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38 results for “reaction analysis”
Methodology for measuring photonuclear reaction cross sections with an electron accelerator based on Bayesian analysis
<p>Measurement data, simulation data and code from the manuscript Braccini et al. "Methodology for measuring photonuclear reaction cross sections with an electron accelerator based on Bayesian analysis" </p> <p>ArXiv preprint arXiv:2309.11270 [nucl-ex] at https://doi.org/10.48550/arXiv.2309.1127</p>
Comparative host transcriptomics as a tool to identify candidate biomarkers for immune reactions in leprosy: A meta-analysis study
<p>The dataset consists of R source code for the individual dataset analysis of the studies and their meta-analysis. It also contains supplementary tables and figure.</p>
Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction. Analysis Code, Numerical and Primary data.
<p>Uploaded under this Zenodo DOI is the following:</p> <p>1. the Analysis Code used for Flow Cytometry analysis in the paper, GO complex analysis (Figure 3) and Hit visualization (Figure 1, 2 S1, S4 Figs).</p> <p>2. The primary Flow Cytometry data from both the initial screen (ScreenFlowFCS) and validation experiments (ValidationFlowFCS) are included as .zip files.</p> <p>3. a .zip folder is uploaded that contains all the analysis code for the ChIP-Seq experiments. </p> <p>4. Excel worksheets that contain the numerical source data for all qPCR bar plots.</p>
Limited sex differences in plastic responses suggest evolutionary conservatism of thermal reaction norms: A meta-analysis in insects
<p>Temperature has a profound effect on the growth and development of ectothermic animals. However, the extent to which ecologically-driven selection pressures can adjust thermal plastic responses in growth schedules is not well understood. Comparing temperature-induced plastic responses between sexes provides a promising but underexploited approach to evaluating the evolvability of thermal reaction norms: males and females share largely the same genes and immature environments but typically experience different ecological selection pressures. We proceed from the idea that substantial sex differences in plastic responses could be interpreted as resulting from sex-specific life-history optimization, whereas similarity among the sexes should rather be seen as evidence of an essential role of physiological constraints. In this study, we performed a meta-analysis of sex-specific thermal responses in insect development times, using data on 161 species with comprehensive phylogenetic and ecological coverage. As a reference for judging the magnitude of sex-specificity in thermal plasticity, we compared the magnitude of sex differences in plastic responses to temperature with those in response to diet. We show that sex-specific responses of development times to temperature variation are broadly similar. We also found no strong evidence for sex-specificity in thermal responses to depend on the magnitude or direction of sex differences in development time. Sex differences in temperature-induced plastic responses were systematically less pronounced than sex differences in responses induced by variations in larval diet. Our results point to the existence of substantial constraints on the evolvability of thermal reaction norms in insects as the most likely explanation. If confirmed, the low evolvability of thermal response is an essential aspect to consider in predicting evolutionary responses to climate warming.</p>
Figure 5 in Quantitative phosphoproteomic analysis of chicken DF-1 cells infected with Eimeria tenella, using tandem mass tag (TMT) and parallel reaction monitoring (PRM) mass spectrometry
Figure 5. KEGG pathways of the differentially expressed phosphorylated proteins. The abscissa indicates the first 10 significantly enriched KEGG pathways and the ordinate indicates the significance of enriched KEGG pathways, the more left, the more significant.
Figure 4 in Quantitative phosphoproteomic analysis of chicken DF-1 cells infected with Eimeria tenella, using tandem mass tag (TMT) and parallel reaction monitoring (PRM) mass spectrometry
Figure 4. Gene ontology annotations of the differentially expressed phosphorylated proteins. The abscissa indicates the enriched GO functional classification, including biological process (A), cellular component (B), and molecular function (C). The ordinate indicates the size of the significance of corresponding to each entry, the more left, the more significant.
Figure 3 in Quantitative phosphoproteomic analysis of chicken DF-1 cells infected with Eimeria tenella, using tandem mass tag (TMT) and parallel reaction monitoring (PRM) mass spectrometry
Figure 3. Clustering heatmap of different expression phosphorylated peptides. Each row represents a phosphorylated peptide segment, each column represents a group of samples. The logarithmic value (logarithmic transformation based on 2) of the significantly differentially expressed phosphorylated peptides in different samples is displayed in the clustering heatmap in different colors. Red represents significant upregulation of phosphorylated peptides; blue represents significant down-regulation of phosphorylated peptides.
Figure 2 in Quantitative phosphoproteomic analysis of chicken DF-1 cells infected with Eimeria tenella, using tandem mass tag (TMT) and parallel reaction monitoring (PRM) mass spectrometry
Figure 2. Volcano plots from different group comparisons. The abscissa indicates difference multiple (logarithmic transformation based on 2), the ordinate indicates the significant of difference (logarithmic transformation based on 10). The red point is significantly upregulated phosphorylated peptide segment, the blue point is significantly downregulated phosphorylated peptide segment and the gray point is a phosphorylated peptide segment with no significant difference.
Fig. 1 in Polymerase chain reaction and gyrA nucleotide sequence analysis of Wolbachia endosymbionts (Rickettsiales: Anaplasmataceae) in various species of Culicidae, Cimex lectularius (Hemiptera: Cimicidae) and Dirofilaria immitis (Rhabditida: Onchocercidae)
Fig. 1. Phylogenetic tree based on Maximum Likelihood depicting the grouping of Wolbachia from various hosts based on analysis of the gyrA gene. The numerical value displayed on branches is the bootstrap value (1,000 replicates), and branches with values below 50% are collapsed. The tree illustrates that gyrA sequences distinguish Wolbachia subtypes based on host taxonomy, demonstrating that this gene may contribute to Wolbachia strain typing projects and future phylogenetic analysis.
Limited sex differences in plastic responses suggest evolutionary conservatism of thermal reaction norms: A meta-analysis in insects
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Diapause is not selected as a bet-hedging strategy in insects: a meta-analysis of reaction norm shapes
<p>Many organisms escape from lethal climatological conditions by entering a resistant resting stage called diapause, and it is essential that this strategy remains optimally timed with seasonal change. Climate change therefore exerts selection pressure on phenology, which is expected to cause the evolution of mean diapause timing, but also phenotypic plasticity and bet-hedging strategies. Especially the latter as a strategy to cope with unpredictability is so far little considered in the context of climate change, and it is unknown whether it can readily evolve.</p> <p>Contemporary patterns of phenological strategies across a geographic range may provide information about their evolvability. We thus extracted 458 diapause reaction norms from 60 studies. First, we correlated mean diapause timing with mean winter onset. Then we partitioned the reaction norm variance into a temporal component (phenotypic plasticity) and among-offspring variance (diversified bet-hedging) and correlated this variance composition with predictability of winter onset. Contrary to our expectation, mean diapause timing correlated only weakly with mean winter onset, as populations at high latitudes failed to track early onsets. Variance among offspring was also limited and correlated only weakly with environmental predictability, indicating little scope for bet-hedging. We conclude that constraints may limit the evolution of phenology in a rapidly changing climate.</p>
Photoactivation of the Orange Carotenoid Protein Requires Two Light-Driven Reactions Mediated by a Metastable Monomeric Intermediate – Absorption Spectra and Global Analysis Results, Molecular Dynamics Simulations
<p>Time-resolved absorption and molecular dynamics trajectory datasets associated with: Rose, J. B.; Gascón, J. A.; Sutter, M.; Sheppard, D. I.; Kerfeld, C. A.; Beck, W. F. Photoactivation of the Orange Carotenoid Protein Requires Two Light-Driven Reactions Mediated by a Metastable Monomeric Intermediate. <i>Phys. Chem. Chem. Phys.</i> <strong>2023</strong>, DOI: 10.1039/d3cp04484j.</p>
Liquid-liquid phase reaction between crystal violet and sodium hydroxide: kinetic study and precipitate analysis
<p>To investigate reaction order and kinetic parameters of the reaction between crystal violet (CV) and sodium hydroxide (NaOH), various concentrations of the reactants were applied. The present work also verifies the unknown solid product produced under highly concentrated conditions. The reaction orders of CV and NaOH were determined to be 1 and 1.17 by pseudo-rate method, respectively, with a rate constant, k, of 0.084 [(M-1.17) s-1]. In addition to pseudo-rate method, the half-life approach is use to calculated the overall reaction order to verify the accuracy of pseudo-rate method. The overall reaction order is determined to be 1.9 by half-life method. Compare reaction order gained from both methods, the overall reaction order is determined as ~2. The precipitate formation was observed when high concentrations of CV (0.01~0.1 M) and NaOH (1.0 M) were applied. Fourier transform infrared (FTIR) spectroscopy was used to compare the spectra of the precipitate generated and a commercial solvent violet 9 (SV9). Based on the FTIR spectra, it was confirmed that the molecular structure of the precipitate matched that of solvent violet 9.</p>
Figure 1 in Quantitative phosphoproteomic analysis of chicken DF-1 cells infected with Eimeria tenella, using tandem mass tag (TMT) and parallel reaction monitoring (PRM) mass spectrometry
Figure 1. Proportion of serine, threonine, and tyrosine in phosphorylation sites.
ReaxANA: Analysis of Reactive Dynamics Trajectories for Reaction Network Generation
<p><span>ReaxFF simulations, QM calculation input/output files, and Jupyter notebooks for data analysis and visualization.</span></p>
The role of chloroplast movement in C4 photosynthesis: A theoretical analysis using a 3-D reaction-diffusion model for maize
<p>Chloroplast movement within mesophyll (M) cells in C<sub>4</sub> plants is hypothesized to enhance the CO<sub>2</sub> concentrating mechanism (CCM), but this is difficult to verify experimentally. A three-dimensional (3-D) leaf model can help analyze how chloroplast movement influences the operation of CCM. The first volumetric reaction-diffusion model of C<sub>4</sub> photosynthesis that incorporates: detailed 3-D leaf anatomy, light propagation, ATP and NADPH production and CO<sub>2</sub>, O<sub>2</sub> and bicarbonate concentration driven by diffusional and assimilation/emission processes, was developed and implemented for maize leaves to simulate various chloroplast movement scenarios within M cells: the movement of all M chloroplasts towards bundle-sheath (BS) cells (aggregative movement) and movement of only those of interveinal M cells towards BS cells (avoidance movement). Light absorbed by bundle-sheath (BS) chloroplasts relative to M chloroplasts increased in both cases. Avoidance movement decreased light absorption by M chloroplasts considerably. Consequently, total ATP and NADPH production and net photosynthesis rate increased for aggregative movement and decreased for avoidance movement case compared to the default case of no chloroplast movement at high light intensities. Leakiness increased in both chloroplast movement scenarios due to the imbalance in energy production and demand in M and BS cells. These results suggest the need to design strategies for coordinated increases in electron transport and Rubisco activities for an efficient CCM at very high light intensities.</p>
The role of chloroplast movement in C4 photosynthesis: A theoretical analysis using a 3-D reaction-diffusion model for maize
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Liquid-liquid phase reaction between crystal violet and sodium hydroxide: kinetic study and precipitate analysis
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Diapause is not selected as a bet-hedging strategy in insects: a meta-analysis of reaction norm shapes
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Quantitative analysis of electroporation-mediated intracellular delivery via bioorthogonal luminescent reaction
<p>The data of the paper entitled "Quantitative analysis of electroporation-mediated intracellular delivery via bioorthogonal luminescent reaction"</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.