Metabolic profiling by ultra-performance liquid chromatography-mass spectrometry and parallel factor analysis for the determination of disease biomarkers in Eucalyptus

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Interferon-gamma production by human neutrophils upon stimulation by IL-12, IL-15 and IL-18 and challenge with Paracoccidioides brasiliensis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Multi-scale lacunarity as an alternative to quantify and diagnose the behavior of prostate cancer

Prostate cancer is a serious public health problem accounting for up to 30% of clinical tumors in men. The diagnosis of this disease is made with clinical, laboratorial and radiological exams, which may indicate the need for transrectal biopsy. Prostate biopsies are discerningly evaluated by pathologists in an attempt to determine the most appropriate conduct. This paper presents a set of techniques for identifying and quantifying regions of interest in prostatic images. Analyses were performed using multi-scale lacunarity and distinct classification methods: decision tree, support vector machine and polynomial classifier. The performance evaluation measures were based on area under the receiver operating characteristic curve (AUC). The most appropriate region for distinguishing the different tissues (normal, hyperplastic and neoplasic) was defined: the corresponding lacunarity values and a rule's model were obtained considering combinations commonly explored by specialists in clinical practice. The best discriminative values (AUC) were 0.906, 0.891 and 0.859 between neoplasic versus normal, neoplasic versus hyperplastic and hyperplastic versus normal groups, respectively. The proposed protocol offers the advantage of making the findings comprehensible to pathologists. (C) 2014 Elsevier Ltd. All rights reserved.

Description and performance of track and primary-vertex reconstruction with the CMS tracker

A description is provided of the software algorithms developed for the CMS tracker both for reconstructing charged-particle trajectories in proton-proton interactions and for using the resulting tracks to estimate the positions of the LHC luminous region and individual primary-interaction vertices. Despite the very hostile environment at the LHC, the performance obtained with these algorithms is found to be excellent. For t (t) over bar events under typical 2011 pileup conditions, the average track-reconstruction efficiency for promptly-produced charged particles with transverse momenta of p(T) > 0.9GeV is 94% for pseudorapidities of vertical bar eta vertical bar < 0.9 and 85% for 0.9 < vertical bar eta vertical bar < 2.5. The inefficiency is caused mainly by hadrons that undergo nuclear interactions in the tracker material. For isolated muons, the corresponding efficiencies are essentially 100%. For isolated muons of p(T) = 100GeV emitted at vertical bar eta vertical bar < 1.4, the resolutions are approximately 2.8% in p(T), and respectively, 10 m m and 30 mu m in the transverse and longitudinal impact parameters. The position resolution achieved for reconstructed primary vertices that correspond to interesting pp collisions is 10-12 mu m in each of the three spatial dimensions. The tracking and vertexing software is fast and flexible, and easily adaptable to other functions, such as fast tracking for the trigger, or dedicated tracking for electrons that takes into account bremsstrahlung.

Toward Satellite-Based Land Cover Classification Through Optimum-Path Forest

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Compartmentalized gene expression of toll-like receptors 2, 4 and 9 in the brain and peripheral lymphoid organs during canine visceral leishmaniasis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Harmony Search applied for Support Vector Machines Training Optimization

Since the beginning, some pattern recognition techniques have faced the problem of high computational burden for dataset learning. Among the most widely used techniques, we may highlight Support Vector Machines (SVM), which have obtained very promising results for data classification. However, this classifier requires an expensive training phase, which is dominated by a parameter optimization that aims to make SVM less prone to errors over the training set. In this paper, we model the problem of finding such parameters as a metaheuristic-based optimization task, which is performed through Harmony Search (HS) and some of its variants. The experimental results have showen the robustness of HS-based approaches for such task in comparison against with an exhaustive (grid) search, and also a Particle Swarm Optimization-based implementation.

Interface para classificação de dados por máquinas de vetores de suporte

In this project the Pattern Recognition Problem is approached with the Support Vector Machines (SVM) technique, a binary method of classification that provides the best solution separating the data in the better way with a hiperplan and an extension of the input space dimension, as a Machine Learning solution. The system aims to classify two classes of pixels chosen by the user in the interface in the interest selection phase and in the background selection phase, generating all the data to be used in the LibSVM library, a library that implements the SVM, illustrating the library operation in a casual way. The data provided by the interface is organized in three types, RGB (Red, Green and Blue color system), texture (calculated) or RGB + texture. At last the project showed successful results, where the classification of the image pixels was showed as been from one of the two classes, from the interest selection area or from the background selection area. The simplest user view of results classification is the RGB type of data arrange, because it’s the most concrete way of data acquisition

Explorando abordagens de múltiplos rótulos por floresta de caminhos ótimos

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Introducing the Discriminative Paraconsistent Machine (DPM)

This paper introduces a new tool for pattern recognition. Called the Discriminative Paraconsistent Machine (DPM), it is based on a supervised discriminative model training that incorporates paraconsistency criteria and allows an intelligent treatment of contradictions and uncertainties. DPMs can be applied to solve problems in many fields of science, using the tests and discussions presented here, which demonstrate their efficacy and usefulness. Major difficulties and challenges that were overcome consisted basically in establishing the proper model with which to represent the concept of paraconsistency.

Segurança em redes sem fio: estudo sobre o desenvolvimento de conjuntos de dados para comparação de IDS

Pós-graduação em Engenharia Elétrica - FEIS

RANKL expression is differentially modulated by TLR2 and TLR4 signaling in fibroblasts and osteoblasts

Resident, non-immune cells express various pattern-recognition receptors and produce inflammatory cytokines in response to microbial antigens, during the innate immune response. Alveolar bone resorption is the hallmark of destructive periodontitis and it is caused by the host response to bacteria and their mediators present on the biofilm. The balance between the expression levels of receptor activator of nuclear factorkappa B ligand (RANKL) and osteoprotegerin (OPG) is pivotal for osteoclast differentiation and activity and has been implicated in the progression of bone loss in periodontitis. To assess the contribution of resident cells to the bone resorption mediated by innate immune signaling, we stimulated fibroblasts and osteoblastic cells with LPS from. Escherichia coli (TLR4 agonist), Porphyromonas gingivalis (TLR2 and -4 agonist), and interleukin-1 beta (as a control for cytokine signaling through Toll/IL-1receptor domain) in time-response experiments. Expression of RANKL and OPG mRNA was studied by RT-PCR, whereas the production of RANKL protein and the activation of p38 MAPK and NF-kB signaling pathways were analyzed by western blot. We used biochemical inhibitors to assess the relative contribution of p38 MAPK and NF-kB signaling to the expression of RANKL and OPG induced by TLR2, -4 and IL1β in these cells. Both p38 MAPK and NFkB pathways were activated by these stimuli in fibroblasts and osteoblasts, but the kinetics of this activation varied in each cell type and with the nature of the stimulation. E. coli LPS was a stronger inducer of RANKL mRNA in fibroblasts, whereas LPS from P. gingivalis downregulated RANKL mRNA in periodontal ligament cells but increased its expression in osteoblasts. IL-1β induced RANKL in both cell types and without a marked effect on OPG expression. p38 MAPK was more relevant than NF-kB for the expression of RANKL and OPG in these cell types.

Interleukin-18 increases TLR4 and mannose receptor expression and modulates cytokine production in human monocytes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Paracoccidioides brasiliensis interferes on dendritic cells maturation by inhibiting PGE(2) production

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Learning kernels for support vector machines with polynomial powers of sigmoid

In the pattern recognition research field, Support Vector Machines (SVM) have been an effectiveness tool for classification purposes, being successively employed in many applications. The SVM input data is transformed into a high dimensional space using some kernel functions where linear separation is more likely. However, there are some computational drawbacks associated to SVM. One of them is the computational burden required to find out the more adequate parameters for the kernel mapping considering each non-linearly separable input data space, which reflects the performance of SVM. This paper introduces the Polynomial Powers of Sigmoid for SVM kernel mapping, and it shows their advantages over well-known kernel functions using real and synthetic datasets.