cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k2vh732
title: Data from: New MRI contrast agents based on silicon nanotubes loaded with superparamagnetic iron oxide nanoparticles

description: This article describes the preparation and fundamental properties of a new
 possible material as a MRI contrast agent based on the incorporation of
 preformed iron oxide nanocrystals into hollow silicon nanotubes.
 Specifically, superparamagnetic iron oxide nanoparticles Fe3O4 of two
 different average sizes (5 nm and 8 nm) were loaded into silicon nanotubes
 of two different shell thicknesses (40 nm and 70 nm). To achieve proper
 aqueous solubility, the nanotubes were functionalized with an outer
 polyethylene glycol (PEG)-diacid (600) moiety via an aminopropyl linkage.
 Relaxometry parameters r1 and r2 were measured, with the corresponding
 r2/r1 ratios in PBS confirming the expected negative contrast agent
 behaviour for these materials. For a given nanocrystal size, the observed
 r2 values are found to be inversely proportional to nanotube wall
 thickness, thereby demonstrating the role of nanostructured silicon
 template on associated relaxometry properties.
description: T1T2_datasetSet of original T1 and T2 data for Fe3O4 nanocrystals and nanocrystals loaded into silicon nanotubes.
DOI: 10.5061/dryad.m6383tr
title: Data from: Population correlates of rapid captive-induced maladaptation in a wild fish

description: Understanding the extent to which captivity generates maladaptation in
 wild species can inform species recovery programs and elucidate wild
 population responses to novel environmental change. Though rarely
 quantified, effective population size (Ne) and genetic diversity should
 influence the magnitude of plastic and genetic changes manifested in
 captivity that reduce wild fitness. Sexually-dimorphic traits might also
 mediate consequences of captivity. To evaluate these relationships, we
 generated &gt;600 full- and half-sibling families from nine wild brook
 trout populations, reared them for one generation under common, captive
 environmental conditions, and contrasted several fitness-related traits in
 wild vs. captive lines. We found substantial variation in lifetime success
 (lifetime survival and reproductive success) and life history traits among
 wild populations after just one captive generation (fourteen- and
 three-fold ranges across populations, respectively). Populations with
 lower heterozygosity showed lower captive lifetime success, suggesting
 that captivity generates maladaptation within one generation. Greater
 male-biased mortality in captivity occurred in populations having
 disproportionately higher growth rates in males than females. Wild
 population Ne and allelic diversity had little or no influence on captive
 trait expression and lifetime success. Our results have four conservation
 implications: (i) Trait values and lifetime success were highly variable
 across populations following one generation of captivity. (ii)
 Maladaptation induced by captive breeding might be particularly intense
 for the very populations practitioners are most interested in conserving,
 such as those with low heterozygosity. (iii) Maladaptive sex differences
 in captivity might be associated with population-dependent growth costs of
 reproduction. (iv) Heterozygosity can be a good indicator of short-term,
 intraspecific responses to novel environmental change.
description: Cape Race_final SNP
 dataCape Race_microsatellite
 data_from 2009 to 2015_with additional popnsCape Race brook
 trout_female_eggsize_wild and captiveCape Race brook
 trout_female_fecundity_wild and captiveCape Race
 survival_progeny of captive born adults in a common hatchery
 environmentCape Race wild
 population survival in captivity to one year 2011 and
 2014Cape Race wild
 population survival in captivity_egg to yolk absorption_2011 and 2014_six
 populationsCape Race wild
 populations in captivity_lengthalltimeallpopCape Race wild
 populations in captivity_lengthweightallpop18monthsCape Race wild
 populations in
 captivity_obs_freq(mortality_by_sex_by_pop)Cape Race wild
 populations in captivity_weightlengthallpop3Cape Race wild
 populations in captivity_weightlengthallpop7Cape Race wild
 populations in captivity_weightlengthallpop12Cape
 Race_female_GSI_captive_wild
DOI: 10.5061/dryad.h7t4dq0
title: Data from: The influence of evaluative right/wrong feedback on phonological and semantic processes in word learning

description: Feedback is typically incorporated in word learning paradigms, in both
 research studies and commercial language learning apps. While the
 common-sense view is that feedback is helpful during learning, relatively
 little empirical evidence about the role of feedback in spoken vocabulary
 learning exists. Some work has suggested that long-term word learning is
 not enhanced by the presence of feedback, and that words are best learned
 implicitly. It is also plausible that feedback might have differential
 effects when learners focus on learning semantic facts, or when they focus
 on learning a new phonological sequence of sounds. In this study, we
 assess how providing evaluative (right/wrong) feedback on a spoken
 response influences two different components of vocabulary learning, the
 learning of a new phonological form, and the learning of a semantic
 property of the phonological form. We find that receiving evaluative
 feedback improves retention of phonological forms, but not of semantic
 facts.
description: TrainingData_LastBlock_ErrorThis is the data file to conduct the error analysis reported in the paper.FinalTestThis is the data from testing conducted a week after training.TrainingDataThis is the data from the training phase of the experiment.
DOI: 10.5061/dryad.18
title: Data from: The role of pleiotropy in the maintenance of sex in yeast

description: In facultatively sexual species, lineages that reproduce asexually for a
 period of time can accumulate mutations that reduce their ability to
 undergo sexual reproduction when sex is favorable. We propagated
 Saccharomyces cerevisiae asexually for ~800 generations, after which we
 measured the change in sexual ﬁtness, measured as the proportion of asci
 observed in sporulation medium. The sporulation rate in cultures
 propagated asexually at small population size declined by 8%, on average,
 over this time period, indicating that the majority of mutations that
 affect sporulation rate are deleterious. Interestingly, the sporulation
 rate in cultures propagated asexually at large population size improved by
 11%, on average, indicating that selection on asexual function effectively
 eliminated most of the mutations deleterious to sporulation ability. These
 results suggest that pleiotropy between mutations’ effects on asexual
 ﬁtness and sexual ﬁtness was predominantly positive, at least for the
 mutations accumulated in this experimental evolution study. A positive
 correlation between growth rate and sporulation rate among lines also pro-
 vided evidence for positive pleiotropy. These results demonstrate that, at
 least under certain circum- stances, selection acting on asexual ﬁtness
 can help to maintain sexual function.
description: Maximum Likelihood
 EstimatorMathematica file that
 summarizes and plots results of the program mlgenomeu.c to infer maximum
 likelihood estimates of the mutation rate and effect size, using two
 fitness assays (sporulation rate, growth rate).MLanalysis.nbStatistical AnalyzerMathematica file that contains all of the growth rate data obtained from the Bioscreen as well as all of the sporulation data. This file performs all of the major statistical analyses on these datasets reported in Hill and Otto (2007).sliding window 06 NEW.nbSporulation Rate Datasporedata.xls
DOI: 10.5061/dryad.1800
title: Data from: Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales

description: The extent to which the distribution of soil bacteria is controlled by
 local environment versus spatial factors (e.g., dispersal, colonisation
 limitation, evolutionary events) is poorly understood and widely debated.
 Our understanding of biogeographic controls in microbial communities is
 likely hampered by the enormous environmental variability encountered
 across spatial scales and the broad diversity of microbial life histories.
 Here we constrained environmental factors (soil chemistry, climate,
 above-ground plant community) to investigate the specific influence of
 space, by fitting all other variables first, on bacterial communities in
 soils over distances from m to 102 km. We found strong evidence for a
 spatial component to bacterial community structure that varies with scale
 and organism life history (dispersal and survival ability). Geographic
 distance had no influence over community structure for organisms known to
 have survival stages, but the converse was true for organisms thought to
 be less hardy. Community function (substrate utilisation) was also shown
 to be highly correlated to community structure, but not to abiotic
 factors, suggesting non-stochastic determinants of community structure are
 important Our results support the view that bacterial soil communities are
 constrained by both edaphic factors and geographic distance, and further
 show that the relative importance of such constraints depends critically
 on the taxonomic resolution used to evaluate spatio-temporal patterns of
 microbial diversity, as well as life-history of the groups being
 investigated, much as is the case for macro-organisms.
description: Arraycellfiles.rar
DOI: 10.5061/dryad.2168568
title: Data from: Advancing mite phylogenomics: designing ultraconserved elements for Acari phylogeny

description: Mites (Acari) are one of the most diverse groups of life on Earth, yet
 their evolutionary relationships are poorly understood. Also, the
 resolution of broader arachnid phylogeny has been hindered by an
 underrepresentation of mite diversity in phylogenomic analyses. To further
 our understanding of Acari evolution,we design targeted ultraconserved
 genomic elements (UCEs) probes, intended for resolving the complex
 relationships between mite lineages and closely related arachnids. We then
 test our Acari UCE baits in-silico by constructing a phylogeny using 13
 existing Acari genomes, as well as 6 additional taxa from a variety of
 genomic sources. Our Acari-specific probe kit improves the recovery of
 loci within mites over an existing general arachnid UCE probe set. Our
 initial phylogeny recovers the major mite lineages, yet finds mites to be
 non-monophyletic overall, with Opiliones (harvestmen) and Ricinuleidae
 (hooded tickspiders) rendering Parasitiformes paraphyletic.
description: mite-UCE-probe-setfasta of UCE probes designed to work across mitesmite-v2-master-probe-list-DUPE-SCREENED.fasta
DOI: 10.5061/dryad.9p4r16m
title: Data from: The time geography of segregation during working hours

description: Understanding segregation is essential to develop planning tools for
 building more inclusive cities. Theoretically, segregation at the work
 place has been described as lower compared to residential segregation
 given the importance of skill complementarity among other productive
 factors shaping the economies of cities. This paper tackles segregation
 during working hours from a dynamical perspective by focusing on the
 movement of urbanites across the city. In contrast to measuring
 residential patterns of segregation, we used mobile phone data to infer
 home-work trajectory networks and apply a community detection algorithm to
 the example city of Santiago, Chile. We then describe qualitatively and
 quantitatively outlined communities, in terms of their socio economic
 composition. We then evaluate segregation for each of these communities as
 the probability that a person from a specific community will interact with
 a co-worker from the same community. Finally, we compare these results
 with simulations where a new work location is set for each real user,
 following the empirical probability distributions of home-work distances
 and angles of direction for each community. Methodologically, this study
 shows that segregation during working hours for Santiago is unexpectedly
 high for most of the city with the exception of its central and business
 district. In fact, the only community that is not statistically segregated
 corresponds to the downtown area of Santiago, described as a zone of
 encounter and integration across the city.
description: HW Commuting in Santiago
 Chile from cellphone CDR dataColumn are as following.
 numa_id: user id; tower_w: cellphone tower at work place; tower_h
 cellphone tower at home place ;X_w: work location easting ;Y_w: work
 location northing;X_h: home location easting;Y_h: home location
 northing;Distance: commuting distance ;angle angle of commuting w/ respect
 to east direction.HW_20days_dataset.csvCommunities by dayCommunities detected from HW commuting behaviour in Santiago Chile.
DOI: 10.5061/dryad.pt3b974
title: Data from: Inferring selection in instances of long‐range colonization: the Aleppo pine (Pinus halepensis) in the Mediterranean Basin

description: Teasing apart the effects of natural selection and demography on current
 allele frequencies is challenging, due to both processes leaving a similar
 molecular footprint. In particular, when attempting to identify selection
 in species that have undergone a recent range expansion, the increase of
 genetic drift at the edges of range expansions (“allele surfing”) can be a
 confounded factor. To address this potential issue, we first assess the
 long-range colonisation history of the Aleppo pine across the
 Mediterranean Basin, using molecular markers. We then look for single
 nucleotide polymorphisms (SNPs) involved in local adaptation using: (i)
 environmental correlation methods (Bayenv2), focusing on bioclimatic
 variables important for the species’ adaptation (i.e. temperature,
 precipitation and water availability); and (ii) FST-related methods
 (PCAdapt). In order to assess the rate of false positives caused by the
 allele surfing effect, these results are compared with results from
 simulated SNP data that mimics the species’ past range expansions and the
 effect of genetic drift, but with no selection. We find that the Aleppo
 pine shows a previously unsuspected complex genetic structure across its
 range, as well as evidence of selection acting on SNPs involved with the
 response to bioclimatic variables such as drought. This study uses an
 original approach to disentangle the confounding effects of drift and
 selection in range margin populations. It also contributes to the
 increased evidence that plant populations are able to adapt to new
 environments despite the expected accumulation of deleterious mutations
 that takes place during long-range colonisations.
description: SSR_genotypesEight nuclear SSRs genotyped in the 44 populations of the Aleppo pine.SNP_genotypes294 SNPs genotyped in the 46 populations of the Aleppo pine.Environmental_DataBioclimatic variables, water availability and aridity indexes.
DOI: 10.6084/m9.figshare.31157827
title: Absolute Force and the Geometric Genesis of Dimensional Walls: A Cryptographically Secured Field Study

description: This record establishes the mathematical hardening of dimensional boundaries under compounded absolute force. Using a high-resolution field simulation, the data demonstrates the transition from fluid wave-forms to rigid geometric constraints at a 0.92 threshold. These results are categorized under Mathematical physics and Information and computing sciences, specifically focusing on the mathematical aspects of field theory and computational integrity. Every state change is verified via SHA-256 cryptographic hashing to ensure the structural conclusions are immutable and accountable.
DOI: 10.6084/m9.figshare.31157827.v1
title: Absolute Force and the Geometric Genesis of Dimensional Walls: A Cryptographically Secured Field Study

description: This record establishes the mathematical hardening of dimensional boundaries under compounded absolute force. Using a high-resolution field simulation, the data demonstrates the transition from fluid wave-forms to rigid geometric constraints at a 0.92 threshold. These results are categorized under Mathematical physics and Information and computing sciences, specifically focusing on the mathematical aspects of field theory and computational integrity. Every state change is verified via SHA-256 cryptographic hashing to ensure the structural conclusions are immutable and accountable.
DOI: 10.5061/dryad.61g8620
title: Data from: Molecular mechanism of viscoelastic polymer enhanced-oil-recovery in nanopores

description: Polymer flooding is a promising chemical enhanced oil recovery method,
 which realizes more efficient extraction in porous formations
 characterized with nanoscale porosity and complicated interfaces.
 Understanding the molecular mechanism of viscoelastic polymer
 enhanced-oil-recovery in nanopores is of great significance for the
 advancement of oil exploitation. Using molecular dynamics simulations, we
 investigated the detailed process of the viscoelastic polymer displacing
 oil at the atomic scale. We found that the interactions between polymer
 chains and oil provide an additional pulling effect on extracting the
 residual oil trapped in dead-end nanopores, which plays a key role in
 increasing the oil displacement efficiency. Our results also demonstrate
 that the oil displacement ability of polymer can be reinforced with the
 increasing chain length and viscoelasticity. In particular, polymer with
 longer chain length exhibits stronger elastic property, which enhances the
 foregoing pulling effect. These findings can help to enrich our
 understanding on the molecular mechanism of polymer enhanced-oil-recovery
 and provide guidance for oil extraction engineering.
description: code_and_dataThis file provides codes and data for analyzing the simulation results.
DOI: 10.5061/dryad.g52m65t
title: Data from: BAMM at the court of false equivalency: a response to Meyer and Wiens

description: The software program BAMM has been widely used to study rates of
 speciation, extinction, and phenotypic evolution on phylogenetic trees.
 The program implements a model-based clustering algorithm to identify
 clades that share common macroevolutionary rate dynamics and to estimate
 parameters. A recent simulation study by Meyer and Wiens (M&W)
 claimed that (i) a simple inference framework ("MS") performs
 much better than BAMM, and (ii) evolutionary rates inferred with BAMM are
 poorly correlated with true rates. I address two statistical concerns with
 their assessment that affect the generality of their conclusions. These
 considerations are not specific to BAMM and apply to other methods for
 estimating parameters from empirical data where the true grouping
 structure of the data is unknown. M&W constrain roughly half of
 the parameters in their MS analyses to their true values, but BAMM is
 given no such information and must estimate all parameters from the data.
 This information disparity results in a substantial degrees-of-freedom
 advantage for the MS estimators. When both methods are given equivalent
 information, BAMM outperforms the MS estimators.
description: dryad-submit-may14Scripts to replicate analysis and figures from "BAMM at the court of false equivalency: a response to Meyer and Wiens"rabosky-2018-kangaroo.zip
DOI: 10.5061/dryad.n0j5b19
title: Data from: Plastic responses to competition: does bacteriocin production increase in the presence of nonself competitors?

description: Anticompetitor traits such as the production of allelopathic toxins can
 confer significant competitive benefits but are often costly to produce.
 Evolution of these traits may be facilitated by environment‐specific
 induction; however, the extent to which costly anticompetitor traits are
 induced by competitors is not well explored. Here, we addressed this
 question using bacteriocins, which are highly specific, proteinaceous
 anticompetitor toxins, produced by most lineages of bacteria and archaea.
 We tested the prediction that bacteriocin production is phenotypically
 plastic and induced by the presence of competitors by examining
 bacteriocin production in the presence and absence of nonself competitors
 over the course of growth of a producing strain. Our results show that
 bacteriocin production is detectable only at high cell densities, when
 competition for resources is high. However, the amount of bacteriocin
 activity was not significantly different in the presence vs. the absence
 of nonself competitors. These results suggest that bacteriocin production
 is either (a) canalized, constitutively produced by a fixed frequency of
 cells in the population or (b) induced by generic cues of competition,
 rather than specific self/nonself discrimination. Such a nonspecific
 response to competition could be favored in the natural environment where
 competition is ubiquitous.
description: Figure 3 Raw
 DataThe data file associated
 with figure 3 in the manuscript.Figure 3
 AnalysisSAS code used to analyze
 data for figure 3.Figure 4 Raw
 DataData file associated
 with Figure 4.Figure 4
 AnalysisSAS code associated with
 Figure 4Figure 5 Raw
 DataData associated with
 Figure 5 in the manuscriptFigure 5
 AnalysisSAS code used to analyze
 the data presented in Figure 5Figure S1 Raw
 DataRaw data used in
 Supplementary Materials, Figure S1.Figure S1
 AnalysisSAS code used to analyze
 data in Supplemental Figure S1.Figure S2 Raw
 DataData file associated
 with Supplemental Figure S2.Figure S2
 AnalysisSAS code associated with
 Supplemental Figure S2.
DOI: 10.5061/dryad.d79c4cs
title: Data from: The changing nature of collaboration in tropical ecology and conservation

description: Collaboration can improve conservation initiatives through increases in
 article impact and by the building scientific understating required for
 conservation practice. We investigated temporal trends in collaboration in
 the tropical ecology and conservation literature by examining patterns of
 authorship for 2,271 articles published from 2000 to 2016 in Biotropica
 and the Journal of Tropical Ecology. Consistent with trends in other
 studies and scientific disciplines, we found that the mean number of
 authors per article increased from 2.6 in 2000 to 4.2 in 2015. We modeled
 changes in multi-national collaboration in articles using a generalized
 linear model, finding that the mean number of author-affiliated countries
 increased from 1.3 (± 0.6 SD) to 1.7 (± 0.8 SD) over time, and that
 increases were best explained by the number of authors per article. The
 proportion of authors based in tropical countries increased, but the
 probability of tropical-extratropical collaboration did not, and was best
 explained solely by the number of authors per article. Overall, our
 analyses suggest that only certain types of collaboration are increasing,
 and that these increases coincide with a general increase in the number of
 authors per article. Such changes in author numbers and collaboration
 could be the result of increased data-sharing, changes in the scope of
 research questions, changing authorship criteria, or scientific migration.
 We encourage tropical conservation scientists continue to build
 collaborative ties, particularly with researchers based in
 underrepresented tropical countries, to ensure that tropical ecology and
 conservation remains inclusive and effective.
description: Collaboration in
 tropical ecology datasetA .csv containing
 columns for year of publication, authors' first country of
 affiliation, authors' names, article title, and the journal where the
 article was published.Tropical.Authorship.Dataset.csv