<p>Antibodies are proteins capable of specific interactions to a wide range of molecules. These interactions are facilitated by the complementary determining regions (CDR).</p><p>Carcinomas are the most common of human cancers and they release significant amount of cytokeratins (CK) in the necrotic areas of the tumors. The CKs stay in the tumor, since they have low solubility. The antibody studied in this thesis, the anti-CK 8 antibody TS1, has shown to be effective in tumor targeting and is proposed to be useful in therapy.</p><p>Single-chain antibodies (scFv) are recombinant antibodies which are much smaller than the intact IgG. This is an advantage when used in tumor therapy, since they can penetrate the tumors more easily than the larger IgG. Moreover, they are expressed by one single gene which make them easy to modify, for example by site-directed mutagenesis.</p><p>The anti-idiotypic antibody αTS1 can be used to clear the TS1 form the circulation and thereby clear the body from non-tumor bound TS1 in therapy. To be able to modify the binding of an antibody to its antigen and or anti-idiotype, these interactions must be studied. In this study this is accomplished by chemical modifications of the IgGs TS1 and αTS1 and the antigen CK 8. Guided by these results, amino acid residues were mutated by using site-directed mutagenesis in the TS1-218 scFv and the effects were studied. From mutational study results, the functional epitope could be mapped and it was found that there are mainly tyrosines, but also charged residues, serine and a tryptophan that are important for both interactions. The binding of TS1-218 to both αTS1 and CK 8 could be improved by changing the negatively charged side-chains by mutations to their corresponding amide or alanine.</p><p>Both the IgG and scFv versions of TS1 were administered in vivo. The IgG αTS1 was used to clear the TS1 from the circulation by forming immune complexes. The immune complexes, consisting of four or more antibodies, were mainly metabolized by the liver. The scFv TS1-218 could localize to the tumor in a tumor xenograft mouse model, although a higher uptake would be desired in a therapeutic strategy. The scFv was cleared rapidly by the kidneys, but the clearance could be slowed by pre-formed immune complexes with anti-TS1 scFv in vitro, prior to administration in vivo.</p>

<p>In directed forgetting research, participants are instructed to forget information recently learned, and asked instead to remember new information given later. When asked to recall both the to-be-remembered and the to-be-forgotten information, participants successfully exhibit directed forgetting by recalling more to-be-remembered material, than to-be-forgotten material. In the present study, two directed forgetting list method experiments were conducted on undergraduate students of psychology (n = 25; n = 78). The aim of the study was to see if retrieval inhibition between participants with or without traumatic childhood experiences differed, when presented with negative or positive words. All participants were screened for childhood trauma with the CTQ-SF. The participants in the second experiment were additionally screened for dissociation with the DES-II. While Experiment 1, possibly due to small sample size failed to attain a directed forgetting effect, Experiment 2 succeeded. The issue of childhood trauma did not influence the directed forgetting effect.</p>

Personal file retrieval – the task of locating and opening files on a computer – is a common task for all computer users. A range of interfaces are available to assist users in retrieving files, such as navigation within a file browser, search interfaces and recent items lists. This thesis examines two broad goals in file retrieval: understanding current file retrieval behaviour, and improving file retrieval by designing improved user interfaces. A thorough understanding of current file retrieval behaviour is important to the design of any improved retrieval tools, however there has been surprisingly little research about the ways in which users interact with common file retrieval tools. To address this, this thesis describes a longitudinal field study that logs participants' file retrieval behaviour across a range of methods, using a specially developed logging tool called FileMonitor. Results confirm findings from previous research that search is used as a method of last resort, while providing new results characterising file retrieval. These include analyses of revisitation behaviour, file browser window reuse, and interactions between retrieval methods, as well as detailed characterisations of the use of navigation and search. Knowledge gained from this study assists in the design of three improvements to file navigation: Icon Highlights, Search Directed Navigation and Hover Menus. Icon Highlights highlight items that are considered the most likely to be accessed next. These highlights are determined using a new algorithm, AccessRank, which is designed to produce a set of results that is both accurate and stable over time. Search Directed Navigation highlights items that match, or contain items that match, a filename search query, allowing users to rehearse the mechanisms for expert performance in order to aid future retrievals, and providing greater context than the results of a traditional search interface. Hover Menus appear when hovering the mouse cursor above a folder, and provide shortcuts to highly ranked files and folders located at any depth within the folder. This allows users to reduce navigation times by skipping levels of the file hierarchy. These interfaces are evaluated in lab and field studies, allowing for both precise analysis of their relative strengths and weaknesses, while also providing a high degree of external validity. Results of the lab study show that all three techniques reduce retrieval times and are subjectively preferred by participants. For the field study, fully functional versions of Icon Highlights and Search Directed Navigation are implemented as part of Finder Highlights, a plugin to OS X's file manager. Results indicate that Icon Highlights significantly reduce file retrieval times, and that Search Directed Navigation was useful to those who used it, but faces barriers to adoption. Key contributions of this thesis include a review of previous literature on file management, a thorough characterisation of file retrieval behaviour, improved algorithms for predicting user behaviour and three improved interfaces for file retrieval. This research has the potential to improve a tedious activity that users perform many times a day, while also providing generalisable algorithms and interface concepts that are applicable to a wide range of interfaces beyond file management.

Convergent evidence suggests that the dorsal medial prefrontal cortex (dmPFC) makes an important contribution to goal-directed action selection. The dmPFC is also part of a network of brain regions that becomes compromised in old age. It was hypothesized that during decision-making, some process of comparison takes place in the dmPFC between the representation of available actions and associated values, and that this process is changed with aging. These hypotheses were tested in aged and young adult rats performing a novel 3-choice, 2-cue decision task. Neuron and local field potential activity revealed that the dmPFC experienced different states during decision and outcome phases of the task, with increased local inhibition and oscillatory (gamma and theta) activity during cue presentation, and increased excitatory neuron activity (among regular firing neurons) at goal zones. Although excitatory and inhibitory activity appeared anti-correlated over phases of the decision task, cross-correlations and the prominent gamma oscillation revealed that excitation and inhibition were highly correlated on the millisecond scale. This "micro-scale" coupling between excitation and inhibition was altered in aged rats and the observed changes were correlated with changes in decision and movement speeds of the aged animals, suggesting a putative mechanism for age-related behavioral slowing. With respect to decision-making, both aged and young adult rats learned over multiple days to follow the rewarded cue in the 3-choice, 2-cue task. Support for the hypothesis that the dmPFC simultaneously represents alternative actions was not found; however, neuron activity selective for particular goal zones was observed. Interestingly, goal-selective neural activity during the decision period was more likely to take place on error trials, particularly on high-performing sessions and when rats exhibited a preference for a particular feeder. A possible interpretation of these patterns is that goal representations in the dmPFC might have sometimes overruled learned habits, which are likely to be involved in following the correct cue and which are known to be supported by other brain regions. These results describe fundamental properties of network dynamics and neural coding in the dmPFC, and have important implications for the neural basis of processing speed and goal-directed action.

The use of enzymes as catalysts for chemical transformations has emerged as a “greener” alternative to traditional organic synthesis. An issue to solve though, is that enzymes are designed by nature to catalyze reactions in a living cell and therefore, in many cases, do not meet the requirements of a suitable biocatalyst. By mimicking Darwinian evolution these problems can be addressed in vitro by different types of directed evolution strategies. α-Hydroxy aldehydes and α-hydroxy ketones are important building blocks in the synthesis of natural products, fine chemicals and pharmaceuticals. In this thesis, two alcohol dehydrogenases, FucO and ADH-A, have been studied. Their potentials to serve as useful biocatalysts for the production of these classes of molecules have been investigated, and shown to be good. FucO for its strict regiospecificity towards primary alcohols and that it strongly prefers the S-enantiomer of diol substrates. ADH-A for its regiospecificity towards secondary alcohols, its enantioselectivity and that is has the ability to use a wide variety of bulky substrates. The kinetic mechanisms of these enzymes were investigated using pre-steady state kinetics, product inhibition, kinetic isotope effects and solvent viscosity effects, and in both cases, the rate limiting steps were pin-pointed to conformational changes occurring at the enzyme-nucleotide complex state. These characterizations provide an important foundation for further studies on these two enzymes.   FucO is specialized for activity with small aliphatic substrates but is virtually inactive with aryl-substituted compounds. By the use of iterative saturation mutagenesis, FucO was re-engineered and several enzyme variants active with S-3-phenylpropane-1,2-diol and phenylacetaldehyde were obtained. It was shown that these variants capability to act on larger substrates are mainly due to an enlargement of the active site cavity. Furthermore, several amino acids which are important for catalysis and specificity were identified. Phe254 interacts with aryl-substituted substrates through π-π stacking and may be essential for activity with these larger substrates. One mutation caused a loss in the interactions made between the enzyme and the nucleotide and thereby enhanced the turnover number for the preferred substrate

Oligonucleotides enable many biotechnological applications; however they are easily degraded by nucleases. Many nucleotides modified at the 2’ position are degraded at decreased rates which improves oligonucleotide utility. Most applications of oligonucleotides rely on enzymatic synthesis. Unfortunately, native DNA polymerases do not recognize most useful modified nucleotide substrates. Directed evolution has been used to identify mutants of Taq DNA polymerase I (Taq) that recognize substrates with 2’ modifications. While mutant enzymes capable of modified nucleotide addition have been identified, to date, all of these enzymes are limited by their inability to synthesize full length modified DNA. Despite considerable efforts to evolve new activity there has been little work done to quantitatively characterize these evolved enzymes. This thesis work presents efforts to synthesize modified primers that will help comparatively and quantitatively characterize three enzymes previously evolved to recognize 2’ modified substrates. Using the methods developed in this thesis project, our lab will be able to characterize the relationship between the number of modified nucleotides in the primer terminus and the rate of modified and unmodified nucleotide addition. Future work will identify key enzymatic steps that limit extension in these enzymes with implications for the future design of Taq mutants capable of synthesizing long 2’ modified oligonucleotides.

The aim of this thesis is to determine the changes in BOLD signal of the human brain during various stages of reinforcement learning. In order to accomplish that goal two probabilistic reinforcement-learning tasks were developed and assessed with healthy participants by using functional magnetic resonance imaging (fMRI). For both experiments the brain imaging data of the participants were analysed by using a combination of univariate and model–based techniques. In Experiment 1 there were three types of stimulus-response pairs where they predict either a reward, a neutral or a monetary loss outcome with a certain probability. The Experiment 1 tested the following research questions: Where does the activity occur in the brain for expecting and receiving a monetary reward and a punishment ? Does avoiding a loss outcome activate similar brain regions as gain outcomes and vice a verse does avoiding a reward outcome activate similar brain regions as loss outcomes? Where in the brain prediction errors, and predictions for rewards and losses are calculated? What are the neural correlates of reward and loss predictions for reward and loss during early and late phases in learning? The results of the Experiment 1 have shown that expectation for reward and losses activate overlapping brain areas mainly in the anterior cingulate cortex and basal ganglia but outcomes of rewards and losses activate separate brain regions, outcomes of losses mainly activate insula and amygdala whereas reward activate bilateral medial frontal gyrus. The model-based analysis also revealed early versus late learning related changes. It was found that predicted-value in early trials is coded in the ventro-medial orbito frontal cortex but later in learning the activation for the predicted value was found in the putamen. The second experiment was designed to find out the differences in processing novel versus familiar reward-predictive stimuli. The results revealed that dorso-lateral prefrontal cortex and several regions in the parietal cortex showed greater activation for novel stimuli than for familiar stimuli. As an extension to the fourth research question of Experiment 1, reward predictedvalues of the conditional stimuli and prediction errors of unconditional stimuli were also assessed in Experiment 2. The results revealed that during learning there is a significant activation of the prediction error mainly in the ventral striatum with extension to various cortical regions but for familiar stimuli no prediction error activity was observed. Moreover, predicted values for novel stimuli activate mainly ventro-medial orbito frontal cortex and precuneus whereas the predicted value of familiar stimuli activates putamen. The results of Experiment 2 for the predictedvalues reviewed together with the early versus later predicted values in Experiment 1 suggest that during learning of CS-US pairs activation in the brain shifts from ventro-medial orbito frontal structures to sensori-motor parts of the striatum.

The term quantization refers to the process of estimating a given probability by a discrete probability supported on a finite set. The quantization dimension Dr of a probability is related to the asymptotic rate at which the expected distance (raised to the rth power) to the support of the quantized version of the probability goes to zero as the size of the support is allowed to go to infinity. This assumes that the quantized versions are in some sense ``optimal'' in that the expected distances have been minimized. In this dissertation we give a short history of quantization as well as some basic facts. We develop a generalized framework for the quantization dimension which extends the current theory to include a wider range of probability measures. This framework uses the theory of thermodynamic formalism and the multifractal spectrum. It is shown that at least in certain cases the quantization dimension function D(r)=Dr is a transform of the temperature function b(q), which is already known to be the Legendre transform of the multifractal spectrum f(a). Hence, these ideas are all closely related and it would be expected that progress in one area could lead to new results in another. It would also be expected that the results in this dissertation would extend to all probabilities for which a quantization dimension function exists. The cases considered here include probabilities generated by conformal iterated function systems (and include self-similar probabilities) and also probabilities generated by graph directed systems, which further generalize the idea of an iterated function system.

A study and analysis of high energy laser (HEL) systems aboard tactical aircraft is performed. The FA-18E/F Hornet and F-35 Joint Strike Fighter (JSF), equipped with solid-state HEL systems, are the main subjects of the study. Considerations of power generation and thermal management for a fighter-sized HEL system and aero-optic effects on beam propagation from high and medium altitude platforms are examined. An overview of system capabilities details how the HEL system will be more difficult to incorporate into legacy strike aircraft, but may be feasible for future aircraft such as the JSF. Tactical flight simulations are used to study and develop potential concepts of operation (CONOPS), using realistic scenarios and threat environments. Results show that a tactical HEL will not be a stand-alone weapon in combat, but will have many potentially useful tactical applications. Another study of a high energy free electron laser (FEL) system aboard C-130J-30 Hercules shows that such a system is feasible. Finally, a study of the FEL shows that strong field extraction can be optimized using undulator tapering. / US Marien Corps (USMC) author.

Renormalization group analysis is a useful tool for studying critical behaviour of stochastic systems. In this thesis, field-theoretic renormalization group will be applied to the scalar model representing directed percolation, known as Gribov model, in presence of the random velocity field. Turbulent mixing will be modelled by the compressible form of stochastic Navier-Stokes equation where the compressibility is described by an additional field related to the density. The task will be to find corresponding scaling properties.