MUMAL: multivariate analysis in shotgun proteomics using machine learning techniques.

BACKGROUND: The shotgun strategy (liquid chromatography coupled with tandem mass spectrometry) is widely applied for identification of proteins in complex mixtures. This method gives rise to thousands of spectra in a single run, which are interpreted by computational tools. Such tools normally use a protein database from which peptide sequences are extracted for matching with experimentally derived mass spectral data. After the database search, the correctness of obtained peptide-spectrum matches (PSMs) needs to be evaluated also by algorithms, as a manual curation of these huge datasets would be impractical. The target-decoy database strategy is largely used to perform spectrum evaluation. Nonetheless, this method has been applied without considering sensitivity, i.e., only error estimation is taken into account. A recently proposed method termed MUDE treats the target-decoy analysis as an optimization problem, where sensitivity is maximized. This method demonstrates a significant increase in the retrieved number of PSMs for a fixed error rate. However, the MUDE model is constructed in such a way that linear decision boundaries are established to separate correct from incorrect PSMs. Besides, the described heuristic for solving the optimization problem has to be executed many times to achieve a significant augmentation in sensitivity. RESULTS: Here, we propose a new method, termed MUMAL, for PSM assessment that is based on machine learning techniques. Our method can establish nonlinear decision boundaries, leading to a higher chance to retrieve more true positives. Furthermore, we need few iterations to achieve high sensitivities, strikingly shortening the running time of the whole process. Experiments show that our method achieves a considerably higher number of PSMs compared with standard tools such as MUDE, PeptideProphet, and typical target-decoy approaches. CONCLUSION: Our approach not only enhances the computational performance, and thus the turn around time of MS-based experiments in proteomics, but also improves the information content with benefits of a higher proteome coverage. This improvement, for instance, increases the chance to identify important drug targets or biomarkers for drug development or molecular diagnostics

Nature of singularity formed by the gravitational collapse in Husain space-time with electromagnetic field and scalar field

In this work, we have investigated the outcome of gravitational collapse in Husain space-time in the presence of electro-magnetic and a scalar field with potential. In order to study the nature of the singularity, global behavior of radial null geodesics have been taken into account. The nature of singularities formed has been thoroughly studied for all possible variations of the parameters. These choices of parameters has been presented in tabular form in various dimensions. It is seen that irrespective of whatever values of the parameters chosen, the collapse always results in a naked singularity in all dimensions. There is less possibility of formation of a black hole. Hence this work is a significant counterexample of the cosmic censorship hypothesis.Comment: 9 pages, 19 figure

Modelling of Optical Detection of Spin-Polarized Carrier Injection into Light-Emitting Devices

We investigate the emission of multimodal polarized light from Light Emitting Devices due to spin-aligned carriers injection. The results are derived through operator Langevin equations, which include thermal and carrier-injection fluctuations, as well as non-radiative recombination and electronic g-factor temperature dependence. We study the dynamics of the optoelectronic processes and show how the temperature-dependent g-factor and magnetic field affect the polarization degree of the emitted light. In addition, at high temperatures, thermal fluctuation reduces the efficiency of the optoelectronic detection method for measuring spin-polarization degree of carrier injection into non-magnetic semicondutors.Comment: 15 pages, 7 figures, replaced by revised version. To appear in Phys. Rev.

Serum Lipid Profile Of Broilers Fed Diets With Inclusion Of Mango Waste Meal

We evaluated the effect of including 2.5, 5.0, 7.5 and 10.0% mango waste meal (MWM) variety UBA in corn and soybean meal-based diet son the serum lipid profile of broilers. The experimental design was completely randomized, with five treatments and six replicates with 20 birds per experimental unit. Concentrations of creatinine, albumin, total protein, total cholesterol, triacylglycerols (TAG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and very-low-density lipoprotein cholesterol (VLDL-C), were evaluated at the ages of 14, 28 and 42 days, with 30 birds evaluated per age. At 14 days, there was no difference serum creatinine, total cholesterol, HDL, triacylglycerols, total proteins or VLDL-C concentrations as compared with control. Albumin concentration was the highest at the MWM inclusion levels of 5.0, 7.5 and 10.0%. At 28 days, triacylglycerols, VLDL-C and LDL-C were the lowestat 7.5% inclusion whereas at 42 days, these same variables were the lowest with addition of 10.0% meal. At 14, 28 and 42 days of age, the VLDL-C, LDL-C and total TAG contents were found to decrease at mango waste meal inclusion levels of 5.0 and 7.5% in the diets, which maybe considered an indicator of improvements in the metabolic conditions of broilers.3753327333

Bounds on the mass of the b' quark, revisited

Recent results from the DELPHI collaboration led us to review the present bounds on the b' quark mass. We use all available experimental data for m_b' > 96 GeV to constrain the b' quark mass as a function of the Cabibbo-Kobayashi-Maskawa elements in a sequential four generations model. We find that there is still room for a b' with a mass larger than 96 GeV.Comment: 9 pages and 7 figures. REVTEX

Integridade estrutural de compósitos laminados em fibra de carbono sujeitos a diferentes taxas de desgaste e absorção de água : protótipo de máquina de testes

Trabalho final de mestrado para obtenção do grau de Mestre em Engenharia MecânicaDesde sempre no panorama do ciclismo de alta competição se fizeram todos os esforços para melhorar os resultados dos atletas. Grande parte destes trabalhos está no desenvolvimento das bicicletas e seus componentes. A empresa Morphis Composites que está em fase de desenvolvimento de carretos de desviador em fibra de carbono. Estando estes componentes em material compósito laminado expostos à atmosfera, poderá estar em causa a sua integridade estrutural pois sabe-se que irão absorver água por difusão e se vão desgastar de forma diferente de carretos de outros materiais. Tudo isto poderá levar ao aumento do seu atrito na transmissão, sendo que é necessária a criação de meios para a avaliação desta temática. No presente trabalho faz-se o projecto e construção de um protótipo para medição de atrito em transmissões de bicicleta. Inclui-se uma breve pesquisa bibliográfica sobre correntes de rolos industriais e de ciclismo, o seu funcionamento e mecanismos de atrito. Além disto fez-se também uma breve pesquisa sobre os efeitos da absorção de água na fibra de carbono. Para o dimensionamento do sistema de medição procuraram-se resultados de trabalhos similares de forma a aferir as grandezas a medir e a sensibilidade necessária. O protótipo deve medir a potência conduzida à transmissão para esta rodar em vazio a uma velocidade constante que foi fixada neste caso em 60 rpm, sendo que quanto mais baixa a potencia medida menor o atrito da transmissão. O sensor usado é uma roseta colada a +45 e -45 graus no veio que fornece movimento ao sistema. O sinal é retirado do veio em rotação através de um sistema de anéis deslizantes em bronze onde se usaram escovas de grafite e de filamentos de cobre. Após a construção do protótipo fez-se a calibração estática dos sistemas de medição com bons resultados de sensibilidade e repetibilidade. Estes resultados empíricos também foram comparados com os resultados teóricos não tendo havido discrepâncias relevantes, provando a qualidade das medições de binário obtidas pelos extensómetros. No entanto, devido ao ruído introduzido no sinal pelas escovas em movimento, não foi possível obter resultados de qualidade nos ensaios dinâmicos para a potência e atrito na transmissão em rotação com o presente protótipo. No final apresentam-se sugestões para melhoria em trabalhos futuros.Ever since the beginning of high competition in cycling, that every erffort has been made to improve the results of the athletes. Much of this work is in the development of bicycles and their components. The company Morphis Composites is in the development stage of carbon fiber rear derailleur sprockets. These components made of laminated composite material are exposed to the atmosphere, thus their structural integrity may be affected because it is known that they will absorb water by diffusion and will wear differently from sprockets made of other materials, such as metals. All this can lead to the increase of its friction in the transmission, and it is necessary to create means for the evaluation of this situation. In the present work, the design and construction of a prototype for measuring friction in bicycle transmissions is done. A brief literature review on industrial roller and cycling chains, their operation and friction mechanisms is included. In addition, a brief research was also made on the effects of water absorption on carbon fiber. For the sizing of the measurement system, results of similar work were sought in order to understand the quantities to be measured and the required sensitivity. The prototype shall measure the power delivered to the transmission to idle at a constant speed which has been set at 60 rpm in this case, the lower the measured power the lower the transmission friction. The sensor used is a rosette glued to +45 and -45 degrees in a section of the main shaft before the main sprocket. The signal is drawn from the rotating shaft through a bronze slip ring system where graphite brushes and copper filaments were used. Upon prototype building the static calibration of the measurement systems was made with good results of sensitivity and repeatability. These empirical results were also compared with what would theoretically be expected and there were no relevant discrepancies, proving the quality of the torque measurements obtained by the extensometers. However, due to the noise introduced into the signal by the moving brushes, it was not possible to obtain quality results in the dynamic tests for power and friction in the rotational transmission with the present prototype. At the end, suggestions are presented for improvement in future work.N/

Electrochemical behavior of Ti/Al2O3 interfaces produced by diffusion bonding

In the field of biomedical applications a special interest exists regarding the study of the physicochemical and mechanical behaviour of materials, with special focus on the electrochemical degradation of metal/ceramic interfaces. In fact, etal/ceramic interfaces may be present in several biomedical devices, ranging from external or implantable sensors, to dental implants. Diffusion bonding represents an important technique since, in opposition to other production technologies, such as active metal brazing, avoid the possible liberation of certain chemical components harmful to health. The aim of this work is to study the electrochemical degradation of the interface formed between commercially pure Ti and Al2O3 produced by diffusion bonding, in contact with a physiological solution. The present approach included the evaluation of the contribution of individual and pairs of interfacial layers on the global degradation processes. For this propose d.c. electrochemical techniques were used to monitor the open-circuit potential, and to perform potentiodynamic polarization and galvanic corrosion evaluation. Also, electrochemical impedance spectroscopy was used as a complementary technique of the corrosion behaviour of the interface. Chemical composition and morphology of samples and corrosion products were evaluated by SEM and EDS analysis. According to experimental results, two principal reaction layers were formed in the interface: TiAl and Ti3Al. The TiAl layer appears to be the responsible for the strong increase in corrosion rate of the interface.Fundação para a Ciência e Tecnologia -POCTI/CTM/33384/2000; SFRH/BPD/ 5518/2001

Field theoretic approach to metastability in the contact process

A quantum field theoretic formulation of the dynamics of the Contact Process on a regular graph of degree z is introduced. A perturbative calculation in powers of 1/z of the effective potential for the density of particles phi(t) and an instantonic field psi(t) emerging from the quantum formalism is performed. Corrections to the mean-field distribution of densities of particles in the out-of-equilibrium stationary state are derived in powers of 1/z. Results for typical (e.g. average density) and rare fluctuation (e.g. lifetime of the metastable state) properties are in very good agreement with numerical simulations carried out on D-dimensional hypercubic (z=2D) and Cayley lattices.Comment: Final published version; 20 pages, 5 figure

Alpha-decay branching ratios of near-threshold states in 19Ne and the astrophysical rate of 15O(alpha,gamma)19Ne

The 15O(alpha,gamma)19Ne reaction is one of two routes for breakout from the hot CNO cycles into the rp process in accreting neutron stars. Its astrophysical rate depends critically on the decay properties of excited states in 19Ne lying just above the 15O + alpha threshold. We have measured the alpha-decay branching ratios for these states using the p(21Ne,t)19Ne reaction at 43 MeV/u. Combining our measurements with previous determinations of the radiative widths of these states, we conclude that no significant breakout from the hot CNO cycle into the rp process in novae is possible via 15O(alpha,gamma)19Ne, assuming current models accurately represent their temperature and density conditions