The purpose of this study is to determine the effects of pedestrian movement on vehicle flow at signalized intersections. Specifically, a computer simulation model written in General Purpose Simulation System language was developed to calculate vehicle seconds of delay at two-lane by four-lane street intersections with fixed-time signal cycles. Two intersections, operating under different conditions, were simulated at various pedestrian and vehicle flow volumes. Possible warrants, based on simulation output, for the inclusion of a separate pedestrian signal in the signal cycle for the two intersections studied were discussed. / M.S.

Oomycetes are fungi-like eukaryotic microorganisms, which are actually phylogenetic relatives of diatoms and brown algae, within the kingdom Stramenopila. Many oomycete species, mainly in the genera Phytophthora, Pythium and downy mildews, are devastating plant pathogens that cause multibillion-dollar losses to agriculture annually in the world. Some oomycetes are also animal pathogens, causing severe losses in aquaculture and fisheries, and occasionally causing dangerous infections of humans. Phytophthora species, represented by the Irish Potato Famine pathogen P. infestans and the soybean pathogen P. sojae, are arguably the most destructive pathogens of dicotyledonous plants among the oomycete species and thus have been extensively studied. This dissertation focuses on the model oomycete pathogen P. sojae to investigate specific aspects of its molecular biology and establish an efficient genetic manipulation tool. Specifically, in Chapter 1, I briefly introduce the basic concepts of oomycete biology and pathology, and summarize the experimental techniques used for studies of oomycete genetics over the past two decades. Because the approach to studying fungi and oomycetes are similar (indeed they were incorrectly placed in the same taxonomic group until recently), a special section reviews the emerging genome editing technology CRISPR/Cas system in these organisms together. Chapter 2 and Chapter 3 focus on one of the most important intracellular activities, nuclear localization of proteins, and describe the characterization of nuclear localization signals (NLSs) in P. sojae. This focus stemmed from my early work on genome editing in P. sojae, when I discovered that conventional NLS signals from SV40 used to target the TAL effector nuclease (TALEN) to the nucleus worked poorly in P. sojae. In the first part of this work (Chapter 2), I used confocal microscopy to identify features of nuclear localization in oomycetes that differ from animals, plants and fungi, based on characterization of two classes of nuclear localization signals, cNLS and PY-NLS, and on characterization of several conserved nuclear proteins. In the second part (Chapter 3), I determined that the nuclear localization of the P. sojae bZIP1 transcription factor is mediated by multiple weak nuclear targeting motifs acting together. In Chapter 4 and Chapter 5, I describe my implementation of nuclease-based technology for genetic modification and control of P. sojae. In Chapter 4, I describe the first use of the CRISPR system in an oomycete, including its use to validate the function of a host specificity gene. This is of particular importance because molecular techniques such as gene knockouts and gene replacements, widely used in other organisms, were not previously possible in oomycetes. The successful implementation of CRISPR provides a major new research capability to the oomycete community. Following up on the studies described in Chapter 4, in Chapter 5, I describe the generalization and simplification of the CRISPR/Cas9 expression strategy in P. sojae as well as methods for mutant screening. I also describe several optimized methodologies for P. sojae manipulation based on my 5 years of experience with P. sojae. / Ph. D. / Oomycetes (water molds) are eukaryotic microorganisms that resemble filamentous fungi (molds), but are actually relatives of diatoms and brown algae, within a different kingdom of life named Stramenopila. The functional relationship between oomycetes and fungi is similar to that between fish and dolphins, which also acquired similar functions via different evolutionary paths. Many families of oomycetes are devastating plant pathogens that cause multibillion-dollar losses to agriculture annually in the world. Other families of oomycetes are animal pathogens, causing severe losses in aquaculture and fisheries, and occasionally causing dangerous infections of humans. <i>Phytophthora</i> species, represented by the Irish Potato Famine pathogen <i>P. infestans</i> and the soybean pathogen <i>P. sojae</i>, are among the most destructive oomycete pathogens of plants and thus have been extensively studied. This dissertation is focused on the model oomycete pathogen <i>P. sojae</i>. It investigates specific aspects of its molecular biology and establishes an efficient genetic manipulation tool. All complex organisms (eukaryotes) package their genetic material in nuclei, which contain proteins as well as DNA. In the first part of my research (Chapter 2 and Chapter 3), I focused on the mechanisms used by <i>P. sojae</i> to target nuclear proteins into the nucleus, particularly the tags (called nuclear localization signals, or NLSs) that are identify the proteins that must travel to the nucleus. I showed that nuclear targeting mechanisms in oomycetes differ in distinct ways from well-studied eukaryotes such as humans. In particular, the nuclear targeting signals in <i>P. sojae</i> proteins are diffused over multiple sites on the proteins, whereas in human proteins there’s usually just a single signal. For one particular oomycete protein, a transcription factor, nuclear targeting involves four weak signals that cooperate synergistically. Two of these four weak signals define a new class of nuclear localization signal. In the second part of my research (Chapter 4 and Chapter 5), I implemented and further optimized a genome editing technology for genetic modification and control of <i>P. sojae</i>. This technology is based on the CRISPR system that has revolutionized genome editing in plants and animals over the last three years. This is of particular importance because genome editing techniques were not previously possible in oomycetes. The successful implementation of CRISPR technology in <i>P. sojae</i> has provided a major new research capability to the oomycete community. In Chapter 5, I also describe several optimized methodologies for <i>P. sojae</i> genetic manipulation based on my 5 years of experience with <i>P. sojae</i>.

Yes / Attempts have been made to treat nonsense-associated genetic disorders by chemical agents and hence an improved mechanistic insight into the decoding of readthrough signals is essential for the identification and characterisation of factors for the treatment of these disorders. To identify either novel compounds or genes that modulate translation readthrough, we have employed dual reporter-based high-throughput screens that use enzymatic and fluorescence activities and screened bio-active NINDS compounds (n = 1000) and siRNA (n = 288) libraries. Whilst siRNAs targeting kinases such as CSNK1G3 and NME3 negatively regulate readthrough, neither the bio-active NINDS compounds nor PTC124 promote readthrough. Of note, PTC124 has previously been shown to promote readthrough. Furthermore, the impacts of G418 on the components of eukaryotic selenocysteine incorporation machinery have also been investigated. The selenocysteine machinery decodes the stop codon UGA specifying selenocysteine in natural selenoprotein genes. We have found that the eukaryotic SelC gene promotes the selenocysteine insertion sequence (SECIS)-mediated readthrough but inhibits the readthrough activity induced by G418. We have previously reported that SECIS-mediated readthrough at UGA codons follows a non-processive mechanism. Here, we show that G418-mediated promotion of readthrough also occurs through a non-processive mechanism which competes with translation termination. Based on our observations, we suggest that proteins generated through a non-processive mechanism may be therapeutically beneficial for the resolution of nonsense-associated genetic disorders. / Fellowship (awarded to MTN) from the Department of Health via the NIHR Comprehensive Biomedical Research Centre award to Guy’s & St Thomas’ NHS Foundation Trust in partnership with King’s College London, Heptagon Life Science Proof of Concept Fund (grant KCL24 to MTN), the Great Britain Sasakawa 22 Foundation (grant B70 to MTN), the Royal Society (grant 43049 to MTN) and the University of Bradford (grants 003200 and DH005 to MTN).

Thesis (MPhil (Philosophy))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: This study investigated the practice of language use on road signs in Switzerland. The language used in public spaces constitutes our image of a specific place to a remarkable degree. We are constantly exposed to signs, whether road signs, advertisements or notifiers. These signs not only convey information such as “Caution”, “Final sale” or “Speed limit 60 here”, but also highlight aspects of culture and, where written text appear on them, aspects of the language(s) used in that area. Language use within the public space enables us to conceptualize, as well as recognize, the ways in which language use occurs, often (but not always) informing us whether a country is monolingual, bilingual or multilingual. In addition, these signs also indicate how language use is linked to other processes such as globalisation, social change and cultural heritage. The main purpose of this thesis was to establish how language is used on road signs in presentday, officially multilingual Switzerland. In this regard, three Swiss cantons (in which bilingual or multilingual societies are found) were investigated as to the language(s) – or lack thereof – which appear on their road signs, as well as to the order in which these languages appear. Specifically, bilingual or multilingual signs, as well as so-called Bildersprache (“picture language”, in other words on a board or plaque with a picture, symbol or other image on it), were studied in these cantons. Data for this research consists of photographic material (taken during visits to the study areas) as well as interview data. It was found that the social and political identities, as well as the economic interests, of language groups in a particular area affect the design and placement of road signs in that area. The results of this study serve as a framework for future research, and the photo material enables us, to a certain extent, to see how an apparently stable language system (such as the multilingualism found in Switzerland) encounters changes due to internal and external influences, but also how creative language can be. / AFRIKAANSE OPSOMMING: In hierdie studie is die taalgebruik op padtekens in Switserland ondersoek. Die taalgebruik in openbare plekke vorm tot ’n merkwaardige mate die beeld wat ons van ’n spesifieke plek het. Ons word konstant blootgestel aan tekens, hetsy padtekens, advertensies of kennisgewings. Hierdie tekens verskaf nie net inligting soos “Versigtig”, “Finale uitverkoping” of “Spoedgrens 60” nie, maar beklemtoon ook kulturele aspekte en, in daardie gevalle waarin geskrewe teks op tekens verskyn, ook aspekte van taal/tale wat in die betrokke gebied gebesig word. Taalgebruik in die openbare ruimte help ons om die wyses waarop taalgebruik voorkom te konseptualiseer en te herken, en dui gereeld (maar nie altyd nie) vir ons aan of ’n land eentalig, tweetalig of veeltalig is. Verder gee die tekens ook ’n aanduiding van hoe taalgebruik gekoppel is aan prosesse soos globalisasie, sosiale verandering en kulturele erfenis. Die hoof doel van hierdie tesis was om te bepaal hoe taal in die hedendaagse Switzerland op padtekens gebruik word. Drie Switserse kantons (met tweetalige en veeltalige gemeenskappe) is in hierdie verband ondersoek in terme van die taal/tale – of die gebrek daaraan – wat op padtekens verskyn asook die volgorde waarin hierdie tale op die padtekens verskyn. Spesifiek tweetalige of veeltalige tekens asook sogenaamde Bildersprache (“prentetaal”, met ander woorde ’n bord met ’n prent, simbool of ander voorstelling daarop) is in hierdie kantons bestudeer. Die data vir hierdie navorsing bestaan uit fotografiese materiaal (wat verkry is tydens besoeke aan die studie-areas) sowel as inligting wat verkry is deur onderhoudvoering. Daar is bevind dat die sosiale en politiese identiteite, sowel as die ekonomiese belange, van taalgroepe in ’n spesifieke area die ontwerp en plasing van padtekens in daardie area beïnvloed. Die resultate van hierdie studie dien as ’n raamwerk vir toekomstige navorsing en die fotomateriaal stel ons tot ’n sekere mate in staat om vas te stel hoe ’n klaarblyklik stabiele taalsisteem (soos die veeltalige een wat in Switserland aangetref word) veranderinge weens interne en eksterne invloede kan ervaar, maar ook hoe kreatief taal kan wees.

Nos estudos sobre a teoria da Seleção Sexual, as libélulas têm sido amplamente estudadas devido à grande variedade de padrões comportamentais, de coloração e táticas reprodutivas. Como forma de demonstrar táticas reprodutivas adotadas por duas espécies de libélulas, esta dissertação teve como objetivos principais: i) investigar o papel de traços secundários como a coloração corporal na competição intra-sexual de uma espécie territorial e ii) analisar se os traços corporais como tamanho e morfologia das asas predizem a tática de acasalamento adotada por machos de uma espécie nãoterritorial. Sugere-se que a coloração corporal pode predizer o resultado de lutas e também se correlacionar positivamente com a condição física dos machos territoriais de Tigriagrion aurantinigrum. Ademais, traços corporais como o tamanho e a morfologia das asas influenciam na tática reprodutiva utilizada por machos não-territoriais de Epipleoneura williamsoni. Portanto, com os resultados obtidos, conclui-se que a variação nos sinais visuais exerce um papel essencial na comunicação animal e na resolução de conflitos, indicando ainda que pode haver uma sinalização da condição física dos machos. Além disso, os resultados mostraram evidências em como diferentes táticas reprodutivas se relacionam com traços corporais como agilidade e tamanho corporal, os quais podem influenciar no sucesso reprodutivo dos indivíduos. / In studies concerning Sexual Selection theory, dragonflies and damselflies have been well studied due to their wide range of behavioral, color and reproductive tactics patterns. To demonstrate reproductive tactics adopted by two damselfly species, this study aimed to: i) investigate the role of secondary traits such as body coloration in intrasexual competition of a territorial species and ii) analyze if body traits such as size and wing morphology predicts the adopted tactic by non-territorial males. It is suggested that body coloration can predict the fight outcome and also positively correlates with males physical condition in territorial males of Tigriagrion aurantinigrum and body traits such as body size and wing morphology influence the reproductive tactic adopted by non-territorial males of Epipleoneura williamsoni. Therefore, with these results, it is concluded that the visual signalling variation plays an important role on the animal comunication and conflict resolution, which also may indicate that there is a signalling on the males physical condition. Furthermore, the results showed evidence in how different reproductive tactics are related to body traits such as agility and size, which can influence on individuals reproductive success.

Nos estudos sobre a teoria da Seleção Sexual, as libélulas têm sido amplamente estudadas devido à grande variedade de padrões comportamentais, de coloração e táticas reprodutivas. Como forma de demonstrar táticas reprodutivas adotadas por duas espécies de libélulas, esta dissertação teve como objetivos principais: i) investigar o papel de traços secundários como a coloração corporal na competição intra-sexual de uma espécie territorial e ii) analisar se os traços corporais como tamanho e morfologia das asas predizem a tática de acasalamento adotada por machos de uma espécie nãoterritorial. Sugere-se que a coloração corporal pode predizer o resultado de lutas e também se correlacionar positivamente com a condição física dos machos territoriais de Tigriagrion aurantinigrum. Ademais, traços corporais como o tamanho e a morfologia das asas influenciam na tática reprodutiva utilizada por machos não-territoriais de Epipleoneura williamsoni. Portanto, com os resultados obtidos, conclui-se que a variação nos sinais visuais exerce um papel essencial na comunicação animal e na resolução de conflitos, indicando ainda que pode haver uma sinalização da condição física dos machos. Além disso, os resultados mostraram evidências em como diferentes táticas reprodutivas se relacionam com traços corporais como agilidade e tamanho corporal, os quais podem influenciar no sucesso reprodutivo dos indivíduos. / In studies concerning Sexual Selection theory, dragonflies and damselflies have been well studied due to their wide range of behavioral, color and reproductive tactics patterns. To demonstrate reproductive tactics adopted by two damselfly species, this study aimed to: i) investigate the role of secondary traits such as body coloration in intrasexual competition of a territorial species and ii) analyze if body traits such as size and wing morphology predicts the adopted tactic by non-territorial males. It is suggested that body coloration can predict the fight outcome and also positively correlates with males physical condition in territorial males of Tigriagrion aurantinigrum and body traits such as body size and wing morphology influence the reproductive tactic adopted by non-territorial males of Epipleoneura williamsoni. Therefore, with these results, it is concluded that the visual signalling variation plays an important role on the animal comunication and conflict resolution, which also may indicate that there is a signalling on the males physical condition. Furthermore, the results showed evidence in how different reproductive tactics are related to body traits such as agility and size, which can influence on individuals reproductive success.

Les soins parentaux sont observés dans de nombreux taxons et sont exprimés de façon plus ou moins complexe. L’étude de ces comportements chez les arthropodes, en particulier chez les araignées, nous permet de mieux comprendre comment les soins à la progéniture se sont mis en place au cours de l’évolution. Au cours de cette thèse nous avons étudié le comportement d’une espèce errante Pardosa saltans (Lycosidae) vis-à-vis de son cocon, puis de ses jeunes. Nous avons décrit les comportements manifestés par la mère pendant toute la période de soin au cocon (période de développement embryonnaire et postembryonnaire des jeunes). Notre étude a permis de mettre en évidence qu’il existe une ontogenèse comportementale dans le cadre des soins parentaux chez cette espèce. Elle a permis également d’évaluer les dépenses énergétiques subies par la mère pendant cette période. Et enfin nous avons identifié, pour la première fois, les composés chimiques présents à la surface du cocon. Nos expériences montrent que ces composés chimiques associés aux vibrations émises par les juvéniles à l’intérieur du cocon sont utilisés par la mère détecter l’état de développement de sa progéniture. / Parental care is widespread among animal kingdom and is more or less expressed. Thus, the study of these behaviours among primitive species, can let us understand how parental behaviours were implemented during evolution. In this thesis we studied maternal behaviour in a wandering spider Pardosa saltans (Lycosidae) with her egg-sac and her young which she actively transports. We have described maternal behaviour towards the egg-sac and highlighted the presence of ontogeny of maternal behavior in this species. Furthermore, we were able to evaluate some of the physiological and ecological investment associated with maternal care of the egg-sac and young. Finally, we have, for the first time, identify chemical compounds on the surface of the silk egg-sac, and placed in evidence the presence of a chemical and vibrational communication between the mother and her cocoon.

The Flashing Yellow Arrow Left Turn signal is quickly becoming prominent in Central Florida as a new method of handling left turns at traffic signals. While the concept of a protected-permitted left turn is not groundbreaking, the departure from the typical display of a five-section signal head is, for this type of operation. The signal head introduced is a four-section head with a flashing yellow arrow between the yellow and green arrows. With this signal head quickly becoming the standard, there is a need to re-evaluate the operational characteristics of the left turning vehicle and advance the knowledge of the significant parameters that may affect the ability for a driver to make a left turn at a signalized intersection. With previous research into the behavioral and operational characteristics of the flashing yellow arrow conducted, there is more information becoming available about the differences between this signal and the previously accepted method of allowing left turns at an intersection. The protected-permitted signal is typically displayed at an intersection with up to two through lanes and generally a protected signal is installed when the number of through lanes increases above two unless specific criteria is met. With the advent of larger arterials and more traffic on the highway networks, the push to operate these intersections at their maximum efficiency has resulted in more of these protected-permitted signals being present at these larger intersections, including the flashing yellow arrow. The core of the research that follows is a comparative analysis of the operation and parameters that affect the left turn movement of the intersection with larger geometry to that of the smaller geometry. The significant parameters of the left turn movement were examined through means of collecting, organizing and analyzing just over 68 hours of field data. This research details the determining of the significant parameters based on the generation of a simulation model of the protected left turn using Synchro, a traffic simulation package, and regression models using field driven data to determine the significant parameters for predicting the number of left turns that can be made in the permitted phase under specific operating conditions. Intuitively, there is an expectation that a larger intersection will not allow for as many permitted lefts as a smaller intersection with all conditions remaining the same. The conclusions drawn from this analysis provide the framework to understanding the similarities and the differences that are encountered when the intersection geometry differs and help to more efficiently manage traffic at signalized intersections. The work of this field promises to enhance the operations of the left turning movement for traffic control devices. With an understanding of the statistical models generated, a broader base of knowledge is gained as to the significant parameters that affect a driver's ability to make the left turn. A discussion of the statistical differences and between the models generated from the small and large geometry intersections is critical to drive further research into standards being developed for the highway transportation network and the treatment of these large signalized intersections. The exploration of specific parameters to predict the number of permitted left turns will yield results as to if there is more to be considered with larger intersections moving forward as they become a standard sight on the roadway network.

Photonics and Optical techniques have advanced recently by a great extend to play an important role in Microwave and Radar applications. Antenna array of modern active phased array radars consist of multiple low power transmit and receive mod- ules. This demands distribution of the various Local Oscillator(LO) signals for up conversion of transmit signals and down conversion of receive signals during various modes of operation of a radar system. Additionally, these receivers require control and clock signals which are digital and low frequency analog, for the synchronization between receive modules. This is normally achieved through RF cables with complex distribution networks which add significantly higher additional weight to the arrays. During radar operations, radio frequency (RF) transmit signal needs to be distributed through the same modules which will in turn get distributed to all antenna elements of the array using RF cables. This makes the system bulky and these large number of cables are prone to Electromagnetic Interference (EMI) and need additional shielding. Therefore it is very desirable to distribute a combination of these RF, analog and digital signals using a distribution network that is less complex, light in weight and immune to EMI. Advancements in Optical and Microwave photonics area have enabled carrying of higher datarate signals on a single fiber due to its higher bandwidth capability including RF signals. This is achieved by employing Wavelength Division Multi- plexing (WDM) that combine high speed channels at different wavelengths. This work proposes, characterizes and evaluates an optical Wavelength Division Multiplexed(WDM) distribution network that will overcome the above mentioned problems in a phased array radar application. The work carries out a feasibility analysis supported with experimental measurements of various physical parameters like am- plitude, delay, frequency and phase variation for various radar waveforms over WDM links. Different configurations of optical distribution network are analyzed for multipoint distribution of both digital and RF signals. These network configurations are modeled and evaluated against various parameters that include power level, loss, cost and component count. A configuration which optimizes these parameters based on the application requirements is investigated. Considerable attention is paid to choose a configuration which does not provide excess loss, which is economically viable, compact and can be realized with minimum component count. After analysing the link configuration, multiplexing density of the WDM link is considered. In this work, since the number of signals to be distributed in radar systems are small, a coarse WDM(CWDM) scheme is considered for evaluation. A comparative study is also performed between coarse and dense WDM (DWDM) links for selection of a suitable multiplexing scheme. These configurations are modeled and evaluated with power budgeting. Even though CWDM scheme does not permit the utilisation of the available bandwidth to the fullest extent, these links have the advantage of having less hardware complexity and easiness of implementation. As the application requires signal distribution to thousands of transmit-receive modules, amplifiers are necessary to compensate for the reduction of signal level due to the high splitting ratio. Introduction of commonly available optical amplifiers like Erbium Doped Fiber Amplifier (EDFA), affect the CWDM channel output powers adversely due to their non-flat gain spectrum. Unlike DWDM systems, the channel separation of CWDM systems are much larger causing significantly high channel gain differences at the EDFA output. So an analysis is carried out for the selection of a suitable wavelength for CWDM channels to minimize the EDFA output power variation. If the gain difference is still significant, separate techniques needs to be implemented to flatten the output power at the antenna end. A CWDM configuration using C-band and L-band EDFAs is proposed and is supported with a feasibility analysis. As a part of evaluation of these links for radar applications, a mathematical model of the WDM link is developed by considering both the RF and digital sig- nals. A generic CWDM system consisting of transmitters, receivers, amplifiers, multiplexers/ demultiplexers and detectors are considered for the modeling. For RF signal transmission, the transmitters with external modulators are considered. Mod- eling is done based on a bottom-top approach where individual component models are initially modeled as a function of input current/power and later cascaded to obtain the link model. These models are then extended to obtain the wavelength dependent model ( spectral response) of the hybrid signal distribution link Further mathematical analysis of the developed link model revealed its variable separable nature in terms of the input power and wavelength. This led to significant reduction in the link equation complexity and development of some approximation techniques to easily represent the link behavior. The reduced form of the link spectral model was very essential as the initially developed wavelength model had a lot of parametric dependency on the component models. This mathematical reduction process led to simplification of the spectral model into a product of two independent functions, the input current and wavelength. It is also noticed that the total link power within specific wavelength range can be obtained by the integrating these functions over a specific link input power. After the mathematical modelling, an experimental prototype physical link is set up and characterized using various radar signals like continuous wave (CW) RF, pulsed RF, non linear frequency modulated signal (NLFM) etc. Additionally a proof of concept Radio-Over-Fiber (RoF) link is established to prove the superior transmission of microwave signal through an optical link. The analysis is supported with measurements on amplitude, delay, frequency and phase variations. The NLFM waveforms transmissions are further analysed using a matched _ltering process to confirm the side lobe requirement. Further a prototype WDM link is built to study the performance when digitally modulated channels are also multiplexed into the link. The link is again validated for signal levels, delay, frequency and phase parameters. Since amplitude and delay are deterministic, it is proposed that these parameter variations can be compensated by using suitable components either in the electrical or the optical domain. Radar systems use low frequency digital signals of different duty-cycles for synchronization and control across various transmit-receive modules. In the proposed link, these digital signals also modulate a WDM channel and hence the link is called a hybrid system. As the proposed link has EDFA to compensate for the splitting losses, there are chances of transient effects at the EDFA output for these low bitrate channels. Owing to the long carrier lifetime, low bitrate digital channels are prone to EDFA transient effects under specific signal and pump power conditions. Additionally, the synchronization signals used in radar application vary the duty-cycle over time, which is found to introduce variations in transient output. This practical challenge is further studied and the thesis for the first time, includes an analysis of EDFA transient e_ects for variable duty-cycle pulsed signals. The analysis is carried out for various parameters like bitrate, input power, pump power and duty-cycle. Investigations on EDFA transients on variable duty-cycle signals help in proposing a viable method to predict the lower duty-cycle transients from higher duty-cycle transients. The predicted transients were again validated against simulated transients and experimental results. As these transient effects are not desirable for radar signals, we propose a novel transient suppression techniques in optical and electrical domain which are validated with simulation and experimental measures. One suppression technique tries to avoid transient effect by keeping the optical input to EDFA always constant by feeding an inverted version of the original pulse into the EDFA along with the actual pulse. It is observed that as the wavelength of the inverted pulse is closer to the original input pulse, the transient effect settles faster. These EDFA transients are evaluated with WDM link configurations, where both high and low bitrate signals are co-propagated. Another challenging aspect of the link operation is the non-at gain spectrum of EDFA. i.e., EDFA provides unequal power level for various signals at WDM link output. This is especially true in the case of local oscillator signals, where it is preferable to have the same amplitude signals before feeding it to the mixer stages. But in the radar applications, this will require additional hardware circuits to equalize the signal level within a phased array antenna. This work also proposes some of the power equalization methods that can be used along with the WDM links. This part of the work is also supported with simulation model and experimental results. The analytical and experimental study of this thesis aids the evaluation process of a suitable optical Wavelength Division Multiplexed(WDM) distribution network that can be used for the distribution of both RF and digital signals. The optical WDM links being superior with its light weight, less loss and EMI/ EMC immunity provides a better solution to future class of radars.

Physiological signals, electroencephalogram (EEG) and heart rate variability (HRV), are generated by complex self-regulating systems. These signals are extremely inhomogeneous and nonstationary, and fluctuate in an irregular and highly complex manner. These fluctuations are due to underlying dynamics of the system. The synchronous neural activity measured as scalp EEG indicates underlying neural dynamics of the brain. Hence, quantitative EEG analysis has become a very useful tool in interpreting results from physiological experiments. The analysis of HRV provides valuable information to assess the autonomous nervous system (ANS). The HRV can be significantly affected by physiological state changes and many disease states. Hence, HRV analysis is becoming a major experimental and diagnostic tool. In this thesis, we focus on the study of EEG and HRV time series using tools from nonlinear time series analysis with special emphasis on its implications in detecting physiological state changes such as, in diseases like epileptic seizure and schizophrenia, and in altered states of consciousness as in sleep and meditation. The proposed nonlinear techniques are used in discriminating different physiological states from control states. Artifact processing of EEG signal Interferences (artifacts) from various sources unavoidably contaminate EEG recordings. In quantitative analysis, results can differ significantly by these artifacts, which may lead to wrong interpretation of the results. In this part of the thesis, we have devised methods to minimize ocular and muscle artifacts in EEG. The artifact correction methods are based on blind source separation (BSS) techniques such as singular value decomposition (SVD), algorithm for multiple signal extraction (AMUSE), canonical correlation analysis (CCA), information maximization (INFOMAX) independent component analysis (ICA) and joint approximate diagonalization of eigen-matrices (JADE) ICA. We have proposed a method to simulate clean and artifact corrupted EEG data based on the BSS methods. In order to enhance the performance of BSS methods, a technique called wavelet-filtered component inclusion method has been introduced. In addition, second-order statistics (SOS) and higher-order statistics (HOS) based BSS methods have been studied considering less number of EEG channels; and performance comparison of these methods has also been made. We have also addressed the problem of simultaneous correction of ocular and muscle artifacts in EEG recordings using the BSS methods. Irrespective of the BSS methods, the component elimination method has introduced high spectral error in all the bands after reconstruction of clean EEG. However, the wavelet filtered component inclusion method has retained almost all spectral powers of EEG channels in theta, alpha, and beta bands after ocular artifact minimization. When the number of EEG channels is very less, the enhanced CCA (SOS BSS) has given superior artifact minimization results than HOS BSS methods, especially in delta band. The component elimination method is used in muscle artifact minimization, and hence the SVD method cannot be used for this purpose since it leads to large spectral distortion of reconstructed EEG. The AMUSE and CCA methods have given comparable performance in muscle artifact minimization. In addition, the JADE method has introduced less mean spectral error compared to other methods. The CCA method has shown superior performance in simultaneous minimization of ocular and muscle artifacts, and AMUSE and JADE methods have given comparable results. Furthermore, the less computation time of wavelet enhanced SOS BSS methods make them very useful in real clinical environments. Fractal characterization of time series In biomedical signal analysis, fractal dimension (FD) is used as a quantitative measure to estimate complexity of physiological signals. Such analysis helps to study physiological processes of underlying systems. The FD can also be used to study dynamics of transitions between different states of systems like brain and ANS, in various physiological and pathological states. In this part, we have proposed a method to estimate FD of time series, called multiresolution box-counting (MRBC) method. A modification of this method resulted in multiresolution length (MRL) method. The estimation performance of the proposed methods is compared with that of Katz, Sevcik, and Higuchi methods, by simulating mathematically defined fractal signals, and also the computation time is compared between the methods. The MRBC and MRL methods have given comparable performance to that of Higuchi method, in estimating FD of waveforms, with the advantage of less computational time. In addition, various properties of the FD are studied and discussed in connection with classical signal processing concepts such as amplitude, frequency, sampling frequency, effect of noise, band width, correlation, etc. The FD value of signals has increased with number of harmonics, noise variance, band-width, and mid-band frequency, and decreased with degree of correlation in AR signal. An analogy between Katz FD and smoothed Teager energy operator has also been made. Application of fractal analysis to EEG and HRV time series The fluctuation of EEG potentials normally depends upon degree of alertness, and varies in amplitude and frequency. Hence, the EEG is an important clinical tool for studying sleep and sleep related disorders, epileptic seizures, schizophrenia, and meditation. In this part of the thesis, we have used FD which gives signal complexity, and detrended fluctuation analysis (DFA) which gives multiscale exponent of time series to quantify EEG. We have extended the concept of FD to multiscale FD to compute complexity of time series at multiple scales. The main applications of the proposed method are epileptic seizure detection, sleep stage detection, schizophrenia EEG analysis, and analysis of heart rate variability during meditation. For seizure detection, we have used intracranial EEG recordings with seizure-free and seizure intervals. In sleep EEG analysis, whole-night sleep EEG is used and results are compared with the manually scored hypnogram. The schizophrenia symptom is further categorized into positive and negative symptoms and complexity is estimated using FD and DFA. We have also analyzed HRV data of Chi and Kundalini meditation using FD and DFA techniques. In all the applications considered, we have tested for statistical significance of the computed parameters, between the case of interest and corresponding control cases, to discriminate between the physiological states. The ocular artifact has reduced FD while muscle artifact increased FD of EEG. The FD of seizure EEG has shown high value compared to that of seizure-free EEG. In addition, the seizure-free EEG has more DFA exponent-1 than seizure EEG. The value of FD of EEG is decreased with deepening of sleep, wake state having high FD value. The FD of REM state sleep EEG showed value between that of wake and state-1. The DFA exponent-1 has increased with deepening of sleep state, having small value for wake state. The REM state has given exponent-1 value between wake and state-1. The schizophrenia subjects have shown lower FD value than healthy controls in all the EEG channels except the bilateral temporal and occipital regions. The positive symptom sub-group has shown comparatively high FD values than healthy controls as well as overall schizophrenia sample in the bilateral tempero-parietal-occipital region. In addition, the positive symptom sub-group has shown significantly higher regional FD values than negative symptom sub-group especially in right temporal region. The overall schizophrenia samples as well as the positive and negative subgroup have shown least FD values in the bilateral frontal region. The values of DFA exponent-2 have shown significant high value in schizophrenia samples. In addition, the schizophrenia group has shown less DFA exponent-1 in bilateral temporal region than healthy control. The FD, multiscale FD, DFA exponents have shown significant performance in discriminating different physiological states from control states. The FD value of HRV time series during meditation is less compared to pre-meditation state in both Chi and Kundalini meditation. Irrespective of the type of meditation, meditation state has shown significantly high DFA exponent-1 than pre-meditation state, and significantly high DFA exponent-2 in pre-meditation state compared to meditation state. Functional connectivity analysis of brain during meditation In functionally related regions of the brain, even in those regions separated by substantial distances, the EEG fluctuations are synchronous, which is termed as functional connectivity. In this part, a novel application of functional connectivity analysis of brain using graph theoretic approach has been made on the EEG recorded from meditation practitioners. We have used 16 channel EEG data from subjects while performing Raja Yoga meditation. The pre-meditation condition is used as control state, against which meditation state is compared. For finding connectivity between EEG of various channels, we have computed pair-wise linear correlation and mutual information between the EEG channels, to form a connection matrix of size 16x16. Then, various graph parameters, such as average connection density, degree of nodes, characteristic path length, and cluster index, are computed from the connection matrix. The computed parameters are projected on to the scalp to get topographic head maps that give spatial variation of the parameter, and results are compared between meditation and pre-meditation states. The meditation state has shown low average connection density, less characteristic path length, and high average degree in fronto-central and central regions. Furthermore, high cluster index is shown in frontal and central regions than pre-meditation state. The parameters such as complexity, characteristic path length and average connection density are used as features in quadratic discriminant classifier to classify meditation and pre-meditation state, and have given good accuracy performance. Connectivity analysis using mutual information has given high average connection density in meditation state in theta, alpha and beta bands compared to pre-meditation state. The characteristic path length is high in delta, alpha and beta bands in meditation state. In addition, the meditation state has shown high degree and cluster index in theta and beta bands compared to pre-meditation state. Nonlinear dynamical characterization of HRV during meditation The cardiovascular system is influenced by internal dynamics as well as from various external factors, which makes the system more dynamic and nonlinear. In this part of the thesis, a novel application of using HRV data for studying Chi and Kundalini meditation has been made. The HRV time series are embedded into higher dimensional phase-space using Takens’ embedding theorem to reconstruct the attractor. After estimating the minimum embedding dimension to unfold the attractor dynamics, the complexity of the attractor is computed using correlation dimension, Lyapunov exponent, and nonlinearity scores. In all the analyses, the pre-meditation state is used as control state against which meditation state is compared. The statistical significance of the parameters estimated is tested to discriminate meditation state from control state. The HRV time series of both pre-meditation and meditation have shown similar minimum embedding dimensions in both Chi and Kundalini meditation. Irrespective of the type of meditation, the meditation state has shown high correlation dimension, largest Lyapunov exponent, and low nonlinearity score compared to pre-meditation state. Recurrent quantification analysis of HRV during meditation In this part, a novel application of recurrent quantification analysis (RQA) to HRV during meditation is studied. Here, the time series is embedded into a higher dimensional phase-space and Euclidean distance between the embedded vectors is calculated to form a distance matrix. The matrix is converted into binary matrix by applying a suitable threshold, and plotted as image to get recurrence plot. Various parameters are extracted from the recurrence plot such as percent recurrence rate, diagonal parameters (determinism, divergence, entropy, ratio), and vertical or horizontal parameters (laminarity, trapping time, maximal vertical line length). The procedure is applied to HRV data during meditation and pre-meditation (control) to discriminate between the states. The HRV of meditation state has shown more diagonal line structure whereas more black patches are observed in pre-meditation state. In addition, at low embedding dimensions, the meditation state has shown low recurrence rate, high determinism, low divergence, low entropy, high ratio, high laminarity, high trapping time, and less maximal vertical line length compared to pre-meditation state. These RQA parameters have shown superior performance in discriminating meditation state from control state.