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94 results for “methods: data analysis”
Data from: Cladistic analysis of Caseidae (Caseasauria, Synapsida): using the gap-weighting method to include taxa based on incomplete specimens
Occupying the role of primary consumer and having an early–middle Permian age range, caseids (Caseasauria, Synapsida) are fundamental to the interpretation of the early history of terrestrial vertebrate ecosystems. Despite this importance, no comprehensive, species-level phylogenetic study of Caseidae has yet been performed. Herein, we present a phylogenetic analysis of the group, using gap weighting to include poorly known taxa. Besides the description and comments on the resultant topologies, some more general issues concerning cladistic methodologies are briefly addressed. This study highlights the importance of a total-evidence approach, including as many within-group taxa and characters as possible. Continuously varying characters, in the form of indices derived from measurement of individual skeletal elements, proved to be highly important, adding significantly to the resolution of, and support for, recovered trees. The utility of the postcranial skeleton in understanding relationships among basal synapsids is highlighted.
Data from: Quantification and statistical analysis methods for vessel wall components from stained images with Masson's trichrome
Purpose: To develop a digital image processing method to quantify structural components (smooth muscle fibers and extracellular matrix) in the vessel wall stained with Masson's trichrome, and a statistical method suitable for small sample sizes to analyze the results previously obtained. Methods: The quantification method comprises two stages. The pre-processing stage improves tissue image appearance and the vessel wall area is delimited. In the feature extraction stage, the vessel wall components are segmented by grouping pixels with a similar color. The area of each component is calculated by normalizing the number of pixels of each group by the vessel wall area. Statistical analyses are implemented by permutation tests, based on resampling without replacement from the set of the observed data to obtain a sampling distribution of an estimator. The implementation can be parallelized on a multicore machine to reduce execution time. Results: The methods have been tested on 48 vessel wall samples of the internal saphenous vein stained with Masson's trichrome. The results show that the segmented areas are consistent with the perception of a team of doctors and demonstrate good correlation between the expert judgments and the measured parameters for evaluating vessel wall changes. Conclusion: The proposed methodology offers a powerful tool to quantify some components of the vessel wall. It is more objective, sensitive and accurate than the biochemical and qualitative methods traditionally used. The permutation tests are suitable statistical techniques to analyze the numerical measurements obtained when the underlying assumptions of the other statistical techniques are not met.
Data from: Dynamic analysis of liquid annular seals with herringbone grooves on the rotor based on perturbation method
Annular seals have significant effects on the hydraulic and rotordynamic performances turbomachinery. In this paper, an analysis method for calculating the leakage rate and dynamic characterisitcs of liquid annular seals with herringbone grooves on the rotor is proposed and verified. Leakage flow rates and dynamic characteristics of the model seals under different operating conditions are theoretically analyzed and compared to those of the plain and spiral-grooved seals of the same size. Besides, the influence of geometric parameters such as spiral angle and the lengths of the constituent parts on the sealing and rotordynamic coefficients of seals with herringbone grooves are also discussed in this paper. The results show that seals with herringbone grooves have better sealing performance, while providing bigger support actions and better damping characteristics than the other two seal types under the same operating conditions. The seal geometric parameters including spiral angle, the lengths of the constituent parts and the clearance value have great influence on the dynamic characteristics of seals with herringbone grooves.
Data from: Optimizing methods for PCR-based analysis of predation
Molecular methods have become an important tool for studying feeding interactions under natural conditions. Despite their growing importance, many methodological aspects have not yet been evaluated but need to be considered to fully exploit the potential of this approach. Using feeding experiments with high alpine carabid beetles and lycosid spiders, we investigated how PCR annealing temperature affects prey DNA detection success and how post-PCR visualization methods differ in their sensitivity. Moreover, the replicability of prey DNA detection among individual PCR assays was tested using beetles and spiders that had digested their prey for extended times postfeeding. By screening all predators for three differently sized prey DNA fragments (range 116–612 bp), we found that only in the longest PCR product, a marked decrease in prey detection success occurred. Lowering maximum annealing temperatures by 4 °C resulted in significantly increased prey DNA detection rates in both predator taxa. Among the three post-PCR visualization methods, an eightfold difference in sensitivity was observed. Repeated screening of predators increased the total number of samples scoring positive, although the proportion of samples testing positive did not vary significantly between different PCRs. The present findings demonstrate that assay sensitivity, in combination with other methodological factors, plays a crucial role to obtain robust trophic interaction data. Future work employing molecular prey detection should thus consider and minimize the methodologically induced variation that would also allow for better cross-study comparisons.
Data to accompany "Evaluation of Spatial Audio Reproduction Methods (Part 2): Analysis of Listener Preference", J. AES, 2016
<p>This work was supported by the EPSRC Programme Grant S3A: Future Spatial Audio for an Immersive Listener Experience at Home (EP/L000539/1). Details about the data underlying this work, along with the terms for data access, are available from http://dx.doi.org/10.15126/surreydata.00809533</p> <p>If you use the data, please cite the following paper:</p> <p>J. Francombe, T. Brookes, and R. Mason, 2016: Evaluation of Spatial Audio Reproduction Methods (Part 2): Analysis of Listener Preference. Journal of the Audio Engineering Society</p>
Data from: Generalized Frequency Coding: A Method of Preparing Polymorphic Multistate Characters for Phylogenetic Analysis
A new method of coding polymorphic multistate characters for phylogenetic analysis is presented. By dividing such characters into subcharacters, their frequency distributions can be represented with discrete states. Differential weighting is employed to counter the effect of using multiple characters to represent one character. The new method, termed generalized frequency coding (GFC), is potentially superior to previously used methods in that it incorporates more information and can be applied to both qualitative and quantitative characters. The method was applied to a previously published data set that includes both types of polymorphic multistate characters, and performed well according to congruence with other studies and the g1 and nonparametric bootstrap statistics. The data set was also used to compare GFC to both gap-weighting and Manhattan distance step matrix coding. On these grounds and for philosophical reasons, GFC was found to be a better estimator of phylogeny.
Data and R Code from "PAT-GEOM: A Software Package for the Analysis of Animal Patterns" (published in Methods in Ecology and Evolution)
<p>Datasets for Figures 2 and 4 in the article "PAT-GEOM: A Software Package for the Analysis of Animal Patterns" (published in Methods in Ecology and Evolution) and the R code used to perform the analysis described in the article.</p>
Data from: Testing Phylogenetic Methods with Tree Congruence: Phylogenetic Analysis of Polymorphic Morphological Characters in Phrynosomatid Lizards
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Data from: Relative accuracy of three common methods of parentage analysis in natural populations
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Data from: Flow cytometric methods for indirect analysis and quantification of gametogenesis in Chlamydomonas reinhardtii (Chlorophyceae)
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Data from: Generalized Frequency Coding: A Method of Preparing Polymorphic Multistate Characters for Phylogenetic Analysis
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Data from: Optimizing methods for PCR-based analysis of predation
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Data from: Comparing analysis methods in functional calcium imaging of the insect brain
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Data from: Dynamic analysis of liquid annular seals with herringbone grooves on the rotor based on perturbation method
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Data from: Comparative finite-element analysis: a single computational modeling method can reliably estimate the mechanical properties of porcine and human vertebrae
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Data from: Making soil particle size analysis by laser diffraction compatible with standard soil texture determination methods
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Data from: Quantification and statistical analysis methods for vessel wall components from stained images with Masson's trichrome
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Data from: Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model
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Data from: High throughput method for analysis of repeat number for 28 phase variable loci of Campylobacter jejuni strain NCTC11168
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Data from: CLIP test: a new fast, simple and powerful method to distinguish between linked or pleiotropic quantitative trait loci in linkage disequilibria analysis
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