HBV core sequence: definition of genotype-specific variability and correlation with geographical origin

There are eight genotypes and nine subtypes of HBV. Small differences in geographical origin are associated with sequence changes in the surface gene. Here, we compared core gene sequences from different genotypes and geographical regions. Specific combinations of 24 amino acid substitutions at nine residues allowed allocation of a sequence to a subtype. Six of these nine residues were located in different T cell epitopes depending on HBV geographical area and/or genotype. Thirty-seven nucleotide changes were associated uniquely with specific genotypes and subtypes. Unique amino acid and nucleotide variants were found in a majority of sequences from specific countries as well as within subtype ayw2 and adr. Specific nucleotide motifs were defined for Korean, Indian, Chinese, Italian and Pacific region isolates. Finally, we observed amino acid motifs that were common to either South-east Asian or Western populations, irrespective of subtype. We believe that HBV strains spread within constrained ethnic groups, result in selection pressures that define sequence variability within each subtype. It suggests that particular T cell epitopes are specific for geographical regions, and thus ethnic groups; this may affect the design of immunomodulatory therapies.

On the adoption decision and the intensity of use of complementary innovations: The intra firm diffusion of management practices across UK establishments

This paper contributes to the literature on the intra-firm diffusion of innovations by investigating the factors that affect the firm’s decision to adopt and use sets of complementary innovations. We define complementary innovations those innovations whose joint use generates super additive gains, i.e. the gain from the joint adoption is higher than the sum of the gains derived from the adoption of each innovation in isolation. From a theoretical perspective, we present a simple decision model, whereby the firm decides ‘whether’ and ‘how much’ to invest in each of the innovations under investigation based upon the expected profit gain from each possible combination of adoption and use. The model shows how the extent of complementarity among the innovations can affect the firm’s profit gains and therefore the likelihood that the firm will adopt these innovations jointly, rather than individually. From an empirical perspective, we focus on four sets of management practices, namely operating (OMP), monitoring (MMP), targets (TMP) and incentives (IMP) management practices. We show that these sets of practices, although to a different extent, are complementary to each other. Then, we construct a synthetic indicator of the depth of their use. The resulting intra-firm index is built to reflect not only the number of practices adopted but also the depth of their individual use and the extent of their complementarity. The empirical testing of the decision model is carried out using the evidence from the adoption behaviour of a sample of 1,238 UK establishments present in the 2004 Workplace Employment Relations Survey (WERS). Our empirical results show that the intra-firm profitability based model is a good model in that it can explain more of the variability of joint adoption than models based upon the variability of adoption and use of individual practices. We also investigate whether a number of firm specific and market characteristics by affecting the size of the gains (which the joint adoption of innovations can generate) may drive the intensity of use of the four innovations. We find that establishment size, whether foreign owned, whether exposed to an international market and the degree of homogeneity of the final product are important determinants of the intensity of the joint adoption of the four innovations. Most importantly, our results point out that the factors that the economics of innovation literature has been showing to affect the intensity of use of a technological innovation do also affect the intensity of use of sets of innovative management practices. However, they can explain only a small part of the diversity of their joint adoption use by the firms in the sample.

Country-specific determinants of horizontal and vertical intra-industry agri-food trade: the case of Bulgaria and Romania

The article analyses patterns and country-specific determinants of agri-food trade of Bulgaria and Romania with the European Union. As literature focusing on agricultural aspects of the topic is limited, the paper seeks to contribute to the literature by providing up to date results and suggestions as well as by identifying the determinants of horizontal and vertical intra-industry trade of the Bulgaria and Romania after EU accession. Results suggest that intra-industry agri-food trade is mainly of vertical nature, referring to trade of different quality products. Results verify that determinants of horizontal and vertical IIT are similar and suggest that economic size and FDI are positively, while factor endowments and distance are negatively related to both sides of IIT. Results are mainly in line with the majority of empirical literature in the field.

Intra- and interannual variability in seagrass carbon and nitrogen stable isotopes from south Florida, a preliminary study

δ13C and δ15N values were determined for the seagrassThalassia testudinum at four permanent seagrass monitoring stations in southFlorida, USA, through a quarterly sampling program over 3-years (1996–1998). All sites are seagrass beds with water depths of less than 6 m. Two sites are located on the Florida Bay side of the Florida Keys, and the other two sites are on the Atlantic side. The data analyzed over the 3 year study period display unique patterns associated with seasonal changes in primary productivity and potentially changes in the N and C pools. The mean carbon and nitrogenisotope values of T. testudinum from all four stations vary from −7.2 to −10.4‰ and 1.1 to 2.2‰, respectively. However, certain stations displayed anomalously depleted nitrogenisotope values (as low as −1.2‰). These values may indicate that biogeochemical processes like N fixation, ammonification and denitrification cause temporal changes in the isotopic composition of the source DIN. Both δ13C and δ15N values displayed seasonal enrichment-depletion patterns, with maximum enrichment occurring during the summer to early fall. The intra-annual variations of δ13C values from the different stations ranged from about 1 to 3.5‰; whereas variations in δ15N ranged from about 1 to 4.9‰. Certain sites showed a positive relationship between isotope values and productivity. These data indicate δ13C values display a high degree of seasonal variability as related to changes in productivity. δ15N values show clear intra-annual variations, but the observed changes do not necessarily follow a distinct seasonal cycle, indicating that changes in DIN will need further investigation.

The constancy of global regulation across a species: the concentrations of ppGpp and RpoS are strain-specific in Escherichia coli

Background: Sigma factors and the alarmone ppGpp control the allocation of RNA polymerase to promoters under stressful conditions. Both ppGpp and the sigma factor sigma(S) (RpoS) are potentially subject to variability across the species Escherichia coli. To find out the extent of strain variation we measured the level of RpoS and ppGpp using 31 E. coli strains from the ECOR collection and one reference K-12 strain. Results: Nine ECORs had highly deleterious mutations in rpoS, 12 had RpoS protein up to 7-fold above that of the reference strain MG1655 and the remainder had comparable or lower levels. Strain variation was also evident in ppGpp accumulation under carbon starvation and spoT mutations were present in several low-ppGpp strains. Three relationships between RpoS and ppGpp levels were found: isolates with zero RpoS but various ppGpp levels, strains where RpoS levels were proportional to ppGpp and a third unexpected class in which RpoS was present but not proportional to ppGpp concentration. High-RpoS and high-ppGpp strains accumulated rpoS mutations under nutrient limitation, providing a source of polymorphisms. Conclusions: The ppGpp and sigma(S) variance means that the expression of genes involved in translation, stress and other traits affected by ppGpp and/or RpoS are likely to be strain-specific and suggest that influential components of regulatory networks are frequently reset by microevolution. Different strains of E. coli have different relationships between ppGpp and RpoS levels and only some exhibit a proportionality between increasing ppGpp and RpoS levels as demonstrated for E. coli K-12.

Systematic Management of Variability in UML-based Software Product Lines

This paper presents SMarty, a variability management approach for UML-based software product lines (PL). SMarty is supported by a UML profile, the SMartyProfile, and a process for managing variabilities, the SMartyProcess. SMartyProfile aims at representing variabilities, variation points, and variants in UML models by applying a set of stereotypes. SMartyProcess consists of a set of activities that is systematically executed to trace, identify, and control variabilities in a PL based on SMarty. It also identifies variability implementation mechanisms and analyzes specific product configurations. In addition, a more comprehensive application of SMarty is presented using SEI's Arcade Game Maker PL. An evaluation of SMarty and related work are discussed.

Environmental and grazing influence on spatial variability of intertidal biofilm on subtropical rocky shores

Epilithic biofilm on rocky shores is regulated by physico-chemical and biological factors and is important as a source of food for benthic organisms. The influences of environmental and grazing pressure on spatial variability of biomass of biofilm were evaluated on shores on the north coast of Sao Paulo State (SE Brazil). A general trend of greater abundance of microalgae was observed lower on the shore, but neither of the environmental factors evaluated (wave exposure and shore level) showed consistent effects, and differences were found among specific shores or times (September 2007 and March 2008). The abundance of slow-moving grazers (limpets and littorinids) showed a negative correlation with chlorophyll a concentration on shores. However, experimental exclusion of these grazers failed to show consistent results at small spatial scales. Observations of divergent abundances of the isopod Ligia exotica and biomass of biofilm on isolated boulders on shores led to a short exclusion experiment, where the grazing pressure by L. exotica significantly decreased microalgal biomass. The result suggests that grazing activities of this fast-moving consumer probably mask the influence of slow-moving grazers at small spatial scales, while both have an additive effect at larger scales that masks environmental influences. This is the first evaluation of the impact of the fast-moving herbivore L. exotica on microalgal biomass on rocky shores and opens an interesting discussion about the role of these organisms in subtropical coastal environments.

Flow rate sprinkler development for site-specific irrigation

Due to the rapid depletion of water resources, water must be used more efficiently in agriculture to maintain current levels of yield in irrigated areas. The efficiency of irrigation systems can be increased by adjusting the amount of water applied to specific conditions of soil and crop, which may vary in a field. Taking into account spatial and temporal variability, it is evident that an equipment capable of providing different irrigation levels is necessary to meet the water requirement of the soil. This work aims to develop and evaluate a flow rate sprinkler to be used in center pivots or linear moving irrigation systems, with potential for utilization in irrigation scheduling. A prototype was developed by duplicating its calibrations, and discharge coefficient adjustment was carried out in the laboratory. To predict the flow rate, a successful model that represented the operation of the flow rate sprinkler was established. The calibration of the flow rate sprinkler prototype showed satisfactory statistical and technical results. Automation of the prototype was achieved by driving a step motor using communication from the parallel port of a microcomputer, which was controlled by a software developed for this purpose. The results were satisfactory and technically feasible.

Within-stand and seasonal variations of specific leaf area in a clonal Eucalyptus plantation in the Republic of Congo

Specific leaf area (SLA; m(leaf)(2) kg(leaf)(-1)) is a key ecophysiological parameter influencing leaf physiology, photosynthesis, and whole plant carbon gain. Both individual tree-based models and other forest process-based models are generally highly sensitive to this parameter, but information on its temporal or within-stand variability is still scarce. In a 2-4-year-old Eucalyptus plantation in Congo, prone to seasonal drought, the within-stand and seasonal variability in SLA were investigated by means of destructive sampling carried out at 2-month intervals, over a 2-year period. Within-crown vertical gradients of SLA were small. Highly significant relationships were found between tree-average SLA (SLA(t)) and tree size (tree height, H(t), or diameter at breast height, DBH): SLA(t) ranged from about 9 m(2) kg(-1) for dominant trees to about 14-15 m(2) kg(-1) for the smallest trees. The decrease in SLA(t) with increasing tree size was accurately predicted from DBH using power functions. Stand-average SLA varied by about 20% during the year, with lowest values at the end of the 5-month dry season, and highest values about 2-3 months after the onset of the wet season. Variability in leaf water status according to tree size and season is discussed as a possible determinant of both the within-stand and seasonal variations in SM. (C) 2009 Elsevier B.V. All rights reserved.

Evaluation of Environmental Mycobacteria Contamination in a Specific Pathogen Free Animal Facility from a Tropical Country

P>With the evidence showing the protection variability of bacille Calmette-Guerin, new potential vaccines for tuberculosis have been tested around the world. One of the general concerns in tuberculosis vaccine development is the possibility of priming the host immune system with prior exposure to environmental mycobacteria antigens, which can change the efficacy of subsequent vaccination. As there is a great homology between the species from Mycobacterium genera, the previous contact of experimental animals with environmental mycobacteria could sensitize the mice and, in this way, could influence subsequent vaccine research. The aim of our study was to investigate critical points in an animal facility to search for environmental mycobacteria that eventually could be in direct or indirect contact with the experimental animals. Samples were collected from surfaces of walls, floor, animal cages and shelves and analysed using the Ogawa-Kudoh decontamination method. Samples of drinking water, food and sawdust were collected for analysis by the NALC/NaOH decontamination method. Also, the samples were cultivated directly in broth medium, without any method for decontamination. After decontamination methods, we observed bacterial colony growth in 4.31% of the total of samples analysed. These samples were stained with Ziehl-Neelsen and we did not detect any acid-fast bacilli, suggesting that the animal facility analysed is free from contamination by environmental mycobacteria and is not a source of mycobacterial antigens. Furthermore, our study showed a new paradigm in tuberculosis vaccine development: concern about the animal facility environment in terms of immune system priming of experimental animals by nascent bacterial contaminants.

Antigen-specific suppression of inflammatory arthritis by dendritic cells

Purpose Antigen-specific suppression of a previously primed immune response is a major challenge for immunotherapy of autoimmune disease. We have shown that NF-κB inactivation in dendritic cells (modified DC) converts them into cells that tolerize rather than immunize to specific antigen [1]. Antigen-exposed modified DC prevent priming of immunity, and they suppress previously primed immune responses. Regulatory CD4+ T cells, which can transfer antigen-specific tolerance in an IL-10-dependent fashion, mediate the tolerance. We hypothesized that modified DC exposed to arthritogenic antigen would suppress clinical arthritis after disease onset. Methods Antigen-induced arthritis was induced in C57/Bl6 mice by priming to methylated bovine serum albumin (mBSA) antigen followed by challenge injection of mBSA to one knee. Knee swelling was apparent within 2 days, with peak clinical signs apparent at 5 days. Mice were treated with antigen-exposed modified DC between 2 and 6 days after mBSA challenge to the knee joint. Results Clinical arthritis was suppressed in each group receiving mBSA-exposed modified DC within 4 days compared with mice that received either no DC or keyhole limpet hemocyanin-exposed modified DC. Clinical improvement was associated with mBSA-specific tolerance in mice receiving mBSA-exposed modified DC. Tolerance induction was not impaired by concomitant administration of anti-tumor necrosis factor alpha monoclonal antibody. Subsequent rechallenge with intra-articular IL-1 induced flare of arthritis in all groups, which could be effectively suppressed by a second administration of mBSA-exposed modified DC. Conclusions The data indicate that modified DC induce antigen-specific immune suppression in this model of inflammatory arthritis, even after full clinical expression of the disease. These observations have important implications for antigen-specific therapy of autoimmunity.

Age and Method-dependent Variability of Predicted Oxygen Consumption in Congenital Heart Disease

Background and Purpose. There has been a lot of debate about the use of predicted oxygen consumption to calculate pulmonary vascular resistance using the Fick principle. We therefore comparatively analyzed predicted oxygen consumption in infants and children in specific age groups, using different methods (formulas), as an attempt to better understand the usefulness and limitations of predictions. Methods and Results. Four models (LaFarge & Miettinen, Bergstra et al., Lindahl, and Lundell et al.) were used to predict oxygen consumption in 200 acyanotic patients with congenital cardiac defects aged 0-2.0, > 2.0-4.0, > 4.0-6.0, and > 6.0-8.75 years (median 2.04 years). Significant differences were observed between the age groups (P < .001) and between the methods (P < .001), not related to diagnoses. Differences between methods were more impressive in the first age group (P < .01). In patients aged 0-2.0 years, the lowest values of oxygen consumption (corresponding to the highest estimates of pulmonary vascular resistance) were obtained with the method of Lindahl; above this age, any method except that of Lundell et al. Conclusions. Although measuring oxygen consumption is always preferable, a rational use of predictions, using different methods, may be of help in situations where measurements are definitely not possible.

Evaluation of RET polymorphisms in a six-generation family with G533C RET mutation: specific RET variants may modulate age at onset and clinical presentation

P>Context We previously described a six-generation family with G533C RET mutation and medullary thyroid carcinoma, in the largest family reported do date. Of particular interest, phenotype variability regarding the age of onset and clinical presentation of the disease, was observed. Objective We evaluate whether single SNPs within RET oncogene or haplotype comprising the RET variants (defined by Haploview) could predispose to early development of MTC in this family and influence the clinical manifestation. Design Eight SNPs were selected based on their previous association with the clinical course of hereditary or sporadic MTC, in particular promoting an early onset of disease. The variants were initially tested in 77 G533C-carriers and 100 controls using either PCR-direct sequencing or PCR-RFLP. Association between a SNP or haplotype and age at diagnosis or presence of lymph node metastasis was tested in 34 G533C-carries with MTC. Different bioinformatic tools were used to evaluate the potential effects on RNA splicing. Results An association was found between IVS1-126G > T and age at diagnosis. The variant [IVS8 +82A > G; 85-86 insC] was associated with the presence of lymph node metastases at diagnosis. In silico analysis suggested that this variant may induce abnormal splicing. This in silico analysis predicted that the [IVS8 +82A > G; 85-86 insC] could alter the splicing by disrupting and/or creating exonic splicing enhancer motifs. Conclusions We here identified two RET variants that were associated with phenotype variability in G533C-carriers, which highlights the fact that the modifier effect of a variant might depend on the type of mutation.

Reliability assessment of Cobb angle measurements using manual and digital methods

BACKGROUND CONTEXT: The vertebral spine angle in the frontal plane is an important parameter in the assessment of scoliosis and may be obtained from panoramic X-ray images. Technological advances have allowed for an increased use of digital X-ray images in clinical practice. PURPOSE: In this context, the objective of this study is to assess the reliability of computer-assisted Cobb angle measurements taken from digital X-ray images. STUDY DESIGN/SETTING: Clinical investigation quantifying scoliotic deformity with Cobb method to evaluate the intra- and interobserver variability using manual and digital techniques. PATIENT SAMPLE: Forty-nine patients diagnosed with idiopathic scoliosis were chosen based on convenience, without predilection for gender, age, type, location, or magnitude of the curvature. OUTCOME MEASURES: Images were examined to evaluate Cobb angle variability, end plate selection, as well as intra- and interobserver errors. METHODS: Specific software was developed to digitally reproduce the Cobb method and calculate semiautomatically the degree of scoliotic deformity. During the study, three observers estimated the Cobb angle using both the digital and the traditional manual methods. RESULTS: The results showed that Cobb angle measurements may be reproduced in the computer as reliably as with the traditional manual method, in similar conditions to those found in clinical practice. CONCLUSIONS: The computer-assisted method (digital method) is clinically advantageous and appropriate to assess the scoliotic curvature in the frontal plane using Cobb method. (C) 2010 Elsevier Inc. All rights reserved.

Valproic acid has temporal variability in urinary clearance of metabolites

The reasons for the intra- and interindividual variability in the clearance of valproic acid (VPA) have not been completely characterized. The aim of this study was to examine day-night changes in the clearance of 3-oxo-valproate (3-oxo-VPA), 4-hydroxy-valproate (4-OH-VPA), and valproic acid glucuronides under steady state. Six diurnally active healthy male volunteers ingested 200 mg sodium valproate 12 hourly, at 0800 and 2000, for 28 days. On the last study day, two sequential 12-h urine samples were collected commencing at 2000 the evening before. Plasma samples were obtained at the end of each collection. Following alkaline hydrolysis, urine was analyzed for concentrations of VPA, 3-oxo-VPA, and 4-OH-VPA. A separate aliquot was assayed for creatinine (CR). The plasma concentrations of VPA, 3-oxo-VPA, 2-en-VPA, and CR were determined. The analysis of VPA and its metabolites was performed by CC-MS. There was an increase in plasma 3-oxo-VPA concentration at 0800, sampling as compared to 2000 sampling (p < .05). The urinary excretion of 3-oxo-VPA and VPA glucuronides were decreased between 2000 and 0800, compared to between 0800, and 2000, by 30% and 50% respectively (p < .05). These results indicate a nocturnal decrease in renal clearance of 3-oxo-VPA rather than a decrease in the beta -oxidation of VPA at night. These differences were not explained by differences between the sampling periods in CR excretion. These results indicate the importance of collecting samples of 24-h duration when studying metabolic profiles of VPA.