Investigating the immunoglobulin repertoire is a means of understanding the adaptive immune response to infectious disease or vaccine challenge. The data examined are typically generated using high-throughput sequencing on samples of immunoglobulin variable-region genes present in blood or tissue collected from human or animal subjects. The analysis of these large, diverse collections provides a means of gaining insight into the specific molecular mechanisms involved in generating and maintaining a protective immune response. It involves the characterization of distinct clonal populations, specifically through the inference of founding alleles for germline gene segment recombination, as well as the lineage of accumulated mutations acquired during the development of each clone. Germline gene segment inference is currently performed by aligning immunoglobulin sequencing reads against an external reference database and assigning each read to the entry that provides the best score according to the metric used. The problem with this approach is that allelic diversity is greater than can be usefully accommodated in a static database. The absence of the alleles used from the database often leads to the misclassification of single-nucleotide polymorphisms as somatic mutations acquired during affinity maturation. This trend is especially evident with the rhesus macaque, but also affects the comparatively well-catalogued human databases, whose collections are biased towards samples from individuals of European descent. Our project presents novel statistical methods for immunoglobulin repertoire analysis which allow for the de novo inference of germline gene segment libraries directly from next-generation sequencing data, without the need for external reference databases. These methods follow a Bayesian paradigm, which uses an information-theoretic modelling approach to iteratively improve upon internal candidate gene segment libraries. Both candidate libraries and trial analyses given those libraries are incorporated as components of the machine learning evaluation procedure, allowing for the simultaneous optimization of model accuracy and simplicity. Finally, the proposed methods are evaluated using synthetic data designed to mimic known mechanisms for repertoire generation, with pre-designated parameters. We also apply these methods to known biological sources with unknown repertoire generation parameters, and conclude with a discussion on how this method can be used to identify potential novel alleles.

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Secondary choral directors often demonstrate a wide variety of organizational, instructional, and musical skills to promote and nurture thriving programs. Among the many tasks executed, choosing repertoire might be viewed as one of the most important duties performed. Material chosen for study is often the vehicle through which curricular concepts are taught. Multiple factors might influence middle school choral directors’ beliefs about repertoire choices. Ironically, repertoire choices might or might not reflect educators’ actual teaching philosophies; nevertheless, these decisions could influence student learning. This study surveyed a stratified random sampling of Texas middle school choral directors who participated in the 2010 University Interscholastic League Concert and Sight-reading competition (n = 209). Seventy middle school choral directors participated in the study. Each director took an online survey and indicated the degree to which they agreed or disagreed with 14 statements concerning repertoire choice. Many of the belief statements showed teachers were overwhelmingly in concordance with their beliefs (92.9%). Results indicated that beliefs were similar, regardless of who chose the curriculum or the amount of discussion perceived in undergraduate training. The only belief statement that continually showed differences between teachers concerned students’ ability to vote on repertoire.

Background: The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D) J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D) J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens. Characterization of immune repertoires is critical in both basic research and clinical contexts. Recent technological advances in repertoire profiling via high-throughput sequencing have resulted in an explosion of research activity in the field. This has been accompanied by a proliferation of software tools for analysis of repertoire sequencing data. Despite the widespread use of immune repertoire profiling and analysis software, there is currently no standardized format for output files from V(D) J analysis. Researchers utilize software such as IgBLAST and IMGT/High V-QUEST to perform V(D) J analysis and infer the structure of germline rearrangements. However, each of these software tools produces results in a different file format, and can annotate the same result using different labels. These differences make it challenging for users to perform additional downstream analyses. Results: To help address this problem, we propose a standardized file format for representing V(D) J analysis results. The proposed format, VDJML, provides a common standardized format for different V(D) J analysis applications to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format. Conclusions: The VDJML suite will allow users to streamline their V(D) J analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https:// vdjserver. org/ vdjml/. We welcome participation from the community in developing the file format standard, as well as code contributions.

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Master of Music / Department of Music / Steven Maxwell / This report is intended for teachers to use when preparing euphonium solo literature with their students. The solos selected for this report encompass a wide variety of styles and technical abilities, with each solo studied in four sections: Historical Background, Theoretical and Technical Considerations, Suggested Practice, and Educational Gains and Values. The solos studied in this report include Conqueror by Leonard B. Smith, In the Hall of the Mountain King by Edvard Grieg, Allerseelen by Richard Strauss, Pearl by H.A. Vandercook, Andante et Allegro by J. Ed. Barat, Andante et Allegro by J. Guy Ropartz, and Morceau Symphonique by Alexandre Guilmant.

In 1988 Bernardo Adam Ferrero's wind band composition Homenaje a Joaquín Sorolla was premiered at the International Wind Band Contest in Valencia, Spain. This relatively unknown wind band composition combines the elements of visual art and music to create a contemporary work for wind band using oil-canvas paintings of Valencian artist Joaquín Sorolla as the source of inspiration. In this document, the author discusses pertinent biographical information about the composer and the artist, and examines the wind band composition and the paintings through musical and visual analysis to evaluate Ferrero's musical interpretation of programmatic themes of the paintings. Through analysis of the craftsmanship of this composition and its connection to the visual arts, the author advocates for Homenaje a Joaquín Sorolla’s inclusion in the core wind band repertoire.

Magister Artium - MA / Globalization has evidently led to an increase in the flow of immigrants across the world, a fact that has and continues to play a significant role in the development of studies on immigration, immigration patterns and the psycho-social struggles that immigrants face; of which identity negotiation in the new context is included. A number of works have been done on the identity negotiation and identity-forming process of immigrant youth. This study attempts to highlight, rather specifically, the unique challenges that 1.5 generation immigrant youth have in forming their identities. Rumbaut coined the term “one-and-a-half generation” to describe “children of Cuban exiles who were born in Cuba but have come of age in the United States” (1976:8). Thus the 1.5 generation immigrant youth constitutes children who were born in their country of origin but was raised and received the education and important experiences in the host country. Hence, the issue of identity becomes important for adolescents such as the 1.5 generation growing up in Diasporic settings. How they come to define who they are, their place in the world and others’ perception of them have significant implications for their successful integration into their new societies (Ogbuagu, 2013). This study takes a socio-cultural approach to investigating the identity negotiation and construction of 1.5 generation Congolese immigrant youth. Sociocultural linguistics refers to an interdisciplinary field which considers language as a sociocultural phenomenon; hence positioning identity as a phenomenon that is socially constructed through language and hence, performed within interaction and conversations.

A atualidade é marcada pela velocidade de informações e maior contato social promovido pela facilidade e acessibilidade das mídias digitais e pela influência considerável na criatividade dos alunos de cursos superiores em moda. A construção do conjunto de conhecimentos para o processo criativo na área de moda é o tema abordado nesta pesquisa e objetiva colher dados de quais informações os estudantes acessam e como lidam com esse processo a fim de construírem seu repertório para a pesquisa. Para isso foram feitas análises bibliográficas dos processos de criação em artes, design e moda; da influência das mídias digitais; e do estudo de caso dos alunos de Design de Moda da UTFPR-Apucarana. Este trabalho visa contribuir para o processo de criação e consequentemente o desenvolvimento de produto de moda inovador. / Today is considerably marked by the speed of information and greater social contact promoted by the facility and accessibility of the digital media and the considerable influence on the creativity of students of higher education courses in fashion. The construction of the set of knowledge for the creative process in fashion, is the topic of this research and aims to collect data from which students access information and how to deal with this process in order to build their repertoire for research. Through bibliographic analysis of the creation processes in arts, design and fashion, the influence of digital media and the case study of students of Fashion Design UTFPR-of Apucarana. This work aims to contribute to the process of creation and consequently the product development of innovative fashion.

Performance of repertoire is a defining curricular aspect in the band area of music education, upon which students will spend significant time. The act of repertoire selection is a potentially complicated one, carrying the norms, values, and beliefs of the overall band area and band directors themselves. A band director’s personal ensemble experience is steeped in aesthetic traditions and canonical notions of repertoire’s quality and its use in band settings, and these notions may be incompatible with highly varied teaching situations. In this study, I examine these issues using Bourdieu’s concepts of habitus and field. The research questions were: is there a tension between the established norms (habitus) regarding the repertoire used in public schools, and practicing band directors’ professional contextual realities? If so, what is the cause of the tension, what do band directors do in response to it, and is the experience or non-experience of tension manifested differently in distinct professional contextual realities? I used a multi-method design to answer the research questions, collecting survey and interview data. Survey participants were randomly sampled from across New York State. The interview participants were purposefully sampled for variation in teaching situations. The data revealed that a tension exists and is manifested in elemental/structural issues and differences in expressed musical/educational goals. Consistent themes were the influence of collegiate ensemble experiences as main drivers of the tension and a resulting expressed reverence for core repertoire, even though it might not be what participants program. These phenomena did not appear to manifest differently across varied contexts. In addressing the tension, participants expand their habitus to include other repertoire that is more suitable or appropriate for their own situations, regardless of normative notions of quality or core repertoire. Music educators may benefit from a reorientation in teacher education programs that acknowledges the potential for this tension and that prepare them to enter their professional contextual realities and evaluate and choose repertoire in a tension-free process. Such a process would be free from a “one size fits all” conceptualization of repertoire’s quality and its role in a band program. Keywords: band, repertoire selection, tension, Bourdieu, habitus, field, hermeneutic phenomenology.