Digital Commons Network^™

Parallelization Of A Maximum Parsimony Branch And Bound Algorithm For Phylogenetic Inference, Curtis J. Howard

Theses

Phyiogenetic inference involves the reconstruction of evolutionary relationships among species in the form of branching diagrams called trees. Specifically, certain biological structures common to all living organisms, such as morphological characteristics, protein sequences or DNA sequences can be compared Differences and similarities in these characteristics among species are used to reconstruct the evolutionary relationships and draw trees. Many methods of tree reconstruction are currently used. The method of maximum parsimony for phyiogenetic inference is a widely used algorithm which employs the hypothesis that the most likely tree for a given group of data will be the one which uses the …

The Relationship Between Emotional Recognition And Personality Traits, Lyndon A. Mitchell

Theses

This study investigated the relationship between personality traits and the ability to recognize emotions from facial expressions. A sample of undergraduate and graduate students (n = 52) were administered the 16 Personality Factor Questionnaire 5th Edition (16PF-5) (Cattell, 1993) and an abbreviated version of Ekman's Pictures of Facial Affect (Ekman & Friesen, 1976). Pearson product-moment correlations revealed that the personality trait, Apprehension, was associated with the accurate recognition of most of the emotions. Further, regression analyses revealed that the recognition of fear was best predicted by the 16PF factors Dominance, Self Reliance and Apprehension. Personality differences were also identified between …

Tissue Surface Identification For Microwave Imaging System Calibration, Surat Teerakapibal

Theses

The methods used for biomedical imaging include X-ray, magnetic resonance imaging (MRI), ultrasound, and most recently, microwave imaging each with its own advantages and disadvantages for specific application. The frequency dependent nature of the Electromagnetic (EM) waves makes it possible for microwave imaging to achieve a tissue differentiation comparable to that obtained by X-ray and would be superior to ultra sound and MRI.

This work addresses one aspect of an ongoing research effort at Rochester Institute of Technology which is a new methodology for detecting diseased tissues by a non-invasive procedure. The methodology is based on the extraction of the …

Ligevolver: A Tool For Ligand Formulation Using Genetic Algorithm, Priyadarsini Soundararajan

Theses

Human Immunodeficiency Virus type 1 (HIV - 1) has been found to be the cause of Acquired Immune Deficiency Syndrome (AIDS). This virus caused uproar during the 1980's and started a major drug discovery race among the pharmaceutical companies. It also proved to be a milestone in the establishment of the use of computers in rational drug design.

Evolutionary computation is a commonly used computational approach that has been successfully applied to a variety of fields ranging from engineering to life science. The main reason for its effectiveness is that it is driven by the principles of evolution. A genetic …

Analysis Of Effective Mechanical Properties Of Thin Films Used In Microelectromechanical Systems, Ajay Pasupuleti

Theses

This research aims at analyzing the effective mechanical properties of thin film materials that are used in MEMS. Using the effective mechanical properties, reliable simulations of new or slightly altered designs can be performed successfully. The main reason for investigating effective material properties of MEMS devices is that the existing techniques can not provide consistent prediction of the mechanical properties without time-consuming and costly physical prototyping if the device or the fabrication recipe is slightly altered. To achieve this goal, two approaches were investigated: soft computing and analytical. In the soft computing approach, the effective material properties are empirically modeled …

The Effectiveness Of Captive Release Conservation Methods For Spotted Turtles (Clemmys Guttata), Kate Cassim

Theses

The spotted turtle (Clemmys guttata) is categorized as protected and a species of special concern in New York State (Milam 2001). Understanding the habitat use, movement patterns, and life history characteristics of this species will be essential for any future efforts to provide the necessary habitat requirements for their successful recovery and management. Rochester Institute of Technology partnered with the Seneca Park Zoo and the New York Department of Environmental Conservation to investigate the release of captive-bred spotted turtles. The goal of this study was to determine the movements, habitat use, survivorship, and growth of the captive-bred spotted turtles in …

Family Tree Manager, Catherine Sullivan

Theses

Many people are interested in learning about their family history. Discovering who has come before us can help us learn more about who we are, and possibly why we are the way we are. Over the years, more and more people have turned to software products to help them build and manage their family tree information. These products allow users to easily enter and retrieve the information, as well as provide graphical representations without the arduous task of drawing by hand. In addition, some manufacturers have made agreements with genealogy search services, and integrated the process of searching for relatives …

Acoustic Classification Using Independent Component Analysis, James Brock

Theses

This thesis research investigates and demonstrates the feasibility of performing computationally efficient, high-dimensional acoustic classification using Mel-frequency cepstral coefficients and independent component analysis for temporal feature extraction. A process was developed to calculate Mel-frequency cepstral coefficients from samples of acoustic data grouped by either musical genre or spoken world language. Then independent component analysis was employed to extract the higher level temporal features of the coefficients in each class. These sets of unique independent features represent themes, or patterns, over time that are the underlying signals in that class of acoustic data. The results obtained from this process clearly show …

Metaheuristics And Combinatorial Optimization Problems, Gerald Skidmore

Theses

This thesis will use the traveling salesman problem (TSP) as a tool to help present and investigate several new techniques that improve the overall performance of genetic algorithms (GA). Improvements include a new parent selection algorithm, harem select, that outperforms all other parent selection algorithms tested, some by up to 600%. Other techniques investigated include population seeding, random restart, heuristic crossovers, and hybrid genetic algorithms, all of which posted improvements in the range of 1% up to 1100%. Also studied will be a new algorithm, GRASP, that is just starting to enjoy a lot of interest in the research community …

Molecular Viewer Using Spiegel, Pavani Baddepudi

Theses

Study of nucleic acids and proteins has evoked great interest for its role in research involving areas such as human genome and drug design. Understanding the core structure and behavior of these protein molecules requires reading and analyzing large amounts of data about atoms derived from a plethora of experiments. In recent years, computer graphics has gained popularity for its ability to translate these large datasets into three dimensional structures providing easy visualization. This project has implemented one such 3-D molecular viewer to display different models of molecules and study their properties. The project was developed in Java3D using the …

Genetic Music, Ryan Becker

Theses

Algorithmic music composition has long been an active area of research in computer science, but the need for a human element only recently began to be more widely acknowledged. Interactive Evolutionary Computing (IEC), made popular by Karl Sims, effectively solves many high dimension problems, like music composition, involving creative and subjective elements. This work applies several Genetic Algorithm (GA) and Genetic Programming (GP) approaches, inspired by Karl Sims, to algorithmic music composition. The implementation of these IEC algorithms is described and their effectiveness compared.

Faculty Scheduling Using Genetic Algorithms, Kevin Soule

Theses

The problem of developing a class schedule for a faculty has been proven to be NP-complete. Therefore when the schedule is large enough, finding just one feasible solution can be impossible for any direct search algorithm within a reasonable time. This project is geared toward investigating the possibility of using genetic-based algorithms to solve faculty scheduling problems of 100 courses or larger quickly. Multiple versions of genetic algorithms and heuristics are tested. Many parameter levels for these algorithms are optimized for fastest convergence.

An Evolutionary Computation Approach To Optimization Of Isoelectric Point Prediction In Proteins, Chris Parkin

Theses

Computational biology has attacked the problem of isoelectric point prediction with little success, achieving a rough accuracy level of only 30%. In 2005, Matthew Conte performed a study focused on the relationship between sequence characteristics and isoelectric point prediction accuracy. Results indicated that charges between adjacent amino acids could have a significant impact on the overall predicted pi for the protein. In this study we introduce an evolutionary computation approach aimed at accounting for these problem dipeptides. For each possible dipeptide involving charged amino acids (7 chargeable groups -> 49 possibilities), the algorithm predicts a pKa value that, when included …

Recovery From Crisis: Jordan Tourism Facing Political Instability, Rasha Hani Saoudi

Theses

This study outlines tourism crises facing international tourism to Jordan. The study also examines major efforts taken by the public and private sectors to recover from the loss of international tourism arrivals to the country caused mainly by the ongoing political crisis in the Middle East. A number of internal and external tourism challenges are identified based on the opinions of key stakeholders in the Jordanian tourism industry. Different approaches to crisis management, drawn from an overview of recovery marketing literature and studies, are also presented. The study concludes that the continuous cooperation and coordination of tourism stakeholders before, during, …

Shopping Motivations And Their Influence On Shopping Experience In Australia And Indonesia, Tjong Budisantoso

Theses

The main focus of this study is on motivation. In particular, the study aims to investigate the relationship between the in-store experience of shoppers and their motivation for shopping. The in-store experience as defined in this study includes the perception of store atmosphere and cognitive responses. Another interest of the study is to test the relationship between cognitive responses and store atmosphere in two different countries. Lastly, this study explores the relationship between in-store experience and store patronage satisfaction, which in turn can influence shoppers’ repatronage intention. All the hypotheses in this study have been tested in Perth, Australia and …

Assessment Of The Effectiveness Of Available Pollution Control Technologies In Reducing Phenol Level At Enoc Refinery Wastewater Treatment Plant, Waddah Shihab Ghanim Al Hashemi

Theses

Phenols are present in discharge effluents of many heavy industries such as refineries. They are regulated and monitored by environmental authorities. Emirates National Oil Company (ENOC) processes condensate oil and produces wastewater that is treated at the ENOC Processing Company's (EPCL-refinery) wastewater treatment plant (ETP) through the use of physical, chemical and biological treatment processes. This study provides an in-depth description of the unit processes employed to treat the different waste streams generated at the EPCL refinery and identifies the different types of phenols which are formulated in the processes. Characterization of phenol level at EPCL-ETP and assessment of the …

The Analysis And Characterisation Of Rotavirus And Norovirus Circulating In The South Of Ireland, Norma Reidy

Theses

On average more than 3,000 cases of rotavirus diarrhea are detected annually amongst Irish children less than 3 years of age. Rotavirus disease occurs mainly during the winter months, with peak infections detected from February to April. The symptoms of disease are diarrhea and dehydration, with 80% of patients requiring hospitalisation, The mean duration of hospitalisation is 3-4 days, with an average cost per day of €409. Eighteen percent of infections were detected in infants less than 6 months of age, suggesting inadequate maternal derived protection from existing strains, or the existence of novel strains in Ireland with little or …

The Development Of Functional Food Ingredients From Yeast Cell Wall Beta Glucans, Susan Keogh

Theses

The intracellular contents of spent yeast can be used to produce flavours and flavour enhancers. However there still remains after this process, a significant quantity of cell wall material, which makes up 20-25% of the dry weight of yeast biomass. A major component of the yeast cell wall is the polysaccharide P-glucan. This project involved the investigation of the extraction and characterisation of p-glucan as well as its evaluation as a functional food ingredient. A preparation of spent yeast p-glucan was obtained from two types of spent yeast species, Saccharomyces cervisiae (brewers yeast) and Kluyveromyces marxianus (dairy yeast) obtained from …

A Biologically Plausible System For Detecting Saliency In Video, David Burlone

Theses

Neuroscientists and cognitive scientists credit the dorsal and ventral pathways for the capability of detecting both still salient and motion salient objects. In this work, a framework is developed to explore potential models of still and motion saliency and is an extension of the original VENUS system. The early visual pathway is modeled by using Independent Component Analysis to learn a set of Gabor-like receptive fields similar to those found in the mammalian visual pathway. These spatial receptive fields form a set of 2D basis feature matrices, which are used to decompose complex visual stimuli into their spatial components. A …

Proteomic Studies Of Pseudomonas Putida Kt2440 In Carcinogenicity Screening Via 2-Dimensional Gel Electrophoresis, Mingyi Yao

Theses

This project is part of a pilot study designed to establish a two dimensional gel electrophoresis-based protocol, which can be utilized in screening mutagencity/carcinogencity of uncharacterized substances. Currently, the Ames test is the most commonly used method, which is solely based on mutation at the genome level. In contrast to the genome, which is static, protein expression in a cell under a given set of conditions (the proteome) is dynamic. A screening method based on the proteome rather than the genome may prove more reliable and quantitative in predicting mutagenicity and carcinogenicity. In this project, Pseudomonas putida KT2440 was employed …

The Environmental Gradients And Plant Communities Of Bergen Swamp, N.Y., U.S.A., Aaron Hall

Theses

No survey of plant communities has been performed recently in the Bergen Swamp, NY, USA, a unique strongly minerotrophic mire with active marl deposition. In summer 2004, I established an array of randomly placed plots throughout Bergen Swamp survey plant communities. The plant survey included stem counts of herbaceous plant species and shrubs within 1m square quadrats. I performed a Raup and Crick clustering analysis at two different spatial scales to group plant communities and found that there were five communities at the subplot level, and three communities at the plot level. I then used detrended correspondence analysis (DCA), an …

Expert Object Recognition In Video, Matthew S. Mceuen

Theses

A recent computer vision technique for object classification in still images is the biologically-inspired Expert Object Recognition (EOR). This thesis adapts and extends the EOR approach for use with segmented video data. Properties of this data, such as segmentation masks and the visibility of an object over multiple frames, are exploited to decrease human supervision and increase accuracy. Several types of runtime learning are facilitated: class-level learning in which object types that are not included in the training set are given artificial classes; viewpoint-level learning in which novel views of training objects are associated with existing classes; and instance-level learning …

Teaching Strategies, Learning Strategies, And Communication In The Mainstream Biology Classroom. A Study Of The Perspective Of Deaf Students, Denise Lengyel

Theses

This qualitative pilot research study explores the perceptions of deaf students who are a minority in the mainstream college classroom. It focuses upon the effectiveness of teaching and learning strategies used in the biology classroom, and how communication with hearing peers affects the deaf student's ability to learn in the classroom. Through questionnaires and interviews, participants provided insight on their experiences in the mainstream biology setting. Through research articles and interview responses, suggestions for effective teaching, learning, and communication were constructed and are provided to benefit all in the education profession.

The Quality Of Textbooks Used In Science Education: A Study Of Four Schools Serving Deaf Students, Matthew Boyd

Theses

Over the years, science achievement scores in the United States have been declining despite the movement towards reforming science and math education. A review of the literature reveals that the issue of the quality of textbooks used in science education is not often mentioned. In this paper, the author evaluates the quality of textbooks used in science education in four schools and discusses the findings relative to curriculum reform. Two Public and two Deaf Residential schools were surveyed, one each respectively, from the state of New York and Pennsylvania. Only the books used in 11th- 12th grade science classes were …

The Methods Of Teaching Deaf Children With Add And Adhd Disorders: The Applications And The Implications, Tasha Goodrich

Theses

The project will be focused on the exploration of the ways that the teachers use to deal with the deaf students that struggle with an additional disability in form of Attention Deficit Disorder. The teaching and learning strategies will be studied in order to determine the success rate, if any, by implementing the goals and results produced by the methods and the objectives associated with the lessons being taught at the time and to determine the willingness of the educators in working with such said disabilities. The experiences of the deaf students with the disorders will be documented as to …

Guidelines For Parents On Homeschooling Deaf Children, Kalpana Varia

Theses

Many families have turned their family room into classrooms. In 1993, homeschooling became legal in all 50 states, when the number of students staying at home for schooling tripled. This trend continues today because parents want to retain control over the education and socialization of their children. Homeschooling refers to education of school-age children with their parents' guiding, directing, and monitoring them. It replaces full-time attendance at a traditional school. Parents express various reasons for educating their children at home; individualization, family time, strong academic, moral, and religious foundations. The problem with homeschooling, for parents of deaf children, is the …

A Structured And Personalized Listening Program For Deaf And Hard Of Hearing High School Students: A Curriculum Development Project, Susan Bregman

Theses

There are many different kinds of auditory training programs available for use by children who are deaf or hard of hearing. However, there are only a few that are appropriate to be used by high school students and even fewer still that relate to the student's academic courses. An auditory training curriculum for deaf and hard of hearing high school students was developed relating to a New York State regents course in biology using the CardMaster 2020 from Califone. Fifteen key vocabulary words from three biology units were chosen for use in this curriculum. Five of these fifteen words were …

A Study Of Multimedia In An Environmental Science Course, Matthew Stefano

Theses

This study examined the use of sign movies, content movies, and adjunct questions in an instructional unit for Deaf students taking an environmental science course. Pre and post tests of factual recall as well as an attitude measure were administered to detennine if web-based technology benefits Deaf students taking environmental science courses. The results indicate that deaf students learning through web-based technology benefit from embedded American Sign Language explanations and questions as adjunct instructional aids. Implications of using webbased technology are discussed for science teachers having deaf students in their classes.

Characteristics Of Schools For The Deaf That Offer Comprehensive Science Programs: A Descriptive Profile, Patrick Freivald

Theses

Studies documenting the state of science education for deaf students are two decades old. However, these studies give insight into many of the reasons that science education is lacking in so many areas. The present study examined the differences in characteristics between schools for the deaf that offer higher level sciences such as chemistry and physics and schools for the deaf that do not. To this end, a survey was distributed to a sample of schools for the deaf in New York and Pennsylvania in an attempt to identify these differences. The primary finding of this study is that the …

A Proteomic Study Of Pseudomonas Putida By Two-Dimensional Gel Electrophoresis: Establishing Quantitative Standards For Intra-Laboratory Results, Kelly Fowlkes

Theses

Two-dimensional gel electrophoresis (2DE) is the most commonly employed technique in the field of proteomics. The technique is designed to separate thousands proteins in highly complex biological samples. It is largely because of the diversity of the sample that 2DE has encountered problems with reproducibility. This study was designed to address and alleviate many of these problems and also to establish quantitative standards for intra-laboratory results. A universal standard gel of Pseudomonas putida KT2440 was created and tested. The universal standard gel will serve as an intra-laboratory reference to which future experiments will be compared. An acceptable coefficient of variation …