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This dissertation develops technology for microfluidic point-of-care (POC) immunoassay devices, divided into three papers, and explores the use of a quartz crystal microbalance for real time monitoring of blood coagulation in a fourth paper. The concept of POC testing has been well established around the world. With testing conveniently brought to the vicinity of the patient or testing site, results can be obtained in a much shorter time. There has been a global push in recent years to develop POC molecular diagnostics devices for resource-limited regions where well equipped centralized laboratories are not readily accessible. POC testing has applications in medical/veterinary diagnostics, environmental monitoring, as well as defense related testing. In the first paper, we demonstrated the use of latex immunoagglutination assays within a microfluidic chip to be an effective and sensitive method for detecting the bovine viral diarrhea virus. In the second paper the feasibility and general ease of integrating liquid core optical components onto a microfluidic lab-on-a-chip type device, for point-of-care AI diagnosis is demonstrated. In the third paper particle agglutination assays, utilizing light scattering measurements at a fixed angle from incident light delivery, for pathogen detection are explored in both Rayleigh and Mie scatter regimes through scatter intensity simulations and compared to experimental results. In the fourth paper a quartz crystal microbalance was used for real-time monitoring of fibrinogen cross-linking on three model biomaterial surfaces.

This dissertation describes the design, fabrication and testing of an oblique incidence diffuse reflectance spectrometry (OIDRS) system for in-vivo and noninvasive detection of epithelial cancer. Two probes were fabricated using micromachining technology, which plays a significant role in the probe development by enabling device miniaturization, low-cost fabrication and precise assembly. The fist probe was developed and clinically tested for skin cancer detection. This probe consists of three source fibers, two linear array of collection fibers and four micromachined positioning devices for accurate alignment of the fibers. The spatially resolved diffuse reflectance spectra from 167 pigmented and 78 non-pigmented skin abnormalities were measured and used to design a set of classifiers to separate them into benign or malignant ones. These classifiers perform with an overall classification rate of 91%. The absorption and reduced scattering coefficient spectra were estimated to link the anatomic and physiologic properties of the lesions with the optical diagnosis. The melanoma cases presented larger average absorption and reduced scattering spectra than the dysplastic and benign ones. A second probe was designed to demonstrate the feasibility of a miniaturized ?side viewing? optical sensor probe for OIDRS. The sensor probe consists of a lithographically patterned polymer waveguides chip and two micromachined positioning substrates. This miniaturize probe was used to measure twenty ex-vivo esophageal samples. Two statistical classifiers were designed to separate the esophageal cases. The first one distinguishes benign and low dysplastic from high dysplastic and cancerous lesions. The second classifier separates benign lesions from low dysplastic ones. Both classifiers generated a classification rate of 100%.

abstract: An imaging measurement technique is developed using surface plasmon resonance. Plasmonic-based electrochemical current imaging (P-ECi) method has been developed to image the local electrochemical current optically, it allows us to measure the current density quickly and non-invasively [1, 2]. In this thesis, we solve the problems when we extand the P-ECi technique to the field of thin film system. The P-ECi signal in thin film structure was found to be directly proportional to the electrochemical current. The upper-limit of thin film thickness to use the proportional relationship between P-ECi signal and EC current was discussed by experiment and simulation. Furthermore, a new algorithm which can calculate the current density from P-ECi signal without any thickness limitation is developed and tested. Besides, surface plasmon resonance is useful phenomenon which can be used to detect the changes in the refractive index near the gold sensing surface. With the assistance of pH indicator, by applied EC potential on the gold film as the working electrode, the detection of H2 evolution reaction can be enhanced. This measurement technique is useful in analyzing local EC information and H2 evolution. References [1] S. Wang, et al., "Electrochemical Surface Plasmon Resonance: Basic Formalism and Experimental Validation," Analytical Chemistry, vol. 82, pp. 935-941, 2010/02/01 2010. [2] X. Shan, et al., "Imaging Local Electrochemical Current via Surface Plasmon Resonance," Science, vol. 327, pp. 1363-1366, March 12, 2010 2010. / Dissertation/Thesis / M.S. Electrical Engineering 2013

This dissertation discusses the development of inexpensive, easy-to-use, and field-deployable diagnostic techniques and devices for the early detection of various pathogens, commonly found in clinical samples and contaminated food and water. Infectious diseases account for about 90% of world health problems, killing approximately 14 million people annually, the majority of which reside in developing countries. In 2012, the World Health Organization (WHO) published data on the top 10 causes of death across the globe. Although communicable disease is a prevalent cause of fatality, both low-income and high-income countries, pathogen species and transmission are very different. Nearly 60% of deaths in developing countries are caused by food, water, air or blood-borne pathogens. The most prevalent illnesses are diarrheal disease, malaria, and HIV/AIDS. By contrast, the leading causes of death in developed countries (heart disease, cancer, and stroke) are not communicable and are often preventable. However, there is an increasing need for the development of rapid and accurate methods for pathogen identification in clinical samples, due to the growing prevalence of antibiotic-resistant strains. Incorrect, or unneeded antibiotic therapies result in the evolution of extremely aggressive nosocomial (hospital-acquired) infections, such as methicillin- (MRSA) and vancomycin-resistant Staphylococcus aureus (VRSA). The implementation of rapid, easy to use and cost-effective diagnostics will reduce the frequency of pathogen-related deaths in underdeveloped countries, and improve targeted antibiotic treatment in hospital settings, thus decreasing the potential development of more treatment-resistant "super bugs". This research includes novel techniques utilizing two major sensing modalities: serological (i.e. immunological), and nucleic acid amplification testing (NAATs). We first developed a highly sensitive (limit-of-detection = 100 CFU mL-1) particle immunoassay that takes advantage of elastic and inelastic light scatter phenomena, for optical detection of target antigens. This assay is performed upon a unique nanofibrous substrate that promotes multiplexing on a user-friendly platform. We then developed a novel technique, termed emulsion loop-mediated isothermal amplification (eLAMP), in which the target amplicon is detected in real-time, again utilizing light scattering detection and quantification. Both techniques require no sample pre-treatments, and can be combined with smartphone imaging for detection of targets in under 15 minutes. These methods have the potential to improve the speed and sensitivity of early pathogenic identification, thus leading to a reduction in preventative deaths and a decrease in global economic costs associated with infectious disease in clinical and other settings.

Title: Automation of dust charging experiment Author: Radim Pechal Department: Department of Surface and Plasma Science Supervisor: RNDr. Jiří Pavlů, PhD. Supervisor's e-mail address: Jiri.Pavlu@mff.cuni.cz Abstract: Since the dust grains are expected to cause problems during operation of tokamaks, there is a developing research of these devices which raises interest in dust grain charging processes research as well. Clarification of the dust grain charging processes may help with their solutions. This thesis deals with an issue of designing a part of a new experimental setup for dust grain research built at the Department of Surface and Plasma Science, Charles University in Prague. The base of this experimental setup is original linear quadrupole trap enabling dust grain trapping and its charging by electron, ion, and UV beams. In the thesis, a method of stabilization of one part of grain oscillation frequency detection is described. The thesis is focused on a development of a control unit and high voltage power supply for an image intensifier. To measure charging processes tungsten dust grains were used. This material will be probably used in construction of ITER tomakak. Electron equilibrium characteristics and other parameters were measured. Two samples of tungsten dust grains were used for...

The examination of the application and accuracy of optical sensors for the purpose of determining rail lubricity of top-of-rail friction modifier is investigated in this research. A literature review of optical sensors as they relate to detecting thin layers is presented, as well as a literature review of the significant aspect of surface roughness on optical signature. Both commercially available optical sensors and optical devices, such as independent lasers and detectors, are examined in a comprehensive parametric study to determine the most suitable configuration for a prototype with adequate third-body detection. A prototype is constructed considering parameters such as sunlight contamination, vibrations, and angle of detection. The prototype is evaluated in a series of laboratory tests with known lubricity conditions for its accuracy of measurements and susceptibility to environmental conditions, in preparation for field testing. Upon field testing the prototype, the data indicates that it is capable of providing subjective measurements that can help with determining whether a rail is highly lubricated or unlubricated, or it is moderately lubricated. It is anticipated that the device could be used to provide a rail lubricity index. The investigation of the optical response of a rail in various conditions, including top-of-rail friction modifier presence and underlying surface roughness, reveals the behavior of friction modifying material on rail/wheel interactions. It is determined that surface roughness is imperative for distinguishing between scattering due to surface condition and scattering due to third-body layers. Additionally it is revealed that friction modifying materials become entrapped within the surface roughness of the rail, effectively causing a "seasoning" effect instead of a simple third body layer. This provides some explanation on the inadequacy of determining lubricity conditions using contacting methods since they cannot detect the entrapped material that are revealed only when the top of rail undergoes a micro deformation due to a passing wheel. Furthermore, the fluorescent signature of flange grease can be utilized to detect any flange grease contamination on top of rail. The results of the study indicate that it is possible to have practical optical sensors for top-of-rail third body layer detection and any contamination that may exist, initially through spot checking the rail and eventually through in-motion surveying. / Master of Science / Top-of-rail friction modifiers are used in the railway industry for a variety of reasons, including, but not limited to, reduction in wear and fuel savings; although their use has been widely accepted, methods of detection of such materials have not been adequately developed. Presently, methods of measurement of physical aspects of a rail are used in order to deduce the presence or lack of friction modifier on top-of-rail. However, no direct method of measurement exists in the published literature today. This study examines the use of optical sensors for the purpose of determining rail lubricity conditions. The literature is reviewed in this study for all applicable topics pertaining to the optical detection of top-of-rail friction modifier, including the optical theory used and the importance of surface roughness on an optical signature. Different characteristics of optical sensors are examined and a configuration is determined for the construction of a prototype device. This device utilizes laser reflective detectors and a fluorescence sensor in order to distinguish friction modifier presence or other third-body layers. This prototype was tested and evaluated in a series of laboratory tests with known lubricity conditions in preparation for field testing. Additionally, metrics were developed using optical theory in order to quantify the differences between different lubricity conditions. It was seen that this prototype was able to determine the presence of friction modifier by its laser reflective properties, and the presence of flange grease contamination through its fluorescence signature. Field testing with this prototype confirmed the prototype’s ability to distinguish adequate lubricity conditions using these metrics. It is anticipated that the device could be used to provide a rail lubricity index that is able to aid railway professionals in maintenance practices regarding rail lubricity.

This research serves to evaluate the ability of optical detection techniques to ascertain the lubricity of revenue service track from a moving platform for railroad applications. A literature review is presented that covers the rail vehicle dynamics that drive the need of Top-of-Rail lubrication and directly affect the manner in which the Top-of-Rail Friction Modifiers (TORFM) and flange grease both spread down rail and eventually wear away. This literature review also highlights previous research in the field of rail lubrication and the benefits that rail lubricants, specifically TORFM, provide for the railroads. Finally, the literature review covers the governing optical principals inherent to the synchronous spot radiometer that has been developed for use in the research as a gloss ratio instrument and also addresses the drawbacks and challenges inherent to applying this type of instrument in the railroad industry. The research then overviews previous rail lubricity sensors developed by the Railway Technologies Laboratory (RTL) at Virginia Tech and the lessons learned from their application. The preceding field testing conducting with a modified second generation rail lubricity sensor and a rail push car is briefly summarized with emphasis on the drawbacks and issues that were used to develop the third generation sensor used for this research. The development of the third generation sensor is covered, including the issues that it attempts to solve from its predecessor and the governing optical principals that govern the operation of the sensor. The laboratory evaluations conducting to commission the sensor are also covered in preparation for deploying the new third generation sensor in medium speed, medium distance revenue service testing. This includes a shakedown run on a siding in Riverside, VA prior to conducting mainline in-service testing. Finally, this research thesis covers the in-service testing on revenue track conducted with the new third generation rail lubricity sensor and the accompanying remote-controlled (RC) rail cart. The two components, when combined, create a Lubricity Assessment System which is capable of being operated at speeds upwards of 10 mph remotely from a follow hy-rail truck. The data collected from this field test is analyzed for the lubricity assessments that are able to be drawn from this initial phase of field service testing. The conclusions from this testing affirm the ability of optical methods to determine and evaluate Top-of-Rail (TOR) lubricity from a moving platform. Specifically, the new sensor is able to identify several local phenomena that demonstrate the high potential for errant evaluation of rail lubricity evaluation from spot check based methods that are solved by evaluating the track in a continuous, moving fashion. Based on the continuous moving data collected for this test, several new signal traits such as the spatial frequency (wavenumber) associated with the passing freight cart wheels in the lubricity signal and the phantom applicator effect of transient lubricity conditions at the entrances and exits of curves can be detected and investigated. The success of this research indicates the continued evaluation of lubricity signals from a moving platform is warranted and suggests the potential for introducing one of these systems to various track metrology cars deployed throughout the United States railroads. / Master of Science / The United States railroads have been employing rail lubricants to the rails since the beginning of the industry and have recently, in the past 20 years, introduced another type of lubricant: Top-of-Rail Friction Modifiers (TORFM). TORFM creates a third body layer between the train wheels and the Top-of-Rail surface to minimize asset wear of both the wheel and rail and to increase the train efficiency. As the United States railroads embrace Precision Scheduled Railroading (PSR), increased train efficiency can allow the railroads to run longer trains with fewer locomotives. This increases the efficiency and capability of the rail network and also decreases the fuel burned and the amount of rail and wheel wear. TORFM has been proven to be effective and is widely adopted, but the railroads are still in need of tools to determine the presence and absence of these thin and often nearly invisible layers of lubricant on the rail surface. This research uses lasers as tool to quantify the level of lubrication of the rail surface. The presence of rail lubricants, such as TORFM, on the rail surface change the amount of light that is reflected and scattered off the shiny steel surface. These changes are often small but can be captured by photodetectors housed in the instrument. By plotting the detected sensor values, trends in the lubricity signal can be tracked and evaluated to determine the presence or absence of rail lubricants and assess the overall quality of lubrication on the rail at specific locations down track. The research in this thesis takes existing methods that were used for single spot inspections and adapts them to a moving platform. The moving platform is able to continuously scan the Top-of-Rail surface as the instrument moves along and generates continuous moving evaluations of rail lubricity. This can be especially important when the lubricity is not uniform and allows for trends in the data to be analyzed to provide more consistent and precise evaluations of the lubricity trends down rail. Optical tools like this sensor, which are by nature non-contact sensors, can easily be adapted to existing track measurement railcars and deployed system wide. This solves a strong need for railroad engineers: to be able to identify the presence of rail lubricants and evaluate the effectiveness of their lubrication practices.

QC 351 A7 no. 07 / The Meinel Reducing Camera for the U. S. Naval Observatory's 60-inch telescope, Flagstaff, Arizona, comprises an f /10 collimator designed by Meinel and Wilkerson, and a Leica 50-mm f/2 Summicron camera lens. The collimator consists of a thick, 5-inch field lens located close to the focal plane of the telescope, plus four additional elements extending toward the camera. The collimator has an efl of 10 inches, yielding a 1-inch exit pupil that coincides with the camera's entrance pupil, 1.558 inches beyond the final surface of the collimator. There is room between the facing lenses of the collimator and camera to place filters and a grating. The collimated light here is the best possible situation for interference filters. Problems of the collimator design work included astigmatism due to the stop's being so far outside the collimator, and field curvature. Two computer programs were used in development of the collimator design. Initial work, begun in 1964, was with the University of Rochester's ORDEALS program (this was the first time the authors had used such a program) and was continued through July, 1965. Development subsequently was continued and completed on the Los Alamos Scientific Laboratory's program, LASL. The final design, completed January 24, 1966, was evaluated with ORDEALS. This project gave a good opportunity to compare ORDEALS, an "aberration" program, with LASL, a "ray deviation" program. It was felt that LASL was the superior program in this case, and some experimental runs beginning with flat slabs of glass indicated that it could have been used for the entire development of the collimator. Calculated optical performance of the design indicated that the reducing camera should be "seeing limited" for most work. Some astigmatism was apparent, but the amount did not turn out to be harmful in actual astronomical use. After the final design was arrived at, minor changes were made to accommodate actual glass indices of the final melt, and later to accommodate slight changes of radii and thicknesses of the elements as fabricated. An additional small change in spacing between two of the elements was made at the observatory after the reducing camera had been in use for a short time. The fabricated camera is working according to expectations. Some photographs are included in the report to illustrate its performance and utility.

The quantitative measurement of structural alterations at the nanoscale level is important for understanding the physical states of weakly disordered optical mediums such as cells/tissues. Progress in certain diseases, such as cancer or abnormalities in the brain, is associated with the nanoscale structural alterations at basic building blocks of the cells/tissues. Elastic light scattering, especially at visible wavelengths range provides non-invasive ways to probe the cells/tissues up to nanoscale level. Therefore, a mesoscopic physics-based open light scattering technique with added finer focusing, partial wave spectroscopy (PWS), is developed to probe nanoscale changes. Then, molecular-specific light localization technique, a close scattering approach called inverse participation ratio (IPR) is proposed that is sensitive to nano to microstructural cell/tissue alterations. In this dissertation, we have introduced the further engineered PWS system with the finer focus for precise volume scattering and molecular-specific light localization IPR techniques. As an application of PWS, we first probe precise scattering volume in commercially available tissue microarrays (TMA) tissue samples to standardize the existing cancer diagnostic methods by distinguishing the cancer stages. We also apply the PWS technique to probe chemotherapy drug-treated metastasizing cancer patients by xenografting prostate cancer cells using a mouse model and identify drug-sensitive and drug-resistance treatment cases. On the other hand, as an illustration of another mesoscopic physics-based molecular specific light localization technique, Confocal-IPR, we study the effects of a probiotic on chronic alcoholic mice brains by targeting the molecular specific alteration in glial cells, astrocytes and microglia, and chromatin of the brain cells through staining with appropriate dyes/proteins. Using structural disorder of IPR as a biomarker, the results show that probiotics in the presence of alcohol are beneficial and help overall brain health. Finally, a TEM-IPR study was performed using nanoscale resolution TEM imaging to support the optical IPR method by studying the anti-cancerous drug effect in ovarian cancer cells. The result shows that we can quantitatively measure the effect of anti-cancerous drugs in cancer treatment and the level of tumorigenicity far below the diffraction limit, and it has a similar effect and supports the optical IPR method.