Codon usage bias and A+T content variation in human papillomavirus genomes

We analyzed the codon usage bias of eight open reading frames (ORFs) across up to 79 human papillomavirus (HPV) genotypes from three distinct phylogenetic groups. All eight ORFs across HPV genotypes show a strong codon usage bias, amongst degenerately encoded amino acids, toward 18 codons mainly with T at the 3rd position. For all 18 degenerately encoded amino acids, codon preferences amongst human and animal PV ORFs are significantly different from those averaged across mammalian genes. Across the HPV types, the L2 ORFs show the highest codon usage bias (73.2 +/- 1.6% and the E4 ORFs the lowest (51.1 +/- 0.5%), reflecting as similar bias in codon 3rd position A + T content (L2: 76.1 +/- 4.2%; E4: 58.6 +/- 4.5%). The E4 ORF, uniquely amongst the HPV ORFs, is G + C rich, while the other ORFs are A + T rich. Codon usage bias correlates positively with A + T content at the codon 3rd position in the E2, E6, L1 and L2 ORFs, but negatively in the E4 ORFs. A general conservation of preferred codon usage across human and non-human PV genotypes whether they originate from a same supergroup or not, together with observed difference between the preferred codon usage for HPV ORFs and for genes of the cells they infect, suggests that specific codon usage bias and A + T content variation may somehow increase the replicational fitness of HPVs in mammalian epithelial cells, and have practical implications for gene therapy of HPV infection. (C) 2003 Elsevier B.V. All rights reserved.

Learning management systems usage on higher education institutions

Learning Management Systems (LMS) are used all over Higher Education Institutions (HEI) and the need to know and understand its adoption and usage arises. However, there is a lack of information about how LMSs are being used, which are the most adopted, whether there is a country adoption standard and which countries use more LMSs. A research team is developing a project that tries to fill this lack of information and provide the needed answers. With this purpose, on a first phase, it a survey was taken place. The results of this survey are presented in this paper. Another purpose of this paper is to disseminate the ongoing project.

An architecture for an effective usage of data mining in business intelligence systems

Business Intelligence (BI) is one emergent area of the Decision Support Systems (DSS) discipline. Over the last years, the evolution in this area has been considerable. Similarly, in the last years, there has been a huge growth and consolidation of the Data Mining (DM) field. DM is being used with success in BI systems, but a truly DM integration with BI is lacking. Therefore, a lack of an effective usage of DM in BI can be found in some BI systems. An architecture that pretends to conduct to an effective usage of DM in BI is presented.

Probabilistic linkage in household survey on hospital care usage

OBJECTIVE: To evaluate the potential advantages and limitations of the use of the Brazilian hospital admission authorization forms database and the probabilistic record linkage methodology for the validation of reported utilization of hospital care services in household surveys. METHODS: A total of 2,288 households interviews were conducted in the county of Duque de Caxias, Brazil. Information on the occurrence of at least one hospital admission in the year preceding the interview was obtained from a total of 10,733 household members. The 130 records of household members who reported at least one hospital admission in a public hospital were linked to a hospital database with 801,587 records, using an automatic probabilistic approach combined with an extensive clerical review. RESULTS: Seventy-four (57%) of the 130 household members were identified in the hospital database. Yet only 60 subjects (46%) showed a record of hospitalization in the hospital database in the study period. Hospital admissions due to a surgery procedure were significantly more likely to have been identified in the hospital database. The low level of concordance seen in the study can be explained by the following factors: errors in the linkage process; a telescoping effect; and an incomplete record in the hospital database. CONCLUSIONS: The use of hospital administrative databases and probabilistic linkage methodology may represent a methodological alternative for the validation of reported utilization of health care services, but some strategies should be employed in order to minimize the problems related to the use of this methodology in non-ideal conditions. Ideally, a single identifier, such as a personal health insurance number, and the universal coverage of the database would be desirable.

Sistema pericial para o estudo de composição de betões

O betão é o material de construção feito pelo Homem mais utilizado no mundo. A sua composição é um processo complexo que exige um conhecimento teórico sólido e muita experiência prática, pelo que poucas pessoas estão habilitadas para o fazer e são muito requisitadas. No entanto não existe muita oferta actual de software que contemple alguns dos aspectos importantes da composição do betão, nomeadamente para o contexto europeu. Nesse sentido, foi desenvolvido um sistema de apoio à decisão chamado Betacomp, baseado num sistema pericial, para realizar estudos de composição de betão. Este contempla as normas legais portuguesas e europeias, e a partir da especificação do betão apresenta toda a informação necessária para se produzir um ensaio de betão. A aquisição do conhecimento necessário ao sistema contou com a colaboração de um especialista com longa e comprovada experiência na área da formulação e produção do betão, tendo sido construída uma base de conhecimento baseada em regras de produção no formato drl (Drools Rule Language). O desenvolvimento foi realizado na plataforma Drools.net, em C# e VB.net. O Betacomp suporta os tipos de betão mais comuns, assim como adições e adjuvantes, sendo aplicável numa grande parte dos cenários de obra. Tem a funcionalidade de fornecer explicações sobre as suas decisões ao utilizador, auxiliando a perceber as conclusões atingidas e simultaneamente pode funcionar como uma ferramenta pedagógica. A sua abordagem é bastante pragmática e de certo modo inovadora, tendo em conta parâmetros novos, que habitualmente não são considerados neste tipo de software. Um deles é o nível do controlo de qualidade do produtor de betão, sendo feito um ajuste de compensação à resistência do betão a cumprir, proporcional à qualidade do produtor. No caso dos produtores de betão, permite que indiquem os constituintes que já possuem para os poderem aproveitar (caso não haja impedimentos técnicos) , uma prática muito comum e que permitirá eventualmente uma aceitação maior da aplicação, dado que reflecte a forma habitual de agir nos produtores.

Root-locus practical sketching rules for fractional-order system

For integer-order systems, there are well-known practical rules for RL sketching. Nevertheless, these rules cannot be directly applied to fractional-order (FO) systems. Besides, the existing literature on this topic is scarce and exclusively focused on commensurate systems, usually expressed as the ratio of two noninteger polynomials. The practical rules derived for those do not apply to other symbolic expressions, namely, to transfer functions expressed as the ratio of FO zeros and poles. However, this is an important case as it is an extension of the classical integer-order problem usually addressed by control engineers. Extending the RL practical sketching rules to such FO systems will contribute to decrease the lack of intuition about the corresponding system dynamics. This paper generalises several RL practical sketching rules to transfer functions specified as the ratio of FO zeros and poles. The subject is presented in a didactic perspective, being the rules applied to several examples.

Projecto e concepção de instalação frigorífica a NH3, para uma unidade de congelação de frangos em contínuo, na Venezuela

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Mecânica

Constraint solving over multi-valued logics - application to digital circuits

Due to usage conditions, hazardous environments or intentional causes, physical and virtual systems are subject to faults in their components, which may affect their overall behaviour. In a ‘black-box’ agent modelled by a set of propositional logic rules, in which just a subset of components is externally visible, such faults may only be recognised by examining some output function of the agent. A (fault-free) model of the agent’s system provides the expected output given some input. If the real output differs from that predicted output, then the system is faulty. However, some faults may only become apparent in the system output when appropriate inputs are given. A number of problems regarding both testing and diagnosis thus arise, such as testing a fault, testing the whole system, finding possible faults and differentiating them to locate the correct one. The corresponding optimisation problems of finding solutions that require minimum resources are also very relevant in industry, as is minimal diagnosis. In this dissertation we use a well established set of benchmark circuits to address such diagnostic related problems and propose and develop models with different logics that we formalise and generalise as much as possible. We also prove that all techniques generalise to agents and to multiple faults. The developed multi-valued logics extend the usual Boolean logic (suitable for faultfree models) by encoding values with some dependency (usually on faults). Such logics thus allow modelling an arbitrary number of diagnostic theories. Each problem is subsequently solved with CLP solvers that we implement and discuss, together with a new efficient search technique that we present. We compare our results with other approaches such as SAT (that require substantial duplication of circuits), showing the effectiveness of constraints over multi-valued logics, and also the adequacy of a general set constraint solver (with special inferences over set functions such as cardinality) on other problems. In addition, for an optimisation problem, we integrate local search with a constructive approach (branch-and-bound) using a variety of logics to improve an existing efficient tool based on SAT and ILP.

Data mining languages for business intelligence

Doctoral Thesis in Information Systems and Technologies Area of Engineering and Manag ement Information Systems

Derivation methods for hybrid knowledge bases with rules and ontologies

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

Adaption of the Creative Commons approach and the roaming concept to spatial data infrastructures (SDI)

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

Comparison of internet usage habits in two generations of higher education students: a case study

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