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72 results for “usage data”
Data from: Complex genome evolution in A. coluzzii associated with increased insecticide usage in Mali
In certain cases, a species may have access to important genetic variation present in a related species via adaptive introgression. These novel alleles may interact with their new genetic background, resulting in unexpected phenotypes. In this study, we describe a selective sweep on standing variation on the X chromosome in the mosquito Anopheles coluzzii, a principal malaria vector in West Africa. This event may have been influenced by the recent adaptive introgression of the insecticide resistance gene known as kdr from the sister species Anopheles gambiae. Individuals carrying both kdr and a nearly fixed X-linked haplotype, encompassing at least four genes including the P450 gene CYP9K1 and the cuticular protein CPR125, have rapidly increased in relative frequency. In parallel, a reproductively isolated insecticide-susceptible A. gambiae population (Bamako form) has been driven to local extinction, likely due to strong selection from increased insecticide-treated bed net usage.
Data of the Paper: Stateful Depletion and Scheduling of Containers on Cloud Nodes for Efficient Resource Usage
<p>This is the online artifact containing the code, data and evaluation log of the experiment performed for the research paper accepted at IEEE QRS 2022 with the title: </p> <p><strong>Stateful Depletion and Scheduling of Containers on Cloud Nodes for Efficient Resource Usage</strong></p> <p><strong>Abstract:</strong> Container scheduling is a fundamental part of today’s service and cloud-based applications. Schedulers operate at different levels depending on how much control the system developers have. On the one hand, container orchestration managers such as Google Kubernetes manage the scheduling of containers to different nodes. On the other hand, serverless managers, such as Google Autopilot, take care of the underlying infrastructure automatically, and developers do not need to manage the nodes. However, when it comes to container depletion, i.e., removing the assigned cloud resources to an idle container, current scheduling technologies have limitations. In this paper, we propose our approach to managing cloud resource usage when containers are idle efficiently. For this purpose, we deplete idle containers statefully, i.e., propose a novel manager that monitors idle containers, saves their state, and efficiently depletes them. This manager reconstructs a depleted container using the saved state when reconstruction is needed. In our approach, we suggest an Infrastructure as Code component to automate the creation of new nodes if a depleted container cannot be scheduled on the same node, e.g., because of being overloaded. We provide an analytical model for the stateful depletion of containers and their rescheduling and empirically evaluate the accuracy of our model. For this purpose, we ran an experiment on a private cloud infrastructure and Google Cloud Platform. Our model has a low error rate of 4.28% averaged over public and private clouds.</p>
Gym lifestyle factors and male reproductive health: a study into young adult usage and perceptions - Survey data
<p>Survey data for the manuscript Gym lifestyle factors and male reproductive health: a study into young adult usage and perceptions</p>
Pre-Workshop Survey Report | 21-22 April 2023 OA Book Usage Data Exchange and Use Guidelines and Principles Meeting
<p>This document contains anonymous data collected through two pre-event surveys of invited event participants. The file was shared with and discussed among participants at the 21-22 April 2023 OA Book Usage Data Exchange and Use Guidelines and Principles Meeting. </p>
Data from: Usage of unscheduled hospital care by homeless individuals in Dublin, Ireland: a cross-sectional study
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Data from: Habitat usage of Daubenton's bat (Myotis daubentonii), common pipistrelle (Pipistrellus pipistrellus), and soprano pipistrelle (Pipistrellus pygmaeus) in a North Wales upland river catchment
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Data from: Exploring temporal patterning of psychological skills usage during the week leading up to competition: lessons for developing intervention programmes
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The value of increased spatial resolution of pesticide usage data for assessing risk to endangered species: Data, notebooks, and results
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Data from: Complex genome evolution in A. coluzzii associated with increased insecticide usage in Mali
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Data from: Variation in host plant usage and diet breadth predict sibling preference and performance in the neotropical tortoise beetle Chelymorpha alternans (Coleoptera: Chrysomelidae: Cassidinae)
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Does autotext usage decrease documentation time among resident physicians? A retrospective analysis of EHR usage data
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Data from: Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution
Background. The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. To understand the evolution of MARV at the codon level, we report a comprehensive analysis of synonymous codon usage patterns in MARV genomes. Multiple codon analysis approaches and statistical methods were performed to determine overall codon usage patterns, biases in codon usage, and influence of various factors, including mutation pressure, natural selection, and its two hosts, Homo sapiens and Rousettus aegyptiacus. Results. Nucleotide composition and relative synonymous codon usage (RSCU) analysis revealed that MARV shows mutation bias and prefers U- and A-ended codons to code amino acids. Effective number of codons analysis indicated that overall codon usage among MARV genomes is slightly biased. The Parity Rule 2 plot analysis showed that GC and AU nucleotides were not used proportionally which accounts for the presence of natural selection. Codon usage patterns of MARV were also found to be influenced by its hosts. This indicates that MARV have evolved codon usage patterns that are specific to both of its hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU patterns was found to be dominant compared with that from H. sapiens. Overall, mutation pressure was found to be the most important and dominant force that shapes codon usage patterns in MARV. Conclusions. To our knowledge, this is the first detailed codon usage analysis of MARV and extends our understanding of the mechanisms that contribute to codon usage and evolution of MARV.
Data from: Gene expression levels are correlated with synonymous codon usage, amino acid composition and gene architecture in the red flour beetle, Tribolium castaneum
Gene expression levels correlate with multiple aspects of gene sequence and gene structure in phylogenetically diverse taxa suggesting an important role of gene expression levels in the evolution of protein-coding genes. Here we present results of a genome-wide study of the influence of gene expression on synonymous codon usage, amino acid composition and gene structure in the red flour beetle, Tribolium castaneum. Consistent with the action of translational selection, we find that synonymous codon usage bias increases with gene expression. However, the correspondence between tRNA gene copy number and optimal codons is weak. At the amino acid level, translational selection is suggested by the positive correlation between tRNA gene numbers and amino acid usage which is stronger for highly expressed genes. In addition, there is a clear trend for increased use of metabolically cheaper, less complex, amino acids as gene expression increases. tRNA gene numbers also correlate negatively with amino acid size/complexity score indicating the coupling between translational selection and selection to minimize the use of large/complex amino acids. Interestingly, the correlation between tRNA gene numbers and amino acid size/complexity score appears to be widespread given our analyses of 10 additional genomes and might be explained by selection against negative consequences of protein misfolding. At the level of gene structure, three major trends are detected 1) CDS length increases across low and intermediate expression levels but decreases in highly expressed genes; 2) the average intron size shows the opposite trend, first decreasing with expression, followed by a slight increase in highly expressed genes and 3) intron density remains nearly constant across all expression levels. These changes in gene architecture are only in partial agreement with selection favoring reduced cost of biosynthesis.
Data from: Antagonistic relationships between intron content and codon usage bias of genes in three mosquito species: functional and evolutionary implications
Genome biology of mosquitoes holds potential in developing knowledge-based control strategies against vector-borne diseases such as malaria, dengue, West Nile Virus and others. Although the genomes of three major vector mosquitoes have been sequenced, attempts to elucidate the relationship between intron and codon usage bias across species in phylogenetic contexts are limited. In this study, we investigated the relationship between intron content and codon bias of orthologous genes among three vector mosquito species. We found an antagonistic relationship between codon usage bias and the intron number of genes in each mosquito species. The pattern is further evident among the intronless and the intron-containing orthologous genes associated with either low or high codon bias among the three species. Furthermore, the co-variance between codon bias and intron number has a directional component associated with the species phylogeny when compared with other non-mosquito insects. By applying a maximum likelihood based continuous regression method, we show that codon bias and intron content of genes vary among the insects in a phylogeny dependent manner but with no evidence of adaptive radiation or species-specific adaptation. We discuss the functional and evolutionary significance of antagonistic relationships between intron content and codon bias.
Data from: Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates
Synonymous codon usage (SCU) patterns are shaped by a balance between mutation, drift, and natural selection. To date, detection of translational selection in vertebrates has proven to be a challenging task, obscured by small long-term effective population sizes in larger animals and the existence of isochores in some species. The consensus is that, in such species, natural selection is either completely ineffective at overcoming mutational pressures and genetic drift or perhaps is effective but so weak that it is not detectable. The aim of this research is to understand the interplay between mutation, selection, and genetic drift in vertebrates. We observe that although variation in mutational bias is undoubtedly the dominant force influencing codon usage, translational selection acts as a weak additional factor influencing synonymous codon usage. These observations indicate that translational selection is a widespread phenomenon in vertebrates and is not limited to a few species.
Data for "Quantifying Discourse Marker Usage in Oral and Literary Discourse"
<p>Anonymized data for the paper "Quantifying Discourse Marker Usage in Oral and Literary Discourse" (currently under blind review)</p>
Data from: Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias
Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea to resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino-acid data provide implicit support for the respective optimal topologies. By analyzing the nucleotide data, we found that the 3rd codon positions are more saturated than the 1st and 2nd codon positions, and excluding these from the analyses leads to a topology congruent with that obtained using amino-acid data. Further, we determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a non-stationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoids the effects of synonymous mutations that underlie codon-usage bias, again recovered liverworts being sister to the remaining land plants. These analyses indicate that the discrepancy between the nucleotide-based and the amino acid-based trees is caused by the lineage specific, parallel compositional bias, or synonymous mutations driving codon-usage bias, as well as saturation in the 3rd codon positions. While genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein coding gene data and their amino-acids translations, by analyzing data modeling compositional bias, and by excluding nucleotide noisy signals due to saturation or codon-usage bias. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even when analyzing large-scale data sets, no matter how well-supported, without fully exploring the effects of substitution models.
Yamada et al Zylazine Usage Survey Data
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Data from: Modelling the impact of curtailing antibiotic usage in food animals on antibiotic resistance in humans
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Data from: Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution
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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)
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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.