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3,878 results for “Molecular data”
Data from: Diversity and molecular evolution of non-visual opsin genes across environmental, developmental, and morphological adaptations in frogs
<p>Dataset for the article Diversity and molecular evolution of non-visual opsin genes across environmental, developmental, and morphological adaptations in frogs. Includes non-visual opsin coding sequences from frogs, sequence alingments, phylogenetics trees, and raw PAML results files.</p>
Supporting molecular simulations data for "A combined molecular dynamics and experimental study of two-step process enabling low-temperature formation of phase-pure α-FAPbI3"
<p>Supplementary data for "A combined molecular dynamics and experimental study of two-step process enabling low-temperature formation of phase-pure α-FAPbI3: <a href="https://doi.org/10.1126/sciadv.abe3326">10.1126/sciadv.abe3326</a>"</p>
Data: The genesis of OH-stretching vibrational circular dichroism in chiral molecular crystals
<p>This data supplements our article "The genesis of OH-stretching vibrational circular dichroism in chiral molecular crystals"</p>
Figure 1 in Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data
Figure 1. Guidelines for studies of cetacean taxonomy based on genetic data.
Supporting Data for "Thermal Transport Through CTAB- and MTAB-Functionalized Gold Interfaces using Molecular Dynamics Simulations"
<p>This gzipped tar archive contains initial configurations and parameters used for the simulations in the manuscript:</p> <p>"Thermal Transport Through CTAB- and MTAB-Functionalized Gold Interfaces using Molecular Dynamics Simulations", by Sydney A. Shavalier, and J. Daniel Gezelter</p> <p>A note on naming conventions. All simulations have filenames with with two numbers - one that signifies simulation replica (1-5), and another that signified which step of equilibration/RNEMD was being performed. For example, lowmtab111_3opt4 would signify the third simulation replica of a low coverage MTAB system and a (111) gold facet, which was on its fourth equilibration step after optimization.</p> <p>The OpenMD simulation engine utilizes a number of file extensions that are present in this archive:</p> <p><strong>.omd</strong> : A combined MetaData and configuration file that is used to start a simulation <br><strong>.frc</strong> : a force field parameter file<br><strong>.eor</strong> : an 'end of run' or final configuration (same format as .omd)<br><strong>.stat</strong> : status file with instantaneous information about energies, temperatures, etc. These are generally large and have not been included, as they can be regenerated easily from the .omd file.<br><strong>.report </strong>: a post-simulation file containing thermodynamic averages from the .stat file<br><strong>.dump</strong> : a full trajectory file containing positions and velocities sampled at a 'sampleTime' specified in the .omd file. These are generally very large and have not been included, as they can be regenerated from the .omd file.<br><strong>.rnemd</strong> : Contains spatial information about temperatures, densities, etc. for simulations run under reverse non-equilibrium molecular dynamics</p> <p>Other data analyis or utility file extensions:</p> <p><strong> .pack</strong> : Files for creating systems with Packmol<br><strong> .z</strong> : Density \rho(z) for specific selected atom types<br><strong> .r </strong> : Density \rho(r) for specific selected atom types<br><strong> .p2z</strong> : Legendre Polynomial Correlation using z as reference axis<br><strong> .p2r</strong> : Legendre Polynomial Correlation using radial vector as reference axis<br> <strong>.chargez</strong> : Charge density as a function of z-axis<br> <strong>.charger</strong> : Charge density as a function of radius<br> <strong>.agr</strong> : Grace graphing package data<br><strong> .xyz </strong> : XYZ (Cartesian) coordinates for visualization<br> </p> <p>The archive is organized as follows:</p> <p> ./CTAB/111: Simulations of Au(111) functionalized with CTAB<br> final systems begin with "highctab"<br> RNEMD simulations are in ./CTAB/111/RNEMD<br> ./CTAB/110: Simulations of Au(110) functionalized with CTAB<br> final systems begin with "highctab"<br> RNEMD simulations are in ./CTAB/110/RNEMD<br> ./CTAB/100: Simulations of Au(100) functionalized with CTAB<br> final systems begin with "highctab"<br> RNEMD simulations are in ./CTAB/100/RNEMD<br> ./MTAB/111: Simulations of Au(111) functionalized with MTAB <br> final systems begin with "highmtab" or "lowmtab"<br> RNEMD simulations are in ./MTAB/111/RNEMD<br> ./MTAB/110: Simulations of Au(110) functionalized with MTAB<br> final systems begin with "highmtab" or "lowmtab"<br> RNEMD simulations are in ./MTAB/110/RNEMD<br> ./MTAB/100: Simulations of Au(100) functionalized with MTAB <br> final systems begin with "highmtab" or "lowmtab"<br> RNEMD simulations are in ./MTAB/100/RNEMD<br> ./MTAB/NP/R10: Simulations of Au Nanoparticles (r = 10 angstroms),<br> functionalized with MTAB<br> final systems begin with "highmtab" or "lowmtab"<br> RNEMD simulations are in ./MTAB/NP/R10/RNEMD</p> <p>Systems that were run with metal polarizability turned on have 'fq' as part of their filenames.</p>
Dispersal patterns in black howler monkeys (Alouatta pigra): Integrating multi-year demographic and molecular data
<p>Dispersal is a fundamental process in the functioning of animal societies as it regulates the degree to which closely related individuals are spatially concentrated. A species' dispersal pattern can be complex as it emerges from individuals' decisions shaped by the cost-benefit tradeoffs associated with either remaining in the natal group or dispersing. Given the potential complexity, combining long-term demographic information with molecular data can provide important insights into dispersal patterns of a species. Based on a 15-year study that integrates multi-year demographic data on six groups with longitudinal and cross-sectional genetic sampling of 20 groups (N=169 individuals, N=21 polymorphic microsatellite loci), we describe the various dispersal strategies of male and female black howler monkeys (<i>Alouatta pigra</i>) inhabiting Palenque National Park, Mexico. Genetically confirmed dispersal events (N=21 of 59 males; N=6 of 65 females), together with spatial autocorrelation analyses revealed that the dispersal pattern of black howlers is bisexual with strong sex-biases in both dispersal rate (males disperse more often than females) and dispersal distance (females disperse farther than males). Observational and genetic data confirm that both males and females can successfully immigrate into established groups, as well as form new groups with other dispersing individuals. Additionally, both males and females may disperse singly, as well as in pairs, and both may also disperse secondarily. Overall, our findings suggest multiple dispersal trajectories for black howler males and females, and longer multi-year studies are needed to unravel which demographic, ecological, and social factors underlie individuals' decisions about whether to disperse and which dispersal options to take.</p>
Data for: Molecular mechanisms behind safranal's toxicity to liver cancer cells from dual omics
<p>The spice saffron (<em>Crocus sativus</em>) has anticancer activity in several human tissues, but the molecular mechanisms underlying potential therapeutic effects are poorly understood. We investigated the impact of safranal, a small molecule secondary metabolite from saffron, on the HCC cell line HEP-G2 using untargeted metabolomics (HPLC-MS) and transcriptomics (RNAseq). Increases in glutathione disulfide and other biomarkers for oxidative damage contrasted with lower levels of the antioxidants biliverdin IX (139-fold decrease, p=5.3E-5), the ubiquinol precursor 3-4-dihydroxy-5-all-trans-decaprenylbenzoate (3-fold decrease, p=1.9E-5), and resolvin E1 (-3,282-fold decrease, p=4E-5), which indicates sensitization to reactive oxygen species. We observed a significant increase in intracellular hypoxanthine (538-fold increase, p=7.7E-6) that may be primarily responsible for oxidative damage in HCC after safranal treatment. The accumulation of free fatty acids and other biomarkers, such as S-methyl-5'-thioadenosine, are consistent with safranal-induced mitochondrial de-uncoupling and explain the sharp increase in hypoxanthine we observed. Overall, the dual omics datasets describe routes to widespread protein destabilization and DNA damage from safranal-induced oxidative stress in HCC cells.</p>
Mutation and methylation data for study: Assessment of the molecular heterogeneity of E-cadherin expression in invasive lobular breast cancer
<p>Processed mutation data and DNA methylation beta values published with this study.</p>
Simulation Input Data for "Molecular simulation of lignin-related aromatic compound permeation through Gram-negative bacterial outer membranes"
<p>This is the reduced data behind an upcoming manuscript investigating permeability across the outer membranes of Gram-negative bacteria. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was:</p> <pre><code class="language-bash">tar --exclude="*BAK" --exclude="*dcd" --exclude="*xsc" --exclude="*vel" --exclude="*coor" --exclude="*csv" --exclude="*old" --exclude="*log" --exclude="*state" --exclude="*watpos/*npz" --exclude="*new*png" --exclude="*frame*png" --exclude="*ppm" --exclude="*mp4" --exclude="*bayesdata*npy" --exclude="*run.npy" -zcvf OM.tgz OuterMembrane</code></pre> <p>Within the OuterMembrane directory, there are 3 primary subdirectories.</p> <ul> <li><strong>Build </strong>contains the scripts and files to build the simulation systems, including the CHARMM-GUI output</li> <li><strong>Equilibrium</strong> contains the equilibrium simulation inputs and the analysis scripts (subdirectory <strong>Analysis</strong>)</li> <li><strong>REUS2</strong>, which has the replica exchange inputs and essential output. It also contains an <strong>Analysis</strong> subdirectory that carries out the analysis within the text.</li> </ul>
Raw data: multispecies amplicon sequencing (Loera, Studer, and Kölliker, 2021, Molecular Ecology Resources)
<p>Grasslands cover close to two fifths of Earth's land. They provide many ecosystem services related to the maintenance of soil integrity, and the regulation of water, carbon and nitrogen flows. Grasslands constitute the basis for sustainable roughage production for ruminant feeding. In Switzerland, grasslands cover more than 70% of the total agricultural land, which highlights their importance in the domestic food production chains.</p> <p>Plant genetic diversity (PGD), a component of biodiversity, influences ecosystem functioning in grasslands. High levels of grassland PGD are related to resistance against invasive plants and yield stabilization during environmental stress (e.g., drought or frost). The PGD of grasses and legumes —the two most economically relevant plant families found in grasslands, which naturally grow in a wide climate spectrum— harbors valuable genetic resources for forage breeding. Nevertheless, most PGD studies of natural or semi-natural grasslands (i.e., grasslands that are not sown) focus on a single or a few related species. Traditional PGD monitoring methods (e.g., simple sequence repeats, or SSRs) are ill-suited for large-scale, multispecies assessments. This limits our ability to study the ecological effects of grassland PGD, its spatiotemporal patterns, and its significance for grassland management.</p> <p>Looking to provide cost-effective tools for multispecies PGD monitoring in grasslands, we performed a sequence capture assay targeting 611 single-copy nuclear loci, followed by multispecies amplicon sequencing (i.e., amplicon sequencing using primer pairs that can be used in multiple species) on eleven selected loci.</p> <p>Our results indicate that multispecies amplicon sequencing is a cost-effective tool for genetic diversity assessment in grassland plant species. Furthermore, the sequence capture data provides the means to extend the number of multispecies amplicons for further research.</p>
Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics: 35 Binding Site Data
<p>This is the original data for the manuscript "Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics" by J Bryan IV, I Sgouralis, and S Presse. This repository contains movies of DNA origami with 35 binding sites.</p>
Data associated to the article "Effects of fluoride salt addition to the physico-chemical properties of the MgCl2-NaCl-KCl heat transfer fluid : a molecular dynamics study"
<p>Contains input file and data used to generate the figures of the article:</p> <p>Effects of fluoride salt addition to the physico-chemical properties of the MgCl<sub>2</sub>-NaCl-KCl heat transfer fluid : a molecular dynamics study</p> <p>Weiguang Zhou, Yanping Zhang, Mathieu Salanne</p> <p>https://chemrxiv.org/engage/chemrxiv/article-details/618e903a2bf8a950c7d98e5d</p> <p>The files <em>data.inpt</em> and <em>runtime.inpt </em>are used to simulate the system using the software MetalWalls</p> <p>The files <em>MgNaKCl.txt, MgNaKClF01.txt, MgNaKClF05.txt, MgNaKClF10.txt, MgNaKClF20.txt</em> contain the computed densities, viscosities and thermal conductivities at various temperatures for several compositions (provided in the header of the files)</p>
Source molecular simulation data for calculating energy and friction profiles and permeability coefficients through model lipid membranes
<p>Energy files from GROMACS molecular dynamics simulations with enhanced free energy sampling contain time-dependent evolution of the free energy profiles and friction profiles (and other energies and simulation properties) that were used for calculating permeability coefficients in the publication https://www.biorxiv.org/content/10.1101/2021.07.16.452599v1</p> <p>Simulation system contains a lipid POPC or DPPC bilayer with a varying amount of cholesterol (specified as mol% in the file name). Hydrophobic level of the permeating particle is specified as "level-I", "level-II" etc. When unspecified in the file name, the particle is hydrophobic level "III". Lipids D-C14-PC denote PC lipids with both tails monounsaturated of length 14 carbon atoms. DOPC is equivalent to D-C18-PC. (Detailed description in the publication)</p> <p>Adaptive Weighted Histogram (AWH) method was used to sample the free energy profile of translocating small molecule through the lipid bilayer.</p> <p>GROMACS tool `gmx awh` reads the files and provides the described profiles.</p> <p>Files were generated by GROMACS `mdrun` simulation engine version 2019.3.</p> <p> </p> <p>Coarse-grained MARTINI 3.0 model was used for modeling the biomolecular interactions.</p> <p>Scripts to perform the simulations and the files with initial configurations and simulation settings are stored in a public GitHub repository depozited on Zenodo.org: <a href="https://doi.org/10.5281/zenodo.5082249">https://doi.org/10.5281/zenodo.5082249</a>.</p> <p> </p> <p>Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).</p> <p>Lindahl, V., Lidmar, J. & Hess, B. Accelerated weight histogram method for exploring free energy landscapes. J. Chem. Phys. 141, 044110 (2014).</p> <p>Souza, P. C. T. et al. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat. Methods 18, 382–388 (2021).</p> <p>Melcr, J. Git repository with analysis scripts for MD simulations of permeability through lipid membranes. (2021) doi:<a href="https://doi.org/10.5281/zenodo.5082249">https://doi.org/10.5281/zenodo.5082249</a>.</p>
Raw Data for the article: A retrospective molecular epidemiological scenario of carbapenemase-producing Klebsiella pneumoniae clinical isolates in a Sicilian transplantation hospital shows a swift polyclonal divergence among sequence types, resistome and virulome
<p>In this work, we assessed and characterized the epidemiological scenario of carbapenem-resistant Klebsiella pneumoniae strains (CR-Kp) at IRCCS-ISMETT, a transplantation hospital in Palermo, Italy, from 2008 to 2017. A total of 288 K. pneumoniae clinical isolates were selected based on their resistance to carbapenems. Molecular characterization was also done in terms of the presence of virulence and resistance genes. All patients were inpatients from our facility and clinical isolates were collected from several sources, either from infection or colonization cases. We observed that, in agreement with the Italian epidemiological scenario, initially only ST258 and ST512 clade II (but not from clade I) were identified from 2008 to 2011. From 2012 onwards, other STs have been observed, including the clinically relevant ST101 and ST307, but also others not previously observed in other Italian health settings, such as ST220 and ST753. The presence of genes involved in resistance and virulence was confirmed, and a heterogeneous genetic resistance profile throughout the years was observed. Our work highlights that resistance genes are rapidly disseminating between different and novel K. pneumoniae clones which, combined with resistance to multiple antibiotics, can derive into more aggressive and pathogenic multidrug-resistant strains of clinical importance. Our results stress the importance of continuous surveillance of CR Enterobacterales in health facilities so that novel STs carrying resistance and virulence genes that may become increasingly pathogenic can be identified and adequate therapies to adopted to avoid their dissemination and derived pathologies.</p>
Raw Data for the article: Clinical and Molecular-Based Approach in the Evaluation of Hepatocellular Carcinoma Recurrence after Radical Liver Resection
<p><strong>Background: </strong>Hepatic resection remains the treatment of choice for patients with early-stage HCC with preserved liver function. Unfortunately, however, the majority of patients develop tumor recurrence. While several clinical factors were found to be associated with tumor recurrence, HCC pathogenesis is a complex process of accumulation of somatic genomic alterations, which leads to a huge molecular heterogeneity that has not been completely understood. The aim of this study is to complement potentially predictive clinical and pathological factors with next-generation sequencing genomic profiling and loss of heterozygosity analysis.</p> <p><strong>Methods: </strong>124 HCC patients, who underwent a primary hepatic resection from January 2016 to December 2019, were recruited for this study. Next-generation sequencing (NGS) analysis and allelic imbalance assessment in a case-control subgroup analysis were performed. A time-to-recurrence analysis was performed as well by means of Kaplan-Meier estimators.</p> <p><strong>Results: </strong>Cumulative number of HCC recurrences were 26 (21%) and 32 (26%), respectively, one and two years after surgery. Kaplan-Meier estimates for the probability of recurrence amounted to 37% (95% C.I.: 24-47) and to 51% (95% C.I.: 35-62), after one and two years, respectively. Multivariable analysis identified as independent predictors of HCC recurrence: hepatitis C virus (HCV) infection (HR: 1.96, 95%C.I.: 0.91-4.24, <em>p</em> = 0.085), serum bilirubin levels (HR: 5.32, 95%C.I.: 2.07-13.69, <em>p</em> = 0.001), number of nodules (HR: 1.63, 95%C.I.: 1.12-2.38, <em>p</em> = 0.011) and size of the larger nodule (HR: 1.11, 95%C.I.: 1.03-1.18, <em>p</em> = 0.004). Time-to-recurrence analysis showed that loss of heterozygosity in the <em>PTEN</em> loci (involved in the PI3K/AKT/mTOR signaling pathway) was significantly associated with a lower risk of HCC recurrence (HR: 0.35, 95%C.I.: 0.13-0.93, <em>p</em> = 0.036).</p> <p><strong>Conclusions: </strong>multiple alterations of cancer genes are associated with HCC progression. In particular, the evidence of a specific AI mutation presented in 20 patients seemed to have a protective effect on the risk of HCC recurrence.</p>
Supporting molecular simulations data for "Pseudo-halide anion engineering for α-FAPbI3 perovskite solar cells"
<p>Supporting molecular simulations data for "Pseudo-halide anion engineering for α-FAPbI3 perovskite solar cells"</p>
Molecular Genetic Analysis of SARS-CoV-2 Lineages in Armenia - additional data
<p>Sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this study, we performed whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina short-read sequencing to describe the circulation of the virus lineage in Armenia.</p> <p>This dataset contains Nextstrain configuration files, the auspice JSON file, BEAST output logs, and trees files, and resulting log and tree files as well as R scripts and data files used in phylogenetic and functional analyses. </p> <p> </p>
Fig. 2 in Taxonomic Position Of Anastrangalia Reyi And A. Sequensi (Coleoptera, Cerambycidae) Based On Molecular And Morphological Data
Fig. 2. Phylogenetic tree of the genus Anastrangalia (with C. cerdo and C. scopolii as outgrouped).
Data from: Molecular identification of an avian predator of mimetic salamanders
<p>Natural field observations of salamander predation are uncommon, in some cases limiting the ability of scientists to study the evolution of toxicity, aposematism, and mimicry in these amphibians. Here, we document field observations of a recently depredated <em>Pseudotriton ruber </em>(Red Salamander) and two <em>Gyrinophilus porphyriticus </em>(Spring Salamanders), members of a putative Müllerian mimetic complex involving <em>Notophthalmus viridescens</em> (Eastern Newts). We use molecular methods to identify the likely avian predator of the Spring Salamanders and underscore the opportunities for future research enabled by the pairing of traditional natural history with modern molecular techniques.</p>
The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade
The use of molecular data for living groups is vital for interpreting fossils, especially when morphology-only analyses retrieve problematic phylogenies for living forms. These topological discrepancies impact on the inferred phylogenetic position of many fossil taxa. In Crocodylia, morphology-based phylogenetic inferences differ fundamentally in placing <i>Gavialis</i> basal to all other living forms, whereas molecular data consistently unite it with crocodylids. The Cenomanian <i>Portugalosuchus azenhae </i>was recently described as the oldest crown crocodilian, with affinities to <i>Gavialis</i>, based on morphology-only analyses, thus representing a potentially important new molecular clock calibration. Here we performed analyses incorporating DNA data into these morphological datasets, using scaffold and supermatrix (total evidence) approaches, in order to evaluate the position of basal crocodylians including <i>Portugalosuchus</i>. Our analyses incorporating DNA data robustly recovered <i>Portugalosuchus</i> outside Crocodylia (as well as thoracosaurs, planocraniids and <i>Borealosuchus</i> spp.), questioning the status of <i>Portugalosuchus</i> a crown crocodilian and any future use as a node calibration in molecular clock studies. Finally, we discuss how, with the increasing size of phylogenomic datasets, the molecular scaffold might be an efficient (though imperfect) approximation of more rigorous but demanding supermatrix analyses.
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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.