Classification of the mechanomyogram signal using a wavelet packet transform and singular value decomposition

Title on author’s file: Classification of mechanomyogram signal using wavelet packet transform and singular value decomposition for multifunction prosthesis control2008-2009 > Academic research: refereed > Publication in refereed journalAccepted ManuscriptPublishe

Holographic Fourier domain diffuse correlation spectroscopy

Diffuse correlation spectroscopy (DCS) is a non-invasive optical modality which can be used to measure cerebral blood flow (CBF) in real-time. It has important potential applications in clinical monitoring, as well as in neuroscience and the development of a non-invasive brain-computer interface. However, a trade-off exists between the signal-to-noise ratio (SNR) and imaging depth, and thus CBF sensitivity, of this technique. Additionally, as DCS is a diffuse optical technique, it is limited by a lack of inherent depth discrimination within the illuminated region of each source-detector pair, and the CBF signal is therefore also prone to contamination by the extracerebral tissues which the light traverses. Placing a particular emphasis on scalability, affordability, and robustness to ambient light, in this work I demonstrate a novel approach which fuses the fields of digital holography and DCS: holographic Fourier domain DCS (FD-DCS). The mathematical formalism of FD-DCS is derived and validated, followed by the construction and validation (for both in vitro and in vivo experiments) of a holographic FD-DCS instrument. By undertaking a systematic SNR performance assessment and developing a novel multispeckle denoising algorithm, I demonstrate the highest SNR gain reported in the DCS literature to date, achieved using scalable and low-cost camera-based detection. With a view to generating a forward model for holographic FD-DCS, in this thesis I propose a novel framework to simulate statistically accurate time-integrated dynamic speckle patterns in biomedical optics. The solution that I propose to this previously unsolved problem is based on the Karhunen-Loève expansion of the electric field, and I validate this technique against novel expressions for speckle contrast for different forms of homogeneous field. I also show that this method can readily be extended to cases with spatially varying sample properties, and that it can also be used to model optical and acoustic parameters

Computing Network of Diseases and Pharmacological Entities through the Integration of Distributed Literature Mining and Ontology Mapping

The proliferation of -omics (such as, Genomics, Proteomics) and -ology (such as, System Biology, Cell Biology, Pharmacology) have spawned new frontiers of research in drug discovery and personalized medicine. A vast amount (21 million) of published research results are archived in the PubMed and are continually growing in size. To improve the accessibility and utility of such a large number of literatures, it is critical to develop a suit of semantic sensitive technology that is capable of discovering knowledge and can also infer possible new relationships based on statistical co-occurrences of meaningful terms or concepts. In this context, this thesis presents a unified framework to mine a large number of literatures through the integration of latent semantic analysis (LSA) and ontology mapping. In particular, a parameter optimized, robust, scalable, and distributed LSA (DiLSA) technique was designed and implemented on a carefully selected 7.4 million PubMed records related to pharmacology. The DiLSA model was integrated with MeSH to make the model effective and efficient for a specific domain. An optimized multi-gram dictionary was customized by mapping the MeSH to build the DiLSA model. A fully integrated web-based application, called PharmNet, was developed to bridge the gap between biological knowledge and clinical practices. Preliminary analysis using the PharmNet shows an improved performance over global LSA model. A limited expert evaluation was performed to validate the retrieved results and network with biological literatures. A thorough performance evaluation and validation of results is in progress

Improved time-frequency de-noising of acoustic signals for underwater detection system

The capability to communicate and perform target localization efficiently in underwater environment is important in many applications. Sound waves are more suitable for underwater communication and target localization because attenuation in water is high for electromagnetic waves. Sound waves are subjected to underwater acoustic noise (UWAN), which is either man-made or natural. Optimum signal detection in UWAN can be achieved with the knowledge of noise statistics. The assumption of Additive White Gaussian noise (AWGN) allows the use of linear correlation (LC) detector. However, the non-Gaussian nature of UWAN results in the poor performance of such detector. This research presents an empirical model of the characteristics of UWAN in shallow waters. Data was measured in Tanjung Balau, Johor, Malaysia on 5 November 2013 and the analysis results showed that the UWAN has a non-Gaussian distribution with characteristics similar to 1/f noise. A complete detection system based on the noise models consisting of a broadband hydrophone, time-frequency distribution, de-noising method, and detection is proposed. In this research, S-transform and wavelet transform were used to generate the time-frequency representation before soft thresholding with modified universal threshold estimation was applied. A Gaussian noise injection detector (GNID) was used to overcome the problem of non-Gaussianity of the UWAN, and its performance was compared with other nonlinear detectors, such as locally optimal (LO) detector, sign correlation (SC) detector, and more conventionally matched filter (MF) detector. This system was evaluated on two types of signals, namely fixed-frequency and linear frequency modulated signals. For de-noising purposes, the S-transform outperformed the wavelet transform in terms of signal-to-noise ratio and root-mean-square error at 4 dB and 3 dB, respectively. The performance of the detectors was evaluated based on the energy-to-noise ratio (ENR) to achieve detection probability of 90% and a false alarm probability of 0.01. Thus, the ENR of the GNID using S-transform denoising, LO detector, SC detector, and MF detector were 8.89 dB, 10.66 dB, 12.7dB, and 12.5 dB, respectively, for the time-varying signal. Among the four detectors, the proposed GNID achieved the best performance, whereas the LC detector showed the weakest performance in the presence of UWAN

A multimodal lens into vascular recovery in a preclinical model of peripheral arterial disease

In the week of February 2nd (21 days into gestation) my parents Ali, and Aicha heard my first heart beat. This shouldn't be a surprise as the heart is the first organ to form and function during the developmental stages of the fetus. In the embryo, newly formed blood vessels provide the growing organs with the vital oxygen and nutrients required for them to flourish. During adulthood, angiogenesis---the process by which new blood vessels form---remains largely quiescent until the delicate balance between pro- and anti-angiogenic factors is disrupted, either through injury or disease. Cardiovascular complications are among the leading causes of morbidity and mortality in diabetic patients, and account for over 80\% of diabetes-associated deaths. One of the most serious is peripheral arterial disease (PAD), which is defined as a narowing of the peripheral vasculature. In this thesis, I will employ a range of imaging modalities to study PAD, investigating methods that may one day enable earlier detection of the disease, and exploring the therapeutic potential of stem cells to treat vascular complications associated with diabetes. This document is divided into four main chapters. The first chapter describes the biological characterization of two different imaging probes targeted, respectively, at hypoxia and \avbt activity, as well as a new power Doppler ultrasound imaging technique capable of detecting small spatiotemporal changes in blood perfusion within muscle. The second chapters applies the \cuProbe peptide targeted at \avbt, to establish an optimal preclinical model of PAD. The third chapter builds on the first and second, by developing a multimodal approach for vascular imaging that enables simultaneous evaluation of molecular and physiological changes during angiogenesis. Finally, the fourth chapter turns its attention toward the mitigation of diabetes-associated PAD. In it, we show that a targeted stem cell-based therapy can exert far reaching effects on the ischemic tissue microenvironment, and may provide clinical improvement for PAD patients in the future

Interrogating spatiotemporal patterns of resting state neuronal and hemodynamic activity in the awake mouse model

Since the advent of functional magnetic resonance imaging (fMRI) and the rise in popularity of its use for resting state functional connectivity mapping (rs-FCM) to non-invasively detect correlated networks of brain activity in human and animal models, many resting state FCM studies have reported differences in these networks under pathologies such as Alzheimer’s or schizophrenia, highlighting the potential for the method’s diagnostic relevance. A common underlying assumption of this analysis, however, is that the blood oxygen level dependent (BOLD) signal of fMRI is a direct measurement of local neural activity. The BOLD signal is in fact a measurement of the local changes in concentration of deoxy-hemoglobin (HbR). Thus, it is imperative that neurovascular coupling—the relationship between neuronal activity and subsequent hemodynamic activity—be better characterized to enable accurate interpretation of resting state fMRI in the context of clinical usage. This dissertation first describes the development and utility of WFOM paradigm for the robust and easily adaptable imaging of simultaneous neuronal and hemodynamic activity in awake mouse models of health or disease in strains with genetically encoded fluorescent calcium reporters. Subsequent exploration of resting state WFOM data collected in Thy1-GCaMP3 and Thy1-GCaMP6f mouse strains is then presented, namely the characterization of spatiotemporal patterns of neuronal and hemodynamic activity and different modulatory depths of neuronal activity via a toolbox of unsupervised blind source separation (e.g. k-means clustering) and supervised (e.g. non-negative least squares, Pearson correlation) analysis tools. The presence of these different modulatory depths of neuronal activity were then confirmed in another Thy1-jRGECO1a mouse strain using the same imaging scheme. Finally, the dissertation documents the application of the WFOM paradigm and select analysis tools to a novel mouse model of diffusely infiltrating glioma, through which neuronal and hemodynamic activity changes during diffusely infiltrating glioma development which impact temporal coherence of the tumor region activity relative to non-tumor regions activity were recorded and analyzed. The paradigm also allowed for recording of numerous spontaneous occurrences of interictal neuronal activity during which neurovascular coupling is modified in the tumor, as well as occurrences of non-convulsive generalized seizure activity (during which neurovascular is non-linear and cortex eventually suffers hypoxia). The detection of spatiotemporal patterns and different modulatory depths of activity in the awake mouse cortex, as well as observation of changes in functional activity in the context of diffusely infiltrating glioma, provide us with new insights into the possible mechanisms underlying variations in resting state connectivity networks found in resting state fMRI studies comparing health and disease states

Neuroinformatics in Functional Neuroimaging

This Ph.D. thesis proposes methods for information retrieval in functional neuroimaging through automatic computerized authority identification, and searching and cleaning in a neuroscience database. Authorities are found through cocitation analysis of the citation pattern among scientific articles. Based on data from a single scientific journal it is shown that multivariate analyses are able to determine group structure that is interpretable as particular “known ” subgroups in functional neuroimaging. Methods for text analysis are suggested that use a combination of content and links, in the form of the terms in scientific documents and scientific citations, respectively. These included context sensitive author ranking and automatic labeling of axes and groups in connection with multivariate analyses of link data. Talairach foci from the BrainMap ™ database are modeled with conditional probability density models useful for exploratory functional volumes modeling. A further application is shown with conditional outlier detection where abnormal entries in the BrainMap ™ database are spotted using kernel density modeling and the redundancy between anatomical labels and spatial Talairach coordinates. This represents a combination of simple term and spatial modeling. The specific outliers that were found in the BrainMap ™ database constituted among others: Entry errors, errors in the article and unusual terminology

Optical Methods in Sensing and Imaging for Medical and Biological Applications

The recent advances in optical sources and detectors have opened up new opportunities for sensing and imaging techniques which can be successfully used in biomedical and healthcare applications. This book, entitled ‘Optical Methods in Sensing and Imaging for Medical and Biological Applications’, focuses on various aspects of the research and development related to these areas. The book will be a valuable source of information presenting the recent advances in optical methods and novel techniques, as well as their applications in the fields of biomedicine and healthcare, to anyone interested in this subject

Algoritmos de Enjambre para la Optimización de HMM en la Detección de Soplos Cardíacos en Señales Fonocardiográficas Usando Representaciones Derivadas del Análisis de Vibraciones

Este trabajo presenta una metodología para desarrollar un sistema automático de apoyo en la clasificación de señales fonocardiográficos (PCG). En primer lugar, las señales PCG fueron pre-procesadas. Luego descompuestas por medio de la técnica descomposición modo empírico (EMD) con algunas de sus variantes y el análisis de vibración por descomposición de Hilbert (HVD) de forma independiente, donde se comparó el costó computacional y el error en la reconstrucción de la señal original generando constructos a partir de las IMFs. A continuación, se extrajeron las características con los momentos estadísticos de los datos generados por la transformada de Hilbert-Huang (HHT), además de los coeficientes cepstrales en las frecuencias de Mel (MFCC) y cuatro de sus variantes. Por último, un subconjunto de características fue seleccionado usando conjuntos de aproximación difusos (FRS), análisis de componentes principales (PCA) y selección secuencial flotante hacia adelante (SFFS) de manera simultánea para ser utilizadas como entradas del modelo oculto de Markov (HMM) ergódico ajustado con optimización por enjambre de partículas (PSO), con el fin de proporcionar un mecanismo objetivo y preciso para mejorar la fiabilidad en la detección de soplos en el corazón, obteniendo resultados en la clasificación de alrededor del 96% con valores de sensibilidad superiores a 0.8 y de especificidad mayores a 0.9, utilizando validación cruzada (70/30 con 30 fold)This study presents a methodology for developing an automated support system in the classification of phonographic signals (PCG). First, the PCG signals were preprocessed. You then decomposed by the decomposition technique empirically (EMD) with some of its variants and vibration analysis by decomposition of Hilbert (HVD) independently, where the computational cost and the error was compared in the reconstruction of the original signal generating constructs from IMFs. Then the characteristics of the statistical moments data generated by the Hilbert-Huang Transform (HHT), plus cepstral coeffcients at frequencies of Mel (MFCC) and four of its variants were extracted. Finally, a subset of features was selected using sets of fuzzy approximation (FRS), principal component analysis (PCA) and floating sequential forward selection (SFFS) simultaneously to be used as inputs to the hidden Markov model (HMM) ergodic adjusted particle swarm optimization (PSO), in order to provide an objective and accurate to improve reliability in detecting heart murmurs mechanism, obtaining results in the classification of about 96% with sensitivity values higher 0.8 and higher specificity to 0.9, using cross-validation (70/30 split with 30 fold)Magister en Automatización y Contro