The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags

Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the information within the human genome in the fight against cancer, we have deposited some two million expressed sequence tags (ESTs) from human tumors and their corresponding normal tissues in the public databases. The data currently define approximate to23,500 genes, of which only approximate to1,250 are still represented only by ESTs. Examination of the EST coverage of known cancer-related (CR) genes reveals that <1% do not have corresponding ESTs, indicating that the representation of genes associated with commonly studied tumors is high. The careful recording of the origin of all ESTs we have produced has enabled detailed definition of where the genes they represent are expressed in the human body. More than 100,000 ESTs are available for seven tissues, indicating a surprising variability of gene usage that has led to the discovery of a significant number of genes with restricted expression, and that may thus be therapeutically useful. The ESTs also reveal novel nonsynonymous germline variants (although the one-pass nature of the data necessitates careful validation) and many alternatively spliced transcripts. Although widely exploited by the scientific community, vindicating our totally open source policy, the EST data generated still provide extensive information that remains to be systematically explored, and that may further facilitate progress toward both the understanding and treatment of human cancers.

Does spatial visualization ability improve after studying technical drawing?

Two studies were carried out to analyze whether learning technical drawing improves a person's ability for spatial visualization. Visualization and inductive reasoning tests were applied at the beginning and end of a course in technical drawing in samples of first year engineering students. In both studies it was observed that a moderate percentage of students improved their Visualization test execution. The improvement was similar in men and women. There was no improvement on the inductive reasoning test. The results support the conclusion that the spatial visualization ability can be improved with training.

Tensor3D: A computer graphics program to simulate 3D real-time deformation and visualization of geometric bodies

Tensor3D is a geometric modeling program with the capacity to simulate and visualize in real-time the deformation, specified through a tensor matrix and applied to triangulated models representing geological bodies. 3D visualization allows the study of deformational processes that are traditionally conducted in 2D, such as simple and pure shears. Besides geometric objects that are immediately available in the program window, the program can read other models from disk, thus being able to import objects created with different open-source or proprietary programs. A strain ellipsoid and a bounding box are simultaneously shown and instantly deformed with the main object. The principal axes of strain are visualized as well to provide graphical information about the orientation of the tensor's normal components. The deformed models can also be saved, retrieved later and deformed again, in order to study different steps of progressive strain, or to make this data available to other programs. The shape of stress ellipsoids and the corresponding Mohr circles defined by any stress tensor can also be represented. The application was written using the Visualization ToolKit, a powerful scientific visualization library in the public domain. This development choice, allied to the use of the Tcl/Tk programming language, which is independent on the host computational platform, makes the program a useful tool for the study of geometric deformations directly in three dimensions in teaching as well as research activities. (C) 2007 Elsevier Ltd. All rights reserved.

Expressed sequence tags from Atta laevigata and identification of candidate genes for the control of pest leaf-cutting ants.

Leafcutters are the highest evolved within Neotropical ants in the tribe Attini and model systems for studying caste formation, labor division and symbiosis with microorganisms. Some species of leafcutters are agricultural pests controlled by chemicals which affect other animals and accumulate in the environment. Aiming to provide genetic basis for the study of leafcutters and for the development of more specific and environmentally friendly methods for the control of pest leafcutters, we generated expressed sequence tag data from Atta laevigata, one of the pest ants with broad geographic distribution in South America. Results: The analysis of the expressed sequence tags allowed us to characterize 2,006 unique sequences in Atta laevigata. Sixteen of these genes had a high number of transcripts and are likely positively selected for high level of gene expression, being responsible for three basic biological functions: energy conservation through redox reactions in mitochondria; cytoskeleton and muscle structuring; regulation of gene expression and metabolism. Based on leafcutters lifestyle and reports of genes involved in key processes of other social insects, we identified 146 sequences potential targets for controlling pest leafcutters. The targets are responsible for antixenobiosis, development and longevity, immunity, resistance to pathogens, pheromone function, cell signaling, behavior, polysaccharide metabolism and arginine kynase activity. Conclusion: The generation and analysis of expressed sequence tags from Atta laevigata have provided important genetic basis for future studies on the biology of leaf-cutting ants and may contribute to the development of a more specific and environmentally friendly method for the control of agricultural pest leafcutters.

Length of resin tags in pit-and-fissure sealants: all-in-one self-etching adhesive vs phosphoric acid etching.

PURPOSE: To investigate the penetration (tags) of adhesive materials into enamel etched with phosphoric acid or treated with a self-etching adhesive, before application of a pit-and-fissure sealant. MATERIALS AND METHODS: The sample comprised six study groups with six specimens each. Before pit-and-fissure sealing with the materials Clinpro SealantTM (Groups I and II), Vitro Seal ALPHA (Groups III and IV) and Fuji II LC (Groups V and VI), the teeth in Groups I, III, and V were etched with 35% phosphoric acid for 30 seconds. Teeth in Groups II, IV, and VI received application of the self-etching adhesive Adper Prompt L-Pop. The treated teeth were sectioned buccolingually, ground to 100-microm thickness, decalcified, and analyzed by conventional light microscopy at 400x magnification. RESULTS: The teeth etched with phosphoric acid exhibited significantly greater penetration than specimens treated with self-etching adhesive. CLINICAL SIGNIFICANCE: When compared with enamel treated with a self-etching adhesive, the penetration (tags) of adhesive materials into enamel was greater when applied on enamel etched with phosphoric acid.

Three-dimensional visualization of human hemoglobin phenotypes with HPLC

Hemoglobinopathies were included in the Brazilian Neonatal Screening Program on June 6, 2001. Automated high-performance liquid chromatography (HPLC) was indicated as one of the diagnostic methods. The amount of information generated by these systems is immense, and the behavior of groups cannot always be observed in individual analyses. Three-dimensional (3-D) visualization techniques can be applied to extract this information, for extracting patterns, trends or relations from the results stored in databases. We applied the 3-D visualization tool to analyze patterns in the results of hemoglobinopathy based on neonatal diagnosis by HPLC. The laboratory results of 2520 newborn analyses carried out in 2001 and 2002 were used. The Fast, F1, F and A peaks, which were detected by the analytical system, were chosen as attributes for mapping. To establish a behavior pattern, the results were classified into groups according to hemoglobin phenotype: normal (N = 2169), variant (N = 73) and thalassemia (N = 279). 3-D visualization was made with the FastMap DB tool; there were two distribution patterns in the normal group, due to variation in the amplitude of the values obtained by HPLC for the F1 window. It allowed separation of the samples with normal Hb from those with alpha thalassemia, based on a significant difference (P > 0.05) between the mean values of the Fast and A peaks, demonstrating the need for better evaluation of chromatograms; this method could be used to help diagnose alpha thalassemia in newborns.

Correlation of the hybrid layer thickness and resin tags length with the bond strength of a self-etching adhesive system.

The objective of this study was to measure the thickness of the hybrid layer (HLT), length of resin tags (RTL) and bond strength (BS) in the same teeth, using a self-etching adhesive system Adper Prompt L Pop to intact dentin and to analyze the correlation between HLTand RTL and their BS. Ten human molars were used for the restorative procedures and each restored tooth was sectioned in mesio-distal direction. One section was submitted to light microscopy analysis of HLT and RTL (400x). Another section was prepared and submitted to the microtensile bond test (0.5 mm/min). The fractured surfaces were analyzed using scanning electron microscopy to determine the failure pattern. Correlation between HLT and RTL with the BS data was analyzed by linear regression. The mean values of HLT, RTL and BS were 3.36 microm, 12.97 microm and 14.10 MPa, respectively. No significant relationship between BS and HLT (R2= 0.011, p>0.05) and between BS and RTL (R2= 0.038) was observed. The results suggested that there was no significant correlation between the HLT and RTL with the BS of the self-etching adhesive to dentin.

Observation of tags and hybrid layer of a single bottle conventional adhesive system and a self-etching adhesive system, on sound dentin.

This experimental light microscopy study investigated the formation of a hybrid layer and resin tags on sound dentin, after utilization of conventional and self-etching adhesive systems. After restorative procedures, the specimens were decalcified in a formic acid and sodium citrate solution, embedded in paraffin, sectioned at 6-microm thickness and stained by the Brown & Brenn method for analysis and measurement by light microscopy (AXIOPHOT) (400x). The results were statistically analyzed by analysis of variance, at a significance level of 5%. Based on the results, it could be concluded that the conventional adhesive allowed the formation of a thicker hybrid layer than the self-etching adhesive, with similar penetration into the dentinal tubules (resin tags).

Information Visualization to support decision making in the context of distance learning: A study with VLE TelEduc

Digital data sets constitute rich sources of information, which can be extracted and evaluated applying computational tools, for example, those ones for Information Visualization. Web-based applications, such as social network environments, forums and virtual environments for Distance Learning, are good examples for such sources. The great amount of data has direct impact on processing and analysis tasks. This paper presents the computational tool Mapper, defined and implemented to use visual representations - maps, graphics and diagrams - for supporting the decision making process by analyzing data stored in Virtual Learning Environment TelEduc-Unesp. © 2012 IEEE.

Design and evaluation of an advanced virtual reality system for visualization of dentistry structures

This paper presents the development of an application created to assist the teaching of dental structures, generate rich content information and different manners of interaction. An ontology was created to provide semantics informations for virtual models. We also used two devices gesture-based interaction: Kinect and Wii Remote. It was developed a system which use intuitive interaction, and it is able to generate three dimensional images, making the experience of teaching / learning motivating. The projection environment used by the system was called Mini CAVE. © 2012 IEEE.

Molecularly designed layer-by-layer (LbL) films to detect catechol using information visualization methods

The control of molecular architectures has been exploited in layer-by-layer (LbL) films deposited on Au interdigitated electrodes, thus forming an electronic tongue (e-tongue) system that reached an unprecedented high sensitivity (down to 10-12 M) in detecting catechol. Such high sensitivity was made possible upon using units containing the enzyme tyrosinase, which interacted specifically with catechol, and by processing impedance spectroscopy data with information visualization methods. These latter methods, including the parallel coordinates technique, were also useful for identifying the major contributors to the high distinguishing ability toward catechol. Among several film architectures tested, the most efficient had a tyrosinase layer deposited atop LbL films of alternating layers of dioctadecyldimethylammonium bromide (DODAB) and 1,2-dipalmitoyl-sn-3-glycero-fosfo-rac-(1-glycerol) (DPPG), viz., (DODAB/DPPG)5/DODAB/Tyr. The latter represents a more suitable medium for immobilizing tyrosinase when compared to conventional polyelectrolytes. Furthermore, the distinction was more effective at low frequencies where double-layer effects on the film/liquid sample dominate the electrical response. Because the optimization of film architectures based on information visualization is completely generic, the approach presented here may be extended to designing architectures for other types of applications in addition to sensing and biosensing. © 2013 American Chemical Society.

Inter-relação do comprimento dos prolongamentos resinosos (tags) e da espessura da camada híbrida de adesão, com a resistência de união de sistemas adesivos ao tecido dentinário

Pós-graduação em Odontologia - FOA

Selantes de fóssulas e fissuras: influência da aplicação prévia de um adesivo autocondicionante ou do condicionamento com ácido fosfórico na formação dos tags resinosos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Visualization of Protein Folding Funnels in Lattice Models

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