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10,735 results for “dependability”
Trait-dependent diversification in angiosperms: Patterns, models and data
<p>Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesized data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to dataset properties – trees that were larger, older, or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics.</p>
Dataset: Core excitations and ionizations of uranyl in Cs2UO2Cl4 from relativistic embedded damped response time-dependent density functional theory and equation of motion coupled cluster calculations
<p>This dataset collects the unprocessed (= outputs from calculations) results discussed in the paper titled "Core excitations and ionizations of uranyl in Cs2UO2Cl4 from relativistic embedded damped response time-dependent density functional theory and equation of motion coupled cluster calculations", by Wilken Aldair Misael and Andre Severo Pereira Gomes. It also contains the figures used in the manuscript.</p>
Meta-analysis shows forest soil CO2 effluxes are dependent on the disturbance regime and biome type
<p class="MsoNormal"><span>F</span><span>orest </span><span>s</span><span>oil CO<sub>2</sub> efflux (F</span><span>CO<sub>2</sub></span><span>)</span><span> is a crucial process in global carbon cycling; however, how F</span><span>CO<sub>2</sub></span><span> responds to disturbance regimes in different forest biomes is poorly understood. </span><span>W</span><span>e quantif</span><span>ied</span><span> the effects of disturbance regimes on F</span><span>CO<sub>2</sub></span><span> </span><span>across boreal, temperate, tropical, and</span><span> Mediterranean</span><span> forests</span><span> based on 1240 observations from 380 studies. Globally, climatic perturbations such as elevated CO<sub>2</sub> concentration, warming, and increased precipitation increase F</span><span>CO<sub>2</sub></span><span> </span><span>by 13 to 25%. F</span><span>CO<sub>2</sub></span><span> is increased by forest conversion to grassland and elevated carbon input by forest management practices but reduced by decreased carbon input, fire, and acid rain. Disturbance also changes soil temperature and water content, which in turn affect the direction and magnitude of disturbance influences on F</span><span>CO<sub>2</sub></span><span>. F</span><span>CO<sub>2</sub></span><span> is disturbance- and biome-type dependent, and such effects should be incorporated into earth system models to improve the projection of the feedback between the terrestrial C cycle and climate change.</span></p>
Long-term coastal macrobenthic Community Trajectory Analysis reveals habitat-dependent stability patterns
<p>Long-term monitoring programs are fundamental to detecting changes in ecosystem health and understanding ecological processes. In the current context of increasing anthropogenic threats on marine ecosystems, understanding the dynamics and response of communities becomes essential. We used data collected over 14 years in the REBENT benthic coastal invertebrates monitoring program, at a regional scale in the North-East Atlantic, covering a total of 26 sites and 979 taxa. Four distinct habitats were studied: two biogenic habitats associated with foundation species in the intertidal and subtidal zones and two bare sedimentary habitats in the same respective tidal zones. We used Community Trajectory Analysis, a statistical approach that allows for quantitative measures and comparisons of temporal trajectories of ecosystems. We compared observed community trajectories to trajectories simulated under a non-directional null model in order to better understand the dynamics of the communities, their potential drivers, and the role of the studied habitats in these dynamics. Despite strong differences in the community compositions between sites and habitats, the communities followed non-directional dynamics during the 14 years monitored, which suggested stability at the regional scale. However, the shape, size, and direction of the trajectories of benthic communities were more similar within than among habitats, also suggesting the influence of the nature of the habitat on community dynamics. Results showed a higher variability in community composition in the first years of the monitoring in the intertidal bare habitat and confirmed the role of biogenic habitats in maintaining temporal stability. They also highlighted the need to apprehend the role of transient and rare species and the scale of observation in temporal beta diversity analyses. Finally, our study confirmed the usefulness of Community Trajectory Analysis to link observed trajectory patterns to fundamental ecological processes.</p>
Data from: Temperature-dependent mechanical behavior of aluminum AM structures generated via multi-layer friction surfacing
<p>This dataset contains the data for the publication " Temperature-dependent mechanical behavior of aluminum AM structures generated via multi-layer friction surfacing "</p>
Supporting data for 'Chemically Reduced Graphene Oxide based Aerogels (rGOAs) - insight on the surface and textural functionalities dependent on handling the synthesis factors'
<p>Experimental data for the 'Chemically Reduced Graphene Oxide based Aerogels (rGOAs) - insight on the surface and textural functionalities dependent on handling the synthesis factors' manuscript/publication.</p> <p>Package contains following data:<br> 1. File with description of the experimental conditions for rGOAs synthesis, format: .pdf, number of files: 1 <br> 2. Data of Boehm titration for graphene oxide used for synthesis of rGOAs, format: .txt, number of files: 12<br> 3. Fourier-transform infrared spectra of rGOA samples and GO used for synthesis, format: .csv, number of files: 16<br> 4. Raw chromatograms of test probes for rGOA samples, format .txt, number of files: 15 folder with 11 files in each</p> <p> </p>
ETV4 mediates dosage-dependent prostate tumor initiation and cooperates with p53 loss to generate prostate cancer
<p>The mechanisms underlying ETS-driven prostate cancer initiation and progression remain poorly understood due to a lack of model systems that recapitulate this phenotype. We generated a genetically engineered mouse with prostate-specific expression of the ETS factor, ETV4, at lower and higher protein dosages through mutation of its degron. Lower-level expression of ETV4 caused mild luminal cell expansion without histologic abnormalities and higher-level expression of stabilized ETV4 caused prostatic intraepithelial neoplasia (mPIN) with 100% penetrance within 1 week. Tumor progression was limited by p53-mediated senescence and Trp53 deletion cooperated with stabilized ETV4. The neoplastic cells expressed differentiation markers such as Nkx3.1 recapitulating luminal gene expression features of untreated human prostate cancer. Single-cell and bulk RNA-sequencing showed stabilized ETV4 induced a novel luminal-derived expression cluster with signatures of the cell cycle, senescence, and epithelial to mesenchymal transition. These data suggest that ETS overexpression alone, at sufficient dosage, can initiate prostate neoplasia.</p>
Data from: The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds
<p><strong><span>Aim</span></strong></p> <p><span>How community composition varies in space and what governs the variation has been extensively investigated in macroorganisms. However, we have only limited knowledge for microorganisms, especially fungi, despite their ecological and economic significance. Based on previous research, we define and test a series of hypotheses regarding the composition of fungal communities, its most influential drivers and their spatial scale dependence. </span></p> <p><strong><span>Location</span></strong></p> <p><span>Czech Republic.</span></p> <p><strong><span>Time period</span></strong></p> <p><span>Present.</span></p> <p><strong><span>Taxa studied</span></strong></p> <p><span>Fungi.</span></p> <p><strong><span>Methods</span></strong></p> <p><span>We analyzed the distance decay relationships, community composition and its drivers (physical distance, litter and soil chemistry, tree composition, climate) in fungi, using multivariate analyses. We compared the results across three fungal ecological guilds (ectomycorrhizal fungi, saprotrophs and yeasts), two forest microhabitats (litter and bulk soil) and six spatial scales (from 5 m to 80 km) that comprehensively cover the Czech Republic.</span></p> <p><strong><span>Results</span></strong></p> <p><span>We found that, similar to macroorganisms, the ectomycorrhizal fungi and saprotrophs showed marked distance-decay relationships</span><span>,</span><span> and their community composition was driven mainly by vegetation and dispersal at local scales, but at regional scales, by environmental effects. In contrast, the third fungal guild, the unicellular yeasts, showed little distance decay, suggesting extraordinary spatial homogeneity, as often seen in microorganisms, such as bacteria.</span></p> <p><strong><span>Main conclusions</span></strong></p> <p><span>Our results underscore the remarkable variation in the community ecology of fungi, which seems to range well-known patterns both from the macro- and the microworld. Knowledge of these patterns advances our understanding of the ecology of fungi, rather understudied organisms of significant ecological and economic importance, which our findings identify as a potentially suitable model for bridging the gaps between the biogeography of micro- and macroorganisms. </span></p>
Data from: Mesocosm experiment reveals scale-dependence of movement tendencies in sticklebacks
<p><span>Habitat fragmentation can have negative impacts on migratory organisms that rely on the functional connectivity between growing and breeding grounds. Quantifying the population-level phenotypic consequences of such fragmentation requires fine-scaled tracking of individual behaviour and movements across relevant scales. We here make use of a natural experiment where some populations of 'migrant' three-spined sticklebacks (<em>Gasterosteus aculeatus</em>) became 'residents', following habitat fragmentation five decades ago. To test whether residents have a lower movement tendency than migrants, we developed a novel experimental platform that allows the automated tracking of individual movements via RFID technology in a semi-natural mesocosm where spatio-temporal scales and environmental conditions can be manipulated. We found that residents moved significantly less than migrants at large but not at small spatial scale. This pattern was consistent across time and contexts (water flow and group size). Our study substantiates prior literature on rapid phenotypic divergence in sticklebacks in response to human-induced isolation and highlights the importance of observing behaviour in ecologically relevant setups that bridge the gap between lab and field studies.</span></p>
Herbaceous vegetation responses to experimental fire in savannas and forests depend on biome and climate
<p>Fire-vegetation feedbacks potentially maintain global savanna and forest distributions. Accordingly, vegetation in savanna and forest ecosystems should have differential responses to fire, but fire response data for herbaceous vegetation has yet to be synthesized across biomes. Here, we examined herbaceous vegetation responses to experimental fire at 30 sites spanning four continents. Across a variety of metrics, herbaceous vegetation increased in abundance where fire was applied, with larger responses to fire in wetter and in cooler and/or less seasonal systems. Compared to forests, savannas were associated with a 4.8 (±0.4) times larger difference in burned versus unburned herbaceous vegetation abundance. In particular, grass cover decreased with fire exclusion in savannas, largely via decreases in C<sub>4</sub> grass cover, whereas changes in fire frequency had a relatively weak effect on grass cover in forests. These differential responses underscore the importance of fire for maintaining the vegetation structure of savannas and forests.</p>
Moonlight synchronous flights across three western palearctic swifts mirror size dependent prey preferences
<p><strong>Abstract</strong></p> <p>Recent studies have suggested the presence of moonlight mediated behaviour in avian aerial insectivores, such as swifts. At the same time swift species also show differences in prey (size) preferences. Here, we use the combined analysis of state-of-the-art activity logger data across three swift species, the Common, Pallid and Alpine swifts, to quantify flight height and activity responses to crepuscular and nocturnal light conditions. Our results show a significant response in flight heights to moonlight illuminance for Common and Pallid swifts, while a moonlight driven response is absent in Alpine swifts. Swift flight responses followed the size dependent altitude gradient of their insect prey. We show a weak relationship between night-time illuminance driven responses and twilight ascending behaviour, suggesting a decoupling of both crepuscular and night-time behaviour. We suggest that swifts optimise their flight behaviour to adapt to favourable night-time light conditions, driven by light responsive and size-dependent vertical insect stratification and weather conditions.</p> <blockquote> <p>You are required to cite both the Zenodo data repository as well as the BioRXiv pre-print when using this data, as:</p> <p>Hufkens et al. 2023. Moonlight synchronous flights across three western palearctic swifts mirror size dependent prey preferences. doi://10.5281/zenodo.7814214</p> <p>Hufkens et al. 2023. Moonlight synchronous flights across three western palearctic swifts mirror size dependent prey preferences. bioRxiv 2023.04.25.538243; doi: https://doi.org/10.1101/2023.04.25.538243</p> </blockquote> <p><strong>Use</strong></p> <p>This is a deposited version of the releases on Github.</p> <p>Either download this Zenodo repository or clone or download the project Github <a href="https://github.com/bluegreen-labs/swift_lunar_synchrony/archive/refs/heads/main.zip">zip file</a>.</p> <pre><code class="language-bash">git clone https://github.com/bluegreen-labs/swift_lunar_synchrony.git</code></pre> <p>Unzip the downloaded data if required. The repository is an `R` project and can be opened in <a href="https://posit.co/download/rstudio-desktop/">RStudio</a>, which will set the correct relative path.</p> <p><strong>Data structure & analysis</strong></p> <p>Analysis data is saved as compressed R serial files (.rds) in the <a href="https://github.com/bluegreen-labs/swift_lunar_synchrony/tree/main/data">`data` folder</a>. Scripts to reproduce the main statistical results are provided in the <a href="https://github.com/bluegreen-labs/swift_lunar_synchrony/tree/main/analysis">`analysis` folder</a>. A matching render of the analysis using the shared data is provided as <a href="http://bluegreen-labs.github.io/swift_lunar_synchrony/">dynamic webpage</a>.</p> <p><strong>Licensing</strong></p> <p>Be mindful of the CC-BY 4.0 license of the data and figures. Reuse is permitted on the condition of proper attribution and documentation of any changes.</p>
Summary statistics for: Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans
<p>Summary statistics of single POE-CpG based and POE-CpG co-methylation module based phenome-wide association analyses for the manuscript "Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans"</p>
Neo4J Maven Central dependency graph
<p>⚠️ Updated archive here: <a href="../records/11104819">https://zenodo.org/records/11104819</a> ⚠️</p> <p>Neo4j dump of the dependency graph of Maven Central as of April 04, 2023.<br> </p>
The trait-mediated trade-off between growth and survival depends on tree sizes and environmental conditions
<p><span>Interspecific relationships between growth and survival are critical determinants of tree species diversity maintenance in forests. The trade-offs between growth and survival in co-occurring tree species are believed to arise along a continuum of life-history strategies. For example, co-occurring species range from those that grow slowly and survive well in resource-poor environments to those that grow quickly but have low survival rates in resource-rich environments. However, uncertainties remain regarding how growth-survival trade-offs are related to species traits, tree sizes, or environmental conditions.</span></p> <p><span>We examined how the relationships between species traits and growth–survival relationships shift in response to changes in stem sizes and across census periods with different climate conditions (frequency of strong winds, drought intensity) across 45 co-occurring tree species based on 23 years of growth and survival records in a warm temperate rain forest on Yakushima Island, Japan. We developed hierarchical Bayesian models of relative growth and survival rates, including leaf traits, wood density, and 95-percentile maximum stem diameter as explanatory variables. We tested the relationships between estimated trait-mediated growth–survival relationships and the intensities of climate events during five census periods.</span></p> <p><span>Each trait's effects on growth–survival relationships differed across the five census periods in response to climate conditions. Interspecific growth–survival relationships affected by a single trait axis for leaves or wood tended to be negative. In contrast, those affected by the maximum stem diameter tended to be positive. Such trends </span><span>increased with more frequent </span><span>strong winds or more intense droughts. The single-trait effects on growth–survival relationships were stronger for smaller sizes than for larger sizes. For all traits combined, we found a significant growth–survival trade-off only for small-sized stems in three of five census periods.</span></p> <p><span>Synthesis: Our results indicate that the effect of species traits on the growth–survival relationships depended on tree sizes, the census periods, or both in response to the frequency or intensity of climate events. We argue the importance of incorporating spatial and temporal variations in environmental conditions into long-term data from tree census to predict forest dynamics.</span></p>
Reforestation of high elevation pines: Direct seeding success depends on seed source and sowing environment
<p>Forest persistence in regions impacted by increasing water and temperature stress will depend upon species' ability to either rapidly adjust to novel conditions or migrate to track ecological niches. Predicted, rapid climate change is likely to outpace the adaptive and migratory capacity of long-lived isolated tree species, and reforestation may be critical to species' persistence. Facilitating persistence both within and beyond a species' range requires identification of seed lots best adapted to the current and future conditions predicted with rapid climate change. We evaluate variation in emergent seedling performance that leads to differential survival among species and populations for three high-elevation five-needle pines. We paired a fully reciprocal field common garden experiment with a greenhouse common garden study to a) quantify variation in seedling emergence and functional traits, b) ask how functional traits affect performance under different establishment conditions, and c) evaluate whether trait and performance variation demonstrates local adaptation and plasticity. Among study species – limber, Great Basin bristlecone, and whitebark pines – we found divergence in emergence and functional traits, though soil moisture was the strongest driver of seedling emergence and abundance across all species. Generalist limber pine had a clear emergence advantage as well as traits associated with drought adaptation, while edaphic specialist bristlecone pine was characterized by low emergence yet high early survival once established. Despite evidence for edaphic specialization, soil characteristics alone did not explain bristlecone success. Across species, trait-environment relationships provided some evidence for local adaptation in drought-adapted traits, but we found no evidence of local adaptation in emergence or survival at this early life stage. For managers looking to promote persistence, sourcing seed from drier environments is likely to impart greater drought resistance into reforestation efforts through strategies such as greater root investment, increasing the probability of early seedling survival. This research demonstrates, through a rigorous reciprocal transplant experimental design, that it may be possible to select climate- and soil-appropriate seed sources for reforestation. However, planting success will ultimately rely on a suitable establishment environment, requiring careful consideration of interannual climate variability for management interventions in these climate- and disturbance-impacted tree species.</p>
Tailoring magnetic hysteresis of Fe-Ni additive manufactured permalloy via multiphysics-multiscale simulations: Temperature-dependent parameters, thermodynamic database, results, and utilities
<p>This dataset contains temperature-dependent parameters and thermodynamic database, supplementary data and utilities of the publication "Tailoring magnetic hysteresis of additive manufactured Fe-Ni permalloy via multiphysics-multiscale simulations of process-property relationships" (<a href="http://doi.org/10.1038/s41524-023-01058-9">Yang et al., 2023</a>).</p> <p>We performed non-isothermal phase-field simulations of SLS process of the Fe<sub>21.5</sub>Ni<sub>78.5</sub> permalloy and subsequential mesoscopic thermo-elasto-plastic calculations and nanoscopic chemical order-disorder (<span>\(\gamma/\gamma'\)</span>) transition simulations as well as micromagnetic hysteresis calculations on nanostructures. Temperature-dependent parameters are employed. We then investigate the dependence of the fusion zone size, the residual stress and plastic strain, and the magnetic hysteresis of AM-produced Fe<sub>21.5</sub>Ni<sub>78.5 </sub>on beam power and scan speed.</p> <p>This dataset contains:</p> <ul> <li><em>feni_cac.tdb</em>: Thermodynamic database of the Fe-Ni binary system based on <a href="https://doi.org/10.1016/j.intermet.2010.02.026">Cacciamani et al., 2010</a></li> <li><em>average_values.csv</em>: Average quantities for creating the contours in Fig. 6a, 6b, 7a, 7b, 8a, and Supp. Fig. 10a, 10b.</li> <li><em>mesostructures.zip</em>: Containing resampled mesostructures from SLS single scan simulations (final timestep) with associated temperature, stress, and strain evolution. Nodal values are explained in Table 1. Naming pattern is <ul> <li>SLS-TEP__<power>-<scan_speed>__.e</li> </ul> </li> <li><em>parameters.zip</em>: Containing temperature-dependent parameters for performing SLS simulations and thermo-elasto-plastic calculations with fine (1K) temperature increments. The same temperature-dependent parameters with coarse temperature increments are already listed as Supp. Table 1, 2.</li> <li><em>sampled_point_data.zip</em>: Containing mechanical quantities on sampled points and corresponding results of nanoscopic <span>\(\gamma'\)</span> phase fraction (<span>\(\Psi_{\gamma'}\)</span>) and magnetic coercivity <span>\(H_\mathrm{c}\)</span>. Naming pattern is <ul> <li>mech__<power>-<scan_speed>__.csv</li> <li>Psi__<power>-<scan_speed>__.csv</li> <li>Hc__<power>-<scan_speed>__.csv</li> </ul> </li> <li><em>utilities.zip</em>: Containing Python utilities to perform calculations of free energy density and related thermodynamic quantities, extracting parameters from <em>feni_cac.tdb. </em><br><strong>Notice: </strong><a href="https://pycalphad.org/docs/latest/">pyCALPHAD</a> (ver 0.8.4) is requested for performing the Python utilities.</li> </ul> <p>Table 1. Nodal values in an exodus file Nodal value name Symbol Meaning Unit T <span>\(T\)</span> Normalized Temperature by <span>\(T_\mathrm{M}\)</span> - c <span>\(\rho\)</span> Substance order parameter - pb <span>\(\xi\)</span> Fusion zone indicator - eps (eps_11, eps_12, eps_13, eps_22, eps_23, eps_33) <span>\({\varepsilon}\)</span> Strain - epsp (epsp_11, epsp_12, epsp_13, epsp_22, epsp_23, epsp_33) <span>\({\varepsilon}_\mathrm{pl}\)</span> Plastic Strain - peeq <span>\(p_\mathrm{e}\)</span> Accumulated plastic strain - sigma (sigma_11, sigma_12, sigma_13, sigma_22, sigma_23, sigma_33) <span>\({\sigma}\)</span> Stress MPa vonmises <span>\(\sigma_\mathrm{e}\)</span> von Mises stress MPa u (u_X, u_Y, u_Z) <span>\(\mathbf{u}\)</span> Displacement μm</p> <p> </p> <p><strong>Notice</strong>: The raw transient outputs are not cured in this dataset due to the vast file size. Please contact the authors to acquire related files/utilities.</p>
Dose-dependent progression of multiple low dose streptozotocin-induced diabetes in mice - DEGs
<p><strong>Differentially expressed genes in mice treated with multiple low doses of streptozotocin.</strong></p> <p> All animals were maintained in accordance with City of Hope Institutional Animal Care and Use Committee protocols (#16047) in accordance with the Guide for the Care and Use of Laboratory Animals (11). Only male C57BL/6J were used due to the varying effectiveness of STZ in female mice. All mice were housed in individually ventilated cages with 3-5 mice/cage. Animals were maintained on 12-h light:dark cycles with <em>ad libitum</em> access to water and standard rodent chow diet.</p> <p> STZ (Sigma-Aldrich S0130-1G; St. Louis, MO, USA) was administered for five consecutive days by intraperitoneal (IP) injections of STZ dissolved right before the injection in saline at either 35 or 55 mg/kg body weight. Saline was administered to 34 mice as a vehicle control, 40 mice received 35 mg/kg STZ, and 38 mice received 55 mg/kg STZ. Equivalent volumes of saline were used in control animals. Approximately 75-100 healthy islets per mouse were picked by hand, washed in cold PBS, and then resuspended in 350 ul of RLT with 1%BME. RNA was isolated using RNeasy micro (Qiagen 7404; Hilden, Germany) kits according to manufacture instructions and DNA was digested by treatment with RNAse-Free DNAse Set (Qiagen 79254). </p> <p> RNA sequencing libraries were prepared using 150 ng total RNA with Kapa RNA mRNA HyperPrep kit (Kapa Biosystems, Cat KR1352; Cape Town, South Africa) to enrich for mRNA according to the manufacturer's protocol with a final PCR cycle of 12x. The RNA fragment time was 8 min at 94 C; 1.0x beads purification was used for the final sequencing library purification. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit. Sequencing was performed on Illumina NovaSeq 6000 by using S4 kit v1.5 with the paired end mode of 2x101cycle. Real-time analysis (RTA) v3.4.4 software was used for base calling. The number of biological replicates were as follows; saline control: 6, STZ, 35 mg/kg: 7, STZ, 55 mg/kg: 8.</p>
Supplementary tables for: Dependent variable selection in phylogenetic generalized least squares regression analysis under Pagel's lambda model
<p class="MsoNormal"><span>Phylogenetic generalized least squares (PGLS) regression is widely used to detect evolutionary correlations. In contrast to the equal treatment of analyzed traits in conventional correlation methods such as Pearson and Spearman's rank tests, we must designate one trait as the independent variable and the other as the dependent variable. However, in our PGLS regression analyses (using Pagel's <em>λ</em> model) of both empirical and simulated datasets, switching independent and dependent variables yielded many conflicting results. A serious problem with PGLS regression that has not been noticed before is that selecting an inappropriate trait as the dependent variable will often result in an error. To assess correlations in simulated data, we established a gold standard by analyzing changes in traits along phylogenetic branches. Next, we tested seven potential criteria for dependent variable selection: log-likelihood, Akaike information criterion, <em>R</em><sup>2</sup>, <em>p</em>-value, Pagel's <em>λ</em>, Blomberg et al.'s <em>K</em>, and the estimated <em>λ</em> in <a name="_Hlk136010442"></a>Pagel's <em>λ</em> model. We determined that the last three criteria performed equally well in selecting the dependent variable and were superior to the other four. For practicality, we suggest using the trait with a higher <em>λ</em></span><span> or <em>K</em> </span><span>value as the dependent variable in future PGLS regressions. In analyzing the evolutionary relationship between two traits, we should designate the trait with a stronger phylogenetic signal as the dependent variable even if it could logically assume the cause in the relationship.</span></p>
pH-dependence of the Plasmodium falciparum chloroquine resistance transporter is linked to the transport cycle
<p>This file contains the original data underpinning the following study:</p> <p>The chloroquine resistance transporter, PfCRT, of the human malaria parasite <em>Plasmodium falciparum </em>displays a strong pH-sensitivity in the weakly acidic range. Consequently, PfCRT operates only at 60% of its maximal drug transport activity at the pH of 5.2 of the digestive vacuole, a proteolytic organelle from which PfCRT expels drugs that interfere with heme detoxification. Despite structural information, the molecular mechanism by which PfCRT senses pH changes has remained unclear. Here we show, by alanine-scanning mutagenesis and functional transport studies, that E207 plays a critical role in pH sensing. The E207A mutant displayed a pH-insensitive transport activity, while preserving drug substrate specificity. Replacement of E207 by Asp or His, but not by any other proteinogenic amino acid, reconstituted pH sensitivity. Molecular dynamics simulations and kinetics analyses suggest an allosteric binding model in which PfCRT can simultaneously accept both protons and chloroquine in a partial non-competitive manner, with increasing proton concentrations reducing the drug transport activity. Molecular dynamics simulations of the open-to-vacuole, the occluded and the open-to-cytosol conformation of PfCRT revealed a drastic relocation of E207 from a peripheral to an engaged location during the transport cycle, resulting in E207 forming a salt bridge with residue K80. We propose that the ionized carboxyl group of E207 acts as a hydrogen acceptor for interactions accelerating progression through the transport cycle and that the pH sensing is a by-product of this function.</p>
Context-dependent memory recall in HMD-based immersive virtual environments
<p>Data represent result of an original VR-based experimental research, which studied human memory recollection in different visual environments. 92 students of psychology using head-mounted VR displays were introduced into a computer-generated virtual environment and asked to memorize presented lists of words. Afterwards, the number of accurate and false memory recollections were measured when participants were placed in the same, respectively different virtual environment. </p> <p> </p>
ScienceDex guides
Understand access before you commit
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.