Physical Sciences and Mathematics Commons^™

Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li

Computer Science Faculty Publications

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …

Development Of A Two-Finger Haptic Robotic Hand With Novel Stiffness Detection And Impedance Control, Vahid Mohammadi, Ramin Shahbad, Mojtaba Hosseini, Mohammad Hossein Gholampour, Saeed Shiry Ghidary, Farshid Najafi, Ahad Behboodi

Mechanical & Aerospace Engineering Faculty Publications

Haptic hands and grippers, designed to enable skillful object manipulation, are pivotal for high-precision interaction with environments. These technologies are particularly vital in fields such as minimally invasive surgery, where they enhance surgical accuracy and tactile feedback: in the development of advanced prosthetic limbs, offering users improved functionality and a more natural sense of touch, and within industrial automation and manufacturing, they contribute to more efficient, safe, and flexible production processes. This paper presents the development of a two-finger robotic hand that employs simple yet precise strategies to manipulate objects without damaging or dropping them. Our innovative approach fused force-sensitive …

A Review Of Piezoelectric Footwear Energy Harvesters: Principles, Methods, And Applications, Bingqi Zhao, Feng Qian, Alexander Hatfield, Lei Zuo, Tian-Bing Xu

Mechanical & Aerospace Engineering Faculty Publications

Over the last couple of decades, numerous piezoelectric footwear energy harvesters (PFEHs) have been reported in the literature. This paper reviews the principles, methods, and applications of PFEH technologies. First, the popular piezoelectric materials used and their properties for PEEHs are summarized. Then, the force interaction with the ground and dynamic energy distribution on the footprint as well as accelerations are analyzed and summarized to provide the baseline, constraints, potential, and limitations for PFEH design. Furthermore, the energy flow from human walking to the usable energy by the PFEHs and the methods to improve the energy conversion efficiency are presented. …

Near Simultaneous Laser Scanning Confocal And Atomic Force Microscopy (Conpokal) On Live Cells, Joree N. Sandin, Surya P. Aryal, Thomas E. Wilkop, Christopher I. Richards, Martha E. Grady

Physiology Faculty Publications

Techniques available for micro- and nano-scale mechanical characterization have exploded in the last few decades. From further development of the scanning and transmission electron microscope, to the invention of atomic force microscopy, and advances in fluorescent imaging, there have been substantial gains in technologies that enable the study of small materials. Conpokal is a portmanteau that combines confocal microscopy with atomic force microscopy (AFM), where a probe "pokes" the surface. Although each technique is extremely effective for the qualitative and/or quantitative image collection on their own, Conpokal provides the capability to test with blended fluorescence imaging and mechanical characterization. Designed …

Protein And Polysaccharide-Based Magnetic Composite Materials For Medical Applications., Elizabeth J Bealer, Kyril Kavetsky, Sierra Dutko, Samuel Lofland, Xiao Hu

Faculty Scholarship for the College of Science & Mathematics

The combination of protein and polysaccharides with magnetic materials has been implemented in biomedical applications for decades. Proteins such as silk, collagen, and elastin and polysaccharides such as chitosan, cellulose, and alginate have been heavily used in composite biomaterials. The wide diversity in the structure of the materials including their primary monomer/amino acid sequences allow for tunable properties. Various types of these composites are highly regarded due to their biocompatible, thermal, and mechanical properties while retaining their biological characteristics. This review provides information on protein and polysaccharide materials combined with magnetic elements in the biomedical space showcasing the materials used, …

Post-Acquisition Processing Confounds In Brain Volumetric Quantification Of White Matter Hyperintensities, Ahmed A. Bahrani, Omar M. Al-Janabi, Erin L. Abner, Shoshana H. Bardach, Richard J. Kryscio, Donna M. Wilcock, Charles D. Smith, Gregory A. Jicha

Neurology Faculty Publications

BACKGROUND: Disparate research sites using identical or near-identical magnetic resonance imaging (MRI) acquisition techniques often produce results that demonstrate significant variability regarding volumetric quantification of white matter hyperintensities (WMH) in the aging population. The sources of such variability have not previously been fully explored.

NEW METHOD: 3D FLAIR sequences from a group of randomly selected aged subjects were analyzed to identify sources-of-variability in post-acquisition processing that can be problematic when comparing WMH volumetric data across disparate sites. The methods developed focused on standardizing post-acquisition protocol processing methods to develop a protocol with less than 0.5% inter-rater variance.

RESULTS: A series …

Dynamic Light Scattering Optical Coherence Tomography To Probe Motion Of Subcellular Scatterers., Nico J J Arezza, Marjan Razani, Michael C Kolios

Medical Biophysics Publications

Optical coherence tomography (OCT) is used to provide anatomical information of biological systems but can also provide functional information by characterizing the motion of intracellular structures. Dynamic light scattering OCT was performed on intact, control MCF-7 breast cancer cells and cells either treated with paclitaxel to induce apoptosis or deprived of nutrients to induce oncosis. Autocorrelations (ACs) of the temporal fluctuations of OCT intensity signals demonstrate a significant decrease in decorrelation time after 24 h in both the paclitaxel-treated and nutrient-deprived cell groups but no significant differences between the two groups. The acquired ACs were then used as input for …

Blood Transfusions In Preterm Infants: Changes On Perfusion Index And Intermittent Hypoxemia, Katrina T. Ibonia, Henrietta S. Bada, Philip M. Westgate, Enrique Gomez Pomar, Prasad Bhandary, Abhijit R. Patwardhan, Elie G. Abu Jawdeh

Pediatrics Faculty Publications

BACKGROUND

Red blood cell (RBC) transfusion decreases intermittent hypoxemia (IH) events beyond the first week of life. This benefit may be related to improved perfusion to the respiratory control network. Perfusion index (PI) is a perfusion measure provided by the pulse oximeter. We hypothesized that the benefit in IH after RBC transfusion is associated with an increase in PI. In addition, we assessed the value of PI and clinical measures in predicting the effect of RBC transfusion on IH.

STUDY DESIGN AND METHODS

We prospectively enrolled infants less than 30 weeks' gestation age. PI and oxygen saturation (SpO₂) …

Using A Respiratory Navigator Significantly Reduces Variability When Quantifying Left Ventricular Torsion With Cardiovascular Magnetic Resonance, Sean M. Hamlet, Christopher M. Haggerty, Jonathan D. Suever, Gregory J. Wehner, Kristin N. Andres, David K. Powell, Richard J. Charnigo, Brandon K. Fornwalt

Electrical and Computer Engineering Faculty Publications

Background: Left ventricular (LV) torsion is an important indicator of cardiac function that is limited by high inter-test variability (50% of the mean value). We hypothesized that this high inter-test variability is partly due to inconsistent breath-hold positions during serial image acquisitions, which could be significantly improved by using a respiratory navigator for cardiovascular magnetic resonance (CMR) based quantification of LV torsion.

Methods: We assessed respiratory-related variability in measured LV torsion with two distinct experimental protocols. First, 17 volunteers were recruited for CMR with cine displacement encoding with stimulated echoes (DENSE) in which a respiratory navigator was used to measure …

Sector Expansion And Elliptical Modeling Of Blue-Gray Ovoids For Basal Cell Carcinoma Discrimination In Dermoscopy Images, Pelin Guvenc, Robert W. Leander, Serkan Kefel, William V. Stoecker, Ryan K. Rader, Kristen A. Hinton, Sherea Monica Stricklin, Harold S. Rabinovitz, Margaret C. Oliviero, Randy Hays Moss

Chemistry Faculty Research & Creative Works

Background: Blue-gray ovoids (B-GOs), a critical dermoscopic structure for basal cell carcinoma (BCC), offer an opportunity for automatic detection of BCC. Due to variation in size and color, B-GOs can be easily mistaken for similar structures in benign lesions. Analysis of these structures could afford accurate characterization and automatic recognition of B-GOs, furthering the goal of automatic BCC detection. This study utilizes a novel segmentation method to discriminate B-GOs from their benign mimics.

Methods: Contact dermoscopy images of 68 confirmed BCCs with B-GOs were obtained. Another set of 131 contact dermoscopic images of benign lesions possessing B-GO mimics provided a …

Slides: Colorado Law: Protecting Water Quantity And Quality, Alan E. Curtis

Monitoring and Protecting Groundwater During Oil and Gas Development (November 26)

Presenter: Alan E. Curtis, White & Jankowski, LLP

23 slides

Event Study Method For Validating Agent-Based Trading Simulations, Shih-Fen Cheng

Research Collection School Of Computing and Information Systems

In this paper, we introduce how one can validate an event-centric trading simulation platform that is built with multi-agent technology. The issue of validation is extremely important for agent-based simulations, but unfortunately, so far there is no one universal method that would work in all domains. The primary contribution of this paper is a novel combination of event-centric simulation design and event study approach for market dynamics generation and validation. In our event-centric design, the simulation is progressed by announcing news events that affect market prices. Upon receiving these events, event-aware software agents would adjust their views on the market …

Analysis Of Globule Types In Malignant Melanoma, Jin Xu, Kapil Kumar Gupta, William V. Stoecker, Yamini Krishnamurthy, Harold S. Rabinovitz, Austin Bangert, David A. Calcara, Margaret C. Oliviero, Joseph M. Malters, Rhett J. Drugge, R. Joe Stanley, Randy Hays Moss, Mehmed Emre Celebi

Chemistry Faculty Research & Creative Works

Objective: To identify and analyze subtypes of globules based on size, shape, network connectedness, pigmentation, and distribution to determine which globule types and globule distributions are most frequently associated with a diagnosis of malignant melanoma. Design: Retrospective case series of dermoscopy images with globules. Setting: Private dermatology practices. Participants: Patients in dermatology practices. Intervention: Observation only. Main Outcome Measure: Association of globule types with malignant melanoma. Results: The presence of large globules (odds ratio [OR], 5.25) and globules varying in size (4.72) or shape (5.37) had the highest ORs for malignant melanoma among all globule types and combinations studied. Classical …

Melanoma And Seborrheic Keratosis Differentiation Using Texture Features, Srinivas V. Deshabhoina, Scott E. Umbaugh, William V. Stoecker, Randy Hays Moss, Subhashini K. Srinivasan

Chemistry Faculty Research & Creative Works

Purpose: To explore texture features in two-dimensional images to differentiate seborrheic keratosis from melanoma.

Methods: A systematic approach to consistent classification of skin tumors is described. Texture features, based on the second-order histogram, were used to identify the features or a combination of features that could consistently differentiate a malignant skin tumor (melanoma) from a benign one (seborrheic keratosis). Two hundred and seventy-one skin tumor images were separated into training and test sets for accuracy and consistency. Automatic induction was applied to generate classification rules. Data analysis and modeling tools were used to gain further insight into the feature space. …