Health Information Technology Commons^™

Tendinopathy Discrimination By Use Of Spatial Frequency Parameters In Ultrasound B-Mode Images, Gregory R. Bashford, Nicholas Tomsen, Shruti Arya, Judith M. Burnfield, Kornelia Kulig

Biomedical Imaging and Biosignal Analysis Laboratory

The structural characteristics of a healthy tendon are related to the anisotropic speckle patterns observed in ultrasonic images. This speckle orientation is disrupted upon damage to the tendon structure as observed in patients with tendinopathy. Quantification of the structural appearance of tendon shows promise in creating a tool for diagnosing, prognosing, or measuring changes in tendon organization over time. The current work describes a first step taken towards this goal—classification of Achilles tendon images into tendinopathy and control categories. Eight spatial frequency parameters were extracted from regions of interest on tendon images, filtered and classified using linear discriminant analysis. Resulting …

Droid: The Drosophila Interactions Database, A Comprehensive Resource For Annotated Gene And Protein Interactions, Jingkai Yu, Svetlana Pacifico, Guozhen Liu, Russell L. Finley Jr

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Charting the interactions among genes and among their protein products is essential for understanding biological systems. A flood of interaction data is emerging from high throughput technologies, computational approaches, and literature mining methods. Quick and efficient access to this data has become a critical issue for biologists. Several excellent multi-organism databases for gene and protein interactions are available, yet most of these have understandable difficulty maintaining comprehensive information for any one organism. No single database, for example, includes all available interactions, integrated gene expression data, and comprehensive and searchable gene information for the important model organism, Drosophila melanogaster. …

Direct Comparison Of Feature Tracking And Autocorrelation For Velocity Estimation, Gregory R. Bashford, Derek J. Robinson

Biomedical Imaging and Biosignal Analysis Laboratory

Feature tracking is an algorithm for estimating tissue motion and blood flow using pulse-echo ultrasound. It was proposed as a computationally simpler alternative to other techniques such as autocorrelation and time-domain cross correlation. The advantage of feature tracking is that it selectively extracts easily identifiable parts of the speckle signal (e.g., the local maxima), reducing the amount of information being processed. Studies on feature tracking to date have used stationary, specklegenerating targets to simulate blood flow. Also, feature tracking has not been compared with accepted commercial methods. This study directly compares feature tracking performance with the complex autocorrelation method, which …

The Genome-Enabled Electronic Medical Record., M A Hoffman

Manuscripts, Articles, Book Chapters and Other Papers

The integration of patient-specific genomic information into the electronic medical record (EMR) will create many opportunities to improve patient care. Key to the successful incorporation of genomic information into the EMR will be the development of laboratory information systems capable of appropriately formatting molecular diagnostic and cytogenetic findings in the EMR. Due to the lack of granular genomics-related content in existing medical vocabularies, the adoption of new standards for describing clinically significant genomic information will be an important step toward recognizing the genome-enabled EMR. Appropriate capture of patient-specific genomic results in the EMR will generate new opportunities to utilize this …

Ocpat: An Online Codon-Preserved Alignment Tool For Evolutionary Genomic Analysis Of Protein Coding Sequences, Guozhen Liu, Monica Uddin, Munirul Islam, Morris Goodman, Lawrence I. Grossman, Roberto Romero, Derek E. Wildman

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence.

Results

Here we report an online codon-preserved alignment tool (OCPAT) that generates …

Single Molecule Detection Systems And Methods, John G. K. Williams, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

A micofluidic system is provided that includes a substrate, a first microchannel disposed in the substrate for providing a reactant to a reaction zone, a second microchannel disposed in the substrate, the third microchannel providing fluid communication between the first and second microchannels. The system also typically includes first and second electrodes, positioned at opposite ends of the second microchannel, for providing an electric field within the second microchannel. In operation, when the reactant is in the reaction zone, a reaction product is produced having a net electric charge different from the electric of the reactant.

Girls' Perception Of Physical Environmental Factors And Transportation: Reliability And Association With Physical Activity And Active Transport To School, Kelly R. Evenson, Amanda Birnbaum, Ariane L. Bedimo-Rung, James Sallis, Carolyn C. Voorhees, Kimberly Ring, John P. Elder

Department of Public Health Scholarship and Creative Works

Background

Preliminary evidence suggests that the physical environment and transportation are associated with youth physical activity levels. Only a few studies have examined the association of physical environmental factors on walking and bicycling to school. Therefore, the purpose of this study was (1) to examine the test-retest reliability of a survey designed for youth to assess perceptions of physical environmental factors (e.g. safety, aesthetics, facilities near the home) and transportation, and (2) to describe the associations of these perceptions with both physical activity and active transport to school.

Methods

Test and retest surveys, administered a median of 12 days later, …

Charge-Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi L. Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation Without interference from unincorporated NPs and Without illuminating the polymerase-DNA complex.

Nucleic Acid Sequencing Using Charge-Switch Nucleotides, John G. K. Williams, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation without interference from unincorporated NPs and without illuminating the polymerase-DNA complex.

Imposed Constraints On The Smith-Waterman Alignment Algorithm For Enhanced Modeling Of A Single-Molecule Dna Sequencer, Patrick G. Humphrey, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An effort has been underway to develop a system for de novo sequencing of single DNA molecules with very long reads. The system operates by optically detecting the passage of fluorescently tagged DNA bases through a detection zone. A successful system would be revolutionary with respect to speed, read length, cost and minimized laboratory infrastructure. An important part of system development is modeling of the detection process. In particular, predicting the expected error from a set of sequencing parameters is helpful in system design. This paper describes variations on the Smith-Waterman algorithm for subsequence alignment used in a single-molecule detection …

Flash Artifact Suppression In Two-Dimensional Ultrasound Imaging, Richard Yung Chiao, Gregory Ray Bashford, Mark Peter Feilen, Cynthia Andrews Owen

Biomedical Imaging and Biosignal Analysis Laboratory

Flash artifacts in ultrasound flow images are suppressed to achieve enhanced flow discrimination. Flash artifacts typically occur as region of elevated signal strength (brightness or equivalent color) within an image. A flash suppression algorithm included the steps of estimating the flash within an image and then suppressing the estimated flash. The mechanism for flash suppression is spatial filtering. An extension of this basic method used information from adjacent frames to estimate the flash and/or to smooth the resulting image sequence. Temporal information from adjacent frames is used as an adjunct to improve performance.

Mining Of Correlated Rules In Genome Sequences, L. Lin, L. Wong, Tze-Yun Leong, P. S. Lai

Research Collection School Of Computing and Information Systems

With the huge amount of data collected by scientists in the molecular genetics community in recent years, there exists a need to develop some novel algorithms based on existing data mining techniques to discover useful information from genome databases. We propose an algorithm that integrates the statistical method, association rule mining, and classification rule mining in the discovery of allelic combinations of genes that are peculiar to certain phenotypes of diseased patients.

Ultrasound Based Quantitative Motion Measurement Using Speckle Size Estimation, James D. Hamilton, Larry Y. L. Mo, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An ultrasound system determines the relative movement in a first direction (F1) of first matter, such as blood flow, and second matter, such as an artery wall, in a subject under study (S). A beam (B1) of ultrasound waves defining a plurality of beam positions (BP1 and BP2) and beam axes (A1 and A2) are moved in scan direction having components parallel to direction F1. First and second blocks of data representing the first and second matter, respectively, are generated. A processor (20) performs an estimation of speckle size on first data to obtain a first result, and performs analysis …

Method And Apparatus For Adaptive Filtering By Counting Acoustic Sample Zeroes In Ultrasound Imaging, Gregory R. Bashford, Edward D. Nonnweiler, David D. Becker, David John Muzilla

Biomedical Imaging and Biosignal Analysis Laboratory

An ultrasound imaging system having an adaptive spatial filter the filter coefficients of which, for particular image parameter sample, are determined by counting the number of neighboring image parameter samples having zero or near-zero values. If the number of zero or near-zero values in a data window is greater than a predetermined threshold, the data in the window is passed, not filtered. This filter has two advantages over other spatial filters. First, image parameter data samples having only zero or near-zero neighboring values (i.e., isolated "point noise") are not smeared. Second, boundaries such as the edge of color in a …

Method And Apparatus For Controlling Acoustic Signal Bandwidth In An Ultrasonic Diagnostic Imaging System, Jeffrey R. Resnick, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An ultrasonic imaging system includes a receive beamformer that generates analog receive signals and a scan converter. A receive signal processing path interconnects the receive beamformer and the scan converter, and this processing path included both an A/D converter characterized by a selectable sampling rate and at least one filter characterized by at least one filter parameter. The filter parameter is selected as a function of the sampling rate to provide enhanced image quality.

Method And Apparatus For Three-Dimensional Ultrasound Imaging Of Biopsy Needle, Syed Omar Ishrak, Mir Said Seyed-Bolorforosh, William Thomas Hatfield, Todd Michael Tillman, Brian Peter Geiser, Gregory R. Bashford, Michael Joseph Washburn

Biomedical Imaging and Biosignal Analysis Laboratory

A method and an apparatus for three-dimensional ultrasound imaging of a needle-like instrument, such as a biopsy needle, inserted in a human body. The instrument is visualized by transmitting ultrasound beams toward the instrument and then detecting the echo signals using a linear array of transducer elements. The problem of ultrasound being reflected from a biopsy needle in a direction away from the transducer array is solved by steering the transmitted ultrasound beams t increase the angle at which the beams impinge upon the biopsy needle. Ideally the ultrasound beams are perpendicular to the needle. This increases the system's sensitivity …

Method And Apparatus For Controlling Acoustic Signal Bandwidth In An Ultrasonic Diagnostic Imaging System, Jeffrey R. Resnick, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An ultrasonic imaging system includes a receive beam former that generates analog receive signals and a scan converter. A receive signal processing path interconnects the receive beamformer and the scan converter, and this processing path includes both an A/D converter characterized by a selectable sampling rate and at least one filter characterized by at least one filter parameter. The filter parameter is selected as a function of the sampling rate to provide enhanced image quality.

Ultrasound Three- Dimensional Velocity Measurements By Feature Tracking, Gregory R. Bashford, Olaf T. Von Ramm

Biomedical Imaging and Biosignal Analysis Laboratory

This article describes a new angle-independent method suitable for three-dimensional (3-D) blood flow velocity measurement that tracks features of the ultrasonic speckle produced by a pulse echo system. In this method, a feature is identified and followed over time to detect motion. Other blood flow velocity measurement methods typically estimate velocity using one- (1-D) or two-dimensional (2-D) spatial and time information. Speckle decorrelation due to motion in the elevation dimension may hinder this estimate of the true 3-D blood flow velocity vector. Feature tracking is a 3-D method with the ability to measure the true blood velocity vector rather than …

The Effects Of Health Related Feedback On A Smoking Cessation Maintenance Program, Janice A. Blalock

University of the Pacific Theses and Dissertations

The present study investigated the effectiveness of health related feedback as a positive reinforcer of abstinence from smoking during the 11 week period following cessation. Fifty-three subjects were randomly assigned to one of three groups: (a) maintenance program plus health related feedback (MF), (b) maintenance program only (M) and, (c) discussion control (D). All groups received an aversive treatment for smoking after which the MP group received coping skills raining and several forms of health related feedback, the M group received coping skills training only, and the D group received discussion. Groups did not differ significantly in abstinence at each …

Some Experiences And Comments About Bio-Medical Data Processing, W. R. Mccrum

Henry Ford Hospital Medical Journal

No abstract provided.