Thermal Quenching of Photoluminescence in ZnO and GaN

Investigation of the thermal quenching of photoluminescence (PL) in semiconductors provides valuable information on identity and characteristics of point defects in these materials, which helps to better understand and improve the properties of semiconductor materials and devices. Abrupt and tunable thermal quenching (ATQ) of PL is a relatively new phenomenon with an unusual behavior of PL. This mechanism was able to explain what a traditional model failed to explain. Usually, in traditional model used to explain “normal” quenching, the slope of PL quenching in the Arrhenius plot determines the ionization energy of the defect causing the PL band. However, in abrupt quenching when the intensity of PL decreases by several orders of magnitude within a small range of temperature, the slope in the Arrhenius plot has no relation to the ionization energy of any defect. It is not known a priori if the thermal quenching of a particular PL band is normal or abrupt and tunable. Studying new cases of unusual thermal quenching, classifying and explaining them helps to predict new cases and understand deeper the ATQ mechanism of PL thermal quenching. Very few examples of abrupt and tunable quenching of PL in semiconductors can be found in literature. The abrupt and tunable thermal quenching, reported here for the first time for high-resistivity ZnO, provides an evidence to settle the dispute concerning the energy position of the LiZn acceptor. In high-resistivity GaN samples, the common PL bands related to defects are the yellow luminescence (YL) band and a broad band in the blue spectral region (BL2). In this work, we report for the first time the observation of abrupt and tunable thermal quenching of the YL band in GaN. The activation energies for the YL and BL2 bands calculated through the new mechanism show agreement with the reported values. From this study we predict that the ATQ phenomenon is quite common for high-resistivity semiconductors

Aging Effect in the Wettability of Nickel Nanorod Arrays

The time-dependent wettability of nickel nanorod arrays was studied by measuring their water contact angles as a function of aging time in air. The nickel nanorod arrays were deposited on silicon substrates by DC magnetron sputtering using an oblique angle of 85° with respect to the substrate normal. By changing the deposition time from 10 to 90 min., the diameter, height, and separation of the nanorods were varied. The water contact angles of each sample were then periodically measured from a minimum aging time of 30 min. after deposition and exposure to air, up to a maximum aging time of three months. The initial water contact angles for all samples were approximately equal to 8o, indicating that the nickel nanorod arrays were initially superhydrophilic. As the samples aged in air, however, they all showed increasing contact angles as a function of time that were nonlinear with different rates. The results can be grouped into two categories: thinner samples with shorter deposition times (10 to 55 min) demonstrated faster rates of increase in contact angle, and thicker samples with longer deposition times (60 and 90 min.) showed slower rates. The increase in contact angle with time indicates that the Ni nanorods become more hydrophobic with aging time in air. Surface chemical analysis demonstrates that this increase in hydrophobicity may be due to oxidization and hydrocarbon contamination, which depend on the nanorod morphology. X-ray photoelectron spectroscopy results indicate that thinner samples (10-55 min. deposition time) have more adsorbed carbon as compared to thicker samples (60 and 90 min.). It appears that the reactivity of the Ni nanorods with air ambient is enhanced for shorter, smaller-diameter nanorods

Density Based Data Clustering

Data clustering is a data analysis technique that groups data based on a measure of similarity. When data is well clustered the similarities between the objects in the same group are high, while the similarities between objects in different groups are low. The data clustering technique is widely applied in a variety of areas such as bioinformatics, image segmentation and market research. This project conducted an in-depth study on data clustering with focus on density-based clustering methods. The latest density-based (CFSFDP) algorithm is based on the idea that cluster centers are characterized by a higher density than their neighbors and by a relatively larger distance from points with higher densities. This method has been examined, experimented, and improved. These methods (KNN-based, Gaussian Kernel-based and Iterative Gaussian Kernel-based) are applied in this project to improve (CFSFDP) density-based clustering. The methods are applied to four milestone datasets and the results are analyzed and compared

Targeting Ataxia telangiectasia mutated (ATM) and DNA dependent protein kinase catalytic subunit (DNA-PKcs) for synthetic lethality application in breast cancer

BRCA1 germ-line mutations predispose to hereditary breast and ovarian cancers. Cells lacking functional BRCA1 protein are deficient in the homologous recombination DNA repair pathway. Base excision repair (BER) is essential for processing base damage induced by endogenous and exogenous sources. Recently, BRCA1 was shown to transcriptionally regulate expression of genes involved in BER. The primary aim of the work described in this thesis was to investigate whether targeting the double-strand break pathway in BRCA1-BER deficient cells using ATM or DNA-PKcs inhibitors would be synthetically lethal. DNA repair gene and protein expression in BRCA1 deficient and proficient cells were investigated. Initially 84 DNA repair genes were investigated. Data demonstrated down-regulation of several DNA repair mRNAs in BRCA1 mutant/knockdown cell lines as compared to proficient cell lines. RT-qPCR was performed for selected DNA repair genes and confirmed statistically significant down-regulation of these genes. Protein expression of the selected group was assessed and showed down-regulation. These results suggest that BRCA1 deficiency may be associated with a global defect in the BER pathway. BRCA1 deficient cells were targeted by ATM/DNA-PKcs inhibitors. BRCA1-BER deficient cells were sensitive to ATM and DNA-PKcs inhibitor treatment either alone or in combination with cisplatin and synthetic lethality was evidenced by DNA double strand breaks accumulation, cell cycle arrest and apoptosis. This in vitro study suggests that a potential synthetic lethality relationship exists between BRCA1 deficiency and ATM/DNA-PKcs inhibition. Moreover, results support the hypothesis that cisplatin increases the efficacy of ATM and DNA-PKcs inhibition in BRCA1 deficient cells. Taken together, this study provides the pre-clinical evidence that ATM and DNA-PKcs could be alternative synthetic lethality targets in BRCA1 deficient breast cancer

FAST NEURAL NETWORK ALGORITHM FOR SOLVING CLASSIFICATION TASKS

Classification is one-out-of several applications in the neural network (NN) world. Multilayer perceptron (MLP) is the common neural network architecture which is used for classification tasks. It is famous for its error back propagation (EBP) algorithm, which opened the new way for solving classification problems given a set of empirical data. In the thesis, we performed experiments by using three different NN structures in order to find the best MLP neural network structure for performing the nonlinear classification of multiclass data sets. A developed learning algorithm used here is the batch EBP algorithm which uses all the data as a single batch while updating the NN weights. The batch EBP speeds up training significantly and this is also why the title of the thesis is dubbed \u27fast NN …\u27. In the batch EBP, and when in the output layer a linear neurons are used, one implements the pseudo-inverse algorithm to calculate the output layer weights. In this way one always finds the local minimum of a cost function for a given hidden layer weights. Three different MLP neural network structures have been investigated while solving classification problems having K classes: one model/K output layer neurons, K separate models/One output layer neuron, and K joint models/One output layer neuron. The extensive series of experiments performed within the thesis proved that the best structure for solving multiclass classification problems is a K joint models/One output layer neuron structure

Single-strand selective monofunctional uracil-DNA glycosylase (SMUG1) deficiency is linked to aggressive breast cancer and predicts response to adjuvant therapy

Uracil in DNA is an important cause of mutagenesis. SMUG1 is a uracil DNA glycosylase that removes uracil through base excision repair. SMUG1 also processes radiation induced oxidative base damage as well as 5-fluorouracil incorporated into DNA during chemotherapy. We investigated SMUG1 mRNA expression in 249 primary breast cancers. SMUG1 protein expression was investigated in 1165 breast tumours randomised into two cohorts [training set (n=583) and test set (n=582)]. SMUG1 and chemotherapy response was also investigated in a series of 315 ER negative tumours (n=315). For mechanistic insights, SMUG1 was correlated to biomarkers of aggressive phenotype, DNA repair, cell cycle and apoptosis. Low SMUG1 mRNA expression was associated with adverse disease specific survival (p=0.008) and disease free survival (p=0.008). Low SMUG1 protein expression (25%) was associated with high histological grade (p<0.0001), high mitotic index (p<0.0001), pleomorphism (p<0.0001), glandular de-differentiation (p=0.0001), absence of hormonal receptors (ER-/PgR-/AR) (p<0.0001), presence of basal-like (p<0.0001) and triple negative phenotypes (p<0.0001). Low SMUG1 protein expression was associated with loss of BRCA1 (p<0.0001), ATM (p<0.0001) and XRCC1 (p<0.0001). Low p27 (p<0.0001), low p21 (p=0.023), mutant p53 (p=0.037), low MDM2 (p<0.0001), low MDM4 (p=0.004), low Bcl-2 (p=0.001), low Bax (p=0.003) and high MIB1 (p<0.0001) were likely in low SMUG1 tumours. Low SMUG1 protein expression was associated with poor prognosis in univariate (p<0.001) and multivariate analysis (p<0.01). In ER+ cohort that received adjuvant endocrine therapy, low SMUG1 protein expression remains associated with poor survival (p<0.01). In ER- cohort that received adjuvant chemotherapy, low SMUG1 protein expression is associated with improved survival (p=0.043). Our study suggests that low SMUG1 expression may correlate to adverse clinicopathological features and predict response to adjuvant therapy in breast cancer

Targeting Ataxia telangiectasia mutated (ATM) and DNA dependent protein kinase catalytic subunit (DNA-PKcs) for synthetic lethality application in breast cancer

BRCA1 germ-line mutations predispose to hereditary breast and ovarian cancers. Cells lacking functional BRCA1 protein are deficient in the homologous recombination DNA repair pathway. Base excision repair (BER) is essential for processing base damage induced by endogenous and exogenous sources. Recently, BRCA1 was shown to transcriptionally regulate expression of genes involved in BER. The primary aim of the work described in this thesis was to investigate whether targeting the double-strand break pathway in BRCA1-BER deficient cells using ATM or DNA-PKcs inhibitors would be synthetically lethal. DNA repair gene and protein expression in BRCA1 deficient and proficient cells were investigated. Initially 84 DNA repair genes were investigated. Data demonstrated down-regulation of several DNA repair mRNAs in BRCA1 mutant/knockdown cell lines as compared to proficient cell lines. RT-qPCR was performed for selected DNA repair genes and confirmed statistically significant down-regulation of these genes. Protein expression of the selected group was assessed and showed down-regulation. These results suggest that BRCA1 deficiency may be associated with a global defect in the BER pathway. BRCA1 deficient cells were targeted by ATM/DNA-PKcs inhibitors. BRCA1-BER deficient cells were sensitive to ATM and DNA-PKcs inhibitor treatment either alone or in combination with cisplatin and synthetic lethality was evidenced by DNA double strand breaks accumulation, cell cycle arrest and apoptosis. This in vitro study suggests that a potential synthetic lethality relationship exists between BRCA1 deficiency and ATM/DNA-PKcs inhibition. Moreover, results support the hypothesis that cisplatin increases the efficacy of ATM and DNA-PKcs inhibition in BRCA1 deficient cells. Taken together, this study provides the pre-clinical evidence that ATM and DNA-PKcs could be alternative synthetic lethality targets in BRCA1 deficient breast cancer

PI-controlled bioreactor as a generalized Lienard system

It is shown that periodic orbits can occur in Cholette's bioreactor model working under the influence of a PI-controller. We find a diffeomorphic coordinate transformation that turns this controlled enzymatic reaction system into a generalized Lienard form. Furthermore, we give sufficient conditions for the existence and uniqueness of limit cycles in the new coordinates. We also perform numerical simulations illustrating the possibility of the existence of a local center (period annulus). A result with possible practical applications is that the oscillation frequency is a function of the integral control gain parameterComment: 15 pages, 5 figures, accepted version at Computers & Chem. En

Computational fluid dynamics analysis of the upper airway after rapid maxillary expansion: a case report

BACKGROUND: Assessment of the upper airway volume, morphology, and mechanics is of great importance for the orthodontic patient. We hypothesize that upper airway dimensions have significant effects on the dynamics of the airway flow and that both the dimensions and mechanics of the upper airway are greatly affected by orthodontic and orthopedic procedures such as rapid maxillary expansion (RME). The aim of the current study was to assess the effect of RME on the airway flow rate and pattern by comparing the fluid dynamics results of pre- and post-treatment finite element models. METHODS: Customized pre- and post-treatment computational fluid dynamics models of the patient's upper airway were built for comparison based on three-dimensional computed tomogram. The inhalation process was simulated using a constant volume flow rate for both models, and the wall was set to be rigid and stationary. Laminar and turbulent analyses were applied. RESULTS: Comparisons between before and after RME airway volume measurements showed that increases were only detected in nasal cavity volume, nasopharynx volume, and the most constricted area of the airway. Pressure, velocity, and turbulent kinetic energy decreased after dental expansion for laminar and turbulent flow. Turbulent flow shows relatively larger velocity and pressure than laminar flow. CONCLUSIONS: RME showed positive effects that may help understand the key reasons behind relieving the symptom of breathing disorders in this patient. Turbulence occurs at both nasal and oropharynx areas, and it showed relatively larger pressure and velocity compared to laminar flow