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.

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.

Avaliação morfométrica da área do epidídimo e dos dúctulos eferentes e ductos epididimários da codorna doméstica, no decorrer do ano

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Trajetória do hospital dia Dr. Elger nunes: um recorte histórico da psiquiatria e saúde mental no Rio Grande do Norte

In Brazil, the mental health network proposed by the Psychiatric Reform inserts the intermediate and replacement services in the pursuit of alignment or resocialization of patients with mental and behavioral disorder in the community. Was adopted, among other services, the Center for Psychosocial Care, Home Therapy, Sheltered Home, Day Hospital and psychiatric beds in general hospital. In this context, the State of Rio Grande do Norte implanted the Day Hospital Dr. Elger Nunes (HDEN) in Natal / RN in 1996, linked to State Department of Public Health. At HDEN happened a multi and interdisciplinary therapeutic work, besides being the scene of disciplinary practices, and extension projects for graduate courses in Higher Education Institutions in the city. However, with the process of decentralization of local services, the hospital was terminated by an administrative state act in 2006, leaving damage to the activities provided to users, disciplinary practices and extension activities. From this breakdown, the objective was to narrate the trajectory of HDEN through a multidisciplinary team of professionals and teachers who used it as a field of disciplinary practices. It is characterized as a documental and qualitative, backed in the technique of thematic oral history, following the phases: authorization of the interviewee, interview recording, transcription, textualization and transcreation of the material obtained. We used documents, ordinances, general reports of activities, among others, plus interviews to fifteen employees who used this service, being thirteen part of the multidisciplinary team of professionals and two graduation professors of health care area, nursing and medicine. The stories collected were organized according to the technique chosen, respecting its steps. In preparing the body subjected to ALCESTE computer program, priority was given to the vital tone for the formation of categories and classes elected by the program, structured in three thematic areas. In the first axis, called Trajectory of HDEN, were recalled the beginning of its activities, the steps of that time, their activities, and its actors - users, families, professionals, and teaching practices. The second axis has dealt with the process of extinction of HDEN, rescuing the feelings of employees, the main reasons given at the time and immediate postextinction scenario. And the third axis revealed in an articulated form the situation of mental health in Natal / RN, listing to the challenges and prospects for the psychosocial care, starting from the trajectory of HDEN with emphasis on activities. Moreover, the trajectory of HDEN provides recognition of the historical basis outlined in the constitution of the network of substitute services present in the current scenario of psychosocial care in the city of Natal and in RN.

Caracterização de estruturas planares com substratos Iso/Anisotrópicos truncados através da técnica da ressonância transversa modificada

This work presents a theoretical and numerical analysis using the transverse resonance technique (TRT) and a proposed MTRT applied in the analysis of the dispersive characteristics of microstrip lines built on truncated isotropic and anisotropic dielectric substrates. The TRT uses the transmission lines model in the transversal section of the structure, allowing to analyze its dispersive behavior. The difference between TRT and MTRT consists basically of the resonance direction. While in the TRT the resonance is calculated in the same direction of the metallic strip normal axis, the MTRT considers the resonance in the metallic strip parallel plane. Although the application of the MTRT results in a more complex equivalent circuit, its use allows some added characterization, like longitudinal section electric mode (LSE) and longitudinal section magnetic mode (LSM), microstrips with truncated substrate, or structures with different dielectric regions. A computer program using TRT and MTRT proposed in this work is implemented for the characterization of microstrips on truncated isotropic and anisotropic substrates. In this analysis, propagating and evanescent modes are considered. Thus, it is possible to characterize both the dominant and higher order modes of the structure. Numerical results are presented for the effective permittivity, characteristic impedance and relative phase velocity for microstrip lines with different parameters and dimensions of the dielectric substrate. Agreement with the results obtained in the literature are shown, as well as experimental results. In some cases, the convergence analysis is also performed by considering the limiting conditions, like particular cases of isotropic materials or structures with dielectric of infinite size found in the literature. The numerical convergence of the formulation is also analyzed. Finally, conclusions and suggestions for the continuity of this work are presented

Desenvolvimento de Modelos no Programa DigSILENT PowerFactoryTM para o Estudo de Estabilidade Transitória em Sistemas Elétricos de Potência com Aerogerador

This work presents a description of models development at DigSILENT PowerFactoryT M program for the transient stability study in power systems with wind turbine. The main goal is to make available means to use a dynamic simulation program in power systems, widely published, and utilize it as a tool that helps in programs results evaluations used for this intent. The process of simulations and analyses results starts after the models setting description phase. The results obtained by the DigSILENT PowerFactoryT M and ATP, program chosen to the validation also international recognized, are compared during this phase. The main tools and guide lines of PowerFactoryT M program use are presented here, directing these elements to the solution of the approached problem. For the simulation it is used a real system which it will be connected a wind farm. Two different technologies of wind turbines were implemented: doublyfed induction generator with frequency converter, connecting the rotor to the stator and to the grid, and synchronous wind generator with frequency converter, interconnecting the generator to the grid. Besides presenting the basic conceptions of dynamic simulation, it is described the implemented control strategies and models of turbine and converters. The stability of the wind turbine interconnected to grid is analyzed in many operational conditions, resultant of diverse kinds of disturbances

Maximização da penetração da geração distribuída através do algoritmo de otimização nuvem de partículas

This work develops a methodology for defining the maximum active power being injected into predefined nodes in the studied distribution networks, considering the possibility of multiple accesses of generating units. The definition of these maximum values is obtained from an optimization study, in which further losses should not exceed those of the base case, i.e., without the presence of distributed generation. The restrictions on the loading of the branches and voltages of the system are respected. To face the problem it is proposed an algorithm, which is based on the numerical method called particle swarm optimization, applied to the study of AC conventional load flow and optimal load flow for maximizing the penetration of distributed generation. Alternatively, the Newton-Raphson method was incorporated to resolution of the load flow. The computer program is performed with the SCILAB software. The proposed algorithm is tested with the data from the IEEE network with 14 nodes and from another network, this one from the Rio Grande do Norte State, at a high voltage (69 kV), with 25 nodes. The algorithm defines allowed values of nominal active power of distributed generation, in percentage terms relative to the demand of the network, from reference values

Antenas planares integradas com FSSs para aplicações em sistemas de comunicações sem fio

This work presents a theoretical and experimental analysis about the properties of microstrip antennas with integrated frequency selective surfaces (Frequency Selective Surface - FSS). The integration occurs through the insertion of the FSS on ground plane of microstrip patch antenna. This integration aims to improve some characteristics of the antennas. The FSS using patch-type elements in square unit cells. Specifically, the simulated results are obtained using the commercial computer program CST Studio Suite® version 2011. From a standard antenna, designed to operate in wireless communication systems of IEEE 802.11 a / b / g / n the dimensions of the FSS are varied to obtain an optimization of some antenna parameters such as impedance matching and selectivity in the operating bands. After optimization of the investigated parameters are built two prototypes of microstrip patch antennas with and without the FSS ground plane. Comparisons are made of the results with the experimental results by 14 ZVB network analyzer from Rohde & Schwarz ®. The comparison aims to validate the simulations performed and show the improvements obtained with the FSS in integrated ground plane antenna. In the construction of prototypes, we used dielectric substrates of the type of Rogers Corporation RT-3060 with relative permittivity equal to 10.2 and low loss tangent. Suggestions for continued work are presented