In shotgun proteomics, the liquid chromatography step is used to separate peptides in order to analyze as few as possible at the same time in the mass spectrometry step. Each peptide has a retention time, that is how long it takes to pass through the chromatography column. Prediction of the retention time can be used to gain increased identification of peptides or in order to create targeted proteomics experiments. Using machine learning methods such as support vector machines has given a high prediction accuracy, but such methods require known features that the retention time depends on. In this thesis we let a convolutional network, learn to rank the retention times instead of predicting the retention times themselves. We also tested how the prediction accuracy depends on the size of the training set. We found that pairwise ranking of peptides outperforms pointwise ranking and that adding more training data increased accuracy until the end without an increase in training time. This implies that accuracy can be further increased by training on even greater training sets.

The Cannibal system, comprised of an activated sludge process integrated with a side stream anaerobic bioreactor, is capable of reducing excess sludge up to 60% compared to the conventional activated sludge process. The hydraulic retention time (HRT) in the Cannibal bioreactor and the interchange rate (the percent of sludge by mass interchanged between the activated sludge system and the bioreactor on daily basis) are the two important operational parameters in the optimization of the Cannibal process. This research was designed to investigate the effect of the Cannibal bioreactor hydraulic retention time and the interchange rate on the solids destruction in the system. The first phase of this study has looked at the effect of three different HRTs, 5 day, 7 day and 10 day. The interchange rate during phase I was 10%. The results showed that the 7 day HRT can be recommended as the minimum retention period for the Cannibal process. The 5 day HRT Cannibal system had some settling problems and high volatile fatty acid content compared to the 7 day HRT Cannibal system. The protein and polysaccharide tests showed that the Cannibal bioreactor is primarily involved in the release of biopolymers which are degraded in the aerobic environment. The second part of this study focused on the effect of the interchange rate (IR) on the solids destruction in the system. The interchange rates that were applied in the system were 15%, 10%, 7%, 5% and 4%.The HRT in the Cannibal bioreactor was 7 day. The results showed that the 10% interchange rate gave maximum solids destruction than the other interchange rates. This implies that 10% is an optimum IR for the Cannibal system. Apart from higher solids wastage, the 4% and 5% IR Cannibal systems had higher volatile fatty acid production. / Master of Science

In this thesis, we propose a new thin-film transistor with trenched body and airgap-insulated structure (AITFT) for one-transistor dynamic random access memory (1T-DRAM) applications and investigate the influence of different materials on the sensing current window and retention time. Its basic operation mechanisms are based on the impact ionization and floating body effects. Due to the generated holes storing in the pseudo neutral region, the threshold voltage (Vth) is lower, resulting in a high drain current for state ¡§1¡¨. So we can recognize the data by sensing the difference of the drain current. According to the ISE TCAD 10.0 simulations, owing to the design of trench and airgap-isolation structure, the AITFT can enhance about 212% sensing current window and 42% retention time compared with the conventional TFT at the channel length of 150 nm and temperature of 300K conditions. Also, owing to the source/drain-tie, the generated heat can be dissipated quickly from the source/drain to the substrate thus the thermal instability is improved. In other words, the AITFT can improve the thermal reliability but without losing control of the short-channel effects.

The study examined the removal mechanism of non-acclimated and acclimated aerobic activated sludge for 29 target organic micropollutants (OMPs) at low concentration. The selection of the target OMPs represents a wide range of physical-chemical properties such as hydrophobicity, charge state as well as a diverse range of classes, including pharmaceuticals, personal care products and household chemicals. The removal mechanisms of OMPs include adsorption, biodegradation, hydrolysis, and vaporization. Adsorption and biodegradation were found to be the main routes for OMPs removal for all target OMPs. Target OMPs responded to the two dominant removal routes in different ways: (1) complete adsorption, (2) strong biodegradation and weak adsorption, (3) medium biodegradation and adsorption, and (4) weak sorption and weak biodegradatio. Kinetic study showed that adsorption of atenolol, mathylparaben and propylparaben well followed first-order model (R2: 0.939 to 0.999) with the rate constants ranging from 0.519-7.092 h-1. For biodegradation kinetics, it was found that benzafibrate, bisphenol A, diclofenac, gemfibrozil, ibuprofen, caffeine and DEET followed zero-order model (K0:1.15E-4 to 0.0142 μg/Lh-1, R2: 0.991 to 0.999), while TCEP, naproxen, dipehydramine, oxybenzone and sulfamethoxazole followed first-order model (K1:1.96E-4 to 0.101 h-1, R2: 0.912 to 0.996). 4 Inhibition by sodium azide (NaN3)and high temperature sterilization was compared, and it was found that high temperature sterilization will damage cells and change the sludge charge state. For the OMPs adaptation removal study, it was found that some of OMPs effluent concentration decreased, which may be due to the slow adaptation of the sludge or the increase of certain bacteria culture; some increased due to chromic toxicity of the chemicals; most of the OMPs had stable effluent concentration trend, it was explained that some of the OMPs were too difficutl to remove while other showed strong quick adaptation. A new module combined of sequencing batch reactor (SBR) and nanofiltration membrane filtration (NF-MBR) was developed to further study the OMPs removal and to exam the concept of compounds (CRT). The NF-MBR was proved to be a promising bioreactor, as OMPs were rejected by NF membrane which leaded to a low OMPs concentration in permeate water, the apparent removal rate was over 80% for most of the OMPs.

The sediment accumulation is an important characteristic in the ageing process of integrated constructed wetlands (ICW). Retained nutrient and other contaminants in wetland sediments have the potential to be remobilized and released to the overlying water column when environmental conditions change. In this study, mesocosms which filled with saturated sediments and planted with Phragmites australis and Agrostis stolonifera were set up to examine nutrient and other contaminants retention and/or release by wetland sediment and substrates. The effects of physico-chemical parameters on sediment-water contaminant exchange were also investigated through the application of multiple regression models, principal component analysis (PCA), redundancy analysis (RDA), and self-organizing map (SOM) model. The results demonstrated an average net release of chemical oxygen demand (COD), ammonianitrogen (NH3-N), nitrate-nitrogen (NO3-N) and molybdate reactive phosphorus (MRP) to the overlying water column, indicating that the ICW sediment and substrates acted as new contaminant sources. According to statistical analysis, electrical conductivity (EC) and redox potential (RP) values affected COD treatment efficiency. Chloride (Cl) concentration and RP value had an impact on NH3-N treatment performance. NO3-N removal was influenced by dissolved oxygen (DO) concentration and RP value. MRP treatment efficiency was related to DO concentration and EC value. The SOM model was selected as prediction tool to provide numerical estimations for the performance of ICW mesocosms. The model was validated, indicating that NH3-N, NO3-N, MRP, and COD treatment efficiencies could be predicted by input variables which are quick and cost-effective to measure. The SOM model can be seen as an appropriate method for monitoring the performance of mature ICWs. The type of vegetation played a minor role in releasing nutrients and other contaminants. However, the mesocosm planted with Phragmites australis outperformed the one planted with Agrostis stolonifera. No water reached bottom outlet of the mesocosm suggesting that there was little potential risk to contaminate groundwater. The clay liner and the biogeochemical processes taking place within sediments proved to be effective in preventing surface water from infiltration. Although no reduction in the overall performance has been observed for the full-scale ICW sites 7 and/or 11, this laboratory-scale study provided valuable warning signs regarding the loss of contaminant sequestration which may contribute to decline in wetland treatment performance over time. The impacts of hydraulic loading rate (HLR) and seasonal temperature fluctuations on contaminant removal efficiencies of a new ICW system receiving domestic wastewater were also assessed. The system showed good overall treatment performance in terms of effluent quality and removal efficiency. The influence of ICW removal efficiencies of the hydraulic loading rate, which was based on overall water balance, was negligible due to large footprint and multi-cellular configuration of the studied system. Relatively low temperature in autumns and winters resulted in decreased biological activities and lower contaminant removal efficiency. The long-term trends in nutrient removal have been investigated to five Wildfowl & Wetlands Trust constructed wetland systems. The results showed less effective removal even release of NO3-N, total oxidised nitrogen (TON), orthophosphate- phosphorus (PO4-P) and total phosphorus (TP) in many of the systems as a result of wetland aging and lack of sediment management.

Water and wastewater treatment solutions incorporating biofilm systems are becoming increasingly popular due to more stringent regulations pertaining to drinking water and wastewater effluent discharge in Canada and in other parts of the world. As a major component of biofilm, extracellular polymeric substances (EPS) have been considered as an important factor affecting the physical and chemical properties of biofilm. Further, the selected method of EPS extraction and the methods of detecting the composition of the EPS have shown to affect the results of EPS measurements. In this research, protocols for EPS extraction and EPS composition analysis were investigated and optimized for nitrifying moving bed biofilm reactor (MBBR) biofilm. In addition, the confocal Raman microscopy (CRM) spectra of EPS in nitrifying MBBR biofilm and the protein, polysaccharide and extracellular DNA (eDNA) percent concentrations of the EPS were investigated at various operating temperatures. Further, the CRM spectra and the protein, polysaccharide and eDNA percent concentration of EPS in nitrifying MBBR biofilm along with the biofilm morphology and thickness and the viability of the embedded cells were investigated at various hydraulic retention times (HRTs). The EPS was characterized at various temperatures and HRTs in order to investigate potential correlation between the EPS components of the nitrifying biofilm and the ammonia removal kinetics. The biofilm morphology and thickness along with the bacterial viability of the biofilm were also investigated at various HRTs. Biofilm morphology images and thickness measurements were acquired using a variable pressure scanning electron microscope (VPSEM). The percentages of viable embedded cells in the biofilm were quantified using live/dead staining in combination with confocal laser microscopy (CLSM) imaging. The research demonstrates that an increase in protein content and subsequently a decrease in polysaccharides and eDNA contents in the EPS of nitrifying MBBR biofilm were observed at the lowest operational HRT and the highest temperature in this work. In particular, the EPS protein to polysaccharide (PN/PS) ratio of nitrifying MBBR systems was shown to significantly decrease below a value of 3 when the system was underloaded (observed at the highest operational temperature in this study) or hydraulically overloaded (observed at the lowest HRT in this study). As such, data obtained at lower operational temperatures, with the system no longer underloaded, and at longer HRTs, with the system no longer hydraulically overloaded, all demonstrate an EPS PN/PS ratio of approximately 3. Correlations were observed between the chemically measured EPS PN/PS ratios and the measured Raman spectra intensity ratios; supporting the concept of higher PN/PS ratios of EPS in more optimal nitrifying MBBR operations. Further, the ammonia removal kinetics and EPS response at HRT values of 0.75 and 1.0 h indicate that nitrifying MBBR systems may be optimized to operate at HRTs as low as 0.75 to 1.0 hour as opposed to conventional HRTs of 2.0 to 6.0 h.

Shotgun Proteomics is the leading technique for protein identification in complexmixtures. However, it produces a large amount of data which results in aextremely high computational cost for identifying the protein. Retention time(RT) is an important factor to be used to enhance the efficiency of protein identification.By predicting the retention time successfully, we could decrease thecomputational cost dramatically. This thesis uses a machine learning method,Gaussian Processes, to predict the retention time of a set of peptide in hand.We also implement a feature extraction method called Bag-of-Words to generatethe features for training the model. In addition, we also investigate theeffect of different types of optimization methods to the model’s parameters.The results show comparable precision of the prediction and relatively lowtime cost when comparing with the state-of-art prediction model.

Managed aquifer recharge (MAR) consists of artificially replenishing groundwater to facilitate reuse and/or the associated environmental benefits. Meanwhile, soil aquifer treatment (SAT) is a process of geo-purification designed and operated to improve the quality of the infiltrating water and is thus a type of MAR. SAT consists of a basin operating under rotation of drying and wetting periods. Often, SAT involves water of impaired quality applied onto soil and consequently it implies various risks of health, geochemical and physical nature with difficult or irreversible remediation. To study the effect of pre-treatment on SAT a pilot plant including conventional activated sludge (CAS), a membrane bioreactor (MBR), tertiary and secondary vertical flow reed beds (VFRB) and SAT soil columns. The sludge retention time (SRT) in the CAS and MBR processes was changed every 6 months to look at the impact of SRT on SAT. Each unit and treatment train effluent was characterised to determine the impact of effluent quality on SAT performance. This study showed that tertiary VFRB, especially when fed with MBR effluent, was the best option for SAT and irrigation reuse as it provided the best compliance with reuse standards and the best fertilisation potential. However, long-term clogging occurred in SAT after tertiary VFRB, suggesting the need for a longer resting period or shorter wetting period. This study also highlighted the importance of total suspended solids (TSS) content for SAT removal mechanisms and infiltration rate. In particular, SAT fed with high TSS content effluent was susceptible to temperature variation. Hence the duration of wetting and flooding periods should be adapted according to the season. Further, variation in SRT only indirectly affected pollutants removal by the system including CAS treatment set up at 6 d SRT where the N compounds balance was favourable to an autotrophic N removal.

Dans les systèmes mettant en jeu des biofilms, le temps de séjour hydraulique (TSH) peut être un élément clé pour le développement du biofilm. Nous avons cherché à caractériser l'influence de ce paramètre sur le développement du biofilm et la compétition entre les bactéries fixées et les bactéries planctoniques. Des Réacteurs Annulaires Rotatifs (RAR) ont été mis en œuvre afin d'estimer expérimentalement la répartition de la biomasse totale entre le liquide et le biofilm. Puis à l'aide d'outils moléculaires (PCR-SSCP) et de traitements statistiques des empreintes moléculaires obtenues, les structures des communautés microbiennes libres et attachées ont été estimées et reliées aux paramètres opératoires. Dans un troisième temps, un modèle microbien simple à une dimension (1D) a été adapté pour intégrer une certaine diversité microbienne (10 espèces). La confrontation entre les données expérimentales et les simulations permet d'expliquer l'évolution de la diversité entre le liquide et le biofilm suivant différentes valeurs du TSH. Les résultats obtenus confirment l'importance du TSH sur la formation du biofilm et l' évolution de la diversité dans le biofilm et la flore planctonique. Si le temps de séjour est élevé (8 heures), alors la croissance dans la phase liquide est importante au détriment de celle du biofilm. Pour des temps de séjour courts (0,3 et 1 heure), la croissance du biofilm est favorisée. La biomasse planctonique est principalement issue du détachement du biofilm. Les sorties du modèle indiquent que la diversité diminue durant la croissance du biofilm. / In biofilm systems, hydraulic retention time (HRT) may have a significant impact on biofilm development. The influence of this parameter on biofilm development and competition between planktonic and attached bacteria has been investigated. Rotating Annular Reactors (RAR) have been used to determine biomass distribution between the bulk phase and the biofilm. Molecular tools (PCR-SSCP) and statistical treatment of molecular fingerprints have been applied to evaluate the impact of operating parameters on the structure of fixed and attached microbial communities. Then, a simple biofilm model (1D) has been adapted to include microbial diversity (10 species). Comparing experimental data and simulation results, it is possible to explain the evolution of diversity at different HRTs. At high HRT, (8 hours) planktonic bacteria are favoured compared to biofilm microorganisms. At low HRT, biofilm growth is favoured by planktonic bacteria wash-out. Simulat ions indicate a decrease of diversity over biofilm growth period.

The focus of the projects presented here was to develop possible solutions to three issues commonly encountered during chemometric analysis of comprehensive two-dimensional liquid chromatography diode array detector (LCxLC-DAD) data. The focus of the first project was to determine a means of performing background correction that removed two background ridges. The methods of simply subtracting out a mean blank sample, singular value decomposition based background correction (SVD-BC) and asymmetrically weighted least squares (AWLS) were compared. AWLS was found to be the only background correction technique to fully remove the ridges. However, AWLS was also found to attenuate the peak intensity by approximately 25% due to over fitting of the background at the lower wavelengths. The focus of the second project was the investigation of five common interpolation strategies for the reconstruction of the sampled first dimension peak. The interpolation strategy that best reproduced the original first dimension retention time was Gaussian fitting. This was expected given that the simulated data set was generated using a Gaussian model for the peak shape. An algorithm, semi-automated alignment method (SAAM), was then developed that allowed for each peak to be aligned independently of the other peaks in the data set. SAAM was validated using both simulated and experimental data. The simulated results indicated that SAAM produced percent recoveries close to 100%. SAAM was also compared to iterative key set factor analysis-alternating least squares (IKSFA-ALS) for the analysis of phenytoin in a waste water treatment plant effluent. SAAM produced a concentration of 26±3 ppb compared to 39±9 ppb from IKSFA-ALS. While these results are very different, the result produced by SAAM is still within the experimental error of the reference 2D-LC/MS/MS method, 42±19. Finally, SAAM was compared to two existing literature methods. A mixture of simulated and experimental data sets was used to measure the accuracy and precision of the results. SAAM was found to be impacted less by intra- and inter-sample retention time shifting then PARAFAC2. SAAM and shifted candecomp/PARAFAC were found to produce very similar results. However, SAAM was found to experience some difficulty producing accurate and precise results with some of the experimental data sets.