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.

Probing the scalar-pseudoscalar mixing in the 125 GeV Higgs particle with current data

LHC has found hints for a Higgs particle of 125 GeV. We investigate the possibility that such a particle is a mixture of scalar and pseudoscalar states. For definiteness, we concentrate on a two-Higgs doublet model with explicit CP violation and soft Z(2) violation. Including all Higgs production mechanisms, we determine the current constraints obtained by comparing h -> yy with h -> VV*, and comment on the information which can be gained by measurements of h -> b (b) over bar. We find bounds vertical bar s(2)vertical bar less than or similar to 0.83 at one sigma, where vertical bar s(2)vertical bar = 0 (vertical bar s(2)vertical bar = 1) corresponds to a pure scalar (pure pseudoscalar) state.

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.

Re-entrant phase behaviour of network fluids: A patchy particle model with temperature-dependent valence

We study a model consisting of particles with dissimilar bonding sites ("patches"), which exhibits self-assembly into chains connected by Y-junctions, and investigate its phase behaviour by both simulations and theory. We show that, as the energy cost epsilon(j) of forming Y-junctions increases, the extent of the liquid-vapour coexistence region at lower temperatures and densities is reduced. The phase diagram thus acquires a characteristic "pinched" shape in which the liquid branch density decreases as the temperature is lowered. To our knowledge, this is the first model in which the predicted topological phase transition between a fluid composed of short chains and a fluid rich in Y-junctions is actually observed. Above a certain threshold for epsilon(j), condensation ceases to exist because the entropy gain of forming Y-junctions can no longer offset their energy cost. We also show that the properties of these phase diagrams can be understood in terms of a temperature-dependent effective valence of the patchy particles. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3605703]

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.

Particle swarm optimization based approaches to vehicle-to-grid scheduling

This paper addresses the problem of energy resources management using modern metaheuristics approaches, namely Particle Swarm Optimization (PSO), New Particle Swarm Optimization (NPSO) and Evolutionary Particle Swarm Optimization (EPSO). The addressed problem in this research paper is intended for aggregators’ use operating in a smart grid context, dealing with Distributed Generation (DG), and gridable vehicles intelligently managed on a multi-period basis according to its users’ profiles and requirements. The aggregator can also purchase additional energy from external suppliers. The paper includes a case study considering a 30 kV distribution network with one substation, 180 buses and 90 load points. The distribution network in the case study considers intense penetration of DG, including 116 units from several technologies, and one external supplier. A scenario of 6000 EVs for the given network is simulated during 24 periods, corresponding to one day. The results of the application of the PSO approaches to this case study are discussed deep in the paper.

A decision-support system based on particle swarm optimization for multiperiod hedging in electricity markets

This paper proposes a particle swarm optimization (PSO) approach to support electricity producers for multiperiod optimal contract allocation. The producer risk preference is stated by a utility function (U) expressing the tradeoff between the expectation and variance of the return. Variance estimation and expected return are based on a forecasted scenario interval determined by a price range forecasting model developed by the authors. A certain confidence level is associated to each forecasted scenario interval. The proposed model makes use of contracts with physical (spot and forward) and financial (options) settlement. PSO performance was evaluated by comparing it with a genetic algorithm-based approach. This model can be used by producers in deregulated electricity markets but can easily be adapted to load serving entities and retailers. Moreover, it can easily be adapted to the use of other type of contracts.

Distributed energy resource short-term scheduling using signaled particle swarm optimization

Distributed Energy Resources (DER) scheduling in smart grids presents a new challenge to system operators. The increase of new resources, such as storage systems and demand response programs, results in additional computational efforts for optimization problems. On the other hand, since natural resources, such as wind and sun, can only be precisely forecasted with small anticipation, short-term scheduling is especially relevant requiring a very good performance on large dimension problems. Traditional techniques such as Mixed-Integer Non-Linear Programming (MINLP) do not cope well with large scale problems. This type of problems can be appropriately addressed by metaheuristics approaches. This paper proposes a new methodology called Signaled Particle Swarm Optimization (SiPSO) to address the energy resources management problem in the scope of smart grids, with intensive use of DER. The proposed methodology’s performance is illustrated by a case study with 99 distributed generators, 208 loads, and 27 storage units. The results are compared with those obtained in other methodologies, namely MINLP, Genetic Algorithm, original Particle Swarm Optimization (PSO), Evolutionary PSO, and New PSO. SiPSO performance is superior to the other tested PSO variants, demonstrating its adequacy to solve large dimension problems which require a decision in a short period of time.

A short-term risk management tool applied to OMEL electricity market using particle swarm optimization

Short-term risk management is highly dependent on long-term contractual decisions previously established; risk aversion factor of the agent and short-term price forecast accuracy. Trying to give answers to that problem, this paper provides a different approach for short-term risk management on electricity markets. Based on long-term contractual decisions and making use of a price range forecast method developed by the authors, the short-term risk management tool presented here has as main concern to find the optimal spot market strategies that a producer should have for a specific day in function of his risk aversion factor, with the objective to maximize the profits and simultaneously to practice the hedge against price market volatility. Due to the complexity of the optimization problem, the authors make use of Particle Swarm Optimization (PSO) to find the optimal solution. Results from realistic data, namely from OMEL electricity market, are presented and discussed in detail.

Particle swarm optimization applied to integrated demand response resources scheduling

The concept of demand response has a growing importance in the context of the future power systems. Demand response can be seen as a resource like distributed generation, storage, electric vehicles, etc. All these resources require the existence of an infrastructure able to give players the means to operate and use them in an efficient way. This infrastructure implements in practice the smart grid concept, and should accommodate a large number of diverse types of players in the context of a competitive business environment. In this paper, demand response is optimally scheduled jointly with other resources such as distributed generation units and the energy provided by the electricity market, minimizing the operation costs from the point of view of a virtual power player, who manages these resources and supplies the aggregated consumers. The optimal schedule is obtained using two approaches based on particle swarm optimization (with and without mutation) which are compared with a deterministic approach that is used as a reference methodology. A case study with two scenarios implemented in DemSi, a demand Response simulator developed by the authors, evidences the advantages of the use of the proposed particle swarm approaches.

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.

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.

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.