Digital Commons Network^™

A Novel Correlation Networks Approach For The Identification Of Gene Targets, Kathryn Dempsey Cooper, Stephen Bonasera, Dhundy Raj Bastola, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Correlation networks are emerging as a powerful tool for modeling temporal mechanisms within the cell. Particularly useful in examining coexpression within microarray data, studies have determined that correlation networks follow a power law degree distribution and thus manifest properties such as the existence of “hub” nodes and semicliques that potentially correspond to critical cellular structures. Difficulty lies in filtering coincidental relationships from causative structures in these large, noise-heavy networks. As such, computational expenses and algorithm availability limit accurate comparison, making it difficult to identify changes between networks. In this vein, we present our work identifying temporal relationships from microarray data …

A Noise Reducing Sampling Approach For Uncovering Critical Properties In Large Scale Biological Networks, Karthik Duraisamy, Kathryn Dempsey Cooper, Hesham Ali, Sanjukta Bhowmick

Interdisciplinary Informatics Faculty Proceedings & Presentations

A correlation network is a graph-based representation of relationships among genes or gene products, such as proteins. The advent of high-throughput bioinformatics has resulted in the generation of volumes of data that require sophisticated in silico models, such as the correlation network, for in-depth analysis. Each element in our network represents expression levels of multiple samples of one gene and an edge connecting two nodes reflects the correlation level between the two corresponding genes in the network according to the Pearson correlation coefficient. Biological networks made in this manner are generally found to adhere to a scale-free structural nature, that …

An Evaluation Of The Usability Of A Computerized Decision Support System For Nursing Homes, M. Fossum, M. Ehnfors, Ann L. Fruhling, A. Ehrenberg

Interdisciplinary Informatics Faculty Publications

Background: Computerized decision support systems (CDSSs) have the potential to significantly improve the quality of nursing care of older people by enhancing the decision making of nursing personnel. Despite this potential, health care organizations have been slow to incorporate CDSSs into nursing home practices.

Objective: This study describes facilitators and barriers that impact the ability of nursing personnel to effectively use a clinical CDSS for planning and treating pressure ulcers (PUs) and malnutrition and for following the suggested risk assessment guidelines for the care of nursing home residents.

Methods: We employed a qualitative descriptive design using varied …

A Comparison Of Forensic Evidence Recovery: Techniques For A Windows Mobile Smart Phone, George Grispos, Tim Storer, William Bradley Glisson

Interdisciplinary Informatics Faculty Publications

Acquisition, decoding and presentation of information from mobile devices is complex and challenging. Device memory is usually integrated into the device, making isolation prior to recovery difficult. In addition, manufacturers have adopted a variety of file systems and formats complicating decoding and presentation.

A variety of tools and methods have been developed (both commercially and in the open source community) to assist mobile forensics investigators. However, it is unclear to what extent these tools can present a complete view of the information held on a mobile device, or the extent the results produced by different tools are consistent.

This paper …

Graduate Academic Catalog (2011-2012), University Of Nebraska At Omaha

Graduate Catalogs

For many, earning a graduate degree is a way to advance in a career, for others it's the next step toward a doctorate degree and for others it's the right thing to do. At the University of Nebraska at Omaha (UNO) you'll experience a university dedicated to being a leading resource for graduate study, one that offers the right learning environment focused on your success.

As a graduate student at UNO, you will have the opportunity to develop independent scholarship and gain greater competence in research and other applied activities. Rigor, combined with real-world experience and innovation help create a …

Trends In Phishing Attacks: Suggestions For Future Research, Ryan M. Schuetzler

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

Deception in computer-mediated communication is a widespread phenomenon. Cyber criminals are exploiting technological mediums to communicate with potential targets as these channels reduce both the deception cues and the risk of detection itself. A prevalent deception-based attack in computer-mediated communication is phishing. Prior phishing research has addressed the “bait” and “hook” components of phishing attacks, the human-computer interaction that takes place as users judge the veracity of phishing emails and websites, and the development of technologies that can aid users in identifying and rejecting these attacks. Despite the extant research on this topic, phishing attacks continue to be successful as …

Role Of Cloud Computing Interventions For Micro-Enterprise Growth: Implications For Global Development, Sajda Qureshi, Mehruz Kamal

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

While the majority of businesses around the world are micro-enterprises, they are the most vulnerable and are often run by people with limited resources, and skills to be able to avail the benefits of Information and Communication Technologies (ICTs). These are a form of small business which employs between 1-5 people and face challenges of limited resources, skills and ability to grow. When they do adopt IT their potential to survive and grow increases as they are then able to participate in the global economy. The challenge for global development lies in enabling these micro-enterprises to adopt the appropriate IT …

Overview And Guidance On Agile Development In Large Organizations, Jordan B. Barlow, Justin Scott Giboney, Mark Jeffrey Keith, David W. Wilson, Ryan Schuetzler, Paul Benjamin Lowry, Anthony Vance

Information Systems and Quantitative Analysis Faculty Publications

A continual debate surrounds the effectiveness of agile software development practices. Some organizations adopt agile practices to become more competitive, improve processes, and reduce costs. Other organizations are skeptical about whether agile development is beneficial. Large organizations face an additional challenge in integrating agile practices with existing standards and business processes. To examine the effects of agile development practices in large organizations, we review and integrate scientific literature and theory on agile software development. We further organize our theory and observations into a framework with guidelines for large organizations considering agile methodologies. Based on this framework, we present recommendations that …

Rigorous Assessment And Integration Of The Sequence And Structure Based Features To Predict Hot Spots, Ruoying Chen, Wenjing Chen, Sixiao Yang, Di Wu, Yong Wang, Yingjie Tian, Yong Shi

Information Systems and Quantitative Analysis Faculty Publications

Background

Systematic mutagenesis studies have shown that only a few interface residues termed hot spots contribute significantly to the binding free energy of protein-protein interactions. Therefore, hot spots prediction becomes increasingly important for well understanding the essence of proteins interactions and helping narrow down the search space for drug design. Currently many computational methods have been developed by proposing different features. However comparative assessment of these features and furthermore effective and accurate methods are still in pressing need.

Results

In this study, we first comprehensively collect the features to discriminate hot spots and non-hot spots and analyze their distributions. We …

Building Spaces To Grow New Ideas: Research 2011, University Office Of Research, South Dakota State University

State of Discovery South Dakota State University's Research Magazine

CONTENTS:

Feeding the World [Page] 2
A Light on New Possibilities [Page] 4
Designing New Tools [Page] 6
Wellness Science [Page] 8
Renovating a Science Resource [Page] 10
Connect World Possibilities [Page] 12
Transfer Research [Page] 14

“Down The Winding Stair”: Victorian Popular Science And Deep Time In “The Golden Key”, Geoffrey Reiter

North Wind: A Journal of George MacDonald Studies

No abstract provided.

How Much Does A Belief Cost?: Revisiting The Marketplace Of Ideas, Gregory Brazeal

Faculty Publications

No abstract provided.

On Noise-Enhanced Distributed Inference In The Presence Of Byzantines, Mukul Gagrani, Pranay Sharma, Satish Iyengar, Venkata Sriram Siddhardh Nadendla, Aditya Vempaty, Hao Chen, Pramod Varshney

Electrical Engineering and Computer Science - All Scholarship

This paper considers the noise-enhanced distributed detection problem in the presence of Byzantine (malicious) nodes by suitably adding stochastic resonance (SR) noise. We consider two metrics - the minimum number of Byzantines (\alpha_{blind}) needed to blind the fusion center as a security metric and the Kullback-Leibler divergence (D_{KL}) as a detection performance metric. We show that \alpha_{blind} increases when SR noise is added at the honest nodes. When Byzantines also start adding SR noise to their observations, we see no gain in terms of \alpha_{blind}. However, the detection performance of the network does improve with SR. We also consider a …

The Journal Of Undergraduate Research: Volume 09

The Journal of Undergraduate Research

This is the complete issue of the South Dakota State University Journal of Undergraduate Research, Volume 13.

The Impact Of A Fundamentals Of Speech Course On Public Speaking Anxiety, Jessica J. Colbeck

The Journal of Undergraduate Research

Thirty to forty percent of Americans suffer from Communication Apprehension (CA) to a degree that impairs their ability and willingness to speak publicly (McCroskey, 1984). McCroskey (1984) defines CA as “an individual’s level of fear or anxiety associated with either real or anticipated communication with another person(s)” (p.13). There are many forms of CA, but “the most common [form] is Public Speaking Anxiety” (McCourt, 2007, p.6), which can be defined as the fear of speaking in front of a group of people. Because research has shown that such fears may hinder career aspirations, personal relationships and self-image, scholarly examination of …

Vibrational Analysis Of An Electromechanical Toothbrush, Mark Wager

The Journal of Undergraduate Research

The effectiveness of an electromechanical toothbrush is based entirely on its ability to remove plaque through vibrations. This paper contests that the three-dimensional motion of more inexpensive models of electromechanical toothbrushes can be accurately modeled in one-dimension so as to predict the motion of future toothbrush designs using simply the material properties, motor specifications, and grip design. Vibrational modeling, mathematical modeling, and experimentation were used in the analysis to confirm the outcome of the study and the assumptions of the model.

Forecast, Winter 2010-2011, Illinois State University, College Of Applied Science And Technology

foreCAST

Magazine of the Illinois State University College of Applied Science and Technology

Evaporation Of Sessile Drops Under Combined Diffusion And Natural Convection, Peter Kelly-Zion, Christopher J. Purcell, Sawan Vaidya, Jaskirat Batra

Engineering Faculty Research

Experiments were conducted to investigate the range of applicability of a commonly used assumption for evaporation models of sessile drops, that the transport mechanism that controls the evaporation is vapor diffusion. The evaporation rates of sessile drops of 3-methylpentane, hexane, cyclohexane, and heptane were measured. The radius of the drop contact line was constant during the measurements and drops of radius from 1 mm to 22 mm were studied. It was found that a diffusion-controlled evaporation model underpredicts the evaporation rate from 36% to 80% depending on the drop size. The increase in the evaporation rate was attributed to a …

Understanding And Improving Lithium Ion Batteries Through Mathematical Modeling And Experiments, Rutooj D. Deshpande

Theses and Dissertations--Chemical and Materials Engineering

There is an intense, worldwide effort to develop durable lithium ion batteries with high energy and power densities for a wide range of applications, including electric and hybrid electric vehicles. For improvement of battery technology understanding the capacity fading mechanism in batteries is of utmost importance. Novel electrode material and improved electrode designs are needed for high energy- high power batteries with less capacity fading. Furthermore, for applications such as automotive applications, precise cycle-life prediction of batteries is necessary.

One of the critical challenges in advancing lithium ion battery technologies is fracture and decrepitation of the electrodes as a result …

Chemical Evolution And Residence Time Of Groundwater In The Wilcox Aquifer Of The Northern Gulf Coastal Plain, Estifanos Haile

Theses and Dissertations--Earth and Environmental Sciences

This study aims to integrate groundwater geochemistry and mathematical modeling to determine the dominant geochemical processes and groundwater residence time within the Wilcox aquifer in the northern Gulf Coastal Plain. Groundwater samples were collected and analyzed for major ion chemistry, stable isotopes (¹⁸O, ²H, and ¹³C), and radioisotope ³⁶Cl content. Geochemical modeling enabled the identification of major sources and sinks of solutes in the aquifer. A two-dimensional, finite-difference, numerical model was used to determine the deep groundwater flow rate and transport of ³⁶Cl in the aquifer. Major ion chemistry shows a chromatographic pattern along …

Arsenic Heterogeneity In Aquifer Sediments From West Bengal, India, Emily Eastridge

Theses and Dissertations--Earth and Environmental Sciences

Multiple studies in the Bengal basin have shown that elevated As in groundwater coincides with reduced, relatively dark sediments of Himalayan provenance. In West Bengal state (India), As concentrations > 10 μg/L tend to occur east of the River Bhagirathi-Hoogly, the main distributary of the Ganges. Associations among sediment chemistry and mineralogy for four cores from either side of the Bhagirathi-Hoogly (cores 1 and 2 to the east, 3 and 4 to the west) in Murshidabad district were investigated. Ten sediment samples were collected from each boring at various depths to a maximum of 38 to 43 m. Sediment chemistry was …

Locating Hot Spots Of Fecal Pollution In An Urban Watershed Of Central Kentucky Using Bacteroides 16s Rrna Markers, Tricia L. Coakley

Theses and Dissertations--Earth and Environmental Sciences

The field of molecular fecal source tracking in the water environment has developed rapidly since the first PCR assays for general and host-­‐specific Bacteroides 16s rRNA markers were published. Numerous host-­‐specific molecular markers and PCR assays have been developed, adding greater specificity, sensitivity and quantitative methods to the array of options. The public demand for readying methods for transfer to the commercial lab, so that they may be used to generate data for public utilities, citizen action groups and regulatory agencies, has fueled the development of an entire new research community. These methods, however plentiful, have not found community agreement …

Fabrication Of Mwcnt Based Gas Sensor Using Site-Selective Growth Of Nanotubes On Gold Patterned Silicon Oxide Substrate, Srikanth Durgamahanty

University of Kentucky Master's Theses

Growth confinement techniques for multi walled carbon nanotubes on Au/SiO₂ surfaces was studied and incorporated into a gas sensor design. A device framework was conceived and a sensor was built to achieve this structure. The fabrication results were analyzed using scanning electron microscopy which confirmed the achievement of highly site-selective growth of carbon nanotubes, exclusively between the interdigitated electrodes. The sensor was then evaluated for its capacitance and conductance response when exposed to NO₂ gas. Variation in sensitivities with frequency and flow rate were analyzed. A mathematical model was derived for such a device structure and the predictions …

Rotate And Hold And Scan (Rahas): Structured Light Illumination For Use In Remote Areas, Eli Ross Crane

University of Kentucky Master's Theses

As a critical step after the discovery of material culture in the field, archaeologists have a need to document these findings with a slew of different physical measurements and photographs from varying perspectives. 3-D imaging is becoming increasingly popular as the primary documenting method to replace the plethora of tests and measurements, but for remote areas 3-D becomes more cumbersome due to physical and environmental constraints. The difficulty of using a 3-D imaging system in such environments is drastically lessened while using the RAHAS technique, since it acquires scans untethered to a computer. The goal of this thesis is to …

Mathematical Modeling Of Clostridium Thermocellum’S Metabolic Responses To Environmental Perturbation, Bless Adotey

Theses and Dissertations--Biosystems and Agricultural Engineering

Clostridium thermocellum is a thermophilic anaerobe that is capable of producing ethanol directly from lignocellulosic compounds, however this organism suffers from low ethanol tolerance and low ethanol yields. In vivo mathematical modeling studies based on steady state traditional metabolic flux analysis, metabolic control analysis, transient and steady states’ flux spectrum analysis (FSA) were conducted on C. thermocellum’s central metabolism. The models were developed in Matrix Laboratory software ( MATLAB^® (The Language of Technical Computing), R2008b, Version 7.7.0.471)) based on known stoichiometry from C. thermocellum pathway and known physical constraints. Growth on cellobiose from Metabolic flux analysis (MFA) and Metabolic …

Parametric Estimation In Competing Risks And Multi-State Models, Yushun Lin

Theses and Dissertations--Statistics

The typical research of Alzheimer's disease includes a series of cognitive states. Multi-state models are often used to describe the history of disease evolvement. Competing risks models are a sub-category of multi-state models with one starting state and several absorbing states.

Analyses for competing risks data in medical papers frequently assume independent risks and evaluate covariate effects on these events by modeling distinct proportional hazards regression models for each event. Jeong and Fine (2007) proposed a parametric proportional sub-distribution hazard (SH) model for cumulative incidence functions (CIF) without assumptions about the dependence among the risks. We modified their model to …

Stochastic Dynamics Of Gene Transcription, Yan Xie

Theses and Dissertations--Statistics

Gene transcription in individual living cells is inevitably a stochastic and dynamic process. Little is known about how cells and organisms learn to balance the fidelity of transcriptional control and the stochasticity of transcription dynamics. In an effort to elucidate the contribution of environmental signals to this intricate balance, a Three State Model was recently proposed, and the transcription system was assumed to transit among three different functional states randomly.

In this work, we employ this model to demonstrate how the stochastic dynamics of gene transcription can be characterized by the three transition parameters. We compute the probability distribution of …

Mechanism And Kinetics Of Covalent Amide-Linked Adduct Formation In Solution And Solid Peptide Formulations, Michael Paul Dehart

Theses and Dissertations--Pharmacy

Peptides and proteins are prone to chemical and physical degradation in solutions and solids. One of the most common chemical degradation pathways involves deamidation of asparagine residues through a reactive succinimide intermediate resulting in the formation of aspartyl and isoaspartyl degradation products.

In this work, kinetic studies in aqueous solutions demonstrated that the succinimide intermediate is susceptible to attack by nucleophiles other than water. This may lead to a variety of alternative degradants. In solutions containing high concentrations of ammonia, the succinimide generated in the deamidation of the model peptides Phe-Asn-Gly and Phe-isoAsn-Gly underwent back-reaction with ammonia leading to peptide …

Profiling Executive Dysfunction In Adolescents With Autism, Nicole R. Rogers

PCOM Psychology Dissertations

Executive Functions (EF) have been assigned a causative role in a number of disorders, including schizophrenia, Tourette syndrome, autism, obsessive compulsive disorder, violent and criminal behavior, and nearly all learning disabilities. While the term executive functions in the professional literature easily yields more than 150 references, empirical research in which executive functions are studied and linked with specific disorders, such as autism, continues to help answer long-held questions about the disorder and adds to the literature base in order to better understand and treat the disorder. The purpose of this study was to review archival data collected using the Behavior …

Encyclopedia Of Snow, Ice And Glaciers, Vijay P. Singh, Pratap Singh, Umesh K. Haritashya

Department of Earth, Environment and Sustainability Faculty Publications

The objective of this encyclopedia is to present the current state of scientific understanding of various aspects of earth’s cryosphere – snow, glaciers, ice caps, ice sheets, ice shelves, sea ice, river and lake ice, and permafrost – and their related interdisciplinary connections under one umbrella. Therefore, every effort has been made to provide a comprehensive coverage of cryosphere by including a broad array of topics, such as the atmospheric processes responsible for snow formation; snowfall observations; snow cover and snow surveys; transformation of snow to ice and changes in their properties; classification of ice and glaciers and their worldwide …