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160 results for “Molecular detection”
On-chip phonon-enhanced IR near-field detection of molecular vibrations
<p>This dataset contains the source data and raw interferograms associated with our manuscript, <em>'On-chip phonon-enhanced IR near-field detection of molecular vibrations</em>' by A. Bylinkin et al. The source data, provided in an .xlsx file, includes the datasets used to generate the figures in both the main text and the Supplementary Information. The raw interferogram dataset, located in the <em>'Interferograms</em>' folder, was used to calculate the experimental spectra shown in Fig. 3b, f, and Suppl. Fig. 13. This dataset was acquired using a NeaSNOM microscope (attocube AG).</p> <p>The data processing procedure for calculating spectra from the interferograms is described in the Methods section of our manuscript.</p>
Data to Reproduce "Robust Automated Equilibration Detection for Molecular Simulations"
<p>Data to reproduce the results from "Robust Automated Equilibration Detection for Molecular Simluations" (see <a href="https://github.com/michellab/Robust-Equilibration-Detection-Paper">https://github.com/michellab/Robust-Equilibration-Detection-Paper</a> and the work linked there). These data are too large to host on GitHub, but are automatically downloaded by the workflow supplied at the above GitHub repository. </p> <p>All data were generated using the code given in the <a href="https://github.com/michellab/Robust-Equilibration-Detection-Paper">GitHub repository</a>, other than the original free energy gradient data <code>gradient_arrays_30ns.pkl</code> which were generated as described in <a title="DOI URL" href="https://doi.org/10.1021/acs.jctc.4c00806">https://doi.org/10.1021/acs.jctc.4c00806</a> (to regenerate, see the code available at: <a href="https://github.com/michellab/Automated-ABFE-Paper">https://github.com/michellab/Automated-ABFE-Paper</a>).</p> <p>The synthetic data used to test all equilibration detection heuristics are given in the <code>compute_equil_times</code> output directories (for example <code>synthetic_data_bound_vanish_with_equil_times.pkl</code>. These are supplied as pickled Python dictionaries with the structures <code>data[dataset_type][system][trace_index]["data"]</code>. For example, to access the first synthetic trace for the T4L system from the "standard" synthetic ensemble, use <code>data["standard"]["T4L"][0]["data"]</code>. For all directories, <code>_free</code> denotes the free vanish multi-window data and <code>_single</code> denotes the bound vanish single-window data - otherwise these are the standard bound vanish multi-window data. However, it is recommended that these data are used as part of the workflow given at <a href="https://github.com/michellab/Robust-Equilibration-Detection-Paper">https://github.com/michellab/Robust-Equilibration-Detection-Paper</a>, which allows the study to be reproduced from scratch.</p>
Simulation data and code used for the publication in Magn. Reson. "Time-domain proton-detected local-field NMR for molecular structure determination in complex lipid membranes"
<p>Simulation data used in the publication Magn. Reson. "Time-domain proton-detected local-field NMR for molecular structure determination in complex lipid membranes". The simulation data set, and the code developed to generate such data, are included. Details in the published paper </p>
Research data supporting: "Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling"
<p>This repository contains the set of data shown in the paper "Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling" published on PNAS (DOI: 10.1073/pnas.2300565120).</p>
Fig. 1 in First Molecular Detection of Giardia duodenalis Assemblage B in a Free-Living European Wildcat (Felis s. silvestris) from Luxembourg
Fig. 1. Neighbor-joining distance analysis of the β-giardin nucleotide sequences. FS1 – sequence of partial β-giardin gene of the isolate from wildcat (KX685669). Reference human isolates: WB and KC8, (X85958 and AY072723); LD18, Nij5, VAN/90/UBC/44, GH- 202 (AY072727, AY072725, KP687755, AB618785); A101 and – cat isolate, (AY647264 and EU769206); P15 – reference cow isolate, (AY072729); A29 and A27 – reference dog isolates (AY545646 and AY545648). G. muris (AY258618) represents an outgroup.
Supplemental files to: Probe-based quantitative PCR and RPA-Cas12a molecular diagnostics for detection of the tomato pest Phthorimaea absoluta (Lepidoptera: Gelechiidae)
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Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
<p>As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suit of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study we show that asymmetric rates of sequence evolution rates lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.</p>
Molecular characterisation of Crimean-Congo haemorrhagic fever virus detected in African blue ticks feeding on cattle in a Ugandan abattoir
<p>CCHFV multiple sequence alignments and maximum likelihood phylogeny treefiles.</p>
Fig. 1 in First molecular detection of Francisella tularensis in turtle (Testudo graeca) and ticks (Hyalomma aegyptium) in Northwest of Iran
Fig. 1. The schematic map of the studied areas, West Azerbaijan (Oshnavieh), Iran.
Underlying data for 'Rapid molecular assays for the detection of the four dengue viruses in infected mosquitoes'
<p>The pantropic emergence of severe dengue disease can partly be attributed to the co-circulation of different dengue viruses (DENVs) in the same geographical location. Effective monitoring for circulation of each of the four DENVs is critical to inform disease mitigation strategies. In low resource settings, this can be effectively achieved by utilizing inexpensive, rapid, sensitive and specific assays to detect viruses in mosquito populations. In this study, we developed four rapid DENV tests with direct applicability for low-resource virus surveillance in mosquitoes. The test protocols utilize a novel sample preparation step, a single-temperature isothermal amplification, and a simple lateral flow detection. Analytical sensitivity testing demonstrated tests could detect down to 1,000 copies/µL of virus-specific DENV RNA, and analytical specificity testing indicated tests were highly specific for their respective virus, and did not detect closely related flaviviruses. All four DENV tests showed excellent diagnostic specificity and sensitivity when used for detection of both individually infected mosquitoes and infected mosquitoes in pools of uninfected mosquitoes. With individually infected mosquitoes, the rapid DENV-1, -2 and -3 tests showed 100% diagnostic sensitivity (95% CI = 69% to 100%, n=8 for DENV-1; n=10 for DENV 2,3) and the DENV-4 test showed 92% diagnostic sensitivity (CI: <span>62% to 100%, n=12</span>) along with 100% diagnostic specificity (CI: 48–100%) for all four tests. Testing infected mosquito pools, the rapid DENV-2, -3 and -4 tests showed 100% diagnostic sensitivity (95% CI = 69% to 100%, n=10) and the DENV-1 test showed 90% diagnostic sensitivity (<span>55.50% to 99.75%, n=10</span>) together with 100% diagnostic specificity (CI: 48–100%). Our tests reduce the operational time required to perform mosquito infection status surveillance testing from > two hours to only 35 minutes, and have potential to improve accessibility of mosquito screening, improving monitoring and control strategies in low-income countries most affected by dengue outbreaks.</p>
Fig. 2 in Molecular detection of Wolbachia endosymbiont in reptiles and their ectoparasites
Fig. 2 Boa constrictor constrictor infested with Ophionyssus natricis (red arrows)
Fig. 1 in Molecular detection of Wolbachia endosymbiont in reptiles and their ectoparasites
Fig. 1 Lacerta bilineata infested with Ixodes ricinus
Dataset for Enantioselective molecular Detection by Surface-Enhanced Raman Scattering at Chiral Gold Helicoids on Grating Surface
<p>This is a dataset for a paper "Enantioselective molecular Detection by Surface-Enhanced Raman Scattering at Chiral Gold Helicoids on Grating Surface". All details about the data are included in the readme file.</p>
Fig. 3 in Evidence of Ehrlichia chaffeensis in Argentina through molecular detection in marsh deer (Blastocerus dichotomus)
Fig. 3. Dead marsh deer with high tick burden.
Fig. 2 in Molecular detection and characterization of a novel Theileria genotype in Dama Gazelle (Nanger dama)
Fig. 2. The clade credibility values of phylogram generated from bayesian analysis.
Data from: Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution
<p class="MsoNormal"><span>Determining the link between genomic and phenotypic change is a </span><span>fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of five statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, greater among-lineage rate variation in the data led to improved performance of all five methods, particularly for Bayesian relaxed-clock analysis when the rate model was mismatched. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.</span></p>
Molecular Diagnostic Methods for Detection of Plasmodium Knowlesi
ClinicalTrials.gov study NCT03988296. IPD Sharing: NO. Countries: 1. Publications: 8.
Data from: A novel molecular toolkit for rapid detection of the pathogen and primary vector of thousand cankers disease
Open the record for dataset details and reuse information.
Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
Open the record for dataset details and reuse information.
Data from: Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution
Open the record for dataset details and reuse information.
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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.