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2,015 results for “context”
Data from: Quantifying individual heterogeneity and its influence on life-history trajectories: different methods for different questions and contexts
Heterogeneity among individuals influences the life-history trajectories we observe at the population level because viability selection, selective immigration and emigration processes, and ontogeny change the proportion of individuals with specific trait values with increasing age. Here, we review the two main approaches that have been proposed to account for these processes in life-history trajectories, contrasting how they quantify ontogeny and selection, and proposing ways to overcome some of their limitations. Nearly all existing approaches to model individual heterogeneity assume either a single normal distribution or a priori known groups of individuals. Ontogenetic processes, however, can vary across individuals through variation in life-history tactics. We show the usefulness of describing ontogenetic processes by modelling trajectories with a mixture model that focuses on heterogeneity in life-history tactics. Additionally, most methods examine individual heterogeneity in a single trait, ignoring potential correlations among multiple traits caused by latent common sources of individual heterogeneity. We illustrate the value of using a joint modelling approach to assess the presence of a shared latent correlation and its influence on life-history trajectories. We contrast the strengths and limitations of different methods for different research questions, and we exemplify the differences among methods using empirical data from long-term studies of ungulates.
Data from: A continuous morphological approach to study the evolution of pollen in a phylogenetic context: an example with the order Myrtales
The study of pollen morphology has historically allowed evolutionary biologists to assess phylogenetic relationships among Angiosperms, as well as to better understand the fossil record. During this process, pollen has mainly been studied by discretizing some of its main characteristics such as size, shape, and exine ornamentation. One large plant clade in which pollen has been used this way for phylogenetic inference and character mapping is the order Myrtales, composed by the small families Alzateaceae, Crypteroniaceae, and Penaeaceae (collectively the "CAP clade"), as well as the large families Combretaceae, Lythraceae, Melastomataceae, Myrtaceae, Onagraceae and Vochysiaceae. In this study, we present a novel way to study pollen evolution by using quantitative size and shape variables. We use morphometric and morphospace methods to evaluate pollen change in the order Myrtales using a time-calibrated, supermatrix phylogeny. We then test for conservatism, divergence, and morphological convergence of pollen and for correlation between the latitudinal gradient and pollen size and shape. To obtain an estimate of shape, Myrtales pollen images were extracted from the literature, and their outlines analyzed using elliptic Fourier methods. Shape and size variables were then analyzed in a phylogenetic framework under an Ornstein-Uhlenbeck process to test for shifts in size and shape during the evolutionary history of Myrtales. Few shifts in Myrtales pollen morphology were found which indicates morphological conservatism. Heterocolpate, small pollen is ancestral with largest pollen in Onagraceae. Convergent shifts in shape but not size occurred in Myrtaceae and Onagraceae and are correlated to shifts in latitude and biogeography. A quantitative approach was applied for the first time to examine pollen evolution across a large time scale. Using phylogenetic based morphometrics and an OU process, hypotheses of pollen size and shape were tested across Myrtales. Convergent pollen shifts and position in the latitudinal gradient support the selective role of harmomegathy, the mechanism by which pollen grains accommodate their volume in response to water loss.
Data from: Adult dietary protein has age- and context-dependent effects on male post-copulatory performance
The highly-conserved effect of dietary protein restriction on life-span and ageing is observed in both sexes and across a vast range of taxa. This extension of life-span is frequently accompanied by a reduction in female fecundity and it has been hypothesised that individuals may reallocate resources away from reproduction and into somatic maintenance. However, effects of dietary protein restriction on male reproduction are less consistent, suggesting that these effects may depend on other environmental parameters. Using the neriid fly, Telostylinus angusticollis, we examined age-specific effects of adult dietary protein restriction on male post-copulatory reproductive performance (fecundity and offspring viability). To explore the context-dependence of these effects, we simultaneously manipulated male larval diet and adult mating history. We found that protein-restricted males sired less viable offspring at young ages, but offspring viability increased with paternal age and eventually exceeded that of fully-fed males. The number of eggs laid by females was not affected by male dietary protein, whereas egg hatching success was subject to a complex interaction of male adult diet, age, larval diet, and mating history. These findings suggest that effects of protein restriction on male reproduction are highly context-dependent, and cannot be explained by a simple reallocation of resources from reproduction to somatic maintenance. Rather, these effects appear to involve changes in the scheduling of male reproductive investment with age.
Data from: Visual landmarks sharpen grid cell metric and confer context specificity to neurons of the medial entorhinal cortex
Neurons of the medial entorhinal cortex (MEC) provide spatial representations critical for navigation. In this network, the periodic firing fields of grid cells act as a metric element for position. The location of the grid firing fields depends on interactions between self-motion information, geometrical properties of the environment and nonmetric contextual cues. Here, we test whether visual information, including nonmetric contextual cues, also regulates the firing rate of MEC neurons. Removal of visual landmarks caused a profound impairment in grid cell periodicity. Moreover, the speed code of MEC neurons changed in darkness and the activity of border cells became less confined to environmental boundaries. Half of the MEC neurons changed their firing rate in darkness. Manipulations of nonmetric visual cues that left the boundaries of a 1D environment in place caused rate changes in grid cells. These findings reveal context specificity in the rate code of MEC neurons.
Data from: Accurate estimation of substitution rates with neighbour-dependent models in a phylogenetic context
Most models and algorithms developed to perform statistical inference from DNA data make the assumption that substitution processes affecting distinct nucleotide sites are stochastically independent. This assumption ensures both mathematical and computational tractability, but is in disagreement with observed data in many situations -- one well-known example being CpG dinucleotide hypermutability in mammalian genomes. In this paper, we consider the class of RN95+YpR substitution models, which allows neighbour-dependent effects -- including CpG hypermutability -- to be taken into account, through transitions between pyrimidine-purine dinucleotides. We show that it is possible to adapt inference methods originally developed under the assumption of independence between sites to RN95+YpR models, using a mathematically rigorous framework provided by specific structural properties of this class of models. We assess how efficient this approach is at inferring the CpG hypermutability rate from aligned DNA sequences. The method is tested on simulated data and compared against several alternatives; the results suggest that it delivers a high degree of accuracy at a low computational cost. We then apply our method to an alignment of ten DNA sequences from primate species. Model comparisons within the RN95+YpR class show the importance of taking into account neighbour-dependent effects. An application of the method to the detection of hypomethylated islands is discussed.
Data from: Adaptation to elevated CO2 in different biodiversity contexts
In the absence of migration, species persistence depends on adaption to a changing environment, but whether and how adaptation to global change is altered by community diversity is not understood. Community diversity may prevent, enhance or alter how species adapt to changing conditions by influencing population sizes, genetic diversity and/or the fitness landscape experienced by focal species. We tested the impact of community diversity on adaptation by performing a reciprocal transplant experiment on grasses that evolved for 14 years under ambient and elevated CO2, in communities of low or high species-richness. Using biomass as a fitness proxy, we find evidence for local adaptation to elevated CO2, but only for plants assayed in a community of similar diversity to the one experienced during the period of selection. Our results indicate that the biological community shapes the very nature of the fitness landscape within which species evolve in response to elevated CO2.
Dataset for Social context modulates idiosyncrasy of behaviour in the gregarious cockroach Blaberus discoidalis
<p>Individuals are different, but they can work together to perform adaptive collective behaviours. Despite emerging evidence that individual variation strongly affects group performance, it is less clear to what extent individual variation is modulated by participation in collective behaviour. We examined light avoidance (negative phototaxis) in the gregarious cockroach Blaberus discoidalis, in both solitary and group contexts. Cockroaches in groups exhibit idiosyncratic light-avoidance performance that persists across days, with some individual cockroaches avoiding a light stimulus 75% of the time, and others avoiding the light just above chance (i.e. ~50% of the time). These individual differences are robust to group composition. Surprisingly, these differences do not persist when individuals are tested in isolation, but return when testing is once again done with groups. During the solo testing phase cockroaches exhibited individually consistent light-avoidance tendencies, but these differences were uncorrelated with performance in any group context. Therefore, we have observed not only that individual variation affects group-level performance, but also that whether or not a task is performed collectively can have a significant, predictable effect on how an individual behaves. That individual behavioural variation is modulated by whether a task is performed collectively has major implications for understanding variation in behaviours that are facultatively social, and it is essential that ethologists consider social context when evaluating individual behavioural differences.</p>
A Context-Driven Approach for Co-Auditing Smart Contracts with The Support of GPT-4
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Socioemotional behavior vs Context
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Dataset of Code Context Models
<p>This is a dataset of code context models. Please refer to README for more information.</p>
CRITICAL ASSESSMENT OF THE THEORY AND PRACTICE OF QUALITIES, TYPES AND COMMUNICATION IN EDUCATIONAL MANAGEMENT AND LEADERSHIP AND ITS APPLICABILITY IN THE CONTEXT OF LEADING PUBLIC COMPULSORY SCHOOLS IN UZBEKISTAN.
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Supplemental Material for Context Switch Sensitive Fault Localization
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Figure 14. Juvenile Stage I in Postembryonic development in freshwater crayfish (Decapoda: Astacidea) in an evolutionary context
Figure 14. Juvenile Stage I of Cambaroides japonicus. (A) Antenna 1, dorsal view; (B) antennal scale, dorsal view; (C) antenna 2, dorsal view; (D) mandible, view of inside of mouth; (E) maxilla 1, oral view; (F) maxilla 2, oral view; (G) first maxilliped, oral view; (H) second maxilliped, oral view; (I) third maxilliped, oral view, (J) pleopod. Scale bars: 0.25 mm.
Figure 8. Juvenile Stage I in Postembryonic development in freshwater crayfish (Decapoda: Astacidea) in an evolutionary context
Figure 8. Juvenile Stage I of Procambarus virginalis. (A) Antenna 1, dorsal view; (B) antennal scale, dorsal view; (C) antenna 2, dorsal view; (D) mandible, view of inside of mouth; (E) maxilla 1, oral view; (F) maxilla 2, oral view; (G) first maxilliped, oral view; (H) second maxilliped, oral view; (I) third maxilliped, oral view; (J) pleopod. Scale bars: 0.25 mm.
Figure 6 in Postembryonic development in freshwater crayfish (Decapoda: Astacidea) in an evolutionary context
Figure 6. Juvenile Stage III of Austropotamobius torrentium. (A) Antenna 1, dorsal view; (B) antennal scale, dorsal view; (C) flagellum of antenna 2, dorsal view; (D) mandible, view of inside of mouth; (E) maxilla 1, oral view; (F) maxilla 2, oral view; (G) first maxilliped, oral view; (H) second maxilliped, oral view; (I) third maxilliped, oral view; (J) pleopod. Scale bars: 0.25 mm, C: 1.0 mm.
How do students respond to different gestures produced by animated pedagogical agents? An investigation of attention, narrative recall, and knowledge transfer within a personalized learning context
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ENGLISH CONJUNCTIONS IN CONTEXT
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Context
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Single-cell multi-omics analysis identifies context specific gene regulatory gates and mechanisms
<p>There is a growing interest in inferring context specific gene regulatory networks from single-cell RNA sequencing (scRNA-seq) data. This involves identifying the regulatory relationships between transcription factors (TFs) and genes in individual cells, and then characterizing these relationships at the level of specific cell types or cell states. <br>In this study, we introduce scGATE (single-cell gene regulatory gate) as a novel computational tool for inferring TF-gene interaction networks and reconstructing Boolean logic gates involving regulatory TFs using scRNA-seq data. In contrast to current Boolean models, scGATE eliminates the need for individual formulations and likelihood calculations for each Boolean rule (e.g., AND, OR, XOR). By employing a Bayesian framework, scGATE infers the Boolean rule after fitting the model to the data, resulting in significant reductions in time-complexities for logic-based studies. <br>We have applied assay for transposase-accessible chromatin with sequencing (scATAC-seq) data and TF DNA binding motifs to filter out non-relevant TFs in gene regulations. By integrating single-cell clustering with these external cues, scGATE is able to infer context specific networks. The performance of scGATE is evaluated using synthetic and real single-cell multi-omic data from mouse tissues and human blood, demonstrating its superiority over existing tools for reconstructing TF-gene networks. Additionally, scGATE provides a flexible framework for understanding the complex combinatorial and cooperative relationships among TFs regulating target genes by inferring Boolean logic gates among them.</p>
ORAL CORPORA FOR BILINGUAL AND PLURILINGUAL CONTEXTS
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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.