Framework para integração semântica de dados geoespaciais: integração de dados geológicos

Pós-graduação em Ciência da Computação - IBILCE

Inteligência cibernética e uso de recursos semânticos na detecção de perfis falsos no contexto do Big Data

Pós-graduação em Ciência da Informação - FFC

The Phylogenetic Relationships and Biogeography of True Porpoises (Mammalia: Phocoenidae) Based On Morphological Data

Prior studies of phylogenetic relationships among phocoenids based on morphology and molecular sequence data conflict and yield unresolved relationships among species. This study evaluates a comprehensive set of cranial, postcranial, and soft anatomical characters to infer interrelationships among extant species and several well-known fossil phocoenids, using two different methods to analyze polymorphic data: polymorphic coding and frequency step matrix. Our phylogenetic results confirmed phocoenid monophyly. The division of Phocoenidae into two subfamilies previously proposed was rejected, as well as the alliance of the two extinct genera Salumiphocaena and Piscolithax with Phocoena dioptrica and Phocoenoides dalli. Extinct phocoenids are basal to all extant species. We also examined the origin and distribution of porpoises within the context of this phylogenetic framework. Phocoenid phylogeny together with available geologic evidence suggests that the early history of phocoenids was centered in the North Pacific during the middle Miocene, with subsequent dispersal into the southern hemisphere in the middle Pliocene. A cooling period in the Pleistocene allowed dispersal of the southern ancestor of Phocoena sinusinto the North Pacific (Gulf of California).

A Model-Based Approach for Making Ecological Inference from Distance Sampling Data

We consider a fully model-based approach for the analysis of distance sampling data. Distance sampling has been widely used to estimate abundance (or density) of animals or plants in a spatially explicit study area. There is, however, no readily available method of making statistical inference on the relationships between abundance and environmental covariates. Spatial Poisson process likelihoods can be used to simultaneously estimate detection and intensity parameters by modeling distance sampling data as a thinned spatial point process. A model-based spatial approach to distance sampling data has three main benefits: it allows complex and opportunistic transect designs to be employed, it allows estimation of abundance in small subregions, and it provides a framework to assess the effects of habitat or experimental manipulation on density. We demonstrate the model-based methodology with a small simulation study and analysis of the Dubbo weed data set. In addition, a simple ad hoc method for handling overdispersion is also proposed. The simulation study showed that the model-based approach compared favorably to conventional distance sampling methods for abundance estimation. In addition, the overdispersion correction performed adequately when the number of transects was high. Analysis of the Dubbo data set indicated a transect effect on abundance via Akaike’s information criterion model selection. Further goodness-of-fit analysis, however, indicated some potential confounding of intensity with the detection function.

Radiocarbon Dating, Chronologic Framework, and Changes in Accumulation Rates of Holocene Estuarine Sediments from Chesapeake Bay

Rapidly accumulating Holocene sediments in estuaries commonly are difficult to sample and date. In Chesapeake Bay, we obtained sediment cores as much as 20min length and used numerous radiocarbon ages measured by accelerator mass spectrometry methods to provide the first detailed chronologies of Holocene sediment accumulation in the bay. Carbon in these sediments is a complex mixture of materials from a variety of sources. Analyses of different components of the sediments show that total organic carbon ages are largely unreliable, because much of the carbon (including coal) has been transported to the bay from upstream sources and is older than sediments in which it was deposited. Mollusk shells (clams, oysters) and foraminifera appear to give reliable results, although reworking and burrowing are potential problems. Analyses of museum specimens collected alive before atmospheric nuclear testing suggest that the standard reservoir correction for marine samples is appropriate for middle to lower Chesapeake Bay. The biogenic carbonate radiocarbon ages are compatible with 210Pb and 137Cs data and pollen stratigraphy from the same sites. Post-settlement changes in sediment transport and accumulation is an important environmental issue in many estuaries, including the Chesapeake. Our data show that large variations in sediment mass accumulation rates occur among sites. At shallow water sites, local factors seem to control changes in accumulation rates with time. Our two relatively deep-water sites in the axial channel of the bay have different long-term average accumulation rates, but the history of sediment accumulation at these sites appears to reflect overall conditions in the bay. Mass accumulation rates at the two deep-water sites rapidly increased by about fourfold coincident with widespread land clearance for agriculture in the Chesapeake watershed.

Inteligência cibernética e uso de recursos semânticos na detecção de perfis falsos no contexto do Big Data

Pós-graduação em Ciência da Informação - FFC

Assessing the gain of biological data integration in gene networks inference

Background: A current challenge in gene annotation is to define the gene function in the context of the network of relationships instead of using single genes. The inference of gene networks (GNs) has emerged as an approach to better understand the biology of the system and to study how several components of this network interact with each other and keep their functions stable. However, in general there is no sufficient data to accurately recover the GNs from their expression levels leading to the curse of dimensionality, in which the number of variables is higher than samples. One way to mitigate this problem is to integrate biological data instead of using only the expression profiles in the inference process. Nowadays, the use of several biological information in inference methods had a significant increase in order to better recover the connections between genes and reduce the false positives. What makes this strategy so interesting is the possibility of confirming the known connections through the included biological data, and the possibility of discovering new relationships between genes when observed the expression data. Although several works in data integration have increased the performance of the network inference methods, the real contribution of adding each type of biological information in the obtained improvement is not clear. Methods: We propose a methodology to include biological information into an inference algorithm in order to assess its prediction gain by using biological information and expression profile together. We also evaluated and compared the gain of adding four types of biological information: (a) protein-protein interaction, (b) Rosetta stone fusion proteins, (c) KEGG and (d) KEGG+GO. Results and conclusions: This work presents a first comparison of the gain in the use of prior biological information in the inference of GNs by considering the eukaryote (P. falciparum) organism. Our results indicates that information based on direct interaction can produce a higher improvement in the gain than data about a less specific relationship as GO or KEGG. Also, as expected, the results show that the use of biological information is a very important approach for the improvement of the inference. We also compared the gain in the inference of the global network and only the hubs. The results indicates that the use of biological information can improve the identification of the most connected proteins.

Tokamak TCABR: Acquisition system, data analysis, and remote participation using MDSplus

Each plasma physics laboratory has a proprietary scheme to control and data acquisition system. Usually, it is different from one laboratory to another. It means that each laboratory has its own way to control the experiment and retrieving data from the database. Fusion research relies to a great extent on international collaboration and this private system makes it difficult to follow the work remotely. The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The choice of MDSplus (Model Driven System plus) is proved by the fact that it is widely utilized, and the scientists from different institutions may use the same system in different experiments in different tokamaks without the need to know how each system treats its acquisition system and data analysis. Another important point is the fact that the MDSplus has a library system that allows communication between different types of language (JAVA, Fortran, C, C++, Python) and programs such as MATLAB, IDL, OCTAVE. In the case of tokamak TCABR interfaces (object of this paper) between the system already in use and MDSplus were developed, instead of using the MDSplus at all stages, from the control, and data acquisition to the data analysis. This was done in the way to preserve a complex system already in operation and otherwise it would take a long time to migrate. This implementation also allows add new components using the MDSplus fully at all stages. (c) 2012 Elsevier B.V. All rights reserved.

Family Management Style Framework and Its Use With Families Who Have a Child Undergoing Palliative Care at Home

Palliative care settings in many countries acknowledge families as their prime focus of care, but in Brazil, to date, researchers have devoted scant attention to that practice setting. In this article, we report the findings of a study that explored how families define and manage their lives when they have a child or adolescent undergoing palliative care at home. Data included individual semistructured interviews with 14 family members of 11 different families. Interviews were transcribed and the coding procedure featured qualitative content analysis methods. The deductive coding was based on the major components of the Family Management Style Framework and the eight dimensions comprising these components. The analysis provides insight into families' daily practices and problems inherent in managing their everyday lives that are encountered when they have a child in palliative care. The article features discussion of implications for the palliative care related development of family nursing practice.

Class-specific metrics for multidimensional data projection applied to CBIR

Content-based image retrieval is still a challenging issue due to the inherent complexity of images and choice of the most discriminant descriptors. Recent developments in the field have introduced multidimensional projections to burst accuracy in the retrieval process, but many issues such as introduction of pattern recognition tasks and deeper user intervention to assist the process of choosing the most discriminant features still remain unaddressed. In this paper, we present a novel framework to CBIR that combines pattern recognition tasks, class-specific metrics, and multidimensional projection to devise an effective and interactive image retrieval system. User interaction plays an essential role in the computation of the final multidimensional projection from which image retrieval will be attained. Results have shown that the proposed approach outperforms existing methods, turning out to be a very attractive alternative for managing image data sets.

A new long-term lifetime distribution induced by a latent complementary risk framework

In this paper, we proposed a new three-parameter long-term lifetime distribution induced by a latent complementary risk framework with decreasing, increasing and unimodal hazard function, the long-term complementary exponential geometric distribution. The new distribution arises from latent competing risk scenarios, where the lifetime associated scenario, with a particular risk, is not observable, rather we observe only the maximum lifetime value among all risks, and the presence of long-term survival. The properties of the proposed distribution are discussed, including its probability density function and explicit algebraic formulas for its reliability, hazard and quantile functions and order statistics. The parameter estimation is based on the usual maximum-likelihood approach. A simulation study assesses the performance of the estimation procedure. We compare the new distribution with its particular cases, as well as with the long-term Weibull distribution on three real data sets, observing its potential and competitiveness in comparison with some usual long-term lifetime distributions.

Parameter recovery for a skew-normal IRT model under a Bayesian approach: hierarchical framework, prior and kernel sensitivity and sample size

Item response theory (IRT) comprises a set of statistical models which are useful in many fields, especially when there is an interest in studying latent variables (or latent traits). Usually such latent traits are assumed to be random variables and a convenient distribution is assigned to them. A very common choice for such a distribution has been the standard normal. Recently, Azevedo et al. [Bayesian inference for a skew-normal IRT model under the centred parameterization, Comput. Stat. Data Anal. 55 (2011), pp. 353-365] proposed a skew-normal distribution under the centred parameterization (SNCP) as had been studied in [R. B. Arellano-Valle and A. Azzalini, The centred parametrization for the multivariate skew-normal distribution, J. Multivariate Anal. 99(7) (2008), pp. 1362-1382], to model the latent trait distribution. This approach allows one to represent any asymmetric behaviour concerning the latent trait distribution. Also, they developed a Metropolis-Hastings within the Gibbs sampling (MHWGS) algorithm based on the density of the SNCP. They showed that the algorithm recovers all parameters properly. Their results indicated that, in the presence of asymmetry, the proposed model and the estimation algorithm perform better than the usual model and estimation methods. Our main goal in this paper is to propose another type of MHWGS algorithm based on a stochastic representation (hierarchical structure) of the SNCP studied in [N. Henze, A probabilistic representation of the skew-normal distribution, Scand. J. Statist. 13 (1986), pp. 271-275]. Our algorithm has only one Metropolis-Hastings step, in opposition to the algorithm developed by Azevedo et al., which has two such steps. This not only makes the implementation easier but also reduces the number of proposal densities to be used, which can be a problem in the implementation of MHWGS algorithms, as can be seen in [R.J. Patz and B.W. Junker, A straightforward approach to Markov Chain Monte Carlo methods for item response models, J. Educ. Behav. Stat. 24(2) (1999), pp. 146-178; R. J. Patz and B. W. Junker, The applications and extensions of MCMC in IRT: Multiple item types, missing data, and rated responses, J. Educ. Behav. Stat. 24(4) (1999), pp. 342-366; A. Gelman, G.O. Roberts, and W.R. Gilks, Efficient Metropolis jumping rules, Bayesian Stat. 5 (1996), pp. 599-607]. Moreover, we consider a modified beta prior (which generalizes the one considered in [3]) and a Jeffreys prior for the asymmetry parameter. Furthermore, we study the sensitivity of such priors as well as the use of different kernel densities for this parameter. Finally, we assess the impact of the number of examinees, number of items and the asymmetry level on the parameter recovery. Results of the simulation study indicated that our approach performed equally as well as that in [3], in terms of parameter recovery, mainly using the Jeffreys prior. Also, they indicated that the asymmetry level has the highest impact on parameter recovery, even though it is relatively small. A real data analysis is considered jointly with the development of model fitting assessment tools. The results are compared with the ones obtained by Azevedo et al. The results indicate that using the hierarchical approach allows us to implement MCMC algorithms more easily, it facilitates diagnosis of the convergence and also it can be very useful to fit more complex skew IRT models.

New insights into Trimezieae (Iridaceae) phylogeny: what do molecular data tell us?

The Neotropical tribe Trimezieae are taxonomically difficult. They are generally characterized by the absence of the features used to delimit their sister group Tigridieae. Delimiting the four genera that make up Trimezieae is also problematic. Previous family-level phylogenetic analyses have not examined the monophyly of the tribe or relationships within it. Reconstructing the phylogeny of Trimezieae will allow us to evaluate the status of the tribe and genera and to examine the suitability of characters traditionally used in their taxonomy. Maximum parsimony and Bayesian phylogenetic analyses are presented for 37 species representing all four genera of Trimezieae. Analyses were based on nrITS sequences and a combined plastid dataset. Ancestral character state reconstructions were used to investigate the evolution of ten morphological characters previously considered taxonomically useful. Analyses of nrITS and plastid datasets strongly support the monophyly of Trimezieae and recover four principal clades with varying levels of support; these clades do not correspond to the currently recognized genera. Relationships within the four clades are not consistently resolved, although the conflicting resolutions are not strongly supported in individual analyses. Ancestral character state reconstructions suggest considerable homoplasy, especially in the floral characters used to delimit Pseudotrimezia. The results strongly support recognition of Trimezieae as a tribe but suggest that both generic- and species-level taxonomy need revision. Further molecular analyses, with increased sampling of taxa and markers, are needed to support any revision. Such analyses will help determine the causes of discordance between the plastid and nuclear data and provide a framework for identifying potential morphological synapomorphies for infra-tribal groups. The results also suggest Trimezieae provide a promising model for evolutionary research.

A novel XML document structure comparison framework based-on sub-tree commonalities and label semantics

XML similarity evaluation has become a central issue in the database and information communities, its applications ranging over document clustering, version control, data integration and ranked retrieval. Various algorithms for comparing hierarchically structured data, XML documents in particular, have been proposed in the literature. Most of them make use of techniques for finding the edit distance between tree structures, XML documents being commonly modeled as Ordered Labeled Trees. Yet, a thorough investigation of current approaches led us to identify several similarity aspects, i.e., sub-tree related structural and semantic similarities, which are not sufficiently addressed while comparing XML documents. In this paper, we provide an integrated and fine-grained comparison framework to deal with both structural and semantic similarities in XML documents (detecting the occurrences and repetitions of structurally and semantically similar sub-trees), and to allow the end-user to adjust the comparison process according to her requirements. Our framework consists of four main modules for (i) discovering the structural commonalities between sub-trees, (ii) identifying sub-tree semantic resemblances, (iii) computing tree-based edit operations costs, and (iv) computing tree edit distance. Experimental results demonstrate higher comparison accuracy with respect to alternative methods, while timing experiments reflect the impact of semantic similarity on overall system performance.

Complete fusion enhancement and suppression of weakly bound nuclei at near barrier energies

We consider the influence of breakup channels on the complete fusion of weakly bound systems in terms of dynamic polarization potentials. It is argued that the enhancement of the cross section at sub-barrier energies may be consistent with recent experimental observations that nucleon transfer, often leading to breakup, is dominant compared to direct breakup. The main trends of the experimental complete fusion cross sections are analyzed in the framework of the DPP approach. The qualitative conclusions are supported by CDCC calculations including a sequential breakup channel, the one neutron stripping of Li-7 followed by the breakup of Li-6.