'An Artificial Immune System as a Recommender System for Web Sites'

Artificial Immune Systems have been used successfully to build recommender systems for film databases. In this research, an attempt is made to extend this idea to web site recommendation. A collection of more than 1000 individuals' web profiles (alternatively called preferences / favourites / bookmarks file) will be used. URLs will be classified using the DMOZ (Directory Mozilla) database of the Open Directory Project as our ontology. This will then be used as the data for the Artificial Immune Systems rather than the actual addresses. The first attempt will involve using a simple classification code number coupled with the number of pages within that classification code. However, this implementation does not make use of the hierarchical tree-like structure of DMOZ. Consideration will then be given to the construction of a similarity measure for web profiles that makes use of this hierarchical information to build a better-informed Artificial Immune System.

Existence and weak-strong uniqueness for the Navier-Stokes-Smoluchowski system over moving domains

This dissertation concerns the well-posedness of the Navier-Stokes-Smoluchowski system. The system models a mixture of fluid and particles in the so-called bubbling regime. The compressible Navier-Stokes equations governing the evolution of the fluid are coupled to the Smoluchowski equation for the particle density at a continuum level. First, working on fixed domains, the existence of weak solutions is established using a three-level approximation scheme and based largely on the Lions-Feireisl theory of compressible fluids. The system is then posed over a moving domain. By utilizing a Brinkman-type penalization as well as penalization of the viscosity, the existence of weak solutions of the Navier-Stokes-Smoluchowski system is proved over moving domains. As a corollary the convergence of the Brinkman penalization is proved. Finally, a suitable relative entropy is defined. This relative entropy is used to establish a weak-strong uniqueness result for the Navier-Stokes-Smoluchowski system over moving domains, ensuring that strong solutions are unique in the class of weak solutions.

Phytoplankton versus macrophyte contribution to primary production and biogeochemical cycles of a coastal mesotidal system. A modelling approach

This study presents an assessment of the contributions of various primary producers to the global annual production and N/P cycles of a coastal system, namely the Arcachon Bay, by means of a numerical model. This 3D model fully couples hydrodynamic with ecological processes and simulates nitrogen, silicon and phosphorus cycles as well as phytoplankton, macroalgae and seagrasses. Total annual production rates for the different components were calculated for different years (2005, 2007 and 2009) during a time period of drastic reduction in seagrass beds since 2005. The total demand of nitrogen and phosphorus was also calculated and discussed with regards to the riverine inputs. Moreover, this study presents the first estimation of particulate organic carbon export to the adjacent open ocean. The calculated annual net production for the Arcachon Bay (except microphytobenthos, not included in the model) ranges between 22,850 and 35,300 tons of carbon. The main producers are seagrasses in all the years considered with a contribution ranging from 56% to 81% of global production. According to our model, the -30% reduction in seagrass bed surface between 2005 and 2007, led to an approximate 55% reduction in seagrass production, while during the same period of time, macroalgae and phytoplankton enhanced their productions by about +83% and +46% respectively. Nonetheless, the phytoplankton production remains about eightfold higher than the macroalgae production. Our results also highlight the importance of remineralisation inside the Bay, since riverine inputs only fulfill at maximum 73% nitrogen and 13% phosphorus demands during the years 2005, 2007 and 2009. Calculated advection allowed a rough estimate of the organic matter export: about 10% of the total production in the bay was exported, originating mainly from the seagrass compartment, since most of the labile organic matter was remineralised inside the bay.

Exchange interaction in chirally coupled quantum dots

We present transport measurements on a system of two lateral quantum dots in a perpendicular magnetic field. Due to edge channel formation in an open conducting region, the quantum dots are chirally coupled. When both quantum dots are tuned into the Kondo regime simultaneously, we observe a change in the temperature dependence of the differential conductance. This is explained by the RKKY exchange interaction between the two dots. As a function of bias the differential conductance shows a splitting of the Kondo resonance which changes in the presence of RKKY interaction.

A biochemical analysis into the co-translational folding of a G protein-coupled receptor; GPR35

The folding and targeting of membrane proteins poses a major challenge to the cell, as they must remain insertion competent while their highly hydrophobic transmembrane (TM) domains are transferred from the ribosome, through the aqueous cytosol and into the lipid bilayer. The biogenesis of a mature membrane protein takes place through the insertion and integration into the lipid bilayer. A number of TM proteins have been shown to gain some degree of secondary structure within the ribosome tunnel and to retain this conformation throughout maturation. Although studies into the folding and targeting of a number of membrane proteins have been carried out to date, there is little information on one of the largest class of eukaryotic membrane proteins; the G-protein-coupled receptors (GPCRs). This project studies the early folding events of the human ortholog of GPR35. To analyse the structure of the 1st TM domain, intermediates were generated and assessed by the biochemical method of pegylation (PEG-MAL). A structurally-similar microbial opsin (Bacterioopsin) was also used to investigate the differences in the early protein folding within eukaryotic and prokaryotic translation systems. Results showed that neither the 1st TM domain of GPR35 nor Bacterioopsin were capable of compacting in the ribosome tunnel before their N-terminus reached the ribosome exit point. The results for this assay remained consistent whether the proteins were translated in a eukaryotic or prokaryotic translation system. To examine the communication mechanism between the ribosome, the nascent chain and the protein targeting pathway, crosslinking experiments were carried out using the homobifunctional lysine cross-linker BS3. Specifically, the data generated here show that the nascent chain of GPR35 reaches the ribosomal protein uL23 in an extended conformation and interacts with the SRP protein as it exits the ribosome tunnel. This confirms the role of SRP in the co-translational targeting of GPR35. Using these methods insights into the early folding of GPCRs has been obtained. Further experiments using site-directed mutagenesis to reduce hydrophobicity in the 1st TM domain of GPR35, highlighted the mechanisms by which GPCRs are targeted to the endoplasmic reticulum. Confirming that hydrophobicity within the signal anchor sequence is essential of SRP-dependent targeting. Following the successful interaction of the nascent GPR35 and SRP, GPR35 is successfully targeted to ER membranes, shown here as dog pancreas microsomes (DPMs). Glycosylation of the GPR35 N-terminus was used to determine nascent chain structure as it is inserted into the ER membrane. These glycosylation experiments confirm that TM1 has obtained its compacted state whilst residing in the translocon. Finally, a site-specific cross-linking approach using the homobifunctional cysteine cross-linker, BMH, was used to study the lateral integration of GPR35 into the ER. Cross-linking of GPR35 TM1 and TM2 could be detected adjacent to a protein of ~45kDa, believed to be Sec61α. The loss of this adduct, as the nascent chain extends, showed the lateral movement of GPR35 TM1 from the translocon was dependent on the subsequent synthesis of TM2.

'An Artificial Immune System as a Recommender System for Web Sites'

Artificial Immune Systems have been used successfully to build recommender systems for film databases. In this research, an attempt is made to extend this idea to web site recommendation. A collection of more than 1000 individuals' web profiles (alternatively called preferences / favourites / bookmarks file) will be used. URLs will be classified using the DMOZ (Directory Mozilla) database of the Open Directory Project as our ontology. This will then be used as the data for the Artificial Immune Systems rather than the actual addresses. The first attempt will involve using a simple classification code number coupled with the number of pages within that classification code. However, this implementation does not make use of the hierarchical tree-like structure of DMOZ. Consideration will then be given to the construction of a similarity measure for web profiles that makes use of this hierarchical information to build a better-informed Artificial Immune System.

Surface acoustic wave streaming in a PDMS microfluidic system: effect of frequency and fluid geometry & A remote ultrasonic glucose sensor

This thesis describes two separate projects. The first is a theoretical and experimental investigation of surface acoustic wave streaming in microfluidics. The second is the development of a novel acoustic glucose sensor. A separate abstract is given for each here. Optimization of acoustic streaming in microfluidic channels by SAWs Surface Acoustic Waves, (SAWs) actuated on flat piezoelectric substrates constitute a convenient and versatile tool for microfluidic manipulation due to the easy and versatile interfacing with microfluidic droplets and channels. The acoustic streaming effect can be exploited to drive fast streaming and pumping of fluids in microchannels and droplets (Shilton et al. 2014; Schmid et al. 2011), as well as size dependant sorting of particles in centrifugal flows and vortices (Franke et al. 2009; Rogers et al. 2010). Although the theory describing acoustic streaming by SAWs is well understood, very little attention has been paid to the optimisation of SAW streaming by the correct selection of frequency. In this thesis a finite element simulation of the fluid streaming in a microfluidic chamber due to a SAW beam was constructed and verified against micro-PIV measurements of the fluid flow in a fabricated device. It was found that there is an optimum frequency that generates the fastest streaming dependent on the height and width of the chamber. It is hoped this will serve as a design tool for those who want to optimally match SAW frequency with a particular microfluidic design. An acoustic glucose sensor Diabetes mellitus is a disease characterised by an inability to properly regulate blood glucose levels. In order to keep glucose levels under control some diabetics require regular injections of insulin. Continuous monitoring of glucose has been demonstrated to improve the management of diabetes (Zick et al. 2007; Heinemann & DeVries 2014), however there is a low patient uptake of continuous glucose monitoring systems due to the invasive nature of the current technology (Ramchandani et al. 2011). In this thesis a novel way of monitoring glucose levels is proposed which would use ultrasonic waves to ‘read’ a subcutaneous glucose sensitive-implant, which is only minimally invasive. The implant is an acoustic analogy of a Bragg stack with a ‘defect’ layer that acts as the sensing layer. A numerical study was performed on how the physical changes in the sensing layer can be deduced by monitoring the reflection amplitude spectrum of ultrasonic waves reflected from the implant. Coupled modes between the skin and the sensing layer were found to be a potential source of error and drift in the measurement. It was found that by increasing the number of layers in the stack that this could be minimized. A laboratory proof of concept system was developed using a glucose sensitive hydrogel as the sensing layer. It was possible to monitor the changing thickness and speed of sound of the hydrogel due to physiological relevant changes in glucose concentration.

A Ride-Sharing System with High Capacity Vehicles and Flexible Meeting Points

In many major cities, fixed route transit systems such as bus and rail serve millions of trips per day. These systems have people collect at common locations (the station or stop), and board at common times (for example according to a predetermined schedule or headway). By using common service locations and times, these modes can consolidate many trips that have similar origins and destinations or overlapping routes. However, the routes are not sensitive to changing travel patterns, and have no way of identifying which trips are going unserved, or are poorly served, by the existing routes. On the opposite end of the spectrum, personal modes of transportation, such as a private vehicle or taxi, offer service to and from the exact origin and destination of a rider, at close to exactly the time they desire to travel. Despite the apparent increased convenience to users, the presence of a large number of small vehicles results in a disorganized, and potentially congested road network during high demand periods. The focus of the research presented in this paper is to develop a system that possesses both the on-demand nature of a personal mode, with the efficiency of shared modes. In this system, users submit their request for travel, but are asked to make small compromises in their origin and destination location by walking to a nearby meeting point, as well as slightly modifying their time of travel, in order to accommodate other passengers. Because the origin and destination location of the request can be adjusted, this is a more general case of the Dial-a-Ride problem with time windows. The solution methodology uses a graph clustering algorithm coupled with a greedy insertion technique. A case study is presented using actual requests for taxi trips in Washington DC, and shows a significant decrease in the number of vehicles required to serve the demand.

Transient scaling and resurgence of chimera states in networks of Boolean phase oscillators.

We study networks of nonlocally coupled electronic oscillators that can be described approximately by a Kuramoto-like model. The experimental networks show long complex transients from random initial conditions on the route to network synchronization. The transients display complex behaviors, including resurgence of chimera states, which are network dynamics where order and disorder coexists. The spatial domain of the chimera state moves around the network and alternates with desynchronized dynamics. The fast time scale of our oscillators (on the order of 100ns) allows us to study the scaling of the transient time of large networks of more than a hundred nodes, which has not yet been confirmed previously in an experiment and could potentially be important in many natural networks. We find that the average transient time increases exponentially with the network size and can be modeled as a Poisson process in experiment and simulation. This exponential scaling is a result of a synchronization rate that follows a power law of the phase-space volume.

A survey on the composition of wines made with grapes produced by an organic system.

Summary There is concern about the health problems caused by pesticides in humans, which has led some grape producers to adopt organic procedures in their vineyards, and a certain amount of these grapes are directed to winemaking. Despite the approval awarded to this organic grape production by the certified organizations, there has been a demand to carry out a survey to determine the physicochemical composition of the wine derived from these products. Some of these wines were made from a single grape variety and others from more than one. For this survey, the samples consisted of five bottles of each type of wine, acquired from wineries and supermarkets in the Serra Gaúcha region, RS, Brazil. The analyses were carried out by physicochemical methods: volatile compounds by gas chromatography; minerals and trace elements by inductively coupled plasma optical emission spectrometry; and pesticide residues by liquid chromatography-mass spectrometry. The results showed that in general the physicochemical composition of these wines was within the limits established by Brazilian legislation. The mineral and trace element concentrations were very low and pesticide residues were not detected (MRL = 10 μg.kg?1) in any of the wines. Resumo: Há preocupação em relação a problemas causados por pesticidas no ser humano, o que levou uma parcela de viticultores a adotar procedimentos de agricultura orgânica em seus vinhedos. Assim, devido a essa preocupação, eles estão produzindo uva pelo sistema orgânico, sendo que uma parte dessa produção é direcionada à elaboração de vinho. Apesar de essas uvas terem sido aprovadas por entidades certificadoras, houve demanda para a realização de um levantamento para determinar a composição dos vinhos delas derivados. Portanto, cinco garrafas de cada tipo de vinho foram coletadas em vinícolas e supermercados da Serra Gaúcha, Rio Grande do Sul, sendo uma parte de vinhos varietais e outra, de cortes de diferentes variedades. As análises foram feitas por métodos físico-químicos: compostos voláteis, por cromatografia gasosa; minerais e elementos-traço, por espectrometria de emissão ótica com plasma acoplado indutivamente, e resíduos de pesticidas, por cromatografia líquida-espectrometria de massa. Os resultados mostram que a composição físico-química desses vinhos e dos minerais situou-se, em geral, dentro dos limites da legislação brasileira. As concentrações de minerais e de elementos-traço foram muito baixas, e não foram detectados resíduos de pesticidas (LMR = 10 μg.kg?1) em nenhum vinho.

Transcription-Coupled DNA Supercoiling in Escherichia Coli: Mechanisms and Biological Functions

Transcription by RNA polymerase can induce the formation of hypernegatively supercoiled DNA both in vivo and in vitro. This phenomenon has been explained by a “twin-supercoiled-domain” model of transcription where a positively supercoiled domain is generated ahead of the RNA polymerase and a negatively supercoiled domain behind it. In E. coli cells, transcription-induced topological change of chromosomal DNA is expected to actively remodel chromosomal structure and greatly influence DNA transactions such as transcription, DNA replication, and recombination. In this study, an IPTG-inducible, two-plasmid system was established to study transcription-coupled DNA supercoiling (TCDS) in E. coli topA strains. By performing topology assays, biological studies, and RT-PCR experiments, TCDS in E. coli topA strains was found to be dependent on promoter strength. Expression of a membrane-insertion protein was not needed for strong promoters, although co-transcriptional synthesis of a polypeptide may be required. More importantly, it was demonstrated that the expression of a membrane-insertion tet gene was not sufficient for the production of hypernegatively supercoiled DNA. These phenomenon can be explained by the “twin-supercoiled-domain” model of transcription where the friction force applied to E. coli RNA polymerase plays a critical role in the generation of hypernegatively supercoiled DNA. Additionally, in order to explore whether TCDS is able to greatly influence a coupled DNA transaction, such as activating a divergently-coupled promoter, an in vivo system was set up to study TCDS and its effects on the supercoiling-sensitive leu-500 promoter. The leu-500 mutation is a single A-to-G point mutation in the -10 region of the promoter controlling the leu operon, and the AT to GC mutation is expected to increase the energy barrier for the formation of a functional transcription open complex. Using luciferase assays and RT-PCR experiments, it was demonstrated that transient TCDS, “confined” within promoter regions, is responsible for activation of the coupled transcription initiation of the leu-500 promoter. Taken together, these results demonstrate that transcription is a major chromosomal remodeling force in E. coli cells.

Physics-Based Modeling of Power System Components for the Evaluation of Low-Frequency Radiated Electromagnetic Fields

The low-frequency electromagnetic compatibility (EMC) is an increasingly important aspect in the design of practical systems to ensure the functional safety and reliability of complex products. The opportunities for using numerical techniques to predict and analyze system’s EMC are therefore of considerable interest in many industries. As the first phase of study, a proper model, including all the details of the component, was required. Therefore, the advances in EMC modeling were studied with classifying analytical and numerical models. The selected model was finite element (FE) modeling, coupled with the distributed network method, to generate the model of the converter’s components and obtain the frequency behavioral model of the converter. The method has the ability to reveal the behavior of parasitic elements and higher resonances, which have critical impacts in studying EMI problems. For the EMC and signature studies of the machine drives, the equivalent source modeling was studied. Considering the details of the multi-machine environment, including actual models, some innovation in equivalent source modeling was performed to decrease the simulation time dramatically. Several models were designed in this study and the voltage current cube model and wire model have the best result. The GA-based PSO method is used as the optimization process. Superposition and suppression of the fields in coupling the components were also studied and verified. The simulation time of the equivalent model is 80-100 times lower than the detailed model. All tests were verified experimentally. As the application of EMC and signature study, the fault diagnosis and condition monitoring of an induction motor drive was developed using radiated fields. In addition to experimental tests, the 3DFE analysis was coupled with circuit-based software to implement the incipient fault cases. The identification was implemented using ANN for seventy various faulty cases. The simulation results were verified experimentally. Finally, the identification of the types of power components were implemented. The results show that it is possible to identify the type of components, as well as the faulty components, by comparing the amplitudes of their stray field harmonics. The identification using the stray fields is nondestructive and can be used for the setups that cannot go offline and be dismantled

Collaborative filtering and deep learning based recommendation system for cold start items

Recommender system is a specific type of intelligent systems, which exploits historical user ratings on items and/or auxiliary information to make recommendations on items to the users. It plays a critical role in a wide range of online shopping, e-commercial services and social networking applications. Collaborative filtering (CF) is the most popular approaches used for recommender systems, but it suffers from complete cold start (CCS) problem where no rating record are available and incomplete cold start (ICS) problem where only a small number of rating records are available for some new items or users in the system. In this paper, we propose two recommendation models to solve the CCS and ICS problems for new items, which are based on a framework of tightly coupled CF approach and deep learning neural network. A specific deep neural network SADE is used to extract the content features of the items. The state of the art CF model, timeSVD++, which models and utilizes temporal dynamics of user preferences and item features, is modified to take the content features into prediction of ratings for cold start items. Extensive experiments on a large Netflix rating dataset of movies are performed, which show that our proposed recommendation models largely outperform the baseline models for rating prediction of cold start items. The two proposed recommendation models are also evaluated and compared on ICS items, and a flexible scheme of model retraining and switching is proposed to deal with the transition of items from cold start to non-cold start status. The experiment results on Netflix movie recommendation show the tight coupling of CF approach and deep learning neural network is feasible and very effective for cold start item recommendation. The design is general and can be applied to many other recommender systems for online shopping and social networking applications. The solution of cold start item problem can largely improve user experience and trust of recommender systems, and effectively promote cold start items.