CE provides evidence of the stereoselective hydroxylation of norketamine in equines

CE with multiple isomer sulfated-CD as selector was used for the simultaneous analysis of the stereoisomers of ketamine, norketamine, 5,6-dehydronorketamine and hydroxylated metabolites of norketamine in liquid/liquid extracts of (i) in vitro incubations with ketamine or norketamine and equine liver microsomes and (ii) plasma and urine of ponies receiving a target-controlled infusion of ketamine under isoflurane anesthesia. Hydroxynorketamine metabolites with the hydroxy group at the cyclohexanone ring could be shown to be formed stereoselectively both in vitro and in vivo. Due to the lack of standard compounds, urinary extracts were fractionated by HPLC followed by characterization of the collected fractions with CE and LC-MS(n) with 0.7 mmu mass discrimination. Comparison of LC-MS(n) data obtained with the fractions, an in vitro microsomal sample, and both pony urine and hydrolyzed pony urine led to the identification of four hydroxylated norketamine metabolites with hydroxylation at the cyclohexanone ring, two with hydroxylation at the aromatic ring and four hydroxylated metabolites of ketamine. Due to the lower detection sensitivity, only the four hydroxynorketamine metabolites with hydroxylation at the cyclohexanone ring were observed by CE. The data suggest that demethylation of ketamine followed by hydroxylation of norketamine at the cyclohexanone ring is the major metabolic pathway in equine species and that the ketamine metabolism is highly stereoselective.

An integrated system for 3D hip joint reconstruction from 2D X-rays: a preliminary validation study

The acquisition of conventional X-ray radiographs remains the standard imaging procedure for the diagnosis of hip-related problems. However, recent studies demonstrated the benefit of using three-dimensional (3D) surface models in the clinical routine. 3D surface models of the hip joint are useful for assessing the dynamic range of motion in order to identify possible pathologies such as femoroacetabular impingement. In this paper, we present an integrated system which consists of X-ray radiograph calibration and subsequent 2D/3D hip joint reconstruction for diagnosis and planning of hip-related problems. A mobile phantom with two different sizes of fiducials was developed for X-ray radiograph calibration, which can be robustly detected within the images. On the basis of the calibrated X-ray images, a 3D reconstruction method of the acetabulum was developed and applied together with existing techniques to reconstruct a 3D surface model of the hip joint. X-ray radiographs of dry cadaveric hip bones and one cadaveric specimen with soft tissue were used to prove the robustness of the developed fiducial detection algorithm. Computed tomography scans of the cadaveric bones were used to validate the accuracy of the integrated system. The fiducial detection sensitivity was in the same range for both sizes of fiducials. While the detection sensitivity was 97.96% for the large fiducials, it was 97.62% for the small fiducials. The acetabulum and the proximal femur were reconstructed with a mean surface distance error of 1.06 and 1.01 mm, respectively. The results for fiducial detection sensitivity and 3D surface reconstruction demonstrated the capability of the integrated system for 3D hip joint reconstruction from 2D calibrated X-ray radiographs.

High-Resolution Chemical Depth Profiling of Solid Material Using a Miniature Laser Ablation/Ionization Mass Spectrometer

High-resolution chemical depth profiling measurements of copper films are presented. The 10 μm thick copper test samples were electrodeposited on a Si-supported Cu seed under galvanostatic conditions in the presence of particular plating additives (SPS, Imep, PEI, and PAG) used in the semiconductor industry for the on-chip metallization of interconnects. To probe the trend of these plating additives toward inclusion into the deposit upon growth, quantitative elemental mass spectrometric measurements at trace level concentration were conducted by using a sensitive miniature laser ablation ionization mass spectrometer (LIMS), originally designed and developed for in situ space exploration. An ultrashort pulsed laser system (τ ∼ 190 fs, λ = 775 nm) was used for ablation and ionization of sample material. We show that with our LIMS system, quantitative chemical mass spectrometric analysis with an ablation rate at the subnanometer level per single laser shot can be conducted. The measurement capabilities of our instrument, including the high vertical depth resolution coupled with high detection sensitivity of ∼10 ppb, high dynamic range ≥10(8), measurement accuracy and precision, is of considerable interest in various fields of application, where investigations with high lateral and vertical resolution of the chemical composition of solid materials are required, these include, e.g., wafers from semiconductor industry or studies on space weathered samples in space research.

SMARTnet: First Experience of Setting Up a Telescope System to Survey the Geostationary Ring

Space debris in geostationary orbits may be detected with optical telescopes when the objects are illuminated by the Sun. The advantage compared to Radar can be found in the illumination: radar illuminates the objects and thus the detection sensitivity depletest proportional to the fourth power of the d istance. The German Space Operation Center, GSOC, together with the Astronomical Institute of the University of Bern, AIUB, are setting up a telescope system called SMARTnet to demonstrate the capability of performing geostationary surveillance. Such a telescope system will consist of two telescopes on one mount: a smaller telescope with an aperture of 20cm will serve for fast survey while the larger one, a telescope with an aperture of 50cm, will be used for follow-up observations. The telescopes will be operated by GSOC from Oberpfaffenhofen by the internal monitoring and control system called SMARTnetMAC. The observation plan will be generated by MARTnetPlanning seven days in advance by applying an optimized planning scheduler, taking into account fault time like cloudy nights, priority of objects etc. From each picture taken, stars will be identified and everything not being a star is treated as a possible object. If the same object can be identified on multiple pictures within a short time span, the trace is called a tracklet. In the next step, several tracklets will be correlated to identify individual objects, ephemeris data for these objects are generated and catalogued . This will allow for services like collision avoidance to ensure safe operations for GSOC’s satellites. The complete data processing chain is handled by BACARDI, the backbone catalogue of relational debris information and is presented as a poster.

Estudio y desarrollo de sensores de fibra óptica para detección de vibraciones en ductos ascendentes submarinos

En esta tesis doctoral se describe el trabajo de investigación enfocado al estudio y desarrollo de sensores de fibra óptica para la detección de presión, flujo y vibraciones en ductos ascendentes submarinos utilizados en la extracción y transporte de hidrocarburos, con el objetivo de aplicarlos en los campos de explotación de aguas profundas en el Golfo de México pertenecientes a la Industria Petrolera Mexicana. El trabajo se ha enfocado al estudio y desarrollo de sensores ópticos cuasi distribuidos y distribuidos. En especial se ha profundizado en el uso y aplicación de las redes de Bragg (FBG) y de reflectómetros ópticos en el dominio del tiempo sensible a la fase (φ-OTDR). Los sensores de fibra óptica son especialmente interesantes para estas aplicaciones por sus ventajosas características como su inmunidad a interferencias electromagnéticas, capacidad de multiplexado, fiabilidad para trabajar en ambientes hostiles, altas temperaturas, altas presiones, ambientes salino-corrosivos, etc. Además, la fibra óptica no solo es un medio sensor sino que puede usarse como medio de transmisión. Se ha realizado un estudio del estado del arte y las ventajas que presentan los sensores ópticos puntuales, cuasi-distribuidos y distribuidos con respecto a los sensores convencionales. Se han estudiado y descrito los interrogadores de redes de Bragg y se ha desarrollado un método de calibración útil para los interrogadores existentes en el mercado, consiguiendo incertidumbres en la medida de la longitud de onda menores de ± 88 nm e incertidumbres relativas (la mas interesante en el campo de los sensores) menores de ±3 pm. Centrándose en la aplicación de las redes de Bragg en la industria del petróleo, se ha realizado un estudio en detalle del comportamiento que presentan las FBGs en un amplio rango de temperaturas de -40 ºC a 500 oC. Como resultado de este estudio se han evaluado las diferencias en los coeficientes de temperatura en diversos tramos de mas mismas, así como para diferentes recubrimientos protectores. En especial se ha encontrado y evaluado las diferencias de los diferentes recubrimientos en el intervalo de temperaturas entre -40 ºC y 60 ºC. En el caso del intervalo de altas temperaturas, entre 100 ºC y 500 ºC, se ha medido y comprobado el cambio uniforme del coeficiente de temperatura en 1pm/ºC por cada 100 ºC de aumento de temperatura, en redes independientemente del fabricante de las mismas. Se ha aplicado las FBG a la medición de manera no intrusiva de la presión interna en una tubería y a la medición del caudal de un fluido en una tubería, por la medida de diferencia de presión entre dos puntos de la misma. Además se ha realizado un estudio de detección de vibraciones en tuberías con fluidos. Finalmente, se ha implementado un sistema de detección distribuida de vibraciones aplicable a la detección de intrusos en las proximidades de los ductos, mediante un φ-OTDR. En este sistema se ha estudiado el efecto negativo de la inestabilidad de modulación que limita la detección de vibraciones distribuidas, su sensibilidad y su alcance. ABSTRACT This thesis describes the research work focused for the study and development of on optical fiber sensors for detecting pressure, flow and vibration in subsea pipes used in the extraction and transportation of hydrocarbons, in order to apply them in deepwater fields in the Gulf of Mexico belonging to the Mexican oil industry. The work has focused on the study and development of optical sensors distributed and quasi distributed. Especially was done on the use and application of fiber Bragg grating (FBG) and optical reflectometers time domain phase sensitive (φ-OTDR). The optical fiber sensors especially are interesting for these applications for their advantageous characteristics such as immunity to electromagnetic interference, multiplexing capability, reliability to work in harsh environments, high temperatures, high pressures, corrosive saline environments, etc. Furthermore, the optical fiber is not only a sensor means it can be used as transmission medium. We have performed a study of the state of the art and the advantages offered by optical sensors point, quasi-distributed and distributed over conventional sensors. Have studied and described interrogators Bragg grating and has developed a calibration method for interrogators useful for the existing interrogators in the market, resulting uncertainty in the measurement of the wavelength of less than ± 0.17 nm and uncertainties (the more interesting in the field of sensors) less than ± 3 pm. Focusing on the application of the Bragg gratings in the oil industry, has been studied in detail the behavior of the FBGs in a wide range of temperatures from -40 °C to 500 oC. As a result of this study we have evaluated the difference in temperature coefficients over various sections of the same, as well as different protective coatings. In particular evaluated and found the differences coatings in the range of temperatures between -40 º C and 60 º C. For the high temperature range between 20 ° C and 500 ° C, has been measured and verified the uniform change of the temperature coefficient at 1pm / ° C for each 100 ° C increase in temperature, in networks regardless of manufacturer thereof. FBG is applied to the non-intrusive measurement of internal pressure in a pipeline and measuring flow of a fluid in a pipe, by measuring the pressure difference between two points thereof. Therefore, has also made a study of detecting vibrations in pipes with fluids. Finally, we have implemented a distributed sensing system vibration applied to intrusion detection in the vicinity of the pipelines, by φ-OTDR. In this system we have studied the negative effect of modulation instability limits the distributed vibration detection, sensitivity and scope.

Specific binding of proinsulin C-peptide to human cell membranes

Recent reports have demonstrated beneficial effects of proinsulin C-peptide in the diabetic state, including improvements of kidney and nerve function. To examine the background to these effects, C-peptide binding to cell membranes has been studied by using fluorescence correlation spectroscopy. Measurements of ligand–membrane interactions at single-molecule detection sensitivity in 0.2-fl confocal volume elements show specific binding of fluorescently labeled C-peptide to several human cell types. Full saturation of the C-peptide binding to the cell surface is obtained at low nanomolar concentrations. Scatchard analysis of binding to renal tubular cells indicates the existence of a high-affinity binding process with Kass > 3.3 × 109 M−1. Addition of excess unlabeled C-peptide is accompanied by competitive displacement, yielding a dissociation rate constant of 4.5 × 10−4 s−1. The C-terminal pentapeptide also displaces C-peptide bound to cell membranes, indicating that the binding occurs at this segment of the ligand. Nonnative d-C-peptide and a randomly scrambled C-peptide do not compete for binding with the labeled C-peptide, nor were crossreactions observed with insulin, insulin-like growth factor (IGF)-I, IGF-II, or proinsulin. Pretreatment of cells with pertussis toxin, known to modify receptor-coupled G proteins, abolishes the binding. It is concluded that C-peptide binds to specific G protein-coupled receptors on human cell membranes, thus providing a molecular basis for its biological effects.

Genetic diversity of Plasmodium falciparum histidine-rich protein 2 (PfHRP2) and its effect on the performance of PfHRP2-based rapid diagnostic tests

Rising costs of antimalarial agents are increasing the demand for accurate diagnosis of malaria. Rapid diagnostic tests (RDTs) offer great potential to improve the diagnosis of malaria, particularly in remote areas. Many RDTs are based on the detection of Plasmodium falciparum histidine-rich protein (PfHRP) 2, but reports from field tests have questioned their sensitivity and reliability. We hypothesize that the variability in the results of PfHRP2-based RDTs is related to the variability in the target antigen. We tested this hypothesis by examining the genetic diversity of PfHRP2, which includes numerous amino acid repeats, in 75 P. falciparum lines and isolates originating from 19 countries and testing a subset of parasites by use of 2 PfHRP2-based RDTs. We observed extensive diversity in PfHRP2 sequences, both within and between countries. Logistic regression analysis indicated that 2 types of repeats were predictive of RDT detection sensitivity (87.5% accuracy), with predictions suggesting that only 84% of P. falciparum parasites in the Asia-Pacific region are likely to be detected at densities

An antigen capture enzyme-linked immunosorbent assay reveals high levels of the dengue virus protein NS1 in the sera of infected patients

We describe the development of a capture enzyme-linked immunosorbent assay for the detection of the dengue virus nonstructural protein NS1. The assay employs rabbit polyclonal and monoclonal antibodies as the capture and detection antibodies, respectively. Immunoaffinity-purified NS1 derived from dengue 2 virus-infected cells was used as a standard to establish a detection sensitivity of approximately 4 ng/ml for an assay employing monoclonal antibodies recognizing a dengue 2 serotype-specific epitope. A number of serotype cross-reactive monoclonal antibodies were also shown to be suitable probes for the detection of NS1 expressed by the remaining three dengue virus serotypes. Examination of clinical samples demonstrated that the assay was able to detect NS1 with minimal interference from serum components at the test dilutions routinely used, suggesting that it could form the basis of a useful additional diagnostic test for dengue virus infection. Furthermore, quantitation of NS1 levels in patient sera may prove to be a valuable surrogate marker for viremia. Surprisingly high levels of NS1, as much as 15 mu g/ml, were found in acute-phase sera taken hom some of the patients experiencing serologically confirmed dengue 2 virus secondary infections but was not detected in the convalescent sera of these patients. In contrast, NS1 could not be detected in either acute-phase or convalescent serum samples taken from patients with serologically confirmed primary infection. The presence of high levels of secreted NS1 in the sera of patients experiencing secondary dengue virus infections, and in the context of an anamnestic antibody response, suggests that NS1 may contribute significantly to the formation of the circulating immune complexes that are suspected to play an important role in the pathogenesis of severe dengue disease.

Identification and relative quantification of tyrosine nitration in a model peptide using two-dimensional infrared spectroscopy

Nitration of tyrosine in proteins and peptides is a post-translational modification that occurs under conditions of oxidative stress. It is implicated in a variety of medical conditions, including neurodegenerative and cardiovascular diseases. However, monitoring tyrosine nitration and understanding its role in modifying biological function remains a major challenge. In this work, we investigate the use of electron-vibration-vibration (EVV) two-dimensional infrared (2DIR) spectroscopy for the study of tyrosine nitration in model peptides. We demonstrate the ability of EVV 2DIR spectroscopy to differentiate between the neutral and deprotonated states of 3-nitrotyrosine, and we characterize their spectral signatures using information obtained from quantum chemistry calculations and simulated EVV 2DIR spectra. To test the sensitivity of the technique, we use mixed-peptide samples containing various levels of tyrosine nitration, and we use mass spectrometry to independently verify the level of nitration. We conclude that EVV 2DIR spectroscopy is able to provide detailed spectroscopic information on peptide side-chain modifications and to detect nitration levels down to 1%. We further propose that lower nitration levels could be detected by introducing a resonant Raman probe step to increase the detection sensitivity of EVV 2DIR spectroscopy. (Graph Presented).

Advanced Techniques for Image Quality Assessment of Modern X-ray Computed Tomography Systems

X-ray computed tomography (CT) imaging constitutes one of the most widely used diagnostic tools in radiology today with nearly 85 million CT examinations performed in the U.S in 2011. CT imparts a relatively high amount of radiation dose to the patient compared to other x-ray imaging modalities and as a result of this fact, coupled with its popularity, CT is currently the single largest source of medical radiation exposure to the U.S. population. For this reason, there is a critical need to optimize CT examinations such that the dose is minimized while the quality of the CT images is not degraded. This optimization can be difficult to achieve due to the relationship between dose and image quality. All things being held equal, reducing the dose degrades image quality and can impact the diagnostic value of the CT examination.

A recent push from the medical and scientific community towards using lower doses has spawned new dose reduction technologies such as automatic exposure control (i.e., tube current modulation) and iterative reconstruction algorithms. In theory, these technologies could allow for scanning at reduced doses while maintaining the image quality of the exam at an acceptable level. Therefore, there is a scientific need to establish the dose reduction potential of these new technologies in an objective and rigorous manner. Establishing these dose reduction potentials requires precise and clinically relevant metrics of CT image quality, as well as practical and efficient methodologies to measure such metrics on real CT systems. The currently established methodologies for assessing CT image quality are not appropriate to assess modern CT scanners that have implemented those aforementioned dose reduction technologies.

Thus the purpose of this doctoral project was to develop, assess, and implement new phantoms, image quality metrics, analysis techniques, and modeling tools that are appropriate for image quality assessment of modern clinical CT systems. The project developed image quality assessment methods in the context of three distinct paradigms, (a) uniform phantoms, (b) textured phantoms, and (c) clinical images.

The work in this dissertation used the “task-based” definition of image quality. That is, image quality was broadly defined as the effectiveness by which an image can be used for its intended task. Under this definition, any assessment of image quality requires three components: (1) A well defined imaging task (e.g., detection of subtle lesions), (2) an “observer” to perform the task (e.g., a radiologists or a detection algorithm), and (3) a way to measure the observer’s performance in completing the task at hand (e.g., detection sensitivity/specificity).

First, this task-based image quality paradigm was implemented using a novel multi-sized phantom platform (with uniform background) developed specifically to assess modern CT systems (Mercury Phantom, v3.0, Duke University). A comprehensive evaluation was performed on a state-of-the-art CT system (SOMATOM Definition Force, Siemens Healthcare) in terms of noise, resolution, and detectability as a function of patient size, dose, tube energy (i.e., kVp), automatic exposure control, and reconstruction algorithm (i.e., Filtered Back-Projection– FPB vs Advanced Modeled Iterative Reconstruction– ADMIRE). A mathematical observer model (i.e., computer detection algorithm) was implemented and used as the basis of image quality comparisons. It was found that image quality increased with increasing dose and decreasing phantom size. The CT system exhibited nonlinear noise and resolution properties, especially at very low-doses, large phantom sizes, and for low-contrast objects. Objective image quality metrics generally increased with increasing dose and ADMIRE strength, and with decreasing phantom size. The ADMIRE algorithm could offer comparable image quality at reduced doses or improved image quality at the same dose (increase in detectability index by up to 163% depending on iterative strength). The use of automatic exposure control resulted in more consistent image quality with changing phantom size.

Based on those results, the dose reduction potential of ADMIRE was further assessed specifically for the task of detecting small (<=6 mm) low-contrast (<=20 HU) lesions. A new low-contrast detectability phantom (with uniform background) was designed and fabricated using a multi-material 3D printer. The phantom was imaged at multiple dose levels and images were reconstructed with FBP and ADMIRE. Human perception experiments were performed to measure the detection accuracy from FBP and ADMIRE images. It was found that ADMIRE had equivalent performance to FBP at 56% less dose.

Using the same image data as the previous study, a number of different mathematical observer models were implemented to assess which models would result in image quality metrics that best correlated with human detection performance. The models included naïve simple metrics of image quality such as contrast-to-noise ratio (CNR) and more sophisticated observer models such as the non-prewhitening matched filter observer model family and the channelized Hotelling observer model family. It was found that non-prewhitening matched filter observers and the channelized Hotelling observers both correlated strongly with human performance. Conversely, CNR was found to not correlate strongly with human performance, especially when comparing different reconstruction algorithms.

The uniform background phantoms used in the previous studies provided a good first-order approximation of image quality. However, due to their simplicity and due to the complexity of iterative reconstruction algorithms, it is possible that such phantoms are not fully adequate to assess the clinical impact of iterative algorithms because patient images obviously do not have smooth uniform backgrounds. To test this hypothesis, two textured phantoms (classified as gross texture and fine texture) and a uniform phantom of similar size were built and imaged on a SOMATOM Flash scanner (Siemens Healthcare). Images were reconstructed using FBP and a Sinogram Affirmed Iterative Reconstruction (SAFIRE). Using an image subtraction technique, quantum noise was measured in all images of each phantom. It was found that in FBP, the noise was independent of the background (textured vs uniform). However, for SAFIRE, noise increased by up to 44% in the textured phantoms compared to the uniform phantom. As a result, the noise reduction from SAFIRE was found to be up to 66% in the uniform phantom but as low as 29% in the textured phantoms. Based on this result, it clear that further investigation was needed into to understand the impact that background texture has on image quality when iterative reconstruction algorithms are used.

To further investigate this phenomenon with more realistic textures, two anthropomorphic textured phantoms were designed to mimic lung vasculature and fatty soft tissue texture. The phantoms (along with a corresponding uniform phantom) were fabricated with a multi-material 3D printer and imaged on the SOMATOM Flash scanner. Scans were repeated a total of 50 times in order to get ensemble statistics of the noise. A novel method of estimating the noise power spectrum (NPS) from irregularly shaped ROIs was developed. It was found that SAFIRE images had highly locally non-stationary noise patterns with pixels near edges having higher noise than pixels in more uniform regions. Compared to FBP, SAFIRE images had 60% less noise on average in uniform regions for edge pixels, noise was between 20% higher and 40% lower. The noise texture (i.e., NPS) was also highly dependent on the background texture for SAFIRE. Therefore, it was concluded that quantum noise properties in the uniform phantoms are not representative of those in patients for iterative reconstruction algorithms and texture should be considered when assessing image quality of iterative algorithms.

The move beyond just assessing noise properties in textured phantoms towards assessing detectability, a series of new phantoms were designed specifically to measure low-contrast detectability in the presence of background texture. The textures used were optimized to match the texture in the liver regions actual patient CT images using a genetic algorithm. The so called “Clustured Lumpy Background” texture synthesis framework was used to generate the modeled texture. Three textured phantoms and a corresponding uniform phantom were fabricated with a multi-material 3D printer and imaged on the SOMATOM Flash scanner. Images were reconstructed with FBP and SAFIRE and analyzed using a multi-slice channelized Hotelling observer to measure detectability and the dose reduction potential of SAFIRE based on the uniform and textured phantoms. It was found that at the same dose, the improvement in detectability from SAFIRE (compared to FBP) was higher when measured in a uniform phantom compared to textured phantoms.

The final trajectory of this project aimed at developing methods to mathematically model lesions, as a means to help assess image quality directly from patient images. The mathematical modeling framework is first presented. The models describe a lesion’s morphology in terms of size, shape, contrast, and edge profile as an analytical equation. The models can be voxelized and inserted into patient images to create so-called “hybrid” images. These hybrid images can then be used to assess detectability or estimability with the advantage that the ground truth of the lesion morphology and location is known exactly. Based on this framework, a series of liver lesions, lung nodules, and kidney stones were modeled based on images of real lesions. The lesion models were virtually inserted into patient images to create a database of hybrid images to go along with the original database of real lesion images. ROI images from each database were assessed by radiologists in a blinded fashion to determine the realism of the hybrid images. It was found that the radiologists could not readily distinguish between real and virtual lesion images (area under the ROC curve was 0.55). This study provided evidence that the proposed mathematical lesion modeling framework could produce reasonably realistic lesion images.

Based on that result, two studies were conducted which demonstrated the utility of the lesion models. The first study used the modeling framework as a measurement tool to determine how dose and reconstruction algorithm affected the quantitative analysis of liver lesions, lung nodules, and renal stones in terms of their size, shape, attenuation, edge profile, and texture features. The same database of real lesion images used in the previous study was used for this study. That database contained images of the same patient at 2 dose levels (50% and 100%) along with 3 reconstruction algorithms from a GE 750HD CT system (GE Healthcare). The algorithms in question were FBP, Adaptive Statistical Iterative Reconstruction (ASiR), and Model-Based Iterative Reconstruction (MBIR). A total of 23 quantitative features were extracted from the lesions under each condition. It was found that both dose and reconstruction algorithm had a statistically significant effect on the feature measurements. In particular, radiation dose affected five, three, and four of the 23 features (related to lesion size, conspicuity, and pixel-value distribution) for liver lesions, lung nodules, and renal stones, respectively. MBIR significantly affected 9, 11, and 15 of the 23 features (including size, attenuation, and texture features) for liver lesions, lung nodules, and renal stones, respectively. Lesion texture was not significantly affected by radiation dose.

The second study demonstrating the utility of the lesion modeling framework focused on assessing detectability of very low-contrast liver lesions in abdominal imaging. Specifically, detectability was assessed as a function of dose and reconstruction algorithm. As part of a parallel clinical trial, images from 21 patients were collected at 6 dose levels per patient on a SOMATOM Flash scanner. Subtle liver lesion models (contrast = -15 HU) were inserted into the raw projection data from the patient scans. The projections were then reconstructed with FBP and SAFIRE (strength 5). Also, lesion-less images were reconstructed. Noise, contrast, CNR, and detectability index of an observer model (non-prewhitening matched filter) were assessed. It was found that SAFIRE reduced noise by 52%, reduced contrast by 12%, increased CNR by 87%. and increased detectability index by 65% compared to FBP. Further, a 2AFC human perception experiment was performed to assess the dose reduction potential of SAFIRE, which was found to be 22% compared to the standard of care dose.

In conclusion, this dissertation provides to the scientific community a series of new methodologies, phantoms, analysis techniques, and modeling tools that can be used to rigorously assess image quality from modern CT systems. Specifically, methods to properly evaluate iterative reconstruction have been developed and are expected to aid in the safe clinical implementation of dose reduction technologies.

Multiscale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probe.

Photoacoustic tomography (PAT) of genetically encoded probes allows for imaging of targeted biological processes deep in tissues with high spatial resolution; however, high background signals from blood can limit the achievable detection sensitivity. Here we describe a reversibly switchable nonfluorescent bacterial phytochrome for use in multiscale photoacoustic imaging, BphP1, with the most red-shifted absorption among genetically encoded probes. BphP1 binds a heme-derived biliverdin chromophore and is reversibly photoconvertible between red and near-infrared light-absorption states. We combined single-wavelength PAT with efficient BphP1 photoswitching, which enabled differential imaging with substantially decreased background signals, enhanced detection sensitivity, increased penetration depth and improved spatial resolution. We monitored tumor growth and metastasis with ∼ 100-μm resolution at depths approaching 10 mm using photoacoustic computed tomography, and we imaged individual cancer cells with a suboptical-diffraction resolution of ∼ 140 nm using photoacoustic microscopy. This technology is promising for biomedical studies at several scales.

Optimisation of a droplet digital PCR assay for the diagnosis of Schistosoma japonicum infection: A duplex approach with DNA binding dye chemistry

Schistosomiasis is a chronically debilitating helminth infection with a significant socio-economic and public health impact. Accurate diagnostics play a pivotal role in achieving current schistosomiasis control and elimination goals. However, many of the current diagnostic procedures, which rely on detection of schistosome eggs, have major limitations including lack of accuracy and the inability to detect pre-patent infections. DNA-based detection methods provide a viable alternative to the current tests commonly used for schistosomiasis diagnosis. Here we describe the optimisation of a novel droplet digital PCR (ddPCR) duplex assay for the diagnosis of Schistosoma japonicum infection which provides improved detection sensitivity and specificity. The assay involves the amplification of two specific and abundant target gene sequences in S. japonicum; a retrotransposon (SjR2) and a portion of a mitochondrial gene (nad1). The assay detected target sequences in different sources of schistosome DNA isolated from adult worms, schistosomules and eggs, and exhibits a high level of specificity, thereby representing an ideal tool for the detection of low levels of parasite DNA in different clinical samples including parasite cell free DNA in the host circulation and other bodily fluids. Moreover, being quantitative, the assay can be used to determine parasite infection intensity and, could provide an important tool for the detection of low intensity infections in low prevalence schistosomiasis-endemic areas.

Systems Modeling of Lung Cancer Screening Programs to Improve Quality

Thesis (Master's)--University of Washington, 2016-08

The development of a photoacoustic Instrument for the monitoring of oil and other hydrocarbons in water.

The present methods for the detection of oil in discharge water are based either on chemical analysis of intermittent samples or bypass pipelines with instrumentation to detect either dissolved or dispersed hydrocarbons by a variety of optical techniques including absorption, scattering and fluorescence. However, test have shown that no single instruments entirely meets either present needs or satisfies the requirements of the future more stringent legislation which may limit total hydrocarbon content to 30 ppm or even less. Hence, in this paper, a detector is devised which can detect both dissolved and dispersed oil products, has a high immunity to scattering and can operate in-line and harsh environments with a detection sensitivity of a few ppm throughout a wide range of operations.

Mapping and modulating spatial attention asymmetries in young and older adults

Healthy young adults demonstrate a group-level, systematic preference for stimuli presented in the left side of space relative to the right (‘pseudoneglect’) (Bowers & Heilman, 1980). This results in an overestimation of features such as size, brightness, numerosity and spatial frequency in the left hemispace, probably as a result of right cerebral hemisphere dominance for visuospatial attention. This spatial attention asymmetry is reduced in the healthy older population, and can be shifted entirely into right hemispace under certain conditions. Although this rightward shift has been consistently documented in behavioural experiments, there is very little neuroimaging evidence to explain this effect at a neuroanatomical level. In this thesis, I used behavioural methodology and electroencephalography (EEG) to map spatial attention asymmetries in young and older adults. I then use transcranial direct current stimulation (tDCS) to modulate these spatial biases, with the aim of assessing age-related differences in response to tDCS. In the first of three experiments presented in this thesis, I report in Chapter Two that five different spatial attention tasks provide consistent intra-task measures of spatial bias in young adults across two testing days. There were, however, no inter-task correlations between the five tasks, indicating that pseudoneglect is at least partially driven by task-dependent patterns of neural activity. In Chapter Three, anodal tDCS was applied separately to the left (P5) and right (P6) posterior parietal cortex (PPC) in young and older adults, with an aim to improve the detection of stimuli appearing in the contralateral visual field. There were no age differences in response to tDCS, but there were significant differences depending on baseline performance. Relative to a sham tDCS protocol, tDCS applied to the right PPC resulted in maintained visual detection across both visual fields in adults who were good at the task at baseline. In contrast, left PPC tDCS resulted in reduced detection sensitivity across both visual fields in poor performers. Finally, in Chapter Four, I report a right-hemisphere lateralisation of EEG activity in young adults that was present for long (but not short) landmark task lines. In contrast, older adults demonstrated no lateralised activity for either line length, thus providing novel evidence of an age-related reduction of hemispheric asymmetry in older adults. The results of this thesis provide evidence of a highly complex set of factors that underlie spatial attention asymmetries in healthy young and older adults.