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1,456 results for “residues”
Data for Deriving WMO cloud classes from ground-based RGB pictures with a residual neural network ensemble
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The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa
<p>Here, we report the first population genetic study to examine the impact of indoor residual spraying (IRS) on Plasmodium falciparum in humans. This study was conducted in an area of high seasonal malaria transmission in Bongo District, Ghana. IRS was implemented during the dry season (November-May) in three consecutive years between 2013 and 2015 to reduce transmission and attempt to bottleneck the parasite population in humans towards lower diversity with greater linkage disequilibrium. The study was done against a background of widespread use of long-lasting insecticidal nets, typical for contemporary malaria control in West Africa. Microsatellite genotyping with 10 loci was used to construct 392 P. falciparum multilocus infection haplotypes collected from two age-stratified cross-sectional surveys at the end of the wet seasons pre- and post-IRS. Three-rounds of IRS, under operational conditions, led to a >90% reduction in transmission intensity and a 35.7% reduction in the P. falciparum prevalence (p < .001). Despite these declines, population genetic analysis of the infection haplotypes revealed no dramatic changes with only a slight, but significant increase in genetic diversity (H<sub>e</sub> : pre-IRS = 0.79 vs. post-IRS = 0.81, p = .048). Reduced relatedness of the parasite population (p < .001) was observed post-IRS, probably due to decreased opportunities for outcrossing. Spatiotemporal genetic differentiation between the pre- and post-IRS surveys (D = 0.0329 [95% CI: 0.0209 - 0.0473], p = .034) was identified. These data provide a genetic explanation for the resilience of P. falciparum to short-term IRS programmes in high-transmission settings in sub-Saharan Africa.</p>
Northern Gulf of Mexico Surface Nutrient Residuals (from Mixing Line)
<p>Northern Gulf of Mexico Surface Nutrient Residuals (from Mixing Line)</p> <p>- DIN, DIP</p>
Local temperature increases reduce soil microbial residues and carbon stocks
<p class="MsoNormal"><span>Warming is known to reduce soil carbon (C) stocks by promoting microbial respiration, which is associated with the decomposition of microbial residue C (MRC). However, the relative contribution of MRC </span><span><span>t</span></span><span>o soil organic C (SOC) across temperature gradients is poorly understood.</span><span><span> </span></span><span><span>Here, we </span></span><span>investigated the contribution of MRC to SOC along two independent elevation gradient</span><span><span>s</span></span><span> of our model system (i.e., the Tibetan Plateau</span><span><span> </span></span><span>and Shennongjia Mountain in China). </span><span>Our results showed that local temperature increases were negatively correlated with </span><span>MRC</span><span><span> </span></span><span>and</span><span><span> </span></span><span>SOC.</span><span><span> </span></span><span>Further analyses revealed that rising temperature reduced SOC via decreasing </span><span>MRC</span><span>,</span><span> which helps to explain future reductions in SOC under climate warming. Our findings</span><span> demonstrate that climate warming has the potential to </span><span><span>reduce C sequestration</span></span><span> </span><span><span>by </span></span><span>increas</span><span><span>ing</span></span><span> the decomposition</span><span> of MRC</span><span>, exacerbating the positive feedback between rising temperature and CO<sub>2</sub></span><span> efflux. Our study also considered the influence of multiple environmental factors such as soil pH and moisture, which were more important in controlling SOC than microbial traits such as microbial life-style strategies and metabolic efficiency. Together, our work suggests an important mechanism underlying long-term soil C sequestration, which has important implications for the microbial-mediated C process in the face of global climate change.</span></p>
Data from: A single residue confers selective loss of sugar sensing in wrynecks
<p>Sensory receptors evolve, and changes to their response profiles can directly impact sensory perception and affect diverse behaviors, from mate choice to foraging decisions. Although receptor sensitivities can be highly contingent on changes occurring early in a lineage's evolutionary history, subsequent shifts in a species' behavior and ecology may exert selective pressure to modify and even reverse sensory receptor capabilities. Neither the extent to which sensory reversion occurs, nor the mechanisms underlying such shifts is well understood. Using receptor profiling and behavioral tests, we uncover both an early gain and an unexpected subsequent loss of sugar sensing in woodpeckers and wrynecks, members of the primarily insectivorous Picidae family of landbirds. Our analyses show that, similar to hummingbirds and songbirds, the ancestors of woodpeckers repurposed their T1R1-T1R3 savory receptor to detect sugars. Importantly, whereas woodpeckers seem to have broadly retained this ability, our experiments demonstrate that wrynecks (an enigmatic ant-eating group sister to all other woodpeckers) selectively lost sugar sensing through a novel mechanism involving a single amino acid change in the T1R3 transmembrane domain. The identification of this molecular microswitch responsible for a sensory shift in taste receptors provides an example of the molecular basis of a sensory reversion in vertebrates and offers novel insights into structure-function relationships during sensory receptor evolution.</p>
Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7
<p>Molecular dynamics simulation systems of publication "Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7" by Akseli Niemelä and Artturi Koivuniemi.</p>
Dataset: Predicting relative agronomic efficiency of phosphorus-rich organic residues
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Datasets for "Detecting rhythmic spiking through the power spectra of point process model residuals"
<p>This repository contains synthetic and empirical datasets that were analyzed in the preprint "Detecting rhythmic spiking through the power spectra of point process model residuals."</p> <p>Relative to the previous version (1.0.0), this new version (1.0.1) only entails changes in the naming of some folders, and the text of an explanatory text file. The changes reflect the reordering of the figures in the newest version of the manuscript.</p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip3p, 310K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip3p water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip4p, 310K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip4p water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, OPC4, 310K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, OPC4 water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip3p, 303K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip3p water model at 303K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p> <p> </p>
MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043), Amber ff99SB-ILDN, tip4p, 303K, Gromacs
<p>MD simulation data for Helicobacter pylori TonB-CTD (residues 194-285) (PDB ID: 5LW8; BMRB entry: 34043). Simulated with Amber ff99SB-ILDN force field, tip4p water model at 303K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
Figure Data for Thermophysical Properties of the North Polar Residual Cap of Mars from MGS TES
<p>Includes comma separated value files for data used to generate paper figures. See 'info.txt' for data description.</p>
Crustal thickness and residual topography data for NE Africa
<p>The files in this gzipped tar file are crustal thicknesses, density anomalies, and residual<br> topography estimates for NE Africa as used in Faccenna et al. (Nature<br> Geoscience, in press, 2019), they are in the Netcdf/GMT grd format.</p> <p>lc.6.grd has crustal thickness in [km], rtl.6.grd the estimated,<br> non-isostatic topography in [km] assuming constant lithospheric<br> thickness and variable density anomalies from CRUST1.0, provided in<br> ades.grd [kg/m^3].</p> <p>Thorsten Becker, UT Austin, 09/2019<br> twb@ig.utexas.edu</p> <p> </p>
Expanding molecular grammar of polar residues and arginine in FUS prion-like domain
<p>Codes to reporoduce simualtion results presented in the paper "Expanding molecular grammar of polar residues and arginine in FUS prion-like domain". </p> <p>Simulation_Codes.zip - Contains python codes for calcualtion of contacts, intrachain distances and angle-distance probability distributions along with files to check the output of the codes. </p> <p>ThT_Assay_Fitting_Scripts.zip - Contains scripts to fit ThT curve.</p>
Figure 11. Residual plots from the regression analyses for the four measurements that had low r in Phylogenetic implications of the morphology of the braincase of caecilian amphibians (Gymnophiona)
Figure 11. Residual plots from the regression analyses for the four measurements that had low r-squared values in their respective regression plots. Species circled represent those that deviate from the expected value of each measurement predicted by the regression plot. Data point labels correspond to the first letter of the genus followed by the first three letters of the species. A, residuals from the regression plot of dorsomedial process length against skull length, for which Typhlonectes natans (T.natans), Chthonerpeton indistinctum (C.indistinctum), and Crotaphatrema lamottei (C.lamottei) possess a process that is shorter than predicted; B, residuals from the regression plot of nasal septum length against skull length, for which T. natans and Ch. indistinctum possess a septum that is shorter than predicted; C, residuals of the regression plot of lateral wall length against skull length, for which Scolecomorphus kirkii (S.kirkii), Scolecomorphus vittatus, and Cr. lamottei possess walls that are longer than predicted; and D, residuals of the regression plot of occipital condyle protrusion against skull length, for which Epicrionops bicolor (E.bicolor), Rhinatrema bivittatum (R.bivittatum), Ichthyophis beddomei (I.beddomei), Ichthyophis kohtaoensis, Caudacaecilia asplenia (C.asplenia), and Scolecomorphus vittatus (S.vittatus) possess less protruded condyles than predicted.
The dataset used in "A max-margin model for predicting residue-base contacts in protein-RNA interactions"
<p>The dataset used in "A max-margin model for predicting residue-base contacts in protein-RNA interactions"</p>
Data Availability for "Function of four tryptophan residues on Cel7A catalytic efficiency: insight into cellulase screening strategy based on natural cellulose or cellulose analogs"
<p><strong>The data support for this article "Function of four tryptophan residues on Cel7A catalytic efficiency: insight into cellulase screening strategy based on natural cellulose or cellulose analogs"</strong></p>
All data support published article "Function of four tryptophan residues on Cel7A catalytic efficiency: insight into cellulase screening strategy based on natural cellulose or cellulose analogs"
<p>There is a high level of conservation of tryptophans within the active site architecture of the cellulase family, whereas the function of the four tryptophans in the catalytic domain of Cel7A is unclear. By mutating four tryptophan residues in the catalytic domain of Cel7A from <em>Penicillium piceum</em> (PpCel7A), the binding affinity between PpCel7A and <em>p-</em>nitrophenol-D-cellobioside (<em>p</em>NPC) was reduced as determined by Michaelis–Menten constants, molecular dynamics simulations, and fluorescence spectroscopy. Furthermore, PpCel7A variants showed a reduced level of cellobiohydrolase activity against cellulose analogs or natural cellulose. Therefore, it could be concluded four tryptophan residues in Cel7A played a critical role in substrate binding. Mutagenesis results indicated that the W390 stacking interactions at the -2 site played an essential role in facilitating substrate distortion to the -1 site. As soon as the function was altered, the mutation would inevitably affect the catalytic activity against the natural substrate. Interestingly, no clear relationship was found between the cellobiohydrolase activity of PpCel7A variants against <em>p</em>NPC and Avicel. <em>p</em>NP contains many electrophilic groups that may result in overestimation of the binding constant between tryptophan residues and <em>p</em>NPC in comparison to the natural substrate. Consequently, screening improved cellulase using cellulose analogs would divert attention from the target direction for lignocellulose biorefinery. Clarifying mechanism of catalytic diversity on the natural cellulose or cellulose analogs may give better insight into cellulase screening and selecting strategy.</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.