Technological enhancements to optometric clinical tests

A sizeable amount of the testing in eye care, requires either the identification of targets such as letters to assess functional vision, or the subjective evaluation of imagery by an examiner. Computers can render a variety of different targets on their monitors and can be used to store and analyse ophthalmic images. However, existing computing hardware tends to be large, screen resolutions are often too low, and objective assessments of ophthalmic images unreliable. Recent advances in mobile computing hardware and computer-vision systems can be used to enhance clinical testing in optometry. High resolution touch screens embedded in mobile devices, can render targets at a wide variety of distances and can be used to record and respond to patient responses, automating testing methods. This has opened up new opportunities in computerised near vision testing. Equally, new image processing techniques can be used to increase the validity and reliability of objective computer vision systems. Three novel apps for assessing reading speed, contrast sensitivity and amplitude of accommodation were created by the author to demonstrate the potential of mobile computing to enhance clinical measurement. The reading speed app could present sentences effectively, control illumination and automate the testing procedure for reading speed assessment. Meanwhile the contrast sensitivity app made use of a bit stealing technique and swept frequency target, to rapidly assess a patient’s full contrast sensitivity function at both near and far distances. Finally, customised electronic hardware was created and interfaced to an app on a smartphone device to allow free space amplitude of accommodation measurement. A new geometrical model of the tear film and a ray tracing simulation of a Placido disc topographer were produced to provide insights on the effect of tear film breakdown on ophthalmic images. Furthermore, a new computer vision system, that used a novel eye-lash segmentation technique, was created to demonstrate the potential of computer vision systems for the clinical assessment of tear stability. Studies undertaken by the author to assess the validity and repeatability of the novel apps, found that their repeatability was comparable to, or better, than existing clinical methods for reading speed and contrast sensitivity assessment. Furthermore, the apps offered reduced examination times in comparison to their paper based equivalents. The reading speed and amplitude of accommodation apps correlated highly with existing methods of assessment supporting their validity. Their still remains questions over the validity of using a swept frequency sine-wave target to assess patient’s contrast sensitivity functions as no clinical test provides the range of spatial frequencies and contrasts, nor equivalent assessment at distance and near. A validation study of the new computer vision system found that the authors tear metric correlated better with existing subjective measures of tear film stability than those of a competing computer-vision system. However, repeatability was poor in comparison to the subjective measures due to eye lash interference. The new mobile apps, computer vision system, and studies outlined in this thesis provide further insight into the potential of applying mobile and image processing technology to enhance clinical testing by eye care professionals.

Generalized Backscattering and the Lax-Phillips Transform

2000 Mathematics Subject Classification: 35P25, 35R30, 58J50.

Highly efficient spectrally encoded imaging using a 45° tilted fiber grating

A novel highly efficient, fiber-compatible spectrally encoded imaging (SEI) system using a 45° tilted fiber grating (TFG) is proposed and experimentally demonstrated for the first time, to the best of our knowledge. The TFG serves as an in-fiber lateral diffraction element, eliminating the need for bulky and lossy free-space diffraction gratings in conventional SEI systems. Under proper polarization control, due to the strong tilted reflection, the 45° TFG offers a diffraction efficiency as high as 93.5%. Our new design significantly reduces the volume of the SEI system and improves energy efficiency and system stability. As a proof-ofprinciple experiment, spectrally encoded imaging of a customer-designed sample (9.6 mm x 3.0 mm) using the TFG-based system is demonstrated. The lateral resolution of the SEI system is measured to be 42 μm in our experiment.

Multimode Analysis of Nanoscale Biomolecular Interactions

Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical calculations have been developed for the analysis of biomolecular interactions. Human neuroglobin (hNgb) and cytochrome c from equine heart (Cyt c) proteins have been used to optimize the customized SPR instrument. The obtained Kd value (~13 µM), from SPR results, for Cyt c-hNgb molecular interactions is in general agreement with a previously published result. The SPR results also confirmed no significant impact of the internal disulfide bridge between Cys 46 and Cys 55 on hNgb binding to Cyt c. Using SPR, E. coli topoisomerase I enzyme turnover during plasmid DNA relaxation was found to be enhanced in the presence of Mg2+. In addition, a new theoretical approach of analyzing biphasic SPR data has been introduced based on analytical solutions of the biphasic rate equations. In order to develop a new label free method to quantitatively study protein-protein interactions, quartz nanopipettes were chemically modified. The derived Kd (~20 µM) value for the Cyt c-hNgb complex formations matched very well with SPR measurements (Kd ~16 µM). The finite element numerical simulation results were similar to the nanopipette experimental results. These results demonstrate that nanopipettes can potentially be used as a new class of a label-free analytical method to quantitatively characterize protein-protein interactions in attoliter sensing volumes, based on a charge sensing mechanism. Moreover, the molecule-based selective nature of hydrophobic and nanometer sized carbon nanotube (CNT) pores was observed. This result might be helpful to understand the selective nature of cellular transport through transmembrane protein pores.

User Effects on Wearable Conformal SCMR System

The performance of a compact, wearable Conformal Strongly Coupled Magnetic Resonance (CSCMR) system is studied when the antenna is in the air and is worn on a user’s arm. The wireless powering system consists of the receiver and load elements designed on a printed circuit board that is attached to a polyester fabric band. The wearable antenna achieves high efficiency, has a small volume, and can be easily printed on substrates. Although the user effect on mobile terminal antennas has been studied in detail, absorption losses in wearable antennas have not been widely investigated. Our results show that efficiency of the antenna in free space is 70% and on a user’s arm is 50%. Human tissue in the close proximity of our wearable Conformal SCMR caused a decrease in radiated efficiency and total efficiency. This undesired degradation in antenna efficiency might be attributed to body loss and absorption losses. Our findings can be used as a reference for future studies on wearable devices and their applications, such as health and sports monitoring.

Prospecção química e avaliação biológica de Banisteriopsis laevifolia (Malpighiaceae)

The Banisteriopsis genus is widespread in traditional medicine. This work aims to contribute with information about the chemical composition and on the evaluation of the biological activity of the essential oil, the ethanol extract of the leaves and partitions of the Banisteriopsis laevifolia. The phytochemical screeningtest of ethanol extract and partitions of leaves indicated the presence of flavonoids, terpenoids, saponins, phenols and steroids compounds. Nitrogenous compounds, characteristic of some species of this family, were not detected. Flavonoids were the predominant metabolite, with the highest concentrations on the partitions ethyl acetate and n-butanol. The antibacterial activity, antifungal and cytotoxicity of the essetial oil, ethanol extract and partitions were assyed by microdilution broth method (MBM), where the minimum inhibitory concentrations (MIC) were calculated. The ethanol extract and partitions did not inhibit growth against to Gram positive bacteria tested, with MIC less than 400 mg L-1. For the Gram negative bacteria tested, the hexane and hydroethanol partitios were more effective against F. nucleatum bacteria (MIC 100 ug mL-1). The ethanol extract showed antifungal activity with MIC of 31.2 mg L-1. Ethyl acetate and n-butanol partitions showed MIC 187.5 mg L-1 and 93.7 mg L-1, respectively, arousing interest for isolation studies. The antioxidant activity was evaluated by the DPPH free radical method. The ethanolic extract, ethyl acetate and n-butanol partitions were active, since they showed EC50 values (4.53 ug mL-1, 4.07 and 8.39 ug mL-1, respectively), values equivalent to the BHT (7.3 mg L-1). The analysis by HPLC-MS/MS of the most active fractions (ethyl acetate and n-butanol) identified phenolic compounds (flavonols and phenolic acids) which exert recognized biological activity. The GC-MS analysis of the essential oils from leaves collected in two periods studied (dry and wet), showed a small variation in the number of compounds. The major classes identified for the oil collected in the dry period were aliphatic alcohols (23,4%), terpenoids (18.7%), sterols (10.4%) and long-chain alkanes (9.2%) compounds. Terpenoids (26.8%) were the major class for the rain season. The major compounds (3Z) -hexenol, phytol and untriacontano are present in the two seasons but in different amounts (19.4%, 9.8% and 7.5% during the dry season, and 17.0 %, 14.9% and 15.3% in the rainy season, respectively). The essential oil from rainy season was not effective against to the oral bacteria Gram positive and Gram negative tested. However, showed significant antifungal activity with MIC 1000 mg L-1 against Candidas. Thus, the promising results with respect to biological assays of ethanolic extract and partitions from B. laevifolia contributed to the chemical and biological knowledge of the species B. laevifolia.

Open-source virtual bronchoscopy for image guided navigation

This thesis describes the development of an open-source system for virtual bronchoscopy used in combination with electromagnetic instrument tracking. The end application is virtual navigation of the lung for biopsy of early stage cancer nodules. The open-source platform 3D Slicer was used for creating freely available algorithms for virtual bronchscopy. Firstly, the development of an open-source semi-automatic algorithm for prediction of solitary pulmonary nodule malignancy is presented. This approach may help the physician decide whether to proceed with biopsy of the nodule. The user-selected nodule is segmented in order to extract radiological characteristics (i.e., size, location, edge smoothness, calcification presence, cavity wall thickness) which are combined with patient information to calculate likelihood of malignancy. The overall accuracy of the algorithm is shown to be high compared to independent experts' assessment of malignancy. The algorithm is also compared with two different predictors, and our approach is shown to provide the best overall prediction accuracy. The development of an airway segmentation algorithm which extracts the airway tree from surrounding structures on chest Computed Tomography (CT) images is then described. This represents the first fundamental step toward the creation of a virtual bronchoscopy system. Clinical and ex-vivo images are used to evaluate performance of the algorithm. Different CT scan parameters are investigated and parameters for successful airway segmentation are optimized. Slice thickness is the most affecting parameter, while variation of reconstruction kernel and radiation dose is shown to be less critical. Airway segmentation is used to create a 3D rendered model of the airway tree for virtual navigation. Finally, the first open-source virtual bronchoscopy system was combined with electromagnetic tracking of the bronchoscope for the development of a GPS-like system for navigating within the lungs. Tools for pre-procedural planning and for helping with navigation are provided. Registration between the lungs of the patient and the virtually reconstructed airway tree is achieved using a landmark-based approach. In an attempt to reduce difficulties with registration errors, we also implemented a landmark-free registration method based on a balanced airway survey. In-vitro and in-vivo testing showed good accuracy for this registration approach. The centreline of the 3D airway model is extracted and used to compensate for possible registration errors. Tools are provided to select a target for biopsy on the patient CT image, and pathways from the trachea towards the selected targets are automatically created. The pathways guide the physician during navigation, while distance to target information is updated in real-time and presented to the user. During navigation, video from the bronchoscope is streamed and presented to the physician next to the 3D rendered image. The electromagnetic tracking is implemented with 5 DOF sensing that does not provide roll rotation information. An intensity-based image registration approach is implemented to rotate the virtual image according to the bronchoscope's rotations. The virtual bronchoscopy system is shown to be easy to use and accurate in replicating the clinical setting, as demonstrated in the pre-clinical environment of a breathing lung method. Animal studies were performed to evaluate the overall system performance.

Ultracompact Retrodirective Antenna Arrays With Superdirective Radiation Patterns

It is shown that the direction-of-arrival (DoA) information carried by an incident electromagnetic (EM) wave can be encoded into the evanescent near field of an electrically small resonance antenna array with a spatial rate higher than that of the incident field oscillation rate in free space. Phase conjugation of the received signal leads to the retrodirection of the near field in the antenna array environment, which in turn generates a retrodirected far-field beam toward the original DoA. This EM phenomenon enables electrically small retrodirective antenna arrays with superdirective, angular super-resolution, auto-pointing properties for an arbitrary DoA. A theoretical explanation of the phenomenon based on first principal observations is given and full-wave simulations demonstrate a realizability route for the proposed retrodirective terminal that is comprised of resonance dipole antenna elements. Specifically, it is shown that a three-element disk-loaded retrodirective dipole array with 0.15\lambda spacings can achieve a 3.4-dBi maximal gain, 3-dBi front-to-back ratio, and 13% return loss fractional bandwidth (at the 10-dB level). Then, it is demonstrated that the radiation gain of a three-element array can be improved to approximately 6 dBi at the expense of the return loss fractional bandwidth reduction (2%).

Multiuser dual-hop relaying over hybrid RF/FSO links

The performance of multiuser dual-hop relaying over mixed radio frequency/free-space optical (RF/FSO) links is investigated. RF links are used for the simultaneous data transmission from m single-antenna sources to the relay, which is equipped with n ≥ m receive antennas and a photo-aperture transmitter. The relay operates under the decode-and-forward protocol and utilizes the popular ordered V-BLAST technique to successively decode each user's transmitted stream. A common norm-based ordering approach is adopted, where the streams are decoded in an ascending order. After the V-BLAST decoding, the relay retransmits the initial information to the destination, which is equipped with a photo-detector, via a point-to-point FSO link in m consecutive timeslots. Analytical expressions for the end-to-end outage probability and average symbol error probability of each user are derived. Some engineering insights are manifested, such as the diversity order, the impact of the pointing error displacement on the FSO link and the severity on the turbulence-induced channel fading.

On-light: optical social network

Social networks are a recent phenomenon of communication, with a high prevalence of young users. This concept serves as a motto for a multidisciplinary project, which aims to create a simple communication network, using light as the transmission medium. Mixed team, composed by students from secondary and higher education schools, are partners on the development of an optical transceiver. A LED lamp array and a small photodiode are the optical transmitter and receiver, respectively. Using several transceivers aligned with each other, this con guration creates a ring communication network, enabling the exchange of messages between users. Through this project, some concepts addressed in physics classes from secondary schools (e.g. photoelectric phenomena and the properties of light) are experimentally veri ed and used to communicate, in a classroom or a laboratory.

Which-path problem for one and two particles with two degrees of freedom and a relation between transverse spatial structure and group velocity of light

Quantum mechanics, optics and indeed any wave theory exhibits the phenomenon of interference. In this thesis we present two problems investigating interference due to indistinguishable alternatives and a mostly unrelated investigation into the free space propagation speed of light pulses in particular spatial modes. In chapter 1 we introduce the basic properties of the electromagnetic field needed for the subsequent chapters. In chapter 2 we review the properties of interference using the beam splitter and the Mach-Zehnder interferometer. In particular we review what happens when one of the paths of the interferometer is marked in some way so that the particle having traversed it contains information as to which path it went down (to be followed up in chapter 3) and we review Hong-Ou-Mandel interference at a beam splitter (to be followed up in chapter 5). In chapter 3 we present the first of the interference problems. This consists of a nested Mach-Zehnder interferometer in which each of the free space propagation segments are weakly marked by mirrors vibrating at different frequencies [1]. The original experiment drew the conclusions that the photons followed disconnected paths. We partition the description of the light in the interferometer according to the number of paths it contains which-way information about and reinterpret the results reported in [1] in terms of the interference of paths spatially connected from source to detector. In chapter 4 we briefly review optical angular momentum, entanglement and spontaneous parametric down conversion. These concepts feed into chapter 5 in which we present the second of the interference problems namely Hong-Ou-Mandel interference with particles possessing two degrees of freedom. We analyse the problem in terms of exchange symmetry for both boson and fermion pairs and show that the particle statistics at a beam splitter can be controlled for suitably chosen states. We propose an experimental test of these ideas using orbital angular momentum entangled photons. In chapter 6 we look at the effect that the transverse spatial structure of the mode that a pulse of light is excited in has on its group velocity. We show that the resulting group velocity is slower than the speed of light in vacuum for plane waves and that this reduction in the group velocity is related to the spread in the wave vectors required to create the transverse spatial structure. We present experimental results of the measurement of this slowing down using Hong-Ou-Mandel interference.

Síntese, caracterização e estudo da regeneração do silicoaluminofosfato-11 (SAPO-11)

heterogeneous catalyst such as a silicoaluminophosphate, molecular sieve with AEL (Aluminophosphate eleven) structure such as SAPO-11, was synthesized through the hydrothermal method starting from silica, pseudoboehmite, orthophosphoric acid (85%) and water, in the presence of a di-isopropylamine organic template. For the preparation of SAPO-11 in a dry basis it was used as reactants: DIPA; H3PO4; SiO4; Pseudoboehmite and distilled water. The crystallization process occurred when the reactive hydrogel was charged into a vessel and autoclaved at 200ºC for a period of 72 hours under autogeneous pressure. The obtained material was washed, dried and calcined to remove the molecular sieves of DIPA. The samples were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), infrared spectroscopy (FT-IR), nitrogen adsorption (BET) and thermal analysis (TG/DTG). The acidic properties were determined using adsorption of nbutylamine followed by programmed thermodessorption. This method revealed that SAPO-11 shows an acidity that ranges from weak to moderate. However, a small quantity of strong acid sites could be detected there. The deactivation of the catalysts was conducted by artificial coking followed by the cracking of the n-hexane in a fixed bed with a continuous flow micro-reactor coupled on line to a gas chromatograph. The main products obtained were: ethane, propane, isobutene, n-butane, n-pentane and isopentane. The Vyazovkin (model-free) kinetics method was used to determine the regeneration and removal of the coke

the plenoptic sensor

In this thesis, we will introduce the innovative concept of a plenoptic sensor that can determine the phase and amplitude distortion in a coherent beam, for example a laser beam that has propagated through the turbulent atmosphere.. The plenoptic sensor can be applied to situations involving strong or deep atmospheric turbulence. This can improve free space optical communications by maintaining optical links more intelligently and efficiently. Also, in directed energy applications, the plenoptic sensor and its fast reconstruction algorithm can give instantaneous instructions to an adaptive optics (AO) system to create intelligent corrections in directing a beam through atmospheric turbulence. The hardware structure of the plenoptic sensor uses an objective lens and a microlens array (MLA) to form a mini “Keplerian” telescope array that shares the common objective lens. In principle, the objective lens helps to detect the phase gradient of the distorted laser beam and the microlens array (MLA) helps to retrieve the geometry of the distorted beam in various gradient segments. The software layer of the plenoptic sensor is developed based on different applications. Intuitively, since the device maximizes the observation of the light field in front of the sensor, different algorithms can be developed, such as detecting the atmospheric turbulence effects as well as retrieving undistorted images of distant objects. Efficient 3D simulations on atmospheric turbulence based on geometric optics have been established to help us perform optimization on system design and verify the correctness of our algorithms. A number of experimental platforms have been built to implement the plenoptic sensor in various application concepts and show its improvements when compared with traditional wavefront sensors. As a result, the plenoptic sensor brings a revolution to the study of atmospheric turbulence and generates new approaches to handle turbulence effect better.

O aqueduto das águas livres como elemento dinamizador e regenerador do eixo Lisboa-Sintra

Dissertação para obtenção do grau de Mestre em Arquitectura com especialização em Urbanismo, apresentada na Universidade de Lisboa - Faculdade de Arquitetura. Assuntos:

Estudos comparativos do ciclo de regeneração de diferentes tipos de silicoaluminofosfatos

Different types of heterogeneous catalysts of the silicoaluminophosphate type, (SAPO-5, SAPO-11, SAPO-31, SAPO-34 and SAPO-41), molecular sieves with a: AFI, AEL, ATO, CHA and AFO structure, respectively, were synthesized through the hydrothermal method. Using sources such as hydrated alumina (pseudobohemita), phosphoric acid, silica gel, water, as well as, different types of organic structural templates, such as: cetyltrimethylammonium bromide (CTMABr), di-isopropylamine (DIPA), di-n- propylamine (DNPA) and tetraethylammonium hydroxide (TEOS), for the respective samples. During the preparation of the silicoaluminophosphates, the crystallization process of the samples occurred at a temperature of approximately 200 ° C, ranging through periods of 18-72 h, when it was possible to obtain pure phases for the SAPOs. The materials were furthermore washed with deionized water, dried and calcined to remove the molecules of the templates. Subsequently the samples were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), absorption spectroscopy in the infrared region (FT-IR), specific surface area and thermal analysis via TG/DTG. The acidic properties were determined using adsorption of n-butylamine followed by programmed termodessorption. These methods revealed that the SAPO samples showed a typically weak to moderate acidity. However, a small amount of strong acid sites was also detected. The deactivation of the catalysts was conducted by artificially coking the samples, followed by n-hexane cracking reactions in a fixed bed with a continuous flow micro-reactor coupled on line to a gas chromatograph. The main products obtained were: ethane, propane, isobutene, n-butane, n-pentane and isopentane. The Vyazovkin (model-free) kinetics method was used to determine the catalysts regeneration and removal of the coke