Integrated BSI bacteria identifier-on-chip using approximate k-mer matching
Esteban Garzón1,2, Victor Galindo2, Yuval Harary2
1Department of Computer Engineering, Modeling, Electronics and Systems Engineering (DIMES), University of Calabria (UNICAL), Rende, 87036, Italy.
Abstract:
Acute graft-versus-host (GVHD) is a deadly disease that can be treated through fecal microbiota transplantation. However, such treatment is often followed by life-threatening bloodstream infections (BSI). Rapid detection of BSI-causing bacteria is critical in preventing BSI-related deaths. PC-CAM is a pathogen identification system-on-chip designed to assist in avoiding BSI by real-time detection of pathogen bacterial genomes using k-mer matching. The core of PC-CAM is an Approximate search-capable (Hamming distance tolerant) Content Addressable Memory (ACAM). PC-CAM was designed and manufactured in a commercial 65nm process. We use PC-CAM for real-time detection of bacteria in blood and stool samples of GVHD patients and evaluate PC-CAM bacteria identification efficiency, performance, silicon area, and power consumption based on silicon measurements. PC-CAM is capable of classifying 960K short DNA reads/sec within a silicon area of 2.38mm[Formula: see text] consuming about 1.27mW. We envision PC-CAM as a platform deployed at points of care to provide real-time, accurate, privacy-preserving, easy-to-operate, and energy-efficient pathogen classification.
Related Concept Videos
Linearization and Approximation
Application of Linearization and Approximation
Sign Test for Matched Pairs
To conduct the sign test, we first calculate the differences in...
Accuracy, limits, and approximation
Accuracy is defined as the closeness of the measured value to the true or actual value. In engineering mechanics, repeated measurements are taken during theoretical or experimental analyses to ensure that the result is precise and accurate.
The accuracy of any solution is based on the...
Linear Approximation in Frequency Domain
In contrast, nonlinear systems do not inherently possess these properties. However, for small deviations around an operating point, a nonlinear system can often be approximated as linear....
Linear Approximation in Time Domain
For a simple pendulum with a mass evenly distributed along its length and the center of mass located at half the pendulum's length,...


