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2,315 results for “maintainability”
Analyzing Static Analysis Metric Trends towards Early Identification of Non-Maintainable Software Components
<p>The provided dataset contains the data used by "Analyzing Static Analysis Metric Trends towards Early Identification of Non-Maintainable Software Components", in order to evaluate the maintainability degree of a software class and identify software components that will eventually become non-maintainable.</p>
Wild kangaroos become more social when caring for young and may maintain long-term affiliations with popular individuals
<p>Kangaroos are an iconic group of Australian fauna. Despite considerable research on kangaroo behaviour, key gaps remain in our understanding of their social organization in the wild. In particular, it remains largely unknown whether kangaroos form long-term social bonds and what factors might prompt individuals to associate or dissociate from one another. Over 6 years, we monitored the social affiliations of individually identified eastern grey kangaroos, Macropus giganteus, in a large wild population. We investigated the short-term and long-term relationships of kangaroos and the extent those relationships varied with age, sex and reproductive state. We found evidence that long-term relationships among eastern grey kangaroos are possible, especially between adult females. Those individuals that were more sociable within years were also more likely to establish affiliations across years. Contrary to previous studies, we observed females actively associating with other mothers in the years in which they had young. These data suggest that the fission-fusion dynamics of eastern grey kangaroo social behaviour allow females to modulate their social position with conspecifics according to their current reproductive state. We highlight the adaptive implications of the formation of long-term bonds and the changes in social behaviour observed in females.</p>
Spider mite resistant maize lines, B75 and B96, maintain resistance under water-stress
<p>Climate variability has major implications for agriculture due to the increase in the frequency and intensity of simultaneous abiotic, namely water-stress, and biotic stresses to crops. Plant water-stress alone harms crops but also can attract outbreaks of herbivores with varied host specialization, and plants succumb to further yield losses dealing with multiple stressors. Host-plant resistance provides a route to lessen yield losses from herbivory; however, our knowledge of the interactions between water-stress and pest resistance is limited, especially for mite herbivores of maize including the generalist two-spotted spider mite (<em>Tetranychus</em> <em>urticae</em>, TSM) and the specialist Banks grass mite (<em>Oligonychus</em> <em>pratensis</em>, BGM). We conducted parallel greenhouse and field experiments whereby a susceptible line (B73) and two TSM-resistant lines (B75 and B96) were subjected to either optimal irrigation or water-stress [50–60% and 5–10% volumetric water content (VWC), and 25–32% and 10–15% VWC, in the greenhouse and field, respectively]. As expected, we found that under optimal irrigation TSM and BGM populations increased readily on B73, while B75 and B96 were largely resistant to the TSM but not BGM. While plant water-stress increased the susceptibility of B73 to both mite species, water-stress did not disrupt initial resistance levels of B75 and B96 maize for either mite species. Elevated protease activity was found in B75 and B96 and may contribute to maize resistance. Our findings that B75 and B96 are highly resistant to the TSM, and maintain resistance to both mite species with water-stress, highlights the importance of including the nuances of multiple stressors within the framework of host-plant resistance.</p>
Dynamic antagonism between key repressive pathways maintains the placental epigenome (source data and custom code)
<p>DNA and Histone-3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb Repressive Complexes regulate the CpG-rich promoters of developmental genes. In contrast to this general framework, the extraembryonic lineages display noncanonical, globally intermediate DNA methylation levels that includes disruption of local Polycomb domains. To better understand this unusual landscape’s molecular properties, we genetically and chemically perturbed major epigenetic pathways in mouse Trophoblast Stem Cells (TSCs). We find that the extraembryonic epigenome reflects ongoing and dynamic de novo methyltransferase recruitment, which is continuously antagonized by Polycomb to maintain intermediate, locally disordered methylation. Despite its disorganized appearance, our data point to a highly controlled equilibrium between counteracting repressors within extraembryonic cells, one that can seemingly persist indefinitely without bistable features typically seen for embryonic forms of epigenetic regulation.</p> <p> </p>
H3K36 methylation maintains cell identity by regulating opposing lineage programs
<p>This upload contains cellranger count outputs and RDS objects of preprocessed scRNAseq data from the publication "H3K36 Methylation Maintains Cell Identity by Regulating Opposing Lineage Programs" for new data published with the paper.</p> <p>These RDS objects are produced by code available here <a href="https://github.com/Michorlab/H3K36_methylation_scRNAseq">https://github.com/Michorlab/H3K36_methylation_scRNAseq</a>. The same GitHub repo contains plots and tables generated from data in these objects.</p>
Data and code for the manuscript:"Female preference for rare males is maintained by indirect selection in Trinidadian guppies"
<p>Data and code for the manuscript "Female preference for rare males is maintained by indirect selection in Trinidadian guppies</p> <p>This project contains three data files and two scripts.</p> <p>Data files:</p> <ul> <li> <p>LL_guppy_data.csv (the mark recapture data from the experimental stream)</p> </li> <li> <p>standardized_locations.csv (the standardized names for pools and riffles each month)</p> </li> <li> <p>pat_data.csv (the classification of male colour patterns by fish id)</p> </li> </ul> <p>Scripts:</p> <ul> <li> <p>data_preparation.R (this script merges the data files, calculates male pattern rarity and novelty, and scores fitness components. RUN THIS FIRST)</p> </li> <li> <p>analysis_and_figures.R (this script builds, runs, and checks the models, summarises the output, and produces the figures. RUN THIS SECOND)</p> </li> </ul>
Sexually antagonistic selection maintains genetic variance when sexual dimorphism evolves
<p>Breeding design data for body size in seed beetles (a sexually antagonistic trait) after 10 generations under different artificial selection conditions to test the effects of selection on the genetic variance of body size. The breeding design and sample size of the study allow us to partition genetic variances into additive autosomal, additive sex-linked, autosomal dominance and X-linked dominance variance.<br><br>See related dataset for body size data of the ancestral population before selection.</p>
Diet-mediated constitutive induction of novel IL4+ ILC2 cells maintains intestinal homeostasis in mice
<p>Group 2 innate lymphoid cells (ILC2s) expressing IL-5 and IL-13 are localized at various mucosal tissues and play critical roles in the induction of type 2 inflammation, response to helminth infection, and tissue repair. Here we reveal a unique ILC2 subset in the mouse intestine that constitutively expresses IL-4 together with GATA3, ST2, KLRG1, IL-17RB, and IL-5. In this subset, IL-4 expression is regulated by mechanisms similar to but distinct from those observed in T cells and is partly affected by IL-25 signaling. Although the absence of the microbiota had marginal effects, feeding mice with a vitamin B1-deficient diet compromised the number of intestinal IL-4+ ILC2s. The decrease in the number of IL-4+ ILC2s caused by the vitamin B1 deficiency was accompanied by a reduction in IL-25-producing tuft cells. Our findings reveal that dietary vitamin B1 plays a critical role in maintaining interaction between tuft cells and IL-4+ ILC2s, a previously uncharacterized immune cell population that may contribute to maintaining intestinal homeostasis.</p>
Data for: Evidence for a maintenance cost for birds maintaining highly flexible basal, but not summit, metabolic rates
<p>Reversible phenotypic flexibility allows organisms to better match phenotypes to prevailing environmental conditions and may produce fitness benefits. Costs and constraints of phenotypic flexibility may limit the capacity for flexible responses but are not well understood or documented. Costs could include expenses associated with maintaining the flexible system or with generating the flexible response. One potential cost of maintaining a flexible system is an energetic cost reflected in the basal metabolic rate (BMR), with elevated BMR in individuals with more flexible metabolic responses. We accessed data from thermal acclimation studies of birds where BMR and/or M<sub>sum</sub> (maximum cold-induced metabolic rate) were measured before and after acclimation, as a measure of metabolic flexibility, to test the hypothesis that flexibility in BMR (ΔBMR), M<sub>sum</sub> (ΔM<sub>sum</sub>), or metabolic scope (M<sub>sum</sub> – BMR; ΔScope) is positively correlated with BMR. When temperature treatments lasted at least three weeks, three of six species showed significant positive correlations between ΔBMR and BMR, one species showed a significant negative correlation, and two species showed no significant correlation. ΔM<sub>sum</sub> and BMR were not significantly correlated for any species and ΔScope and BMR were significantly positively correlated for only one species. These data suggest that support costs exist for maintaining high BMR flexibility for some bird species, but high flexibility in M<sub>sum</sub> or metabolic scope does not generally incur elevated maintenance costs. </p>
Data from: Complex evolutionary processes maintain an ancient chromosomal inversion
<p>Genome re-arrangements such as chromosomal inversions are often involved in adaptation. As such, they experience natural selection, which can erode genetic variation. Thus, whether and how inversions can remain polymorphic for extended periods of time remains debated. Here we combine genomics, experiments, and evolutionary modeling to elucidate the processes maintaining an inversion polymorphism associated with the use of a challenging host plant (Redwood trees) in <em>Timema </em>stick insects. We show that the inversion is maintained by a combination of processes, finding roles for life-history trade-offs, heterozygote advantage, local adaptation to different hosts, and gene flow. We use models to show how such multi-layered regimes of balancing selection and gene flow provide resilience to help buffer populations against the loss of genetic variation, maintaining the potential for future evolution. We further show that the inversion polymorphism has persisted for millions of years and is not a result of recent introgression. We thus find that rather than being a nuisance, the complex interplay of evolutionary processes provides a mechanism for the long-term maintenance of genetic variation.</p>
Mitochondrial MICOS complex genes, implicated in hypoplastic left heart syndrome, maintain cardiac contractility and actomyosin integrity
<p>Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease (CHD) with a likely oligogenic etiology, but our understanding of the genetic complexities and pathogenic mechanisms leading to HLHS is limited. We therefore performed whole genome sequencing (WGS) on a large cohort of HLHS patients and their families to identify candidate genes that were then tested in <em>Drosophila</em> heart model for functional and structural requirements. Bioinformatic analysis of WGS data from an index family comprised of a HLHS proband born to consanguineous parents and postulated to have a homozygous recessive disease etiology, prioritized 9 candidate genes with rare, predicted damaging homozygous variants. Of the candidate HLHS gene homologs tested, cardiac-specific knockdown (KD) of mitochondrial MICOS complex subunit dCHCHD3/6 resulted in drastically compromised heart contractility, diminished levels of sarcomeric actin and myosin, reduced cardiac ATP levels, and mitochondrial fission-fusion defects. Interestingly, these heart defects were similar to those inflicted by cardiac KD of ATP synthase subunits of the electron transport chain (ETC), consistent with the MICOS complex's role in maintaining cristae morphology and ETC complex assembly. Analysis of 183 genomes of HLHS patient-parent trios revealed five additional HLHS probands with rare, predicted damaging variants in CHCHD3 or CHCHD6. Hypothesizing an oligogenic basis for HLHS, we tested 60 additional prioritized candidate genes in these cases for genetic interactions with CHCHD3/6 in sensitized fly hearts. Moderate KD of CHCHD3/6 in combination with Cdk12 (activator of RNA polymerase II), RNF149 (E3 ubiquitin ligase), or SPTBN1 (scaffolding protein) caused synergistic heart defects, suggesting the potential involvement of a diverse set of pathways in HLHS. Further elucidation of novel candidate genes and genetic interactions of potentially-disease-contributing pathways is expected to lead to a better understanding of HLHS and other CHDs.</p>
Data from: Freshwater fishes maintain multi-trait phenotypic stability across an environmental gradient in aqueous calcium
<p>Reductions in a limiting nutrient might be expected to necessitate compromises in the functional traits that depend on that nutrient; yet populations existing in locations with low levels of such nutrients often do not show the expected degradation of functional traits. Indeed, we previously found that fish of three species, Logperch (<em>Percina caprodes</em>),Pumpkinseed Sunfish (<em>Lepomis gibbosus</em>), and Yellow Perch (<em>Perca flavescens</em>) residing in low-calcium water in the Upper St. Lawrence River nevertheless maintained levels of scale calcium comparable to those of conspecific populations in high-calcium water. However, it remains possible that the maintenance of one functional trait under nutrient-limited conditions could come at the expense of maintaining other functional traits that depend on that same nutrient. Hence, we here extend prior work by examining other calcium-dependent traits: skeletal element sizes and bone densities in the same fish species in the same area. Using radiographs of 101 fish from the three species across four locations (two in high-calcium water and two in low-calcium water), we document multi-trait "homeostasis" along the gradient of water calcium. That is, we did not detect any effect of calcium regime (low-calcium versus high-calcium) on any of the measured variables. Further, effect sizes for the skeletal traits were very low – lower even than effect sizes previously documented for scale calcium. Our results thus show that native fishes maintain phenotype stability across a suite of functional traits linked to calcium regulation, perhaps pointing to an "organismal-level homeostasis" scenario rather than a "trait-level homeostasis" scenario. </p>
Figure 11 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina), version 2
Figure 11. Sequential (1-2) views of encounter between the two male forms of Maevia inclemens. Apart from a brief defensive reaction by the grey male (2), no ritual combat ensued and the males did not appear to recognize that they were conspecific.
Figure 9 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina), version 2
Figure 9. Five sequential matings (1-2, 3, 4, 5-6, 7) of the two male forms with the same female Maevia inclemens over the course of five days. 1-2, This mating was interrupted as the male switched from one side to the other, but after an atypical low crawl display with legs I extended, the tufted male quickly recaptured the female and continued to mate on the other side. 5-6, mating on the right and then left sides. Note the many erect spines on the legs of the mating male in each instance.
Figure 10 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina), version 2
Figure 10. Attempted mating by the grey male Maevia inclemens. This sequence shows how the male jumped the female while she was suspended from her dragline, just after capturing a fly (1), and attempted to mate with her (2). The female promptly released her prey, and the male then fed on it for many minutes (3-4), still in a suspended position [23 JUNE 2020 14:09- 14:13]. Three days later this male approached and mated successfully with the female for a second time (Figures 5:1-7, 9:7).
Figure 7 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina), version 2
Figure 7. Sequential positions (1-10) of the tufted male Maevia inclemens as he advanced toward the female in a later mating attempt (after Figure 6).
Figure 3 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina), version 2
Figure 3. Adult male Maevia inclemens, tufted (black) form. The tufts of the dorsal carapace may not be present in all males of this form. Note the lack of stripes on the uniformly-colored legs. 2, Feeding on mosquito (Diptera: Culicidae).
Figure 6 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina), version 2
Figure 6. Sequential positions (1-4) of the tufted male Maevia inclemens as he advanced toward the female. Facing the female, this male maintained an elevated position with the opisthosoma turned down, stepping and waving both legs I and pedipalps. As with the grey male (Figure 5), this male also mated sucessfully with the female (Figure 9:3), jumping and capturing her after advancing to a near position.
Figure 5 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina), version 2
Figure 5. Display by grey males, Maevia inclemens. 1-7, Successive (low crawl) positions of the grey male male from Massachusetts, advancing to successfully mate with the female. When close, this male jumped and captured the female (Figure 9:7). 8, Display by a grey male from Sherburne County, Minnesota, recorded in 1982.
Figure 2 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina), version 2
Figure 2. Adult male Maevia inclemens, grey (striped) form. Note the stripes on the prolateral surface of each femur.
ScienceDex guides
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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.