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The Santa Clara, 2024-10-11, Santa Clara University

The Santa Clara

No abstract provided.

Predictive Mathematical Model For Polyhydroxybutyrate Synthesis In Escherichia Coli, Angela Dixon

Engineering Datasets

Polyhydroxybutyrate has been studied as a potential biodegradable replacement for petrochemical plastics. Polyhydroxybutyrate synthesis is not native to Escherichia coli, but the genes have successfully been inserted through plasmids. However, polyhydroxybutyrate production needs to be more cost-effective before it can be commercially produced. A mathematical model for polyhydroxybutyrate synthesis was developed to identify genes that could be altered to increase polyhydroxybutyrate production. The major metabolic pathways included in the model were glycolysis, acetyl coenzyme-A synthesis, tricarboxylic acid cycle, glyoxylate bypass, and polyhydroxybutyrate synthesis. Reactions were modeled using kinetic mechanisms identified for each enzyme. The transcriptional network was incorporated into the …

Integrating Science And Policy: A Case Study Of The Hubbard Brook Research Foundation Science Links Program, Charles T. Driscoll, Kathy Fallon Lambert, Kathleen C. Weathers

Civil and Environmental Engineering - All Scholarship

Scientists, related professionals, and the public have for decades called for greater interaction among scientists, policymakers, and the media to address contemporary environmental challenges. Practical examples of effective “real-world” programs designed to catalyze interactions and provide relevant science are few. Existing successful models can be used, however, to develop and expand the work of integrating, synthesizing, and communicating ecosystem science for environmental policy and natural-resource management. We provide an overview of the structure and strategies used in the Hubbard Brook Research Foundation Science Links program, now in its thirteenth year as a successful boundary-spanning organization. We detail project activities and …

Development And Prototyping Of A Ground Fault Circuit Interrupter For 3-Phase 480 Volt Systems, Matthew R. Norlander

Master's Theses

Ground Fault Circuit Interrupter (GFCI) technology was first introduced in the NEC in 1971, yet four decades later the technology has not been introduced to a great extent outside of the home environment. This thesis introduces the difficulties encountered in low-voltage three phase ground fault current detection, and adopts a previously patented tripping scheme to develop and prototype a digital relay for 3-phase 480 volt systems capable of the sensitivity and speed required for personnel safety. Results demonstrate the feasibility of the concept and suggest commercial development should be pursued. The prototype is capable of mA sensitivity and reliably detects …

Nebraska Blueprint – Fall/Winter 2011

Nebraska Blueprint (Student Publication)

Table of Contents:

From the Editor

Engi-Briefs

Dean Tim Wei and the Future of Nebraska Engineering

Researching Safety on the Highway – "Cody S. Stolle, a graduate research assistant at UNL's Midwest Roadside Safety Facility, recently conducted research on cable median wires to reduce the number of deadly car highway accidents."

Husker Alum Returns – Dr. Kim Blair, Mechanical Engineering alumnus, spoke as part of the Pierson Lecture Series on innovation and technology development.

Engineering Off the Road – UNL's Baja SAE [Society of Automotive Engineers] team placed 3rd in suspension and traction, 7th in tractor pull, 11th in maneuverability, …

Role Of Ammonia In The Activiation Of Methanol Dehydrogenase/Cytochrome C(L) Enzyme, Ancy Kunjumon

Doctoral Dissertations

Recent advancement in enzyme catalysis has opened ways to design efficient biocatalysts, bio-sensors and bio-fuel cells. An in-depth knowledge about the mechanism of the reaction taking place within the enzymes is of great importance to achieve these goals. In this dissertation, various computation methods are applied to investigate the mechanism behind enzyme catalysis in the presence of compounds called activators.

Methanol dehydrogenase (MDH) is a well-known bio-catalyst that can oxidize excess of methanol from the environment to formaldehyde. The enzyme works well within the bacterial environment, but under in vitro, it loses activity. Ammonia is used as an activator …

Passive Micromixers And Organic Electrochemical Transistors For Biosensor Applications, Senaka Krishna Kanakamedala

Doctoral Dissertations

Fluid handling at the microscale has greatly affected different fields such as biomedical, pharmaceutical, biochemical engineering and environmental monitoring due to its reduced reagent consumption, portability, high throughput, lower hardware cost and shorter analysis time compared to large devices. The challenges associated with mixing of fluids in microscale enabled us in designing, simulating, fabricating and characterizing various micromixers on silicon and flexible polyester substrates. The mixing efficiency was evaluated by injecting the fluids through the two inlets and collecting the sample at outlet. The images collected from the microscope were analyzed, and the absorbance of the color product at the …

Green Residential Stormwater Management Demonstration: An Integrated Stormwater Management And Graywater System To Reduce The Quantity And Improve The Quality Of Residential Water Discharges, Post Co Data Analysis, Ni-Bin Chang, Martin Wanielista, Manoj Chopra, Mike Hardin, Matthew Allen Goolsby

BMP Trains Research and Publications

No abstract provided.

Nitrogen Transport And Transformation Beneath Stormwater Retention Basins In Karst Areas And Effectiveness Of Stormwater Best Management Practices For Reducing Nitrate Leaching To Ground Water In Marion County, Florida, Stormwater Academy

BMP Trains Research and Publications

No abstract provided.

Polymorphic Structures Of Alzheimer's Beta-Amyloid Globulomers, Jie Zheng

Chemical, Biomolecular, and Corrosion Engineering Faculty Research

Misfolding and self-assembly of Amyloid-β (Aβ) peptides into amyloid fibrils is pathologically linked to the development of Alzheimer's disease. Polymorphic Aβ structures derived from monomers to intermediate oligomers, protofilaments, and mature fibrils have been often observed in solution. Some aggregates are on-pathway species to amyloid fibrils, while the others are off-pathway species that do not evolve into amyloid fibrils. Both on-pathway and off-pathway species could be biologically relevant species. But, the lack of atomic-level structural information for these Aβ species leads to the difficulty in the understanding of their biological roles in amyloid toxicity and amyloid formation.

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.

The Bridge Newsletter Winter 2011, Missouri University Of Science And Technology

The Bridge Newsletter

-Living intentionally: Meet the Oerthers
-Making a lasting impact
-Phytoforensics
-The simple things of life

Tertiary-Treated Municipal Wastewater Is A Significant Point Source Of Antibiotic Resistance Genes Into Duluth-Superior Harbor, Patrick J. Mcnamara, Tucker R. Burch, Timothy M. Lapara, David T. Tan, Mi Yan, Jessica J. Eichmiller

Civil and Environmental Engineering Faculty Research and Publications

In this study, the impact of tertiary-treated municipal wastewater on the quantity of several antibiotic resistance determinants in Duluth-Superior Harbor was investigated by collecting surface water and sediment samples from 13 locations in Duluth-Superior Harbor, the St. Louis River, and Lake Superior. Quantitative PCR (qPCR) was used to target three different genes encoding resistance to tetracycline (tet(A), tet(X), and tet(W)), the gene encoding the integrase of class 1 integrons (intI1), and total bacterial abundance (16S rRNA genes) as well as total and human fecal contamination levels (16S rRNA genes specific to the genus Bacteroides …

Climate Change Policy Could Make Keystone Xl Obsolete, Adam Liska

Adam Liska Papers

Clearly the Keystone XL pipeline threatens both surface and ground water that sustains the agricultural economy of Nebraska, but the projected profitability of tar sands oil and the pipeline operation are dependent on the future economics of climate change. Three recent scientific studies estimate the total carbon intensity of tar sands-based gasoline from Alberta (from both production and burning of the fuel) at an average of roughly 22 percent higher than U.S. gasoline in 2005, with the range of average carbon intensities for tar sands-gasoline at 16 to 27 percent higher than most other sources.

Bilateral Assessment Of Functional Tasks For Robot-Assisted Therapy Applications, Michelle J. Johnson, Sarah Wang, Ping Bai, Elaine Strachota, Guennady Tchekanov, Jeff Melbye, John Mcguire

Biomedical Engineering Faculty Research and Publications

This article presents a novel evaluation system along with methods to evaluate bilateral coordination of arm function on activities of daily living tasks before and after robot-assisted therapy. An affordable bilateral assessment system (BiAS) consisting of two mini-passive measuring units modeled as three degree of freedom robots is described. The process for evaluating functional tasks using the BiAS is presented and we demonstrate its ability to measure wrist kinematic trajectories. Three metrics, phase difference, movement overlap, and task completion time, are used to evaluate the BiAS system on a bilateral symmetric (bi-drink) and a bilateral asymmetric (bi-pour) functional task. Wrist …

Region-Of-Interest Material Decomposition From Truncated Energy-Resolved Ct, Taly Gilat Schmidt

Biomedical Engineering Faculty Research and Publications

Purpose: Energy-resolved CT using photon-counting detectors has the potential to provide improved material decomposition compared to dual-kVp approaches. However, available photon-counting detectors are susceptible to pulse-pileup artifacts, especially at the periphery of the field of view (FOV) where the object attenuation is low compared to the center of the FOV. Pulse pileup may be avoided by imaging a region-of-interest (ROI) where the dynamic range is expected to be limited. This work investigated performing material decomposition and reconstructing ROI basis images from truncated energy-resolved data.

Methods: A method is proposed to reconstructimages of basis functions primarily contained within the ROI, such …

A Compressed Sensing Algorithm For Sparse-View Pinhole Single Photon Emission Computed Tomography, Paul Arthur Wolf, Emil Y. Sidky, Taly Gilat Schmidt

Biomedical Engineering Faculty Research and Publications

Single Photon Emission Computed Tomography (SPECT) systems are being developed with multiple cameras and without gantry rotation to provide rapid dynamic acquisitions. However, the resulting data is angularly undersampled, due to the limited number of views. We propose a novel reconstruction algorithm for sparse-view SPECT based on Compressed Sensing (CS) theory. The algorithm models Poisson noise by modifying the Iterative Hard Thresholding algorithm to minimize the Kullback-Leibler (KL) distance by gradient descent. Because the underlying objects of SPECT images are expected to be smooth, a discrete wavelet transform (DWT) using an orthogonal spline wavelet kernel is used as the sparsifying …

A Fixed Robotic Mars Base Architecture, Christie Angunette Alston

Mechanical & Aerospace Engineering Theses & Dissertations

This thesis proposes a fixed Mars base architecture consisting of the following interconnected elements: landing area, power generation, in-situ resource utilization (ISRU), robotic repair and assembly, and a scientific research laboratoiy. The base architecture that has been put forward can be expanded readily to include future elements such as a sustainable human habitat. The base architecture approach was developed assuming that serial Earth-launched lander missions were too expensive and too slow going forward in effecting the systematic exploration of a planet whose surface area constitutes nearly the same area as the land mass of Earth. The fixed base architecture facilitates …

Architecture For A Flexible And Scalable Simulation Engine, Robert C. Holcomb Jr.

Computational Modeling & Simulation Engineering Theses & Dissertations

Simulation is used by many different industries to gain insight on actions and decisions that may be too dangerous or costly to perform in reality. Although the use of computers to assist with modeling and simulation has been studied for quite a while, computer infrastructure, hardware, and capabilities are changing at a rapid pace. Computer software once written is difficult and costly to change, especially in order to take advantage of the advances in computer hardware. This thesis focuses on the design and implementation of a software simulation architecture that allows flexibility in the modeling conducted and scalability in the …

A Survey Of Techniques And Challenges In Underwater Localization, Hwee-Pink Tan, Roee Diamant, Winston K. G. Seah, Marc Waldmeyer

Research Collection School Of Computing and Information Systems

Underwater Wireless Sensor Networks (UWSNs) are expected to support a variety of civilian and military applications. Sensed data can only be interpreted meaningfully when referenced to the location of the sensor, making localization an important problem. While global positioning system (GPS) receivers are commonly used in terrestrial WSNs to achieve this, this is infeasible in UWSNs as GPS signals do not propagate through water. Acoustic communications is the most promising mode of communication underwater. However, underwater acoustic channels are characterized by harsh physical layer conditions with low bandwidth, high propagation delay and high bit error rate. Moreover, the variable speed …

Comparison Of Four Chip-Seq Analytical Algorithms Using Rice Endosperm H3k27 Trimethylation Profiling Data., Brandon M. Malone, Feng Tan, Susan M. Bridges, Zhaohua Peng

BCoE Publications

Chromatin immunoprecipitation coupled with high throughput DNA Sequencing (ChIP-Seq) has emerged as a powerful tool for genome wide profiling of the binding sites of proteins associated with DNA such as histones and transcription factors. However, no peak calling program has gained consensus acceptance by the scientific community as the preferred tool for ChIP-Seq data analysis. Analyzing the large data sets generated by ChIP-Seq studies remains highly challenging for most molecular biology laboratories.Here we profile H3K27me3 enrichment sites in rice young endosperm using the ChIP-Seq approach and analyze the data using four peak calling algorithms (FindPeaks, PeakSeq, USeq, and MACS). Comparison …

Stage-Dependent Transient Storage Of Phosphorus In Alluvial Floodplains, Derek M. Heeren, Garey A. Fox, Ronald B. Miller, Daniel E. Storm, Amanda K. Fox, Chad J. Penn, Todd Halihan, Aaron R. Mittelstet

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Models for contaminant transport in streams commonly idealize transient storage as a well-mixed but immobile system. These transient storage models capture rapid (near-stream) hyporheic storage and transport, but do not account for large-scale, stage-dependent interaction with the alluvial aquifer. The objective of this research was to document transient storage of phosphorus (P) in coarse gravel alluvium potentially influenced by large-scale, stage-dependent preferential flow pathways (PFPs). Long-term monitoring was performed at floodplain sites adjacent to the Barren Fork Creek and Honey Creek in northeastern Oklahoma. Based on results from subsurface electrical resistivity mapping which was correlated to hydraulic conductivity data, observation …

High Ethanol Titers From Cellulose By Using Metabolically Engineered Thermophilic, Anaerobic Microbes, D. Aaron Argyros, Shital A. Tripathi, Trisha F. Barrett, Stephen R. Rogers, Lawrence F. Feinberg, Daniel G. Olson, Justin M. Foden, Bethany B. Miller, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

This work describes novel genetic tools for use in Clostridium thermocellum that allow creation of unmarked mutations while using a replicating plasmid. The strategy employed counter-selections developed from the native C. thermocellum hpt gene and the Thermoanaerobacterium saccharolyticum tdk gene and was used to delete the genes for both lactate dehydrogenase (Ldh) and phosphotransacetylase (Pta). The Δldh Δpta mutant was evolved for 2,000 h, resulting in a stable strain with 40:1 ethanol selectivity and a 4.2-fold increase in ethanol yield over the wild-type strain. Ethanol production from cellulose was investigated with an engineered coculture of organic acid-deficient engineered strains of …

A Comparison Of Finite State Classifier And Mahalanobis-Taguchi System For Multivariate Pattern Recognition In Skin Cancer Detection, Elizabeth A. Cudney, Steven M. Corns

Engineering Management and Systems Engineering Faculty Research & Creative Works

This project presents two methods for image classification for the detection of malignant melanoma: The Mahalanobis-Taguchi System and Finite State Classifiers. the Mahalanobis-Taguchi System is a diagnosis and predictive method for analyzing patterns in multivariate cases, while Finite State Classifiers are a state-based machine learning technique. the goal of this study is to compare the ability of the Mahalanobis-Taguchi System and a Finite State Classifier to discriminate using small data sets. We examine the discriminant ability as a function of data set size using publicly available skin lesion image data. While analysis of the data shows a high degree of …

Cooperative Approaches Indicating To Capacity And Power Control For Ad Hoc Wireless Network, Liuju Wu, Maciej Jan Zawodniok

Electrical and Computer Engineering Faculty Research & Creative Works

In this paper, two integrated schemes for fair capacity allocation and power control for ad hoc wireless network are presented. the game theory approach is utilized to derive a collaborative update law. in the practical wireless network, a non-uniform distribution of nodes results in varying degree of interference among the network links or hops. Such varying mutual interference may lead to unfair allocation of bandwidth and result in network congestion. as a result, some links may become bottlenecks for the entire network. Hence, it is important to fairly allocate resources in the entire network. the proposed schemes aim to address …

Solving The Capacitated Vehicle Routing Problem With Environmental Criteria Based On Real Estimations In Road Transportation: A Case Study, Javier Faulin, Angel Juan, Fernando Lera, Scott Erwin Grasman

Engineering Management and Systems Engineering Faculty Research & Creative Works

One of the most important objectives in company logistics is the optimization of goods distribution considering the whole value chain. There are many algorithms to optimize the capacitated vehicle routing problems (CVRP) associated to problems of road transportation. the objective function of those problems usually involves distance, cost, number of vehicles, or profits, among others. in this contribution we also take into account environmental costs. Here, we want to manage environmental costs estimations based on surveys about road transportation crossing rural areas having valuable biological and natural stock. Thus, we develop some variants (AWEC) to traditional heuristic algorithms, such as …

Radiation Effects Basics For 7750, Robert J. Twiggs

Robert "Bob" Twiggs STEM Education Collection

A PowerPoint presentation created by Professor Bob Twiggs on "Radiation Effects Basics for 7750" on September 25, 2011.

Adaptive Control In Swarm Robotic Systems, Hanyi Dai

The Hilltop Review

Inspired by the collective behavior observed in natural insects, swarm robotics is a new approach in designing control algorithms for a large group of robots performing a certain task. In such robotic systems, an individual robot with only limited capabilities in terms of sensing, computation, and communication can adapt its own behavior so that a desired collective behavior emerges from the local interactions among robots and between robots and the environment. Swarm robotics has been the focus of increased attention recently because of the beneficial features demonstrated in such systems, such as higher group efficiency, robustness against the failures of …

The Effects Of Mental Training On Brain Computer Interface Performance With Distractions, John Larocco

Theses and Dissertations

The overall success of a brain computer interface (BCI) is largely dependent on the features used to make decisions. Noise in the electroencephalography (EEG) increases the difficulty of acquiring meaningful features. Previous literature suggests teaching subjects meditation and relaxation techniques may improve features relevant to BCI operation. The purpose of this study was to investigate performance on several cognitive protocols for both individuals who use meditation techniques and those who do not use these techniques. Both groups were given a motor imagery based BCI protocol, a P300 speller BCI, a verbal learning task, and an N-back test. No significant difference …

Accurate Estimation Of Isoform And Gene Expression Levels From Next Generation Sequencing Data, Marius Nicolae

Master's Theses

Massively parallel transcriptome sequencing is quickly replacing microarrays as the technology of choice for performing gene expression profiling due to its wider dynamic range and digital quantitation capabilities. However, accurate estimation of expression levels from sequencing data remains challenging due to the short read length delivered by current sequencing technologies and still poorly understood protocol- and technology-specific biases.

To date, two main transcriptome sequencing protocols have been proposed in the literature. The most commonly used one, referred to as RNA-Seq, generates short (single or paired) sequencing tags from the ends of randomly generated cDNA fragments. An alternative protocol, referred to …