Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Design And Synthesis Of N-acylated Aza-goniothalamin Derivatives And Evaluation Of Their In Vitro And In Vivo Antitumor Activity.

Herein we describe the synthesis of a focused library of compounds based on the structure of goniothalamin (1) and the evaluation of the potential antitumor activity of the compounds. N-Acylation of aza-goniothalamin (2) restored the in vitro antiproliferative activity of this family of compounds. 1-(E)-But-2-enoyl-6-styryl-5,6-dihydropyridin-2(1H)-one (18) displayed enhanced antiproliferative activity. Both goniothalamin (1) and derivative 18 led to reactive oxygen species generation in PC-3 cells, which was probably a signal for caspase-dependent apoptosis. Treatment with derivative 18 promoted Annexin V/7-aminoactinomycin D double staining, which indicated apoptosis, and also led to G2 /M cell-cycle arrest. In vivo studies in Ehrlich ascitic and solid tumor models confirmed the antitumor activity of goniothalamin (1), without signs of toxicity. However, derivative 18 exhibited an unexpectedly lower in vivo antitumor activity, despite the treatments being administered at the same site of inoculation. Contrary to its in vitro profile, aza-goniothalamin (2) inhibited Ehrlich tumor growth, both on the ascitic and solid forms. Our findings highlight the importance of in vivo studies in the search for new candidates for cancer treatment.

Equity Of Access To Pap Smears: Population-based Study In Campinas, São Paulo, Brazil.

To determine the prevalence of the Papanicolaou exam among women aged 20 to 59 years in the city of Campinas (state of São Paulo, Brazil) and to analyze associations between this test and affiliation to private health insurance plans as well as socioeconomic/demographic variables and health-related behavior. To do so, a population-based, cross-sectional study was carried out. Statistical analyses took the study design into account. Despite the significant socioeconomic differences between women with and without private health plans, no differences between these groups were found regarding having been submitted to the Papanicolaou test. In fact no differences were found as to socioeconomic and health variables analyzed. Among all variables analyzed, only marital status was significantly associated with having undergone the test. The Brazilian public health system accounted for 55.7% of the exams. The present findings indicate social equity in the city of Campinas regarding the preventive exam for cervical cancer in the age group studied.

The ichthyofauna of upper rio Capivari: defining conservation strategies based on the composition and distribution of fish species

Although the rio Capivari basin is recognized as an area of great importance for the ichthyofauna, it lacks virtually every basic requirement for the definition of appropriate conservation strategies, since not even its species composition is known. The objective of this work is to determine the composition and distribution of fish species in the upper rio Capivari basin, relating them to the local physical features, and to evaluate the effectiveness of proposed conservations units, delimited based on areas of native vegetation remains, on the conservation of local ichthyofauna. During 2007, 50 different watercourses were sampled with gillnets, cast nets and kick nets. A total of 1308 individuals belonging to 41 species were captured. Degree of conservation, altitude and width were the parameters that best explained fish species richness. Considering the recently proposed boundaries for potential conservation units in the region only 15 or 20 out of 41 species would be found in the State Park and Environmental Protection Area respectively. In practice, the proposed conservation units would not be effective tools for fish conservation, since it would be located in mountainous areas of high altitude, of headwaters streams and where few species are found. In such context, the conservation of specific stretches of larger rivers is critical.

Analysis of the effects of conical indentation variables on the indentation response of elastic-plastic materials through factorial design of experiment

In this work, the effects of conical indentation variables on the load-depth indentation curves were analyzed using finite element modeling and dimensional analysis. A factorial design 2(6) was used with the aim of quantifying the effects of the mechanical properties of the indented material and of the indenter geometry. Analysis was based on the input variables Y/E, R/h(max), n, theta, E, and h(max). The dimensional variables E and h(max) were used such that each value of dimensionless Y/E was obtained with two different values of E and each value of dimensionless R/h(max) was obtained with two different h(max) values. A set of dimensionless functions was defined to analyze the effect of the input variables: Pi(1) = P(1)/Eh(2), Pi(2) = h(c)/h, Pi(3) = H/Y, Pi(4) = S/Eh(max), Pi(6) = h(max)/h(f) and Pi(7) = W(P)/W(T). These six functions were found to depend only on the dimensionless variables studied (Y/E, R/h(max), n, theta). Another dimension less function, Pi(5) = beta, was not well defined for most of the dimensionless variables and the only variable that provided a significant effect on beta was theta. However, beta showed a strong dependence on the fraction of the data selected to fit the unloading curve, which means that beta is especially Susceptible to the error in the Calculation of the initial unloading slope.

The International LAM Registry: A Component of an Innovative Web-Based Clinician, Researcher, and Patient-Driven Rare Disease Research Platform

Background: A relative friability to capture a sufficiently large patient population in any one geographic location has traditionally limited research into rare diseases. Methods and Results: Clinicians interested in the rare disease lymphangioleiomyomatosis (LAM) have worked with the LAM Treatment Alliance, the MIT Media Lab, and Clozure Associates to cooperate in the design of a state-of-the-art data coordination platform that can be used for clinical trials and other research focused on the global LAM patient population. This platform is a component of a set of web-based resources, including a patient self-report data portal, aimed at accelerating research in rare diseases in a rigorous fashion. Conclusions: Collaboration between clinicians, researchers, advocacy groups, and patients can create essential community resource infrastructure to accelerate rare disease research. The International LAM Registry is an example of such an effort.

Silica-based cationic bilayers as immunoadjuvants

Background: Silica particles cationized by dioctadecyldimethylammonium bromide (DODAB) bilayer were previously described. This work shows the efficiency of these particulates for antigen adsorption and presentation to the immune system and proves the concept that silica-based cationic bilayers exhibit better performance than alum regarding colloid stability and cellular immune responses for vaccine design. Results: Firstly, the silica/DODAB assembly was characterized at 1 mM NaCl, pH 6.3 or 5 mM Tris. HCl, pH 7.4 and 0.1 mg/ml silica over a range of DODAB concentrations (0.001-1 mM) by means of dynamic light scattering for particle sizing and zeta-potential analysis. 0.05 mM DODAB is enough to produce cationic bilayer-covered particles with good colloid stability. Secondly, conditions for maximal adsorption of bovine serum albumin (BSA) or a recombinant, heat-shock protein from Mycobacterium leprae (18 kDa-hsp) onto DODAB-covered or onto bare silica were determined. At maximal antigen adsorption, cellular immune responses in vivo from delayed-type hypersensitivity reactions determined by foot-pad swelling tests (DTH) and cytokines analysis evidenced the superior performance of the silica/DODAB adjuvant as compared to alum or antigens alone whereas humoral response from IgG in serum was equal to the one elicited by alum as adjuvant. Conclusion: Cationized silica is a biocompatible, inexpensive, easily prepared and possibly general immunoadjuvant for antigen presentation which displays higher colloid stability than alum, better performance regarding cellular immune responses and employs very low, micromolar doses of cationic and toxic synthetic lipid.

A nearly optimum linear-phase digital FIR filters design

A new simple method to design linear-phase finite impulse response (FIR) digital filters, based on the steepest-descent optimization method, is presented in this paper. Starting from the specifications of the desired frequency response and a maximum approximation error a nearly optimum digital filter is obtained. Tests have shown that this method is alternative to other traditional ones such as Frequency Sampling and Parks-McClellan, mainly when other than brick wall frequency response is required as a desired frequency response. (C) 2011 Elsevier Inc. All rights reserved.

Embedded DSP-Based Compact Fuzzy System and Its Application for Induction-Motor V/f Speed Control

This paper presents a compact embedded fuzzy system for three-phase induction-motor scalar speed control. The control strategy consists in keeping constant the voltage-frequency ratio of the induction-motor supply source. A fuzzy-control system is built on a digital signal processor, which uses speed error and speed-error variation to change both the fundamental voltage amplitude and frequency of a sinusoidal pulsewidth modulation inverter. An alternative optimized method for embedded fuzzy-system design is also proposed. The controller performance, in relation to reference and load-torque variations, is evaluated by experimental results. A comparative analysis with conventional proportional-integral controller is also achieved.

Fuzzy pole placement based on piecewise Lyapunov functions

This paper presents a controller design method for fuzzy dynamic systems based on piecewise Lyapunov functions with constraints on the closed-loop pole location. The main idea is to use switched controllers to locate the poles of the system to obtain a satisfactory transient response. It is shown that the global fuzzy system satisfies the requirements for the design and that the control law can be obtained by solving a set of linear matrix inequalities, which can be efficiently solved with commercially available softwares. An example is given to illustrate the application of the proposed method. Copyright (C) 2009 John Wiley & Sons, Ltd.

Power imbalance application region method for distributed synchronous generator anti-islanding protection design and evaluation

This paper presents a novel graphical approach to adjust and evaluate frequency-based relays employed in anti-islanding protection schemes of distributed synchronous generators, in order to meet the anti-islanding and abnormal frequency variation requirements, simultaneously. The proposed method defines a region in the power mismatch space, inside which the relay non-detection zone should be located, if the above-mentioned requirements must be met. Such region is called power imbalance application region. Results show that this method can help protection engineers to adjust frequency-based relays to improve the anti-islanding capability and to minimize false operation occurrences, keeping the abnormal frequency variation utility requirements satisfied. Moreover, the proposed method can be employed to coordinate different types of frequency-based relays, aiming at improving overall performance of the distributed generator frequency protection scheme. (C) 2011 Elsevier B.V. All rights reserved.

Automatic tuning method for the design of supplementary damping controllers for flexible alternating current transmission system devices

The design of supplementary damping controllers to mitigate the effects of electromechanical oscillations in power systems is a highly complex and time-consuming process, which requires a significant amount of knowledge from the part of the designer. In this study, the authors propose an automatic technique that takes the burden of tuning the controller parameters away from the power engineer and places it on the computer. Unlike other approaches that do the same based on robust control theories or evolutionary computing techniques, our proposed procedure uses an optimisation algorithm that works over a formulation of the classical tuning problem in terms of bilinear matrix inequalities. Using this formulation, it is possible to apply linear matrix inequality solvers to find a solution to the tuning problem via an iterative process, with the advantage that these solvers are widely available and have well-known convergence properties. The proposed algorithm is applied to tune the parameters of supplementary controllers for thyristor controlled series capacitors placed in the New England/New York benchmark test system, aiming at the improvement of the damping factor of inter-area modes, under several different operating conditions. The results of the linear analysis are validated by non-linear simulation and demonstrate the effectiveness of the proposed procedure.

A novel subwavelength plasmon-polariton optical filter based on tilted coupled structures

This work proposes a completely new approach for the design of resonant structures aiming at wavelength-filtering applications. The structure consists of a subwavelength metal-insulator-metal (MIM) waveguide presenting tilted coupled structures transversely arranged in the midpoint between the input and output ports. The cavity-like response of this device has shown that this concept can be particularly attractive for optical filter design for telecom applications. The extra degree of freedom provided by the tilting of the cavity has proved to be not only very effective on improving the quality factor of these structures, but also to be an elegant way of extending the range of applications for tuning multiple wavelengths, if necessary.

Efficiency and feasibility of product disassembly: A case-based study

The productivity associated with commonly available disassembly methods today seldomly makes disassembly the preferred end-of-life solution for massive take back product streams. Systematic reuse of parts or components, or recycling of pure material fractions are often not achievable in an economically sustainable way. In this paper a case-based review of current disassembly practices is used to analyse the factors influencing disassembly feasibility. Data mining techniques were used to identify major factors influencing the profitability of disassembly operations. Case characteristics such as involvement of the product manufacturer in the end-of-life treatment and continuous ownership are some of the important dimensions. Economic models demonstrate that the efficiency of disassembly operations should be increased an order of magnitude to assure the competitiveness of ecologically preferred, disassembly oriented end-of-life scenarios for large waste of electric and electronic equipment (WEEE) streams. Technological means available to increase the productivity of the disassembly operations are summarized. Automated disassembly techniques can contribute to the robustness of the process, but do not allow to overcome the efficiency gap if not combined with appropriate product design measures. Innovative, reversible joints, collectively activated by external trigger signals, form a promising approach to low cost, mass disassembly in this context. A short overview of the state-of-the-art in the development of such self-disassembling joints is included. (c) 2008 CIRP.

A simulation-based evolutionary multiobjective approach to manufacturing cell formation

The purpose of this paper is to propose a multiobjective optimization approach for solving the manufacturing cell formation problem, explicitly considering the performance of this said manufacturing system. Cells are formed so as to simultaneously minimize three conflicting objectives, namely, the level of the work-in-process, the intercell moves and the total machinery investment. A genetic algorithm performs a search in the design space, in order to approximate to the Pareto optimal set. The values of the objectives for each candidate solution in a population are assigned by running a discrete-event simulation, in which the model is automatically generated according to the number of machines and their distribution among cells implied by a particular solution. The potential of this approach is evaluated via its application to an illustrative example, and a case from the relevant literature. The obtained results are analyzed and reviewed. Therefore, it is concluded that this approach is capable of generating a set of alternative manufacturing cell configurations considering the optimization of multiple performance measures, greatly improving the decision making process involved in planning and designing cellular systems. (C) 2010 Elsevier Ltd. All rights reserved.