Bayesian analysis of skew-t multivariate null intercept measurement error model

The multivariate skew-t distribution (J Multivar Anal 79:93-113, 2001; J R Stat Soc, Ser B 65:367-389, 2003; Statistics 37:359-363, 2003) includes the Student t, skew-Cauchy and Cauchy distributions as special cases and the normal and skew-normal ones as limiting cases. In this paper, we explore the use of Markov Chain Monte Carlo (MCMC) methods to develop a Bayesian analysis of repeated measures, pretest/post-test data, under multivariate null intercept measurement error model (J Biopharm Stat 13(4):763-771, 2003) where the random errors and the unobserved value of the covariate (latent variable) follows a Student t and skew-t distribution, respectively. The results and methods are numerically illustrated with an example in the field of dentistry.

Comparing performance of instrumental drift correction by linear and quadratic adjusting in inductive electromagnetic data

Electromagnetic induction (EMI) method results are shown for vertical magnetic dipole (VMD) configuration by using the EM38 equipment. Performance in the location of metallic pipes and electrical cables is compared as a function of instrumental drift correction by linear and quadratic adjusting under controlled conditions. Metallic pipes and electrical cables are buried at the IAG/USP shallow geophysical test site in Sao Paulo City. Brazil. Results show that apparent electrical conductivity and magnetic susceptibility data were affected by ambient temperature variation. In order to obtain better contrast between background and metallic targets it was necessary to correct the drift. This correction was accomplished by using linear and quadratic relation between conductivity/susceptibility and temperature intending comparative studies. The correction of temperature drift by using a quadratic relation was effective, showing that all metallic targets were located as well deeper targets were also improved. (C) 2010 Elsevier B.V. All rights reserved.

Upper-mantle seismic anisotropy from SKS splitting in the South American stable platform: A test of asthenospheric flow models beneath the lithosphere

Upper-mantle seismic anisotropy has been extensively used to infer both present and past deformation processes at lithospheric and asthenospheric depths. Analysis of shear-wave splitting (mainly from core-refracted SKS phases) provides information regarding upper-mantle anisotropy. We present average measurements of fast-polarization directions at 21 new sites in poorly sampled regions of intra-plate South America, such as northern and northeastern Brazil. Despite sparse data coverage for the South American stable platform, consistent orientations are observed over hundreds of kilometers. Over most of the continent, the fast-polarization direction tends to be close to the absolute plate motion direction given by the hotspot reference model HS3-NUVEL-1A. A previous global comparison of the SKS fast-polarization directions with flow models of the upper mantle showed relatively poor correlation on the continents, which was interpreted as evidence for a large contribution of ""frozen"" anisotropy in the lithosphere. For the South American plate, our data indicate that one of the reasons for the poor correlation may have been the relatively coarse model of lithospheric thicknesses. We suggest that improved models of upper-mantle flow that are based on more detailed lithospheric thicknesses in South America may help to explain most of the observed anisotropy patterns.

The matrix-tolerance hypothesis: an empirical test with frogs in the Atlantic Forest

The matrix-tolerance hypothesis suggests that the most abundant species in the inter-habitat matrix would be less vulnerable to their habitat fragmentation. This model was tested with leaf-litter frogs in the Atlantic Forest where the fragmentation process is older and more severe than in the Amazon, where the model was first developed. Frog abundance data from the agricultural matrix, forest fragments and continuous forest localities were used. We found an expected negative correlation between the abundance of frogs in the matrix and their vulnerability to fragmentation, however, results varied with fragment size and species traits. Smaller fragments exhibited stronger matrix-vulnerability correlation than intermediate fragments, while no significant relation was observed for large fragments. Moreover, some species that avoid the matrix were not sensitive to a decrease in the patch size, and the opposite was also true, indicating significant differences with that expected from the model. Most of the species that use the matrix were forest species with aquatic larvae development, but those species do not necessarily respond to fragmentation or fragment size, and thus affect more intensively the strengthen of the expected relationship. Therefore, the main relationship expected by the matrix-tolerance hypothesis was observed in the Atlantic Forest; however we noted that the prediction of this hypothesis can be substantially affected by the size of the fragments, and by species traits. We propose that matrix-tolerance model should be broadened to become a more effective model, including other patch characteristics, particularly fragment size, and individual species traits (e. g., reproductive mode and habitat preference).

Mitochondrial sequence data and Dipsacales phylogeny: Mixed models, partitioned Bayesian analyses, and model selection

Phylogenetic analyses of chloroplast DNA sequences, morphology, and combined data have provided consistent support for many of the major branches within the angiosperm, clade Dipsacales. Here we use sequences from three mitochondrial loci to test the existing broad scale phylogeny and in an attempt to resolve several relationships that have remained uncertain. Parsimony, maximum likelihood, and Bayesian analyses of a combined mitochondrial data set recover trees broadly consistent with previous studies, although resolution and support are lower than in the largest chloroplast analyses. Combining chloroplast and mitochondrial data results in a generally well-resolved and very strongly supported topology but the previously recognized problem areas remain. To investigate why these relationships have been difficult to resolve we conducted a series of experiments using different data partitions and heterogeneous substitution models. Usually more complex modeling schemes are favored regardless of the partitions recognized but model choice had little effect on topology or support values. In contrast there are consistent but weakly supported differences in the topologies recovered from coding and non-coding matrices. These conflicts directly correspond to relationships that were poorly resolved in analyses of the full combined chloroplast-mitochondrial data set. We suggest incongruent signal has contributed to our inability to confidently resolve these problem areas. (c) 2007 Elsevier Inc. All rights reserved.

Coding behavioural data for cladistic analysis: using dynamic homology without parsimony

Many of the controversies around the concept of homology rest on the subjectivity inherent to primary homology propositions. Dynamic homology partially solves this problem, but there has been up to now scant application of it outside of the molecular domain. This is probably because morphological and behavioural characters are rich in properties, connections and qualities, so that there is less space for conflicting character delimitations. Here we present a new method for the direct optimization of behavioural data, a method that relies on the richness of this database to delimit the characters, and on dynamic procedures to establish character state identity. We use between-species congruence in the data matrix and topological stability to choose the best cladogram. We test the methodology using sequences of predatory behaviour in a group of spiders that evolved the highly modified predatory technique of spitting glue onto prey. The cladogram recovered is fully compatible with previous analyses in the literature, and thus the method seems consistent. Besides the advantage of enhanced objectivity in character proposition, the new procedure allows the use of complex, context-dependent behavioural characters in an evolutionary framework, an important step towards the practical integration of the evolutionary and ecological perspectives on diversity. (C) The Willi Hennig Society 2010.

Comparing finite state machine test coverage criteria

To plan testing activities, testers face the challenge of determining a strategy, including a test coverage criterion that offers an acceptable compromise between the available resources and test goals. Known theoretical properties of coverage criteria do not always help and, thus, empirical data are needed. The results of an experimental evaluation of several coverage criteria for finite state machines (FSMs) are presented, namely, state and transition coverage; initialisation fault and transition fault coverage. The first two criteria focus on FSM structure, whereas the other two on potential faults in FSM implementations. The authors elaborate a comparison approach that includes random generation of FSM, construction of an adequate test suite and test minimisation for each criterion to ensure that tests are obtained in a uniform way. The last step uses an improved greedy algorithm.

Paleomagnetic data and K-Ar ages from Mesozoic units of the Santa Marta massif: A preliminary interpretation for block rotation and translations

We report 6 K-Ar ages and paleomagnetic data from 28 sites collected in Jurassic, Lower Cretaceous and Paleocene rocks of the Santa Marta massif, to test previous hypothesis of rotations and translations of this massif, whose rock assemblage differs from other basement-cored ranges adjacent to the Guyana margin. Three magnetic components were identified in this study. A first component has a direction parallel to the present magnetic field and was uncovered in all units (D 352, I = 25.6, k = 57.35, a95 = 5.3, N = 12). A second component was isolated in Cretaceous limestone and Jurassic volcaniclastic rocks (D = 8.8, I = 8.3, k = 24.71, a95 = 13.7, N = 6), and it was interpreted as of Early Cretaceous age. In Jurassic sites with this component, Early Cretaceous K-Ar ages obtained from this and previous studies are interpreted as reset ages. The third component was uncovered in eight sites of Jurassic volcaniclastic rocks, and its direction indicates negative shallow to moderate inclinations and northeastward declinations. K-Ar ages in these sites are of Early (196.5 +/- 4.9 Ma) to early Late Jurassic age (156.6 +/- 8.9 Ma). Due to local structural complexity and too few Cretaceous outcrops to perform a reliable unconformity test, we only used two sites with (1) K-Ar ages, (2) less structural complexity, and (3) reliable structural data for Jurassic and Cretaceous rocks. The mean direction of the Jurassic component is (D = 20.4, I = -18.2, k = 46.9, a95 = 5.1, n = 18 specimens from two sites). These paleomagnetic data support previous models of northward along-margin translations of Grenvillian-cored massifs. Additionally, clockwise vertical-axis rotation of this massif, with respect to the stable craton, is also documented; the sense of rotation is similar to that proposed for the Perija Range and other ranges of the southern Caribbean margin. More data is needed to confirm the magnitudes of rotations and translations. (C) 2009 Elsevier Ltd. All rights reserved.

Improving data perturbation testing techniques for Web services

The widespread use of service-oriented architectures (SOAs) and Web services in commercial software requires the adoption of development techniques to ensure the quality of Web services. Testing techniques and tools concern quality and play a critical role in accomplishing quality of SOA based systems. Existing techniques and tools for traditional systems are not appropriate to these new systems, making the development of Web services testing techniques and tools required. This article presents new testing techniques to automatically generate a set of test cases and data for Web services. The techniques presented here explore data perturbation of Web services messages upon data types, integrity and consistency. To support these techniques, a tool (GenAutoWS) was developed and applied to real problems. (C) 2010 Elsevier Inc. All rights reserved.

A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets

We propose a likelihood ratio test ( LRT) with Bartlett correction in order to identify Granger causality between sets of time series gene expression data. The performance of the proposed test is compared to a previously published bootstrapbased approach. LRT is shown to be significantly faster and statistically powerful even within non- Normal distributions. An R package named gGranger containing an implementation for both Granger causality identification tests is also provided.