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311 results for “Empirical data”
Data from: Synergism and antagonism of proximate mechanisms enable and constrain the response to simultaneous selection on body size and development time: an empirical test using experimental evolution
Natural selection acts on multiple traits simultaneously. How mechanisms underlying such traits enable or constrain their response to simultaneous selection is poorly understood. We show how antagonism and synergism among three traits at the developmental level enable or constrain evolutionary change in response to simultaneous selection on two focal traits at the phenotypic level. After 10 generations of 25% simultaneous directional selection on all four combinations of body size and development time in Manduca sexta (Sphingidae), the changes in the three developmental traits predict 93% of the response of development time and 100% of the response of body size. When the two focal traits were under synergistic selection, the response to simultaneous selection was enabled by juvenile hormone and ecdysteroids and constrained by growth rate. When the two focal traits were under antagonistic selection, the response to selection was due primarily to change in growth rate and constrained by the two hormonal traits. The approach used here reduces the complexity of the developmental and endocrine mechanisms to three proxy traits. This generates explicit predictions for the evolutionary response to selection that are based on biologically informed mechanisms. This approach has broad applicability to a diverse range of taxa, including algae, plants, amphibians, mammals, and insects.
Data from: Inferring complex phylogenies using parsimony: an empirical approach using three large DNA data sets for angiosperms
To explore the feasibility of parsimony analysis for large data sets, we conducted heuristic parsimony searches and bootstrap analyses on separate and combined DNA data sets for 190 angiosperms and three outgroups. Separate data sets of 18S rDNA (1,855 bp), rbc L (1,428 bp), and atp B (1,450 bp) sequences were combined into a single matrix 4,733 bp in length. Analyses of the combined data set show great improvements in computer run times compared to those of the separate data sets and of the data sets combined in pairs. Six searches of the 18S rDNA rbc L atp B data set were conducted; in all cases TBR branch swapping was completed, generally within a few days. In contrast, TBR branch swapping was not completed for any of the three separate data sets, or for the pairwise combined data sets. These results illustrate that it is possible to conduct a thorough search of tree space with large data sets, given sufficient signal. In this case, and probably most others, sufficient signal for a large number of taxa can only be obtained by combining data sets. The combined data sets also have higher internal support for clades than the separate data sets, and more clades receive bootstrap support of 50% in the combined analysis than in analyses of the separate data sets. These data suggest that one solution to the computational and analytical dilemmas posed by large data sets is the addition of nucleotides, as well as taxa.
Data from: Are extra-pair males different from cuckolded males? An empirical and meta-analytic examination
Traditional models for female extra-pair matings assume that females benefit indirectly from extra-pair mating behaviour. Under these so-called adaptive models, extra-pair males are hypothesized to have more compatible genotypes, larger body size, exaggerated ornaments or to be older than cuckolded males. Alternatively, ('nonadaptive') models that consider female extra-pair matings to be a by-product posit that female extra-pair mating can be maintained even if there is no benefit to females. This could happen if, for example, males gained fitness benefits from extra-pair mating, while female and male extra-pair mating behaviours were genetically correlated. Extra-pair males are also expected to be older and larger if this improves their ability to convince or coerce females to mate. We investigated whether a female's extra-pair mates differed from her cuckolded mate in both genetic and phenotypic traits by analysing data from an insular house sparrow population. We found that extra-pair males were older than cuckolded males, consistent with both models. However, in contrast to the expectations from from adaptive models, extra-pair and cuckolded males were of similar genetic relatedness, and hence expected compatibility, with the female, and had comparable body size and secondary sexual traits. We also updated previous meta-analyses examining differences between extra-pair and cuckolded males. The meta-analytic results matched results from our house sparrow case study. Although we cannot completely exclude indirect benefits for females, nonadaptive models may better explain female extra-pair matings. These neglected alternative models deserve more research attention, and this should improve our understanding of the evolution of mating systems.
Data from: Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totalling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4,274 CR1 retroelements identified from multi-species whole genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other non-ostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.
Replication kit for: Problems with SZZ and Features: An empirical study of the state of practice of defect prediction data collection
<p>This is the replication package for our article "Problems with SZZ and Features: An empirical study of the state of practice of defect prediction data collection". </p> <p>All relevant information is available in the replication-notebook, which is available as executable Jupyter Notebook and as HTML page.</p> <p>The archive release-level-data.tar.gz contains the defect prediction data labeled with IND-JLMIV+R for the 398 releases and is shared for re-use by other researcher for defect prediction experiments. </p> <p>The archive DO_NOT_USE_release-leve-data.tar.gz contains the contains the defect prediction data labeled with 6M-SZZ and should not be re-used. </p> <p>The raw data with the MongoDB required to run the Jupyter Notebook is contained in the SmartSHARK Database release 1.0 (https://smartshark.github.io/dbreleases/ / https://doi.org/10.5281/zenodo.4071448).</p> <p>All materials are licensed under the Apache 2.0 License (see LICENSE file). </p>
Data set for EMPIR project MeDDII Report D2
<p>Data set for the D2 of project MeDDII - Comparison on microflow</p>
Data from: Empirical estimation of skin resistance to water loss in amphibians: agar evaluation as a non-resistance model to evaporation
<p>Total resistance (R<sub>T</sub>) to evaporative water loss (EWL) in amphibians is given by the sum of the boundary layer (<em>r</em><sub>b</sub>) and the skin resistance (<em>r</em><sub>s</sub>). Thus, <em>r</em><sub>s</sub> can be determined if the <em>r</em><sub>b</sub> component is defined (<em>r</em><sub>s</sub> = R<sub>T</sub> - <em>r</em><sub>b</sub>). The use of agar models has become the standard technique to estimate <em>r</em><sub>b</sub> under the assumption that agar surface imposes no barrier to evaporation (<em>r<sub>s</sub></em> = 0). We evaluated this assumption by determining EWL rates and <em>r</em><sub>b</sub> values from exposed surfaces of free water, a physiological solution mimicking the osmotic properties of a generalized amphibian, and agar gels prepared at various concentrations either using water or physiological solution as diluent. Water evaporation was affected by both, the presence of solutes and agar concentration. Models prepared with agar at 5% concentration in water provided the most practical and appropriate proxy for the estimation of <em>r</em><sub>b</sub>.</p> <p> </p> <p> </p>
An empirical study of data constraint implementations in Java
<p>Replication package for eponymous EMSE article.</p>
Adaptive Empirical Modeling Data for "Thin Current Sheet Formation and Reconnection at $X\sim$-10\,R$_E$ during the Main Phase of a Magnetic Storm"
<p>The ZIP file contains results of AM03 model run for the magnetic storm event on 17 June 2012. </p>
Data from: Conventional analysis of trial-by-trial adaptation is biased: empirical and theoretical support using a Bayesian estimator
Research on human motor adaptation has often focused on how people adapt to self-generated or externally-influenced errors. Trial-by-trial adaptation is a person's response to self-generated errors. Externally-influenced errors applied as catch-trial perturbations are used to calculate a person's perturbation adaptation rate. Although these adaptation rates are sometimes compared to one another, we show through simulation and empirical data that the two metrics are distinct. We demonstrate that the trial-by-trial adaptation rate, often calculated as a coefficient in a linear regression, is biased under typical conditions. We tested 12 able-bodied subjects moving a cursor on a screen using a computer mouse. Statistically different adaptation rates arise when sub-sets of trials from different phases of learning are analyzed from within a sequence of movement results. We propose a new approach to identify when a person's learning has stabilized in order to identify steady-state movement trials from which to calculate a more reliable trial-by-trial adaptation rate. Using a Bayesian model of human movement, we show that this analysis approach is more consistent and provides a more confident estimate than alternative approaches. Constraining analyses to steady-state conditions will allow researchers to better decouple the multiple concurrent learning processes that occur while a person makes goal-directed movements. Streamlining this analysis may help broaden the impact of motor adaptation studies, perhaps even enhancing their clinical usefulness.
Data set for EMPIR project MeDDII Paper FMI 73 2020 101729
<p>Data set for EMPIR project MeDDII Paper</p> <p>https://doi.org/10.1016/j.flowmeasinst.2020.101729</p>
Data set for EMPIR project MeDDII Report A2.2.2
<p>Data set for EMPIR project MeDDII Report A2.2.2</p> <p>In-line calibration of in-line pressure sensors</p>
Empirical study on Visual Attention Characteristics of basketball players of different levels during free-throw shooting original data.
<p>不同水平篮球运动员罚球投篮视觉注意特征实证研究的原始数据,包括注视持续时间、注视次数、瞳孔扩张和扫视幅度。</p>
Data from: Economic uncertainty, geopolitical risk and U.S. energy price risk spillover: An empirical study based on the risk spillover model
<p>This data is mainly used to analyze the risk correlation among economic uncertainly,geopolitical risk and energy price,and can also be applied to the TVP-VAR model to analyze the correlation between different variables using the time-varying parameter model,which has great potential for reuse. The risk relationship between economic uncertainly.At the same time,since it is macroeconomic data,it does not involve any moral and ethical issues.</p>
An Empirical Model for Mercury's Field-Aligned Currents Derived from MESSENGER Magnetometer Data
<p>Companion dataset for manuscript titled "An Empirical Model for Mercury’s Field-Aligned Currents Derived from MESSENGER Magnetometer Data" submitted to <em>JGR: Space Physics</em>.</p> <p>The file MESSENGER_MAG_Disturbance_Indices_v12.txt defines the Mercury disturbance index as a function of MESSENGER orbit number.</p> <p>The file rsuns.txt defines the Mercury’s Heliocentric distance as a function of time.</p> <p>The file merge_magrdr_11083_15120_actidx_kt17res.txt contain the processed MESSENGER magnetometer vectors. This file is further broken into quintiles based on the disturbance index.</p>
Data of the Paper: Analytical Modeling and Empirical Validation of Performability of Service- and Cloud-Based Dynamic Routing Architecture Patterns
<p>The online artifacts for the following article accepted at 30th Asia-Pacific Software Engineering Conference (APSEC 2023): </p><p>"Analytical Modeling and Empirical Validation of Performability of Service- and Cloud-Based Dynamic Routing Architecture Patterns"</p><p>Abstract:</p><p>Many dynamic routing architectural patterns are available, including distributed routing, e.g., using the sidecar pattern, or centralized routing, e.g., using event stores or service buses. Different Quality-of-Service (QoS) factors influence routing schemas and technology selection, such as performance, reliability, scalability, and control properties offered by the patterns. An analytical model can formalize the QoS factors and facilitate the architectural decision-making when changing the routing scheme, i.e., to more distributed or centralized routing. So far, the impact of these architectural patterns on performability, i.e., the overall performance of a system with impeded reliability, has not been extensively studied. This is important because deciding to increase performance, e.g., by parallel processing of requests, may lead to decreased reliability because of the added points of a crash. We propose an analytical performability model during component crashes. For the empirical validation of our proposed model, we ran an extensive experiment of 2412 hours of runtime on a private cloud infrastructure and Google Cloud Platform. The low prediction error of 1.75\% indicates the high accuracy of our performability model. These results provide important insights when making architectural decisions regarding service- and cloud-based dynamic routing.</p>
Data from: How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards
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Data from: Are extra-pair males different from cuckolded males? An empirical and meta-analytic examination
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Data from: The evolutionary enigma of mixed mating systems in plants: occurrence, theoretical explanations, and empirical evidence
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Data from: Genetic load, inbreeding depression and hybrid vigor covary with population size: an empirical evaluation of theoretical predictions
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ScienceDex guides
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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.