cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.05358ph
title: Data from: Forest community assembly is driven by different strata-dependent mechanisms along an elevational gradient

description: Aim: The mechanisms driving forest community assembly along elevational
 gradients remain elusive. The distinct strata in heterogeneous forest are
 subject to differing assembly mechanisms. This study aims to evaluate how
 different ecological mechanisms driving forest community assembly across
 strata and spatial scales, and to identify how these assemblages respond
 to different abiotic or biotic variables along an elevational gradient.
 Location: Yulong Mountain within Hengduan Mountains, Southwest China.
 Taxon: Seed plants Methods: We sampled plant species along a 1200 m
 elevational gradient across forest strata (trees, shrubs and herbs) at
 different spatial scales (neighbourhood and community). We integrated
 phylogenetic and functional diversity to disentangle the roles of
 ecological mechanisms in structuring community assembly. We also
 determined the relative effects of climatic, soil and biotic variables and
 their interactions on these community assemblages. Results: The
 phylogenetic and functional diversity of trees was lower at the extremes
 of elevational gradient, where they were constrained by water availability
 or temperature. While communities with higher species diversity exhibited
 an overdispersed structure at mid-elevations. For shrubs, overdispersion
 was exhibited at high elevations despite low species richness, which could
 be consistent with facilitative interactions or competition exclusion.
 However, most communities of herbs appear to have a markedly random
 structure, despite some incongruence between phylogenetic divergence and
 functional convergence, as well as influences from overstory trees and
 local light conditions. The relative effects of abiotic variables on
 community structure were larger at the community scale than at the
 neighbourhood scale. Main conclusions: Our study emphasises the importance
 of considering phylogenies and traits in understanding the strata- and
 scale- dependent mechanisms of forest community assembly. Collectively,
 results indicate that contrasting assembly mechanisms interact across
 different strata along elevational gradients to shape diverse forest
 communities.
description: the matrix of
 sequencesThe matrix of sequences
 which combind the two chloroplast gene regions (rbcL, matK) and the ITS
 nuclear gene regionrbcl_matK_ITS.phyphylogenetic tree of treestree.nexusphylogenetic tree across forest strataphylogenetic tree of shrubsshrub.nexusphylogenetic tree of herbsherb.nexusthe traits of treestreetrait_species level.csvthe traits of shrubsshrubtrait_species level.csvthe traits of herbsherbtrait_species level.csv
DOI: 10.5061/dryad.kc27cm8
title: Data from: Management and outcome of primary CNS lymphoma patients in the modern era. a LOC network study

description: Objective: Studies on primary CNS lymphoma (PCNSL) patients in the “real
 life” are scarce. Our objective was to analyze, in a nationwide
 population-based study, the current medical practice in the management of
 PCNSL. Methods: The LOC database prospectively records all newly diagnosed
 PCNSL from 32 French centers. Data of patients diagnosed between 2011-2016
 were retrospectively analyzed. Results: We identified 1002 immunocompetent
 patients (43% aged&gt;70 years, median KPS 60). First-line treatment
 was high-dose methotrexate-based chemotherapy in 92% of cases, with an
 increasing use of rituximab over time (66%). Patients &lt;60 years old
 received consolidation treatment in 77% of cases, consisting of
 whole-brain radiotherapy (WBRT) (54%) or high-dose chemotherapy with
 autologous stem cell transplantation (HCT-ASCT) (23%). Among the patients
 &gt; 60 years old, WBRT and HCT-ASCT consolidation were administered
 in only 9% and 2%, respectively. The complete response rate to initial
 chemotherapy was 50%. Median progression-free survival was 10.5 months.
 For relapse, second-line chemotherapy, HCT-ASCT, WBRT and palliative care
 were offered to 55%, 17%, 10%, and 18% of patients, respectively. The
 median, 2-year and 5-year overall survival was 25.3 months, 51% and 38%,
 respectively (&lt; 60 years: not reached (NR), 70% and 61%; &gt;
 60 years: 15.4 months, 44% and 28%). Age, KPS, sex and response to
 induction CT were independent prognostic factors in multivariate analysis.
 Conclusions: Our study confirms the increasing proportion of elderly
 within PCNSL and shows comparable outcome in this population-based study
 with those reported by clinical trials, reflecting a notable application
 of recent PCNSL advances in the real life.
description: Supplemental
 data
DOI: 10.5061/dryad.6fd53f8
title: Data from: Parallel genomic architecture underlies repeated sexual signal divergence in Hawaiian Laupala crickets

description: When the same phenotype evolves repeatedly, we can explore the
 predictability of genetic changes underlying phenotypic evolution. Theory
 suggests that genetic parallelism is less likely when phenotypic changes
 are governed by many small-effect loci compared to few of major effect,
 because different combinations of genetic changes can result in the same
 quantitative outcome. However, some genetic trajectories might be favoured
 over others, making a shared genetic basis to repeated polygenic evolution
 more likely. To examine this, we studied the genetics of parallel male
 mating song evolution in the Hawaiian cricket Laupala. We compared
 quantitative trait loci (QTL) underlying song divergence in three species
 pairs varying in phenotypic distance. We tested whether replicated song
 divergence between species involves the same QTL and the likelihood that
 sharing QTL is related to phenotypic effect sizes. Contrary to theoretical
 predictions, we find substantial parallelism in polygenic genetic
 architectures underlying repeated song divergence. QTL overlapped more
 than expected based on simulated QTL analyses. Interestingly, QTL effect
 size did not predict QTL sharing, but did correlate with magnitude of
 phenotypic divergence. We highlight potential mechanisms driving these
 constraints on cricket song evolution and discuss a scenario that
 consolidates empirical quantitative genetic observations with
 micro-mutational theory.
description: QTLreuse_DataFiles.vcf are the filtered SNP data prior to maker selection based on segregation distortion, distance, genotypic similarity, etc. .raw files are data input files for mapmaker. The same genotype matrix was used in JoinMap .RData are the crossfiles used for QTL analysis in r/QTL CrossFile.csv files contain the genotype matrix, the linkage map, and the phenotypes input to create those RData files 6sppQTL_effectsizes_sharing contains the data needed for Fig 2 .prep files are scripts files for mapmaker QTLreuse.r contains all the code for the QTL mapping and the comparative analyses
DOI: 10.5061/dryad.dr32n87
title: Data from: A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs

description: Muscle development and lipid accumulation in muscle critically affect meat
 quality in livestock. Yet, the underlying genetic factors for
 myofiber-type specification and intramuscular fat (IMF) accumulation
 remain to be elucidated. Using two independent intercrosses between
 Western breeds and Korean native pigs (KNPs) and a joint linkage-linkage
 disequilibrium analysis, we here identified a 488.1-kb region on porcine
 chromosome 12 that affects both reddish meat color (a*) and IMF. In this
 critical region, only the MYH3 gene, encoding myosin heavy chain 3, was
 found to be preferentially overexpressed in the skeletal muscle in KNPs.
 Subsequently, MYH3-transgenic mice demonstrated that this gene controls
 both myofiber-type specification and adipogenesis in skeletal muscle. We
 discovered a structural variant in the promotor/regulatory region of MYH3
 for which Q allele carriers exhibited significantly higher values of a*
 and IMF than q allele carriers. Furthermore, chromatin immunoprecipitation
 and co-transfection assays showed the structural variant in the
 5'-UTR of MYH3 abrogated binding of the myogenic regulatory factors
 (MYF5, MYOD, MYOG, and MRF4). The allele distribution of the MYH3 among
 worldwide pig populations indicated that the MYH3 Q allele is of Asian
 origin and likely predates domestication. In conclusion, we identified a
 functional regulatory sequence variant in the porcine MYH3 that provides
 novel insights into the genetic basis of the regulation of myofiber type
 ratios and associated changes in IMF in pigs. The MYH3 variant can play an
 important role to improve pork quality in current breeding programs.
description: PGENE ICC
 HBPPGENE_raw_data_ICC_HBP_etal.zip
DOI: 10.5061/dryad.gm957n1
title: Data from: Strong evidence of an Information-Theoretical Conservation Principle linking all discrete systems

description: Diverse discrete systems share common global properties that lack a
 unifying theoretical explanation. However, constraining the simplest
 measure of total information (Hartley-Shannon) in a statistical mechanics
 framework reveals a principle, the Conservation of Hartley-Shannon
 Information (CoHSI) that directly predicts both known and unsuspected
 common properties of discrete systems, as borne out in the diverse systems
 of computer software, proteins and music.  Discrete systems fall
 into two categories distinguished by their structure: heterogeneous
 systems in which there is a distinguishable order of assembly of the
 system's components from an alphabet of  unique tokens (e.g.
 proteins assembled from an alphabet of amino acids), and homogeneous
 systems in which unique tokens are simply binned, counted and rank
 ordered. Heterogeneous systems are characterized by an implicit
 distribution of component lengths, with sharp unimodal peak (containing
 the majority of components) and a power-law tail, whereas homogeneous
 systems reduce naturally to Zipf's Law but with a drooping tail in
 the distribution.  We also confirm predictions that very long
 components are inevitable for heterogeneous systems; that discrete systems
 can exhibit simultaneously both heterogeneous and homogeneous behavior;
 and that in systems with more than one consistent token alphabet (e.g.
 digital music), the alphabets themselves show a power-law relationship.
description: HattonWarr_RSOS_Jun-2019A complete computational reproducibility package to reproduce all Figures and statistical analyses in the submitted paper.
DOI: 10.5061/dryad.3st9688
title: Data from: GATA2 controls lymphatic endothelial cell junctional integrity and lymphovenous valve morphogenesis through miR-126

description: Mutations in the transcription factor GATA2 cause lymphedema. GATA2 is
 necessary for the development of lymphatic valves (LVs) and lymphovenous
 valves (LVVs), and for the patterning of lymphatic vessels. Here, we
 report that GATA2 is not necessary for valvular endothelial cell (VEC)
 differentiation. Instead, GATA2 is required for VEC maintenance and
 morphogenesis. GATA2 is also necessary for the expression of cell junction
 molecules VE-Cadherin and Claudin5 in lymphatic vessels. We identified
 miR-126 as a target of GATA2, and miR-126-/- embryos recapitulate the
 phenotypes of mice lacking GATA2. Primary human lymphatic endothelial
 cells (HLECs) lacking GATA2 (GATA2ΔHLEC) have altered expression of
 Claudin5 and VE-Cadherin, and blocking miR-126 activity in HLECs
 phenocopies these changes in expression. Importantly, overexpression of
 miR-126 in GATA2ΔHLEC significantly rescues the cell junction defects.
 Thus, our work defines a new mechanism of GATA2 and uncovers miR-126 as a
 novel regulator of mammalian lymphatic vascular development.
description: GATA2KD1RNA-seq data from primary human lymphatic endothelial cells treated with shGATA2 (Sample1).GATA2KD2RNA-seq data from primary human lymphatic endothelial cells treated with shGATA2 (Sample2).GATA2KD3RNA-seq data from primary human lymphatic endothelial cells treated with shGATA2 (Sample3).CONTROL3RNA-seq data from primary human lymphatic endothelial cells treated with pLV control viruses (Sample3).CONTROL2RNA-seq data from primary human lymphatic endothelial cells treated with pLV control viruses (Sample2).CONTROL1RNA-seq data from primary human lymphatic endothelial cells treated with pLV control viruses (Sample1).mir126KD_1RNA-seq data from primary human lymphatic endothelial cells treated with miR-126 sponge viruses (Sample1).mir126KD_2RNA-seq data from primary human lymphatic endothelial cells treated with miR-126 sponge viruses (Sample2).mir126KD_3RNA-seq data from primary human lymphatic endothelial cells treated with miR-126 sponge viruses (Sample3).CTRL_3RNA-seq data from primary human lymphatic endothelial cells treated with pSFFV control viruses (Sample3).CTRL_2RNA-seq data from primary human lymphatic endothelial cells treated with pSFFV control viruses (Sample2).CTRL_1RNA-seq data from primary human lymphatic endothelial cells treated with pSFFV control viruses (Sample1).
DOI: 10.5061/dryad.n8h2fv0
title: Data from: Assessing species boundaries in the open sea: an integrative taxonomic approach to the pteropod genus Diacavolinia

description: To track changes in pelagic biodiversity in response to climate change, it
 is essential to accurately define species boundaries. Shelled pteropods
 are a group of holoplanktonic gastropods that have been proposed as
 bio-indicators because of their vulnerability to ocean acidification. A
 particularly suitable, yet challenging group for integrative taxonomy is
 the pteropod genus Diacavolinia, which has a circumglobal distribution and
 is the most species-rich pteropod genus, with 24 described species. We
 assessed species boundaries in this genus, with inferences based on
 geometric morphometric analyses of shell-shape variation, genetic
 (cytochrome c oxidase subunit I, 28S rDNA sequences) and geographic data.
 We found support for a total of 13 species worldwide, with observations of
 706 museum and 263 freshly collected specimens across a global collection
 of material, including holo‐ and paratype specimens for 14 species. In the
 Atlantic Ocean, two species are well supported, in contrast to the eight
 currently described, and in the Indo‐Pacific we found a maximum of 11
 species, partially merging 13 of the described species. Distributions of
 these revised species are congruent with well-known biogeographic
 provinces. Combining varied datasets in an integrative framework may be
 suitable for many diverse taxa and is an important first step to
 predicting species-specific responses to global change.
description: Supplementary
 Information S1.Sample collection
 information, group assignment using integrative approach, data usage for
 geometric morphometric analyses and GenBank accession codes for each
 Diacavolinia specimen used in this study. Amb. = Ambiguous LDA assignment;
 Unkn. = Unknown integrative group; N.A. = Not
 available.SupplementaryInformationS1.xlsxSupplementary Information S2.Photographs of Diacavolinia specimens included in this study in (A) ventral and (B) lateral orientations.SupplementaryInformationS2.rarSupplementary Information S3.Geometric morphometric data of Diacavolinia specimens: centroid sizes and relative warps in ventral (A: 23 and B: 38 landmarks) and lateral orientations (C: 15 and D: 49 landmarks).SupplementaryInformationS3.xlsxSupplementary Information S4.Ordination of the second and third relative warps (RWs) of Diacavolinia for Indo‐Pacific specimens for (A) lateral orientation with 49 landmarks (LMs; N = 282), (B) ventral orientation with 23 LMs (N = 378), and (C) ventral orientation of a subset with 38 LMs (N = 174). See Figure 4 for symbol definitions. Thin plate splines from the RW positions indicated with black squares are shown below and left of the axes to depict the variation in shell shape, with images of shells and LM positions shown on the right.SupplementaryInformationS4.tifSupplementary Information S5.Alignments of (A) COI nucleotides (N = 89; 658bp; GenBank accession numbers MF974762–MF974847) and (B) 28S (N = 138; 901bp; GenBank accession numbers MF974624–MF974761).SupplementaryInformationS5.zip
DOI: 10.5061/dryad.0rc447b
title: Data from: Show me you care: female mate choice based on egg attendance rather than male or territorial traits

description: Female mate choice is often based on male traits, including signals or
 behaviors, and/or the quality of a male’s territory. In species with
 obligate paternal care, where care directly affects offspring survival,
 females may also base their mate choices on the quality of a sire’s care.
 Here, we quantified male reproductive success in a natural population of
 the glassfrog Hyalinobatrachium cappellei, a species with male parental
 care, to determine the influence of territory quality, male traits, and
 paternal care behaviors on female mate choice. We found that attending
 males have a higher chance of gaining new clutches than non-attending
 males. Our results indicate that females do not select males based only on
 body condition, calling persistence, or territory traits. Instead, our
 findings support the hypothesis that females choose males based on care
 status. Indeed, males already attending a clutch were 70% more likely to
 obtain another clutch, and the time to acquire an additional clutch was
 significantly shorter. We also found that males adjust their parental care
 effort in response to genetic relatedness, by caring only for their own
 offspring; however, remaining close to unrelated clutches serves as a
 strategy to attract females and increase chances of successful mating.
 Thus, males that establish territories that already contain clutches
 benefit from the signal eggs provide to females.
description: <strong>Individuals genotypes</strong>
 Genotypes from collected individuals (males, females, larvae) of
 Hyalinobatrachium cappellei Hyalinobatrachium cappellei
 genotypes.xls
DOI: 10.5061/dryad.513bv1v
title: Asymmetry in kinematic generalization between visual and passive lead-in movements are consistent with a forward model in the sensorimotor system

description: In our daily life we often make complex actions comprised of linked
 movements, such as reaching for a cup of coffee and bringing it to our
 mouth to drink. Recent work has highlighted the role of such linked
 movements in the formation of independent motor memories, affecting the
 learning rate and ability to learn opposing force fields. In these
 studies, distinct prior movements (lead-in movements) allow adaptation of
 opposing dynamics on the following movement. Purely visual or purely
 passive lead-in movements exhibit different angular generalization
 functions of this motor memory as the lead-in movements are modified,
 suggesting different neural representations. However, we currently have no
 understanding of how different movement kinematics (distance, speed or
 duration) affect this recall process and the formation of independent
 motor memories. Here we investigate such kinematic generalization for both
 passive and visual lead-in movements to probe their individual
 characteristics. After participants adapted to opposing force fields using
 training lead-in movements, the lead-in kinematics were modified on random
 trials to test generalization. For both visual and passive modalities,
 recalled compensation was sensitive to lead-in duration and peak speed,
 falling off away from the training condition. However, little reduction in
 force was found with increasing lead-in distance. Interestingly,
 asymmetric transfer between lead-in movement modalities was also observed,
 with partial transfer from passive to visual, but very little vice versa.
 Overall these tuning effects were stronger for passive compared to visual
 lead-ins demonstrating the difference in these sensory inputs in
 regulating motor memories. Our results suggest these effects are a
 consequence of state estimation, with differences across modalities
 reflecting their different levels of sensory uncertainty arising as a
 consequence of dissimilar feedback delays.
description: PlosOne_VisPas_transfer_Dryadhuman movement transfer experiment Matlab analysis programsmatlab for experiments.zipPassive Data Part 4raw data for passive to visual transfer experiments Part 4P4.zipPassive Data Part 3Raw data for passive to visual transfer experiments part 3P3.zipPassive Data Part 2Raw data for passive to visual transfer experiments part 2P2.zipPassive Data Part 1Raw data for passive to visual transfer experiments part 1P1.zipVisual Data Part 4Raw data for visual to passive transfer experiments part 4V4.zipVisual Data Part 3Raw data for visual to passive transfer experiments part 3V3.zipVisual Data Part 2Raw data for visual to passive transfer experiments part 2V2.zipVisual Data Part 1Raw data for visual to passive transfer experiments part 1V1.zip
DOI: 10.5061/dryad.860473k
title: Data from: The dataset of ticks in South America

description: The datasets of records of the distribution of ticks are invaluable tools
 to understand the phylogenetic patterns of evolution of ticks and the
 abiotic traits to which they are associated. Such datasets require an
 exhaustive collection of bibliographical references. In most cases, it is
 necessary the confirmation of reliable identification of ticks, together
 with an update of the scientific names of the vertebrate hosts. For some
 biogeographic regions, these data are not easily available, because many
 records were published in the so-called “grey literature”. We introduce
 the Dataset of Ticks in South America, a repository that collates data on
 more than 7,000 records of ticks, together with a set of abiotic traits,
 curated from satellite-derived information over the complete target
 region. The dataset includes data about ticks collected on wild hosts,
 with a special chapter devoted to species of cattle. It includes details
 of the phylogenetic relationships of the species of hosts, to provide
 researchers with both the biotic and abiotic traits, driving the
 distribution of ticks in South America.
description: Ticks in South
 America   Ticks of the
 Neotropics Details are included in
 the Readme file
DOI: 10.5061/dryad.19st68k
title: Inferring quantity and qualities of superimposed reaction rates from single molecule survival time distributions

description: Actions of molecular species, for example binding of transcription factors
 to chromatin, may comprise several superimposed reaction pathways. The
 number and the rate constants of such superimposed reactions can in
 principle be resolved by inverse Laplace transformation of the
 corresponding distribution of reaction lifetimes. However, current
 approaches to solve this transformation are challenged by
 photobleaching-prone fluorescence measurements of lifetime distributions.
 Here, we present a genuine rate identification method (GRID), which infers
 the quantity, rates and amplitudes of dissociation processes from
 fluorescence lifetime distributions using a dense grid of possible decay
 rates. In contrast to common multi-exponential analysis of lifetime
 distributions, GRID is able to distinguish between broad and narrow
 clusters of decay rates. We validate GRID by simulations and apply it to
 CDX2-chromatin interactions measured by live cell single molecule
 fluorescence microscopy. GRID reveals well-separated narrow decay rate
 clusters of CDX2, in part overlooked by multi-exponential analysis. We
 discuss the amplitudes of the decay rate spectrum in terms of frequency of
 observed events and occupation probability of reaction states. We further
 demonstrate that a narrow decay rate cluster is compatible with a common
 model of TF sliding on DNA.
description: Repository_Data_GRID_CDX2 The compressed folder "Repository_Data_19122" contains tracking data, binding time histograms and short matlab-scripts together with their according descriptions. Repository_Data_191122.zip
description: The dataset was collected by live-cell fluorescence
 microscopy.