Advances in characterisation, calibration and data processing speed of optical coherence tomography systems

This thesis describes advances in the characterisation, calibration and data processing of optical coherence tomography (OCT) systems. Femtosecond (fs) laser inscription was used for producing OCT-phantoms. Transparent materials are generally inert to infra-red radiations, but with fs lasers material modification occurs via non-linear processes when the highly focused light source interacts with the materials. This modification is confined to the focal volume and is highly reproducible. In order to select the best inscription parameters, combination of different inscription parameters were tested, using three fs laser systems, with different operating properties, on a variety of materials. This facilitated the understanding of the key characteristics of the produced structures with the aim of producing viable OCT-phantoms. Finally, OCT-phantoms were successfully designed and fabricated in fused silica. The use of these phantoms to characterise many properties (resolution, distortion, sensitivity decay, scan linearity) of an OCT system was demonstrated. Quantitative methods were developed to support the characterisation of an OCT system collecting images from phantoms and also to improve the quality of the OCT images. Characterisation methods include the measurement of the spatially variant resolution (point spread function (PSF) and modulation transfer function (MTF)), sensitivity and distortion. Processing of OCT data is a computer intensive process. Standard central processing unit (CPU) based processing might take several minutes to a few hours to process acquired data, thus data processing is a significant bottleneck. An alternative choice is to use expensive hardware-based processing such as field programmable gate arrays (FPGAs). However, recently graphics processing unit (GPU) based data processing methods have been developed to minimize this data processing and rendering time. These processing techniques include standard-processing methods which includes a set of algorithms to process the raw data (interference) obtained by the detector and generate A-scans. The work presented here describes accelerated data processing and post processing techniques for OCT systems. The GPU based processing developed, during the PhD, was later implemented into a custom built Fourier domain optical coherence tomography (FD-OCT) system. This system currently processes and renders data in real time. Processing throughput of this system is currently limited by the camera capture rate. OCTphantoms have been heavily used for the qualitative characterization and adjustment/ fine tuning of the operating conditions of OCT system. Currently, investigations are under way to characterize OCT systems using our phantoms. The work presented in this thesis demonstrate several novel techniques of fabricating OCT-phantoms and accelerating OCT data processing using GPUs. In the process of developing phantoms and quantitative methods, a thorough understanding and practical knowledge of OCT and fs laser processing systems was developed. This understanding leads to several novel pieces of research that are not only relevant to OCT but have broader importance. For example, extensive understanding of the properties of fs inscribed structures will be useful in other photonic application such as making of phase mask, wave guides and microfluidic channels. Acceleration of data processing with GPUs is also useful in other fields.

A Note on the “Constructing” of Nonstationary Methods for Solving Nonlinear Equations with Raised Speed of Convergence

This paper is partially supported by project ISM-4 of Department for Scientific Research, “Paisii Hilendarski” University of Plovdiv.

Increasing the Calculation Speed of an Acceleration Scheme for an Age-Structured Diffusion Model

Дойчин Бояджиев, Галена Пеловска - В статията се предлага оптимизиран алгоритъм, който е по-бърз в сравнение с по- рано описаната ускорена (модифицирана STS) диференчна схема за възрастово структуриран популационен модел с дифузия. Запазвайки апроксимацията на модифицирания STS алгоритъм, изчислителното времето се намаля почти два пъти. Това прави оптимизирания метод по-предпочитан за задачи с нелинейност или с по-висока размерност.

Exploratory Study of the Download Speed of Leading University Hospitality and Tourism Department Websites Worldwide

Increased broadband penetration (BP) rates around the world have encouraged web designers to include more web content and additional functions on their web sites, thereby enhancing the richness and playfulness of the information. However, it is often very difficult for web surfers who are still using narrowband connections to access such web sites. Many university web sites target international audiences; therefore their download performance should be considered, as it may directly influence the user experience. This exploratory study examined 331 university hospitality and tourism department web sites in 37 countries. The empirical results showed that entry web pages of universities in Asia, with a medium BP rate (mid-BP), have the slowest download speeds, and those in Australia and New Zealand perform the best. The adoption rate of the Cascade Style Sheet (CSS) in Asia is relatively lower than that of other regions.

Seawater carbonate chemistry and sperm swimming speed of the polychaete Galeolaria caespitosa in lab experiment

The rapidity of ocean acidification intensifies selection pressure for resilient phenotypes, particularly during sensitive early life stages. The scope for selection is greater in species with greater within-species variation in responses to changing environments, thus enhancing the potential for adaptation. We investigated among-male variation in sperm swimming responses (percent motility and swimming speeds) of the serpulid polychaete Galeolaria caespitosa to near- (delta pH 0.3) and far-future ocean acidification (delta pH 0.5). Responses of sperm swimming to acidification varied significantly among males and were overall negative. Robust sperm swimming behavior under near-future ocean acidification in some males may ameliorate climate change impacts, if traits associated with robustness are heritable, and thereby enhance the potential for adaptation to far-future conditions. Reduced sperm swimming in the majority of male G. caespitosa may decrease their fertilization success in a high CO2 future ocean. Resultant changes in offspring production could affect recruitment success and population fitness downstream.

Water-, pH- and temperature relations of germination for the extreme xerophiles Xeromyces bisporus (FRR 0025), Aspergillus penicillioides (JH06THJ), and Eurtotium halophilicum (FRR 2471)

Water activity, temperature and pH are determinants for biotic activity of cellular systems, biosphere function and, indeed, for all life processes. This study was carried out at high concentrations of glycerol, which concurrently reduces water activity and acts as a stress protectant, to characterize the biophysical capabilities of the most extremely xerophilic organisms known. These were the fungal xerophiles: Xeromyces bisporus (FRR 0025), Aspergillus penicillioides (JH06THJ) and Eurotium halophilicum (FRR 2471). High-glycerol spores were produced and germination was determined using 38 media in the 0.995–0.637 water activity range, 33 media in the 2.80–9.80 pH range and 10 incubation temperatures, from 2 to 50°C. Water activity was modified by supplementing media with glycerol+sucrose, glycerol+NaCl and glycerol+NaCl+sucrose which are known to be biologically permissive for X. bisporus, A. penicillioides and E. halophilicum respectively. The windows and rates for spore germination were quantified for water activity, pH and temperature; symmetry/asymmetry of the germination profiles were then determined in relation to supra- and sub-optimal conditions; and pH- and temperature optima for extreme xerophilicity were quantified. The windows for spore germination were ~1 to 0.637 water activity, pH 2.80–9.80 and > 10 and < 44°C, depending on strain. Germination profiles in relation to water activity and temperature were asymmetrical because conditions known to entropically disorder cellular macromolecules, i.e. supra-optimal water activity and high temperatures, were severely inhibitory. Implications of these processes were considered in relation to the in-situ ecology of extreme conditions and environments; the study also raises a number of unanswered questions which suggest the need for new lines of experimentation.

High Pressure Speed of Sound and Related Thermodynamic Properties of 1-Alkyl-3-methylimidazolium Bis[(trifluoromethyl)sulfonyl]imides (from 1-Propyl- to 1-Hexyl-)

The knowledge of thermodynamic high-pressure speed of sound in ionic liquids (ILs) is a crucial way either to study the nature of the molecular interactions, structure and packing effects or to determine other key thermodynamic properties of ILs essential for their applications in any chemical and industrial processes. Herein, we report the speed of sound as a function temperature at pressures up to 101 MPa in four ultrapure ILs: 1-propyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, 1-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, 1-pentyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, and 1-hexyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, taking into consideration their relaxation behavior. Additionally, to further improve the reliability of the speed of sound results, the density, isentropic compressibility, and isobaric heat capacity as a function of temperature and pressure are calculated using an acoustic method.

Critical swimming speed of the southern straight-mouth nase Pseudochondrostoma willkommii (Steindachner, 1866), a potamodromous cyprinid from southern Europe.

Critical swimming speed (Ucrit) of the potamodromous southern straight-mouth nase was assessed in a modified Blazka-type swim tunnel. Forty-one P. willkommii were tested and exhibited a mean± SD Ucrit of 0.54 ± 0.07 m/s. The sex of experimental fish had no effect on Ucrit but a significant positive relationship was found between swimming performance and the body condition of tested fish. Results from this study can be used to improve the current design of fish passes targeting this, or similar, potamodromous fish species.

Robustness of germination analysis methods for Copaifera langsdorffii Desf. (Fabaceae) seeds.

2016

A cohomological approach to Ruelle-Pollicott resonances and speed of mixing of Anosov diffeomorphisms

Given a transitive Anosov diffeomorphism on a closed manifold it is known that, for smooth enough observables, the system is mixing w.r.t. the measure of maximal entropy. Therefore, it makes sense to investigate the speed of decay of correlations and to look for the so-called Ruelle-Pollicott resonances, in order to determine a complete asymptotics for the decay of correlations. In this thesis we are able to find the first terms of that asymptotics and to prove an estimate for the speed of decaying of correlations. The proof is based on a surprising connection between the action of a transfer operator on suitable anisotropic Banach spaces of currents and the action induced by the Anosov map on the de Rham cohomology.

Thermal and moisture content effects on storability and seed dormancy releasing on Brachiaria brizantha cultivars

Brachiaria species normally show a double seed dormancy mechanism, mainly on fresh-harvested seeds, leading to germination percentages lower than those of viability detected by tetrazolium test (TZ) and causing problems as to storage, trading and seed inspection activities. The adoption of the methodology to detect the constants of the viability equation (high storage temperatures and fixed moisture contents) made feasible in this research to isolate the effects of 40, 50 and 65°C on B. brizantha cultivars Marandu, Mulato 1 and Mulato 2 seed dormancy releasing, after storage with moisture contents ranging from 1.9 and 17.8%. Seed samples presented high dormancy levels, detected by TZ and it was complete and partially released by chemical scarification and accelerated ageing test, respectively. No statistical differences were observed as to the speed of germination (T50); however, differences among cultivars were detected as to number of seed per gram. Sorption and desorption isotherm curves were similar for the cultivars. Seed dormancy releasing was better achieved at 40 and 50°C with mc ranging from 7.6 to 10.8%. The temperature of 50°C appears to be adequate for seed dormancy releasing in all mc analyzed. No significant seed dormancy releasing result was observed at 65°C. The cultivar Marandu presented the highest storability throughout the experiment.

Germinação de sementes e otimização de técnicas de micropropagação de umbuzeiro (spondias tuberosa, arr.) anacardiaceae

The brazilian-plum (Spondias tuberosa, His) is a tropical fruit tree that has been consolidated in the market for agribusiness processing, due to its characteristic flavor of fruit. Accordingly, studies to optimize the propagation of plants are necessary for production of seedlings with agronomic and quality assurance measures. This study aimed at determining the efficient techniques for uniform seed germination, as brazilian-plum seed present mechanical dormancy, and establish optimal culture media for multiplication of shoots from the in vitro micropropagation. Firstly, in a greenhouse at the Universidade Federal do Rio Grande do Norte, was evaluated the influence of different methods of breaking dormancy in the emergence of seedlings of brazilian-plum and speed of germination (IVG) of seeds. After 60 days of cultivation, it was found that splay in the distal portion of the seed was the best treatment, with rates of 85.33% in germinability and 3.415 of IVG, compared with the treatment of seed-soaking in water for 12h + humus and the control group. Subsequently, new sources of seedling explants were obtained in studies of tissue culture. Laboratory of Plant Biotechnology that the university, was used stem apex, nodal segments and internodes in search of decontamination with various concentrations of calcium hypochlorite [Ca(OCl)2] and micropropagation, inoculating them in half WPM (1980) with various concentrations of 6-benzylaminopurine (BAP). We used 10 sample units with three replications for different concentrations of [Ca(OCl)2], BAP and explants type. After thirty days, which was observed for the control of contamination, during the establishment in vitro, concentrations of [Ca(OCl)2] between 0.5% and 2.0% were effective in combating exogenous contamination of the apex. In nodal segments and internodes, concentrations of [Ca(OCl)2] between 1.0% and 2.0% and 1.5% and 2.0% were respectively, sufficient to reduce the percentage of losses in these infestations explants. For micropropagation, the culture medium supplemented with 0.1 mg.L-1 BAP promotes better development of multiple shoots per explants from nodal segment. However, success does not get to shoot training in internodal segment

Morfologia e avaliação do crescimento inicial de plântulas de Bactris gasipaes Kunth. (arecaceae) em diferentes substratos

Este trabalho teve por objetivos descrever a morfologia dos diásporos, as fases da germinação e determinar o substrato mais adequado para o crescimento inicial de plântulas de pupunha. Periodicamente, unidades representativas de cada fase de germinação foram retiradas para a descrição da seqüência dos eventos morfológicos. Os substratos usados para o crescimento inicial foram Plantmax HT, areia, terra (latossolo roxo) e outro com proporções iguais de terra, areia e esterco (TAE). Avaliou-se o crescimento inicial das plântulas aos 101 dias após o transplante, com base na sua altura, número de folhas, comprimento e largura das folhas. Observou-se que as sementes são albuminosas, com endosperma oleaginoso e de consistência relativamente dura. O embrião é lateral, periférico e relativamente indiferenciado, de forma cônica. A germinação inicia-se com o desenvolvimento de uma massa de células indiferenciadas na depressão micropilar. Posteriormente, esta massa de células torna-se cilíndrica, com a diferenciação dos primórdios caulinar e radicular. O primórdio caulinar é constituído por três bainhas envolvendo a primeira folha. Estas se abrem sucessivamente, permitindo a emergência da folha primária. Entre os substratos testados, de acordo com os parâmetros avaliados, os mais adequados para crescimento inicial de mudas de Bactris gasipaes Kunth foram o TAE e o Plantmax.

Qualidade física e fisiológica de sementes da leguminosa forrageira Macrotyloma axillare cv. Java

É de interesse prático, quando se dispõe de diferentes lotes de sementes, conhecer a qualidade fisiológica intrínseca a cada um. Objetivou-se determinar a qualidade fisiológica de lotes de sementes da leguminosa forrageira tropical, Macrotyloma axillare cv. Java, com utilização de diferentes metodologias para realização dos testes germinação e vigor. Determinou-se a pureza física dos lotes, o peso de mil sementes, a germinação com e sem escarificação (TG) e o vigor (índice de velocidade de germinação (IVG), primeira contagem, envelhecimento acelerado e condutividade elétrica) de três lotes de sementes. Diferenças na qualidade fisiológica inicial de sementes escarificadas foram observadas pelo teste de germinação. Pelos resultados dos testes de primeira contagem e IVG não foi possível detectar diferenças na qualidade fisiológica das sementes; o envelhecimento acelerado das sementes escarificadas pode ser realizado a 41º C por 72 horas ou a 45º C por 48 horas; o teste de condutividade elétrica mostrou-se adequado para diferenciar os lotes, a partir de 48 horas de embebição.