A maximum likelihood algorithm for genome mapping of cytogenetic loci from meiotic configuration data.

Frequencies of meiotic configurations in cytogenetic stocks are dependent on chiasma frequencies in segments defined by centromeres, breakpoints, and telomeres. The expectation maximization algorithm is proposed as a general method to perform maximum likelihood estimations of the chiasma frequencies in the intervals between such locations. The estimates can be translated via mapping functions into genetic maps of cytogenetic landmarks. One set of observational data was analyzed to exemplify application of these methods, results of which were largely concordant with other comparable data. The method was also tested by Monte Carlo simulation of frequencies of meiotic configurations from a monotelodisomic translocation heterozygote, assuming six different sample sizes. The estimate averages were always close to the values given initially to the parameters. The maximum likelihood estimation procedures can be extended readily to other kinds of cytogenetic stocks and allow the pooling of diverse cytogenetic data to collectively estimate lengths of segments, arms, and chromosomes.

Modeling and optimization of populations subject to time-dependent mutation.

It has become clear that many organisms possess the ability to regulate their mutation rate in response to environmental conditions. So the question of finding an optimal mutation rate must be replaced by that of finding an optimal mutation schedule. We show that this task cannot be accomplished with standard population-dynamic models. We then develop a "hybrid" model for populations experiencing time-dependent mutation that treats population growth as deterministic but the time of first appearance of new variants as stochastic. We show that the hybrid model agrees well with a Monte Carlo simulation. From this model, we derive a deterministic approximation, a "threshold" model, that is similar to standard population dynamic models but differs in the initial rate of generation of new mutants. We use these techniques to model antibody affinity maturation by somatic hypermutation. We had previously shown that the optimal mutation schedule for the deterministic threshold model is phasic, with periods of mutation between intervals of mutation-free growth. To establish the validity of this schedule, we now show that the phasic schedule that optimizes the deterministic threshold model significantly improves upon the best constant-rate schedule for the hybrid and Monte Carlo models.

Avaliação probabilística de riscos à saúde humana em área contaminada por compostos organoclorados

Introdução: Áreas contaminadas por agentes químicos perigosos em regiões urbanas representam riscos importantes à saúde humana e ao ambiente. Vila Carioca, localizada na cidade de São Paulo, é uma área contaminada por pesticidas organoclorados considerada crítica, pela magnitude da contaminação, pela presença de pessoas residentes e pela complexidade de fontes da contaminação. Vários estudos de riscos já foram realizados por uma das empresas contaminadoras, no entanto, ainda há muita incerteza e controvérsias sobre os riscos à saúde da população. Objetivo: Avaliar o incremento de risco de câncer no tempo de vida para população exposta por meio de uma avaliação probabilística. Método: Foram utilizados dados secundários das contaminações obtidos nos estudos de riscos efetuados pela empresa produtora de pesticidas organoclorados e também em documentos oficiais dos órgãos de saúde e meio ambiente do Estado de São Paulo, resultantes do monitoramento da água e do solo na área residencial no período de 1997 a 2012, para 335 substâncias. Foram selecionadas substâncias carcinogênicas presentes na água subterrânea e solo com melhor conjunto de dados. Para a avaliação probabilística foi empregado o método de simulação de Monte Carlo, por meio do software comercial ModelRisk. Foram utilizados os métodos recomendados pela United States Environmental Protection Agency para a avaliação de risco de exposição dérmica e de incremento de riscos de câncer para substâncias mutagênicas. Foram consideradas a ingestão de água e solo, e contato dérmico com água. Resultados: O incremento de risco de câncer no tempo de vida (IRLT) foi de 4,7x10-3 e 4,1x10-2 para o percentil 50% e 95%, respectivamente. As rotas de exposição mais importantes foram ingestão e contato dérmico com a água subterrânea, seguido da ingestão de solo. O grupo etário que apresentou maior risco foi o das crianças de 0 a 2 anos de idade. Conclusão: Os riscos estimados são superiores aos valores considerados toleráveis. A avaliação realizada foi conservativa, mas ressalta-se que a restrição do uso da água subterrânea deve ser mantida e que a população deve ser devidamente informada dos riscos envolvidos na área, em especial, relacionados ao solo contaminado

Numerical test of the Cardy-Jacobsen conjecture in the site-diluted Potts model in three dimensions

We present a microcanonical Monte Carlo simulation of the site-diluted Potts model in three dimensions with eight internal states, partly carried out on the citizen supercomputer Ibercivis. Upon dilution, the pure model’s first-order transition becomes of the second order at a tricritical point. We compute accurately the critical exponents at the tricritical point. As expected from the Cardy-Jacobsen conjecture, they are compatible with their random field Ising model counterpart. The conclusion is further reinforced by comparison with older data for the Potts model with four states.

Equilibrium fluid-solid coexistence of hard spheres

We present a tethered Monte Carlo simulation of the crystallization of hard spheres. Our method boosts the traditional umbrella sampling to the point of making practical the study of constrained Gibbs’ free energies depending on several crystalline order parameters. We obtain high-accuracy estimates of the fluid-crystal coexistence pressure for up to 2916 particles (enough to accommodate fluid-solid interfaces). We are able to extrapolate to infinite volume the coexistence pressure [p_(co) = 11.5727(10)k_(B)T/σ^(3)] and the interfacial free energy [γ_({100}) = 0.636(11)k_(B)T/σ^(2)].

Best Alternatives to Cronbach's Alpha Reliability in Realistic Conditions: Congeneric and Asymmetrical Measurements

The Cronbach's alpha is the most widely used method for estimating internal consistency reliability. This procedure has proved very resistant to the passage of time, even if its limitations are well documented and although there are better options as omega coefficient or the different versions of glb, with obvious advantages especially for applied research in which the ítems differ in quality or have skewed distributions. In this paper, using Monte Carlo simulation, the performance of these reliability coefficients under a one-dimensional model is evaluated in terms of skewness and no tau-equivalence. The results show that omega coefficient is always better choice than alpha and in the presence of skew items is preferable to use omega and glb coefficients even in small samples.

Análise da dinâmica e quantificação metabólica de imagens de medicina nuclear na modalidade PET/CT.

A presença da Medicina Nuclear como modalidade de obtenção de imagens médicas é um dos principais procedimentos utilizados hoje nos centros de saúde, tendo como grande vantagem a capacidade de analisar o comportamento metabólico do paciente, traduzindo-se em diagnósticos precoces. Entretanto, sabe-se que a quantificação em Medicina Nuclear é dificultada por diversos fatores, entre os quais estão a correção de atenuação, espalhamento, algoritmos de reconstrução e modelos assumidos. Neste contexto, o principal objetivo deste projeto foi melhorar a acurácia e a precisão na análise de imagens de PET/CT via processos realísticos e bem controlados. Para esse fim, foi proposta a elaboração de uma estrutura modular, a qual está composta por um conjunto de passos consecutivamente interligados começando com a simulação de phantoms antropomórficos 3D para posteriormente gerar as projeções realísticas PET/CT usando a plataforma GATE (com simulação de Monte Carlo), em seguida é aplicada uma etapa de reconstrução de imagens 3D, na sequência as imagens são filtradas (por meio do filtro de Anscombe/Wiener para a redução de ruído Poisson caraterístico deste tipo de imagens) e, segmentadas (baseados na teoria Fuzzy Connectedness). Uma vez definida a região de interesse (ROI) foram produzidas as Curvas de Atividade de Entrada e Resultante requeridas no processo de análise da dinâmica de compartimentos com o qual foi obtida a quantificação do metabolismo do órgão ou estrutura de estudo. Finalmente, de uma maneira semelhante imagens PET/CT reais fornecidas pelo Instituto do Coração (InCor) do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP) foram analisadas. Portanto, concluiu-se que a etapa de filtragem tridimensional usando o filtro Anscombe/Wiener foi relevante e de alto impacto no processo de quantificação metabólica e em outras etapas importantes do projeto em geral.

Evaluación de la susceptibilidad de las laderas a sufrir inestabilidades inducidas por terremotos: aplicación a la cuenca de drenaje del río Serpis (provincia de Alicante)

Se ha realizado un análisis para estimar la susceptibilidad de las laderas, en suelos de la cuenca de drenaje del río Serpis, a sufrir inestabilidades inducidas por terremotos. Para ello, se ha utilizado el denominado método de Newmark, que ha sido convenientemente modificado para contemplar la variabilidad que, de forma natural, se observa en las propiedades geotécnicas de los materiales. En el cálculo, se ha efectuado una simulación Monte Carlo, donde todas las propiedades geotécnicas que intervienen son tratadas como variables aleatorias. Los resultados obtenidos están expresados como probabilidad de que la aceleración crítica del talud sea menor o igual que 0.1g. Las susceptibilidades más elevadas se observan cuando los materiales están secos, pero en tal caso la extensión de territorio afectado es pequeña. En cambio, cuando el suelo está saturado se observa que gran parte del territorio presenta susceptibilidad Media o Baja, incluso con pendientes de 6 – 10º, frente a susceptibilidad Muy Baja – Nula, que los caracteriza cuando se encuentra seco. Se ha analizado también la posición de las zonas de mayor susceptibilidad con respecto a elementos constructivos existentes en el área.

Background Measurement Techniques and Sensitivity Studies for the SNO+ Neutrinoless Double Beta Decay Search

The control of radioactive backgrounds will be key in the search for neutrinoless double beta decay at the SNO+ experiment. Several aspects of the SNO+ back- grounds have been studied. The SNO+ tellurium purification process may require ultra low background ethanol as a reagent. A low background assay technique for ethanol was developed and used to identify a source of ethanol with measured 238U and 232Th concentrations below 2.8 10^-13 g/g and 10^-14 g/g respectively. It was also determined that at least 99:997% of the ethanol can be removed from the purified tellurium using forced air ow in order to reduce 14C contamination. In addition, a quality-control technique using an oxygen sensor was studied to monitor 222Rn contamination due to air leaking into the SNO+ scintillator during transport. The expected sensitivity of the technique is 0.1mBq/L or better depending on the oxygen sensor used. Finally, the dependence of SNO+ neutrinoless double beta decay sensitivity on internal background levels was studied using Monte Carlo simulation. The half-life limit to neutrinoless double beta decay of 130Te after 3 years of operation was found to be 4.8 1025 years under default conditions.

The burden of major depression avoidable by longer-term treatment strategies

Background: Major depression is the largest single cause of nonfatal disease burden in Australia. Effective drug and psychological treatments exist, yet are underused. Objective: To quantify the burden of disease currently averted in people seeking care for major depression and the amount of disease burden that could be averted in these people under optimal episodic and maintenance treatment strategies. Design: Modeling impact of current and optimal treatment strategies based on secondary analysis of mental health survey data, studies of the natural history of major depression, and meta-analyses of effectiveness data. Monte Carlo simulation of uncertainty in the model. Setting: The cohort of Australian adults experiencing an episode of major depression in 2000 are modeled through "what if" scenarios of no treatment, current treatment, and optimal treatment strategies with cognitive behavioral therapy or antidepressant drug treatment. Main Outcome Measure: Disability-Adjusted Life Year. Results: Current episodic treatment averts 9% (95% uncertainty interval, 6%-12%) of the disease burden of major depression in Australian adults. Optimal episodic treatment with cognitive behavioral therapy could avert 28% (95% uncertainty interval, 19%-39%) of this disease burden, and with drugs 24% (95% uncertainty interval, 19%-30%) could be averted. During the 5 years after an episode of major depression, current episodic treatment patterns would avert 13% (95% uncertainty interval, 10%-17%) of Disability-Adjusted Life Years, whereas maintenance drug treatment could avert 50% (95% uncertainty interval, 40%-60%) and maintenance cognitive behavioral therapy could avert 52% (95% uncertainty interval, 42%-64%), even if adherence of around 60% is taken into account. Conclusions: Longer-term maintenance drug or psychological treatment strategies are required to make significant inroads into the large disease burden associated with major depression in the Australian population.

Colorectal cancer screening in Australia: an economic evaluation of a potential biennial screening program using faecal occult blood tests

Objective: To evaluate whether the introduction of a national, co-ordinated screening program using the faecal occult blood test represents 'value-for-money' from the perspective of the Australian Government as third-party funder. Methods: The annual equivalent costs and consequences of a biennial screening program in 'steady-state' operation were estimated for the Australian population using 1996 as the reference year. Disability-adjusted life years (DALYs) and the years of life lost (YLLs) averted, and the health service costs were modelled, based on the epidemiology and the costs of colorectal cancer in Australia together with the mortality reduction achieved in randomised controlled trials. Uncertainty in the model was examined using Monte Carlo simulation methods. Results: We estimate a minimum or 'base program' of screening those aged 55 to 69 years could avert 250 deaths per annum (95% uncertainty interval 99-400), at a gross cost of $A55 million (95% UI $A46 million to $A96 million) and a gross incremental cost-effectiveness ratio of $A17,000/DALY (95% UI $A13,000/DALY to $A52,000/DALY). Extending the program to include 70 to 74-year-olds is a more effective option (cheaper and higher health gain) than including the 50 to 54-year-olds. Conclusions: The findings of this study support the case for a national program directed at the 55 to 69-year-old age group with extension to 70 to 74-year-olds if there are sufficient resources. The pilot tests recently announced in Australia provide an important opportunity to consider the age range for screening and the sources of uncertainty, identified in the modelled evaluation, to assist decisions on implementing a full national program.

Effects of potential models on the adsorption of ethane and ethylene on graphitized thermal carbon black. Study of two-dimensional critical temperature and isosteric heat versus loading

Adsorption of ethylene and ethane on graphitized thermal carbon black and in slit pores whose walls are composed of graphene layers is studied in detail to investigate the packing efficiency, the two-dimensional critical temperature, and the variation of the isosteric heat of adsorption with loading and temperature. Here we used a Monte Carlo simulation method with a grand canonical Monte Carlo ensemble. A number of two-center Lennard-Jones (LJ) potential models are investigated to study the impact of the choice of potential models in the description of adsorption behavior. We chose two 2C-LJ potential models in our investigation of the (i) UA-TraPPE-LJ model of Martin and Siepmann (J. Phys. Chem. B 1998,102, 25692577) for ethane and Wick et al. (J. Phys. Chem. B 2000,104, 8008-8016) for ethylene and (ii) AUA4-LJ model of Ungerer et al. (J. Chem. Phys. 2000,112, 5499-5510) for ethane and Bourasseau et al. (J. Chem. Phys. 2003, 118, 3020-3034) for ethylene. These models are used to study the adsorption of ethane and ethylene on graphitized thermal carbon black. It is found that the solid-fluid binary interaction parameter is a function of adsorbate and temperature, and the adsorption isotherms and heat of adsorption are well described by both the UA-TraPPE and AUA models, although the UA-TraPPE model performs slightly better. However, the local distributions predicted by these two models are slightly different. These two models are used to explore the two-dimensional condensation for the graphitized thermal carbon black, and these values are 110 K for ethylene and 120 K for ethane.

Prediction of high-pressure adsorption equilibrium of supercritical gases using density functional theory

In this paper, we present the results of the prediction of the high-pressure adsorption equilibrium of supercritical. gases (Ar, N-2, CH4, and CO2) on various activated carbons (BPL, PCB, and Norit R1 extra) at various temperatures using a density-functional-theory-based finite wall thickness (FWT) model. Pore size distribution results of the carbons are taken from our recent previous work 1,2 using this approach for characterization. To validate the model, isotherms calculated from the density functional theory (DFT) approach are comprehensively verified against those determined by grand canonical Monte Carlo (GCMC) simulation, before the theoretical adsorption isotherms of these investigated carbons calculated by the model are compared with the experimental adsorption measurements of the carbons. We illustrate the accuracy and consistency of the FWT model for the prediction of adsorption isotherms of the all investigated gases. The pore network connectivity problem occurring in the examined carbons is also discussed, and on the basis of the success of the predictions assuming a similar pore size distribution for accessible and inaccessible regions, it is suggested that this is largely related to the disordered nature of the carbon.

Process systems modelling and applications in granulation: A review

Granulation is one of the fundamental operations in particulate processing and has a very ancient history and widespread use. Much fundamental particle science has occurred in the last two decades to help understand the underlying phenomena. Yet, until recently the development of granulation systems was mostly based on popular practice. The use of process systems approaches to the integrated understanding of these operations is providing improved insight into the complex nature of the processes. Improved mathematical representations, new solution techniques and the application of the models to industrial processes are yielding better designs, improved optimisation and tighter control of these systems. The parallel development of advanced instrumentation and the use of inferential approaches provide real-time access to system parameters necessary for improvements in operation. The use of advanced models to help develop real-time plant diagnostic systems provides further evidence of the utility of process system approaches to granulation processes. This paper highlights some of those aspects of granulation. (c) 2005 Elsevier Ltd. All rights reserved.

Modelling nucleation in wet granulation

Nucleation is the first stage in any granulation process where binder liquid first comes into contact with the powder. This paper investigates the nucleation process where binder liquid is added to a fine powder with a spray nozzle. The dimensionless spray flux approach of Hapgood et al. (Powder Technol. 141 (2004) 20) is extended to account for nonuniform spray patterns and allow for overlap of nuclei granules rather than spray drops. A dimensionless nuclei distribution function which describes the effects of the design and operating parameters of the nucleation process (binder spray characteristics, the nucleation area ratio between droplets and nuclei and the powder bed velocity) on the fractional surface area coverage of nuclei on a moving powder bed is developed. From this starting point, a Monte Carlo nucleation model that simulates full nuclei size distributions as a function of the design and operating parameters that were implemented in the dimensionless nuclei distribution function is developed. The nucleation model was then used to investigate the effects of the design and operating parameters on the formed nuclei size distributions and to correlate these effects to changes of the dimensionless nuclei distribution function. Model simulations also showed that it is possible to predict nuclei size distributions beyond the drop controlled nucleation regime in Hapgood's nucleation regime map. Qualitative comparison of model simulations and experimental nucleation data showed similar shapes of the nuclei size distributions. In its current form, the nucleation model can replace the nucleation term in one-dimensional population balance models describing wet granulation processes. Implementation of more sophisticated nucleation kinetics can make the model applicable to multi-dimensional population balance models.