Heuristic algorithm for computing reversal distance with multigene families via binary integer programming

Hannenhalli and Pevzner developed the first polynomial-time algorithm for the combinatorial problem of sorting of signed genomic data. Their algorithm solves the minimum number of reversals required for rearranging a genome to another when gene duplication is nonexisting. In this paper, we show how to extend the Hannenhalli-Pevzner approach to genomes with multigene families. We propose a new heuristic algorithm to compute the reversal distance between two genomes with multigene families via the concept of binary integer programming without removing gene duplicates. The experimental results on simulated and real biological data demonstrate that the proposed algorithm is able to find the reversal distance accurately. ©2005 IEEE

Capacity utilisation and profitability: A decomposition of short-run profit efficiency

The principal aim of this paper is to measure the amount by which the profit of a multi-input, multi-output firm deviates from maximum short-run profit, and then to decompose this profit gap into components that are of practical use to managers. In particular, our interest is in the measurement of the contribution of unused capacity, along with measures of technical inefficiency, and allocative inefficiency, in this profit gap. We survey existing definitions of capacity and, after discussing their shortcomings, we propose a new ray economic capacity measure that involves short-run profit maximisation, with the output mix held constant. We go on to describe how the gap between observed profit and maximum profit can be calculated and decomposed using linear programming methods. The paper concludes with an empirical illustration, involving data on 28 international airline companies. The empirical results indicate that these airline companies achieve profit levels which are on average US$815m below potential levels, and that 70% of the gap may be attributed to unused capacity. (C) 2002 Elsevier Science B.V. All rights reserved.

A genetic algorithm based method for deregulated electricity market dispatch

In a deregulated electricity market, optimizing dispatch capacity and transmission capacity are among the core concerns of market operators. Many market operators have capitalized on linear programming (LP) based methods to perform market dispatch operation in order to explore the computational efficiency of LP. In this paper, the search capability of genetic algorithms (GAs) is utilized to solve the market dispatch problem. The GA model is able to solve pool based capacity dispatch, while optimizing the interconnector transmission capacity. Case studies and corresponding analyses are performed to demonstrate the efficiency of the GA model.

Fitting genetic models to twin data with binary and ordered categorical responses: A comparison of structural equation modelling and Bayesian hierarchical models

We compare Bayesian methodology utilizing free-ware BUGS (Bayesian Inference Using Gibbs Sampling) with the traditional structural equation modelling approach based on another free-ware package, Mx. Dichotomous and ordinal (three category) twin data were simulated according to different additive genetic and common environment models for phenotypic variation. Practical issues are discussed in using Gibbs sampling as implemented by BUGS to fit subject-specific Bayesian generalized linear models, where the components of variation may be estimated directly. The simulation study (based on 2000 twin pairs) indicated that there is a consistent advantage in using the Bayesian method to detect a correct model under certain specifications of additive genetics and common environmental effects. For binary data, both methods had difficulty in detecting the correct model when the additive genetic effect was low (between 10 and 20%) or of moderate range (between 20 and 40%). Furthermore, neither method could adequately detect a correct model that included a modest common environmental effect (20%) even when the additive genetic effect was large (50%). Power was significantly improved with ordinal data for most scenarios, except for the case of low heritability under a true ACE model. We illustrate and compare both methods using data from 1239 twin pairs over the age of 50 years, who were registered with the Australian National Health and Medical Research Council Twin Registry (ATR) and presented symptoms associated with osteoarthritis occurring in joints of the hand.

Rough Notes on Programming AVR Microcontrollers in C

These notes follow on from the material that you studied in CSSE1000 Introduction to Computer Systems. There you studied details of logic gates, binary numbers and instruction set architectures using the Atmel AVR microcontroller family as an example. In your present course (METR2800 Team Project I), you need to get on to designing and building an application which will include such a microcontroller. These notes focus on programming an AVR microcontroller in C and provide a number of example programs to illustrate the use of some of the AVR peripheral devices.

Optimal release strategies for biological control agents: an application of stochastic dynamic programming to population management

1. Establishing biological control agents in the field is a major step in any classical biocontrol programme, yet there are few general guidelines to help the practitioner decide what factors might enhance the establishment of such agents. 2. A stochastic dynamic programming (SDP) approach, linked to a metapopulation model, was used to find optimal release strategies (number and size of releases), given constraints on time and the number of biocontrol agents available. By modelling within a decision-making framework we derived rules of thumb that will enable biocontrol workers to choose between management options, depending on the current state of the system. 3. When there are few well-established sites, making a few large releases is the optimal strategy. For other states of the system, the optimal strategy ranges from a few large releases, through a mixed strategy (a variety of release sizes), to many small releases, as the probability of establishment of smaller inocula increases. 4. Given that the probability of establishment is rarely a known entity, we also strongly recommend a mixed strategy in the early stages of a release programme, to accelerate learning and improve the chances of finding the optimal approach.

Binary games with many players

We examine a problem with n players each facing the same binary choice. One choice is superior to the other. The simple assumption of competition - that an individual's payoff falls with a rise in the number of players making the same choice, guarantees the existence of a unique symmetric equilibrium (involving mixed strategies). As n increases, there are two opposing effects. First, events in the middle of the distribution - where a player finds itself having made the same choice as many others - become more likely, but the payoffs in these events fall. In opposition, events in the tails of the distribution - where a player finds itself having made the same choice as few others - become less likely, but the payoffs in these events remain high. We provide a sufficient condition (strong competition) under which an increase in the number of players leads to a reduction in the equilibrium probability that the superior choice is made.

A zero-augmented gamma mixed model for longitudinal data with many zeros

In many occupational safety interventions, the objective is to reduce the injury incidence as well as the mean claims cost once injury has occurred. The claims cost data within a period typically contain a large proportion of zero observations (no claim). The distribution thus comprises a point mass at 0 mixed with a non-degenerate parametric component. Essentially, the likelihood function can be factorized into two orthogonal components. These two components relate respectively to the effect of covariates on the incidence of claims and the magnitude of claims, given that claims are made. Furthermore, the longitudinal nature of the intervention inherently imposes some correlation among the observations. This paper introduces a zero-augmented gamma random effects model for analysing longitudinal data with many zeros. Adopting the generalized linear mixed model (GLMM) approach reduces the original problem to the fitting of two independent GLMMs. The method is applied to evaluate the effectiveness of a workplace risk assessment teams program, trialled within the cleaning services of a Western Australian public hospital.

Segregation in binary and ternary liquid fluidized beds

The mechanism underlying segregation in liquid fluidized beds is investigated in this paper, A binary fluidized bed system not at a stable equilibrium condition. is modelled in the literature as forming a mixed part-corresponding to stable mixture-at the bottom of the bed and a pure layer of excess components always floating on the mixed part. On the basis of this model: (0 comprehensive criteria for binary particles of any type to mix/segregate, and (ii) mixing, segregation regime map in terms of size ratio and density ratio of the particles for a given fluidizing medium, are established in this work. Therefore, knowing the properties of given particles, a second type of particles can be chosen in order to avoid or to promote segregation according to the particular process requirements. The model is then advanced for multicomponent fluidized beds and validated against experimental results observed for ternary fluidized beds. (C) 2002 Elsevier Science B.V. All rights reserved.

Mixed gas equilibrium adsorption on zeolites and energetic heterogeneity of adsorption volume

A model for binary mixture adsorption accounting for energetic heterogeneity and intermolecular interactions is proposed in this paper. The model is based on statistical thermodynamics, and it is able to describe molecular rearrangement of a mixture in a nonuniform adsorption field inside a cavity. The Helmholtz free energy obtained in the framework of this approach has upper and lower limits, which define a permissible range in which all possible solutions will be found. One limit corresponds to a completely chaotic distribution of molecules within a cavity, while the other corresponds to a maximum ordered molecular structure. Comparison of the nearly ideal O-2-N-2-zeolite NaX system at ambient temperature with the system Of O-2-N-2-zeolite CaX at 144 K has shown that a decrease of temperature leads to a molecular rearrangement in the cavity volume, which results from the difference in the fluid-solid interactions. The model is able to describe this behavior and therefore allows predicting mixture adsorption more accurately compared to those assuming energetic uniformity of the adsorption volume. Another feature of the model is its ability to correctly describe the negative deviations from Raoult's law exhibited by the O-2-N-2-CaX system at 144 K. Analysis of the highly nonideal CO2-C2H6-zeolite NaX system has shown that the spatial molecular rearrangement in separate cavities is induced by not only the ion-quadrupole interaction of the CO2 molecule but also the significant difference in molecular size and the difference between the intermolecular interactions of molecules of the same species and those of molecules of different species. This leads to the highly ordered structure of this system.

Personality disorders and adult attachment dimensions in a mixed psychiatric sample: A multivariate study

The associations between personality disorders and adult attachment dimensions were assessed in a sample of 487 consecutively admitted psychiatric subjects. Canonical correlation analysis showed that two sets of moderately correlated canonical variates explained the correlations between personality disorders and adult attachment patterns. The first and second attachment variates closely resembled the avoidance and anxiety attachment dimensions, respectively. The first personality disorder variate was mainly characterized by avoidant, depressive, paranoid, and schizotypal personality disorders, whereas dependent, histrionic, and borderline personality disorders loaded on the second canonical variate. However, these linear combinations of personality disorders were different from those obtained from principal component analysis. The results extend previous studies linking personality disorders and attachment patterns and suggest the importance of focusing on specific constellations of symptoms associated with dimensions of insecurity.