Physical Sciences and Mathematics Commons^™

Knowledge Discovery And Modeling In Genomic Databases, Michael M. Yin

Dissertations

This dissertation research is targeted toward developing effective and accurate methods for identifying gene structures in the genomes of high eukaryotes, such as vertebrate organisms. Several effective hidden Markov models (HMMs) are developed to represent the consensus and degeneracy features of the functional sites including protein-translation start sites, mRNA splicing junction donor and acceptor sites in vertebrate genes. The HMM system based on the developed models is fully trained using an expectation maximization (EM) algorithm and the system performance is evaluated using a 10-way cross-validation method. Experimental results show that the proposed HMM system achieves high sensitivity and specificity in …

Intramural, Collaborative Learning Systems, Robert S. Friedman

Theses

This thesis focuses on three related concepts: problem-based collaborative learning; the use of multimedia tools in learning systems; and participatory design as a software engineering methodology to create multimedia tools to be used in learning systems. A literature review of the three areas is followed by an overview of the pedagogical, technological, and business trends that affect the direction of innovation in education, including problem-based learning. A discussion of a software engineering project to develop a multimedia application that enhances the learning of geography skills and puts the programming, interface design and multimedia systems capabilities of college students into action …

Statistical Image Analysis Of Spotted Arrays, Filippo Posta

Theses

There is a lot of systematic and specific variability in microarray experiments, this variability affects measured gene expression levels, leading to unreliable gene profiling or an heavy load of extra experiment to statistically confirm the data observed in one experiment.

The aim of this work is to systematically analyze, using statistics, the image derived from a cDNA microarray experiment to have a better understanding of this variability and thus a better confidence over the data obtained from an experiment.

Using technologies available at the Center for Applied Genomics, Newark, New Jersey. Selected images derived from different type of microarray experiments …

An Algorithm For Estimating The Quality Of Microarrays, Ajeet S. Sodhi

Theses

Microarray technology is currently one of the most valuable gene expression tools in molecular biology allowing the experimenter to simultaneously quantify the expression of thousands of genes. It is also one of the most difficult tools to use accurately as each microarray produces a large amount of information that needs to be inspected and normalized before analysis. As the size of a microarray or number of replicates increase, the use of manual inspection becomes impractical. The aim of this thesis is to introduce an algorithm that evaluates each feature of a microarray from the scanned data file. A quality score …

Development And Characterization Of Methodology And Technology For The Alignment Of Fmri Time Series, Carlo Ciulla

Dissertations

This dissertation has developed, implemented and tested a novel computer based system (AUTOALIGN) that incorporates an algorithm for the alignment of functional Magnetic Resonance Image (fMRI) time series. The algorithm assumes the human brain to be a rigid body and computes a head coordinate system on the basis of three reference points that lie on the directions correspondent to two of the eigenvectors of inertia of the volume, at the intersections with the head boundary. The eigenvectors are found weighting the inertia components with the voxel's intensity values assumed as mass. The three reference points are found in the same …

Collaborative Problem Solving And Program Development Model, Joanna Defranco-Tommarello

Dissertations

A model to enhance collaborative problem solving and program development is presented. The collaborative model is a detailed cognitive model that takes into consideration the cognitive and social activities that occur during collaborative problem solving and program development. The cognitive activities required for collaborative problem solving and program development are identified and integrated into a six-stage model. An extensive literature review in the associated fields is presented to show the need for the model described in this dissertation. In addition, a comprehensive study of tools to support collaboration during problem solving and program development was also performed as well as …

An Evolving Approach To Learning In Problem Solving And Program Development : The Distributed Learning Model, Idania Espinosa

Theses

Technological advances are paving the way for improvements in many sectors of society. The US education system needs to undergo a transformation of existing pedagogical methods to maximize utilization of new technologies. Traditional education has primarily been teacher driven, lectured-based in one location. Advances in technology are challenging existing paradigms by developing tools and educational environments that reach diverse learning styles and surpass the boundaries of current teaching methods.

Distributed learning is an emerging paradigm today that has promise to contribute significantly to learning and improve overall academic success. This research first explores various systems that provide different modes of …

Simulation And Close-To-Optimal Algorithm For The Static Load Balancing Of A Network Of Heterogeneous Processors, Mark G. Steiner

Theses

A close-to-optimal linear programming-based algorithm for the static load balancing of a network of heterogeneous processors is described and implemented. Experimental results suggest that the amount of time required by the implementation of the algorithm to balance the loads of the servers as a function of the number of servers has polynomial complexity.

Comparative Molecular Field Analysis (Comfa) Of Protonated Methylphenidate Phenyl-Substituted Analogs, Kathleen Mary Gilbert

Theses

Protonated methylphenidate (pMP) and several phenyl-substituted pMP analogs were analyzed using Comparative Molecular Field Analysis (CoMFA) to develop a pharmacophore for dopamine transporter (DAT) binding. This research is a part of an interdisciplinary study on using methylphenidate (MP) analogs to block the binding of cocaine to the DAT as a treatment for addiction.

A random search conformational analysis using key pMP torsional angles was performed to create conformer families representing possible bioactive conformations. The lowest energy pMP conformer of each family was used as a template to create phenyl-substituted pMP analogs.

Partial least squares analysis was used to determine the …

A Tool For Phylogenetic Data Cleaning And Searching, Viswanath Neelavalli

Theses

Data collection and cleaning is a very important part of an elaborate Data Mining System. 'TreeBASE' is a relational database of phylogenetic information at the Harvard University with a keyword based searching interface. 'TreeSearch' is a Structure based search engine implemented at NJIT that can be used for searching phylogenetic data. Phylogenetic trees are extracted from the flat-file database at Harvard University, available at {ftp://herbaria.harvard.edu/pub/piel/Data/files/}. There is huge amount of information present in the files about the trees and the data matrices from which the trees are generated. The search tool implemented at NJIT is interested in using the string …

A Review And Assessment Of Novice Learning Tools For Problem Solving And Program Development, Christopher John Bladek

Theses

There is a great demand for the development of novice learning tools to supplement classroom instruction in the areas of problem solving and program development. Research in the area of pedagogy, the psychology of programming, human-computer interaction, and cognition have provided valuable input to the development of new methodologies, paradigms, programming languages, and novice learning tools to answer this demand.

Based on the cognitive needs of novices, it is possible to postulate a set of characteristics that should comprise the components an effective novice-learning tool. This thesis will discover these characteristics and provide recommendations for the development of new learning …