Human pathogenic streptococcal proteomics and vaccine development

Gram-positive streptococci are non-motile, chain-forming bacteria commonly found in the normal oral and bowel flora of warm-blooded animals. Over the past decade, a proteomic approach combining 2-DE and MS has been used to systematically map the cellular, surface-associated and secreted proteins of human pathogenic streptococcal species. The public availability of complete streptococcal genomic sequences and the amalgamation of proteomic, genomic and bioinformatic technologies have recently facilitated the identification of novel streptococcal vaccine candidate antigens and therapeutic agents. The objective of this review is to examine the constituents of the streptococcal cell wall and secreted proteome, the mechanisms of transport of surface and secreted proteins, and describe the current methodologies employed for the identification of novel surface-displayed proteins and potential vaccine antigens.     

Probabilistic analysis of a grouping algorithm

We study thegrouping by swapping problem, which occurs in memory compaction and in computing the exponential of a matrix. In this problem we are given a sequence ofn numbers drawn from {0,1, 2,...,m?1} with repetitions allowed; we are to rearrange them, using as few swaps of adjacent elements as possible, into an order such that all the like numbers are grouped together. It is known that this problem is NP-hard. We present a probabilistic analysis of a grouping algorithm calledMEDIAN that works by sorting the numbers in the sequence according to their median positions. Our results show that the expected behavior ofMEDIAN is within 10% of optimal and is asymptotically optimal asn/m→∞ or asn/m→0.     

Generalized Adjusted Rand Indices for cluster ensembles

In this paper, Adjusted Rand Index (ARI) is generalized to two new measures based on matrix comparison: (i) Adjusted Rand Index between a similarity matrix and a cluster partition (ARImp), to evaluate the consistency of a set of clustering solutions with their corresponding consensus matrix in a cluster ensemble, and (ii) Adjusted Rand Index between similarity matrices (ARImm), to evaluate the consistency between two similarity matrices. Desirable properties of ARI are preserved in the two new measures, and new properties are discussed. These properties include: (i) detection of uncorrelatedness; (ii) computation of ARImp/ARImm in a distributed environment; and (iii) characterization of the degree of uncertainty of a consensus matrix. All of these properties are investigated from both the perspectives of theoretical analysis and experimental validation. We have also performed a number of experiments to show the usefulness and effectiveness of the two proposed measures in practical applications.     

Informatics challenges of high-throughput microscopy

In this article, we discussed the emerging informatics issues of high-throughput screening (HTS) using automated fluorescence microscopy technology, otherwise known as high-content screening (HCS) in the pharmaceutical industry. Optimal methods of scoring biomarkers and identifying candidate hits have been actively studied in academia and industry, with the exception of data modeling topics. To find candidate hits, we need to score the images associated with different compound interventions. In the application example of RNAi genome-wide screening, we aim to find the candidate effectors or genes which correspond to the images acquired using the three channels. Scoring the effectors is equivalent to scoring the images based on the number of phenotypes existing in those images. Our ultimate objective of studying HTS is to model the relationship between gene networks and cellular phenotypes, investigate cellular communication via protein interaction, and study the disease mechanism beyond the prediction based on the molecular structure of the compound. Finally, computational image analysis has become a powerful tool in cellular and molecular biology studies. Signal processing and modeling for high-throughput image screening is an emerging filed that requires novel algorithms for dynamical system analysis, image processing, and statistical modeling. We hope that this article will motivate the signal processing communities to address challenging data modeling and other informatics issues of HTS.     

Simultaneous all-optical inverted and noninverted wavelength conversion using a single-stage fiber-optical parametric amplifier

We have demonstrated, for the first time to our knowledge, simultaneous all-optical inverted and noninverted wavelength conversion by using a single-stage two-pump fiber-optical parametric amplifier with an extinction ratio between 7 and 14 dB over 24 nm.     

Evaluation of a Computer-Assisted, 2-D Virtual Reality System for Training People With Intellectual Disabilities on How to Shop.

Objective: To evaluate the effectiveness of a 2-D virtual reality (VR) program for training people with intellectual disabilities to shop. Study Design: Pretest and posttest quasi-experimental design. Participants: Sixteen persons with intellectual disabilities (age 17-23 years; IQ = 40-54). Intervention: A VR program or a conventional program training them in supermarket-shopping skills. Main Outcome Measure: Checklist for supermarket-shopping skills. Results: Participants in both training groups showed significant improvement. There was no significant difference in effectiveness between the two methods. Conclusions: The VR program appears effective in training people with intellectual disabilities in an important community living skill. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Three generations of asynchronous microprocessors

We trace the evolution of Caltech asynchronous processors from a simple proof of concept, to a high-performance MIPS-like processor using a different buffer circuit for better performance, to the latest 8051 clone targeting low-energy operation. We describe the control aspects of the evolving circuit styles. We describe these three generations of asynchronous microprocessors (Caltech asynchronous processors, MiniMIPS and Lutonium) and the corresponding circuit families and design methods. The asynchronous circuits we use are called quasidelay-insensitive (QDI) circuits. A QDI circuit involves no assumption about, or knowledge of, delays in operators and wires, except for isochronic forks, which the designer assumes have similar delays on the different branches. QDI circuits are the most conservative asynchronous circuits in terms of delays.     

Estimating light vectors in real time

Capturing the appearance of objects under different lighting conditions is useful in texture acquisition, bidirectional reflectance distribution function (BRDF) measurement, and image-based data acquisition. With the acquired data, we can render virtual objects realistically. During the data capture, we must record both the radiance and the light vector. Measuring the light vector is not necessarily easy. We propose a capturing system that estimates the light vector by applying a vision-based technique. It lets the user freely position a handheld light source during capture. The system estimates light-source orientation in real time through a Web cam mounted on the light source. Software running on an ordinary PC analyzes images from the Web cam to recognize the light source direction (the light vector). Our goal is to design a low-cost, portable, and adaptable system. Vision-based approaches offer such characteristics. We use a pose-estimation system to acquire image-based data for relighting.     

A Six-sigma approach for benchmarking of RP&M processes

This paper presents a methodology of using six-sigma quality tools for benchmarking of rapid prototyping & manufacturing (RP&M) processes. It involves the fabrication of a geometric benchmark part and a methodology to control and identify the best performance of the process to reduce the variablity in the fabricated parts. The approach is demonstrated with a case study based on the direct laser sintering (DLS) process for prototyping using plastic powder. In the case study an identified set of six-sigma/ statistical process control tools is employed to determine and best tune factors affecting the desired outcomes of the built parts.