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Description
Genomic and proteomic sequences, which are in the form of deoxyribonucleic acid (DNA) and amino acids respectively, play a vital role in the structure, function and diversity of every living cell. As a result, various genomic and proteomic sequence processing methods have been proposed from diverse disciplines, including biology, chemistry,

Genomic and proteomic sequences, which are in the form of deoxyribonucleic acid (DNA) and amino acids respectively, play a vital role in the structure, function and diversity of every living cell. As a result, various genomic and proteomic sequence processing methods have been proposed from diverse disciplines, including biology, chemistry, physics, computer science and electrical engineering. In particular, signal processing techniques were applied to the problems of sequence querying and alignment, that compare and classify regions of similarity in the sequences based on their composition. However, although current approaches obtain results that can be attributed to key biological properties, they require pre-processing and lack robustness to sequence repetitions. In addition, these approaches do not provide much support for efficiently querying sub-sequences, a process that is essential for tracking localized database matches. In this work, a query-based alignment method for biological sequences that maps sequences to time-domain waveforms before processing the waveforms for alignment in the time-frequency plane is first proposed. The mapping uses waveforms, such as time-domain Gaussian functions, with unique sequence representations in the time-frequency plane. The proposed alignment method employs a robust querying algorithm that utilizes a time-frequency signal expansion whose basis function is matched to the basic waveform in the mapped sequences. The resulting WAVEQuery approach is demonstrated for both DNA and protein sequences using the matching pursuit decomposition as the signal basis expansion. The alignment localization of WAVEQuery is specifically evaluated over repetitive database segments, and operable in real-time without pre-processing. It is demonstrated that WAVEQuery significantly outperforms the biological sequence alignment method BLAST for queries with repetitive segments for DNA sequences. A generalized version of the WAVEQuery approach with the metaplectic transform is also described for protein sequence structure prediction. For protein alignment, it is often necessary to not only compare the one-dimensional (1-D) primary sequence structure but also the secondary and tertiary three-dimensional (3-D) space structures. This is done after considering the conformations in the 3-D space due to the degrees of freedom of these structures. As a result, a novel directionality based 3-D waveform mapping for the 3-D protein structures is also proposed and it is used to compare protein structures using a matched filter approach. By incorporating a 3-D time axis, a highly-localized Gaussian-windowed chirp waveform is defined, and the amino acid information is mapped to the chirp parameters that are then directly used to obtain directionality in the 3-D space. This mapping is unique in that additional characteristic protein information such as hydrophobicity, that relates the sequence with the structure, can be added as another representation parameter. The additional parameter helps tracking similarities over local segments of the structure, this enabling classification of distantly related proteins which have partial structural similarities. This approach is successfully tested for pairwise alignments over full length structures, alignments over multiple structures to form a phylogenetic trees, and also alignments over local segments. Also, basic classification over protein structural classes using directional descriptors for the protein structure is performed.
ContributorsRavichandran, Lakshminarayan (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Spanias, Andreas S (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Lacroix, Zoé (Committee member) / Arizona State University (Publisher)
Created2011
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Description
The study of acoustic ecology is concerned with the manner in which life interacts with its environment as mediated through sound. As such, a central focus is that of the soundscape: the acoustic environment as perceived by a listener. This dissertation examines the application of several computational tools in the

The study of acoustic ecology is concerned with the manner in which life interacts with its environment as mediated through sound. As such, a central focus is that of the soundscape: the acoustic environment as perceived by a listener. This dissertation examines the application of several computational tools in the realms of digital signal processing, multimedia information retrieval, and computer music synthesis to the analysis of the soundscape. Namely, these tools include a) an open source software library, Sirens, which can be used for the segmentation of long environmental field recordings into individual sonic events and compare these events in terms of acoustic content, b) a graph-based retrieval system that can use these measures of acoustic similarity and measures of semantic similarity using the lexical database WordNet to perform both text-based retrieval and automatic annotation of environmental sounds, and c) new techniques for the dynamic, realtime parametric morphing of multiple field recordings, informed by the geographic paths along which they were recorded.
ContributorsMechtley, Brandon Michael (Author) / Spanias, Andreas S (Thesis advisor) / Sundaram, Hari (Thesis advisor) / Cook, Perry R. (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Digital sound synthesis allows the creation of a great variety of sounds. Focusing on interesting or ecologically valid sounds for music, simulation, aesthetics, or other purposes limits the otherwise vast digital audio palette. Tools for creating such sounds vary from arbitrary methods of altering recordings to precise simulations of vibrating

Digital sound synthesis allows the creation of a great variety of sounds. Focusing on interesting or ecologically valid sounds for music, simulation, aesthetics, or other purposes limits the otherwise vast digital audio palette. Tools for creating such sounds vary from arbitrary methods of altering recordings to precise simulations of vibrating objects. In this work, methods of sound synthesis by re-sonification are considered. Re-sonification, herein, refers to the general process of analyzing, possibly transforming, and resynthesizing or reusing recorded sounds in meaningful ways, to convey information. Applied to soundscapes, re-sonification is presented as a means of conveying activity within an environment. Applied to the sounds of objects, this work examines modeling the perception of objects as well as their physical properties and the ability to simulate interactive events with such objects. To create soundscapes to re-sonify geographic environments, a method of automated soundscape design is presented. Using recorded sounds that are classified based on acoustic, social, semantic, and geographic information, this method produces stochastically generated soundscapes to re-sonify selected geographic areas. Drawing on prior knowledge, local sounds and those deemed similar comprise a locale's soundscape. In the context of re-sonifying events, this work examines processes for modeling and estimating the excitations of sounding objects. These include plucking, striking, rubbing, and any interaction that imparts energy into a system, affecting the resultant sound. A method of estimating a linear system's input, constrained to a signal-subspace, is presented and applied toward improving the estimation of percussive excitations for re-sonification. To work toward robust recording-based modeling and re-sonification of objects, new implementations of banded waveguide (BWG) models are proposed for object modeling and sound synthesis. Previous implementations of BWGs use arbitrary model parameters and may produce a range of simulations that do not match digital waveguide or modal models of the same design. Subject to linear excitations, some models proposed here behave identically to other equivalently designed physical models. Under nonlinear interactions, such as bowing, many of the proposed implementations exhibit improvements in the attack characteristics of synthesized sounds.
ContributorsFink, Alex M (Author) / Spanias, Andreas S (Thesis advisor) / Cook, Perry R. (Committee member) / Turaga, Pavan (Committee member) / Tsakalis, Konstantinos (Committee member) / Arizona State University (Publisher)
Created2013
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Description
E-Strings Academy (www.estringsacademy.wordpress.com) is a resource website intended for the beginning violinist, violist, cellist, and bassist. The mission of the website is to extend musical learning opportunities to students outside of the physical string classroom and to engage first-year string students in musical activities at home that supplement the instruction

E-Strings Academy (www.estringsacademy.wordpress.com) is a resource website intended for the beginning violinist, violist, cellist, and bassist. The mission of the website is to extend musical learning opportunities to students outside of the physical string classroom and to engage first-year string students in musical activities at home that supplement the instruction they receive in a school setting. The current website features five different areas for students to explore: lesson videos, tunes, listening activities, games, and resources. In each area, students have the opportunity to learn and reinforce musical concepts and skill sets that they will need in order to be successful in music, both in their first year of playing and beyond. I created E-Strings Academy with the intention that I use it with my own string students in my future teaching career. It is a flexible website that I will continue to revise, adapt, and enhance to best serve the needs of my students and enrich their musical learning outside of the classroom.
ContributorsCook, Christa Marie (Author) / Schmidt, Margaret (Thesis director) / Tobias, Evan (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor)
Created2015-05
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Description
Jamaican folk music is categorized into three large genres, which may be broken down into smaller more specific subgenres. Work and Social Music (which includes Work Songs, Mento Music, and Social Music), Recreational Music, and Ritual and Ceremonial Music. Rastafarianism, although it is a manifestation of ritual music, is given

Jamaican folk music is categorized into three large genres, which may be broken down into smaller more specific subgenres. Work and Social Music (which includes Work Songs, Mento Music, and Social Music), Recreational Music, and Ritual and Ceremonial Music. Rastafarianism, although it is a manifestation of ritual music, is given its own section due to the large amount of information available on the subject. Included here are historical analysis of the genres, as well as musical examples. Eight folk songs are included, and four drum patterns. This paper is intended as a resource for music educators, and therefore each song includes a Quick Reference Page, which lists solfege, rhythmic motives, genre of song, and if applicable drum rhythms which may be used to accompany the song. In addition, each song includes specific information regarding appropriate performance practice and suggestions for use in the classroom.
ContributorsVillarreal, Alicia Raquel (Author) / Stauffer, Sandra (Thesis director) / Schmidt, Margaret (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor)
Created2015-05
Description
"EP \u2014 Kyan Palmer" is a compilation of three songs, "Hit List," "Queen Cobra," and "Burn Mona Lisa" all written and recorded by Barrett student, Kyan Palmer. The project explores the process involved in creating recorded music and exposes the vulnerability and self-reflection in writing a song. The following depicts

"EP \u2014 Kyan Palmer" is a compilation of three songs, "Hit List," "Queen Cobra," and "Burn Mona Lisa" all written and recorded by Barrett student, Kyan Palmer. The project explores the process involved in creating recorded music and exposes the vulnerability and self-reflection in writing a song. The following depicts the thought process that came about in the creation of each song from the lyrics, to the vocals, to the production. This paper depicts a journal-like writing style outlining the various events that took place while creating EP \u2014 Kyan Palmer. The bulk of this Thesis/Creative Project was the written, produced, and recorded music attached in the appendix. With that said, the following document is intended to be reflective rather than scholarly and acts as an accompaniment to the audio recordings and video entries.
ContributorsPalmer, Kyan (Author) / Swoboda, Deanna (Thesis director) / Tobias, Evan (Committee member) / W. P. Carey School of Business (Contributor) / School of Music (Contributor) / Department of Marketing (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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Description
Rainbow Connection is an integrated choir with members on and off the autism spectrum. It was founded in the spring of 2012 by Barrett students Ali Friedman, Megan Howell, and Victoria Gilman as part of an honors thesis creative project. Rainbow Connection uses the rehearsal process and other creative endeavors

Rainbow Connection is an integrated choir with members on and off the autism spectrum. It was founded in the spring of 2012 by Barrett students Ali Friedman, Megan Howell, and Victoria Gilman as part of an honors thesis creative project. Rainbow Connection uses the rehearsal process and other creative endeavors to foster natural relationship building across social gaps. A process-oriented choir, Rainbow Connection's main goals concern the connections made throughout the experience rather than the final musical product. The authors believe that individual, non-hierarchical relationships are the keys to breaking down systemized gaps between identity groups and that music is an ideal facilitator for fostering such relationships. Rainbow Connection operates under the premise that, like colors in a rainbow, choir members create something beautiful not by melding into one homogenous group, but by collaboratively showcasing their individual gifts. This paper will highlight the basic premise and structure of Rainbow Connection, outline the process of enacting the choir, and describe the authors' personal reactions and takeaways from the project.
ContributorsFriedman, Alexandra (Co-author) / Gilman, Victoria (Co-author) / Howell, Megan (Co-author) / Rio, Robin (Thesis director) / Schildkret, David (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2014-12
Description
Only in the world of acting can an individual be denied a job simply on the basis of their appearance, and in my thesis, I sought to explore alternatives to this through the concept of nontraditional casting and casting against "type", which included the presentation of a full-length production of

Only in the world of acting can an individual be denied a job simply on the basis of their appearance, and in my thesis, I sought to explore alternatives to this through the concept of nontraditional casting and casting against "type", which included the presentation of a full-length production of the musical "Once on this Island" which I attempted to cast based on vocal quality and skill alone rather than taking physical characteristics into account. I researched the history and implementation of nontraditional casting, both in regards to race and other factors such as gender, socio-economic status, and disability. I also considered the legal and intellectual property challenges that nontraditional casting can pose. I concluded from this research that while nontraditional casting is only one solution to the problem, it still has a great deal of potential to create diversity in theater. For my own show, I held the initial auditions via audio recording, though the callback auditions were held in person so that I and my crew could appraise dance and acting ability. Though there were many challenges with our cast after this initial round of auditions, we were able to solidify our cast and continue through the rehearsal process. All things said, the show was very successful. It is my hope that those who were a part of the show, either as part of the production or the audience, are inspired to challenge the concept of typecasting in contemporary theater.
ContributorsBriggs, Timothy James (Author) / Yatso, Toby (Thesis director) / Dreyfoos, Dale (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor)
Created2014-12
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Description
This project creates a possible framework for the application of music therapy to reduce test anxiety in students. Although music therapy has grown in recent years as a treatment method for a variety of mental health and wellness problems, it has yet to be comprehensively applied to the specific issue

This project creates a possible framework for the application of music therapy to reduce test anxiety in students. Although music therapy has grown in recent years as a treatment method for a variety of mental health and wellness problems, it has yet to be comprehensively applied to the specific issue of test anxiety. Some studies have examined the use of music in testing situations in order to reduce anxiety or improve academic performance. However, more in-depth music therapy interventions are a promising, largely untried treatment possibility for students suffering from this type of anxiety.
ContributorsCowan, Sarah Elizabeth (Author) / Crowe, Barbara (Thesis director) / Rio, Robin (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor) / School of International Letters and Cultures (Contributor)
Created2014-12
Description
The music business has constantly evolved since its inception. Sheet music was the first physical form of music sold and was influenced by innovations in printing technology. Recorded music came about in the late 1800s and early 1900s, with Thomas Edison pioneering the phonograph record. Technology shifted from records to

The music business has constantly evolved since its inception. Sheet music was the first physical form of music sold and was influenced by innovations in printing technology. Recorded music came about in the late 1800s and early 1900s, with Thomas Edison pioneering the phonograph record. Technology shifted from records to 8-tracks to cassettes, and finally, digital audio, which revolutionized the entire industry. Compact discs (CDs) skyrocketed in popularity during the 1990s and early 2000s, but so did file-sharing. To combat piracy, record labels began selling and streaming music online. Music sales have plummeted in all formats. Streaming reigns as the most popular form of music distribution, but it produces a mere fraction of the revenue traditional albums once did. The loss affects all those in the industry, especially the artists, who see an average of only $23.40 for every $1000 in music sold. But technology has allowed the independent artist to record and distribute their music to the world for little cost compared to their major label predecessors. Many wonder if the music industry is dead, but as with any other technological change in history, the adaptors and innovators will survive.
ContributorsDamiano, Alec (Author) / Swoboda, Deanna (Thesis director) / Whyte, Rutger (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor) / Walter Cronkite School of Journalism and Mass Communication (Contributor)
Created2015-05