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PubMed1988

A secondary and tertiary structure editor for nucleic acids.

A major difficulty in the evaluation of secondary and tertiary structures of nucleic acids is the lack of convenient methods for their construction and representation. As a first step in a study of the symbolic representation of biopolymers, we report the development of a structure editor written in Pascal, permitting model construction on the screen of a personal computer. The program calculates energies for helical regions, allows user-defined helices and displays the secondary structure of a nucleic acid based on a user-selected set of helices. Screen and printer outputs can be in the form of a backbone or the letters of the primary sequence. The molecule can then be displayed in a format which simulates its three-dimensional structure. Using appropriate glasses, the molecule can be viewed on the screen in three dimensions. Other options include the manipulation of helices and single-stranded regions which results in changes in the spatial relationship between different regions of the molecule. The editor requires an IBM or compatible PC, 640 kbyte memory and a medium or high resolution graphics card.

Algorithms↗
PubMed2005

Illness stories on the Internet: features of websites disclosing breast cancer patients' illness stories in the Dutch language.

OBJECTIVE: To examine the way in which breast cancer patients' illness stories in the Dutch language are disclosed on the Internet. METHODS: Websites containing Dutch illness stories written by breast cancer patients were selected using a search engine on the Internet. A checklist was developed based on a theoretical framework for analysing communication processes in order to examine the selected websites. RESULTS: None of the websites implements search facilities based on either the content of an illness story, or the personal features of the author. A minority of the websites offers information about the illness stories, such as author's genuineness and editor's review. CONCLUSION: The Internet's opportunities are not fully utilized with respect to disclosing breast cancer patients' illness stories. PRACTICE IMPLICATIONS: In order to support a patient in finding appropriate illness stories in the diverse set of available stories, we are in the process of developing an application that combines symbolic and statistical natural language analysis techniques to facilitate content-based retrieval.

Adaptation, Psychological↗
PubMed2003

Does anybody read "evidence-based" articles?

BACKGROUND: The electronic version of the British Medical Journal (eBMJ) has a unique feature in that it provides an electronic record of the number of times an article has been viewed ("hits") in the week after its publication. We sought to compare the relative popularity of primary research and "evidence-based" papers against that of narrative reviews and editorials. We surveyed four broad groupings of articles in 2001: Editorials, Clinical Reviews (which are narrative reviews), Education and Debate, and Papers (which are original research articles and systematic reviews). Clinical Reviews were the most frequently viewed articles, with an average of 4148 hits per article, while Papers were less popular (average of 1168 hits per article). Systematic reviews (23 articles, average of 1190 hits per article) were visited far less often than narrative reviews. Editorials (average of 2537 hits per article) were viewed much more frequently than Papers, even where the editorial was written as an accompanying piece with a direct link to the paper. DISCUSSION: Narrative reviews and editorials are accessed more frequently than primary research papers or systematic reviews in the first week after their publication. These findings may disappoint those who believe that it is important for readers to critically appraise the primary research data. Although the technical quality of journal articles may have been helped by recommendations on structured reporting, the readability of such articles has received little attention. Authors and journal editors must take steps to make research articles and systematic reviews more attractive to readers. This may involve using simpler language, as well as innovative use of web resources to produce shorter, snappier papers, with the methodological or technical details made available elsewhere. CONCLUSION: Primary research and "evidence-based" papers seem to be less attractive to readers than narrative reviews and editorials in the first week after publication. Authors and editors should try to improve the early appeal of primary research papers.

Evidence-Based Medicine↗
PubMed1999

Raising the quality of cost-utility analyses: lessons learnt and still to learn.

Heightened awareness by health care funders of the need to find more efficient ways of using scarce health care resources has led to greater demand for evidence of cost-effectiveness. Implicit in this demand is that evidence is generated using clear reporting and accepted methods. The research reported here updates an earlier review of published cost-utility analyses (CUAs) to address whether previously identified gaps in reporting have diminished over time. Raising CUA standards requires systematic and regular reviews of published material to allow adequate monitoring and evaluation. There is also a need to 'appraise the appraisers' in the sense of reviewing peer-review processes. This is particularly so in those journals which are growing in importance as outlets for economic evaluation information. The findings from this study indicate continuing variation in the quality of reporting. At the lower end of this spectrum improvements could be made in the reporting of comparators, in the clarity of effectiveness evidence, in the assignment of utility weights to health states and in reporting of sensitivity analysis. CUAs published in peer-reviewed specialist medical journals were more likely to be lower in quality suggesting guidance on the appraisal of economic submissions needs to be extended to the editors of these particular journals. These findings could be used to help to target attempts to raise the quality of evidence-based CUA information.

Australia↗
PubMed2000

Ethical responsibilities of editors, reviewers, and authors.

Scientific misconduct, which is neither new nor unique, is prevalent in the medical literature. Although fabrication of data obviously is unethical, and although ethical rules of conduct for certain aspects of medical studies, such as informed consent, are theoretically accepted worldwide, numerous authors do not adhere to ethical rules of conduct. Ethically, the editor is responsible, as a gatekeeper, for ensuring that material to be published is accurate and valid. Thus, the editor's main responsibility is to the reader. Nonetheless, the editor also must serve the author by selecting unbiased reviewers and by providing the assurance that material will be selected for publication based solely on the scientific quality of the material. Peer reviewers are obligated to maintain a posture of confidentiality throughout the review process. Authors are responsible for adequate planning before undertaking a study, and for safeguarding patients' rights during the study. The author must read all cited references completely, strive for accuracy, and be certain that the material reported is valid, because it will be used in the treatment of patients. Hopefully, awareness of the ethical problems related to medical writing will provide a clearer understanding of the ethical aspects of medical writing.

Authorship↗
PubMed1991

Systems face challenges. Interview by Donald E.L. Johnson.

The regional hospital system has become a mainstay in the structuring of health care during the past decade. How will it fare in the next 10 years? In the following interview with Health Care Strategic Management's editor and publisher Donald E.L. Johnson, Fred L. Brown, president and chief executive officer of Christian Health System, the St. Louis, Mo.-based umbrella organization for nine hospitals, six nursing facilities, and one retirement community, predicts a bright future for the health care system. He also discusses the strategies that are unique to the success of such a system.

Christianity↗
PubMed1994

Merger offers IS managers flexibility & less stressful integrating, downsizing, & outsourcing. Interview by Bill Childs.

A merger between two multi-million dollar IS firms in July 1993 created a company with $315 million in sales and a sharp focus on healthcare. National Healthtech Corp., parent firm of MRI, brought the focus to the deal. And Dallas-based Affiliated Computer Services, a data services provider to financial, commercial and healthcare organizations, brought telecommunications and outsourcing expertise. Bill Childs, editor-in-chief, recently spoke with the two firms' principals--Richard A. Montgomery, CEO of National Healthtech Corp., and Steve Carpenter, senior VP of ACS and COO of NHC. Excerpts from their conversation follow.

Contract Services↗
PubMed1990

Risk prediction in medicine and surgery: ethical and practical considerations.

Risk prediction is a subject of increasing clinical interest, and publications in this area are likely to have an important influence on patient care in the near future. A multiplicity of risk prediction systems, many of them computer-based, will raise a number of ethical and practical questions. These questions need to be addressed by the originators of systems, the editors of journals, practising clinicians, and the lay public.

Biomedical Research↗
PubMed2006

Can academic and clinical journals be in financial conflict of interest situations? The case of evidence-based incorporated.

The hypothesis is advanced that scholarly journals can find themselves in conflict of interest positions when they operate business strategies which for commercial reasons may militate against the publication of articles which question the usefulness of the products being sold. It is suggested on the basis of probabilistic reasoning that the more extensive the merchandizing and the greater the commercial profits, the greater is the potential for conflict of interest. The alternative hypothesis is advanced that such a conflict of interest position cannot possibly exist. The current Hypothesis paper is published in order to stimulate debate on the subject of study. The reader is referred to the Editor's Note p. 395.

Conflict of Interest↗
PubMedDate not supplied

Does exchanging comments of Indian and non-Indian reviewers improve the quality of manuscript reviews?

BACKGROUND: The quality of peer reviewing in developing countries is thought to be poor. To examine whether this was so, we compared the performance of Indian and non-Indian reviewers who were sent original and review articles submitted to The National Medical Journal of India. We also tested whether informing reviewers that their comments would be exchanged improved the quality of their reviews. METHODS: In a prospective, randomized, blinded study, we sent 100 manuscripts to pairs of peer reviewers (Indian and non-Indian) of which 78 pairs of completed replies were available for analysis. Thirty-eight pairs of reviews were exchanged and 40 were not. The quality of the reviews was assessed by two editors who were unaware of the reviewers' nationality and whether they had been told that their reviews would be exchanged. The quality of the reviews was scored out of 100 (based on a predesigned evaluation proforma). We also measured the time taken to return a manuscript. RESULTS: Overall, non-Indian reviewers scored higher than Indians (mean scores non-Indians first, 56.7 v. 48.6, p < 0.001), especially those in the non-exchanged group (58.4 v. 47.3, p < 0.001) but not the exchanged group (54.8 v. 50.0, p < 0.06). Being informed that reviews would be exchanged did not affect the quality of reviews by non-Indians (54.8 exchanged v. 58.4 non-exchanged) or of reviews by Indians (50.0 exchanged v. 47.3 non-exchanged). The editors' assessment of the reviewers matched well (r = 0.59, p < 0.001). Non-Indians took the same amount of time as Indians to return their reviews, although the postage time was at least eight days longer. CONCLUSIONS: We found that non-Indian peer reviewers were better than Indians and informing them that their views would be exchanged did not seem to affect the quality of their reviews. We suggest that Indian editors should also use non-Indian reviewers and start training programmes to improve the quality of peer reviews in India.

Humans↗
PubMed2005

Hox genes, digit identities and the theropod/bird transition.

Vargas and Fallon (2005. J Exp Zool (Mol Dev Evol) 304B:86-90) propose that Hox gene expression patterns indicate that the most anterior digit in bird wings is homologous to digit 1 rather than to digit 2 in other amniotes. This interpretation is based on the presence of Hoxd13 expression in combination with the absence of Hoxd12 expression in the second digit condensation from which this digit develops (the first condensation is transiently present). This is a pattern that is similar to that in the developing digit 1 of the chicken foot and the mouse hand and foot. They have tested this new hypothesis by analysing Hoxd12 and Hoxd13 expression patterns in two polydactylous chicken mutants, Silkie and talpid2. They conclude that the data support the notion that the most anterior remaining digit of the bird wing is homologous to digit 1 in other amniotes either in a standard phylogenetic sense, or alternatively in a (limited) developmental sense in agreement with the Frameshift Hypothesis of Wagner and Gautier (1999, i.e., that the developmental pathway is homologous to the one that leads to a digit 1 identity in other amniotes, although it occurs in the second instead of the first digit condensation). We argue that the Hoxd12 and Hoxd13 expression patterns found for these and other limb mutants do not allow distinguishing between the hypothesis of Vargas and Fallon (2005. J Exp Zool (Mol Dev Evol) 304B:86-90) and the alternative one, i.e., the most anterior digit in bird wings is homologous to digit 2 in other amniotes, in a phylogenetic or developmental sense. Therefore, at the moment the data on limb mutants does not present a challenge to the hypothesis, based on other developmental data (Holmgren, 1955. Acta Zool 36:243-328; Hinchliffe, 1984. In: Hecht M, Ostrom JH, Viohl G, Wellnhofer P, editors. The beginnings of birds. Eichstätt: Freunde des Jura-Museum. p 141-147; Burke and Feduccia, 1997. Science 278:666-668; Kundrát et al., 2002. J Exp Zool (Mol Dev Evol) 294B:151-159; Larsson and Wagner, 2002. J Exp Zool (Mol Dev Evol) 294B:146-151; Feduccia and Nowicki, 2002. Naturwissenschaften 89:391-393), that the digits of bird wings are homologous to digits 2,3,4 in amniotes. We recommend further testing of the hypothesis by comparing Hoxd expression patterns in different taxa.

Animals↗
PubMed1987

Three-dimensional reconstruction of biological objects using a graphics engine.

A common problem in the study of biological material is the determination of three-dimensional structure from serial sections. The large number of sections required to obtain sufficient internal detail of a structure results in enormous processing requirements. These requirements can now be satisfied by current graphics engine technology in combination with image-digitizing hardware. The previously onerous tasks of manipulating and displaying 3D objects become routine with this combination of technologies. We report a computer-assisted reconstruction system on a graphics engine-based workstation. The system accepts images from any video source and includes a utility for aligning adjacent video images. Also available is an editor for geometric object entry and editing. More novel in our approach is the use of video interiors in 3D displays in addition to contours and tiled surfaces. Video interiors is a form of display in which digitized pixels interior to objects are revealed by cutaway blocks.

Algorithms↗
PubMed1994

Writing Arden Syntax Medical Logic Modules.

The Arden Syntax for Medical Logic Modules is a language for encoding medical knowledge bases that consist of independent modules. The Arden Syntax has been used to generate clinical alerts, diagnostic interpretations, management messages, and screening for research studies and quality assurance. An Arden Syntax knowledge base consists of rules called Medical Logic Modules (MLMs), which are stored as simple ASCII files that can be written on any text editor. An MLM is made of slots grouped into three categories: maintenance information, library information, and the actual medical knowledge. Most MLMs are triggered by clinical events, evaluate medical criteria, and, if appropriate, perform an action such as sending a message to a health care provider. This paper provides a detailed tutorial on how to write MLMs.

Artificial Intelligence↗
PubMed2003

The battle against SARS: a Chinese story.

SARS is the first major new infectious disease in the 21st century (Rodier, 2003) and is described as a "serious disaster" in mainland China where it caused unprecedented panic and social and economic consequences. A total of 5,327 SARS cases were reported, with 348 deaths (Ministry of Health, 2003a). Although the Chinese government was criticised by the international community for underreporting at the early stages of the SARS epidemic (Editor CMAJ, 2003a), China eventually achieved remarkable success in combating SARS. This paper documents some aspects of the Chinese experience infighting against SARS, based on interviews with my Chinese colleagues, analysed with reference to government policy documents and published articles. My interviewees included health officials at the central, provincial and municipal levels and hospital managers who had been working in the frontline of the battle against SARS.

China↗
PubMed1991

Award showcases programs. Interview by Donald E. L. Johnson.

Mount Zion Hospital and Medical Center, a 290-bed institution in San Francisco, Calif., displayed a commitment to a mission of "caring, grounded in learning, supported by acts of personal kindness" to win the 1990 American Hospital Association's Foster G. McGaw Prize for community service. In the following interview with Health Care Strategic Management's editor and publisher Donald E.L. Johnson, Martin H. Diamond, the hospital's CEO, explains how the institution earned recognition for its community-based programs to aid disenfranchised groups.

American Hospital Association↗