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Acknowledgments I wish to express my greatest thanks to my advisor, John Lafferty. John's excellent guidance has been absolutely essential for the completion of this thesis. From the very beginning, he has treated me as a peer and a friend, and given me the right amount of freedom and guidance. It has been such a joy to work with him. Over the years, I have(More)
Using Blood Oxygen Level Dependent (BOLD) functional MRI (fMRI) to detect deception is feasible in simple laboratory paradigms. A mock sabotage scenario was used to test whether this technology would also be effective in a scenario closer to a real-world situation. Healthy, nonmedicated adults were recruited from the community, screened, and randomized to(More)
BACKGROUND Biomedical literature, e.g., MEDLINE, contains a wealth of knowledge regarding functions of proteins. Major recurring biological concepts within such text corpora represent the domains of this body of knowledge. The goal of this research is to identify the major biological topics/concepts from a corpus of protein-related MEDLINE titles and(More)
BACKGROUND Expression microarray analysis is one of the most popular molecular diagnostic techniques in the post-genomic era. However, this technique faces the fundamental problem of potential cross-hybridization. This is a pervasive problem for both oligonucleotide and cDNA microarrays; it is considered particularly problematic for the latter. No(More)
BACKGROUND Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, a much needed and important task is to determine the functions of the(More)
MOTIVATION The results of initial analyses for many high-throughput technologies commonly take the form of gene or protein sets, and one of the ensuing tasks is to evaluate the functional coherence of these sets. The study of gene set function most commonly makes use of controlled vocabulary in the form of ontology annotations. For a given gene set, the(More)
BACKGROUND Functional magnetic resonance imaging (fMRI) is a technology used to detect brain activity. Patterns of brain activation have been utilized as biomarkers for various neuropsychiatric applications. Detecting deception based on the pattern of brain activation characterized with fMRI is getting attention - with machine learning algorithms being(More)
We present the metrics for assessing overall functional coherence of a group of proteins based on associated biomedical literature. A probabilistic topic model is applied to extract biologic concepts from a corpus of protein-related biomedical literature. Bipartite protein semantic networks are constructed, so that the functional coherence of a protein(More)
MOTIVATION The Gene Ontology (GO) is a controlled vocabulary designed to represent the biological concepts pertaining to gene products. This study investigates the methods for identifying informative subsets of GO terms in an automatic and objective fashion. This task in turn requires addressing the following issues: how to represent the semantic context of(More)
Most stored neuropeptide cannot be released from nerve terminals suggesting the existence of a refractory pool of dense core vesicles (DCVs). Past fluorescence photobleaching recovery, single particle tracking and release experiments suggested that the refractory neuropeptide pool corresponds to a distinct immobile fraction of cytoplasmic DCVs. However,(More)