Phase II clinical trials aim to potentially screen out ineffective and identify effective therapies to move forward to randomized phase III trials. Single-arm studies remain the most utilized design in phase II oncology trials, especially in scenarios where a randomized design is simply not practical. Due to concerns regarding excessive toxicity or ineffective new treatment strategies, interim analyses are typically incorporated in the trial, and the choice of statistical methods mainly depends on the type of primary endpoints. For oncology trials, the most common primary objectives in phase II trials include tumor response rate (binary endpoint) and progression disease-free survival (time-to-event endpoint). Interim strategies are well-developed for both endpoints in single-arm phase II trials. The advent of molecular targeted therapies, often with lower toxicity profiles from traditional cytotoxic treatments, has shifted the drug development paradigm into establishing evidence of biological activity, target modulation and pharmacodynamics effects of these therapies in early phase trials. As such, these trials need to address simultaneous evaluation of safety as well as proof-of-concept of biological marker activity or changes in continuous tumor size instead of binary response rates. In this dissertation, we extend a predictive probability design for binary outcomes in the single-arm clinical trial setting and develop two interim designs for continuous endpoints, such as continuous tumor shrinkage or change in a biomarker over time. The two-stage design mainly focuses on the futility stopping strategies, while it also has the capacity of early stopping for efficacy. Both optimal and minimax designs are presented for this two-stage design. The multi-stage design has the flexibility of stopping the trial early either due to futility or efficacy. Due to the intense computation and searching strategy we adopt, only the minimax design is presented for this multi-stage design. The multi-stage design allows for up to 40 interim looks with continuous monitoring possible for large and moderate effect sizes, requiring an overall sample size less than 40. The stopping boundaries for both designs are based on predictive probability with normal likelihood and its conjugated prior distributions, while the design itself satisfies the pre-specified type I and type II error rate constraints. From simulation results, when compared with binary endpoints, both designs well preserve statistical properties across different effect sizes with reduced sample size. We also develop an R package, PPSC, and detail it in chapter four, so that both designs can be freely accessible for use in future phase II clinical trials with the collaborative efforts of biostatisticians. Clinical investigators and biostatisticians have the flexibility to specify the parameters from the hypothesis testing framework, searching ranges of the boundaries for predictive probabilities, the number of interim looks involved and if the continuous monitoring is preferred and so on.

BackgroundAtrazine suppression of the LH surge slowly develops over time and peaks after 4 days; sensitivity to atrazine decreases after 8 or 14 days of dosing. Adaptation of the LH response was correlated with increased phase I and phase II liver enzyme activity/expression. MethodsThe effect of atrazine on the LH surge was evaluated in female Sprague-Dawley rats administered 100 mg/kg/day atrazine by gavage for 1, 2, 3, or 4 consecutive days or 6.5, 50, or 100 mg/kg/day atrazine for 4, 8, or 14 days. ResultsNo statistically significant effects of atrazine were seen on peak plasma LH or LH area under the curve (AUC) after one, two, or three doses of 100 mg/kg/day. Four daily doses of 50 or 100 mg/kg atrazine significantly reduced peak LH and LH AUCs, whereas 6.5 mg/kg/day had no effect. After 8 or 14 days of treatment, statistically significantly reduced peak LH and LH AUC were observed in the 100 mg/kg/day dose group, but not in the 6.5 or 50 mg/kg/day dose groups, although significantly reduced LH was observed in one sample 9 hr after lights-on in the 50 mg/kg/day dose group on day 14. The number of days of treatment required to achieve a significant suppression of the LH surge is consistent with the repeat-dose pharmacokinetics of the chlorotriazines. ConclusionThe apparent adaptation to the effect of atrazine on the LH surge after 8 or 14 days may be related to the induction of phase I or, more likely, phase II metabolism observed in this study after 8 days, or to a decreased sensitivity of the hypothalamic-pituitary-adrenal axis or an homeostatic adaption of the effect of atrazine on the LH surge mechanism. Birth Defects Research 110:246-258, 2018. (c) 2017 The Authors. Birth Defects Research Published by Wiley Periodicals, Inc.

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Am Large Hadron Collider und am ATLAS-Detektor werden umfangreiche Aufrüstungsarbeiten vorgenommen. Diese Arbeiten sind in mehrere Phasen gegliedert und umfassen unter Anderem Änderungen an der Ausleseelektronik der Flüssigargonkalorimeter; insbesondere ist es geplant, während der letzten Phase ihren Primärpfad vollständig auszutauschen. Die Elektronik besteht aus einem analogen und einem digitalen Teil: während ersterer die Signalpulse verstärkt und sie zur leichteren Abtastung verformt, führt letzterer einen Algorithmus zur Energierekonstruktion aus. Beide Teile müssen während der Aufrüstung verbessert werden, damit der Detektor interessante Kollisionsereignisse präzise rekonstruieren und uninteressante effizient verwerfen kann. In dieser Dissertation werden Simulationsstudien präsentiert, die sowohl die analoge als auch die digitale Auslese der Flüssigargonkalorimeter optimieren. Die Korrektheit der Simulation wird mithilfe von Kalibrationsdaten geprüft, die im sog. Run 2 des ATLAS-Detektors aufgenommen worden sind. Der Einfluss verschiedener Parameter der Signalverformung auf die Energieauflösung wird analysiert und die Nützlichkeit einer erhöhten Abtastrate von 80 MHz untersucht. Des Weiteren gibt diese Arbeit eine Übersicht über lineare und nichtlineare Energierekonstruktionsalgorithmen. Schließlich wird eine Auswahl von ihnen hinsichtlich ihrer Leistungsfähigkeit miteinander verglichen. Es wird gezeigt, dass ein Erhöhen der Ordnung des Optimalfilters, der gegenwärtig verwendete Algorithmus, die Energieauflösung um 2 bis 3 % verbessern kann, und zwar in allen Regionen des Detektors. Der Wiener Filter mit Vorwärtskorrektur, ein nichtlinearer Algorithmus, verbessert sie um bis zu 10 % in einigen Regionen, verschlechtert sie aber in anderen. Ein Zusammenhang dieses Verhaltens mit der Wahrscheinlichkeit fälschlich detektierter Kalorimetertreffer wird aufgezeigt und mögliche Lösungen werden diskutiert.:1 Introduction 2 An Overview of High-Energy Particle Physics 2.1 The Standard Model of Particle Physics 2.2 Verification of the Standard Model 2.3 Beyond the Standard Model 3 LHC, ATLAS, and the Liquid-Argon Calorimeters 3.1 The Large Hadron Collider 3.2 The ATLAS Detector 3.3 The ATLAS Liquid-Argon Calorimeters 4 Upgrades to the ATLAS Liquid-Argon Calorimeters 4.1 Physics Goals 4.2 Phase-I Upgrade 4.3 Phase-II Upgrade 5 Noise Suppression With Digital Filters 5.1 Terminology 5.2 Digital Filters 5.3 Wiener Filter 5.4 Matched Wiener Filter 5.5 Matched Wiener Filter Without Bias 5.6 Timing Reconstruction, Optimal Filtering, and Selection Criteria 5.7 Forward Correction 5.8 Sparse Signal Restoration 5.9 Artificial Neural Networks 6 Simulation of the ATLAS Liquid-Argon Calorimeter Readout Electronics 6.1 AREUS 6.2 Hit Generation and Sampling 6.3 Pulse Shapes 6.4 Thermal Noise 6.5 Quantization 6.6 Digital Filters 6.7 Statistical Analysis 7 Results of the Readout Electronics Simulation Studies 7.1 Statistical Treatment 7.2 Simulation Verification Using Run-2 Data 7.3 Dependence of the Noise on the Shaping Time 7.4 The Analog Readout Electronics and the ADC 7.5 The Optimal Filter (OF) 7.6 The Wiener Filter 7.7 The Wiener Filter with Forward Correction (WFFC) 7.8 Final Comparison and Conclusions 8 Conclusions and Outlook Appendices / The Large Hadron Collider and the ATLAS detector are undergoing a comprehensive upgrade split into multiple phases. This effort also affects the liquid-argon calorimeters, whose main readout electronics will be replaced completely during the final phase. The electronics consist of an analog and a digital portion: the former amplifies the signal and shapes it to facilitate sampling, the latter executes an energy reconstruction algorithm. Both must be improved during the upgrade so that the detector may accurately reconstruct interesting collision events and efficiently suppress uninteresting ones. In this thesis, simulation studies are presented that optimize both the analog and the digital readout of the liquid-argon calorimeters. The simulation is verified using calibration data that has been measured during Run 2 of the ATLAS detector. The influence of several parameters of the analog shaping stage on the energy resolution is analyzed and the utility of an increased signal sampling rate of 80 MHz is investigated. Furthermore, a number of linear and non-linear energy reconstruction algorithms is reviewed and the performance of a selection of them is compared. It is demonstrated that increasing the order of the Optimal Filter, the algorithm currently in use, improves energy resolution by 2 to 3 % in all detector regions. The Wiener filter with forward correction, a non-linear algorithm, gives an improvement of up to 10 % in some regions, but degrades the resolution in others. A link between this behavior and the probability of falsely detected calorimeter hits is shown and possible solutions are discussed.:1 Introduction 2 An Overview of High-Energy Particle Physics 2.1 The Standard Model of Particle Physics 2.2 Verification of the Standard Model 2.3 Beyond the Standard Model 3 LHC, ATLAS, and the Liquid-Argon Calorimeters 3.1 The Large Hadron Collider 3.2 The ATLAS Detector 3.3 The ATLAS Liquid-Argon Calorimeters 4 Upgrades to the ATLAS Liquid-Argon Calorimeters 4.1 Physics Goals 4.2 Phase-I Upgrade 4.3 Phase-II Upgrade 5 Noise Suppression With Digital Filters 5.1 Terminology 5.2 Digital Filters 5.3 Wiener Filter 5.4 Matched Wiener Filter 5.5 Matched Wiener Filter Without Bias 5.6 Timing Reconstruction, Optimal Filtering, and Selection Criteria 5.7 Forward Correction 5.8 Sparse Signal Restoration 5.9 Artificial Neural Networks 6 Simulation of the ATLAS Liquid-Argon Calorimeter Readout Electronics 6.1 AREUS 6.2 Hit Generation and Sampling 6.3 Pulse Shapes 6.4 Thermal Noise 6.5 Quantization 6.6 Digital Filters 6.7 Statistical Analysis 7 Results of the Readout Electronics Simulation Studies 7.1 Statistical Treatment 7.2 Simulation Verification Using Run-2 Data 7.3 Dependence of the Noise on the Shaping Time 7.4 The Analog Readout Electronics and the ADC 7.5 The Optimal Filter (OF) 7.6 The Wiener Filter 7.7 The Wiener Filter with Forward Correction (WFFC) 7.8 Final Comparison and Conclusions 8 Conclusions and Outlook Appendices

Cancer is the second leading cause of death after cardiovascular diseases in the world. Many of the chemical carcinogens need metabolic activation that catalyzed by cytochrome P450 and Phase II enzymes in order to exert their genotoxic and carcinogenic effects. Hence one possible mechanism is that phenolic compounds may alter anticarcinogenic effects is through an interaction with these enzymes either by the inhibition or activation of certain forms, leading to a reduced production of the ultimate carcinogen. Therefore anti-carcinogen activity of tannic acid, a hydrolyzable plant polyphenol, has a crucial importance to prevent conversion of pro-carcinogens to their carcinogenic form. Tannic acid is produced from secondary metabolism of plants and is found in edible vegetables, fruits and nuts, especially tea, cocoa, coffee and wine. In the present work, modulation of rabbit liver and kidney microsomal P450 dependent aniline 4-hydroxylase, N-nitrosodimethylamine N-demethylase and p-nitrophenol hydroxylase activities and cytosolic phase II enzymes / glutathione S-transferase (GST), NAD(P)H:quinone oxidoreductase:1 (NQO1) were studied in the presence of tannic acid at concentrations ranging from 0.5 &micro / M to 150 &micro / M in the reaction medium. The results obtained in this study were shown that tannic acid significantly inhibited the activities of p-nitrophenol hydroxylase, aniline 4-hydroxylase, NDMA N-demethylase, glutathione S-transferase, NAD(P)H:quinine oxidoreductase 1. Tannic acid was found to be the most potent inhibitor of cytosolic glutathione S-transferase with IC50 of 0.33 &micro / M and the least potent inhibitor of microsomal aniline 4-hydroxylase.with IC50 of 60.26 &micro / M. Effect of tannic acid on enzyme activities was further studied for both mode and type of inhibition. For this purpose various concentrations of the substrate were examined at various tannic acid concentrations. Lineweaver-Burk and Dixon plots were then generated from the resulting data sets. The Km value and inhibition constants (KI) were determined from double reciprocal and Dixon plot of the enzyme activity versus substrate and inhibitor concentration, respectively. Tannic acid was shown to be a noncompetitive inhibitor for liver cytosolic GST, NQO1 and microsomal aniline 4- hydroxylase enzymes with KI of 0.3 &micro / M, 41 &micro / M and 54.7 &micro / M, respectively. On the other hand, in kidney tissues, tannic acid was an uncompetitive inhibitor of cytosolic GST, while it was noncompetitive inhibitor for cytosolic NQO1 with a KI of 12.6 &micro / M. These results indicate that tannic acid may modulate cytochrome P450 dependent and Phase II enzymes and influence the metabolic activation of xenobiotics mediated by these enzymes.

Sulforaphane is an isothiocyanate found in high concentrations in cruciferous vegetables like broccoli. Sulforaphane has received much attention due to the evidence that it inhibits phase I carcinogen-bioactivating enzymes and/or induces phase II antioxidant enzymes as well as metallothioneins (MTs) (Perocco et al., 2006; Clarke et al., 2008; Yeh & Yen, 2009). Since MTs and antioxidant enzymes are involved in the scavenging of reactive oxygen species (ROS), the question was raised whether sulforaphane can provide protection against increased oxidative stress and if sulforaphane exposure of a human hepatocellular carcinoma cell line, like HepaRG cells, will have a negative impact on phase I and II biotransformation in these cells. Oxidative stress was exogenously induced in HepaRG cells with tert- Butyl hydroperoxide (t-BHP). Phase I and phase II biotransformation pathways were assessed with caffeine, paracetamol, aspirin, sodium benzoate, and paraaminobenzoic acid, respectively, as probe substances. Through the use of a liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) assay, the biotransformation of caffeine in phase I and the formation of paracetamol, aspirin, sodium benzoate and para-aminobenzoic acid conjugates in phase II were investigated. This involved elucidating the time it took for the whole probe to be completely biotransformed during phase I biotransformation and the unique conjugates formed during phase II biotransformation in HepaRG cells. The optimal t-BHP concentration and exposure time in HepaRG cells were standardized with a 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. LC-ESI-MS/MS assays to monitor phase I and phase II biotransformation were optimized and validated. The optimal sulforaphane concentration and exposure time in HepaRG cells were standardized with a MTT assay. To evaluate the possible protective effect of sulforaphane against oxidative stress, HepaRG cells were pre-incubated with sulforaphane followed by the induction of oxidative stress with t-BHP and the quantification of the amount of viable cells with a MTT assay. To investigate the effect of sulforaphane on phase I and phase II biotransformation pathways, HepaRG cells were first pre-incubated with sulforaphane followed by the addition of a specific probe substance and the assessment of the biotransformation of the probe with a LC-ESI-MS/MS assay. The results partially supported the hypothesis of the study that sulforaphane will protect HepaRG cells against oxidative stress without negatively influencing phase I and phase II biotransformation. The results indicated that sulforaphane provided partial protection against t-BHP induced oxidative stress and had no effect on phase II paracetamol biotransformation in HepaRG cells. / Thesis, MSc (Biochemistry), North-West University, Potchefstroom Campus, 2013.

Sulforaphane is an isothiocyanate found in high concentrations in cruciferous vegetables like broccoli. Sulforaphane has received much attention due to the evidence that it inhibits phase I carcinogen-bioactivating enzymes and/or induces phase II antioxidant enzymes as well as metallothioneins (MTs) (Perocco et al., 2006; Clarke et al., 2008; Yeh & Yen, 2009). Since MTs and antioxidant enzymes are involved in the scavenging of reactive oxygen species (ROS), the question was raised whether sulforaphane can provide protection against increased oxidative stress and if sulforaphane exposure of a human hepatocellular carcinoma cell line, like HepaRG cells, will have a negative impact on phase I and II biotransformation in these cells. Oxidative stress was exogenously induced in HepaRG cells with tert- Butyl hydroperoxide (t-BHP). Phase I and phase II biotransformation pathways were assessed with caffeine, paracetamol, aspirin, sodium benzoate, and paraaminobenzoic acid, respectively, as probe substances. Through the use of a liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) assay, the biotransformation of caffeine in phase I and the formation of paracetamol, aspirin, sodium benzoate and para-aminobenzoic acid conjugates in phase II were investigated. This involved elucidating the time it took for the whole probe to be completely biotransformed during phase I biotransformation and the unique conjugates formed during phase II biotransformation in HepaRG cells. The optimal t-BHP concentration and exposure time in HepaRG cells were standardized with a 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. LC-ESI-MS/MS assays to monitor phase I and phase II biotransformation were optimized and validated. The optimal sulforaphane concentration and exposure time in HepaRG cells were standardized with a MTT assay. To evaluate the possible protective effect of sulforaphane against oxidative stress, HepaRG cells were pre-incubated with sulforaphane followed by the induction of oxidative stress with t-BHP and the quantification of the amount of viable cells with a MTT assay. To investigate the effect of sulforaphane on phase I and phase II biotransformation pathways, HepaRG cells were first pre-incubated with sulforaphane followed by the addition of a specific probe substance and the assessment of the biotransformation of the probe with a LC-ESI-MS/MS assay. The results partially supported the hypothesis of the study that sulforaphane will protect HepaRG cells against oxidative stress without negatively influencing phase I and phase II biotransformation. The results indicated that sulforaphane provided partial protection against t-BHP induced oxidative stress and had no effect on phase II paracetamol biotransformation in HepaRG cells. / Thesis, MSc (Biochemistry), North-West University, Potchefstroom Campus, 2013.

Clinical drug trials are costly and time-consuming. Bayesian methods alleviate the inefficiencies in the testing process while providing user-friendly probabilistic inference and predictions from the sampled posterior distributions, saving resources, time, and money. We propose a dynamic linear model to estimate the mean response at each dose level, borrowing strength across dose levels. Our model permits nonmonotonicity of the dose-response relationship, facilitating precise modeling of a wider array of dose-response relationships (including the possibility of toxicity). In addition, we incorporate an adaptive approach to the design of the clinical trial, which allows for interim decisions and assignment to doses based on dose-response uncertainty and dose efficacy. The interim decisions we consider are stopping early for success and stopping early for futility, allowing for patient and time savings in the drug development process. These methods complement current clinical trial design research.