cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h3r45
title: Data from: Preoperative falls predict postoperative falls and other adverse patient-reported outcomes

description: BACKGROUND: Falls are common and linked to morbidity. Our objectives were
 to characterize postoperative falls, and determine whether preoperative
 falls independently predicted postoperative falls (primary outcome),
 functional dependence, quality of life, complications, and readmission.
 METHODS: This prospective cohort study included 7982 unselected patients
 undergoing elective surgery. Data were collected from the medical record,
 a baseline survey, and follow-up surveys approximately 30days and one year
 after surgery. RESULTS: Fall rates (per 100 person-years) peaked at 175
 (hospitalization), declined to 140 (30-day survey), and then to 97
 (one-year survey). After controlling for confounders, a history of one,
 two, and ≥three preoperative falls predicted postoperative falls at 30days
 (adjusted odds ratios [aOR] 2.3, 3.6, 5.5) and one year (aOR 2.3, 3.4,
 6.9). One, two, and ≥three falls predicted functional decline at 30days
 (aOR 1.2, 2.4, 2.4) and one year (aOR 1.3, 1.5, 3.2), along with
 in-hospital complications (aOR 1.2, 1.3, 2.0). Fall history predicted
 adverse outcomes better than commonly-used metrics, but did not predict
 quality of life deterioration or readmission. CONCLUSIONS: Falls are
 common after surgery, and preoperative falls herald postoperative falls
 and other adverse outcomes. A history of preoperative falls should be
 routinely ascertained.
description: outcomesv2alldataNOPHIdryad2This is the raw dataset provided by the informaticist, after we added missing BMI and surgery dates that were available in the chart, calculated time interval variables, changed age &gt; 89 years to 89 years, and then removed all other PHI (dates, zip code). The variables in this dataset have not been recoded or imputed. The codebook for the variable names is provided on the second sheet of the excel file.
DOI: 10.5061/dryad.n7n71
title: Data from: Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms

description: Background: Earthworms (Crassiclitellata) are a diverse group of annelids
 of substantial ecological and economic importance. Earthworms are
 primarily terrestrial infaunal animals, and as such are probably rather
 poor natural dispersers. Therefore, the near global distribution of
 earthworms reflects an old and likely complex evolutionary history.
 Despite a long-standing interest in Crassiclitellata, relationships among
 and within major clades remain unresolved. Methods: In this study, we
 evaluate crassiclitellate phylogenetic relationships using 38 new
 transcriptomes in combination with publicly available transcriptome data.
 Our data include representatives of nearly all extant earthworm families
 and a representative of Moniligastridae, another terrestrial annelid group
 thought to be closely related to Crassiclitellata. We use a series of
 differentially filtered data matrices and analyses to examine the effects
 of data partitioning, missing data, compositional and branch-length
 heterogeneity, and outgroup inclusion. Results and discussion: We recover
 a consistent, strongly supported ingroup topology irrespective of
 differences in methodology. The topology supports two major earthworm
 clades, each of which consists of a Northern Hemisphere subclade and a
 Southern Hemisphere subclade. Divergence time analysis results are
 concordant with the hypothesis that these north-south splits are the
 result of the breakup of the supercontinent Pangaea. Conclusions: These
 results support several recently proposed revisions to the classical
 understanding of earthworm phylogeny, reveal two major clades that seem to
 reflect Pangaean distributions, and raise new questions about earthworm
 evolutionary relationships.
description: Data
 FilesPlease see ReadMe
 file.data_files.zipTree FilesPlease see ReadMe file.tree_files.zipDating AnalysesPlease see ReadMe file.dating.zipDetailed MethodsMicrosoft Word file that describes laboratory and computational approaches.DetailedMethods.docxScriptsPlease see ReadMe file.scripts_used.zip
DOI: 10.5061/dryad.h4s6t
title: Data from: Does one model fit all? patterns of beech mortality in natural forests of three European regions

description: Large uncertainties characterize forest development under global climate
 change. Although recent studies have found widespread increased tree
 mortality, the patterns and processes associated with tree death remain
 poorly understood, thus restricting accurate mortality predictions. Yet,
 projections of future forest dynamics depend critically on robust
 mortality models, preferably based on empirical data rather than
 theoretical, not well-constrained assumptions. We developed parsimonious
 mortality models for individual beech (Fagus sylvatica) trees and
 evaluated their potential for incorporation in Dynamic Vegetation Models
 (DVMs). We used inventory data from nearly 19′000 trees from unmanaged
 forests in Switzerland, Germany and Ukraine, representing the largest
 dataset used to date for calibrating such models. Tree death was modelled
 as a function of size and growth, i.e., stem diameter (dbh) and relative
 basal area increment (relBAI), using generalized logistic regression
 accounting for unequal re-measurement intervals. To explain the spatial
 and temporal variability in mortality patterns, we considered a large set
 of environmental and stand characteristics. Validation with independent
 datasets was performed to assess model generality. Our results demonstrate
 strong variability in beech mortality that was independent of
 environmental or stand characteristics. Mortality patterns in Swiss and
 German strict forest reserves were dominated by competition processes as
 indicated by J-shaped mortality over tree size and growth. The Ukrainian
 primeval beech forest was additionally characterized by windthrow and a
 U-shaped size-mortality function. Unlike the mortality model based on
 Ukrainian data, the Swiss and German models achieved good discrimination
 and acceptable transferability when validated against each other. We thus
 recommend these two models to be incorporated and examined in DVMs. Their
 mortality predictions respond to climate change via tree growth, which is
 sufficient to capture the adverse effects of water availability and
 competition on the mortality probability of beech under current
 conditions.
description: Data from: Does one
 model fit all? patterns of beech mortality in natural forests of three
 European regionsCH_reduced.csvData from: Does one model fit all? patterns of beech mortality in natural forests of three European regionsCH.csvData from: Does one model fit all? patterns of beech mortality in natural forests of three European regionsDE.csvData from: Does one model fit all? patterns of beech mortality in natural forests of three European regionsUA.csv
DOI: 10.5061/dryad.t1k4q
title: Data from: Mechanisms of resilience: empirically quantified positive feedbacks produce alternate stable states dynamics in a model of a tropical reef

description: Alternate stable states (ASS) theory is a dominant conceptual framework
 for understanding processes that support resilience of ecological
 communities in the face of multiple anthropogenic disturbances. For
 decades, coral reefs have been cited as a classic example of ASS, yet this
 position remains highly controversial, largely because convincing
 empirical evaluations have been elusive. Using a combination of empirical
 measurements of positive feedback processes and simulation modelling, we
 assessed ASS in coral reefs of the Eastern Tropical Pacific (ETP) by
 identifying the potential for multiple basins of attraction from a
 mechanistic perspective. Using bioassays of algal growth and consumption,
 we quantified two spatially localized positive feedback mechanisms on
 coral reefs: increasing herbivore activity associated with higher coral
 abundances and amelioration of nutrient limitation leading to higher algal
 growth in areas with higher algal abundance. Analysis of a model of
 benthic community dynamics incorporating these feedbacks showed they were
 central to producing hysteresis and bistability in the model, two
 hallmarks of ASS. Further, reefs simulated with conditions matching those
 measured at Isla Contadora, Panamá, displayed ASS dynamics while producing
 spatial patterns matching field observations. This provides model-derived
 support, based on empirically measured conditions of ETP reefs, for the
 presence of ASS. Synthesis. The combination of experimental bioassays to
 measure feedback strengths and simulation models to evaluate the influence
 of those feedbacks provides a novel, non-destructive approach to
 evaluating ASS dynamics that can be applied in threatened ecosystems where
 classic approaches are not viable.
description: Compressed data archive
 for empirical data, model code and simulation outputsThis compressed archive
 includes multiple other files with several data sets from empirical
 studies (in .csv format for tabular data), the R code for a cellular
 automaton model of coral reef benthic community dynamics (a .R script),
 and a set of data files that are the model outputs used to produce figures
 in the manuscript (as .rdata files which can be read using R). Specific
 descriptions of each file are supplied in the ReadMe.txt
 file.Mutukrishnan_et_al_reef_community_dynamics.zip
DOI: 10.5061/dryad.8kn73
title: Data from: The quick and the dead: microbial demography at the yeast thermal limit

description: The niche of microorganisms is determined by where their populations can
 expand. Populations can fail to grow because of high death or low birth
 rates, but these are challenging to measure in microorganisms. We
 developed a novel technique that enables single cell measurement of
 age-structured birth and death rates in the budding yeast, Saccharomyces
 cerevisiae, and used this method to study responses to heat stress in a
 genetically diverse panel of strains. We find that individual cells show
 significant heterogeneity in their rates of birth and death during heat
 stress. Genotype-by-environment effects on processes that regulate
 asymmetric cell division contribute to this heterogeneity. These lead to
 either premature senescence or early life mortality during heat stress,
 and we find that a mitochondrial inheritance defect explains the early
 life mortality phenotype of one of the strains we studied. This study
 demonstrates how the interplay of physiology, genetic variation, and
 environmental variables influence where microbial populations survive and
 flourish.
description: Estimated growth of
 strains using growth curves2016-Maxwell-Magwene-100genomes-temperature-growth.csvRaw Tecan Sunrise growth curve data2016-Maxwell-Magwene-100genomes-temperatures-raw.csvStrains identified as sensitive to heat stress2016-Maxwell-Magwene-heat-stress-candidates.csvMitochondrial morphology scoring2016-Maxwell-Magwene-mito-morphology-scoring.csvMitochondrial morphology plus TrackScar2016-Maxwell-Magwene-mito-trackscar.csvMapping from PMY to YJM strain numbers2016-Maxwell-Magwene-PMY-to-YJM.csvThree color TrackScar data2016-Maxwell-Magwene-three-color-trackscar.csvTwo color TrackScar timeseries data2016-Maxwell-Magwene-two-color-trackscar-timeseries.csvTwo color TrackScar data2016-Maxwell-Magwene-two-color-trackscar.csvCode used to generate figures and statisticsThis archive should be unzipped in the same folder as the data files. The file README.org contains the code used to generate the statistics in the paper and was used to generate the README.html files associated with the rest of the submission.R-code.zip
DOI: 10.5061/dryad.73q8s
title: Data from: Control at stability's edge minimizes energetic costs: expert stick balancing

description: Stick balancing on the fingertip is a complex voluntary motor task that
 requires the stabilization of an unstable system. For seated expert stick
 balancers, the time delay is 0.23 s, the shortest stick that can be
 balanced for 240 s is 0.32 m and there is a Embedded Image° dead zone for
 the estimation of the vertical displacement angle in the saggital plane.
 These observations motivate a switching-type, pendulum–cart model for
 balance control which uses an internal model to compensate for the time
 delay by predicting the sensory consequences of the stick's
 movements. Numerical simulations using the semi-discretization method
 suggest that the feedback gains are tuned near the edge of stability. For
 these choices of the feedback gains, the cost function which takes into
 account the position of the fingertip and the corrective forces is
 minimized. Thus, expert stick balancers optimize control with a
 combination of quick manoeuvrability and minimum energy expenditures.
description: Milton_Insperger_sup_materialData for Figures 2b, 3 and 4. Stick balancing data for a 0.56m stick for E1, E2, E3 and E4. Matlab programs used to estimate sensory dead zone and to generate lots shown in Figures 5 and 6.
DOI: 10.5061/dryad.3v71f
title: Data from: Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod

description: Organisms may respond to changing environments through phenotypic
 plasticity or adaptive evolution. These two processes are not mutually
 exclusive and may either dampen or strengthen each other's effects,
 depending on the genetic correlation between trait values and the slopes
 of their norms of reaction. To examine the effect of adaptation to heat
 stress on the plasticity of heat tolerance, we hybridized populations of
 the crustacean Tigriopus californicus that show divergent phenotypes for
 heat tolerance. We then selected for increased heat tolerance in hybrids
 and measured heat tolerance and the phenotypic plasticity of heat
 tolerance in both selected lines and unselected controls. To test whether
 the changes in phenotypic plasticity were associated with changes in the
 plasticity of gene expression, we also sequenced transcriptomes of
 selected and unselected lines, both under heat shock and at ambient
 temperatures. We observed increased heat tolerance in selected lines, but
 also lower phenotypic and transcriptional plasticity in response to heat
 stress. The plastic response to heat stress was highly enriched for
 hydrolytic and catalytic activities, suggesting a prominent role for
 degradation of misfolded proteins. Our findings have important
 implications for biological responses to climate change: if adaptation to
 environmental stress reduces plasticity, then plasticity and adaptive
 evolution will make overlapping, rather than additive contributions to
 buffering populations from environmental change.
description: Transcriptome
 assembliesTranscriptome assemblies
 for Salt Point in northern California, USA, (SA, 39˚20’N, 123˚33’W) and
 Bird Rock in southern California (BD, 32˚49’N, 117˚16’W)Tigriopus
 populationsassemblies.zipAnnotationsAnnotations associated with Tigriopus californicus transcriptome assembliesannotations.zipDE gene analysis in RData files and R-scripts for DE gene analysisLT50_analysisData files and R scripts for heat tolerance LT-50 analysis
DOI: 10.5061/dryad.h0h4s
title: Data from: Maximum likelihood implementation of an isolation-with-migration model for three species

description: We develop a maximum likelihood (ML) method for estimating migration rates
 between species using genomic sequence data. A species tree is used to
 accommodate the phylogenetic relationships among three species, allowing
 for migration between the two sister species, while the third species is
 used as an out-group. A Markov chain characterization of the genealogical
 process of coalescence and migration is used to integrate out the
 migration histories at each locus analytically, whereas Gaussian
 quadrature is used to integrate over the coalescent times on each
 genealogical tree numerically. This is an extension of our early
 implementation of the symmetrical isolation-with-migration model for three
 species to accommodate arbitrary loci with two or three sequences per
 locus and to allow asymmetrical migration rates. Our implementation can
 accommodate tens of thousands of loci, making it feasible to analyze
 genome-scale data sets to test for gene flow. We calculate the posterior
 probabilities of gene trees at individual loci to identify genomic regions
 that are likely to have been transferred between species due to gene flow.
 We conduct a simulation study to examine the statistical properties of the
 likelihood ratio test for gene flow between the two in-group species and
 of the ML estimates of model parameters such as the migration rate.
 Inclusion of data from a third out-group species is found to increase
 dramatically the power of the test and the precision of parameter
 estimation. We compiled and analyzed several genomic data sets from the
 Drosophila fruit flies. Our analyses suggest no migration from D.
 melanogaster to D. simulans, and a significant amount of gene flow from D.
 simulans to D. melanogaster, at the rate of ~0.02 migrant individuals per
 generation. We discuss the utility of the multispecies coalescent model
 for species tree estimation, accounting for incomplete lineage sorting and
 migration.
description: Supplementary
 InformationSupplementary tables and
 figuresUSYB-2016-042.Dalquen.SI.pdfDrosophila datasetsDatasests D1-D5 from the Drosophila analysisdrosophila_datasets.tar.gz
DOI: 10.5061/dryad.g7rk5
title: Data from: Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep

description: Fat-tailed sheep have commercial value because consumers prefer
 high-protein and low-fat food and producers care about feed conversion
 rate. However, fat-tailed sheep still have some scientific significance,
 as the fat tail is commonly regarded as a characteristic of environmental
 adaptability. Finding the candidate genes associated with fat tail
 formation is essential for breeding and conservation. To identify these
 candidate genes, we applied FST and hapFLK approaches in fat- and
 thin-tailed sheep with available 50K SNP genotype data. These two methods
 found 6.24 Mb of overlapped regions and 43 genes that may associated with
 fat tail development. Gene annotation showed that HOXA11, BMP2, PPP1CC,
 SP3, SP9, WDR92, PROKR1 and ETAA1 may play important roles in fat tail
 formation. These findings provide insight into tail fat development and a
 guide for molecular breeding and conservation.
description: 6_population6sheeppopulation50Kdata.zip
DOI: 10.5061/dryad.03622
title: Data from: Monograph of Aframomum (Zingiberaceae)

description: Aframomum (Zingiberaceae, subfamily Alpinioideae) is a genus of 61 species
 of herbs, occurring naturally in Africa and Madagascar. Historically the
 seeds have been an important item in international trade under the names
 “grains of paradise” or “melegueta.” The important characters in
 identification of the species are discussed, and special instructions on
 collecting specimens of the genus are provided. Keys to fruiting and
 flowering specimens are presented. Each species account includes
 nomenclature, description, distribution, and specimen citations.
 Preliminary IUCN conservation assessments are made based on herbarium
 records for each species. Twelve new species, Aframomum dhetchuvii, A.
 fragrans, A. hirsutum, A. kamerunicum, A. kodmin, A. lutarium, A.
 parvulum, A. plicatum, A. rotundum, A. scalare, A. submontanum, and A.
 tchoutoui, are described.
description: Aframomum_specimens
 Harris Wortley 2018This text file contains
 data on herbarium specimens, herbaria where housed, and collecting
 localities.Aframomum_specimens_Harris Wortley 2018This csv file saved in microsoft excel contains herbarium specimen data, herbaria where housed, and collecting localities. It is the same data as the txt file with the same name on dryad.
DOI: 10.5061/dryad.tt5q1
title: Data from: Bees use the taste of pollen to determine which flowers to visit

description: Pollen plays a dual role as both a gametophyte and a nutritional reward
 for pollinators. Although pollen chemistry varies across plant species,
 its functional significance in pollination has remained obscure, in part
 because little is known about how floral visitors assess it. Bees rely on
 pollen for protein, but whether foragers evaluate its chemistry is
 unclear, as it is primarily consumed by larvae. We asked whether the
 chemical composition of pollen influences bumblebees' foraging
 behaviour. Using putatively sweet and bitter pollen blends, we found that
 chemical composition influenced two aspects of bee behaviour relevant to
 plant fitness: the amount of pollen collected and the likelihood of
 subsequently visiting a visually similar flower. These findings offer a
 new perspective on the nutritional ecology of plant–pollinator
 interactions, as they show that pollen's taste may mediate its
 collection and transfer.
description: All data from Biol Lett
 MSThis includes data from
 all parts of the experiment (behavioural, thermal) - notes within file
 describing dataDryad_data_Muth et
 al.xlsx
DOI: 10.5061/dryad.bh330
title: Data from: Reflections of the social environment in chimpanzee memory: applying rational analysis beyond humans

description: In cognitive science, the rational analysis framework allows modelling of
 how physical and social environments impose information-processing demands
 onto cognitive systems. In humans, for example, past social contact among
 individuals predicts their future contact with linear and power functions.
 These features of the human environment constrain the optimal way to
 remember information and probably shape how memory records are retained
 and retrieved. We offer a primer on how biologists can apply rational
 analysis to study animal behaviour. Using chimpanzees (Pan troglodytes) as
 a case study, we modelled 19 years of observational data on their social
 contact patterns. Much like humans, the frequency of past encounters in
 chimpanzees linearly predicted future encounters, and the recency of past
 encounters predicted future encounters with a power function. Consistent
 with the rational analyses carried out for human memory, these findings
 suggest that chimpanzee memory performance should reflect those
 environmental regularities. In re-analysing existing chimpanzee memory
 data, we found that chimpanzee memory patterns mirrored their social
 contact patterns. Our findings hint that human and chimpanzee memory
 systems may have evolved to solve similar information-processing problems.
 Overall, rational analysis offers novel theoretical and methodological
 avenues for the comparative study of cognition.
description: stevens_etal_2016_RSOSThese data were extracted from 19 years of data from the Kanyawara community of chimpanzees in Kibale National Park, Uganda from July 1988 to June 2006. The data rows are dyads of chimpanzees and columns are days. Cell values represent whether the dyad was observed together (1) or not (0) on that day. If neither chimpanzee was observed for more than 70% of the day or if the chimpanzees could not possibly have been in contact (e.g., at least one was not living), the values are blank.