Digital Commons Network^™

Long-Term Trends From Ecosystem Research At The Hubbard Brook Experimental Forest, John L. Campbell, Charles T. Driscoll, Christopher Eagar, Gene E. Likens, Thomas G. Siccama, Chris E. Johnson, Timothy J. Fahey, Steven P. Hamburg, Richard T. Holmes, Amey S. Bailey, Donald C. Buso

Civil and Environmental Engineering - All Scholarship

The Hubbard Brook Experimental Forest was established by the U.S. Forest Service in 1955 as a major center for hydrologic research in the Northeast. The Hubbard Brook Ecosystem Study originated 8 years later with the idea of using the small watershed approach to study element flux and cycling and the response of forest ecosystems to disturbance. Since that time, the research program at Hubbard Brook has expanded to include various physical, chemical and biological measurements collected by researchers from a number of cooperating institutions. Collaborative, long-term data are the keystone of the Hubbard Brook Ecosystem Study and have provided invaluable …

Simulation And Fabrication Of Three Novel Micromechanical Sensors, Yanqing Lu

Doctoral Dissertations

This work focuses on the simulation, fabrication and characterization of novel microdevices for chemical and biological sensors for improved sensitivity, enhanced performance and applicability. Specifically, microbridge and microcoil sensors have been fabricated via advanced microfabrication technologies. Due to the potential application in chemical and biological sensing, the growth of gold and platinum nanowires during an electrolysis process have also been investigated.

A microbridge can be considered as the head-to-head fusion of two cantilevers and the middle of the bridge would deform in a way similar to a microcantilever. The microbridge sensing device is more stable than the microcantilever, especially in …

Ribosome Kinetics And Aa-Trna Competition Determine Rate And Fidelity Of Peptide Synthesis, Aaron Fluitt, Elsje Pienaar, Hendrik J. Viljoen

Hendrik J. Viljoen Publications

It is generally accepted that the translation rate depends on the availability of cognate aa-tRNAs. In this study it is shown that the key factor that determines translation rate is the competition between near-cognate and cognate aa-tRNAs. The transport mechanism in the cytoplasm is diffusion, thus the competition between cognate, near-cognate and non-cognate aa-tRNAs to bind to the ribosome is a stochastic process. Two competition measures are introduced; C (i) and R (i) (i = 1, 64) are quotients of the arrival frequencies of near-cognates vs. cognates and noncognates vs. cognates, respectively. Furthermore, the reaction …

Gene Synthesis, Cloning, Expression, Purification And Biophysical Characterization Of The C2 Domain Of Human Tensin, Kiran Sukumar Gajula

Doctoral Dissertations

Tensin is a large "docking" protein found in the adhesive junctions of animal cells and recruited early in the development of cell-substrate contacts. There it binds to the cytoplasmic domain of integrin β1 and caps the barbed ends of filamentous actin. This forms a rational basis for its implication in a direct role in the mechanics of membrane-cytoskeleton interactions. Tensin provides a physical link between the actin cytoskeleton, integrins, and other proteins at the cell-substrate contacts. Its overall biochemical properties are a function of its domain composition and architecture, i.e., the domains that are present and their relative positions in …

Trade-Off Between Sample Size And Accuracy: Case Of Static Measurements Under Interval Uncertainty, Hung T. Nguyen, Vladik Kreinovich

Departmental Technical Reports (CS)

In many practical situations, we are not satisfied with the accuracy of the existing measurements. There are two possible ways to improve the measurement accuracy:

first, instead of a single measurement, we can make repeated measurements; the additional information coming from these additional measurements can improve the accuracy of the result of this series of measurements;

second, we can replace the current measuring instrument with a more accurate one; correspondingly, we can use a more accurate (and more expensive) measurement procedure provided by a measuring lab -- e.g., a procedure that includes the use of a higher quality reagent.

In …

Trade-Off Between Sample Size And Accuracy: Case Of Dynamic Measurements Under Interval Uncertainty, Hung T. Nguyen, Olga Kosheleva, Vladik Kreinovich, Scott Ferson

Departmental Technical Reports (CS)

In many practical situations, we are not satisfied with the accuracy of the existing measurements. There are two possible ways to improve the measurement accuracy:

first, instead of a single measurement, we can make repeated measurements; the additional information coming from these additional measurements can improve the accuracy of the result of this series of measurements;

second, we can replace the current measuring instrument with a more accurate one; correspondingly, we can use a more accurate (and more expensive) measurement procedure provided by a measuring lab -- e.g., a procedure that includes the use of a higher quality reagent.

In …

Gold Nanorods Mediate Tumor Cell Death By Compromising Membrane Integrity, Ling Tong, Yan Zhao, Terry B. Huff, Matthew N. Hansen, Alexander Wei, Ji-Xin Cheng

Other Nanotechnology Publications

Folate-conjugated gold nanorods targeted to tumor cell surfaces produced severe membrane damage upon near-infrared irradiation. Photoinduced injury to the plasma membrane resulted in a rapid increase in intracellular calcium (shown in green) with subsequent disruption of the actin network, featured prominently by the formation of membrane blebs.

Study Of Interaction Between Indium Species And Dna In The Formation Of Dna -Templated Nanowires, Shivashankar Suryanarayanan

Doctoral Dissertations

A primary goal of semiconductor industry is to improve device performance and capability by downscaling feature size and upscaling packaging density. As optical-lithography, the mainstream technology for microfabrication, is being stretched to its limit, new unconventional fabrication techniques are being explored as alternatives. A "Bottom-up" approach for manufacturing is emerging as an answer to limitations posed by the traditional "Top-down" approach. Nanowires, bearing the potential of being the basic building blocks for such an approach, are gaining tremendous attention in nanoelectronics. Metal nanowires fabricated using DNA as templates have potential for precise control of length, diameter and positioning. However, wires …

Design And Development Of Microcantilever As A Platform For Moisture Sensing, Qi Chen

Doctoral Dissertations

Ultra-sensitive and selective moisture sensors are needed in various industries for processing control or environmental monitoring. As an outstanding sensor platform, microcantilevers have potential application in moisture detection due to their advantages, such as low-level moisture detection limits, high accuracy, quick response time, high reproducibility, good recovery rate and low in cost. Our research results will lead to the first of its kind for the commercialization of a microcantilever-based moisture sensor used for industrial and household applications. The novelty of the present work is the development of SiO2 and Si cantilevers, which were fabricated using developed processes and modified with …

A Comparison Of State Policies For Complying With The Endangered Species Act, Lenahan O'Connell, Ted Grossardt

Kentucky Transportation Center Research Report

In recent years the number of biological assessments (BAs) for the presence of endangered species conducted by KYTC has risen significantly. This was primarily due to new/additional restrictions imposed by the United States Fish and Wildlife Service (USFWS) in 2005. The most consequential restriction was the listing of the Indiana bat as potentially present in all Kentucky counties. Previously BAs for the Indiana bat were only conducted when a project occurred in a county in which the Indiana bat had been observed (a known occurrence). This study reviewed the policies of the states adjacent to Kentucky, as well as those …

A Site-Wide Perspective On Uranium Geochemistry At The Hanford Site, John M. Zachara, C. Brown, J. Christensen, J.A. Davis, E. Dresel, Chongxuan Liu, S. Kelly, James Mckinley, J. Serne, W. Um

United States Department of Energy: Publications

Uranium (U) is an important risk-driving contaminant at the Hanford Site. Over 200,000 kg have been released to the vadose zone over the course of site operations, and a number of vadose zone and groundwater plumes containing the uranyl cation [UO₂²⁺, U(VI)] have been identified. U is recognized to be of moderate-to-high mobility, conditions dependent. The site is currently making decisions on several of these plumes with long-lasting implications, and others are soon to come.

Uranium is one of nature’s most intriguing and chemically complex elements. The fate and transport of U(VI) has been studied over the …

A Survey Of Neural Computation On Graphics Processing Hardware, Ryan J. Meuth, Donald C. Wunsch

Electrical and Computer Engineering Faculty Research & Creative Works

Modern graphics processing units (GPU) are used for much more than simply 3D graphics applications. From machine vision to finite element analysis, CPU's are being used in diverse applications, collectively called general purpose graphics processor utilization. This paper explores the capabilities and limitations of modern GPU's and surveys the neural computation technologies that have been applied to these devices.

Inference Of Genetic Regulatory Networks With Recurrent Neural Network Models Using Particle Swarm Optimization, Rui Xu, Donald C. Wunsch, Ronald L. Frank

Electrical and Computer Engineering Faculty Research & Creative Works

Genetic regulatory network inference is critically important for revealing fundamental cellular processes, investigating gene functions, and understanding their relations. The availability of time series gene expression data makes it possible to investigate the gene activities of whole genomes, rather than those of only a pair of genes or among several genes. However, current computational methods do not sufficiently consider the temporal behavior of this type of data and lack the capability to capture the complex nonlinear system dynamics. We propose a recurrent neural network (RNN) and particle swarm optimization (PSO) approach to infer genetic regulatory networks from time series gene …

Signaling Pathways Activated By Interleukin-2 And Interluekin-4 Receptors Mediate T Lymphocyte Clonal Expansion, Kristen K. Comfort

Chemical and Materials Engineering Faculty Publications

Cells sense and respond to chemical and physical stimuli through signal transduction pathways, which mediate cell proliferation, differentiation, migration, and survival. The cytokines interleukin-2 (IL-2) and interleukin-4 (IL-4) are key regulators of the adaptive immune system, particularly influencing the clonal expansion and differentiation of T cells. At least in culture, both synergistic and antagonistic effects of IL-2 and IL-4 co-stimulation have been reported; the antagonism, when observed, is thought to arise from the utilization of a common subunit shared by IL-2 and IL-4 receptors. We have sought to characterize IL-2 and IL-4 signaling at the level of intracellular pathways activated …

Cs 141: Computer Programming - I, Michael Ondrasek

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.

Ceg 476/676: Computer Graphics I, Thomas Wischgoll

Computer Science & Engineering Syllabi

By the end of this quarter, you will have learned techniques for constructing 2-D and 3-D objects as well as manipulating and rendering the objects using OpenGL.

Ceg 402/602: Introduction To Computer Communication, Bin Wang

Computer Science & Engineering Syllabi

This course provides an introduction to basic concepts of communication networks, different types of networks, protocols over different layers, and network applications through lectures, labs, homework, and reading on relevant materials.

You will

• Understand networking principles, protocols, and technologies.

• Understand some design and performance issues involved in providing a network service.

• Acquire background for supporting e-commerce, e-government, and e-education.

• Gain hands-on experience with programming techniques for network protocols.

• Obtain background for original research in computer networks.

Cs/Bio 471/671: Algorithms For Bioinformatics, Michael L. Raymer

Computer Science & Engineering Syllabi

Theory-oriented approach to the application of contemporary algorithms to bioinformatics. Graph theory, complexity theory, dynamic programming and optimization techniques are introduced in the context of application toward solving specific computational problems in molecular genetics. 4 credit hours.

Bactericidal Effects Of Cold Plasma Technology On Geobacillus Stearothermophilus And Bacillus Cereus Microorganisms, Angela D. Morris, Gayle B. Mccombs, Susan L. Tolle, Mounir Laroussi, Wayne L. Hynes

Dental Hygiene Faculty Publications

Cold plasma is a state of matter that contains a large number of particles that are electrically charged. Plasmas generate chemically reactive species and ultraviolet radiation making them useful in decontamination applications (Kong & Laroussi, 2003). Research regarding the inactivation of gram-positive bacteria by cold plasma has been studied by Laroussi et al (2003); however, there is limited research regarding the germicidal effectiveness of cold plasma on Geobacillus stearothermophilus and Bacillus cereus microorganisms. The purpose of this study was to determine if cold plasma technology inactivates Geobacillus stearothermophilus and Bacillus cereus vegetative cells and spores. This study consisted of 981 …

Rapid Detection Of Analytes With Improved Selectivity Using Coated Microcantilever Chemical Sensors And Estimation Theory, Michael J. Wenzel, Fabien Josse Phd, Edwin E. Yaz, Stephen M. Heinrich, P. G. Datskos

Civil and Environmental Engineering Faculty Research and Publications

Rapid detection of analytes with improved selectivity is achieved though the use of estimation theory to analyze the response of polymer-coated microcantilever chemical sensors. In general, chemical sensors exhibit partial selectivity and can have relatively long response times. Using estimation theory, it is possible to make short-term response predictions from past data. This makes it possible to use the transient information (response time), often unique to an analyte/coating pair, to achieve an improvement in analyte species recognition while simultaneously allowing for a reduction in the time required for identification and quantification. An extended Kalman filter is used as a recursive …

Bioluminescence Imaging For Assessment And Normalization In Transfected Cell Arrays, Angela K. Pannier, Eric A. Ariazi, Abigail D. Bellis, Zain Bengali, V. Craig Jordan, Lonnie D. Shea

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Transfected cell arrays (TCAs) represent a high-throughput technique to correlate gene expression with functional cell responses. Despite advances in TCAs, improvements are needed for the widespread application of this technology. We have developed a TCA that combines a two-plasmid system and dual-bioluminescence imaging to quantitatively normalize for variability in transfection and increase sensitivity. The two-plasmids consist of: (i) normalization plasmid present within each spot, and (ii) functional plasmid that varies between spots, responsible for the functional endpoint of the array. Bioluminescence imaging of dual-luciferase reporters (renilla, firefly luciferase) provides sensitive and quantitative detection of cellular response, with minimal post-transfection processing. …

Neighborhood Defined Adaboost Based Mixture Of Color Components For Efficient Skin Segmentation, Ramya Reddy Maaram

Electrical & Computer Engineering Theses & Dissertations

A skin segmentation algorithm robust to illumination changes and skin-like backgrounds is developed in this thesis. So far skin pixel classification has been limited to only individual color spaces and there has not been a comprehensive evaluation of which color components or combination of color components would provide the best classification accuracy, Color components in a given color space form the feature set for the classification of skin pixels. The combination of the color components or the features present within a single color space may not be the best when it comes to skin pixel classification as the discriminatory power …

Microfabrication Of An Optical Chamber For Exposing Living Cells To Pulsed Electric Fields, Saleh Sheikh

Electrical & Computer Engineering Theses & Dissertations

I have fabricated a chamber which enables the application of Nanosecond Pulsed Electric Fields (nsPEFs) to living cells while monitoring their real time fluorescence with an inverted microscope. The No. I thickness (150µm nominal) coverslip glass substrate used for fabrication allows the use of high numerical aperture oil immersion objectives for imaging intracellular organelles. Electrodes are fabricated by first evaporating a chromium adhesion layer, followed by a nickel seed layer. Subsequently, an ultra-thick positive photoresist is applied and patterned to create a 30µm thick electroplating mold. The electrodes are then electrodeposited into the mold from a nickel sulfamate plating bath. …

Electroactive Polymers (Eap): Simulation Studies Of The Actuation Mechanisms In A Cantilever Cellulose Electroactive Paper, Fatim A. Mbaye

Electrical & Computer Engineering Theses & Dissertations

Electroactive polymers (EAPs) exhibit large strain in response to an external electric field and have attracted a great deal of attention in recent years for sensor and actuator applications. Favorable properties include soft actuation, ease and simplicity in manufacturing, being light-weight, low power consumption, and the ability to withstand harsh environments. However, this is an emerging material, and several aspects, including the fundamental mechanisms for piezoelectric deflections, remain unclear. This project studies the internal electromechanical factors that contribute to the voltage induced deflections of electro-active paper (EAPap). Experimental measurements of bias dependent deflections and water absorption as a function of …

Parmela Based Simulations On Jefferson Lab Free Electron Laser Injector, Deepesh Kumar Koppunuru

Electrical & Computer Engineering Theses & Dissertations

Free Electron Lasers (FELs) have many applications and are under continuing development to meet various needs and in areas from materials processing to life sciences research. This is because of its unique capability of generating high-average power, coherent, and wavelength tunable light by employing relativistic beam of un-bounded electrons. The main challenge in FEL development is the generation of a high intensity, high-quality electron beam in an injector. Further acceleration to relativistic energies is accomplished in a linear accelerator (LINAC) for producing laser light in a device known as wiggler. The Jefferson Lab FEL team intents to increase the injector …

Stochastic Optimization Formulations For Structure Design, Shivanandini Tanuku

Mechanical & Aerospace Engineering Theses & Dissertations

The production process and the operational environment of a product usually involve many unpredictable elements, such as the manufacturing tolerance, the service loads, the maintenance schedule, etc. Furthermore, the targeted functionality of a product can also be alternated or enhanced in its service life due to the technology advancement, new demands, or new regulation. It is thus a challenge to a designer to include these uncertainties in the early design stage of a product.

This thesis uses a simple three-bar truss problem as a vehicle to investigate the qualities of the optimal solutions resulted from various stochastic programming formulations. The …

Chronic Hypoxia-Induced Pulmonary Hypertension Does/Does Not Lead To Loss Of Pulmonary Vasculature, Marlene Rabinovitch, Naomi Chesler, Robert C. Molthen

Biomedical Engineering Faculty Research and Publications

No abstract provided.

A Pulse-Based Feature Extractor For Spike Sorting Neural Signals, Christy L. Rogers, John G. Harris, Jose C. Principe, Justin C. Sanchez

Electrical and Computer Engineering Faculty Research & Creative Works

Spike sorting is often required for analyzing neural recordings to isolate the activity of single neurons. Wave shape analysis in the spike sorting procedure provides a means to detect spikes while minimizing the influence of false alarms. As neural recording techniques allow for recording hundreds of electrodes, power is too limited in neural implants for current spike sorting algorithms. Even with spike sorting at the back end where more power is available, the bandwidth is too limited to transmit enough information for current spike sorting techniques. A low-power pulse-based feature extractor presented in the paper is a solution to the …

Wireless, In Vivo Neural Recording Using A Custom Integrated Bioamplifier And The Pico System, David Cheney, Aik Goh, Jie Xu, Karl Gugel, John G. Harris, Justin C. Sanchez, Jose C. Principe

Electrical and Computer Engineering Faculty Research & Creative Works

This paper describes a wireless system for sampling multiple channels of neural activity based on a low-power, custom 80dB-gain integrated bio amplifier, Texas Instrument's MSP430 microprocessors, and Nordic Semiconductor's ultra-low power, high bandwidth RF transmitter/receivers. The system's features are presented as well as results of spike potentials from a live subject. © 2007 IEEE.

Effect Of Hydrofluoric Acid In Oxidizing Acid Mixtures On The Hydroxylation Of Silicon Surface, Sanjukta Guhathakurta, Anuradha Subramanian

Anuradha Subramanian Publications

Silicon (100) wafers, predipped in 1:20 (v/v) HF water, were treated separately with four different acid mixtures, viz., HNO₃, H₂SO₄–H₂O₂, HNO₂–HF, and H₂SO₄–H₂O₂–HF, for different time durations. Subsequent vigorous rinsing with deionized water rendered the wafer surfaces with hydroxyl termination. Synthesized surfaces were characterized by diffuse-reflectance infrared Fourier transform spectroscopy (DRIFTS), ellipsometry, contact angle and atomic force microscopy. Surfaces treated with HN0₃ and H₂SO₂–H₂O₂ showed increasing hydrophilicity at room temperature due to …