Physical Sciences and Mathematics Commons^™

A Study Of Correlations Between The Definition And Application Of The Gene Ontology, Yuji Mo

Computer and Electronics Engineering: Dissertations, Theses, and Student Research

When using the Gene Ontology (GO), nucleotide and amino acid sequences are annotated by terms in a structured and controlled vocabulary organized into relational graphs. The usage of the vocabulary (GO terms) in the annotation of these sequences may diverge from the relations defined in the ontology. We measure the consistency of the use of GO terms by comparing GO's defined structure to the terms' application. To do this, we first use synthetic data with different characteristics to understand how these characteristics influence the correlation values determined by various similarity measures. Using these results as a baseline, we found that …

Water Quality Models For Stormwater Runoff In Two Lincoln, Nebraska Urban Watersheds, Jake Fisher

Department of Civil and Environmental Engineering: Dissertations, Theses, and Student Research

Water quality monitoring was conducted in two urban watersheds (Colonial Hills and Taylor Park) located in southeast Lincoln, NE over a three year period spanning from October 2008 through September 2011. In-line probes continuously measured for turbidity, conductivity, dissolved oxygen, and water temperature while other water quality constituents were analyzed for discrete water samples collected using grab and automatic sampling techniques. The water quality data was used to calculate event mean concentrations (EMCs) for sixteen storm events sampled over the duration of the project period. Three types of stormwater quality multiple linear regression models were developed for the estimation of …

Location Cheating: A Security Challenge To Location-Based Social Network Services, Mai Ren

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Location-based mobile social network services such as Foursquare and Gowalla have grown exponentially over the past several years. These location-based services utilize the geographical position to enrich user experiences in a variety of contexts, including location-based searching and location-based mobile advertising. To attract more users, the location-based mobile social network services provide real-world rewards to the user, when a user checks in at a certain venue or location. This gives incentives for users to cheat on their locations.

In this thesis, we investigate the threat of location cheating attacks, find the root cause of the vulnerability, and outline the possible …

Relational Neighborhood Inverse Consistency For Constraint Satisfaction: A Structure-Based Approach For Adjusting Consistency & Managing Propagation, Robert J. Woodward

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Freuder and Elfe [1996] introduced Neighborhood Inverse Consistency (NIC) as a local consistency property defined on the values in the variables' domains of a Constraint Satisfaction Problem (CSP). Debruyne and Bessiere [2011] showed that enforcing NIC on binary CSPs is ineffective on sparse graph and too costly on dense graphs. In this thesis, we propose Relational Neighborhood Inverse Consistency (RNIC), an extension of NIC defined as a local consistency property on the tuples of the relations of a CSP. We characterize RNIC for both binary and non-binary CSPs, and propose an algorithm for enforcing it whose complexity is bounded by …

Efficient Traffic Crash And Snow Complaint Gis System, Anthony B. Ngo

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

We describe the design and implementation of a traffic crash and snow complaint GIS system developed for the Lincoln Public Works department. We also describe a novel geocoding algorithm that was used to move data from the older Criminal Justice Information System, which is a relational database, to the new GIS system. In addition, we describe the implementation of several indexing algorithms that enable the system to efficiently answer rectangular range queries and queries about the relative locations of moving objects. Finally, in many applications (on-line analysis or mobile GIS), we need to execute spatial query efficiently (fast and small), …

Thermodynamics Of Magnetic Multilayers, Tathagata Mukherjee

Department of Physics and Astronomy: Dissertations, Theses, and Student Research

Our interest in thermodynamics of magnetic thin film heterostructure began by exploring the possibility to use magnetic nanostructures in the search for optimized magnetocaloric materials for potential room temperature refrigeration. In the present thesis magnetic thin film heterostructures are experimentally realized by Molecular Beam Epitaxy (MBE) and Pulsed Laser Deposition (PLD). Co/Cr and Fe/Cr superlattices were fabricated using mean-field theoretical concepts as guiding principles. The potential of artificial antiferromagnets for near room-temperature refrigeration is explored. Magnetocaloric properties are deduced from measurements of the temperature and field dependence of the magnetization of our samples. The effects of intra-plane and inter-plane exchange …

Domain Size And Structure In Exchange Coupled [Co/Pt]/Nio/[Co/Pt] Multilayers, Andrew G. Baruth, Shireen Adenwalla

Shireen Adenwalla Papers

We investigate the competing effects of interlayer exchange coupling and magnetostatic coupling in the magnetic heterostructure ([Co/Pt]/NiO/[Co/Pt]) with perpendicular magnetic anisotropy (PMA). This particular heterostructure is unique among coupled materials with PMA in directly exhibiting both ferromagnetic and antiferromagnetic coupling, oscillating between the two as a function of spacer layer thickness. By systematically tuning the coupling interactions via a wedge-shaped NiO spacer layer, we explore the energetics that dictate magnetic domain formation using high resolution magnetic force microscopy coupled with the magneto-optical Kerr effect. This technique probes the microscopic and macroscopic magnetic behavior as a continuous function of thickness and …

Classification For Mass Spectra And Comprehensive Two-Dimensional Chromatograms, Xue Tian

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Mass spectra contain characteristic information regarding the molecular structure and properties of compounds. The mass spectra of compounds from the same chemically related group are similar. Classification is one of the fundamental methodologies for analyzing mass spectral data. The primary goals of classification are to automatically group compounds based on their mass spectra, to find correlation between the properties of compounds and their mass spectra, and to provide a positive identification of unknown compounds.

This dissertation presents a new algorithm for the classification of mass spectra, the most similar neighbor with a probability-based spectrum similarity measure (MSN-PSSM). Experimental results demonstrate …

Molecular Dynamics Simulation Based On Hadoop Mapreduce, Chen He

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Molecular Dynamics (MD) simulation is a computationally intensive application used in multiple fields. It can exploit a distributed environment due to inherent computational parallelism. However, most of the existing implementations focus on performance enhancement. They may not provide fault-tolerance for every time-step.

MapReduce is a framework first proposed by Google for processing huge amounts of data in a distributed environment. The simplicity of the programming model and fault- tolerance for node failure during run-time make it very popular not only for commercial applications but also in scientific computing.

In this thesis, we develop a novel communication-free and each time-step fault- …

Real-Time Divisible Load Scheduling For Cluster Computing, Anwar Mamat

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Cluster computing has become an important paradigm for solving large-scale problems. However, as the size of a cluster increases, so does the complexity of resource management and maintenance. Therefore, automated performance control and re- source management are expected to play critical roles in sustaining the evolution of cluster computing. The current cluster scheduling practice is similar in sophistication to early supercomputer batch scheduling algorithms, and no consideration is given to desired quality-of-service (QoS) attributes. To fully avail the power of computational clusters, new scheduling algorithms that provides high performance, QoS assurance, fault-tolerance, energy savings and streamlined management of the cluster …

Identifying Changes In Climatic Trends And The Fingerprints Of Landuse And Landcover Changes In The High Plains Of The Usa, Denis Mutiibwa

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Human activities such as conversion of natural ecosystem to croplands and urban-centers, deforestation and afforestation impact biophysical properties of land surface such as albedo, energy balance, and surface roughness. Alterations in these properties affect the heat and moisture exchanges between the land surface and atmospheric boundary layer. The objectives of this research were; (i) to quantitatively identify the High plains’ regional climate change in temperatures over the period 1895 to 2006, (ii) detect the signatures of anthropogenic forcing of LULC changes on the regional climate change of the High Plains, and (iii) examine the trends in evolving regional latent heat …

A Reservation-Based Smart Parking System, Hongwei Wang

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

In metropolitan areas, parking management influences drivers search time and cost for parking spaces, parking revenue, and traffic congestion. The wide deployment of wireless parking meters with sensing and communications capabilities allows the parking authority to monitor the state of each parking space in real time and optimize the parking management.

In this thesis, we study state-of-the-art parking policies in smart parking systems, and show that the smart parking system needs to be "smarter". Our design goals of the smart parking systems include: (1) simplify the operations of parking systems, (2) improve drivers' satisfaction, (3) increase parking revenue, and (4) …

A Study On Facility Planning Using Discrete Event Simulation: Case Study Of A Grain Delivery Terminal., Sarah M. Asio

Department of Industrial and Management Systems Engineering: Dissertations, Theses, and Student Research

The application of traditional approaches to the design of efficient facilities can be tedious and time consuming when uncertainty and a number of constraints exist. Queuing models and mathematical programming techniques are not able to capture the complex interaction between resources, the environment and space constraints for dynamic stochastic processes. In the following study discrete event simulation is applied to the facility planning process for a grain delivery terminal. The discrete event simulation approach has been applied to studies such as capacity planning and facility layout for a gasoline station and evaluating the resource requirements for a manufacturing facility. To …

The Green, Blue And Grey Water Footprint Of Crops And Derived Crop Products, Mesfin Mekonnen, Arjen Y. Hoekstra

Daugherty Water for Food Global Institute: Faculty Publications

Abstract. This study quantifies the green, blue and grey water footprint of global crop production in a spatially-explicit way for the period 1996–2005. The assessment improves upon earlier research by taking a high-resolution approach, estimating the water footprint of 126 crops at a 5 by 5 arc minute grid. We have used a grid-based dynamic water balance model to calculate crop water use over time, with a time step of one day. The model takes into account the daily soil water balance and climatic conditions for each grid cell. In addition, the water pollution associated with the use of nitrogen …

Campus Grids: A Framework To Facilitate Resource Sharing, Derek J. Weitzel

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

It is common at research institutions to maintain multiple clusters. These might fulfill different needs and policies, or represent different owners or generations of hard- ware. Many of these clusters are under utilized while researchers at other departments may require these resources. This may be solved by linking clusters with grid mid- dleware. This thesis describes a distributed high throughput computing framework to link clusters without changing security or execution environments. The framework initially keeps jobs local to the submitter, overflowing if necessary to the campus, and regional grid. The framework is implemented spanning two campuses at the Holland Computing …

National Water Footprint Accounts: The Green, Blue And Grey Water Footprint Of Production And Consumption. Volume 1: Main Report, Mesfin Mekonnen, Arjen Y. Hoekstra

Daugherty Water for Food Global Institute: Faculty Publications

This study quantifies and maps the water footprints of nations from both a production and consumption perspective and estimates international virtual water flows and national and global water savings as a result of trade. The entire estimate includes a breakdown of water footprints, virtual water flows and water savings into their green, blue and grey components. The main finding of the study can be summarized as:

The global water footprint in the period 1996-2005 was 9087 Gm3/yr (74% green, 11% blue, 15% grey). Agricultural production contributes 92% to this total footprint.

About one fifth of the global water footprint relates …

National Water Footprint Accounts: The Green, Blue And Grey Water Footprint Of Production And Consumption. Volume 2: Appendices, Mesfin Mekonnen, Arjen Y. Hoekstra

Daugherty Water for Food Global Institute: Faculty Publications

Contents

Appendix I. The water footprint of national production (Mm³/yr)

Appendix II. Virtual-water flows related to trade in crop, animal and industrial products, per country (Mm³/yr)

Appendix III. International virtual-water flows per product category (Mm³/yr)

Appendix IV. National water saving related to trade in agricultural and industrial products per country (Mm³/yr)

Appendix V. Global water saving related to trade in agricultural and industrial products, per product (Mm³/yr)

Appendix VI. The average water footprint per ton of commodity per country, weighted based on origin (WF* in m³/ton)

Appendix VII. …

Protein Structure – Based Method For Identification Of Horizontal Gene Transfer In Bacteria, Swetha Billa

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Horizontal Gene Transfer is defined as the movement of genetic material from one strain of species to another. Bacteria, being an asexual organism were always believed to transfer genes vertically. But recent studies provide evidence that shows bacteria can also transfer genes horizontally.

HGT plays a major role in evolution and medicine. It is the major contributor in bacterial evolution, enabling species to acquire genes to adapt to the new environments. Bacteria are also believed to develop drug resistance to antibiotics through the phenomenon of HGT. Therefore further study of HGT and its implications is necessary to understand the effects …

Ontology For Psychophysiological Dysregulation Of Anger/Aggression, Swathi Vasanthapuram

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

The advancement of Information Technology in the last four decades led to the use of computers in medicine. A new area called Medical Informatics has emerged. This area comprises the application of IT to healthcare with the aim of creating tools that help healthcare personnel diagnose and treat patients more accurately and efficiently. IT not only provides tools for storing, integrating, and updating patient information base but also for processing information efficiently. One of such tools is a Clinical Decision Support System. Ontologies are an integral part of clinical decision support systems because they help formalize and integrate domain knowledge. …

Understanding User Generated Content Characteristics : A Hot-Event Perspective, Miao Wang, Guodong Li, Jie Feng, Lisong Xu, Byrav Ramamurthy, Wei Li, Xiaohong Guan

CSE Conference and Workshop Papers

Nowadays, millions of Internet users watch and upload a large number of videos on User Generated Content (UGC) sites (e.g., Youtube) everyday. Moreover, online videos about hot events, such as breaking news and Olympic games, attract lots of users. In this paper, we study the characteristics of hot-event videos by collecting video traces of the largest UGC site in China for 28 days. We first empirically study statistical properties of such videos and find that hot-event videos contribute a large number of views, even though the total number of hotevent videos is relatively small. In addition, there exist extremely active …

Multi-Channel Peer-To-Peer Streaming Systems As Resource Allocation Problems, Miao Wang

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

In the past few years, the Internet has witnessed the success of Peer-to-Peer (P2P) streaming technology, which has attracted millions of users. More recently, commercial P2P streaming systems have begun to support multiple channels and a user in such systems is allowed to watch more than one channel at a time. We refer to such systems as multi-channel P2P streaming systems. In this dissertation, we focus on designing multi-channel P2P streaming systems with the goal of providing optimal streaming quality for all channels, termed as system-wide optimal streaming quality. Specifically, we design the systems from the perspective of how to …

Offline Optimization Of Advance Reservation Of Bandwidth Over Dynamic Circuit Networks, Pragatheeswaran Angu

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

E-science projects require very high-speed and reliable networks to transfer data across various destinations in the world. Dynamic Circuit Network (DCN) is a networking service to make advance reservation of bandwidth between a source and a destination in a network. In this thesis we solve the problem of advance reservation of bandwidth in next-generation wavelength-division multiplexing (WDM) networks using a simulation based approach.
We implement a greedy algorithm and a genetic algorithm in parallel, in separate threads. The request for advance reservation is processed by both but the user gets the response only from the greedy algorithm. The genetic algorithm …

Review Of A Dry Oasis: Institutional Adaptation To Climate On The Canadian Plains. Edited By Gregory P. Marchildon., Siân Mooney

Great Plains Research: A Journal of Natural and Social Sciences

A Dry Oasis examines past and potential future climate challenges on the Canadian Plains. The book provides extensive discussion, data, and analysis of challenges related to water supply and management within the South Saskatchewan River Basin (SSRB). Past challenges, experiences, and institutional responses are described and used to frame possible future adaptation pathways under expected future climate change. The book provides an excellent grounding in the historical settlement and development of the SSRB, paying particular attention to the ways that the economy, society, and institutions have adapted in response to climatic variability.

Estimation Of Land Surface Evapotranspiration With A Satellite Remote Sensing Procedure, Ayse Kilic, Ian Ratcliffe, Pariskhit Ranade, Kenneth Hubbard, Ramesh K. Singh, Babuarao Kamble, Jeppe Kjaersgaard

Great Plains Research: A Journal of Natural and Social Sciences

There are various methods available for estimating magnitude and trends of evapotranspiration. Bowen ratio energy balance system and eddy correlation techniques offer powerful alternatives for measuring land surface evapotranspiration. In spite of the elegance, high accuracy, and theoretical attractions of these techniques for measuring evapotranspiration, their practical use over large areas can be limited due to the number of sites needed and the related expense. Application of evapotranspiration mapping from satellite measurements can overcome the limitations. The objective of this study was to utilize the METRIC^TM (Mapping Evapotranspiration at High Resolution using Internalized Calibration) model in Great Plains environmental …

Polygonal Spatial Clustering, Deepti Joshi

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Clustering, the process of grouping together similar objects, is a fundamental task in data mining to help perform knowledge discovery in large datasets. With the growing number of sensor networks, geospatial satellites, global positioning devices, and human networks tremendous amounts of spatio-temporal data that measure the state of the planet Earth are being collected every day. This large amount of spatio-temporal data has increased the need for efficient spatial data mining techniques. Furthermore, most of the anthropogenic objects in space are represented using polygons, for example – counties, census tracts, and watersheds. Therefore, it is important to develop data mining …

Propeller: A Scalable Metadata Organization For A Versatile Searchable File System, Lei Xu, Hong Jiang, Xue Liu, Lei Tian, Yu Hua, Jian Hu

CSE Technical Reports

The exponentially increasing amount of data in file systems has made it increasingly important for users, administrators and applications to be able to fast retrieve files using file-search services, instead of replying on the standard file system API to traverse the hierarchical namespaces. The quality of the file-search services is significantly affected by the file-indexing overhead, the file-search performance and the accuracy of search results. Unfortunately, the existing file-search solutions either are so poorly scalable that their performance degrades unacceptably when the systems scale up, or incur so much crawling delays that they produce acceptably inaccurate results. We believe that …

Identifying Horizontal Gene Transfer Using Anomalies In Protein Structures And Sequences, Venkat Ram B. Santosh

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Genetics has traditionally focused on vertical gene transfer, which is the passing of the genetic material of an organism to its offspring. However, recent studies in genetics increased the awareness that horizontal gene transfer, which is the passing of the genetic material of an organism to another organism that is not its offspring, is also a significant phenomenon. Horizontal gene transfer is thought to play a major role in the natural evolution of bacteria, such as, when several different types of bacteria all suddenly develop the same drug resistance genes. Artificial horizontal gene transfer occurs in genetic engineering.

This thesis …

Meeting Reports: Research On Coupled Human And Natural Systems (Chans): Approach, Challenges, And Strategies, Marina Alberti, Heidi Asbjornsen, Lawrence A. Baker, Nicholas Brozovic, Laurie E. Drinkwater, Scott A. Drzyzga, Claire A. Jantz, José Fragoso, Daniel S. Holland, Timothy A. Kohler, Jianguo Liu, William J. Mcconnell, Herbert D.G. Maschner, James D.A. Millington, Michael Monticino, Guillermo Podestá, Robert Gilmore Pontius, Charles L. Redman, Nicholas J. Reo, David Sailor, Gerald Urquhart

Daugherty Water for Food Global Institute: Faculty Publications

Understanding the complexity of human–nature interactions is central to the quest for both human well-being and global sustainability. To build an understanding of these interactions, scientists, planners, resource managers, policymakers, and communities increasingly are collaborating across wide-ranging disciplines and knowledge domains. Scientists and others are generating new integrated knowledge on top of their requisite specialized knowledge to understand complex systems in order to solve pressing environmental and social problems (e.g., Carpenter et al. 2009). One approach to this sort of integration, bringing together detailed knowledge of various disciplines (e.g., social, economic, biological, and geophysical), has become known as the study …

The Water Footprint Assessment Manual: Setting The Global Standard, Arjen Y. Hoekstra, Ashok K. Chapagain, Maite M. Aldaya, Mesfin Mekonnen

Daugherty Water for Food Global Institute: Faculty Publications

This book contains the global standard for 'water footprint assessment' as developed and maintained by the Water Footprint Network (WFN). It covers a comprehensive set of definitions and methods for water footprint accounting. It shows how water footprints are calculated for individual processes and products, as well as for consumers, nations and businesses. It also includes methods for water footprint sustainability assessment and a library of water footprint response options. A shared standard on definitions and calculation methods is crucial given the rapidly growing interest in companies and governments to use water footprint accounts as a basis for formulating sustainable …

Diagnosis Of Multiple Scan-Chain Faults In The Presence Of System Logic Defects, Zhen Chen, Sharad C. Seth, Dong Xiang, Bhargab B. Bhattacharya

CSE Conference and Workshop Papers

We present a combined hardware-software based approach to scan-chain diagnosis, when the outcome of a test may be affected by system faults occurring in the logic outside of the scan chain. For the hardware component we adopt the double-tree scan (DTS) chain architecture, which has previously been shown to be effective in reducing power, volume, and application time of tests for stuck-at and delay faults. We develop a version of flush test which can resolve a multiple fault in a DTS chain to a small number of suspect candidates. Further resolution to a unique multiple fault is enabled by the …