Electrocardiogram (ECG/EKG) using FPGA

FPGAs (Field Programmable Gate Arrays) are finding wide acceptance in medical systems for their ability for rapid prototyping of a concept that requires hardware/software co-design, for performing custom processing in parallel at high data rates and be programmed in the field after manufacturing. Based on the market demand, the FPGA design can be changed and no new hardware needs to be purchased as was the case with ASICs (Application Specific Integrated Circuit) and CPLDs (Complex Programmable Logic Device). Medical companies can now move over to FPGAs saving cost and delivering highly-efficient upgradable systems. ECG (Electrocardiogram) is considered to be a must have feature for a medical diagnostic imaging system. This project attempts at implementing ECG heart-rate computation in an FPGA. This project gave me exposure to hardware engineering, learning about the low level chips like Atmel UC3A3256 micro-controller on an Atmel EVK1105 board which is used as a simulator for generating the ECG signal, the operational amplifiers for amplifying and level-shifting the ECG signal, the A/D converter chip for analog to digital conversion of the ECG signal, the internal workings of FPGA, how different hardware components communicate with each other on the system and finally some signal processing to calculate the heart rate value from the ECG signal

Real-time VLSI architecture for bio-medical monitoring

This paper discusses the architecture and implementation of SSS2, a high-performance real-time signal processing system developed with a hybrid ESL/RTL methodology and targeted to biomedical image processing. Traditional methodologies, as well as new tools, such as Cebatech's C2R untimed-C synthesizer have been employed in the design of the system. The SSS2 platform specifies a parametric number of scalar processing elements, based on multiple 32-bit Sparc-compliant engines, augmented with LE2, an ESL-designed 2-way LIW/SIMD accelerator. LE2, which is purely designed in C, exposes a consistent interface to its SIMD datapath directly which is directly derived from the C-source of open-source image processing codes. It is synthesized to Verilog RTL with C2R. Behaviorally-synthesized SIMD datapaths are then 'plugged-in' into the exposed LE2 datapath interface. The LE2 memory interface can be either a cache- based configurable vector load/store unit or a multi-banked, multi-channel streaming local memory system. Results drawn from this work strongly suggest a shift towards a hybrid approach in designing multi-core systems for high bandwidth streaming and for dealing with large scale medical image transfers and non-linear bio-signal processing algorithms

Mars Observer mission

The Mars Observer mission will extend the exploration and characterization of Mars by providing new and systematic measurements of the atmosphere, surface, and interior of the planet. These measurements will be made from a low-altitude polar orbiter over a period of 1 Martian year, permitting repetitive observations of the surface and of the seasonal variations of the atmosphere. The mission will be conducted in a manner that will provide new and valuable scientific data using a distributed data system that minimizes operational complexity and cost

Doctor of Philosophy

dissertationThis work describes the use of second harmonic generation (SHG) and ultraviolet-visible sum-frequency generation (UV-Vis SFG) to directly detect ligand-protein recognitions and drug-membrane associations. First, SHG spectroscopy was employed to detect protein-ligand binding for several model systems: avidin, streptavidin, neutrAvidinTM and anti-biotin antibody binding to biotin. The equilibrium binding affinities of these model systems were measured and compared with those values reported in literature to validate the ability of SHG to detect protein-ligand interactions without any chemical modification. Furthermore, the energetics of the protein-ligand binding and the protein nonspecific adsorption were evaluated to provide useful information about these protein-ligand pairs which are commonly used in many bioanalytical applications. Next, UV-Vis SFG spectroscopy was developed and utilized to detect drug-lipid membrane association for four drugs: ibuprofen, azithromycin, tetracaine, and tolnaftate. Drug association was measured on planar supported lipid bilayers composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine. The drugs' equilibrium association constants were obtained and correlated with the drugs' partition coefficients in the membrane-water system. Furthermore, the drug surface excess in the lipid membrane was quantitatively determined using the combination of the UV-Vis SFG and the bulk partition coefficient. It was shown that UV-Vis SFG is a powerful and novel technique to directly measure the association of drugs to a lipid membrane without chemical modification. Finally, SHG imaging was employed in the label-free detection of the interactions between tetracaine and a multicomponent planar supported lipid bilayer array (MLBA). The MLBAs allowed the effects of lipid phase and cholesterol content on tetracaine binding to be examined simultaneously. Additionally, tetracaine binding at different charge states and the effect of the charged lipids were investigated. The maximum surface excess of tetracaine in the lipid bilayers was also determined. This demonstrates that SHG imaging is a sensitive technique which can directly image and quantitatively measure the association of tetracaine in a high-throughput manner. This work has demonstrated that SHG and UV-Vis SFG are valuable alternatives in detection of biomolecular interactions at a lipid bilayer surface. The use of SHG or UV-Vis SFG imaging in combination with the MLBAs offer potential applications in high-throughput screenings of proteins and small molecules

Nanobiotechnologie: Werkzeuge für die Proteomik : molekulare Organisation und Manipulation von Proteinen und Proteinkomplexen in Nanodimensionen

First milestone of this Ph.D. thesis was the successful extension of conventional NTA/His-tag technique to self-assembling, multivalent chelator thiols for high-affinity recognition as well as stable and uniform immobilization of His-tagged proteins on chip surfaces. Bis-NTA was linked via an oligoethylene glycol to alkyl thiols by an efficient modular synthesis strategy yielding a novel, multivalent compound for formation of mixed SAMs with anti-adsorptive matrix thiols on gold. Multivalent chelator chips allow a specific, high-affinity, reversible, long-term immobilization of His-tagged proteins. In AFM studies reversibility of the specific protein immobilization process was visualized at single molecule level. The entire control over the orientation of the immobilized protein promotes this chip surface to an optimal platform for studies focusing on research targets at single molecule level and nanobiotechnology. Based on the constructed protein chip platform above and a novel AFM mode (contact oscillation mode, COM) – developed during the current Ph.D. work – protein nanolithography under physiological conditions enabling fabrication of active biomolecular patterns in countless variety has been established. Reversible COM-mediated nanostructuring is exceptionally suitable for multiplexed patterning of protein assemblies in situ. The first selfassembled protein layer acts as a biocompatible and ductile patterning material. Immobilized proteins can be replaced by the AFM tip applying COM, and the generated structures can be erased and refilled with different proteins, which are immobilized in a uniform and functional manner. Multi-protein arrays can be systematically fabricated by iterative erase-and-write processes, and employed for protein-protein interaction analysis. Fabrication of two-dimensionally arranged nanocatalytic centres with biological activity will establish a versatile tool for nanobiotechnology. As an alternative chip fabrication approach, the combined application of methodologies from surface chemistry, semiconductor technology, and chemical biology demonstrated successfully how pre-patterned templates for micro- and nanoarrays for protein chips are fabricated. The surface physical, as well the biophysical experiments, proved the functionality of this technology. The promises of such process technology are fast and economic fabrication of ready-to-use nanostructured biochips at industrial scale. Membrane proteins are complicated in handling and hence require sophisticated solutions for chip technological application. A silicon-on-insulator (SOI) chip substrate with microcavities and nanopores was employed for first technological investigation to construct a protein chip suitable for membrane proteins. The formation of an artificial lipid bilayer using vesicle fusion on oxidized SOI cavity substrates was verified by CLSM. Future AFM experiments will give further insights into the chip architecture and topography. This will provide last evidence of the sealing of the cavity by the lipid bilayer. Transmembrane proteins will be employed for reconstitution experiments on this membrane protein chip platform. Highly integrated microdevices will find application in basic biomedical and pharmaceutical research, whereas robust and portable point-of-care devices will be used in clinical settings.Erster Meilenstein der vorliegenden Arbeit war die erfolgreiche Erweiterung des konventionellen NTA/His-tag-Konzepts auf selbst-assemblierende, multivalente Chelatorthiole für die hochaffine Erkennung und stabile, einheitliche Immobilisierung His-getaggter Proteine auf Chipoberflächen. Mittels einer effizienten, modularen Synthesestrategie wurden Bis-NTA-Module über Oligoethylenglykoleinheiten an Alkylthiole angebunden. Diese Chelatorthiole wurden zusammen mit antiadsorptiven Matrixthiolen zur Ausbildung gemischter selbst-assemblierender Monolagen (SAMs) auf Goldoberflächen eingesetzt. Die multivalenten Chelatorchips erlauben eine spezifische, hochaffine, umkehrbare und langfristige Immobilisierung His-getaggter Proteine. Die Umkehrbarkeit der spezifischen Proteinimmobilisierung wurde in rasterkraftmikroskopischen (AFM) Studien bis zur Einzel-Molekül-Ebene visualisiert. Die vollständige Kontrolle über die Orientierung immobilisierter Proteine qualifiziert diese entwickelte Chipoberfläche zu einer optimalen Plattform für Anwendungsbereiche der Einzelmolekülbiochemie und Nanobiotechnologie. Basierend auf dieser Plattform für Proteinchips und einem – im Rahmen dieser Arbeit – neuentwickelten AFM-Modus (Kontaktoszillationsmodus, COM) wurde die „Protein-Nanolithographie“ etabliert, welche die Fabrikation von aktiven, biomolekularen Strukturen in unzähliger Vielfalt ermöglicht. Die umkehrbare COM-vermittelte Nanolithographie ist insbesondere für die multiplexe Anordnung von Proteinverbänden in situ geeignet. Die erste Schicht immobilisierter Proteine fungiert als ein biokompatibles und verformbares Strukturierungsmaterial. Diese immobilisierten Proteine können nun im Kontaktoszillationsmodus mit der AFM-Spitze lokal entfernt („Löschen“) und gegen andere Proteine – die an die freigelegte Chipoberfläche ebenfalls spezifisch und funktional immobilisieren – ausgetauscht werden („Schreiben“). Arrays, bestehend aus mehreren unterschiedlichen Proteinen können nun systematisch in iterativen Lösch-und-Schreib-Vorgängen fabriziert und für Proteininteraktionsanalysen eingesetzt werden. Die Fabrikation von zwei-dimensional arrangierten nanokatalytischen Zentren mit biologischer Aktivität wird von großem Nutzen für die Nanobiotechnologie sein. Eine alternative Herstellungsmethode aus einer Kombination von Oberflächenchemie, Halbleitertechnologie und chemischer Biologie wurde für die Fabrikation von vorstrukturierten Templaten für Mikro- und Nanoarrays entwickelt. Die Funktionalität dieser Chipplattform wurde anhand oberflächen- und biophysikalischer Experimente erfolgreich gezeigt. Zukünftiges Ziel ist die Anfertigung vorstrukturierter Template in der Dimension weniger Nanometer zur Ausbildung von Bio-Arrays mit einzelnen Molekülen. Ein weiteres Ziel besteht in der kompletten Verlagerung des Herstellungsprozesses in die Gasphase. Eine Produktion in der Gasphase verspricht eine schnelle und wirtschaftliche Erzeugung sofort einsatzbereiter nanostrukturierter Biochips im industriellen Maßstab. Der Umgang mit Membranproteinen verlangt besondere Vorkehrungen im experimentellen Milieu, ebenso speziell sind die Bedürfnisse in den entsprechenden Chip-Anwendungen. Ein Chip mit Mikrokavitäten und Nanoporen, basierend auf der „Silicon-on-Insulator“ (SOI)-Technologie, wurde für erste technologische Studien zum Entwurf eines Proteinchips für Membranproteine eingesetzt. Künstliche Lipidmembranen wurden auf der SOI-Oberfläche mittels Vesikelfusion ausgebildet und mit konfokaler Laser-Scanning-Mikroskopie gezeigt. Zukünftige AFM-Experimente werden weitere Einsichten in die Chiparchitektur und Topographie ermöglichen. Transmembranproteine werden in Rekonstitutionsexperimenten für funktionale Studien der Membranproteinchips eingesetzt. Anwendungsbereiche solcher hochintegrierten Mikrosysteme sind sowohl in der biologischen Grundlagenforschung als auch in mobilen Diagnostikgeräten im klinischen Einsatz zu finden

Cassini atmospheric chemistry mapper. Volume 1. Investigation and technical plan

The Cassini Atmospheric Chemistry Mapper (ACM) enables a broad range of atmospheric science investigations for Saturn and Titan by providing high spectral and spatial resolution mapping and occultation capabilities at 3 and 5 microns. ACM can directly address the major atmospheric science objectives for Saturn and for Titan, as defined by the Announcement of Opportunity, with pivotal diagnostic measurements not accessible to any other proposed Cassini instrument. ACM determines mixing ratios for atmospheric molecules from spectral line profiles for an important and extensive volume of the atmosphere of Saturn (and Jupiter). Spatial and vertical profiles of disequilibrium species abundances define Saturn's deep atmosphere, its chemistry, and its vertical transport phenomena. ACM spectral maps provide a unique means to interpret atmospheric conditions in the deep (approximately 1000 bar) atmosphere of Saturn. Deep chemistry and vertical transport is inferred from the vertical and horizontal distribution of a series of disequilibrium species. Solar occultations provide a method to bridge the altitude range in Saturn's (and Titan's) atmosphere that is not accessible to radio science, thermal infrared, and UV spectroscopy with temperature measurements to plus or minus 2K from the analysis of molecular line ratios and to attain an high sensitivity for low-abundance chemical species in the very large column densities that may be achieved during occultations for Saturn. For Titan, ACM solar occultations yield very well resolved (1/6 scale height) vertical mixing ratios column abundances for atmospheric molecular constituents. Occultations also provide for detecting abundant species very high in the upper atmosphere, while at greater depths, detecting the isotopes of C and O, constraining the production mechanisms, and/or sources for the above species. ACM measures the vertical and horizontal distribution of aerosols via their opacity at 3 microns and, particularly, at 5 microns. ACM recovers spatially-resolved atmospheric temperatures in Titan's troposphere via 3- and 5-microns spectral transitions. Together, the mixing ratio profiles and the aerosol distributions are utilized to investigate the photochemistry of the stratosphere and consequent formation processes for aerosols. Finally, ring opacities, observed during solar occultations and in reflected sunlight, provide a measurement of the particle size and distribution of ring material. ACM will be the first high spectral resolution mapping spectrometer on an outer planet mission for atmospheric studies while retaining a high resolution spatial mapping capability. ACM, thus, opens an entirely new range of orbital scientific studies of the origin, physio-chemical evolution and structure of the Saturn and Titan atmospheres. ACM provides high angular resolution spectral maps, viewing nadir and near-limb thermal radiation and reflected sunlight; sounds planetary limbs, spatially resolving vertical profiles to several atmospheric scale heights; and measures solar occultations, mapping both atmospheres and rings. ACM's high spectral and spatial resolution mapping capability is achieved with a simplified Fourier Transform spectrometer with a no-moving parts, physically compact design. ACM's simplicity guarantees an inherent stability essential for reliable performance throughout the lengthy Cassini Orbiter mission

Doctor of Philosophy

dissertationThe importance of lipid bilayers to the structure and function of cellular membranes coupled with their inherent complexity has driven the development of analytical techniques capable of high-throughput investigation of these surfaces. This work describes a continuous flow microspotter (CFM) that was modified to create micropatterned lipid bilayer arrays (MLBAs). This dissertation is divided into four main parts, with the first chapter focusing on the characterization of MLBAs using fluorescence microscopy to ensure bilayer formation and integrity. The individually addressable nature of the CFM was also demonstrated using a multi-ligand array containing ganglioside GM1, dinitrophenyl (DNP) and biotin. A multiple protein-ligand assay was performed using the ligand array to detect three different fluorescently labeled proteins (cholera toxin b (CTb), anti-DNP antibody and NeutrAvidin) from solution simultaneously. The second part of this dissertation concentrates on creating stable MLBAs using a polymerizable lipid, poly(bis-SorbPC) in order to generate a more robust biosensing platform. The poly(lipid) arrays were compared directly to the MLBAs prepared without the polymerizable lipids using fluorescence microscopy to demonstrate their superior stability. A multiple protein-ligand assay was also performed to demonstrate the utility of these arrays and their potential application as a sensor substrate. iv Next, the MLBAs were used to investigate the impact of fifteen different lipid components on small molecule-membrane binding. The lipophilic dye merocyanine 540 (MC540) was used as a model small molecule and its binding was monitored by fluorescence microscopy. These studies demonstrate the potential of using MLBAs to investigate drug membrane interactions while preserving time and cost-effectiveness. Finally, sum-frequency vibrational imaging (SFVI) was developed to provide a surface specific noninvasive, analytical technique capable of monitoring lipid structure and dynamics in a high-throughput manner. The vibrational sensitivity of SFVI was investigated with an asymmetric lipid bilayer patterned by ultraviolet (UV) radiation lithographically. The phase behavior of three different binary mixtures in a MLBA was successfully investigated using SFVI. The SFVI setup had the sensitivity, resolution and field of view required for exploring lipid bilayer properties in an array format. This dissertation presents a new approach for assembling lipid bilayer arrays in combination with a powerful analytical technique to allow exploration of the physical properties of lipid membranes in a high-throughput and noninvasive manner

Hardware Implementaion of Image Acquisition system using FPGA & ARM

In this paper, image data acquisition system has been introduced. In this task, a system of high-speed image data acquisition based on ARM and FPGA is designed according to the needs of actual system in image data transmission, which can be used in data monitoring and surveillance systems. The choice of ARM is a 32-bit embedded RISC microprocessor architecture, which has a rich instruction set and programming flexibility. FPGA has a great advantage in the speed and parallel computing, suitable for real-time requirements of image processing. The interface between camera module and FPGA as well as interface between FPGA and ARM is done using UART. Image from ARM is transmitted to PC using Ethernet

The use of Unmanned Aerial Vehicle based photogrammetric point cloud data for winter wheat intra-field variable retrieval and yield estimation in Southwestern Ontario

Precision agriculture uses high spatial and temporal resolution soil and crop information to control the crop intra-field variability to achieve optimal economic benefit and environmental resources sustainable development. As a new imagery collection platform between airborne and ground measurements, Unmanned Aerial Vehicle (UAV) is used to collect high spatial resolution images at a user selected period for precision agriculture. Most studies extract crop parameters from the UAV-based orthomosaic imagery using spectral methods derived from the satellite and airborne based remote sensing. The new dataset, photogrammetric point cloud data (PCD), generated from the Structure from Motion (SfM) methods using the UAV-based images contains the feature’s structural information, which has not been fully utilized to extract crop’s biophysical information. This thesis explores the potential for the applications of the UAV-based photogrammetric PCD in crop biophysical variable retrieval and in final biomass and yield estimation. First, a new moving cuboid filter is applied to the voxel of UAV-based photogrammetric PCD of winter wheat to eliminate noise points, and the crop height is calculated from the highest and lowest points in each voxel. The results show that the winter wheat height can be estimated from the UAV-based photogrammetric PCD directly with high accuracy. Secondly, a new Simulated Observation of Point Cloud (SOPC) method was designed to obtain the 3D spatial distribution of vegetation and bare ground points and calculate the gap fraction and effective leaf area index (LAIe). It reveals that the ground-based crop biophysical methods are possible to be adopted by the PCD to retrieve LAIe without ground measurements. Finally, the SOPC method derived LAIe maps were applied to the Simple Algorithm for Yield estimation (SAFY) to generate the sub-field biomass and yield maps. The pixel-based biomass and yield maps were generated in this study revealed clearly the intra-field yield variation. This framework using the UAV-based SOPC-LAIe maps and SAFY model could be a simple and low-cost alternative for final yield estimation at the sub-field scale. The results of this thesis show that the UAV-based photogrammetric PCD is an alternative source of data in crop monitoring for precision agriculture