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Discovering Gene Functional Relationships Using Faun (Feature Annotation Using Nonnegative Matrix Factorization), Elina Tjioe, Michael W. Berry, Ramin Homayouni 2010 University of Tennessee - Knoxville

Discovering Gene Functional Relationships Using Faun (Feature Annotation Using Nonnegative Matrix Factorization), Elina Tjioe, Michael W. Berry, Ramin Homayouni

Faculty Publications and Other Works -- EECS

Background

Searching the enormous amount of information available in biomedical literature to extract novel functional relationships among genes remains a challenge in the field of bioinformatics. While numerous (software) tools have been developed to extract and identify gene relationships from biological databases, few effectively deal with extracting new (or implied) gene relationships, a process which is useful in interpretation of discovery-oriented genome-wide experiments.

Results

In this study, we develop a Web-based bioinformatics software environment called FAUN or Feature Annotation Using Nonnegative matrix factorization (NMF) to facilitate both the discovery and classification of functional relationships among genes. Both the computational complexity ...


The Impact Of Multiple Computing And Digital Arts Degrees On Undergraduate Recruitment, Amber Settle, Liz Friedman, Mary Jo Davidson 2010 DePaul University

The Impact Of Multiple Computing And Digital Arts Degrees On Undergraduate Recruitment, Amber Settle, Liz Friedman, Mary Jo Davidson

Amber Settle

In this paper, we describe a two-year study of the factors influencing freshman and first-year transfer student enrollment at the College of Computing and Digital Media (CDM) at DePaul University. Our results show that the reputation of the institution, the particular degree programs at DePaul CDM, and to a lesser degree the diversity of degree programs available, were all positive factors for application and enrollment at DePaul. Factors that were not of primary importance included parental influence, the fact that DePaul is a liberal arts institution, and recommendations from relatives and friends. 


Absolute Blood Velocity Measured With A Modified Fundus Camera, Donald D. Duncan, Paul Lemaillet, Mohamed Ibrahim, Quan D. Nguyen, Matthias Hiller, Jessica C. Ramella-Roman 2010 Portland State University

Absolute Blood Velocity Measured With A Modified Fundus Camera, Donald D. Duncan, Paul Lemaillet, Mohamed Ibrahim, Quan D. Nguyen, Matthias Hiller, Jessica C. Ramella-Roman

Electrical and Computer Engineering Faculty Publications and Presentations

We present a new method for the quantitative estimation of blood flow velocity, based on the use of the Radon transform. The specific application is for measurement of blood flow velocity in the retina. Our modified fundus camera uses illumination from a green LED and captures imagery with a high-speed CCD camera. The basic theory is presented, and typical results are shown for an in vitro flow model using blood in a capillary tube. Subsequently, representative results are shown for representative fundus imagery. This approach provides absolute velocity and flow direction along the vessel centerline or any lateral displacement therefrom ...


Auxiliary State Variables For Rotor Crack Detection, Zbigniew Kulesza, Jerzy T. Sawicki 2010 Bialystok University of Technology

Auxiliary State Variables For Rotor Crack Detection, Zbigniew Kulesza, Jerzy T. Sawicki

Mechanical Engineering Faculty Publications

In the present study, a new model-based method for rotor crack detection and crack location is proposed. The finiteelement model of the rotor-bearing system accounts for the breathing mechanism of the crack. The model of the rotor system is augmented with an auxiliary single-degree-of-freedom oscillator. The observer is designed and the estimates of its two auxiliary state variables are proposed as crack indicators. The crack location along the shaft is determined by designing a set of observers, which calculate the values of these indicators for different possible crack locations along the shaft. The proposed method is validated numerically and the ...


Do Surfaces With Mixed Hydrophilic And Hydrophobic Areas Enhance Pool Boiling?, Amy Rachel Betz, Jie Xu, Huihe Qiu, Daniel Attinger 2010 Columbia University

Do Surfaces With Mixed Hydrophilic And Hydrophobic Areas Enhance Pool Boiling?, Amy Rachel Betz, Jie Xu, Huihe Qiu, Daniel Attinger

Daniel Attinger

We demonstrate that smooth and flat surfaces combining hydrophilic and hydrophobicpatterns improve pool boiling performance. Compared to a hydrophilicsurface with 7° wetting angle, the measured critical heat flux and heat transfer coefficients of the enhanced surfaces are, up to respectively, 65% and 100% higher. Different networks combining hydrophilic and hydrophobic regions are characterized. While all tested networks enhance the heat transfer coefficient, large enhancements of critical heat flux are typically found for hydrophilic networks featuring hydrophobic islands. Hydrophilic networks indeed are shown to prevent the formation of an insulating vapor layer.


A Review Of Zero Discharge Wastewater Treatment Systems Using Reed Willow Bed Combinations In Ireland, Sean O'Hogain, Liam McCarton, Anna Reid, John Turner 2010 Dublin Institute of Technology

A Review Of Zero Discharge Wastewater Treatment Systems Using Reed Willow Bed Combinations In Ireland, Sean O'Hogain, Liam Mccarton, Anna Reid, John Turner

Conference papers

The concept of a reed willow bed combination has the potential to achieve a zero discharge wastewater treatment system. This paper will present results from a two year study to monitor the performance of a reed willow bed facility at Lynches Lane, Co. Dublin, Ireland. Outline design specifications for the facility will be presented. Monitoring results for a two year period including influent and effluent parameters, rainfall, potential evapotranspiration, and soil classification will be presented and discussed. During the two year monitoring period the system achieved a zero discharge. This paper will discuss the potential widespread application of similar systems ...


Perpetual Exploration Of Relational Information And Enhanced Star Glyphs For Multi-Source Data Visualization, Andrew Crowell 2010 Rowan University

Perpetual Exploration Of Relational Information And Enhanced Star Glyphs For Multi-Source Data Visualization, Andrew Crowell

Theses and Dissertations

Information Visualization is an area of research concerned with the presentation of abstract data in a visual format. It has many diverse applications in fields of software engineering, information sciences, biology, chemistry, and medical, among others. This thesis is primarily concerned with the application of information visualization to the display of directed graphs and to the display of multivariate data for analysis. Two novel applications will be presented that are both advancements in the field of information visualization. The first application applies to the visualization and navigation of large or infinite graphs and networks. The quality of a graph drawing ...


Research On Non-Analytical Arc Welding Robot Control Algorithm And System-Thesis, G. Zhang 2010 Selected Works

Research On Non-Analytical Arc Welding Robot Control Algorithm And System-Thesis, G. Zhang

Jing Wu

No abstract provided.


Safe Inter-Domain Routing Under Diverse Commercial Agreements, Yong Liao, Lixin Gao, Roch A. Guérin, Zhi-Li Zhang 2010 University of Massachusetts - Amherst

Safe Inter-Domain Routing Under Diverse Commercial Agreements, Yong Liao, Lixin Gao, Roch A. Guérin, Zhi-Li Zhang

Lixin Gao

Commercial agreements drive the routing policies used in today's Internet. The two most extensively studied commercial agreements are transit and peering; however, they are only two of many diverse and continuously evolving commercial agreements that ISPs enter into. So far, the only known practical safe and robust routing policy is Gao and Rexford's policy guideline, which is applicable to transit and peering agreements only. It is, therefore, of importance to identify routing policies that are safe and robust and at the same time capable of accommodating the diverse commercial agreements existing in the Internet. In particular, this paper ...


On The Feasibility And Efficacy Of Protection Routing In Ip Networks, Kin-Wah (Eric) Kwong, Lixin Gao, Roch A. Guérin, Zhi-Li Zhang 2010 University of Pennsylvania

On The Feasibility And Efficacy Of Protection Routing In Ip Networks, Kin-Wah (Eric) Kwong, Lixin Gao, Roch A. Guérin, Zhi-Li Zhang

Lixin Gao

With network components increasingly reliable, routing is playing an ever greater role in determining network reliability. This has spurred much activity in improving routing stability and reaction to failures, and rekindled interest in centralized routing solutions, at least within a single routing domain. Centralizing decisions eliminates uncertainty and many inconsistencies, and offers added flexibility in computing routes that meet different criteria. However, it also introduces new challenges; especially in reacting to failures where centralization can increase latency. This paper leverages the flexibility afforded by centralized routing to address these challenges. Specifically, we explore when and how standby backup forwarding options ...


Fpga-Based Fuzzy Inference System For Real-Time Embedded Applications, Philadelphia University 2010 Philadelphia University

Fpga-Based Fuzzy Inference System For Real-Time Embedded Applications, Philadelphia University

Philadelphia University, Jordan

No abstract provided.


Handling External Events Efficiently In Gillespie's Stochastic Simulation Algorithm, Brad Geltz 2010 Virginia Commonwealth University

Handling External Events Efficiently In Gillespie's Stochastic Simulation Algorithm, Brad Geltz

Theses and Dissertations

Gillespie's Stochastic Simulation Algorithm (SSA) provides an elegant simulation approach for simulating models composed of coupled chemical reactions. Although this approach can be used to describe a wide variety biological, chemical, and ecological systems, often systems have external behaviors that are difficult or impossible to characterize using chemical reactions alone. This work extends the applicability of the SSA by adding mechanisms for the inclusion of external events and external triggers. We define events as changes that occur in the system at a specified time while triggers are defined as changes that occur to the system when a particular condition ...


Programmable Periodicity Of Quantum Dot Arrays With Dna Origami Nanotubes, Hieu Bui, Craig Onodera, Carson Kidwell, YerPeng Tan, Elton Graugnard, Wan Kuang, Jeunghoon Lee, William B. Knowlton, Bernard Yurke, William L. Hughes 2010 Boise State University

Programmable Periodicity Of Quantum Dot Arrays With Dna Origami Nanotubes, Hieu Bui, Craig Onodera, Carson Kidwell, Yerpeng Tan, Elton Graugnard, Wan Kuang, Jeunghoon Lee, William B. Knowlton, Bernard Yurke, William L. Hughes

Elton Graugnard

To fabricate quantum dot arrays with programmable periodicity, functionalized DNA origami nanotubes were developed. Selected DNA staple strands were biotin-labeled to form periodic binding sites for streptavidin-conjugated quantum dots. Successful formation of arrays with periods of 43 and 71 nm demonstrates precise, programmable, large-scale nanoparticle patterning; however, limitations in array periodicity were also observed. Statistical analysis of AFM images revealed evidence for steric hindrance or site bridging that limited the minimum array periodicity.


Accident In Bhopal: Observations 20 Years Later, Ronald J. Willey, Dennis C. Hendershot, Scott Berger 2010 Northeastern University

Accident In Bhopal: Observations 20 Years Later, Ronald J. Willey, Dennis C. Hendershot, Scott Berger

Ronald J. Willey

The most influential process safety accident passed its 20th anniversary on Dec 3, 2004. At an international symposium to mark the event in Kanpur, India during the week of this anniversary, process safety practitioners from around the world assembled to discuss progress in resolving the Bhopal tragedy and in advancing the practice of process safety worldwide. This paper reports the main conclusions from the conference, and provides insight into the Bhopal site as attendees found it in December 2004. Since 1984, many positive steps worldwide have been made in regards to improvements in process safety and protection of personnel within ...


Study Of Load Transfer Efficiency Of Airfield Rigid Pavement Joints Based On Stresses And Deflections, Ashish Wadkar 2010 Rowan University

Study Of Load Transfer Efficiency Of Airfield Rigid Pavement Joints Based On Stresses And Deflections, Ashish Wadkar

Theses and Dissertations

The concept of joint load transfer efficiency is very important and fundamental to Federal Aviation Administration's (FAA) airfield rigid pavement thickness design procedures. The FAA procedure assumes 25% of stress applied to the edge is transferred to the adjoining slab. Moreover, since it is not convenient or practical to measure stress-based load transfer efficiency [LTE (S)], field measurement of load transfer efficiency includes computation of the ratio of unloaded slab deflection to loaded slab deflection. Falling weight deflectometer (FWD) generally serves the purpose of measurement of deflection-based load transfer efficiency [LTE (6)]. The true load transfer is defined by ...


The Virtual Hip: An Anatomically Accurate Finite Element Model Based On The Visible Human Dataset, Jonathan M. Ford 2010 University of South Florida

The Virtual Hip: An Anatomically Accurate Finite Element Model Based On The Visible Human Dataset, Jonathan M. Ford

Graduate Theses and Dissertations

The purpose of this study is to determine if element decimation of a 3-D anatomical model affects the results of Finite Element Analysis (FEA). FEA has been increasingly applied to the biological and medical sciences. In order for an anatomical model to successfully run in FEA, the 3-D model’s complex geometry must be simplified, resulting in a loss of anatomical detail. The process of decimation reduces the number of elements within the structure and creates a simpler approximation of the model. Using the National Library of Medicine’s Visible Human Male dataset, a virtual 3-D representation of several structures ...


Flooded Grain And Other Harvest Issues, Charles R. Hurburgh, Roger Elmore, Alison E. Robertson 2010 Iowa State University

Flooded Grain And Other Harvest Issues, Charles R. Hurburgh, Roger Elmore, Alison E. Robertson

Integrated Crop Management News

Harvest is underway and a few issues stemming from the unusual weather patterns last summer are coming up. On September 30 the Iowa Department of Agriculture and Land Stewardship (IDALS), as the state representative for the U.S. Food and Drug Administration, issued a statement saying that grain submerged (over the grain) in flood waters was to be considered contaminated and therefore not eligible for entry into food-feed markets. Ethanol is a feed market because of the dried distillers grains with solubles (DDGS). This is the same policy that was used for grain in storage that was submerged in 2008 ...


Assessment Of State Recycling Regulations In The United States, Nazli Yesiller, James L. Hanson, Samuel A. Vigil 2010 California Polytechnic State University, San Luis Obispo

Assessment Of State Recycling Regulations In The United States, Nazli Yesiller, James L. Hanson, Samuel A. Vigil

Civil and Environmental Engineering

This investigation was conducted to identify the current status of state recycling regulations in U.S. using an extensive survey. Questions were included regarding: baseline waste generation and recycling trends; recycling regulatory trends; quantitative thresholds; integration of science, engineering, and economic principles; material properties; and legislative status of regulations. The majority of the surveyed states had regulations for recycling activities, which were less strict than solid waste regulations, and required permits for operation of recycling facilities. A low percentage of the states regulated generators, transporters, and handlers and a high percentage regulated recyclers. In general, transfer stations and recycling centers ...


Selection And Recognition Of Landmarks Using Terrain Spatiograms, Damian M. Lyons 2010 Fordham University

Selection And Recognition Of Landmarks Using Terrain Spatiograms, Damian M. Lyons

Faculty Publications

A team of robots working to explore and map an area may need to share information about landmarks so as to register their local maps and to plan effective exploration strategies. In previous papers we have introduced a combined image and spatial representation for landmarks: terrain spatiograms. We have shown that for manually selected views, terrain spatiograms provide an effective, shared representation that allows for occlusion filtering and a combination of multiple views.

In this paper, we present a landmark saliency architecture (LSA) for automatically selecting candidate landmarks. Using a dataset of 21 outdoor stereo images generated by LSA, we ...


P2pstm: A Peer-To-Peer Software Transactional Memory, Phil Pratt-Szeliga, Jim Fawcett 2010 Syracuse University

P2pstm: A Peer-To-Peer Software Transactional Memory, Phil Pratt-Szeliga, Jim Fawcett

Electrical Engineering and Computer Science

Peer-to-Peer network topologies are such that there is no centralized server in a distributed system but rather each peer is part server and part client. This idea was originally popularized with peer-to-peer file sharing. If one were to distribute computation on a peer-to-peer network topology, consistency of shared data among peers is a problem. Software Transactional Memory (STM) is a lock free mechanism of assuring consistency of memory among threads of execution that has favorable performance over locked methods when the number of threads is large. This paper presents a method to use STM methods with a peer-to-peer network architecture ...


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