Performance evaluation of image processing algorithms on the GPU

The graphics processing unit (GPU), which originally was used exclusively for visualization purposes, has evolved into an extremely powerful co-processor. In the meanwhile, through the development of elaborate interfaces, the GPU can be used to process data and deal with computationally intensive applications. The speed-up factors attained compared to the central processing unit (CPU) are dependent on the particular application, as the GPU architecture gives the best performance for algorithms that exhibit high data parallelism and high arithmetic intensity. Here, we evaluate the performance of the GPU on a number of common algorithms used for three-dimensional image processing. The algorithms were developed on a new software platform called "CUDA", which allows a direct translation from C code to the GPU. The implemented algorithms include spatial transformations, real-space and Fourier operations, as well as pattern recognition procedures, reconstruction algorithms and classification procedures. In our implementation, the direct porting of C code in the GPU achieves typical acceleration values in the order of 10-20 times compared to a state-of-the-art conventional processor, but they vary depending on the type of the algorithm. The gained speed-up comes with no additional costs, since the software runs on the GPU of the graphics card of common workstations.     

Computational exploration of structural information from cryo-electron tomograms

Cryo-electron tomography aims to act as an interface between in vivo cell imaging and techniques achieving atomic resolution. This attempt to bridge the resolution gap is facilitated by recent software and hardware advances. Information provided by atomically resolved macromolecules and molecular interaction data need to be put into a common framework in order to create a hybrid multidimensional cellular image. A major partner in this enterprise is the development of regularization and pattern recognition techniques, which try to identify macromolecular complexes as a function of their structural signature in cryo-electron tomograms of living cells.     

Efficacy of a Multi-level Intervention to Reduce Injecting and Sexual Risk Behaviors among HIV-Infected People Who Inject Drugs in Vietnam: A Four-Arm Randomized Controlled Trial

IntroductionInjecting drug use is a primary driver of HIV epidemics in many countries. People who inject drugs (PWID) and are HIV infected are often doubly stigmatized and many encounter difficulties reducing risk behaviors. Prevention interventions for HIV-infected PWID that provide enhanced support at the individual, family, and community level to facilitate risk-reduction are needed.Methods455 HIV-infected PWID and 355 of their HIV negative injecting network members living in 32 sub-districts in Thai Nguyen Province were enrolled. We conducted a two-stage randomization: First, sub-districts were randomized to either a community video screening and house-to-house visits or standard of care educational pamphlets. Second, within each sub-district, participants were randomized to receive either enhanced individual level post-test counseling and group support sessions or standard of care HIV testing and counseling. This resulted in four arms: 1) standard of care; 2) community level intervention; 3) individual level intervention; and 4) community plus individual intervention. Follow-up was conducted at 6, 12, 18, and 24 months. Primary outcomes were self-reported HIV injecting and sexual risk behaviors. Secondary outcomes included HIV incidence among HIV negative network members.ResultsFewer participants reported sharing injecting equipment and unprotected sex from baseline to 24 months in all arms (77% to 4% and 24% to 5% respectively). There were no significant differences at the 24-month visit among the 4 arms (Wald = 3.40 (3 df); p = 0.33; Wald = 6.73 (3 df); p = 0.08). There were a total of 4 HIV seroconversions over 24 months with no significant difference between intervention and control arms.DiscussionUnderstanding the mechanisms through which all arms, particularly the control arm, demonstrated both low risk behaviors and low HIV incidence has important implications for policy and prevention programming.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01689545","term_id":"NCT01689545"}}NCT01689545     

Stimulation of polyunsaturated fatty acid oxidation in myocytes by regulating its cellular uptake. On the rate limiting step of polyunsaturated fatty acid oxidation in heart.

In order to investigate the regulation of polyunsaturated fatty acid oxidation in the heart, the effect of the phosphodiesterase inhibitor enoximone on the oxidation of [1-14C] arachidonic acid, and [1-14C] arachidonyl-CoA, were studied in adult rat myocytes, and isolated rat heart mitochondria. Enoximone stimulated arachidonate oxidation by 94%, at a concentration of 0.25 mM. The apparent Vmax value of arachidonate oxidation in the presence of enoximone (6.98 nmol/mg protein/30 min), was approximately 75% higher than the value observed with the control (4.0 nmol/mg protein/30 min) in isolated myocytes. Also, enoximone stimulated arachidonate uptake by 27% at a concentration of 0.25 mM. On the other hand, enoximone had no effect on the oxidation of [1-14C] arachidonyl-CoA in isolated rat heart mitochondria. These results suggest that the oxidation of polyunsaturated fatty acids in myocytes is regulated by the rate of uptake of these acids across sarcolemmal membranes.     

A relation between myocardial taurine contest and pulmonary wedge pressure in dogs with heart failure

Myocardial taurine levels were correlated with pulmonary wedge pressure (PWP) in dogs with congestive heart failure (CHF). Heart failure was induced by creating an infrarenal aortocaval fistula. PWP ranged from 6.6 to 28 mm Hg, suggesting a wide range in severity of heart failure in those dogs. Compared to taurine levels of normal dogs, levels of the CHF group were significantly elevated in both left and right ventricles. Linear regression analysis of ventricular taurine content yielded a highly significant direct relation to PWP. The results suggest that myocardial taurine content increases as heart failure becomes more severe.     

Dissociation of neonatal rat brain by dispase for preparation of primary astrocyte cultures

We describe the use of the neutral protease Dispase for the dissociation of neonatal rat brain tissue for the preparation of primary monolayer astrocyte cultures. The method involves 5 to 6 successive extractions with careful separation of sedimenting, undissociated tissue. This method gives an initial cell suspension of high viability (93.7±1.7% cells exclude trypan blue). In comparison trypsin (0.25%) dissociated tissue gave a cell suspension that showed a lower viability of 58.2±7.6%. Identical saturation densities of 1.1 to 1.2×10⁴ cells/cm² after two weeks in culture were obtained for a range of seeding densities from 1 to 4×10⁴ cells/cm² of the Dispase dissociated tissue. Staining for glial fibrillary acidic protein showed that 90–100% cells were positive for this astroglial marker. Thus, the use of Dispase for the initial dissociation of rat brain tissue seems to give primary astrocyte cultures which are very reproducible and homogeneous.