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.

Calculation of converged rovibrational energies and partition function for methane using vibrational-rotational configuration interaction

The rovibration partition function of CH4 was calculated in the temperature range of 100-1000 K using well-converged energy levels that were calculated by vibrational-rotational configuration interaction using the Watson Hamiltonian for total angular momenta J=0-50 and the MULTIMODE computer program. The configuration state functions are products of ground-state occupied and virtual modals obtained using the vibrational self-consistent field method. The Gilbert and Jordan potential energy surface was used for the calculations. The resulting partition function was used to test the harmonic oscillator approximation and the separable-rotation approximation. The harmonic oscillator, rigid-rotator approximation is in error by a factor of 2.3 at 300 K, but we also propose a separable-rotation approximation that is accurate within 2% from 100 to 1000 K. (C) 2004 American Institute of Physics.

A policy model for secure information flow

When a computer program requires legitimate access to confidential data, the question arises whether such a program may illegally reveal sensitive information. This paper proposes a policy model to specify what information flow is permitted in a computational system. The security definition, which is based on a general notion of information lattices, allows various representations of information to be used in the enforcement of secure information flow in deterministic or nondeterministic systems. A flexible semantics-based analysis technique is presented, which uses the input-output relational model induced by an attacker's observational power, to compute the information released by the computational system. An illustrative attacker model demonstrates the use of the technique to develop a termination-sensitive analysis. The technique allows the development of various information flow analyses, parametrised by the attacker's observational power, which can be used to enforce what declassification policies.

Understanding cumulative risk

This paper summarizes the theory of simple cumulative risks—for example, the risk of food poisoning from the consumption of a series of portions of tainted food. Problems concerning such risks are extraordinarily difficult for naı¨ve individuals, and the paper explains the reasons for this difficulty. It describes how naı¨ve individuals usually attempt to estimate cumulative risks, and it outlines a computer program that models these methods. This account predicts that estimates can be improved if problems of cumulative risk are framed so that individuals can focus on the appropriate subset of cases. The paper reports two experiments that corroborated this prediction. They also showed that whether problems are stated in terms of frequencies (80 out of 100 people got food poisoning) or in terms of percentages (80% of people got food poisoning) did not reliably affect accuracy.

Predicting natural ventilation in a two-zone building driven by combined forces.

Natural ventilation relies on less controllable natural forces so that it needs more artificial control, and thus its prediction, design and analysis become more important. This paper presents both theoretical and numerical simulations for predicting the natural ventilation flow in a two-zone building with multiple openings which is subjected to the combined natural forces. To our knowledge, this is the first analytical solutions obtained so far for a building with more than one zones and in each zone with possibly more than 2 openings. The analytical solution offers a possibility for validating a multi-zone airflow program. A computer program MIX is employed to conduct the numerical simulation. Good agreement is achieved. Different airflow modes are identified and some design recommendations are also provided.

Spatial expansion and population structure of the neotropical malaria vector, Anopheles darlingi (Diptera: Culicidae)

Extensive population structuring is known to occur in Anopheles darlingi, the primary malaria vector of the Neotropics. We analysed the phylogeographic structure of the species using the mitochondrial cytochrome oxidase I marker. Diversity is divided into six main population groups in South America: Colombia, central Amazonia, southern Brazil, south-eastern Brazil, and two groups in north-east Brazil. The ancestral distribution of the taxon is hypothesized to be central Amazonia, and there is evidence of expansion from this region during the late Pleistocene. The expansion was not a homogeneous front, however, with at least four subgroups being formed due to geographic barriers. As the species spread, populations became isolated from each other by the Amazon River and the coastal mountain ranges of south-eastern Brazil and the Andes. Analyses incorporating distances around these barriers suggest that the entire South American range of An. darlingi is at mutation-dispersal-drift equilibrium. Because the species is distributed throughout such a broad area, the limited dispersal across some landscape types promotes differentiation between otherwise proximate populations. Moreover, samples from the An. darlingi holotype location in Rio de Janeiro State are substantially derived from all other populations, implying that there may be additional genetic differences of epidemiological relevance. The results obtained contribute to our understanding of gene flow in this species and allow the formulation of human mosquito health protocols in light of the potential population differences in vector capacity or tolerance to control strategies. (C) 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 854-866.

Forest-obligate Sabethes mosquitoes suggest palaeoecological perturbations

The origin of tropical forest diversity has been hotly debated for decades. Although specific mechanisms vary, many such explanations propose some vicariance in the distribution of species during glacial cycles and several have been supported by genetic evidence in Neotropical taxa. However, no consensus exists with regard to the extent or time frame of the vicariance events. Here, we analyse the cytochrome oxidase II mitochondrial gene of 250 Sabethes albiprivus B mosquitoes sampled from western Sao Paulo in Brazil. There was very low population structuring among collection sites (Phi(ST) = 0.03, P = 0.04). Historic demographic analyses and the contemporary geographic distribution of genetic diversity suggest that the populations sampled are not at demographic equilibrium. Three distinct mitochondrial clades were observed in the samples, one of which differed significantly in its geographic distribution relative to the other two within a small sampling area (similar to 70 x 35 km). This fact, supported by the inability of maximum likelihood analyses to achieve adequate fits to simple models for the population demography of the species, suggests a more complex history, possibly involving disjunct forest refugia. This hypothesis is supported by a genetic signal of recent population growth, which is expected if population sizes of this forest-obligate insect increased during the forest expansions that followed glacial periods. Although a time frame cannot be reliably inferred for the vicariance event leading to the three genetic clades, molecular clock estimates place this at similar to 1 Myr before present.

Analytical Assessment of a Home Made Capillary Electrophoresis Equipment with Linear Charge Coupled Device for Visible Light Absorption Detection in the Determination of Food Dyes

The performance of modular home made capillary electrophoresis equipment with spectrophotometric detection, at a visible region by means of a miniaturized linear charge coupled device, was evaluated for the determination of four food dyes. This system presents a simple but efficient home made cell detection scheme. A computer program that converts the spectral data after each run into the electropherograms was developed to evaluate the analytical parameters. The dyes selected for analytical evaluation of the system were Brilliant Blue FCF, Fast Green FCF, Sunset Yellow FCF, and Amaranth. Separation was carried out in a 29cm length and 75 mu m I.D fused silica capillary, using 10mmolL-1 borate buffer at pH 9, with separation voltage of 7.5kV. The detection limits for the dyes were between 0.3 and 1.5mgL-1 and the method presented adequate linearity over the ranges studied, with correlation coefficients greater than 0.99. The method was applied for determination and quantification of these dyes in fruit juices and candies.

Un estudio sociolingüístico sobre el catalán : Los efectos de la inmersión lingüística

This thesis analyzes the current state of the language immersion program in Catalonia after its implementation 30 years ago, and after the immigration wave of the last decade. The language immersion is a method of teaching a second language using a language of instruction different than the students’ mother tongue. The Catalan authorities use this as a method for preserving Catalan in the society.The aim of this study is to examine the use of Catalan at school and outside of school by students who have followed the language immersion program. Language attitudes play an important role for the maintenance of a minority language, as Catalan. Therefore, in this study, the informants’ attitudes towards Catalan have also been measured. The method applied is a quantitative method where the informants have answered a written questionnaire. The results show a high level of knowledge of Catalan and its frequent use in the classroom. In contrast, outside of school the Castilian language is more often used. The informants seem to have a positive attitude towards Catalan.The conclusion is that the language immersion works satisfactory in a school context but often fails outside of school.

Solcellsdrivet FTX-system för miljonprogramshus : Tjärna Ängar, Borlänge

Projektet omfattade undersökning och framtagande av ett solcellssystem med förmåga att försörja ett FTX-system i ett flerbostadshus från miljonprogrammet med el. För att kunna bedöma storlek och utformning av komponenter har information tagits genom: Informationssökning via databaser, kurslitteratur och intervjuer Simuleringar av solceller i datorprogrammet PVSYST Modulering av ventilationskanaler i datorprogrammet MagiCAD Syftet var främst att undersöka om det gick att få fram ett teoretiskt fungerande system med avseende på både solceller och ventilation. Beroende på vad resultatet blev skulle även ekonomin i projektet undersökas. Undersökningen visade att det teoretiskt ska gå att installera solceller för elframställning som klarar av att täcka FTX-systemets elbehov på årsbasis. Solcellerna bedöms även producera tillräckligt med el för viss övrig elkrävande utrustning under stora delar av året. Det visade sig även att det skulle gå att få solcellerna ekonomiskt lönsamma om en kalkyltid på 14 år används. Metoden som använts för dessa resultat är noga beskriven och är med små förändringar tillämpbar för ett stort antal byggnader i det svenska byggnadsbeståndet. En viktig slutsats är att om fastighetsägarna kan se 15 år fram i tiden för en investering i solenergi, skulle det innebära inte bara miljömässiga utan även ekonomiska vinster. Det finns redan idag kunnande, teknik och produkter för att utvinna en stor del av fastigheternas elbehov genom solens energi.

Evaluation of the usefulness of 'Marvin'; a computerized assessment tool for investigative interviewers of children

This study examined the usefulness of a computerized developmental assessment tool, designed to provide investigative interviewers with knowledge about children's understanding of spatial, temporal, numerical, and color terms that may be relevant to the forensic setting. Specifically, the effect of the computer program (compared to a standard verbal and no assessment) was examined on 4- to 5-year-old children's recall of an independent event and their enjoyment of the interview process. In addition, children's performance on the computerized and verbal developmental assessment was compared with their performance when recalling the independent event. Overall, the children rated the assessment conducted on computer more favorably than the verbal assessment. Further, the verbal assessment elicited responses that were more consistent with their responses about the event than the computerized assessment. However, there was no difference in the accuracy and detail of children's responses about the independent event, irrespective of whether the children received the computerized or verbal assessment, or no assessment. Directions for future research are discussed.

Eliciting children's recall of events: how do computers compare with humans?

This study investigated the usefulness of an interactive computer program in eliciting children's reports about an event. Fifty-four 5–6- and fifty-nine  7–8-year old children participated in an event with their regular class teacher which involved several activities and a mildly negative secret. Four days and again 14 days later, the children were interviewed individually by computer (alone) or by a human interviewer. The computer program incorporated animation and audio whereby an animated figure asked the questions and the children were required to provide a verbal response. The accuracy and detail of the children’s reports was similar across the interview conditions. The children were more willing to review their answers with the computer than the adult interviewer. However, responses to the computer were less consistent across the interviews, and the children were less willing to disclose the secret in the second interview to the computer compared with the human interviewer. Overall, the computer revealed little benefit in eliciting children’s recall of the event over the standard face-to-face interview.

How well does club head speed correlate with gold handicaps?

The velocity at which a golf club impacts with a golf ball is known as club head speed. Although club head speed has been used to measure performance changes in a number of golf studies, it has not been validated as a golf performance measure. As handicap is the usual measure of performance, the purpose of this study was to investigate the relationship between club head speed and handicap, and to determine whether club head speed at impact is a valid measure of golfing performance. Forty-five male golfers aged 18–80 years, all with registered golfing handicaps (2–27), participated in this study. Each golfer performed 10 golf swings captured by a high-speed camera. Golfers' club head speeds were determined using Video Expert 2, a biomechanical computer program. Golfers with a lower handicap (ie, a better skill level) had faster club head speeds than higher handicap golfers. Linear regression analysis found club head speed to be highly correlated with handicap (r= 0.950). This relationship was described by the equation: In (club head speed)= 4.065 − 0.0214 x handicap. In conclusion, this study has shown that club head speed is a valid indicator of performance in golfers and may therefore be a useful performance measure in future laboratory-based studies.

Accuracy of body size estimation: Role of biopsychosocial variables

This study evaluated factors related to the perceptual disturbances of body image. Using a digital body image computer program, 191 participants (107 women, 82 men) adjusted an image of their body to the perceived actual size at five body regions; chest, waist, hips, thighs and calves. A neutral object (a vase) was also adjusted to partial out the level of perceptual distortion present with a neutral object. Men and women overestimated the size of the neutral object and their body image. Among women, overestimation was primarily predicted by high levels of depression, and media and peer influences to be thinner and increase muscles. Among men, overestimation was predicted by high BMI, media influences to lose weight and increase muscles, and peer influences to increase muscles. These findings suggest that perceptual accuracy of body image is primarily predicted by biopsychosocial influences.