Learning gene regulatory networks using gaussian process emulator and graphical LASSO.

Large amounts of research efforts have been focused on learning gene regulatory networks (GRNs) based on gene expression data to understand the functional basis of a living organism. Under the assumption that the joint distribution of the gene expressions of interest is a multivariate normal distribution, such networks can be constructed by assessing the nonzero elements of the inverse covariance matrix, the so-called precision matrix or concentration matrix. This may not reflect the true connectivity between genes by considering just pairwise linear correlations. To relax this limitative constraint, we employ Gaussian process (GP) model which is well known as computationally efficient non-parametric Bayesian machine learning technique. GPs are among a class of methods known as kernel machines which can be used to approximate complex problems by tuning their hyperparameters. In fact, GP creates the ability to use the capacity and potential of different kernels in constructing precision matrix and GRNs. In this paper, in the first step, we choose the GP with appropriate kernel to learn the considered GRNs from the observed genetic data, and then we estimate kernel hyperparameters using rule-of-thumb technique. Using these hyperparameters, we can also control the degree of sparseness in the precision matrix. Then we obtain kernel-based precision matrix similar to GLASSO to construct kernel-based GRN. The findings of our research are used to construct GRNs with high performance, for different species of Drosophila fly rather than simply using the assumption of multivariate normal distribution, and the GPs, despite the use of the kernels capacity, have a much better performance than the multivariate Gaussian distribution assumption.

Survival rate of AIDS disease and mortality in HIV-infected patients: a meta-analysis.

BACKGROUND: The life expectancy of patients with human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) reported by several epidemiological studies is inconsistent. This meta-analysis was conducted to estimate the survival rate from HIV diagnosis to AIDS onset and from AIDS onset to death. METHODS: The electronic databases PubMed, Web of Science and Scopus were searched to February 2016. In addition, the reference lists of included studies were checked to identify further references, and the database of the International AIDS Society was also searched. Cohort studies addressing the survival rate in patients diagnosed with HIV/AIDS were included in this meta-analysis. The outcomes of interest were the survival rate of patients diagnosed with HIV progressing to AIDS, and the survival rate of patients with AIDS dying from AIDS-related causes with or without highly active antiretroviral therapy (HAART). The survival rate (P) was estimated with 95% confidence intervals based on random-effects models. RESULTS: In total, 27,862 references were identified, and 57 studies involving 294,662 participants were included in this meta-analysis. Two, 4-, 6-, 8-, 10- and 12-year survival probabilities of progression from HIV diagnosis to AIDS onset were estimated to be 82%, 72%, 64%, 57%, 26% and 19%, respectively. Two, 4-, 6-, 8- and 10-year survival probabilities of progression from AIDS onset to AIDS-related death in patients who received HAART were estimated to be 87%, 86%, 78%, 78%, and 61%, respectively, and 2-, 4- and 6-year survival probabilities of progression from AIDS onset to AIDS-related death in patients who did not receive HAART were estimated to be 48%, 26% and 18%, respectively. Evidence of considerable heterogeneity was found. The majority of the studies had a moderate to high risk of bias. CONCLUSION: The majority of HIV-positive patients progress to AIDS within the first decade of diagnosis. Most patients who receive HAART will survive for >10 years after the onset of AIDS, whereas the majority of the patients who do not receive HAART die within 2 years of the onset of AIDS.

How much excess body weight, blood sugar, or age can double the risk of hypertension?

BACKGROUND: Despite the well-known impact of advanced age, excess body weight, and raised blood glucose on blood pressure, the level of exposure to these risk factors that is necessary to double the risk hypertension is not widely investigated, but was explored in this study. STUDY DESIGN: Cross-sectional study. METHODS: This study reports the results of a screening program conducted on a large population of adults to assess the prevalence of diabetes and hypertension and their associated risk factors. The participants were people aged 30 years or older referring to 16 health centers in Tehran. A standard questionnaire was used to collect data on blood pressure, body mass index (BMI), waist-hip ratio (WHR), fasting blood sugar (FBS), smoking status, and demographic characteristics (age and gender) based on WHO STEPS manual. RESULTS: Of the 7611 people who participated in the screening program, 696 (9.1%) had raised blood pressure. The level of exposure to risk factors for high blood pressure that is necessary to replicate the OR of 2.0 indicated that an OR of 2.0 corresponds to an increase in age of about 9.4 years, an increase in BMI of about 10.3 kg/m(2), an increase in waist-to-hip ratio of about 0.5, and an increase in fasting blood sugar (FBS) of about 85.8 mg/dl. CONCLUSIONS: This study indicated how much increase in age, BMI, waist-hip ratio, and FBS can double the risk of hypertension. These results may be helpful for public health policy and prioritizing effective prevention programs to reduce the burden of high blood pressure.

Classification of Death Rate due to Women's Cancers in Different Countries.

BACKGROUND: The two most frequently diagnosed cancers among women worldwide are breast and cervical cancers. The objective of the present study was to classify the different countries based on the death rates from sex specific cancers. METHODS: In this cross-sectional study, we used dataset regarding death rate from breast, cervical, uterine, and ovarian cancers in 190 countries worldwide reported by World Health Organization. Normal mixture models were fitted with different numbers of components to these data. The model's parameters estimated using the EM algorithm. Then, appropriate number of components was determined and was selected the best-fit model using the BIC criteria. Next, model-based clustering was used to allocate the world countries into different clusters based on the distribution of women's cancers. The MIXMOD program using MATLAB software was used for data analysis. RESULTS: The best model selected with four components. Then, countries were allocated into four clusters including 43 (23%) in the first cluster, 28 (14%) in the second cluster, 75 (39%) in the third cluster, and 44 (24%) in the fourth cluster. Most countries in South America were to the first cluster. In addition, most countries in Africa, Central, and Southeast Asia were located to the third cluster. Furthermore, the fourth cluster consisted of Pacific continent, North America and European countries. CONCLUSION: Considering the benefits of clustering based on normal mixture models, it seems that can be applied this method in wide variety of medical and public heath contexts.

Cholesteryl ester transfer protein (CETP) -629C/A polymorphism and it's effects on the serum lipid levels in metabolic syndrome patients.

Metabolic syndrome is a relatively common disorder with significant morbidity worldwide. Cholesteryl ester transfer protein (CETP) plays a central role in the metabolism of lipoproteins. In this study the effect of -629C/A polymorphism on the concentration of CETP and plasma lipids pattern was elicited in metabolic syndrome patients and control subjects. For this, a sample of 200 patients diagnosed with metabolic syndrome disorder was studied in comparison with 200 healthy controls. This study was performed by using polymerase chain reaction and restriction fragment length polymorphisms. Genotype distribution and allelic frequencies were determined and compared in metabolic syndrome and healthy controls. To determine the relationship between -629C/A polymorphism and lipid levels, lipids and CETP concentration were measured in metabolic syndrome and normal subjects. The results showed a significant difference between two groups in terms of FBS, cholesterol, TG, HDL-C, LDL-C levels as well as BMI, waist circumference, systolic and diastolic blood pressure. The genotype frequencies for this polymorphism differed significantly between metabolic syndrome patients and controls (in control group: CC% 20.5, CA% 76, AA% 3.5 and in patient group: CC% 28.5, CA% 53.5, AA% 18) (p < 0.05) while there was no significant difference in the frequency of the alleles. In the two groups, the levels of the cholesteryl ester transfer protein in AA genotype were lower than other genotypes. In the control group, individuals with AA genotype had the highest levels of LDL-C and TC plasma concentration. Considering the results of this study, it can be concluded that the -629 AA genotype was associated with high cholesterol; high LDL-C and low CETP level, so that it can be related to metabolic syndrome.

Effects of velocity and particles load on efficiency of cyclone in the stone crushing units at azendarian area.

BACKGROUND: The traditional cyclone has been developed for the removal of airborne silica particles from local exhaust ventilation (LEV). The objective of this research was to evaluate the effects of velocity and particles load on efficiency of cyclone in the Stone Crushing Units at Azendarian Area. METHODS: After the designing and installing the traditional cyclone, downstream and upstream samples of the apparatus were obtained. The mass of all samples collected was determined gravimetrically using EPA method with cascade Impactor. RESULTS: The relation between inlet total and respirable dust concentration to cyclone and cyclone overall efficiency is statistically significant (P= 0.005) and the relation between inlet air velocity to cyclone and cyclone pressure loss is statistically significant (P= 0.002). There was a significant correlation between the inlet concentration loaded to cyclone and the efficiency of cyclone. CONCLUSION: Increase of respirable dust concentration and also total concentration cause to increase efficiency of cyclone.

Estimation of illuminance on the South facing surfaces for clear skies in iran.

BACKGROUND: Daylight availability data are essential for designing effectively day lighted buildings. In respect to no available daylight availability data in Iran, illuminance data on the south facing vertical surfaces were estimated using a proper method. METHODS: An illuminance measuring set was designed for measuring vertical illuminances for standard times over 15 days at one hour intervals from 9 a.m. to 3 p.m. at three measuring stations (Hamadan, Eshtehard and Kerman). Measuring data were used to confirm predicted by the IESNA method. RESULTS: Measurement of respective illuminances on the south vertical surfaces resulted in minimum values of 10.5 KLx, mean values of 33.59 KLx and maximum values of 79.6 KLx. CONCLUSION: In this study was developed a regression model between measured and calculated data of south facing vertical illuminance. This model, have a good linear correlation between measured and calculated values (r= 0.892).

Environmental exposure to xylenes in drivers and petrol station workers by urinary methylhippuric Acid.

BACKGROUND: The aims of this study were evaluation of exposed to xylenes in low concentration and compare urinary level of methyl hippuric acid in taxi drivers and petrol stations workers in West of Iran. METHODS: This observation study was carried out on samples of the exposed men to xylenes in two occupational groups in Hamadan City (west of Iran) from March 2003 to March 2004. Subjects included 45 taxi drivers and 25 petrol station workers. The study group was selected from 54 workers at petrol stations and 300 drivers by simple random sampling. Xylenes was analyzed using gas chromatography equipped with a Flame Ionization Detector (FID). The urinary methyl hippuric acid (MHA) was analyzed with High performance Liquid Chromatography (HPLC) equipped with an ultraviolet (UV) detector. RESULTS: Total xylene exposure was 1.05±0.55 ppm (mean±SD) with a range of 0.20-2.55 ppm that was about 4 times more than taxi drivers' exposure. The poor correlation coefficient was seen between xylenes concentration and urinary MHA for drivers (r2= 0.09 to 0.42) but significant associations were noted between urinary MHA and xylene in the breathing zone of petrol station workers (r2= 0.69 to 0.77; P< 0.05). CONCLUSION: High xylenes levels are emitted in petrol stations at Iran. Urinary MHA level has a poor correlation with exposure to xylenes in drivers but has good correlation in petrol station workers.

Bacterial, fungal and parasitic contamination of cockroaches in public hospitals of Hamadan, Iran.

BACKGROUND & OBJECTIVES: To determine the possible role of cockroaches in dissemination of medically important microorganisms, a study was carried out in public hospitals and residential areas of Hamadan city, west of Iran. Bacteria, fungi and parasites of medical importance were isolated and identified. The total number of Blattella germanica collected from hospitals were 133 as the case group. The cockroaches collected from residential areas were 45 as the control group. METHODS: A total of 178 cockroaches were collected, over a period of two years (133 from hospitals; and 45 from residential areas) in Hamadan. Medically important microorganisms were isolated from external and internal surfaces using standard methods. RESULTS: In the case group, 130 out of 133 (98%) Blattella germanica showed contamination with high bacterial load (more than 1 x 10(3)) whereas only 2 out of 45 (4.45%) cockroaches of the control group were carrying medically important bacteria with high bacterial load. Bacteriological examinations revealed that almost all test cockroaches had at least one of the following microorganisms either in their body surface or digestive tract. Enterobacter (22.6%), Klebsiela (21%), Enterococcus (17.3%), Staphylococcus (16.5%), Esherichia coli and Streptococcus (8.3%), Pseudomonas (3%), and also Shigella, Haemophilus and group A beta-hemolytic Streptococcus each less than 1%. In addition the results showed (74.4.%) of test cockroaches harboured fungi-Candida (48.9%), Mucor (10.5%), Aspergillus niger (7.5%), Rhizopus (4.5) and also Penicillium and Aspergillus fumigans each 1.5%. Some parasitic worms of medical importance were also isolated from the test cockroaches, but carriage rates were low. INTERPRETATION & CONCLUSION: The data from this study emphasise the importance of cockroaches as potential vectors of medically important microorganisms such as pathogenic bacteria and fungi in hospital environments.

Serum lipid level in Iranian patients with psoriasis.

BACKGROUND: Psoriasis is a common, chronic, inflammatory and proliferative skin disease associated with abnormal lipid metabolism. Previous studies have demonstrated that patients with psoriasis may have an increased risk of occlusive vascular disease. OBJECTIVES: The aim of this study was to determine lipid profile in Iranian patients with psoriasis. SUBJECTS AND METHODS: A cross-sectional study was performed in 30 patients with approved psoriasis diagnosis attending the Dermatology Outpatient Department at Sina Hospital, Hamedan, Iran and 30 matched healthy individuals. Fasting blood sugar (FBS), triglyceride, cholesterol, high-density lipoprotein (HDL), low-density lipoprotein (LDL) and very low-density lipoprotein (VLDL) were measured using standard enzymatic method. The psoriasis activity was evaluated by psoriasis area and severity index (PASI Index). RESULTS: FBS levels were higher in patients with psoriasis diagnosis but the differences were not significant (P-value = 0.284). There were no significant differences between serum levels of triglyceride and cholesterol in two groups. There were no differences in lipoproteins (HDL, LDL, VLDL) compared with control subjects. (P-value > 0.05) PASI Index and lipid profile did not have any significant correlation. The correlation between duration of disease and LDL were significant (P-value = 0.033). CONCLUSION: Lipid profile in Iranian patients with psoriasis did not differ compared with control-matched subjects.

Road traffic noise model.

BACKGROUND: The recognition of road traffic noise as one of the main sources of environmental pollution has led to develop models that enable to predict noise level from fundamental variables. Traffic noise prediction models are required as aids for designing roads and highways. In addition, sometimes are used in the assessment of existing or envisaged changes in traffic noise conditions. In this paper a statistical modelling approach has been used for predicting road traffic noise in Iranian road conditions. METHODS: The study was performed during 2005-2006 in Hamadan city, in the west of Iran. The data set consisted of 282 noise measurements. The entire data set was utilized to develop a new model for Iranian condition using regression analysis. RESULTS: The developed model has twelve explanatory variables in order to achieve a proper fit for measured values of Leq (r2= 0.913). CONCLUSION: The proposed road traffic noise model can be effectively used as a decision support tools for prediction of traffic noise index of Leq(30min), in Iran's cities.

Tobacco smoking and oral cancer: a meta-analysis.

BACKGROUND: Several epidemiological studies suggest that tobacco smoking increases the risk of oral cancer. No systematic review, however, has been reported to examine how consistent the evidence is across the studies. We undertook a meta-analysis of epidemiological studies investigating the magnitude relationship between tobacco smoking and oral cancer. METHODS: Primary studies were identified through a computerized literature search of Medline. Articles abstracted were all epidemiological studies published as original articles in English during 1990-2007 provided the summary estimates of odds ratios (OR) of tobacco smoking for oral cancer compared to that of non-smokers. A total of 15 case-control studies were used for this meta-analysis. Summary of OR was calculated based on random effects model. RESULTS: The combined odds ratio for tobacco smoking related to oral cancer was 4.65 (95%CI, 3.19-6.77). Also, the highest combined odds ratio was belong to America continents (OR= 7.65; 95%CI, 5.11-11.45) and the lowest was in Asia (OR= 1.88; 95%CI, 0.95-3.71). There was heterogeneity in the pooled OR estimate across the studies. CONCLUSION: Our results clearly indicate that tobacco smokers are at increased risk of oral cancer. The cancer risk can be reduced by controlling of tobacco smoking in different countries.

Association between Alcohol Consumption and Gastric Cancer: A Meta-Analysis.

BACKGROUND: Gastric cancer is the second most common cause of death from cancer. As conflicting studies have recently been published, we aimed to evaluate the magnitude of the epidemiological evidence for an association between alcohol consumption and gastric cancer. METHODS: This study is a meta-analysis of case-control studies which have been performed during 1989 to 2007. We systematically reviewed the literature on the association between alcohol consumption and gastric cancer. Published case-control studies were identified in Pub Med and reference lists. Random effects meta-analysis was used to pool effects from twenty studies. RESULTS: The odds ratio (OR) for the overall association between alcohol and gastric cancer was 1.77 (95%CI: 1.46-2.15). The pooled OR for alcohol consumption related to gastric cancer for men was 2.17 (95%CI: 1.67-2.83). The odds ratio of beer or liquor was 1.16 which is not statistically related to gastric cancer risk (P> 0.05). Whereas, the odds ratio of vodka, wine and other types of alcohol intake related to gastric cancer were respectively 3.26, 1.69, and 1.77 (P< 0.01). CONCLUSION: Overall, based on the results of pooled analysis, it is reassuring that this meta-analysis shows a direct effect of alcohol associated with gastric cancer. Knowledge on the level of exposure to different alcohol constituents provides a deeper understanding of the real role of alcohol on cancer risk and ultimately allows the design of safer beverages.

Meta-analysis of case-referent studies of specific environmental or occupational pollutants on lung cancer.

BACKGROUND: Meta-analysis is a statistical tool for combining and integrating the results of independent studies of a given scientific issue. The present investigation was initiated to investigate case-referent studies of lung cancer risk from specific environmental and occupational pollutants, using detailed individual exposure data. MATERIALS AND METHODS: To examine the risk of lung cancer associated with environmental and occupational pollutants, a meta-analysis of published case-control studies was undertaken using a random effects model. For this study, the papers were selected for review from electronic search of PubMed, Medline and Google Scholar during 1990-2006. The principal outcome measure was the odds ratio for the risk of lung cancer. Twelve study reports detailing the relationship between the lung cancer and the type of exposure were identified. RESULTS: The odds ratio of asbestos, cooking fuel, cooking fumes, motor and diesel exhaust related to lung cancer were 1.67, 1.99, 2.52 and 1.42 (P < 0.001), respectively. The odds ratio of metal fumes related to lung cancer was 1.28 (0.001 P < 0.01). The combined odds ratio for the environmental and occupational exposure related to lung cancer was 1.67 (P < 0.001). CONCLUSIONS: The meta-analysis of the present study shows the magnitude association between asbestos, cooking fumes, cooking fuels, motor and diesel exhaust, with lung cancer risk. Lung cancer risk may be reduced by controlling exposure levels.

Comparative study of lung function in Iranian factory workers exposed to silica dust.

The study compared lung function among 322 workers in pottery, ceramic, stone-cutter and stone-grinder factories in the west of the Islamic Republic of Iran. Concentrations of silica particles <2 microm were measured in the ambient air of factories. Forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) were significantly lower in stone-grinders compared with pottery, ceramic or stone-cutter workers and a control group. No difference in lung function was found in pottery and stone-cutter workers with less than 20 years occupation compared with controls. The prevalence of respiratory symptoms in stone-grinders was higher than other workers. The concentration of silica particles of stone-grinder factories was 40-110 times higher than in ceramic and potteries factories. More attention is needed to ventilation systems and health care of stone-grinders.

Comparative study of lung function in Iranian factory workers exposed to silica dust

The study compared lung function among 322 workers in pottery, ceramic, stone-cutter and stone-grinder factories in the west of the Islamic Republic of Iran. Concentrations of silica particles <2 microm were measured in the ambient air of factories. Forced expiratory volume in 1 second [FEV1] and forced vital capacity [FVC] were significantly lower in stone-grinders compared with pottery, ceramic or stone-cutter workers and a control group. No difference in lung function was found in pottery and stone-cutter workers with less than 20 years occupation compared with controls. The prevalence of respiratory symptoms in stone-grinders was higher than other workers. The concentration of silica particles of stone-grinder factories was 40-110 times higher than in ceramic and potteries factories. More attention is needed to ventilation systems and health care of stone-grinders