Bayesian model comparison with un-normalised likelihoods

Models for which the likelihood function can be evaluated only up to a parameter-dependent unknown normalizing constant, such as Markov random field models, are used widely in computer science, statistical physics, spatial statistics, and network analysis. However, Bayesian analysis of these models using standard Monte Carlo methods is not possible due to the intractability of their likelihood functions. Several methods that permit exact, or close to exact, simulation from the posterior distribution have recently been developed. However, estimating the evidence and Bayes’ factors for these models remains challenging in general. This paper describes new random weight importance sampling and sequential Monte Carlo methods for estimating BFs that use simulation to circumvent the evaluation of the intractable likelihood, and compares them to existing methods. In some cases we observe an advantage in the use of biased weight estimates. An initial investigation into the theoretical and empirical properties of this class of methods is presented. Some support for the use of biased estimates is presented, but we advocate caution in the use of such estimates.

Bayesian coalescent analysis reveals a high rate of molecular evolution in GB virus C

GB virus C/hepatitis G (GBV-C) is an RNA virus of the family Flaviviridae. Despite replicating with an RNA-dependent RNA polymerase, some previous estimates of rates of evolutionary change in GBV-C suggest that it fixes mutations at the anomalously low rate of similar to 100(-7) nucleotide substitution per site, per year. However, these estimates were largely based on the assumption that GBV-C and its close relative GBV-A (New World monkey GB viruses) codiverged with their primate hosts over millions of years. Herein, we estimated the substitution rate of GBV-C using the largest set of dated GBV-C isolates compiled to date and a Bayesian coalescent approach that utilizes the year of sampling and so is independent of the assumption of codivergence. This revealed a rate of evolutionary change approximately four orders of magnitude higher than that estimated previously, in the range of 10(-2) to 10(-3) sub/site/year, and hence in line with those previously determined for RNA viruses in general and the Flaviviridae in particular. In addition, we tested the assumption of host-virus codivergence in GBV-A by performing a reconciliation analysis of host and virus phylogenies. Strikingly, we found no statistical evidence for host-virus codivergence in GBV-A, indicating that substitution rates in the GB viruses should not be estimated from host divergence times.

Endogenous protection in Mercosul: an empirical analysis

This paper analyses the equilibrium structure of protection in Mercosul, developing empirical analyses based on the literature ensuing from the sequence of models set forth by Grossman and Helpman since 1994. Not only Mercosul’s common external tariff (CET) may be explained under a political economy perspective, but the existence of deviations, both at the level of the external tariffs and at that of the internal ones, make it interesting to contrast several structures under this approach. Different general equilibrium frameworks, in which governments are concerned with campaign contributions and with the welfare of the average voter, while organized special-interest groups care only about the welfare of their members, are used as the theoretical basis of the empirical tests. We build a single equation for explaining the CET and two fourequations systems (one equation for each member) for explaining deviations from the CET and from the internal free trade between members. The results (at the two-digit level) shed an interesting light on the sectoral dynamics of protection in each country; notably, Brazil seems to fit in better in the model framework, followed by Uruguay. In the case of the CET, and of deviations from it, the interaction between the domestic lobbies in the four countries plays a major role. There is also suggestion that the lobby structure that bid for deviations, be they internal or external, differs from the one which bid for the CET.

Real spectra for the non-Hermitian Dirac equation in 1+1 dimensions with the most general coupling

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Evolução tectono-estrutural do Campo de Xaréu (Sub-bacia de Mundaú, Bacia do Ceará - NE do Brasil: abordagem multiescala e pluriferramental

The Xaréu Oil Field, located in the center-southern portion of the Mundaú Sub-Basin (eastern portion of the Ceará Basin), is characterized by a main Iramework of NW-trending and NE-dipping faults. The faults in the Xaréu Oil Field, among which the Xaréu Fautt stands out, are arranged according to an extensional-listriclan, rooted on a detachment surface corresponding to the Mundaú Fault, the border fautt of Mundaú Sub-Basin. During the tectonic-structural evolution of the Xaréu Oil Field and the Mundaú Sub-Basin, the Mundaú Fault played a crucial role on the control of the geometry of both compartments. The main carbonatic unit in the Xaréu Oil Field, named the Trairí Member(Paracuru Formation of Late Aptian to Early Albian age), contains the largest oil volume in the field, concentrated in structurally-controlled accumulations. The Trairí Member is composed by a variety of carbonatic rocks (massive, bedded or laminated calcilutites, ostracodites, calcarenites and carbonatic rudites, all of them presenting variable degrees of dolomitization). The carbonatic rocks are interbedded into thick packages of black shales and marls, besides local beds of siliciclastic conglomerates, sandstones, siltnes and argillites. From the spatial association and the genetic relationships between the carbonatic and siliciclastic units, it is possible to group them in three lithofacies associations (Marginal Plain, Ramp and Lacustrine Interior) that, together, were developed in a lacustrine system associated to a marginal sabkha. Structural studies based on drill coresthat sample the Trairí Member in the Xaréu Oil Field allowed to characterize two generations of meso- to microscale structures: the D1 group presents a typical hydroplastic character, being characterized by intra/interstratal to oblique-bedding shear zones. The hydroplastic character related to these structures allowed to infer their development at an early-lithilication stage of the Trairí Member, leading to infer an Early Cretaceous age to them. The second group of structures identified in the drill cores, nominated D2 and ascribed to a Neogene age, presents a strictly brttle character, being typilied by normal faults and slickenfibers of re-crystallized clayminerals, ali olthem displaying variable orientations. Although the present faults in the Xaréu Oil Field (and, consequently, in the Mundaú Sub-Basin) were classically relerred as struetures of essentially normal displacement, the kinematics analysis of the meso-to microscaie D1 struetures in the drill cores led to deline oblique displacements (normal with a clockwise strike-slip component) to these faults, indicating a main tectonic transport to ENE. These oblique movements would be responsible for the installation of a transtensive context in the Mundaú Sub-Basin, as part of the transcurrent to translormant opening of the Atlantic Equatorial Margin. The balancing of four struetural cross-sections ofthe Xaréu Oil Field indicates that the Mundaú Fault was responsible for more than 50% of the total stretching (ß factor) registered during the Early Aptian. At the initial stages of the "rifting", during Early Aptianuntil the Holocene, the Mundaú Sub-Basin (and consequently the Xaréu Oil Fleld) accumulated a total stretching between 1.21 and 1.23; in other words, the crust in this segment of the Atlantic Equatorial Margin was subjeeted to an elongation of about 20%. From estimates of oblique displacements related to the faults, it ws possible to construct diagrams that allow the determination of stretching factors related to these displacements. Using these diagrams and assuming the sense 01 dominant teetonictransport towards ENE, it was possible to calculate the real stretching lactors related to the oblique movement 0 of the faults in the Mundaú Sub-Basin. which reached actual values between 1.28 and 1.42. ln addnion to the tectonic-structural studies in the Xaréu Oil Field, the interpretation of remote sensing products, coupled wnh characterization of terrain analogues in seleeted areas along the northern Ceará State (continental margins of the Ceará and Potiguar basins), provided addnional data and constraints about the teetonic-structural evolution of the oil lield. The work at the analogue sites was particularly effective in the recognition and mapping, in semidetail scale, several generations of struetures originated under a brittle regime. Ali the obtained information (from the Xaréu Oil Field, the remote sensor data and the terrain analogues) were jointly interpreted, culminating with the proposnion of an evolutionary model lor this segment of the Atlantic Equatorial Margin; this model that can be applied to the whole Margin, as well. This segmentof the Atlantic Equatorial Margin was delormedin an early E-W (when considered lhe present-day position of the South American Plate) transcurrent to transform regime with dextral kinematics, started Irom, at least, the Early Aptian, which left its record in several outcrops along the continental margin of the Ceará State and specilically in the Xaréu off Field. The continuous operation of the regime, through the Albian and later periods, led to the definitive separation between the South American and African plates, with the formation of oceanic lithosphere between the two continental blocks, due to the emplacement off spreading centers. This process involved the subsequent transition of the transcurrent to a translorm dextral regime, creating lhe Equatorial Atlantic Oceano With the separation between the South American and African plates already completed and the increasing separation between lhe continental masses, other tecton ic mechanisms began to act during the Cenozoic (even though the Cretaceous tectonic regime lasted until the Neogene), like an E-W compressive stress líeld (related to the spreading olthe oceanic floor along lhe M id-Atlantic Ridge and to the compression of the Andean Chain) effective Irom the Late Cretaceous, and a state of general extension olthe horizontal surface (due to the thermal uplift ofthe central portion of Borborema Province), effective during the Neogene. The overlap of these mechanisms during the Cenozoic led to the imprint of a complex tectonic framework, which apparently influenced the migration and entrapment 01 hydrocarbon in the Ceará Basin

A General Solution of the Fokker-Planck Equation

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

General method for reducing the two-body Dirac equation

A semirelativistic two-body Dirac equation with an enlarged set of phenomenological potentials, including Breit-type terms, is investigated for the general case of unequal masses. Solutions corresponding to definite total angular momentum and parity are shown to fall into two classes, each one being obtained by solving a system of four coupled first-order radial differential equations. The reduction of each of these systems to a pair of coupled Schrödinger-type equations is also discussed. © 1992 American Institute of Physics.

Applying the National Institute for Clinical Excellence criteria to patients treated with the Genous (TM) Bio-engineered R stent (TM): a sub-study of the e-HEALING (Healthy Endothelial Accelerated Lining Inhibits Neointimal Growth) worldwide registry

The National Institute for Clinical Excellence (NICE) guidelines recommend the use of bare-metal stents (BMS) in non-complex lesions with a low risk of restenosis (diameter a parts per thousand yen3 mm and lesion length a parts per thousand currency sign15 mm) and the use of drug-eluting stents (DES) in more complex lesions with a high risk of restenosis (diameter < 3.0 mm or lesion length > 15 mm). However, the guidelines were created based on studies evaluating BMS and DES only. We performed an analysis of patients undergoing non-urgent percutaneous coronary intervention with the novel endothelial cell capturing stent (ECS). The ECS is coated with CD34(+) antibodies that attract circulating endothelial progenitor cells to the stent surface, thereby accelerating the endothelialization of the stented area. We analyzed all patients enrolled in the worldwide e-HEALING registry that met the NICE criteria for either low-risk or high-risk lesions and were treated with a parts per thousand yen1 ECS. The main study outcome was target vessel failure (TVF) at 12-month follow-up, defined as the composite of cardiac death or MI and target vessel revascularization (TVR). A total of 4,241 patients were assessed in the current analysis. At 12-month follow-up, TVF occurred in 7.0% of the patients with low-risk lesions and in 8.8% of the patients with high-risk lesions (p = 0.045). When evaluating the diabetic patients versus the non-diabetic patients per risk group, no significant differences were found in TVF, MI or TVR in either risk group. The ECS shows good clinical outcomes in lesions carrying either a high or a low risk of restenosis according to the NICE guidelines with comparable rates of cardiac death, myocardial infarction, and stent thrombosis. The TVF rate with ECS was slightly higher in patients with high-risk lesions, driven by higher clinically driven TLR. The risk of restenosis with ECS in patients carrying high-risk lesions needs to be carefully considered relative to other risks associated with DES. Furthermore, the presence of diabetes mellitus did not influence the incidence of TVF in either risk group.

Human thermal comfort: an irreversibility-based approach emulating empirical clothed-body correlations and the conceptual energy balance equation

Exergetic analysis can provide useful information as it enables the identification of irreversible phenomena bringing about entropy generation and, therefore, exergy losses (also referred to as irreversibilities). As far as human thermal comfort is concerned, irreversibilities can be evaluated based on parameters related to both the occupant and his surroundings. As an attempt to suggest more insights for the exergetic analysis of thermal comfort, this paper calculates irreversibility rates for a sitting person wearing fairly light clothes and subjected to combinations of ambient air and mean radiant temperatures. The thermodynamic model framework relies on the so-called conceptual energy balance equation together with empirical correlations for invoked thermoregulatory heat transfer rates adapted for a clothed body. Results suggested that a minimum irreversibility rate may exist for particular combinations of the aforesaid surrounding temperatures. By separately considering the contribution of each thermoregulatory mechanism, the total irreversibility rate rendered itself more responsive to either convective or radiative clothing-influenced heat transfers, with exergy losses becoming lower if the body is able to transfer more heat (to the ambient) via convection.

Essays on Bayesian Inference for Social Networks

This thesis presents Bayesian solutions to inference problems for three types of social network data structures: a single observation of a social network, repeated observations on the same social network, and repeated observations on a social network developing through time. A social network is conceived as being a structure consisting of actors and their social interaction with each other. A common conceptualisation of social networks is to let the actors be represented by nodes in a graph with edges between pairs of nodes that are relationally tied to each other according to some definition. Statistical analysis of social networks is to a large extent concerned with modelling of these relational ties, which lends itself to empirical evaluation. The first paper deals with a family of statistical models for social networks called exponential random graphs that takes various structural features of the network into account. In general, the likelihood functions of exponential random graphs are only known up to a constant of proportionality. A procedure for performing Bayesian inference using Markov chain Monte Carlo (MCMC) methods is presented. The algorithm consists of two basic steps, one in which an ordinary Metropolis-Hastings up-dating step is used, and another in which an importance sampling scheme is used to calculate the acceptance probability of the Metropolis-Hastings step. In paper number two a method for modelling reports given by actors (or other informants) on their social interaction with others is investigated in a Bayesian framework. The model contains two basic ingredients: the unknown network structure and functions that link this unknown network structure to the reports given by the actors. These functions take the form of probit link functions. An intrinsic problem is that the model is not identified, meaning that there are combinations of values on the unknown structure and the parameters in the probit link functions that are observationally equivalent. Instead of using restrictions for achieving identification, it is proposed that the different observationally equivalent combinations of parameters and unknown structure be investigated a posteriori. Estimation of parameters is carried out using Gibbs sampling with a switching devise that enables transitions between posterior modal regions. The main goal of the procedures is to provide tools for comparisons of different model specifications. Papers 3 and 4, propose Bayesian methods for longitudinal social networks. The premise of the models investigated is that overall change in social networks occurs as a consequence of sequences of incremental changes. Models for the evolution of social networks using continuos-time Markov chains are meant to capture these dynamics. Paper 3 presents an MCMC algorithm for exploring the posteriors of parameters for such Markov chains. More specifically, the unobserved evolution of the network in-between observations is explicitly modelled thereby avoiding the need to deal with explicit formulas for the transition probabilities. This enables likelihood based parameter inference in a wider class of network evolution models than has been available before. Paper 4 builds on the proposed inference procedure of Paper 3 and demonstrates how to perform model selection for a class of network evolution models.

Empirical and fundamental mechanical tests in the evaluation of dough and bread rheological properties

Bread dough and particularly wheat dough, due to its viscoelastic behaviour, is probably the most dynamic and complicated rheological system and its characteristics are very important since they highly affect final products’ textural and sensorial properties. The study of dough rheology has been a very challenging task for many researchers since it can provide numerous information about dough formulation, structure and processing. This explains why dough rheology has been a matter of investigation for several decades. In this research rheological assessment of doughs and breads was performed by using empirical and fundamental methods at both small and large deformation, in order to characterize different types of doughs and final products such as bread. In order to study the structural aspects of food products, image analysis techniques was used for the integration of the information coming from empirical and fundamental rheological measurements. Evaluation of dough properties was carried out by texture profile analysis (TPA), dough stickiness (Chen and Hoseney cell) and uniaxial extensibility determination (Kieffer test) by using a Texture Analyser; small deformation rheological measurements, were performed on a controlled stress–strain rheometer; moreover the structure of different doughs was observed by using the image analysis; while bread characteristics were studied by using texture profile analysis (TPA) and image analysis. The objective of this research was to understand if the different rheological measurements were able to characterize and differentiate the different samples analysed. This in order to investigate the effect of different formulation and processing conditions on dough and final product from a structural point of view. For this aim the following different materials were performed and analysed: - frozen dough realized without yeast; - frozen dough and bread made with frozen dough; - doughs obtained by using different fermentation method; - doughs made by Kamut® flour; - dough and bread realized with the addition of ginger powder; - final products coming from different bakeries. The influence of sub-zero storage time on non-fermented and fermented dough viscoelastic performance and on final product (bread) was evaluated by using small deformation and large deformation methods. In general, the longer the sub-zero storage time the lower the positive viscoelastic attributes. The effect of fermentation time and of different type of fermentation (straight-dough method; sponge-and-dough procedure and poolish method) on rheological properties of doughs were investigated using empirical and fundamental analysis and image analysis was used to integrate this information throughout the evaluation of the dough’s structure. The results of fundamental rheological test showed that the incorporation of sourdough (poolish method) provoked changes that were different from those seen in the others type of fermentation. The affirmative action of some ingredients (extra-virgin olive oil and a liposomic lecithin emulsifier) to improve rheological characteristics of Kamut® dough has been confirmed also when subjected to low temperatures (24 hours and 48 hours at 4°C). Small deformation oscillatory measurements and large deformation mechanical tests performed provided useful information on the rheological properties of samples realized by using different amounts of ginger powder, showing that the sample with the highest amount of ginger powder (6%) had worse rheological characteristics compared to the other samples. Moisture content, specific volume, texture and crumb grain characteristics are the major quality attributes of bread products. The different sample analyzed, “Coppia Ferrarese”, “Pane Comune Romagnolo” and “Filone Terra di San Marino”, showed a decrease of crumb moisture and an increase in hardness over the storage time. Parameters such as cohesiveness and springiness, evaluated by TPA that are indicator of quality of fresh bread, decreased during the storage. By using empirical rheological tests we found several differences among the samples, due to the different ingredients used in formulation and the different process adopted to prepare the sample, but since these products are handmade, the differences could be account as a surplus value. In conclusion small deformation (in fundamental units) and large deformation methods showed a significant role in monitoring the influence of different ingredients used in formulation, different processing and storage conditions on dough viscoelastic performance and on final product. Finally the knowledge of formulation, processing and storage conditions together with the evaluation of structural and rheological characteristics is fundamental for the study of complex matrices like bakery products, where numerous variable can influence their final quality (e.g. raw material, bread-making procedure, time and temperature of the fermentation and baking).

Essays on the Empirical Analysis of Economic and Political Development in Sub-Saharan Africa

In Sub-Saharan Africa, non-democratic events, like civil wars and coup d'etat, destroy economic development. This study investigates both domestic and spatial effects on the likelihood of civil wars and coup d'etat. To civil wars, an increase of income growth is one of common research conclusions to stop wars. This study adds a concern on ethnic fractionalization. IV-2SLS is applied to overcome causality problem. The findings document that income growth is significant to reduce number and degree of violence in high ethnic fractionalized countries, otherwise they are trade-off. Income growth reduces amount of wars, but increases its violent level, in the countries with few large ethnic groups. Promoting growth should consider ethnic composition. This study also investigates the clustering and contagion of civil wars using spatial panel data models. Onset, incidence and end of civil conflicts spread across the network of neighboring countries while peace, the end of conflicts, diffuse only with the nearest neighbor. There is an evidence of indirect links from neighboring income growth, without too much inequality, to reduce the likelihood of civil wars. To coup d'etat, this study revisits its diffusion for both all types of coups and only successful ones. The results find an existence of both domestic and spatial determinants in different periods. Domestic income growth plays major role to reduce the likelihood of coup before cold war ends, while spatial effects do negative afterward. Results on probability to succeed coup are similar. After cold war ends, international organisations seriously promote democracy with pressure against coup d'etat, and it seems to be effective. In sum, this study indicates the role of domestic ethnic fractionalization and the spread of neighboring effects to the likelihood of non-democratic events in a country. Policy implementation should concern these factors.

Social cognition as a mediator variable between neurocognition and functional outcome in schizophrenia: empirical review and new results by structural equation modeling

Cognitive impairments are currently regarded as important determinants of functional domains and are promising treatment goals in schizophrenia. Nevertheless, the exact nature of the interdependent relationship between neurocognition and social cognition as well as the relative contribution of each of these factors to adequate functioning remains unclear. The purpose of this article is to systematically review the findings and methodology of studies that have investigated social cognition as a mediator variable between neurocognitive performance and functional outcome in schizophrenia. Moreover, we carried out a study to evaluate this mediation hypothesis by the means of structural equation modeling in a large sample of 148 schizophrenia patients. The review comprised 15 studies. All but one study provided evidence for the mediating role of social cognition both in cross-sectional and in longitudinal designs. Other variables like motivation and social competence additionally mediated the relationship between social cognition and functional outcome. The mean effect size of the indirect effect was 0.20. However, social cognitive domains were differentially effective mediators. On average, 25% of the variance in functional outcome could be explained in the mediation model. The results of our own statistical analysis are in line with these conclusions: Social cognition mediated a significant indirect relationship between neurocognition and functional outcome. These results suggest that research should focus on differential mediation pathways. Future studies should also consider the interaction with other prognostic factors, additional mediators, and moderators in order to increase the predictive power and to target those factors relevant for optimizing therapy effects.

Predictors of surgical, general and follow-up complications in lumbar spinal stenosis relative to patient age as emerged from the Spine Tango Registry

Published opinions regarding the outcomes and complications in older patients have a broad spectrum and there is a disagreement whether surgery in older patients entails a higher risk. Therefore this study examines the risk of surgery for lumbar spinal stenosis relative to age in the pooled data set of the Spine Tango registry.