A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites "pattern-heterogeneity" to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate- variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program.

Conformational heterogeneity of tripeptides containing Boc-Leu-Aib as corner residues in the solid state

A critical analysis of single crystal X-ray diffraction studies on a series of terminally protected tripeptides containing a centrally positioned Aib (alpha-aminoisobutyric acid) residue has been reported. For the tripeptide series containing Boc-Ala-Aib as corner residues, all the reported peptides formed distorted type II beta-turn structures. Moreover, a series of Phe substituted analogues ( tripeptides with Boc-Phe-Aib) have also shown different beta-turn conformations. However, the Leu-modified analogues (tripeptides with Boc-Leu-Aib) disrupt the concept of beta-turn formation and adopt various conformations in the solid state. X-ray crystallography sheds some light on the conformational heterogeneity at atomic resolution. (c) 2007 Elsevier Ltd. All rights reserved.

Analytical and compositional aspects of isoflavones in food and their biological effects

This paper provides an overview of analytical techniques used to determine isoflavones (IFs) in foods and biological fluids with main emphasis on sample preparation methods. Factors influencing the content of IFs in food including processing and natural variability are summarized and an insight into IF databases is given. Comparisons of dietary intake of IFs in Asian and Western populations, in special subgroups like vegetarians, vegans, and infants are made and our knowledge on their absorption, distribution, metabolism, and excretion by the human body is presented. The influences of the gut microflora, age, gender, background diet, food matrix, and the chemical nature of the IFs on the metabolism of IFs are described. Potential mechanisms by which IFs may exert their actions are reviewed, and genetic polymorphism as determinants of biological response to soy IFs is discussed. The effects of IFs on a range of health outcomes including atherosclerosis, breast, intestinal, and prostate cancers, menopausal symptoms, bone health, and cognition are reviewed on the basis of the available in vitro, in vivo animal and human data.

Linguistic heterogeneity in Williams syndrome

Williams syndrome (WS) is a rare genetic disorder resulting from a deletion on chromosome 7. A number of studies have shown that individuals with WS have a superior linguistic profile compared to their non-verbal abilities, however the evidence has been inconclusive, as many studies have disputed such a profile. The vast majority of studies on WS have assumed a single, homogeneous WS linguistic profile in order to support various theoretical viewpoints. The present study investigated the linguistic profiles of 5 individuals with WS on a number of standardized verbal measures and in conversational settings. The results indicated substantially variable performance in all aspects of the verbal domain, which supports the view that WS, linguistically, is a rather heterogeneous condition and this should be taken into consideration when referring to it in theoretical accounts of language acquisition and debates on modularity.

Obesity and health in Europeans aged 50 years and older

Background: Obesity is increasing globally across all population groups. Limited data are available on how obesity patterns differ across countries. Objective: To document the prevalence of obesity and related health conditions for Europeans aged 50 years and older, and to estimate the association between obesity and health outcomes across 10 European countries. Methods: Data were obtained from the 2004 Survey of Health, Ageing and Retirement in Europe, a cross-national survey of 22 777 Continental Europeans over the age of 50 years. The health outcomes included self-reported health, disability, doctor-diagnosed chronic health conditions and depression. Multivariate regression analysis was used to predict health outcomes across weight classes (defined by body mass index [BMI] from self-reported weight and height) in the pooled sample and individually in each country. Results: The prevalence of obesity (BMI >= 30) ranged from 12.8% in Sweden to 20.2% in Spain for men and from 12.3% in Switzerland to 25.6% in Spain for women. Adjusting for compositional differences across countries changed little in the observed large heterogeneity in obesity rates throughout Europe. Compared with normal weight individuals, men and women with greater BMI had significantly higher risks for all chronic health conditions examined except heart disease in overweight men. Depression was linked to obesity in women only. Particularly pronounced risks of impaired health and chronic health conditions were found among severely obese people. The effects of obesity on health did not vary significantly across countries. Conclusions: Cross-country differences in the prevalence of obesity in older Europeans are substantial and exceed socio-demographic differentials in excessive body weight. Obesity is associated with significantly poorer health outcomes among Europeans aged 50 years and over, with effects similar across countries. Large heterogeneity in obesity throughout Europe should be investigated further to identify areas for effective public policy. (C) 2007 Published by Elsevier Ltd on behalf of The Royal Institute of Public Health.

Modeling the effects of node heterogeneity on the performance of a real grid application

The performance benefit when using Grid systems comes from different strategies, among which partitioning the applications into parallel tasks is the most important. However, in most cases the enhancement coming from partitioning is smoothed by the effect of the synchronization overhead, mainly due to the high variability of completion times of the different tasks, which, in turn, is due to the large heterogeneity of Grid nodes. For this reason, it is important to have models which capture the performance of such systems. In this paper we describe a queueing-network-based performance model able to accurately analyze Grid architectures, and we use the model to study a real parallel application executed in a Grid. The proposed model improves the classical modelling techniques and highlights the impact of resource heterogeneity and network latency on the application performance.

Modeling the effects of node heterogeneity on the performance of grid applications

The performance benefit when using grid systems comes from different strategies, among which partitioning the applications into parallel tasks is the most important. However, in most cases the enhancement coming from partitioning is smoothed by the effects of synchronization overheads, mainly due to the high variability in the execution times of the different tasks, which, in turn, is accentuated by the large heterogeneity of grid nodes. In this paper we design hierarchical, queuing network performance models able to accurately analyze grid architectures and applications. Thanks to the model results, we introduce a new allocation policy based on a combination between task partitioning and task replication. The models are used to study two real applications and to evaluate the performance benefits obtained with allocation policies based on task replication.

A compositional framework for hardware/software co-design

We describe a compositional framework, together with its supporting toolset, for hardware/software co-design. Our framework is an integration of a formal approach within a traditional design flow. The formal approach is based on Interval Temporal Logic and its executable subset, Tempura. Refinement is the key element in our framework because it will derive from a single formal specification of the system the software and hardware parts of the implementation, while preserving all properties of the system specification. During refinement simulation is used to choose the appropriate refinement rules, which are applied automatically in the HOL system. The framework is illustrated with two case studies. The work presented is part of a UK collaborative research project between the Software Technology Research Laboratory at the De Montfort University and the Oxford University Computing Laboratory.

Compositional technique for synthesising multi-phase regular arrays

We describe a high-level design method to synthesize multi-phase regular arrays. The method is based on deriving component designs using classical regular (or systolic) array synthesis techniques and composing these separately evolved component design into a unified global design. Similarity transformations ar e applied to component designs in the composition stage in order to align data ow between the phases of the computations. Three transformations are considered: rotation, re ection and translation. The technique is aimed at the design of hardware components for high-throughput embedded systems applications and we demonstrate this by deriving a multi-phase regular array for the 2-D DCT algorithm which is widely used in many vide ocommunications applications.

The effect of surface heterogeneity on cloud absorption estimates

This study presents a systematic and quantitative analysis of the effect of inhomogeneous surface albedo on shortwave cloud absorption estimates. We used 3D radiative transfer modeling over a checkerboard surface albedo to calculate cloud absorption. We have found that accounting for surface heterogeneity enhances cloud absorption. However, the enhancement is not sufficient to explain the reported difference between measured and modeled cloud absorption.

The impact of price promotions on producer strategies in markets with large product heterogeneity

Although current research indicates that increasing the number of options has negative effects on the cognitive ability of consumers, little understanding has been given to the consequences on producers and their strategic behavior. This article tests whether a large portfolio of products is beneficial to producers by observing UK consumer response to price promotions. The article shows that discounts induce mainly segment switching (74% of the total impact), with a limited effect on stockpiling (26%) and no impact on purchase incidence. Consequently, consumers prefer to “follow the discount” rather than purchase multiple units of the same wine. This result seems to explain the current structure of the market, and suggests that discounts may conflict with segment loyalty, a situation that disfavors producers, particularly in very populated segments. Results also casts doubts on the economic sustainability of competition based on an intense product differentiation in the wine sector.

Sequence heterogeneity of an mpb70 gene analogue in Mycobacterium kansasii

The protein antigen MPB70 is a major component of culture supernatants of Mycobacterium bovis and Is an active ingredient of bovine PPD used for skin-testing cattle for tuberculosis. we have shown that Mycobacterium kansasii possesses a similar gene that cross-reacts in a PCR test for M. bovis. Single strand conformational polymorphism analysis, and the DNA sequence of the PCR product, shows differences between M. kansasii strains, supporting the suggestion that M. kansasii is not a homogeneous species.