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1,456 results for “residues”
Data from: Nets versus spraying: a spatial modelling approach reveals indoor residual spraying targets Anopheles mosquito habitats better than mosquito nets in Tanzania
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Data from: Multiple-trait genome-wide association study based on principal component analysis for residual covariance matrix
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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
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Measuring resilience and resistance in aging and Alzheimer disease using residual methods: A systematic review and meta-analysis
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BfR calculator for estimating consumer exposure to biocide residues in food
<p>This calculator has been developed by the German Federal Institute for Risk Assessment (BfR) (1) to support competent authorities and industry when performing dietary risk assessment for biocidal products. It presents a tool to facilitate the estimation of dietary risk from consumer exposure to biocidal active substances used in domestic households as described in the Guidance on Estimating Dietary Risk from Transfer of Biocidal Active Substances into Foods - Non-professional Uses (Guidance Non-professional Uses) (2). It applies assumptions and default values as given in the guidance document.</p> <p>The exposure models presented in this calculator are not a comprehensive collection of scenarios. During evaluation it must be ensured that the chosen scenario is applicable to the intended use to be evaluated. Adjustment of existing scenarios or development of new scenarios will be required on a case-by-case basis. The list of scenarios in this calculator may be extended as more active substances and their uses in biocidal products are evaluated.</p> <p>The "Examples" spreadsheet contains calculations for various scenarios to illustrate the use of this calculator. Results for the examples given in the Guidance Non-professional Uses may slightly deviate from results produced by this calculator due to rounding differences.</p> <p><strong>Link: https://www.bfr.bund.de/cm/349/bfr-calculator-for-estimating-transfer-of-biocideresidues-into-foods-non-professional-uses.xlsx</strong></p>
Dataset for: Deciphering the selectivity of inhibitor MKC9989 towards residue K907 in IRE1α; a multiscale in silico approach
<p>Dataset from the study of pKa values and pre- and post-Schiff base formation properties in the reaction between IRE1 inhibitor MKC9989 and Lysine 907.</p> <p>File contents: </p> <p>- "QMMM" contains the input files prepared to perform QMMM optimization on RNase IRE1 (residues 830-964) and to scan the potential energy surface (PES) along the hydrogen bond direction using Gaussian 16.<br> - "MCCE" contains the input files for Multi-Conformation Continuum Electrostatics simulation using MCCE-v2.7.<br> - "CovDock" contains the output files form MacroModel (file: mmod_csearch_1) using MacroModel-v12.5, and Covalent docking using Glide-v8.4, and input structure for MD simulation (file: CovDocked.pdb) using Desmond-v5.9.</p>
Clustering and kernel density estimation for assessment of measurable residual disease by flow cytometry
<p>Flow cytometry raw data and supplementary table S1.</p>
Sealing in light cream terracotta, showing a seated female figure on a throne, with an inscription; impresson made from a coin (of the Kuṣāṇa king Vasishka, circa CE 246-67); on the reverse, the residual impression of a document
<p>Sealing in light cream terracotta, showing a seated female figure on a throne, with an inscription; impresson made from a coin (of the Kuṣāṇa king Vasishka, circa CE 246-67); on the reverse, the residual impression of a document. British Museum 1960,0517.1.17.</p>
Data for article "Tracking Charge Transfer to Residual Metal Clusters in Conjugated Polymers for Photocatalytic Hydrogen Evolution"
<p>Data presented in the publication "Tracking Charge Transfer to Residual Metal Clusters in Conjugated Polymers for Photocatalytic Hydrogen Evolution", published in the Journal of the American Chemical Society. The published article is available at <a href="https://doi.org/10.1021/jacs.0c06104">https://doi.org/10.1021/jacs.0c06104</a></p>
Data from: Sexual dimorphism explains residual variance around the survival-reproduction tradeoff in lizards: implications for sexual conflict over life-history evolution
The tradeoff between survival and reproduction is a central feature of life-history variation, but few studies have sought to explain why females of some species exhibit relatively lower survival than expected for a given level of reproductive effort. Intralocus sexual conflict theory proposes that sex differences in selection on survival and reproductive effort may, by virtue of shared genes underlying these components of fitness, prevent females from optimizing this life-history tradeoff. To test this hypothesis, we used a phylogenetically based comparative analysis of published estimates for mean annual survival and reproductive effort from females of 82 lizard species to (1) characterize the tradeoff between survival and reproduction, and (2) test whether variation around this tradeoff is explained by sexual size dimorphism (SSD), a potential proxy for sexual conflict over life-history traits. Across species, we found a strong negative correlation between mean annual survival and reproductive effort, confirming this classic life-history tradeoff. Although residual variance around this tradeoff is unrelated to the absolute magnitude of SSD, it is strongly related to the direction of SSD. Specifically, we found that females have lower survival than expected for a given level of reproductive effort in female-larger species, whereas they have higher survival than expected in male-larger species. Given that female-larger SSD is thought to reflect selection for increased fecundity, our results suggest that intralocus sexual conflict may be particularly likely to constrain female life-history evolution in situations where increased reproductive effort is favored, but the phenotypes that facilitate this increase (e.g., body size) are constrained by antagonistic selection on males.
Data from: Gain-of-function experiments in bacteriophage lambda uncover residues under diversifying selection in nature
Viral gain-of-function mutations frequently evolve during laboratory experiments. Whether the specific mutations that evolve in the lab also evolve in nature and whether they have the same impact on evolution in the real world is unknown. We studied a model virus, bacteriophage λ, that repeatedly evolves to exploit a new host receptor under typical laboratory conditions. Here we demonstrate that two residues of λ's J protein are required for the new function. In natural λ variants, these amino acid sites are highly diverse and evolve at high rates. Insertions and deletions at these locations are associated with phylogenetic patterns indicative of ecological diversification. Our results show that viral evolution in the laboratory mirrors that in nature and that laboratory experiments can be coupled with protein sequence analyses to identify the causes of viral evolution in the real world. Furthermore, our results provide evidence for widespread host-shift evolution in lambdoid viruses.
Data from: Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis
Identification of residue-residue contacts from primary sequence can be used to guide protein structure prediction. Using Escherichia coli CcdB as the test case, we describe an experimental method termed saturation-suppressor mutagenesis to acquire residue contact information. In this methodology, for each of five inactive CcdB mutants, exhaustive screens for suppressors were performed. Proximal suppressors were accurately discriminated from distal suppressors based on their phenotypes when present as single mutants. Experimentally identified putative proximal pairs formed spatial constraints to recover >98% of native-like models of CcdB from a decoy dataset. Suppressor methodology was also applied to the integral membrane protein, diacylglycerol kinase A where the structures determined by X-ray crystallography and NMR were significantly different. Suppressor as well as sequence co-variation data clearly point to the X-ray structure being the functional one adopted in vivo. The methodology is applicable to any macromolecular system for which a convenient phenotypic assay exists.
Long-term logging residue loadings affect tree growth but not soil nutrients in lodgepole pine forests
<p>Both above- and below-ground characteristics are affected by logging residue loadings. Long-term monitoring of tree growth and soil nutrients was conducted. We found that tree growth but not soil nutrients were affected. There were dynamic relationships between tree growth and logging residue loadings.</p>
Data from: Environmental stress correlates with increases in both genetic and residual variances: a meta-analysis of animal studies
Adaptive evolutionary responses are determined by the strength of selection and the amount of genetic variation within traits, however, both are known to vary across environmental conditions. As selection is generally expected to be strongest under stressful conditions, understanding how the expression of genetic variation changes across stressful and benign environmental conditions is crucial for predicting the rate of adaptive change. While theory generally predicts increased genetic variation under stress, previous syntheses of the field has found limited support for this notion. These studies have focused on heritability, which is dependent on other environmentally sensitive, but non-genetic, sources of variation. Here, we aim to complement these studies with a meta-analysis where we examine changes in coefficient of variation (CV) in maternal, genetic, and residual variances across stressful and benign conditions. Confirming previous analyses, we did not find any clear direction in how heritability changes across stressful and benign conditions. However, when analyzing CV, we found higher genetic and residual variance under highly stressful conditions in life-history traits but not in morphological traits. Our findings are of broad significance to contemporary evolution suggesting that rapid evolutionary adaptive response may be mediated by increased evolutionary potential in stressed populations.
Data from: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity
Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825,767,562 bp in 8,260 scaffolds with an N50 scaffold size of 713,602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49,124 high confidence gene models representing 37,740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158,367 Solanaceae genes and 1,897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding.
Data from: Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions
The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced "superacceptor" activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD) motif in the catalytic loop and the Asp-Phe-Gly (DFG) motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not limited to the ATP site, and may enhance allosteric cooperativity with the substrate binding region by increasing communication capabilities of mediating residues.
Data from: Molecular analysis of caffeoyl residues related to pigmentation in green cotton fibers
The pigment components in green cotton fibers were isolated and identified as 22-O-caffeoyl-22-hydroxymonodocosanoin and 22-O-caffeoyl-22-hydroxydocosanoic acid. The concentration of 22-O-caffeoyl-22-hydroxymonodocosanoin was correlated positively with the degree of green fibers of color, indicating a role of caffeoyl derivatives in pigmentation of green cotton fibers. Upland cotton (Gossypium hirsutum L.) contains four genes (Gh4CL1 to Gh4CL4) encoding 4-coumarate:CoA ligase (4CL), key enzymes of the phenylpropanoid biosynthesis pathway. In 15 to 24 days-post anthesis fibers, the expression level of Gh4CL1 was very low, Gh4CL3 had a similar expression level between the white and green cottons, Gh4CL2 had a significantly higher expression level in the green fibers than in the white fibers, whereas Gh4CL4 seemed to have a higher expression level in the white fibers than in the green fibers. According to enzyme kinetics analysis, Gh4CL1 displayed a preference for 4-coumarate, Gh4CL3 and Gh4CL4 exhibited a somewhat low but still prominent activity towards ferulate, while Gh4CL2 had a strong preference for caffeate and ferulate. These results suggest that Gh4CL2 might be involved in the metabolism of caffeoyl residues and related to pigment biosynthesis in green cotton fibers. Our findings provide insights for understanding biochemical and molecular mechanisms of pigmentation in green cotton fibers.
Data from: Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information
Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likelihood based method to covary across protein-protein interfaces in the 50S ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex provided that the number of aligned sequences is greater than the average of the lengths of the two proteins. We use this method to make subunit contact predictions for an additional 36 protein complexes with unknown structures, and present models based on these predictions for the tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite efflux system, the pyruvate formate lyase-activating enzyme complex, and the methionine ABC transporter.
Data from: The interaction of fatigue cracks with a residual stress field using thermoelastic stress analysis and synchrotron x-ray diffraction experiments
This article presents an experimental study on the fatigue behaviour of cracks emanating from cold-expanded holes utilising thermoelastic stress analysis (TSA) and synchrotron x-ray diffraction (SXRD) techniques with the aim of resolving the long-standing ambiguity in the literature regarding potential relaxation, or modification, of beneficial compressive residual stresses as a result of fatigue crack propagation. The crack growth rates are found to be substantially lower as the crack tip moved through the residual stress zone induced by cold expansion. The TSA results demonstrated that the crack tip plastic zones were reduced in size by the presence of the residual compressive stresses induced by cold expansion. The crack tip plastic zones were found to be insignificant in size in comparison to the residual stress zone resulting from cold expansion, which implied that they were unlikely to have had a notable impact on the surrounding residual stresses induced by cold expansion. The residual stress distributions measured along the direction of crack growth, using SXRD, showed no signs of any significant stress relaxation or redistribution, which validates the conclusions drawn from the TSA data. Fractographic analysis qualitatively confirmed the influence on crack initiation of the residual stresses induced by the cold expansion. It was found that the application of single compressive overload caused a relaxation, or reduction in the residual stresses, which has wider implications for improving the fatigue life.
Data from: A high-efficiency hydrocyclone designed by response surface methodology for acid hydrolysis residue recycling
A high-efficiency hydrocyclone was designed by response surface methodology to evaluate the recycling of acid hydrolysis residues from titanium dioxide (TiO2) production as a study case. TiO2 is an important product and the world's best white pigment. During its production from ilmenite (FeTiO3) by the sulphuric acid method, the incomplete reaction produces large amounts of residue, which also contain unreacted ilmenite. Large amounts of residue are generally accumulated without any treatment. Hydrocycloneuse is regarded as a method for separating and recovering chemicals from process residues by which the unreacted components can be recycled efficiently. However, hydrocyclones designed by conventional procedures may have some limitations regarding classification sharpness. In this paper, numerical experiments and laboratory tests were performed to evaluate the classification sharpness of various hydrocyclone designs. Response surface methodology was used to optimize hydrocyclones with different structural configurations. Based on the response models, a designed hydrocyclone with a high sharpness of classification of particles was constructed. The sharpness of the newly designed hydrocyclone increased from 80.5 % to 93.3 %. The vortex finder separated approximately 89.9 % of the fine particles in impurities, while 51.0 % of TiO2was recycled by the spigot. The hydrocyclone proposed in this paper properly minimizes the risk of environmental pollution caused by TiO2 production and provides a significant estimated cost savings.
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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.