Correlation filters (CFs) are well established and useful tools for a variety of tasks in signal processing and pattern recognition, including automatic target recognition and tracking, biometrics, landmark detection, and human action recognition. Traditionally, CFs have been designed and implemented efficiently in the frequency domain using the discrete Fourier transform (DFT). However, the element-wise multiplication of two DFTs in the frequency domain corresponds to a circular correlation, which results in aliasing (i.e., distortion) in the correlation output. Prior CF research has largely ignored these aliasing effects by making the assumption that linear correlation is approximated by circular correlation. In this work, we investigate in detail the topic of aliasing in CFs. First, we illustrate that the current formulation of CFs in the frequency domain is inherently flawed, as it unintentionally assumes circular correlation during the design phase. This means that existing CFs are not truly optimal. We introduce zero-aliasing correlation filters (ZACFs) which fix this formulation issue by ensuring that each CF formulation problem corresponds to a linear correlation rather than a circular correlation. By adopting the ZACF design modifications, we show that the recognition and localization performance of conventional CF designs can be significantly improved. We demonstrate these benefits using a variety of data sets and present solutions to the computational challenges associated with computing ZACFs. After a CF is designed, it is used for object recognition by correlating it with a test signal. We investigate the use of the well-known overlap-add (OLA) and overlap-save (OLS) algorithms to improve the computation and memory requirements of this correlation operation for high dimensional applications (e.g., video). Through this process, we highlight important tradeoffs between these two algorithms that have previously been undocumented. To improve the computation and memory requirements of OLA and OLS, we introduce a new block filtering scheme, denoted partial-aliasing OLA (PAOLA) that intentionally introduces aliasing into the output correlation. This aliasing causes conventional CFs to perform poorly. To remedy this, we introduce partial-aliasing correlation filters (PACFs), which are specifically designed to minimize this aliasing. We demonstrate through numerical results that PACFs outperform conventional CFs in the presence of aliasing.

Tat1-72, is an intrinsically disordered protein at pH 4.1 as previously indicated by NMR chemical shifts and coupling constants, and confirmed by 15N-relaxation parameters. The presence of SDS elicits a conformational change to α-helicity in Tat1-72. In the presence of the non-ionic DDM detergent and zinc, Tat was found to be soluble at pH 4 when bound to TAR RNA; TAR binding also elicits a conformational shift to α-helicity in Tat1-72. The β-sheet content of Tat1-72 is increased in the presence of NaCl. In similar conditions, Tat1-72 aggregates stained with Congo Red displayed a yellow-green birefringence and a red-shift in the Congo Red absorbance that is typical of β-amyloid fibril. The web-based algorithm “WALTZ” identifies the majority of the Tat1-72 hydrophobic core region as amyloidogenic. The helical propensity of Tat1-72 in TFE was determined by two-dimensional NMR spectroscopy.

Sensitivity to differential motion components, shearing and compressive (opposed) motion, was examined. The hypothesis that the visual system contains local mechanisms specifically sensitive to these types of motion was tested. Stimuli consisted of two moving sinusoidal gratings. Sensitivity to shear and compression was compared with sensitivity for linear motion. Lower thresholds of motion and contrast sensitivities were obtained. Subjects were more sensitive to opposed than to non-opposed motion for a range of grating orientations and different grating spatial frequencies. However sensitivity for opposed motion decreased in the presence of a second added linear motion. The hypothesis of local shear and compression mechanisms was rejected in favour of antagonistic (opponent) interactions between local motion mechanisms. Motion capture was examined. Stimuli were made up of a circular test grating surrounded by another grating. Subjects were required to judge the direction of motion of the test grating. Experiments examined the effects on motion capture of: centre grating size; orientation of surround; relative contrast of centre and surround; plaids in the surround. Conditions favouring motion capture were: with the smallest centre grating; with surround and centre orientations within thirty degrees; with surround had higher contrast than the centre; and only when a plaid surround contained a component of similar orientation as the centre. For conditions of motion capture relative to those of no-capture, increased velocity thresholds for judging the centre direction were found. This was associated with a shift in the bias point between opposed directions with no change in overall sensitivity to motion. It is suggested that a cooperative network of local motion mechanisms featuring centre-surround opponency can account for all the results of this study.

Circular source and detector trajectories in cone-beam computed tomography (CT) are known to collect insufficient data for accurate object reconstruction. One model predicts that the lacking information corresponds to a shift-variant cone of missing spatial frequency components in the local Fourier domain. These predictions were experimentally verified by imaging small, localized objects and observing their Fourier transforms. Measurements indicated that the internal angle of the ‘missing cone’ varies as the angle of locally intersecting x rays with respect to the horizontal plane, as expected. Object recovery was also found to depend greatly on the distribution of the object’s frequency spectrum relative to the missing cone, as predicted. Findings agreed with more anatomically relevant phantoms, which showed preferential intensity discrepancies at gradients oriented within or near the missing cone. Methods for artefact correction are in general limited to approximation unless a priori information is incorporated.

Circular source and detector trajectories in cone-beam computed tomography (CT) are known to collect insufficient data for accurate object reconstruction. One model predicts that the lacking information corresponds to a shift-variant cone of missing spatial frequency components in the local Fourier domain. These predictions were experimentally verified by imaging small, localized objects and observing their Fourier transforms. Measurements indicated that the internal angle of the ‘missing cone’ varies as the angle of locally intersecting x rays with respect to the horizontal plane, as expected. Object recovery was also found to depend greatly on the distribution of the object’s frequency spectrum relative to the missing cone, as predicted. Findings agreed with more anatomically relevant phantoms, which showed preferential intensity discrepancies at gradients oriented within or near the missing cone. Methods for artefact correction are in general limited to approximation unless a priori information is incorporated.

Photocopy of typescript. / Thesis (Ph. D.)--University of Hawaii at Manoa, 1979. / Bibliography: leaves 174-182. / Microfiche. / xvi, 182 leaves ill. 29 cm

The broad aim of this thesis is to generate fundamental knowledge about the structure and function of cyclotides, which are a topologically unique family of proteins. A long-term goal is to use the fundamental knowledge to assist in the development of drugs based on the stable cyclotide framework. Cyclotides are small proteins that are characterised by a cyclic cystine knot (CCK) motif, which is defined as a circular backbone combined with a cystine knot core. So far cyclotides have been found in plants of the Violaceae (violet) and Rubiaceae (coffee) plant families, and are believed to have a defence-related function. From an application perspective, the CCK framework has potential as a drug scaffold, being an ultra-stable alternative to linear peptide models. The reasons why cyclotides show promise as a drug template are three-fold – they have naturally high sequence diversity, suggesting that their framework can accommodate a range of epitopes; they are remarkably stable under various chemical, enzymatic and thermal conditions, which means that they have increased bioavailability; and they have a diverse range of bioactivities, supporting the notion that they can be used in a number of therapeutic applications. These three reasons are intimately linked to three core knowledge domains of cyclotide research, namely cyclotide sequences, structures and interactions. Thus, fundamental research into these three domains, as investigated in this thesis, is important as it may assist in the development of drugs based on the CCK scaffold. Chapter 1 of this thesis provides the background information to define the molecules studied and to highlight their importance. Chapter 2 describes the main experimental techniques that were used in this thesis, including nuclear magnetic resonance spectroscopy and mass spectrometry. The development of the CCK technology may benefit from a thorough understanding of the natural diversity of cyclotide sequences and the significance of this diversity on activity. Chapter 3 reports on the discovery of cyclotides in Viola yedoensis, a Chinese violet that is interesting because it is widely used in Traditional Chinese Medicine to treat a number of illnesses including swelling and hepatitis. In this study, a total of eight cyclotides was characterised, including five novel sequences. Based on anti-HIV and haemolytic assays, a strong relationship between surface hydrophobicity and activity was established. The stability of cyclotides, which underpins their potential as a drug scaffold, is examined at a structural level in Chapter 4. The solution structure of varv F, a cyclotide from the European field pansy, Viola arvensis, was solved and compared to the crystal structure of the same peptide, confirming the core structural features of cyclotides responsible for their stability, including the topology of the cystine knot, which has previously attracted some debate. From a comparison of biophysical measurements of a representative group of five cyclotides, a conserved network of hydrogen bonds, which also stabilises the cyclotide framework, was defined. A subset of hydrogen bonds involving the highly conserved Glu in loop 1 of cyclotides was examined in more detail by solving the structure of kalata B12, the only naturally occurring cyclotide with an Asp instead of a Glu in loop 1. By comparison with the prototypical cyclotide kalata B1 and an Ala mutant E7A-kalata B1, it was shown that the highly conserved Glu is important for both stability and activity. Chapter 5 reports on studies that add to our understanding of the mechanism of action of cyclotides, which is believed to involve membrane interactions. Spin-label experiments were performed for two cyclotides, kalata B2 and cycloviolacin O2, which are representative cyclotides from the two cyclotide sub-families, Möbius and bracelet, respectively. This study showed that different cyclotides have different but very specific binding modes at the membrane surface. Currently, it is believed that for Möbius cyclotides at least (e.g. kalata B1 and kalata B2), self-association may lead to the formation of membrane pores. Oligomerisation of cyclotides was also studied in this chapter using NMR relaxation. A computer program, NMRdyn, was developed to extract microdynamic and self-association parameters from NMR relaxation data. This program was used to analyse 13C relaxation data on kalata B1, providing clues about the tetramer structure of kalata B1. Although the three areas of cyclotide research examined in this thesis – sequence, structure and interactions – are reported in separate sections, the areas are not independent of each other. For example, the mechanism of action of cyclotides, which is reported in Chapter 3, requires an understanding of cyclotide structures, which is reported in Chapter 4. Chapter 6 describes a database, CyBase, which integrates sequence/structure/activity data on cyclotides so that relationships between the three areas can be examined. The database also provides tools to assist in discovery and engineering of cyclic proteins. In summary, several key areas that are fundamental to our understanding of cyclotides have been investigated in this thesis, ranging from cyclotide sequence diversity to their mechanism of action. The work described in this thesis represents a significant advance in our current understanding of cyclotides by providing, for example, explanations to their observed structural stability and how they work through interactions with other biomolecules. The information presented in this thesis is potentially useful in facilitating the long-term goal of developing peptide therapeutics based on the stable cyclotide framework.

Thesis (D. Sc.)--University of Sydney, 2003. / Title from title screen (viewed Apr. 28, 2008). Submitted in fulfilment of the requirements for the degree of Doctor of Science to the School of Chemistry, Faculty of Science. Degree awarded 2003; thesis submitted 2002. Includes bibliographical references. Also available in print form.

Thesis (Ph. D.)--University of Chicago, Dept. of Economics, August 1997. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves 224-231).