cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1q8h3
title: Data from: Mobile phone reminders and peer counseling improve adherence and treatment outcomes of patients on ART in Malaysia: a randomized clinical trial

description: Background: Adherence to treatment remains the cornerstone of long term
 viral suppression and successful treatment outcomes among patients
 receiving Antiretroviral Therapy (ART). Objective(s): Evaluate the
 effectiveness of mobile phone reminders and peer counseling in improving
 adherence and treatment outcomes among HIV positive patients on ART in
 Malaysia. Methods: A single-blind, parallel group RCT conducted in
 Hospital Sungai Buloh, Malaysia in which 242 adult Malaysian patients were
 randomized to intervention or control groups. Intervention consisted of a
 reminder module delivered through SMS and telephone call reminders by
 trained research assistants for 24 consecutive weeks (starting from date
 of ART initiation), in addition to adherence counseling at every clinic
 visit. The length of intended follow up for each patient was 6 months.
 Data on adherence behavior of patients was collected using specialized,
 pre-validated Adult AIDS Clinical Trial Group (AACTG) adherence
 questionnaires. Data on weight, clinical symptoms, CD4 count and viral
 load tests were also collected. Data was analyzed using SPSS version 22
 and R software. Repeated measures ANOVA, Friedman’s ANOVA and Multivariate
 regression models were used to evaluate efficacy of the intervention.
 Results: The response rate after 6 months follow up was 93%. There were no
 significant differences at baseline in gender, employment status, income
 distribution and residential location of respondents between the
 intervention and control group. After 6 months follow up, the mean
 adherence was significantly higher in the intervention group (95.7; 95%
 CI: 94.39–96.97) as compared to the control group (87.5; 95% CI:
 86.14–88.81). The proportion of respondents who had Good (&gt;95%)
 adherence was significantly higher in the intervention group (92.2%)
 compared to the control group (54.6%). A significantly lower frequency in
 missed appointments (14.0% vs 35.5%) (p = 0.001), lower viral load (p =
 0.001), higher rise in CD4 count (p = 0.017), lower incidence of
 tuberculosis (p = 0.001) and OIs (p = 0.001) at 6 months follow up, was
 observed among patients in the intervention group. Conclusion: Mobile
 phone reminders (SMS and telephone call reminders) and peer counseling are
 effective in improving adherence and treatment outcomes among HIV positive
 patients on ART in Malaysia. These findings may be of potential benefit
 for collaborative adherence planning between patients and health care
 providers at ART commencement.
description: Adherence research in
 MalaysiaAdherence research in
 MalaysiaAdherence
 research_.sav
DOI: 10.5061/dryad.56b32
title: Data from: Diet complexity in early life affects survival in released pheasants by altering foraging efficiency, food choice, handling skills and gut morphology

description: 1. Behavioural and physiological deficiencies are major reasons why
 reintroduction programmes suffer from high mortality when captive animals
 are used. Mitigation of these deficiencies is essential for successful
 reintroduction programmes. 2. Our study manipulated early developmental
 diet to better replicate foraging behaviour in the wild. Over 2 years, we
 hand-reared 1800 pheasants (Phasianus colchicus), from 1 day old, for 7
 weeks under different dietary conditions. In year one, 900 pheasants were
 divided into three groups and reared with (i) commercial chick crumb, (ii)
 crumb plus 1% live mealworm or (iii) crumb plus 5% mixed seed and fruit.
 In year two, a further 900 pheasants were divided into two groups and
 reared with (i) commercial chick crumb or (ii) crumb plus a combination of
 1% mealworm and 5% mixed seed and fruit. In both years, the commercial
 chick crumb acted as a control treatment, whilst those with live prey and
 mixed seeds and fruits mimicking a more naturalistic diet. After 7 weeks
 reared on these diets, pheasants were released into the wild. 3.
 Postrelease survival was improved with exposure to more naturalistic diets
 prior to release. We identified four mechanisms to explain this. Pheasants
 reared with more naturalistic diets (i) foraged for less time and had a
 higher likelihood of performing vigilance behaviours, (ii) were quicker at
 handling live prey items, (iii) were less reliant on supplementary feed
 which could be withdrawn and (iv) developed different gut morphologies. 4.
 These mechanisms allowed the pheasants to (i) reduce the risk of predation
 by reducing exposure time whilst foraging and allowing more time to be
 vigilant; (ii) be better at handling and discriminating natural food items
 and not be solely reliant on supplementary feed; and (iii) have a better
 gut system to cope with the natural forage after the cessation of
 supplementary feeding in the spring. 5. Learning food discrimination,
 preference and handling skills by the provision of a more naturalistic
 diet is essential prior to the release of pheasants in a reintroduction
 programme. Subsequent diet, foraging behaviour, gut morphology and
 digestive capabilities all work together as one nutritional complex.
 Simple manipulations during early development can influence these
 characteristics to better prepare an individual for survival upon release.
description: Whiteside et al Diet
 DataEach sheet refers to a
 separate analysis performed in the associated paper. Analysis is
 identified in the worksheet tab name.
DOI: 10.5061/dryad.753d06g
title: Data from: Hibernation constrains brain size evolution in mammals

description: The expensive brain hypothesis predicts that the lowest stable level of
 steady energy input acts as a strong constraint on a species’ brain size,
 and thus that periodic troughs in net energy intake should select for
 reduced brain size relative to body mass. Here, we test this prediction
 for the extreme case of hibernation. Hibernators drastically reduce food
 intake for up to several months, and are therefore expected to have
 smaller relative brain sizes than non‐hibernating species. Using a
 comparative phylogenetic approach on brain size estimates of 1104
 mammalian species, and controlling for possible confounding variables, we
 indeed found that the presence of hibernation in mammals is correlated
 with decreased relative brain size. This result adds to recent comparative
 work across mammals and amphibians supporting the idea that environmental
 seasonality (where in extremis hibernation is necessary for survival)
 imposes an energetic challenge, and thus acts as an evolutionary
 constraint on relative brain size.
description: Supplementary material
 to the manuscript: “Hibernation constrains brain size evolution in
 mammals” Sandra A. Heldstab, Karin Isler, and Carel P. van
 SchaikList of species and data
 used for this study (1104 mammalian species) including references for
 brain mass, body mass, hibernation, diurnality, substrate use, diet and
 mid-latitude of geographical distribution dataSupplementary
 material.xlsx
DOI: 10.5061/dryad.fd5q0p68
title: Data from: On the ancestral recruitment of metalloproteinases into the venom of snakes

description: Tracing the evolutionary history of proteins can reveal insights into gene
 alterations responsible for changes in structure and function. Here, the
 origin of snake venom metalloproteinases was rigorously reassessed using
 phylogenetics and the reconstruction of ancestral sequences. Basal SVMPs
 are most closely related to ADAM 7, 28 and decysin 1 proteins.
 Reconstructing the evolutionary history of these proteins and their
 hypothetical ancestors elucidates progressive alterations in the amino
 acid composition and structural characteristics of ADAMs/SVMPs through
 evolutionary time.
description: Casewell_metalloproteinase_alignment.fasAn amino acid sequence alignment of ADAM and ADAMTS proteins isolated from the genomes of Homo sapiens, Danio rerio and Anolis carolinensis with basal snake venom metalloproteinases isolated from Elapidae and Atractaspidinae
DOI: 10.5061/dryad.r9693
title: Data from: Genetic differentiation among isolates of Teredinibacter turnerae, a widely occurring intracellular endosymbiont of shipworms

description: Teredinibacter turnerae is a cultivable intracellular endosymbiont of
 xylotrophic (wood-feeding) bivalves of the Family Teredinidae (shipworms).
 Although T. turnerae has been isolated from many shipworm taxa collected
 in many locations, no systematic effort has been made to explore genetic
 diversity within this symbiont species across the taxonomic and
 geographical range of its hosts. The mode of symbiont transmission is
 unknown. Here, we examine sequence diversity in fragments of six genes
 (16S rRNA, gyrB, sseA, recA, rpoB and celAB) among 25 isolates of T.
 turnerae cultured from 13 shipworm species collected in 15 locations in
 the Atlantic, Pacific and Indian Oceans. While 16S rRNA sequences are
 nearly invariant between all examined isolates (maximum pairwise
 difference &lt;0.26%), variation between examined protein-coding loci
 is greater (mean pairwise difference 2.2–5.9%). Phylogenetic analyses
 based on each protein-coding locus differentiate the 25 isolates into two
 distinct and well-supported clades. With five exceptions, clade
 assignments for each isolate were supported by analysis of alleles of each
 of the five protein-coding loci. These exceptions include (i) putative
 recombinant alleles of the celAB and gyrB loci in two isolates
 (PMS-535T.S.1b.3 and T8510), suggesting homologous recombination between
 members of the two clades; and (ii) evidence for a putative lateral gene
 transfer event affecting a second locus (recA) in three isolates (T8412,
 T8503 and T8513). These results demonstrate that T. turnerae isolates do
 not represent a homogeneous global population. Instead, they indicate the
 emergence of two lineages that, although distinct, likely experience some
 level of genetic exchange with each other and with other bacterial
 species.
description: Figure 1 Bayesian
 treesZIP file containing
 Figure 1 Bayesian trees and alignments in Nexus format.Figure S2 Bayesian
 treesZIP file containing
 Figure S2 trees and alignments in Nexus format.Figure S3 ML
 treesZIP file containing
 Figure S3 Maximum Likelihood trees and alignments in Nexus
 format.Figure S4_recA1 A2
 Bayesian treeFigure S4 tree and
 alignment in Nexus format.recA of Teredinibacter
 turnerae strains T8412, T8503, and T8513Sequence alignment of
 recA loci of Teredinibacter turnerae strains T8412, T8503, and
 T8513
DOI: 10.5061/dryad.v74t1
title: Data from: The financial needs vs. the realities of in situ conservation: an analysis of federal funding for protected areas in Brazil’s Caatinga

description: In situ conservation is an effective strategy to protect biodiversity, and
 Brazil has one of the largest protected area (PA) systems in the world.
 However, the distribution of Brazilian PAs is uneven and the Caatinga
 drylands are poorly protected. As financial resources are essential for
 effectively managing PAs, we analyzed the Brazilian Government's
 budget allocated to 20 federal PAs in the Caatinga between 2008 and 2014,
 which ranged from 231,575 USD in 2008 to 13.5 Mi USD in 2011. Neither
 expenses, nor the availability of funds, were homogeneous among PAs or
 throughout the years. Land acquisition in a single PA consumed ~75% of the
 budget, and the two smallest PAs received proportionally the most money.
 Excluding land acquisition, the 20 PAs received 0.50 USD/ha/year. Funds
 were allocated not to biodiversity conservation per se but mainly to
 securing offices, cars, and equipment. From 2012 onwards, the PA budget
 was reduced. Even including salaries, the budget allocated for these PAs
 is ~13 times lower than what the Ministry of the Environment declared
 necessary for the basic operation of protected areas in Brazil, 1.5 times
 lower than values spent worldwide, up to 5 times lower than spent in Latin
 American and African parks, and up to 72 times lower than spent in the
 European Union, exposing one cause of the precarious situation of the
 Caatinga PAs.
description: TableS1Budget expenses for 20 federal protected areas in Brazil´s Caatinga drylands, between 2008 and 2014. PA_Code = protected area´s administrative code used by the Brazilian Government. PA_Name = name of the protected area. PA_Category = category of the protected areas, APA: Área de Proteção Ambiental (Protected Area); ESEC: Estação Ecológica (Ecological Station); FLONA: Floresta Nacional (National Forest); PARNA: Parque Nacional (National Park); MN: Monumento Natural (Natural Monument); REBIO: Reserva Biológica (Biological Reserve). PA_Type = type of the protected area, sustainable use (uso sustentável) or strict protection (proteção integral). PA_Area = area in hectares of the protected area. Expenses_(Portuguese) = expenses as described in the original, in Portuguese. Expenses_(Translated) = expenses translated to English. Expense_Category = CA means “Capital Assets” and CU means "costs". Value_2008 to Value_2014 = values spent per year (2008 to 2014). All values in Brazilian Reais (BRL or R$). Comma used to separate 10,000 and points to cents.
DOI: 10.5061/dryad.jr4dc
title: Data from: A trade-off between oxidative stress resistance and DNA repair plays a role in the evolution of elevated mutation rates in bacteria

description: The dominant paradigm for the evolution of mutator alleles in bacterial
 populations is that they spread by indirect selection for linked
 beneficial mutations when bacteria are poorly adapted. In this paper, we
 challenge the ubiquity of this paradigm by demonstrating that a clinically
 important stressor, hydrogen peroxide, generates direct selection for an
 elevated mutation rate in the pathogenic bacterium Pseudomonas aeruginosa
 as a consequence of a trade-off between the fidelity of DNA repair and
 hydrogen peroxide resistance. We demonstrate that the biochemical
 mechanism underlying this trade-off in the case of mutS is the elevated
 secretion of catalase by the mutator strain. Our results provide the first
 experimental evidence that direct selection can favour mutator alleles in
 bacterial populations, and pave the way for future studies to understand
 how mutation and DNA repair are linked to stress responses and how this
 impacts the evolution of bacterial mutation rates.
description: Catalase
 activityAmplex® Red Catalase
 Assay fluorescence measures of catalase activity of supernatant of P.
 aeruginosa mutators and WT.Fitness mutators vs
 WTCompetition experiments
 between P. aeruginosa PAO1 wild-type and mutators (GmR) in the presence
 and absence of hydrogen peroxide.H2O2 effect on cell
 densityViable cells of P.
 aeruginosa mutators and WT using BacTiter-Glo™ Reagent (Promega) after
 treatment with H2O2 relative to viable cells in
 H2O-treatedMutation rate with
 hydrogen peroxideMutation rate of P.
 aeruginosa WT and mutators before treatment and after treatment with
 hydrogen peroxide washing and non washing the cells calculated with the
 MSS maximum likelihood method.Mutation rate with hydr
 perox.ods
DOI: 10.5061/dryad.fk376
title: Data from: Germination performance of native and non-native Ulmus pumila populations

description: Germination is a crucial step for invasive plants to extend their
 distribution under different environmental conditions in a new range.
 Therefore, information on germination characteristics of invasive plant
 species provides invaluable knowledge about the factors which might
 contribute to the invasion success. Moreover, intra-specific comparisons
 under controlled conditions will show if different responses between
 non-native and native populations are caused by evolutionary changes or by
 phenotypic plasticity towards different environmental influences. This
 paper focuses on the germination of native and non-native Ulmus pumila
 populations. We expected that non-native populations would be
 characterized by their higher final germination percentage and enhanced
 germination rate, which might indicate an influence due to corresponding
 climatic conditions. Germination experiments with a moderate and a warm
 temperature treatment did not reveal significant differences in final
 germination percentage. However, seeds from the North American non-native
 range germinated significantly faster than native seeds (p &lt;
 0.001). Additionally, mean time to germination in both ranges was
 significantly negatively correlated with annual precipitation (p = 0.022).
 At the same time, this relationship is stronger in the native range
 whereas mean time to germination in non-native populations seems to be
 less influenced by climatic conditions. Different germination responses of
 the North American populations could be caused by a fast evolutionary
 change mediating a higher tolerance to current climatic conditions in the
 non-native range. However, our findings could also be caused by artificial
 selection during the introduction process and extensive planting of Ulmus
 pumila in its non-native range. Nevertheless, we assume that the faster
 germination rate of non-native populations is one potential explanation
 for the invasion success of Ulmus pumila in its new range since it might
 provide a competitive advantage during colonization of new sites.
description: Hirsch et al. -
 germination dataGermination records used
 for the survival analysis. For each seed the corresponding origin
 (population and range), the day of germination (germination_day), the
 status in regards to the right censoring (1 = germinated; 0 =
 non-germinated but viable at the end of the experiment) and the
 corresponding temperature condition during the experiment
 (temperature_treatment) are provided.germination paper
 data2.xlsx
DOI: 10.5061/dryad.qt2kt
title: Data from: Mammal-induced trophic cascades in invertebrate food webs are modulated by grazing intensity in subalpine grassland

description: 1. Even though mammalian herbivores can exert strong indirect effects on
 other animals by altering the vegetation, the study of trophic cascades
 retains a focus on apex predators and their top-down forces. Bottom-up
 trophic interaction chains induced by mammalian herbivores, particularly
 in invertebrate food webs, remain largely unexplored. 2. We tested whether
 effects of mammalian herbivores on the vegetation ricochet back up several
 trophic levels of the invertebrate food web. We further tested two
 alternative hypotheses: the strength of herbivore-induced indirect
 interactions either increases with plant productivity because of a
 concurrent higher grazing intensity, or it decreases because of a higher
 plant tolerance to grazing. 3. We progressively excluded large, medium,
 and small herbivorous mammals from replicated plots of 6 m2 in productive,
 intensively grazed short-grass vegetation and less productive, less
 intensively grazed tall-grass vegetation of subalpine grasslands. We
 measured vegetation quantity, quality, structure, and composition, and
 determined the abundance of invertebrate herbivores, detritivores,
 omnivores, and predators. We used Structural Equation Modelling to test
 vegetation-mediated cascading effects of the different mammalian
 herbivores across different trophic groups of invertebrates. 4. In the
 short-grass vegetation, mammals caused changes in vegetation quantity and
 thickness. These changes directly affected detritivorous and predatory
 invertebrate abundance, yet indirectly affected predatory and omnivorous
 invertebrates through a bottom-up trophic cascade via changes in
 herbivorous invertebrate abundance. In the tall-grass vegetation,
 mammal-induced changes in vegetation quality and composition affected
 detritivorous invertebrates and in turn omnivorous invertebrates, but
 these cascading effects were weaker than those in the short-grass
 vegetation. Smaller mammals were at least as important as large mammals in
 structuring the invertebrate food web. 5. Our results demonstrate that
 differently sized mammalian herbivores can trigger trophic cascades in the
 local invertebrate food web. Our findings further support the hypothesis
 that herbivore-induced indirect interactions are stronger in more
 productive systems because of higher foraging intensity, as opposed to the
 hypothesis that a higher grazing tolerance of plants should dampen
 herbivore-induced indirect interactions in productive systems.
description: Data_JAE-2016-00436.R4
DOI: 10.5061/dryad.f51bb
title: Data from: The carnivorous plant described as Sarracenia alata contains two cryptic species

description: Modern methods for species delimitation provide biologists with the power
 to detect cryptic diversity in nearly any system. To illustrate the
 application of such methods, we collected data (21 sequence loci) from a
 carnivorous plant in southeastern North America and applied several
 recently developed methods (Gaussian clustering, Structurama, BPP,
 spedeSTEM). The pale pitcher plant Sarracenia alata inhabits the
 southeastern USA along the northern coast of the Gulf of Mexico.
 Sarracenia alata populations are separated by the Mississippi River and
 Atchafalaya Basin, a known biogeographical barrier in this region, but the
 cohesiveness of S. alata as currently classified has not been tested
 rigorously. Multiple analytical approaches (including allelic clustering
 and species trees methods) suggest that S. alata comprises two cryptic
 lineages that correspond to the eastern and western portions of the
 plant's distribution. That such clear genetic evidence for cryptic
 diversity exists within S. alata and is in conflict with other sources of
 data (e.g. morphology, environmental differentiation) illustrates a
 conundrum faced by those who investigate species boundaries: genetic data
 are often the first type of data to accumulate evidence of
 differentiation, but most existing taxonomic treatments are based on
 nongenetic data. Our results suggest that S. alata as currently described
 contains two cryptic species, and we recommend the elevation of the
 western populations to species status.
description: Dryad-SalataBLJSZip file containing input files from Structurama, Gaussian clustering, BPP, and spedeSTEM. Also contains nexus files for each of 21 loci.
DOI: 10.5061/dryad.k5b1j
title: Data from: Cultural transmission of tool use combined with habitat specializations leads to fine-scale genetic structure in bottlenose dolphins

description: [No abstract entered]
description: Kopps et al 2014
 genotypes