Employing 2D Projections for Fast Visual Exploration of Large Fiber Tracking Data

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Morphometric and bioacoustic data on three species of Pseudopaludicola Miranda-Ribeiro, 1926 (Anura: Leptodactylidae: Leiuperinae) described from chapada dos guimarães, mato Grosso, Brazil, with the revalidation of pseudopaludicola ameghini (Cope, 1887)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Oral squamous carcinoma cells secrete RANKL directly supporting osteolytic bone loss

Objective: Local invasion of bone is a frequent complication of oral squamous cell carcinoma (OSCC). Development of these osteolytic lesions is mediated by osteoclasts. Receptor activation of NF-kappa B ligand (RANKL) signaling, counteracted by osteoprotegerin (OPG), regulates osteoclastogenesis. Previous studies in rodent models have demonstrated that inhibition of RANKL decreases tumor growth and lesions within bone. However, the contributory role of OSCC cells to this disease process has yet to be defined.Methods: RANKL expression was assessed in a panel of OSCC cell lines by qPCR, flow cytometry, and ELISA. Induction of osteoclastogenesis was assessed by co-culture with macrophages or with OSCC-derived conditioned medium. In an animal model of bone invasion, nude mice were injected intratibially with UMSCC-11B cells expressing a RANKL luciferase promoter to detect tumor-derived RANKL activity. Osteolytic lesions were analyzed by X-ray, micro-CT, and histological methods. RANKL expression was assessed in human OSCC tissues by immunohistochemistry.Results: We demonstrated that OSCCs express varied levels of all RANKL isoforms, both membrane-bound and soluble RANKL. Both co-culture and treatment with OSCC-conditioned media induced osteoclastogenesis. In mice, we demonstrated human RANKL promoter activity during bone invasion. Over the course of the experiment, animals suffered osteolytic lesions as RANKL-driven luciferase expression increased with time. After 8 weeks, human-derived RANKL was detected in areas of bone resorption by immunohistochemistry. Similar epithelial RANKL expression was detected in human OSCC tissues.Conclusion: These data demonstrate the ability of OSCCs to produce RANKL, directly altering the tumor microenvironment to increase osteoclastogenesis and mediate local bone invasion. (C) 2012 Elsevier Ltd. All rights reserved.

Microstrain Around Dental Implants Supporting Fixed Partial Prostheses Under Axial and Non-Axial Loading Conditions, In Vitro Strain Gauge Analysis

The current study used strain gauge analysis to perform an in vitro evaluation of the effect of axial and non-axial loading on implant-supported fixed partial prostheses, varying the implant placement configurations and the loading points. Three internal hexagon implants were embedded in the center of each polyurethane block with in-line and offset placements. Microunit abutments were connected to the implants using a torque of 20 N.cm, and plastic prosthetic cylinders were screwed onto the abutments, which received standard patterns cast in Co-Cr alloy (n = 10). Four strain gauges (SGs) were bonded onto the surfaces of the blocks, tangentially to the implants: SG 01 mesially to implant 1, SG 02 and SG 03 mesially and distally to implant 2, respectively, and SG 04 distally to implant 3. Each metallic structure was screwed onto the abutments using a 10-N.cm torque, and axial and non-axial loads of 30 kg were applied at 5 predetermined points. The data obtained from the strain gauge analyses were analyzed statistically through the repeated measures analysis of variance and the Tukey test, with a conventional level of significance of P < 0.05. The results showed a statistically significant difference for the loading point (P = 0.0001), with point E (nonaxial) generating the highest microstrain (327.67 mu epsilon) and point A (axial) generating the smallest microstrain (208.93 mu epsilon). No statistically significant difference was found for implant placement configuration (P = 0.856). It was concluded that the offset implant placement did not reduce the magnitude of microstrain around the implants under axial and non-axial loading conditions, although loading location did influence this magnitude.

Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Zirconia-based dental crown to support a removable partial denture: a three-dimensional finite element analysis using contact elements and micro-CT data

Veneer fracture is the most common complication in zirconia-based restorations. The aim of this study was to evaluate the mechanical behavior of a zirconia-based crown in a lower canine tooth supporting removable partial denture (RPD) prosthesis, varying the bond quality of the veneer/coping interface. Microtomography (μCT) data of an extracted left lower canine were used to build the finite element model (M) varying the core material (gold core - MAu; zirconia core - MZi) and the quality of the veneer/core interface (complete bonded - MZi; incomplete bonded - MZi-NL). The incomplete bonding condition was only applied for zirconia coping by using contact elements (Target/Contact) with 0.3 frictional coefficients. Stress fields were obtained using Ansys Workbench 10.0. The loading condition (L = 1 N) was vertically applied at the base of the RPD prosthesis metallic support towards the dental apex. Maximum principal (σmax) and von Mises equivalent (σvM) stresses were obtained. The σmax (MPa) for the bonded condition was similar between gold and zirconia cores (MAu, 0.42; MZi, 0.40). The incomplete bonded condition (MZi-NL) raised σmax in the veneer up to 800% (3.23 MPa) in contrast to the bonded condition. The peak of σvM increased up to 270% in the MZi-NL. The incomplete bond condition increasing the stress in the veneer/zirconia interface.

Green training supporting eco-innovation in three Brazilian companies: practices and levels of integration

Purpose – The purpose of this paper is to show results from the relationship between green/environmental training and the development of three projects of low-carbon eco-innovations in top Brazilian companies. Design/methodology/approach – This study includes three organizational projects for low-carbon eco-innovations in products (A, B and C) with the objective of reducing their impact on GHG emissions, the so-called low-carbon products. Data were collected from several sources of evidence, including in-depth interviews, document analyses and direct observations. Findings – The authors verified that the environmental training interface for mitigating climate change is relevant for the systematic development of low-carbon products in most of the cases studied. Originality/value – Low-carbon eco-innovations are a trend in the corporate world; however, there is not enough literature and practical evidence on this subject. Thus, this paper adds new evidence to the literature.

Sofya: Supporting Rapid Development of Dynamic Program Analyses for Java

Dynamic analysis is an increasingly important means of supporting software validation and maintenance. To date, developers of dynamic analyses have used low-level instrumentation and debug interfaces to realize their analyses. Many dynamic analyses, however, share multiple common high-level requirements, e.g., capture of program data state as well as events, and efficient and accurate event capture in the presence of threading. We present SOFYA – an infra-structure designed to provide high-level, efficient, concurrency-aware support for building analyses that reason about rich observations of program data and events. It provides a layered, modular architecture, which has been successfully used to rapidly develop and evaluate a variety of demanding dynamic program analyses. In this paper, we describe the SOFYA framework, the challenges it addresses, and survey several such analyses.

Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.

Semantic integration of gene expression analysis tools and data sources using software connectors

Abstract Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.

Supporting semantic web technologies in the pervasive service ecosystems middleware

Semantic Web technologies are strategic in order to fulfill the openness requirement of Self-Aware Pervasive Service Ecosystems. In fact they provide agents with the ability to cope with distributed data, using RDF to represent information, ontologies to describe relations between concepts from any domain (e.g. equivalence, specialization/extension, and so on) and reasoners to extract implicit knowledge. The aim of this thesis is to study these technologies and design an extension of a pervasive service ecosystems middleware capable of exploiting semantic power, and deepening performance implications.

Development of new tools and devices for CMB and foreground data analysis and future experiments

The discovery of the Cosmic Microwave Background (CMB) radiation in 1965 is one of the fundamental milestones supporting the Big Bang theory. The CMB is one of the most important source of information in cosmology. The excellent accuracy of the recent CMB data of WMAP and Planck satellites confirmed the validity of the standard cosmological model and set a new challenge for the data analysis processes and their interpretation. In this thesis we deal with several aspects and useful tools of the data analysis. We focus on their optimization in order to have a complete exploitation of the Planck data and contribute to the final published results. The issues investigated are: the change of coordinates of CMB maps using the HEALPix package, the problem of the aliasing effect in the generation of low resolution maps, the comparison of the Angular Power Spectrum (APS) extraction performances of the optimal QML method, implemented in the code called BolPol, and the pseudo-Cl method, implemented in Cromaster. The QML method has been then applied to the Planck data at large angular scales to extract the CMB APS. The same method has been applied also to analyze the TT parity and the Low Variance anomalies in the Planck maps, showing a consistent deviation from the standard cosmological model, the possible origins for this results have been discussed. The Cromaster code instead has been applied to the 408 MHz and 1.42 GHz surveys focusing on the analysis of the APS of selected regions of the synchrotron emission. The new generation of CMB experiments will be dedicated to polarization measurements, for which are necessary high accuracy devices for separating the polarizations. Here a new technology, called Photonic Crystals, is exploited to develop a new polarization splitter device and its performances are compared to the devices used nowadays.

Five-year results of a randomized controlled clinical trial comparing zirconia and titanium abutments supporting single-implant crowns in canine and posterior regions

OBJECTIVES: To test the survival rates, and the technical and biological complication rates of customized zirconia and titanium abutments 5 years after crown insertion. MATERIAL AND METHODS: Twenty-two patients with 40 single implants in maxillary and mandibular canine and posterior regions were included. The implant sites were randomly assigned to zirconia abutments supporting all-ceramic crowns or titanium abutments supporting metal-ceramic crowns. Clinical examinations were performed at baseline, and at 6, 12, 36 and 60 months of follow-up. The abutments and reconstructions were examined for technical and/or biological complications. Probing pocket depth (PPD), plaque control record (PCR) and Bleeding on Probing (BOP) were assessed at abutments (test) and analogous contralateral teeth (control). Radiographs of the implants revealed the bone level (BL) on mesial (mBL) and distal sides (dBL). Data were statistically analyzed with nonparametric mixed models provided by Brunner and Langer and STATA (P < 0.05). RESULTS: Eighteen patients with 18 zirconia and 10 titanium abutments were available at a mean follow-up of 5.6 years (range 4.5-6.3 years). No abutment fracture or loss of a reconstruction occurred. Hence, the survival rate was 100% for both. Survival of implants supporting zirconia abutments was 88.9% and 90% for implants supporting titanium abutments. Chipping of the veneering ceramic occurred at three metal-ceramic crowns supported by titanium abutments. No significant differences were found at the zirconia and titanium abutments for PPD (meanPPD(ZrO2) 3.3 ± 0.6 mm, mPPD(T) (i) 3.6 ± 1.1 mm), PCR (mPCR(Z) (rO) (2) 0.1 ± 0.3, mPCR(T) (i) 0.3 ± 0.2) and BOP (mBOP(Z) (rO) (2) 0.5 ± 0.3, mBOP(T) (i) 0.6 ± 0.3). Moreover, the BL was similar at implants supporting zirconia and titanium abutments (mBL(Z) (rO) (2) 1.8 ± 0.5, dBL(Z) (rO) (2) 2.0 ± 0.8; mBL(T) (i) 2.0 ± 0.8, dBL(T) (i) 1.9 ± 0.8). CONCLUSIONS: There were no statistically or clinically relevant differences between the 5-year survival rates, and the technical and biological complication rates of zirconia and titanium abutments in posterior regions.