17 research outputs found

    Development of mathematical methods for modeling biological systems

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    A Small Acoustic Goniometer for General Purpose Research

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    Understanding acoustic events and monitoring their occurrence is a useful aspect of many research projects. In particular, acoustic goniometry allows researchers to determine the source of an event based solely on the sound it produces. The vast majority of the acoustic goniometry research projects used custom hardware targeted to the specific application under test. Unfortunately, due to the wide range of sensing applications, a flexible general purpose hardware/firmware system does not exist for this research. This dissertation focuses on the development of such a system which encourages the continued exploration of general purpose hardware/firmware and lowers barriers to research in projects requiring the use of acoustic goniometry. Simulations have been employed to verify system feasibility, and a complete hardware implementation of the acoustic goniometer has been designed and field tested. The results are reported, and suggested areas for improvement and further exploration are discussed

    Probabilistic analysis of the human transcriptome with side information

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    Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient sharing of research material through community databases have opened up new views to the study of living organisms and the structure of life. In this thesis, novel computational strategies have been developed to investigate a key functional layer of genetic information, the human transcriptome, which regulates the function of living cells through protein synthesis. The key contributions of the thesis are general exploratory tools for high-throughput data analysis that have provided new insights to cell-biological networks, cancer mechanisms and other aspects of genome function. A central challenge in functional genomics is that high-dimensional genomic observations are associated with high levels of complex and largely unknown sources of variation. By combining statistical evidence across multiple measurement sources and the wealth of background information in genomic data repositories it has been possible to solve some the uncertainties associated with individual observations and to identify functional mechanisms that could not be detected based on individual measurement sources. Statistical learning and probabilistic models provide a natural framework for such modeling tasks. Open source implementations of the key methodological contributions have been released to facilitate further adoption of the developed methods by the research community.Comment: Doctoral thesis. 103 pages, 11 figure

    NASA patent abstracts bibliography: A continuing bibliography. Section 2: Indexes (supplement 13)

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    This issue of the Index Section contains entries for 3386 patent and application for patent citations covering the period May 1969 through June 1978. The Index Section contains five indexes --- subject, inventor, source, number, and accession number

    NASA patent abstracts bibliography: A continuing bibliography. Section 2: Indexes (supplement 14)

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    This issue of the Index Section contains entries for 3512 patent and applications for patent citations covering the period May 1969 through December 1978. The Index Section contains five indexes --- subject, inventor, source, number, and accession number

    Epithelial specific transcriptome map of the human prostate

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    The prostate has a zonal anatomy, with differing susceptibilities to disease (benign prostatic hyperplasia originates from the transition zone, prostate cancer largely arises in the peripheral zone). The molecular reasons for this are not understood. Previous prostate cancer microarray studies have used whole benign, diseased or tissue adjacent to the carcinoma as normal controls, for what is an epithelial disease. This study provides a gene expression profile of normal, non-diseased prostate, or a ‘reference prostate gene expression profile’. This has been compared to prostate cancer to identify novel biomarkers of disease. This study also investigates zonal differences in gene expression between different anatomical zones of the prostate. I used normal, human donor prostate tissue, laser capture microdissection (LCM), and Affymetrix gene expression arrays to achieve these aims. Eight LCM prostate epithelial samples from 3 donor prostates were used. The gene expression data was validated by low density real-time PCR and immunohistochemistry on a prostate tissue microarray. Major differences in gene expression were discovered between whole tissue and LCM epithelium only prostate using homology tables. Novel prostate adenocarcinoma genes were identified using a publicly available LCM prostate cancer gene expression array dataset. 9318 genes showed significant differential expression in normal vs. cancer datasets. Three targets, MCM2, NR1D1 and ABCA1 were validated at the protein level. Expression of NR1D1 and ABCA1 were increased in cancer, suggesting they are novel epithelial biomarkers of prostate cancer. An analysis of zonal differences in gene expression found significant differences between zones. Zonal specific markers included TGM4 (central zone), LPL (peripheral zone), and COL9A1 (transition zone). This study provides: (i) a gene expression profile of the normal prostate epithelium (ii) novel, prostate adenocarcinoma specific gene and protein markers and (iii) the first gene expression profile of normal epithelium on the basis of zonal anatomy of the prostate

    Safety and Reliability - Safe Societies in a Changing World

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    The contributions cover a wide range of methodologies and application areas for safety and reliability that contribute to safe societies in a changing world. These methodologies and applications include: - foundations of risk and reliability assessment and management - mathematical methods in reliability and safety - risk assessment - risk management - system reliability - uncertainty analysis - digitalization and big data - prognostics and system health management - occupational safety - accident and incident modeling - maintenance modeling and applications - simulation for safety and reliability analysis - dynamic risk and barrier management - organizational factors and safety culture - human factors and human reliability - resilience engineering - structural reliability - natural hazards - security - economic analysis in risk managemen

    NASA patent abstracts bibliography: A continuing bibliography. Section 2: Indexes (supplement 18)

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    Entries for 3900 patents and patent applications citations for the period May 1980 through December 1980 are listed. Indexes for subject, invention, source, number, and accession number are included
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