Statistical Methods for Conservation and Alignment Quality in Proteins

Construction of multiple sequence alignments is a fundamental task in Bioinformatics. Multiple sequence alignments are used as a prerequisite in many Bioinformatics methods, and subsequently the quality of such methods can be critically dependent on the quality of the alignment. However, automatic construction of a multiple sequence alignment for a set of remotely related sequences does not always provide biologically relevant alignments.Therefore, there is a need for an objective approach for evaluating the quality of automatically aligned sequences. The profile hidden Markov model is a powerful approach in comparative genomics. In the profile hidden Markov model, the symbol probabilities are estimated at each conserved alignment position. This can increase the dimension of parameter space and cause an overfitting problem. These two research problems are both related to conservation. We have developed statistical measures for quantifying the conservation of multiple sequence alignments. Two types of methods are considered, those identifying conserved residues in an alignment position, and those calculating positional conservation scores. The positional conservation score was exploited in a statistical prediction model for assessing the quality of multiple sequence alignments. The residue conservation score was used as part of the emission probability estimation method proposed for profile hidden Markov models. The results of the predicted alignment quality score highly correlated with the correct alignment quality scores, indicating that our method is reliable for assessing the quality of any multiple sequence alignment. The comparison of the emission probability estimation method with the maximum likelihood method showed that the number of estimated parameters in the model was dramatically decreased, while the same level of accuracy was maintained. To conclude, we have shown that conservation can be successfully used in the statistical model for alignment quality assessment and in the estimation of emission probabilities in the profile hidden Markov models.

Determinação da estrutura molecular do ciclooctano por métodos ab initio e difração de elétrons na fase gasosa

The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase and ab initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions.

Estudo do estado fundamental de aglomerados de silício via redes neurais

We introduce a global optimization method based on the cooperation between an Artificial Neural Net (ANN) and Genetic Algorithm (GA). We have used ANN to select the initial population for the GA. We have tested the new method to predict the ground-state geometry of silicon clusters. We have described the clusters as a piling of plane structures. We have trained three ANN architectures and compared their results with those of pure GA. ANN strongly reduces the total computational time. For Si10, it gained a factor of 5 in search speed. This method can be easily extended to other optimization problems.

Energy efficiency parameters in variable speed drives

The main purpose of this thesis is to measure and evaluate how accurately the current energy saving calculation in ABB’s new variable speed drive ACS850 works. The main topic of this thesis is energy-efficiency parameters. At the beginning of this thesis centrifugal pump, squirrel cage motor and variable speed drive, including some equations related to them, are being introduced. Also methods of throttling control and variable speed drive control of centrifugal pumps are being introduced. These subjects are introduced because the energy saving calculation in ACS850 is related to the centrifugal pumps usually driven by squirrel cage motors. The theory also includes short section about specific energy of pumping. Before measurements the current energy saving calculation of ACS850 is being introduced and analyzed. The measurements part includes introduction of measuring equipment, measurement results, summary and analysis of the measurements. At the end of this thesis a proposal for an improvement to the current energy saving calculation is being introduced and few proposals are made for new energy-efficiency parameters, which could be added to variable speed drives. At the end are also thoughts

On the effects of welding parameters on weld quality of plasma arc keyhole welding of structural steels

The possibility and the usefulness of applying plasma keyhole welding to structural steels with different compositions and material thicknesses, and in various welding positions has been examinated. Single pass butt welding with I groove in flat, horizontal vertical and vertical positions and root welding with V , Y and U grooves of thick plate material in flat position have been studied and the welds with high quality has been obtained. The technological conditions for successful welding are presented. The single and interactive effects of welding parameters on weld quality, especially on surface weld defects, geometrical form errors, internal defects and mechanical properties (strength, ductility, impact toughness, hardness and bendability) of weld joint, are presented. Welding parameter combinations providing the best quality welds are also presented.

Swarm Intelligent Selection and Optimization of Machining System Parameters for Microchannel Fabrication in Medical Devices

Current technology trends in medical device industry calls for fabrication of massive arrays of microfeatures such as microchannels on to nonsilicon material substrates with high accuracy, superior precision, and high throughput. Microchannels are typical features used in medical devices for medication dosing into the human body, analyzing DNA arrays or cell cultures. In this study, the capabilities of machining systems for micro-end milling have been evaluated by conducting experiments, regression modeling, and response surface methodology. In machining experiments by using micromilling, arrays of microchannels are fabricated on aluminium and titanium plates, and the feature size and accuracy (width and depth) and surface roughness are measured. Multicriteria decision making for material and process parameters selection for desired accuracy is investigated by using particle swarm optimization (PSO) method, which is an evolutionary computation method inspired by genetic algorithms (GA). Appropriate regression models are utilized within the PSO and optimum selection of micromilling parameters; microchannel feature accuracy and surface roughness are performed. An analysis for optimal micromachining parameters in decision variable space is also conducted. This study demonstrates the advantages of evolutionary computing algorithms in micromilling decision making and process optimization investigations and can be expanded to other applications

The effects of real time control of welding parameters on weld quality in plasma arc keyhole welding

Joints intended for welding frequently show variations in geometry and position, for which it is unfortunately not possible to apply a single set of operating parameters to ensure constant quality. The cause of this difficulty lies in a number of factors, including inaccurate joint preparation and joint fit up, tack welds, as well as thermal distortion of the workpiece. In plasma arc keyhole welding of butt joints, deviations in the gap width may cause weld defects such as an incomplete weld bead, excessive penetration and burn through. Manual adjustment of welding parameters to compensate for variations in the gap width is very difficult, and unsatisfactory weld quality is often obtained. In this study a control system for plasma arc keyhole welding has been developed and used to study the effects of the real time control of welding parameters on gap tolerance during welding of austenitic stainless steel AISI 304L. The welding tests demonstrated the beneficial effect of real time control on weld quality. Compared with welding using constant parameters, the maximum tolerable gap width with an acceptable weld quality was 47% higher when using the real time controlled parameters for a plate thickness of 5 mm. In addition, burn through occurred with significantly larger gap widths when parameters were controlled in real time. Increased gap tolerance enables joints to be prepared and fit up less accurately, saving time and preparation costs for welding. In addition to the control system, a novel technique for back face monitoring is described in this study. The test results showed that the technique could be successfully applied for penetration monitoring when welding non magnetic materials. The results also imply that it is possible to measure the dimensions of the plasma efflux or weld root, and use this information in a feedback control system and, thus, maintain the required weld quality.

Photometric and Halpha observations of LSI+61·303: detection of a 26 day V and JHK band modulation

We present new optical and infrared photometric observations and high resolution H α spectra of the periodic radio star LSI+61◦303. The optical photometric data set covers the time interval 1985-1993 and amounts to about a hundred nights. A period of ∼26 days is found in the V band. The infrared data also present evidence for a similar periodicity, but with higher amplitude of variation ((0.m 2). The spectroscopic observations include 16 intermediate and high dispersion spectra of LSI+61◦303 collected between January 1989 and February 1993. The H α emission line profile and its variations are analyzed. Several emission line parameters -- among them the H α EW and the width of the H α red hump -- change strongly at or close to radio maximum, and may exhibit periodic variability. We also observe a significant change in the peak separation. The H α profile of LSI+61◦303 does not seem peculiar for a Be star. However, several of the observed variations of the H α profile can probably be associated with the presence of the compact, secondary star.

Physicochemical parameters of Amazon Melipona honey

Stingless bees produce a honey that is different from the Apis honey in terms of composition. There aren't enough data to establish quality control parameters for this product, mainly due to lack of research results. The aim of this work is to evaluate some physicochemical parameters that can be used for the characterization and for the quality control of the Meliponinae honey. Four different samples were collected in the Amazon region of Brazil in 2004 (Melipona compressipes manaoense bee and Melipona seminigra merribae bee). Honey analyses were performed as described by the official methods. The mean results were: moisture (30.13%), pH (3.65), acidity (24.57 mEq/kg), water activity (0.75), fructose (31.91%), glucose (29.30%) and sucrose (0.19%). These results reinforce the need for a specific regulation for stingless bee honey. This will only be feasible when enough data is available to establish upper and lower limits for the physicochemical parameters used for quality control.

Leaving the Dark ages with AMIGA

We present an Analytic Model of Intergalactic-medium and GAlaxy (AMIGA) evolution since the dark ages. AMIGA is in the spirit of the popular semi-analytic models of galaxy formation, although it does not use halo merger trees but interpolates halo properties in grids that are progressively built. This strategy is less memory-demanding and allows one to start modeling at sufficiently high redshifts and low halo masses to have trivial boundary conditions. The number of free parameters is minimized by making a causal connection between physical processes usually treated as independent of each other, which leads to more reliable predictions. However, the strongest points of AMIGA are the following: (1) the inclusion of molecular cooling and metal-poor, population III (Pop III) stars with the most dramatic feedback and (2) accurate follow up of the temperature and volume filling factor of neutral, singly ionized, and doubly ionized regions, taking into account the distinct halo mass functions in those environments. We find the following general results. Massive Pop III stars determine the intergalactic medium metallicity and temperature, and the growth of spheroids and disks is self-regulated by that of massive black holes (MBHs) developed from the remnants of those stars. However, the properties of normal galaxies and active galactic nuclei appear to be quite insensitive to Pop III star properties due to the much higher yield of ordinary stars compared to Pop III stars and the dramatic growth of MBHs when normal galaxies begin to develop, which cause the memory loss of the initial conditions.

Usando um Jogo Digital na Sala de Aula do Ensino Fundamental: Visão dos Professores

A digital game was created as a resource for cognitive learning and afterwards it was used in primary schools in order to survey its active users. The methods used to recollect data were observation, in-depth interviews and focus groups. The main target of this study is to collect points of view of different primary school teachers. Conclusions show us how the group of study members perceive the use of digital games in the classroom.

Disseny i muntatge d'un mòdul d'entrades digitals per comunicació modbus

Actualment l’exigència i la competitivitat del mercat, obliguen les industries a modernitzar-se i automatitzar tots els seus processos productius. En aquests processos les dades i paràmetres de control són dades fonamentals a verificar. Amb aquest treball final de carrera, es pretén realitzar un mòdul d’entrades digitals, per tal de gestionar les dades rebudes d’un procés automatitzat. L’objectiu d’aquest TFC ha estat dissenyar un mòdul d’entrades digitals capaç de gestionar dades de qualsevol tipus de procés automatitzat i transmetre-les a un mestremitjançant un bus de comunicació Modbus. El projecte però, s’ha centrat en el cas específic d’un procés automatitzat per al tractament de la fusta. El desenvolupament d’aquest sistema, comprèn el disseny del circuit, la realització de la placa, el software de lectura de dades i la implementació del protocol Modbus. Tot el mòdul d’entrades està controlat per un microcontrolador PIC 18F4520. El disseny és un sistema multiplataforma per tal d’adaptar-se a qualsevol procés automàtic i algunes de les seves característiques més rellevants són: entrades aïllades multitensió, control de fugues, sortides a relé, i memòria externa de dades, entre altres. Com a conclusions cal dir que s’han assolit els objectius proposats amb èxit. S’ha aconseguit un disseny robust, fiable, polivalent i altament competitiu en el mercat. A nivell acadèmic, s’han ampliat els coneixements en el camp del disseny i de la programació.

Inversion and assimilation methods with applications in geophysical remote sensing

Stratospheric ozone can be measured accurately using a limb scatter remote sensing technique at the UV-visible spectral region of solar light. The advantages of this technique includes a good vertical resolution and a good daytime coverage of the measurements. In addition to ozone, UV-visible limb scatter measurements contain information about NO2, NO3, OClO, BrO and aerosols. There are currently several satellite instruments continuously scanning the atmosphere and measuring the UVvisible region of the spectrum, e.g., the Optical Spectrograph and Infrared Imager System (OSIRIS) launched on the Odin satellite in February 2001, and the Scanning Imaging Absorption SpectroMeter for Atmospheric CartograpHY (SCIAMACHY) launched on Envisat in March 2002. Envisat also carries the Global Ozone Monitoring by Occultation of Stars (GOMOS) instrument, which also measures limb-scattered sunlight under bright limb occultation conditions. These conditions occur during daytime occultation measurements. The global coverage of the satellite measurements is far better than any other ozone measurement technique, but still the measurements are sparse in the spatial domain. Measurements are also repeated relatively rarely over a certain area, and the composition of the Earth’s atmosphere changes dynamically. Assimilation methods are therefore needed in order to combine the information of the measurements with the atmospheric model. In recent years, the focus of assimilation algorithm research has turned towards filtering methods. The traditional Extended Kalman filter (EKF) method takes into account not only the uncertainty of the measurements, but also the uncertainty of the evolution model of the system. However, the computational cost of full blown EKF increases rapidly as the number of the model parameters increases. Therefore the EKF method cannot be applied directly to the stratospheric ozone assimilation problem. The work in this thesis is devoted to the development of inversion methods for satellite instruments and the development of assimilation methods used with atmospheric models.

ARSÊNIO E ARROZ: TOXICIDADE, METABOLISMO E SEGURANÇA ALIMENTAR

Arsenic is considered a semimetal, and its wide distribution in the Earth's crust in different chemical forms, including organic and inorganic species, has a great deal of influence on the mechanisms of toxicity. Exposure to arsenic can be either through occupational practice (use of pesticides) or by the consumption of water and food containing the element. Rice is considered a fundamental constituent of the basic diet of Brazilians and is usually cultivated in flooded conditions. Such a plantation system results in an increased amount of As in the soil and hence a greater accumulation of As in the plant, which is highlighted by the inorganic species' classification as highly toxic. Besides the use of mitigation techniques to reduce the toxicological risk, monitoring the concentration of As and its chemical species in rice and rice products is required through the establishment of legislation in the area. Thus, some world organizations are conducting improved research to determine and establish acceptable concentrations of As and its chemical species in rice, e. g., in 2012, FDA researchers described a chemical speciation methodology for As in rice and rice products. Hence, the application of existing chemical speciation methods and the establishment of parameters for ensuring food security and exposure risk assessment deserve particular consideration.