948 resultados para local sequence alignment problem
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Brazil s semi-arid region is an immense territory characterized by a mosaic of natural environments and human settlements. Inside this multifaceted framework, there are problems that are specific to the region (the water resources situation, for example) while others are more universal (such as the inequality between men and women). The circumstances that give rise to these problems are complex and require a holistic view so that our understanding can go beyond the simple concept that this is a problem region . The semi-arid must be perceived as a viable area in need of a new analysis, taking into account its successes, limitations, challenges and the strategic public policy framework that guarantees its sustainable development. The dissertation analyzes, from a sustainable local development perspective, the experience of the Northeastern Brazil Groundwater Project (PROASNE), carried out from 2001 to 2003, in partnership with the Waters and Sewers Company of Rio Grande do Norte (CAERN) in the rural community of Mirandas, municipality of Caraúbas/RN, situated in the middle of the northeastern Brazil semi-arid region
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The intervalar arithmetic well-known as arithmetic of Moore, doesn't possess the same properties of the real numbers, and for this reason, it is confronted with a problem of operative nature, when we want to solve intervalar equations as extension of real equations by the usual equality and of the intervalar arithmetic, for this not to possess the inverse addictive, as well as, the property of the distributivity of the multiplication for the sum doesn t be valid for any triplet of intervals. The lack of those properties disables the use of equacional logic, so much for the resolution of an intervalar equation using the same, as for a representation of a real equation, and still, for the algebraic verification of properties of a computational system, whose data are real numbers represented by intervals. However, with the notion of order of information and of approach on intervals, introduced by Acióly[6] in 1991, the idea of an intervalar equation appears to represent a real equation satisfactorily, since the terms of the intervalar equation carry the information about the solution of the real equation. In 1999, Santiago proposed the notion of simple equality and, later on, local equality for intervals [8] and [33]. Based on that idea, this dissertation extends Santiago's local groups for local algebras, following the idea of Σ-algebras according to (Hennessy[31], 1988) and (Santiago[7], 1995). One of the contributions of this dissertation, is the theorem 5.1.3.2 that it guarantees that, when deducing a local Σ-equation E t t in the proposed system SDedLoc(E), the interpretations of t and t' will be locally the same in any local Σ-algebra that satisfies the group of fixed equations local E, whenever t and t have meaning in A. This assures to a kind of safety between the local equacional logic and the local algebras
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This work presents a algorithmic study of Multicast Packing Problem considering a multiobjective approach. The first step realized was an extensive review about the problem. This review serverd as a reference point for the definition of the multiobjective mathematical model. Then, the instances used in the experimentation process were defined, this instances were created based on the main caracteristics from literature. Since both mathematical model and the instances were definined, then several algoritms were created. The algorithms were based on the classical approaches to multiobjective optimization: NSGA2 (3 versions), SPEA2 (3 versions). In addition, the GRASP procedures were adapted to work with multiples objectives, two vesions were created. These algorithms were composed by three recombination operators(C1, C2 e C3), two operator for build solution, a mutation operator and a local search procedure. Finally, a long experimentation process was performed. This process has three stages: the first consisted of adjusting the parameters; the second was perfomed to indentify the best version for each algorithm. After, the best versions for each algorithm were compared in order to identify the best algorithm among all. The algorithms were evaluated based on quality indicators and Hypervolume Multiplicative Epsilon
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Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTEs were assembled into 81,429 contigs. of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTEs sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTEs coincided with DNA regions predicted as encoding exons by GENSCAN.
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The merozoite surface protein-2 (MSP-2) of Plasmodium falciparum comprises repeats flanked by dimorphic domains defining the allelic families FC27 and IC1. Here, we examined sequence diversity at the msp-2 locus in Brazil and its impact on MSP-2 antibody recognition by local patients. Only 25 unique partial sequences of msp-2 were found in 61 isolates examined. The finding of identical msp-2 sequences in unrelated parasites, collected 6-13 years apart, suggests that no major directional selection is exerted by variant-specific immunity in this malaria-endemic area. To examine antibody cross-reactivity, recombinant polypeptides derived from locally prevalent and foreign MSP-2 variants were used in ELISA. Foreign IC1-type variants, such as 3D7 (currently tested for human vaccination), were less frequently recognized than FC27-type and local IC1-type variants. Antibodies discriminated between local and foreign IC1-type variants, but cross-recognized structurally different local IC1-type variants. The use of evolutionary models of MSP-2 is suggested to design vaccines that minimize differences between local parasites and vaccine antigens. (C) 2004 Elsevier B.V. All rights reserved.
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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
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INTRODUÇÃO: Nestes últimos anos, descobriu-se a complexidade dos mecanismos que influenciam a atividade óssea, e grande parte das pesquisas direcionou-se para o estudo de fatores capazes de modular as funções ósseas. Essa expansão da pesquisa deve-se, em parte, ao reconhecimento da osteoporose como importante problema na velhice. A osteoporose constitui uma das osteopatias mais comuns, caracterizando-se pela redução da massa óssea, determinada, por sua vez, pelo desequilíbrio entre reabsorção e neoformação. OBJETIVO: Apresentar uma revisão da literatura sobre os principais aspectos da remodelação e da reparação associados à deficiência estrogênica. Remodelação óssea: O osso apresenta processo contínuo de remodelação, entretanto anormalidades nesse processo ocorrem em algumas doenças, entre elas a osteoporose, sendo que a deficiência estrogênica parece ter o papel principal na sua gênese. Reparação óssea: Tal processo envolve uma cascata complexa de respostas biológicase, assim como a remodelação, é afetado por fatores locais e externos e regulado pela interação de diferentes mecanismos. Portanto, o aumento ou o decréscimo da capacidade de reparação óssea têm sido relacionados a alterações ocorridas na remodelação. Deficiência estrogênica e metabolismo ósseo: A maioria dos autores sugere uma redução na capacidade de remodelação e de reparação do tecido. DISCUSSÃO: Ainda não está determinado qual estágio da reparação é mais alterado, se a fase inicial de formação do calo ósseo, se a de mineralização ou se a fase tardia da reparação, a remodelação óssea. CONCLUSÃO: Como os mecanismos fisiológicos e a patogênese das alterações ósseas causadas pela deficiência estrogênica não estão completamente estabelecidos, novas pesquisas ainda são necessárias.
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We show that by introducing appropriate local Z(N)(Ngreater than or equal to13) symmetries in electroweak models it is possible to implement an automatic Peccei-Quinn symmetry, at the same time keeping the axion protected against gravitational effects. Although we consider here only an extension of the standard model and a particular 3-3-1 model, the strategy can be used in any kind of electroweak model. An interesting feature of this 3-3-1 model is that if we add (i) right-handed neutrinos, (ii) the conservation of the total lepton number, and (iii) a Z(2) symmetry, the Z(13) and the chiral Peccei-Quinn U(1)P-Q symmetries are both accidental symmetries in the sense that they are not imposed on the Lagrangian but are just a consequence of the particle content of the model, its gauge invariance, renormalizability, and Lorentz invariance. In addition, this model has no domain wall problem.
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We show that by imposing local Z(13)circle timesZ(3) symmetries in an SU(2)circle timesU(1) electroweak model we can implement an invisible axion in such a way that (i) the Peccei-Quinn symmetry is an automatic symmetry of the classical Lagrangian, and (ii) the axion is protected from semiclassical gravitational effects. In order to be able to implement such a large discrete symmetry, and at the same time allow a general mixing in each charge sector, we introduce right-handed neutrinos and enlarge the scalar sector of the model. The domain wall problem is briefly considered.
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Some dynamic properties for a light ray suffering specular reflections inside a periodically corrugated waveguide are studied. The dynamics of the model is described in terms of a two dimensional nonlinear area preserving map. We show that the phase space is mixed in the sense that there are KAM islands surrounded by a large chaotic sea that is confined by two invariant spanning curves. We have used a connection with the Standard Mapping near a transition from local to global chaos and found the position of these two invariant spanning curves limiting the size of the chaotic sea as function of the control parameter.
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O problema de minimização de troca de ferramentas (MTSP) busca uma sequência de processamento de um conjunto de tarefas, de modo a minimizar o número de trocas de ferramentas requeridas. Este trabalho apresenta uma nova heurística para o MTSP, capaz de produzir bons limitantes superiores para um algoritmo enumerativo. Esta heurística possui duas fases: uma fase construtiva que é baseada em um grafo em que os vértices correspondem a ferramentas e existe um arco k = (i, j) que liga os vértices i e j se e somente se as ferramentas i e j são necessárias para a execução de alguma tarefa k; e uma fase de refinamento baseada na meta-heurística Busca Local Iterativa. Resultados computacionais mostram que a heurística proposta tem um bom desempenho para os problemas testados, contribuindo para uma redução significativa no número de nós gerados de um algoritmo enumerativo.
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The extended linear complementarity problem (XLCP) has been introduced in a recent paper by Mangasarian and Pang. In the present research, minimization problems with simple bounds associated to this problem are defined. When the XLCP is solvable, their solutions are global minimizers of the associated problems. Sufficient conditions that guarantee that stationary points of the associated problems are solutions of the XLCP will be proved. These theoretical results support the conjecture that local methods for box constrained optimization applied to the associated problems could be efficient tools for solving the XLCP. (C) 1998 Elsevier B.V. All rights reserved.
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The code STATFLUX, implementing a new and simple statistical procedure for the calculation of transfer coefficients in radionuclide transport to animals and plants, is proposed. The method is based on the general multiple-compartment model, which uses a system of linear equations involving geometrical volume considerations. Flow parameters were estimated by employing two different least-squares procedures: Derivative and Gauss-Marquardt methods, with the available experimental data of radionuclide concentrations as the input functions of time. The solution of the inverse problem, which relates a given set of flow parameter with the time evolution of concentration functions, is achieved via a Monte Carlo Simulation procedure.Program summaryTitle of program: STATFLUXCatalogue identifier: ADYS_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADYS_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: noneComputer for which the program is designed and others on which it has been tested: Micro-computer with Intel Pentium III, 3.0 GHzInstallation: Laboratory of Linear Accelerator, Department of Experimental Physics, University of São Paulo, BrazilOperating system: Windows 2000 and Windows XPProgramming language used: Fortran-77 as implemented in Microsoft Fortran 4.0. NOTE: Microsoft Fortran includes non-standard features which are used in this program. Standard Fortran compilers such as, g77, f77, ifort and NAG95, are not able to compile the code and therefore it has not been possible for the CPC Program Library to test the program.Memory, required to execute with typical data: 8 Mbytes of RAM memory and 100 MB of Hard disk memoryNo. of bits in a word: 16No. of lines in distributed program, including test data, etc.: 6912No. of bytes in distributed Program, including test data, etc.: 229 541Distribution format: tar.gzNature of the physical problem: the investigation of transport mechanisms for radioactive substances, through environmental pathways, is very important for radiological protection of populations. One such pathway, associated with the food chain, is the grass-animal-man sequence. The distribution of trace elements in humans and laboratory animals has been intensively studied over the past 60 years [R.C. Pendlenton, C.W. Mays, R.D. Lloyd, A.L. Brooks, Differential accumulation of iodine-131 from local fallout in people and milk, Health Phys. 9 (1963) 1253-1262]. In addition, investigations on the incidence of cancer in humans, and a possible causal relationship to radioactive fallout, have been undertaken [E.S. Weiss, M.L. Rallison, W.T. London, W.T. Carlyle Thompson, Thyroid nodularity in southwestern Utah school children exposed to fallout radiation, Amer. J. Public Health 61 (1971) 241-249; M.L. Rallison, B.M. Dobyns, F.R. Keating, J.E. Rall, F.H. Tyler, Thyroid diseases in children, Amer. J. Med. 56 (1974) 457-463; J.L. Lyon, M.R. Klauber, J.W. Gardner, K.S. Udall, Childhood leukemia associated with fallout from nuclear testing, N. Engl. J. Med. 300 (1979) 397-402]. From the pathways of entry of radionuclides in the human (or animal) body, ingestion is the most important because it is closely related to life-long alimentary (or dietary) habits. Those radionuclides which are able to enter the living cells by either metabolic or other processes give rise to localized doses which can be very high. The evaluation of these internally localized doses is of paramount importance for the assessment of radiobiological risks and radiological protection. The time behavior of trace concentration in organs is the principal input for prediction of internal doses after acute or chronic exposure. The General Multiple-Compartment Model (GMCM) is the powerful and more accepted method for biokinetical studies, which allows the calculation of concentration of trace elements in organs as a function of time, when the flow parameters of the model are known. However, few biokinetics data exist in the literature, and the determination of flow and transfer parameters by statistical fitting for each system is an open problem.Restriction on the complexity of the problem: This version of the code works with the constant volume approximation, which is valid for many situations where the biological half-live of a trace is lower than the volume rise time. Another restriction is related to the central flux model. The model considered in the code assumes that exist one central compartment (e.g., blood), that connect the flow with all compartments, and the flow between other compartments is not included.Typical running time: Depends on the choice for calculations. Using the Derivative Method the time is very short (a few minutes) for any number of compartments considered. When the Gauss-Marquardt iterative method is used the calculation time can be approximately 5-6 hours when similar to 15 compartments are considered. (C) 2006 Elsevier B.V. All rights reserved.
Sequence, evolution and ligand binding properties of mammalian Duffy antigen/receptor for chemokines
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The Duffy antigen/receptor for chemokine, DARC, acts as a widely expressed promiscuous chemokine receptor and as the erythrocyte receptor for Plasmodium vivax. To gain insight into the evolution and structure/function relations of DARC, we analyzed the binding of anti-human Fy monoclonal antibodies (mAbs) and human chemokines to red blood cells (RBCs) from 11 nonhuman primates and two nonprimate mammals, and we elucidated the structures of the DARC genes from gorilla, gibbon, baboon, marmoset, tamarin, night monkey and cattle. CXCL-8 and CCL-5 chemokine binding analysis indicated that the promiscuous binding profile characteristic of DARC is conserved across species. Among three mAbs that detected the Fy6 epitope by flow cytometric analysis of human and chimpanzee RBCs, only one reacted with night monkey and squirrel monkey. Only chimpanzee RBCs bound a significant amount of the anti-Fy3 mAb. Fy3 was also poorly detected on RBCs from gorilla, baboon and rhesus monkey, but not from new world monkeys. Alignment of DARC homologous sequences allowed us to construct a phylogenetic tree in which all branchings were in accordance with current knowledge of primate phylogeny. Although DARC was expected to be under strong internal and external selection pressure, in order to maintain chemokine binding and avoid Plasmodium vivax binding, respectively, our present study did not provide arguments in favor of a selection pressure on the extracellular domains involved in ligand specificity. The amino acid variability of DARC-like polypeptides was found to be well correlated with the hydrophylicity indexes, with the highest divergence on the amino-terminal extracellular domain. Analysis of the deduced amino acid sequences highlighted the conservation of some amino acid residues, which should prove to be critical for the structural and functional properties of DARC.
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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)