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13,587 results for “specification”
Domain-specific Language for Data-driven Design Time Analyses and Result Mappings for Logic Programs - Data Set
<p>This data set contains additional information to the master thesis of Sebastian Hahner. This includes the prototypical implementation of the domain-specific language (DSL) as well as sample scenarios and mapping results.</p>
Divalent cations bind to phosphoinositides to induce ion and isomer specific propensities for nano-cluster initiation in bilayer membranes
<p>We report all-atom molecular dynamics simulations of physiologically composed asymmetric bilayers containing phosphoinositides in the presence of monovalent and divalent cations. We have characterized the molecular mechanism by which these divalent cations interact with phosphoinositides. Calcium desolvates more readily, consistent with single-molecule calculations, and forms a network of ionic-like bonds that serve as a "molecular glue'' that allows a single ion to coordinate with up to three phosphatidylinositol-(4,5)-bisphosphate lipids. The phosphatidylinositol-(3,5)-bisphosphate isomer shows no such effect and neither does PI(4,5)P2 in the presence of Mg. The resulting network of Ca-mediated lipid-lipid bonds grows to span the entire simulation space and therefore has implications for the lateral distribution of phosophoinositides in the bilayer. We observe context-specific differences in lipid diffusion rates, lipid surface densities, and bilayer structure. The molecular-scale delineation of ion-lipid arrangements reported here provides insight into similar nanocluster formation induced by peripheral proteins to regulate the formation of functional signaling complexes on the membrane.</p>
Contrasting influences on bacterial symbiont specificity by co-occurring deep-sea mussels and tubeworms
<p>Relationships between deep-sea invertebrates and bacterial symbionts, fueled by sulfide and methane, are well known, yet factors influencing symbiont specificity remain cryptic. For animals that obtain their symbionts from the environment, both host identity and geographic location can impact the ultimate symbiont partner. Bacterial symbionts were analyzed for 3 co-occurring species each of <i>Bathymodiolus</i> mussels and vestimentiferan tubeworms, from three deep methane seeps off the west coast of Costa Rica. The bacterial internal transcribed spacer gene was analyzed via direct and barcoded amplicon sequencing to reveal fine-scale symbiont diversity. Each of the three mussel species (<i>B. earlougheri, B. billschneideri </i>and<i> B. nancyschneideri</i>) hosted genetically-distinct thiotrophic endosymbionts, despite living nearly side-by-side in their habitat, suggesting that host identity is influential in driving symbiont specificity.<b> </b>The dominant thiotrophic symbiont of co-occurring tubeworms <i>Escarpia spicata</i> and <i>Lamellibrachia (L. barhami </i>and<i> L. donwalshi)</i>, on the other hand, was identical regardless of host species or sample location, suggesting lack of influence by either factor on symbiont selectivity in this group of animals. These findings highlight the specific, yet distinct, influences on the environmental acquisition of symbionts in two foundational invertebrates with similar lifestyles, and provide a rapid and precise method of examining symbiont identities.</p>
Sex-specific transgenerational plasticity II: Grandpaternal effects are lineage- and sex-specific in threespined sticklebacks
<p>1. Transgenerational plasticity (TGP) occurs when the environment encountered by one generation (F0) alters the phenotypes of one or more future generations (e.g. F1 and F2). Sex selective TGP, via specific lineages or to only male or female descendants, has been underexplored in natural systems, and may be adaptive if it allows past generations to fine-tune the phenotypes of future generations in response to sex-specific life history strategies. </p> <p>2. We sought to understand if exposing males to predation risk can influence grandoffspring via sperm in threespined stickleback (Gasterosteus aculeatus). We specifically tested the hypothesis that grandparental effects are transmitted in a sex-specific way down the male lineage, from paternal grandfathers to F2 males. </p> <p>3. We reared F1 offspring of unexposed and predator-exposed F0 males under 'control' conditions and used them to generate F2s with control grandfathers, a predator-exposed maternal grandfather (i.e., predator-exposed F0 males to F1 daughters to F2 offspring), a predator-exposed paternal grandfather (i.e., predator-exposed F0 males to F1 sons to F2 offspring), or two predator-exposed grandfathers. We then assayed male and female F2s for a variety of traits related to antipredator defense. </p> <p>4. We found little evidence that transgenerational effects were mediated to only male descendants via the paternal lineage. Instead, grandpaternal effects depended on lineage and were mediated largely across sexes, from F1 males to F2 females and from F1 females to F2 males. When their paternal grandfather was exposed to predation risk, female F2s were heavier and showed a reduced change in behavior in response to a simulated predator attack relative to offspring of control, unexposed grandparents. In contrast, male F2s showed reduced antipredator behavior when their maternal grandfather was exposed to predation risk. However, these patterns were only evident when one grandfather, but not both grandfathers, was exposed to predation risk, suggesting the potential for non-additive interactions across lineages.</p> <p>5. If sex-specific and lineage effects are common, then grandparental effects are likely underestimated in the literature. These results draw attention to the importance of sex-selective inheritance of environmental effects and raise new questions about the proximate and ultimate causes of selective transmission across generations.</p>
Species-specific effects of thermal stress on the expression of genetic variation across a diverse group of plant and animal taxa under experimental conditions
<p>Assessing the genetic adaptive potential of populations and species is essential for better understanding evolutionary processes. However, the expression of genetic variation may depend on environmental conditions, which may speed up or slow down evolutionary responses. Thus, the same selection pressure may lead to different responses. Against this background, we here investigate the effects of thermal stress on genetic variation, mainly under controlled laboratory conditions. We estimated additive genetic variance (<i>V<sub>A</sub></i>), narrow-sense heritability (<i>h</i><sup>2</sup>), and the coefficient of genetic variation (<i>CV<sub>A</sub></i>) under both benign control and stressful thermal conditions. We included six species spanning a diverse range of plant and animal taxa and a total of 25 morphological and life-history traits. Our results show that (1) thermal stress reduced fitness components, (2) the majority of traits showed significant genetic variation, and that (3) thermal stress affected the expression of genetic variation (<i>V<sub>A</sub></i>, <i>h</i><sup>2</sup> or <i>CV<sub>A</sub></i>) in only one third of the cases (25 of 75 analyses, mostly in one clonal species). Moreover, effects were highly species-specific, with genetic variation increasing in 11 and decreasing in 14 cases under stress. Our results hence indicate that thermal stress does not generally affect the expression of genetic variation under laboratory conditions but, nevertheless, increases or decreases genetic variation in specific cases. Consequently, predicting the rate of genetic adaptation might not be generally complicated by environmental variation, but requires a careful case-by-case consideration.</p>
Temperature drives caste-specific morphological clines in ants
The morphology of organisms relates to most aspects of their life history and autecology. In particular, morphology can reflect adaptation to the abiotic environment in which species occur. As such, elucidating the drivers of morphological variation along environmental gradients might give insight into processes limiting species distributions. In eusocial organisms, the concept of morphology is more complex than in solitary organisms. Eusocial insects such as ants exhibit drastic morphological differences between reproductive and worker castes. How environmental selection operates on the morphology of each caste, and whether caste-specific selection has fitness consequences is largely unknown, but potentially crucial to understand what limits ant species' distributions. Here, we used 26,472 georeferenced morphometric measurements from 2206 individual ants belonging to 32 closely related North American species in the genus Formica to assess how ant morphology relates to geographic variation in the abiotic environment. Although precipitation and seasonality explained some of the geographic variation in morphology, temperature was the best predictor. Specifically, geographic variation in body size was positively related to temperature, meaning that ants are smaller in cold than in warm environments. Moreover, the strength of the relationship between size and temperature was stronger for the reproductive castes (i.e. queens and males) than for the worker caste. The shape of workers and males also varied along these large-scale abiotic gradients. Specifically, the relative length of workers' legs, thoraxes and antennae positively related to temperature, meaning that they had shorter appendages in cold environments. In contrast, males had smaller heads, but larger thoraxes in more seasonal environments. Overall, our results suggest that geographic variation in ambient temperature influences the morphology of ants, but that the strength of this effect is caste-specific. The effect of temperature on the queen caste may play an important role in determining colony fitness, and perhaps, limiting northern distributional limits. In conclusion, whereas ant ecology has traditionally focused on the worker caste, our study shows that considering the ecology of the reproductive castes is imperative to move forward in this field. 04-Aug-2020
Social competition stimulates cognitive performance in a sex-specific manner
Social interactions are thought to be a critical driver in the evolution of cognitive ability. Cooperative interactions, such as pair bonding, rather than competitive interactions have been largely implicated in the evolution of increased cognition. This is despite competition traditionally being a very strong driver of trait evolution. Males of many species track changes in their social environment and alter their reproductive strategies in response to anticipated levels of competition. We predict this to be cognitively challenging. Using a Drosophila melanogaster model we are able to distinguish between the effects of a competitive environment versus generic social contact by exposing flies to same-sex same-species competition vs different species partners, shown to pose non-competitive contacts. Males increase olfactory learning/memory and visual memory after exposure to conspecific males only, a pattern echoed by increased expression of synaptic genes and an increased need for sleep. For females, largely not affected by mating competition, the opposite pattern was seen. The results indicate that specific social contacts dependent on sex, not simply generic social stimulation, may be an important evolutionary driver for cognitive ability in fruit flies.
Data and R code used in Delory et al (2020) Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants
<p>This repository contains the data and R markdown files supporting the findings presented in Delory et al (2020) Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants.</p>
Fig. 2 in Gender-Specific Reproductive Tissue in Ratites and Tyrannosaurus rex
Fig. 2. Dinosaur and ratite comparative views. (A) Freshly broken fragment of MOR 1125 shows laminar ELB separating CB and MB. Bone tissues decrease in density internal to the ELB, because of increased vascularity. (B) Emu tibia, midshaft section. Erosion rooms extending into ELB are secondarily filled by MB. (C) Ostrich bone, mid shaft. MB is distinct from CB, but no obvious ELB is visible and several large vascular sinuses are seen. (D) Higher magnification of MB region of MOR 1125, showing increased porosity and more random orientation of MB than CB or ELB. (E) Emu, stained (14) to distinguish bone from infiltrating marrow fat. MB is more vascular than overlying CB and exhibits a random, whorled pattern. (F) Ostrich MB, showing relationship of bony spicules to invading blood sinuses, colored red from remnant blood. (G) Ground section of MOR 1125. Dense cortical Haversian bone shows second- and third-generation remodeling. ELB separates Haversian bone from more vascular MB. (H) Similar orientation of emu femur shows dense CB, distinct ELB, and a thin layer of MB. (I) Ostrich MB appears more laminar than in (C) or (F) because of the longitudinal orientation of tubelike medullary spicules.
Data from: Genotype-specific effects of ericoid mycorrhizae on floral traits and reproduction in Vaccinium corymbosum
PREMISE OF THE STUDY: Most plants interact with mycorrhizal fungi and animal pollinators simultaneously. Yet, the effects of mycorrhizae on pollination are poorly understood. Here, we examined how inoculation with ericoid mycorrhizal fungi affected flowering phenology, floral traits, and reproductive success among eight genotypes of Vaccinium corymbosum (Ericaceae). We asked three overarching questions: 1) do genotypes differ in response to inoculation? 2) How does inoculation affect floral and flowering traits? 3) Are inoculated plants more attractive to pollinators and thus less pollen limited than non-inoculated plants of the same genotype? METHODS: To examine these questions, we experimentally inoculated plants with fungal spores at planting, grew them in the field, and took flowering and floral measurements over two years. In year two, we conducted a hand-pollination experiment to test if plants differed in pollen limitation. KEY RESULTS: Our results demonstrated that inoculated plants had significantly higher levels of colonization for some genotypes but not all, and there were significant floral trait changes in inoculated plants for some genotypes as well. On average, inoculated plants produced significantly larger floral displays, more fruits/inflorescence, and heavier fruits with lower sugar content, than non-inoculated, control plants. Hand pollination enhanced the production of fruits, and fruit mass, for non-inoculated plants but not for those that were inoculated. CONCLUSIONS: Our results demonstrate that ericoid mycorrhizal fungi enhance flowering and alter investment in reproduction in genotype-specific ways. These findings underscore the importance of examining belowground symbionts to fully understand the drivers of aboveground interactions.
Assigning the sex-specific markers via genotyping-by-sequencing onto the Y chromosome for a torrent frog Amolops mantzorum
<p><span>We use a genotyping-by-sequencing (GBS) approach to identify sex-linked markers in a torrent frog (<i>Amolops mantzorum</i>) using wild-caught individuals of 21 males and 19 females from the same population. A total of 141 putatively sex-linked markers were screened from 1,015,964 GBS tags through three approaches, respectively based on sex differences in allele frequencies, sex difference in heterozygosity, and sex-limited occurrence. With validations, 69 sex-linked markers were confirmed, all of which point to male heterogamety. The male specificity of eight sex markers was further verified by PCR amplifications with a large number of additional individuals covering the whole geographic distribution of the species. Y chromosome (No. 5) was microdissected under a light microscope, amplified by whole-genome amplification, and assembled a draft Y genome. 55 out of 69 sex-linked markers could be mapped to the Y chromosome assembly (i.e 79.7 %). Thus the chromosome 5 could be added as candidate chromosomes that particularly favored to recruit for sex determination than others among frogs. Three sex-linked markers that mapped on Y chromosome were aligned to three different promoter regions of <i>Rana rugosa</i> CYP19A1 gene, which might be considered as a candidate gene to trigger sex determination in <i>A</i>.<i> mantzorum</i>.</span></p>
Mitogenomes reveal alternative initiation codons and lineage-specific gene order conservation in echinoderms
<p>Sample information, gene alignments and concatenated matrix</p>
Raw fitness data (offspring number and weight), main dataset for manuscript: Female-specific resource limitation does not make the opportunity for selection more female biased
<p>The present dataset contains the entirety of the raw empirical data used in the manuscript entitled: "Female-specific resource limitation does not make the opportunity for selection more female biased". This data is composed of offspring count and weight, which represent proxys of fitness. Fitness was assessed for males and females independently, and across three different experimental treatments. These fitness measures are used to calculate the opportunity for selection, as the variance in realtive fitness. Detailed methods regarding data collection can be found in the main manuscript.</p>
Template for bundle-specific tractography
<p><strong>Bundle-specific tractography</strong></p> <p>This data is made to be used with the following script: <a href="https://github.com/scilus/scilpy/blob/master/scripts/scil_generate_priors_from_bundle.py">scil_generate_priors_from_bundle.py</a><br> This <a href="https://github.com/scilus/bstflow/">Nextflow pipeline</a> is made to simplify the execution.</p> <p>The script/pipeline and provided dataset are the same used in this publication:</p> <p><em>Rheault, Francois, et al. "Bundle-specific tractography with incorporated anatomical and orientational priors." NeuroImage 186 (2019): 382-398.</em><br> </p>
SNPs markers of Trypoxylus dichotomus developed by using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques
<p>The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high-resolution single nucleotide polymorphisms (SNPs) for genotyping.</p>
Controlled Experiment in Crosscutting Concerns Identification from Software Requirements Specification
<p>The concern is a group of requirements with the same purpose, which are known as crosscutting concerns when they are scattered and tangled in the system. Identifying and separating these concerns is a matter of huge importance to software maintainability and evolution. For this, some approaches are proposed. There are few experimental studies comparing and analyzing these approaches in detail. In this paper, our aim is to provide empirical evidence about two approaches in this context. We conducted a controlled experiment to compare the effectiveness of two approaches, which identify crosscutting concerns in the requirements specification, followed by an assessment of its perceived utility and ease of use. Our results indicate that, in this given context and planned scenario, there are significant differences between the effectiveness of ObasCId and Theme/Doc approaches.</p>
Targeting diamondback moth in greenhouses by attracting specific native parasitoids with herbivory-induced plant volatiles
<p>We investigated whether recruitment of specific parasitoids using a specific blend of synthetic herbivory-induced plant volatiles (HIPVs) could be a novel method of pest control in greenhouses. In the Miyama rural area in Kyoto, Japan,diamondback moth (DBM) (<i>Plutella xylostella</i>) larvae are an important pest of cruciferous crops in greenhouses, and <i>Cotesia vestalis</i>, a larval parasitoid of DBM, are found in the surrounding areas. Dispensers of HIPVs that attracted <i>C. vestalis</i> and honey feeders were set inside greenhouses (treated greenhouses). The monthly incidence of DBM in the treated greenhouses was significantly lower than that in the untreated greenhouses across a two-year period. The monthly incidences of <i>C. vestalis</i> and DBM were not significantly different in the untreated greenhouses, whereas the monthly incidence of <i>C. vestalis</i> was significantly higher than that of DBM in the treated greenhouses. Poisson regression analyses showed that, in both years, a significantly higher number of <i>C. vestalis</i> was recorded in the treated greenhouses than in the untreated greenhouses when the number of DBM adults increased. We concluded that DBM was suppressed more effectively by <i>C. vestalis</i> in the treated greenhouses than in the untreated greenhouses.</p>
Fast and accurate estimation of species-specific diversification rates using data augmentation
Diversification rates vary across species as a response to various factors, including environmental conditions and species-specific features. Phylogenetic models that allow accounting for and quantifying this heterogeneity in diversification rates have proven particularly useful for understanding clades diversification. Recently, we introduced the cladogenetic diversification rate shift model (ClaDS), which allows inferring subtle rate variations across lineages. Here we present a new inference technique for this model that considerably reduces computation time through the use of data augmentation and provide an implementation of this method in Julia. In addition to drastically reducing computation time, this new inference approach provides a posterior distribution of the augmented data, that is the tree with extinct and unsampled lineages as well as associated diversification rates. In particular, this allows extracting the distribution through time of both the mean rate and the number of lineages. We assess the statistical performances of our approach using simulations and illustrate its application on the entire bird radiation.
Sex-specific sterility caused by extreme temperatures is likely to create cryptic changes to the operational sex ratio in Drosophila virilis
<p>Climate change is increasing the frequency and severity of short-term heat shocks that threaten the persistence of natural populations. The effect of thermal stress on natural selection is a common topic of debate, but high temperatures can also influence sexual selection. Typically, males and females of a species can survive at similar extreme temperatures, but males have been shown to lose fertility at lower temperatures than females. Here, we examine how a brief exposure of pupae to high temperatures in the fruit fly Drosophila virilis affects adult fertility in both males and females. We find strong sexual dimorphism in temperature-induced sterility. This has the potential to quickly and unpredictably create populations composed of mostly sterile males and fertile females, resulting in changes to the operational sex ratio (OSR). These disruptions are likely to be cryptic and difficult to measure in the wild, especially considering that males can eventually recover fertility and that sterile males of some species can still copulate. Changes to the OSR in this way are likely to influence sexual selection by favouring females that can discriminate between fertile and sterilised males, and possibly leading to female-female conflict over a limited pool of fertile males. Further research on how cryptic disruptions to the OSR affect sexual selection dynamics is critical for understanding the impact of environmental change on biodiversity.</p>
Protocol and data analysis scripts for high-throughput phenotyping of specific root respiration
<p>This repository contains a PDF written protocol with figures describing a method for measuring root respiration using an infrared gas analyzer (LI-850) and the R script necessary for processing the text files to derive CO<sub>2</sub> flux. Just download the ZIP file, unzip locally, open either the PDF or the .R file.</p> <p><strong>root_respiration_protocol.pdf </strong>- The illustrated protocol includes instruments and parts needed.</p> <p><strong>root_respiration_script.R - </strong>A script for processing the included 15 <em>.txt </em>files as examples from a LI-850 Gas Analyzer and extract absolute CO<sub>2</sub> flux with example code for how to incorporate root mass or length to derive specific root respiration. It is intended to run directly in RStudio and will automatically set the working directory in that case.</p> <p><strong>Please cite this repository if the protocol or R script is used in your work. </strong></p> <p>Guo, H., Ayalew, H., Seethepalli, A., Dhakal, K., Griffiths, M., Ma, X., York, L. M. (2020). Protocol and data analysis scripts for high-throughput phenotyping of specific root respiration [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4247873</p> <p><strong>The first manuscript using and describing this method is available:</strong></p> <p>Guo, H., Ayalew, H., Seethepalli, A., Dhakal, K., Griffiths, M., Ma, X., York, L. M. (2021). Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture. <em><a href="https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.17329">New Phytologist. DOI: 10.1111/nph.17329</a></em></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.