Biologically Inspired Approaches to Automated Feature Extraction and Target Recognition

Ongoing research at Boston University has produced computational models of biological vision and learning that embody a growing corpus of scientific data and predictions. Vision models perform long-range grouping and figure/ground segmentation, and memory models create attentionally controlled recognition codes that intrinsically cornbine botton-up activation and top-down learned expectations. These two streams of research form the foundation of novel dynamically integrated systems for image understanding. Simulations using multispectral images illustrate road completion across occlusions in a cluttered scene and information fusion from incorrect labels that are simultaneously inconsistent and correct. The CNS Vision and Technology Labs (cns.bu.edulvisionlab and cns.bu.edu/techlab) are further integrating science and technology through analysis, testing, and development of cognitive and neural models for large-scale applications, complemented by software specification and code distribution.

Rule Extraction, Fuzzy ARTMAP, and Medical Databases

This paper shows how knowledge, in the form of fuzzy rules, can be derived from a self-organizing supervised learning neural network called fuzzy ARTMAP. Rule extraction proceeds in two stages: pruning removes those recognition nodes whose confidence index falls below a selected threshold; and quantization of continuous learned weights allows the final system state to be translated into a usable set of rules. Simulations on a medical prediction problem, the Pima Indian Diabetes (PID) database, illustrate the method. In the simulations, pruned networks about 1/3 the size of the original actually show improved performance. Quantization yields comprehensible rules with only slight degradation in test set prediction performance.

Rapid separation of biologically important low molecular weight compounds by microchip electrophoresis and ultra-fast performance liquid chromatography

The research work in this thesis reports rapid separation of biologically important low molecular weight compounds by microchip electrophoresis and ultrahigh liquid chromatography. Chapter 1 introduces the theory and principles behind capillary electrophoresis separation. An overview of the history, different modes and detection techniques coupled to CE is provided. The advantages of microchip electrophoresis are highlighted. Some aspects of metal complex analysis by capillary electrophoresis are described. Finally, the theory and different modes of the liquid chromatography technology are presented. Chapter 2 outlines the development of a method for the capillary electrophoresis of (R, S) Naproxen. Variable parameters of the separation were optimized (i.e. buffer concentration and pH, concentration of chiral selector additives, applied voltage and injection condition).The method was validated in terms of linearity, precision, and LOD. The optimized method was then transferred to a microchip electrophoresis system. Two different types of injection i.e. gated and pinched, were investigated. This microchip method represents the fastest reported chiral separation of Naproxen to date. Chapter 3 reports ultra-fast separation of aromatic amino acid by capillary electrophoresis using the short-end technique. Variable parameters of the separation were optimized and validated. The optimized method was then transferred to a microchip electrophoresis system where the separation time was further reduced. Chapter 4 outlines the use of microchip electrophoresis as an efficient tool for analysis of aluminium complexes. A 2.5 cm channel with linear imaging UV detection was used to separate and detect aluminium-dopamine complex and free dopamine. For the first time, a baseline, separation of aluminium dopamine was achieved on a 15 seconds timescale. Chapter 5 investigates a rapid, ultra-sensitive and highly efficient method for quantification of histamine in human psoriatic plaques using microdialysis and ultrahigh performance liquid chromatography with fluorescence detection. The method utilized a sub-two-micron packed C18 stationary phase. A fluorescent reagent, 4-(1-pyrene) butyric acid N-hydroxysuccinimide ester was conjugated to the primary and secondary amino moieties of histamine. The dipyrene-labeled histamine in human urine was also investigated by ultrahigh pressure liquid chromatography using a C18 column with 1.8 μm particle diameter. These methods represent one of the fastest reported separations to date of histamine using fluorescence detection.

Silica bonded stationary phases: Innovative functionalization methods and novel chromatographic separations based on molecular recognition

The research work included in this thesis examines the synthesis, characterization and chromatographic evaluation of novel bonded silica stationary phases. Innovative methods of preparation of silica hydride intermediates and octadecylsilica using a “green chemistry” approach eliminate the use of toxic organic solvents and exploit the solvating power and enhanced diffusivity of supercritical carbon dioxide to produce phases with a surface coverage of bonded ligands which is comparable to, or exceeds, that achieved using traditional organic solvent-based methods. A new stationary phase is also discussed which displays chromatographic selectivity based on molecular recognition. Chapter 1 introduces the chemistry of silica stationary phases, the retention mechanisms and theories on which reversed-phase liquid chromatography and hydrophilic interaction chromatograpy are based, the art and science of achieving a well packed liquid chromatography column, the properties of supercritical carbon dioxide and molecular recognition chemistry. Chapter 2 compares the properties of silica hydride materials prepared using supercritical carbon dioxide as the reaction medium with those synthesized in an organic solvent. A higher coverage of hydride groups on the silica surface is seen when a monofunctional silane is reacted in supercritical carbon dioxide while trifunctional silanes result in a phase which exhibits different properties depending on the reaction medium used. The differing chromatographic behaviour of these silica hydride materials prepared using supercritical carbon dioxide and using organic solvent are explored in chapter 3. Chapter 4 focusses on the preparation of octadecylsilica using mono-, di- and trifunctional alkoxysilanes in supercritical carbon dioxide and in anhydrous toluene. The surface coverage of octadecyl groups, as calculated using thermogravimetric analysis and elemental analysis, is highest when a trifunctional alkoxysilane is reacted with silica in supercritical carbon dioxide. A novel silica stationary phase is discussed in chapter 5 which displays selectivity for analytes based on their hydrogen bonding capabilities. The phase is also highly selective for barbituric acid and may have a future application in the solid phase extraction of barbiturates from biological samples.

Synthesis and characterisation of novel superficially porous silica based stationary phases for use in liquid chromatography

The concept of pellicular particles was suggested by Horváth and Lipsky over fifty years ago. The reasoning behind the idea of these particles was to improve column efficiency by shortening the pathways analyte molecules can travel, therefore reducing the effect of the A and C terms. Several types of shell particles were successfully marketed around this time, however with the introduction of high quality fully porous silica under 10 μm, shell particles faded into the background. In recent years a new generation of core shell particles have become popular within the separation science community. These particles allow fast and efficient separations that can be carried out on conventional HPLC systems. Chapter 1 of this thesis introduces the chemistry of chromatographic stationary phases, with an emphasis on silica bonded phases, particularly focusing on the current state of technology in this area. The main focus is on superficially porous silica particles as a support material for liquid chromatography. A summary of the history and development of these particles over the past few decades is explored, along with current methods of synthesis of shell particles. While commercial shell particles have a rough outer surface, Chapter 2 focuses on the novel approach to growth of smooth surface superficially porous particles in a step-by-step manner. From the Stöber methodology to the seeded growth technique, and finally to the layer-bylayer growth of the porous shell. The superficially porous particles generated in this work have an overall diameter of 2.6 μm with a 350 nm porous shell; these silica particles were characterised using SEM, TEM and BET analysis. The uniform spherical nature of the particles along with their surface area, pore size and particle size distribution are examined in this chapter. I discovered that these smooth surface shell particles can be synthesised to give comparable surface area and pore size in comparison to commercial brands. Chapter 3 deals with the bonding of the particles prepared in Chapter 2 with C18 functionality; one with a narrow and one with a wide particle size distribution. This chapter examines the chromatographic and kinetic performance of these silica stationary phases, and compares them to a commercial superficially porous silica phase with a rough outer surface. I found that the particle size distribution does not seem to be the major contributor to the improvement in efficiency. The surface morphology of the particles appears to play an important role in the packing process of these particles and influences the Van Deemter effects. Chapter 4 focuses on the functionalisation of 2.6 μm smooth surface superficially porous particles with a variety of fluorinated and phenyl silanes. The same processes were carried out on 3.0 μm fully porous silica particles to provide a comparison. All phases were accessed using elemental analysis, thermogravimetric analysis, nitrogen sorption analysis and chromatographically evaluated using the Neue test. I observed comparable results for the 2.6 μm shell pentaflurophenyl propyl silica when compared to 3.0 μm fully porous silica. Chapter 5 moves towards nano-particles, with the synthesis of sub-1 μm superficially porous particles, their characterisation and use in chromatography. The particles prepared are 750 nm in total with a 100 nm shell. All reactions and testing carried out on these 750 nm core shell particles are also carried out on 1.5 μm fully porous particles in order to give a comparative result. The 750 nm core shell particles can be synthesised quickly and are very uniform. The main drawback in their use for HPLC is the system itself due to the backpressure experienced using sub – 1 μm particles. The synthesis of modified Stöber particles is also examined in this chapter with a range of non-porous silica and shell silica from 70 nm – 750 nm being tested for use on a Langmuir – Blodgett system. These smooth surface shell particles have only been in existence since 2009. The results displayed in this thesis demonstrate how much potential smooth surface shell particles have provided more in-depth optimisation is carried out. The results on packing studies reported in this thesis aims to be a starting point for a more sophisticated methodology, which in turn can lead to greater chromatographic improvements.

Profiling phytochemical and nutritional components of potato

Potatoes (Solanum Tuberosum L.) contain secondary metabolites that may have an impact on human health. The aim of this study was to assess the levels of some of these compounds in a wide range of varieties, including rare, heritage and commercial cultivars. Vitamin C, total carotenoids, phenolics, flavonoids, antioxidant activity and glycoalkaloids were determined, using spectroscopy and chromatography, in the skin and flesh of tubers grown in field trials. Transcript levels of key synthetic enzymes were assessed by qPCR. Accumulation of selected metabolites was higher in the skin than in the flesh of tubers, except ascorbate, which was undetected in the skin. Differences were on average 2.5 to 3-fold for carotenoids, 6-fold for phenolics, 15 to 16-fold for flavonoids, 21-fold for glycoalkaloids and 9 to 10-fold for antioxidant activity. Higher contents of carotenoids were associated with yellow skin or flesh, and higher values of phenolics, flavonoids and antioxidant activity with blue flesh. Variety ‘Burren’ had maxima values of carotenoids in skin and flesh, variety ‘Nicola’ of ascorbate, variety ‘Congo’ of phenolics, flavonoids and antioxidant activity in both tissues, except antioxidant activity in the skin, which was higher in ‘Edzell Blue’. Varieties ‘May Queen’ and ‘International Kidney’ had highest glycoalkaloid content in skin and flesh respectively. The effect of the environment was diverse: year of cultivation was significant for all metabolites, but site of cultivation was not for carotenoids and glycoalkaloids. Levels of expression of phenylalanine ammonia-lyase and chalcone synthase were higher in varieties accumulating high contents of phenolic compounds. However, levels of expression of phytoene synthase and L-galactono-1,4-lactone dehydrogenase were not different between varieties showing contrasting levels of carotenoids and ascorbate respectively. This work will help identify varieties that could be marketed as healthier and the most suitable varieties for extraction of high-value metabolites such as glycoalkaloids.

3D refraction correction and extraction of clinical parameters from spectral domain optical coherence tomography of the cornea.

Capable of three-dimensional imaging of the cornea with micrometer-scale resolution, spectral domain-optical coherence tomography (SDOCT) offers potential advantages over Placido ring and Scheimpflug photography based systems for accurate extraction of quantitative keratometric parameters. In this work, an SDOCT scanning protocol and motion correction algorithm were implemented to minimize the effects of patient motion during data acquisition. Procedures are described for correction of image data artifacts resulting from 3D refraction of SDOCT light in the cornea and from non-idealities of the scanning system geometry performed as a pre-requisite for accurate parameter extraction. Zernike polynomial 3D reconstruction and a recursive half searching algorithm (RHSA) were implemented to extract clinical keratometric parameters including anterior and posterior radii of curvature, central cornea optical power, central corneal thickness, and thickness maps of the cornea. Accuracy and repeatability of the extracted parameters obtained using a commercial 859nm SDOCT retinal imaging system with a corneal adapter were assessed using a rigid gas permeable (RGP) contact lens as a phantom target. Extraction of these parameters was performed in vivo in 3 patients and compared to commercial Placido topography and Scheimpflug photography systems. The repeatability of SDOCT central corneal power measured in vivo was 0.18 Diopters, and the difference observed between the systems averaged 0.1 Diopters between SDOCT and Scheimpflug photography, and 0.6 Diopters between SDOCT and Placido topography.

Analysis of ocean power extraction capabilites of a rotary wave energy conversion system

Gemstone Team WAVES (Water and Versatile Energy Systems)

Extraction of polydispersity information from photon correlation data

Photon correlation spectroscopy (PCS) is a light-scattering technique for particle size diagnosis. It has been used mainly in the investigation of hydrosol particles since it is based on the measurement of the correlation function of the light scattered from the Brownian motion of suspended particles. Recently this technique also proved useful for studying soot particles in flames and similar aerosol systems. In the case of a polydispersed system the problem of recovering the particle size distribution can be reduced to the problem of inverting the Laplace transform. In this paper we review several methods introduced by the authors for the solution of this problem. We present some numerical results and we discuss the resolution limits characterizing the reconstruction of the size distributions. © 1989.

Extraction of polydispersity information in photon correlation spectroscopy

info:eu-repo/semantics/published

Inorganic sulphate extraction from SO2-impacted Andosols

info:eu-repo/semantics/published

A coarse grid extraction of sound signals for computational aeroacoustics

Sound waves are propagating pressure fluctuations, which are typically several orders of magnitude smaller than the pressure variations in the flow field that account for flow acceleration. On the other hand, these fluctuations travel at the speed of sound in the medium, not as a transported fluid quantity. Due to the above two properties, the Reynolds averaged Navier–Stokes equations do not resolve the acoustic fluctuations. This paper discusses a defect correction method for this type of multi-scale problems in aeroacoustics. Numerical examples in one dimensional and two dimensional are used to illustrate the concept. Copyright (C) 2002 John Wiley & Sons, Ltd.

Numerical investigation of a source extraction technique based on an acoustic correction method

An aerodynamic sound source extraction from a general flow field is applied to a number of model problems and to a problem of engineering interest. The extraction technique is based on a variable decomposition, which results to an acoustic correction method, of each of the flow variables into a dominant flow component and a perturbation component. The dominant flow component is obtained with a general-purpose Computational Fluid Dynamics (CFD) code which uses a cell-centred finite volume method to solve the Reynolds-averaged Navier–Stokes equations. The perturbations are calculated from a set of acoustic perturbation equations with source terms extracted from unsteady CFD solutions at each time step via the use of a staggered dispersion-relation-preserving (DRP) finite-difference scheme. Numerical experiments include (1) propagation of a 1-D acoustic pulse without mean flow, (2) propagation of a 2-D acoustic pulse with/without mean flow, (3) reflection of an acoustic pulse from a flat plate with mean flow, and (4) flow-induced noise generated by the an unsteady laminar flow past a 2-D cavity. The computational results demonstrate the accuracy for model problems and illustrate the feasibility for more complex aeroacoustic problems of the source extraction technique.