Ensemble methods for stochastic networks with special reference to the biological clock of Neurospora crassa.

A major challenge in systems biology is to infer the parameters of regulatory networks that operate in a noisy environment, such as in a single cell. In a stochastic regime it is hard to distinguish noise from the real signal and to infer the noise contribution to the dynamical behavior. When the genetic network displays oscillatory dynamics, it is even harder to infer the parameters that produce the oscillations. To address this issue we introduce a new estimation method built on a combination of stochastic simulations, mass action kinetics and ensemble network simulations in which we match the average periodogram and phase of the model to that of the data. The method is relatively fast (compared to Metropolis-Hastings Monte Carlo Methods), easy to parallelize, applicable to large oscillatory networks and large (~2000 cells) single cell expression data sets, and it quantifies the noise impact on the observed dynamics. Standard errors of estimated rate coefficients are typically two orders of magnitude smaller than the mean from single cell experiments with on the order of ~1000 cells. We also provide a method to assess the goodness of fit of the stochastic network using the Hilbert phase of single cells. An analysis of phase departures from the null model with no communication between cells is consistent with a hypothesis of Stochastic Resonance describing single cell oscillators. Stochastic Resonance provides a physical mechanism whereby intracellular noise plays a positive role in establishing oscillatory behavior, but may require model parameters, such as rate coefficients, that differ substantially from those extracted at the macroscopic level from measurements on populations of millions of communicating, synchronized cells.

Younger age, recent HIV diagnosis, no welfare support and no annual sexually transmissible infection screening are associated with nonuse of antiretroviral therapy among HIV-positive gay men in Australia.

OBJECTIVES: With the increasing momentum to maximize the benefits of antiretroviral therapy (ART), better understanding of opportunities and challenges in increasing ART coverage and promoting early ART initiation is urgently needed. Key sociodemographic, clinical and behavioural factors associated with Australian HIV-positive gay men's current nonuse of ART were systematically examined. METHODS: Data were based on 1911 responses from HIV-positive men who had participated in the Australian Gay Community Periodic Surveys (GCPS) between 2010 and 2012. Stratified univariate analysis and multivariate logistic regression were used. RESULTS: A majority of the participants were recruited from gay community venues and events and self-identified as gay or homosexual. On average, they were 44 years old and had been living with HIV for at least 10 years. Close to 80% (n=1555) were taking ART, with >90% further reporting an undetectable viral load at the time of the survey. From 2010 to 2012, there had been a moderate increase in ART uptake [adjusted odds ratio (AOR) 1.40; 95% confidence interval (CI) 1.20-1.65]. In addition, younger age (AOR 1.66; 95% CI 1.45-1.92), recent HIV diagnosis (AOR 1.78; 95% CI 1.59-1.98), not receiving any social welfare payments (AOR 2.20; 95% CI 1.05-2.54) and no annual screening for sexually transmissible infections (AOR 1.55; 95% CI 1.03-2.34) were independently associated with ART nonuse. CONCLUSIONS: Current ART coverage among HIV-positive gay men in Australia is reasonably high. To further increase ART coverage and promote early ART initiation in this population, better clinical care and sustained structural support are needed for HIV management throughout their life course.

Trends in health services utilization in eight provinces in China, 1989-1993.

Continued pursuit of market-oriented reforms in China seems to have resulted in increasing income disparities. This has raised concerns about possible declines in the use of health services by the poor. Using data from three waves of the China Health and Nutrition Survey (1989, 1991, 1993), we examine whether people age 20-45 in eight provinces became less likely to seek care when ill. We carried out three probit estimations of seeking care when ill; the predictor variables include individual and workplace characteristics, a measure of the severity of illness and community level factors. Health care is broadly defined to include basic level clinics as well as urban hospitals. We find no evidence that health care utilization is decreasing. Rather, for people in a community survey reporting mainly mild or moderate illness, health care continues to be accessible. We consider possible limits of our study and discuss extensively the implications of the use of illness reports from the three cross-sectional surveys as health status indicators.

Frequent microsatellite alterations at chromosomes 9p21 and 3p14 in oral premalignant lesions and their value in cancer risk assessment.

To better understand genetic alterations in oral premalignant lesions, we examined 84 oral leukoplakia samples from 37 patients who had been enrolled in a chemoprevention trial. The samples were analyzed for two microsatellite markers located at chromosomes 9p21 and 3p14. Loss of heterozygosity (LOH) at either or both loci was identified in 19 of the 37 (51%) patients. Of these 19 patients, seven (37%) have developed head and neck squamous cell carcinoma (HNSCC) while only one of 18 (6%) of patients without LOH developed HNSCC. Our data suggest that clonal genetic alterations are common in oral premalignant lesions; that multiple genetic alterations have already occurred in oral premalignant lesions, allowing at least a focal clonal expansion; and that losses of the 9p21 and 3p14 regions may be related to early processes of tumorigenesis in HNSCC. These genetic alterations in premalignant tissues may serve as markers for cancer risk assessment.

Molecular assessment of histopathological staging in squamous-cell carcinoma of the head and neck.

BACKGROUND: Surgical oncologists rely heavily on the histopathological assessment of surgical margins to ensure total excision of the tumor in patients with head and neck cancer. However, current techniques may not detect small numbers of cancer cells at the margins of resection or in cervical lymph nodes. METHODS: We used molecular techniques to determine whether clonal populations of infiltrating tumor cells harboring mutations of the p53 gene could be detected in histopathologically negative surgical margins and cervical lymph nodes of patients with squamous-cell carcinoma of the head and neck. RESULTS: We identified 25 patients with primary squamous-cell carcinoma of the head and neck containing a p53 mutation who appeared to have had complete tumor resection on the basis of a negative histopathological assessment. In 13 of these 25 patients, molecular analysis was positive for a p53 mutation in at least one tumor margin. In 5 of 13 patients with positive margins by this method (38 percent), the carcinoma has recurred locally, as compared with none of 12 patients with negative margins (P = 0.02 by the log-rank test). Furthermore, molecular analysis identified neoplastic cells in 6 of 28 lymph nodes (21 percent) that were initially negative by histopathological assessment. CONCLUSIONS: Among specimens initially believed to be negative by light microscopy, a substantial percentage of the surgical margins and lymph nodes from patients with squamous-cell carcinoma of the head and neck contained p53 mutations specific for the primary tumor. Patients with these positive margins appear to have a substantially increased risk of local recurrence. Molecular analysis of surgical margins and lymph nodes can augment standard histopathological assessment and may improve the prediction of local tumor recurrence.

In vivo assessment of left ventricular remodelling after myocardial infarction by digital video contrast angiography in the rat.

OBJECTIVE: The aim was to develop a digital video contrast angiographic method for assessing global left ventricular function and volume in vivo in the rat and then to apply it to a study of ventricular remodelling after coronary occlusion, with and without reperfusion. METHODS: Digital contrast angiography was performed on 29 rats, including the following groups: sham operated (n = 11), non-transmural myocardial infarction produced by reperfusion (n = 8), and transmural infarction produced by permanent occlusion (n = 10). Under anaesthesia three weeks later, biplane fluoroscopic images were acquired following venous contrast injection. Levophase images were digitised, and left ventricular end diastolic and end systolic volumes and ejection fractions were obtained using an area-length method. Left ventricular ejection fraction data also were calculated by videodensitometry from video density curves. RESULTS: Compared to the sham operated group, the reperfused group showed a significant decrease in left ventricular ejection fraction, at 53(SD 7) v 70(5)% (p < 0.01), and an increase in end diastolic volume. The permanent occlusion group showed a further decrease in the ejection fraction [40(8)%] and a further significant increase in end diastolic volume compared to the reperfused group (p < 0.01). Left ventricular ejection fraction correlated inversely with percent infarct size (r = 0.882) and showed a positive correlation with the spared epicardial area (r = 0.721). Most haemodynamic variables, including maximum left ventricular dP/dt, failed to discriminate between the groups. The methods showed reasonable accuracy when tested in vitro using contrast filled balloons. In vivo, the left ventricular ejection fraction calculated by densitometry showed adequate interobserver variability (2 SD +/- 8.5 percentage points), but the area-length method showed somewhat more scatter. CONCLUSIONS: Digital video contrast angiography is a feasible method for the assessing global left ventricular function in the rat and should be useful in other small animal models. Significant differences in left ventricular volumes and ejection fractions were detected between reperfused and permanent occlusion groups, whereas haemodynamic variables showed non-significant trends. Reperfusion after 45 min of occlusion caused sparing of the epicardium, prevented unfavourable remodelling, and improved the ejection fraction compared to permanent occlusion.