Digital Commons Network^™

Improving The Performance Of Promol By Integrating Communal Database Access, Alexander Grier

Theses

The ability of structural genomics consortia to determine protein structures more quickly than the proteins can be functionally annotated by conventional experimental means has generated a significant bottleneck that inhibits the progress of certain areas of biological and medical research. This issue is currently being addressed in part by the development of computational resources, which can suggest functions for proteins of interest based on their structure. ProMOL is such a resource, and the method that it employs is based on detecting, in structures of unknown function, motifs of known function from a template library. Access to ProMOL results has been …

The Transverse Musculocutaneous Gracilis Flap For Breast Reconstruction Educational Illustration Series, Ryan Steenberg

Theses

Advancements in medicine have allowed surgeons a menu of options in post-mastectomy breast reconstruction. A conundrum exists, however, in flap selection when faced with varying patient body types. In the case of the athletic patient who does not have the appropriate amount of donor site tissue to warrant a Transverse Rectus Abdominus Musculocutaneuos Flap (TRAM) the Transverse Musculocutaneous Gracilis Flap (TMG) is an appropriate alternative due to its functional and aesthetic benefits. An intricate and timely process, the TMG procedure can be difficult to understand for the layperson. Therefore, a need for a condensed and standardized description exists. By breaking …

Libdetector: Version Identification Of Libraries In Android Applications, Zhihao Mike Chi

Theses

In the Android ecosystem today, code is often reused by developers in the form of software libraries. This practice not only saves time, but also reduces the complexity of software development. However, like all other software, software libraries are prone to bugs, design flaws, and security vulnerabilities. They too undergo incremental updates to not only add/change features, but also to address their flaws. Unfortunately, the knowledge gap between consumers and maintainers of software libraries presents a barrier to the timely adoption of important library updates.

Therefore we present LibDetector, a tool for identifying the specific version of Java libraries used …

Hyperspectral Vehicle Brdf Learning: An Exploration Of Vehicle Re Ectance Variation And Optimal Measures Of Spectral Similarity For Vehicle Reacquisition And Tracking Algorithms, Joseph Svejkosky

Theses

The spectral signatures of vehicles in hyperspectral imagery exhibit temporal variations due to the preponderance of surfaces with material properties that display non-Lambertian bi-directional reflectance distribution functions (BRDFs). These temporal variations are caused by changing illumination conditions, changing sun-target-sensor geometry, changing road surface properties, and changing vehicle orientations. To quantify these variations and determine their relative importance in a sub-pixel vehicle reacquisition and tracking scenario, a hyperspectral vehicle BRDF sampling experiment was conducted in which four vehicles were rotated at different orientations and imaged over a six-hour period. The hyperspectral imagery was calibrated using novel in-scene methods and converted to …

The Realization And Study Of Optical Wings, Alexandra Brae Artusio-Glimpse

Theses

Consider the airfoil: a carefully designed structure capable of stable lift in a uniform air flow. It so happens that air pressure and radiation (light) pressure are similar phenomena because each transfer momentum to flow-disturbing objects. This, then, begs the question: does an optical analogue to the airfoil exist? Though an exceedingly small effect, scientists harness radiation pressure in a wide gamut of applications from micromanipulation of single biological particles to the propulsion of large spacecrafts called solar sails. We introduce a cambered, refractive rod that is subjected to optical forces analogous to those seen in aerodynamics, and I call …

An Empirical Demonstration Of The Probabilistic Upper Bound Of The Adaptive Boosting Test Error, Paige Houston

Theses

Statistical machine learning uses data to model a relationship between many parameters, or explanatory variables, and a response variable. The adaptive boosting algorithm is a machine learning method that can be used to model relationships of classification data. This method uses a weak base learner to improve accuracy of predicting the correct response class from a set of variables. Because of its learnability, adaptive boosting yields an exponentially decreasing empirical error. From this, an empirical error bound can be derived from the boosting algorithm. This empirical error bound inspires us to see if there is a generalized error bound and …

Electronic Cigarette Topography: A Quantitative Validation Study Of The Wireless Personal Use Monitor, Karina Roundtree

Theses

Background: Electronic cigarettes are battery powered nicotine vaporizers built with a heating element that atomizes an e-liquid solution. Studies have been conducted to understand user nicotine exposure however, replicating realistic use patterns, puff topography, is necessary to conduct accurate emissions studies. Previous studies have been conducted in the laboratory environment using the CReSS Micro System however, this instrument has limitations making it impractical to measure natural use behavior. The Wireless Personal Use Monitor (wPUM), developed at RIT can overcome the CReSS limitations to capture usage behavior in the natural environment. The wPUM was deployed in 2015 to measure the usage …

The Opportunity: A 3d Animation About Karma, Mark J. Reisch

Theses

The Opportunity is a three dimensional animation that illustrates the idea that by helping others you can inadvertently help yourself. The story is told using an animated sunflower, bees, tulip, and farmer. In a sunflower garden, a sunflower tries to entice a bee to pollinate it, but a tulip (that is not supposed to be in the sunflower garden) attracts all of the bees. The tulip sees the farmer coming to weed out any unwanted plants. Seeing the fear in the tulip’s eyes, the sunflower helps disguise the tulip. The farmer is tricked and the tulip is saved. With the …

Investigating The Role Of Anaerobic Bacteria In Colorectal Carcinoma, Oluwadara Coker

Theses

Colorectal cancer (CRC), with multifactorial influences of genetic, molecular, inflammatory, and environmental factors, is a leading cause of cancer-related deaths. Due to the high diversity and concentration of microbes found in the human colon, the microbiome has become a prime suspect of being a biological contributor. This prompts the need to investigate the relationship between microorganisms and CRC. Recent studies have shown that Fusobacterium nucleatum, Campylobacter showae, Leptrotrichia buccalis, and Selenomonas sputigena are overrepresented in colon tumors. These anaerobes have known associations to the oral microbiome and cause infections. Here, these findings are further expanded in an experimental attempt to …

Detection Of Anomalous Vehicle Loading, Troy Mckay

Theses

Determining the mass of a vehicle from ground based passive sensor data is important for many security and traffic safety reasons. A vehicle consists of multiple dependent and independent systems that each respond differently to changes in vehicle mass. In some cases, the responses of these vehicle systems can be measured remotely. If these remotely sensed system responses are correlated to the vehicle's mass, and the required vehicle parameters were known, it would be possible to calculate the mass of the vehicle as a function of these responses.

The research described here investigates multiple vehicle phenomenologies and their correlation to …

Identifying The Presence Of Known Vulnerabilities In The Versions Of A Software Project, Craig Cabrey

Theses

As the world continues to embrace a completely digital society in all aspects of life, the ever present threat of a security flaw in a software system looms. Especially with a stream of high profile security flaws and breaches, the public is more aware of the risk now than ever before.

However, the realities of any software project is that there are engineering concerns of the utmost importance that all demand simultaneous attention. To balance and manage these challenges, software engineering has developed patterns of industry activities and best practices. Yet even as engineers rely on these practices to stay …

Humberto: The Fire Next Time, John David Fournie

Theses

“The Fire Next Time” is the opening section of a novel, Humberto, that tells the story of a group of people working at a biomedical engineering firm in St. Louis. The section follows Charles, a well-respected employee and leader whose marriage is slowly disintegrating. In the first chapter, a larger-than-life employee, the Priest, joins the company. He befriends Charles while working closely with him. The Priest, however, begins an affair with Charles’ wife, Linda. Charles is put in a difficult position: how should he work with a man he both hates and admires? As Charles struggles with this dilemma, a …

An Empirical Study On Code Comprehension: Dci Compared To Oo, Hector A. Valdecantos

Theses

Comprehension of source code affects software development, especially its maintenance where reading code is the most time consuming performed activity. A programming paradigm imposes a style of arranging the source code that is aligned with a way of thinking toward a computable solution. Then, a programming paradigm with a programming language represents an important factor for source code comprehension. Object-Oriented (OO) is the dominant paradigm today. Although, it was criticized from its beginning and recently an alternative has been proposed. In an OO source code, system functions cannot escape outside the definition of classes and their descriptions live inside multiple …

Evaluating The Relationship Between Derived Relational Responding, Verbal Operant Development, And Linguistic Structure: Correlating The Peak-E-Pa, The Ablls-R, And The Told-I:4, Bridget Munoz

Theses

The increasing prevalence of Autism Spectrum Disorder has produced a longstanding relevance for continued progressive measures towards a systematic approach to the treatment of deficient language repertoires. Current behavior analytic assessments, such as the Assessment of Basic Language and Learning Skills-Revised (ABLLS-R), have demonstrated utility in providing relative measures of the functional characteristics of an individual’s language and learner repertoire, as consistent with a traditional Skinnerian approach. Further assessments have been created under other existing theoretical frameworks, such as the Test of Language Development (TOLD), and the Promoting the Emergence of Advanced Knowledge Relational Training System (PEAK). Each assessment was …

Characterization And Reduction Of Noise In Manifold Representations Of Hyperspectral Imagery, Can Jin

Theses

A new workflow to produce dimensionality reduced manifold coordinates based on the improvements of landmark Isometric Mapping (ISOMAP) algorithms using local spectral models is proposed. Manifold space from nonlinear dimensionality reduction better addresses the nonlinearity of the hyperspectral data and often has better per- formance comparing to the results of linear methods such as Minimum Noise Fraction (MNF). The dissertation mainly focuses on using adaptive local spectral models to fur- ther improve the performance of ISOMAP algorithms by addressing local noise issues and perform guided landmark selection and nearest neighborhood construction in local spectral subsets. This work could benefit the …

Bayesian Inference With Combined Dynamic And Sparsity Models: Application In 3d Electrophysiological Imaging, Jingjia Xu

Theses

Data-driven inference is widely encountered in various scientific domains to convert the observed measurements into information that cannot be directly observed about a system. Despite the quickly-developing sensor and imaging technologies, in many domains, data collection remains an expensive endeavor due to financial and physical constraints. To overcome the limits in data and to reduce the demand on expensive data collection, it is important to incorporate prior information in order to place the data-driven inference in a domain-relevant context and to improve its accuracy.

Two sources of assumptions have been used successfully in many inverse problem applications. One is the …

Learning For Cross-Layer Resource Allocation In The Framework Of Cognitive Wireless Networks, Wenbo Wang

Theses

The framework of cognitive wireless networks is expected to endow wireless devices with a cognition-intelligence ability with which they can efficiently learn and respond to the dynamic wireless environment. In this dissertation, we focus on the problem of developing cognitive network control mechanisms without knowing in advance an accurate network model. We study a series of cross-layer resource allocation problems in cognitive wireless networks. Based on model-free learning, optimization and game theory, we propose a framework of self-organized, adaptive strategy learning for wireless devices to (implicitly) build the understanding of the network dynamics through trial-and-error.

The work of this dissertation …

Modelling Of Information Flow And Resource Utilization In The Edge Distributed Web System, Bryan Thomas Meyers

Theses

The adoption of Distributed Web Systems (DWS) into modern engineering design process has dramatically increased in recent years. The Engineering Design Guide and Environment (EDGE) is one such DWS, intended to provide an integrated set of tools for use in the development of new products and services. Previous attempts to improve the efficiency and scalability of DWS focused largely on hardware utilization (i.e. multithreading and virtualization) and software scalability (i.e. load balancing and cloud services). However, these techniques are often limited to analysis of the computational complexity of the algorithms implemented.

This work seeks to improve the understanding of efficiency …

Deadly Pleasure, Chunhui Bao

Theses

In this work, a girl’s father is one of the victims in the mass political persecution by Emperor Yongzheng, 18 A.D., and he is killed in front of his family. The Emperor is present during his murder and he notices the girl and her gorgeous, long hair. Because of this the girl survives the massacre of her entire family and is sent away and trained to become a concubine. It becomes the goal of the girl to work hard to become a chosen concubine by the Emperor so she can avenge the murder of her family with her gorgeous, magical …

Scent Of Geranium, Naghmeh Farzaneh

Theses

“Scent of Geranium” is an animated graduate thesis film, with a runtime of 4 minutes and 41 seconds. This film is a completion of an unfinished project from 2011, the year that I immigrated to the United States of America, called “The Whole World Is Watching”. Scent of Geranium is an autobiography about the challenges, fears, unexpected events and adaptation process that I experienced after my immigration. This film captures a series of memories and events that were significant to me and that have affected me in a certain way.

This film is a full color, hand-drawn animation that was …

Regulation Of Star Formation Amidst Heating And Cooling In Galaxies And Galaxy Clusters, Sravani Vaddi

Theses

Galaxy clusters are the largest gravitationally bound systems in the Universe and often host the largest galaxies (known as the brightest cluster galaxies (BCG)) at its centers. These BCG’s are embedded in hot 1-10 keV X-ray gas. A subset of galaxy clusters known as cool-core clusters show sharply peaked X-ray emission and high central densities, demonstrating cooling of the surrounding halo gas in timescales much shorter than a Hubble time. These observations led to the development of a simple cooling flow model. In the absence of an external heating process, a cooling flow model predicts that the hot intracluster medium …

Bioclimatic Design For Global Projects: The Case Of Maranatha One-Day Church, Cibele Eller Rodrigues

Theses

Bioclimatic design is an effective architectural approach for creating environmentally responsive buildings, improving comfort and quality of life for its users while using fewer resources. However, globalization of construction strategies and standardized systems are often applied to various locations without considering the specificity of each climate and site. Thus, working contrary to bioclimatic premises and reducing the overall building performance. This work analyzes the case of the One-Day Church (ODC) global project from Maranatha Volunteers International (MVI), which consists of building churches around the world using a standard roof and frame kit, and local materials. It proposes design improvements for …

Joint Source-Channel Coding Optimized On End-To-End Distortion For Multimedia Source, Ebrahim Jarvis

Theses

In order to achieve high efficiency, multimedia source coding usually relies on the use of predictive coding. While more efficient, source coding based on predictive coding has been considered to be more sensitive to errors during communication. With the current volume and importance of multimedia communication, minimizing the overall distortion during communication over an error-prone channel is critical. In addition, for real-time scenarios, it is necessary to consider additional constraints such as fix and small delay for a given bit rate. To comply with these requirements, we seek an efficient joint source-channel coding scheme.

In this work, end-to-end distortion is …

The Effect Of Directing Attention Externally Toward A Visible Or Imagined Object, Masahiro Yamada

Theses

Utilization of an external focus of attention has been proved to be beneficial in the motor learning literature. When people focus on the effects of the movement (i.e., external focus of attention), the motor skill is enhanced compared to directing attention to the body movements (i.e., internal focus of attention). Previous studies that have examined the effect of focus of attention on learning a motor skill often used visible or imagined objects to elicit an external focus of attention. However, the effects of these different types of external focus instruction have not been investigated thoroughly. It was unclear prior to …

Macro And Micro Skills In Second Language Academic Writing: A Study Of Vietnamese Learners Of English, Ha Thi Thanh Nguyen

Theses

The ability to write in a second language is one of the major skills required in academic settings. However, research about the effectiveness of academic programs on second language writing in long term perspective is rather scarce and the findings are mixed (e.g. Archibald, 2001; Elder & O’Loughlin, 2003; Hu, 2007; Knoch et al., 2014, 2015; Storch 2007). The present study aimed to contribute further empirical evidence about the effectiveness of academic training on the development of the writing skills of Vietnamese second language learners enrolled in an undergraduate English program. The investigation was designed in view of the L2 …

Characterizing The Transient Profile Shapes And Deposition Patterns Of Desiccating Colloidal Droplets, Marcette Sapphira Greyson

Theses

As a droplet containing colloidal material dries on a surface, the suspended particles are deposited onto it. Aqueous colloidal droplets often leave the majority of particles at the periphery of the deposition area. This phenomenon is known as the coffee ring effect, and it arises when a radially outward evaporative flows dominates within a droplet as it dries. This deposition non-uniformity can impact a diverse range of applications. In medical diagnostic testing, it can introduce uncertainty into microarray test results, while in inkjet printing it can produce finer printed circuitry. Controlling colloidal deposition could allow for higher-quality medical diagnostics and …

A Thermosiphon Loop For High Heat Flux Removal Using Flow Boiling Of Ethanol In Open Microchannel Manifold (Omm) With Taper, Sanskar S. Panse

Theses

Open Microchannel Manifold (OMM) with taper has proved instrumental in enhancing heat transfer performance in flow boiling while keep the pressure drop to a minimum. This makes it applicable in developing a low pressure drop system like a thermosiphon loop. To this end, a gravity-driven flow boiling system developed earlier was tested at low flow rates using ethanol. Based on the pressure drop and heat transfer data, a two-phase thermosiphon loop with a small ethanol head below 0.2 m was developed and tested with OMM configuration. A maximum heat flux of 136 W/cm2 was recorded at a wall superheat of …

Modeling The Radar Return Of Powerlines Using An Incremental Length Diffraction Coefficient Approach, Douglas Macdonald

Theses

A method for modeling the signal from cables and powerlines in Synthetic Aperture Radar (SAR) imagery is presented. Powerline detection using radar is an active area of research. Accurately identifing the location of powerlines in a scene can be used to aid pilots of low flying aircraft in collision avoidance, or map the electrical infrastructure of an area. The focus of this research was on the forward modeling problem of generating the powerline SAR signal from first principles. Previous work on simulating SAR imagery involved methods that ranged from efficient but insufficiently accurate, depending on the application, to more exact …

Gaze Guidance, Task-Based Eye Movement Prediction, And Real-World Task Inference Using Eye Tracking, Srinivas Sridharan

Theses

The ability to predict and guide viewer attention has important applications in computer graphics, image understanding, object detection, visual search and training. Human eye movements provide insight into the cognitive processes involved in task performance and there has been extensive research on what factors guide viewer attention in a scene. It has been shown, for example, that saliency in the image, scene context, and task at hand play significant roles in guiding attention.

This dissertation presents and discusses research on visual attention with specific focus on the use of subtle visual cues to guide viewer gaze and the development of …

Understanding The Impact Of Diversity In Software Bugs On Bug Prediction Models, Harold Valdivia-Garcia

Theses

Nowadays, software systems are essential for businesses, users and society. At the same time such systems are growing both in complexity and size. In this context, developing high-quality software is a challenging and expensive activity for the software industry. Since software organizations are always limited by their budget, personnel and time, it is not a trivial task to allocate testing and code-review resources to areas that require the most attention. To overcome the above problem, researchers have developed software bug prediction models that can help practitioners to predict the most bug-prone software entities. Although, software bug prediction is a very …