Distributed Smart Camera (DSC) networks are power constrained real-time distributed embedded systems that perform computer vision using multiple cameras. Providing data aggregation techniques that is criti-cal for running complex image processing algorithms on DSCs is a challenging task due to complexity of video and image data. Providing highly desirable SQL APIs for sophisticated query processing in DSC networks is also challenging for similar reasons. Research on DSCs to date have not addressed the above two problems. In this thesis, we develop a novel SOA based middleware framework on a DSC network that uses Distributed OSGi to expose DSC network services as web services. We also develop a novel web service composition scheme that aid in data aggregation and a SQL query interface for DSC net-works that allow sophisticated query processing. We validate our service orchestration concept for data aggregation by providing query primitive for face detection in smart camera network.

Protein aggregation and physical stability are perpetual concerns in medicine and industry. Misfolded protein can form ordered protein aggregates, amyloids, which are associated with a host of neurodegenerative diseases in mammals and control heritable traits in fungi and yeast. Industrially, amorphous aggregates reduce the efficacy of protein-based therapeutics and activity of enzymes during production and storage. This work studies ion-specific and solvent-based effects on protein physical stability. We show that ion-specificity significantly affects amyloid formation kinetics, aggregate morphology, thermostability, frangibility, and, most intriguingly, prion infectivity in vivo. Forming amyloid in chaotropic or kosmotropic solutions generates predominately weak or strong prion variants, respectively. Ion-specific effects also influenced amorphous aggregation of model proteins and antibodies. To quantify protein - protein stability/affinity, we developed a rapid and reliable diffusion-based technique. Our technique was able to resolve relative differences in colloidal stability between various saline and saccharide solutions. In all, this dissertation expands our understanding of ion-specific and water-mediated interactions with prion proteins and protein dispersions.

The disturbances and abnormalities occurring in the components of the Acetylcholine (ACh) neurocycle are considered one of the main features of cholinergic sicknesses like Parkinson’s and Alzheimer’s diseases. A fundamental understanding of the ACh neurocycle is therefore very critical in order to design drugs that keep the ACh concentrations in the normal physiological range. In this dissertation, a novel two-enzyme-two-compartment model is proposed in order to explore the bifurcation, dynamics, and chaotic characteristics of the ACh neurocycle. The model takes into consideration the physiological events of the choline uptake into the presynaptic neuron and the ACh release in the postsynaptic neuron. In order to approach more realistic behavior, two complete kinetic mechanisms for enzymatic processes pH-dependent are built: the first mechanism is for the hydrolysis reaction catalyzed by the acetylcholinesterase (AChE) and the other is for the synthesis reaction catalyzed by the cholineacetyltransferase (ChAT). The effects of hydrogen ion feed concentrations, AChE activity, ChAT activity, feed ACh concentrations, feed choline concentrations, and feed acetate concentrations as bifurcation parameters, on the system performance are studied. It was found that hydrogen ions play an important role, where they create potential differences through the plasma membranes. The concentrations of ACh, choline and acetate in compartments 1 and 2 are affected by the activity of AChE through a certain range of their concentrations, where the activity of AChE is inhibited completely after reaching certain values. A detailed bifurcation analysis over a wide range of parameters is carried out in order to uncover some important features of the system, such as hysteresis, multiplicity, Hopf bifurcation, period doubling, chaotic characteristics, and other complex dynamics. The effects of the feed choline concentrations and the feed acetate concentrations as bifurcation parameters are studied in this dissertation. It is found that the feed choline concentrations play an important role and have a direct effect on the ACh neurocycle through a certain important range of the parameters. However, the feed acetate concentrations have less effect. It is concluded from the results that the feed choline is a more important factor than the feed acetate in ACh processes. The effects of ChAT activity and the choline recycle ratio as bifurcation parameters, on the system performance are investigated. It was found that as the ChAT activity increases, ACh concentrations in compartments 1 and 2 increase continuously. The effect of the choline recycle ratio shows that choline reuptake plays a very critical role in the synthesis of ACh in compartment 1, where it supplies the choline as a substrate for the synthesis reaction by ChAT. The concentrations of ACh, choline and acetate in compartments 1 and 2 are affected by the choline recycle ratio through a certain range of the choline recycle ratio; then, they become constant as the choline recycle ratio increases further. It is concluded from our results that choline uptake is the rate limiting step in the ACh processes in both compartments in comparison to ChAT activity. Based on partial dissociation of the acetic acid in compartments 1, and 2 of the ACh cholinergic system, the two-parameter continuation technique has been applied to investigate the pH range to be closer to physiological ranges of pH values. In addition, static/dynamic solutions of the ACh cholinergic neurocycle system based on feed choline concentration as the main bifurcation parameter in both compartments have been investigated. The findings of the above studies are related to the real phenomena occurring in the neurons, like periodic stimulation of neural cells and non-regular functioning of ACh receptors. It was found that ACh, choline, acetate, and pH exist inside the physiological range associated with taking into consideration the partial dissociation of the acetic acid. The disturbances and irregularities (chaotic attractors) occurring in the ACh cholinergic system may be good indications of cholinergic diseases such as Alzheimer’s and Parkinson’s diseases. The results have been compared to the results of physiological experiments and other published models. As there is strong evidence that cholinergic brain diseases like Alzheimer’s disease and Parkinson’s disease are related to the concentration of ACh, the present findings are useful for uncovering some of the characteristics of these diseases and encouraging more physiological research.

The disturbances and abnormalities occurring in the components of the Acetylcholine (ACh) neurocycle are considered one of the main features of cholinergic sicknesses like Parkinson’s and Alzheimer’s diseases. A fundamental understanding of the ACh neurocycle is therefore very critical in order to design drugs that keep the ACh concentrations in the normal physiological range. In this dissertation, a novel two-enzyme-two-compartment model is proposed in order to explore the bifurcation, dynamics, and chaotic characteristics of the ACh neurocycle. The model takes into consideration the physiological events of the choline uptake into the presynaptic neuron and the ACh release in the postsynaptic neuron. In order to approach more realistic behavior, two complete kinetic mechanisms for enzymatic processes pH-dependent are built: the first mechanism is for the hydrolysis reaction catalyzed by the acetylcholinesterase (AChE) and the other is for the synthesis reaction catalyzed by the cholineacetyltransferase (ChAT). The effects of hydrogen ion feed concentrations, AChE activity, ChAT activity, feed ACh concentrations, feed choline concentrations, and feed acetate concentrations as bifurcation parameters, on the system performance are studied. It was found that hydrogen ions play an important role, where they create potential differences through the plasma membranes. The concentrations of ACh, choline and acetate in compartments 1 and 2 are affected by the activity of AChE through a certain range of their concentrations, where the activity of AChE is inhibited completely after reaching certain values. A detailed bifurcation analysis over a wide range of parameters is carried out in order to uncover some important features of the system, such as hysteresis, multiplicity, Hopf bifurcation, period doubling, chaotic characteristics, and other complex dynamics. The effects of the feed choline concentrations and the feed acetate concentrations as bifurcation parameters are studied in this dissertation. It is found that the feed choline concentrations play an important role and have a direct effect on the ACh neurocycle through a certain important range of the parameters. However, the feed acetate concentrations have less effect. It is concluded from the results that the feed choline is a more important factor than the feed acetate in ACh processes. The effects of ChAT activity and the choline recycle ratio as bifurcation parameters, on the system performance are investigated. It was found that as the ChAT activity increases, ACh concentrations in compartments 1 and 2 increase continuously. The effect of the choline recycle ratio shows that choline reuptake plays a very critical role in the synthesis of ACh in compartment 1, where it supplies the choline as a substrate for the synthesis reaction by ChAT. The concentrations of ACh, choline and acetate in compartments 1 and 2 are affected by the choline recycle ratio through a certain range of the choline recycle ratio; then, they become constant as the choline recycle ratio increases further. It is concluded from our results that choline uptake is the rate limiting step in the ACh processes in both compartments in comparison to ChAT activity. Based on partial dissociation of the acetic acid in compartments 1, and 2 of the ACh cholinergic system, the two-parameter continuation technique has been applied to investigate the pH range to be closer to physiological ranges of pH values. In addition, static/dynamic solutions of the ACh cholinergic neurocycle system based on feed choline concentration as the main bifurcation parameter in both compartments have been investigated. The findings of the above studies are related to the real phenomena occurring in the neurons, like periodic stimulation of neural cells and non-regular functioning of ACh receptors. It was found that ACh, choline, acetate, and pH exist inside the physiological range associated with taking into consideration the partial dissociation of the acetic acid. The disturbances and irregularities (chaotic attractors) occurring in the ACh cholinergic system may be good indications of cholinergic diseases such as Alzheimer’s and Parkinson’s diseases. The results have been compared to the results of physiological experiments and other published models. As there is strong evidence that cholinergic brain diseases like Alzheimer’s disease and Parkinson’s disease are related to the concentration of ACh, the present findings are useful for uncovering some of the characteristics of these diseases and encouraging more physiological research.

Sensor networks are innovative wireless networks consisting of a large number of low-cost, resource-constrained sensor nodes that collect, process, and transmit data in a distributed and collaborative way. There are numerous applications for wireless sensor networks, and security is vital for many of them. However, sensor nodes suffer from many constraints, including low computation capability, small memory, limited energy resources, susceptibility to physical capture, and the lack of infrastructure, all of which impose formidable security challenges and call for innovative approaches. In this thesis, we present our research results on three important aspects of securing sensor networks: lightweight entity authentication, distributed node clone detection, and secure data aggregation. As the technical core of our lightweight authentication proposals, a special type of circulant matrix named circulant-P2 matrix is introduced. We prove the linear independence of matrix vectors, present efficient algorithms on matrix operations, and explore other important properties. By combining circulant-P2 matrix with the learning parity with noise problem, we develop two one-way authentication protocols: the innovative LCMQ protocol, which is provably secure against all probabilistic polynomial-time attacks and provides remarkable performance on almost all metrics except one mild requirement for the verifier's computational capacity, and the HB$^C$ protocol, which utilizes the conventional HB-like authentication structure to preserve the bit-operation only computation requirement for both participants and consumes less key storage than previous HB-like protocols without sacrificing other performance. Moreover, two enhancement mechanisms are provided to protect the HB-like protocols from known attacks and to improve performance. For both protocols, practical parameters for different security levels are recommended. In addition, we build a framework to extend enhanced HB-like protocols to mutual authentication in a communication-efficient fashion. Node clone attack, that is, the attempt by adversaries to add one or more nodes to the network by cloning captured nodes, imposes a severe threat to wireless sensor networks. To cope with it, we propose two distributed detection protocols with difference tradeoffs on network conditions and performance. The first one is based on distributed hash table, by which a fully decentralized, key-based caching and checking system is constructed to deterministically catch cloned nodes in general sensor networks. The protocol performance of efficient storage consumption and high security level is theoretically deducted through a probability model, and the resulting equations, with necessary adjustments for real application, are supported by the simulations. The other is the randomly directed exploration protocol, which presents notable communication performance and minimal storage consumption by an elegant probabilistic directed forwarding technique along with random initial direction and border determination. The extensive experimental results uphold the protocol design and show its efficiency on communication overhead and satisfactory detection probability. Data aggregation is an inherent requirement for many sensor network applications, but designing secure mechanisms for data aggregation is very challenging because the aggregation nature that requires intermediate nodes to process and change messages, and the security objective to prevent malicious manipulation, conflict with each other to a great extent. To fulfill different challenges of secure data aggregation, we present two types of approaches. The first is to provide cryptographic integrity mechanisms for general data aggregation. Based on recent developments of homomorphic primitives, we propose three integrity schemes: a concrete homomorphic MAC construction, homomorphic hash plus aggregate MAC, and homomorphic hash with identity-based aggregate signature, which provide different tradeoffs on security assumption, communication payload, and computation cost. The other is a substantial data aggregation scheme that is suitable for a specific and popular class of aggregation applications, embedded with built-in security techniques that effectively defeat outside and inside attacks. Its foundation is a new data structure---secure Bloom filter, which combines HMAC with Bloom filter. The secure Bloom filter is naturally compatible with aggregation and has reliable security properties. We systematically analyze the scheme's performance and run extensive simulations on different network scenarios for evaluation. The simulation results demonstrate that the scheme presents good performance on security, communication cost, and balance.

It has been proved from several studies that the genetic influence has been the most significant factor for having preeclampsia (PE). Still there are many uncertainties about origin and magnitude of the genetic effects as no specific inheritance patterns have been established. In this study, heritage risk of PE is in both the woman’s family and her partner’s family to her risk of PE is examined, along women and men own history with same and different partners. Moreover it is also examined whether timing of onset of PE is also has any impact on familial clustering of PE. Here, we used the population based Danish birth and multi generation registers to identify a cohort of women who have given birth during 1978 to 2008; which consisted of 1,79,69,28 singleton deliveries. This information is linked with pedigree information from the Danish Family Relation Database to define both maternal and paternal relationships. Risk ratios were estimated comparing women with and without various PE histories. It is found that the recurrence risk of a woman suffering from PE is 12.4 with 95% confidence limits (11.9, 12.8). Woman's recurrence risk diminishes only slightly when she changes partner means that particularly maternal genetic factors play the largest role, compared to male partner whose recurrence risk almost diminishes if he changes his female partner. Women and men from families with PE contribute to risk of PE in pregnancies they are involved in. The woman’s family history is still more important compared to man family history of PE; except for increased rick in pregnancies fathered by men who were born to preeclamptic mothers.  The recurrence risk of a women suffering from PE, if she already has suffered from this condition before 34 weeks is found to be very high (RR=25.4 with 95% confidence limits (21.8, 29.1)) with same male partner. It is found that early-onset PE and later-onset varieties have a clear genetic component but the intensity of early onset is stronger than late onset varieties. There are both maternal and paternal genetic contributions to early-onset PE, with the maternal ones seeming to be stronger.

Copepod species are distributed throughout the ocean by many factors, including chemical, biological, and physical effects. Turbulence in the ocean has been suggested as a factor that vertically partitions some species of copepod. Copepods may seek calmer waters by sinking to deeper levels as the surface waters become more turbulent, or may maintain their position in turbulent waters. The goal of this study is to determine the behavioral effects of turbulence on three species of copepod, Calanus finmarchicus, Acartia tonsa, and Temora longicornis. Experiments consisted of exposing each of the species to stagnant water plus four levels of turbulence intensity. The experiments were conducted in a laboratory apparatus that mimics oceanic turbulence. The turbulence characteristics have been previously characterized by particle image velocimetry (PIV), that show the turbulence to be nearly isotropic and homogeneous in the observation region. Behavior responses were quantified via several measures, including the number of animals phototactically aggregating per minute, the number of escape events, the swimming speed, and the net-to-gross-displacement ratio. There are important conclusions about the effect of laboratory turbulence on copepods. The size of the copepod has a significant effect on its aggregation and swimming capability with increasing turbulence. The smaller copepods had less ability to overcome a strong flow field, and they were more likely to be advected by the stronger flow fields. Swim style also can influence how a copepod reacts to increased turbulence. If the copepod is a hop and sink traveler, then the copepod continues to hop and sink more than its cruising counterparts as turbulence increases. The cruise and sink travelers did not alter the number of escapes in response to turbulence.

Wireless sensor networks (WSNs) are characterized by limited amount of energy supply at sensor nodes. Hence, energy efficiency is an important issue in system design and operation of WSNs. In this work we focus on solving the energy efficiency problems of data gathering processes in WSNs. We first address this problem on a macroscopic level by investigating the efficiency of data gathering trees when data sent by different sensors are correlated. Such correlation aware data gathering strategies typically shift the aggregation structure from a default shortest-path tree (SPT) to a steiner minimum tree (SMT) in order to achieve the required efficiency. We study the energy efficiency of correlation aware data aggregation trees under various sensor network conditions and the tradeoffs involved in using them. Comprehensive simulation results as well as inferences and theoretical analysis of those results are presented in the thesis. Based on the insights gained through the investigation, we propose a simple, scalable and distributed correlation aware aggregation structure that achieves good energy performance across a wide range of sensor network configurations, and at the same time addresses the practical challenges of establishing a correlation aware data aggregation structure in resource-constrained WSNs. On a microscopic level, we propose a novel communication strategy called Communication through Silence (CtS) to achieve energy-efficient data gathering without significant degradation on overall throughput in WSNs. The proposed scheme primarily uses time, along with a minimal amount of energy to deliver information among sensors. CtS can be used to replace the conventional energy-based transmissions between each pair of sensor nodes during a data gathering process. We analyze in detail the primary energy-throughput tradeoff inherent in this approach as well as other challenges related to the realization of the proposed communication strategy. Finally, we propose a practical realization of CtS strategy that includes radio technology, MAC layer, and higher layer solutions. Performance evaluation results prove that this solution effectively realizes the CtS strategy in a WSN setting, at the same time achieves considerable energy savings compared to conventional communication strategies.

About half a century ago, Főrster and Kasper discovered that traditional organic chromophore such as pyrene was weakened with an increase in its solution concentration. It was soon recognized that this was a general phenomenon for many aromatic compounds. This concentration-quenching effect was found to be caused by the formation of sandwich-shaped (disc-like) excimers and exciplexes aided by the collisional interactions between the aromatic molecules in the excited and ground states. In 2001, Tang¡¦group discovered such a system, in which luminogen aggregation played a constructive, instead of a destructive, role in the light-emitting process: a series of silole molecules were found to be non-luminescent in the solution state but emissive in the aggregated state. They coined the term ¡¥¡¥aggregation-induced emission¡¦¡¦ (AIE) or ¡§AIE enhancement¡¨ (AIEE) for this novel phenomenon which originated from the restricted intramolecular rotation (RIR) inherent from the chemical structures of the luminescent materials. To verify the effect of molecular structure on the AIE properties of organic and polymeric materials, four approaches were attempted in this research. (I) Aggregation-Induced Emission in Tetraphenylthiophene-Derived Organic Molecules and Vinyl Polymer Organic molecules of tetraphenylthiophene (TP) and the derived model compound of TP-Qu and vinyl polymer of PS-Qu with the pendant group of TP-Qu were prepared and characterized to identify their photoluminescent responses toward the effect of AIE. During aggregate formation, the corresponding TP solutions greatly gained the emission intensity. In contrast, TP-Qu and PS-Qu in isolated or aggregated states emitted strongly with nearly the same emission intensity. RIR is the key factor deciding the AIE effect in different states. With four small phenyl rotors around the central thiophene stator, the RIR of the TP molecules in dilute solution is low but increases upon aggregate formations. In contrast, the bulky C-2 quinoline rotor of the TP-Qu molecule enhances the RIR in isolated state. With the inherent TP-Qu pendant groups, the emissive behavior of vinyl polymer PS-Qu is similar to the TP-Qu molecule. (II) Aggregation-Induced Emission Enhancement of Diblock Copolymer Containing Tetraphenylthiophene-Quinoline Pendant Fluorphores by Selective Solvent Pairs In this study, diblock copolymer of PSQu-PBS containing 25 mol% of fluorescent PSQu segments was synthesized and its aggregation-induced emission enhancement (AIEE) behavior was characterized and compared to PSQu homopolymer with 100 mol% of fluorescent units. With fewer (25 %) fluorescent units, solutions of diblock PSQu-PBS copolymer actually have higher (or comparable) emission intensities than the homopolymer PSQu solutions. Solutions of PSQu-PBS in THF/H2O of varied compositions emit essentially with the same intensity but in contrast, emissions of PSQu-PBS in THF/hexane increase with the increasing hexane content. Copolymer micelles formed in THF/hexane mixtures are supposed to have higher extent of aggregation, leading to more pronounced AIEE effect than micelles formed in THF/H2O. (III) Tetraphenylthiophene-Functionalized Poly(N-isopropylacrylamide): Probing LCST with Aggregation-Induced Emission A hydrophobic TP center with novel AIE property was chemically linked to two poly(N-isopropylacrylamide) (PNIPAM) chains to obtain thermoresponsive polymers to study the relationships between the lower critical solution transitions (LCSTs) and the AIE-operative fluorenscence emission. Three ethynyl-terminated PNIPAMs with different molecular weights were synthesized via controlled atom transfer radical polymerization (ATRP) using ethynyl-functionalized initiator. The PNIPAMs were then coupled with diazide-funtionalized TP (TPN3) via click reaction to obtain the desired TP-embedded polymers of Px (x = 1, 2, and 3). All three polymers show AIE-property from their solution fluorescence behavior in THF/hexane mixtures. In the aqueous solution, the TP-center served as a fluorogenic probe that reveals the LCSTs of polymers and its relation to the degree of TP labeling in terms of polymer concentration. The thermoresponsiveness of Px was demonstrated by the complete emission quench when heated at temperatures above LCST. Dissociation of the TP aggregates above LCST is responsible for the emission quench. (IV) Influence of Molecular Weight on the Aggregation-Induced Emission of Vinyl Polymers Containing the Fluorescent 2,4,6-Triphenylpyridine Pendant Groups Molecular weight effect on the AIEE property of vinyl polymers containing fluorescent 2,4,6-triphenylpyridine (TPP) pendant groups was evaluated in the fourth topic. The high and low Mw vinyl polymers of PDMPS¡VL and ¡VH were prepared through Click chemistry between azide¡VTPP derivative and acetylene¡Vfunctionalized polystyrenes. Solutions of the low Mw PDMPS¡VL exhibited the normal AIEE effect with continuous emission gains with increasing extent of aggregation upon nonsolvent inclusion. On the contrast, the high Mw PDMPS¡VH solutions emitted with constant intensity on all solutions with different extent of aggregation. Despite the varied solution behavior, the solid PDMPS-L and ¡VH films are all strong deep-blue emitter with high quantum yields of 84 and 82.5%, respectively. The emission behavior was explained by the conformational difference between the PDMPS¡VL and ¡VH chains, which were approached by computer simulation in this topic.

In this study, tetraphenylthiophenen (TP) with aggregation-induced emission enhancement (AIEE) property is served as terminal and central fluorophores of poly(£^-benzyl-L-glutamate) (PBLG)-based polymers of TP1PBLG and TP2PBLG, respectively, to probe for the relationship between the secondary structure (£\-helix) of polypeptides and the ALEE-operative fluorescence (FL). Intermolecular aggregation of the central TP unit in the di-substituted TP2PBLG is sterically blocked by the large £\-helical PBLG chains, which lead to the reduced AIEE-oriented FL. On the contrast, the terminal TP units in TP1PBLG can easily approach each other to form aggregates with strong FL. Factor (e.g. solvent annealing) controlling the fraction of £\-helix chain also varies the corresponding emission intensity. Conformational difference between TP1PBLG and TP2PBLG evaluated from the infrared and the X-ray (wide- and small-angle) diffraction spectra is also used to verify its influence on the AIEE-operative FL behavior.