Evaluation of computational methods for the reconstruction of HLA haplotypes

Human leukocyte antigen (HLA) haplotypes are frequently evaluated for population history inferences and association studies. However, the available typing techniques for the main HLA loci usually do not allow the determination of the allele phase and the constitution of a haplotype, which may be obtained by a very time-consuming and expensive family-based segregation study. Without the family-based study, computational inference by probabilistic models is necessary to obtain haplotypes. Several authors have used the expectation-maximization (EM) algorithm to determine HLA haplotypes, but high levels of erroneous inferences are expected because of the genetic distance among the main HLA loci and the presence of several recombination hotspots. In order to evaluate the efficiency of computational inference methods, 763 unrelated individuals stratified into three different datasets had their haplotypes manually defined in a family-based study of HLA-A, -B, -DRB1 and -DQB1 segregation, and these haplotypes were compared with the data obtained by the following three methods: the Expectation-Maximization (EM) and Excoffier-Laval-Balding (ELB) algorithms using the arlequin 3.11 software, and the PHASE method. When comparing the methods, we observed that all algorithms showed a poor performance for haplotype reconstruction with distant loci, estimating incorrect haplotypes for 38%-57% of the samples considering all algorithms and datasets. We suggest that computational haplotype inferences involving low-resolution HLA-A, HLA-B, HLA-DRB1 and HLA-DQB1 haplotypes should be considered with caution.

Branching processes and computational collapse of discretized unimodal mappings

In computer simulations of smooth dynamical systems, the original phase space is replaced by machine arithmetic, which is a finite set. The resulting spatially discretized dynamical systems do not inherit all functional properties of the original systems, such as surjectivity and existence of absolutely continuous invariant measures. This can lead to computational collapse to fixed points or short cycles. The paper studies loss of such properties in spatial discretizations of dynamical systems induced by unimodal mappings of the unit interval. The problem reduces to studying set-valued negative semitrajectories of the discretized system. As the grid is refined, the asymptotic behavior of the cardinality structure of the semitrajectories follows probabilistic laws corresponding to a branching process. The transition probabilities of this process are explicitly calculated. These results are illustrated by the example of the discretized logistic mapping.

Computational differentiation of N-terminal signal peptides and transmembrane helices

Signal peptides and transmembrane helices both contain a stretch of hydrophobic amino acids. This common feature makes it difficult for signal peptide and transmembrane helix predictors to correctly assign identity to stretches of hydrophobic residues near the N-terminal methionine of a protein sequence. The inability to reliably distinguish between N-terminal transmembrane helix and signal peptide is an error with serious consequences for the prediction of protein secretory status or transmembrane topology. In this study, we report a new method for differentiating protein N-terminal signal peptides and transmembrane helices. Based on the sequence features extracted from hydrophobic regions (amino acid frequency, hydrophobicity, and the start position), we set up discriminant functions and examined them on non-redundant datasets with jackknife tests. This method can incorporate other signal peptide prediction methods and achieve higher prediction accuracy. For Gram-negative bacterial proteins, 95.7% of N-terminal signal peptides and transmembrane helices can be correctly predicted (coefficient 0.90). Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 99% (coefficient 0.92). For eukaryotic proteins, 94.2% of N-terminal signal peptides and transmembrane helices can be correctly predicted with coefficient 0.83. Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 87% (coefficient 0.85). The method can be used to complement current transmembrane protein prediction and signal peptide prediction methods to improve their prediction accuracies. (C) 2003 Elsevier Inc. All rights reserved.

Computational evaluation of hydraulic system behaviour with entrapped air under rapid pressurization

The pressurization of hydraulic systems containing entrapped air is considered a critical condition for the infrastructure's security due to transient pressure variations often occurred. The objective of the present study is the computational evaluation of trends observed in variation of maximum surge pressure resulting from rapid pressurizations. The comparison of the results with those obtained in previous studies is also undertaken. A brief state of art in this domain is presented. This research work is applied to an experimental system having entrapped air in the top of a vertical pipe section. The evaluation is developed through the elastic model based on the method of characteristics, considering a moving liquid boundary, with the results being compared with those achieved with the rigid liquid column model.

Computational evaluation of hydraulic system behaviour with entrapped air under rapid pressurization

The pressurization of hydraulic systems containing entrapped air is considered a critical condition for the infrastructure's security due to transient pressure variations often occurred. The objective of the present study is the computational evaluation of trends observed in variation of maximum surge pressure resulting from rapid pressurizations. The comparison of the results with those obtained in previous studies is also undertaken. A brief state of art in this domain is presented. This research work is applied to an experimental system having entrapped air in the top of a vertical pipe section. The evaluation is developed through the elastic model based on the method of characteristics, considering a moving liquid boundary, with the results being compared with those achieved with the rigid liquid column model.

How can we help students to improve their creativity? – lessons learned from a case study

One of the main concerns of today’s organizations is to cope with the rapid pace of change while maintaining their competitive advantage. This means that firms must be innovative, create new knowledge and have new ideas constantly. Similarly, one of the main concerns of lecturers is to help students to develop creativity. According to some authors, new ideas, new thoughts, innovation can arise in an appropriate environment and with the development and train of adequate competences and skills. This means that although some persons were born more creative than others, it is possible to help those less creative to improve their innovative capacities and competences. The question that remains now is “how”. How can we, as lecturers and educators help our students to become more creative? In this paper we describe a Portuguese case study that took place at ISCAP (School of Accountancy and Administration of Porto – Portugal), in the course of Business Communication, in the unit “Marketing Communication” (3rd year (1st Bologna cycle), 1st semester). We will describe and characterize the situation at the beginning of the semester (situation A), explain the tasks and activities proposed to students and the final result (situation A2). We will discuss differences between situation A and A2, formulate some hypotheses concerning differences and draw some recommendations.

Creativity and digital spaces in the intercultural society

In Permanent Transit: Discourses and Maps of the Intercultural Experience builds interdisciplinary approaches to the study of migrations, traffics, globalization, communication, regulations, arts, literature, and other intercultural processes, in the context of past and present times. The book offers a convergence of perspectives, combining conceptual and empirical work by sociologists, anthropologists, historians, linguists, educators, lawyers, media, specialists, and literary studies writers, in their shared attempt to understand the many routes of the intercultural experience. In Permanent Transit: Discourses and Maps of the Intercultural Experience builds interdisciplinary approaches to the study of migrations, traffics, globalization, communication, regulations, arts, literature, and other intercultural processes, in the context of past and present times. The book offers a convergence of perspectives, combining conceptual and empirical work by sociologists, anthropologists, historians, linguists, educators, lawyers, media, specialists, and literary studies writers, in their shared attempt to understand the many routes of the intercultural experience.

Technology for creativity and innovation: tools, techniques and applications

It is widely accepted that organizations and individuals must be innovative and continually create new knowledge and ideas to deal with rapid change. Innovation plays an important role in not only the development of new business, process and products, but also in competitiveness and success of any organization. Technology for Creativity and Innovation: Tools, Techniques and Applications provides empirical research findings and best practices on creativity and innovation in business, organizational, and social environments. It is written for educators, academics and professionals who want to improve their understanding of creativity and innovation as well as the role technology has in shaping this discipline.