Parallelizing exact motif finding algorithms on multi-core

The motif finding problem is one of the important and challenging problems in bioinformatics. A variety of sequential algorithms have been proposed to find exact motifs, but the running time is still not suitable due to high computational complexity of finding motifs. In this paper we parallelize three efficient sequential algorithms which are HEPPMSprune, PMS5 and PMS6. We implement the algorithms on a Dual Quad-Core machine using openMP to measure the performance of each algorithm. Our experiment on simulated data show that: (1) the parallel PMS6 is faster than the other algorithms in case of challenging instances, while the parallel HEPPMSprune is faster than the other algorithms in most of solvable instances; (2) the scalability of parallel HEPPMSprune is linear for all instances, while the scalability of parallel PMS5 and PMS6 is linear in case of challenging instances only; (3) the memory used by HEPPMSprune is less than that of the other algorithms.     

Hall effect on unsteady couette flow with heat transfer under exponential decaying pressure gradient

The unsteady Couette flow of an electrically conducting, viscous, incompressible fluid bounded by two parallel non-conducting porous plates is studied with heat transfer taking the Hall effect into consideration. An external uniform magnetic field and a uniform suction and injection are applied perpendicular to the plates while the fluid motion is subjected to an exponential decaying pressure gradient. The two plates are kept at different but constant temperatures while the Joule and viscous dissipations are included in the energy equation. The effect of the ion slip and the uniform suction and injection on both the velocity and temperature distributions is examined.     

In vitro analysis of inflammatory responses following environmental exposure to pharmaceuticals and inland waters

Pharmaceuticals are regularly released into the environment; in particular non-steroidal anti-inflammatory drugs (NSAIDs) and antibiotics. Erythromycin, naproxen, furosemide and atenolol are reported to be stable for up to 1 year in the environment, which increases the risk for accumulation. In the present study we have measured the occurrence and concentration of pharmaceuticals in river Viskan (Jössabron) downstream of a sewage treatment plant in Borås, Sweden. Pharmaceuticals and water samples were tested for potential human risk by evaluating inflammatory responses (NF-κB and AP-1) using human T24 bladder epithelial cells and Jurkat T-cells. NF-κB activity in T24 cells was significantly reduced by all NSAIDs analysed (diclofenac, ketoprofen, naproxen, ibuprophen and dextropropoxyphene), but also by trimethoprim, using environmentally relevant concentrations. NF-κB and AP-1 activation was further analysed in response to water samples collected from different locations in Sweden. Dose-dependent down-regulation of AP-1 activity in Jurkat cells was observed at all locations. At two locations (Jössabron and Almenäs) down-regulation of NF-κB was observed. In contrast, the NF-κB response was potentiated by exposure to water from both locations following activation of NF-κB by treatment with heat-killed Escherichia coli. To determine the involvement of pharmaceuticals in the responses, T24 cells were exposed to the pharmaceutical mixture, based on the determined levels at Jössabron. This resulted in reduction of the NF-κB response following exposure to the pharmaceutical mixture alone while no potentiation was observed when cells were co-exposed to heat killed E. coli and pharmaceuticals. The obtained results demonstrate that the identified pharmaceuticals affect the inflammatory responses and furthermore indicate the presence of unknown substance(s) with the ability to potentiate inflammatory responses.     

Dual image watermarking using a multi-level thresholding and selective zone-quantization for copyright protection,authentication and recovery applications

Multimedia Tools and Applications - Image watermarking has been developed, recently, to meet the various concerns in multimedia copyright protection and forgery detection due to the explosive...     

[18F]Flurpiridaz: Facile and Improved Precursor Synthesis for this Next-Generation Cardiac Positron Emission Tomography Imaging Agent

[¹⁸F]Flurpiridaz is a recently developed positron emission tomography tracer that is currently being investigated in phase III clinical trials to measure myocardial blood flow. The relatively long physical half-life of fluorine-18 alongside the high spatial resolution and outstanding myocardium-to-background ratio fuels its potential to be the next gold standard for the early detection of coronary artery disease. Notwithstanding the expected widespread use of [¹⁸F]flurpiridaz, the reported multistep synthesis of its precursor for radiofluorination involves a hazardous alkylation step using carcinogenic ethylene oxide, and a low overall chemical yield of 7 %. In this work, we have improved the overall yield more than fivefold and concurrently replaced the hazardous step. Specificity of binding of [¹⁸F]flurpiridaz to mitochondrial complex 1 was demonstrated by in vitro autoradiography on mouse heart tissue sections. These results thus pave the way for assessing myocardial blood flow and coronary flow reserve in mouse models of cardiovascular disease.