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266 results for “selection analysis”
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>
PanDDA analysis of SP100 screened against selection of Maybridge Fragment Library
<p>Nulear auto-antigen SP-100 screened against a selection of the Maybridge Fragment Library by X-ray crystallography.</p>
Binding of Cholesterol to the N-terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerisation-Related Binding Selectivity and Loop Mutations
<p>Input files, topologies and trajectories of the work "Binding of Cholesterol to the N-terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerisation-Related Binding Selectivity and Loop Mutations". </p>
Population Genomics Analysis of 30 Samples from Each of Multiple Populations Reveals Signatures of Selection from Breeding for Rapid Growth and Apical Dominance in Paulownia fortunei
<p><i>Paulownia fortunei</i> is an ecologically and economically valuable tree cultivated for its rapid growth and high-quality timber. To enhance <i>Paulownia</i> germplasm, we have developed the elite variety QingT with patented advantages in growth rate and apical dominance. To illuminate the genetic basis of QingT's superior traits, here we harness comparative population genomics to analyze genomic variation patterns between QingT and common <i>Paulownia</i>. We performed whole-genome re-sequencing of 30 QingT and 30 common samples, detecting 15.6 million SNPs and 2.6 million indels. Phylogeny and population structure analyses robustly partitioned common and QingT into distinct groups which indicate robust genome stabilization. QingT exhibited reduced heterozygosity and linkage disequilibrium decay compared to common <i>Paulownia</i>, reflecting high recombination, indicating hybridizing effects with common white-flowered string is the source of its patented advantages. Genome selection scans uncovered 25 regions of 169 genes with elevated nucleotide diversity, indicating selection sweeps among groups. Functional analysis of sweep genes revealed upregulation of ribosomal, biosynthesis and growth pathways in QingT, implicating enhanced protein production and developmental processes in its rapid growth phenotype. This study's insights comprehensively chart genomic variation during <i>Paulownia</i> breeding, localizing candidate loci governing agronomic traits, and underpinnings of future molecular breeding efforts to boost productivity. </p>
Statistical analysis of data determining minimal selective concentration of Amoxicillin, doxycycline and enrofloxacin
<p>This repository is containing the datasets with statistical analysis of the paper: "Selection for amoxicillin, doxycycline and enrofloxacin resistant Escherichia coli at concentrations lower tha nthe ECOFF in rich media and in broiler-derived fecal fermenations."</p> <p><em>The phenotypic analysis</em></p> <ul> <li>Phenotypic amoxicillin <ul> <li>R-file: Phenotypic Amox mixed models, CSV-file: Phenotypic data Amox</li> </ul> </li> <li>Phenotypic doxycycline <ul> <li>R-file: Phenotypic Dox mixed models, CSV-file: Phenotypic data Dox</li> </ul> </li> <li>Phenotypic enrofloxacin <ul> <li>R-file: Phenotypic Enro mixed models, CSV-file: Phenotypic data Enro</li> </ul> </li> </ul> <p><em>The resistome analysis </em></p> <ul> <li>two CSV-files: Resistoom workfile and resistome_reference_file</li> <li>one R-file: Resistome_analysis_antimicrobial_classes</li> </ul> <p><em>Microbiome analysis<br></em></p> <ul> <li>Alpha- and beta-diversity analysis<br> <ul> <li>R-file Biom analysis, CSV-file: metadata2, biom-file: reads_fermentation</li> </ul> </li> <li>Microbial abundance analysis <ul> <li>R-file: Abundance plot, CSV-file: metadata2. biom-file: reads_fermentation2.biom</li> </ul> </li> </ul>
Why the long teeth? Morphometric analysis suggests different selective pressures on functional occlusal traits in Plio-Pleistocene African suids
<p>Neogene and Pleistocene African suids displayed convergent evolutionary trends in the third molar (M3) morphology, with increasingly elongated and higher crowns through time. While these features can prevent premature loss of masticatory functionality and potentially increase long-term reproductive success, changes in dental occlusal traits such as enamel complexity and thickness can also improve chewing efficiency and increase short-term energetic return. While both long-term and short-term benefits can contribute to the thriving of a lineage, the selective pressures associated with each category can be different. To examine how crown elongation correlates with these functional occlusal traits, we selected M3s of Kolpochoerus, Notochoerus, and Metridiochoerus from Kenya and South Africa, dated between 3.0 Ma and 0.4 Ma. To account for dental wear, we used micro-CT imaging of unworn/slightly worn M3s to simulate wear progression within each tooth. We compared morphometric representatives of occlusal enamel complexity and thickness among the specimens following their respective wear trajectories. We found that M3 elongation correlates with higher occlusal complexity and thinner enamel in Notochoerus and Metridiochoerus lineages through time. In Kolpochoerus, enamel complexity and thickness were generally maintained through time, despite M3 elongation. The differences in M3 morphometric trends suggest that Kolpochoerus likely experienced a different set of selective pressures on functional occlusal traits compared to Notochoerus and Metridiochoerus. The shared evolutionary trends of M3 specialization among Notochoerus and Metridiochoerus suggest similar selective pressures on their chewing efficiency and the possibility of a dietary niche overlap in more xeric habitats.</p>
Dataset for an analysis of selected studies on software development and reuse in the field of software documentation
<p>The data record contains bibliographical metadata from 2012 to 2023, which have been extracted from the databases ScienceDirect, SpringerLink and IEEE Xplore. It was created in the context of a master thesis which will be published later. The aim was to make a selection of studies on software documentation from the perspective of software development based on the master thesis.</p>
12 selected stations from NVE Hydra II for QDF analysis
<p>Streamflow data, in cubic meters per second, and date in YYYMMDD/HHMM for twelve hydrologic gauging stations in Norway. </p> <p>Filename - station name:</p> <p>35_2000013 - Sjodalsvatn</p> <p>35_6000010 - Gryta</p> <p>35_11000004 - Elgtjern</p> <p>35_12000070 - Etna</p> <p>35_16000066 - Grosettjern</p> <p>35_19000079 - Gravå</p> <p>35_55000004 - Røykenes</p> <p>35_55000005 - Dyrdalsvatn</p> <p>35_83000002 - Viksvatn</p> <p>35_122000017 - Hugdal Bru</p> <p>35_138000001 - Øyungen</p> <p>35_206000003 - Manndalen Bru</p>
Gene Enrichment Map Data from gProfiler Analysis - Selected MPK Interactions of Arabidopsis thaliana
<p>Gene enrichment analysis results for the selected predicted MPK interactions are included in the supplementary materials.</p>
Elasto-plastic residual stress analysis of selective laser sintered porous materials based on 3D-multilayer thermo-structural phase-field simulations
<p>The supporting data and utilities from the publication "Elasto-plastic residual stress analysis of selective laser sintered porous materials based on 3D-multilayer thermo-structural phase-field simulations" are recorded in this dataset. </p> <p>Non-isothermal phase-field simulations of SLS process on SS316L material and subsequent elasto-plastic calculations were performed to analyze the development of plastic deformation and residual stress in SLS produced components during the processing. The dependence of the fusion zone, residual stress and plastic strain on the processing parameters namely, Beam power (Unit: Watts) and Scan speed (Unit: mm/s) were investigated. </p> <p>To promote FAIR research data principles, the processed simulation data from the thermo-elasto-plastic calculations for all the process parameter sets (hereby refered as P-v sets) are curated in this dataset. The raw temporal data obtained from the processing simulations and the elasto-plastic could not be included in this dataset due to its high volume. However, the corresponding raw data can be requested by contacting the creators of this dataset (Yangyiwei Yang: <a href="mailto:yangyiwei.yang@mfm.tu-darmstadt.de">yangyiwei.yang@mfm.tu-darmstadt.de</a> and Somnath Bharech: <a href="mailto:somnath.bharech@tu-darmstadt.de">somnath.bharech@tu-darmstadt.de</a>).</p> <p>This dataset includes: </p> <ul> <li><code>average_value.csv</code>: Contains average values of mechanical properties (such as residual stress, plastic strain) for the powder bed and the fused strut of all the process parameter sets.</li> <li><code>mesostructures_tep_sls.zip</code> : Contains resampled mesostructures obtained at the last time step of the SLS processing simulations with thermo-elasto-plastic calculations for the P-v sets reported in the aforementioned investigation. Nomenclature of the sub-directories indicating the P-v sets follows: <code>tep_<beam power>-<scan speed></code>. Each of these sub-directories contain the mesostructures from last time step of the thermo-elasto-plastic analysis of each of the four layer scans and is named as: <code>TP_layer{1..4}_output_final.e</code>. These files can be opened using Paraview v.5.8.1 or higher. The nodal values are explained as follows:</li> </ul> <table> <tbody> <tr> <td><strong>Nodal value name</strong></td> <td><strong>Symbol</strong></td> <td><strong>Description</strong></td> <td><strong>Unit</strong></td> </tr> <tr> <td>T</td> <td>\(T\)</td> <td>Temperature field normalized by \(T_M\)</td> <td>-</td> </tr> <tr> <td>c</td> <td>\(\rho\)</td> <td>Substance order parameter</td> <td>-</td> </tr> <tr> <td>eps_ij </td> <td>\(\varepsilon\)</td> <td>Strain</td> <td>-</td> </tr> <tr> <td>epsp_ij</td> <td>\(\varepsilon^\text{pl}\)</td> <td>Plastic strain</td> <td>-</td> </tr> <tr> <td>peeq</td> <td>\(p_\text{e}\)</td> <td>Accumulated plastic strain</td> <td>-</td> </tr> <tr> <td>sigma_ij </td> <td>\(\sigma\)</td> <td>Stress</td> <td>MPa</td> </tr> <tr> <td>vonmises</td> <td>\(\sigma_\text{e}\)</td> <td>von Mises stress </td> <td>MPa</td> </tr> <tr> <td>u</td> <td>\(\mathbf{u}\)</td> <td>Displacement</td> <td>µm</td> </tr> </tbody> </table> <p> </p>
Selection pressure analysis of dengue virus complete genome and E gene nucleotide sequences from Pakistan
<p>This dataset comprises 43 E gene and 44 complete genome nucleotide sequences of the dengue virus from serotypes DENV-1 to DENV-4, representing all documented sequences in Pakistan to date, sourced from the Virus Pathogen Resource (ViPR) database and NCBI. The E gene is critical as it is involved in serotype changes of the dengue virus, making it a pivotal target for understanding shifts in viral pathogenicity and immune escape mechanisms. The aim of compiling this dataset is to facilitate comprehensive genetic analysis and enhance understanding of the evolutionary dynamics of the dengue virus within the region. To assess the evolutionary pressures acting on these sequences, we conducted a selection pressure analysis utilizing computational methods. These methods include the Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), adaptive Branch Site Random Effects Likelihood (aBSREL), Mixed Effects Model of Evolution (MEME), and the Genetic Algorithm for Recombination Detection (GARD), all implemented in the HyPhy software package. Our analysis focused on identifying genomic sites under both positive and negative selection pressures, providing insights into the adaptive evolutionary processes affecting the E gene of the dengue virus in Pakistan. Understanding the molecular evolution of this gene is crucial for predicting serotype evolution, potentially aiding in the development of effective vaccines and therapeutic strategies.</p>
Social selection analysis reveals limited effect of neighbors' traits in Tree swallows
<p>Social interactions are ubiquitous in nature and can shape fitness of individuals through social selection. This type of selection arises when phenotypes of neighbors influence the fitness of a focal individual. Quantifying social selection is crucial to better characterise the overall selective landscape. For example, if intraspecific competition is strong, traits that are beneficial for an individual could be detrimental for competitors. In this study, we quantified social selection acting on four key ecological traits (body mass, wing length, laying date and clutch size) in wild Tree swallow (<em>Tachycineta bicolor)</em> females. We used reproductive success measured at three stages throughout the breeding season as fitness proxies to assess selection acting at those decisive moments. We also quantified the effects of environment on selection using measures of conspecifics' density, type of agricultural landscape and presence of interspecific competitors. Overall, we found no strong evidence of social selection on these traits in our study system, although there were marginally non-significant selection gradients suggesting positive effect of larger neighbors. Environmental variables affected reproductive success but did not affect social selection gradients. Our study calls for more social selection estimates to be reported across environments to better understand its importance in wild populations.</p>
Statistical Analysis of Selected Mixtures of Alkali-activated Materials Exposed to Thermal
<p>Alkaline-activated materials have come to the forefront of the interest of construction experts in recent decades.<br>It is a composite material, an alternative to concrete, where the binder component can be a by-product (with pozzolanic or<br>latent hydraulic properties) of some industrial processes instead of ecologically disadvantageous cement. The work is<br>focused on the statistical analysis of the compressive strength of alkali-activated materials exposed to temperature stress,<br>where the first part contains three mixtures of alkali-activated composites that were subjected to the frost resistance test,<br>and the second part follows the functional dependence of the compressive strength of the selected mixture of the alkaliactivated system on exposure to high temperatures with the selection of the optimal statistical model.</p>
The application of a mode of double preconcentration and double stripping steps in combination with a flow system to decrease the detection limit and increase the selectivity of determinations in stripping analysis of As(III)
<p><span>Due to the fact that arsenic </span><span>has very harmful and toxic effects on living organisms </span><span>monitoring of its content in various environmental samples </span><span>at trace level concentrations</span><span> </span><span>is desirable and highly recommended. Such advantages as low cost and portable instrumentation, achieving low detection limits and most of all the possibility of the direct determination of As(III) with no separation step make stripping voltammetry suitable for the determination of arsenic.</span><span> </span><span> <br></span></p> <p><span>These data concer the application of double deposition and double stripping steps mode in combination with a flow system for anodic stripping voltammetric determination of As(III) ions. An advantage of the proposed way of the voltammetric measurements is a decrease of the detection limit as compared to the values obtained using a traditional three-electrode system thanks to an initial preconcentration of the analyte on the first working electrode as well as the significant increase in a selectivity of As(III) determination thanks to the possibility of solution exchange after the first deposition step.</span></p> <p><span><span>The proposed way of the voltammetric measurements leads to the following analytical advantages: (i) a decrease of the detection limit as compared to the values obtained using traditional three-electrode system by an initial preconcentration of the analyte using the large-surface area electrode; (ii) an increase of the selectivity of voltammetric determinations thanks to the application of a flow system and exchange the solution after the first deposition step; (iii) simplification of performing the measurements in comparison to the original version of double accumulation and stripping steps mode due to the lack of a need to change the position of the first working electrode; (iv) the possibility of analysis of samples with a complex matrix thanks to the use of a flow system leading to minimization of matrix effects in the second deposition step. The developed procedure of As(III) determination offers a wide linear dynamic range in the range from 1 × 10<sup>-9</sup> to 5 × 10<sup>-8</sup> mol L<sup>-1</sup> at a deposition time of 120 s at both working electrodes. The detection limit for As(III) determination was 4.8 × 10<sup>-10</sup> mol L<sup>-1</sup>. The undoubted advantage of the described procedure is its high selectivity. The tolerable limit of excess of Cu(II), which is the main interferent in the course of anodic stripping voltammetric As(III) determination, was significantly increased thanks to the solution exchange after the first deposition step. The correctness of the proposed procedure was confirmed by analysis of a real water sample and lake water certified reference material by obtaining satisfactory recovery values. The additional advantage of the proposed procedure is a miniaturization of the measurement system and the use of environmentally friendly electrodes.</span></span></p>
Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors - Inputs and Analysis
<p>Supplementary data of "Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors" paper.</p> <p>This dataset consists of the parametrized ligand (covalent and noncovalent form of ICR, ICK, ICL, IKR) and complexes files, sample of input files used for Molecular dynamics simulations and analysis procedures, and the raw data of results. </p>
Supplementary Table S1. Combined analysis of variance containing the degrees of freedom (DF), mean squares (MS), P value (P val.), mean, coefficient of experimental variation (CEV%) and selective accuracy (SA) for the traits of luminosity (L*), chromaticity a* (a*), chromaticity b* (b*), grain length (length, mm), grain width (width, mm), grain thickness (thickness, mm), mass of 100 grains (Mass, g), normal grains (Ng, %), water absorption (absorption, %), cooking time (Ct, min:s), and concentrations of potassium (K, g kg-1 dry matter - DM), phosphorus (P, g kg-1 DM), calcium (Ca, g kg-1 DM), magnesium (Mg, g kg-1 DM), iron (Fe, mg kg-1 DM), zinc (Zn, mg kg-1 DM), and copper (Cu, mg kg-1 DM) obtained in 25 common bean cultivars evaluated in four experiments carried out from 2019 to 2021
<p><strong><span>Table S1.</span></strong><span> Combined analysis of variance.</span></p> <p><strong><span>Indirect selection for multiple technological and nutritional traits in common bean cultivars under different degrees of multicollinearity</span></strong></p> <p><strong><span>Bragantia, 2024.</span></strong></p>
Figure 1. Landmarks and curves selection. A. Fore wing. B. Hind wing. C in Geometric morphometric analysis of Eysarcoris guttiger, E. annamita and E. ventralis (Hemiptera: Pentatomidae)
Figure 1. Landmarks and curves selection. A. Fore wing. B. Hind wing. C. Pygophore.
Lichens as bioindicators of monitoring of the selective air pollution, Zabrze (Poland) - XRF analysis results.
<p>XRF analyses were performed by the BRUKER S8 TIGER series 2 WD-XRF spectrometer with a 1kW Rh X-ray tube. The system is equipped with five analyzing crystals (LiF200, PET, XS–55, LIF-220 & Ge) and two detectors (flow and scintillation counter). The samples were measured by best detection mode (18min analysis time), and the results were evaluated in Quant-Express (fundamental parameters) and SPECTRAplus Software.<br> Dr Ewa Szram, employed at the Institute of Earth Sciences, Faculty of Natural Sciences, Silesian University in Katowice, carried out the project. This research was funded by the National Science Centre, Poland MINIATURA-6 2022/06/X/ST10/00338 “Lichens as bioindicators of monitoring of the selective air pollution”</p>
Data from: Delineating seasonal shifts in Reindeer habitat and diet selection by integrating GPS telemetry and stable Isotope 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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