Optical wireless communication systems based on ultraviolet (UV)-band has a lot inherent advantages, such as low background solar radiation, low device dark noise. Besides, it also has small restrictive requirements for PAT (pointing, acquisition, and tracking) because of its high atmospheric scattering with molecules and aerosols. And these advantages are driving people to explore and utilize UV band for constructing and implementing a high-data-rate, less PAT communication links, such as diffuse-line-of-sight links (diffuse-LOS) and non-line-of-sight (NLOS). The responsivity of the photodetector at UV range is far lower than that of visible range, high power UV transmitters which can be easily modulated are under investigation. These factors make it is hard to realize a high-data-rate diffuse-LOS or NLOS UV communication links. To achieve a UV link mentioned above with current devices and modulation schemes, this thesis presents some efficient modulation schemes and available devices for the time being. Besides, a demonstration of ultraviolet-B (UVB) communication link is implemented utilizing quadrature amplitude modulation (QAM) orthogonal frequency-division multiplexing (OFDM). The demonstration is based on a 294-nm UVB-light-emitting-diode (UVB-LED) with a full-width at half-maximum (FWHM) of 9 nm, and according to the measured L-I-V curve, we set the bias voltage as 7V for maximum the ac amplitude and thus get a high signal-noise-ratio (SNR) channel, and the light output power is 190 μW with such bias voltage. Besides, there is a unique silica gel lens on top of the LED to concentrate the beam. A -3-dB bandwidth of 29 MHz was measured and a high-speed near-solar-blind communication link with a data rate of 71 Mbit/s was achieved using 8-QAM-OFDM at perfect alignment, and 23.6 Mbit/s using 2-QAM-OFDM when the angle subtended by the pointing direction of the UVB-LED and photodetector (PD) is 12 degrees, thus establishing a diffuse-line-of-sight (LOS) link. The measured bit-error rate (BER) of 2.8 × 10−4 and 2.4 × 10−4, respectively, are well below the forward error correction (FEC) criterion of 3.8 × 10−3. The demonstrated high data-rate OFDM-based UVB communication link paves the way for realizing high-speed non-line-of-sight free-space optical (FSO) communications.

Diffuse optical tomography uses near infrared (NIR) light as the probing media to recover the distributions of tissue optical properties. It has a potential to become an adjunct imaging modality for breast and brain imaging, that is capable of providing functional information of the tissue under investigation. As NIR light propagation in the tissue is dominated by scattering, the image reconstruction problem (inverse problem) tends to be non-linear and ill-posed, requiring usage of advanced computational methods to compensate this. Traditional image reconstruction methods in diffuse optical tomography employ l2 –norm based regularization, which is known to remove high frequency noises in the re-constructed images and make them appear smooth. The recovered contrast in the reconstructed image in these type of methods are typically dependent on the iterative nature of the method employed, in which the non-linear iterative technique is known to perform better in comparison to linear techniques. The usage of non-linear iterative techniques in the real-time, especially in dynamical imaging, becomes prohibitive due to the computational complexity associated with them. In the rapid dynamic diffuse optical imaging, assumption of a linear dependency in the solutions between successive frames results in a linear inverse problem. This new frame work along with the l1–norm based regularization can provide better robustness to noise and results in a better contrast recovery compared to conventional l2 –based techniques. Moreover, it is shown that the proposed l1-based technique is computationally efficient compared to its counterpart(l2 –based one). The proposed framework requires a reasonably close estimate of the actual solution for the initial frame and any suboptimal estimate leads to erroneous reconstruction results for the subsequent frames. Modern diffuse optical imaging systems are multi-modal in nature, where diffuse optical imaging is combined with traditional imaging modalities such as MRI, CT, and Ultrasound. A novel approach that can more effectively use the structural information provided by the traditional imaging modalities in these scenarios is introduced, which is based on prior image constrained- l1 minimization scheme. This method has been motivated by the recent progress in the sparse image reconstruction techniques. It is shown that the- l1 based frame work is more effective in terms of localizing the tumor region and recovering the optical property values both in numerical and gelatin phantom cases compared to the traditional methods that use structural information.

Diffuse optical tomography (DOT) is one of the promising imaging modalities that pro- vides functional information of the soft biological tissues in-vivo, such as breast and brain tissues. The near infrared (NIR) light (600-1000 nm) is the interrogating radiation, which is typically delivered and collected using fiber bundles placed on the boundary of the tissue. The internal optical property distribution is estimated via model-based image reconstruction algorithm using these limited boundary measurements. Image reconstruction problem in DOT is known to be non-linear, ill-posed, and some times under-determined due to the multiple scattering of NIR light in the tissue. Solving this inverse problem requires regularization to obtain meaningful results, with Tikhonov-type regularization being the most popular one. The choice of the regularization parameter dictates the reconstructed optical image quality and is typically chosen empirically or based on prior experience. An automated method for optimal selection of regularization parameter that is based on regularized minimal residual method (MRM) is proposed and is compared with the traditional generalized cross-validation method. The results obtained using numerical and gelatin phantom data indicate that the MRM-based method is capable of providing the optimal regularization parameter. A new approach that can easily incorporate any generic penalty function into the diffuse optical tomographic image reconstruction is introduced to show the utility of non-quadratic penalty functions. The penalty functions that were used include, quadratic (`2), absolute (`1), Cauchy, and Geman-McClure. The regularization parameter in each of these cases were obtained automatically using the generalized cross-validation (GCV) method. The reconstruction results were systematically compared with each other via utilization of quantitative metrics, such as relative error and Pearson correlation. The reconstruction results indicate that while quadratic penalty may be able to provide better separation between two closely spaced targets, it's contrast recovery capability is limited and the sparseness promoting penalties, such as `1, Cauchy, Geman-McClure have better utility in reconstructing high-contrast and complex-shaped targets with Geman-McClure penalty being the most optimal one. Effective usage of image guidance by incorporating the refractive index (RI) variation in computational modeling of light propagation in tissue is investigated to assess its impact on optical-property estimation. With the aid of realistic patient breast three-dimensional models, the variation in RI for different regions of tissue under investigation is shown to influence the estimation of optical properties in image-guided diffuse optical tomography (IG-DOT) using numerical simulations. It is also shown that by assuming identical RI for all regions of tissue would lead to erroneous estimation of optical properties. The a priori knowledge of the RI for the segmented regions of tissue in IG-DOT, which is difficult to obtain for the in vivo cases, leads to more accurate estimates of optical properties. Even inclusion of approximated RI values, obtained from the literature, for the regions of tissue resulted in better estimates of optical properties, with values comparable to that of having the correct knowledge of RI for different regions of tissue. Image reconstruction in IG-DOT procedure involves reduction of the number of optical parameters to be reconstructed equal to the number of distinct regions identified in the structural information provided by the traditional imaging modality. This makes the image reconstruction problem to be well-determined compared to traditional under- determined case. Still, the methods that are deployed in this case are same as the one used for traditional diffuse optical image reconstruction, which involves regularization term as well as computation of the Jacobian. A gradient-free Nelder-Mead simplex method was proposed here to perform the image reconstruction procedure and shown to be providing solutions that are closely matching with ones obtained using established methods. The proposed method also has the distinctive advantage of being more efficient due to being regularization free, involving only repeated forward calculations.

Water companies are continually adopting catchment management as a way of improving the quality of raw water prior to treatment. The catchments from which raw water is abstracted are often heterogeneous which regularly presents multiple pollutant issues and variability in the spatial distribution of pollutant-contributing areas. For catchment management to be effective, it is crucial that water companies select and target appropriate interventions at multi-pollutant high risk areas. Within this thesis a conceptual framework is developed to disaggregate and compare multiple pollutant risks in drinking water catchments to aid water companies in this decision making process. A review of pollutant processes highlights links between pollutants often mitigated using catchment management and therefore confirms the feasibility for a multi- pollutant framework. Criteria were developed with water industry catchment management professionals to determine framework requirements. No current framework or model fully meets these criteria.

A diffuse-interface finite-element method has been applied to simulate the flow of two-component rheologically complex fluids. It treats the interfaces as having a finite thickness with a phase-field parameter varying continuously from one phase to the other. Adaptive meshing is applied to produce fine grid near the interface and coarse mesh in the bulk. It leads to accurate resolution of the interface at modest computational costs. An advantage of this method is that topological changes such as interfacial rupture and coalescence happen naturally under a short-range force resembling the van der Waals force. There is no need for manual intervention as in sharp-interface model to effect such event. Moreover, this energy-based formulation easily incorporates complex rheology as long as the free energy of the microstructures is known. The complex fluids considered in this thesis include viscoelastic fluids and nematic liquid crystals. Viscoelasticity is represented by the Oldroyd-B model, derived for a dilute polymer solution as linear elastic dumbbells suspended in a Newtonian solvent. The Leslie-Ericksen model is used for nematic liquid crystals，which features distortional elasticity and viscous anisotropy. The interfacial dynamics of such complex fluids are of both scientific and practical significance. The thesis describes seven computational studies of physically interesting problems. The numerical simulations of monodisperse drop formation in microfluidic devices have reproduced scenarios of jet breakup and drop formation observed in experiments. Parametric studies have shown dripping and jetting regimes for increasing flow rates, and elucidated the effects of flow and rheological parameters on the drop formation process and the final drop size. A simple liquid drop model is used to study the neutrophil, the most common type of white blood cell, transit in pulmonary capillaries. The cell size, viscosity and rheological properties are found to determine the transit time. A compound drop model is also employed to account for the cell nucleus. The other four cases concern drop and bubble dynamics in nematic liquid crystals, as determined by the coupling among interfacial anchoring, bulk elasticity and anisotropic viscosity. In particular, the simulations reproduce unusual bubble shapes seen in experiments, and predict self-assembly of microdroplets in nematic media. / Applied Science, Faculty of / Chemical and Biological Engineering, Department of / Graduate

The efficacy of therapeutic modalities for non-Hodgkin’s lymphoma have been tested and improved throughout the 19th century through various series of drug trials aimed at eliminating cellular malignancies, first through chemotherapy treatment, and more recently through immunotherapy. While to an extent successful in eliminating cancerous lesions and affected cells, chemotherapy treatments have shown to influence the induction of new malignancies, through genetic mutation, as well as unwanted toxic effects of systemic poisoning. The purpose of this thesis is to compare treatment methods in terms of their biomolecular activity, precision of intended results, and possible drawbacks, as well as their application to specific populations of Non-Hodgkin lymphoma diagnoses, including Follicular and Diffuse Large B-Cell lymphomas. In the following sections on contributing factors specific to Diffuse Large B-Cell lymphomas and Follicular lymphoma, elements of disease prognosis will be analyzed from a molecular and clinical point of view. This includes a focus on the impact of genetic mutation, the immunohistochemical evidence these changes present, as well as the variances in immune cell functionality, and finally a description of symptoms with direction to specific underlying causes. An analysis of standard of care chemotherapy, and monoclonal antibody treatments will then be provided for each occurrence. The second segment will discuss novel techniques being developed for the treatment of lymphoma including but not limited to new monoclonal antibodies, synthetic lethality modulation, inhibition of selected chemokine receptors, DNA vector immunization for production of internal host antibodies, concepts of cell mediated bispecific antibody induced destruction, and new generations of Immunomodulatory drugs. With the recent development of cost effective sequencing technology, included is a discussion of the shift towards personalized medicine treatments, targeting appropriate phenotypic specific populations for optimal results, as it relates to therapies for Diffuse Large B-Cell lymphoma and Follicular lymphoma.

In the last two decades, advances in the dark field detectors and microscopes of scanning transmission electron microscopy (STEM) have inspired a resurgence of interest in quantitative STEM analysis. One promising avenue is the use of STEM as a nanothermometric probe. In this application, thermal diffuse scattering, captured by a CCD camera or an annular dark field detector, acts as an indirect measurement of the specimen temperature. One challenge with taking such a measurement is achieving adequate sensitivity to quantify a change in scattered electron signal on the order of 1% or less of the full electron beam. Another difficulty is decoupling the thermal effect on electron scattering from scattering changes due to differing specimen thicknesses and materials. To address these issues, we have developed a method using STEM, combined with electron energy loss spectroscopy (EELS), to produce a material-specific calibration curve. On silicon, across the range 89 K to 294 K, we measured a monotonically increasing HAADF signal ranging from 4.0% to 4.4% of the direct beam intensity at a thickness-to-mean-free-path ratio of 0.5. This yielded a calibration curve of temperature versus full-beam-normalized, thickness-normalized HAADF signal. The method enables thermal measurements on a specimen of varying local thickness at a spatial resolution of a few nanometers. We demonstrated the potential of the technique for testing electron scattering models by applying single-electron scattering theory to the data collected to extract a measurement of the mean atomic vibration amplitude in silicon at 294 K. The measured value, 0.00738 ± 0.00002 nm, agrees well with reported measurement using X-rays.

Orientador: Alexandre Dal Pai / Resumo: O presente trabalho sugere modelos de correção para a irradiância solar difusa medida com o disco de sombreamento. A irradiância global foi medida por um piranômetro Eppley-PSP; a irradiância normal direta por um pireliômetro Eppley-NIP adaptado a um dispositivo de rastreamento solar ST-3 e irradiância difusa por um piranômetro Eppley-PSP instalado em um disco de sombreamento. O Laboratório de Radiometria Solar da Universidade Estadual Paulista forneceu as medições durante os anos de 1997 a 2000. Os resultados mostraram que ambos os modelos sugeridos, o modelo para todas as coberturas de céu e o modelo para as diferentes coberturas de céu melhoram a medida da irradiância difusa pelo método do disco de sombreamento permitindo a geração de um banco de dados de radiação global, direta e difusa, sem altos investimentos financeiros. A medida da Irradiância difusa sem correção apresentou um MBE de -4,64% e um RMSE de 12,23%, enquanto que os modelos de correção para todas as coberturas de céu e para as diferentes coberturas de céu obtiveram MBE de 0,48% e 0,85 e RMSE de 10,52% e 9,91%, respectivamente. / Doutor

A dissertation submitted to the Faculty of Health Sciences, University of Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science in the branch of Anatomical Pathology. 21 July 2017. / Aims and objectives The study design aimed to assess and validate various laboratory techniques in the detection of EBV in HIV positive patients with diffuse large B cell lymphoma. The sensitivity and specificity of each technique was determined, as was the presence of an asymptomatic (latent) or lytic phase infection and the viral strain. DLBL samples occurring in HIV seropositive patients were used as a vehicle for these laboratory procedures which included chromogenic in situ hybridisation (EBER), immunohistochemistry (EBNA 2, LMP 1), real time PCR, (EBNA 1, LMP 2 and BZLF 1) and nested PCR (EBNA 2). Materials and Methods 46 cases of previously diagnosed DLBL from HIV positive individuals were identified and retrieved from the archives of the Department of Anatomical Pathology of the University of Witwatersrand and NHLS. All in-situ hybridisation, immunohistochemical and PCR laboratory procedures were carried out in accordance with the Standard Operating Procedures of the Anatomical Pathology Molecular Laboratory, using appropriate negative and positive controls throughout. Ethical clearance was obtained (M140273). Results/Conclusion A 20% frequency of EBV in HIV positive DLBL cases was established. All EBV infections were found to be in the lytic phase, with an almost equal distribution of latency patterns II and III and an equal distribution of EBV strains 1 and 2. EBER in situ hybridisation was confirmed to be the most sensitive and reliable method of viral detection, and the presence of the BZLF 1 gene determined by real time PCR was found to be a reliable indicator of a lytic infection. / LG2018

Thesis advisor: Udayan Mohanty / The conformational dynamics plays a significant role in a wide range of biological systems, from small RNA molecules to the large-scale ribonucleoprotein assemblies, in which ions are found critical and have notable structural and functional impacts. In the glass-forming liquids, the structural dynamics also calls for further investigations and deeper understandings. To this end, using four distinct chapters, this dissertation discusses the ion-related conformational dynamics in various scales of biomolecular systems, as well as the fluctuation effects in the glass-forming liquids. In chapter 1, we investigate the dynamics of ions and water molecules in the outer solvation sphere of a widely studied 58-nucleotide rRNA fragment. Molecular dynamics (MD) simulations with explicit solvent molecules and atomic details are performed for the RNA fragment in ionic solution. We determine all of the association sites and spatial distributions of residence times for Mg2+, K+, and water molecules in those sites. In accordance to the analysis of the dynamics of the RNA fragment, we provide insights into how the dynamics of ions and water molecules are intricately linked with the kinetics of the RNA fragment. In addition, the long-lived sites for Mg2+ ions identified from the simulation agree with the metal ion locations determined in the X-ray structure. The excess ion atmosphere around the RNA fragment is calculated and compared with the experimental measures. The results from this study indicate that the 58-mer rRNA fragment in ionic solution forms a complex polymer that is encased by a fluctuating network of ions and water. In chapter 2, the conformational dynamics of a large-scale ribonucleoprotein assembly, ribosome, is studied with molecular dynamics simulations with a newly developed model that accounts for electrostatic and ionic effects on the biomolecules. In this study, an all-atom structure based model is constructed with explicit representations of non-hydrogen atoms from biomolecules and diffuse ions. Implicit treatment is applied to the solvent molecules with the solvation effect associated with diffuse ions described by effective potentials. Parameters in this model are refined against explicit solvent simulations and experimental measures. This model with refined parameters is able to capture the excess Mg2+ ions for prototypical RNA systems and their dependence on the Mg2+ concentrations. Motivated by this, we apply the model to a bacterial ribosome and find that the position of the extended L1 stalk region can be controlled by the diffuse ions. This simulation also indicated ion-induced long-range interactions between L1 stalk and tRNA, which provides insights into the impact of ions on the functional rearrangements of ribosome. In chapter 3, we focus on the dynamics of the glass-forming liquids. In this study, we generalized the Adam-Gibbs model of relaxation in glass-forming liquids and take into account the fluctuations in the number of molecules inside the cooperative rearranging region. We obtain the expressions of configurational fractions at the glass-transition temperature with and without the fluctuation effect in Adam-Gibbs model, and determine the configurational fraction for several glass-forming liquids at glass-transition temperature in the absence of fluctuation effects. A connection between the β Kohlrausch-Williams-Watts parameters and the configurational fraction at the glass-transition temperature is also reported in this study. In chapter 4, we apply the model developed in chapter 2 to a ribosome structure to investigate the effects of diffuse ions on the aminoacyl-tRNA (aa-tRNA) accommodation process. The aa-tRNA accommodation is a critical step in the tRNA selection process which serves the purpose of protein synthesis in the ribosome. Experimental and computational efforts were made to reveal the mechanism and the energetic properties of the accommodation process, while the effects from diffuse ions on this process remain elusive. To this end, we design and perform MD simulations of ribosome structure with different treatment of electrostatics and diffuse ions in the system. Simulations with various ionic concentrations are also performed to study the concentration effects. The simulation trajectories indicate that diffuse ions can facilitate the aa-tRNA accommodation process and stabilize the accommodated configurations. In addition, we observe that Mg2+ ions play critical roles in stabilizing the accommodated configurations and a few millimolar change of Mg2+ concentration can alter the tendency of the tRNA configurational change during the accommodation process. This result shed light on the investigations of suitable ionic environment for the tRNA selection in the ribosome. It will be fruitful to extend this strategy into the investigations of other conformational rearrangements in the ribosome, such as tRNA translocation and subunit rotation, which will provide us with deeper understanding about the functional mechanism of the ribosome. / Thesis (PhD) — Boston College, 2021. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.