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538 results for “Vector data”
Data, plotting scripts, and figures for "Accelerating Reactive-Flow Simulations using Vectorized Chemistry Integration"
<p>Data, plotting scripts, and figures for the article "Accelerating Reactive-Flow Simulations using Vectorized Chemistry Integration".</p>
Dynamic implicit modeling of tunnel unfavorable geology based on multi-source data fusion using support vector machine
<p>This is the relevant data of the article "Dynamic implicit modeling of tunnel unfavorable geology based on multi-source data fusion using support vector machine"</p>
Research data and example scripts for the paper "Bayesian Target-Vector Optimization for Efficient Parameter Reconstruction"
<p><strong>Bayesian Target-Vector Optimization for Efficient Parameter Reconstruction</strong></p> <p>This publication contains the research data and example scripts for the paper “Bayesian Target-Vector Optimization for Efficient Parameter Reconstruction” [1]. The research data is found in the directory <code>research_data</code>, the example scripts are found in the directory <code>example_scripts</code>.</p> <p>The research data contains all necessary information to be able to reconstruct the figures and values given in the paper, as well as all result figures shown. Where possible, the directories contain the necessary scripts to recreate the results themselves, up to stochastic variations.</p> <p>The example scripts are intended to show how one can (i), perform a least-square type optimization of a model function (here we focus our efforts on the analytical model functions MGH17 and Gauss3, as described in the paper) using various methods (BTVO, LM, BO, L-BFGS-B, NM, including using derivative information when applicable), and (ii), perform Markov chain Monte Carlo (MCMC) sampling around the found maximum likelihood estimate (MLE) to estimate the uncertainties of the MLE parameter (both using a surrogate model of the actual model function, as well as using the actual model function directly).</p> <p> </p> <p><strong>Research data</strong></p> <p>Contained are directories for the experimental problem GIXRF, and the two analytical model functions MGH17 and Gauss3. What follows is a listing of directories and the contents:</p> <ul> <li><code>gauss3_optimization</code>: Optimization logs for the Gauss3 model function for BTVO, LM, BO, L-BFGS-B, NM (with derivatives when applicable), .npy files used for generating the plots, a <code>benchmark.py</code> file used for the generation of the data, as well as the plots shown in the paper.</li> <li><code>mgh17_optimization</code>: Optimization logs for the MGH17 model function for BTVO, LM, BO, L-BFGS-B, NM (with derivatives when applicable), .npy files used for generating the plots, a <code>benchmark.py</code> file used for the generation of the data, as well as the plots shown in the paper.</li> <li><code>mgh17_mcmc_analytical</code>: Scripts for the creation of the plots (does not use an optimization log), as well as plots shown in the paper. This uses the model function directly to perform the MCMC sampling.</li> <li><code>mgh17_mcmc_surrogate</code>: Optimization log of the MGH17 function used for the creation of the MCMC plots, scripts for the creation of the plots (use the optimization log), as well as plots shown in the paper. This uses a surrogate model to perform the MCMC sampling.</li> <li><code>gixrf_optimization</code>: <code>benchmark.py</code> file to perform the optimization, the optimization logs for the various methods (BTVO, LM, BO, L-BFGS-B, NM), .npy files and scripts used for the creation of the plots, and the plots shown in the paper.</li> <li><code>gixrf_mcmc_supplement</code>: optimization log used for the creation of the plot, pickle file used for the creation of the plot, script to create the MCMC plot.</li> <li><code>gixrf_optimum_difference_supplement</code>: optimization logs of BTVO optimization of the GIXRF problem, scripts to create the difference/error plots shown for the GIXRF problem in the supplement, and the plots themselves.</li> </ul> <p><strong>Employed software for creating the research data</strong></p> <p>The software used in the creation is:</p> <ul> <li>JCMsuite Analysis and Optimization toolkit, development version, commit d55e99b (the closest commercial release is found in JCMsuite version 5.0.2)</li> <li>A list of Python packages installed (excerpt from <code>conda list</code>, name and version) <ul> <li>corner 2.1.0</li> <li>emcee 3.0.2</li> <li>jax 0.2.22</li> <li>jaxlib 0.1.72</li> <li>matplotlib 3.2.1</li> <li>numba 0.40.1</li> <li>numpy 1.18.1</li> <li>pandas 0.24.1</li> <li>python 3.7.11</li> <li>scikit-optimize 0.7.4</li> <li>scipy 1.7.1</li> <li>tikzplotlib 0.9.9</li> </ul> </li> <li>JCMsuite 4.6.3 for the evaluation of the experimental model</li> </ul> <p> </p> <p><strong>Example scripts</strong></p> <p>This directory contains a few sample files that show how parameter reconstructions can be performed using the JCMsuite analysis and optimization toolbox, with a particular focus on the Bayesian target-vector optimization method shown in the paper.</p> <p>It also contains example files that show how an uncertainty quantification can be performed using MCMC, both directly using a model function, as well as using a surrogate model of the model function.</p> <p>What follows is a listing of the contents of the directory:</p> <ul> <li><code>mcmc_mgh17_analytical.py</code>: performs a MCMC analysis of the MGH17 model function directly, without constructing a surrogate model. Uses <code>emcee</code>.</li> <li><code>mcmc_mgh17_surrogate.py</code>: performs a MCMC analysis of the MGH17 model function by constructing a surrogate model of the model function. Uses the JCMsuite analysis and optimization toolbox.</li> <li><code>opt_gauss3.py</code>: performs a parameter reconstruction of the Gauss3 model function using various methods (BTVO, LM, BO, L-BFGS-B, NM, with derivatives when applicable).</li> <li><code>opt_mgh17.py</code>: performs a parameter reconstruction of the MGH17 model function using various methods (BTVO, LM, BO, L-BFGS-B, NM, with derivatives when applicable).</li> <li><code>util/model_functions.py</code>: contains the MGH17 and Gauss3 model functions, their (automatic) derivatives, and objective functions used in the optimizations.</li> </ul> <p><strong>Requirements to execute the example scripts</strong></p> <p>These scripts have been developed and tested under Linux, Debian 10. We have tried to make sure that they would also work in a Windows environment, but can unfortunately give no guarantees for that.</p> <p>We mainly use Python to run the reconstructions. To execute the files, a few Python packages have to be installed. In addition to the usual scientific Python stack (NumPy, SciPy, matplotlib, pandas, etc.), the packages <code>jax</code> and <code>jaxlib</code> (for automatic differentiation of Python/NumPy functions), <code>emcee</code> and <code>corner</code> (for MCMC sampling and subsequent plotting of the results) have to be installed.</p> <p>This can be achieved for example using pip, e.g.</p> <pre><code>pip install -r requirements.txt</code></pre> <p>Additionally, JCMsuite has to be installed. For this you can visit [2] and download a free trial version.</p> <p>On Linux, the installation has to be added to the PATH, e.g. by adding the following to your <code>.bashrc</code> file:</p> <pre><code>export JCMROOT=/FULL/PATH/TO/BASE/DIRECTORY export PATH=$JCMROOT/bin:$PATH export PYTHONPATH=$JCMROOT/ThirdPartySupport/Python:$PYTHONPATH</code></pre> <p> </p> <p><strong>Bibliography</strong></p> <p>[1] <span>M. Plock</span>, <span> K. Andrle</span>, <span> S. Burger</span>, <span> P.-I. Schneider</span>, <span>Bayesian Target-Vector Optimization for Efficient Parameter Reconstruction</span>. <em>Adv. Theory Simul.</em> <strong><span>5</span></strong>, 2200112 (2022).</p> <p>[2] https://jcmwave.com/</p>
Supporting data and code for "A new look at the potential role of marine plastic debris as a global vector of toxic benthic algae".
<p>R code and dataset for: Leite I.P., Menegotto A., Lana P.C. & Mafra Jr LL. 2022. A new look at the potential role of marine plastic debris as a global vector of toxic benthic algae. Science of the Total Environment, 838, 156262.</p>
ROS and SGI data for manuscript "The perception and evolution of flagellin, cold shock protein, and elongation factor Tu from vector-borne bacterial plant pathogens"
<p>This contains raw data for the ROS and seedling growth inhibition (SGI) assays collected for the manuscript "The perception and evolution of flagellin, cold shock protein, and elongation factor Tu from vector-borne bacterial plant pathogens". For a quick reference, there are two spreadsheets listing all the Max RLUs and Z-scores for the experiments, but the actual output of each plate reader is also included. </p>
South Sulawesi vector data
<p>This file contains shapefiles that were used to built the bear cuscus habitat model in the southern landscape of South Sulawesi using MaxEnt in the WGS 84/UTM zone 50S coordinate system, i.e.:</p> <ol> <li>The model area</li> <li>Rivers in South Sulawesi</li> <li>Settlements in South Sulawesi</li> <li>Roads in South Sulawesi, Bantimurung Bulusaraung National Park, and Hasanuddin University Educational Forest (consist of patrol roads (footpaths), local roads (rural roads), and arterial roads (highways)).</li> </ol>
Compound data sets for support vector machine and regression modeling
<p>Provided are compound data sets used for support vector machine and support vector regression modeling and associated information.</p>
Data from: Genetic diversity and population structure of the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: implications for vector control
Uganda is the only country where the chronic and acute forms of human African Trypanosomiasis (HAT) or sleeping sickness both occur and are separated by < 100 km in areas north of Lake Kyoga. In Uganda, Glossina fuscipes fuscipes is the main vector of the Trypanosoma parasites responsible for these diseases as well for the animal African Trypanosomiasis (AAT), or Nagana. We used highly polymorphic microsatellite loci and a mitochondrial DNA (mtDNA) marker to provide fine scale spatial resolution of genetic structure of G. f. fuscipes from 42 sampling sites from the northern region of Uganda where a merger of the two disease belts is feared. Based on microsatellite analyses, we found that G. f. fuscipes in northern Uganda are structured into three distinct genetic clusters with varying degrees of interconnectivity among them. Based on genetic assignment and spatial location, we grouped the sampling sites into four genetic units corresponding to northwestern Uganda in the Albert Nile drainage, northeastern Uganda in the Lake Kyoga drainage, western Uganda in the Victoria Nile drainage, and a transition zone between the two northern genetic clusters characterized by high level of genetic admixture. An analysis using HYBRIDLAB supported a hybrid swarm model as most consistent with tsetse genotypes in these admixed samples. Results of mtDNA analyses revealed the presence of 30 haplotypes representing three main haplogroups, whose location broadly overlaps with the microsatellite defined clusters. Migration analyses based on microsatellites point to moderate migration among the northern units located in the Albert Nile, Achwa River, Okole River, and Lake Kyoga drainages, but not between the northern units and the Victoria Nile drainage in the west. Effective population size estimates were variable with low to moderate sizes in most populations and with evidence of recent population bottlenecks, especially in the northeast unit of the Lake Kyoga drainage. Our microsatellite and mtDNA based analyses indicate that G. f. fuscipes movement along the Achwa and Okole rivers may facilitate northwest expansion of the Rhodesiense disease belt in Uganda. We identified tsetse migration corridors and recommend a rolling carpet approach from south of Lake Kyoga northward to minimize disease dispersal and prevent vector re-colonization. Additionally, our findings highlight the need for continuing tsetse monitoring efforts during and after control.
Data from: Analysis-ready datasets for insecticide resistance phenotype and genotype frequency in African malaria vectors
The impact of insecticide resistance in malaria vectors is poorly understood and quantified. Here a series of geospatial datasets for insecticide resistance in malaria vectors are provided so that trends in resistance in time and space can be quantified and the impact of resistance found in wild populations on malaria transmission in Africa can be assessed. Data are also provided for common genetic markers of resistance to support analyses of whether these genetic data can improve the ability to monitor resistance in low resource settings. Specifically, data have been collated and geopositioned for the prevalence of insecticide resistance, as measured by standard bioassays, in representative samples of individual species or species complexes. Data are provided for the Anopheles gambiae species complex, the Anopheles funestus subgroup, and for nine individual vector species. In addition, allele frequencies for known resistance associated markers in the Voltage-gated sodium channel (Vgsc) are provided. In total, eight analysis-ready, standardised, geopositioned datasets encompassing over 20,000 African mosquito collections between 1957 and 2017 are provided.
Data from: Sympatric diversification vs. immigration: deciphering host-plant specialization in a polyphagous insect, the stolbur phytoplasma vector Hyalesthes obsoletus (Cixiidae)
The epidemiology of vector transmitted plant diseases is highly influenced by dispersal and the host-plant range of the vector. Widening the vector's host range may increase transmission potential, whereas specialization may induce specific disease cycles. The process leading to a vector's host shift and its epidemiological outcome is therefore embedded in the frameworks of sympatric evolution vs. immigration of preadapted populations. In this study, we analyse whether a host shift of the stolbur phytoplasma vector, Hyalesthes obsoletus from field bindweed to stinging nettle in its northern distribution range evolved sympatrically or by immigration. The exploitation of stinging nettle has led to outbreaks of the grapevine disease bois noir caused by a stinging nettle-specific phytoplasma strain. Microsatellite data from populations from northern and ancestral ranges provide strong evidence for sympatric host-race evolution in the northern range: Host-plant associated populations were significantly differentiated among syntopic sites (0.054 < FHT < 0.098) and constant over 5 years. While gene flow was asymmetric from the old into the predicted new host race, which had significantly reduced genetic diversity, the genetic identity between syntopic host-race populations in the northern range was higher than between these populations and syntopic populations in ancestral ranges, where there was no evidence for genetic host races. Although immigration was detected in the northern field bindweed population, it cannot explain host-race diversification but suggests the introduction of a stinging nettle-specific phytoplasma strain by plant-unspecific vectors. The evolution of host races in the northern range has led to specific vector-based bois noir disease cycles.
Data from: Automated identification of insect vectors of Chagas disease in Brazil and Mexico: the Virtual Vector Lab
Identification of arthropods important in disease transmission is a crucial, yet difficult, task that can demand considerable training and experience. An important case in point is that of the 150+ species of Triatominae, vectors of Trypanosoma cruzi, causative agent of Chagas disease across the Americas. We present a fully automated system that is able to identify triatomine bugs from Mexico and Brazil with an accuracy consistently above 80%, and with considerable potential for further improvement. The system processes digital photographs from a photo apparatus into landmarks, and uses ratios of measurements among those landmarks, as well as (in a preliminary exploration) two measurements that approximate aspects of coloration, as the basis for classification. This project has thus produced a working prototype that achieves reasonably robust correct identification rates, although many more developments can and will be added, and—more broadly—the project illustrates the value of multidisciplinary collaborations in resolving difficult and complex challenges.
Data from: Quantifying (non)parallelism of microbial community change using multivariate vector analysis
<p>Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have limited knowledge of whether parallel evolution of host organisms is accompanied by parallel changes of their associated microbial communities (i.e., microbiotas), which are crucial for their hosts' ecology and evolution. Determining the extent of microbiota parallelism in nature can improve our ability to identify the factors that are associated with (putatively adaptive) shifts in microbial communities. While it has been emphasized that (non)parallel evolution is better considered as a quantitative continuum rather than a binary phenomenon, quantitative approaches have rarely been used to study microbiota parallelism. We advocate using multivariate vector analysis (i.e., phenotypic change vector analysis) to quantify direction and magnitude of microbiota changes and discuss the applicability of this approach for studying parallelism. We exemplify its use by reanalyzing gut microbiota data from multiple fish species that exhibit parallel shifts in trophic ecology. This approach provides an analytical framework for quantitative comparisons across host lineages, thereby providing the potential to advance our capacity to predict microbiota changes. Hence, we encourage the development and application of quantitative measures, such as multivariate vector analysis, to better understand the role of microbiota dynamics during their hosts' adaptive evolution, particularly in settings of parallel evolution.</p>
IG. 6. Ordination diagram of PCA of the Patagonian bat assemblage for craniodental variables using A) data set not size-corrected; and B) data set size-corrected. Polygons include specimens from each species: H. macrotus (▲), H. magellanicus (), H. montanus (▲), L. varius (■), M. chiloensis (●), and T. brasiliensis (£). Vectors show the strengh of correlation of each variable with the plane of PC1 and PC2. See text for abbreviations in Ecomorphological diversity in the Patagonian assemblage of bats from Argentina
IG. 6. Ordination diagram of PCA of the Patagonian bat assemblage for craniodental variables using A) data set not size-corrected; and B) data set size-corrected. Polygons include specimens from each species: H. macrotus (▲), H. magellanicus (), H. montanus (▲), L. varius (■), M. chiloensis (●), and T. brasiliensis (£). Vectors show the strengh of correlation of each variable with the plane of PC1 and PC2. See text for abbreviations
A first high-quality vector data of buildings in East Asian countries based on a comprehensive large-scale mapping framework
<p>We generate a high-quality and complete vector data of buildings in East Asian regions, including China, Japan, North Korea, South Korea and Mongolia, filling the gaps in the existing public buildings data.</p>
Data from: 2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador
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Data from: Dispersing hemipteran vectors have reduced arbovirus prevalence
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Data from: Infection with Haemoproteus iwa affects vector movement in a hippoboscid fly – frigatebird system
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Data from: Pathogens manipulate the preference of vectors, slowing disease spread in a multi-host system
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Data from: Effective population size of malaria mosquitoes: large impact of vector control
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Data from: Seasonal effects and fine-scale population dynamics of Aedes taeniorhynchus, a major disease vector in the Galapagos Islands
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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.