Digital Commons Network^™

Yeast Pheromone Pathway Modeling Using Petri Nets, Stephen D. Scott, Abhishek Majumdar, Jitender S. Deogun, Steven D. Harris

School of Computing: Conference and Workshop Papers

Background: Our environment is composed of biological components of varying magnitude. The relationships between the different biological elements can be represented as a biological network. The process of mating in S. cerevisiae is initiated by secretion of pheromone by one of the cells. Our interest lies in one particular question: how does a cell dynamically adapt the pathway to continue mating under severe environmental changes or under mutation (which might result in the loss of functionality of some proteins known to participate in the pheromone pathway). Our work attempts to answer this question. To achieve this, we first propose a …

A Comparison Of A Campus Cluster And Open Science Grid Platforms For Protein- Guided Assembly Using Pegasus Workflow Management System, Natasha Pavlovikj, Kevin Begcy, Sairam Behera, Malachy Campbell, Harkamal Walia, Jitender S. Deogun

School of Computing: Conference and Workshop Papers

Scientific workflows are a useful tool for managing large and complex computational tasks. Due to its intensive resource requirements, the scientific workflows are often executed on distributed platforms, including campus clusters, grids and clouds. In this paper we build a scientific workflow for blast2cap3, the protein-guided assembly, using the Pegasus Workflow Management System (Pegasus WMS). The modularity of blast2cap3 allows us to decompose the existing serial approach on multiple tasks, some of which can be run in parallel. Afterwards, this workflow is deployed on two distributed execution platforms: Sandhills, the University of Nebraska Campus Cluster, and the Open Science …

Use Of Innovative Techniques To Enhance The Hydraulic Disinfection Efficiency Of Drinking Water Contact Tanks, J. J. Kattnig, S. K. Venayagamoorthy

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

The focus of this study was to understand the complex nature of flow dynamics within water disinfection contact tanks and to use this understanding in the development of beneficial tank modifications. Methods involved in this process included the use of computational fluid dynamics (CFD) and physical conservative tracer studies. Attempted tank alterations included the installation of baffles, inlet modification, and the use of industrial packing material. Tested modifications aimed at altering existing velocity fields to increase the hydraulic disinfection efficiency of a given system. Hydraulic efficiency was measured through the use of residence time distribution (RTD) curves and the well-known …

Role Of Solids Retention Time On Complete Nitrification: Mechanistic Understanding And Modeling, Guoqiang Liu, Jianmin Wang

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

Effects of solids retention time (SRT) on both steps of the nitrification process (e.g., ammonia oxidation and nitrite oxidation) and the nitrifier community in a complete-mix activated sludge process were studied. At a SRT less than or equal to 20 days, the effluent ammonia concentration was lower than the effluent nitrite concentration. At the 40-day SRT, however, the effluent nitrite concentration became equal to or less than the effluent ammonia concentration. Quantitative Polymerase Chain Reaction (QPCR) assays indicated that increasing SRT significantly increased nitrite-oxidizing bacteria/ammonia-oxidizing bacteria (NOB/AOB) ratio. Further investigation indicated that Nitrosomonas europaea/eutropha were the dominant AOB for ammonia …

An Instrument To Assess Individual Capacity For System Thinking, Ra'ed M. Jaradat

Engineering Management & Systems Engineering Theses & Dissertations

The purpose of this research was to develop and deploy a new systems thinking instrument to assess individual capacity for systems thinking using an inductive research design. While technology has been increasing exponentially, the corresponding methods to harness those technological advances, and the problems they have spawned, is lagging. While there is a broad collection of systems based methods, techniques, technologies, and tools that can be used in dealing with complex problems, these are predicated on an individual's capacity for engaging a level of systems thinking commensurate with their effective, deployment. Research based methods to determine individual capacity for systems …

Effect Of Magnetic Nanoparticle Heating On Cortical Neuron Viability, Christopher J. Rivet, Yuan Yuan, Ryan J. Gilbert, Diana Andra Borca-Tasciuc

Chemical and Biochemical Engineering Faculty Research & Creative Works

Purpose: Superparamagnetic iron oxide nanoparticles are currently approved for use as an adjunctive treatment to glioblastoma multiforme radiotherapy. Radio frequency stimulation of the nanoparticles generates localized hyperthermia, which sensitizes the tumor to the effects of radiotherapy. Clinical trials reported thus far are promising, with an increase in patient survival rate; however, what are left unaddressed are the implications of this technology on the surrounding healthy tissue. Methods and materials: Amino silane-coated iron oxide nanoparticles suspended in culture medium were applied to chick embryonic cortical neuron cultures. Cultures were heated to 37 °C or 45 °C by an induction coil system …

Coupling Graphs, Efficient Algorithms And B-Cell Epitope Prediction, Liang Zhao, Steven C. H. Hoi, Zhenhua Li, Limsoon Wong, Hung Nguyen

Research Collection School Of Computing and Information Systems

Coupling graphs are newly introduced in this paper to meet many application needs particularly in the field of bioinformatics. A coupling graph is a two-layer graph complex, in which each node from one layer of the graph complex has at least one connection with the nodes in the other layer, and vice versa. The coupling graph model is sufficiently powerful to capture strong and inherent associations between subgraph pairs in complicated applications. The focus of this paper is on mining algorithms of frequent coupling subgraphs and bioinformatics application. Although existing frequent subgraph mining algorithms are competent to identify frequent subgraphs …

Synthesis Of Radioactive And Nonradioactive Nanostructures Through Radiolytic And Wet Chemistry, Jessika Viviana Rojas Marin

Doctoral Dissertations

"In this work the synthesis of non radioactive and radioactive nanoparticles (NPs) through radiolytic and wet chemistry was studied. Non radioactive NPs of rhenium, iridium, and rhodium were synthesized from aqueous solutions containing the metal salt precursors by gamma irradiation. The solutions were irradiated to generate reducing species that led to the nucleation and growth of the nanoparticles. Amorphous rhenium oxide nanoparticles with average sizes ranging from 10 nm to 55 nm were obtained. Metallic iridium and rhodium nanoparticles were produced in polyvinyl-pyrrolidone (PVP) having narrow particle size distributions and average particle sizes from 2 nm to 6 nm. The …

Impact Of Slickwater Fracturing Fluid Compositions On The Petrophysical Properties Of Shale And Tightsand, Yongpeng Sun

Doctoral Dissertations

"A tight reservoir always requires hydraulic fracturing before production to increase production rate. The additives in hydraulic fluids are highly considerable for a successful stimulation. A friction reducer is often used to reduce the flowing friction in the wellbore during hydraulic fracturing. Extensive researches have been conducted to examine the extent it can reduce the fluid friction in tubings; however, no research has been reported on its behavior in a reservoir, which is related to the fracture extension. A breaker is also pumped into the formation to degrade the friction reducer. However, it is not clear that what is the …

Predicting Pressure Distribution Between Transfemoral Prosthetic Socket And Residual Limb Using Finite Element Analysis, Rajesh Surapureddy

UNF Graduate Theses and Dissertations

In this study, a non-linear Finite Element (FE) model was created and analyzed to determine the pressure distribution between the residual limb and the prosthetic socket of a transfemoral amputee. This analysis was performed in an attempt to develop a process allowing healthcare providers and engineers to simulate the fit and comfort of transfemoral prosthetics to reduce the number of re-fittings needed for the amputees. The analysis considered the effects of interference due to insertion of the limb into the prosthesis, referred to as donning, and also the effects due to the body weight of the amputee. A non-linear finite …

Evaluation Of Upper Extremity Movement Characteristics During Standardized Pediatric Functional Assessment With A Kinect®-Based Markerless Motion Analysis System, Jacob R. Rammer, Joseph J. Krzak, Susan A. Riedel, Gerald F. Harris

Biomedical Engineering Faculty Research and Publications

A recently developed and evaluated upper extremity (UE) markerless motion analysis system based on the Microsoft® Kinect® has potential for improving functional assessment of patients with hemiplegic cerebral palsy. 12 typically-developing adolescents ages 12-17 were evaluated using both the Kinect-based system and the Shriners Hospitals for Children Upper Extremity Evaluation (SHUEE), a validated measure of UE motion. The study established population means of UE kinematic parameters for each activity. Statistical correlation analysis was used to identify key kinematic metrics used to develop automatic scoring algorithms. The Kinect motion analysis platform is technically sound and can be applied to standardized task-based …

A Modular Low-Clearance Wrist Orthosis For Improving Wrist Motion In Children With Cerebral Palsy, Devon Holley, Michelle Johnson, Gerald F. Harris, Scott A. Beardsley

Biomedical Engineering Faculty Research and Publications

Children with Cerebral Palsy (CP) often exhibit impairments in the coordination of the grip and lift phases of arm movements that directly impact their ability to perform activities of daily living (ADLs). The application of assistive robotic therapy to children with spastic hemiplegic CP has shown that augmented movement training can lead to improved functional outcomes and improved arm kinematics. Assistive robotic therapy of the wrist has been shown to help improve motor skills in stroke patients, but the devices employed are often large and obtrusive, focusing on a repeated motion rather than a task-based itinerary. Here, we propose a …

Emerging Optical Techniques For Detection Of Oral, Cervical And Anal Cancer In Low-Resource Settings, Bing Yu, Daron G. Ferris, Yang Liu, Vivek K. Nagarajan

Biomedical Engineering Faculty Research and Publications

Cancers of the oral and anogenital regions are a growing global health problem that disproportionately impact women and men living in developing countries. The high death rate in developing countries is largely due to the fact that these countries do not have the appropriate medical infrastructure and resources to support the organized screening and diagnostic programs that are available in the developed world. Emerging optical diagnostics techniques, such as optical spectroscopy, reflectance imaging, and fluorescence imaging, are noninvasive techniques that are sensitive to multiple cancer biomarkers and have shown the potential as a cost–effective and fast tool for diagnosis of …

Dissolution Behavior Of Phosphate Glasses, Li Na Ma

Doctoral Dissertations

"The solubility of phosphate glasses in aqueous solutions can be tailored through compositional control to obtain a wide range of ion release rates required for a variety of applications. The principal objective of this dissertation is to advance the understanding of the dissolution behavior of phosphate glasses in aqueous environments.

Two families of glasses, sodium-iron phosphate (NFP) glasses and sodium-calcium phosphate (NCP) glasses, were evaluated. The dissolution behavior depends on the phosphate anions that constitute the glass structure and the associated metal (Me) cations. The phosphate glass structure, defined by the distribution and average size of phosphate anions and depending …

Femtosecond Laser Micro-Machined Optical Fiber Based Embeddable Strain And Temperature Sensors For Structural Monitoring, Armadeep Kaur

Doctoral Dissertations

"Structural monitoring technology is becoming increasingly important for managing all types of structures. Embedding sensors while constructing new structures or repairing the old ones allows for continual monitoring of structural health thus giving an estimate of remaining utility. Along with being embeddable, miniaturized sensors that are easy to handle are highly sought after in the industry where in-situ monitoring is required in a harsh environment (corrosive atmosphere, high temperatures, high pressure etc.).

This dissertation demonstrates the use of femtosecond laser-fabricated Fabry-Perot interferometer (FPI) based optical fiber sensors for embedded applications like structural health monitoring. Two types of Fabry-Perot interferometer sensors, …

Which Design And Biomaterial Factors Affect Clinical Wear Performance Of Total Disc Replacements? A Systematic Review, Sai Y. Veruva, Marla J. Steinbeck, Jeffrey M. Toth, Dominik D. Alexander, Steven M. Kurtz

Biomedical Engineering Faculty Research and Publications

Background

Total disc replacement was clinically introduced to reduce pain and preserve segmental motion of the lumbar and cervical spine. Previous case studies have reported on the wear and adverse local tissue reactions around artificial prostheses, but it is unclear how design and biomaterials affect clinical outcomes.

Questions/purposes

Which design and material factors are associated with differences in clinical wear performance (implant wear and periprosthetic tissue response) of (1) lumbar and (2) cervical total disc replacements?

Methods

We performed a systematic review on the topics of implant wear and periprosthetic tissue response using an advanced search in MEDLINE and Scopus …

Evaluating Electronic Market Designs: The Effects Of Competitive Arousal And Social Facilitation On Electronic Group Buying, Yuecheng Yu, Karl R. Lang, Alex Pelaez

Research Collection School Of Computing and Information Systems

This article presents an evaluation approach foralternative electronic market designs and examines theimpact of competitive arousal under time pressure onmarket performance in a group-buying setting. Drawingon theory from economics, decision theory, andinformation systems, we present a competitive arousalmodel for a social buying setting that posits thatintroducing competitive arousal among buyers reducesbuyer profits and that social facilitation can mitigate thesecosts through better task completion and time tocompletion rates. Using an economic experiment, wefound that rivalry has a negative effect on buyer profitsbut also that competitive arousal increases the efficiencyof social facilitation in terms of group formation. Wediscuss the implications of these …

Role Of Surface Chemistry In Nanoscale Electrokinetic Transport, Secuk Atalay

Mechanical & Aerospace Engineering Theses & Dissertations

This dissertation work presents the efforts to study the electrofluidics phenomena, with a focus on surface charge properties in nanoscale systems with the potential applications in imaging, energy conversion, ultrafiltration, DNA analysis/sequencing, DNA and protein transport, drug delivery, biological/chemical agent detection and micro/nano chip sensors.

Since the ion or molecular or particle transport and also liquid confinement in nano-structures are strongly dominated by the surface charge properties, in regards of the fundamental understanding of electrofluidics at nanoscale, we have used surface charge chemistry properties based on 2-pK charging mechanism. Using this mechanism, we theoretically and analytically showed the surface charge …

Gold-Magnetite Nanoparticle-Biomolecule Conjugates: Synthesis, Properties And Toxicity Studies, Akshay Pariti

Masters Theses

"This thesis study focuses on synthesizing and characterizing gold-magnetite optically active magnetic nanoparticle and its conjugation with biomolecules for biomedical applications, especially magnetic fluid hyperthermia treatment for cancerous tissue. Gold nanoparticles have already displayed their potential in the biomedical field. They exhibit excellent optical properties and possess strong surface chemistry which renders them suitable for various biomolecule attachments. Studies have showed gold nanoparticles to be a perfect biocompatible vector. However, clinical trials for gold mediated drug delivery and treatment studied in rat models identified some problems. Of these problems, the low retention time in bloodstream and inability to maneuver externally …

Potential Acid Mine Drainage Treatment Utilizing Acidophilic Sulfate Reducing Bacteria In An Upflow Bioreactor, Elise Fay Kittrell

Masters Theses

"During coal and iron mining, pyrite is often exposed to oxygen, causing acid mine drainage (AMD). Acid mine drainage has characteristic traits of: a rust color, low pH levels (around 3 or 4) and high concentrations of sulfate, metal sulfates and heavy metals.

Sulfate reducing bacteria (SRB) are often utilized in acid mine drainage treatment by implementing them into biochemical reactors (BCR). As SRB break down various carbon sources, bicarbonate is produced, raising the pH and generating hydrogen sulfide which reacts with numerous metals. This approach can be troublesome, as SRBs do not thrive at low pH levels often associated …

Polydopamine As Active Templates For Fabrication Of Conductive Of Copper Line Pattern, Raweewan Thongprachan

Chulalongkorn University Theses and Dissertations (Chula ETD)

In this research, copper conductive patterns were fabricated on polyethylene terephthalate (PET) substrate by combination of spray drying of polydopamine nanoparticles, and consequently electroless plating process. The polydopamine nanoparticle ink was synthesized by self-polymerization of dopamine hydrochloride at different initial pH 8, 8.5, 9 and 10. The patterns were deposited by site-selective Cu electroless plating process on top of the PDA pattern at the controlled temperature 30 C. The effects of plating time in electroless plating and storage time were studied. Moreover, the adhesion and aspect ratio were also investigated. The conductive lines fabricated were characterized by two-point probe measurement, …

การผลิตไบโอบิวทานอลจากการย่อยสลายของเปลือกถั่วเหลือง, มานพ บุญเจริญ

Chulalongkorn University Theses and Dissertations (Chula ETD)

งานวิจัยนี้ทำการศึกษาการย่อยสลายเปลือกถั่วเหลืองด้วยกรดเพื่อใช้เป็นสารตั้งต้นในการผลิตอะซิโตน เอทานอล และบิวทานอล ด้วยเชื้อ Clostridium saccharobutylicum ATCC BAA 117 การย่อยสลายทำในหม้อนึ่งไอน้ำความดันสูงที่ความเข้มข้น อัตราส่วนของแข็งต่อของเหลว และเวลาในการทำปฏิกิริยาที่ค่าต่างๆ สภาวะที่ดีที่สุดสำหรับการผลิตน้ำตาลรีดิวซ์ที่สูงและสารยับยั้งที่ต่ำ มีดังนี้ ความเข้มข้นกรดร้อยละ 5 โดยปริมาตร อัตราส่วนของแข็งต่อของเหลว 1 ต่อ 5 เวลาการย่อยสลาย 15 นาที น้ำตาลไฮโดรไลเซทประกอบด้วยน้ำตาลรีดิวซ์รวม 31.86 กรัมต่อลิตร รวมทั้งเฟอร์ฟูรัล 0.66 กรัมต่อลิตร และไฮดรอกซีเมทิลเฟอร์ฟูรัล 0.059 กรัมต่อลิตร เฟอร์ฟูรัลที่ความเข้มข้น 0.05 กรัมต่อลิตร ได้แสดงฤทธิ์ยับยั้งการเจริญเติบโตของ C. saccharobutylicum ATCC BAA 117 แต่ไฮดรอกซีเมทิลเฟอร์ฟูรัลไม่มีผลกระทบ การบำบัดโดยใช้ Overliming ด้วยแคลเซียมไฮดรอกไซด์ และการดูดซับด้วยเรซิน XAD-4 และถ่านกัมมันต์ ช่วยปรับปรุงน้ำตาลไฮโดรไลเซทให้สามารถใช้ในการหมักได้อย่างมีนัยสำคัญ การหมักแบบกะที่อุณหภูมิ 35 องศาเซลซียส ค่าความเป็นกรดด่าง 5.5 เมื่อใช้น้ำตาลไฮโดรไลเซท (30-65 กรัมต่อลิตร) ที่ชนิดแหล่งและความเข้มข้นแหล่งไนโตรเจนต่างๆ การผลิตตัวทำละลายที่เหมาะสมจะได้รับจากที่สภาวะอุณหภูมิ 35 องศาเซลเซียส ค่าความเป็นกรดด่าง 5.5 ในอาหารน้ำตาลไฮโดรไลเซทที่ประกอบด้วยน้ำตาลรีดิวซ์ 65 กรัมต่อลิตร ยีตส์สกัด แอมโมเนียมอะซิเตทและน้ำแช่ข้าวโพด ตัวทำละลายรวมมีค่า 15.69 กรัมต่อลิตร ประกอบด้วยอะซิโตน บิวทานอล และเอทานอลเท่ากับ 12.15, 15.69 และ 2.39 กรัมต่อลิตร ตามลำดับ มีผลได้ตัวทำละลายเท่ากับ 0.46 และอัตราการผลิตตัวทำละลาย 0.37 กรัมต่อลิตรต่อชั่วโมง ในงานวิจัยนี้แสดงให้เห็นว่าเปลือกถั่วเหลืองสามารถใช้เป็นแหล่งคาร์บอนที่มีศักยภาพสำหรับการหมักเพื่อผลิตอะซิโตน เอทานอล และบิวทานอล

An Intelligent System For High Resolution Radar Systems, Janette C. Briones

Open Access Theses & Dissertations

Cognitive radio is a recent, novel approach that integrates machine perception software into wireless systems. The term cognitive radio was first used by Joe Mitola. The concept and the term cognitive radio quickly caught the attention and interest of many in the communications field. Cognitive radios are capable of making decisions and selecting or modifying the operating parameters of a radio. Given these capabilities, it is feasible to build a cognitive radar system as introduced by Simon Haykin in 2006. Cognitive radar, as described by Haykin, is an intelligent system that must be aware of its environment, uses prior knowledge, …

Natural Selectivity Of Nickel And Vanadium In Crude Oil, Olienka P. De La O Fernandez

Open Access Theses & Dissertations

Nickel and Vanadium have always been found in crude oil all around the world. The metal content is found mainly in porphyrin structures in the asphaltene fraction of the petroleum. In order to determine the reason for this natural preference, a set of experiments testing thermodynamics, kinetics, and other factors were performed. Candidate metalloporphyrins containing Vanadyl, Chromium, Iron, Nickel, Copper and Zinc were analyzed through chemical reactions characterized using Silica Column Chromatography, HPLC, MS and UV-Visible. Theoretical analysis of the stability of metalloporphyrins was conducted using DFT/NRLMOL for computational calculation. The analysis of all factors leads us to conclude that …

Optimized Integrated Software Package For Classification Of Small Airway Dysfunction Using Genetic Algorithms, Elias Estrada

Open Access Theses & Dissertations

Due to the similarity in the symptoms of respiratory disorders, an accurate diagnosis could be a difficult task. Regarding asthma as the main focus of this research, early detection of small airway impairment could represent a better opportunity for timely diagnosis. An integrated software package (ISP) based on the impulse oscillometry technique, has been developed to serve as an important tool for clinicians during classification of asthma severities on children [1]. The current version of the ISP was tested with data obtained during several years by Dr. Homer Nazeran and Dr. Michael Goldman from 110 Hispanic children [2], providing an …

Design Of Three Different Particle Size Distributions In Silver Paste Through Computer Simulation For Higher Electrical Conductivity, Kyungdeok Jang

Open Access Theses & Dissertations

In the field of printed electronics technology, researchers have tried to print highly conductive electrodes with fine width and height in order to manufacture high performance devices.

The purpose of this research is to print particle monolayer silver patterns which have better electrical conductivity than existing ones. The key idea of this experiment is to analyze silver inks with different sized particles. Let us consider a particle monolayer pattern printed with silver ink consisting of mono-sized particles. Inside of the pattern, there are some vacant spaces between the particles, which can lead to low electrical conductivity and discontinuity of the …

Design And Development Of Implantable And Remote Controlled Distraction Osteogenesis Device For Limb Lengthening Practice In Children, Mario Eduardo Rodriguez De La O

Open Access Theses & Dissertations

Recent technology improvements have been positively affecting medical industry in recent years since procedures and equipment are more precise and reliable. Nevertheless, there are still surgical procedures and medical devices that not fully address specific needs according to medical experts. One of those necessities is focused on options available for children patients when subjected to a surgical procedure named distraction osteogenesis. In general, distraction osteogenesis is performed when skeletal deformities need to be corrected or when bone lengthening is required, typically a mechanism is utilized to elongate bone at a controlled rate. The existing osteodistraction methods for limb lengthening and …

Master's In Electrical Engineering, Ricardo Xavier Rodriguez

Open Access Theses & Dissertations

This project is a focus on characterizing the process for actualizing three dimensional structures out of a carbon nanostructure composite via a direct print additive manufacturing process. Manufacturing parts additively enables for realization of geometrically complex shapes that often times cannot be manufactured any other way. The specificity of a material's properties have to be such, that the processing method can precisely place and bond material to itself in a highly repeatable manner. Commercial materials for additive manufacturing are have been optimized with these goals in mind and, therefore, often times lack the rigor and robustness for many applications.

The …

Use Of Cosine Modulated Filter Bank To Quantify Human Muscle Fatigue Using Electromyography Signals Obtained During Isometric Voluntary Contractions, Liza Stephanie Rodriguez

Open Access Theses & Dissertations

As technology continues to advance, there continues to be an interest in applying engineering theories to solve medical problems. Technology has allowed researchers to investigate the properties and characteristics of the human body in hopes of emulating their complexities. The rising interest in the study of biopotentials for use in prosthetic limbs, exoskeletons and machine interfacing has led to a necessity to validate that the understanding of these signals is accurate. The study of biopotentials generated by muscles via a method known as electromyography (EMG) has improved the understanding of effects of rehabilitative treatments, assisted in diagnosing diseases, control of …

Multi-Objective Border Patrolling Optimization Using Game Theory And Evolutionary Algorithms, Franciso Oswaldo Aguirre

Open Access Theses & Dissertations

Border security has evolved significantly since the days when no more than 75 Mounted Guards patrolled the U.S. border in the early 1900's. The border region includes thousands of miles of both land and maritime borders that must be controlled, as well as commercial transportation networks. One of the primary components of the Department of Homeland Security (DHS) is the U.S. Customs and Border Protection (CBP) agency. One of the most typical activities performed by CBP is patrolling the expansive open areas in between official points of entry (POEs) to prohibit illegal entry attempts. Roving patrols are routinely conducted by …