Dissertations / Theses on the topic 'Fold'
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1
Grando, Gianluca. "Growth fold systems in deep water fold thrust belts." Thesis, Royal Holloway, University of London, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.417783.
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Turner, Jacqueline. "Into the fold." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape15/PQDD_0022/MQ31308.pdf.
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McStravick, Michael. "Microwave pulse compression using 3-fold and 5-fold helically corrugated waveguides." Thesis, University of Strathclyde, 2012. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=25510.
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The use of an over-moded circular waveguide with helical corrugations of its inner surface as a dispersive medium enables compression of frequency-modulated microwave pulses. The helical corrugation couples a pair of partial modes of the circular waveguide having significantly different group velocities. As a result of the resonant coupling an eigenmode of the helically corrugated waveguide appears which has a strongly frequency dependent group velocity, which is favourable for the pulse compression. Two helically corrugated waveguide structures were investigated as sweep-frequency microwave pulse compressors for X-band microwave radiation. The investigation comprised the analytical, numerical and experimental study of the eigenwave and group velocity dispersion characteristics for the 3-fold and 5-fold helically corrugated waveguide compressors. Sweep-frequency based microwave pulse compression experiments were carried out at low (mW) and medium (kW) power levels. A 3-fold helically corrugated waveguide system resonantly coupled the fasttravelling counter-rotating TE1,1 mode and TE2,1 near cut-off mode. A 5.6 kW, 80 ns input pulse with 5 % frequency modulation from a conventional TWT was compressed to a maximum peak power of 140 kW, 1.5 ns pulse resulting in a peak power amplification of 22.5 ± 2.5 times, where 42 ± 5 % of the input energy was compressed to the main body of the output pulse. A larger diameter 5-fold helically corrugated waveguide system was designed to compress microwave pulses with frequency-modulation within the frequency interval 9.0 GHz to 9.6 GHz and simultaneously provide low reflection of the input radiation within a frequency interval of 8.0 GHz to 10.0 GHz. The 5-fold helically corrugated waveguide resonantly coupled the fast-travelling counter-rotating TE3,1 mode and TE2,2 near cut-off mode. An input pulse of 5.8 kW, 85 ns duration was compressed to a maximum peak power of 144 kW, 1.5 ns pulse resulting in a peak power compression ratio of 22.3 ± 2.5 and compression efficiency of 40 ± 5 %.
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Abeln, Sanne. "Protein fold evolution on completed genomes : distinguishing between young and old folds." Thesis, University of Oxford, 2007. http://ora.ox.ac.uk/objects/uuid:b520fd65-e829-4ae0-bed6-47d642909889.
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We review fold usage on completed genomes in order to explore protein structure evolution and assess the evolutionary relevance of current structural classification systems (SCOP and CATH). We assign folds on a set of 150 completed genomes using fold recognition methods (PSI-BLAST, SUPERFAMILY and Gene3D). The patterns of presence or absence of folds on genomes gives us insights into the relationships between folds and how we have arrived at the set of folds we see today. In particular, we develop a technique to estimate the relative ages of a protein fold based on genomic occurrence patterns in a phylogeny. We find that SCOP's `alpha/beta' class has relatively fewer distinct folds on large genomes, and that folds of this class tend to be older; folds of SCOP's `small protein' class follow opposite trends. Usage patterns show that folds with many copies on a genome are generally old, but that old folds do not necessarily have many copies. In addition, longer domains tend to be older and hydrophobic amino acids have high propensities for older folds whereas, polar - but non-charged - amino acids are associated with younger folds. Generally domains with stabilising features tend to be older. We also show that the reliability of fold recognition methods may be assessed using occurrence patterns. We develop a method, that detects false positives by identifying isolated occurrences in a phylogeny of species, and is able to improve genome wide fold recognition assignment sets. We use a structural fragment library to investigate evolutionary links between protein folds. We show that 'older' folds have relatively more such links than 'younger' folds. This correlation becomes stronger for longer fragment lengths suggesting that such links may reflect evolutionary relatedness.
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Thomas, Geraint Llewllyn. "Ab initio protein fold prediction." Thesis, University of Leeds, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.436019.
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Smith, Richard E. "An approach to fold recognition." Thesis, University of Essex, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.397732.
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Lin, Guang. "Protein fold recognition using neural networks." Thesis, Open University, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.273307.
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Zhang, Yao, and Peng Yang. "Automatic Carry Fold Ladders for Attics." Thesis, Blekinge Tekniska Högskola, Institutionen för maskinteknik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:bth-11977.
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Data shows that elderly people are more likely to live alone than younger people, meanwhile the percentage of elderly people with disabilities increases significantly with age. These trends and facts bring a number of issues. One of these we would like to solve is that it is difficult and dangerous for them to lift the heavy loads through ladder. Sometimes it is also very dangerous for normal people, not to mention to people with reduced mobility. In order to solve these issues and reduce the possibility of accident, we have come up with a new ladder used for attics that can transport the heavy loads automatically. As transmission part we use a rack and pinion mechanism to achieve a smooth transport and a ratchet mechanism for stopper to avoid sudden accident drops. The ladder also can be hidden when not using it.
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Bosworth, Jeff. "Investigation of a stop-fold tiltrotor." Thesis, Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/29662.
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Thesis (M. S.)--Aerospace Engineering, Georgia Institute of Technology, 2010.Committee Chair: Hodges, Dewey; Committee Member: Bauchau, Olivier; Committee Member: Sankar, Lakshmi. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Vucic, Vladimir. "Image Analysis for Nail-fold Capillaroscopy." Thesis, KTH, Skolan för elektro- och systemteknik (EES), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-174868.
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Detection of diseases in an early stage is very important since it can make the treatment of patients easier, safer and more ecient. For the detection of rheumatic diseases, and even prediction of tendencies towards such diseases, capillaroscopy is becoming an increasingly recognized method. Nail-fold capillaroscopy is a non-invasive imaging technique that is used for analysis of microcirculation abnormalities that may lead todisease like systematic sclerosis, Reynauds phenomenon and others. The main goal of this master thesis project is to provide new tools and techniques for the analysis of capillaroscopy images from the nail-fold area. Image processing and machine learning techniques are applied to images obtained by digital microscopes, like Mediscope as produced by Optilia Instruments AB, Sollentuna. This thesis oers a novel way for segmentation of capillaries from images as well as (semi)automatic capillary width calculation and automatic annotation of capillaries. These tools provide new insights into the structure of capillaries and also reduce the time required for measurement/annotation of capillaries.
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Terry, Aaron David. "Modeling Vocal Fold Intravascular Flow with Synthetic Replicas." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/8820.
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Communication by voice is foundational in our society and many rely on their voices for their occupations. Voice disorders affect a significant number of individuals each year, and diagnosis and treatment improvements are therefore sought via advancements in voice research. Contained in this thesis is a description of work intended to contribute to vocal fold research by using synthetic, self-oscillating vocal fold replicas to study the impact of replica vibration on perfusion fluid flow through the replica. Methods for manufacturing vocal fold replicas containing imbedded channels allowing for fluid perfusion are discussed. Experimental procedures developed for delivering perfusion fluid to the imbedded channel at a constant pressure during replica vibration are described. Methods for measuring perfusion parameters of perfusion fluid pressure, imbedded channel diameter, flow rate, and vibration parameters (subglottal pressure, frequency, amplitude, channel length, and glottal width) are detailed. Experiments performed using both stationary and vibrating vocal fold replicas are presented. Correlations between perfusion pressure and channel diameter are discussed. Vibration parameters were correlated to perfusion flow parameters and it is shown that perfusion flow rate through the channels decreased significantly with model vibration. Potential mechanisms for changes in perfusion flow resistance with vibration are discussed and analyzed. Output of a theoretical model, developed to incorporate some of the possible flow resistance mechanisms, was compared to vibrating replica experimental data.
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Yu, Libo. "Consensus Fold Recognition by Predicted Model Quality." Thesis, University of Waterloo, 2005. http://hdl.handle.net/10012/1124.
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Protein structure prediction has been a fundamental challenge in the biological field. In this post-genomic era, the need for automated protein structure prediction has never been more evident and researchers are now focusing on developing computational techniques to predict three-dimensional structures with high throughput.
Consensus-based protein structure prediction methods are state-of-the-art in automatic protein structure prediction. A consensus-based server combines the outputs of several individual servers and tends to generate better predictions than any individual server. Consensus-based methods have proved to be successful in recent CASP (Critical Assessment of Structure Prediction).
In this thesis, a Support Vector Machine (SVM) regression-based consensus method is proposed for protein fold recognition, a key component for high throughput protein structure prediction and protein function annotation. The SVM first extracts the features of a structural model by comparing the model to the other models produced by all the individual servers. Then, the SVM predicts the quality of each model. The experimental results from several LiveBench data sets confirm that our proposed consensus method, SVM regression, consistently performs better than any individual server. Based on this method, we developed a meta server, the Alignment by Consensus Estimation (ACE).
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Dehzangi, Abdollah. "Protein Fold Recognition Using Segmentation-based Features." Thesis, Griffith University, 2015. http://hdl.handle.net/10072/366423.
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Proteins are considered to be one of the most important biological macromolecules and play a wide range of vital roles in most biological interactions. Therefore, determining how they function is an important task in biology and biomedical science. Protein fold recognition is defined as assigning a given protein to a fold (among a finite number of folds) that represents its functionality as well as its major tertiary structure. Despite all the efforts made over the last two decades, finding an effective computational approach to solve this problem still remains challenging for computational biology and bioinformatics.
In this study we enhance the protein fold prediction accuracy by employing evolutionary and structural information for feature extraction. Based on our previously proposed feature extraction techniques to extract physicochemical-based features, we develop segmented distribution and segmented auto-covariance feature extraction methods to extract local evolutionary and structural information. By applying an SVM to our extracted features, we enhance the protein fold prediction accuracy up to 7.2% better than the best result found in the literature. In conclusion, we develop several segmentation-based feature extraction techniques that enable us to extract local discriminatory information for protein fold recognition better than previously proposed approaches to achieve this goal.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Institute for Integrated and Intelligent Systems
Science, Environment, Engineering and Technology
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Samlan, Robin Amy. "Kinematic Modeling of Asymmetric Vocal Fold Vibration." Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/232456.
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Asymmetries of the vocal folds and vocal fold vibration are key features underlying unilateral vocal fold motion impairment (VFMI). The knowledge of what particular asymmetries contribute to breathy voice and which asymmetries must be eliminated to re-establish normal voice will be important to improving evaluation and treatment of VFMI. It was hypothesized that several structural and vibratory asymmetries should lead to predictable changes in the glottal area, flow, and acoustic waveforms, and subsequently a perceived breathy voice quality. The purpose of this project was threefold: 1) to determine how specific vocal fold structural and vibratory asymmetries alter vocal function and perceived voice quality, 2) to determine the improvement in vocal function and voice quality in an abnormal voice with elimination of individual asymmetries, and 3) to develop a battery of vocal function measures that vary with dysphonia in a predictable manner. The approach was to use a computational kinematic model of vocal fold vibration that allows for differential left/right control of parameters such as vocal fold adduction, medial surface bulging, vibratory nodal point, phase, amplitude of vibration, and fundamental frequency. The resultant signals were subjected to aerodynamic and acoustic measurement as well as perceptual rating of voice quality. Results revealed that the degree of vocal process separation was the most influential parameter tested, though asymmetry of bulging, nodal point ratio, and starting phase worsened normal voice quality. Conversely, increased symmetry of bulging, nodal point ratio, amplitude of vibration and starting phase improved disordered voice quality. The amount of improvement to disordered voices varied based on the number of other asymmetries present. None of the six vocal function measures tested were primarily responsive to one particular model parameter, though four measures generally decreased as vocal process separation increased: maximum flow declination rate (MFDR), spectral slope (B0-B2), cepstral peak prominence (CPP), and harmonics-to-noise ratio (HNR). Two of the measures, MFDR and CPP, co-varied with each of the five parameters and robustly correlated with perceived severity.
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Stevens, Kimberly Ann. "Geometry and Material Properties of Vocal Fold Models." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/5595.
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Voiced communication plays a fundamental role in society. Voice research seeks to improve understanding of the fundamental physics governing voice production, with the eventual goal of improving methods to diagnose and treat voice disorders. For this thesis, three different aspects of voice production research were studied. First, porcine vocal fold medial surface geometry was determined, and the three-dimensional geometric distortion induced by freezing the larynx, especially in the region of the vocal folds, was quantified. It was found that porcine vocal folds are qualitatively geometrically similar to canine and human vocal folds, as well as commonly used models, and that freezing of tissue in the larynx causes distortion of around 5%. Second, a setup of multiple high-resolution cameras and a stereo-endoscopy system simultaneously recorded positions on the superior surface of synthetic, self-oscillating vocal fold models to estimate the error in the measurement of the three-dimensional location by the stereo-endoscopy system. The error was found to be low in the transverse plane, whereas the error was relatively large in the inferior-superior direction, suggesting that the stereo-endoscope is applicable for in vivo measurements of absolute distances of the glottis in the transverse plane such as glottal length, width, and area. Third, a function for strain-varying Poisson's ratio for silicone was developed from experimental data. It is anticipated that the findings herein can aid voice researchers as they study voice production, leading to improved voice care.
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Toledo, Patino Saacnicteh [Verfasser], and Birte [Akademischer Betreuer] Höcker. "On the emergence of the hemD-like fold and its use for fold-chimeragenesis / Saacnicteh Toledo Patino ; Betreuer: Birte Höcker." Tübingen : Universitätsbibliothek Tübingen, 2019. http://d-nb.info/1196617252/34.
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Nosaka, Takefumi. "4-fold symmetric quandle invariants of 3-manifolds." 京都大学 (Kyoto University), 2012. http://hdl.handle.net/2433/157740.
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Chan, Alfred. "Vocal fold vibration measurements using laser Doppler vibrometry." Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=106574.
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The objective of this study was to measure the velocity of the superior surface of human vocal folds during phonation using laser Doppler vibrometry (LDV). A custom-made endoscopic laser beam deflection unit was designed and fabricated. An in vivo clinical experimental procedure was developed and performed at the Montreal General Hospital Voice Laboratory in order to simultaneously collect velocity data from the LDV and video from endoscopy. The velocity along the direction of the laser beam, ie. the inferior-superior direction, was captured and found to be synchronous with electroglottograph (EGG) and sound level meter data. Recorded phonation onset/offset times were found to be commensurate with reported data obtained using EGG and high-speed imaging. The vibration energy of the vocal folds was determined to be significant up to a frequency of 3 kHz. The velocity amplitude was found to be approximately 45 mm/s and was consistent between subjects. A sparse map of the vocal fold surface velocity was obtained, which showed that the velocity amplitude did not change significantly with location. Different characteristic vibration waveforms were identified and attributed to the presence of a mucosal wave over the vocal fold surface. Laser Doppler vibrometry offers potential as a diagnostic tool for the early detection of vocal disorders. It may provide online biofeedback for voice professionals, and help them to tune their laryngeal tension to obtain the desired voice output.La présente étude avait pour but de mesurer directement la vitesse des cordes vocales de la voix humaine en utilisant la vibrométrie laser (VL). Une buse endoscopique pour la re-direction du faisceau laser a été conçue et construite. Un protocole expérimental de mesures en clinique a été développé et mis en oeuvre afin d'obtenir des signaux de vitesse simultanément avec des images vidéoendoscopiques. Les mesures furent prises au laboratoire de la voix de l'Hôpital Général de Montréal. La vitesse mesurée est dans l'axe du faisceau laser, soit dans la direction inférieure-supérieure. Des signaux synchrones provenant d'un électroglottogramme (EGG) et d'un microphone furent recueillis pour fins de comparaisons et de vérifications. Les signaux provenant du VL sont parfaitement corrélés et consistants avec les signaux du EGG et microphone ainsi que les informations provenant du vidéo. L'énergie vibratoire semble être présente dans un bande de fréquence allant jusqu'à 3 kHz. La vitesse est de 45 mm/s dans les trois cas étudiés, pour toute fréquence, amplitude et position. Différents modes vibratoires avec des formes d'ondes distinctes furent identifiés, probablement dus à la propagation d'ondes sur la surface supérieure des cordes vocales. Les résultats suggèrent que l'utilisation du VL pourrait mener à des applications intéressantes pour la détection de problèmes tels que des lésions. La VL pourrait aussi sans doute fournir une rétroaction à des professionnels de la voix qui leur permettrait d'ajuster la tension et la position de leur cordes vocales afin d'obtenir le timbre ou l'intonation désirée.
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Cotton, James Timothy. "Salt tectonics in compressional fold and thrust belts." Thesis, Imperial College London, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.267734.
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Goodyer, Eric N. "The biomechancial properties of the human vocal fold." Thesis, De Montfort University, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.502514.
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Phonation is a complex process requiring the controlled exhalation of air through the larynx. Within the larynx there is a specialist tissue structure known as the vocal folds, which under muscular control captures energy within the airflow and transfers it to a dynamic phenomena, analogous to a static fluid wave, known as the mucosal wave. This mucosal wave causes the vocal folds to open and close rhythmically, thus modulating the airflow, which can then be manipulated in the vocal tract to create the sounds that we know as speech. The purpose of the research detailed in this thesis is the quantification of the biomechanical properties of the vocal folds. There is a major gap in knowledge relating to the elastic properties of the vocal fold as the only reliable apparatus available to determine these properties rely on dissecting the tissue out of anatomical context. The author's research is dedicated to developing methods to measure these properties from intact larynges, and from patients in vivo. This is to enable a better understanding of how this complex tissue structure works; to assist with the derivation of mathematical models of phonation; and to provide methods to assess objectively the effectiveness of tissue engineering therapies used to repair scarred vocal folds.
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Hadley, Caroline. "Exploiting functional information for improved protein fold recognition." Thesis, University of Warwick, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247416.
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Jawad-Alami, Zahra. "Structure and evolution of the β-propeller fold." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615810.
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Goodyer, Erin N. "The biomechanical properties of the human vocal fold." Thesis, De Montfort University, 2008. http://hdl.handle.net/2086/4344.
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Phonation is a complex process requiring the controlled exhalation of air through the larynx. Within the larynx there is a specialist tissue structure known as the vocal folds, which under muscular control captures energy within the airflow and transfers it to a dynamic phenomena, analogous to a static fluid wave, known as the mucosal wave. This mucosal wave causes the vocal folds to open and close rhythmically, thus modulating the airflow, which can then be manipulated in the vocal tract to create the sounds that we know as speech. The purpose of the research detailed in this thesis is the quantification of the biomechanical properties of the vocal folds. There is a major gap in knowledge relating to the elastic properties of the vocal fold as the only reliable apparatus available to determine these properties rely on dissecting the tissue out of anatomical context. The author's research is dedicated to developing methods to measure these properties from intact larynges, and from patients in vivo. This is to enable a better understanding of how this complex tissue structure works; to assist with the derivation of mathematical models of phonation; and to provide methods to assess objectively the effectiveness of tissue engineering therapies used to repair scarred vocal folds. The author devised a new and novel apparatus to obtain data from excised tissue and in vivo. A key principle of these devices is that they directly measure the mechanical properties of intact larynges, which contrasts to methods reported by the majority of other researchers. The author also managed a number of research grant funded projects, in his capacity as PI, which deployed the devices. The author developed most of the software and the mathematical techniques used to analyse the data. Details of the apparatus devised to obtain data from both excised larynges and in vivo are given, which required the derivation of devices capable of measuring micrograms of force and displacement resolutions at micron level. Also given are the mathematical models used to transform the raw data into the fundamental material property known as shear modulus. The results include measurements of the shear modulus of a group of 20 excised vocal folds, of varying ages and both sexes. Also given are the results of similar data obtained from eight volunteer patients in vivo. The anisotropic nature of vocal fold tissue is quantified and iso-contour maps presented showing the variation of elasticity with respect to anatomical position. Early results are given that quantify the change in vocal fold tension with respect to electrical stimulation of the recurrent and superior laryngeal nerves in a canine model.A lso given are the resultso f a study that demonstratedth at hyaluronica cid tissue augmentation could restore vocal fold pliability in a rabbit model.
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Djurdjević, Dušan. "Ab initio protein fold prediction using evolutionary algorithms." Thesis, University of Edinburgh, 2006. http://hdl.handle.net/1842/13660.
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A comprehensive study was undertaken for ab initio protein fold prediction using a fully atomistic protein model and a physicochemical potential. Twenty four EA designs where initially assessed on polyalanine, a prototypical α-helical polypeptide. Design aspects varied include the encoding alphabet, crossover operator, replacement strategy and selection strategy. By undertaking a comprehensive parameter study, the best performing designs and associated control parameter values were identified for polyalanine. The scaling between the performance and polyalinine size was also identified for these best designs. This initial study was followed by a similar parametric study for met-enkephalin, a five residue polypeptide that has long been used as a de facto standard test case for protein structure prediction algorithms. It was found that the control parameter scalings identified from the polyalinine study were transferable to this real protein, and that the EA is superior to all existing ab initio approaches for met-enkephalin. The best design was finally applied to a series of real proteins ranging in size up to 45 residues to more generally assess the EA’s performance. The thesis is concluded with consideration of the future work required to extend the EA to larger proteins and ab initio structure prediction for non-native environments such as at interfaces, which are of relevance to, for example, biosensors.
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Hill, Jamie Richard. "Fold recognition and alignment in the 'twilight zone'." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:353a9832-b2a4-41fb-a9f2-f3cae1a30039.
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At present, the most accurate approach to predicting protein structure, comparative modelling, builds a model of a target sequence using known protein structures as templates. Comparative modelling becomes markedly less accurate in the ‘twilight zone’, where the target protein shares little sequence identity with all known templates. There are two main causes of this inaccuracy: first, it becomes difficult to identify good structural templates; second, it becomes difficult to determine which amino acids in the template are structurally equivalent to those in the target. These are problems of fold recognition and target-template alignment respectively. In this thesis, new approaches are developed to address both these problems. The alignment problem is investigated in the special case of membrane proteins. These are key modelling targets as they resist structure determination and are pharmaceutically important. The approach taken here is to use ‘environment specific substitution tables’ (ESSTs)– that is, to alter the alignment scoring system for each local environment of the template structure. We show how ESSTs can be made for membrane proteins, tested for robustness of construction, and used to infer the most important evolutionary pressures acting on protein structure. The incorporation of ESSTs into a multiple sequence alignment method leads to more accurate alignments of membrane proteins, and so to more accurate models. Recently, algorithms have been developed that predict contacts in protein structures from a multiple sequence alignment of homologous sequences. We explore the potential of these predictions for fold recognition by developing an algorithm that makes no use of amino acid identity, and so should be agnostic to the existence of a ‘twilight zone’. We show that whilst this is not the case, our method is complementary to state-of-the-art approaches.
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Willis, Joshua Jerome. "27th Immunoglobulin Domain: Fold Catastrophes and Hydrogen Bonding." Case Western Reserve University School of Graduate Studies / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=case1332855603.
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Volkar, Carie L. "Patterns of Vocal Fold Closure in Professional Singers." Cleveland State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=csu1494258620137297.
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Drechsel, James S. "Characterization of synthetic, self-oscillating vocal fold models /." Diss., CLICK HERE for online access, 2007. http://contentdm.lib.byu.edu/ETD/image/etd2339.pdf.
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Wurzbacher, Tobias. "Vocal fold dynamics : quantification and model-based classification /." Aachen : Shaker Verlag, 2008. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=016315367&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.
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Ward, Shelby Charisse. "Refinement and Characterization of Synthetic Vocal Fold Models." BYU ScholarsArchive, 2014. https://scholarsarchive.byu.edu/etd/4225.
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Understanding vocal fold mechanics is an integral part of voice research and synthetic vocal fold models are an essential tool in characterizing vocal fold mechanics. These models contain multiple layers with varying stiffness, much like human vocal folds. The purpose of this thesis is to improve the current models and modeling techniques, as well as investigate the impact of asymmetry on model vibration. A new design for an MRI-based model is detailed. This model has a more realistic geometry than the simplified models and mimics some of the vibratory characteristics observed in human vocal folds. The MRI-based model was used to investigate left-right stiffness asymmetry in multiple layers of the model. A zipper-like motion was observed during vibration of the MRI-based models. A phase shift was present in the asymmetric models, with the less stiff side leading the stiffer side. A new expendable mold fabrication process is described. This new process provides more freedom in designing vocal fold models and experiments. Additionally, the new process enables fabrication of models without the use of release agent, a factor which has, in the past, adversely impacted manufacturing yield and prohibited the incorporation of certain biological materials into the synthetic models. The new process also allows for more convenient geometry variation than what has previously been feasible. Finally, the new process was used to investigate cover layer geometry variation and asymmetry in a simplified model. Cover layer thickness was found to be a significant factor in governing the motion of the vocal fold model. Anterior-posterior asymmetry was found to induce the same zipper-like motion observed in the MRI-based models.
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Drechsel, James S. "Characterization of Synthetic, Self-Oscillating Vocal Fold Models." BYU ScholarsArchive, 2008. https://scholarsarchive.byu.edu/etd/1590.
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The vocal folds are essential for speech production, and a better understanding of vocal fold vibration characteristics may help improve treatments of voice disorders. However, studying real vocal folds presents significant challenges. In-vivo studies are limited by access and safety issues. Excised larynges have a short useable lifetime (on the order of minutes) and are difficult to parameterize. In contrast, synthetic vocal fold models have long useable lifetimes and can be easily parameterized. In this thesis, a series of tests performed on recently developed synthetic, self-oscillating models of the human vocal folds are discussed. These tests include measurements of vibration frequency, sub-glottal pressure, and time-averaged flow rate. The differences between one-layer and two-layer synthetic models are evaluated. Comparisons are made between synthetic model and real vocal fold behavior. The synthetic model is shown to have vibrated at frequencies, pressures, and flow rates consistent with human phonation. The influence of sub-glottal tube length on model vibration frequency is examined. Motion is observed using high-speed imaging. Velocity measurements of the glottal jet using particle image velocitmetry (PIV) were performed with and without an idealized vocal tract, including the effects of the false folds, for various cases of vocal tract asymmetry. Glottal jet velocities measured using PIV were consistent with velocities measured using excised larynges. A starting vortex was observed in all test cases. The presence of the false folds acted to restrain the sides of the starting vortex, and in some cases created new vortical structures shed from the false folds. An algorithm was created to calculate and visualize the jet core centerline. In the vocal tract cases, the glottal jet tended to skew toward the nearest wall; in the false fold cases, the opposite trend was observed as the jet skewed away from the nearest wall (towards the midplane). Plots of RMS velocity showed distinct regions of shear layer and jet core. Vocal tract cases at pressures much greater than phonation onset pressure showed significant increases in RMS velocities compared to open jet and false fold cases.
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Avila, Alex. "Origami-Based Design of Fold States and Stability." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7036.
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Origami is a potentially elegant and powerful source of inspiration for many engineering designs. The viable shapes (fold states) of a single device allow it to perform multiple, seemingly contradictory, functions. The fold state is a large factor in the device's performance, but there are challenges in selecting and maintaining those fold states. In this thesis we analyze existing concepts for overcoming these challenges. Those concepts are compared with those that occur in origami-based devices. From this analysis fundamental gaps were identified, specifically, shortcoming in the terminology used to refer to (1) non-flat origami states and (2) sets of facets and creases. Likewise we found a need for a comprehensive categorization method of fold states. Fold states are divided into seven types based on the set of fold angles they contain: U, P, F, UP, UF, PF, and UPF. The origami-based devices are analyzed based on their functional fold states, showing an emphasis on P and PF fold states. The fold states and their functions are tabulated. We demonstrate the table as a tool in an origami-based design method. Selecting fold states for an application is just the first step for effective use of origami. Once selected, the origami fold state must be maintained during use to perform its functions. This thesis also outlines the Origami Stability Integration Method (OSIM) for integrating a wealth of stability techniques. These techniques are categorized and analyzed to assist designers in selecting a technique for a device's application. Both methods, the fold-state selection method and the OSIM, are demonstrated in designing an origami-based ballistic barrier. The barrier is designed to stow in a compact fold state and deploy to a partially folded state to provide protection during armed conflicts. Quick deployment and a stable structure make the barrier a valuable example of origami-based design, demonstrating these two methods in addressing some of origami's design challenges.
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Tristan, Julie Antonia de [Verfasser]. "Indication for vocal fold medialization in patients with unilateral vocal fold paralysis (thyroplasty versus fat injection) / Julie Antonia de Tristan geb. Kraas." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2011. http://d-nb.info/1010757717/34.
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Ren, Bin. "Crystallographic studies on redox enzymes containing the thioredoxin fold /." Stockholm, 1999. http://diss.kib.ki.se/1999/91-628-3302-2/.
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Anzur, Matthew Paul. "k-star decomposition of lambda-fold complete multipartite graphs." Auburn, Ala., 2007. http://repo.lib.auburn.edu/07M%20Dissertations/ANZUR_MATTHEW_39.pdf.
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Menke, Matthew Ewald 1978. "Predicting the beta-trefoil fold from protein sequence data." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/30093.
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Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.Includes bibliographical references (p. 45-47).
A method is presented that uses [beta]-strand interactions at both the sequence and the atomic level, to predict the beta-structural motifs in protein sequences. A program called Wrap-and-Pack implements this method, and is shown to recognize β-trefoils, an important class of globular β-structures, in the Protein Data Bank with 92% specificity and 92.3% sensitivity in cross-validation. It is demonstrated that Wrap-and-Pack learns each of the ten known SCOP β-trefoil families, when trained primarily on β-structures that are not β-trefoils, together with 3D structures of known β-trefoils from outside the family. Wrap-and-Pack also predicts many proteins of unknown structure to be β-trefoils. The computational method used here may generalize to other β-structures for which strand topology and profiles of residue accessibility are well conserved.
by Matthew Ewald Menke.
S.M.
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Gottlieb, Alexis Hope. "FOLD : an open platform for adding context to stories." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/101840.
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Thesis: S.M., Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2015.Cataloged from PDF version of thesis.
Includes bibliographical references.
News is important. It gives us the information we need to make decisions, provides common ground to share with others around us, and helps us become global citizens. However, there are many important stories we shy away from because we lack the background needed to understand them. Some of the most important news stories we encounter-like the Israel- Palestine conflict, the recent unrest in Ukraine, or the ongoing Ebola outbreak-are complex and require context to understand. Traditionally, news relies on a storytelling structure called the inverted pyramid, where key facts are introduced in the first paragraph, with subsequent paragraphs providing background information. This structure worked well for the era of paper-based journalism, so the story could be shortened to fit space constraints without compromising emerging facts. But is this the way that news should be now, or is this the result of using ink and paper procedures in a world where digital technologies allow for more flexibility? This thesis presents FOLD, a publishing platform that uses visual structure to address the problem of including context alongside stories. FOLD allows writers to tell stories by weaving together different pieces of information from across the web in the form of "cards." There are two types of cards: narrative cards, and context cards. Narrative cards are arranged vertically to form the "backbone" of a story. Context cards are positioned perpendicular to the narrative cards, providing alternate axes for reading. The use and reception of this tool within the context of a 3-month public beta is discussed, and opportunities for future work are presented.
by Alexis Hope Gottlieb.
S.M.
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Unnikrishnan, Harikrishnan. "ANALYSIS OF VOCAL FOLD KINEMATICS USING HIGH SPEED VIDEO." UKnowledge, 2016. http://uknowledge.uky.edu/ece_etds/82.
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Vocal folds are the twin in-folding of the mucous membrane stretched horizontally across the larynx. They vibrate modulating the constant air flow initiated from the lungs. The pulsating pressure wave blowing through the glottis is thus the source for voiced speech production. Study of vocal fold dynamics during voicing are critical for the treatment of voice pathologies. Since the vocal folds move at 100 - 350 cycles per second, their visual inspection is currently done by strobosocopy which merges information from multiple cycles to present an apparent motion. High Speed Digital Laryngeal Imaging(HSDLI) with a temporal resolution of up to 10,000 frames per second has been established as better suited for assessing the vocal fold vibratory function through direct recording. But the widespread use of HSDLI is limited due to lack of consensus on the modalities like features to be examined. Development of the image processing techniques which circumvents the need for the tedious and time consuming effort of examining large volumes of recording has room for improvement. Fundamental questions like the required frame rate or resolution for the recordings is still not adequately answered. HSDLI cannot get the absolute physical measurement of the anatomical features and vocal fold displacement. This work addresses these challenges through improved signal processing. A vocal fold edge extraction technique with subpixel accuracy, suited even for hard to record pediatric population is developed first. The algorithm which is equally applicable for pediatric and adult subjects, is implemented to facilitate user inspection and intervention. Objective features describing the fold dynamics, which are extracted from the edge displacement waveform are proposed and analyzed on a diverse dataset of healthy males, females and children. The sampling and quantization noise present in the recordings are analyzed and methods to mitigate them are investigated. A customized Kalman smoothing and spline interpolation on the displacement waveform is found to improve the feature estimation stability. The relationship between frame rate, spatial resolution and vibration for efficient capturing of information is derived. Finally, to address the inability to measure physical measurement, a structured light projection calibrated with respect to the endoscope is prototyped.
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Kumirov, Vlad K. "Mechanisms and Consequences of Evolving a New Protein Fold." Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/605218.
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The ability of mutations to change the fold of a protein provides evolutionary pathways to new structures. To study hypothetical pathways for protein fold evolution, we designed intermediate sequences between Xfaso1 and Pfl6, two homologous Cro proteins that have 40% sequence identity but adopt all–α and α+β folds, respectively. The designed hybrid sequences XPH1 and XPH2 have 70% sequence identity to each other. XPH1 is more similar in sequence to Xfaso1 (86% sequence identity) while XPH2 is more similar to Pfl6 (80% sequence identity). NMR solution ensembles show that XPH1 and XPH2 have structures intermediate between Xfaso1 and Pfl6. Specifically, XPH1 loses α-helices 5 and 6 of Xfaso1 and incorporates a small amount of β-sheet structure; XPH2 preserves most of the β-sheet of Pfl6 but gains a structure comparable to helix 6 of Xfaso1. These findings illustrate that the sequence space between two natural protein folds may encode a range of topologies, which may allow a protein to change its fold extensively through gradual, multistep mechanisms. Evolving a new fold may have consequences, such as a strained conformation. Here we show that Pfl6 represents an early, strained form of the α+β Cro fold resulting from an ancestral remnant of the all-α Cro proteins retained after the fold switch. This nascent fold can be stabilized through deletion mutations in evolution, which can relieve the strain but may also negatively affect DNA-binding function. Compensatory mutations that increase dimerization appear to offset these effects to maintain function. These findings suggest that new folds can undergo mutational editing through evolution, which may occur in parallel pathways with slightly different outcomes.
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Walton, Chloe. "Unilateral vocal fold paralysis : Voice therapy and voice outcomes." Phd thesis, Australian Catholic University, 2018. https://acuresearchbank.acu.edu.au/download/0232c3d9f0f647c7ef485011cb64a90856682aa7dcac1def5faeb4794abe62b6/7120437/Walton_2018_Unilateral_vocal_fold_paralysis_voice_therapy.pdf.
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Unilateral vocal fold paralysis (UVFP) is a debilitating condition arising from a recurrent laryngeal nerve injury due to iatrogenic, idiopathic or other intrinsic or extrinsic causes. The loss of voluntary vocal fold movement can result in marked changes in voice quality and performance (dysphonia) and have a significant impact on quality of life. UVFP is estimated to affect approximately 0.5% of the population - with dysphonia reported in 86.6% of all cases. Treatment for UVFP aims to improve the voice quality and restore the glottal sufficiency either through voice therapy, surgical intervention or a combination of the two. Selection of treatment type for UVFP is based on the severity of the glottal insufficiency, the associated dysphonia and the vocal requirements of the individual. However, there is currently limited evidence available to support decision making around the management of dysphonia for people with UVFP. There are a number of potential reasons for the current limitation in evidence, including: (1) inadequate development and documentation of the voice therapy program characteristics and (2) variable and inadequate application of voice outcome measures to determine treatment effect.
The first aim of my PhD is therefore to investigate the content, timing and dosage characteristics of voice therapy provided (by speech pathologists) to patients with dysphonia due to UVFP. This has resulted in three studies in my thesis: (1) a systematic review of the current relevant literature; (2) a cross-section international survey of current practice and (3) an in-depth qualitative study of expert practice. The findings of the three studies highlighted the lack of consistency in the application of voice therapy in the literature (Study 1), and then provided key information that informed the development of a schema that outlined the key stages involved in voice therapy treatment for patients with UVFP (Study 2 and Study 3) Key elements of this schema described factors that influence decision making and goal setting for voice therapy, the timing and intensity of therapy, the measurement of therapy outcomes, and decision making for the cessation of therapy. The schema could inform both future research into the efficacy of voice therapy in UVFP and clinical practice Together these studies will provide a triangulation of evidence to formulate a clear and prescriptive direction for voice therapy treatment for future efficacy studies, as well as for clinical practice.
The second aim of my PhD is to critically evaluate voice outcome measures that are used with patients with UVFP to determine treatment effects. There are a large number of potential voice outcomes to choose from (more than 50), across multiple dimensions of voicing (e.g. acoustic, aerodynamic, auditory-perceptual and patient self-rated measures) and therefore there is a need for clarity on the most appropriate means of detecting voice change over time. A systematic review was conducted to address the second aim. The systematic review critically evaluated the voice outcome measures used in the existing literature with respect to reliability, validity and responsiveness to change, as well as multidimensionality and procedural/protocol accuracy. The systematic review identified set of voice outcome measures with good psychometric properties that demonstrated their responsiveness to the treatment effect. The set of outcome measures could therefore be used for future research in UVFP.
Together the findings of this thesis provide the best evidence for the voice therapy management of UVFP and have identified several multi-dimensional voice outcome measures which are responsive to the treatment effect.
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Wang, Chen. "Video Processing for Nail-fold Capillary Blood Velocity Detection." Thesis, KTH, Skolan för elektro- och systemteknik (EES), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-174869.
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Microcirculation plays an essential and functional role in the human body and reflects people’s physical status with microscopic detail. For peripheral microcirculation, nail-fold microscopy is a convenient and non-invasive tool since the capillaries in the nail-fold are well arranged and parallel to the skin, which is advantageous for microscopic visualization. Further, nail-fold capillaroscopy information is widely useful. In diagnosis, various diseases such as systemic lupus erythematosus and cardiac diseases can be detected and predicted at an early stage with capillaroscopic patterns and capillary blood velocity. For medical experiments, capillaroscopic information can be used to monitor drug effects and other medical treatments. Though nail-fold capillaroscopy is of significant convenience, it is not widely used. Currently, there is no commercial product with those functions due to the limitations of the equipment, such as microscope resolution and lens magnification. Besides, there is no concrete standard for measurement procedures or objective rules for quantitive data analysis. This thesis proposes a reliable system estimating nail-fold capillary blood flow velocity. It is tested and applied to the microscope from Optilia. In this work, various image and video processing methods are discussed in detail and tested in practice. Taking computational load and equipment limitations into consideration, the system applies frame enhancement and video stabilization. It uses dual-window and correlation methods to estimate the velocity of red blood cells in nail-fold capillaries. In order to test the reliability of the system, the obtained results are compared with the outcome of direct observation. It turns out that the chosen methods employed in the system provide rational results within 5 pixel bias.
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Merritt, Jonathan Karl. "Efforts Towards the Directed Evolution of a Protein Fold." Thesis, The University of Arizona, 2012. http://hdl.handle.net/10150/244476.
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More than a thousand different protein folds are known to exist, many of which have been characterized through dedicated research; however, there is little evidence of how these numerous structural forms arose through evolution. One approach to elucidating possible evolutionary pathways of protein structure is to perform directed evolution experiments on ancestrally related protein families which occupy different folds. One approach to the directed evolution of a protein fold is to follow a destroy-and-rebuild scheme where protein stability is knocked out through protein engineering, random mutagenesis is used to resurrect stability, and stable variants are selected through the powerful method of phage display coupled to proteolysis. The Cordes lab has previously identified a case suitable for such an investigation in the Cro protein family where two small DNA binding proteins, Xfaso 1 and P 6, occupy different folds yet retain high sequence identity. Previous work has identified deletion mutations which destroy the stability of the ancestral α-helical fold, but are also known to be compatible with the descendant β-sheet fold. Here, error prone PCR is presented as a possible method of resurrecting stability through random mutagenesis in Cro protein variants destabilized through these deletions. A protocol has been optimized for the production of mutant libraries of these genes Through EP-PCR. Test clones of these libraries into a prototype pCANTAB B phagemid vector for later phage display investigations have been successful, and sequencing has revealed that the implemented protocol yields an acceptable nucleotide substitution rate of 2.9%.
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Nielson, Joseph R. "Three Dimensional Characterization of Vocal Fold Fluid Structure Interactions." BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/3662.
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Voice quality is strongly linked to quality of life; those who suffer from voice disorders are adversely affected in their social, family, and professional relationships. An effort has been made to more fully understand the physics behind how the voice is created, specifically the fluid structure interactions that occur during vocal fold vibration. Many techniques have been developed and implemented to study both the motion of the vocal folds and the airflow that creates the motion. Until recently these techniques have sought to understand a highly three-dimensional phenomenon with 1D or 2D perspectives.This research focuses on the development and implementation of an experimental technique to obtain three-dimensional characterizations of vocal fold motion and fluid flow. Experiments were performed on excised human vocal fold models at the University Hospital Erlangen Medical School in Erlangen, Germany. A novel technique for tracking the motion of the vocal folds using multiple camera viewpoints and limited user interaction was developed. Four high-speed cameras (2000 fps) recorded an excised vocal fold model vibrating at 250 Hz. Based on the images from these four cameras a fully 3D reconstruction of the superior surface of the vocal folds was achieved. The 3D reconstruction of 70 consecutive time steps was assembled to characterize the motion of the vocal folds over eight cycles. The 3D reconstruction accurately modeled the observed behavior of vocal fold vibration with a clearly visible mucosal wave. The average reprojection error for this technique was on par with other contemporary techniques (~20 micrometers). A whole field, time resolved, three-dimensional reconstruction of the vocal fold fluid flow was obtained using synthetic aperture particle image velocimetry. Simultaneous 3D flow fields, subglottal pressure waves, and superior surface motion were presented for 2 consecutive cycles of oscillation. The vocal fold fluid flow and motion measurements correlated with behavior observed in previous three-dimensional studies. A higher resolution view of one full cycle of oscillation was compiled from 16 time resolved data sets via pressure data. The result was a full three-dimensional characterization of the evolution and disintegration of the glottal jet.
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Chappell, B. W. "Chemical evolution and origin of granites in the Lachlan Fold Belt." Thesis, Canberra, ACT : The Australian National University, 1990. http://hdl.handle.net/1885/139081.
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The author has been involved in studying the granites of the Lachlan Fold Belt (LFB) since
1963 with this being the main focus of his scientific studies since 1973. This thesis brings together
many of the publications that have arisen from that work and those 20 papers that are being
submitted for examination are listed in Section 1 (pp. 2-3) and are bound together at the back of this
volume. A complete list of the 114 publications for which this writer is an author is given in Section
10 (pp. 43-51). That list is comprehensive and again includes the 20 papers being examined. The
remaining 94 papers are listed in support of the candidacy. Among those other papers, 37 deal with
various aspects of granite studies, both in the LFB and elsewhere, and the remainder with a variety
of geological and geochemical subjects.
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Romero, Ryan Gregory. "Development and Analysis of 3D-Printed Synthetic Vocal Fold Models." BYU ScholarsArchive, 2019. https://scholarsarchive.byu.edu/etd/7727.
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Vocal fold models are valuable for studying voice production. They provide an alternative method of studying the mechanics of the voice that does not require in vivo experimentation or the use of excised human or animal tissue. In this thesis, a new method of creating vocal fold models through additive manufacturing is described. The purpose of this research was to reduce model fabrication time, to decrease the number of model failures during manufacturing, and to lay the foundation for creating models with more lifelike geometric and material properties. This research was conducted in four stages. First, a suitable silicone additive manufacturing technique using a UV-curable silicone was chosen. The technique chosen was called freeform reversible embedding (FRE) and involved embedding liquid silicone material into a gel-like medium named organogel. The UV-curable silicone's material properties were identified to confirm its utility in vocal fold model design. Second, an open-source, fused deposition modeling slicing software was selected to create g-code for the printer. Applicable software settings were tuned through qualitative printing tests to find their optimal values for use in FRE printing. Third, 3D-printed cubes were used in tensile tests to characterize the material properties of FRE-printed, silicone material. The cubes were found to be anisotropic, exhibiting different modulus values corresponding to the layer orientation of the printed material. Fourth, vocal fold models were FRE-printed in two different layer orientations and were used in phonation tests to gather data for onset pressure, vibratory frequency, amplitude, and flow rate. The printed models self-oscillated and withstood the strains induced by phonation. These tests showed that layer direction affects the phonation properties of the models, demonstrating that models with layers in the coronal plane had slightly lower frequencies and onset pressures than models with layers in the sagittal plane. The models' onset pressures were higher than what is found in human vocal folds. However, their frequencies were within a comparable range. These tests showed the effectiveness of additive manufacturing in the application of vocal fold fabrication, reducing production effort by allowing researchers to go directly from model design to fabrication in a single manufacturing step. It is anticipated that this method will be modified to incorporate printing of multiple stiffnesses of silicone to better mimic the material properties of vocal fold tissue, and that the anisotropy of 3D-printed material will be leveraged to model the anisotropy of human vocal folds. This work also has potential application areas outside of voice research.
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Bächtold, Michael Johannes. "Fold-type solution singularities and characteristic varieties of nonlinear PDEs /." [S.l.] : [s.n.], 2009. http://opac.nebis.ch/cgi-bin/showAbstract.pl?sys=000292630.
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Dillon, Matthew Lee. "Substitute teacher training and videotaped instruction : the two-fold intervention /." Full text available from ProQuest UM Digital Dissertations, 2008. http://0-proquest.umi.com.umiss.lib.olemiss.edu/pqdweb?index=0&did=1850440211&SrchMode=1&sid=1&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1278084170&clientId=22256.
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Thesis (Ph.D.)--University of Mississippi, 2008.Typescript. Vita. "July 2008." Advisor: Dr. Susan McClelland Includes bibliographical references (leaves 63-69). Also available online via ProQuest to authorized users.
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Levefelt, Christer. "A Fold Recognition Approach to Modeling of Structurally Variable Regions." Thesis, University of Skövde, School of Humanities and Informatics, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-902.
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A novel approach is proposed for modeling of structurally variable regions in proteins. In this approach, a prerequisite sequence-structure alignment is examined for regions where the target sequence is not covered by the structural template. These regions, extended with a number of residues from adjacent stem regions, are submitted to fold recognition. The alignments produced by fold recognition are integrated into the initial alignment to create a multiple alignment where gaps in the main structural template are covered by local structural templates. This multiple alignment is used to create a protein model by existing protein modeling techniques.
Several alternative parameters are evaluated using a set of ten proteins. One set of parameters is selected and evaluated using another set of 31 proteins. The most promising result is for loop regions not located at the C- or N-terminal of a protein, where the method produces an average RMSD 12% lower than the loop modeling provided with the program MODELLER. This improvement is shown to be statistically significant.
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Bon, Ramos Adriana. "QueF and QueF-like: Diverse Chemistries in a Common Fold." PDXScholar, 2016. http://pdxscholar.library.pdx.edu/open_access_etds/3101.
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The tunneling fold (T-Fold) superfamily is a small superfamily of enzymes found in organisms encompassing all kingdoms of life. Seven members have been identified thus far. Despite sharing a common three-dimensional structure these enzymes perform very diverse chemistries.
QueF is a bacterial NADPH-dependent oxidoreductase that catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ0) to a primary amine (preQ1) in the queuosine biosynthetic pathway. Previous work on this enzyme has revealed the mechanism of reaction but the cofactor binding residues remain unknown. The experiments discussed herein aim to elucidate the role of residues lysine 80, lysine 83, and arginine 125 (B. subtilis numbering) in NADPH binding. The biological role of the disulfide bond between the conserved residues cysteine 55 and cysteine 99 observed in several crystal structures is also examined.
Characterization of QueF mutants K80A, K83, R125A and R125K revealed lysine 80, lysine 83 and arginine 125 are required for turnover. Further analysis of turnover rates for R125K are consistent with this residue and both lysines being involved in cofactor binding presumably by interacting with the negatively charged phosphate tail of NADPH and are therefore involved in cofactor binding. Based on bond angles and energies, the disulfide bond between Cys55 and Cys99 was characterized as non-structural. Enzyme oxidation assays were consistent with the bond serving to protect QueF against irreversible oxidation of Cys55, which would render the enzyme inactive. This is the only known example of a stress protective mechanism in the Tunneling-fold superfamily.
QueF-like is an amidinotransferase found in some species of Crenarchaeota and involved in the biosynthesis of archaeosine-tRNA. The work presented here is focused on the preliminary characterization of this enzyme, including the elucidation of the natural substrate as well as the source of ammonia. The structure of the enzyme was solved and is also discussed.
Substrate analysis for QueF-like indicated this enzyme is capable of binding both preQ0 and preQ0-tRNA and reacting to form a thioimide intermediate analogous to QueF but only the latter serves as a substrate for the reaction. This makes QueF-like the first example of a nucleic acid binding enzyme in the Tunneling-fold superfamily. Ammonia, glutamine and asparagine were tested as nitrogen sources and unlike most known amidotransferases, QueF-like can only use free ammonia to produce the archaeosine-tRNA product. The crystal structure of P. calidifontis QueF-like indicates the functional enzyme is a dimer of pentamers pinned together by a large number of salt bridges. The structure presents a high degree of similarity to that of QueF albeit the higher twist of the QueF-like pentamers with respect to QueF results in a more compact structure.
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DiSantis, Nicholas E. "Rub, fold, and abrasion resistance testing of digitally printed documents /." Online version of thesis, 2007. http://hdl.handle.net/1850/4489.
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