Massively Multithreaded Maxflow for Image Segmentation on the Cray XMT-2.

Image segmentation is a very important step in the computerized analysis of digital images. The maxflow mincut approach has been successfully used to obtain minimum energy segmentations of images in many fields. Classical algorithms for maxflow in networks do not directly lend themselves to efficient parallel implementations on contemporary parallel processors.

Reassortment Networks and the evolution of pandemic H1N1 swine-origin influenza.

Prior research developed Reassortment Networks to reconstruct the evolution of segmented viruses under both reassortment and mutation. We report their application to the swine-origin pandemic H1N1 virus (S-OIV). A database of all influenza A viruses, for which complete genome sequences were available in Genbank by October 2009, was created and dynamic programming was used to compute distances between all corresponding segments.

Reassortment networks for investigating the evolution of segmented viruses.

Many viruses of interest, such as influenza A, have distinct segments in their genome. The evolution of these viruses involves mutation and reassortment, where segments are interchanged between viruses that coinfect a host. Phylogenetic trees can be constructed to investigate the mutation-driven evolution of individual viral segments.

Evaluation of regional lymph node dissection in patients with upper urinary tract urothelial cancer.

Objective: The role of the lymph node dissection (LND) in conjunction with nephroureterectomy (NU) in upper tract urothelial cell carcinoma (UT-UCC) remains undefined. We evaluated the manner in which the LND was applied at NU, the patterns of lymph node (LN) involvement and the preoperative variables that could identify patients at high risk for lymph node metastasis (LNM).

Methods: We examined clinical, radiological and pathological records of patients who underwent NU for UT-UCC between 1985 and 2004.

Parallelizing a DNA simulation code for the Cray MTA-2.

The Cray MTA-2 (Multithreaded Architecture) is an unusual parallel supercomputer that promises ease of use and high performance. We describe our experience on the MTA-2 with a molecular dynamics code, SIMU-MD, that we are using to simulate the translocation of DNA through a nanopore in a silicon based ultrafast sequencer. Our sequencer is constructed using standard VLSI technology and consists of a nanopore surrounded by Field Effect Transistors (FETs).

A parallel graph decomposition algorithm for DNA sequencing with nanopores.

Motivation: With the potential availability of nanopore devices that can sense the bases of translocating single-stranded DNA (ssDNA), it is likely that 'reads' of length approximately 10(5) will be available in large numbers and at high speed. We address the problem of complete DNA sequencing using such reads. We assume that approximately 10(2) copies of a DNA sequence are split into single strands that break into randomly sized pieces as they translocate the nanopore in arbitrary orientations.

Staphylococcus aureus and MRSA nasal carriage in general population.

Objective: Assessment of Staphylococcus aureus (S. aureus) and MRSA nasal carriage in our general population.

Design: Cross-sectional analytical study.

Antimicrobial resistance of community and hospital acquired Staphylococcus aureus isolates to oxacillin and glycopeptides.

Objective: To determine sensitivity pattern of Staphylococcus aureus isolates from the community and hospitals to methicillin, glycopeptides and other antimicrobial agents.

Design: Descriptive study.

Place And Duration Of Study: Private Pathology Laboratory in Lahore from January 2001 to April 2002.