cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f3b04rm
title: Data from: Beyond novelty effect: a mixed-methods exploration into the motivation for long-term activity tracker use

description: Objectives: Activity trackers hold the promise to support people in
 managing their health through quantified measurements about their daily
 physical activities. Monitoring personal health with quantified activity
 tracker-generated data provides patients with an opportunity to
 self-manage their health. Many activity tracker user studies have been
 conducted within short time frames, however, which makes it difficult to
 discover the impact of the activity tracker’s novelty effect or the
 reasons for the device’s long-term use. This study explores the impact of
 novelty effect on activity tracker adoption and the motivation for
 sustained use beyond the novelty period. Materials and Methods: This study
 uses a mixed-methods approach that combines both quantitative activity
 tracker log analysis and qualitative one-on-one interviews to develop a
 deeper behavioral understanding of 23 Fitbit device users who have used
 their trackers for at least two months (range of use = 69 - 1073 days).
 Results: Log data from users’ Fitbit devices revealed two stages in their
 activity tracker use: the novelty period and the long-term use period. The
 novelty period for Fitbit users in this study was approximately three
 months, during which they might have discontinued using their devices.
 Discussion: The qualitative interview data identified various factors that
 motivate users to continuously use Fitbit devices in different stages. The
 discussion of these results provides design implications to guide future
 development of activity tracking technology. Conclusion: This study
 reveals important dynamics emerging over long-term activity tracker use,
 contributes new knowledge to consumer health informatics and
 human-computer interaction, and offers design implications to guide future
 development of similar health-monitoring technologies that better account
 for long-term use in support of patient care and health self-management.
description: Summary of Analysis of
 Participants’ Exercise Performance DataSummary of Analysis of
 Participants’ Exercise Performance DataSummary of Analysis of
 Participants Data.docxTwo Groups’ Device Usage
 Patterns Over TimeTwo Groups’ Device Usage
 Patterns Over Time (High-usage group vs Low-usage
 group)Step Differences Between
 the Two Groups Over TimeLattice Graph: Step
 Differences Between the Two Groups Over Time
DOI: 10.5061/dryad.1b736
title: Data from: Unraveling the determinants of insular body size shifts

description: The island rule, a pattern of size shifts on islands, is an oft-cited but
 little understood phenomenon of evolutionary biology. Here we explore the
 evolutionary mechanisms behind the rule in 184 mammal species, testing
 climatic, ecological, and phylogenetic hypotheses in a robust quantitative
 framework. Our findings confirm the importance of species’ ecological
 traits in determining both the strength and the direction of body size
 changes on islands. Although the island rule pattern appears relatively
 weak overall, we find strongest support for models incorporating trait,
 climatic, and geographic factors in a phylogenetic context, lending
 support to the idea that the island rule is a complex phenomenon driven by
 interacting intrinsic and extrinsic mechanisms. Overall we find that
 different clades may be evolutionarily predisposed to dwarfism or
 gigantism but the magnitude of size changes depends more on adaptation to
 the local environment.
description: Insular Size Ratios of
 Mammals with Environmental Dataisland.csvR Code For AnalysesMcClain_etal_Islands_BioLett_Code.R
DOI: 10.5061/dryad.m777t
title: Data from: Long-term monitoring dataset of fish assemblages impinged at nuclear power plants in northern Taiwan

description: The long-term species diversity patterns in marine fish communities are
 garnering increasing attention from ecologists and conservation
 biologists. However, current databases on quantitative abundance
 information lack consistent long-term time series, which are particularly
 important in exploring the possible underlying mechanism of community
 changes and evaluating the effectiveness of biodiversity conservation
 measures. Here we describe an impinged fish assemblage dataset containing
 1, 283, 707 individuals from 439 taxa. Once a month over 19 years
 (1987–1990 and 2000–2014), we systematically collected the fish killed by
 impingement upon cooling water intake screens at two nuclear power plants
 on the northern coast of Taiwan. Because impingement surveys have low
 sampling errors and can be carried out over many years, they serve as an
 ideal sampling tool for monitoring how fish diversity and community
 structure vary over an extended period of time.
description: Impinged fish dataset
 1987-1990Impinged fish dataset
 2000-2014
DOI: 10.5061/dryad.9nc22
title: Data from: Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates

description: Ecological and evolutionary studies largely assume that island populations
 display low levels of neutral genetic variation. However, this notion has
 only been formally tested in a few cases involving plant taxa, and the
 confounding effect of selection on genetic diversity (GD) estimates based
 on putatively neutral markers has typically been overlooked. Here, we
 generated nuclear microsatellite and plastid DNA sequence data in
 Periploca laevigata, a plant taxon with an island-mainland distribution
 area, to (i) investigate whether selection affects GD estimates of
 populations across contrasting habitats and (ii) test the long-standing
 idea that island populations have lower GD than their mainland
 counterparts. Plastid data showed that colonization of the Canary Islands
 promoted strong lineage divergence within P. laevigata, which was
 accompanied by selective sweeps at several nuclear microsatellite loci.
 Inclusion of loci affected by strong divergent selection produced a
 significant downward bias in the GD estimates of the mainland lineage, but
 such underestimates were substantial (&gt;14%) only when more than one
 loci under selection were included in the computations. When loci affected
 by selection were removed, we did not find evidence that insular Periploca
 populations have less GD than their mainland counterparts. The analysis of
 data obtained from a comprehensive literature survey reinforced this
 result, as overall comparisons of GD estimates between island and mainland
 populations were not significant across plant taxa (N=66), with the only
 exception of island endemics with narrow distributions. This study
 suggests that identification and removal of markers potentially affected
 by selection should be routinely implemented in estimates of GD,
 particularly if different lineages are compared. Furthermore, it provides
 compelling evidence that the expectation of low GD cannot be generalized
 to island plant populations.
description: Periploca
 populationsGeographical location,
 coordinates, vouchers and collector(s) of the Periploca populations
 sampled in this studyPeriploca pops
 data.txtPeriploca microsatellite
 data matrixGenotyping of 661
 Periploca individuals using 13 microsatellite nuclear loci (Genetix
 format). Population codes correspond with those provided in the
 "Periploca populations" text filePeriploca_nSSR.txtPeriploca cpDNA sequence dataConcantenated sequence data of four plastid regions (rbcL+trnTL+matK+psba-trnH) from 99 Periploca individuals (N = 33 populations)Periploca99samples_4cpDNAregions.txt
DOI: 10.5061/dryad.j958j
title: Data from: Census parcels cropping system classification from multitemporal remote imagery: a proposed universal methodology

description: A procedure named CROPCLASS was developed to semi-automate census parcel
 crop assessment in any agricultural area using multitemporal remote
 images. For each area, CROPCLASS consists of a) a definition of census
 parcels through vector files in all of the images; b) the extraction of
 spectral bands (SB) and key vegetation index (VI) average values for each
 parcel and image; c) the conformation of a matrix data (MD) of the
 extracted information; d) the classification of MD decision trees (DT) and
 Structured Query Language (SQL) crop predictive model definition also
 based on preliminary land-use ground-truth work in a reduced number of
 parcels; and e) the implementation of predictive models to classify
 unidentified parcels land uses. The software named CROPCLASS-2.0 was
 developed to semi-automatically perform the described procedure in an
 economically feasible manner. The CROPCLASS methodology was validated
 using seven GeoEye-1 satellite images that were taken over the LaVentilla
 area (Southern Spain) from April to October 2010 at 3- to 4-week
 intervals. The studied region was visited every 3 weeks, identifying 12
 crops and others land uses in 311 parcels. The DT training models for each
 cropping system were assessed at a 95% to 100% overall accuracy (OA) for
 each crop within its corresponding cropping systems. The DT training
 models that were used to directly identify the individual crops were
 assessed with 80.7% OA, with a user accuracy of approximately 80% or
 higher for most crops. Generally, the DT model accuracy was similar using
 the seven images that were taken at approximately one-month intervals or a
 set of three images that were taken during early spring, summer and
 autumn, or set of two images that were taken at about 2 to 3 months
 interval. The classification of the unidentified parcels for the
 individual crops was achieved with an OA of 79.5%.
description: CROPCLASS-2.0
 softwareAdd-on for ENVI5.0 which
 develop semiautomatically the crop classification based on census parcel
 and multiemporal remote imagescropclass2.savInstalation CROPCLASS-2.0 Decembre2014 ENGLISHObjectives, achievments and installation procedure of CROPCLASS-2.0 software (an extension of ENVI5.0)Odd parcels FINAL data 156 parcels last 07April2014Field data set of the articleVentillas 156 parcels data & variables definitionField data and variables definition
DOI: 10.5061/dryad.23f21
title: Data from: Cross-taxa generalities in the relationship between population abundance and ambient temperatures

description: Identifying patterns in the effects of temperature on species'
 population abundances could help develop a general framework for
 predicting the consequences of climate change across different communities
 and realms. We used long-term population time series data from
 terrestrial, freshwater, and marine species communities within central
 Europe to compare the effects of temperature on abundance across a broad
 range of taxonomic groups. We asked whether there was an average
 relationship between temperatures in different seasons and annual
 abundances of species in a community, and whether species attributes
 (temperature range of distribution, range size, habitat breadth, dispersal
 ability, body size, and lifespan) explained interspecific variation in the
 relationship between temperature and abundance. We found that, on average,
 warmer winter temperatures were associated with greater abundances in
 terrestrial communities (ground beetles, spiders, and birds) but not
 always in aquatic communities (freshwater and marine invertebrates and
 fish). The abundances of species with large geographical ranges, larger
 body sizes, and longer lifespans tended to be less related to temperature.
 Our results suggest that climate change may have, in general, positive
 effects on species’ abundances within many terrestrial communities in
 central Europe while the effects are less predictable in aquatic
 communities.
description: Species_specific_temp_effects_on_abundanceThis files contains species-level estimates of the effect of average ambient temperatures and precipitation amounts in different seasons on subsequent population abundances. The columns are (1) species names; (2) dataset/taxa - see Table 1 in the article for details; (3) The weather variable and season; (4) The regression coefficient estimate of the effect of each weather variable on the population abundance of each species, as tested in a statistical model including AR(1) errors and a continuous 'year' effect to account for long-term trends due to unrelated drivers; (5) SD -The standard deviation of the regression estimate and (6) and (7) the lower and upper 95% confidence intervals of the regression coefficient.
DOI: 10.5061/dryad.vf1ms
title: Data from: The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes

description: The evolution of convergent phenotypes is one of the most interesting
 outcomes of replicate adaptive radiations. Remarkable cases of convergence
 involve the thick-lipped phenotype found across cichlid species flocks in
 the East African Great Lakes. Unlike most other convergent forms in
 cichlids, which are restricted to East Africa, the thick-lipped phenotype
 also occurs elsewhere, e.g. in the Central American Midas Cichlid
 assemblage. Here we use an ecological genomic approach to study the
 function, the evolution and the genetic basis of this phenotype in two
 independent cichlid adaptive radiations on two continents. We applied
 phylogenetic, demographic, geometric morphometric and stomach-content
 analyses to an African (Lobochilotes labiatus) and a Central American
 (Amphilophus labiatus) thick-lipped species. We found that similar
 morphological adaptations occur in both thick-lipped species and that the
 ‘fleshy’ lips are associated with hard-shelled prey in the form of
 mollusks and invertebrates. We then used comparative Illumina RNA
 sequencing of thick versus normal lip tissue in East African cichlids and
 identified a set of 141 candidate genes that appear to be involved in the
 morphogenesis of this trait. A more detailed analysis of six of these
 genes led to three strong candidates: Actb, Cldn7 and Copb. The function
 of these genes can be linked to the loose connective tissue constituting
 the fleshy lips. Similar trends in gene expression between African and
 Central American thick-lipped species appear to indicate that an
 overlapping set of genes was independently recruited to build this
 particular phenotype in both lineages.
description: stomach_content_analysisdata from the stomach content analysesqPCR1raw data from the qPCR analysesqPCR2data from the quantitative real-time experimentsAmphilophusTropheini
DOI: 10.34740/kaggle/dsv/14631808
title: different vegetation restoration
DOI: 10.5061/dryad.vn0gc
title: Data from: Genomic repeat abundances contain phylogenetic signal

description: A large proportion of genomic information, particularly repetitive
 elements, is usually ignored when researchers are using next-generation
 sequencing. Here we demonstrate the usefulness of this repetitive fraction
 in phylogenetic analyses, utilising comparative graph-based clustering of
 next-generation sequence reads, which results in abundance estimates of
 different classes of genomic repeats. Phylogenetic trees are then inferred
 based on the genome-wide abundance of different repeat types treated as
 continuously varying characters; such repeats are scattered across
 chromosomes and in angiosperms can constitute a majority of nuclear
 genomic DNA. In six diverse examples, five angiosperms and one insect,
 this method provides generally well-supported relationships at
 interspecific and intergeneric levels that agree with results from more
 standard phylogenetic analyses of commonly used markers. We propose that
 this methodology may prove especially useful in groups where there is
 little genetic differentiation in standard phylogenetic markers. At the
 same time as providing data for phylogenetic inference, this method
 additionally yields a wealth of data for comparative studies of genome
 evolution.
description: Online Appendix
 1Read
 data quality and high-copy assembly parameters.Online Appendix
 2ML
 analyses for all datasets.Online Appendix
 3Analysis with
 non-standardised data.
DOI: 10.5061/dryad.t0q94
title: Data from: The evolution of primate general and cultural intelligence

description: There are consistent individual differences in human intelligence,
 attributable to a single ‘general intelligence’ factor, g. The
 evolutionary basis of g and its links to social learning and culture
 remain controversial. Conflicting hypotheses regard primate cognition as
 divided into specialized, independently evolving modules versus a single
 general process. To assess how processes underlying culture relate to one
 another and other cognitive capacities, we compiled ecologically relevant
 cognitive measures from multiple domains, namely reported incidences of
 behavioural innovation, social learning, tool use, extractive foraging and
 tactical deception, in 62 primate species. All exhibited strong positive
 associations in principal component and factor analyses, after
 statistically controlling for multiple potential confounds. This highly
 correlated composite of cognitive traits suggests social, technical and
 ecological abilities have coevolved in primates, indicative of an
 across-species general intelligence that includes elements of cultural
 intelligence. Our composite species-level measure of general intelligence,
 ‘primate gs’, covaried with both brain volume and captive learning
 performance measures. Our findings question the independence of cognitive
 traits and do not support ‘massive modularity’ in primate cognition, nor
 an exclusively social model of primate intelligence. High general
 intelligence has independently evolved at least four times, with
 convergent evolution in capuchins, baboons, macaques and great apes.
description: Electronic Supplementary
 MaterialElectronic Supplementary
 Material (ESM) accompanying the paper.ESM_ReaderHagerLalandPhilTrans2011_rstb20100342supp1.pdfDatasetPlease refer to ReadMe file.Data_ReaderHagerLalandPhilTrans2011.csv
DOI: 10.5061/dryad.4k078
title: Data from: strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence

description: strap (Stratigraphic Tree Analysis for Palaeontology) is a new package for
 the freely available statistical programming language R designed to
 perform three main tasks: (1) to time-scale phylogenies of fossil taxa;
 (2) to plot those time-scaled trees against stratigraphy; and (3) to
 assess congruence between phylogenies and stratigraphy. Time-scaling is
 performed with the DatePhylo function, with three approaches offered.
 Plotting trees against a choice of five different geological time scaless
 is possible using the geoscalePhylo function. Finally, the function
 StratPhyloCongruence calculates stratigraphic congruence measures for one
 or more input phylogenies, with no taxon limit. All three major congruence
 measures are offered: Stratigraphic Consistency Index (SCI), Manhattan
 Stratigraphic Measure (MSM*) and the gap excess ratio (GER; including GERt
 and GER*), as well as the pseudocongruence measure, the Relative
 Completeness Index (RCI). Each measure has an accompanying significance
 test that works by comparing the input trees against a user-defined number
 of randomly generated topologies with the same taxon set and age ranges.
 Additional options for generating these random topologies allow the user
 to fix the outgroup or retain the input tree shape to make fairer
 comparisons. A tutorial that assumes no prior knowledge of R showcases all
 three functions using two different example data sets.
description: Dipnoi
 treeThe single favoured MPT
 from Lloyd et al., 2012.Dipnoi.treDipnoi agesUpper and lower bounds from the first appearance for the taxa in the tree contained in Dipnoi.tre.Dipnoi.txtAsaphidae treesAll 162 MPTs of the trilobite Family Asaphidae from Bell and Braddy, 2012.Asaphidae.treAsaphidae stratigraphic rangesFirst and last appearance datums for all species within the Asaphidae.tre file.Asaphidae.txtBell and Lloyd - Strap tutorialTutorial describing usage of main functions of strap (v 1.4) package for R.Bell and Lloyd - SI Tutorial.pdf
DOI: 10.5061/dryad.8164
title: Data from: Evaluating the reliability of microsatellite genotyping from low-quality DNA templates with a polynomial distribution model

description: Molecular studies using trace DNA, such as from museum specimens, ancient
 or forensic samples and samples obtained noninvasively, often have a
 common problem of low quality of DNA templates. Amplification errors, such
 as allelic dropout and false allele, may arise during polymerase chain
 reaction (PCR) using such samples. A mathematical model which treats
 homozygotes and heterozygotes discriminately has been developed to measure
 sample quality and compute the confidence level of using multiple-tube
 approaches. We use plucked hair samples collected from 26 individual
 Sichuan snub-nosed monkeys (Rhinopithecus roxellana) to test the model. In
 this case, a confidence level of 99% can be achieved by three positive
 PCRs. If the sample quality is very poor and requires many PCR replicates,
 an alternative multiple-step genotyping method is recommended. This model
 enables researchers to optimize experimental protocols through pilot
 studies and obtain reliable genetic information using noninvasive sampling
 method.
description: Consensus
 GenotypeGenotype file of 26
 individuals at 5 SSR loci.Calculation_Program_of_Fig.3 (C Program Source File)Source file of the program calculating the estimated number of replicates and the reduction in the number of replicates of heterozygotes and homozygotes using multiple-steps method at the 99% confidence level.Calculation_Program_of_Fig.3.cData of Fig.3The estimated number of replicates and the reduction in the number of replicates of heterozygotes and homozygotes using multiple-steps method at the 99% confidence level. Sheet1 are the estimated numbers of replicates of heterozygotes. Sheet1 are the estimated numbers of replicates of homozygotes. Sheet3 and Sheet4 are selected genotyping approaches.Fig.3 data.xlsCalculation Program of Fig.3 (win32 application)Calculation Program of Fig.3 (win32 application compiled with Visual Studio 2008)Calculation Program of Fig.3 win32.exeReliability Calculator (win32 application)Reliability Calculator (win32 application complied with Visual Studio 2008) Reliability Calculator for Microsatellite Genotyping Using low quality DNA templates Functions: 1. Generate a table of minimum thresholds of R1 and R2 at a given confidence level; 2. Find approaches reach a given confidence level for given R1 and R2; 3. Generate a table of minimum thresholds of R1 and R2 at a given confidence level (P(E1) is calculated by equation (4)); 4. Find approaches reach a given confidence level for given R1 and R2 (P(E1) iscalculated by equation (4)); 5. Calculate the lower limit of one-sided confidence interval; 6. Simulate the expected number of replicates for given R1, R2, ms and ns;Reliability Calculator win32.exeReliability Calculator (C Program Source File)Reliability Calculator (C Program Source File)Reliability Calculator.c