Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Plant-antivenom: Database of anti-venom medicinal plants

Plant-antivenom is a computational Websystem about medicinal plants with anti-venom properties. The system consists of a database of these plants, including scientific publications on this subject and amino acid sequences of active principles from venomous animals. The system relates these data allowing their integration through different search applications. For the development of the system, the first surveys were conducted in scientific literature, allowing the creation of a publication database in a library for reading and user interaction. Then, classes of categories were created, allowing the use of tags and the organization of content. This database on medicinal plants has information such as family, species, isolated compounds, activity, inhibited animal venoms, among others. Provision is made for submission of new information by registered users, by the use of wiki tools. Content submitted is released in accordance to permission rules defined by the system. The database on biological venom protein amino acid sequences was structured from the essential information from National Center for Biotechnology Information (NCBI). Plant-antivenom`s interface is simple, contributing to a fast and functional access to the system and the integration of different data registered on it. Plant-antivenom system is available on the Internet at http://gbi.fmrp.usp.br/plantantivenom.

Elementary Petri net inside RFID distributed database (PNRD)

Usually, a Petri net is applied as an RFID model tool. This paper, otherwise, presents another approach to the Petri net concerning RFID systems. This approach, called elementary Petri net inside an RFID distributed database, or PNRD, is the first step to improve RFID and control systems integration, based on a formal data structure to identify and update the product state in real-time process execution, allowing automatic discovery of unexpected events during tag data capture. There are two main features in this approach: to use RFID tags as the object process expected database and last product state identification; and to apply Petri net analysis to automatically update the last product state registry during reader data capture. RFID reader data capture can be viewed, in Petri nets, as a direct analysis of locality for a specific transition that holds in a specific workflow. Following this direction, RFID readers storage Petri net control vector list related to each tag id is expected to be perceived. This paper presents PNRD cornerstones and a PNRD implementation example in software called DEMIS Distributed Environment in Manufacturing Information Systems.

Integration of Ligand- and Target-Based Virtual Screening for the Discovery of Cruzain Inhibitors

A myriad of methods are available for virtual screening of small organic compound databases. In this study we have successfully applied a quantitative model of consensus measurements, using a combination of 3D similarity searches (ROCS and EON), Hologram Quantitative Structure Activity Relationships (HQSAR) and docking (FRED, FlexX, Glide and AutoDock Vina), to retrieve cruzain inhibitors from collected databases. All methods were assessed individually and then combined in a Ligand-Based Virtual Screening (LBVS) and Target-Based Virtual Screening (TBVS) consensus scoring, using Receiving Operating Characteristic (ROC) curves to evaluate their performance. Three consensus strategies were used: scaled-rank-by-number, rank-by-rank and rank-by-vote, with the most thriving the scaled-rank-by-number strategy, considering that the stiff ROC curve appeared to be satisfactory in every way to indicate a higher enrichment power at early retrieval of active compounds from the database. The ligand-based method provided access to a robust and predictive HQSAR model that was developed to show superior discrimination between active and inactive compounds, which was also better than ROCS and EON procedures. Overall, the integration of fast computational techniques based on ligand and target structures resulted in a more efficient retrieval of cruzain inhibitors with desired pharmacological profiles that may be useful to advance the discovery of new trypanocidal agents.

SOFT TISSUE INTEGRATION IN THE NECK AREA OF TITANIUM IMPLANTS - AN ANIMAL TRIAL

Dental implant materials are required to enable good apposition of bone and soft tissues. They must show sufficient resistance to chemical, physical and biological stress in the oral cavity to achieve good long-term outcomes. A critical issue is the apposition of the soft tissues, as they have provided a quasi-physiological closure of oral cavity. The present experiment was performed to study the peri-implant tissue response to non-submerged (1-stage) implant installation procedures. Two different implants types (NobelBiocare, NobelReplace (R) Tapered Groovy 4.3 x 10 mm and Replace (R) Select Tapered TiU RP 4.3 x 10 mm) were inserted into the right and left sides of 8 domestic pigs (Sus scrofa domestica) mandibles, between canines and premolars and immediately provided with a ceramic crown. Primary implant stability was determined using ressonance frequency analysis. Soft tissue parameters were assessed: sulcus depth (SDI) and junctional epithelium (JE). Following 70 days of healing, jaw sections were processed for histology and histomorphometric examination. Undecalcified histological sections demonstrated osseointegration with direct bone contact. The soft tissue parameters revealed no significant differences between the two implant types. The peri-implant soft tissues appear to behave similarly in both implant types.

On the functional integration between postural and supra-postural tasks on the basis of contextual cues and task constraint

In order to evaluate the effects of uncertainty about direction of mechanical perturbation and supra-postural task constraint on postural control young adults had their upright stance perturbed while holding a tray in a horizontal position Stance was perturbed by moving forward or backward a supporting platform contrasting situations of certainty versus uncertainty of direction of displacement Increased constraint on postural stability was Imposed by a supra-postural task of equilibrating a cylinder on the tray Performance was assessed through EMG of anterior leg muscles angular displacement of the main Joints involved in the postural reactions and displacement of the tray Results showed that both certainty on the direction of perturbation and Increased supra-postural task constraint led to decreased angular displacement of the knee and the hip Furthermore combination of certainty and high supra-postural task constraint produced shorter latency of muscular activation Such postural responses were paralleled by decreased displacement of the tray Thesi results suggest a functional integration between the tasks with central set priming reactive postural responses from contextual cues and Increased stability demand (C) 2010 Elsevier B V All rights reserved

Online Mammographic Images Database for Development and Comparison of CAD Schemes

Considering the difficulties in finding good-quality images for the development and test of computer-aided diagnosis (CAD), this paper presents a public online mammographic images database free for all interested viewers and aimed to help develop and evaluate CAD schemes. The digitalization of the mammographic images is made with suitable contrast and spatial resolution for processing purposes. The broad recuperation system allows the user to search for different images, exams, or patient characteristics. Comparison with other databases currently available has shown that the presented database has a sufficient number of images, is of high quality, and is the only one to include a functional search system.

Fault Detection in Power Distribution Systems Using Automated Integration of Computational Intelligence Tools

The main purpose of this paper is to present architecture of automated system that allows monitoring and tracking in real time (online) the possible occurrence of faults and electromagnetic transients observed in primary power distribution networks. Through the interconnection of this automated system to the utility operation center, it will be possible to provide an efficient tool that will assist in decisionmaking by the Operation Center. In short, the desired purpose aims to have all tools necessary to identify, almost instantaneously, the occurrence of faults and transient disturbances in the primary power distribution system, as well as to determine its respective origin and probable location. The compilations of results from the application of this automated system show that the developed techniques provide accurate results, identifying and locating several occurrences of faults observed in the distribution system.

Digital control and integration of a 192 MW wind farm with doubly fed induction generator into the Brazilian power system

This paper reports on design of digital control for wind turbines and its relation to the quality of power fed into the Brazilian grid on connecting to it a 192 MW wind farm equipped with doubly fed induction generators. PWM converters are deployed as vector controlled regulated current voltage sources for their rotors, for independent control of both active and reactive power of those generators. Both speed control and active power control strategies are analyzed, in the search for maximum efficiency of conversion of wind kinetic energy into electric power and enhanced quality of delivered power. (C) 2009 Elsevier B.V. All rights reserved.

Robust integration of real time optimization with linear model predictive control

Here, we study the stable integration of real time optimization (RTO) with model predictive control (MPC) in a three layer structure. The intermediate layer is a quadratic programming whose objective is to compute reachable targets to the MPC layer that lie at the minimum distance to the optimum set points that are produced by the RTO layer. The lower layer is an infinite horizon MPC with guaranteed stability with additional constraints that force the feasibility and convergence of the target calculation layer. It is also considered the case in which there is polytopic uncertainty in the steady state model considered in the target calculation. The dynamic part of the MPC model is also considered unknown but it is assumed to be represented by one of the models of a discrete set of models. The efficiency of the methods presented here is illustrated with the simulation of a low order system. (C) 2010 Elsevier Ltd. All rights reserved.

MODELING ELECTRODIALYSIS AND A PHOTOCHEMICAL PROCESS FOR THEIR INTEGRATION IN SALINE WASTEWATER TREATMENT

Oxidation processes can be used to treat industrial wastewater containing non-biodegradable organic compounds. However, the presence of dissolved salts may inhibit or retard the treatment process. In this study, wastewater desalination by electrodialysis (ED) associated with an advanced oxidation process (photo-Fenton) was applied to an aqueous NaCl solution containing phenol. The influence of process variables on the demineralization factor was investigated for ED in pilot scale and a correlation was obtained between the phenol, salt and water fluxes with the driving force. The oxidation process was investigated in a laboratory batch reactor and a model based on artificial neural networks was developed by fitting the experimental data describing the reaction rate as a function of the input variables. With the experimental parameters of both processes, a dynamic model was developed for ED and a continuous model, using a plug flow reactor approach, for the oxidation process. Finally, the hybrid model simulation could validate different scenarios of the integrated system and can be used for process optimization.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis x Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

FtsH2 and FtsH5: two homologous subunits use different integration mechanisms leading to the same thylakoid multimeric complex

P>The Arabidopsis thylakoid FtsH protease complex is composed of FtsH1/FtsH5 (type A) and FtsH2/FtsH8 (type B) subunits. Type A and type B subunits display a high degree of sequence identity throughout their mature domains, but no similarity in their amino-terminal targeting peptide regions. In chloroplast import assays, FtsH2 and FtsH5 were imported and subsequently integrated into thylakoids by a two-step processing mechanism that resulted in an amino-proximal lumenal domain, a single transmembrane anchor, and a carboxyl proximal stromal domain. FtsH2 integration into washed thylakoids was entirely dependent on the proton gradient, whereas FtsH5 integration was dependent on NTPs, suggesting their integration by Tat and Sec pathways, respectively. This finding was corroborated by in organello competition and by antibody inhibition experiments. A series of constructs were made in order to understand the molecular basis for different integration pathways. The amino proximal domains through the transmembrane anchors were sufficient for proper integration as demonstrated with carboxyl-truncated versions of FtsH2 and FtsH5. The mature FtsH2 protein was found to be incompatible with the Sec machinery as determined with targeting peptide-swapping experiments. Incompatibility does not appear to be determined by any specific element in the FtsH2 domain as no single domain was incompatible with Sec transport. This suggests an incompatible structure that requires the intact FtsH2. That the highly homologous type A and type B subunits of the same multimeric complex use different integration pathways is a striking example of the notion that membrane insertion pathways have evolved to accommodate structural features of their respective substrates.

Biochemistry of the Envenomation Response-a Generator Theme for Interdisciplinary Integration

The understanding of complex physiological processes requires information from many different areas of knowledge. To meet this interdisciplinary scenario, the ability of integrating and articulating information is demanded. The difficulty of such approach arises because, more often than not, information is fragmented through under graduation education in Health Sciences. Shifting from a fragmentary and deep view of many topics to joining them horizontally in a global view is not a trivial task for teachers to implement. To attain that objective we proposed a course herein described Biochemistry of the envenomation response aimed at integrating previous contents of Health Sciences courses, following international recommendations of interdisciplinary model. The contents were organized by modules with increasing topic complexity. The full understanding of the envenoming pathophysiology of each module would be attained by the integration of knowledge from different disciplines. Active-learning strategy was employed focusing concept map drawing. Evaluation was obtained by a 30-item Likert-type survey answered by ninety students; 84% of the students considered that the number of relations that they were able to establish as seen by concept maps increased throughout the course. Similarly, 98% considered that both the theme and the strategy adopted in the course contributed to develop an interdisciplinary view.