cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k486f
title: Data from: Hybrid EEG/EOG-based brain/neural hand exoskeleton restores fully independent daily living activities after quadriplegia

description: Direct brain control of advanced robotic systems promises substantial
 improvements in health care, for example, to restore intuitive control of
 hand movements required for activities of daily living in quadriplegics,
 like holding a cup and drinking, eating with cutlery, or manipulating
 different objects. However, such integrated, brain- or neural-controlled
 robotic systems have yet to enter broader clinical use or daily life
 environments. We demonstrate full restoration of independent daily living
 activities, such as eating and drinking, in an everyday life scenario
 across six paraplegic individuals (five males, 30 ± 14 years) who used a
 noninvasive, hybrid brain/neural hand exoskeleton (B/NHE) to open and
 close their paralyzed hand. The results broadly suggest that
 brain/neural-assistive technology can restore autonomy and independence in
 quadriplegic individuals’ everyday life.
description: Output dataset of
 EEG/EOG B/NHE controlOutput dataset of hybrid
 EEG/EOG brain/neural hand exoskeleton control.Soekadar2016_ZIP2.zipSource Codes and Software for EEG/EOG B/NHE control used in Soekadar et al. 2016This data container includes the custom-made modules for EEG/EOG-based B/NHE control that were embedded into the BCI2000 environment used in Soekadar et al. 2016. Please see the included tutorial for instructions on how to install and run the software.Soekadar2016_ZIP1.zip
DOI: 10.5061/dryad.7vt36
title: Data from: Long-term climate and competition explain forest mortality patterns under extreme drought

description: Rising temperatures are amplifying drought-induced stress and mortality in
 forests globally. It remains uncertain, however, whether tree mortality
 across drought-stricken landscapes will be concentrated in particular
 climatic and competitive environments. We investigated the effects of
 long-term average climate [i.e. 35-year mean annual climatic water deficit
 (CWD)] and competition (i.e. tree basal area) on tree mortality patterns,
 using extensive aerial mortality surveys conducted throughout the forests
 of California during a 4-year statewide extreme drought lasting from 2012
 to 2015. During this period, tree mortality increased by an order of
 magnitude, typically from tens to hundreds of dead trees per km2, rising
 dramatically during the fourth year of drought. Mortality rates increased
 independently with average CWD and with basal area, and they increased
 disproportionately in areas that were both dry and dense. These results
 can assist forest managers and policy-makers in identifying the most
 drought-vulnerable forests across broad geographic areas.
description: Young_et_al_DataGridded tree mortality data based on annual aerial surveys conducted from 2009 to 2015, along with environmental variables used to explain mortality patterns. The data file contains one row per unique 3.5 km grid cell & year combination. The data frame covers all grid cells within the state of California where at least one Aerial Detection Survey (ADS) flight was taken between 2009 and 2015, so each grid cell position has between 1 and 7 years of data (reflected as 1 to 7 rows in the data file per grid cell position). The main response variables are mort.bin (presence of any mortality) and mort.tph (number of dead trees/ha reported for the given grid cell & year combination). The main predictor variables are a set of climatic and forest structure variables at the same spatial scale, as described in the primary publication. This file is an Excel workbook with two worksheets: the first worksheet describes the variables, and the second worksheet contains the data. This data file was created by compiling and processing various publicly-available data sources into a standardized grid; the R code used for this is included in this repository as "Young_et_al_Data_preparation.R". The code used for statistical analyses and plots based on this data file ("Young_et_al_Analysis.R") is included as well.Young_et_al_Data_preparationCode for generating the data file (also contained in this repository) by compiling and processing publicly-available data sources.Young_et_al_AnalysisCode for performing statistical analyses and producing plots based on the gridded mortality data (also included in this repository).
DOI: 10.5061/dryad.q1d1s
title: Data from: Novel opsin gene variation in large-bodied, diurnal lemurs

description: Some primate populations include both trichromatic and dichromatic
 (red–green colour blind) individuals due to allelic variation at the
 X-linked opsin locus. This polymorphic trichromacy is well described in
 day-active New World monkeys. Less is known about colour vision in
 Malagasy lemurs, but, unlike New World monkeys, only some day-active
 lemurs are polymorphic, while others are dichromatic. The evolutionary
 pressures underlying these differences in lemurs are unknown, but aspects
 of species ecology, including variation in activity pattern, are
 hypothesized to play a role. Limited data on X-linked opsin variation in
 lemurs make such hypotheses difficult to evaluate. We provide the first
 detailed examination of X-linked opsin variation across a lemur clade
 (Indriidae). We sequenced the X-linked opsin in the most strictly diurnal
 and largest extant lemur, Indri indri, and nine species of smaller,
 generally diurnal indriids (Propithecus). Although nocturnal Avahi (sister
 taxon to Propithecus) lacks a polymorphism, at least eight species of
 diurnal indriids have two or more X-linked opsin alleles. Four
 rainforest-living taxa—I. indri and the three largest Propithecus
 species—have alleles not previously documented in lemurs. Moreover, we
 identified at least three opsin alleles in Indri with peak spectral
 sensitivities similar to some New World monkeys.
description: Sequence data for exons
 3 and 5 of the X-linked opsin gene (Indriidae)Sequence alignments for
 exons 3 and 5 of the X-linked opsin gene. Data include consensus sequences
 for ten species of Indriidae. Alignments were generated in Geneious. The
 three key functional sites (180: exon 3, 277 and 285: exon 5) are
 highlighted (added in Adobe Illustrator).Indriidae exons 3 and 5
 X-linked opsin gene
 alignments.pdfNucleotide alignment for
 exon 5 of the X-linked opsin gene (Indriidae)Nucleotide alignment of
 consensus sequences for exon 5 of the X-linked opsin gene (Plain Text file
 in FASTA format generated in Geneious). Sequences represent 10 species of
 Indriidae.Nucleotide alignment Indriidae
 exon 5 X-linked opsin
 gene.fasta.txtNucleotide alignment for
 exon 3 of the X-linked opsin gene (Indriidae)Nucleotide alignment of
 consensus sequences for exon 3 of the X-linked opsin gene (Plain Text file
 in FASTA format generated in Geneious). Sequences represent 10 species of
 Indriidae.Nucleotide alignment Indriidae
 exon 3 X-linked opsin gene.fasta.txt
DOI: 10.5061/dryad.53m76
title: Data from: Miocene flooding events of western Amazonia

description: There is a considerable controversy about whether western Amazonia was
 ever covered by marine waters during the Miocene [23 to 5 Ma (million
 years ago)]. We investigated the possible occurrence of Miocene marine
 incursions in the Llanos and Amazonas/Solimões basins, using
 sedimentological and palynological data from two sediment cores taken in
 eastern Colombia and northwestern Brazil together with seismic
 information. We observed two distinct marine intervals in the Llanos
 Basin, an early Miocene that lasted ~0.9 My (million years) (18.1 to 17.2
 Ma) and a middle Miocene that lasted ~3.7 My (16.1 to 12.4 Ma). These two
 marine intervals are also seen in Amazonas/Solimões Basin (northwestern
 Amazonia) but were much shorter in duration, ~0.2 My (18.0 to 17.8 Ma) and
 ~0.4 My (14.1 to 13.7 Ma), respectively. Our results indicate that shallow
 marine waters covered the region at least twice during the Miocene, but
 the events were short-lived, rather than a continuous full-marine
 occupancy of Amazonian landscape over millions of years.
description: Online File 1
 gplates: GPlates
 Project. Online File 2 R code
 geological time: R code to transfer
 stratigraphic position into geological time. 
 Online File 3
 graphcor: Graphic Correlation
 Project. Online File 4 events
 Correlation Saltarin and 105 AM: Events of the Line of
 Correlation. Online File 5
 description cores 105AM and Saltarin: Lithological description
 of cores 105AM and Saltarin. Online File 6 all supp
 tables: All supplementary tables
 in excel format.
DOI: 10.5061/dryad.52636
title: Data from: A unifying comparative phylogenetic framework including traits coevolving across interacting lineages

description: Models of phenotypic evolution fit to phylogenetic comparative data are
 widely used to make inferences regarding the tempo and mode of trait
 evolution. A wide range of models is already available for this type of
 analysis, and the field is still under active development. One of the most
 needed development concerns models that better account for the effect of
 within- and between-clade interspecific interactions on trait evolution,
 which can result from processes as diverse as competition, predation,
 parasitism, or mutualism. Here, we begin by developing a very general
 comparative phylogenetic framework for (multi)-trait evolution that can be
 applied to both ultrametric and nonultrametric trees. This framework not
 only encapsulates many previous models of continuous univariate and
 multivariate phenotypic evolution, but also paves the way for the
 consideration of a much broader series of models in which lineages
 coevolve, meaning that trait changes in one lineage are influenced by the
 value of traits in other, interacting lineages. Next, we provide a
 standard way for deriving the probabilistic distribution of traits at tip
 branches under our framework. We show that a multivariate normal
 distribution remains the expected distribution for a broad class of models
 accounting for interspecific interactions. Our derivations allow us to fit
 various models efficiently, and in particular greatly reduce the
 computation time needed to fit the recently proposed phenotype matching
 model. Finally, we illustrate the utility of our framework by developing a
 toy model for mutualistic coevolution. Our framework should foster a new
 era in the study of coevolution from comparative data.
description: OnlineAppendixV2We provide here the full, uncut, Online Appendix to our paper entitled "A unifying comparative phylogenetic framework including traits coevolving across interacting lineages". The first section is exposed in the attached appendix of the paper, but we let it here for the sake of self-containment. Note that simple equation numbering (e.g. equation (5)) refers to equations printed in the main text, whereas equations exposed in this appendix are designated as, e.g. equation (S5).
DOI: 10.5061/dryad.vs370
title: Data from: Widespread genetic incompatibilities between first-step mutations during parallel adaptation of Saccharomyces cerevisiae to a common environment

description: Independently evolving populations may adapt to similar selection
 pressures via different genetic changes. The interactions between such
 changes, such as in a hybrid individual, can inform us about what course
 adaptation may follow and allow us to determine whether gene flow would be
 facilitated or hampered following secondary contact. We used Saccharomyces
 cerevisiae to measure the genetic interactions between first-step
 mutations that independently evolved in the same biosynthetic pathway
 following exposure to the fungicide nystatin. We found that genetic
 interactions are prevalent and predominantly negative, with the majority
 of mutations causing lower growth when combined in a double mutant than
 when alone as a single mutant (sign epistasis). The prevalence of sign
 epistasis is surprising given the small number of mutations tested and
 runs counter to expectations for mutations arising in a single
 biosynthetic pathway in the face of a simple selective pressure.
 Furthermore, in one third of pairwise interactions, the double mutant grew
 less well than either single mutant (reciprocal sign epistasis). The
 observation of reciprocal sign epistasis among these first adaptive
 mutations arising in the same genetic background indicates that partial
 postzygotic reproductive isolation could evolve rapidly between
 populations under similar selective pressures, even with only a single
 genetic change in each. The nature of the epistatic relationships was
 sensitive, however, to the level of drug stress in the assay conditions,
 as many double mutants became fitter than the single mutants at higher
 concentrations of nystatin. We discuss the implications of these results
 both for our understanding of epistatic interactions among beneficial
 mutations in the same biochemical pathway and for speciation.
description: Data package about
 incompatibilities between adaptive mutations in yeastThis package contains
 files and scripts related to the publication "Widespread Genetic
 Incompatibilities Between First-Step Mutations During Parallel Adaptation
 of Saccharomyces cerevisiae to a Common Environment". Raw data and
 analyses are included.DryadSubmission.zip
DOI: 10.5061/dryad.2gn8c
title: Data from: Oxidative stress-mediated NFκB phosphorylation upregulates p62/SQSTM1 and promotes retinal pigmented epithelial cell survival through increased autophagy

description: p62 is a scaffolding adaptor implicated in the clearance of protein
 aggregates by autophagy. Reactive oxygen species (ROS) can either
 stimulate or inhibit NFκB-mediated gene expression influencing cellular
 fate. We studied the effect of hydrogen peroxide (H2O2)-mediated oxidative
 stress and NFκB signaling on p62 expression in the retinal pigment
 epithelium (RPE) and investigated its role in regulation of autophagy and
 RPE survival against oxidative damage. Cultured human RPE cell line
 ARPE-19 and primary human adult and fetal RPE cells were exposed to
 H2O2-induced oxidative stress. The human apolipoprotein E4
 targeted-replacement (APOE4) mouse model of AMD was used to study
 expression of p62 and other autophagy proteins in the retina. p62, NFκB
 p65 (total, phosphorylated, nuclear and cytoplasmic) and ATG10 expression
 was assessed by mRNA and protein analyses. Cellular ROS and mitochondrial
 superoxide were measured by CM-H2DCFDA and MitoSOX staining respectively.
 Mitochondrial viability was determined using MTT activity. qPCR-array
 system was used to investigate autophagic genes affected by p62. Nuclear
 and cytoplasmic levels of NFκB p65 were evaluated after cellular
 fractionation by Western blotting. We report that p62 is up-regulated in
 RPE cells under H2O2-induced oxidative stress and promotes autophagic
 activity. Depletion of endogenous p62 reduces autophagy by downregulation
 of ATG10 rendering RPE more susceptible to oxidative damage. NFκB p65
 phosphorylation at Ser-536 was found to be critical for p62 upregulation
 in response to oxidative stress. Proteasome inhibition by H2O2 causes
 p62-NFκB signaling as antioxidant pre-treatment reversed p62 expression
 and p65 phosphorylation when RPE was challenged by H2O2 but not when by
 Lactacystin. p62 protein but not RNA levels are elevated in APOE4-HFC AMD
 mouse model, suggesting reduction of autophagic flux in disease
 conditions. Our findings suggest that p62 is necessary for RPE
 cytoprotection under oxidative stress and functions, in part, by
 modulating ATG10 expression. NFκB p65 activity may be a critical upstream
 initiator of p62 expression in RPE cells under oxidative stress.
description: Supporting
 DataWestern Blots, qRT PCR
 and assay values, Immunohistochemistry and Immunocytochemistry
 SlidesData_Set.zip
DOI: 10.5061/dryad.n4k76
title: Data from: Fixation probability in a haploid-diploid population

description: Classical population genetic theory generally assumes either a fully
 haploid or fully diploid life cycle. However, many organisms exhibit more
 complex life cycles, with both free-living haploid and diploid stages.
 Here we ask what the probability of fixation is for selected alleles in
 organisms with haploid-diploid life cycles. We develop a genetic model
 that considers the population dynamics using both the Moran model and
 Wright-Fisher model. Applying a branching process approximation, we obtain
 an accurate fixation probability assuming that the population is large and
 the net effect of the mutation is beneficial. We also find the diffusion
 approximation for the fixation probability, which is accurate even in
 small populations and for deleterious alleles, as long as selection is
 weak. These fixation probabilities from branching process and diffusion
 approximations are similar when selection is weak for beneficial mutations
 that are not fully recessive. In many cases, particularly when one phase
 predominates, the fixation probability differs substantially for
 haploid-diploid organisms compared to either fully haploid or diploid
 species.
description: Supplementary
 Mathematica FileMathematica file
 deriving key results in the manuscript, including the simulations reported
 in the figures.SupplementaryFile.nbSupplementary Mathematica File (PDF)PDF version of the Mathematica file deriving key results in the manuscript, including the simulations reported in the figures.SupplementaryFile.pdf
DOI: 10.5061/dryad.1310
title: Data from: Biogeography and evolution of body size and life history of African frogs: phylogeny of squeakers (Arthroleptis) and long-ﬁngered frogs (Cardioglossa) estimated from mitochondrial data

description: The evolutionary history of living African amphibians remains poorly
 understood. This study estimates the phylogeny within the frog genera
 Arthroleptis and Cardioglossa using approximately 2400 bases of mtDNA
 sequence data (12S, tRNA-Valine, and 16S genes) from half of the described
 species. Analyses are conducted using parsimony, maximum likelihood, and
 Bayesian methods. The effect of alignment on phylogeny estimation is
 explored by separately analyzing alignments generated with different gap
 costs and a consensus alignment. The consensus alignment results in
 species paraphyly, low nodal support, and incongruence with the results
 based on other alignments, which produced largely similar results. Most
 nodes in the phylogeny are highly supported, yet several topologies are
 inconsistent with previous hypotheses. The monophyly of Cardioglossa and
 of miniature species previously assigned to Schoutedenella was further
 examined using Templeton and Shimodaira–Hasegawa tests. Cardioglossa
 monophyly is rejected and C. aureoli is transferred to Arthroleptis. These
 tests do not reject Schoutedenella monophyly, but this hypothesis receives
 no support from non-parametric bootstrapping or Bayesian posterior
 probabilities. This phylogeny provides a framework for reconstructing
 historical biogeography and analyzing the evolution of body size and life
 history. Direct development and miniaturization appear at the base of
 Arthroleptis phylogeny concomitant with a range expansion from Central
 Africa to throughout most of sub-Saharan Africa.
description: Alignment representing
 consensus of three other alignmentsConsensus alignment
 generated by removing nucleotide positions for which the alignment
 differed when comparing three alignments generated via ClustalX (with gap
 costs of 10, 15, and 20).Blackburn2008_consensus.nexAlignment with character set denoting excluded base pairsAlignment with a charset specifying nucleotide positions differing between three alignments generated using different gap costs in ClustalX. These sites were excluded to make the consensus alignment.Blackburn2008_excludedbp.nexAlignment generated using a gap cost of 10Blackburn2008_gc10alignment.nexAlignment generated using a gap cost of 15Blackburn2008_gc15alignment.nex.nexAlignment generated using a gap cost of 20Blackburn2008_gc20alignment.nex
DOI: 10.5061/dryad.mb4nd
title: Data from: Temporal shifts and temperature sensitivity of avian spring migratory phenology: a phylogenetic meta-analysis

description: There are wide reports of advances in the timing of spring migration of
 birds over time and in relation to rising temperatures, though
 phenological responses vary substantially within and among species. An
 understanding of the ecological, life-history and geographic variables
 that predict this intra- and interspecific variation can guide our
 projections of how populations and species are likely to respond to future
 climate change. Here, we conduct phylogenetic meta-analyses addressing
 slope estimates of the timing of avian spring migration regressed on (i)
 year and (ii) temperature, representing a total of 413 species across five
 continents. We take into account slope estimation error and examine
 phylogenetic, ecological and geographic predictors of intra- and
 interspecific variation. We confirm earlier findings that on average birds
 have significantly advanced their spring migration time by 2·1 days per
 decade and 1·2 days °C−1. We find that over time and in response to warmer
 spring conditions, short-distance migrants have advanced spring migratory
 phenology by more than long-distance migrants. We also find that larger
 bodied species show greater advance over time compared to smaller bodied
 species. Our results did not reveal any evidence that interspecific
 variation in migration response is predictable on the basis of
 species' habitat or diet. We detected a substantial phylogenetic
 signal in migration time in response to both year and temperature,
 suggesting that some of the shifts in migratory phenological response to
 climate are predictable on the basis of phylogeny. However, we estimate
 high levels of species and spatial variance relative to phylogenetic
 variance, which is consistent with plasticity in response to climate
 evolving fairly rapidly and being more influenced by adaptation to current
 local climate than by common descent. On average, avian spring migration
 times have advanced over time and as spring has become warmer. While we
 are able to identify predictors that explain some of the true
 among-species variation in response, substantial intra- and interspecific
 variation in migratory response remains to be explained.
description: Avian spring migration
 phenology global metadataGlobal metadata gathered
 from published studies on avian spring migration timing over time and with
 respect to temperature. Also includes publication data, methodological,
 geographical and species' ecological factors used in
 analysis.Usui_et_al_2016_metadata_dryad.csv