GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

Computational detection of TF binding patterns has become an indispensable tool in functional genomics research. With the rapid advance of new sequencing technologies, large amounts of protein-DNA interaction data have been produced. Analyzing this data can provide substantial insight into the mechanisms of transcriptional regulation. However, the massive amount of sequence data presents daunting challenges. In our previous work, we have developed a novel algorithm called Hybrid Motif Sampler (HMS) that enables more scalable and accurate motif analysis. Despite much improvement, HMS is still time-consuming due to the requirement to calculate matching probabilities position-by-position. Using the NVIDIA CUDA toolkit, we developed a graphics processing unit (GPU)-accelerated motif analysis program named GPUmotif. We proposed a “fragmentation" technique to hide data transfer time between memories. Performance comparison studies showed that commonly-used model-based motif scan and de novo motif finding procedures such as HMS can be dramatically accelerated when running GPUmotif on NVIDIA graphics cards. As a result, energy consumption can also be greatly reduced when running motif analysis using GPUmotif. The GPUmotif program is freely available at http://sourceforge.net/projects/gpumotif

Microwave-assisted leaching for copper recovery from the chalcopyrite concentrate of Sarcheshmeh copper complex

Microwave applications in mining and process metallurgy have been the subject of many studies over the past two decades. This paper reviews the microwave-assisted leaching of copper from high-grade sulfide concentrate of the Sarcheshmeh copper complex. Response surface methodology (RSM) is used to optimize the leaching process. In this research, leaching experiments were carried out in a multi-mode cavity, and times in the presence of varying concentrations of H2O2 with microwave assistance after the leaching process parameters including type and concentration of the oxidizing agent, NaCl concentration, and leaching temperature, were optimized using Taguchi orthogonal array design method. Conventional leaching experiments were also performed to evaluate the influence of microwave radiation. It has been recognized that microwave technology has great potential to improve the extraction efficiency of metals in terms of both reductions in required leaching time and the recovery of valuable metals. Under the optimized conditions, the leaching efficiencies of copper were 75.3% and 42.5% in 3 hours by microwave assistance and conventional leaching methods, respectively.

COMPARATIVE EFFECTS OF NITRAZEPAM AND ACTH ON THE TREATMENT OF INFANTILE SPASM

ObjectiveInfantile spasms (IS) or West syndrome is a convulsive disease characterized by brief, symmetric axial muscle contractions (neck, trunk, and/or extremities).The therapy universally recognized as most effective in the treatment of IS, is treatment with the adrenocorticotropic hormone (ACTH) or oral corticosteroids. This therapy however has important side effects. Many studies have sought to find alternative therapies with fewer side effects. Nitrazepam, it has been proven, can be as effective as ACTH in controlling infantile spasms. The aim of this study was to evaluate and compare the efficacy of Nitrazepam and ACTH on the treatment of infantile spasms. Materials & MethodsThis randomized controlled clinical trial, enrolled sixty patients with newly diagnosed and previously untreated IS; diagnosis was made based on the criteria of The International Classification of Epilepsies of the International League Against Epilepsy (ILAE). Prior to treatment, all patients underwent Electro encephalo graphs (EEGs) and CT scans. Patients were randomized to receive 0.5-1 mg/kg Nitrazpam (NZP) in three daily doses or 40 IU Depot ACTH in a single morning dose. Complete cessation of spasms was considered to be as optimal response.ResultsOf the sixty patients studied, 24 (40%) were girls and 36(60%) were boys. All patients in the both groups were matched for age and sex.There were no differences between the both groups regarding age and sex (non-significant). Following treatments, at the end of the 6-week duration therapy, optimal response (Cessation of spasms) was obtained in 19 (63%) patients of NZP group and 9 (30%) patients of ACTH group, (

Effects of ANG II and its receptor blockers on nasal salt gland secretion and arterial blood pressure in conscious perkin ducks (Anas plalytrhynchos)

grantor: University of TorontoThe vertebrate renin-angiotensin system (RAS) controls cardiovascular, renal and osmoregulatory functions. Angiotensin II (ANG II) is the most potent hormone of the RAS. However in some vertebrates, Angiotensin III ( (Val\sp4) -ANG III) also has significant activity. The effects of angiotensins with different amino acid sequences and mammalian ANG II receptor antagonists on nasal salt gland function and arterial blood pressure in conscious white Pekin ducks were investigated in the present study. There was a positive linear correlation: between nasal fluid (Na\sp+) and osmolality, between (Na\sp+) and (K\sp+) and between the rate of nasal salt gland fluid secretion (NFS) and (Na\sp+) and (K\sp+). (Asp\sp1, Val\sp5) -ANG II (l nmol.kg\sp{-1} i.v.) inhibited NFS but did not change ionic concentrations. (Val\sp4) -ANG III (1 or 5 nmol.kg\sp{-1}) and ANG I (1-7) (20 nmol.kg\sp{-1}) had no effect on NFS. SARILE acted as an ANG II receptor agonist and resulted in a prolonged and complete inhibition of NFS. The AT\sb1 receptor antagonist-losartan (DuP 753) and the AT\sb2 receptor antagonist-PD 123319 both failed to block the inhibitory effect of (Asp\sp1, Val\sp5) -ANG II on the nasal salt glands. (Asp\sp1, Val\sp5) -ANG II(2 nmol.kg\sp{-1} i.v.) increased mean arterial blood pressure by about 40% (MABP) whereas the same dose of (Asn\sp1, Val\sp5) -ANG II (teleost) had only 30% of the pressor effect of (Asp\sp1, Val\sp5) -ANG II. Neither 1 nor 5 nmol.kg\sp{-1} of (Val\sp4) -ANG III i.v. nor 20 nmol.kg\sp{-1} of ANG I(1-7) had any measurable effect on MABP. SARILE completely blocked the pressor response to (Asp\sp1, Val\sp5) -ANG II, but the AT\sb1 antagonists losartan and CGP 48933 and the AT\sb2 antagonist PD 123319 all failed to block the pressor response to (Asp\sp1, Val\sp5) -ANG II.M.Sc

Prevalence of Unwanted Pregnancy and its Related Demographic Factors in Kurdistan - 2012

Introduction and Aims: Unwanted pregnancy is associated with induced abortion, Preterm birth and Low birth weight. Also produce Psychosocial, economic and health consequences for women and families and is considered as an important problem of Public health. Therefore this study had been conducted with the aim of investigate the prevalence of unwanted pregnancy and factors related with among women in Kurdistan.Methods: In this sectional study, 1134 person participated. In every city sampling ratio had been done in Maternity hospitals and other obstetric facility centers. Required data collected by interviews. Information analyzed by using SPSS 11.5 software, Chi-square statistic test and Logistic Regression.Results: A significant relationship was found between unwanted pregnancy with age (P<0.001), education levels (P<0.001), Education levels of spouse (P= 0.003) and methods of contraception (P<0.001). And There was no significant association with unwanted pregnancy with habitat (P<0.971) and job (P= 0.55). In Analyzing by Logistic Regression, Those who were older (P =0.001) and those who had lower education (P= 0.01), being involved in Unwanted pregnancy more. Thus, there is need to raise awareness and give proper training to women and their partners with broader and more comprehensive programs.Conclusion: Older age and lower educational levels were associated with unwanted pregnancy. Therefore, we need a broader program to raise awareness among women and their partners.*Corresponding author: Farnaz Zandvakili, Assistant Professor, Gynecology Department, Kurdistan University of medical sciences.Email: [email protected]