Digital Commons Network^™

Clustering Of High-Dimensional Gene Expression Data With Feature Filtering Methods And Diffusion Maps, Rui Xu, Steven Damelin, Boaz Nadler, Donald C. Wunsch

Electrical and Computer Engineering Faculty Research & Creative Works

The importance of gene expression data in cancer diagnosis and treatment by now has been widely recognized by cancer researchers in recent years. However, one of the major challenges in the computational analysis of such data is the curse of dimensionality, due to the overwhelming number of measures of gene expression levels versus the small number of samples. Here, we use a two-step method to reduce the dimension of gene expression data. At first, we extract a subset of genes based on the statistical characteristics of their corresponding gene expression measurements. For further dimensionality reduction, we then apply diffusion maps, …

Contributions Of Online Visual Feedback To The Learning And Generalization Of Novel Finger Coordination Patterns, Xiaolin Liu, Robert A. Scheidt

Biomedical Engineering Faculty Research and Publications

We explored how people learn new ways to move objects through space using neuromuscular control signals having more degrees of freedom than needed to unambiguously specify object location. Subjects wore an instrumented glove that recorded finger motions. A linear transformation matrix projected joint angle signals (a high-dimensional control vector) onto a two-dimensional cursor position on a video monitor. We assessed how visual information influences learning and generalization of novel finger coordination patterns as subjects practiced using hand gestures to manipulate cursor location. Three groups of test subjects practiced moving a visible cursor between different sets of screen targets. The hand-to-screen …

A Laboratory Study Of Streambed Stability In Bottomless Culverts, Brian Mark Crookston

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Traditional culvert designs, in many cases, have become habitat barriers to aquatic animal species. In response, environmentally sensitive culvert designs have been developed to function as ecological bridges. Bottomless and buried invert culverts are examples of such designs and are commonly used for fish passage. Additional design guidance specific to streambed stability in buried-invert or bottomless culverts under high flow events is needed. This study investigated incipient motion conditions for four substrate materials in a 2-ft (0.61-m) diameter circular bottomless arch culvert and in a 1-ft (0.30-m) wide rectangular flume in a laboratory setting. General scour of the streambed within …

A Field Programmable Gate Array Based Finite-Domain Constraint Solver, Prasad Subramanian

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Constraint satisfaction and optimization techniques are commonly employed in scheduling, industrial manufacturing, and automation processes where concepts from Operations Research (OR) and Artificial Intelligence (AI) are applied. In embedded systems, Constraint Satisfaction Problem (CSP) finds use in design, synthesis, and optimization. However, most application areas of CSP employ offline solving techniques where design requirements and constraints are captured before the system is deployed online. There is a significant amount of pre-planning and human intervention required.

In embedded systems, online constraint solving techniques are primarily used as onboard control software in order to enable a system that can dynamically adapt to …

Calculated Surface Velocity Coefficients For Prismatic Open Channels By Three-Dimensional Hydraulic Modeling, Nat Marjang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

A turbulence model was developed for computing surface velocity coefficients and discharge under steady, uniform flow conditions for rectangular and compound open-channel cross sections. Reynolds-Average Navier-Stokes (RANS) equations, Reynolds stress equations, and kinetic energy and dissipation equations were applied in the model using the finite-volume method with the SIMPLER algorithm. The models show graphical results of the velocity distributions in the longitudinal bed slope direction, secondary velocities, pressure, turbulence kinetic energy, and kinetic energy dissipation rate across the cross section. Also, the surface velocity coefficients were computed at increments of one-eighth of the base width from the vertical walls to …

Nutrient Mobility From Biosolids Land Application Sites, Mai Anh Vu Tran

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Three types of biosolids (lime-stabilized, aerobically digested, and anaerobically digested biosolids) were applied on 0.13-ha test plots on disturbed rangelands in Western Utah at rates of up to twenty times (20X) the estimated N-based agronomic rate. Soil samples at depths up to 1.5 m were collected and analyzed for nitrogen, phosphorus, regulated metals, pH, and electrical conductivity for up to two years after biosolids application.

NH₄-N at the soil surface (0.2 m) was primarily lost through ammonia volatilization and nitrification. This observation was consistent with reported increases in nitrate (NO₃-N) concentrations found within the soil surface …

Seepage Evaluations In Cache Valley Irrigation Canals, Katerine N. Molina

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Estimation of seepage was done in 39 selected reaches of 11 irrigation canals in the Logan and Blacksmith Fork Irrigation Systems of Cache Valley, Utah. The measurements were performed from June to October, 2008, which includes part of the irrigation season for these canals. The inflow-outflow method was used to measure seepage, in which area and velocities were measured under steady flow conditions. Velocity measurements were done with an acoustic flow meter and the mean velocity was determined using the reduced-point method (velocity measurements at 0.2, 0.6 and or 0.8 of the depth from the water surface).

As a result, …

Development Of A Microelectrode Array Sensing System For Water Quality Monitoring, Robert D. Gardner

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This thesis reports the design and fabrication of a low-cost reliable microelectrode array sensing platform and its application toward water quality monitoring, including heavy metal ion detection. Individually addressable microelectrodes were designed in a planar array on a nonconductive glass substrate by a photolithography method. The size, shape, composition, and functionality of the microelectrodes were theoretically explored in order to maximize performance.

The microelectrode array sensing platform was proven and characterized in the K3Fe(CN)₆ electrochemical standard using cyclic voltammetry. The sensor platform exhibited well defined voltammograms and had increased sensitivity relative to a commercially available microelectrode of similar size. …

Developing Lcfs For Biofuels: Getting It Right For Corn Ethanol, Kenneth Cassman, Adam Liska

Adam Liska Papers

• Corn ethanol will be first to test the newly developed LCFS assessment methods; substantial amounts of other biofuels will come several years later

• Accurate valuation of direct-effect GHG emissions from corn ethanol is the foundation of the LCFS process; these affects vary with ethanol biorefinery type and corn feedstock supply

• Different reference GHG emissions values are needed for each major class of ethanol plants

• The BESS model provides the most up-to-date, scientifically sound estimate of corn-ethanol GHG emissions; can BESS and GREET reach agreement?

• Certification and compliance tools are also needed

The Draft Genome Of The Transgenic Tropical Fruit Tree Papaya ( Carica Papaya Linnaeus), Ray Ming, Shaobin Hou, Yun Feng, Qinguyi Yu, Jyothi Thimmapuram

Cyber Center Publications

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3 draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree¹ to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far may account for the smaller papaya gene number in …

2008 - The Thirteenth Annual Symposium Of Student Scholars

Symposium of Student Scholars Program Books

The full program book from the Thirteenth Annual Symposium of Student Scholars, held on April 14, 2008. Includes abstracts from the presentations and posters.

Water-Soluble Iron Oxide Nanoparticles For Nanomedicine, Christy L. Cooper, Lisa M. Reece, J Key, Donald E. Bergstrom, James F. Leary

Birck Poster Sessions

Monodisperse iron oxide nanoparticles (MION) are easily synthesized in organic solvents for industrial applications. However, biological applications require that the particles by readily dispersed in aqueous solutions. To improve their dispersion in aqueous solution, MION particles can be conjugated to water soluble polymers. These water soluble particles can then be used for nanomedicine, which utilizes nanometer scale constructs to treat diseases at the cellular level. Here we report the synthesis of a monodisperse iron oxide nanoparticle construct for breast cancer applications.

2008 Directory Of Indiana State, County, City And Town Officials Responsible For Road And Street Work, Indiana Ltap

Indiana Local Technical Assistance Program (LTAP) Directory

Contact information for agency officials and employees responsible for Indiana’s local road infrastructure.

Implementing Mass Nutrient Balance Procedures On Swine Production Facilities, Richard Koelsch, Alan Sutton

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Whole Farm Nutrient Balance (WFNB) approaches have been used to provide a measure of environmental performance (Aarts et al., 1992; Lanyon and Beegle, 1993; Klausner, 1995). Whole farm balance concepts are used as part of the Netherlands Mineral Accounting System public policy that includes compulsory mineral input and output reports from livestock farms and levies for excess imbalances (Jongbloed and Lenis, 1998). Procedures for measuring WFNB will be followed in measurements made on commercial swine facilities for 2006 and 2007. The conclusions developed based upon data from 13 for 2006 include:

• On average, the participating swine producers import 1.5 units …

42nd Conference On Senior Engineering Design Projects, College Of Engineering And Applied Sciences

Senior Engineering Design Conference

The 42nd Conference on Senior Engineering Design Projects was held on April 15, 2008 at the College of Engineering and applied Sciences on the Parkview Campus of Western Michigan University. The college sponsors the conference to showcase the work of its graduating seniors, who are required to complete a capstone project that puts into practice what they have learned. Many of the projects are sponsored by business and industry.

Modeling And Characterization Of Adaptive Lanthanum-Modified Lead Zirconate Titanate (Plzt) Microlenses, Yasser A. Abdelaziez, Partha P. Banerjee

Electrical and Computer Engineering Faculty Publications

We report the modeling and characterization of adaptive voltage controlled electro-optic microlenses. First, we utilize finite element analysis (FEA) to simulate the induced electro-optic effect in lanthanum-modified lead zirconate titanate (PLZT). FEA simulation provides microlens parameters such as phase and focal length. A simple z-scan method is developed to fully characterize the adaptive voltage controlled linear lens. Experimental z-scan results are shown to match the theoretical predictions from FEA.

Opportunistic Checkpoint Intervals To Improve System Performance, Sarala Arunagiri, John T. Daly, Patricia J. Teller, Seetharami Seelam, Ron A. Oldfield, Maria Ruiz Varela, Rolf Riesen

Departmental Technical Reports (CS)

The massive scale of current and next-generation massively parallel processing (MPP) systems presents significant challenges related to fault tolerance. For applications that perform periodic checkpoints, the choice of the checkpoint interval, the period between checkpoints, can have a significant impact on the execution time of the application. Finding the optimal checkpoint interval that minimizes the wall clock execution time, has been a subject of research over the last decade. In an environment where there are concurrent applications competing for access to the network and storage resources, in addition to application execution times, contention at these shared resources need to be …

Real-Time Telemetry Options For Ocean Observing Systems, Bridget Benson, G. Chang, F. Spada, D. Manov, R. Kastner

Electrical Engineering

Ocean observing systems provide a means to monitor oceanic variables on a variety of temporal and spatial scales. Data from ocean observing systems are most useful when they are collected in real-time; real-time data allow the detection of important events as they occur. Various real-time telemetry options exist for transferring data from sea to shore and from the subsurface to the surface. We survey these telemetry options to highlight the research problems associated with subsea to surface to shore networking and include a comparison of existing real-time technologies for three specific ocean observing system network topologies with respect to data …

Fabrication Of Bioactive Osteogenic Controlled-Release Systems, Cellular Platforms, And Cellular Capsules Using Layer -By -Layer Nanoassembly, Skylar Stewart-Clark

Doctoral Dissertations

There is an ever-increasing awareness that the field of tissue engineering offers many potential solutions to clinical problems. While advances along these lines have been made, the design and implementation of an "off the shelf" tissue is yet to be realized. Thus, the objectives of this work were largely aimed at the design and fabrication of biocompatible, bioactive structures which could be integrated into existing biomaterial products.

The electrostatic layer-by-layer (LbL) self-assembly technique was used to incorporate biologically relevant molecules within controlled release systems, cell culture platforms, and 3-D cellular capsules. Two delivery systems were investigated to determine the release …

Interfaces, Volume 10, Issue 1 - Spring 2008

INTERFACES: Newsletter of the Nebraska Center for Materials and Nanoscience

CONTENTS
From the Director
Facility Focus: Nano-Fabrication Facility
Recent Achievements of Center Researchers
Magnetic Nanoclusters Put in Order – Insights with Scanning Tunneling Microscopy
NCMN Welcomes Eva Franke Schubert
Research Spotlight: Barry Cheung
UNL Hosts 54th Annual Midwest Solid State Conference
Published Books
Engineers Part of $9 Million Project Studying Cell Context of Genes

Incorporation Of Space Syntax Theory In Determining Safe And Efficient Construction Site Layout, Minsuck Cho

Masters Theses

Facility layout is an important to determine a proper arrangement of temporary facilities in a construction site. It significantly impacts productivity and safety of construction. The objectives of layout planning are to minimize travel distance and time, to decrease the facility transportation and setup costs, and to improve site safety. Despite the importance of facility layout, it is often overlooked in the planning phase. Several models have been developed taking some of these factors into consideration; however, construction managers and site planners often regard cost as the most important factor in layout planning and pay less attention to safety and …

Oxygen Diffusion Through Natural Extracellular Matrices: Implications For Estimating "Critical Thickness" Values In Tendon Tissue Engineering, Caroline Androjna, Jorge E. Gatica, Joanne M. Belovich, Kathleen A. Derwin

Chemical & Biomedical Engineering Faculty Publications

Oxygen is necessary for maintaining cell proliferation and viability and extracellular matrix (ECM) production in 3-dimensional tissue engineering. Typically, diffusion is the primary mode for oxygen transport in vitro; thus, ensuring an adequate oxygen supply is essential. In this study, we determined the oxygen diffusion coefficients of 3 natural ECMs that are being investigated as construct scaffolds for tendon tissue engineering: small-intestine submucosa (SIS), human dermis (Alloderm (R)), and canine fascia lata. Diffusion coefficients were determined using a standard diffusion cell system. The ranges for each matrix type were: SIS: 7 x 10(-6) - 2 x 10(-5) cm(2)/s, Alloderm (R): …

Modeling The Cellular Level Of Natural Sensing With The Functional Basis For The Design Of Biomimetic Sensor Technology, Jacquelyn K. Stroble, Robert B. Stone, Daniel A. Mcadams, L. H. Shu, Steve Eugene Watkins

Electrical and Computer Engineering Faculty Research & Creative Works

After surveying biology for natural sensing solutions six main types of extraneous sensing were identified across the biological kingdoms. Natural sensing happens at the cellular level with receptor cells that respond to photo, chemo, eletro, mechano, thermo and magnetoreceptor-type stimuli. At the highest level, all natural sensing systems have the same reaction sequence to stimuli: perception, transduction, and response. This research is exploring methods for knowledge transfer between the biological and engineering domains. With the use of the Functional Basis, a well-defined modeling language, the ingenuity of natural sensing can be captured through functional models and crossed over into the …

Cs 141-01: Computer Programming - I, Jay Dejongh

Computer Science & Engineering Syllabi

This course provides a general introduction to the fundamentals of computer programming. Examples from and applications to a broad range of problems are given. No prior knowledge of programming is assumed. The concepts covered will be applied to the Java programming language. Students must register for both lecture and one laboratory section. 4 credit hours. Prerequisite: MTH 127 (College Algebra) or equivalent.

Cs/Bio 271: Introduction To Bioinformatics, Michael L. Raymer, Dan E. Krane

Computer Science & Engineering Syllabi

No abstract provided.

Ceg 355-01: Introduction To The Design Of Information Technology Systems, Thomas C. Hartrum

Computer Science & Engineering Syllabi

Introduction to the design of information systems comprising modern technologies such as SQL database programming, networks, and distributed computing with CORBA, electronic and hypertext (HTML) documents, and multimedia.

Improving Query Efficiency Of Multiresolution Data Aggregation For Analytical Exploration Of Large Relational Dataset, Yu-Ting Huang

Masters Theses

Tree structures are developed to organize the data more efficiently by using fewer resources for searching records. This thesis investigates the tree's actual structure on the hard disk to see the influence of different kinds of structures on the tree building time and query execution time. In order to improve efficiency, one multi-file structure and two reorganization structures, BFS and DFS, are examined to achieve this goal. The results indicate that two reorganization structures on KDB-tree structure can significantly improve the query execution time in large data sets and multi-file structure can slightly improve the TPIE lover level building time.

Systems Methodology And Framework For Problem Definition In Mobile Ad Hoc Networks, Reghu Anguswamy, Maheswaran Thiagarajan, Cihan H. Dagli

Engineering Management and Systems Engineering Faculty Research & Creative Works

Mobile Ad Hoc Networks are communication networks built up of a collection of mobile devices which can communicate through wireless connections. Mobile Ad Hoc Networks have many challenges such as routing, which is the task of directing data packets from a source node to a given destination. This task is particularly hard in Mobile Ad Hoc Networks: due to the mobility of the network elements and the lack of central control, robustness and adaptability in routing algorithms and work in a decentralized and self organizing way. Through the principles of systems architecting and Engineering; the problem statement in Mobile Ad …

Substrates Preparation From Woody Tropical Waste Biomass For Biohydrogen Production, Dwi Susilaningsih, Theresia Umi Harwati, Khairul Anam, Yopi Yopi

Makara Journal of Technology

Substrates Preparation from Woody Tropical Waste Biomass for Biohydrogen Production. Addressing to the global warming problem, energy crisis and pollution, hydrogen production by micro-organisms using biotechnological approach should be considered, since it fulfils the recent society requirement to safely produce, renewable and environmental friendly energy. Hydrogen is one of the most promising green energy sources, because it is easily converted to electricity and cleanly combustible. There are three types of micro-organisms for hydrogen production, the first is cyanobacteria through the photosynthesis process, the second is anaerobic bacteria, which use organic substances as electron donor and energy and convert them to …

Biomass Production Chlorella Vulgaris Buitenzorg Using Series Of Bubble Column Photo Bioreactor With A Periodic Illumination, Anondho Wijanarko, Dianursanti Dianursanti, Muryanto Muryanto, Josia Simanjuntak, Praswasti Pembangun Dyah Kencana Wulan, Heri Hermansyah, Misri Gozan, Roekmijati Widaningroem Soemantojo

Makara Journal of Technology

Chlorella vulgaris Buitenzorg cultivation using three bubble column photo bioreactors arranged in series with a volume of 200 mL for 130 hours shows an increase of biomass production of Chlorella vulgaris Buitenzorg up to 1.20 times and a decrease of the ability of CO2 fixation compared to single reactor at a periodic sun illumination cycle. The operation conditions on cultivation are as following: T, 29.0oC; P,1 atm.; UG, 2.40 m/h; CO2, 10%; Benneck medium; and illumination source by Phillip Halogen Lamp 20W /12V/ 50Hz. Other research parameters such as microbial carbon dioxide transferred rate (qco2), CO2 transferred rate (CTR), energy …