bluuebunny/crossref_metadata_2025 huggingface dataset:
Does Personal Experience in a Community Increase or Decrease Newspaper Reading?
Authors: Demers David Pearce
Published: December 2011

Many agenda-setting researchers argue that personal experience with issues or events in a community diminishes use of mass media. This study challenges this notion and, drawing on the community attachment model, hypothesizes that personal experience normally will increase newspaper reading. Personal experience increases reading because rarely is it identical or isomorphic with news coverage, especially in pluralistic systems, and because, like social ties in general, personal experience often stimulates additional needs for information. Data support the key hypothesis when it comes to reading of the local community weekly and student newspapers, but not for the metropolitan newspaper.
Communication, Community Attachment, and Involvement
Authors: Rothenbuhler Eric W. , Mullen Lawrence J. , DeLaurell Richard , Ryu Choon Ryul
Published: December 2011

A long tradition of social theory has emphasized the importance of communication to individuals' ties to their communities. Two major types of such ties are treated here: affective attachment and cognitive and active involvement. Data from a sample survey of 400 adult residents of Iowa are used to examine a structural equation model linking community attachment and involvement to newspaper use, local television news use, age, education, number of children in the home, localism, and population density. Among the results, we show that newspaper reading makes important contributions to both attachment and involvement, independently of the other variables in the model, while television news viewing does not. Error paths and correlations between the errors of the equations are estimated to aid future modeling work.
The Wisconsin Press and Woman Suffrage, 1911–1919: An Analysis of Factors Affecting Coverage by Ten Diverse Newspapers
Authors: Burt Elizabeth V.
Published: December 2011

This study combines quantitative and qualitative methods in its analysis of ten Wisconsin newspapers during six week-long periods in which a significant woman suffrage event took place. It attempted to identify those factors that might have influenced individual newspapers' coverage of the suffrage movement, including the personal positions of their publishers and editors, their political affiliations, the demographic characteristics of their readership area, circulation size, place of publication, and sources of the stories they published on suffrage. The study found that these examples of the “mainstream press,” far from representing a united ideological voice, represented a diversity of voices influenced, in part, by these factors.
Community Newspapers, Community Structural Pluralism, and Local Conflict with Nonlocal Groups
Authors: Hindman Douglas Blanks
Published: December 2011

This important study of how newspapers address conflict contributes to an understanding of how the content of local newspapers is related to community conditions. In periods of change, newspaper content reflects the concerns of powerful groups within and beyond the community. Ultimately, newspaper reports of both internal conflict and conflict with outside groups contribute to the maintenance of community stability and community adjustment to change in the larger social environment.
VNRs and Air Checks: A Content Analysis of the Use of Video News Releases in Television Newscasts
Authors: Cameron Glen T. , Blount David
Published: December 2011

Forty-seven television news stories generated by a video news release (VNR) were content analyzed to determine how television gatekeepers use various elements included in VNRs. A survey was also done to obtain station resource data that might predict greater use of packaged elements from a VNR. Results suggest that the production costs for a packaged story in a VNR may be wasted. Extensive use was made of B-roll, public service announcements (PSAs), and footage from planned events like news conferences that reporters are accustomed to covering. When the packaged story was used, it was heavily edited or truncated. Contrary to common wisdom, resource-poor stations did not make greater use of the packaged story in the VNR.
Public Perceptions of Journalists' Ethical Motivations
Authors: Voakes Paul S.
Published: December 2011

Telephone surveys of 376 residents and 60 daily journalists in the same Midwestern county revealed starkly different conceptions of journalistic ethics. Members of the public seemed to believe that journalists' ethics are guided primarily by their occupational norms and competitive pressures, whereas the journalists themselves cited organizational policies, the relevant law, and their own individual reasoning as the primary influences on their ethical decision making. Journalists and public respondents showed surprisingly high agreement, however, on the unacceptability of specific, ethically controversial actions.
The Locus of Metaphorical Persuasion: An Empirical Test
Authors: Hitchon Jacqueline C.
Published: December 2011

The use of metaphor has been accepted as an effective persuasive device in many forms of communication since Aristotle first introduced the figure. Yet, the psychological process by which metaphor influences persuasion has received comparatively little attention. Based on a review of the literature regarding the impact of metaphor on attitudes, this study presents pretests and an experiment that test whether the locus of persuasion lies in the valence of B, as widely assumed, or in the valence of the metaphor ground, what A and B share. Findings indicate that global affect toward B does not transfer onto A, and that metaphorical persuasion is a distinct process meriting further investigation.
Minority Presence and Portrayal in Mainstream Magazine Advertising: An Update
Authors: Bowen Lawrence , Schmid Jill
Published: December 2011

This research analyzes inclusion, portrayal, and integration of minorities in mainstream magazine advertising. Nine mass-circulation magazines for 1987 and 1992 constituted the sample frame: four issues of each magazine for each year for a total of seventy-two issues, yielding 1, 969 “populated” advertisements. Each ad was examined for minority presence, gender, age, occupation, and product category. When minorities and Whites appeared together in the same ad, the relationship depicted was also coded. Overall, when compared with earlier studies, the number of Black models used in magazine advertisements has increased. The use of Hispanic and Asian models was extremely small. There were few differences in portrayal by gender or age. Blacks were more likely to appear as athletes or musicians and to be featured in public-service or government-sponsored ads. In mixed-ethnic ads, Whites typically outnumbered minorities, and the relationships depicted were set in formal or work settings with very little face-to-face interaction.
An Editorial Comment
Authors: Folkerts Jean , Gomery Douglas , Steele Janet
Published: December 2011

This issue features four articles in a special section titled “Media History.” The articles were reviewed and edited by an editorial board of three people, including Jean Folkerts, director of the School of Media and Public Affairs at The George Washington University and editor of Journalism & Mass Communication Quarterly; Douglas Gomery, professor in the College of Journalism at the University of Maryland; and Janet Steele, associate professor of media and public affairs at The George Washington University.
Changing Theoretical Perspectives on Women's Media Images: The Emergence of Patterns in a new Area of Historical Scholarship
Authors: Kitch Carolyn
Published: December 2011

This interpretive, historiographic essay surveys the past twenty-five years of historical research on images of women in American mass media, a growing field of inquiry in communication history. It places this work into four categories of scholarship - the stereotypes approach, the search for alternative images, the examination of imagery as ideology, and the “reading” of images as polysemic texts - that provide a temporal framework for discussing the trajectory of critical perspectives on the subject. It argues that significant patterns have already emerged in this relatively new area, and that these trends illustrate larger issues in historical research. Indeed, the range of content revealed by this survey is less significant than the array of theoretical models that, when considered together, point to important concerns underlying all media history scholarship: how we define our mission as scholars, what counts as historical evidence, and who controls the meaning of mass-media imagery.
Rethinking TV History
Authors: Gomery Douglas
Published: December 2011

The writing of the early history of U.S. television has long concentrated on the rise of dominating national networks. Based on principles of social, demographic, policy, and urban history, I propose we rethink historical analysis, and begin at the local level. To illustrate the power of this approach, I offer a case study of the place of Washington, D.C., as a site for network news. In the mid-1950s, it was also an important example of live locally produced country music. As a community, Washington presents an important site where forces such as migration and suburbanization shaped the early history of television.
Considering Interacting Factors in the Third-Person Effect: Argument Strength and Social Distance
Authors: White H. Allen
Published: December 2011

This study explores the possible relationship among issue involvement, argument strength, and the third-person effect. The study examines Petty and Cacioppo's Elaboration Likelihood Model and the third-person effect hypothesis. The hypothesis in this laboratory experiment was that perceived issue involvement in others would interact with argument strength in a written persuasive message to affect the nature of the third-person effect. That is, it was hypothesized and found that people tend to believe that “others” will be more affected than themselves by a persuasive message that contains weak argumentation, but that “others” will be less affected than themselves by a persuasive message that contains strong argumentation.
Candidate Images in Spanish Elections: Second-Level Agenda-Setting Effects
Authors: McCombs Maxwell , Llamas Juan Pablo , Lopez-Escobar Esteban , Rey Federico
Published: December 2011

Traditional agenda-setting theory is about the influence of mass media on the public's focus of attention, who and what people are thinking about. The expanded theory of agenda setting tested here during the 1995 regional and municipal elections in Spain elaborates the influence of the mass media on how people think about persons and topics in the news. Combining content analysis and survey data, this study documents the influence of newspapers, TV news, and both TV and newspaper political advertising on Spanish voters' images of political candidates.
Browsing and the Hypermedia Interaction Cycle: A Model of Self- Efficacy and Goal Dynamics
Authors: Fredin Eric S. , David Prabu
Published: December 2011

The Hypermedia Interaction Cycle (HIC) proposed in this paper is an iterative, self-regulatory model that captures the dynamics of hypermedia interaction from a user's perspective. The interaction cycle was divided into three distinct phases: preparation, exploration, and consolidation. The dynamics between two motivational components, namely self-efficacy factors and goal conditions, were examined within the HIC using a browsing task that involved searching for news-story ideas on the World Wide Web. Findings suggest that a cyclical model involving shifting states of goals and self-efficacy can capture some of the dynamics of motivation within the HIC. Furthermore, there was evidence of a self-regulatory pattern between the motivational components in the model.
Framing the Candidates in Presidential Primaries: Issues and Images in Press Releases and News Coverage
Authors: Miller M. Mark , Andsager Julie L. , Riechert Bonnie P.
Published: December 2011

Media coverage of presidential primaries is crucial to voters, and candidates often complain that news coverage fails to present their positions. This study used computerized content analysis to examine how the 1996 GOP presidential candidates framed themselves in press releases and how elite newspapers covered them. The analysis reveals that (1) candidate images were distinct in press releases and news stories; (2) candidate positions were represented differently in both; and (3) candidates were differentially successful in getting news media to reflect their positions. News media covered substantive concerns that were not included in candidate press releases.
Civic Journalism and Nonelite Sourcing: Making Routine Newswork of Community Connectedness
Authors: Massey Brian L.
Published: December 2011

Civic journalism's routine use of bringing more “average” citizens into the news was tested by comparing the Tallahassee (FL) Democrat, a nationally recognized civic-journalism newspaper, with its past, traditional-journalism self and a traditionalist contemporary. Nonelite information sources were elevated to numerical parity with elite sources in the civic journalism Democrat, but the frequency and directness of their news voices were largely unchanged. The news-voice profile of elites was diminished in the civic-journalism paper. Routine civic journalism at the Democrat did more to tone down the newsworthiness of elites than to raise the volume for nonelites.
The Birth of a Notion: Media Coverage of Contraception, 1915–1917
Authors: Flamiano Dolores
Published: December 2011

This article analyzes the emergence of media discourses on contraception from 1915 to 1917, focusing on coverage in the New York Times, The New Republic, and Harper's Weekly. Considered legally obscene and unfit for public discussion, contraception first made headlines as a result of Margaret Sanger's birth control activism and ensuing legal troubles. After the New York Times covered Sanger's activities, several magazines began to publish articles on the contraception debate. This early coverage of birth control emphasized its scientific and social utility, virtually ignoring controversial issues of gender, sexuality, and power.
The Influence of Political Talk Radio on Confidence in Democratic Institutions
Authors: Pfau Michael , Moy Patricia , Holbert R. Lance , Szabo Erin A. , Lin Wei-Kuo , Zhang Weiwu
Published: December 2011

This study compares people's use of political talk radio to that of other mass communication sources and to their confidence in democratic institutions. The paper argues that communication modalities (e.g., political talk radio) serve as important sources of secondary socialization: negative depictions of democratic institutions by specific sources cultivate negative perceptions of those institutions among users of these modalities. In order to test this position, the investigation employs a broad interconnected approach, combining a content analysis of references to specific democratic institutions across mass communication sources with a survey of people's media use patterns and their confidence in institutions. The results indicate that political talk radio depicts most institutions negatively, and that listeners manifest reduced confidence in those institutions. The implications of these findings for this nation's “crisis of confidence” in political institutions are explored.
Does Web Advertising Work? Memory for Print vs. Online Media
Authors: Sundar S. Shyam , Narayan Sunetra , Obregon Rafael , Uppal Charu
Published: December 2011

Is memory for an advertisement related to the medium in which the ad was viewed? A between-subjects experiment (N = 48) was designed to answer this question. One-half of the subjects was exposed to a print newspaper front-page with two news stories and one advertisement whereas the other half was exposed to the online version of the same content. Results showed that print subjects remembered significantly more ad material than online subjects.
Medicine, Media, and Celebrities: News Coverage of Breast Cancer, 1960–1995
Authors: Corbett Julia B. , Mori Motomi
Published: December 2011

This research investigated the relationship between medical activities, public events, and media coverage of breast cancer during a thirty-six-year period.1 There was substantial support for medical attention preceding media attention to breast cancer, and some evidence of medical attention following media coverage. There were extremely high, significant correlations between numbers of medical journal articles and newspaper, magazine, and TV coverage. Time-series analysis revealed a two-way, concurrent relationship between breast cancer funding and media coverage. Public events (prominent women acknowledging their breast cancer) significantly affected media coverage. There was a two-way concurrent relationship between breast cancer incidence and TV coverage.
Exploring Receivers' Criteria for Perception of Print and Online News
Authors: Sundar S. Shyam
Published: December 2011

This study investigates the factor structure underlying receivers' perceptions of news content. Exploratory analyses of readers' ratings of a wide variety of news stories reveals that receivers implicitly use at least four key variables in their perception of printed and online news stimuli. This article explicates the four criteria used by news receivers—Credibility, Liking, Quality, and Representativeness—and offers measures for future empirical research on news perception.
Placing Alcohol Warnings before, during, and after TV Beer Ads: Effects on Knowledge and Responses to the Ads and the Warnings
Authors: Slater Michael D. , Rouner Donna , Karan David , Murphy Kevin , Beauvais Frederick
Published: December 2011

This experiment compared the effects of warnings placed before, during, or after television beer advertisements. Warnings before or after the ads led to higher knowledge scores and fewer negative comments about the warning presentation than did warnings scrolled during the ads; warnings after and during but not before the ads significantly decreased positive comments about the ads. Earlier findings regarding effects of warning topic and quantitative information in the warnings were replicated.
Who Do You Think You Are? Personal Home Pages and Self-Presentation on the World Wide Web
Authors: Dominick Joseph R.
Published: December 2011

Personal home pages on the World Wide Web make it possible for anyone to be a mass communicator. They represent an unprecedented chance to study the audience as producers of mass communication content rather than as consumers. The current study content analyzed 319 personal home pages and identified their most popular features. In addition, personal home pages were examined as new channels of self-presentation, a topic that has received much research attention from psychologists. Findings indicated that most personal web pages did not contain much personal information. The typical page had a brief biography, a counter or guest book, and links to other pages. The same strategies of self-presentation were employed on personal pages with the same frequency as they were in the interpersonal setting. There were also gender differences in self-presentation that were consistent with research findings from social psychology.
Professional Opinions on Violence Against Women and Femicide in Spain
Authors: Gonzalez-Mendez Rosaura , Santana-Hernandez Juana Dolores
Published: December 2011

This qualitative study explores the opinions of professionals on the causes of femicide in Spain through a structured interview with open questions. The participants were 29 professionals from various agencies for women’s protection, police services and law courts (Tenerife, Canary Islands). Participants gave their views on four main topics: (a) opinions on intimate partner violence and femicide, (b) opinions on women who suffer violence, (c) opinions on offenders, and (d) opinions concerning the protection system. These professionals described a complex reality and pointed out several weaknesses in the system. Findings have implications for policies intended to combat gender-based violence.
Radon Exposure Assessment for Sewerage System’s Workers in Naples, South Italy
Authors: Pugliese M. , Quarto M. , De Cicco F. , De Sterlich C. , Roca V.
Published: December 2011

An indoor radon survey has been carried out in 17 workplaces of sewerage system of Naples city using E-Perm detectors in long-term configuration. The main objective was to assess the mean effective dose for workers. The measured indoor radon concentration ranged from 1714 to 3789 Bq m−3 in the rooms located on second level underground, from 138 to 5772 Bq m−3 in the rooms on first level underground and from 53 to 913 Bq m−3 in the ground floor. The mean annual effective doses in the ground floor, first and second level underground were found to be 0.85 mSv, 0.29 mSv and 0.43 mSv, respectively. These values are less than the lower limit of International Commission on Radiological Protection (ICRP) recommended action levels of 3–10 mSv y−1.
Deciding to use the law in social work practice
Authors: Braye Suzy , Preston-Shoot Michael , Wigley Veronica
Published: December 2011

• Summary: This article reviews evidence on how social workers incorporate legal rules in their decision-making. It draws on a small empirical study in which practitioners shared with each other, in peer interviews, examples of their own casework, followed by individual interviews with a researcher. Taken together, the conversations cast light on the extent to which legal knowledge is foregrounded in practitioners’ accounts of their work.

• Findings: The findings show that references to law are more likely to be implicit than explicit, particularly in adult social care, and that absence of legal references is a striking feature of the social workers’ narratives. The article draws on related literature to interrogate the potential reasons for the relatively low profile of ‘law talk’ and identifies four factors – lack of legal knowledge and confidence, reliance on organizational and procedural approaches, assumptions about the role of law in different service contexts, and individual orientations to practice – as significant factors in determining whether and how legal rules are relied upon. Thus it presents a more nuanced analysis of the relationship between law and practice than has hitherto been available.

• Applications: The findings are significant in casting light on the complex range of factors that present barriers to the robust and consistent implementation of legal rules in social work. They have implications – in particular for the role of organizational management in the audit, development and supervision of practice – that are particularly topical in the context of the work in England of the Social Work Reform Board.
“All Our Kids Get Better Jobs Tomorrow”: The North American Free Trade Agreement in The New York Times
Authors: Goss Brian Michael
Published: December 2011

This investigation examines over 300 articles in The New York Times from 1993 that concern the North American Free Trade Agreement (NAFTA). In constructing a critical analysis of The Times's discourse on NAFTA, I begin with an overview of the factors that impact on contemporary media-government relations in the United States (e.g., “information subsidy,” stereotyped narrative forms into which news accounts are typically organized). Thereafter, I demonstrate how the private sector's and Clinton government's emphatic support for the agreement was regularly insinuated into The Times's coverage. Despite “legitimate controversy” that surrounded NAFTA, The Times's sourcing patterns distinctly shaded toward pro-NAFTA sources. Moreover, the Clinton government's “market/democracy” and “economic invasion” appeals for NAFTA became prominent storylines in The Times despite their implausibility. Conversely, The Times's treatment of the NAFTA opposition (most particularly, the opposition of unions and Ross Perot) was harsh and encased within personalized narratives that skirted away from substantive analysis. Given the stakes involved in this complex, high profile, and consequential issue, I conclude by theorizing what The Times's NAFTA discourse implies about journalism and U.S. democracy.
Anti-Communism, Race, and Structuration: Newspaper Coverage of the Labor and Desegregation Movements in the South, 1932–40 and 1953–61
Authors: Durham Frank D.
Published: December 2011

The Southern labor and desegregation movements were organized at the Highlander Folk School in Tennessee between 1932–40 and 1953–61, respectively. This historical sociology examines the role of journalism within the process of social reform by focusing on the labor and desegregation movements as racial “hot spots” of ideological tension and pragmatic transformation. A comparison of the relationship in news coverage in each movement period between the rhetoric of anti-Communism and the newspapers' normative fight against desegregation provides a point of critical analysis. In the interpretation of the resulting process of reforms, Anthony Giddens' (1984) theory of structuration supports the analysis of interactions between movement activists and their normative counterparts at the state's newspapers that ultimately produced social and institutional reforms.
First Amendment Values in Fair Use Analysis
Authors: Olson Kathleen K.
Published: December 2011

This monograph examines the status of the fair use doctrine as a “First Amendment safeguard” used to maintain the proper constitutional balance between authors' rights and public access to creative works. In particular, it examines the role that First Amendment values have played in the courts' analysis of fair use cases since enactment of the 1976 Copyright Act, focusing on a subset of cases involving secondary uses of copyrighted material of the types of speech that would receive greater protection under traditional First Amendment analysis. Cases involving fair use disputes over news reporting and comment and criticism, including political speech and parody, are examined in order to determine the underlying purpose of fair use and its role in preserving First Amendment values within the copyright system.
Wonderlic, Race, and the NFL Draft
Authors: Gill Andrew , Brajer Victor
Published: December 2011

Extending the work of Berri and Simmons on the National Football League (NFL) player draft and the Scouting Combine, the authors use the Wonderlic cognitive ability test to test one implication of a simple Phelps model of statistical discrimination in the NFL draft. The authors treat Wonderlic scores as a noisy signal of a player’s adaptability to the NFL game that may be more informative for White players than it is for Black players. The authors find that Wonderlic scores are important in explaining relative draft position for quarterbacks, offensive linemen, and tight ends. At the same time, the authors find limited evidence to support statistical discrimination based on Wonderlic scores.
Treatment, risk factors, and outcome of adults with relapsed AML after reduced intensity conditioning for allogeneic stem cell transplantation
Authors: Schmid Christoph , Labopin Myriam , Nagler Arnon , Niederwieser Dietger , Castagna Luca , Tabrizi Reza , Stadler Michael , Kuball Jürgen , Cornelissen Jan , Vorlicek Jiri , Socié Gerard , Falda Michele , Vindeløv Lars , Ljungman Per , Jackson Graham , Kröger Nicolaus , Rank Andreas , Polge Emmanuelle , Rocha Vanderson , Mohty Mohamad ,   on behalf of the Acute Leukaemia Working Party of the European Group for Blood and Marrow Transplantation (EBMT)
Published: December 2011

Because information on management and outcome of AML relapse after allogeneic hematopoietic stem cell transplantation (HSCT) with reduced intensity conditioning (RIC) is scarce, a retrospective registry study was performed by the Acute Leukemia Working Party of EBMT. Among 2815 RIC transplants performed for AML in complete remission (CR) between 1999 and 2008, cumulative incidence of relapse was 32% ± 1%. Relapsed patients (263) were included into a detailed analysis of risk factors for overall survival (OS) and building of a prognostic score. CR was reinduced in 32%; remission duration after transplantation was the only prognostic factor for response (P = .003). Estimated 2-year OS from relapse was 14%, thereby resembling results of AML relapse after standard conditioning. Among variables available at the time of relapse, remission after HSCT > 5 months (hazard ratio [HR] = 0.50, 95% confidence interval [CI], 0.37-0.67, P < .001), bone marrow blasts less than 27% (HR = 0.53, 95% CI, 0.40-0.72, P < .001), and absence of acute GVHD after HSCT (HR = 0.67, 95% CI, 0.49-0.93, P = .017) were associated with better OS. Based on these factors, 3 prognostic groups could be discriminated, showing OS of 32% ± 7%, 19% ± 4%, and 4% ± 2% at 2 years (P < .0001). Long-term survival was achieved almost exclusively after successful induction of CR by cytoreductive therapy, followed either by donor lymphocyte infusion or second HSCT for consolidation.
Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows
Authors: Barriuso Jorge , Valverde Jose R , Mellado Rafael P
Published: December 2011

Background

Next generation sequencing (NGS) enables a more comprehensive analysis of bacterial diversity from complex environmental samples. NGS data can be analysed using a variety of workflows. We test several simple and complex workflows, including frequently used as well as recently published tools, and report on their respective accuracy and efficiency under various conditions covering different sequence lengths, number of sequences and real world experimental data from rhizobacterial populations of glyphosate-tolerant maize treated or untreated with two different herbicides representative of differential diversity studies.

Results

Alignment and distance calculations affect OTU estimations, and multiple sequence alignment exerts a major impact on the computational time needed. Generally speaking, most of the analyses produced consistent results that may be used to assess differential diversity changes, however, dataset characteristics dictate which workflow should be preferred in each case.

Conclusions

When estimating bacterial diversity, ESPRIT as well as the web-based workflow, RDP pyrosequencing pipeline, produced good results in all circumstances, however, its computational requirements can make method-combination workflows more attractive, depending on sequence variability, number and length.
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
Authors: Zhao Qiong-Yi , Wang Yi , Kong Yi-Meng , Luo Da , Li Xuan , Hao Pei
Published: December 2011

Background

With the fast advances in nextgen sequencing technology, high-throughput RNA sequencing has emerged as a powerful and cost-effective way for transcriptome study. De novo assembly of transcripts provides an important solution to transcriptome analysis for organisms with no reference genome. However, there lacked understanding on how the different variables affected assembly outcomes, and there was no consensus on how to approach an optimal solution by selecting software tool and suitable strategy based on the properties of RNA-Seq data.

Results

To reveal the performance of different programs for transcriptome assembly, this work analyzed some important factors, including k-mer values, genome complexity, coverage depth, directional reads, etc. Seven program conditions, four single k-mer assemblers (SK: SOAPdenovo, ABySS, Oases and Trinity) and three multiple k-mer methods (MK: SOAPdenovo-MK, trans-ABySS and Oases-MK) were tested. While small and large k-mer values performed better for reconstructing lowly and highly expressed transcripts, respectively, MK strategy worked well for almost all ranges of expression quintiles. Among SK tools, Trinity performed well across various conditions but took the longest running time. Oases consumed the most memory whereas SOAPdenovo required the shortest runtime but worked poorly to reconstruct full-length CDS. ABySS showed some good balance between resource usage and quality of assemblies.

Conclusions

Our work compared the performance of publicly available transcriptome assemblers, and analyzed important factors affecting de novo assembly. Some practical guidelines for transcript reconstruction from short-read RNA-Seq data were proposed. De novo assembly of C. sinensis transcriptome was greatly improved using some optimized methods.
Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies
Authors: Shimizu Masaaki , Nagamochi Hiroshi , Akutsu Tatsuya
Published: December 2011

Background

Enumeration of chemical graphs satisfying given constraints is one of the fundamental problems in chemoinformatics and bioinformatics since it leads to a variety of useful applications including structure determination of novel chemical compounds and drug design.

Results

In this paper, we consider the problem of enumerating all tree-like chemical graphs from a given set of feature vectors, which is specified by a pair of upper and lower feature vectors, where a feature vector represents the frequency of prescribed paths in a chemical compound to be constructed. This problem can be solved by applying the algorithm proposed by Ishida et al. to each single feature vector in the given set, but this method may take much computation time because in general there are many feature vectors in a given set. We propose a new exact branch-and-bound algorithm for the problem so that all the feature vectors in a given set are handled directly. Since we cannot use the bounding operation proposed by Ishida et al. due to upper and lower constraints, we introduce new bounding operations based on upper and lower feature vectors, a bond constraint, and a detachment condition.

Conclusions

Our proposed algorithm is useful for enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies.
Application of magnifying narrow-band imaging endoscopy for diagnosis of early gastric cancer and precancerous lesion
Authors: Zhang Jing , Guo Shi-Bin , Duan Zhi-Jun
Published: December 2011

Background

Gastric carcinoma is the second commonest cause of cancer deaths worldwide. Early detection and diagnosis of gastric cancer in the stomach is important for improving the prognosis of gastric cancer. This retrospective study was designed to investigate the value of magnifying narrow-band imaging (NBI) in the diagnosis of precancerous lesions and early gastric cancer.

Methods

This study included 122 patients who were diagnosed with early gastric cancer or precancerous gastric lesions by endoscopy. The patients underwent an examination with conventional endoscopy, magnifying NBI, and magnifying chromoendoscopy. Images resolution was evaluated, and the morphology, pit patterns and blood capillary forms of lesions were analyzed. The presence of gastric carcinoma and high grade intraepithelial neoplasia in the biopsy samples was considered as a positive pathological result, which is used to assess accuracy of endoscopic diagnosis.

Results

For image resolution, magnifying NBI and magnifying chromoendoscopy were significantly superior to magnifying conventional endoscopy in morphology, pit pattern and blood capillary form (P < 0.01), and magnifying NBI was significantly superior to magnifying chromoendoscopy in blood capillary form (P < 0.01). IV, V1, and VI type of gastric pit pattern were detected in 14 cases, 43 cases, and 17 cases in patients with high grade intraepithelial neoplasia, respectively. V1and VI type of gastric pit pattern were detected in 9 cases and 39 cases in patients with early gastric cancer, respectively. The presence of irregular minute vessels and variation in the caliber of vessels was found in 109 cases. The accuracy, sensitivity, specificity, false positive rate and false negative rate for diagnosis of early gastric cancer and precancerous gastric lesions were 68.9%, 95.1%, 63.1%, 24.5%, and 32.4% for conventional endoscopy, 93.6%, 92.7%, 94.5%, 5.7%, and 6.9% for magnifying NBI, and 91.3%, 88.6%, 93.2%, 13.2%, and 21.48% for magnifying chromoendoscopy, respectively.

Conclusions

This study demonstrates that magnifying NBI is superior to conventional endoscopy in the diagnosis of early gastric cancer and precancerous gastric lesions, and can be used for screening early malignancies of the stomach.
Successful management of cryptococcosis of the bilateral adrenal glands and liver by unilateral adrenalectomy with antifungal agents: a case report
Authors: Matsuda Yayoi , Kawate Hisaya , Okishige Yuka , Abe Ichiro , Adachi Masahiro , Ohnaka Keizo , Satoh Naoichi , Inokuchi Junichi , Tatsugami Katsunori , Naito Seiji , Nomura Masatoshi , Takayanagi Ryoichi
Published: December 2011

Background

Cryptococcusspecies usually affect the central nervous system and lungs in immunocompromised hosts. Although the adrenal glands can be involved in disseminated cryptococcosis, primary adrenal insufficiency caused by the fungal infection is uncommon.

Case presentation

We present a case of primary adrenal insufficiency with bilateral adrenal masses and liver invasion in a 43-year-old man with mild type 2 diabetes mellitus. Cryptococcosis was diagnosed by fine-needle aspiration biopsy of the liver mass. The serum cryptococcal antigen titer was elevated to 1:256. After 6 months of antifungal therapy with fluconazole and amphotericin B, the size of the liver mass was decreased, but no significant changes were observed in the bilateral adrenal masses and the serum cryptococcal antigen titer remained elevated at 1:128. To control the cryptococcosis, a laparoscopic left adrenalectomy was performed, followed by antifungal therapy. After the unilateral adrenalectomy, the size of the remaining right adrenal mass was reduced and the serum cryptococcal antigen titer declined to 1:4.

Conclusions

This is the first report describing adrenal cryptococcosis with adrenal insufficiency and liver invasion without central nervous system involvement. Adrenal cryptococcosis should be considered in the differential diagnosis for patients with bilateral adrenal masses with primary adrenal deficiency. Unilateral adrenalectomy was quite effective in controlling the cryptococcosis in this case. Even in patients with bilateral adrenal cryptococcosis, unilateral adrenalectomy should be an option for treatment of disseminated cryptococcosis.
Rate and determinants of treatment response to different antiretroviral combination strategies in subjects presenting at HIV-1 diagnosis with advanced disease
Authors: Esposito Antonella , Floridia Marco , d'Ettorre Gabriella , Pastori Daniele , Fantauzzi Alessandra , Massetti Paola , Ceccarelli Giancarlo , Ajassa Camilla , Vullo Vincenzo , Mezzaroma Ivano
Published: December 2011

Background

The optimal therapeutic strategies for patients presenting with advanced disease at HIV-1 diagnosis are as yet incompletely defined.

Methods

All patients presenting at two outpatient clinics in 2000-2009 with an AIDS-defining clinical condition or a CD4+ T cell count < 200/μL at HIV-1 diagnosis were analyzed for the presence of combined immunovirological response, defined by the concomitant presence of an absolute number of CD4+ T cells > 200 cells/μL and a plasma HIV-1 RNA copy number < 50/mL after 12 months of HAART.

Results

Among 102 evaluable patients, first-line regimens were protease inhibitors [PI]-based in 78 cases (77%) and efavirenz-based in 24 cases (23%). The overall response rate was 65% (95% CI: 55-74), with no differences by gender, age, nationality, route of transmission, hepatitis virus coinfections, presence of AIDS-defining clinical events, baseline HIV-1 viral load, or type of regimen (response rates with PI-based and efavirenz-based therapy: 63% and 71%, respectively, p = 0.474). Response rate was significantly better with higher baseline CD4+ T cell counts (78% with CD4+ ≥ 100/μL, compared to 50% with CD4+ < 100/μL; odds ratio: 3.5; 95% CI: 1.49-8.23, p = 0.003). Median time on first-line antiretroviral therapy was 24 months (interquartile range: 12-48). Switch to a second line treatment occurred in 57% of patients, mainly for simplification (57%), and was significantly more common with PI-based regimens [adjusted hazard ratios (AHR) with respect to efavirenz-based regimens: 3.88 for unboosted PIs (95% CI: 1.40-10.7, p = 0.009) and 4.21 for ritonavir-boosted PI (95%CI 1.7-10.4, p = 0.002)] and in older subjects (≥ 50 years) (AHR: 1.83; 95% CI: 1.02-3.31, p = 0.044). Overall mortality was low (3% after a median follow up of 48 months).

Conclusions

Our data indicate that a favorable immunovirological response is possible in the majority of naive patients presenting at HIV-1 diagnosis with AIDS or low CD4+ T cell counts, and confirm that starting HAART with a more compromised immune system may be associated with a delayed and sometimes partial immune recovery. Simpler regimens may be preferable in this particular population.
A novel mutation in STK11 gene is associated with Peutz-Jeghers Syndrome in Chinese patients
Authors: Wang Zhiqing , Chen Yulan , Wu Baoping , Zheng Haoxuan , He Jiman , Jiang Bo
Published: December 2011

Background

Peutz-Jeghers syndrome (PJS) is caused by mutations in the tumor suppressor gene, STK11, and is characterized by gastrointestinal hamartomas, melanin spots on the lips, and an increased risk of developing cancer.

Methods

Blood samples were collected from two unrelated Chinese PJS families totaling 20 individuals (9 male and 11 females), including 6 PJS patients. The entire coding region of the STK11 gene was amplified by polymerase chain reaction and analyzed by direct sequencing.

Results

A novel mutation, c.904C > T, in exon 7 was identified in both families. A C > T substitution changed codon 302 from CAG (glutamine) to TAG (stop), truncating the STK11 protein, thus leading to the partial loss of the kinase domain and complete loss of the α-helix C-terminus. Furthermore, one PJS patient from each family was diagnosed with a visceral cancer, a colon cancer and a liver cancer respectively.

Conclusion

We predict that this novel mutation, p.Q302X, is most likely responsible for development of the PJS phenotype and may even contribute to malignancy.
The association between parity, infant gender, higher level of paternal education and preterm birth in Pakistan: a cohort study
Authors: Shaikh Kiran , Premji Shahirose S , Rose Marianne S , Kazi Ambreen , Khowaja Shaneela , Tough Suzanne
Published: December 2011

Background

High rates of antenatal depression and preterm birth have been reported in Pakistan. Self reported maternal stress and depression have been associated with preterm birth; however findings are inconsistent. Cortisol is a biological marker of stress and depression, and its measurement may assist in understanding the influence of self reported maternal stress and depression on preterm birth.

Methods

In a prospective cohort study pregnant women between 28 to 30 weeks of gestation from the Aga Khan Hospital for Women and Children completed the A-Z Stress Scale and the Centre for Epidemiology Studies Depression Scale to assess stress and depression respectively, and had a blood cortisol level drawn. Women were followed up after delivery to determine birth outcomes. Correlation coefficients and Wilcoxon rank sum test was used to assess relationship between preterm birth, stress, depression and cortisol. Logistic regression analysis was used to determine the key factors predictive of preterm birth.

Results

132 pregnant women participated of whom 125 pregnant women had both questionnaire and cortisol level data and an additional seven had questionnaire data only. Almost 20% of pregnant women (19·7%, 95% CI 13·3-27·5) experienced a high level of stress and nearly twice as many (40·9%, 95% CI 32·4-49·8%) experienced depressive symptoms. The median of cortisol level was 27·40 ug/dl (IQR 22·5-34·2). The preterm birth rate was 11·4% (95% CI 6·5-18). There was no relationship between cortisol values and stress scale or depression. There was a significant positive relationship between maternal depression and stress. Preterm birth was associated with higher parity, past delivery of a male infant, and higher levels of paternal education. Insufficient numbers of preterm births were available to warrant the development of a multivariable logistic regression model.

Conclusions

Preterm birth was associated with higher parity, past delivery of a male infant, and higher levels of paternal education. There was no relationship between stress, and depression, cortisol and preterm birth. There were high rates of stress and depression among this sample suggesting that there are missed opportunities to address mental health needs in the prenatal period. Improved methods of measurement are required to better understand the psychobiological basis of preterm birth.
Association of ADAMTS13 polymorphism with cerebral malaria
Authors: Kraisin Sirima , Naka Izumi , Patarapotikul Jintana , Nantakomol Duangdao , Nuchnoi Pornlada , Hananantachai Hathairad , Tsuchiya Naoyuki , Ohashi Jun
Published: December 2011

Background

Cerebral malaria is one of the most severe manifestations of Plasmodium falciparum malaria. The sequestration of parasitized red blood cells (PRBCs) to brain microvascular endothelium has been shown to contribute to the pathophysiology of cerebral malaria. Recent studies reported increased levels of von Willebrand factor (VWF) and reduced activity of VWF-cleaving protease, ADAMTS13 (a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13), in patients with cerebral malaria.

Methods

Association of six single nucleotide polymorphisms (SNPs) of the ADAMTS13 gene with cerebral malaria was examined in 708 Thai patients with P. falciparum malaria.

Results

Among six SNPs, the derived allele of a SNP located in intron 28, rs4962153-A, was significantly associated with protection against cerebral malaria when 115 cerebral malaria patients were compared with 367 mild malaria patients (Fisher's exact P-value = 0.0057; OR = 0.27; 95% CI = 0.096-0.76). Significant association was also detected between 115 cerebral malaria and 593 non-cerebral malaria (226 non-cerebral severe malaria and 367 mild malaria) patients (Fisher's exact P-value = 0.012; OR = 0.30; 95% CI = 0.11-0.83).

Conclusions

Excessive adhesion of PRBCs to the platelet-decorated ultra-large VWF (ULVWF) appears to enhance the sequestration of PRBCs to cerebral microvascular endothelium. The genetic association observed in the present study implies that the regulation of platelet-decorated ULVWF strings by ADAMTS13 may play a role in the development of cerebral malaria.