Laser enhanced high-intensity focused ultrasound thrombolysis: An in vitro study

This is the Published Version made available with the permission of the publisher. Copyright, Ecological Society of America.Laser-enhanced thrombolysis by high intensity focused ultrasound (HIFU) treatment was studied in vitro with bovine blood clots. To achieve laser-enhanced thrombolysis, laser light was employed to illuminate the sample concurrently with HIFU radiation, and ultrasound and laser parameters were optimized to achieve better thrombolysis efficiency. The results indicated that the thrombolysis efficiency increased when pulse length of HIFU wave, HIFU pressure, or laser fluence increases. Also, with the presence of laser, an enhanced effect of thrombolysis was observed.This study was supported in part byNIH Grant No. 1R03EB015077-01A1

Exploiting Parallel R in the Cloud with SPRINT

BACKGROUND: Advances in DNA Microarray devices and next-generation massively parallel DNA sequencing platforms have led to an exponential growth in data availability but the arising opportunities require adequate computing resources. High Performance Computing (HPC) in the Cloud offers an affordable way of meeting this need. OBJECTIVES: Bioconductor, a popular tool for high-throughput genomic data analysis, is distributed as add-on modules for the R statistical programming language but R has no native capabilities for exploiting multi-processor architectures. SPRINT is an R package that enables easy access to HPC for genomics researchers. This paper investigates: setting up and running SPRINT-enabled genomic analyses on Amazon’s Elastic Compute Cloud (EC2), the advantages of submitting applications to EC2 from different parts of the world and, if resource underutilization can improve application performance. METHODS: The SPRINT parallel implementations of correlation, permutation testing, partitioning around medoids and the multi-purpose papply have been benchmarked on data sets of various size on Amazon EC2. Jobs have been submitted from both the UK and Thailand to investigate monetary differences. RESULTS: It is possible to obtain good, scalable performance but the level of improvement is dependent upon the nature of algorithm. Resource underutilization can further improve the time to result. End-user’s location impacts on costs due to factors such as local taxation. Conclusions: Although not designed to satisfy HPC requirements, Amazon EC2 and cloud computing in general provides an interesting alternative and provides new possibilities for smaller organisations with limited funds

PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature

Summary: PDQ Wizard automates the process of interrogating biomedical references using large lists of genes, proteins or free text. Using the principle of linkage through co-citation biologists can mine PubMed with these proteins or genes to identify relationships within a biological field of interest. In addition, PDQ Wizard provides novel features to define more specific relationships, highlight key publications describing those activities and relationships, and enhance protein queries. PDQ Wizard also outputs a metric that can be used for prioritization of genes and proteins for further research

SUrgical versus PERcutaneous Bypass: SUPERB-trial; Heparin-bonded endoluminal versus surgical femoro-popliteal bypass: study protocol for a randomized controlled trial

Contains fulltext : 96315.pdf (publisher's version ) (Open Access)BACKGROUND: Endovascular treatment options for the superficial femoral artery are evolving rapidly. For long lesions, the venous femoropopliteal bypass considered to be superior above the prosthetic bypass. An endoluminal bypass, however, may provide equal patency rates compared to the prosthetic above knee bypass. The introduction of heparin-bonded endografts may further improve patency rates. The SUrgical versus PERcutaneous Bypass (SuperB) study is designed to assess whether a heparin-bonded endoluminal bypass provides equal patency rates compared to the venous bypass and to prove that it is associated with improved quality of life, related to a decreased complication rate, or not. METHODS/DESIGN: Two-hundred-twenty-two patients with peripheral arterial occlusive disease, category 3-6 according to Rutherford, will be randomized in two treatment arms; 1. the surgical femoro-popliteal bypass, venous whenever possible, and 2. the heparin-bonded endoluminal bypass. The power analysis was based on a non-inferiority principle, with an effect size of 90% and 10% margins (alpha 5%, power 80%). Patients will be recruited from 5 teaching hospitals in the Netherlands during a 2-year period. The primary endpoint is primary patency and quality of life evaluated by the RAND-36 questionnaire and the Walking Impairment Questionnaire. Secondary endpoints include secondary patency, freedom-from-TLR and complications. DISCUSSION: The SuperB trial is a multicentre randomized controlled trial designed to show non-inferiority in patency rates of the heparin-bonded endograft compared to the surgical bypass for treatment of long SFA lesions, and to prove a better quality of life using the heparin bonded-endograft compared to surgically treatment, related to a reduction in complications. TRIAL REGISTRATION: Clinicaltrials: NCT01220245

PEDRo: A database for storing, searching and disseminating experimental proteomics data

Abstract Background Proteomics is rapidly evolving into a high-throughput technology, in which substantial and systematic studies are conducted on samples from a wide range of physiological, developmental, or pathological conditions. Reference maps from 2D gels are widely circulated. However, there is, as yet, no formally accepted standard representation to support the sharing of proteomics data, and little systematic dissemination of comprehensive proteomic data sets. Results This paper describes the design, implementation and use of a Proteome Experimental Data Repository (PEDRo), which makes comprehensive proteomics data sets available for browsing, searching and downloading. It is also serves to extend the debate on the level of detail at which proteomics data should be captured, the sorts of facilities that should be provided by proteome data management systems, and the techniques by which such facilities can be made available. Conclusions The PEDRo database provides access to a collection of comprehensive descriptions of experimental data sets in proteomics. Not only are these data sets interesting in and of themselves, they also provide a useful early validation of the PEDRo data model, which has served as a starting point for the ongoing standardisation activity through the Proteome Standards Initiative of the Human Proteome Organisation

Type II Endoleak Following Endovascular Repair of Infrarenal Abdominal Aortic Aneurysm: Innovative Transgraft Approach to Contemporary Management

Elective endovascular aneurysm repair (EVAR) is the first-line therapeutic option for patients with infrarenal abdominal aortic aneurysm. However, endoleaks –– persistent blood flow outside the lumen of the stent graft (or endograft) but within the aneurysm sac or adjacent vascular segment being treated by the graft –– continue to be a persistent problem in the post-EVAR setting. The type II endoleak is the most common of these and can be a demanding challenge to address by standard endovascular techniques. Currently, two prominent endovascular techniques exist for the management of type II endoleaks: direct translumbar embolization and transarterial embolization. Both of these are fraught with their own limitations and complications. In this review, we describe the contemporary trends in management of type II endoleaks and introduce a novel endovascular technique to treat this challenging and common EVAR complication

Parity Assignment of the Pronounced Structure in the Radiative Capture of Neutrons by /sup 238/U below 100 keV

Some years ago, Perez and de Saussure reported evidence for intermediate structure in the radiative capture cross sections of /sup 238/U. More recently, these and additional data, obtained by a different experimental technique but which showed the same non-statistical behavior, were analyzed by Perez et al. Under the assumption that the structure could be attributed to doorway states in the p/sup 3/2/ neutron channel. The results of an experimental determination of the parity of the structure, using neutron capture-gamma ray spectroscopy are reported. Much of the structure below 50 keV appears to be due to s-wave interactions. The magnitude of the fluctuations is much larger than can be calculated with the usual unresolved - resonance treatment unless the average neutron and radiative-capture widths are correlated. It is shown that such an apparent correlation can arise as a result of multiple-scattering enhancement of radiative capture in the samples used, and it is concluded that the evidence for intermediate structure in the capture of neutrons by /sup 238/U is not yet firmly established