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PubMed2003

QAlign: quality-based multiple alignments with dynamic phylogenetic analysis.

Integrating different alignment strategies, a layout editor and tools deriving phylogenetic trees in a 'multiple alignment environment' helps to investigate and enhance results of multiple sequence alignment by hand. QAlign combines algorithms for fast progressive and accurate simultaneous multiple alignment with a versatile editor and a dynamic phylogenetic analysis in a convenient graphical user interface.

Algorithms↗
PubMed1993

Mismatch recognition in chromosomal interactions and speciation.

Homologous chromosomes interact during meiosis by means of proteins involved in recombination and in the recognition and repair of mismatched base pairs. Recombination proteins bring homologous chromosomes or chromosomal regions together by facilitating the search for DNA homology and by catalyzing strand exchange between homologous molecules or regions. Mismatch recognition and repair proteins act as editors of recombination and appear to disrupt those DNA associations that contain mismatched base pairs. Thus, it may be that, as chromosomes diverge in their primary sequence and become increasingly polymorphic, recombinational interactions leading to chromosome pairing and recombination tend to be inhibited. Decreasing homologous interactions within and between chromosomes will clearly contribute to maintaining the integrity of individual chromosomes and may ultimately lead, as a result of sterile meioses, to the reproductive isolation of closely related species.

Biological Evolution↗
PubMed1998

P-CAPE: a high-level tool for entering and processing clinical practice guidelines. Partners Computerized Algorithm and Editor.

The Partners Computerized Algorithm Processor and Editor (P-CAPE) is a high-level tool intended to remove the programming bottleneck for implementing practice guidelines in our computer-based record system, and to integrate guideline-based advice into the clinician's workflow. P-CAPE has three major components: 1) An Editor that allows an analyst to enter the parameters of a guideline in the form of an algorithm; 2) A Navigator that processes the steps of the guideline and logs all transactions in a patient-specific file; and 3) A clinician Notifier that sends messages to a patient's covering clinician, seeking data or presenting recommendations and order sets that can be processed by the system. P-CAPE's guideline object model was adapted from the InterMed Collaboratory GuideLine Interface Format (GLIF).

Algorithms↗
PubMed1997

[Improving the editing of medical journals and the World Association of Medical Editors (WAME)].

Medical journal editing is a task with many facets. The role of the editors includes organizing and evaluating a peer-review system as a main tool for their decision making in selecting manuscripts to be published. The International Congress on Biomedical Peer Review and Global Communications was held in September, 1997, in Prague, Czech Republic, organized by JAMA, the BMJ and Project HOPE, and sponsored by several other organizations. A meeting of the World Association of Medical Editors took place during this Congress and its institutional objectives and membership were discussed and enlarged, based on the previous foundation Conference held in Bellagio, Italy, in March 1995. The main goals of this Association: "To facilitate worldwide cooperation and communication among editors of peer-reviewed medical journals; to improve editorial standards, to promote professionalism in medical editing through education, self-criticism and self-regulation; and to encourage research on the principles and practices of medical editing" were accomplished in a warm and friendly atmosphere, with over 300 participants from 46 countries and every continent. Revista Médica de Chile was represented in these meetings by its former and present Editors. An analysis of the meetings by the editorial team will lead to changes intended to improve the editorial process in our journal.

Peer Review↗
PubMed1995

Methods of reporting statistical results from medical research studies.

There has recently been vigorous debate about the most appropriate way to report statistical results from medical studies, particularly concerning the relative merits of significance tests, confidence intervals, or other methods such as likelihood. Arguing that p values have often been abused in the past, some biomedical journals now require authors to emphasize confidence intervals instead. A review of the debate reveals points in favor of each of the proposed methods, and more than one type of analysis may be required to obtain a full perspective on the data. Furthermore, a change in editorial policy alone is unlikely to eliminate future statistical errors. It therefore appears unsatisfactory and coercive of editors to mandate the exclusive use of any one approach, based on speculative estimates of the likely rate of its correct usage by future authors. Instead, further work is needed to better understand how consumers of medical research interpret studies, particularly how they are influenced by the authors' methods of summarizing the data. Until then, editorial flexibility is required, so that authors can provide readers with enough information to form their own conclusions from a given set of results. Evidence from papers recently published in the American Journal of Epidemiology suggests that authors are now tending to report results using both significance testing and estimation techniques. This seems entirely appropriate, to avoid the strictures implied by rigid adherence to only one method.

Confidence Intervals↗
PubMed1997

Classification of user expertise level by neural networks.

A neural network approach to low-level user modeling is described, in the context of text editing tasks using the Jove editor. Knowledge of a user's expertise is extracted automatically, based on their interaction with Jove over a two week period. A MLP classifier which uses rprop learning and incorporates output data fuzzification is developed to classify users into one of five expertise levels. Classification into the correct level is achieved in around 80% of the cases, with misclassification being restricted to adjacent classes. The neurofuzzy system is seen to outperform not only the binary classifier of Beale [1989], but also production rule and inductive expert systems developed especially for comparison purposes in this study.

Artificial Intelligence↗
PubMedDate not supplied

[Structure and content of the radiological report: an audit of 94 reports from a university education center].

Efficient communication between the radiologist and the referring clinician is an essential feature of high quality radiology practice. The written report, the only result of the radiological investigation most clinicians will see, should therefore comply with a number of quality criteria. As far as reporting in Dutch is concerned, these criteria have not been clearly defined. Articles on the radiology report are scarce and mostly focus on reporting in English. We have investigated the quality of radiology reporting in a university hospital in Flanders, the Dutch speaking part of Belgium. A weighed sample of 94 reports of 24 radiologists (staff members and radiologists-in-training) was blinded and evaluated by a qualified radiologist with ten years of experience as a writer and editor-in-chief medical magazines. A scoring system was applied, based on five criteria: comprehensible, problem-oriented, correct Dutch, concise, and direct. This article gives an overview of the results and takes a closer look at three of the 94 reports examined.

Humans↗
PubMed2002

[Anales Españoles de Pediatría 2001. Bibliometric indicators of scientific quality].

UNLABELLED: BACKGROUND. One important objective of Anales Españoles de Pediatría (An Esp Pediatr) is to be included in Journal Citation Reports-Science Citation Index and the main step to achieve this is to increase the scientific quality of this Spanish journal. Bibliometric indicators are important tools used to determine the quality of scientific publications. MATERIAL AND METHODS: A bibliometric study of all the original articles published in An Esp Pediatr in 2001 (n 76) was performed; bibliometric indicators were classified into quantitative and qualitative (statistical analyses and level of scientific evidence). The results were compared with the original articles published in the journal from 1994 to June 2000 (n 733) and with the original articles published in Pediatrics in 2001 (n 276). RESULTS: The differences found in An Esp Pediatr between the two study periods were the following in 2001: greater collaboration between epidemiologists and/or biostatisticians in the authorship of articles (19.7 %), increased complexity of statistical analyses (statistical accessibility > 7 in 25 %) and greater use of evidence-based methodological concepts (19.7 %). However, no improvement was found in the scientific evidence (evidence was good in only 1.4 % and average in 25.7 %). Other aspects of interest were a lower number of original articles (due to an increase in other types of articles, such as Letters to the Editor or Special Articles) and a greater percentage of articles on evidence-based medicine or articles using its methodology. The differences in bibliometric indicators of quality found between An Esp Pediatr and Pediatrics continued to be considerable: statistical accessibility, evidence-based methodological concepts and scientific evidence (for example, good evidence was 22 times more frequent in Pediatrics). CONCLUSIONS: The scientific quality of An Esp Pediatr improved in 2001 compared with that of previous years, but the differences found between this journal and the gold standard of Pediatrics are still considerable. We found greater interest in articles related to the new scientific paradigm of evidence-based medicine, which uses the medical literature more effectively to guide medical practice.

Bibliometrics↗
PubMed1999

Clinical testing of restorative materials: some historical landmarks.

OBJECTIVES: The aim of the study was to review the historical background of the methodologies currently in use for clinical investigations of contemporary tooth coloured dental restorative materials and techniques, and to attempt to identify the likely general direction of such research projects in the future. DATA SOURCES: Published articles obtained as a result of a wide ranging literature search of both dental and medical journals. STUDY SELECTION: Historical and contemporary accounts of clinical trial management, upon which an overview of the key events important in the evolution of clinical methods of evaluation of dental restorative materials, and a prediction of possible future trends in this area, could be based. CONCLUSIONS: Publication of dental restoratives clinical research has not kept up with that in medicine, where editors of leading journals require that clinical trials be run in accordance with the Consolidated Standards of Reporting Trials (CONSORT) guidelines. The current trend towards evidence based treatment in dentistry can be expected to initiate more statistically powerful clinical studies of dental restoratives, and the merit of involving general dentists in practice based research can also be anticipated to become increasingly recognised in the future.

Clinical Trials as Topic↗
PubMed2000

Writing a case report: an editor's eye view.

'That was a nice presentation. Why not write it up for a journal?' With such words a thousand case reports are born. But they are like birds tossed over a stormy ocean: only a few gain a foothold in the rigging of passing ships--for the rest, oblivion. So, how do you persuade an editor to accept your wonderful case report? Here are some reflections from the editor's standpoint.

Evidence-Based Medicine↗
PubMed2005

Integration of HTML documents into an XML-based knowledge repository.

The Emergency Patient Instruction Generator (EPIG) is an electronic content compiler / viewer / editor developed by Intermountain Health Care. The content is vendor-licensed HTML patient discharge instructions. This work describes the process by which discharge instructions where converted from ASCII-encoded HTML to XML, then loaded to a database for use by EPIG.

Database Management Systems↗
PubMed1999

Indirect reference limits estimated from patients' results by three mathematical procedures.

Presently, only a few clinical laboratories produce their own reference values, while the great majority use reference intervals reported in the literature. An alternative to this unsatisfactory situation is to estimate indirect reference limits by means of mathematical/statistical procedures from patients' results obtained routinely in the laboratory. The procedures of Bhattacharya (A simple method of resolution of a distribution into Gaussian components. Biometrics 1967;23:115-135) Martin et al. (Reference values based on populations accessible to hospitals. In: Gräsbeck R, Alström T, editors. Reference Values in Laboratory Medicine. Chischester: Wiley, 1981:233-262) and Kairisto et al. (Generation of reference values for cardiac enzymes from hospital admission laboratory data. Eur J Clin Chem Clin Biochem 1994;32:789-796) were applied to 14 biochemical quantities. In order to verify these procedures, the indirect reference limits obtained from patients' results were validated by statistical comparison with reference limits estimated from a reference sample according to recommendations of the International Federation of Clinical Chemistry (IFCC). Calculated indirect reference limits for most quantities studied were reliable, but indirect reference limits for bilirubins and potassium ion substance concentrations, alanine aminotransferase, and aspartate aminotransferase catalytic concentrations in serum were not suitable. We conclude that indirect reference limits can be obtained from patients' results by all procedures studied when skewness and kurtosis of mixed distribution are not too large, but other factors also seem to have an influence on the reliability of these procedures.

Adult↗
PubMedDate not supplied

Informatics in Radiology (infoRAD): radiology report entry with automatic phrase completion driven by language modeling.

Keyboard entry or correction of radiology reports by radiologists and transcriptionists remains necessary in many settings despite advances in computerized speech recognition. A report entry system that implements an automated phrase completion feature based on language modeling was developed and tested. The special text editor uses context to predict the full word or phrase being typed, updating the displayed prediction after each keystroke. At any point, pressing the tab key inserts the predicted phrase without having to type the remaining characters of the phrase. Successive words of the phrase are predicted by a trigram language model. Phrase lengths are chosen to minimize the expected number of keystrokes as predicted by the language model. Operation is highly and automatically customized to each user. The language model was trained on 36,843 general radiography reports, which were consecutively generated and contained 1.48 million words. Performance was tested on 200 randomly selected reports outside of the training set. The phrase completion technique reduced the average number of keystrokes per report from 194 to 58; the average reduction factor was 3.3 (geometric mean) (95% confidence interval, 3.2-3.5). The algorithm significantly reduced the number of keystrokes required to generate a radiography report (P <.00005).

Algorithms↗
PubMed1991

New institute shoots for the moon.

The Institute of Medicine's (IOM) exhaustive study on the computerized patient record is finally complete. One of the study's first recommendations is to establish an institute for the computer-based patient record to get the ball rolling. Computers in Healthcare Editor Carolyn Dunbar asks a key leader of the IOM study, Richard Dick, Ph.D., why the ball is now rolling and picking up speed rapidly toward a true electronic medical record.

Academies and Institutes↗
PubMed1999

Ideas and ideals in medicine: fruits of reason or props of power?

Editors of medical journals play a central role in the promotion -- or suppression -- of ideas and ideals in medicine. Recently eminent among these have been the advocacies of the Evidence-based Medicine (EBM) movement and others concerned with evidence and guidelines for health care. With regard to these topics, it still remains for editors of journals either to advance or to retard even the consolidation of the associated core concepts, most notably those of evidence in medicine, scientific medicine, and rational medicine. I present, first, a case study on the conduct of the editors of three medical journals, specifically their assumption of the role of authority on the scholarly fundamentals of evidence in medicine and their responding to propositions on the topic with commentaries well below the intellectual standards that should prevail in the journals of a learned profession. Then, following a brief review of the Flexnerian and EBM ideas and ideals on the practice of medicine, supplemented by observations drawn from medical sociology and the precepts of the philosophy of science, I posit a way of understanding such behaviour by editors of medical journals. They can have a temptation, and apparently some propensity, to play a regressive role in the development of the fundamentals of medicine. This is prone to occur whenever reason constitutes a threat to power, whether solely to the editors' own or to that of the profession at large. A full realization of the dream of reason in medicine requires an immense integrity of its journal editors and of its other intellectual leaders.

Evidence-Based Medicine↗