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opencc-zeroJul 2023View details →

Data from: Shifts in mutation bias promote mutators by altering the distribution of fitness effects

Recent experimental evidence demonstrates that shifts in mutational biases, for example increases in transversion frequency, can change the distribution of fitness effects of mutations (DFE). In particular, reducing or reversing a prevailing bias can increase the probability that a de novo mutation is beneficial. It has also been shown that mutator bacteria are more likely to emerge if the beneficial mutations they generate have a larger effect-size than observed in the wildtype. Here, we connect these two results, demonstrating that mutator strains that reduce or reverse a prevailing bias have a positively-shifted DFE, which in turn can dramatically increase their emergence probability. Since changes in mutation rate and bias are often coupled through the gain and loss of DNA repair enzymes, our results predict that the invasion of mutator strains will be facilitated by shifts in mutation bias that offer improved access to previously under-sampled beneficial mutations.

opencc-by-4.0Jul 2023View details →

MMT/Binospec Spectroscopic Survey of Two z~0.8 Galaxy Clusters: Galaxy Spectra Figures and FITS Data

This dataset includes MMT/Binospec spectra of all 371 galaxies observed in 2019 and 2022, which were already discussed in the research paper (J. Di et al.) where you just got this dataset link. To quickly look at our spectra, we reduced our spectra in the JPG format. We also attached the raw FITS format 1D and 2D spectra of two years' observations.

opencc-zeroJul 2023View details →

Is my model fit for purpose? Validating a population model for predicting freshwater fish responses to flow management

Models based on ecological processes ("process-explicit models") are often used to predict ecosystem responses to environmental changes or management scenarios. However, models are imperfect and need to be validated, ideally by testing their assumptions and outputs against independent empirical data sets. Examples of validation of process-explicit models are rare. Recently, stochastic population models have been developed to predict the likely responses (over 10-120 years) of a riverine fish (golden perch, Macquaria ambigua) to flow management in the Murray-Darling Basin (MDB) in eastern Australia, one of the world's most regulated river basins. Declines of golden perch (and other species) are a direct consequence of altered hydrology, and managers require information to predict how fish will respond to possible future hydrological conditions to guide the substantial investments in flow management. Here, we use two independent field data sets to validate our population model. We compared model predictions to observed trends to ask: (1) how do predicted population sizes and growth rates compare to observed data? (2) does the correlation between predicted and observed population sizes and growth rates vary among populations? (3) does the correlation between predicted and observed population sizes and growth rates vary across observed hydrological conditions? and (4) how do modelled and observed fish movement rates compare? We found reasonable correlations between fish population sizes and growth rates as predicted by the model and observed in independent data sets for several populations (Aim 1) but the strength of these correlations varied among populations (Aim 2) and hydrological conditions (Aim 3). Predicted and observed fish movement rates were strongly correlated (Aim 4). Population models are frequently used in conservation decision-making but are rarely validated. We demonstrate that: (1) validation can identify model strengths and weaknesses; (2) observed data sets often have inherent limitations that can preclude robust validations; (3) validation is likely be more common if appropriate observed data sets are available; and (4) validation should consider the purpose of modelling. Wider consideration of these messages would contribute to more critical examinations of models so they can be most appropriately used in conservation decision-making.

opencc-by-4.0Jul 2023View details →

TOI-332: chains from the MCMC fit

The 5 chains from the MCMC analysis of the TOI-332 system (paper in review). Chain files are 50,000 steps (rows), with no burn-in removed (1,000 steps are removed in our analysis). Parameters are given in the column headers, and described below: <ul> <li>The lightcurve means (mean_tess28, mean_tess12, mean_lco1, mean_lco2, mean_lco3, mean_lco4, mean_lco5,  mean_lco6)</li> <li>Intervals for the uniform priors (u_star_quadlimbdark____0, u_star_quadlimbdark____1, m_star_interval__ ,  r_star_interval__, logr_interval__, b_impact__, period_interval__, t0_interval__, logK_interval__, offset_harps_interval__)</li> <li>And posterior values: <ul> <li>Log of the jitter on the HARPS data (where jitter is in m/s): log_jitter_harps    </li> <li>The limb darkening: u_star__0, u_star__1    </li> <li>Stellar mass (Msun): m_star</li> <li>Stellar radius (Rsun): r_star</li> <li>Log of the planet radius (where radius is in Rsun): logr    </li> <li>Radius of the planet (Rsun): r_pl</li> <li>Planet-to-star radius ratio: ror</li> <li>Impact parameter: b</li> <li>Planet period (days): period</li> <li>Reference time of midtransit (BJD-2457000): t0</li> <li>Log of the RV semi-amplitude (where semi-amplitude is in m/s): logK</li> <li>Offset on the HARPS data (m/s): offset_harps</li> </ul> </li> </ul>

opencc-by-2.0Aug 2023View details →

Fitness and cold tolerance of Spodoptera frugiperda fed on corn and two winter crops (Original data)

草地贪夜蛾(FAW)草地贪夜蛾是一种主要的迁徙和多噬性害虫。FAW的越冬、迁徙和定植性状与植被和寄主适应性密切相关。在这项研究中,我们调查了春夏作物(玉米)和两种冬季作物(卷心菜,芸苔属和油菜,油菜,油菜)的产卵偏好,喂养偏好,适应性和耐寒性。结果表明,FAW可以通过喂食卷心菜和油菜来完成其生命周期,尽管健康状况不如玉米。以卷心菜为食的FAW存活率、雌蛹质量和宿主适宜性指数高于油菜,幼虫更喜欢以油菜叶为食,雌性更喜欢在油菜植株上产卵。此外,与玉米和油菜相比,以卷心菜为食的FAW幼虫从寒晕中恢复的时间最短,表明以卷心菜为食可提高FAW幼虫的耐寒性。因此,卷心菜可能是FAW的理想宿主,需要在冬季生存和繁殖。研究结果提高了我们对FAW寄主选择和适应的理解,为预测FAW冬季繁殖区奠定了基础。

opencc-zeroAug 2023View details →

Fitness, risk taking, and spatial behavior covary with boldness in experimental vole populations

Individuals of a population may vary along a pace-of-life syndrome from highly fecund, short-lived, bold, dispersive 'fast' types at one end of the spectrum to less fecund, long-lived, shy, plastic 'slow' types at the other end. Risk-taking behaviour might mediate the underlying life-history trade-off but empirical evidence supporting this hypothesis is still ambiguous. Using experimentally created populations of common voles (Microtus arvalis) - a species with distinct seasonal life-history trajectories - we aimed to test whether individual differences in boldness behaviour co-vary with risk-taking, space use, and fitness. We quantified risk taking, space use (via automated tracking), survival and reproductive success (via genetic parentage analysis) in 8 to 14 experimental, mixed-sex populations of 113 common voles of known boldness type in large grassland enclosures over a significant part of their adult life span and two reproductive events. Populations were assorted to contain extreme boldness types (bold or shy) of both sexes. Bolder individuals took more risks than shyer ones, which did not affect survival. Bolder males but not females produced more offspring than shy conspecifics. Daily home range and core area sizes, based on 95% and 50% Kernel density estimates (20 ± 10 per individual, n = 54 individuals), were highly repeatable over time. Individual space use unfolded differently for sex-boldness type combinations over the course of the experiment. While day ranges decreased for shy females, they increased for bold females and all males. Space use trajectories may, hence, indicate differences in coping styles when confronted with a novel social and physical environment. Thus, inter-individual differences in boldness predict risk taking under near natural conditions and have consequences for fitness in males, which have a higher reproductive potential than females. Given extreme inter- and intra-annual fluctuations in population density in the study species and its short life span, density-dependent fluctuating selection operating differently on the sexes might maintain (co)variation in boldness, risk taking and pace-of-life.

opencc-zeroAug 2023View details →

Linking temperature dependence in fitness effects of mutations to thermal niche adaptation

Fitness effects of mutations may generally depend on temperature that influences all rate-limiting biophysical and biochemical processes. Earlier studies suggested that high temperatures may increase the availability of beneficial mutations ("more beneficial mutations"), or allow beneficial mutations to show stronger fitness effects ("stronger beneficial mutation effects"). The "more beneficial mutations" scenario would inevitably be associated with increased proportion of conditionally beneficial mutations at higher temperatures. This in turn predicts that populations in warm environments show faster evolutionary adaptation but suffer fitness loss when faced with cold conditions, and those evolving in cold environments become thermal-niche generalists ("hotter is narrower"). Under the "stronger beneficial mutation effects" scenario, populations evolving in warm environments would show faster adaptation without fitness costs in cold environments, leading to a "hotter is (universally) better" pattern in thermal niche adaptation. We tested predictions of the two competing hypotheses using an experimental evolution study in which populations of two model bacterial species, Escherichia coli and Pseudomonas fluorescens, evolved for 2,400 generations at three experimental temperatures. Results of reciprocal transplant experiments with our P. fluorescens populations were largely consistent with the "hotter is narrower" prediction. Results from the E. coli populations clearly suggested stronger beneficial mutation effects at higher assay temperatures, but failed to detect faster adaptation in populations evolving in warmer experimental environments (presumably because of limitation in the supply of genetic variation). Our results suggest that the influence of temperature on mutational effects may provide insight into the patterns of thermal niche adaptation and population diversification across thermal conditions.

opencc-by-4.0Sep 2023View details →

The effect of microplastics on Daphnia fitness – systematic review and meta-analysis.

Systematic review on studies on micro/nanoplastic effect on Daphnia published up to 27 April 2022, including a meta-analysis on the effect of micro/nanoplastics on Daphnia reproduction.

opencc-by-4.0Sep 2023View details →

MCMC chains representing stellar halo fits for Lane et al. (2023) paper published in MNRAS

Results for the paper entitled "The stellar mass of the Gaia-Sausage/Enceladus accretion remnant" published in MNRAS by Lane, Bovy, & Mackereth. The results are in the form of MCMC posterior chains, which are used to generate the results recorded in Table 1 of the manuscript. The process used to generate these data is outlined in section 2 (data & sample preparation), section 3 (Density modelling framework), and section 4 (Presentation of results) of the manuscript. The data are contained within a single gzipped .tar file, organized in two directories: gse/ containing the results for fits to the GS/E kinematic samples, and all/ containing the results for the fits to the whole halo sample. In the gse/ directory, there are three directories: eLz/, AD/, and JRLz/, containing the results for the fits to each of the respective kinematically defined subsamples. Within these directories, as well as within all/, are a final set of directories for each of the eight density profiles considered in the work. Within each of these directories are a single file named "samples.npy" which is a binary file (see <a href="https://numpy.org/doc/stable/reference/generated/numpy.lib.format.html#module-numpy.lib.format">this link</a> for format information) containing a numpy array of shape (# of parameters, # of posterior samples). The number of posterior samples is the number of walkers (100) times the number of samples per walker (10,000), minus the number of burn-in steps per walker (1,000) = 900,000. The number of parameters can be inferred from the density profiles definitions in section 3 of the manuscript, and the ordering of the parameters is the same as in Table 1. The units of the parameters are as in Table 1, except for the parameters theta and phi which are scaled such that they are defined on the interval (0,1), representing the intervals (0,2pi) and (0,pi) respectively.

opencc-by-4.0Sep 2023View details →

Cloud Factory - Skeletonizing and Analyzing Pipeline Tutorial Fits Files

Fits files used in the tutorial notebooks that skeletonizes and analyzes clouds within a Cloud Factory grid. These files are the post-processed version of one grid (see Binary to Fits tutorial) with precomputed outputs of the pipeline (thresholded_data.fits and skeleton.fits). The grid is a 500x500x500 pc region of the Feedback-Dominated grid, with the total volume density of hydrogen nuclei (nhtot), volume density of carbon monoxide (nCO), molecular hydrogen (nH2), ionized hydrogen (nHP), atomic hydrogen (nH1), the gas tempearture (temp), and effective cooling from dust (tdust).

opencc-by-4.0Nov 2022View details →

figure of habitus (Palma, 1863) fits the concept of Merodon aberrans. in Integrative taxonomy of the Merodon aberrans (Diptera, Syrphidae) species group: distribution patterns and description of three new species

figure of habitus (Palma, 1863) fits the concept of Merodon aberrans.

opencc-zeroOct 2023View details →

Data from: Large fitness benefits of social nesting in a small carpenter bee

Facultatively social insects are an optimal model group for the study of the emergence of cooperation between individuals. Factors influencing the fitness benefits of social nesting are still debated. Non-reproductive subordinates can benefit from indirect fitness benefits due to increasing reproductive success of related individuals or direct fitness benefits due to direct future reproduction. Here, we studied the costs and benefits of social nesting in the small carpenter bee Ceratina albosticta. From demographic data and within-nest relatedness we obtained key parameters for assessing the fitness of solitary females, social primaries, and social secondaries. C. albosticta were found to usually mate with one male and multiple mating is not common although exists at low frequencies. Social nests usually contain two females, which were found to be related (full sisters), but also some females were unrelated to each other. Patterns of parentage from microsatellite loci revealed that only one female reproduces in social nests. Our results show that relatedness, per capita brood productivity, and offspring survival strongly increase the fitness benefits of social nesting strategies. Social secondaries, when related to the social primaries, have higher inclusive fitness than solitary females, but unrelated social nesting females had no indirect fitness and much reduced inclusive fitness compared to solitary females. Interestingly, average fitness benefits of the social secondary were higher than solitary females. This study provides important empirical data on the costs and benefits of sociality in a facultatively social bee and sets the stage for future comparative studies.

opencc-zeroOct 2023View details →

The impact of helping experience on helper life-history and fitness in a cooperatively breeding bird

The data and accompanying .R scripts were used to test whether having experience as a helper affected a number of different breeding and fitness related parameters in the Seychelles warbler (Acrocephalus sechellensis) in the paper "The impact of helping experience on helper life-history and fitness in a cooperatively breeding bird." Datasets statusInfo.xlsx: data collected over a focal individual's lifetime. natalInfo.xlsx: data pertaining to the natal environment of the focal bird. lastSeen.xlsx: data used to calculate when the bird was last seen alive. summerIndex.xlsx: data used to determine whether a particular field period was during a summer or winter season. territoryQuality.xlsx: data used to determine the territory quality of each territory during a particular field period. Statistical analyses experiencePrep.R: the script used to prepare the data and calculate the necessary model variables prior to running the analyses. experienceAnalyses.R: the script used to run the analyses and generate the related graphs. More detailed information regarding the contents of each dataset can be found in the READ.ME From this, we found that helping experience had no significant association with any of the metrics considered, except that individuals with helping experience had an older age at first dominance, and dominant females with helping experience had longer lifespans than those that had never helped. In addition, we found that females with co-breeding experience produced more adult offspring (≥1 year old) after acquiring dominance, and had a higher lifetime reproductive success than females that had never co-bred.

opencc-zeroOct 2023View details →

Nectar robbing by bees affects the reproductive fitness of the distylous plant Tirpitzia sinensis (Linaceae)

Nectar robbing can affect plant reproductive success directly by influencing female and male fitness, and indirectly by affecting pollinator behavior. Flowers have morphological and chemical features that may protect them from nectar robbers. Previous studies on nectar robbing have focused mainly on homotypic plants. It remains unclear how nectar robbing affects the reproductive success of distylous plants, and whether defense strategies of two morphs are different. Nectar robbing rates on the long- and short- styled morph (L-morph, S-morph) of the distylous Tirpitzia sinensis were investigated. We compared floral traits, the temporal pattern of change in nectar volume and sugar concentration, nectar secondary metabolites and sugar composition between robbed and unrobbed flowers of two morphs. We tested direct effects of nectar robbing on female and male components of plant fitness and the indirect effects of nectar robbing via pollinators. Nectar robbing rates did not differ between the two morphs. Flowers with smaller sepals and petals were more easily robbed. The floral tube diameter and thickness were greater in L-morphs than in S-morphs, and the nectar rob holes were significantly smaller in L-morphs than in S-morphs. Nectar robbing significantly decreased nectar replenishment rate but did not affect nectar sugar concentration or sugar composition. After robbery the quantities and diversity of secondary compounds in the nectar of S-morphs increased significantly and the total relative contents of secondary compounds in L-morphs showed no obvious changes. Nectar robbing could decrease female fitness by decreasing pollen germination and thus decreasing seed set. Nectar robbing had no significant effects on male fitness. Robbed flowers were less likely to be visited by hawkmoth pollinators, especially in S-morphs. These results suggest that nectar robbing could directly and indirectly decrease the female fitness of T. sinensis, and different morphs have evolved different defense mechanisms in response to nectar robbing pressure.

opencc-zeroDec 2022View details →

Sexually concordant selection on floral traits despite greater opportunity for selection through male fitness

Pollinators are important drivers of floral trait evolution, yet plant populations are not always perfectly adapted to their pollinators. Such apparent maladaptation may result from conflicting selection through male and female sexual functions in hermaphrodites. We studied sex-specific mating patterns and phenotypic selection on floral traits in Aconitum gymnandrum. After genotyping 1786 offspring, we partitioned individual fitness into sex-specific selfed and outcrossed components and estimated phenotypic selection acting through each. Relative fitness increased with increasing mate number, and more so for male function. This led to greater opportunity for selection through outcrossed male fitness, though patterns of phenotypic selection on floral traits tended to be similar, and with better support for selection through female rather than male fitness components. We detected directional selection through one or more fitness components for larger flower number, larger flowers, and more negative nectar gradients within inflorescences. Our results are consistent with Bateman's principles for sex-specific mating patterns and illustrate that, despite the expected difference in opportunity for selection, patterns of variation in selection across traits can be rather similar for the male and female sexual functions. These results shed new light on the effect of sexual selection on the evolution of floral traits.

opencc-by-nc-nd-4.0Oct 2023View details →

Supplementary Data for "Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation"

Supplementary data for publication "Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation".Includes:<ul><li>All input structures used in the the retrospective benchmark dataset as well as the (at most) 5 best scoring output models.</li><li>Input structures and output models for IFD-MD predictions of SSTR2, SSTR4, and SSTR5 complexes.</li><li>Output FEP+ maps (in fmp format) for SSTR2, SSTR4, and SSTR5 best models (representative runs shown in publication).</li></ul>

closedIPD-NOFeb 2026View details →

Effects of Exercise Training Intensity on Fitness and Insulin Sensitivity in African Americans

ClinicalTrials.gov study NCT02892331. IPD Sharing: NO. Countries: 1. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

Enhancing Fitness in Older Pre-diabetic Veterans

ClinicalTrials.gov study NCT00594399. IPD Sharing: Not stated. Countries: 1. Publications: 7.

closedIPD-NOFeb 2026View details →

Gerofit Exercise Intervention for Older Adults With Sickle Cell Disease (SICKLE-FIT Study)

ClinicalTrials.gov study NCT05714098. IPD Sharing: NO. Countries: 1. Publications: 8.