Principal Coordinates OrdinationCharacterDataCharacter matrixBootstrapValuescontains bootstrap data for each ordination axisbootstrapvalues.csv
DOI: 10.5281/zenodo.18350909
title: INRIM_Brand1_60F_4_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 60F SC sample 4 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.18350908
title: INRIM_Brand1_60F_4_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 60F SC sample 4 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.69k0b3r
title: Data from: The effects of haploid selection on Y chromosome evolution in two closely related dioecious plants

description: The evolution of sex chromosomes is usually considered to be driven by
 sexually antagonistic selection in the diploid phase. However, selection
 during the haploid gametic phase of the lifecycle has recently received
 theoretical attention as possibly playing a central role in sex chromosome
 evolution, especially in plants where gene expression in the haploid phase
 is extensive. In particular, male-specific haploid selection might favour
 the linkage of pollen beneficial alleles to male sex determining regions
 on incipient Y chromosomes. This linkage might then allow such alleles to
 further specialise for the haploid phase. Purifying haploid selection is
 also expected to slow the degeneration of Y-linked genes expressed in the
 haploid phase. Here, we examine the evolution of gene expression in flower
 buds and pollen of two species of Rumex to test for signatures of haploid
 selection acting during plant sex chromosome evolution. We find that genes
 with high ancestral pollen expression bias occur more often on sex
 chromosomes than autosomes and that genes on the Y chromosome are more
 likely to become enriched for pollen expression bias. We also find that
 genes with low expression in pollen are more likely to be lost from the Y
 chromosome. Our results suggest that sex-specific haploid selection during
 the gametophytic stage of the lifecycle may be a major contributor to
 several features of plant sex chromosome evolution.
description: Differential expression
 and ASE dataDryad
 data.tarBioProject for Rumex
 transcriptome sequencingRespository including
 files containing raw reads from illumina transcriptome sequencing of
 several tissues in two species of Rumex.
DOI: 10.5061/dryad.h8r2629
title: Data from: Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model

description: In order to understand patterns and processes of the diversification of
 life we require an accurate understanding of taxa interrelationships.
 Recent studies have suggested that analyses of morphological character
 data using the Bayesian and Maximum likelihood Mk model provide
 phylogenies of higher accuracy compared to parsimony methods. These
 studies have proved controversial, particularly simulating morphology-data
 under Markov models that assume shared branch lengths for characters, as
 it is claimed this leads to bias favouring the Bayesian or Maximum
 likelihood Mk model over parsimony models which do not explicitly make
 this assumption. We avoid these potential issues by employing a simulation
 protocol in which character states are randomly assigned to tips, but
 datasets are constrained to an empirically-realistic distribution of
 homoplasy as measured by the Consistency Index. Datasets were analysed
 with equal-weights and implied weights parsimony, and the Maximum
 Likelihood and Bayesian Mk model. We find that consistent (low homoplasy)
 datasets render method choice largely irrelevant, as all methods perform
 well with high consistency (low homoplasy) datasets, but the largest
 discrepancies in accuracy occur with low consistency datasets (high
 homoplasy). In such cases, the Bayesian Mk model is significantly more
 accurate than alternative models, and Implied weights parsimony never
 significantly out-performs the Bayesian Mk model. When poorly-supported
 branches are collapsed, the Bayesian Mk model recovers trees with higher
 resolution compared to other methods. Since it is not possible to assess
 homoplasy independently of a tree estimate, the Bayesian Mk model emerges
 as the most reliable method for categorical morphological analyses.
description: README file for Puttick
 et al. 2018supplementalCodeR code to simulate data matricesempirical.CIData from the survey of Consistency Indices from empirical matrices of morphological dataRCode_exampleExample of how data were simulated in the manuscriptsimulateBinaryR code to simulate all binary matricessimulateMultiStateR code to simulate all binary + multistate matricesPuttick_et_al_supp_figuresAll supplementary figures referenced in Puttick et al. 2018Puttick_et_al_supp_tablesAll supplementary tables referenced in Puttick et al. 2018
DOI: 10.5061/dryad.16r2v07
title: Data from: Emergence and evolution of novel reassortant influenza A viruses in canines in southern China

description: The capacity of influenza A viruses (IAVs) to host jump from animal
 reservoir species to humans presents an ongoing pandemic threat. Birds and
 swine are considered major reservoirs of viral genetic diversity, whereas
 equines and canines have historically been restricted to one or two stable
 IAV lineages with no transmission to humans. Here, by sequencing the
 complete genomes of 16 IAVs obtained from canines in southern China
 (Guangxi Zhuang Autonomous Region [Guangxi]) in 2013 to 2015, we
 demonstrate that the evolution of canine influenza viruses (CIVs) in Asian
 dogs is increasingly complex, presenting a potential threat to humans.
 First, two reassortant H1N1 virus genotypes were introduced independently
 from swine into canines in Guangxi, including one genotype associated with
 a zoonotic infection. The genomes contain segments from three lineages
 that circulate in swine in China: North American triple reassortant H3N2,
 Eurasian avian-like H1N1, and pandemic H1N1. Furthermore, the swine-origin
 H1N1 viruses have transmitted onward in canines and reassorted with the
 CIV-H3N2 viruses that circulate endemically in Asian dogs, producing three
 novel reassortant CIV genotypes (H1N1r, H1N2r, and H3N2r [r stands for
 reassortant]). CIVs from this study were collected primarily from pet dogs
 presenting with respiratory symptoms at veterinary clinics, but dogs in
 Guangxi are also raised for meat, and street dogs roam freely, creating a
 more complex ecosystem for CIV transmission. Further surveillance is
 greatly needed to understand the full genetic diversity of CIV in southern
 China, the nature of viral emergence and persistence in the region’s
 diverse canine populations, and the zoonotic risk as the viruses continue
 to evolve.
description: PB2
 xmlXML file used to infer
 MCC tree for PB2 sequences (pandemic H1N1 lineage)CIV.PB2p.xmlPB1 xmlXML file used to infer MCC tree for PB1 sequences (pandemic H1N1 lineage)CIV.PB1p.xmlPA xmlXML file used to infer MCC tree for PA sequences (pandemic H1N1 lineage)CIV.PAp.xmlHA xmlXML file used to infer MCC tree for HA sequences (Eurasian swine lineage)CIV.H1e.xmlNP xmlXML file used to infer MCC tree for NP sequences (pandemic H1N1 lineage)CIV.NPp.xmlNA xmlXML file used to infer MCC tree for NA sequences (Eurasian swine H1N1 lineage)CIV.N1e.xmlMP xmlXML file used to infer MCC tree for MP sequences (pandemic H1N1 lineage)CIV.MPe.xmlNS xmlXML file used to infer MCC tree for NS sequences (North American swine triple reassortant lineage), with phylogeography/Markov jumpsCIV.NS.xml
DOI: 10.5061/dryad.41kf6ps
title: Data from: Cryptic niche switching in a chemosymbiotic gastropod

description: Life stages of some animals, including amphibians and insects, are so
 different that they have historically been seen as different species.
 ‘Metamorphosis’ broadly encompasses major changes in organism bodies and,
 importantly, concomitant shifts in trophic strategies. Many marine animals
 have a biphasic lifestyle, with small pelagic larvae undergoing one or
 more metamorphic transformations before settling into a permanent, adult
 morphology on the benthos. Post-settlement, the hydrothermal vent
 gastropod Gigantopelta chessoia experiences a further, cryptic
 metamorphosis at body sizes around 5-7 mm. The terminal adult stage is
 entirely dependent on chemoautotrophic symbionts; smaller individuals do
 not house symbionts, and presumably depend on grazing. Using high
 resolution x-ray microtomography to reconstruct the internal organs in a
 growth series, we show this sudden transition in small but sexually mature
 individuals dramatically reconfigures the organs, but is in no way
 apparent from external morphology. We introduce the term
 ‘cryptometamorphosis’ to identify this novel phenomenon of a major body
 change and trophic shift, not related to sexual maturity, transforming
 only the internal anatomy. Understanding energy flow in ecosystems depends
 on the feeding ecology of species; the present study highlights the
 possibility for adult animals to make profound shifts in biology that
 influence energy dynamics.
description: Video_S1_CryptometamorphosisVideo S1. A video illustrating a hypothesised scenario of isometric growth post-settlement in Gigantopelta chessoia versus the observed cryptometamorphosis, showing changes in the anatomy of the digestive system around the point of transition (3.5 mm to 12.2 mm body length). Simulated growth and rendering was done in Blender v2.79b.
DOI: 10.5061/dryad.3m58sk3
title: Data from: Dobzhansky-Muller incompatibilities, dominance drive, and sex-chromosome introgression at secondary contact zones: a simulation study

description: Dobzhansky-Muller (DM) incompatibilities involving sex chromosomes have
 been proposed to account for Haldane’s rule (lowered fitness among hybrid
 offspring of the heterogametic sex) as well as Darwin’s corollary
 (asymmetric fitness costs with respect to the direction of the cross). We
 performed simulation studies of a hybrid zone to investigate the effects
 of different types of DM incompatibilities on cline widths and positions
 of sex-linked markers. From our simulations, X-Y incompatibilities
 generate steep clines for both X-linked and Y-linked markers; random
 effects may produce strong noise in cline center positions when migration
 is high relative to fitness costs, but X- and Y-centers always coincide
 strictly. X-autosome and Y-autosome incompatibilities also generate steep
 clines, but systematic shifts in cline centers occur when migration is
 high relative to selection, as a result of a dominance drive linked to
 Darwin’s corollary. Interestingly, sex-linked genes always show farther
 introgression than the associated autosomal genes. We discuss ways of
 disentangling the potentially confounding effects of sex biases in
 migration, we compare our results to those of a few documented contact
 zones, and we stress the need to study independent replicates of the same
 contact zone.
description: Cline parameters of the
 simulated hybrid zonesCline widths and centers
 (as well as their confidence intervals) for each locus (X: X-linked; Y:
 Y-linked; N: autosomal, neutral; A: autosomal, involved in DMIs), for each
 simulation, under different types of DMI (neut = none; xa: X-autosome; ya:
 Y-autosome, xy: X-Y), sex-biased dispersal (sex.disp), dispersal rate
 (disp.rate), hybrid fitness (h.fit) and selection (s) and the
 corresponding sigma and sqrt(sigma) (SS) for each locus. Simulation were
 performed in Quantinemo and clines were fitted with
 hzar.Data_Sciuchetti_et_al.txt