bluuebunny/crossref_metadata_2025 huggingface dataset:
Poverty, Literacy, and Politics: Living in the USA
Authors: Shannon Patrick
Published: December 2009

The following article by Patrick Shannon is the second installment of a three-part series on literacy and educational policy in jlr's Critical Issues section. Previously (Volume 23, Number 2), Judith Green with Carol Dixon, David Pearson, and Sharon Quint commented respectively on the ideas they believed to be crucial for policymakers to know about literacy, from their view as literacy researchers. At the same time, we published Donna Alvermann's reaction to the views of the three researchers. Patrick Shannon now addresses how poverty and social disadvantages relate to literacy research and policy issues. In the next issue of jlr (Volume 23, Number 4), we will publish the comments of several high-ranking policymakers who have been asked to respond to the literacy researchers' views on literacy and educational policy.

We hope that this series of “Critical Issues” pieces will stimulate increased dialogue about educational policy among researchers interested in literacy and between researchers and policymakers. Toward that end, we encourage readers to ponder the perspectives and ideas presented in this series and to consider adding their own insights by submitting letters to the editor, which will be considered for publication.
The Children's Literature Hour: A Social-Constructivist Approach to Family Literacy
Authors: Neuman Susan B. , Celano Donna , Fischer Robyn
Published: December 2009

Pursued from a social-constructivist perspective, this study reports the results of a series of peer group discussions with adolescent parents enrolled in a family literacy program. The purpose of these discussions was to provide opportunities for learners to critically reflect on their goals and their literacy strengths and needs, as well as their needs for their children. We engaged a total of 18 adolescent mothers in 1-hour discussion sessions of multicultural children's literature books. Analysis of the conversations indicated that literacy was seen as important because it served as a tool to address economic and social concerns. Parents' goals for themselves focused on independence, being a role model to their children, and self-respect. For their children, they wished to convey a sense of cultural pride, independence from peer pressure, and a “gift of childhood.” The social aspects of the discussions seemed to strengthen and expand the possibilities for meaningful interaction between parents, creating a space for discourses which included their shared realities. It is suggested that family literacy programs should build on these issues and be context specific, working collaboratively with participants to create new visions that challenge the status quo.
Assessing Adult Literacy by Telephone
Authors: Sticht Thomas G. , Hofstetter C. Richard , Hofstetter Carolyn H.
Published: December 2009

Several industrialized nations have conducted expensive door-to-door surveys of adult literacy. Following a critique of the role of knowledge in literacy, the research presented here examined the construct and action validity of the use of simple checklists to assess the declarative knowledge component of adult's literacy by telephone. Significant relationships were found among knowledge when assessed either by listening (telephone) or by reading (mailed questionnaire) modality. The telephone data showed similar relationships to demographic variables that have been found in the 1993 National Adult Literacy Survey and other literacy surveys during the last half-century. It was concluded that the telephone method may provide a valid, cost-effective alternative to door-to-door assessments of literacy.
A Study of the Spelling Development of Adult Literacy Learners Compared with That of Classroom Children
Authors: Viise Neva M.
Published: December 2009

This study compared the spelling development of 195 child and 124 adult literacy learners through a comparison of spelling errors. These errors occurred across 24 word features, which included examples of phonetic patterns, visual patterns, and word relationships ranging from beginning consonant sound (dig) to root constancy matches such as the vowel in accented and unaccented syllables (compete/competition). The order of mastery of the 24 spelling features examined was assessed through the Guttman scale analysis. This analysis indicated a similar developmental pattern occurring in both child and adult spellers especially at the early spelling levels. The differences that occurred in the two groups showed the adults better at identifying visual patterns and understanding some word concepts. They fell behind the children in their correct representation of certain phonetic features because of a tendency to depart from the phonics of the word in their spellings. However, because the adults showed no tendency to skip or shortcut the developmental pattern, it lends support to the theory that adult spelling acquisition, like that of children, needs careful assessment as an essential part of the instructional process.
Prediction of Reading Ability: A Cross-Validation Study of the Simple View of Reading
Authors: Chen Ru San , Vellutino Frank R.
Published: December 2009

The Simple View of Reading, as originally articulated by Gough and Tunmer (1986), proposes that reading comprehension ability can be predicted by the product term of two components: decoding and listening comprehension (R = D × L). Based on a longitudinal study evaluating developmental reading in bilingual children, Hoover and Gough (1990) reported results providing initial support for the model. The present study attempted to cross-validate the Simple View of Reading using a sample of children with English as their first language. Results support the idea that reading comprehension ability can be decomposed into decoding and listening comprehension abilities, but they do not support the assumption that all or most of the substantive variance in reading comprehension can be explained by the multiplicative combination of decoding and listening comprehension. They do, however, support a more complicated version of the model, which requires the inclusion of both the linear and the product terms in predicting reading comprehension from decoding and language comprehension (R = D + L + D × L).
Investigating the Processes of Reading-to-Assess among Dutch Legislators
Authors: Neutelings Rob , Maat Henk Pander
Published: December 2009

This study investigated the reading of policy documents by Dutch legislators. Its first aim was to investigate reading-to-assess processes using methods that address the limitations of previous studies. Its second aim was to analyze the reading-to-assess processes of the legislators to extend existing models and theories of reading in professional contexts. Data were gathered from 8 Dutch legislators who thought aloud while reading a policy document. Three methods of data analysis were employed: analyses of information-seeking behaviors, cognitive processes, and reading goals. Results indicated that the legislators read efficiently, focusing on relatively small portions of the policy documents in a nonlinear fashion, and that their processing of the text was devoted to elaborating and evaluating in relation to their goals for reading. Findings are discussed in relation to existing models of reading texts in professional life.
“Do You Want to Be in My Story?”: Collaborative Writing in an Urban Elementary Classroom
Authors: Schultz Katherine
Published: December 2009

Based on a year-long interpretive research project, this article describes the arrangements for collaborative writing in an urban elementary classroom. In contrast to typical descriptions of collaboration, this study suggests a more complex view, one that includes a range of ways for students to participate in writing together. This study begins to answer the following questions: What happens when teachers allow students to talk as they write? What does a classroom look like when collaboration is conceptualized as more than a technique, but as a way to understand students as members of a writing community? In this classroom, collaborative writing included the following arrangements: Students wrote alone and shared their work with others; they wrote in pairs or small, consistent groups called networks; and they worked together to author a single text. Brief case studies are used to illustrate each of these types of collaboration. This study describes the ways students responded to opportunities for collaboration. Collaboration was more than a technique; through interactions with peers, students developed their own voices and ways of writing.
Perspectives on Learning History: A Case Study
Authors: Simpson Michele L. , Nist Sherrie L.
Published: December 2009

The purpose of this case study was to generate a description of the elements that supported students' performance in a university history course. Throughout the study, the researchers were guided by a phenomen-ographic theoretical framework. Taking the role of observers, the researchers collected data over a 10-week period in the form of lecture notes, fieldnotes, and documents. In addition, multiple interviews from both the history professor and the 10 informants, who were chosen in a purposive manner, were transcribed. Data were subjected to a qualitative content analysis. Three categories that emerged as salient were students' belief systems, students' strategic knowledge, and students' ability to be flexible. Informants differed on these beliefs depending on whether they were in the high-performance, low-performance, or improved-performance group. One of the major conclusions drawn from this case study was that students who were flexible in their belief systems about learning and history, perceptions of task, and strategic approaches were the ones who succeeded in the course. In addition, students who performed better in the course shared the professor's perceptions of learning and task.
Learning from Classroom Questions and Answers: Teachers' Uncertainties about Children's Language
Authors: Edwards Barbara , Davis Boyd
Published: December 2009

This article examines the interaction of language varieties with teachers' perceptions and evaluations of how k-2 students answer classroom questions. Using both qualitative and quantitative methodology, we trace the processes, findings, and reflections from 2 years of collaboration with teachers in a low-income, multiethnic, inner-city school where all students spoke marginalized or stigmatized varieties of English, including Appalachian/rural and African-American English, or Ebonics. Among other findings, we and the teachers discovered ambiguity in their questions which created problems for students accustomed to different discourse practices. We noticed examples of Delpit's “silenced dialogue” when young White teachers would not listen to the exhortations of an experienced Black teacher that they should show students exactly what they wanted as answers. We worked with the teachers to uncover their concerns about racism and classism to discover what they heard and valued in students' answers and to modify their ways of listening to children. Implications include the need to query our own teaching practices relative to creating “culturally composite classrooms” where speakers of all dialects are respected.
Some Complexities of Gendered Talk about Texts
Authors: Moore David W.
Published: December 2009

In this study, I reanalyzed classroom discussion data. I approached this inquiry with a social-enactment theoretical orientation and a substantive framework based on gendered classroom interactions, multiple subjectivities, and power relationships. The data sources consisted of three videotaped class discussions and interviews about the discussions as well as fieldnotes produced during my weekly observations conducted during an academic year in an Advanced Placement English class. I analyzed the actions and interactions of two highly visible 12th graders. The students accepted and contested traditional gender-based expectations, indicating some complexities of gendered talk about texts. Locating literacy events theoretically at the confluence of external forces and individual actions helped me explain these actions and interactions and suggest possible classroom practices. I close this report with concerns and questions.
Partial Word Knowledge and Vocabulary Growth during Reading Comprehension
Authors: Schwanenflugel Paula J. , Stahl Steven A. , McFalls Elisabeth L.
Published: December 2009

The experiment investigated the development of vocabulary knowledge in elementary school children as a function of story reading for partially known and unknown words. Fourth graders participated in a vocabulary checklist in which they provided definitions or sentences for words they knew (known words) and checked off words they did not know the meaning of but were familiar with (partially known words). Children then read stories containing some of these words. The remaining words served as a control. Vocabulary growth was small but even for both partially known and unknown words. However, the characteristics of the words being learned themselves (particularly, part of speech and concreteness) were more important in determining this growth than aspects of the texts.
Evaluation of Workplace Literacy Programs: A Profile of Effective Instructional Practices
Authors: Mikulecky Larry , Lloyd Paul
Published: December 2009

This study introduces and examines a model for evaluating workplace literacy programs by assessing the impact of workplace literacy instruction in a variety of settings. The model was developed in reaction to the particular assessment difficulties associated with workplace literacy programs to address 2 questions: (a) Are learners in workplace literacy classes able to demonstrate gains between premeasures and postmeasures in areas related to literacy practices? (b) For gains to occur, how much of several instructional practices (e.g., reading/writing practice, use of workplace examples, etc.) do classes need to incorporate? The study focuses on changes in literacy practices, beliefs about personal effectiveness with literacy, reading processes, literacy abilities, and changes in educational plans. Programs were most effective at improving learner literacy performance, literacy strategies and processes, and beliefs and plans related to literacy. Analysis of gains in relation to course characteristics allowed the development of a data-driven profile of thresholds for effective program practices. This profile provides evidence that gains are linked to an environment intense with the literacy practice, some use of workplace reading and writing materials, and providing discussion and feedback.
Critical Issues Literacy Connections between School and Home: How Should We Evaluate Them?
Authors: Serpell Robert
Published: December 2009

The value of a partnership between teachers and parents in the promotion of children's literacy appears self-evident. It symbolizes both the school's accountability to the community it serves and the complementary responsibility of families to support the school's agenda of empowering their children with the tools of civilization. Many parents and teachers across the world perceive, however, that there is something amiss with the relations between them. On the one hand, they share an interest in the literacy development of the same children, and in some sense, they subscribe to an implicit contract to share responsibility for promoting it. Yet, disagreement frequently arises about how this contract is to be executed in practice. In this eclectic review of research, I consider three complementary ways in which the nature of the connection between children's homes and the schools they attend can be problematized, each focusing on a different criterial dimension for evaluating the home-school connection: (a) congruence of family life with the agenda of schooling, (b) intimacy, or depth of understanding, between teachers and parents, and (c) sociocultural productivity of the interaction between the school and its students' home communities.
 as Signifier: Considering the Semantic Field of School Literacy
Authors: Dressman Mark , McCarty Laurie , Benson Jonathan
Published: December 2009

This article examines the use of the term  within the educational and national media and by the newspaper and interested parties in 1 college town. Data collected include articles in literacy journals; a search of 5 daily newspapers in the US and other periodicals and TV news; a search of 1 local newspaper; and interviews with 70 teachers, administrators, university faculty, and “concerned citizens” in a mid-sized city in the Southwestern us with a major public university. Using the “discourse-centered approach to culture” proposed by Sherzer (1987) as a revision of the Sapir-Whorf hypothesis, our interpretive analysis of the data argues that the disputes surrounding the term  have as much to do with cultural, political, and economic issues confronting the US, and in particular the Southwest, as they do with any philosophical or professional conversation about the “best way” to teach children to read. The implication is that if literacy research is to retain both its legitimacy and its relevance within discussions about literacy, researchers need to become more open about their own cultural and political biases in the stands they take, and more aware of how those positions might be perceived and used by others and by the national media.
Introduction: Appropriating and Creating Space for Difference in Literacy Research
Authors: García Georgia Earnest , Willis Arlette Ingram , Harris Violet J.
Published: December 2009

Have you ever hurt about baskets? I have, seeing my grandmother weaving for a long time. Have you ever hurt about work? I have, because my father works too hard and tells how he works. Have you ever hurt about cattle? I have, because my grandfather has been working on the cattle for a long time. Have you ever hurt about school? I have, because I have learned a lot of words from my school, And they are not my words.
Experiencing Literacy in and Out of School: Case Studies of Two American Indian Youths
Authors: Noll Elizabeth
Published: December 2009

This case-study research focused on the role of multiple literacies in the lives of Lakota and Dakota (Sioux) young adolescents who lived and attended school in a predominately White, rural community in the upper Midwest. In addition to examining the participants' uses of reading and writing, this study explored the ways in which the participants constructed meaning through music, dance, and art. Also studied was the influence of multiple cultures - American Indian culture, school culture, and mainstream popular culture - on the adolescents' transactions with literacy. Data were collected both in and out of school over a period of 7 months. Primary collection techniques included participant observation and fieldnotes; interviews with the participants and their parents, peers, teachers, and administrators; and examination of artifacts. The findings of this study indicate that literacy supported important personal and social needs in the lives of the adolescents. Specifically, through literacy, they explored and expressed their sense of identity and examined critical issues related to prejudice, racism, and discrimination.

Numerous questions remain as to the different ways persons experience literacy and illiteracy. How often is literacy defined in relation to illiteracy? How often does it actually signify academic literacy? How do diverse individuals become literate in an inequitable world? - Maxine Greene (1991, p. 129)
Diverse Learners, Diverse Texts: Exploring Identity and Difference through Literary Encounters
Authors: Athanases Steven Z.
Published: December 2009

This article reports from a yearlong ethnography that examined two urban loth-grade English classes of ethnically diverse students in which the teachers diversified literature selections for newly designed ethnic literature curricula. The study reports texts students found most memorable and meaningful and analyzes the values students found in their encounters with these literary works. When students identified with characters and texts, they reflected on personal concerns, including family nostalgia and loss; adolescent challenges; and culture, gender, and sexual-identity formation. Literary encounters also fostered discoveries about diverse groups (identified by race, ethnicity, gender, religion, and sexual orientation) that helped students move past stereotyped notions of others. Choices of meaningful works were often tied integrally to ways in which the texts were treated during class time-particularly to activities involving the social processes of constructing meaning, exploring interpretation, and openly discussing issues of culture and identity. The results remind researchers of the need to include in cur-ricular theorizing the importance of instruction that fosters students' thinking about literature, identity, and diversity.
First Graders' Use of Analogy in Word Reading
Authors: Wang Chiung-Chu , Gaffhey Janet S.
Published: December 2009

This study investigated first graders' use of analogy in word decoding. All students were given three tasks, Letter Identification, Ohio Word Test, and Dictation, from Clay's Observation Survey (1993). They were asked to read three types of words - analogous, non-analogous, and misanalogous - twice. The first time, children were asked to read the words and received no help from the researcher. The second time, they were shown and told clue words before reading. Students read more words correctly after exposure to analogous clue words. In addition, the Dictation task accounted for a large proportion of variance on the decoding of analogous words. This study clarified the results of previous research, specifically, the helpfulness of clue words in decoding by analogy and the abilities of first graders that may contribute to this strategy.
The National Reading Conference: The College and Adult Reading Years
Authors: Stahl Norman A. , Smith-Burke M. Trika
Published: December 2009

The National Reading Conference has a long and honored history spanning a period of nearly 50 years. This article delves into the birth, childhood, and adolescence of the organization with direct attention given to the germination of the Journal of Reading Behavior.
As if Women Writing
Authors: Luce-Kapler Rebecca
Published: December 2009

When we write literary texts such as fiction, poetry, autobiography, or memoir, we initiate performances of meaning that subjunctivize reality. Because the subjunctive traffics in human possibilities rather than settled certainties (Bruner, 1986), writing becomes a site of possibility, an “as if” that works in multiple ways with, through, and beyond the text. What such contingency does is broaden the possibilities for experiencing, acting, understanding, and creating. If there is no “solid” sense of self, but rather an ever evolving story of identity that is always in revision, then our stories about ourselves are fraught with possibility - the subjunctive possibility of writing. Women, using the fluidity of writing to express a variety of experiences, shape a story of subjectivity where they begin to see themselves as having multiple possibilities for understanding and acting. This article explores some of the possibilities of writing that the author realized from working with women writers and describes how, as a result of this work, she has revised her thinking about writing and the teaching of writing.
A Cross-Linguistic Perspective on Imagery and Affect in Reading: Dual Coding in Chinese and English
Authors: Steffensen Margaret S. , Goetz Ernest T. , Cheng Xiaoguang
Published: December 2009

Three studies of bilingual readers' nonverbal responses were conducted in China. Participants read a text in either English or Chinese about a train trip, then gave reports of imagery experienced during reading and rated text segments for vividness of imagery. These procedures were repeated for emotional responses. In the first experiment, readers of the English version reported fewer images and emotional responses than did those reading the Chinese version. In the second study, readers of the English version were allowed to write their reports in Chinese, but there was no increase in number of reports. In the third study, English readers wrote their reports in Chinese. No significant difference was found in the ratings or number of reports of affect, but English readers still produced fewer reports of imagery. Qualitative analysis of these reports showed that English readers did not understand the passage as well as the Chinese readers did. However, imagery and affect were formed even in the absence of total understanding, showing they are fundamental aspects of foreign language reading.
Public and Personal Voices in Adolescents' Classroom Talk
Authors: Phelps Stephen , Weaver Dera
Published: December 2009

In a reanalysis of data from a year-long study of classroom discussion of text, we looked at the factors that influenced the degree to which students' personal voices became part of the public talk of two classrooms, one an 11th-grade U.S. history class in a large urban high school, and the other an 8th-grade language arts class in a Southern university town. Data consisted of observation field notes, videotapes and audiotapes of class sessions, and interviews with students and teachers. Our reanalysis probed the factors that seemed to inhibit students' public voices, the evidence of silenced students' potential to make contributions to classroom talk, and the implications both for individual students and for the classroom community when students do not participate in classroom discussion. Our findings suggest that student participation in discussion is influenced by competing discourses in a classroom, including peer and gender relations and differing conceptions of teaching and knowledge. We also found that encouraging students to exercise their personal voices in the public forum of the classroom entails risks for both students and teachers.
Critical Issues: Reading and the New Literacy Studies: Reframing the National Academy of Sciences Report on Reading
Authors: Gee James Paul
Published: December 2009

This article is a reflection on the recent report from the National Academy of Sciences, Preventing Reading Difficulties in Young Children. This report, typical of many recent discussions of early reading instruction, centers on psycholinguistic aspects of reading having to do with phonological awareness, decoding, word recognition, and literal comprehension. I seek to reframe the report from the perspective of the New Literacy Studies, an interdisciplinary effort that takes a sociocultural approach to language and literacy. My approach is to stress tensions internal to the report itself as pressure points around which one could imagine a different sort of report being written, one more in the spirit of the New Literacy Studies. I take up issues such as whether or not there is a consensus in the reading field; the nature of the “literacy crisis”; relationships among reading, poverty, racism, and culture; whether or not technology leads to higher literacy demands; learning to read as against learning content; and the connections among phonological awareness, early language abilities, and the use of specific genres and registers in school.
Metacognitive Responses of an Intermediate Speller While Performing Three Literacy Tasks
Authors: Sabey Brenda L.
Published: December 2009

This case study explored verbal reflections of a competent fifth-grade speller as he performed word sorts, spelling lists, and creative writing activities. The student was asked to “think aloud” as he completed the three literacy activities, which represented three levels of applying orthographic knowledge. Videotapes, transcriptions, field notes, written work, and teacher interviews suggested eight categories of responses. The responses revealed two conclusions: (a) the accuracy or inaccuracy of the participant's statements were related to his level of spelling development, and (b) each literacy task appeared to have a predominant category of responses. These findings support previous research regarding the developmental acquisition of spelling knowledge and instruction at appropriate developmental levels.
Critical Issues: Crafting State Educational Policy: The Slippery Role of Research and Researchers
Authors: Allington Richard L.
Published: December 2009

For most of the past decade, there have been rumblings in the nrc membership around the question: Should nrc be involved in attempting to influence educational policy making? This question has been posed at Town Meetings, in campaign statements, committee reports, conference forums, symposia, and papers. It has been debated at board meetings, Vital Issues, and in nrc publications. The debate continues, but that debate often seems grounded in one or more unwarranted assumptions. In this article, some of those assumptions are challenged, primarily through the use of descriptive case studies of educational policy making in two states - Texas and California.
Visual speech aids: A British survey of use and evaluation by speech and language therapists
Authors: Coventry Kenny R. , Clibbens John , Cooper Margaret , Rood Ben
Published: December 2009

One hundred and eighty speech and language therapists throughout the UK completed a postal questionnaire which asked for ratings of visual speech aids (VSAs) on a number of dimensions together with information regarding frequency of use of such aids, comments on the range of applicability of each type of aid and other demographic data relating to the diversity of client groups covered in case loads. The results (using analysis of variance) revealed a main effect of VSA type. There was also a main effect of question type; all VSAs scored poorly on some dimensions as compared with others. Furthermore there was a significant interaction between type of VSA and dimension type. This suggests that VSAs not only tend to be built for particular client groups, but that the makers tend to focus on some specific design criteria to the detriment of others. These results are discussed with respect to the future design of VSAs, and with respect to their testing and future evaluation.
The use of graphic language intervention among young children in Norway
Authors: von Tetzchner Stephen
Published: December 2009

Knowledge about graphic communication intervention and use among young disabled children has been sparse. The present study is based on a thorough search, and provides reliable information about children who are 10 years old or younger who have graphic communication (for example, photographs, drawings, Blissymbols, PIC, traditional orthography) as their main form of communication. The study covers all such children in three Norwegian counties, comprising a population of 1.1 million people. Detailed descriptions of the children, the systems they use, and their educational settings are presented, and implications for the organisation of habilitation services are discussed.
Bordetella evades the host immune system by inducing IL-10 through a type III effector, BopN
Authors: Nagamatsu Kanna , Kuwae Asaomi , Konaka Tadashi , Nagai Shigenori , Yoshida Sei , Eguchi Masahiro , Watanabe Mineo , Mimuro Hitomi , Koyasu Shigeo , Abe Akio
Published: December 2009

The inflammatory response is one of several host alert mechanisms that recruit neutrophils from the circulation to the area of infection. We demonstrate that Bordetella, a bacterial pathogen, exploits an antiinflammatory cytokine, interleukin-10 (IL-10), to evade the host immune system. We identified a Bordetella effector, BopN, that is translocated into the host cell via the type III secretion system, where it induces enhanced production of IL-10. Interestingly, the BopN effector translocates itself into the nucleus and is involved in the down-regulation of mitogen-activated protein kinases. Using pharmacological blockade, we demonstrated that BopN-induced IL-10 production is mediated, at least in part, by its ability to block the extracellular signal-regulated kinase pathway. We also showed that BopN blocks nuclear translocation of nuclear factor κB p65 (NF-κBp65) but, in contrast, promotes nuclear translocation of NF-κBp50. A BopN-deficient strain was unable to induce IL-10 production in mice, resulting in the elimination of bacteria via neutrophil infiltration into the pulmonary alveoli. Furthermore, IL-10–deficient mice effectively eliminated wild-type as well as BopN mutant bacteria. Thus, Bordetella exploits BopN as a stealth strategy to shut off the host inflammatory reaction. These results explain the ability of Bordetella species to avoid induction of the inflammatory response.
Intestinal CD103+, but not CX3CR1+, antigen sampling cells migrate in lymph and serve classical dendritic cell functions
Authors: Schulz Olga , Jaensson Elin , Persson Emma K. , Liu Xiaosun , Worbs Tim , Agace William W. , Pabst Oliver
Published: December 2009

Chemokine receptor CX3CR1+ dendritic cells (DCs) have been suggested to sample intestinal antigens by extending transepithelial dendrites into the gut lumen. Other studies identified CD103+ DCs in the mucosa, which, through their ability to synthesize retinoic acid (RA), appear to be capable of generating typical signatures of intestinal adaptive immune responses. We report that CD103 and CX3CR1 phenotypically and functionally characterize distinct subsets of lamina propria cells. In contrast to CD103+ DC, CX3CR1+ cells represent a nonmigratory gut-resident population with slow turnover rates and poor responses to FLT-3L and granulocyte/macrophage colony-stimulating factor. Direct visualization of cells in lymph vessels and flow cytometry of mouse intestinal lymph revealed that CD103+ DCs, but not CX3CR1-expressing cells, migrate into the gut draining mesenteric lymph nodes (LNs) under steady-state and inflammatory conditions. Moreover, CX3CR1+ cells displayed poor T cell stimulatory capacity in vitro and in vivo after direct injection of cells into intestinal lymphatics and appeared to be less efficient at generating RA compared with CD103+ DC. These findings indicate that selectively CD103+ DCs serve classical DC functions and initiate adaptive immune responses in local LNs, whereas CX3CR1+ populations might modulate immune responses directly in the mucosa and serve as first line barrier against invading enteropathogens.
Estimating DNA coverage and abundance in metagenomes using a gamma approximation
Authors: Hooper Sean D. , Dalevi Daniel , Pati Amrita , Mavromatis Konstantinos , Ivanova Natalia N. , Kyrpides Nikos C.
Published: December 2009

Motivation: Shotgun sequencing generates large numbers of short DNA reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. These reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). The feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative abundances of their source genomes in the microbial community. A low coverage suggests that most of the genomic DNA in the sample has not been sequenced, but it is often difficult to estimate either the extent of the uncaptured diversity or the amount of additional sequencing that would be most efficacious. In this work, we regard a metagenome as a population of DNA fragments (bins), each of which may be covered by one or more reads. We employ a gamma distribution to model this bin population due to its flexibility and ease of use. When a gamma approximation can be found that adequately fits the data, we may estimate the number of bins that were not sequenced and that could potentially be revealed by additional sequencing. We evaluated the performance of this model using simulated metagenomes and demonstrate its applicability on three recent metagenomic datasets.

Contact:  sean.d.hooper@genpat.uu.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
sORF finder: a program package to identify small open reading frames with high coding potential
Authors: Hanada Kousuke , Akiyama Kenji , Sakurai Tetsuya , Toyoda Tetsuro , Shinozaki Kazuo , Shiu Shin-Han
Published: December 2009

Summary: sORF finder is a program package for identifying small open reading frames (sORFs) with high-coding potential. This application allows the identification of coding sORFs according to the nucleotide composition bias among coding sequences and the potential functional constraint at the amino acid level through evaluation of synonymous and non-synonymous substitution rates.

Availability: Online tools and source codes are freely available at http://evolver.psc.riken.jp/

Contact:  kohanada@psc.riken.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
An Introduction to the Augmented Inverse Propensity Weighted Estimator
Authors: Glynn Adam N. , Quinn Kevin M.
Published: December 2009

In this paper, we discuss an estimator for average treatment effects (ATEs) known as the augmented inverse propensity weighted (AIPW) estimator. This estimator has attractive theoretical properties and only requires practitioners to do two things they are already comfortable with: (1) specify a binary regression model for the propensity score, and (2) specify a regression model for the outcome variable. Perhaps the most interesting property of this estimator is its so-called “double robustness.” Put simply, the estimator remains consistent for the ATE if either the propensity score model or the outcome regression is misspecified but the other is properly specified. After explaining the AIPW estimator, we conduct a Monte Carlo experiment that compares the finite sample performance of the AIPW estimator to three common competitors: a regression estimator, an inverse propensity weighted (IPW) estimator, and a propensity score matching estimator. The Monte Carlo results show that the AIPW estimator has comparable or lower mean square error than the competing estimators when the propensity score and outcome models are both properly specified and, when one of the models is misspecified, the AIPW estimator is superior.
Perspectives of Future Physicians on Disaster Medicine and Public Health Preparedness: Challenges of Building a Capable and Sustainable Auxiliary Medical Workforce
Authors: Kaiser Heather E. , Barnett Daniel J. , Hsu Edbert B. , Kirsch Thomas D. , James James J. , Subbarao Italo
Published: December 2009

Background: Although the training of future physicians in disaster preparedness and public health issues has been recognized as an important component of graduate medical education, medical students receive relatively limited exposure to these topics. Recommendations have been made to incorporate disaster medicine and public health preparedness into medical school curricula. To date, the perspectives of future physicians on disaster medicine and public health preparedness issues have not been described.

Methods: A Web-based survey was disseminated to US medical students. Frequencies, proportions, and odds ratios were calculated to assess perceptions and self-described likelihood to respond to disaster and public health scenarios.

Results: Of the 523 medical students who completed the survey, 17.2% believed that they were receiving adequate education and training for natural disasters, 26.2% for pandemic influenza, and 13.4% for radiological events, respectively; 51.6% felt they were sufficiently skilled to respond to a natural disaster, 53.2% for pandemic influenza, and 30.8% for radiological events. Although 96.0% reported willingness to respond to a natural disaster, 93.7% for pandemic influenza, and 83.8% for a radiological event, the majority of respondents did not know to whom they would report in such an event.

Conclusions: Despite future physicians' willingness to respond, education and training in disaster medicine and public health preparedness offered in US medical schools is inadequate. Equipping medical students with knowledge, skills, direction, and linkages with volunteer organizations may help build a capable and sustainable auxiliary workforce. (Disaster Med Public Health Preparedness. 2009;3:210–216)
Fatal Work Injuries Involving Natural Disasters, 1992–2006
Authors: Fayard Gregory M.
Published: December 2009

Objective: Although a goal of disaster preparedness is to protect vulnerable populations from hazards, little research has explored the types of risks that workers face in their encounters with natural disasters. This study examines how workers are fatally injured in severe natural events.

Methods: A classification structure was created that identified the physical component of the disaster that led to the death and the pursuit of the worker as it relates to the disaster. Data on natural disasters from the Census of Fatal Occupational Injuries for the years 1992 through 2006 were analyzed.

Results: A total of 307 natural disaster deaths to workers were identified in 1992–2006. Most fatal occupational injuries were related to wildfires (80 fatalities), hurricanes (72 fatalities), and floods (62 fatalities). Compared with fatal occupational injuries in general, natural disaster fatalities involved more workers who were white and more workers who were working for the government. Most wildfire fatalities stemmed directly from exposure to fire and gases and occurred to those engaged in firefighting, whereas hurricane fatalities tended to occur more independently of disaster-produced hazards and to workers engaged in cleanup and reconstruction. Those deaths related to the 2005 hurricanes occurred a median of 36.5 days after landfall of the associated storm. Nearly half of the flood deaths occurred to passengers in motor vehicles. Other disasters included tornadoes (33 fatalities), landslides (17), avalanches (16), ice storms (14), and blizzards (9).

Conclusions: Despite an increasing social emphasis on disaster preparation and response, there has been little increase in expert knowledge about how people actually perish in these large-scale events. Using a 2-way classification structure, this study identifies areas of emphasis in preventing occupational deaths from various natural disasters. (Disaster Med Public Health Preparedness. 2009;3:201–209)
Epidemiological Characteristics of Human Stampedes
Authors: Hsieh Yu-Hsiang , Ngai Ka Ming , Burkle Frederick M. , Hsu Edbert B.
Published: December 2009

Objective: The potential for deadly human stampedes to occur at any mass gathering event highlights this unique form of crowd disaster as deserving of special attention from both scientific and planning perspectives. Improved understanding of human stampedes is indispensable in the mitigation of this type of mass casualty. With relatively few peer-reviewed reports on deadly human stampedes, information from news reports and the Internet is essential to increased collective understanding. Without incorporating nontraditional sources, no other way to reasonably acquire sufficient data is available. This study analyzed human stampede events from 1980 to 2007 to identify epidemiological characteristics associated with increased mortality.

Methods: A LexisNexis search was followed by sequential searches of multiple Internet-based English-language news agencies. Date, country, geographical region, time of occurrence, type of event, location, mechanism, number of participants, number injured, and number of deaths were recorded. Bivariate analyses of number of deaths or injuries were conducted using a nonparametric Wilcoxon rank test. Multivariate regression was performed to determine the factors associated with increased number of fatalities during stampede events.

Results: A total of 215 human stampede events were reported from 1980 to 2007, resulting in 7069 deaths and at least 14,078 injuries from 213 events with available fatality information and 179 events with injury information. In bivariate analysis, stampedes occurring in the Middle East, in developing countries, outdoors, or associated with religious events had the highest median number of deaths. In multivariate analysis, events that occurred in developing countries and outdoors were associated with increased number of fatalities. Stampedes that occurred in the context of sports, religious, music, and political events, or that had a unidirectional mechanism, also increased the relative number of deaths.

Conclusions: Several epidemiological features of human stampedes associated with increased mortality are identified. Standardized collection of epidemiological data pertaining to human stampedes is strongly recommended, and further study of this recurrent, distinctive disaster is warranted. (Disaster Med Public Health Preparedness. 2009;3:217–223)
Neuronal SIRT1 regulates endocrine and behavioral responses to calorie restriction
Authors: Cohen Dena E. , Supinski Andrea M. , Bonkowski Michael S. , Donmez Gizem , Guarente Leonard P.
Published: December 2009

Mammalian life span can be extended by both calorie restriction (CR) and mutations that diminish somatotropic signaling. Sirt1 is a mediator of many effects of CR in mammals, but any role in controlling somatotropic signaling has not been shown. Since the somatotropic axis is controlled by the brain, we created mice lacking Sirt1 specifically in the brain and examined the impacts of this manipulation on somatotropic signaling and the CR response. These mutant mice displayed defects in somatotropic signaling when fed ad libitum, and defects in the endocrine and behavioral responses to CR. We conclude that Sirt1 in the brain is a link between somatotropic signaling and CR in mammals.
A novel histone fold domain-containing protein that replaces TAF6 in Drosophila SAGA is required for SAGA-dependent gene expression
Authors: Weake Vikki M. , Swanson Selene K. , Mushegian Arcady , Florens Laurence , Washburn Michael P. , Abmayr Susan M. , Workman Jerry L.
Published: December 2009

The histone acetyltransferase complex SAGA is well characterized as a coactivator complex in yeast. In this study of Drosophila SAGA (dSAGA), we describe three novel components that include an ortholog of Spt20, a potential ortholog of Sgf73/ATXN7, and a novel histone fold protein, SAF6 (SAGA factor-like TAF6). SAF6, which binds directly to TAF9, functions analogously in dSAGA to TAF6/TAF6L in the yeast and human SAGA complexes, respectively. Moreover, TAF6 in flies is restricted to TFIID. Mutations in saf6 disrupt SAGA-regulated gene expression without disrupting acetylated or ubiquitinated histone levels. Thus, SAF6 is essential for SAGA coactivator function independent of the enzymatic activities of the complex.