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3,937 results for “number”
Data from: The basic-reproduction number of infectious diseases in spatially structured host populations
<p>The spatial structure of a host population has a profound effect on the dynamics of infectious diseases. The basic reproduction number, a central quantity in the study of epidemic dynamics, is affected by host clustering as well as host density. Several authors have developed methods to quantify the basic reproduction number in a spatially structured host population. The methods used and the expressions derived are however difficult to apply to real life spatial host structures. In this paper we introduce an explicit expression for the basic reproduction number using the O-ring statistic, developed in spatial statistics, that quantifies the host density as a function of the distance from a randomly selected host individual. The O-ring statistic is frequently used in the study of the ecology of spatially structured plant populations, being a convenient summary of the properties of a landscape by way of a single function. The connection we develop between spatial statistics and epidemic dynamics can be used to study the effect of host spatial pattern on the basic reproduction number of infectious diseases. As well as showing how explicit expressions for the basic reproduction number can be derived for landscapes with standard structures, our expression for the basic reproduction number is tested against a simulation model. The model structure in our simulation is motivated by the spread of a plant disease epidemic, although it is applicable more broadly. The agreement between our analytic expression for the basic reproduction number and the corresponding numeric quantity extracted from simulations is close to perfect across a wide range of landscape structures and model parameterisations, and including cases in which more than one species of host is at risk of infection.</p>
Dataset related to the article "Binary classification of copy number alteration profiles in liquid biopsy with potential clinical impact in advanced NSCLC"
<p>This record contains original data used in the article "Binary classification of copy number alteration profiles in liquid biopsy with potential clinical impact in advanced NSCLC" to develop a linear support vector machine (SVM) classifier to predict chromosomal instability. </p> <p>We retrospectively evaluated the results of plasma NGS analysis performed at our Institution by using the AVENIO ctDNA Expanded Kit, a panel of 77 genes, which detects the major classes of genetic alterations. Binary classification, into “stable” (SCP) or “unstable” (UCP) chromosomal profiles, was initially performed by visual inspection of individual CNV alteration profiles by two independent professionals of our group. Then we decided to implement a support vector machine (SVM) classifier to automatically classify CNV profiles as SCP or UCP, beyond operators’ experience. We considered the segmented log2 ratios (.cns) files provided by the CNV kit software and computed three features (Segments, Size, Chromosomes). An alteration (“occurrence of instability”) in the CNV profile was defined each time we found a DNA segment of any size with absolute value of the log2 copy ratio exceeding a fixed cut-off. Two different cut-off values on log2 copy ratio were examined: 0.1 and 0.2. Once the cut-off was defined, three features were considered as covariates in the SVM classifier: 1) number of altered segments (Segments), 2) total length of altered regions (Size) and 3) number of affected chromosomes (Chromosomes).</p> <p>The “dataset_0.1.txt” and “dataset_0.2.txt” files are the original data matrices obtained by considering a cut-off of 0.1 and 0.2, respectively, on the absolute value of the log2 copy ratio.</p> <p>Rows represent available samples in our study (n=177). Columns contain the following variables: anonymized sample IDs (Sample), the class, “stable” or “unstable”, as assigned by two independent professionals of our group (Class), the corresponding binary label (Label: 0 for “stable”, 1 for “unstable”), the three features used as covariates in the SVM classifier and computed as described above (Segments, Size, Chromosomes).</p> <p><br>For the detailed results of our work, please refer to the full article.</p>
Size-dependent Copy Number Analysis Data
<p>Data<strong> </strong>used for analysis described in <em><span>Pan-cancer copy number analysis identifies optimized size thresholds and co-occurrence models for individualized risk stratification</span></em></p> <p><strong>MeningiomaSegs.zip </strong>contains the generated copy number segmentation from the sesame pipeline for 565 meningioma samples used in this project</p> <p><strong>MeningiomaClinical.xlsx </strong>contains deidentified clinical outcomes and relevant molecular data for meningioma samples</p> <p><strong>blank_CNV_table.xlsx </strong>is a blank template loaded in several R scripts in this project</p> <p><strong>hg38.14_chrom_arms_manual.txt </strong>Details the starting and ending points of chromosome arms</p> <p><strong>sampleinventory_excluded.xlsx</strong> Lists the TCGA cancer types and how many samples have both copy number and clinical data after manual exclusion of other samples</p>
Improvements to the dynamic wake meandering model by incorporating the turbulent Schmidt number
<p>Data to replicate the figures in Brugger, P., Markfort, C., and Porté-Agel, F.: Improvements to the Dynamic Wake Meandering Model by incorporating the turbulent Schmidt number, Wind Energ. Sci. Discuss. [preprint], https://doi.org/10.5194/wes-2023-150, 2023.</p>
Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen - Supplementary Data files
<p>Supplementary Data file 3-4 included in the manuscript Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen. </p>
Fig. 2 in Celebration time: here's to 500 numbers of Far Eastern Entomologist
Fig. 2. Prof. Sergey Yu. Storozhenko – Editor-in-Chief of the journal since 1994.
Fig. 4 in Celebration time: here's to 500 numbers of Far Eastern Entomologist
Fig. 4. Number of authors of the journal "Far Eastern Entomologist" by countries.
Data from: Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers, and life history
<p>The Major Histocompatibility Complex (MHC) multigene family encodes key pathogen-recognition molecules of the vertebrate adaptive immune system. Hyper-polymorphism of MHC genes is <em>de novo</em> generated by point mutations, but new haplotypes may also arise by re-shuffling of existing variation through intra- and inter-locus gene conversion. Although the occurrence of gene conversion at the MHC has been known for decades, we still have limited understanding of its functional importance. Here, I took advantage of extensive genetic resources (~9000 sequences) to investigate a broad scale macroevolutionary patterns in gene conversion processes at the MHC across nearly 200 avian species. Gene conversion was found to constitute a universal mechanism in birds, as 83% of species showed footprints of gene conversion at either MHC class and 25% of all allelic variants were attributed to gene conversion. Gene conversion processes were stronger at MHC-II than MHC-I, but inter-specific variation at both MHC classes was explained by similar evolutionary scenarios, reflecting fluctuating selection towards different optima and drift. Gene conversion showed uneven phylogenetic distribution across birds and was driven by gene copy number variation, supporting significant role of inter-locus gene conversion processes in the evolution of the avian MHC. Finally, MHC gene conversion was stronger in species with fast life histories (high fecundity) and in long-distance migrants, likely reflecting variation in population sizes and host-pathogen coevolutionary dynamics. The results provide a robust comparative framework for understanding macroevolutionary variation in gene conversion at the avian MHC and reinforce important contribution of this mechanism to functional MHC diversity.</p>
Mutation frequency and copy number alterations determine prognosis and metastatic tropism in 60.000 clinical cancer samples
<p>The intricate interplay between somatic mutations and copy number alterations critically influences tumour evolution and patient prognosis. Traditional genomic studies often overlook this interplay by analysing these two biomarker types in isolation. We developed INCOMMON, a computational method to detect allele-specific copy number alterations from clinical targeted panels without matched normal, discover recurrent tumour-specific patterns of co-existing mutations and copy-number alterations, and stratify patients based on these composite genotypes for downstream analyses of survival, metastatic propensity and organotropism. The tool can be used as an open-source R package available at <a href="https://github.com/caravagnalab/INCOMMON">https://github.com/caravagnalab/INCOMMON</a>, and a shiny application available at <a href="https://ncalonaci.shinyapps.io/incommon/" target="_blank" rel="noopener">https://ncalonaci.shinyapps.io/incommon/</a>. This repository contains all the scripts that we used to analyse PCAWG, TCGA, MSK-MetTropism and AACR GENIE-Dfci data, and all the relevant results in the form of data tables.<strong></strong></p>
Fig. 1 in Number And Dynamics Of Zooplankton Taxa In The Daugava River And Pļaviņas Reservoir
Fig. 1. Localities of sampling sities in 2014 and 2015.
Data from: The influence of the number of tree searches on maximum likelihood inference in phylogenomics
<p>Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., ten) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was ≥ 10. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6 /15 phylogenomic datasets. Lastly, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.</p>
Extirpated species in Berlin, dates of last detections, habitats, and number of Berlin's inhabitants
<p>Species loss is highly scale-dependent, following the species-area relationship. We analysed spatio-temporal patterns of species' extirpation on a multitaxonomic level using Berlin, the capital city of Germany. Berlin is one of the largest cities in Europe and has experienced a strong urbanisation trend since the late 19th century. We expected species' extirpation to be exceptionally high due to the long history of urbanisation. Analysing regional Red Lists of Threatened Plants, Animals, and Fungi of Berlin (covering 9498 species), we found that 16 % of species were extirpated, a rate 5.9 times higher than at the German scale, and 47.1 times higher than at the European scale. Species' extirpation in Berlin is comparable to that of another German city with a similarly broad taxonomic coverage, but much higher than in regional areas with less human impact. The documentation of species' extirpation started in the 18th century and is well documented for the 19th and 20th centuries. We found an average annual extirpation of 3.6 species in the 19th century, 9.6 species in the 20th century, and the same number of extirpated species as in the 19th century were documented in the 21th century, despite the much shorter time period. Our results showed that species' extirpation is higher at small than on large spatial scales, and might be negatively influenced by urbanisation, with different effects on different taxonomic groups and habitats. Over time, we found that species' extirpation is highest during periods of high human alterations and is negatively affected by the number of people living in the city. But, there is still a lack of data to decouple the size of the area and the human impact of urbanisation. However, cities might be suitable systems for studying species' extirpation processes due to their small scale and human impact.</p>
Activational and organizational effects of testosterone on the number of mating partners and reproductive success in males of a social rodent
<p>The timing of exposure to the steroid hormone, testosterone, produces activational and organizational effects in vertebrates. These activational and organizational effects are hypothesized to relate with the number of female mating partners and reproductive success in males. We tested this hypothesis by examining 151 wild degu (<em>Octodon degus</em>) males across a 10-year study. We quantified the association between adult serum testosterone levels (i.e., an indirect index of adult activational effects) and anogenital distance (AGD) length (i.e., a direct index of fetal organizational effects), and their interaction on the number of female mating partners and reproductive success. We found no evidence of an association between adult male serum testosterone levels and the number of female mating partners, or between adult male serum testosterone levels and reproductive success. However, male AGD was positively associated with reproductive success, but not so with the number of female mating partners. Additionally, the positive association between male AGD and male reproductive success was mediated by the number of mates. Our findings do not support major roles of activational or organizational effects of testosterone on the number of female mating partners and its consequences on male reproductive success. Instead, our results suggest that compared with individual male attributes, the female social environment plays a more important role in driving male reproductive success.</p>
Toward a better understanding of curve number and initial abstraction ratio values from a large-dataset of watersheds perspective
<p>The code within this repository is founded on the analysis of the Natural Resources Conservation Service Curve Number (NRCS-CN) method and its parameters. The analyses make use of the [CARAVAN dataset and your extensios] (<a href="../records/6578598" rel="nofollow">https://zenodo.org/records/6578598</a>). The separation of streamflow into baseflow and runoff is based on the methodology established by Xie et al. (2020) (<a href="https://doi.org/10.1016/j.jhydrol.2020.124628" rel="nofollow">https://doi.org/10.1016/j.jhydrol.2020.124628</a>).</p> <p>Contained within this repository are 5 Jupyter Notebooks, each focused on the application of the NRCS-CN method using distinct data analysis approaches:</p> <ul> <li>Principal Components Analysis</li> <li>Random Forest</li> <li>NRCS-NEH</li> <li>NRCS-ASYMPTOTIC </li> <li>NRCS-LEAST-SQUARES</li> </ul> <p>Additionally, the results of the metrics from applying these methods can be found in the files Metrics_runoff_G1 and Metrics_runoff_G2. The folder Times_series contains the time series of simulated runoff using the NRCS methods.</p> <p>Channel Log: </p> <p> Version v2 - Version of the official paper release. No changes in the data but added a static copy of the accompanying code of the paper. </p> <p>Version 1.0 - In this version, the Asymptotic method was considered with natural data</p>
Copy number variation heterogeneity & hierarchical cancer classifications
<p>This is the CNV data from progenetix on the NCIt morphology tree used in the study Copy number variation heterogeneity reveals biological inconsistency in hierarchical cancer classifications. The columns are separated by tabs, and the values indicate the max CNV value of the biosample on the corresponding bin (1MB) of the genome.</p>
Dataset for "Aerosol mixing state, new particle formation, and cloud droplet number concentration in an urban environment "
<p>Inverted HTDMA data, parcel model input, and parcel model output associated with the manuscript. HTDMA data are from the TRACER campaign and inverted using the LSQ1 or LSQ2 method described in Petters (2021). Model input is a 4 lognormal aerosol mode representation of the aerosol size distribution during TRACER, obtained by fitting measured size distributions obtained from mobility-based and optical-based sensors. Hygroscopicity is assigned for each mode based on observed size-resolved hygroscopicity from the HTDMA measurements. Model output refers to parcel model simulations using the pyrcel model (Rothenberg and Iompar).</p> <p>Petters, M. D.: Revisiting matrix-based inversion of scanning mobility particle sizer (SMPS) and humidified tandem differential mobility analyzer (HTDMA) data, Atmos. Meas. Tech., 14, 7909–7928, https://doi.org/10.5194/amt-14-7909-2021, 2021. </p> <p>Rothenberg, D. and lompar: darothen/pyrcel: Pyrcel v1.3.2, , https://doi.org/10.5281/zenodo.8378595, 2023.563</p>
Crater diameter of granular polystyrene layer with various diameter of grains and Weber number of water droplet
<p>Datas about experiments of impacts made in 2021-2023. A water droplet impacting a polystyrene granular layer of 4 differents grains diameters. These datas give the crater diameter obtain in function of the Weber number of the droplet. A file from tomography of the granular layer before impact is added.</p>
Figure 1-Validation of a Web Application by Using a Limited Number of Web Pages
<p>Figure 1 shows the GARWA for this example.</p>
Human-related ignitions increase the number of large wildfires across U.S. ecoregions
<p>This data was used in the analysis in the article "Human-related ignitions increase the number of large wildfires across U.S. ecoregions" by R. Chelsea Nagy, Emily Fusco, Bethany Bradley, John T. Abatzoglou, and Jennifer Balch. This article was accepted for publication in the journal Fire on 22 January 2018.</p>
Evolutionary mechanisms of varying chromosome numbers in the radiation of Erebia butterflies
<p>This is the dataset for the study with the same title published at MDPI Genes (please see the paper for all details).</p> <p>To test for a phylogenetic signal of varying chromosome numbers in Erebia butterflies (Lucek submitted), I reconstructed a phylogeny using a subset of Peña et al. Biol J Linn Soc 2016 for which chromosome numbers were available. Data for an additional 5 species was taken from GenBank. Chromosome numbers used are included.<br> The final alignment comprised sequence data for four genes: 620 bp of the mitochondrial cytochrome oxidase subunit I (COI), 598 bp of the nuclear glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 565 bp of the nuclear ribosomal protein S5 (RpS5) and 343 bp of the nuclear wingless gene.</p> <p>I used PartitionFinder 2 (Lanfear et al. Mol Biol Evol 2017) to infer the best partition scheme and associated substitution model for each codon position and gene. The output of PartitionFinder is provided in the data file. The resulting best partitioning scheme for the Bayesian inference is given in each nexus file. For the maximum likelihood (ML) based phylogeny I used the GTR model with invariant sites and gamma correction (GTR+I+G) in RAXML 8.2.8 (Stamatakis, Bioinformatics 2014) with the corresponding partition scheme from PartitionFinder. I further used 1000 bootstrap replicates to assess significance. I ran RAXML for the dataset comprising either all four genes, the mitochondrial COI gene only or the three nuclear genes. In the latter case, data was only available for 35 taxa. I conducted the Bayesian analysis in MrBayes 3.2.2 (Ronquist et al. Syst Biol 2012) for either dataset using in each case, 5’000’000 generations with four chains – three heated and one cold. Trees were sampled every 1’000 generations.<br> Provided are the input and output files of MrBayes and RAXML for all genes combined (subfolder all), the mitochondrial COI gene only (subfolder mtdna) or the three nuclear genes (subfolder nuclear).</p>
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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)
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.