Assessment of the role of genetic polymorphism in venous thrombosis through artificial neural networks

PURPOSE

To assess the role of genetic polymorphisms in venous thrombosis events (VTE) using Artificial Neural Networks (ANNs), a model for solving non-linear problems frequently associated with complex biological systems, due to interactions between biological, genetic and environmental factors.

METHODS

A database was generated from a case-control study of venous thrombosis, using 238 patients and 211 controls. The database of 64 variables included age, gender and a panel of 62 genetic variants. Three different ANNs were compared, with logistic regression for the accuracy of predicting cases and controls.

RESULTS

ANNs yielded a better performance than the logistic regression algorithm. Indeed, through ANNs models, the 62 variables related to genetic variants were first reduced to a set of 9, and then of 3 (MTHFR 677 C/T, FV arg506gln, ICAM1 gly214arg).

CONCLUSIONS

The findings of this study illustrate the power of ANN in evaluating multifactorial data, and show that the different sensitivities of the models of elaboration are related to the characteristics of the data. This may contribute to a better understanding of the role played by genetic polymorphisms in VTE, and help to define, if possible, a test panel of genetic variants to estimate an individual's probability of developing the disease.

Food consumption and nutrient intakes with a special focus on milk product consumption in early pubertal girls in Central Finland

OBJECTIVE

To evaluate the current status of dietary intakes in early pubertal girls with a special focus on milk products.

DESIGN

Cross-sectional data using 3-day food records.

SUBJECTS

Eight hundred and sixty girls, aged 10-12 years, at Tanner maturation stage I-III.

RESULTS

The mean consumption of milk products (620 g day(-1)) was similar to that of a Finnish study in the 1980s, while the consumption of non-milk drinks (403 g day(-1)) had increased. Twelve per cent of the girls had a dairy-restricted diet and consumed significantly less milk products than girls with a non-restricted diet (465 vs. 644 g day(-1), P<0.001). Girls with low milk product consumption had the highest non-milk drinks consumption (P<0.001). The mean energy intake was 7.1 MJ day(-1). No major changes were found in the sources of nutrients. The shares of energy for nutrients were close to recommendations except for saturated fat (13.9 vs. 10% of energy) and carbohydrates (51.5 vs. 55-60% of energy). The mean calcium intake (1117 mg day(-1)) was above the recommendation, while the vitamin D intake (3.1 microg day(-1)) of 88% of the girls was below the recommendation.

CONCLUSIONS

The diet quality of early pubertal girls is close to the recommendations and has improved with respect to fat compared with the 1980s. Consumption of milk products is high although the consumption of non-milk drinks has increased. We found a subgroup of girls who compensate their low milk product consumption with a higher consumption of non-milk drinks. Following a dairy-restricted diet is the main reason for low consumption of milk products.

Influence of physical activity and maturation status on bone mass and geometry in early pubertal girls

This study aimed to evaluate the influence of leisure-time physical activity on the development of bone mass and density in early pubertal girls. Scores of physical activity were obtained from 242 Finnish girls (10-12 years old within Tanner Stages I-II) using a questionnaire. Bone mass and density were assessed using different densitometric techniques. At Tanner Stage I, active girls had significantly higher bone mineral mass (BMC) and areal bone mineral density (aBMD) of the whole body and cortical volumetric BMD and thickness of the tibial shaft compared with sedentary girls (P<0.05). On the other hand, the active girls at Tanner Stage II showed significantly higher values only in BMC and aBMD at the lumbar spine (P=0.017 and P=0.007, respectively). These indicated that girls at Tanner Stage I with higher leisure-time physical activity level benefited more from physical activity in terms of their bone development than their less active counterparts. Our results provide evidence that the most beneficial time for physical exercise to exhibit its effect on bone development is in the earlier pubertal period for normal school children, but the positive effect on the lumbar spine is also demonstrated in Tanner Stage II.

Comparison of three ultrasonic axial transmission methods for bone assessment

This study compared three approaches to bone assessment using ultrasonic axial transmission. In 41 fresh human radii, velocity of the first arriving signal was measured with a commercial device (Sunlight Omnisense) operating at 1.25 MHz, a prototype based on 1-MHz bidirectional axial transmission and a low-frequency (200 kHz) prototype, also measuring the velocity of a slower wave. Cortical and trabecular bone mineral density, cortical thickness and cross-sectional area were determined by peripheral quantitative computed tomography. Significant but modest correlation between velocities reflects differences in the nature of the propagating waves and methodological differences. Of the higher frequency devices, bidirectional measurements provided stronger correlations with bone properties than did conventional measurements. High-frequency devices were less sensitive to cortical thickness than was the low-frequency device, because higher frequency waves interrogate thinner cortical layers. The results suggest that different axial transmission approaches reflect different bone properties. Therefore, a multifrequency technique might be useful in probing different bone properties.

Interaction between metabolic syndrome and PON1 polymorphisms as a determinant of the risk of coronary artery disease

The enzyme serum paraoxonase plays an important role in antioxidant defences and prevention of atherosclerosis. Metabolic syndrome (MS) is a clinical condition associated with increased oxidant stress and cardiovascular mortality. Two common polymorphisms of serum paraoxonase, PON1 Leu(55)Met and Gln(192)Arg, have been postulated to modulate the cardiovascular risk. We studied 915 subjects with angiographic documentation: 642 subjects with coronary atherosclerosis and 273 with normal coronary arteries. Two hundred and twenty-four subjects met the diagnostic criteria of MS. We found a significant interaction between MS and both the PON1 polymorphisms in determining the risk of coronary artery disease (P<0.05 by likelihood-ratio test). The 55Leu and the 192Arg alleles, associated with reduced protection against lipid peroxidation, were associated with coronary artery disease only in the MS subgroup. Subjects with MS and both 55Leu and 192Arg alleles had significantly increased risk (OR=9.38 with 95% CI=3.02-29.13 after adjustment by multiple logistic regression) as compared to subjects without MS and with 55Met/Met-192Gln/Gln genotype. No increased risk was found for subjects with MS and the 55Met/Met-192Gln/Gln genotype. This study highlights a potential example of genetic (paraoxonase polymorphisms)-clinical (MS) interaction influencing cardiovascular risk.

Mortality in New Zealand workers exposed to phenoxy herbicides and dioxins

AIMS

To evaluate mortality in New Zealand phenoxy herbicide producers and sprayers exposed to dioxins.

METHODS

Phenoxy herbicide producers (n = 1025) and sprayers (n = 703) were followed up from 1 January 1969 and 1 January 1973 respectively to 31 December 2000. A total of 813 producers and 699 sprayers were classified as exposed to dioxin and phenoxy herbicides. Standardised mortality ratios (SMR) were calculated using national mortality rates.

RESULTS

At the end of follow up, 164 producers and 91 sprayers had died. Cancer mortality was reduced for sprayers (SMR = 0.82, 95% CI 0.57 to 1.14) and increased in exposed production workers (SMR = 1.24, 95% CI 0.90 to 1.67), especially for synthesis workers (SMR = 1.69), formulation and lab workers (SMR = 1.64), and maintenance/waste treatment/cleaning workers (SMR = 1.46). Lymphohaematopoietic cancer mortality was increased in exposed production workers (SMR = 1.65, 95% CI 0.53 to 3.85), especially for multiple myeloma (SMR = 5.51, 95% CI 1.14 to 16.1). Among sprayers, colon cancer (SMR = 1.94, 95% CI 0.84 to 3.83) showed increased mortality.

CONCLUSIONS

Results showed 24% non-significant excess cancer mortality in phenoxy herbicide producers, with a significant excess for multiple myeloma. Associations were stronger for those exposed to multiple agents including dioxin during production. Overall cancer mortality was not increased for producers and sprayers mainly handling final technical products, although they were likely to have been exposed to TCDD levels far higher than those currently in the general New Zealand population.

Assessment of Candida albicans genes expressed during infections as a tool to understand pathogenesis

Candida albicans is the most common fungal opportunistic pathogen of humans and causes mucocutaneous, bloodstream and deep organ infections. Screening for C. albicans genes that are preferentially expressed within infected hosts represents a strategy to identify novel virulence factors and define global expression patterns relevant to pathogenesis. Until recently, C. albicans has not been amenable to screening using existing technologies. This has begun to change with the development of new molecular genetic tools and the sequencing of the C. albicans genome. In this paper, we review studies using recently developed techniques to identify genes expressed by C. albicans during infections, as well as work from our laboratory using a human antibody-based strategy. Along with others, we have shown that selected in vivo expressed genes encode known and previously unrecognized candidal virulence factors. Future studies in this area will identify additional novel virulence factors, as well as advance our understanding of pathogenesis.

Mortality and cancer incidence in New Zealand meat workers

AIMS

To ascertain whether there is an increased risk of cancers of the lung and lymphohaematopoietic tissue in workers employed in the New Zealand meat processing industry, and to identify exposures associated with any increased risks.

METHODS

A cohort of 6647 individuals assembled from personnel records from three plants was followed from 1988 until 2000. The observed number of deaths and cancer registrations was compared with expected numbers using five year age and gender specific rates for the New Zealand population. Subgroup analyses evaluated the effect of duration of exposure to selected agents, based on job titles and departments.

RESULTS

Vital status was determined for 84% of the cohort, and 92% of the total possible person-years. Mortality from all causes and all cancers was increased, and there was a significant excess of lung cancer. There were significant trends of increasing risk of lung and lymphohaematopoietic cancer with increasing duration of exposure to biological material.

CONCLUSIONS

Excess risks were observed for mortality from all causes, all cancers, and lung cancer. Although the increased risk of lung cancer may be partly due to confounding by smoking, it is unlikely to be entirely due to this cause. Furthermore, the dose-response relation observed for lung cancer suggests the effect is related to exposure to biological material contained in animal urine, faeces, and blood. Although numbers were small, the risk of lymphohaematopoietic cancer was also associated with increasing duration and level of exposure to biological material.

Comparison of inhibitory effects of oxygen radicals and calf serum protein on surfactant activity

The effects of the reactive oxygen species (ROS) superoxide anion (O2*-) and hydroxyl radical (*OH) on the surface tension lowering properties of bovine lipid extract surfactant (BLES) were compared to the effects of calf serum protein (CSP) in a captive bubble surfactometer (CBS). O2*- was generated from xanthine/xanthine oxidase (X/XO), and *OH was generated by the Fenton reaction. ROS were demonstrated by electron spin resonance (ESR) using 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) as the spin trap. Lipid peroxidation was measured using the thiobarbituric acid method. *OH had broad inhibitory effects on surface tension parameters, including adsorption, minimum surface tension, percentage film area change and film compressibility. O2*- showed inhibitory effects on adsorption, film area change and film compressibility but had no significant effect on minimum surface tension. Both O2*- and *OH treatment were associated with a large 'squeezeout' plateau around 20-25 mN/m in the surface tension-area relation, indicating poor film organization during the compression phase. At the concentrations used, ROS were associated with lipid peroxidation of BLES, which also demonstrated radical scavenging properties. Calf serum protein produced inhibitory effects on adsorption, minimum surface tension and percentage film area change that were quantitatively similar to those produced by *OH. The effects on film compression were significantly greater and qualitatively different from those seen with either O2*- or *OH. We conclude that the inhibition of BLES surface activity by ROS and inhibitory proteins can be distinguished in the captive bubble surfactometer and, particularly, by changes in the film compressibility modulus.

Dual wavelength demultiplexing by coupling and decoupling of photonic crystal waveguides

We demonstrate that the fundamental mode of the two coupled photonic crystal waveguides (PCWs) can be odd parity in a triangular photonic crystal and their dispersion curves do intersect. Thus, the PCWs are decoupled at the crossing point. By employing the decoupling at the crossing-point frequency and ultra short coupling length for another frequency, we designed a dual-wavelength demultiplexer with a coupling length of only two wavelengths and output power ratio as high as 15 dB. A loop-shape PCW is adapted to eliminate the backward energy flow.

Myelin associated glycoprotein cross-linking triggers its partitioning into lipid rafts, specific signaling events and cytoskeletal rearrangements in oligodendrocytes

Myelin-associated glycoprotein (MAG) has been implicated in inhibition of nerve regeneration in the CNS. This results from interactions between MAG and the Nogo receptor and gangliosides on the apposing axon, which generates intracellular inhibitory signals in the neuron. However, because myelin-axon signaling is bidirectional, we undertook an analysis of potential MAG-activated signaling in oligodendrocytes (OLs). In this study, we show that antibody cross-linking of MAG on the surface of OLs (to mimic axonal binding) leads to the redistribution of MAG into detergent (TX-100)-insoluble complexes, hyperphosphorylation of Fyn, dephosphorylation of serine and threonine residues in specific proteins, including lactate dehydrogenase and the beta subunit of the trimeric G-protein-complex, and cleavage of alpha-fodrin followed by a transient depolymerization of actin. We propose that these changes are part of a signaling cascade in OLs associated with MAG function as a mediator of axon-glial communication which might have implications for the mutual regulation of the formation and stability of axons and myelin.

Interaction between smoking and PON2 Ser311Cys polymorphism as a determinant of the risk of myocardial infarction

BACKGROUND

Increased oxidative stress is thought to play a role in the pathogenesis of the atherothrombotic process. Paraoxonases (PONs) are closely related antioxidant enzymes encoded by clustered genes on chromosome 7q. We evaluated three PON polymorphisms (PON1 Leu55Met and Gln192Arg; PON2 Ser311Cys) as possible risk factors for coronary atherosclerotic disease (CAD) and/or its main thrombotic complication, myocardial infarction (MI).

MATERIALS AND METHODS

We studied 890 subjects with angiographic documentation of coronary vessels (272=CAD-free; 618=CAD). In the CAD group, 341 subjects had a previous MI.

RESULTS

Frequencies of various genotypes were not significantly different between CAD-free subjects and the entire CAD population. In the latter group, there were more carriers of the PON2 311Cys variation among those who had suffered a MI than among those who had not (P<0.01 by chi2). The adjusted OR for MI among PON2 311Cys carriers was 1.5 (95%CI, 1.03-2.19). A gene-environmental interaction was found between PON2 Ser311Cys and smoking. Smoking by itself was associated with an increased MI risk. Among smokers, however, the MI risk was related to PON2 genotype: Cys/Cys homozygotes (OR=5.3; 95%CI, 1.7-16.4) and Ser/Cys heterozygotes (OR=2.1; 95%CI, 1.3-3.6) were at greater risk than Ser/Ser subjects (OR=1.2; 95%CI, 0.8-1.8). The PON2 polymorphism did not influence the MI risk among nonsmokers.

CONCLUSIONS

In CAD subjects, a proportion of the risk of MI may be influenced by the interaction between smoking and a polymorphism in the antioxidant enzyme PON2.

Pollen counts in relation to the prevalence of allergic rhinoconjunctivitis, asthma and atopic eczema in the International Study of Asthma and Allergies in Childhood (ISAAC)

BACKGROUND

Although pollens are major allergens associated with allergic rhinoconjunctivitis and asthma, there is little information about the relative prevalence of these conditions in populations with different pollen exposures.

OBJECTIVE

The purpose of this study was to investigate the relationship between pollen exposure and allergic symptoms among children in different countries.

METHODS

An ecological analysis was conducted to see whether pollen exposure (pollen counts, and duration and severity of pollen seasons) is associated with symptoms of allergic rhinoconjunctivitis, asthma and atopic eczema in 28 centres within 11 countries (nine being in Europe). Data on the prevalence of symptoms in 13-14-year olds were based on the responses to the written questionnaires from the International Study of Asthma and Allergies in Childhood (ISAAC). The analysis was adjusted for gross national product and mean annual relative humidity.

RESULTS

There was little relationship between pollen exposure and symptom prevalence, except for a significant inverse association between grass pollen counts and lifetime prevalence of the symptoms of allergic rhinitis (P=0.03). Almost all the regression coefficients were negative. The associations were even weaker and all non-significant when the analyses were conducted within countries, using a random intercept fixed slope model, but there was still no evidence of a positive association between pollen exposure and symptoms.

CONCLUSION

There is a weak but consistent tendency for the prevalence of allergic symptoms to be inversely associated with pollen exposure. This finding accords with evidence from several countries, suggesting that the prevalence of hayfever and asthma tends to be lower in rural than in urban areas, and lowest among people living on farms. Exposure to allergenic pollen in early life does not appear to increase the risk of acquiring symptoms of respiratory allergy, and may even give some protection against them.

Assessment of the tibia using ultrasonic guided waves in pubertal girls

The purpose of this study was to compare low frequency ultrasonic guided wave measurements with established ultrasound and bone density measurements in terms of their ability to characterize the tibia in pubertal girls. Subjects were 12-14-year-old girls ( n=106) who were participating in a calcium and vitamin D intervention study. A prototype low frequency pulse transmission device consisting of a uniaxial scanning mechanism and low frequency transducers orientated perpendicularly to the limb was used to measure two ultrasound velocities in the tibia. The first velocity, V1, was that of the first arriving signal, similar to that measured by existing commercial tibial ultrasound devices. The second velocity, V2, was that of a slower wave propagating at 1,500-2,000 m/s, which has been shown elsewhere to be consistent with the lowest order antisymmetric guided mode in the bone. In addition, commercial ultrasound devices (Omnisense, Sunlight Ltd.; QUS-2, Quidel Corp.) were used to measure the speed of sound (SOS) in the tibia and the radius and attenuation (BUA) in the calcaneus. Cortical bone cross-sectional area (CSA), mineral density (BMD) and cortical thickness (cTh) of the tibia were measured using pQCT, site-matched to the ultrasound measurements. Both V1 and V2 correlated significantly with cortical BMD and with cTh and CSA. On the other hand, tibial SOS correlated with BMD, but not with cTh and CSA. These results indicate that the prototype device using guided waves captures aspects of tibial cortical bone geometry in addition to bone density, thereby potentially offering increased diagnostic information compared to existing tibial ultrasound devices.

Characterization of HLA DR2 and DQ8 transgenic mouse with a new engineered mouse class II deletion, which lacks all endogenous class II genes

Human autoimmune diseases are a class of complex immune system disorders characterized by loss of tolerance to self-antigens. HLA class II molecules play a central role in the initiation, propagation and prolongation of the disease process. HLA class II transgenic mice with mouse endogenous class II gene Ab knockout were used successfully in several mouse models for human autoimmune diseases, such as IDDM, SLE and EAE in our Lab. However, these mice carry the functional mouse Eb gene from the Abeta(0/0) construct and could express Ebeta/DRalpha(Ealpha) molecules and shape the T cell repertoire in these mice. Recently, we have obtained the new MHCII(Delta/Delta) mice that are devoid of all endogenous conventional mouse MHC class II genes. When these mice are mated with our HLA class II transgenic mice, only human class II genes are expressed. The DR and DQ molecules expressed in these mice shape the T cell repertoire and regulate the immune response. Therefore, this new class of HLA transgenic mice is the first to be completely "humanized" in their MHC class II genes and will be an invaluable mouse model for human MHC class II associated autoimmune diseases.

Factor V Leiden polymorphism and the rate of fibrosis development in chronic hepatitis C virus infection

BACKGROUND

The rate of progression to cirrhosis varies among individuals chronically infected with the hepatitis C virus (HCV). Coagulation pathway activation in models of hepatic fibrosis suggests variation in coagulation pathway components may influence the rate of fibrosis. We hypothesised that polymorphisms of the coagulation factors II and V affect the rate of progression to cirrhosis in HCV infected subjects.

METHODS

We studied the relationship between rate of fibrosis (calculated by dividing the fibrosis stage by duration of infection) and genotypes of specific coagulation pathway genes in 352 White European patients infected with HCV. Genotyping was performed using reverse line blot hybridisation.

RESULTS

The rate of fibrosis was significantly higher in patients with the factor V Leiden genotype (Arg560Gln) (ANOVA, p=0.004). In disease association studies, a significant association was seen (Fisher's exact test, p=0.029; odds ratio 3.28 for fast progression to cirrhosis (expected to reach cirrhosis in less than 30 years) if heterozygous for factor V Leiden). No associations were seen between factor II genotype and fibrosis rate.

CONCLUSIONS

Possession of the factor V Leiden polymorphism significantly increases the risk of rapid disease progression in HCV, suggesting a role for the coagulation system in the pathogenesis of fibrotic liver disease.