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Sapphire fiber has been studied intensively for harsh environment sensing in the past two decades due to its supreme mechanical, physical and optical properties. It is by far the most reported and likely the best optical fiber based sensing technology for sensing applications in temperature beyond 1000°C. Several sensing schemes have been proposed and studied to date including sapphire fiber extrinsic and intrinsic Fabry-Perot interferometers, fiber Bragg gratings and long period gratings inscribed in sapphire fibers. Lacking the cladding, sapphire fiber is highly multi-moded which renders sapphire fiber based sensor fabrication much more difficult than those based on silica fibers. Among all the reported work on sapphire fiber sensing, the vast majority is for single point temperature measurement. In this work, different sensing schemes are proposed to enhance the capability of the sapphire fiber based sensing technology. For the single point sensing, a miniaturized sapphire fiber temperature sensor for embedded sensing applications was proposed and studied. The sensors are no more than 75 µm in diameter and are ideal for non-invasive embedded sensing applications. Unlike existing sapphire fiber sensors, the thin film sensors are batch-fabrication oriented and thus have a potential to permit mass production with low cost. In addition to single point sensors, multiplexed sapphire fiber sensing systems are investigated for the first time. Two multiplexed sensing solutions, named frequency-multiplexing and spatial-multiplexing, are proposed and studied to achieve multiplexed sensing based on sapphire fibers. / Ph. D.

Made available in DSpace on 2016-03-15T19:38:10Z (GMT). No. of bitstreams: 1 Mauricio Moderno de Carvalho.pdf: 2212181 bytes, checksum: 274e2da279304668d738afe9e3483c45 (MD5) Previous issue date: 2008-08-06 / Fundo Mackenzie de Pesquisa / By adopting a ring topology and optical switches we propose a novel protection mechanism for time division multiplexed passive optical network (TDM-PON) that provides resilience against multiple network fails. Some protection schemes have been proposed in order to give resilience for passive optical network (PON) as defined at ITU-T Recommendation G983.1. However that recommendation defines the optical distribution network (ODN) and equipment duplication to protect it against multiple points of fail. We propose a ring topology with dual fibers paths capable to protect the network by switching these lines individually according to the local alarms detected by each optical network unit (ONU). According to our proposal neither equipment nor network should be duplicated to provide survivability to the system. / Adotando uma topologia em anel e chaves ópticas, estamos propondo um novo mecanismo de proteção para redes ópticas passivas TDM (Time Division Multiplexed) que possibilita a proteção da rede contra múltiplos pontos de falha. Muitos esquemas de proteção foram propostos para dar confiabilidade para as redes ópticas passivas como definido pela recomendação ITUT G.983.1. Para permitir proteção contra múltiplos pontos de falhas a recomendação ITU-T define a duplicação da rede óptica (ODN) e equipamento. Apresentamos, então, uma topologia em anel com dois caminhos ópticos distintos protegendo a rede pela comutação individual destas linhas de acordo com a detecção de alarmes locais por cada Optical Network Unit (ONU). Conforme nossa proposta, nem o equipamento ou a rede precisam ser duplicadas para prover proteção do sistema.

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abstract: This work describes efforts made toward the development of a compact, quantitative fluorescence-based multiplexed detection platform for point-of-care diagnostics. This includes the development of a microfluidic delivery and actuation system for multistep detection assays. Early detection of infectious diseases requires high sensitivity dependent on the precise actuation of fluids. Methods of fluid actuation were explored to allow delayed delivery of fluidic reagents in multistep detection lateral flow assays (LFAs). Certain hydrophobic materials such as wax were successfully implemented in the LFA with the use of precision dispensed valves. Sublimating materials such as naphthalene were also characterized along with the implementation of a heating system for precision printing of the valves. Various techniques of blood fractionation were also investigated and this work demonstrates successful blood fractionation in an LFA. The fluid flow of reagents was also characterized and validated with the use of mathematical models and multiphysics modeling software. Lastly intuitive, user-friendly mobile and desktop applications were developed to interface the underlying Arduino software. The work advances the development of a system which successfully integrates all components of fluid separation and delivery along with highly sensitive detection and a user-friendly interface; the system will ultimately provide clinically significant diagnostics in a of point-of-care device. / Dissertation/Thesis / Masters Thesis Biomedical Engineering 2018

The wavelength-division-multiplexed passive optical network (WDM-PON) offers many advantages such as large bandwidth per user, easy management, high network security and low insertion loss enabling long-reach and/or high split-ratio. However, with the rapid development and growing interest for deployment of WDM-PON, the PON systems are becoming increasingly vulnerable to various failures. Therefore, network supervision becomes extremely important to guarantee an appropriate level of network reliability performance. The aim of PON supervision is to provide automated test and diagnostic capability without compromising the available bandwidth for services. An essential function is to detect any kind of deterioration in the network that can cause suspended services and to remotely localize these faults in order to avoid the high cost arising from troubleshooting. In this thesis, we evaluate several existing WDM PON supervision methods, based on which two simple and cost-effective new solutions are proposed to localize fiber failures in WDM PON systems. In the first solution, a conventional optical time domain reflectometry (OTDR) and a switch unit are employed, while in the second method, a novel architecture based on N×N arrayed waveguide grating (AWG) is proposed. Both methods are able to localize failures in feeder fiber and drop fibers without e.g. using expensive tunable OTDRs. A patent has been filed based on the second solution. The first proposed method is validated by simulations using VPI Transmission Maker. According to the results, this supervision method is able to give accurate measurement of many different types of failures that may happen in a fiber link. Furthermore, VPI is examined in terms of its future applicability in modeling complete PON supervision methods based on OTDR.

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Data acquisition from multiple analog channels is an important function in many embedded devices used in avionics, medical electronics, robotics and space applications. It is desirable to engineer these systems to reduce their size, power consumption, heat dissipation and cost. The goal of this research is to explore designs that exploit a priori knowledge of the input signals in order to achieve these objectives. Sparsity is a commonly observed property in signals that facilitates sub-Nyquist sampling and reconstruction through compressed sensing, thereby reducing the number of A to D conversions. New architectures are proposed for the real-time, compressed acquisition of streaming signals. A. It is demonstrated that by sampling a collection of signals in a multiplexed fashion, it is possible to efficiently utilize all the available sampling cycles of the analogue-to-digital converters (ADCs), facilitating the acquisition of multiple signals using fewer ADCs. The proposed method is modified to accommodate more general signals, for which spectral leakage, due to the occurrence of non-integral number of cycles in the reconstruction window, violates the sparsity assumption. When the objective is to only detect the constituent frequencies in the signals, as against exact reconstruction, it can be achieved surprisingly well even in the presence of severe noise (SNR ~ 5 dB) and considerable undersampling. This has been applied to the detection of the carrier frequency in a noisy FM signal. Information redundancy due to inter-signal correlation gives scope for compressed acquisition of a set of signals that may not be individually sparse. A scheme has been proposed in which the correlation structure in a set of signals is progressively learnt within a small fraction of the duration of acquisition, because of which only a few ADCs are adequate for capturing the signals. Signals from the different channels of EEG possess significant correlation. Employing signals taken from the Physionet database, the correlation structure of nearby EEG electrodes was captured. Subsequent to this training phase, the learnt KLT matrix has been used to reconstruct signals of all the electrodes with reasonably good accuracy from the recordings of a subset of electrodes. Average error is below 10% between the original and reconstructed signals with respect to the power in delta, theta and alpha bands: and below 15% in the beta band. It was also possible to reconstruct all the channels in the 10-10 system of electrode placement with an average error less than 8% using recordings on the sparser 10-20 system. In another design, a set of signals are collectively sampled on a finer sampling grid using ADCs driven by phase-shifted clocks. Thus, each signal is sampled at an effective rate that is a multiple of the ADC sampling rate. So, it is possible to have a less steep transition between the pass band and the stop band, thereby reducing the order of the anti-aliasing filter from 30 to 8. This scheme has been applied to the acquisition of voltages proportional to the deflection of the control surfaces in an aerospace vehicle. The idle sampling cycles of an ADC that performs compressive sub-sampling of a sparse signal, can be used to acquire the residue left after a coarse low-resolution sample is taken in the preceding cycle, like in a pipelined ADC. Using a general purpose, low resolution ADC, a DAC and a summer, one can acquire a sparse signal with double the resolution of the ADC, without having to use a dedicated pipelined ADC. It has also been demonstrated as to how this idea can be applied to achieve a higher dynamic range in the acquisition of fetal electrocardiogram signals. Finally, it is possible to combine more than one of the proposed schemes, to handle acquisition of diverse signals with di_erent kinds of sparsity. The implementation of the proposed schemes in such an integrated design can share common hardware components so as to achieve a compact design.

abstract: Over the past several decades, there has been a growing interest in the use of fluorescent probes in low-cost diagnostic devices for resource-limited environments. This dissertation details the design, development, and deployment of an inexpensive, multiplexed, and quantitative, fluorescence-based lateral flow immunoassay platform, in light of the specific constraints associated with resource-limited settings. This effort grew out of the need to develop a highly sensitive, field-deployable platform to be used as a primary screening and early detection tool for serologic biomarkers for the high-risk human papillomavirus (hrHPV) infection. A hrHPV infection is a precursor for developing high-grade cervical intraepithelial neoplasia (CIN 2/3+). Early detection requires high sensitivity and a low limit-of-detection (LOD). To this end, the developed platform (DxArray) takes advantage of the specificity of immunoassays and the selectivity of fluorescence for early disease detection. The long term goal is to improve the quality of life for several hundred million women globally, at risk of being infected with hrHPV. The developed platform uses fluorescent labels over the gold-standard colorimetric labels in a compact, high-sensitivity lateral flow assay configuration. It is also compatible with POC settings as it substitutes expensive and bulky light sources for LEDs, low-light CMOS cameras, and photomultiplier tubes for photodiodes, in a transillumination architecture, and eliminates the need for expensive focusing/transfer optics. The platform uses high-quality interference filters at less than $1 each, enabling a rugged and robust design suitable for field use. The limit of detection (LOD) of the developed platform is within an order of magnitude of centralized laboratory diagnostic instruments. It enhances the LOD of absorbance or reflectometric and visual readout lateral flow assays by 2 - 3 orders of magnitude. This system could be applied toward any chemical or bioanalytical procedure that requires a high performance at low-cost. The knowledge and techniques developed in this effort is relevant to the community of researchers and industry developers looking to deploy inexpensive, quantitative, and highly sensitive diagnostic devices to resource-limited settings. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2018

Silicon-based electric DNA chip arrays were utilized to fast identify pathogenic microorganisms with respect to the capacity to produce toxins involved in foodborne poisoning and infections. Bacteria of the B. cereus and the enterohemorrhagic E. coli (EHEC) groups contain different set-ups of various virulence factors that are encoded by the corresponding genes. The purpose of this work was to develop a fast and simple method for determination of the presence of these virulence genes in a colony from primary enrichment cultures. A target gene is detected through hybridization to a surface-immobilized specific capture probe and biotin-labeled detection probe. Following binding of an enzyme conjugate to this sandwich hybrid complex, a current signal is generated by electronic redox recycling of the enzymatic product paminophenol (pAP). Two versions of the assay were developed. In the first version the capture probes were immobilized on magnetic beads, which carried out all reactions until the pAP generation, while the final electric signal was created by transferring pAP to a single-electrode chip surface. In the second version a silicon chip array with 16 parallel sensing electrode positions each of them functionalized by capture probes, carried out all assay steps on the chip surface. This instrument can realize automatic and multiplexed gene detection. The kinetics of bacterial cell disruption and impact of DNA fragmentation by ultrasound were determined. The experimental data suggested that the increased signal after first minutes of ultrasonication were due to the accumulation of released DNA amount, while the further signal increase resulted from the improved hybridization with the shortened target DNA strands. Studies on probe localization on the 16-electrode chip assays indicated that the probe-targeting site, which was located at the 5’-end of strands, gave rise to the highest signal level due to the efficient targetprobes hybridization and the following enzyme binding. When these functionalized chip arrays were exposed to the cell homogenates, the sensing electrodes were fouled by cellular proteins and therefore led to dramatically decreased redox-recycling current. To circumvent this, samples were treated by DNA extraction after the 1st sonication and then DNA fragmentation by a 2nd time sonication. The DNA extract removed most of the interfering components from bacterial cell. This sample treatment was applied to characterize one “diarrheal” and one “emetic” strain of B. cereus with the chip arrays functionalized by eight DNA probes. The signal patterns of eight virulence genes from chip assays agreed well with PCR control analyses for both strains. By simply adding the SDS detergent to cell homogenates, chip surface blocking effect can be significantly reduced even without DNA extraction treatment. After optimization of some critical factors, the 16-electrode DNA chips with the improved sensing performance can directly detect multiple virulence genes from a single E. coli colony in 25 min after the introduction of supernatant of ultrasonicated cell lysate. / QC 20100824