Statistical analysis and meta-analysis of microarray data

The microarray technology provides a high-throughput technique to study gene expression. Microarrays can help us diagnose different types of cancers, understand biological processes, assess host responses to drugs and pathogens, find markers for specific diseases, and much more. Microarray experiments generate large amounts of data. Thus, effective data processing and analysis are critical for making reliable inferences from the data. ^ The first part of dissertation addresses the problem of finding an optimal set of genes (biomarkers) to classify a set of samples as diseased or normal. Three statistical gene selection methods (GS, GS-NR, and GS-PCA) were developed to identify a set of genes that best differentiate between samples. A comparative study on different classification tools was performed and the best combinations of gene selection and classifiers for multi-class cancer classification were identified. For most of the benchmarking cancer data sets, the gene selection method proposed in this dissertation, GS, outperformed other gene selection methods. The classifiers based on Random Forests, neural network ensembles, and K-nearest neighbor (KNN) showed consistently god performance. A striking commonality among these classifiers is that they all use a committee-based approach, suggesting that ensemble classification methods are superior. ^ The same biological problem may be studied at different research labs and/or performed using different lab protocols or samples. In such situations, it is important to combine results from these efforts. The second part of the dissertation addresses the problem of pooling the results from different independent experiments to obtain improved results. Four statistical pooling techniques (Fisher inverse chi-square method, Logit method. Stouffer's Z transform method, and Liptak-Stouffer weighted Z-method) were investigated in this dissertation. These pooling techniques were applied to the problem of identifying cell cycle-regulated genes in two different yeast species. As a result, improved sets of cell cycle-regulated genes were identified. The last part of dissertation explores the effectiveness of wavelet data transforms for the task of clustering. Discrete wavelet transforms, with an appropriate choice of wavelet bases, were shown to be effective in producing clusters that were biologically more meaningful. ^

Design and implementation of a multisite data repository for pediatric epilepsy

This dissertation established a software-hardware integrated design for a multisite data repository in pediatric epilepsy. A total of 16 institutions formed a consortium for this web-based application. This innovative fully operational web application allows users to upload and retrieve information through a unique human-computer graphical interface that is remotely accessible to all users of the consortium. A solution based on a Linux platform with My-SQL and Personal Home Page scripts (PHP) has been selected. Research was conducted to evaluate mechanisms to electronically transfer diverse datasets from different hospitals and collect the clinical data in concert with their related functional magnetic resonance imaging (fMRI). What was unique in the approach considered is that all pertinent clinical information about patients is synthesized with input from clinical experts into 4 different forms, which were: Clinical, fMRI scoring, Image information, and Neuropsychological data entry forms. A first contribution of this dissertation was in proposing an integrated processing platform that was site and scanner independent in order to uniformly process the varied fMRI datasets and to generate comparative brain activation patterns. The data collection from the consortium complied with the IRB requirements and provides all the safeguards for security and confidentiality requirements. An 1-MR1-based software library was used to perform data processing and statistical analysis to obtain the brain activation maps. Lateralization Index (LI) of healthy control (HC) subjects in contrast to localization-related epilepsy (LRE) subjects were evaluated. Over 110 activation maps were generated, and their respective LIs were computed yielding the following groups: (a) strong right lateralization: (HC=0%, LRE=18%), (b) right lateralization: (HC=2%, LRE=10%), (c) bilateral: (HC=20%, LRE=15%), (d) left lateralization: (HC=42%, LRE=26%), e) strong left lateralization: (HC=36%, LRE=31%). Moreover, nonlinear-multidimensional decision functions were used to seek an optimal separation between typical and atypical brain activations on the basis of the demographics as well as the extent and intensity of these brain activations. The intent was not to seek the highest output measures given the inherent overlap of the data, but rather to assess which of the many dimensions were critical in the overall assessment of typical and atypical language activations with the freedom to select any number of dimensions and impose any degree of complexity in the nonlinearity of the decision space.

Pulsed parabolic equation model of acoustic transmission (PPEMAT)

Underwater sound is very important in the field of oceanography where it is used for remote sensing in much the same way that radar is used in atmospheric studies. One way to mathematically model sound propagation in the ocean is by using the parabolic-equation method, a technique that allows range dependent environmental parameters. More importantly, this method can model sound transmission where the source emits either a pure tone or a short pulse of sound. Based on the parabolic approximation method and using the split-step Fourier algorithm, a computer model for underwater sound propagation was designed and implemented. This computer model differs from previous models in its use of the interactive mode, structured programming, modular design, and state-of-the-art graphics displays. In addition, the model maximizes the efficiency of computer time through synchronization of loosely coupled dual processors and the design of a restart capability. Since the model is designed for adaptability and for users with limited computer skills, it is anticipated that it will have many applications in the scientific community.

Intelligent retrieval system for conditions of contract documents in construction

The outcome of this research is an Intelligent Retrieval System for Conditions of Contract Documents. The objective of the research is to improve the method of retrieving data from a computer version of a construction Conditions of Contract document. SmartDoc, a prototype computer system has been developed for this purpose. The system provides recommendations to aid the user in the process of retrieving clauses from the construction Conditions of Contract document. The prototype system integrates two computer technologies: hypermedia and expert systems. Hypermedia is utilized to provide a dynamic way for retrieving data from the document. Expert systems technology is utilized to build a set of rules that activate the recommendations to aid the user during the process of retrieval of clauses. The rules are based on experts knowledge. The prototype system helps the user retrieve related clauses that are not explicitly cross-referenced but, according to expert experience, are relevant to the topic that the user is interested in.

In Vivo Characterization of Myocardial Tissue Post Myocardial Infarction Using Combined Fluorescence and Diffuse Reflectance Spectroscopy

Accurately assessing the extent of myocardial tissue injury induced by Myocardial infarction (MI) is critical to the planning and optimization of MI patient management. With this in mind, this study investigated the feasibility of using combined fluorescence and diffuse reflectance spectroscopy to characterize a myocardial infarct at the different stages of its development. An animal study was conducted using twenty male Sprague-Dawley rats with MI. In vivo fluorescence spectra at 337 nm excitation and diffuse reflectance between 400 nm and 900 nm were measured from the heart using a portable fiber-optic spectroscopic system. Spectral acquisition was performed on - (1) the normal heart region; (2) the region immediately surrounding the infarct; and (3) the infarcted region - one, two, three and four weeks into MI development. The spectral data were divided into six subgroups according to the histopathological features associated with various degrees / severities of myocardial tissue injury as well as various stages of myocardial tissue remodeling, post infarction. Various data processing and analysis techniques were employed to recognize the representative spectral features corresponding to various histopathological features associated with myocardial infarction. The identified spectral features were utilized in discriminant analysis to further evaluate their effectiveness in classifying tissue injuries induced by MI. In this study, it was observed that MI induced significant alterations (p < 0.05) in the diffuse reflectance spectra, especially between 450 nm and 600 nm, from myocardial tissue within the infarcted and surrounding regions. In addition, MI induced a significant elevation in fluorescence intensities at 400 and 460 nm from the myocardial tissue from the same regions. The extent of these spectral alterations was related to the duration of the infarction. Using the spectral features identified, an effective tissue injury classification algorithm was developed which produced a satisfactory overall classification result (87.8%). The findings of this research support the concept that optical spectroscopy represents a useful tool to non-invasively determine the in vivo pathophysiological features of a myocardial infarct and its surrounding tissue, thereby providing valuable real-time feedback to surgeons during various surgical interventions for MI.

Optimal kernel development for real-time communications

The purpose of this research is to develop an optimal kernel which would be used in a real-time engineering and communications system. Since the application is a real-time system, relevant real-time issues are studied in conjunction with kernel related issues. The emphasis of the research is the development of a kernel which would not only adhere to the criteria of a real-time environment, namely determinism and performance, but also provide the flexibility and portability associated with non-real-time environments. The essence of the research is to study how the features found in non-real-time systems could be applied to the real-time system in order to generate an optimal kernel which would provide flexibility and architecture independence while maintaining the performance needed by most of the engineering applications. Traditionally, development of real-time kernels has been done using assembly language. By utilizing the powerful constructs of the C language, a real-time kernel was developed which addressed the goals of flexibility and portability while still meeting the real-time criteria. The implementation of the kernel is carried out using the powerful 68010/20/30/40 microprocessor based systems.

Content-aware compression for big textual data analysis

A substantial amount of information on the Internet is present in the form of text. The value of this semi-structured and unstructured data has been widely acknowledged, with consequent scientific and commercial exploitation. The ever-increasing data production, however, pushes data analytic platforms to their limit. This thesis proposes techniques for more efficient textual big data analysis suitable for the Hadoop analytic platform. This research explores the direct processing of compressed textual data. The focus is on developing novel compression methods with a number of desirable properties to support text-based big data analysis in distributed environments. The novel contributions of this work include the following. Firstly, a Content-aware Partial Compression (CaPC) scheme is developed. CaPC makes a distinction between informational and functional content in which only the informational content is compressed. Thus, the compressed data is made transparent to existing software libraries which often rely on functional content to work. Secondly, a context-free bit-oriented compression scheme (Approximated Huffman Compression) based on the Huffman algorithm is developed. This uses a hybrid data structure that allows pattern searching in compressed data in linear time. Thirdly, several modern compression schemes have been extended so that the compressed data can be safely split with respect to logical data records in distributed file systems. Furthermore, an innovative two layer compression architecture is used, in which each compression layer is appropriate for the corresponding stage of data processing. Peripheral libraries are developed that seamlessly link the proposed compression schemes to existing analytic platforms and computational frameworks, and also make the use of the compressed data transparent to developers. The compression schemes have been evaluated for a number of standard MapReduce analysis tasks using a collection of real-world datasets. In comparison with existing solutions, they have shown substantial improvement in performance and significant reduction in system resource requirements.

Extending Science Gateway Frameworks to Support Big Data Applications in the Cloud

Cloud computing offers massive scalability and elasticity required by many scien-tific and commercial applications. Combining the computational and data handling capabilities of clouds with parallel processing also has the potential to tackle Big Data problems efficiently. Science gateway frameworks and workflow systems enable application developers to implement complex applications and make these available for end-users via simple graphical user interfaces. The integration of such frameworks with Big Data processing tools on the cloud opens new oppor-tunities for application developers. This paper investigates how workflow sys-tems and science gateways can be extended with Big Data processing capabilities. A generic approach based on infrastructure aware workflows is suggested and a proof of concept is implemented based on the WS-PGRADE/gUSE science gateway framework and its integration with the Hadoop parallel data processing solution based on the MapReduce paradigm in the cloud. The provided analysis demonstrates that the methods described to integrate Big Data processing with workflows and science gateways work well in different cloud infrastructures and application scenarios, and can be used to create massively parallel applications for scientific analysis of Big Data.

Two-Path All-pass Based Half-Band Infinite Impulse Response Decimation Filters and the Effects of Their Non-Linear Phase Response on ECG Signal Acquisition

This paper is based on the novel use of a very high fidelity decimation filter chain for Electrocardiogram (ECG) signal acquisition and data conversion. The multiplier-free and multi-stage structure of the proposed filters lower the power dissipation while minimizing the circuit area which are crucial design constraints to the wireless noninvasive wearable health monitoring products due to the scarce operational resources in their electronic implementation. The decimation ratio of the presented filter is 128, working in tandem with a 1-bit 3rd order Sigma Delta (ΣΔ) modulator which achieves 0.04 dB passband ripples and -74 dB stopband attenuation. The work reported here investigates the non-linear phase effects of the proposed decimation filters on the ECG signal by carrying out a comparative study after phase correction. It concludes that the enhanced phase linearity is not crucial for ECG acquisition and data conversion applications since the signal distortion of the acquired signal, due to phase non-linearity, is insignificant for both original and phase compensated filters. To the best of the authors’ knowledge, being free of signal distortion is essential as this might lead to misdiagnosis as stated in the state of the art. This article demonstrates that with their minimal power consumption and minimal signal distortion features, the proposed decimation filters can effectively be employed in biosignal data processing units.

Compositional data analysis of Holocene sediments from the West Bengal Sundarbans, India: Geochemical proxies for grain-size variability in a delta environment

This paper is part of a special issue of Applied Geochemistry focusing on reliable applications of compositional multivariate statistical methods. This study outlines the application of compositional data analysis (CoDa) to calibration of geochemical data and multivariate statistical modelling of geochemistry and grain-size data from a set of Holocene sedimentary cores from the Ganges-Brahmaputra (G-B) delta. Over the last two decades, understanding near-continuous records of sedimentary sequences has required the use of core-scanning X-ray fluorescence (XRF) spectrometry, for both terrestrial and marine sedimentary sequences. Initial XRF data are generally unusable in ‘raw-format’, requiring data processing in order to remove instrument bias, as well as informed sequence interpretation. The applicability of these conventional calibration equations to core-scanning XRF data are further limited by the constraints posed by unknown measurement geometry and specimen homogeneity, as well as matrix effects. Log-ratio based calibration schemes have been developed and applied to clastic sedimentary sequences focusing mainly on energy dispersive-XRF (ED-XRF) core-scanning. This study has applied high resolution core-scanning XRF to Holocene sedimentary sequences from the tidal-dominated Indian Sundarbans, (Ganges-Brahmaputra delta plain). The Log-Ratio Calibration Equation (LRCE) was applied to a sub-set of core-scan and conventional ED-XRF data to quantify elemental composition. This provides a robust calibration scheme using reduced major axis regression of log-ratio transformed geochemical data. Through partial least squares (PLS) modelling of geochemical and grain-size data, it is possible to derive robust proxy information for the Sundarbans depositional environment. The application of these techniques to Holocene sedimentary data offers an improved methodological framework for unravelling Holocene sedimentation patterns.

Automated Collection of Sign Inventory Information by Integrating Global Positioning System (GPS) with Videologging Data Collection Activities, 1995

Advances in communication, navigation and imaging technologies are expected to fundamentally change methods currently used to collect data. Electronic data interchange strategies will also minimize data handling and automatically update files at the point of capture. This report summarizes the outcome of using a multi-camera platform as a method to collect roadway inventory data. It defines basic system requirements as expressed by users, who applied these techniques and examines how the application of the technology met those needs. A sign inventory case study was used to determine the advantages of creating and maintaining the database and provides the capability to monitor performance criteria for a Safety Management System. The project identified at least 75 percent of the data elements needed for a sign inventory can be gathered by viewing a high resolution image.

High-performance parallel systems for data-intensive computing

Thesis (Ph.D.)--University of Washington, 2016-08

Strategies for protecting intellectual property when using CUDA applications on graphics processing units

Recent advances in the massively parallel computational abilities of graphical processing units (GPUs) have increased their use for general purpose computation, as companies look to take advantage of big data processing techniques. This has given rise to the potential for malicious software targeting GPUs, which is of interest to forensic investigators examining the operation of software. The ability to carry out reverse-engineering of software is of great importance within the security and forensics elds, particularly when investigating malicious software or carrying out forensic analysis following a successful security breach. Due to the complexity of the Nvidia CUDA (Compute Uni ed Device Architecture) framework, it is not clear how best to approach the reverse engineering of a piece of CUDA software. We carry out a review of the di erent binary output formats which may be encountered from the CUDA compiler, and their implications on reverse engineering. We then demonstrate the process of carrying out disassembly of an example CUDA application, to establish the various techniques available to forensic investigators carrying out black-box disassembly and reverse engineering of CUDA binaries. We show that the Nvidia compiler, using default settings, leaks useful information. Finally, we demonstrate techniques to better protect intellectual property in CUDA algorithm implementations from reverse engineering.

Configurable Web Warehouses construction through BPM Systems

The process of building Data Warehouses (DW) is well known with well defined stages but at the same time, mostly carried out manually by IT people in conjunction with business people. Web Warehouses (WW) are DW whose data sources are taken from the web. We define a flexible WW, which can be configured accordingly to different domains, through the selection of the web sources and the definition of data processing characteristics. A Business Process Management (BPM) System allows modeling and executing Business Processes (BPs) providing support for the automation of processes. To support the process of building flexible WW we propose a two BPs level: a configuration process to support the selection of web sources and the definition of schemas and mappings, and a feeding process which takes the defined configuration and loads the data into the WW. In this paper we present a proof of concept of both processes, with focus on the configuration process and the defined data.

The Implication of Using NVivo Software in Qualitative Data Analysis: Evidence-Based Reflections

For a long time, electronic data analysis has been associated with quantitative methods. However, Computer Assisted Qualitative Data Analysis Software (CAQDAS) are increasingly being developed. Although the CAQDAS has been there for decades, very few qualitative health researchers report using it. This may be due to the difficulties that one has to go through to master the software and the misconceptions that are associated with using CAQDAS. While the issue of mastering CAQDAS has received ample attention, little has been done to address the misconceptions associated with CAQDAS. In this paper, the author reflects on his experience of interacting with one of the popular CAQDAS (NVivo) in order to provide evidence-based implications of using the software. The key message is that unlike statistical software, the main function of CAQDAS is not to analyse data but rather to aid the analysis process, which the researcher must always remain in control of. In other words, researchers must equally know that no software can analyse qualitative data. CAQDAS are basically data management packages, which support the researcher during analysis.