Supporting contexts in program refinement

A program can be refined either by transforming the whole program or by refining one of its components. The refinement of a component is, for the main part, independent of the remainder of the program. However, refinement of a component can depend on the context of the component for information about the variables that are in scope and what their types are. The refinement can also take advantage of additional information, such as any precondition the component can assume. The aim of this paper is to introduce a technique, which we call program window inference, to handle such contextual information during derivations in the refinement calculus. The idea is borrowed from a technique, called window inference, for handling context in theorem proving. Window inference is the primary proof paradigm of the Ergo proof editor. This tool has been extended to mechanize refinement using program window inference. (C) 1997 Elsevier Science B.V.

Dynamics of Hepatitis D (delta) virus genotype 3 in the Amazon region of South America

Hepatitis delta virus (HDV) is widely distributed and associated with fulminant hepatitis epidemics in areas with high prevalence of HBV. Several studies performed in the 1980s showed data on HDV infection in South America, but there are no studies on the viral dynamics of this virus. The aim of this study was to conduct an evolutionary analysis of hepatitis delta genotype 3 (HDV/3) prevalent in South America: estimate its nucleotide substitution rate, determine the time of most recent ancestor (TMRCA) and characterize the epidemic history and evolutionary dynamics. Furthermore, we characterized the presence of HBV/HDV infection in seven samples collected from patients who died due to fulminant hepatitis from Amazon region in Colombia and included them in the evolutionary analysis. This is the first study reporting HBV and HDV sequences from the Amazon region of Colombia. Of the seven Colombian patients, five were positive for HBV-DNA and HDV-RNA. Of them, two samples were successfully sequenced for HBV (subgenotypes F3 and Fib) and the five samples HDV positive were classified as HDV/3. By using all HDV/3 available reference sequences with sampling dates (n = 36), we estimated the HDV/3 substitution rate in 1.07 x 10(-3) substitutions per site per year (s/s/y), which resulted in a time to the most recent common ancestor (TMRCA) of 85 years. Also, it was determined that HDV/3 spread exponentially from early 1950s to the 1970s in South America. This work discusses for the first time the viral dynamics for the HDV/3 circulating in South America. We suggest that the measures implemented to control HBV transmission resulted in the control of HDV/3 spreading in South America, especially after the important raise in this infection associated with a huge mortality during the 1950s up to the 1970s. The differences found among HDV/3 and the other HDV genotypes concerning its diversity raises the hypothesis of a different origin and/or a different transmission route. (C) 2011 Elsevier B.V. All rights reserved.

Classification System of Raman Spectra using Cluster Analysis to Diagnose Coronary Artery Lesions

The traditional methods employed to detect atherosclerotic lesions allow for the identification of lesions; however, they do not provide specific characterization of the lesion`s biochemistry. Currently, Raman spectroscopy techniques are widely used as a characterization method for unknown substances, which makes this technique very important for detecting atherosclerotic lesions. The spectral interpretation is based on the analysis of frequency peaks present in the signal; however, spectra obtained from the same substance can show peaks slightly different and these differences make difficult the creation of an automatic method for spectral signal analysis. This paper presents a signal analysis method based on a clustering technique that allows for the classification of spectra as well as the inference of a diagnosis about the arterial wall condition. The objective is to develop a computational tool that is able to create clusters of spectra according to the arterial wall state and, after data collection, to allow for the classification of a specific spectrum into its correct cluster.

Assessing Interethnic Admixture Using an X-Linked Insertion-Deletion Multiplex

In this study, a PCR multiplex was optimized, allowing the simultaneous analysis of 13 X-chromosome Insertion/deletion polymorphisms (INDELs). Genetic variation observed in Africans, Europeans, and Native Americans reveals high inter-population variability. The estimated proportions of X-chromosomes in an admixed population from the Brazilian Amazon region show a predominant Amerindian contribution (congruent to 41%), followed by European (congruent to 32%) and African (congruent to 27%) contributions. The proportion of Amerindian contribution based on X-linked data is similar to the expected value based on mtDNA and Y-chromosome information. The accuracy for assessing interethnic admixture, and the high differentiation between African, European, and Native American populations, demonstrates the suitability of this INDEL set to measure ancestry proportions in three-hybrid populations, as it is the case of Latin American populations. Am. J. Hum. Biol. 21:707-709, 2009. (C) 2009 Wiley-Liss, Inc.

Evaluation of computational methods for the reconstruction of HLA haplotypes

Human leukocyte antigen (HLA) haplotypes are frequently evaluated for population history inferences and association studies. However, the available typing techniques for the main HLA loci usually do not allow the determination of the allele phase and the constitution of a haplotype, which may be obtained by a very time-consuming and expensive family-based segregation study. Without the family-based study, computational inference by probabilistic models is necessary to obtain haplotypes. Several authors have used the expectation-maximization (EM) algorithm to determine HLA haplotypes, but high levels of erroneous inferences are expected because of the genetic distance among the main HLA loci and the presence of several recombination hotspots. In order to evaluate the efficiency of computational inference methods, 763 unrelated individuals stratified into three different datasets had their haplotypes manually defined in a family-based study of HLA-A, -B, -DRB1 and -DQB1 segregation, and these haplotypes were compared with the data obtained by the following three methods: the Expectation-Maximization (EM) and Excoffier-Laval-Balding (ELB) algorithms using the arlequin 3.11 software, and the PHASE method. When comparing the methods, we observed that all algorithms showed a poor performance for haplotype reconstruction with distant loci, estimating incorrect haplotypes for 38%-57% of the samples considering all algorithms and datasets. We suggest that computational haplotype inferences involving low-resolution HLA-A, HLA-B, HLA-DRB1 and HLA-DQB1 haplotypes should be considered with caution.

Role of the bed nucleus of the stria terminalis in the cardiovascular responses to acute restraint stress in rats

The aim of this work was to test the hypothesis that the bed nucleus of the stria terminalis (BST) and noradrenergic neurotransmission therein mediate cardiovascular responses to acute restraint stress in rats. Bilateral microinjection of the non-specific synaptic blocker CoCl2 (0.1nmol/100nl) into the BST enhanced the heart rate (HR) increase associated with acute restraint without affecting the blood pressure increase, indicating that synapses within the BST influence restraint-evoked HR changes. BST pretreatment with the selective 1-adrenoceptor antagonist WB4101 (15nmol/100nl) caused similar effects to cobalt, indicating that local noradrenergic neurotransmission mediates the BST inhibitory influence on restraint-related HR responses. BST treatment with equimolar doses of the 2-adrenoceptor antagonist RX821002 or the -adrenoceptor antagonist propranolol did not affect restraint-related cardiovascular responses, reinforcing the inference that 1-adrenoceptors mediate the BST-related inhibitory influence on HR responses. Microinjection of WB4101 into the BST of rats pretreated intravenously with the anticholinergic drug homatropine methyl bromide (0.2mg/kg) did not affect restraint-related cardiovascular responses, indicating that the inhibitory influence of the BST on the restraint-evoked HR increase could be related to an increase in parasympathetic activity. Thus, our results suggest an inhibitory influence of the BST on the HR increase evoked by restraint stress, and that this is mediated by local 1-adrenoceptors. The results also indicate that such an inhibitory influence is a result of parasympathetic activation.

Nasal allergies in the Latin American population: Results from the Allergies in Latin America survey

Allergies in Latin America is the first cross-national survey that describes the symptoms, impact, and treatment of nasal allergies (NAs) in individuals >= 4 years old in Latin America (LA). In total, 22,012 households across the Latin American countries of Argentina, Brazil, Chile, Colombia, Ecuador, Mexico, Peru, and Venezuela were screened for children, adolescents, and adults with a diagnosis of NA and either symptoms or treatment in the past 12 months. A total of 1088 adults and 457 children and adolescents were included and the sample was probability based to ensure valid statistical inference to the population. Approximately 7% of the LA population was diagnosed with NAs with two of three respondents stating that their allergies were seasonal or intermittent in nature. A general practice physician or otolaryngologist diagnosed the majority of individuals surveyed. Nasal congestion was the most common and bothersome symptom of NAs. Sufferers indicated that their symptoms affected productivity and sleep and had a negative impact on quality of life. Two-thirds of patients reported taking some type of medication for their NAs, with a roughly equal percentage of patients reporting taking over-the-counter versus prescription medications. Changing medications was most commonly done in those reporting inadequate efficacy. The most common reasons cited for dissatisfaction with current medications were related to inadequate effectiveness, effectiveness wearing off with chronic use, failure to provide 24-hour relief, and bothersome side effects (e.g., unpleasant taste and retrograde drainage into the esophagus). Findings from this cross-national survey on NAs have confirmed a high prevalence of physician-diagnosed NAs and a considerable negative impact on daily quality of life and work productivity as well as substantial disease management challenges in LA. Through identification of disease impact on the LA population and further defining treatment gaps, clinicians in LA may better understand and treat NAs, thus leading to improvements in overall patient satisfaction and quality of life. (Allergy Asthma Proc 31:S9-S27, 2010; doi: 10.2500/aap.2010.31.3347)

A Comparison of Bayesian and Sampling Theory Inferences in a Probit Model

HE PROBIT MODEL IS A POPULAR DEVICE for explaining binary choice decisions in econometrics. It has been used to describe choices such as labor force participation, travel mode, home ownership, and type of education. These and many more examples can be found in papers by Amemiya (1981) and Maddala (1983). Given the contribution of economics towards explaining such choices, and given the nature of data that are collected, prior information on the relationship between a choice probability and several explanatory variables frequently exists. Bayesian inference is a convenient vehicle for including such prior information. Given the increasing popularity of Bayesian inference it is useful to ask whether inferences from a probit model are sensitive to a choice between Bayesian and sampling theory techniques. Of interest is the sensitivity of inference on coefficients, probabilities, and elasticities. We consider these issues in a model designed to explain choice between fixed and variable interest rate mortgages. Two Bayesian priors are employed: a uniform prior on the coefficients, designed to be noninformative for the coefficients, and an inequality restricted prior on the signs of the coefficients. We often know, a priori, whether increasing the value of a particular explanatory variable will have a positive or negative effect on a choice probability. This knowledge can be captured by using a prior probability density function (pdf) that is truncated to be positive or negative. Thus, three sets of results are compared:those from maximum likelihood (ML) estimation, those from Bayesian estimation with an unrestricted uniform prior on the coefficients, and those from Bayesian estimation with a uniform prior truncated to accommodate inequality restrictions on the coefficients.

Maned wolf survival rate in central Brazil

Although many carnivores are of conservation concern, most are poorly studied. The maned wolf Chrysocyon brachyurus Illiger, 1811 is the largest South American canid with a broad distribution; however, the largest portion of its range is in the Brazilian Cerrado savannah, where due to intensive agricultural expansion, it is threatened by habitat loss. Maned wolf population trends are virtually unknown. We analyzed radio telemetry data from a 13-year study in Emas National Park, central Brazil, with Burnham`s live recapture/dead recovery models in the program MARK to obtain the first analytically sound estimate of the apparent maned wolf survival rate. We constructed 16 candidate models including variation in survival rate and resighting probability associated with an individual`s sex or age and year of study. Apparent adult survival rate throughout the study ranged from 0.28 (se=0.08) to 0.97 (se=0.06). There was no evidence for sex specificity but strong support for time variation. Model weights supported an age effect and the subadult survival rate was 0.63 (se=0.15). Results indicate similar life patterns for male and female maned wolves and similar mortality risks for adults and subadults in the study area. The observed temporal fluctuations of adult survival rate are important for population dynamics as they decrease average population growth rates. Population dynamics are central for conservation planning and our results are an important step towards a better understanding of the maned wolf`s ecology.

Do Low-shrink Composites Reduce Polymerization Shrinkage Effects?

Progress in polymer science has led to continuous reduction of polymerization shrinkage, exemplified by a new generation of ""low-shrink composites"". The common inference that shrinkage stress effects will be reduced in teeth restored with such restoratives with lower shrinkage was tested in extracted human premolars. Mesio-occluso-distal slot-shaped cavities were cut and restored with a conventional (SupremePlus) or low-shrink (RefleXions, Premise, Kalore, and LS) composite (N = 5). We digitized the coronal surfaces before and 10 min after restoration to determine cuspal deflection from the buccal and lingual volume change/area. We also determined the main properties involved (total shrinkage, post-gel shrinkage, degree of conversion, and elastic modulus), as well as microleakage, to verify adequate bonding. It was shown that, due to shrinkage stresses, buccal and lingual surfaces pulled inward after restoration (9-14 microns). Only Kalore and LS resulted in significantly lower tooth deformation (ANOVA/Student-Newman-Keuls post hoc, p = 0.05). The other two low-shrink composites, despite having the lowest and highest total shrinkage values, did not cause significant differences in cuspal deflection. Deflection seemed most related to the combination of post-gel shrinkage and elastic modulus. Therefore, even for significantly lower total shrinkage values, shrinkage stress is not necessarily reduced.

Simpson's paradox: A logically benign, empirically treacherous hydra

This article examines Simpson's paradox as applied to the theory of probabilites and percentages. The author discusses possible flaws in the paradox and compares it to the Sure Thing Principle, statistical inference, causal inference and probabilistic analyses of causation.

Platyhelminth phylogenetics - a key to understanding parasitism?

The comparative method, the inference of biological processes from phylogenetic patterns, is founded on the reliability of the phylogenetic tree. In attempting to apply the comparative method to the understanding of the evolution of parasitism in the phylum Platyhelminthes, we have highlighted several points we consider to be of value along with many problems. We discuss four of these topics. Firstly, we view the group at a phylum level, in particular discussing the importance of establishing the sister taxon to the obligate parasite group, the Neodermata, for addressing such questions as the monophyly, parasitism or the endo or ectoparasitic nature of the early parasites. The variety of non-congruent phylogenetic trees presented so far, utilising either or both morphological and molecular data, gives rise to the suggestion that any evolutionary scenarios presented at this stage be treated as interesting hypotheses rather than well-supported theories. Our second point of discussion is the conflict between morphological and molecular estimates of monogenean evolution. The Monogenea presents several well-established morphological autapomorphies, such that morphology consistently estimates the group as monophyletic, whereas molecular sequence analyses indicate paraphyly, with different genes giving different topologies. We discuss the problem of reconciling gene and species trees. Thirdly, we use recent phylogenetic results on the tapeworms to interpret the evolution of strobilation, proglottization, segmentation and scolex structure. In relation to the latter, the results presented indicate that the higher cestodes are diphyletic, with one branch difossate and the other tetrafossate. Finally, we use a SSU rDNA phylogenetic tree of the Trematoda as a basis for the discussion of an aspect of the digenean life-cycle, namely the nature of the first intermediate host. Frequent episodes of host-switching, between gastropod and bivalve hosts or even into annelids, are indicated.

The nature and evolution of the association among digeneans, molluscs and fishes

Patterns of association of digenean families and their mollusc and vertebrate hosts are assessed by way of a new database containing information on over 1000 species of digeneans for lift-cycles and over 5000 species from fishes. Analysis of the distribution of digenean families in molluscs suggests that the group was associated primitively with gastropods and that infection of polychaetes, bivalves and scaphopods are all the results of host-switching. For the vertebrates. infections of agnathans and chondrichthyans are apparently the result of host-switching from teleosts. For digenean families the ratio of orders of fishes infected to superfamilies of molluscs infected ranges from 0.5 (Mesometridae) to 16 (Bivesiculidae) and has a mean of 5.6. Individual patterns of host association of 13 dipenean families and superfamilies are reviewed. Two, Bucephalidae and Sanguinicolidae. are exceptional in infecting a range of first intermediate hosts qualitatively as broad as their range of definitive hosts. No well-studied taxon shows narrower association with vertebrate than with mollusc clades. The range of definitive hosts of digeneans is characteristically defined by eco-physiological similarity rather than phylogenetic relationship. The range of associations of digenean families with mollusc taxa is generally much narrower. These data are considered in the light of ideas about the significance of different forms of host association. If Manter's Second Rule (the longer the association with a host group, the mure pronounced the specificity exhibited by the parasite group) is invoked, then the data may suggest that the Digenea first parasitised molluscs before adopting vertebrate hosts. This interpretation is consistent with most previous ideas about the evolution of the Digenea but contrary to current interpretations based on the monophyly of the Neodermata. The basis of Manter's Second Rule is. however, considered too flimsy for this interpretation to be robust. Problems of the inference of the evolution of patterns of parasitism in the Neodermata al-e discussed and considered so intractable that the truth may be presently unknowable. (C) 2001 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All rights reserved.

Effects of alcohol consumption on indices of iron stores and of iron stores on alcohol intake markers

Background: Alcohol increases body iron stores. Alcohol and iron may increase oxidative stress and the risk of alcohol-related liver disease. The relationship between low or safe levels of alcohol use and indices of body iron stores, and the factors that affect the alcohol-iron relationship, have not been fully characterized. Other aspects of the biological response to alcohol use have been reported to depend on iron status. Methods: We have measured serum iron, transferrin, and ferritin as indices of iron stores in 3375 adult twin subjects recruited through the Australian Twin Registry. Information on alcohol use and dependence and smoking was obtained from questionnaires and interviews. Results: Serum iron and ferritin increased progressively across classes of alcohol intake. The effects of beer consumption were greater than those of wine or spirits. Ferritin concentration was significantly higher in subjects who had ever been alcohol dependent. There was no evidence of interactions between HFE genotype or body mass index and alcohol. Alcohol intake-adjusted carbohydrate-deficient transferrin was increased in women in the lowest quartile of ferritin results, whereas adjusted gamma -glutamyltransferase, aspartate aminotransferase, and alanine aminotransferase values were increased in subjects with high ferritin. Conclusions: Alcohol intake at low level increases ferritin and, by inference, body iron stores. This may be either beneficial or harmful, depending on circumstances. The response of biological markers of alcohol intake can be affected by body iron stores; this has implications for test sensitivity and specificity and for variation in biological responses to alcohol use.

On surrogate methods for detecting lateral gene transfer

Surrogate methods for detecting lateral gene transfer are those that do not require inference of phylogenetic trees. Herein I apply four such methods to identify open reading frames (ORFs) in the genome of Escherichia coli K12 that may have arisen by lateral gene transfer. Only two of these methods detect the same ORFs more frequently than expected by chance, whereas several intersections contain many fewer ORFs than expected. Each of the four methods detects a different non-random set of ORFs. The methods may detect lateral ORFs of different relative ages; testing this hypothesis will require rigorous inference of trees. (C) 2001 Federation of European Microbiological Societies. Published by Elsevier Science BN. All rights reserved.