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3,202 results for “Maintenance”
Data from: Food supplementation fails to reveal a trade-off between incubation and self-maintenance in female house wrens
Incubating birds must allocate their time and energy between maintaining egg temperature and obtaining enough food to meet their own metabolic demands. We tested the hypothesis that female house wrens (Troglodytes aedon) face a trade-off between incubation and self-maintenance by providing females with supplemental food during incubation. We predicted that food supplementation would increase the amount of time females devoted to incubating their eggs, lower their baseline plasma corticosterone levels (a measure of chronic stress), and increase their body mass, haematocrit (a measure of anaemia), and reproductive success relative to control females. As predicted, food-supplemented females spent a greater proportion of time incubating their eggs than control females. Contrary to expectation, however, there was no evidence that food supplementation significantly influenced female baseline plasma corticosterone levels, body mass, haematocrit, or reproductive success. However, females with high levels of corticosterone at the beginning of incubation were more likely to abandon their nesting attempt after capture than females with low levels. Corticosterone significantly increased between the early incubation and early nestling stages of the breeding cycle in all females. These results suggest that although food supplementation results in a modest increase in incubation effort, it does not lead to significantly lower levels of chronic stress as reflected in lower baseline corticosterone levels. We conclude that female house wrens that begin the incubation period with low levels of plasma corticosterone can easily meet their own nutritional needs while incubating their eggs, and that any trade-off between incubation and self-feeding does not influence female reproductive success under the conditions at the time of our study.
Data from: Maintenance of species boundaries in a Neotropical radiation of Begonia
A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by-product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in Begonia by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between B. heracleifolia and B. nelumbiifolia are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between B. heracleifolia and B. sericoneura contains a higher proportion of F1s, but little evidence of introgression. The lack of later-generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that Begonia demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.
Data from: Lifetime fitness, sex-specific life history, and the maintenance of a polyphenism
Polyphenisms, alternative morphs produced through plasticity, can reveal the evolutionary and ecological processes that initiate and maintain diversity within populations. We examined lifetime fitness consequences of two morphs in a polyphenic population of Arizona Tiger Salamanders using a 27-year data set with 1,317 adults and 6,862 captures across eight generations. Larval salamanders develop into either an aquatic paedomorph that retains larval traits and stays in its natal pond or a terrestrial metamorph that undergoes metamorphosis. To evaluate the adaptive significance of this polyphenism, we compared lifetime reproductive success of each morph and assessed how life history strategies and spatiotemporal variation explained fitness. We found sex-specific differences in lifetime fitness between morphs. For males, paedomorphs had more reproductive opportunities than metamorphs when we accounted for the potential mating advantage of larger males. For females, in contrast, metamorphs had higher estimated egg production than paedomorphs. Life history strategies differed between morphs largely because the morphs maximize different ends of the trade-off between age at first reproduction and longevity. Spatiotemporal variation affected larval more than adult life history traits with little to no effect on lifetime fitness. Thus, environmental variation likely explains differences in morph production across time and space but contributes little to lifetime fitness differences between morphs and sexes. Our long-term study and measures of lifetime fitness provide unique insight into the complex selective regimes potentially acting on each morph and sex. Our findings motivate future work to examine how sex-specific selection may contribute to the maintenance of polyphenism.
Data from: Evolution of Drosophila resistance against different pathogens and infection routes entails no detectable maintenance costs
Pathogens exert a strong selective pressure on hosts, entailing host adaptation to infection. This adaptation often affects negatively other fitness-related traits. Such trade-offs may underlie the maintenance of genetic diversity for pathogen resistance. Trade-offs can be tested with experimental evolution of host populations adapting to parasites, using two approaches: (1) measuring changes in immunocompetence in relaxed-selection lines and (2) comparing life-history traits of evolved and control lines in pathogen-free environments. Here, we used both approaches to examine trade-offs in Drosophila melanogaster populations evolving for over 30 generations under infection with Drosophila C Virus or the bacterium Pseudomonas entomophila, the latter through different routes. We find that resistance is maintained after up to 30 generations of relaxed selection. Moreover, no differences in several classical life-history traits between control and evolved populations were found in pathogen-free environments, even under stresses such as desiccation, nutrient limitation, and high densities. Hence, we did not detect any maintenance costs associated with resistance to pathogens. We hypothesize that extremely high selection pressures commonly used lead to the disproportionate expression of costs relative to their actual occurrence in natural systems. Still, the maintenance of genetic variation for pathogen resistance calls for an explanation.
Sexual signal loss, pleiotropy, and maintenance of a male reproductive polymorphism in crickets
<p>Pleiotropy between male signals and female preferences can facilitate evolution of sexual communication by maintaining coordination between the sexes. Alternatively, it can favor variation in the mating system, such as a reproductive polymorphism. It is unknown how common either of these scenarios are in nature. In Pacific field crickets (<i>Teleogryllus oceanicus</i>) on Kauai, Hawaii, a mutation (<i>flatwing</i>) that segregates as a single locus is responsible for the rapid loss of song production in males. We used outbred cricket colonies fixed for male wing morph to investigate whether homozygous <i>flatwing</i> and <i>normal-wing</i> (wild-type) females differ in responsiveness to male calling song and propensity to mate when paired with either a <i>flatwing</i> or <i>normal-wing</i> male in the presence or absence of courtship song. <i>Flatwing</i> females were less likely to mount a male than <i>normal-wing</i> females. Females of both genotypes showed a preference for <i>normal-wing</i> males and were more likely to mate in the presence of courtship song; n<i>ormal-wing </i>females<i> </i>were<i> </i>particularly likely to mate with song. Our results show that negative pleiotropy between obligate male silence and female mating behavior can constrain the evolution of sexual signal loss and contribute to the maintenance of a male reproductive polymorphism in the wild. </p>
Data from: Factors leading to the evolution and maintenance of a male ornament in territorial species
Male ornamentation is assumed to have evolved primarily from selection by female mate choice. Yet this is only one possible reason for ornament evolution. Ornaments might also be useful in aggressive competition by improving opponent assessment between males, or they might function to enhance signal detection by making males more conspicuous in the environment. We tested both these ideas in territorial Anolis lizards in which female choice is either absent or secondary to males competing for territories that overlap female home ranges. Male tail crests only evolved in species in which territory neighbors were distant, consistent with the signal detection hypothesis. Once the tail crest had evolved, however, it seems to have become a signal in itself, with variation in the frequency and size of tail crests within species correlating with variables predicted by the aggressive competition hypothesis. Our study presents an apparent example of a male ornament in which the selection pressure leading to variation among species in ornament expression is different from the selection pressure acting on variation within species. The Anolis tail crest is therefore likely to be an exaptation. We caution that conclusions made on the evolution of male ornaments are dependent on the phylogenetic perspective adopted by a study. Studies restricted to single species are useful for identifying selection pressures in contemporary settings (i.e., the current utility of traits), but may lead to erroneous conclusions on the factors that initially lead to the origin of traits.
Data from: Herbivore-mediated interaction promotes the maintenance of trichome dimorphism through negative frequency-dependent selection
Natural plant populations exhibit genetic variation in defense traits against herbivores. Despite a growing body of evidence for herbivore-mediated selection on plant defenses, we still know little about how genetic variation persists in antiherbivore defense traits. Here we present field and experimental evidence for herbivore-mediated frequency-dependent selection that promotes the maintenance of trichome-producing (hairy) and trichomeless (glabrous) plants of Arabidopsis halleri subsp. gemmifera. First, in a natural population where the specialist leaf beetle Phaedon brassicae was prevalent, hairy plants were damaged less when the frequency of neighboring glabrous plants increased. Furthermore, temporal variation in the frequency of the two plant morphs showed that rarer morphs increased in frequency at the scale of 1-m-diameter patches between survey years. Using a mesocosm experiment, we demonstrated a rare-morph advantage for defense (leaf damage and herbivore abundance) and reproduction (flower and clone production) between hairy and glabrous plants in the presence of P. brassicae. However, this rare-morph advantage was not detected when beetles were absent, with glabrous plants having higher reproduction than hairy plants under these conditions regardless of frequency conditions. These findings highlight the overlooked but potentially critical role of herbivore-mediated apparent interaction in maintaining plant defense polymorphism.
Data from: Metabolome dynamics of diapause in the butterfly Pieris napi: distinguishing maintenance, termination and post-diapause phases
Diapause is a deep resting stage facilitating temporal avoidance of unfavourable environmental conditions that is used by many insects to adapt their life cycle to seasonal variation. Although considerable work has been invested in trying to understand each of the major diapause stages (induction, maintenance and termination), we know very little about the transitions between stages, especially diapause termination. Understanding diapause termination is critical for modelling and predicting spring emergence and winter physiology of insects, including many pest insects. In order to gain these insights we investigated metabolome dynamics across diapause development in pupae of the butterfly Pieris napi, which exhibits adaptive latitudinal variation in the length of endogenous diapause that is uniquely well characterized. By employing a time-series experiment we show that the whole-body metabolome is highly dynamic throughout diapause and differs between pupae kept at a diapause-terminating (low), or at a diapause-maintaining (high) temperature. We show major physiological transitions through diapause, separated temperature-dependent from temperature-independent processes and identified significant patterns of metabolite accumulation and degradation. Together the data show that while the general diapause phenotype (suppressed metabolism, increased cold tolerance) is established in a temperature-independent fashion, diapause termination is temperature-dependent and requires a cold signal. This revealed several metabolites that are only accumulated in diapause terminating conditions and degraded in a temperature-unrelated fashion during diapause termination. In conclusion, our findings indicate that some metabolites, in addition to functioning as e.g. cryoprotectants, are candidates for having regulatory roles as metabolic clocks or time-keepers during diapause.
Data from: Assortative mating and the maintenance of population structure in a natural hybrid zone
Understanding the factors that give rise to natural hybrid zones and govern their dynamics and structure is important to predicting the evolutionary consequences of hybridization. Here we use a combination of multi-generational population genetic data, mating patterns from a natural population, behavioral assays, and mark-recapture data within clinal hybrid zones of the genus Xiphophorus to test the role of assortative mating in maintaining population structure and the potential for ongoing genetic exchange between heterospecifics. Our data demonstrate that population structure is temporally robust and driven largely by assortative mating stemming from pre-copulatory isolation between pure species. Furthermore, mark-recapture data revealed that rates of migration within the same stream reach are far below the level needed to support population structure. Contrasting with many empirical studies of natural hybrid zones, there appeared to be no hybrid male dysfunction nor discrimination against hybrid males by pure parental females, and hybrid females mated and associated with pure species and hybrid males at random. Despite strong isolation between pure parentals, hybrids therefore can act as a conduit for genetic exchange between heterospecifics, which has been shown to increase the tempo of evolutionary change. Additionally, our findings highlight the complexity of natural hybrid zone dynamics, demonstrating that multivariate selection can give rise to patterns that do not fit classical models of hybrid zone evolution.
Dataset of light microscopy and image processing for ruthenium red staining - Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants
<p>This contains additional data relative to version 1, corresponding to a new versio of the manuscript. </p> <p>This dataset contains darkfield light microscopy images from ruthenium red stained <em>Arabidopsis thaliana </em>dark grown hypocotyls of various wildtype and mutant plants, along with the prossessing and quantified data (including segmented masks, corrected masks, raw quantification and processed quantification) reported in the study "Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants" (<a href="https://www.biorxiv.org/content/10.1101/2024.11.26.625362v1">https://www.biorxiv.org/content/10.1101/2024.11.26.625362v1</a>). Data was acquired following the method described in the publication. Processing of the raw data was perfomed using the RRQuant workflow (<a href="https://doi.org/10.5281/zenodo.14173186">10.5281/zenodo.14173186</a>).</p>
Supplementary Data for "Exploring the Integration of Large Language Models in Industrial Test Maintenance Processes"
<p>This package contains supplementary data not directly included in the paper, including per-commit results for each prototype and the prompts used in the proof-of-concept implementations.</p>
Refactoring Code Smells in Open Source Projects: A Hands-on Approach to Teaching Software Maintenance
<p>Code smells are suboptimal code structures that can undermine software quality and maintainability. On the one hand, software engineers commonly apply refactoring techniques to address these deficiencies and improve internal quality attributes. On the other hand, when performed manually and without discipline, refactoring can lead to code degradation. Despite its importance, refactoring and code smells are rarely explored in depth in undergraduate computing courses, which can be reflected in industry practices. To address this gap, this paper presents a hands-on approach to teaching code smell refactoring through contributions to Open Source Software (OSS) projects, an environment where developers with diverse skill levels collaborate, and maintaining code quality is particularly challenging. Code smells accumulate over time in such scenarios, hindering software evolution and collaboration. Our study in two undergraduate Software Quality and Software Maintenance courses expands on previous findings by incorporating an in-depth analysis of students’ learning experiences. The results indicate that: (i) students rec- ognized improvements in code quality after refactoring; (ii) they identified strong connections between refactoring, testing, and debugging; (iii) their confidence decreased when refactoring required changes across multiple files; (iv) code complexity posed a significant challenge to refactoring; (v) students’ choices of refactoring techniques were influenced by project structure and personal preferences, often combining multiple techniques to address a single smell; (vi) in some cases, refactoring introduced new code smells; (vii) the longest refactoring efforts were also the most likely to reintroduce code smells; (viii) contributing to OSS projects improved students’ programming skills and fostered a sense of professional growth; (ix) students faced challenges in understanding OSS contribution processes, particularly regarding issue resolution, adherence to contribution guidelines, and responding to maintainer feedback; (x) automated checks and review workflows varied across projects, affecting students’ ability to submit successful contributions; and (xi) despite these challenges, engagement with OSS enabled students to gain practical experience in collaborative software development. Our findings offer valuable insights for software engineering educators seeking to integrate refactoring practices into coursework while leveraging OSS contributions as an educational tool.</p>
Towards Identifying Python Proficiency to Foster Software Maintenance and Evolution
Open the record for dataset details and reuse information.
DT-MAS architecture for smart maintenance of aircraft fuel distribution systems
<p><strong>Project Goal:</strong> Develop a digital twin architecture using a multi-agent system and AI for smart maintenance of aircraft distribution systems.</p> <p><strong>Objective:</strong> Build a reliable model that accurately represents the real system in an offline environment.</p> <p><strong>Methodology : </strong></p> <ul> <li>Developed a simulation based on an aircraft distribution system model, mimicking real system behavior.</li> <li>Created a dataset with four runs, five scenarios per run, and five operating points per scenario.</li> <li>Simulated healthy and faulty conditions using MATLAB-injected faults across various categories.</li> <li>Focused on four system components: hydraulic pump, tanks, engines, and pumps.</li> <li>Generated data for 11 healthy and faulty scenarios, including six fault types: <ul> <li>Noise on instruments</li> <li>Abnormal instrument readings</li> <li>Minor service problems</li> <li>External leakage</li> <li>Parameter deviation</li> <li>Structural deficiency</li> </ul> </li> <li>Features used for analysis: <ul> <li>Pump flow for pumps</li> <li>Pump motor speed for hydraulic pumps</li> <li>Driver power</li> <li>Tank volume and temperature</li> </ul> </li> </ul> <p><strong>Expected Results:</strong></p> <ul> <li>Compare performance of different asset health estimation models.</li> <li>Develop new predictive maintenance strategies.</li> <li>Predict and emulate complex aircraft behavior through multi-agent systems and AI.</li> </ul>
Replication Package for 'Analyzing the Evolution and Maintenance of ML Models on Hugging Face'
<p>Replication Package attached to the 'Analyzing the Evolution and Maintenance of ML Models on Hugging Face' article. Within the README and accompanying scripts, you will find detailed instructions to guide you through the analysis conducted in the article.</p>
Supporting Software Maintenance with Dynamically Generated Document Hierarchies
Open the record for dataset details and reuse information.
Supporting for "Bivalve Resilience to Ocean Acidification: Active H+ Efflux as a Mechanism for Shell Growth Maintenance"
<p><span>Summary: </span></p> <p><span>This dataset encompasses a comprehensive collection of responses from the Manila clam <em>Ruditapes philippinarum</em> to ocean acidification. Key metrics included in this dataset are oxygen consumption rate, Ammonia-N excretion rate, intracellular pH, H⁺ flux, expression and activity of acid-base regulatory genes, and individual growth measurements.</span></p> <p><span> </span><span>The data was systematically compiled from both field mesocosm and laboratory experiments aimed at elucidating the physiological responses and underlying mechanisms by which bivalves adapt to the stressors associated with ocean acidification.</span></p> <p><span> </span><span>Data generation occurred primarily between 2020 and 2023. This dataset serves as a valuable resource for enhancing our mechanistic understanding of the responses and adaptive potential of marine bivalves in the context of escalating ocean acidification.</span></p>
Dataset and code from tensile test experiments - Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants
<p>This data set contains brightfield light microscopy images, extensometer reading and other measurments associated with tensile test experiment performed on <em>Arabidopsis thaliana </em>dark grown hypocotyls of various wildtype and mutant plants, along with the prossessing and quantified data as reported in the study "Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants" (<a href="https://www.biorxiv.org/content/10.1101/2024.11.26.625362v1">https://www.biorxiv.org/content/10.1101/2024.11.26.625362v1</a>). Data was acquired following the method described in the publication. Processing of the raw data was perfomed using the RRQuant workflow (<a href="https://doi.org/10.5281/zenodo.14173186">10.5281/zenodo.14173186</a>).</p>
Reproduction package for the paper "Analyzing long-term maintenance releases of the Linux kernel"
<p>This is the reproduction package of the paper "Analyzing long-term maintenance releases of the Linux kernel". This package includes the datasets and the software for methods presented in the paper.</p>
Evidence from automixis with inverted meiosis for the maintenance of sex by loss of complementation
<p>The adaptive value of sexual reproduction is still debated. A short-term disadvantage of asexual reproduction is loss of heterozygosity, which leads to the unmasking of recessive deleterious mutations. The cost of this loss of complementation is predicted to be higher than the twofold cost of meiosis for most types of asexual reproduction. Automixis with terminal fusion of sister nuclei is especially vulnerable to the effect of loss of complementation. It is found, however, in some taxa including oribatid mites, the most prominent group of ancient asexuals. Here I show that automixis with terminal fusion is stable if it is associated with inverted meiosis, and that this appears to be the case in nature, notably in oribatid mites. The existence of automixis with terminal fusion, and its co-occurrence with inverted meiosis, therefore, is consistent with the hypothesis that loss of complementation is important in the evolution of sexual reproduction.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.