cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.03c0c
title: Data from: Comparison of methodological quality of positive versus negative comparative studies published in Indian medical journals: a systematic review

description: Objectives: Published negative studies should have the same rigour of
 methodological quality as studies with positive findings. However, the
 methodological quality of negative versus positive studies is not known.
 The objective was to assess the reported methodological quality of
 positive versus negative studies published in Indian medical journals.
 Design: A systematic review (SR) was performed of all comparative studies
 published in Indian medical journals with a clinical science focus and
 impact factor &gt;1 between 2011 and 2013. The methodological quality
 of randomised controlled trials (RCTs) was assessed using the Cochrane
 risk of bias tool, and the Newcastle-Ottawa scale for observational
 studies. The results were considered positive if the primary outcome was
 statistically significant and negative otherwise. When the primary outcome
 was not specified, we used data on the first outcome reported in the
 history followed by the results section. Differences in various
 methodological quality domains between positive versus negative studies
 were assessed by Fisher's exact test. Results: Seven journals with
 259 comparative studies were included in this SR. 24% (63/259) were RCTs,
 24% (63/259) cohort studies, and 49% (128/259) case–control studies. 53%
 (137/259) of studies explicitly reported the primary outcome. Five studies
 did not report sufficient data to enable us to determine if results were
 positive or negative. Statistical significance was determined by p value
 in 78.3% (199/254), CI in 2.8% (7/254), both p value and CI in 11.8%
 (30/254), and only descriptive in 6.3% (16/254) of studies. The overall
 methodological quality was poor and no statistically significant
 differences between reporting of methodological quality were detected
 between studies with positive versus negative findings. Conclusions: There
 was no difference in the reported methodological quality of positive
 versus negative studies. However, the uneven reporting of positive versus
 negative studies (72% vs 28%) indicates a publication bias in Indian
 medical journals with an impact factor of &gt;1.
description: positive versus negative
 studies indiaPositive vs negative data
 collection all studies.txt
DOI: 10.5061/dryad.v5p11
title: Data from: Size-dependent ejaculation strategies and reproductive success in the yellow dung fly, Scathophaga stercoraria

description: Theory predicts that sperm competition will favour the production of
 larger ejaculates. However, because the benefits of greater reproductive
 investment are balanced by the costs of spermatogenesis, expenditure
 should depend on male physiology, mating rate and the relationship between
 additional investment and fertilization gains. In the yellow dung fly,
 Scathophagastercoraria, males adopt size-dependent alternative mating
 tactics that are associated with discrete ecological resources (foraging
 and oviposition substrates), although males switch between these
 environments throughout their lives. By copulating on foraging substrate
 (fruit or flowers), males can bypass intense mate competition that occurs
 at oviposition sites (cow dung), but as a consequence, must occupy a
 disfavoured mating role (i.e. face a greater risk that their ejaculate
 will be displaced from storage prior to fertilization). Small males often
 mate on foraging substrate, whereas large males mate in this environment
 only during feeding bouts. Optimal ejaculate expenditure should therefore
 depend on male size and their current mating role. By measuring copula
 duration (i.e. ejaculate expenditure) of natural matings and assigning
 paternity to resulting offspring, we confirmed that copulations on dung
 sire approximately three times as many offspring as those on foraging
 substrate. Furthermore, large males reduced copula duration on fruit, as
 predicted, since this strategy enables greater investment into high-payoff
 matings on dung. Conversely, small males copulated for shorter durations
 on dung than on foraging substrate, perhaps to minimize the risk of being
 displaced from copula by a rival. These patterns of ejaculate expenditure
 translated into greater offspring production for large males on dung and
 for small males on fruit. We discuss the possible proximate factors
 driving these size- and context-dependent patterns of ejaculate allocation
 by yellow dung fly males. Together, our findings shed light on the
 allocation strategies and reproductive consequences of alternative mating
 tactics.
description: Gress.Pitnick.AB.dataRaw copula durations for pomace males (m1.cop.dur) and dung males (m2.cop.dur) were recorded in the field, as was ambient temperature (temp1 = temperature during pomace mating, temp2 = temperature during dung mating); Portion of offspring sired by male 1 and 2 (P1 and P2); m1.progeny and m2.progeny represent the absolute number of offspring sired by male 1 and 2 in the subsequent female clutch; male hind tibia length was measured in the lab (m1.ru and m2.ru raw values, m1.htl.mm and m2.htl.mm are divided by 32 to convert to mm); sperm1 and sperm2 are estimates of the number of sperm transferred per ejaculate using known relationships between male htl and sperm transfer rate (0.0018 (htl^3) - 0.003) * 826.85
DOI: 10.5061/dryad.fh8hs
title: Data from: Characteristics of patients with smear-negative pulmonary tuberculosis (TB) in a region with high TB and HIV prevalence

description: Introduction: Smear-negative pulmonary TB (SNPT) represents 30–60% of all
 pulmonary TB cases. The mortality of these patients can reach 25% in
 populations with high prevalence of HIV infection, and 10–20% of TB
 transmission at the population level are attributable to SNPT cases.
 Methods: We conducted a retrospective study to evaluate epidemiological,
 clinical, and radiological characteristics of patients with SNPT and to
 compare these with patients who were diagnosed as having smear-positive
 pulmonary TB (SPPT). All adult patients (≥ 18 years old) with a positive
 culture for Mycobacterium tuberculosis, and a diagnosis of pulmonary TB
 were included in the study. Results: 198 patients met the inclusion
 criteria (positive culture for Mycobacterium tuberculosis) and were
 included in the analysis. Of these patients, 69 (34.8%) were smear
 positive (SPPT) and 129 (65.2%) were smear negative (SNPT). In univariate
 analysis, cough, dyspnea, and hemoptysis were less frequent in SNPT
 patients in comparison with SPPT patients. In a multivariate model, having
 no cough and no radiographic pattern typical of TB were the
 characteristics independently associated with a diagnosis of SNPT.
 Conclusions: We found a very high prevalence of SNPT among patients with
 TB in a setting with high TB and HIV prevalence. The absence of cough in
 the presence of other symptoms suggestive of TB, and having no
 radiographic pattern typical of TB where independent predictors of SNPT.
description: BD_28.04.2016
DOI: 10.5061/dryad.9719r
title: Data from: Spatiotemporal dynamics and genome-wide association analysis of desiccation tolerance in Drosophila melanogaster

description: Water availability is a major environmental challenge to a variety of
 terrestrial organisms. In insects, desiccation tolerance varies
 predictably over spatial and temporal scales and is an important
 physiological determinant of fitness in natural populations. Here, we
 examine the dynamics of desiccation tolerance in North American
 populations of Drosophila melanogaster using: 1) natural populations
 sampled across latitudes and seasons; 2) experimental evolution in field
 mesocosms over seasonal time; 3) genome-wide associations to identify
 SNPs/genes associated with variation for desiccation tolerance; and 4)
 subsequent analysis of patterns of clinal/seasonal enrichment in existing
 pooled sequencing data of populations sampled in both North America and
 Australia. A cline in desiccation tolerance was observed, for which
 tolerance exhibited a positive association with latitude; tolerance also
 varied predictably with culture temperature, demonstrating a significant
 degree of thermal plasticity. Desiccation tolerance evolved rapidly in
 field mesocosms, although only males showed differences in desiccation
 tolerance between spring and autumn collections from natural populations.
 Water loss rates did not vary significantly among latitudinal or seasonal
 populations; however, changes in metabolic rates during prolonged exposure
 to dry conditions are consistent with increased tolerance in higher
 latitude populations. Genome wide associations in a panel of inbred lines
 identified twenty-five SNPs in twenty-one loci associated with
 sex-averaged desiccation tolerance, but there is no robust signal of
 spatially varying selection on genes associated with desiccation
 tolerance. Together, our results suggest that desiccation tolerance is a
 complex and important fitness component that evolves rapidly and
 predictably in natural populations.
description: Desiccation tolerance in
 natural populations of Drosophila melanogasterData on latitudinal
 variations in desiccation tolerance in six natural populations of
 Drosophila melanogaster from North America. Cultures were grown at three
 different temperatures (18, 25, and 30 °C) and assays were performed on
 3-4 days old adults at 25 °C.Desiccation
 tolerance_Geographical variations-Thermal Plasticity and Diapause
 conditions.xlsxSeasonal variations in
 desiccation tolerance in Drosophila melanogaster.Data on seasonal
 variations in desiccation tolerance in three natural populations of
 Drosophila melanogaster from North America.Desiccation tolerance_Seasonal
 variations.xlsx
DOI: 10.5061/dryad.p1h2b
title: Data from: Vocal plasticity in mallards: multiple signal changes in noise and the evolution of the Lombard effect in birds

description: Signal plasticity is a building block of complex animal communication
 systems. A particular form of signal plasticity is the Lombard effect, in
 which a signaler increases its vocal amplitude in response to an increase
 in the background noise. The Lombard effect is a basic mechanism for
 communication in noise that is well-studied in human speech and which has
 also been reported in other mammals and several bird species. Sometimes,
 but not always, the Lombard effect is accompanied by additional changes in
 signal parameters. However, the evolution of the Lombard effect and other
 related vocal adjustments in birds are still unclear because so far only
 three major avian clades have been studied. We report the first evidence
 for the Lombard effect in an anseriform bird, the mallard (Anas
 platyrhynchos). In association with the Lombard effect, the fifteen
 ducklings in our experiment also increased the peak frequency of their
 calls in noise. However, they did not change the duration of call
 syllables or their call rates as has been found in other bird species. Our
 findings support the notion that all extant birds use the Lombard effect
 to solve the common problem of maintaining communication in noise, i.e. it
 is an ancestral trait shared among all living avian taxa, which means that
 it has evolved more than 70 million years ago within that group. At the
 same time, our data suggest that parameter changes associated with the
 Lombard effect follow more complex patterns, with marked differences
 between taxa, some of which might be related to proximate constraints..
description: Dorado-Correaetal.DATA.ducks.2017Call characteristics of ducklings exposed to three different noise treatments.
DOI: 10.5061/dryad.1q413
title: Data from: Heterogeneous distributional responses to climate warming: evidence from rodents along a subtropical elevational gradient

description: Background: Understanding whether species' elevational range is
 shifting in response to directional changes in climate and whether there
 is a predictable pattern in that response is one of the major challenges
 in ecology. However, so far very little is known about the distributional
 responses of subtropical species to climate change, especially for small
 mammals. In this study, we examined the elevational range shifts at three
 range points (upper and lower range limits and abundance-weighted range
 centre) of rodents over a 30-year period (1986 to 2014-2015), in a
 subtropical forest of Southwest China. We also examined the influences of
 four ecological traits (body mass, habitat breadth, diet and daily
 activity pattern) on the upslope shifts in species'
 abundance-weighted range centres. Results: Despite the warming trend
 between 1986 and 2015, the eleven rodent species in analysis displayed
 heterogeneous dynamics at each of the three range points. Species which
 have larger body sizes and narrower habitat breadths, show both diurnal
 and nocturnal activities and more specialized dietary requirements, are
 more likely to exhibit upslope shifts in abundance-weighted range centres.
 Conclusions: Species' distributional responses can be heterogeneous
 even though there are directional changes in climate. Our study indicates
 that climate-induced alleviation of competition and lag in response may
 potentially drive species' range shift, which may not conform to the
 expectation from climate change. Difference in traits can lead to
 different range dynamics. Our study also illustrates the merit of
 multi-faceted assessment in studying elevational range shifts.
description: BMC_wen_datadryad
DOI: 10.5061/dryad.hk2gc
title: Data from: Scale-dependent role of demography and dispersal on the distribution of populations in heterogeneous landscapes

description: Both dispersal and local demographic processes determine a
 population's distribution among habitats of varying quality, yet most
 theory, experiments, and field studies have focused on the former. We use
 a generic model to show how both processes contribute to a
 population's distribution, and how the relative importance of each
 mechanism depends on scale. In contrast to studies only considering
 habitat-dependent dispersal, we show that predictions of ideal free
 distribution (IFD) theory are relevant even at landscape scales, where the
 assumptions of IFD theory are violated. This is because scales that
 inhibit one process, promote the other's ability to drive populations
 to the IFD. Furthermore, because multiple processes can generate IFDs, the
 pattern alone does not specify a causal mechanism. This is important
 because populations with IFDs generated by dispersal or demography respond
 much differently to shifts in resource distributions.
description: Model output of Ideal
 Free Distribution simulationsThe data file contains
 the model output of the Combined Model. Each row represents one
 simulation. The first four columns are model parameters that were varied
 in the simulations (see table A1 in the Appendix for parameter
 descriptions), and the fifth column is the recorded IFD slope of that
 simulation. All simulations were run in NetLogo.IFD dryad data
 Final.csv
DOI: 10.5061/dryad.r7j2k42
title: Data from: The development of integration in marsupial and placental limbs

description: The morphological interdependence of traits, or their integration, is
 commonly thought to influence their evolution. As such, study of
 morphological integration and the factors responsible for its generation
 form an important branch of the field of morphological evolution. However,
 most research to date on post-cranial morphological integration has
 focused on adult patterns of integration. This study investigates patterns
 of correlation (i.e., morphological integration) among skeletal elements
 of the fore- and hind limbs of developing marsupial and placental mammals.
 The goals of this study are to establish how patterns of limb integration
 vary over development in marsupials and placentals, and identify factors
 that are likely responsible for their generation. Our results indicate
 that although the overall pattern of correlation among limb elements is
 consistent with adult integration throughout mammalian development,
 correlations vary at the level of the individual element and stage. As a
 result, the relative integration among fore- and hind limb elements varies
 dynamically between stages during development in both marsupial and
 placental mammals. Therefore, adult integration studies of the limbs may
 not be indicative of developmental integration. Results are also
 consistent with integration during early limb development being more
 heavily influenced by genetic and developmental factors, and later by
 function. Additionally, results are generally consistent with a constraint
 on marsupial forelimb evolution caused by the functional requirements of
 the crawl to the teat that operates by limiting morphological variation
 before and at the time of birth, and not after.
description: Length_dataLength calculations from landmarks for all specimens.mckenna.csv
DOI: 10.5061/dryad.5q3b3
title: Data from: Genetic connectivity for two bear species at wildlife crossing structures in Banff National Park

description: Roads can fragment and isolate wildlife populations, which will eventually
 decrease genetic diversity within populations. Wildlife crossing
 structures may counteract these impacts, but most crossings are relatively
 new, and there is little evidence that they facilitate gene flow. We
 conducted a three-year research project in Banff National Park, Alberta,
 to evaluate the effectiveness of wildlife crossings to provide genetic
 connectivity. Our main objective was to determine how the Trans-Canada
 Highway and crossing structures along it affect gene flow in grizzly
 (Ursus arctos) and black bears (Ursus americanus). We compared genetic
 data generated from wildlife crossings with data collected from greater
 bear populations. We detected a genetic discontinuity at the highway in
 grizzly bears but not in black bears. We assigned grizzly bears that used
 crossings to populations north and south of the highway, providing
 evidence of bidirectional gene flow and genetic admixture. Parentage tests
 showed that 47% of black bears and 27% of grizzly bears that used
 crossings successfully bred, including multiple males and females of both
 species. Differentiating between dispersal and gene flow is difficult, but
 we documented gene flow by showing migration, reproduction and genetic
 admixture. We conclude that wildlife crossings allow sufficient gene flow
 to prevent genetic isolation.
description: Banff Bear DNA
 DataMicrosatellite data for
 105 black bears and 134 grizzly bears detected in Banff National Park.
 Excel file contains 3 worksheets (description, black bear data, grizzly
 bear data)
DOI: 10.5061/dryad.82gj124
title: Data from: Temperature dependent effects of cutaneous bacteria on a frog's tolerance of fungal infection

description: Defense against pathogens is one of many benefits that bacteria provide to
 animal hosts. A clearer understanding of how changes in the environment
 affect the interactions between animals and their microbial benefactors is
 needed in order to predict the impact and dynamics of emerging animal
 diseases. Due to its dramatic effects on the physiology of animals and
 their pathogens, temperature may be a key variable modulating the level of
 protection that beneficial bacteria provide to their animal hosts. Here we
 investigate how temperature and the makeup of the skin microbial community
 impact the susceptibility of amphibian hosts to infection by
 Batrachochytrium dendrobatidis, one of two fungal pathogens known to cause
 the disease chytridiomycosis. To do this, we manipulated the skin
 bacterial communities of susceptible hosts, northern cricket frogs (Acris
 crepitans), prior to exposing these animals to Batrachochytrium
 dendrobatidis under two different ecologically relevant temperatures. Our
 manipulations included one treatment where antibiotics were used to reduce
 the skin bacterial community, one where the bacterial community was
 augmented with the antifungal bacterium, Stenotrophomonas maltophilia, and
 one in which the frog's skin bacterial community was left intact. We
 predicted that frogs with reduced skin bacterial communities would be more
 susceptible (i.e., less resistant to and/or tolerant of Bd infection), and
 frogs with skin bacterial communities augmented with the known antifungal
 bacterium would be less susceptible to Bd infection and chytridiomycosis.
 However, we also predicted that this interaction would be
 temperature-dependent. We found a strong effect of temperature but not of
 skin microbial treatment on the probability and intensity of infection
 in Bd-exposed frogs. Whether temperature impacted survival,
 however, differed among our skin microbial treatment groups, with animals
 having more S. maltophilia on their skin surviving longer at 14 but not at
 26 °C. Our results suggest that temperature was the predominant factor
 influencing Bd's ability to colonize the host (i.e., resistance) but
 that the composition of the cutaneous bacterial community was important in
 modulating the host's ability to survive (i.e., tolerate) a heavy Bd
 infection.
description: Robak_and_Richards_Zawacki_2018_data This file contains data on survival, body condition, <em>Batrachochytrium</em> <em>dendrobatidis</em> load, and <em>Stenotrophomonas</em> <em>maltophilia</em> load on <em>Acris</em> <em>crepitans</em> frogs involved in the experiment described in Robak & Richards-Zawacki (2018).
DOI: 10.5061/dryad.42d2r
title: Data from: Pollination benefits are maximized at intermediate nutrient levels

description: Yield production in flowering crops depends on both nutrient resource
 availability and pollination but their relative roles and potential
 interactions are poorly understood. We measured pollination benefits to
 yield in sunflower, combining a gradient in insect pollination (0, 25, 50,
 100%) with a continuous gradient in nitrogen (N) fertilization (from 0 to
 150 kg N ha-1) in an experiment under realistic soil field conditions. We
 found that pollination benefits to yield were maximized at intermediate
 levels of N availability, bolstering yield by a c. 25% compared to
 complete pollinator exclusion. Interestingly, we found little decrease in
 yield when insect visits were reduced by 50% indicating that the
 incremental contribution of pollination by insects to yield is greater
 when the baseline pollination service provision is very low. Our findings
 shed light on the processes that drive crop production, providing evidence
 for non-linear relationships between pollination and resource
 availability. Our results support ecological intensification as a
 promising strategy for sustainable management of agroecosystems. In
 particular, we found optimal level of pollination to potentially
 compensate for lower N applications.
description: Tamburini et al.
 DATASunflower yield, yield
 parameters and visitation rateTamburini et al.
 Flowering durationFlowering
 duration