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This article provides recommendations for new and experienced reviewers based on the authors' experiences as editors, authors, and peer reviewers. By adherence to the techniques below, reviewers can make positive contributions to the professional community in addition to improving their personal publication, reviewing, and writing skills.
The ribosomal differentiation of medical micro-organisms (RIDOM) web server, first described by Harmsen et al. [Harmsden,D., Rothganger,J., Singer,C., Albert,J. and Frosch,M. (1999) Lancet, 353, 291], is an evolving electronic resource designed to provide micro-organism differentiation services for medical identification needs. The diagnostic procedure begins with a specimen partial small subunit ribosomal DNA (16S rDNA) sequence. Resulting from a similarity search, a species or genus name for the specimen in question will be returned. Where the first results are ambiguous or do not define to species level, hints for further molecular, i.e. internal transcribed spacer, and conventional phenotypic differentiation will be offered ('sequential and polyphasic approach'). Additionally, each entry in RIDOM contains detailed medical and taxonomic information linked, context-sensitive, to external World Wide Web services. Nearly all sequences are newly determined and the sequence chromatograms are available for intersubjective quality control. Similarity searches are now also possible by direct submission of trace files (ABI or SCF format). Based on the PHRED/PHRAP software, error probability measures are attached to each predicted nucleotide base and visualised with a new 'Trace Editor'. The RIDOM web site is directly accessible on the World Wide Web at http://www.ridom.de/. The email address for questions and comments is webmaster@ridom.de.
SUMMARY: A visual Java-based tool for drawing and annotating biological pathways was developed. This tool integrates the possibilities of charting elements with different attributes (size, color, labels), drawing connections between elements in distinct characteristics (color, structure, width, arrows), as well as adding links to molecular biology databases, promoter sequences, information on the function of the genes or gene products, and references. It is easy to use and system independent. The result of the editing process is a PNG (portable network graphics) file for the images and XML (extended markup language) file for the appropriate links.
The evidence-based medicine movement has received enthusiastic endorsement from editors of major medical journals. Hardly anyone can disagree with the aim of helping clinicians to make judicious use of the best scientific evidence for decisions in patient care. Evidence-based medicine, however, because of its dependence on randomized trials, cannot be applied to all individuals seen in daily practice. Specifically, patients may differ in age, severity of illness, presence of comorbidity and myriad of other clinical nuances. In response to these limitations, decision analysis, a technique which allows to consider multiple health outcomes, such as the patient's preferences for different states of health, and to measure the consequences of many strategies for which randomized trials are not feasible, provides a rational means of allowing health professionals to move from finding evidence to implementing it. Such formal approach may reconcile evidence-based medicine with 'real life' and patient's preference. It should therefore be considered complementary to evidence-based medicine.
To determine the progress women have made in the last 20 years in terms of contributions to the knowledge base (i.e., authorship) and reputations as leading contributors (i.e., appointments as editors and editorial board members) in educational psychology, we analyzed data from six journals: the American Educational Research Journal, Contemporary Educational Psychology, the Educational Psychologist, Educational Psychology Review, the Journal of Experimental Education, and the Journal of Educational Psychology. Results indicated that (a) women's progress in terms of authorships could be predicted by their increasing representation as educational psychologists, (b) opportunities for females to become editorial board members seem to be getting better, and (c) opportunities for females to become editors seem to be getting worse. Copyright 1998 Academic Press.
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The purpose of this systematic literature search was to evaluate how the evidence-based approach appears in German-language dental journals. All volumes of 28 dental journals published between 1997 and 2003 were searched by hand; for 15 of these journals, an additional electronic search was made. The focus of the search was all articles, editorials or letters to the Editor dealing with topics related to evidence-based dentistry (EBD)/medicine or using its terminology. Of the 1776 journal issues that were scrutinised, 368 relevant publications were found. After a low, albeit slightly increasing, number of pertinent contributions published between 1997 and 1999, there was a sharp rise in 2000 and 2001, culminating in 2003. Our findings indicate a rising awareness of the concept of EBD in the German-language dental literature. Nonetheless, its reception within the German-speaking dental community is still modest.
CONTEXT: While medical journals strive to ensure accuracy and the acknowledgment of limitations in articles, press releases may not reflect these efforts. METHODS: Telephone interviews conducted in January 2001 with press officers at 9 prominent medical journals and analysis of press releases (n = 127) about research articles for the 6 issues of each journal preceding the interviews. RESULTS: Seven of the 9 journals routinely issue releases; in each case, the editor with the press office selects articles based on perceived newsworthiness and releases are written by press officers trained in communications. Journals have general guidelines (eg, length) but no standards for acknowledging limitations or for data presentation. Editorial input varies from none to intense. Of the 127 releases analyzed, 29 (23%) noted study limitations and 83 (65%) reported main effects using numbers; 58 reported differences between study groups and of these, 26 (55%) provided the corresponding base rate, the format least prone to exaggeration. Industry funding was noted in only 22% of 23 studies receiving such funding. CONCLUSIONS: Press releases do not routinely highlight study limitations or the role of industry funding. Data are often presented using formats that may exaggerate the perceived importance of findings.
Transient extracellular pH changes accompany the exchange of chloride for sulfate across the erythrocyte membrane. The direction of the extracellular pH change during chloride efflux and sulfate influx depends on experimental conditions. When bicarbonate is present, the extracellular pH drops sharply at the outset of the anion exchange and tends to follow the partial ionic equilibrium described by Wilbrandt (W. Wilbrandt, 1942. Pfluegers Arch. 246:291). When bicarbonate is absent, however, the anion exchange causes the pH to rise, indicating that protons are cotransported with sulfate during chloride-sulfate exchange. The pH rise can be reversed by the addition of HCO(-3) (4 muM) or 2,4-dinitrophenol (90 muM). This demonstrates that the proton-sulfate cotransport can drive proton transport uphill. The stoichiometry of the transport is that one chloride exchanges for one sulfate plus one proton. These results support the titratable carrier model proposed by Gunn (Gunn, R.B. 1972, In: Oxygen Affinity of Hemoglobin and Red Cell Acid-Base Status. M. Rorth and P. Astrup, editors. p. 823. Munksgaard, Copenhagen) for erythrocyte membrane anion exchange.
The present state of the German editions of Freud is described and documented as the result of a historical development taking place in three phases: the history of editions as history of persecution. Based on her longstanding personal experience as editor of Freud, the author relates the third phase (since 1960).
BACKGROUND: The Clinical Pharmacogenetics Implementation Consortium published an updated guideline for opioids and CYP2D6, OPRM1, and COMT in December 2020. These guidelines include recommendations to avoid key opioids in patients who are ultrarapid or poor metabolizers of CYP2D6 to avoid toxicity and optimize efficacy. CASE REPORT: An older woman encountered a letter to the editor in a family magazine regarding genomically based responses to opioids. She reached out for more information and assistance, attesting to continued lack of analgesia to opioids prescribed during occasions of severe pain over the course of many years. A pharmacogenomic analysis proved to be the key to solving her mystery. CONCLUSION: Pharmacogenomic results may provide life-altering information transforming a patient's perspective on health care. Personalized medicine may be a key component in providing objective evidence for opioid treatment efficacy. There is a critical need for both provider and patient education to increase awareness of pharmacogenomics and how it can be applied to effective pharmacotherapy. Research is needed to explore appropriate, effective educational methods.
We developed a program to automatically screen patients' medication profiles for pairs of interacting drugs. Since some drug-drug interactions are indicated by changes in physiological parameters (e.g., ciprofloxacin and theophylline leading to an elevation of theophylline levels), the program considered the patients' relevant laboratory parameters prior to generating the alerts. We developed an editor to facilitate maintenance of the knowledge base. We evaluated the program for 3 weeks in two satellite pharmacies. The program reported 160 alerts of which 5 resulted in a change in the patients' therapies (one per 500 patient-days of care). These five interactions were potentially very serious. An additional 3 alerts led to changes in medication administration times. Subjectively, the program is well received and continues to be in routine clinical use.
Harmonic analysis of the pressure and wall responses of a blood vessel exposed to a dynamic pressure input signal required the development of a software application which could properly synchronize the data gathered by two separate microcomputers. In order to accomplish this task, the Pressure-Image Editor was developed. The first computer is used to generate a swept frequency sinusoidal dynamic pressure input signal while at the same time monitoring the resulting response pressures. The second computer is used to record the physical (visual) response of the artery to the pressure signal via a high speed CCD camera and video digitizer. Using the Pressure-Image Editor, 256 animated images along with 65,536 pressure points can be combined and synchronized based on the camera frame rate, input trigger frequency, and any internal timing delays. The Pressure-Image Editor is a object-oriented application written in C++ and includes a window based graphical user interface.
Health research on race and ethnicity has been criticized for lacking rigor in conceptualization, terminology, and analysis. Scientific journals' editorial processes help determine research quality. This survey assessed editors' awareness of current debates, attitudes toward recent recommendations, and involvement in developing editorial policies. Twenty-nine editors of health journals with impact factors of > or = 1 (based on citation ratings) were sent a questionnaire including four key problems identified in research literature and recommendations from federal agencies; 23 (79%) responded. Seven editors relevant policies. Two had read the federal directive on racial and ethnic classification; one was aware of its current review. Most perceived the four key problems as uncommon. The majority agreed with Public Health Service recommendations on race and ethnicity research, except for analyzing effects of racism. Approximately 20% had discussed issues with co-editors, editorial boards, or reviewers. About 40% saw further discussion as beneficial; four planned to draft guidelines. Editors' potential for helping resolve problems in race/ethnicity research is not being realized. Greater participation would be beneficial to public health research and practice.
BACKGROUND: Despite the pivotal role of peer review in the scientific process, there has never been a formal study of the way in which reviewers' opinions are elicited. This article describes such a study and makes recommendations for a more standardized approach to the peer review process. We hope, through this publication and related efforts, to encourage such a process in Preventive Medicine and in other journals. METHOD: The study population included the top 100 journals (as rated by the 1989 Institute for Scientific Information citation frequency index). Only journals with primarily U.S.-based editorial offices are included (n = 73). Participants provided their reviewer forms, cover letters for reviewers, and instructions for reviewers that were used routinely. All data were collected in February 1992. RESULTS: The response rate was 97.3%. Journals varied substantially in many of their reviewer requests. While 96% of journals asked reviewers to recommend acceptance or rejection, only 72% asked reviewers to assess manuscripts' novelty, 69% requested assessments of clarity, and only 51% asked for assessments of the reasonableness of manuscripts' conclusions. Similarly, only 46% of journals reminded reviewers that manuscripts were confidential documents, 51% provided a separate cover letter, and 25% provided extensive (>1 full page) reviewer instructions. CONCLUSIONS: While review uniformity is not requisite, differences between review protocols may not be a function of specific journals' needs, but of some journals' excluding important review components from explicit mention. Based in part on the Council of Biology Editors' recommendations, standard components of reviews and of instructions for reviewers are suggested. If editors' expectations were more explicit, reviewers' comments could better serve editorial needs.
OBJECTIVE: To assess whether manuscripts received by JAMA in 1991 possessed differing peer review and manuscript processing characteristics, or had a variable chance of acceptance, associated with the gender of the participants in the peer review process. DESIGN: Retrospective cohort study of 1851 research articles. SETTING: JAMA editorial office. PARTICIPANTS: Eight male and five female JAMA editors, 2452 male and 930 female reviewers, and 1698 male and 462 female authors. MAIN OUTCOME MEASURE: Statistically significant gender bias. RESULTS: Female editors were assigned manuscripts from female corresponding authors more often than were male editors (P < .001). Female editors used more reviewers per manuscript if sent for other review. Male reviewers assisted male editors more often than female editors, and male reviewers took longer to return manuscripts than did their female counterparts (median, 25 vs 22 days). Content reviewer recommendations were independent of corresponding author and review gender, while male statistical reviewers recommended the highest and lowest categories more frequently than did female statistical reviewers (P < .001). Manuscripts handled by female editors were rejected summarily at higher rates (P < .001). Articles submitted to JAMA in 1991 were not accepted at significantly different rates based on the gender of the corresponding author or the assigned editor (P < .4). CONCLUSIONS: Gender differences exist in editor and reviewer characteristics at JAMA with no apparent effect on the final outcome of the peer review process or acceptance for publication.
BACKGROUND: The term evidence-based medicine (EBM) is increasingly being used. Physicians, journal editors, insurance companies, and patients are applying its tenets to clinical decision making. Although there are concerns about the overly zealous application of EBM to clinical situations, many of the basic concepts are important in improving decision making. OBJECTIVE: To define evidence-based medicine and to review potential problems in basing decision making entirely on less-than-ideal evidence. METHODS: We reviewed the EBM literature and looked for examples in dermatology of pitfalls in decision making based on poor evidence. RESULTS: Following a definition of EBM, we review problems inherent in anecdotes and uncontrolled trials, including the placebo effect. Examples of medical practice that have been altered by doing more rigorous studies are provided. CONCLUSIONS: Concepts of EBM as currently defined should be considered by dermatologic surgeons in assessing the available information for clinical decision making.
Large DNA sequences are now routinely sequenced by the cloning of randomly generated fragments into single-stranded DNA phage vectors (the 'shotgun' method). Various programs exist for computerized assembly of such fragments, including the phases of data entry, homology searching and gel-management/editing. Many gel-management editors are rudimentary in nature, using either line-editing techniques or using unnatural displays or command systems. Others are available only on restricted types of computer system. The program VTUTIN makes full screen editing along the lines of modern text editors available for the complex data type of sets of sequence gels and their consensus. Not only are the data displayed on the VDU screen in a natural manner, but VTUTIN has also been written to model the command system of a well-established text editor (PDP-11 KED or VAX/VMS EDT) to simplify editor use and learning. VTUTIN has been written in Pascal in a modular form so that wide-spread portability is facilitated. VTUTIN is currently implemented to work on VT-100 type terminals although the modularity of the code should allow straightforward conversion for other terminal types and should also permit simple alteration to model any other text editor.