PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Background: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions: PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

Damage detection and quantification using transmissibility

Structures experience various types of loads along their lifetime, which can be either static or dynamic and may be associated to phenomena of corrosion and chemical attack, among others. As a consequence, different types of structural damage can be produced; the deteriorated structure may have its capacity affected, leading to excessive vibration problems or even possible failure. It is very important to develop methods that are able to simultaneously detect the existence of damage and to quantify its extent. In this paper the authors propose a method to detect and quantify structural damage, using response transmissibilities measured along the structure. Some numerical simulations are presented and a comparison is made with results using frequency response functions. Experimental tests are also undertaken to validate the proposed technique. (C) 2011 Elsevier Ltd. All rights reserved.

Finite element studies of the mechanical behaviour of the diaphragm in normal and pathological cases

The diaphragm is a muscular membrane separating the abdominal and thoracic cavities, and its motion is directly linked to respiration. In this study, using data from a 59-year-old female cadaver obtained from the Visible Human Project, the diaphragm is reconstructed and, from the corresponding solid object, a shell finite element mesh is generated and used in several analyses performed with the ABAQUS 6.7 software. These analyses consider the direction of the muscle fibres and the incompressibility of the tissue. The constitutive model for the isotropic strain energy as well as the passive and active strain energy stored in the fibres is adapted from Humphrey's model for cardiac muscles. Furthermore, numerical results for the diaphragmatic floor under pressure and active contraction in normal and pathological cases are presented.

Methods for automatic and assisted image annotation

Personal memories composed of digital pictures are very popular at the moment. To retrieve these media items annotation is required. During the last years, several approaches have been proposed in order to overcome the image annotation problem. This paper presents our proposals to address this problem. Automatic and semi-automatic learning methods for semantic concepts are presented. The automatic method is based on semantic concepts estimated using visual content, context metadata and audio information. The semi-automatic method is based on results provided by a computer game. The paper describes our proposals and presents their evaluations.

Typical load profiles in the smart grid context – a clustering methods comparison

The present research paper presents five different clustering methods to identify typical load profiles of medium voltage (MV) electricity consumers. These methods are intended to be used in a smart grid environment to extract useful knowledge about customer’s behaviour. The obtained knowledge can be used to support a decision tool, not only for utilities but also for consumers. Load profiles can be used by the utilities to identify the aspects that cause system load peaks and enable the development of specific contracts with their customers. The framework presented throughout the paper consists in several steps, namely the pre-processing data phase, clustering algorithms application and the evaluation of the quality of the partition, which is supported by cluster validity indices. The process ends with the analysis of the discovered knowledge. To validate the proposed framework, a case study with a real database of 208 MV consumers is used.

Technical and economic resources management in smart grids using heuristic optimization methods

Intensive use of Distributed Generation (DG) represents a change in the paradigm of power systems operation making small-scale energy generation and storage decision making relevant for the whole system. This paradigm led to the concept of smart grid for which an efficient management, both in technical and economic terms, should be assured. This paper presents a new approach to solve the economic dispatch in smart grids. The proposed methodology for resource management involves two stages. The first one considers fuzzy set theory to define the natural resources range forecast as well as the load forecast. The second stage uses heuristic optimization to determine the economic dispatch considering the generation forecast, storage management and demand response

Electricity markets: transmission prices methods

In the context of electricity markets, transmission pricing is an important tool to achieve an efficient operation of the electricity system. The electricity market is influenced by several factors; however the transmission network management is one of the most important aspects, because the network is a natural monopoly. The transmission tariffs can help to regulate the market, for this reason transmission tariffs must follow strict criteria. This paper presents the following methods to tariff the use of transmission networks by electricity market players: Post-Stamp Method; MW-Mile Method Distribution Factors Methods; Tracing Methodology; Bialek’s Tracing Method and Locational Marginal Price. A nine bus transmission network is used to illustrate the application of the tariff methods.

Comparison between deterministic and meta-heuristic methods applied to ancillary services dispatch

This paper proposes two meta-heuristics (Genetic Algorithm and Evolutionary Particle Swarm Optimization) for solving a 15 bid-based case of Ancillary Services Dispatch in an Electricity Market. A Linear Programming approach is also included for comparison purposes. A test case based on the dispatch of Regulation Down, Regulation Up, Spinning Reserve and Non-Spinning Reserve services is used to demonstrate that the use of meta-heuristics is suitable for solving this kind of optimization problem. Faster execution times and lower computational resources requirements are the most relevant advantages of the used meta-heuristics when compared with the Linear Programming approach.

Ancillary services market clearing simulation: a comparison between deterministic and heuristic methods

Electricity market players operating in a liberalized environment requires access to an adequate decision support tool, allowing them to consider all the business opportunities and take strategic decisions. Ancillary services represent a good negotiation opportunity that must be considered by market players. For this, decision support tool must include ancillary market simulation. This paper proposes two different methods (Linear Programming and Genetic Algorithm approaches) for ancillary services dispatch. The methodologies are implemented in MASCEM, a multi-agent based electricity market simulator. A test case based on California Independent System Operator (CAISO) data concerning the dispatch of Regulation Down, Regulation Up, Spinning Reserve and Non-Spinning Reserve services is included in this paper.

Online versus postal questionnaires: a comparison between two data collection methods

Objectives : The purpose of this article is to find out differences between surveys using paper and online questionnaires. The author has deep knowledge in the case of questions concerning opinions in the development of survey based research, e.g. the limits of postal and online questionnaires. Methods : In the physician studies carried out in 1995 (doctors graduated in 1982-1991), 2000 (doctors graduated in 1982-1996), 2005 (doctors graduated in 1982-2001), 2011 (doctors graduated in 1977-2006) and 457 family doctors in 2000, were used paper and online questionnaires. The response rates were 64%, 68%, 64%, 49% and 73%, respectively. Results : The results of the physician studies showed that there were differences between methods. These differences were connected with using paper-based questionnaire and online questionnaire and response rate. The online-based survey gave a lower response rate than the postal survey. The major advantages of online survey were short response time; very low financial resource needs and data were directly loaded in the data analysis software, thus saved time and resources associated with the data entry process. Conclusions : The current article helps researchers with planning the study design and choosing of the right data collection method.

A comparison of two attenuation correction methods in 111In-Pentetriotide abdominal SPECT

Tomographic image can be degraded, partially by patient based attenuation. The aim of this paper is to quantitatively verify the effects of attenuation correction methods Chang and CT in 111In studies through the analysis of profiles from abdominal SPECT, correspondent to a uniform radionuclide uptake organ, the left kidney.

A model updating technique based on FRFs for damped structures

Model updating methods often neglect that in fact all physical structures are damped. Such simplification relies on the structural modelling approach, although it compromises the accuracy of the predictions of the structural dynamic behaviour. In the present work, the authors address the problem of finite element (FE) model updating based on measured frequency response functions (FRFs), considering damping. The proposed procedure is based upon the complex experimental data, which contains information related to the damped FE model parameters and presents the advantage of requiring no prior knowledge about the damping matrix structure or its content, only demanding the definition of the damping type. Numerical simulations are performed in order to establish the applicability of the proposed damped FE model updating technique and its results are discussed in terms of the correlation between the simulated experimental complex FRFs and the ones obtained from the updated FE model.

Derivative-free optimization and filter methods to solve nonlinear constrained problems

In real optimization problems, usually the analytical expression of the objective function is not known, nor its derivatives, or they are complex. In these cases it becomes essential to use optimization methods where the calculation of the derivatives, or the verification of their existence, is not necessary: the Direct Search Methods or Derivative-free Methods are one solution. When the problem has constraints, penalty functions are often used. Unfortunately the choice of the penalty parameters is, frequently, very difficult, because most strategies for choosing it are heuristics strategies. As an alternative to penalty function appeared the filter methods. A filter algorithm introduces a function that aggregates the constrained violations and constructs a biobjective problem. In this problem the step is accepted if it either reduces the objective function or the constrained violation. This implies that the filter methods are less parameter dependent than a penalty function. In this work, we present a new direct search method, based on simplex methods, for general constrained optimization that combines the features of the simplex method and filter methods. This method does not compute or approximate any derivatives, penalty constants or Lagrange multipliers. The basic idea of simplex filter algorithm is to construct an initial simplex and use the simplex to drive the search. We illustrate the behavior of our algorithm through some examples. The proposed methods were implemented in Java.

Numerical experiments with a modified regularization scheme for mathematical programs with complementarity constraints

On this paper we present a modified regularization scheme for Mathematical Programs with Complementarity Constraints. In the regularized formulations the complementarity condition is replaced by a constraint involving a positive parameter that can be decreased to zero. In our approach both the complementarity condition and the nonnegativity constraints are relaxed. An iterative algorithm is implemented in MATLAB language and a set of AMPL problems from MacMPEC database were tested.

Numerical Uncertainty and Its Implications

Copyright © 2014 António F. Rodrigues, Nuno O. Martins. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In accordance of the Creative Commons Attribution License all Copyrights © 2014 are reserved for SCIRP and the owner of the intellectual property António F. Rodrigues, Nuno O. Martins. All Copyright © 2014 are guarded by law and by SCIRP as a guardian.