Histological analysis of gallbladder diseases in relation to opisthorchiasis in endemic areas of Thailand

Chronic gallbladder disease frequently accompanies infection with the liver fluke, Opisthorchis viverrini, in Northeast Thailand. However, the pathology and pathogenesis of the gallbladder disease have not been described. Accordingly, gallbladder specimens from 187 consecutive patients who had undergone cholecystectomy at a referral hospital in an endemic area in Thailand were histologically characterized in relation to O. viverrini infection. The infection was assessed by the presence of parasite eggs in the bile and/or antibody response to the liver fluke. The average level of parasite-specific IgG was significantly higher in patients with Opisthorchis eggs in the bile than those without (P < 0.001). The main histopathologic features of the gallbladder included inflammation, mucosal atrophy/or hyperplasia, goblet cell metaplasia, mucous gland hyperplasia, Rokitansky-Aschoff sinus formation, dysplasia and fibrosis. The fibrosis was strongly associated with elevated levels of Opisthorchis-specific antibody (P < 0.001) but not with the presence of parasite eggs. Other pathologic features did not vary in frequency or severity with parasitological status. Our results show that severe fibrosis of the gallbladder is a more common histologic feature of cholecystitis among those with O. viverrini infection compared to those without infection. The close relationship between parasite-specific IgG and severe fibrosis suggests that specific immune response to the parasite play an important role in the pathogenesis of the fibrotic change. (C) 2003 Elsevier B.V. All rights reserved.

Computational analysis of base composition pattern and promoter elements in the putative promoter regions in relation to expression profiles of 682 human genes on chromosome 22

The base composition pattern (BCP) in the putative promoter region (PPRs) up to 5 Kb lengths of 682 human genes on Chromosome 22 (Chr22) was examined. Two-dimensional (2D) and three-dimensional (3D) functions were designed to delineate the DNA base composition, with four major patterns identified. It is found that 17.6% genes include TATA box, 28.0% GC box, 18.9% CAAT box and 38.4% CpG islands, and approximately 10% genes have one of four putative initiator (Inr) motifs. The occurrence of the promoter elements is tightly associated with the base composition features in the promoter regions, and the associations of the base composition features with occurrence of the promoter elements in the promoter regions mediate tissue-wide expression of the genes in human. The occurrence of two or more promoter elements in the promoter regions is required for the medium- and wide-range expression profiles of the human genes on Chr22. Thus, the reported data shed light on the characteristics of the PPRs of the human genes on Chr22, which may improve our understanding of regulatory roles of the PPRs with occurrence of the promoter elements in gene expression.

Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome

The chromodomain is 40-50 amino acids in length and is conserved in a wide range of chromatic and regulatory proteins involved in chromatin remodeling. Chromodomain-containing proteins can be classified into families based on their broader characteristics, in particular the presence of other types of domains, and which correlate with different subclasses of the chromodomains themselves. Hidden Markov model (HMM)-generated profiles of different subclasses of chromodomains were used here to identify sequences encoding chromodomain-containing proteins in the mouse transcriptome and genome. A total of 36 different loci encoding proteins containing chromodomains, including 17 novel loci, were identified. Six of these loci (including three apparent pseudogenes, a novel HP1 ortholog, and two novel Msl-3 transcription factor-like proteins) are not present in the human genome, whereas the human genome contains four loci (two CDY orthologs and two apparent CDY pseuclogenes) that are not present in mouse. A number of these loci exhibit alternative splicing to produce different isoforms, including 43 novel variants, some of which lack the chromodomain. The likely functions of these proteins are discussed in relation to the known functions of other chromodomain-containing proteins within the same family.

Perceptual and instrumental analysis of laryngeal function after traumatic brain injury in childhood

Objective: To investigate laryngeal function and phonatory disturbance in children with traumatic brain injury (TBI), using both perceptual and instrumental techniques. Design and participants: The performance of 16 individuals with moderate to severe TBI acquired in childhood and 16 nonneurologicatly impaired control subjects was compared on a battery of perceptual (Frenchay Dysarthria Assessment, speech sample analysis) and instrumental (Aerophone II, laryngograph) assessments. Results and conclusions: As a group, the children with TBI demonstrated normal, or only minimally impaired laryngeal function, when compared with the control group, which contrasts with the significant laryngeal impairment noted in adults after TBI. Several reasons for the different findings in relation to laryngeal function in adults and children after TBI are postulated: (1) differing types of injury usually incurred by adults and children may result in a relatively decreased degree of neurologic impairment in these children, (2) differences in recovery potential between adults and children, and (3) the pediatric larynx is still developing, hence it may be better able to compensate for any impairment incurred.

Socioeconomic causes of loss of animal genetic diversity: analysis and assessment

The proximate causes and processes involved in loss of breeds are outlined. The path-dependent effect and Swanson's dominance-effect are discussed in relation to lock-in of breed selection. These effects help to explain genetic erosion. It is shown that the extension of markets and economic globalisation have contributed significantly to the loss of breeds. The decoupling of animal husbandry from surrounding natural environmental conditions is further eroding the stock of genetic resources. Recent trends in animal husbandry raise serious sustainability issues, apart from animal welfare concerns. The extension of markets and economic globalisation have contributed significantly to the rapid loss of domestic breeds, especially livestock. (C) 2003 Elsevier Science B.V. All rights reserved.

Development of a controlled drinking self-efficacy scale and appraising its relation to alcohol dependence

There is no specific self-efficacy measure that has been developed primarily for problem drinkers seeking a moderation drinking goal. In this article, we report the factor structure of a 20-item Controlled Drinking Self-Efficacy Scale (CDSES Sitharthan et al., 1996; Sitharthan et al., 1997). The results indicate that the CDSES is highly reliable, and the factor analysis using the full sample identified four factors: negative affect, positive mood/social context, frequency of drinking, and consumption quantity. A similar factor structure was obtained for the subsample of men. In contrast, only three factors emerged in the analysis of data on female participants. Compared to women, men had low self-efficacy to control their drinking in situations relating to positive mood/social context, and subjects with high alcohol dependence had low self-efficacy for situations relating to negative affect, social situations, and drinking less frequently. The CDSES can be a useful measure in treatment programs providing a moderation drinking goal. (C) 2003 Wiley Periodicals, Inc.

Graduate attributes in relation to curriculum design and delivery in a Bachelor of Materials Engineering Programme

This paper presents a critical analysis of the Bachelor of Materials Engineering programme compared with the expectations of the Institution of Engineers Australia (IEAust) and of UQ. To set the scene, the graduate attributes are listed, the programme framework is presented and the educational culture and available facilities are described Then, the programme delivery is described; this includes an analysis of the learning opportunities that allow students to develop the graduate attributes. Finally, an assessment is made of programme outcomes relating to graduate attributes.

The utility and limitations of chloroplast DNA analysis for identifying native British oak stands and for guiding replanting strategy

We report a method using variation in the chloroplast genome (cpDNA) to test whether oak stands of unknown provenance are of native and/or local origin. As an example, a sample of test oaks, of mostly unknown status in relation to nativeness and localness, were surveyed for cpDNA type. The sample comprised 126 selected trees, derived from 16 British seed stands, and 75 trees, selected for their superior phenotype (201 tree samples in total). To establish whether these two test groups are native and local, their cpDNA type was compared with that of material from known autochthonous origin (results of a previous study which examined variation in 1076 trees from 224 populations distributed across Great Britain). In the previous survey of autochthonous material, four cpDNA types were identified as native; thus if a test sample possessed a new haplotype then it could be classed as non-native. Every one of the 201 test samples possessed one of the four cpDNA types found within the autochthonous sample. Therefore none could be proven to be introduced and, on this basis, was considered likely to be native. The previous study of autochthonous material also found that cpDNA variation was highly structured geographically and, therefore, if the cpDNA type of the test sample did not match that of neighbouring autochthonous trees then it could be considered to be non-local. A high proportion of the seed stand group (44.2 per cent) and the phenotypically superior trees (58.7 per cent) possessed a cpDNA haplotype which matched that of the neighbouring autochthonous trees and, therefore, can be considered as local, or at least cannot be proven to be introduced. The remainder of the test sample could be divided into those which did not grow in an area of overall dominance (18.7 per cent of seed stand trees and 28 per cent of phenotypically superior) and those which failed to match the neighbouring autochthonous haplotype (37.1 per cent and 13.3 per cent, respectively). Most of the non-matching test samples were located within 50 km of an area dominated by a matching autochthonous haplotype (96.0 per cent and 93.5 per cent, respectively), and potentially indicates only local transfer. Whilst such genetic fingerprinting tests have proven useful for assessing the origin of stands of unknown provenance, there are potential limitations to using a marker from the chloroplast genome (mostly adaptively neutral) for classifying seed material into categories which have adaptive implications. These limitations are discussed, particularly within the context of selecting adaptively superior material for restocking native forests.

Relation between cell disruption conditions, cell debris particle size, and inclusion body release

The efficiency of physical separation of inclusion bodies from cell debris is related to cell debris size and inclusion body release and both factors should be taken into account when designing a process. In this work, cell disruption by enzymatic treatment with lysozyme and cellulase, by homogenization, and by homogenization with ammonia pretreatment is discussed. These disruption methods are compared on the basis of inclusion body release, operating costs, and cell debris particle size. The latter was measured with cumulative sedimentation analysis in combination with membrane-associated protein quantification by SDS-PAGE and a spectrophotometric pepticloglycan quantification method. Comparison of the results obtained with these two cell debris quantification methods shows that enzymatic treatment yields cell debris particles with varying chemical composition, while this is not the case with the other disruption methods that were investigated. Furthermore, the experiments show that ammonia pretreatment with homogenization increases inclusion body release compared to homogenization without pretreatment and that this pretreatment may be used to control the cell debris size to some extent. The enzymatic disruption process gives a higher product release than homogenization with or without ammonia pretreatment at lower operating costs, but it also yields a much smaller cell debris size than the other disruption process. This is unfavorable for centrifugal inclusion body purification in this case, where cell debris is the component going to the sediment and the inclusion body is the floating component. Nevertheless, calculations show that centrifugal separation of inclusion bodies from the enzymatically treated cells gives a high inclusion body yield and purity. (C) 2004 Wiley Periodicals, Inc.

An investigation into effects of long-distance seed dispersal on organelle population genetic structure and colonization rate: a model analysis

A simulation-based modelling approach is used to examine the effects of stratified seed dispersal (representing the distribution of the majority of dispersal around the maternal parent and also rare long-distance dispersal) on the genetic structure of maternally inherited genomes and the colonization rate of expanding plant populations. The model is parameterized to approximate postglacial oak colonization in the UK, but is relevant to plant populations that exhibit stratified seed dispersal. The modelling approach considers the colonization of individual plants over a large area (three 500 km x 10 km rolled transects are used to approximate a 500 km x 300 km area). Our approach shows how the interaction of plant population dynamics with stratified dispersal can result in a spatially patchy haplotype structure. We show that while both colonization speeds and the resulting genetic structure are influenced by the characteristics of the dispersal kernel, they are robust to changes in the periodicity of long-distance events, provided the average number of long-distance dispersal events remains constant. We also consider the effects of additional physical and environmental mechanisms on plant colonization. Results show significant changes in genetic structure when the initial colonization of different haplotypes is staggered over time and when a barrier to colonization is introduced. Environmental influences on survivorship and fecundity affect both the genetic structure and the speed of colonization. The importance of these mechanisms in relation to the postglacial spread and genetic structure of oak in the UK is discussed.

Better prediction of protein contact number using a support vector regression analysis of amino acid sequence

Background: Protein tertiary structure can be partly characterized via each amino acid's contact number measuring how residues are spatially arranged. The contact number of a residue in a folded protein is a measure of its exposure to the local environment, and is defined as the number of C-beta atoms in other residues within a sphere around the C-beta atom of the residue of interest. Contact number is partly conserved between protein folds and thus is useful for protein fold and structure prediction. In turn, each residue's contact number can be partially predicted from primary amino acid sequence, assisting tertiary fold analysis from sequence data. In this study, we provide a more accurate contact number prediction method from protein primary sequence. Results: We predict contact number from protein sequence using a novel support vector regression algorithm. Using protein local sequences with multiple sequence alignments (PSI-BLAST profiles), we demonstrate a correlation coefficient between predicted and observed contact numbers of 0.70, which outperforms previously achieved accuracies. Including additional information about sequence weight and amino acid composition further improves prediction accuracies significantly with the correlation coefficient reaching 0.73. If residues are classified as being either contacted or non-contacted, the prediction accuracies are all greater than 77%, regardless of the choice of classification thresholds. Conclusion: The successful application of support vector regression to the prediction of protein contact number reported here, together with previous applications of this approach to the prediction of protein accessible surface area and B-factor profile, suggests that a support vector regression approach may be very useful for determining the structure-function relation between primary sequence and higher order consecutive protein structural and functional properties.

Rethinking the "diseases of affluence" paradigm: Global patterns of nutritional risks in relation to economic development

Background Cardiovascular diseases and their nutritional risk factors-including overweight and obesity, elevated blood pressure, and cholesterol-are among the leading causes of global mortality and morbidity, and have been predicted to rise with economic development. Methods and Findings We examined age-standardized mean population levels of body mass index (BMI), systolic blood pressure, and total cholesterol in relation to national income, food share of household expenditure, and urbanization in a cross-country analysis. Data were from a total of over 100 countries and were obtained from systematic reviews of published literature, and from national and international health agencies. BMI and cholesterol increased rapidly in relation to national income, then flattened, and eventually declined. BMI increased most rapidly until an income of about I$5,000 (international dollars) and peaked at about I$12,500 for females and I$17,000 for males. Cholesterol's point of inflection and peak were at higher income levels than those of BMI (about I$8,000 and I$18,000, respectively). There was an inverse relationship between BMI/cholesterol and the food share of household expenditure, and a positive relationship with proportion of population in urban areas. Mean population blood pressure was not correlated or only weakly correlated with the economic factors considered, or with cholesterol and BMI. Conclusions When considered together with evidence on shifts in income-risk relationships within developed countries, the results indicate that cardiovascular disease risks are expected to systematically shift to low-income and middle-income countries and, together with the persistent burden of infectious diseases, further increase global health inequalities. Preventing obesity should be a priority from early stages of economic development, accompanied by population-level and personal interventions for blood pressure and cholesterol.

Syntactic complexity measures and their relation to oral proficiency in Japanese as a foreign language

The study reported in this article is a part of a large-scale study investigating syntactic complexity in second language (L2) oral data in commonly taught foreign languages (English, German, Japanese, and Spanish; Ortega, Iwashita, Rabie, & Norris, in preparation). In this article, preliminary findings of the analysis of the Japanese data are reported. Syntactic complexity, which is referred to as syntactic maturity or the use of a range of forms with degrees of sophistication (Ortega, 2003), has long been of interest to researchers in L2 writing. In L2 speaking, researchers have examined syntactic complexity in learner speech in the context of pedagogic intervention (e.g., task type, planning time) and the validation of rating scales. In these studies complexity is examined using measures commonly employed in L2 writing studies. It is assumed that these measures are valid and reliable, but few studies explain what syntactic complexity measures actually examine. The language studied is predominantly English, and little is known about whether the findings of such studies can be applied to languages that are typologically different from English. This study examines how syntactic complexity measures relate to oral proficiency in Japanese as a foreign language. An in-depth analysis of speech samples from 33 learners of Japanese is presented. The results of the analysis are compared across proficiency levels and cross-referenced with 3 other proficiency measures used in the study. As in past studies, the length of T-units and the number of clauses per T-unit is found to be the best way to predict learner proficiency; the measure also had a significant linear relation with independent oral proficiency measures. These results are discussed in light of the notion of syntactic complexity and the interfaces between second language acquisition and language testing. Adapted from the source document