Refactoring object-z specifications

Object-Z offers an object-oriented means for structuring formal specifications. We investigate the application of refactoring rules to add and remove structure from such specifications to forge object-oriented designs. This allows us to tractably move from an abstract functional description of a system toward a lower-level design suitable for implementation on an object-oriented platform.

Predicting structural disruption of proteins caused by crossover

We present a machine learning model that predicts a structural disruption score from a protein’s primary structure. SCHEMA was introduced by Frances Arnold and colleagues as a method for determining putative recombination sites of a protein on the basis of the full (PDB) description of its structure. The present method provides an alternative to SCHEMA that is able to determine the same score from sequence data only. Circumventing the need for resolving the full structure enables the exploration of yet unresolved and even hypothetical sequences for protein design efforts. Deriving the SCHEMA score from a primary structure is achieved using a two step approach: first predicting a secondary structure from the sequence and then predicting the SCHEMA score from the predicted secondary structure. The correlation coefficient for the prediction is 0.88 and indicates the feasibility of replacing SCHEMA with little loss of precision. ©2005 IEEE

EAD: O POLO DE APOIO PRESENCIAL COMO ESPAÇO ORGANIZADOR DA AÇÃO EDUCATIVO-CULTURAL

Esta pesquisa estuda a organização e estruturação de três polos de apoio presencial ligados a modalidade a distância, bem como os processos de gestão e autonomia no contexto em que atuam. Trata-se, portanto, de dois momentos de análise, considerando que o primeiro se relaciona a um estudo descritivo-exploratório no que se refere a organização e estruturação dos polos, a partir de diretrizes preestabelecidas e da discussão sobre a realidade cultural e, ao mesmo tempo contingencial existente neste espaço; o segundo, relacionado à utilização da técnica da entrevista para a análise do processo de gestão e autonomia existente nos polos pesquisados. Para a aplicação da pesquisa, foram realizadas visitas aos polos de apoio presencial (dois localizados no Estado de São Paulo e um no Estado do Paraná) e entrevistas com seus coordenadores, sendo importante destacar que dois destes polos estão ligados à realidade privada e um deles à realidade pública. Respectivamente, tais análises e entrevistas indicaram que apesar das diretrizes preestabelecidas, os polos pesquisados possuem um modelo contingencial e, portanto, cultural de adaptação à realidade em que se instalam; sendo que no caso das entrevistas semiestruturadas e, respectivamente do processo de gestão, existe uma proposta clara por parte dos coordenadores no exercício em se fazer EAD, compreendendo assim, uma gestão voltada a adequações e readequações diante de um contexto em constante desenvolvimento. No que se refere ao processo de autonomia, os fatores que merecem atenção estão diretamente relacionados à compreensão dos sujeitos sobre a existência de trâmites não negociáveis, respectivamente relacionados às bases legais que regulamentam a existência dos polos de apoio presencial, contudo, estabelecidos estes parâmetros, a autonomia se determina pela tomada de decisão deste gestor diante da realidade em que se instala.

The oxidation behaviour of sintered iron

The oxidation behaviour of porous, sintered iron was studied by thermo-gravimetric analysis (TGA), at temperatures between 300oC and 700oC, in a flowing atmosphere of 20% O2/80% N2. Samples for TGA tests were compacted from pure iron powder, at 150MPa to 550MPa, and vacuum sintered at 1120oC. The mass gain of samples during oxidation was recorded continuously for a period of 24 hours. It was found that the oxidation mass gain of PM samples depended on the permeability of the pore structure and the temperature. At low temperatures, the oxidising gas was able to permeate through the pore structure, causing the oxidation of a large active surface area. At high temperatures the active surface area was smaller, because oxygen diffusing into the pore structure, from the external atmosphere, was adsorbed by pore surfaces close to the external surface of the compact. Although the weight of the external oxide scale on compacts increased with increasing oxidation temperature, the absence of oxide in the core porosity in compacts oxidised at higher temperatures resulted in smaller mass gains than were observed for compacts oxidised at lower temperatures. The heat generated by the oxidation of the large active surface areas of porous samples was studied by thermo-calorimetric analysis (TCA). It was determined that this phenomenon could raise the core temperature of samples significantly above the ambient furnace temperature, and affecting the morphology of the oxide scale formed. The effects (on oxidation behaviour at 500oC) of small, elemental alloy additions of Al, Cu, P and Si to pure iron powder were studied. It was found that elements that promote pore rounding during sintering caused a significant reduction in the mass gain rate of the PM alloys, compared to the PM pure iron. The oxidation resistance due to these elements prevented pore closure by oxide growth, so that the active surface area of these PM alloys remained high. The PM alloys were also studied by thermo-mechanical analysis (TMA, dilatometry), to determine their dimensional stability during sintering and subsequent elevated temperature service. The oxidation experiment was augmented with optical and electron microscopy, and X-ray analysis of alloy and scale compositions.

Design and synthesis of potential antimicrobial agents

Tuberculosis is one of the most devastating diseases in the world primarily due to several decades of neglect and an emergence of multidrug-resitance strains (MDR) of M. tuberculosis together with the increased incidence of disseminated infections produced by other mycobacterium in AIDS patients. This has prompted the search for new antimycobacterial drugs. A series of pyridine-2-, pyridine-3-, pyridine-4-, pyrazine and quinoline-2-carboxamidrazone derivatives and new classes of carboxamidrazone were prepared in an automated fashion and by traditional synthesis. Over nine hundred synthesized compounds were screened for their anti mycobacterial activity against M. fortutium (NGTG 10394) as a surrogate for M. tuberculosis. The new classes of amidrazones were also screened against tuberculosis H37 Rv and antimicrobial activities against various bacteria. Fifteen tested compounds were found to provide 90-100% inhibition of mycobacterium growth of M. tuberculosis H37 Rv in the primary screen at 6.25 μg mL-1. The most active compound in the carboxamidrazone amide series had an MIG value of 0.1-2 μg mL-1 against M. fortutium. The enzyme dihydrofolate reductase (DHFR) has been a drug-design target for decades. Blocking of the enzymatic activity of DHFR is a key element in the treatment of many diseases, including cancer, bacterial and protozoal infection. The x-ray structure of DHFR from M. tuberculosis and human DHFR were found to have differences in substrate binding site. The presence of glycerol molecule in the Xray structure from M. tuberculosis DHFR provided opportunity to design new antifolates. The new antifolates described herein were designed to retain the pharmcophore of pyrimethamine (2,4- diamino-5(4-chlorophenyl)-6-ethylpyrimidine), but encompassing a range of polar groups that might interact with the M. tuberculosis DHFR glycerol binding pockets. Finally, the research described in this thesis contributes to the preparation of molecularly imprinted polymers for the recognition of 2,4-diaminopyrimidine for the binding the target. The formation of hydrogen bonding between the model functional monomer 5-(4-tert-butyl-benzylidene)-pyrimidine-2,4,6-trione and 2,4-diaminopyrimidine in the pre-polymerisation stage was verified by 1H-NMR studies. Having proven that 2,4-diaminopyrimidine interacts strongly with the model 5-(4-tert-butylbenzylidene)- pyrimidine-2,4,6-trione, 2,4-diaminopyrimidine-imprinted polymers were prepared using a novel cyclobarbital derived functional monomer, acrylic acid 4-(2,4,6-trioxo-tetrahydro-pyrimidin-5- ylidenemethyl)phenyl ester, capable of multiple hydrogen bond formation with the 2,4- diaminopyrimidine. The recognition property of the respective polymers toward the template and other test compounds was evaluated by fluorescence. The results demonstrate that the polymers showed dose dependent enhancement of fluorescence emissions. In addition, the results also indicate that synthesized MIPs have higher 2,4-diaminopyrimidine binding ability as compared with corresponding non-imprinting polymers.

Structural optimization

The non-linear programming algorithms for the minimum weight design of structural frames are presented in this thesis. The first, which is applied to rigidly jointed and pin jointed plane frames subject to deflexion constraints, consists of a search in a feasible design space. Successive trial designs are developed so that the feasibility and the optimality of the designs are improved simultaneously. It is found that this method is restricted lo the design of structures with few unknown variables. The second non-linear programming algorithm is presented .in a general form. This consists of two types of search, one improving feasibility and the other optimality. The method speeds up the 'feasible direction' approach by obtaining a constant weight direction vector that is influenced by dominating constraints. For pin jointed plane and space frames this method is used to obtain a 'minimum weight' design which satisfies restrictions on stresses and deflexions. The matrix force method enables the design requirements to be expressed in a general form and the design problem is automatically formulated within the computer. Examples are given to explain the method and the design criteria are extended to include member buckling. Fundamental theorems are proposed and proved to confirm that structures are inter-related. These theorems are applicable to linear elastic structures and facilitate the prediction of the behaviour of one structure from the results of analysing another, more general, or related structure. It becomes possible to evaluate the significance of each member in the behaviour of a structure and the problem of minimum weight design is extended to include shape. A method is proposed to design structures of optimum shape with stress and deflexion limitations. Finally a detailed investigation is carried out into the design of structures to study the factors that influence their shape.

Simulation of surface EMG for the analysis of muscle activity during whole body vibratory stimulation

This study aims to reproduce the effect of motor-unit synchronization on surface EMG recordings during vibratory stimulation to highlight vibration evoked muscle activity. The authors intended to evaluate, through numerical simulations, the changes in surface EMG spectrum in muscles undergoing whole body vibration stimulation. In some specific bands, in fact, vibration induced motion artifacts are also typically present. In addition, authors meant to compare the simulated EMGs with respect to real recordings in order to discriminate the effect of synchronization of motor units discharges with vibration frequencies from motion artifacts. Computations were performed using a model derived from previous studies and modified to consider the effect of vibratory stimulus, the motor unit synchronization and the endplates-electrodes relative position on the EMG signal. Results revealed that, in particular conditions, synchronization of MUs' discharge generates visible peaks at stimulation frequency and its harmonics. However, only a part of the total power of surface EMGs might be enclosed within artifacts related bands (±1. Hz centered at the stimulation frequency and its superior harmonics) even in case of strong synchronization of motor units discharges with the vibratory stimulus. © 2013 Elsevier Ireland Ltd.

Inverse space-dependent force problems for the wave equation

The determination of the displacement and the space-dependent force acting on a vibrating structure from measured final or time-average displacement observation is thoroughly investigated. Several aspects related to the existence and uniqueness of a solution of the linear but ill-posed inverse force problems are highlighted. After that, in order to capture the solution a variational formulation is proposed and the gradient of the least-squares functional that is minimized is rigorously and explicitly derived. Numerical results obtained using the Landweber method and the conjugate gradient method are presented and discussed illustrating the convergence of the iterative procedures for exact input data. Furthermore, for noisy data the semi-convergence phenomenon appears, as expected, and stability is restored by stopping the iterations according to the discrepancy principle criterion once the residual becomes close to the amount of noise. The present investigation will be significant to researchers concerned with wave propagation and control of vibrating structures.

The mediating effect of innovation on the relationship between corporate reputation and performance in U.S. firms

In recent years, corporate reputation has gained the attention of many scholars in the strategic management and related fields. There is a general consensus that higher corporate reputation is positively related to firm success or performance. However, the link is not always straightforward; as a result, it calls for researchers to dedicate their efforts to investigate the causes and effects of firm reputation and how it is related to performance. In this doctoral dissertation, innovation is suggested as a mediating variable in this relationship. Innovation is a critical factor for firm success and survival. Highly reputed firms are in a more advantageous position to attract critical resources for innovation such as human and financial capital. These firms face constant pressure from external stakeholders, e.g. the general public, or customers, to achieve and remain at high levels of innovativeness. As a result, firms are in constant search, internally or externally, for new technologies expanding their knowledge base. Consequently, these firms engage in firms acquisitions. In the dissertation, the author assesses the effects of domestic versus international acquisitions as well as related versus unrelated acquisitions on the level of innovativeness and performance. Building upon an established measure of firm-level degree of internationalization (DOI), the dissertation proposes a more detailed and enhanced measure for the firm's DOI. It is modeled as an interaction effect between corporate reputation and resources for innovation. More specifically, firms with higher levels of internationalization will have access to resources for innovation, i.e. human and financial capital, at a global scale. Additionally, the distance between firms and higher education institutions, i.e. universities, is considered as another interaction effect for the human capital attraction. The dissertation is built on two theoretical frameworks, the resource-based view of the firm and institutional theory. It studies 211 U.S. firms using a longitudinal panel data structure from 2006 to 2012. It utilizes a linear dynamic panel data estimation methodology for its hypotheses analyses. Results confirm the hypotheses proposed in the study.

Análise estrutural e avaliação do efeito condroitim sulfato extraído de tilápia (Oreochromis niloticus) em modelo de peritonite aguda

Chondroitin sulfate (CS) is a naturally glycosaminoglycan found in the extracellular matrix of connective tissues and it may be extracted and purified those tissues. CS is involved in various biological functions, which may be related to the having structural variability, despite the simplicity of the linear chain structure from this molecule. Researches in biotechnology and pharmaceutical field with wastes from aquaculture has been developed in Brazil. In recent decades, tilapia (Oreochromis niloticus), native fish from Africa, has been one of the most cultivated species in various regions of the world, including Brazil. The tilapia farming is a cost-effective activity, however, it generates large amount of wastes that are discarded by producers. It is understood that waste from tilapia can be used in research as a source of molecules with important biotechnological applications, which also helps in reducing environmental impacts and promote the development of an ecofriendly activity. Thus, nile tilapia viscera were subjected to proteolysis, then the glycosaminoglycans were complexed with ion exchange resin (Lewatit), it was fractionated with increasing volumes of acetone and purified by ion exchange chromatography DEAE-Sephacel. Further, the fraction was analyzed by agarose gel electrophoresis and nuclear magnetic resonance (NMR). The electrophoretic profile of the compound together the analysis of 1H NMR spectra and the HSQC correlation allow to affirm that the compound corresponds to a molecule like chondroitin sulfate. MTT assay was used to assess cell viability in the presence of CS tilapia isolated and showed that the compound is not cytotoxic to normal cells such as cells from the mouse embryo fibroblast (3T3). Then, this compound was tested for the ability to reduce the influx of leukocytes in model of acute peritonitis (in vivo) induced by sodium thioglycolate. In this context, it was done total and differential leukocytes counting in the blood and peritoneal fluid collected respectively from vena cava and the peritoneal cavity of the animals subjected to the experiment. The chondroitin sulfate for the first time isolated from tilapia (CST ) was able to reduce the migration of leukocytes to the peritoneal cavity of inflamed mice until 80.4 per cent at a dose 10µg/kg. The results also show that there was a significant reduction (p<0.001) of the population of polymorphonuclear leukocytes from peritoneal cavity in the three tested doses (0.1µg/kg; 1µg/kg and 10µg/kg) when it was compared to the positive control (just thioglycolate). Therefore, since the CST structure and mechanism of action has been completely elucidated, this compound may have potential for therapeutic use in inflammatory diseases

Estudo do aproveitamento de resíduos PAE no desenvolvimento de materiais cerâmicos

This work presents a new ceramic material obtained through the incorporation of solid waste from the steel industry and known as dedusting powder PAE - in ceramic formulations based on clay, potassium and sodium feldspars, kaolin and talc. Formulations were prepared with ceramic residue levels of 0% (basic mass - MB), 2%, 4% and 8%, subjected to firing at temperatures of 1000 ° C, 1050ºC, 1100ºC and 1150ºC for periods of 15 min. and 120 min. The physicchemical and mechanical properties of these ceramic formulations were determined based on the firing temperature, residence time in the oven and the percentage of waste. Since the physicochemical and mechanical properties of the sintered materials were evaluated by chemical analysis techniques (fluorescence X-rays - FRX), particle size distribution, specific surface area, apparent density, structural analysis by diffraction of X-rays (DRX) and characterization of surface by scanning electron microscopy (SEM). The magnetic response characteristics and the pattern of magnetic ferrites of the samples were analyzed in the assay conditions, having noticed that the saturation magnetic susceptibility depend on the sintering temperature of the material and it is associated with its crystal structure. From the analysis results, it was concluded that the ceramic material with better physical and mechanical properties is obtained when the 8% from PAE residue is added to standard formulation under the burn time of 15 minutes and temperature of 1150ºC.

New Advancements of Scalable Statistical Methods for Learning Latent Structures in Big Data

Constant technology advances have caused data explosion in recent years. Accord- ingly modern statistical and machine learning methods must be adapted to deal with complex and heterogeneous data types. This phenomenon is particularly true for an- alyzing biological data. For example DNA sequence data can be viewed as categorical variables with each nucleotide taking four different categories. The gene expression data, depending on the quantitative technology, could be continuous numbers or counts. With the advancement of high-throughput technology, the abundance of such data becomes unprecedentedly rich. Therefore efficient statistical approaches are crucial in this big data era.

Previous statistical methods for big data often aim to find low dimensional struc- tures in the observed data. For example in a factor analysis model a latent Gaussian distributed multivariate vector is assumed. With this assumption a factor model produces a low rank estimation of the covariance of the observed variables. Another example is the latent Dirichlet allocation model for documents. The mixture pro- portions of topics, represented by a Dirichlet distributed variable, is assumed. This dissertation proposes several novel extensions to the previous statistical methods that are developed to address challenges in big data. Those novel methods are applied in multiple real world applications including construction of condition specific gene co-expression networks, estimating shared topics among newsgroups, analysis of pro- moter sequences, analysis of political-economics risk data and estimating population structure from genotype data.

Strength of the Iberian intraplate lithosphere: Cenozoic deformations and seismicity

Previous studies about the strength of the lithosphere in the Iberia centre fail to resolve the depth of earthquakes because of the rheological uncertainties. Therefore, new contributions are considered (the crustal structure from a density model) and several parameters (tectonic regime, mantle rheology, strain rate) are checked in this paper to properly examine the role of lithospheric strength in the intraplate seismicity and the Cenozoic evolution. The strength distribution with depth, the integrated strength, the effective elastic thickness and the seismogenic thickness have been calculated by a finite element modelling of the lithosphere across the Central System mountain range and the bordering Duero and Madrid sedimentary basins. Only a dry mantle under strike-slip/extension and a strain rate of 10-15 s-1, or under extension and 10-16 s-1, causes a strong lithosphere. The integrated strength and the elastic thickness are lower in the mountain chain than in the basins. These anisotropies have been maintained since the Cenozoic and determine the mountain uplift and the biharmonic folding of the Iberian lithosphere during the Alpine deformations. The seismogenic thickness bounds the seismic activity in the upper–middle crust, and the decreasing crustal strength from the Duero Basin towards the Madrid Basin is related to a parallel increase in Plio–Quaternary deformations and seismicity. However, elasto–plastic modelling shows that current African–Eurasian convergence is resolved elastically or ductilely, which accounts for the low seismicity recorded in this region.

Power relations and good governance: a social network analysis of the evolution of the integrity in public office act in the Commonwealth of Dominica

La Banque mondiale propose la bonne gouvernance comme la stratégie visant à corriger les maux de la mauvaise gouvernance et de faciliter le développement dans les pays en développement (Carayannis, Pirzadeh, Popescu & 2012; & Hilyard Wilks 1998; Leftwich 1993; Banque mondiale, 1989). Dans cette perspective, la réforme institutionnelle et une arène de la politique publique plus inclusive sont deux stratégies critiques qui visent à établir la bonne gouvernance, selon la Banque et d’autres institutions de Bretton Woods. Le problème, c’est que beaucoup de ces pays en voie de développement ne possèdent pas l’architecture institutionnelle préalable à ces nouvelles mesures. Cette thèse étudie et explique comment un état en voie de développement, le Commonwealth de la Dominique, s’est lancé dans un projet de loi visant l’intégrité dans la fonction publique. Cette loi, la Loi sur l’intégrité dans la fonction publique (IPO) a été adoptée en 2003 et mis en œuvre en 2008. Cette thèse analyse les relations de pouvoir entre les acteurs dominants autour de évolution de la loi et donc, elle emploie une combinaison de technique de l’analyse des réseaux sociaux et de la recherche qualitative pour répondre à la question principale: Pourquoi l’État a-t-il développé et mis en œuvre la conception actuelle de la IPO (2003)? Cette question est d’autant plus significative quand nous considérons que contrairement à la recherche existante sur le sujet, l’IPO dominiquaise diverge considérablement dans la structure du l’IPO type idéal. Nous affirmons que les acteurs "rationnels," conscients de leur position structurelle dans un réseau d’acteurs, ont utilisé leurs ressources de pouvoir pour façonner l’institution afin qu’elle serve leurs intérêts et ceux et leurs alliés. De plus, nous émettons l’hypothèse que: d’abord, le choix d’une agence spécialisée contre la corruption et la conception ultérieure de cette institution reflètent les préférences des acteurs dominants qui ont participé à la création de ladite institution et la seconde, notre hypothèse rivale, les caractéristiques des modèles alternatifs d’institutions de l’intégrité publique sont celles des acteurs non dominants. Nos résultats sont mitigés. Le jeu de pouvoir a été limité à un petit groupe d’acteurs dominants qui ont cherché à utiliser la création de la loi pour assurer leur légitimité et la survie politique. Sans surprise, aucun acteur n’a avancé un modèle alternatif. Nous avons conclu donc que la loi est la conséquence d’un jeu de pouvoir partisan. Cette recherche répond à la pénurie de recherche sur la conception des institutions de l’intégrité publique, qui semblent privilégier en grande partie un biais organisationnel et structurel. De plus, en étudiant le sujet du point de vue des relations de pouvoir (le pouvoir, lui-même, vu sous l’angle actanciel et structurel), la thèse apporte de la rigueur conceptuelle, méthodologique, et analytique au discours sur la création de ces institutions par l’étude de leur genèse des perspectives tant actancielles que structurelles. En outre, les résultats renforcent notre capacité de prédire quand et avec quelle intensité un acteur déploierait ses ressources de pouvoir.

Flexible modeling and estimation for high-dimensional graphs

Thesis (Ph.D.)--University of Washington, 2016-08