TWENTY-FIVE YEARS OF SCHOLARSHIP ON SECOND LANGUAGE COMPOSING PROCESSES: 1976-2000

This work is divided into two sections: (1) an annotated bibliography of full-length, published, (mostly) basic research on second language writing and overviews thereof, and (2) an unannotated bibliography of both basic and applied research (mostly unpublished) and commentary on second language composing. Both sections have been arranged in chronological order to allow readers to follow the development of scholarship in this area. Entries are listed alphabetically within a given year. While this bibliography is extensive, it is not meant to be exhaustive, and while the focus here is on research, many of the studies included address pedagogical matters in a substantive manner

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

The trans-ancestral genomic architecture of glycemic traits

Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 x 10(-8)), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution. A trans-ancestry meta-analysis of GWAS of glycemic traits in up to 281,416 individuals identifies 99 novel loci, of which one quarter was found due to the multi-ancestry approach, which also improves fine-mapping of credible variant sets.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

publication en ligne. Article dans revue scientifique avec comité de lecture. nationale.National audienceThe human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

ESL writing in twentieth-century United States higher education: The formation of an interdisciplinary field

The number of second language writers in US higher education has been increasing continuously during the latter half of the 20th century. Today, there are over 480,000 international students, the majority of whom come from countries where English is not the dominant language. In addition, there is an equally significant number of permanent residents and refugees as well as native-born and naturalized citizens of the United States who grew up speaking languages other than English at home and in their communities. Thus, it is becoming increasingly likely that writing teachers at one point or another in their career will encounter ESL writers in their classrooms. While ESL students are similar in many ways to native-English-speaking writers, there also are many significant differences that make working with these students challenging for writing teachers. Yet, the preparation of writing teachers generally does not include the teaching of writing to ESL writers, and composition theory and research, for the most part, continue to be uninformed about the needs and characteristics of second language writers and writing. The lack of attention to second language writing issues in composition studies, I argue, is related to how those issues have been positioned in relation to two closely related intellectual formations: composition studies and second language studies—or more specifically, Teaching English as a Second Language (TESL). To construct a view of the interdisciplinary relationship that is conducive to meeting the needs of second language writers, this study investigates the historical development of second language writing issues in 20th-century US higher education. In addition to constructing an identity for the field of second language writing as a site of disciplinary and instructional practices, this study contributes an understanding of the historical context in which second language writing theory and pedagogy have developed, thus providing a basis for the critique of existing disciplinary and instructional practices. The first dissertation-length examination of the history of second language writing, this study also contributes historical insights into second language issues in composition studies and writing issues in second language studies

Reading an ESL Writer’s Text

This paper focuses on reading as a central act of communication in the tutorial session. Writing center tutors without extensive experience reading writing by second language writers may have difficulty getting past the many differences in surface-level features, organization, and rhetorical moves. After exploring some of the sources of these differences in writing, the authors present strategies that writing tutors can use to work effectively with second language writers

Considering the Impact of the WPA Outcomes Statement on Second Language Writers

Book chapter on considerations on the impact of the Council of Writing Program Administrators (WPA) Outcomes Statement (OS) on second language writers. This chapter examines the extent to which the WPA OS reflects (or does not reflect) the presence and needs of second language writers

Exploring Composition Studies Sites, Issues, Perspectives

Intro -- Contents -- Foreword: Defining Composition Studies . . . Again, and Again - Andrea A. Lunsford -- Introduction: How Did We Get Here? - Kelly Ritter and Paul Kei Matsuda -- I: The State of the Field(s) -- 1. Creation Myths and Flash Points: Understanding Basic Writing through Conflicted Stories - Linda Adler-Kassner and Susanmarie Harrington -- 2. Teaching Composition in the Multilingual World: Second Language Writing in Composition Studies - Paul Kei Matsuda -- 3. Remapping Professional Writing: Articulating the State of the Art and Composition Studies - Tim Peeples and Bill Hart-Davidson -- 4. Writing Center Scholarship: A "Big Cross-Disciplinary Tent" - Lauren Fitzgerald -- 5. WAC's Disappearing Act - Rita Malenczyk -- 6. Scholarly Positions in Writing Program Administration - Jeanne Gunner -- II: Innovations, Advancements, and Methodologies -- 7. Reimagining the Nature of FYC Trends in Writing-about-Writing Pedagogies - Doug Downs and Elizabeth Wardle -- 8. Transfer, Portability, Generalization: (How) Does Composition Expertise "Carry"? - Christiane Donahue -- 9. Writing Assessment in the Early Twenty-first Century: A Primer - Kathleen Blake Yancey -- 10. Studying Literacy in Digital Contexts: Computers and Composition Studies - Gail E. Hawisher and Cynthia L. Selfe -- 11. "What Goes On Here?": The Uses of Ethnography in Composition Studies - Elizabeth Chiseri-Strater -- 12. Archival Research in the Field of Rhetoric and Composition - Barbara L'Eplattenier and Lisa S. Mastrangelo -- 13. Writing Pedagogy Education: Instructor Development in Composition Studies - Heidi Estrem and E. Shelley Reid -- Afterword: Redefining the Ineffable -- Or, Creating Scholarly Presence and a Usable Future: An Editor's Perspective - Deborah H. Holdstein -- Works Cited -- Index -- About the AuthorsDescription based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries

Second Language Writing Research Perspectives on the Process of Knowledge Construction

This book consists of original chapters on various methodological issues in second language writing research.Cover -- Half Title -- Title Page -- Copyright Page -- Dedication -- Table of Contents -- Preface -- I. Research as Situated Knowledge Construction -- 1. On the Philosophical Bases of Inquiry in Second Language Writing: Metaphysics, Inquiry Paradigms, and the Intellectual Zeitgeist -- From Practice to Theory -- The Philosophical Tradition -- Ideology -- Inquiry Paradigms -- Types of Inquiry -- Types of Empirical Designs -- Multimodal Inquiry -- The Intellectual Zeitgeist -- Conclusion -- References -- 2. Uses of Narrative in L2 Writing Research -- The Role of Narrative in Structuring and Interpreting Experience -- Narrative in L2 Writing Research -- Metadisciplinary Narratives (The Stories of the Field) -- Narrative Inquiry as a Research Approach -- Reports of Research as Narrative -- Narratives as Data -- Pedagogical Narratives -- Conclusion -- References -- 3. Historical Inquiry in Second Language Writing -- Historical Inquiry in Second Language Studies -- The Making of a Disciplinary History -- Toward Communal Dialectic -- References -- II. Conceptualizing L2 Writing Research -- 4. Situated Qualitative Research and Second Language Writing -- Defining Situated Qualitative Research -- The Study: Textual Ownership in a College Context in India -- Conclusion: Doing the Impossible -- References -- 5. A Multimethod Approach to Research Into Processes of Scholarly Writing for Publication -- Background of the Research -- Specific Research Objectives -- The Research Outputs -- The Quantitative Survey -- The Qualitative In-Depth Interview Study -- The Editors' Interview Paper -- The NNES Writer Case Study Paper -- Textual Analysis -- Conclusion -- Acknowledgments -- References -- 6. Hypothesis Generation and Hypothesis Testing: Two Complementary Studies of EFL Writing Processes -- Sasaki (2000): An Exploratory Study -- Preparatory Steps -- A Pilot StudyConducting Sasaki (2000) -- Results of Sasaki (2000) -- Getting Sasaki (2000) Published -- Sasaki (2002): A Confirmatory Study -- Preparatory Steps -- Conducting Sasaki (2002) -- Getting Sasaki (2002) Published -- Questions for Further Studies -- References -- 7. Talking About Writing: Cross-Modality Research and Second Language Speaking/Writing Connections -- Types of Cross-Modality Studies -- Problems in Cross-Modality Research -- Sociocultural Theory and the L2 Speech/Writing Connection -- Conclusion -- References -- 8. Researching Teacher Evaluation of Second Language Writing via Prototype Theory -- Part I: How Big Testing Operations Categorize Essay Writing Skills -- Part II: How Researchers and Teachers might Categorize Essay Writing Skills -- References -- 9. Composing Culture in a Fragmented World: The Issue of Representation in Cross-Cultural Research -- References -- III. Collecting and Analyzing Data -- 10. Qualitative Research as Heuristic: Investigating Documentation Practices in a Medical Setting -- Target Study: Appropriation of Professional Writing Skills in a Medical Setting -- Issue 1: Emergent Design: Navigating Through the Funnel -- Target Study: Appropriation of Professional Writing Skills -- Issue 2: Representativeness of Data -- Target Study: Appropriation of Professional Writing Skills -- Issue 3: Researcher Stance and the Role of Theory -- Target Study: Appropriation of Professional Writing Skills -- Conclusion -- References -- 11. Mucking Around in the Lives of Others: Reflections on Qualitative Research -- Choices -- Match Between Researcher and Research Approach -- Positives -- Negatives -- Composition, not Literacy -- Literacy, not Composition -- Bad News -- Conclusion -- References -- 12. Coding Data in Qualitative Research on L2 Writing: Issues and Implications -- The Study and its Underpinnings -- The Coding ProcessCoding Scheme 1: Parse Before You Pigeonhole -- Coding Scheme 2: Categorize In Order To Unitize -- Establishing the Reliability of Coding Scheme 2 -- Problem 1: I Know More Than My Peer Rater Does -- Problem 2: I am More Attuned to Participants' Language Use than my Peer Coder -- Discussion: The Relationship Between Coding and Dependability, Reconfigured -- References -- 13. Digging Up Texts and Transcripts: Confessions of a Discourse Analyst -- Framing the Issue -- Selecting Methods -- The Text Data -- The Interview Data -- Some Thoughts on Analysis -- Conclusions -- References -- 14. Using Concurrent Protocols to Explore L2 Writing Processes: Methodological Issues in the Collection and Analysis of Data -- Data-Collection Procedures -- The Rationale Behind the Choice of Concurrent Protocols -- The Writing Tasks -- Order of Tasks and Practice Effect -- The Retrospective Questionnaires -- Preparing the Data for Coding/Analysis: The Transcriptions of Protocols -- Data Analysis: Setting Up the Coding Scheme -- Deciding What Part of the Protocols Is Going to Be Subjected to Analysis -- Establishing the Categories and Setting up the Coding Scheme -- Conclusion -- References -- 15. Taking on English Writing in a Bilingual Program: Revisiting, Reexamining, Reconceptualizing the Data -- The Original Study -- Forays into English and Additional Questions -- Ten Years Later: Revisioning the Study Through New Perspectives -- Research Questions -- Data-Collection Methods -- Our Interpretations -- Conclusions -- References -- IV. Coda -- 16. Tricks of the Trade: The Nuts and Bolts of L2 Writing Research -- Background: My Own Research Experience -- What I Have Learned: Nuts and Bolts -- Identifying a Focus for Research -- Selecting Research Paradigms -- Disseminating Research -- Obtaining Research Support -- Working CollaborativelySummary: If I Can Do It, Anyone Can -- References -- Contributors -- Author Index -- Subject IndexThis book consists of original chapters on various methodological issues in second language writing research.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries