cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bh123
title: Data from: Bypass of genetic constraints during mutator evolution to antibiotic resistance

description: Genetic constraints can block many mutational pathways to optimal
 genotypes in real fitness landscapes, yet the extent to which this can
 limit evolution remains to be determined. Interestingly, mutator bacteria
 elevate only specific types of mutations, and therefore could be very
 sensitive to genetic constraints. Testing this possibility is not only
 clinically relevant, but can also inform about the general impact of
 genetic constraints in adaptation. Here, we evolved 576 populations of two
 mutator and one wild-type Escherichia coli to doubling concentrations of
 the antibiotic cefotaxime. All strains carried TEM-1, a β-lactamase enzyme
 well known by its low availability of mutational pathways. Crucially, one
 of the mutators does not elevate any of the relevant first-step mutations
 known to improve cefatoximase activity. Despite this, both mutators
 displayed a similar ability to evolve more than 1000-fold resistance.
 Initial adaptation proceeded in parallel through general multi-drug
 resistance mechanisms. High-level resistance, in contrast, was achieved
 through divergent paths; with the a priori inferior mutator exploiting
 alternative mutational pathways in PBP3, the target of the antibiotic.
 These results have implications for mutator management in clinical
 infections and, more generally, illustrate that limits to natural
 selection in real organisms are alleviated by the existence of multiple
 loci contributing to fitness.
description: Supplementary
 MaterialThe file includes two
 figures and three tables. Supplementary
 Material.pdf
DOI: 10.5061/dryad.r7865
title: Data from: Patients’ experiences with and attitudes towards a diabetes patient web portal

description: Objective: A diabetes patient web portal allows patients to access their
 personal health record and may improve diabetes outcomes; however,
 patients’ adoption is slow. We aimed to get insight into patients’
 experiences with a web portal to understand how the portal is being used,
 how patients perceive the content of the portal and to assess whether
 redesign of the portal might be needed. Materials and Methods: A survey
 among 1500 patients with type 1 and type 2 diabetes with a login to a
 patient portal. Setting: 62 primary care practices and one outpatient
 hospital clinic, using a combined patient portal. We compared patients who
 requested a login but never used it or once (‘early quitters’) with
 patients who used it at least two times (‘persistent users’). Results: 632
 patients (42.1%) returned the questionnaire. Their mean age was 59.7
 years, 63.1% was male and 81.8% had type 2 diabetes. 413 (65.3%) people
 were persistent users and 34.7% early quitters. In the multivariable
 analysis, insulin use (OR2.07; 95%CI[1.18–3.62]), experiencing more
 frequently hyperglycemic episodes (OR1.30;95%CI[1.14–1.49]) and better
 diabetes knowledge (OR1.02, 95%CI[1.01–1.03]) do increase the odds of
 being a persistent user. Persistent users perceived the usefulness of the
 patient portal significantly more favorable. However, they also more
 decisively declared that the patient portal is not helpful in supporting
 life style changes. Early quitters felt significantly more items not
 applicable in their situation compared to persistent users. Both
 persistent users (69.8%) and early quitters (58.8%) would prefer a
 reminder function for scheduled visits. About 60% of both groups wanted
 information about medication and side-effects in their portal.
 Conclusions: The diabetes patient web portal might be improved
 significantly by taking into account the patients’ experiences and
 attitudes. We propose creating separate portals for patients on insulin or
 not.
description: DB_PWP_Users_EnglishQuestionnaire to patients with diabetes mellitus about the use of a patient web portal.
DOI: 10.5061/dryad.qq541
title: Data from: Towards an integrated database on Canadian ocean resources: benefits, current states, and research gaps

description: Oceanic ecosystem services support a range of human benefits, and Canada
 has extensive research networks producing growing data sets. We present a
 first effort to compile, link, and harmonize available information to
 provide new perspectives on the status of Canadian ocean ecosystems and
 corresponding research. The metadata database currently includes 1094
 individual assessments and data sets from government (n = 716),
 nongovernment (n = 320), and academic sources (n = 58), comprising
 research on marine species, natural drivers and resources, human
 activities, ecosystem services, and governance, with data sets spanning
 1979–2012 on average. Overall, research shows a strong prevalence towards
 single-species fishery studies, with an underrepresentation of economic
 and social aspects, and of the Arctic region in general. Nevertheless, the
 number of studies that are multispecies or ecosystem-based have increased
 since the 1960s. We present and discuss two illustrative case studies —
 marine protected area establishment in Canada and herring resource use by
 the Heiltsuk First Nation — highlighting the potential use of
 multidisciplinary data sets drawn from metadata records. Identifying
 knowledge gaps is key to achieving the comprehensive, accessible and
 interdisciplinary data sets and subsequent analyses necessary for new
 sustainability policies that meet both ecological and socioeconomic needs.
description: OceanCanada Marine
 Research MetadataThis dataset is an
 integrated list of marine-related assessments and reports produced for the
 Canadian Arctic, Atlantic, and Pacific Oceans. These include stock
 assessments, fisheries statistics, spatial use data, research frameworks,
 and ecosystem evaluations and projections, compiled from Canadian
 government, intergovernmental, non-government, and academic sources.
 Subjects covered include marine species and ecosystem service production,
 value, and status, and data contained in each assessment may be available
 for use as indicated.Meta
 Dryad.xlsx
DOI: 10.5061/dryad.4fv2v
title: Data from: Influences of species interactions with aggressive ants and habitat filtering on nest colonization and community composition of arboreal twig-nesting ants

description: Ant community assembly is driven by many factors including species
 interactions (e.g. competition, predation, parasitism), habitat filtering
 (e.g. vegetation differences, food and nesting resources), and dispersal.
 Canopy ant communities, including dominant and twig-nesting ants, are
 structured by all these different factors, but we know less about the
 impacts of species interactions and habitat filters acting at the
 colonization or recruitment stage. We examined occupation of artificial
 twig nests placed in shade trees in coffee agroecosystems. We asked
 whether species interactions -- aggression from the dominant canopy ant,
 Azteca sericeasur (Hymenoptera: Formicidae) -- or habitat filtering --
 species of tree where nests were placed, tree size, or surrounding
 vegetation -- influence colonization, species richness, and community
 composition of twig-nesting ants. We found 20 species of ants occupying
 artificial nests. Nest occupation was lower on trees with A. sericeasur,
 but did not differ depending on tree species or surrounding vegetation.
 Yet, there were species-specific differences in occupation depending on A.
 sericeasur presence and tree species. Ant species richness did not vary
 with A. sericeasur presence or tree species. Community composition varied
 with A. sericeasur presence, tree height, and surrounding vegetation. Our
 results suggest that species interactions with dominant ants are important
 determinants of colonization and community composition of twig-nesting
 ants. Habitat filtering by tree species did not affect twig-nesting ants,
 but changes in tree size or coffee management may contribute to
 differences in community composition with important implications for ant
 conservation in agricultural landscapes, as well as biological control of
 coffee pests.
description: Philpott_Serber_DelaMora_EnvEnt_DryadDataThe data file has three tabs - in the Metadata - please see descriptions of the variables in the other two tabs. In GLMData, please find data for the occupancy analysis. In NMDSSppData, please find data for the species analyses.
DOI: 10.5061/dryad.pn8mn
title: Data from: An antibody screen of a Plasmodium vivax antigen library identifies novel merozoite proteins associated with clinical protection

description: Background. Elimination of Plasmodium vivax malaria would be greatly
 facilitated by the development of an effective vaccine. A comprehensive
 and systematic characterization of antibodies to P. vivax antigens in
 exposed populations is useful in guiding rational vaccine design.
 Methodology/Principal Findings. In this study, we investigated antibodies
 to a large library of P. vivax entire ectodomain merozoite proteins in 2
 Asia-Pacific populations, analysing the relationship of antibody levels
 with markers of current and cumulative malaria exposure, and socioeconomic
 and clinical indicators. 29 antigenic targets of natural immunity were
 identified. Of these, 12 highly-immunogenic proteins were strongly
 associated with age and thus cumulative lifetime exposure in Solomon
 Islanders (P&lt;0.001-0.027). A subset of 6 proteins, selected on the
 basis of immunogenicity and expression levels, were used to examine
 antibody levels in plasma samples from a population of young Papua New
 Guinean children with well-characterized individual differences in
 exposure. This analysis identified a strong association between reduced
 risk of clinical disease and antibody levels to P12, P41, and a novel
 hypothetical protein that has not previously been studied, PVX_081550 (IRR
 0.46-0.74; P&lt;0.001-0.041). Conclusion/Significance. These data
 emphasize the benefits of an unbiased screening approach in identifying
 novel vaccine candidate antigens. Functional studies are now required to
 establish whether PVX_081550 is a key component of the naturally-acquired
 protective immune response, a biomarker of immune status, or both.
description: SI_factorialData from comprehensive screen.SI_reactivity_screenData from reactivity screen.
DOI: 10.5061/dryad.v4h76
title: Data from: Sexually coercive male chimpanzees sire more offspring

description: In sexually reproducing animals, male and female reproductive strategies
 often conflict. In some species, males use aggression to overcome female
 choice, but debate persists over the extent to which this strategy is
 successful. Previous studies of male aggression toward females among wild
 chimpanzees have yielded contradictory results about the relationship
 between aggression and mating behavior. Critically, however, copulation
 frequency in primates is not always predictive of reproductive success. We
 analyzed a 17-year sample of behavioral and genetic data from the Kasekela
 chimpanzee (Pan troglodytes schweinfurthii) community in Gombe National
 Park, Tanzania, to test the hypothesis that male aggression toward females
 increases male reproductive success. We examined the effect of male
 aggression toward females during ovarian cycling, including periods when
 the females were sexually receptive (swollen) and periods when they were
 not. We found that, after controlling for confounding factors, male
 aggression during a female’s swollen periods was positively correlated
 with copulation frequency. However, aggression toward swollen females was
 not predictive of paternity. Instead, aggression by high-ranking males
 toward females during their nonswollen periods was positively associated
 with likelihood of paternity. This indicates that long-term patterns of
 intimidation allow high-ranking males to increase their reproductive
 success, supporting the sexual coercion hypothesis. To our knowledge, this
 is the first study to present genetic evidence of sexual coercion as an
 adaptive strategy in a social mammal.
description: Aggression rate by
 swollen state data setContains dyadic
 aggression rates during female swollen and non-swollen periods, used to
 test whether dyadic aggression rates changed between female swollen and
 non-swollen periods.Regression analysis data
 setData set used for
 regression analysis to determine factors predicting both dyadic copulation
 rates and paternity odds.
DOI: 10.5061/dryad.8p1t6
title: Data from: Impact of microRNA expression in human atrial tissue in patients with atrial fibrillation undergoing cardiac surgery

description: Background: Although microRNA (miRNA) regulates initiation and/or
 progression of atrial fibrillation (AF) in canine AF models, the
 underlying mechanism in humans remains unclear. We speculated that certain
 miRNAs in atrial tissue are related to AF, and evaluated the relationship
 of miRNA expression in human atrial tissue in cardiac surgery patients.
 Methods: Right atrial tissues from 29 patients undergoing cardiovascular
 surgery were divided into 3 groups [A: chronic AF or unsuccessful maze,
 n=6; B: successful maze, n=10; C: sinus rhythm (SR) n=13]. miRNA
 expression was determined using high density microarrays and with Reverse
 transcriptase-polymerase chain reaction (RT-PCR). Fibrosis was examined
 using Masson trichrome staining. Results: miRNA microarray analysis showed
 elevated miRNA-21, miRNA-23b, miRNA-199b, and miRNA-208b in AF as compared
 to SR groups. RT-PCR showed elevated miRNA-21 (1.9-fold) and miRNA-208b
 (4.2-fold) in AF as compared to the SR groups. miRNA-21 expression
 increased from Group C to A (A: 2.1-fold, B: 1.8-fold, C: 1.0-fold).
 Fibrosis increased from C to A (A: 43.0±12.9%, B: 21.3±6.1%, C:
 11.9±3.1%). Percent fibrosis and miRNA-21 expression were correlated
 (r=0.508, p&lt;0.05). The plasma levels of miRNA-21 in AF patients was
 significantly decreased as compared to the healthy volunteers
 (p&lt;0.05). Conclusion: The expression of miRNA-21 in human atrial
 tissue was found to be related to atrial fibrosis and might affect AF
 occurrence, indicating its usefulness as a biomarker for cardiac surgery
 management.
description: Nishi Microarray
 dataOriginal microarray data
 (AF patients and Control patients)Nishi Microarray deposited data
 final.xlsx
DOI: 10.5061/dryad.b77tv
title: Data from: Peripatric speciation in an endemic Macaronesian plant after recent divergence from a widespread relative

description: The Macaronesian Scrophularia lowei is hypothesized to have arisen from
 the widespread S. arguta on the basis of several phylogenetic studies of
 the genus, but sampling has been limited. Although these two annual
 species are morphologically distinct, the origin of S. lowei is unclear
 because genetic studies focused on this Macaronesian species are lacking.
 We studied 5 S. lowei and 25 S. arguta populations to determine the
 relationship of both species and to infer the geographical origin of S.
 lowei. The timing of S. lowei divergence and differentiation was inferred
 by dating analysis of the ITS region. A phylogenetic analysis of two
 nuclear (ITS and ETS) and two chloroplast (psbJ–petA and psbA–trnH) DNA
 regions was performed to study the relationship between the two species,
 and genetic differentiation was analysed by AMOVA. Haplotype network
 construction and Bayesian phylogeographic analysis were conducted using
 chloroplast DNA regions and a spatial clustering analysis was carried out
 on a combined dataset of all studied regions. Our results indicate that
 both species constitute a well-supported clade that diverged in the
 Miocene and differentiated in the Late Miocene-Pleistocene. Although S.
 lowei constitutes a well-supported clade according to nDNA, cpDNA revealed
 a close relationship between S. lowei and western Canarian S. arguta, a
 finding supported by the spatial clustering analysis. Both species have
 strong population structure, with most genetic variability explained by
 inter-population differences. Our study therefore supports a recent
 peripatric speciation of S. lowei—a taxon that differs morphologically and
 genetically at the nDNA level from its closest relative, S. arguta, but
 not according to cpDNA, from the closest Macaronesian populations of that
 species. In addition, a recent dispersal of S. arguta to Madeira from
 Canary Islands or Selvagens Islands and a rapid morphological
 differentiation after the colonization to generate S. lowei is the most
 likely hypothesis to explain the origin of the last taxon.
description: Slowei_Data_Peripatric
 speciationZip file containing the
 matrix and data used in the phylogenetic, population genetic and spatial
 clustering analysesSlowei_Data_DRYAD.zip
DOI: 10.5061/dryad.hs37s
title: Data from: Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus)

description: Characterizing movement dynamics and spatial aspects of gene flow within a
 species permits inference on population structuring. As patterns of
 structuring are products of historical and current demographics and gene
 flow, assessment of structure through time can yield an understanding of
 evolutionary dynamics acting on populations that are necessary to inform
 management. Recent dramatic population declines in hibernating bats in
 eastern North America from white-nose syndrome have prompted the need for
 information on movement dynamics for multiple bat species. We
 characterized population genetic structure of the little brown bat, Myotis
 lucifugus, at swarming sites in southeastern Canada using 9 nuclear
 microsatellites and a 292-bp region of the mitochondrial genome. Analyses
 of FST, ΦST, and Bayesian clustering (STRUCTURE) found weak levels of
 genetic structure among swarming sites for the nuclear and mitochondrial
 genome (Global FST = 0.001, P &lt; 0.05, Global ΦST = 0.045, P
 &lt; 0.01, STRUCTURE K = 1) suggesting high contemporary gene flow.
 Hierarchical AMOVA also suggests little structuring at a regional
 (provincial) level. Metrics of nuclear genetic structure were not found to
 differ between males and females suggesting weak asymmetries in gene flow
 between the sexes. However, a greater degree of mitochondrial structuring
 does support male-biased dispersal long term. Demographic analyses were
 consistent with past population growth and suggest a population expansion
 occurred from approximately 1250 to 12,500 BP, following Pleistocene
 deglaciation in the region. Our study suggests high gene flow and thus a
 high degree of connectivity among bats that visit swarming sites whereby
 mainland areas of the region may be best considered as one large gene pool
 for management and conservation.
description: MYLU microsatellite
 dataMicrosatellite loci data
 as coded as an input file for GENEPOPMYLU_microsatellites_GENEPOP.txtMYLU mtDNA Arlequin infileMitchondrial haplotypes of the Hypervariable II area of the control region for Myotis lucifugus. Data are in the form of an Arlequin infile.MYLU_mtDNA_arlequin_infile.txtSTRUCTURE MYLU infileMicrosatellite data for Myotis lucifugus from Eastern Canada coded as an infile for the program STRUCTURE.STRUCTURE_MYLU_infile.txtSTRUCTURE MYLU mainparamsParameters used in the program STRUCTURE for the analysis of the microsatellite data.STRUCTURE_MYLU_mainparams.txt
DOI: 10.5061/dryad.6cm5d7f
title: Data from: Global drivers of tree seedling establishment at alpine treelines in a changing climate

description: Alpine and Arctic treeline expansion depends on establishment of tree
 seedlings beyond the current treeline, which is expected to occur with
 climate warming. However, treelines often fail to respond to higher
 temperatures, and it is therefore likely that other environmental factors
 are important for seedling establishment. We aimed to analyse our current
 understanding of how temperature and a range of other environmental
 drivers affect tree seedling establishment at the alpine and Arctic
 treelines worldwide, and to assess the relative importance of temperature
 compared with other factors and how they interact. We collected 366
 observations from 76 experimental and observational papers for a
 qualitative analysis of the role of a wide range of environmental factors
 on tree seed germination, tree seedling growth, survival and natural
 occurrence. For a subset of these studies, where the experimental design
 allowed, we conducted formal meta-analyses to reveal if there were global
 drivers for different seedling life traits. The analyses showed that a
 wide range of abiotic and biotic factors affected tree seedling
 establishment besides from temperature, including water, snow, nutrients,
 light, and surrounding vegetation. The meta-analyses showed that different
 seedling life stages do not respond similarly to environmental factors.
 For example, temperature had positive effects on growth, while tree
 seedling survival and germination showed mixed responses to warming.
 Further, warming was as often as not the strongest factor controlling tree
 seedling establishment, when compared to with one of five other
 environmental factors. Moreover, warming effects often depended on other
 factors such as moisture or the presence of surrounding vegetation. Our
 results suggests that population dynamics of trees at the alpine and
 Arctic treeline are responsive to environmental changes and show that
 there is a clear need for multi-factorial studies if we want to fully
 understand and predict the interplay between warming and other
 environmental factors and their effect on tree seedling establishment
 across current treelines.
description: tree seedling responses
 to environmental factors at alpine and arctic treelineIncludes data collected
 from studies on tree seedling survival, growth and germination at alpine
 and Arctic treelines. Includes means, standards and sample size for
 control and treatment of various field manipulations as well as various
 moderators. Also includes data from a wider range of papers that can be
 used to evaluate if tree seedlings and seed germination responds
 positively, negatively or neutrally to a range of environmental
 factors.Lett and
 Dorrepaal.xlsx
DOI: 10.5061/dryad.n6g3q
title: Data from: Scale-dependent phenological synchrony between songbirds and their caterpillar food source

description: In seasonal environments, the timing of reproduction has important fitness
 consequences. Our current understanding of the determinants of
 reproductive phenology in natural systems is limited because studies often
 ignore the spatial scale on which animals interact with their environment.
 When animals use a restricted amount of space and the phenology of
 resources is spatially variable, selection may favor sensitivity to
 small-scale environmental variation. Population-level studies of how
 songbirds track the changing phenology of their food source have been
 influential in explaining how populations adjust to changing climates but
 have largely ignored the spatial scale at which phenology varies. We
 explored whether individual great tits (Parus major) synchronize their
 breeding with phenological events in their local environment and
 investigated the spatial scale at which this occurs. We demonstrate marked
 variation in the timing of food availability, at a spatial scale relevant
 to individual birds, and that such local variation predicts the breeding
 phenology of individuals. Using a 45-year data set, we show that measures
 of vegetation phenology at very local scales are the most important
 predictors of timing of breeding within years, suggesting that birds can
 fine-tune their phenology to that of other trophic levels. Knowledge of
 the determinants of variation in reproductive behavior at different
 spatial scales is likely to be critical in understanding how selection
 operates on breeding phenology in natural populations.
description: Great tit breeding
 attempts, oak and caterpillar phenology dataData collected in the
 field (Wytham Woods, Oxford, UK)Hinks et al Am Nat
 data.xlsx