Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection

The time passed since the infection of a human immunodeficiency virus (HIV)-infected individual (the age of infection) is an important but often only poorly known quantity. We assessed whether the fraction of ambiguous nucleotides obtained from bulk sequencing as done for genotypic resistance testing can serve as a proxy of this parameter.

Gene duplication: a drive for phenotypic diversity and cause of human disease

Gene duplication is one of the key factors driving genetic innovation, i.e., producing novel genetic variants. Although the contribution of whole-genome and segmental duplications to phenotypic diversity across species is widely appreciated, the phenotypic spectrum and potential pathogenicity of small-scale duplications in individual genomes are less well explored. This review discusses the nature of small-scale duplications and the phenotypes produced by such duplications. Phenotypic variation and disease phenotypes induced by duplications are more diverse and widespread than previously anticipated, and duplications are a major class of disease-related genomic variation. Pathogenic duplications particularly involve dosage-sensitive genes with both similar and dissimilar over- and underexpression phenotypes, and genes encoding proteins with a propensity to aggregate. Phenotypes related to human-specific copy number variation in genes regulating environmental responses and immunity are increasingly recognized. Small genomic duplications containing defense-related genes also contribute to complex common phenotypes.

Writing center handbooks and travel guidebooks : redesigning instructional texts for multicultural, multilingual, and multinational contexts

In an increasingly interconnected world characterized by the accelerating interplay of cultural, linguistic, and national difference, the ability to negotiate that difference in an equitable and ethical manner is a crucial skill for both individuals and larger social groups. This dissertation, Writing Center Handbooks and Travel Guidebooks: Redesigning Instructional Texts for Multicultural, Multilingual, and Multinational Contexts, considers how instructional texts that ostensibly support the negotiation of difference (i.e., accepting and learning from difference) actually promote the management of difference (i.e., rejecting, assimilating, and erasing difference). As a corrective to this focus on managing difference, chapter two constructs a theoretical framework that facilitates the redesign of handbooks, guidebooks, and similar instructional texts. This framework centers on reflexive design practices and is informed by literacy theory (Gee; New London Group; Street), social learning theory (Wenger), globalization theory (Nederveen Pieterse), and composition theory (Canagarajah; Horner and Trimbur; Lu; Matsuda; Pratt). By implementing reflexive design practices in the redesign of instructional texts, this dissertation argues that instructional texts can promote the negotiation of difference and a multicultural/multilingual sensibility that accounts for twenty-first century linguistic and cultural realities. Informed by the theoretical framework of chapter two, chapters three and four conduct a rhetorical analysis of two forms of instructional text that are representative of the larger genre: writing center coach handbooks and travel guidebooks to Hong Kong. This rhetorical analysis reveals how both forms of text employ rhetorical strategies that uphold dominant monolingual and monocultural assumptions. Alternative rhetorical strategies are then proposed that can be used to redesign these two forms of instructional texts in a manner that aligns with multicultural and multilingual assumptions. These chapters draw on the work of scholars in Writing Center Studies (Boquet and Lerner; Carino; DiPardo; Grimm; North; Severino) and Technical Communication (Barton and Barton; Dilger; Johnson; Kimball; Slack), respectively. Chapter five explores how the redesign of coach handbooks and travel guidebooks proposed in this dissertation can be conceptualized as a political act. Ultimately, this dissertation argues that instructional texts are powerful heuristic tools that can enact social change if they are redesigned to foster the negotiation of difference and to promote multicultural/multilingual world views.