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High Sensitivity Rna Pseudoknot Prediction, Xiaolu Huang, Hesham Ali

Information Systems and Quantitative Analysis Faculty Publications

Most ab initio pseudoknot predicting methods provide very few folding scenarios for a given RNA sequence and have low sensitivities. RNA researchers, in many cases, would rather sacrifice the specificity for a much higher sensitivity for pseudoknot detection. In this study, we introduce the Pseudoknot Local Motif Model and Dynamic Partner Sequence Stacking (PLMM_DPSS) algorithm which predicts all PLM model pseudoknots within an RNA sequence in a neighboring-region-interferencefree fashion. The PLM model is derived from the existing Pseudobase entries. The innovative DPSS approach calculates the optimally lowest stacking energy between two partner sequences. Combined with the Mfold, PLMM_DPSS can also …

Original Investigation Correlated Joint Fluctuations Can Influence The Selection Of Steady State Gait Patterns In The Elderly, Max J. Kurz, Nikolaos Stergiou

Journal Articles

This investigation utilized a Markov model to investigate the relationship of correlated lower extremity joint fluctuations and the selection of a steady state gait pattern in the young and elderly. Our model simulated the neuromuscular system by predicting the behavior of the joints for the next gait cycle based on the behavior exhibited in the preceding gait cycles. Such dependencies in the joint fluctuations have been noted previously in the literature. We speculated that compared to the young model, the characteristics of the correlated fluctuations in the elderly model would result in the selection of a different steady state gait …

Genomeblast: A Web Tool For Small Genome Comparison, Guoqing Lu, Liying Jiang, Resa M. K. Helikar, Thaine W. Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N. Moriyama

Biology Faculty Publications

Background: Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes.

Results: GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each …

Optimal Movement Variability: A New Theoretical Perspective For Neurologic Physical Therapy, Nikolaos Stergiou, Regina T. Harbourne, James T. Cavanaugh

Journal Articles

Variability is a natural and important feature of human movement. Using existing theoretical frameworks as a foundation, we propose a new model to explain movement variability as it relates to motor learning and health. We contend that mature motor skills and healthy states are associated with an optimal amount of movement variability. This variability also has form and is characterized by a chaotic structure. Less than optimal movement variability characterizes biological systems that are overly rigid and unchanging, whereas greater than optimal variability characterizes systems that are noisy and unstable. Both situations characterize systems that are less adaptable to perturbations, …

Robotic Surgery And Training: Electromyographic Correlates Of Robotic Laparoscopic Training, Timothy N. Judkins, D. Oleynikov, N. Karazaki, Nikolaos Stergiou

Journal Articles

Background: Robotic laparoscopic surgery has been shown to decrease task completion time, reduce errors, and decrease training time when compared to manual laparoscopic surgery. However, current literature has not addressed physiological effects, in particular muscle responses, to training with a robotic surgical system. We seek to determine the frequency response of electromyographic (EMG) signals of specific arm and hand muscles with training using the da Vinci Surgical System (dVSS).

Methods: Seven right-handed medical students were trained in three tasks with da Vinci Surgical System over four weeks. These subjects, along with eight controls, were tested before and after …

Narrowed Tcr Repertoire And Viral Escape As A Consequence Of Heterologous Immunity, Markus Cornberg, Alex T. Chen, Lee A. Wilkinson, Michael A. Brehm, Sung-Kwon Kim, Claudia Calcagno, Dario Ghersi, Roberto Puzone, Franco Celada, Raymond M. Welsh, Liisa K. Selin

Interdisciplinary Informatics Faculty Publications

Why some virus-specific CD8 TCR repertoires are diverse and others restricted or “oligoclonal” has been unknown. We show here that oligoclonality and extreme clonal dominance can be a consequence ofTcell crossreactivity. Lymphocytic choriomeningitis virus (LCMV) and Pichinde virus (PV) encode NP205–212 epitopes that induce different but highly cross-reactive diverseTCRrepertoires. Homologous viral challenge ofimmune mice only slightly skewed the repertoire and enriched for predictable TCR motifs. However, heterologous viral challenge resulted in a narrow oligoclonal repertoire with dominant clones with unpredictableTCRsequences.This shift in clonal dominance varied with the private, i.e., unique, specificity of the host’s TCR repertoire and was simulated using …

Method Of Predicting Splice Sites Based On Signal Interactions, Alexander Churbanov, Igor B. Rogozin, Jitender S. Deogun, Hesham Ali

Information Systems and Quantitative Analysis Faculty Publications

Background: Predicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan.

Results: …

Hper Biomechanics Laboratory 2005 Annual Report, Issue 4, Nebraska Biomechanics Core Facility

Biomechanics Annual Report

This issue features Dr. Stergiou Receives a K25 Award from the National Institutes of Health, Training Methods to Improve Robotic Laparoscopic Surgery, Progress Update for Federal Grant: The Development of Sitting Posture in Children with Cerebral Palsy, Pioneering Gait Analysis Research, Collaboration with UNMC Department of Surgery and VA Hospital: The Effects of Peripheral Arterial Disease on Gait, Sabbatical Strengthened Collaborations in Orthopedics, Computer Modeling with Dynamic Toys Reveals Human Gait Patterns, Prestigious Awards to Dr. Stergiou, Teachers Enriched During Final Year of Banneker 2000, New Staff Joins the HPER Biomechanics Laboratory, Noteworthy Events, Internationally Recognized Bioengineer Visited HPER Biomechanics …

Follow-Up Evaluation 2 Years After Acl Reconstruction With Bone–Patellar Tendon–Bone Graft Shows That Excessive Tibial Rotation Persists, Stavros Ristanis, Nikolaos Stergiou, Kostas Patras, Elias Tsepis, Constantina O. Moraiti, Anastasios D. Georgoulis

Journal Articles

Objective: To investigate in vivo if the increased tibial rotation found in anterior cruciate ligament (ACL)-deficient patients before surgery is restored 2 years after the reconstruction, during 2 high-demanding activities.

Design: Prospective follow-up study.

Setting: A gait analysis laboratory.

Participants: Nine subjects with unilateral ACL rupture, reconstructed with a bone–patellar tendon–bone (BPTB) graft, and 10 healthy control subjects.

Interventions: All the ACL-deficient patients underwent a unilateral ACL reconstruction after prereconstruction data acquisition.

Main Outcome Measurements: Using a 6-camera motion analysis system, kinematics were collected as subjects (1) descended from a stair and, after foot …

A Novel Approach To Measure Variability In The Anterior Cruciate Ligament Deficient Knee During Walking: The Use Of The Approximate Entropy In Orthopaedics, Anastasios D. Georgoulis, Constantina O. Moraiti, Stavros Ristanis, Nikolaos Stergiou

Journal Articles

Objective. The evaluation of variability of biological rhythmic activities through measures such as Approximate Entropy (ApEn) has provided important information regarding pathology in disciplines such as cardiology and neurology. This research lead to the “loss of complexity hypothesis” where decreased variability is associated with loss of healthy flexibility rendering the system more rigid and unable to adapt to stresses. ApEn as a measure of variability and complexity, correlates well with pathology while, in some cases, it is predictive of subsequent clinical changes. The study of human gait could benefit from the application of ApEn since it is also a …

Recovery Of Postural Control After Cerebral Concussion: New Insights Using Approximate Entropy, James T. Cavanaugh, Kevin M. Guskiewicz, Carol Giuliani, Stephen Marshall, Vicki S. Mercer, Nikolaos Stergiou

Journal Articles

Context: The return-to-play decision after sport-related cerebral concussion depends in part on knowing when an athlete has fully recovered postural control after injury.

Objective: To describe the postconcussion recovery of postural control using approximate entropy (ApEn), a regularity statistic from nonlinear dynamics.

Design: Retrospective case series analysis.

Setting: Sports medicine research laboratory.

Patients or Other Participants: Collegiate athletes from whom center-of-pressure and symptom data were collected at preseason, less than 48 hours after injury, and 48 to 96 hours after injury.

Main Outcome Measure(s): Approximate entropy values reflecting the amount of randomness contained in center-of-pressure oscillations were calculated for anterior-posterior …

Identification Of A Family Of Bsp-A Like Surface Proteins Of Entamoeba Histolytica With Novel Leucine Rich Repeats., Paul H. Davis, Zhi Zhang, Minghe Chen, Xiaochun Zhang, Subhra Chakraborty, Samuel L. Stanley Jr.

Biology Faculty Publications

Leucine rich repeats serve as recognition motifs for surface proteins from bacteria and eukaryotes. The BspA protein from Bacteroides forsythus mediates bacterial binding to fibronectin and contains leucine rich repeats of the Treponema pallidum (TpLRRP) family. Here we show that the protozoan parasite Entamoeba histolytica contains multiple BspA-like proteins, including a family of surface proteins which possess a new form of a leucine rich repeat that differs from the standard Treponema pallidum- like leucine rich repeat (TpLRRP) by possessing two conserved cysteine residues.

Sight-Reading Versus Repertoire Performance On The Piano: A Case Study Using High-Speed Motion Analysis, Brenda Wristen, Sharon Evans, Nikolaos Stergiou

Journal Articles

The purpose of the study was to examine whether differences exist in the motions employed by pianists when they are sight-reading versus performing repertoire and determine whether these differences could be quantified using high speed motion capture technology. A secondary question of interest was whether or not an improvement in the efficiency of motion could be observed between two sight-reading trials of the same musical excerpt. This case study employed a six digital infrared camera system (Motion Analysis, Inc.) to capture the motion of pianists playing two trials of a repertoire piece and two trials of a sight-reading excerpt. Angular …

An Improved Surrogate Method For Detecting The Presence Of Chaos In Gait, David J. Miller, Nikolaos Stergiou, Max J. Kurz

Journal Articles

It has been suggested that the intercycle variability present in the time series of biomechanical gait data is of chaotic nature. However, the proper methodology for the correct determination of whether intercycle fluctuations in the data are deterministic chaos or random noise has not been identified. Our goal was to evaluate the pseudoperiodic surrogation (PPS) [Small et al., 2001. Surrogate test for pseudoperiodic time series data. Physical Review Letters 87(18), 188,101–188,104], and the surrogation algorithms of Theiler et al. [1992. Testing for nonlinearity in time series: the method of surrogate data. Physica D 58(1–4), 77–94] and of Theiler and Rapp …