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1.  Photoletter to the editor: Hyperkeratosis lenticularis perstans (Flegel's disease) with unusual clinical presentation. Response to isotretinoin therapy. 
Hyperkeratosis lenticularis perstans also known as Flegel's disease is a keratinisation disorder characterized by small keratotic papules with horny scales. Most cases have been reported in Europe with age of presentation between 35 and 60 years. We report a case of a 25-year-old man, who presented with 1-5 mm multiple asymptomatic hyperkeratotic papules of 15 years duration on both legs and hand along with lichenified plaques with Koebner phenomenon in the axillary folds, anticubital and popliteal fossae. Similar lesions were present in the eyelids also. There was no involvement elsewhere. Similar illness was found in the younger brother aged 13 years with the duration of illness for the past 5 years. Histopathology confirmed the clinical diagnosis. Patient was treated with oral isotretinoin in a daily dose of 20 mg per day to which he responded immediately with clearing of the lesions in two weeks.
doi:10.3315/jdcr.2012.1111
PMCID: PMC3470798  PMID: 23091588
Flegel's disease; hyperkeratosis lenticularis perstans; Koebner phenomenon; isotretinoin
2.  Science and policy on endocrine disrupters must not be mixed: a reply to a “common sense” intervention by toxicology journal editors 
Environmental Health  2013;12:69.
The “common sense” intervention by toxicology journal editors regarding proposed European Union endocrine disrupter regulations ignores scientific evidence and well-established principles of chemical risk assessment. In this commentary, endocrine disrupter experts express their concerns about a recently published, and is in our considered opinion inaccurate and factually incorrect, editorial that has appeared in several journals in toxicology. Some of the shortcomings of the editorial are discussed in detail. We call for a better founded scientific debate which may help to overcome a polarisation of views detrimental to reaching a consensus about scientific foundations for endocrine disrupter regulation in the EU.
doi:10.1186/1476-069X-12-69
PMCID: PMC3765603  PMID: 23981490
Endocrine disrupting chemicals; Environment; Health; Precautionary principle; Regulatory toxicology
3.  Photoletter to the editor: Diffuse cocaine-related purpura 
Diffuse purpura is an uncommon skin manifestation found in platelet and coagulation disorders, meningococcemia, vasculitides and cocaine use. Reports of cocaine-related purpura predominantly involve adulteration with the anti-helminthic, levamisole. Levamisole enhances the effects of cocaine and is known to cause vasculitis. Recently, the CDC also released an advisory of oxymorphone being used intravenously causing thrombogenic thrombocytopenic purpura (TTP). We report the case of a patient with diffuse purpura ultimately diagnosed with cocaine-related thrombogenic vasculopathy. In the current environment of adulterated cocaine usage and increased prescription narcotic abuse, it is crucial to investigate substance abuse as a cause of diffuse purpura.
doi:10.3315/jdcr.2013.1159
PMCID: PMC3888784  PMID: 24421868
cocaine; levamisole; oxymorphone; purpura
4.  A survey of the awareness, knowledge, policies and views of veterinary journal Editors-in-Chief on reporting guidelines for publication of research 
Background
Wider adoption of reporting guidelines by veterinary journals could improve the quality of published veterinary research. The aims of this study were to assess the knowledge and views of veterinary Editors-in-Chief on reporting guidelines, identify the policies of their journals, and determine their information needs. Editors-in-Chief of 185 journals on the contact list for the International Association of Veterinary Editors (IAVE) were surveyed in April 2012 using an online questionnaire which contained both closed and open questions.
Results
The response rate was 36.8% (68/185). Thirty-six of 68 editors (52.9%) stated they knew what a reporting guideline was before receiving the questionnaire. Editors said they had found out about reporting guidelines primarily through articles in other journals, via the Internet and through their own journal. Twenty of 57 respondents (35.1%) said their journal referred to reporting guidelines in its instructions to authors. CONSORT, REFLECT, and ARRIVE were the most frequently cited. Forty-four of 68 respondents (68.2%) believed that reporting guidelines should be adopted by all refereed veterinary journals. Qualitative analysis of the open questions revealed that lack of knowledge, fear, resistance to change, and difficulty in implementation were perceived as barriers to the adoption of reporting guidelines by journals. Editors suggested that reporting guidelines be promoted through communication and education of the veterinary community, with roles for the IAVE and universities. Many respondents believed a consensus policy on guideline implementation was needed for veterinary journals.
Conclusions
Further communication and education about reporting guidelines for editors, authors and reviewers has the potential to increase their adoption by veterinary journals in the future.
doi:10.1186/1746-6148-10-10
PMCID: PMC3922819
Veterinary journals; Veterinary research; Reporting guidelines; Reporting quality; Editors; Editorial policies; Views; Barriers
5.  A Diagram Editor for Efficient Biomedical Knowledge Capture and Integration 
Understanding the molecular mechanisms underlying complex disorders requires the integration of data and knowledge from different sources including free text literature and various biomedical databases. To facilitate this process, we created the Biomedical Concept Diagram Editor (BCDE) to help researchers distill knowledge from data and literature and aid the process of hypothesis development. A key feature of BCDE is the ability to capture information with a simple drag-and-drop. This is a vast improvement over manual methods of knowledge and data recording and greatly increases the efficiency of the biomedical researcher. BCDE also provides a unique concept matching function to enforce consistent terminology, which enables conceptual relationships deposited by different researchers in the BCDE database to be mined and integrated for intelligible and useful results. We hope BCDE will promote the sharing and integration of knowledge from different researchers for effective hypothesis development.
PMCID: PMC3041526  PMID: 21347131
6.  Skyline: an open source document editor for creating and analyzing targeted proteomics experiments 
Bioinformatics  2010;26(7):966-968.
Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools.
Availability: Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.
Contact: brendanx@u.washington.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btq054
PMCID: PMC2844992  PMID: 20147306
7.  Authors, editors, and the signs, symptoms and causes of plagiarism 
Saudi Journal of Anaesthesia  2011;5(3):303-307.
Plagiarism and inadequate citing appear to have reached epidemic proportions in research publication. This article discusses how plagiarism is defined and suggests some possible causes for the increase in the plagiarism disease. Most editors do not have much tolerance for text re-use with inadequate citation regardless of reasons why words are copied from other sources without correct attribution. However, there is now some awareness that re-use of words in research articles to improve the writing or “the English” (which has become a common practice) should be distinguished from intentional deceit for the purpose of stealing other authors’ ideas (which appears to remain a very rare practice). Although it has become almost as easy for editors to detect duplicate text as it is for authors to re-use text from other sources, editors often fail to consider the reasons why researchers resort to this strategy, and tend to consider any text duplication as a symptom of serious misconduct. As a result, some authors may be stigmatized unfairly by being labeled as plagiarists. The article concludes with practical advice for researchers on how to improve their writing and citing skills and thus avoid accusations of plagiarism.
doi:10.4103/1658-354X.84107
PMCID: PMC3168350  PMID: 21957412
Plagiarism; editors; authors
8.  Photoletter to the editor: Dermoscopy for discriminating between pityriasis rubra pilaris and psoriasis 
Pityriasis rubra pilaris (PRP) is a relatively uncommon entity that often has to be clinically differentiated from other erythematosquamous skin diseases, such as psoriasis. Dermoscopy has already been shown to enhance clinical evaluation of inflammatory skin conditions and dermoscopic patterns of various diseases, including psoriasis, have been documented. In the current manuscript we present the dermoscopic findings observed in two patients suffering from PRP and psoriasis, respectively. The dermoscopic pattern of PRP consisted of round/oval yellowish areas surrounded by vessels of mixed morphology. The latter findings are clearly distinct from the dermoscopic features of psoriasis, which have been extensively investigated previously and are presented also in the psoriatic patient herein. This observation represents an initial indication that dermoscopy could be of value in differentiating between the two entities.
doi:10.3315/jdcr.2013.1131
PMCID: PMC3622511  PMID: 23580911
blood vessels; dermatoscopy; dermoscopy; pityriasis rubra pilaris; psoriasis
9.  PREP-Mt: predictive RNA editor for plant mitochondrial genes 
BMC Bioinformatics  2005;6:96.
Background
In plants, RNA editing is a process that converts specific cytidines to uridines and uridines to cytidines in transcripts from virtually all mitochondrial protein-coding genes. There are thousands of plant mitochondrial genes in the sequence databases, but sites of RNA editing have not been determined for most. Accurate methods of RNA editing site prediction will be important in filling in this information gap and could reduce or even eliminate the need for experimental determination of editing sites for many sequences. Because RNA editing tends to increase protein conservation across species by "correcting" codons that specify unconserved amino acids, this principle can be used to predict editing sites by identifying positions where an RNA editing event would increase the conservation of a protein to homologues from other plants. PREP-Mt takes this approach to predict editing sites for any protein-coding gene in plant mitochondria.
Results
To test the general applicability of the PREP-Mt methodology, RNA editing sites were predicted for 370 full-length or nearly full-length DNA sequences and then compared to the known sites of RNA editing for these sequences. Of 60,263 cytidines in this test set, PREP-Mt correctly classified 58,994 as either an edited or unedited site (accuracy = 97.9%). PREP-Mt properly identified 3,038 of the 3,698 known sites of RNA editing (sensitivity = 82.2%) and 55,956 of the 56,565 known unedited sites (specificity = 98.9%). Accuracy and sensitivity increased to 98.7% and 94.7%, respectively, after excluding the 489 silent editing sites (which have no effect on protein sequence or function) from the test set.
Conclusion
These results indicate that PREP-Mt is effective at identifying C to U RNA editing sites in plant mitochondrial protein-coding genes. Thus, PREP-Mt should be useful in predicting protein sequences for use in molecular, biochemical, and phylogenetic analyses. In addition, PREP-Mt could be used to determine functionality of a mitochondrial gene or to identify particular sequences with unusual editing properties. The PREP-Mt methodology should be applicable to any system where RNA editing increases protein conservation across species.
doi:10.1186/1471-2105-6-96
PMCID: PMC1087475  PMID: 15826309
10.  FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data 
BMC Systems Biology  2009;3:26.
Background
Genomics research produces vast amounts of experimental data that needs to be integrated in order to understand, model, and interpret the underlying biological phenomena. Interpreting these large and complex data sets is challenging and different visualization methods are needed to help produce knowledge from the data.
Results
To help researchers to visualize and interpret integrated genomics data, we present a novel visualization method and bioinformatics software tool called FORG3D that is based on real-time three-dimensional force-directed graphs. FORG3D can be used to visualize integrated networks of genome scale data such as interactions between genes or gene products, signaling transduction, metabolic pathways, functional interactions and evolutionary relationships. Furthermore, we demonstrate its utility by exploring gene network relationships using integrated data sets from a Caenorhabditis elegans Parkinson's disease model.
Conclusion
We have created an open source software tool called FORG3D that can be used for visualizing and exploring integrated genome scale data.
doi:10.1186/1752-0509-3-26
PMCID: PMC2651117  PMID: 19239683
11.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench 
Bioinformatics  2009;25(9):1189-1191.
Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.
Availability: The Jalview 2 Desktop application and JalviewLite applet are made freely available under the GPL, and can be downloaded from www.jalview.org
Contact: g.j.barton@dundee.ac.uk
doi:10.1093/bioinformatics/btp033
PMCID: PMC2672624  PMID: 19151095
12.  An editor for pathway drawing and data visualization in the Biopathways Workbench 
BMC Systems Biology  2009;3:99.
Background
Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface.
Results
The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server . Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system.
Conclusion
Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.
doi:10.1186/1752-0509-3-99
PMCID: PMC2763869  PMID: 19799790
13.  The publication of ethically uncertain research: attitudes and practices of journal editors 
BMC Medical Ethics  2012;13:4.
Background
Publication of ethically uncertain research occurs despite well-published guidelines set forth in documents such as the Declaration of Helsinki. Such guidelines exist to aide editorial staff in making decisions regarding ethical acceptability of manuscripts submitted for publication, yet examples of ethically suspect and uncertain publication exist. Our objective was to survey journal editors regarding practices and attitudes surrounding such dilemmas.
Methods
The Editor-in-chief of each of the 103 English-language journals from the 2005 Abridged Index Medicus list publishing original research were asked to complete a survey sent to them by email between September-December 2007.
Results
A response rate of 33% (n = 34) was obtained from the survey. 18% (n = 6) of respondents had published ethically uncertain or suspect research within the last 10 years. 85% (n = 29) of respondents stated they would always reject ethically uncertain articles submitted for publication on ethical grounds alone. 12% (n = 4) of respondents stated they would approach each submission on a case-by-case basis. 3% (n = 1) stated they would be likely to publish such research, but only with accompanying editorial. Only 38% (n = 13) give reviewers explicit instruction to reject submissions on ethical grounds if found wanting.
Conclusions
Editorial compliance with the Declaration of Helsinki in rejecting research that is conducted unethically was difficult to ascertain because of a poor response rate despite multiple attempts using different modalities. Of those who did respond, the majority do reject ethically suspect research but few explicitly advise reviewers to do so. In this study editors did not take advantage of the opportunity to describe their support for the rejection of the publication of unethical research.
doi:10.1186/1472-6939-13-4
PMCID: PMC3378458  PMID: 22494972
Editors; Ethics; Publication ethics
14.  What do letters to the editor publish about randomized controlled trials? A cross-sectional study 
BMC Research Notes  2013;6:414.
Background
To identify published letters to the editor (LTE) written in response to randomized controlled trials (RCTs), determine the topics addressed in the letters, and to examine if these topics were affected by the characteristics and results of the RCTs.
Methods
Comparative cross-sectional study of a representative sample of RCTs from a set of high-impact medical journals (BMJ, Lancet, NEJM, JAMA, and Annals of Internal Medicine). RCTs and their published LTE were searched from these 5 journals in 2007. Data were collected on RCTs and their characteristics (author affiliation, funding source, intervention, and effect on the primary outcome) and the topics addressed in published LTE related to these RCTs. Analysis included chi-square and regression analysis (RCT characteristics) and thematic analysis (LTE topics).
Results
Of 334 identified RCTs, 175 trials had at least one LTE. Of these, 381 published LTE were identified. Most RCTs, tested drug interventions (68%), were funded by government (54%) or industry (33%), and described an intervention that had a positive impact on the primary outcome (62%). RCT authors were primarily affiliated with an academic centre (78%). Ninety percent of the 623 LTE topics concerned methodological issues regarding the analysis, intervention, and population in the RCT. There was a significant association between funding source and impact on outcomes (p = 0.002) or type of intervention tested (p = 0.001) in these trials. Clinical and “Other” LTE topics were more likely to be published in response to a government funded RCT (p = 0.005 and p = 0.033, respectively); no other comparisons were significant.
Conclusions
This study showed that most LTE are about methodological topics, but found little evidence to support that these topics are affected by the characteristics or results of the RCTs. The lack of association may be explained by editorial censorship as a small proportion of LTE that are submitted are actually published.
doi:10.1186/1756-0500-6-414
PMCID: PMC3852599  PMID: 24124753
Letters to the editor; Randomized controlled trials; Journalogy
15.  “Hardly worth the effort”? Medical journals’ policies and their editors’ and publishers’ views on trial registration and publication bias: quantitative and qualitative study 
Objectives To determine the proportion of medical journals requiring trial registration and to understand their reasons for adopting (or not adopting) such policies and other measures designed to reduce publication bias.
Design Quantitative study of journals’ instructions to authors (in June 2012) and qualitative study of editors’ and publishers’ views on trial registration and publication bias (carried out in Autumn 2012).
Setting Random selection of 200 medical journals publishing clinical trials identified from the Cochrane CENTRAL database.
Participants Editors (n=13) and publishers (n=3) of journals with different policies on trial registration (and with recently changed policies) identified from the survey of their instructions to authors.
Results Only 55/200 journals (28%) required trial registration according to their instructions and a further three (2%) encouraged it. The editors and publishers interviewed explained their journals’ reluctance to require registration in terms of not wanting to lose out to rival journals, not wanting to reject otherwise sound articles or submissions from developing countries, and perceptions that such policies were not relevant to all journals. Some interviewees considered that registration was unnecessary for small or exploratory studies.
Conclusions Although many major medical journals state that they will only publish clinical trials that have been prospectively registered, and such policies have been associated with a dramatic increase in the number of trials being registered, most smaller journals have not adopted such policies. Editors and publishers may be reluctant to require registration because they do not understand its benefits or because they fear that adopting such a policy would put their journal at a disadvantage to competitors.
doi:10.1136/bmj.f5248
PMCID: PMC3805489  PMID: 24014339
16.  Are reviewers suggested by authors as good as those chosen by editors? Results of a rater-blinded, retrospective study 
BMC Medicine  2006;4:13.
Background
BioMed Central (BMC) requires authors to suggest four reviewers when making a submission. Editors searching for reviewers use these suggestions as a source. The review process of the medical journals in the BMC series is open – authors and reviewers know each other's identity – although reviewers can make confidential comments to the editor. Reviews are published alongside accepted articles so readers may see the reviewers' names and recommendations.
Our objective was to compare the performance of author-nominated reviewers (ANR) with that of editor-chosen reviewers (ECR) in terms of review quality and recommendations about submissions in an online-only medical journal.
Methods
Pairs of reviews from 100 consecutive submissions to medical journals in the BMC series (with one author-nominated and one editor-chosen reviewer and a final decision) were assessed by two raters, blinded to reviewer type, using a validated review quality instrument (RQI) which rates 7 items on 5-point Likert scales. The raters discussed their ratings after the first 20 pairs (keeping reviewer type masked) and resolved major discrepancies in scoring and interpretation to improve inter-rater reliability. Reviewers' recommendations were also compared.
Results
Reviewer source had no impact on review quality (mean RQI score (± SD) 2.24 ± 0.55 for ANR, 2.34 ± 0.54 for ECR) or tone (mean scores on additional question 2.72 ANR vs 2.82 ECR) (maximum score = 5 in both cases). However author-nominated reviewers were significantly more likely to recommend acceptance (47 vs 35) and less likely to recommend rejection (10 vs 23) than editor-chosen reviewers after initial review (p < 0.001). However, by the final review stage (i.e. after authors had responded to reviewer comments) ANR and ECR recommendations were similar (65 vs 66 accept, 10 vs 14 reject, p = 0.47). The number of reviewers unable to decide about acceptance was similar in both groups at both review stages.
Conclusion
Author-nominated reviewers produced reviews of similar quality to editor-chosen reviewers but were more likely to recommend acceptance during the initial stages of peer review.
doi:10.1186/1741-7015-4-13
PMCID: PMC1482713  PMID: 16734897
17.  What do the JAMA editors say when they discuss manuscripts that they are considering for publication? Developing a schema for classifying the content of editorial discussion 
Background
In an effort to identify previously unrecognized aspects of editorial decision-making, we explored the words and phrases that one group of editors used during their meetings.
Methods
We performed an observational study of discussions at manuscript meetings at JAMA, a major US general medical journal. One of us (KD) attended 12 editorial meetings in 2003 as a visitor and took notes recording phrases from discussion surrounding 102 manuscripts. In addition, editors attending the meetings completed a form for each manuscript considered, listing the reasons they were inclined to proceed to the next step in publication and reasons they were not (DR attended 4/12 meetings). We entered the spoken and written phrases into NVivo 2.0. We then developed a schema for classifying the editors' phrases, using an iterative approach.
Results
Our classification schema has three main themes: science, journalism, and writing. We considered 2,463 phrases, of which 87 related mainly to the manuscript topic and were not classified (total 2,376 classified). Phrases related to science predominated (1,274 or 54%). The editors, most of whom were physicians, also placed major weight on goals important to JAMA's mission (journalism goals) such as importance to medicine, strategic emphasis for the journal, interest to the readership, and results (729 or 31% of phrases). About 16% (n = 373) of the phrases used related to writing issues, such as clarity and responses to the referees' comments.
Conclusion
Classification of editorial discourse provides insight into editorial decision making and concepts that need exploration in future studies.
doi:10.1186/1471-2288-7-44
PMCID: PMC2121101  PMID: 17894854
18.  Letter to the editor: healthy alternatives to trans fats 
Consumption of trans fats is associated with an increase of cardiovascular disease (CVD) risk. To comply with regulatory policies and public health authorities recommendations, trans fats should be replaced in food products. The study by Sundram et al. (Nutrition & Metabolism 2007, 4:3) reporting the effect on CVD risk factors of interesterified fat (IE) and partially hydrogenated soybean oil (PHSO) compared to palm olein (POL) has been critically analyzed. The study design and in particular the composition of the tested fats was not suitable to properly answer the question raised regarding the effect of alternative ingredients to trans fats on plasma lipids. The observed effects are divergent with predicted data derived from the literature model consolidated using the individual results of 60 randomized clinical trials. The results of the study published by Sundram and co-workers have to be considered with awareness.
doi:10.1186/1743-7075-4-10
PMCID: PMC1867814  PMID: 17462099
19.  Representation of authors and editors from countries with different human development indexes in the leading literature on tropical medicine: survey of current evidence 
BMJ : British Medical Journal  2004;328(7450):1229-1232.
Objective To assess the current international representation of members of editorial and advisory boards and authors in the leading peer reviewed literature on tropical medicine.
Design Systematic review.
Main outcome measures Country affiliations, as classified by the human development index, of editorial and advisory board members of all tropical medicine journals referenced by the Institute of Scientific Information (ISI) as of late 2003 and of all contributing authors of full articles published in the six leading journals on tropical medicine in 2000-2.
Results Sixteen (5.1%) of the 315 editorial and advisory board members from the 12 ISI referenced journals on tropical medicine are affiliated to countries with a low human development index and 223 (70.8%) to countries with a high index. Examination of the 2384 full articles published in 2000-2 in the six highest ranking tropical medicine journals showed that 48.1% of contributing authors are affiliated to countries with a high human development index, whereas the percentage of authors from countries with a low index was 13.7%. Articles written exclusively by authors from low ranked countries accounted for 5.0%. Our data indicate that research collaborations between a country with a high human development index and one that has either a medium or a low index are common and account for 26.5% and 16.1% of all full articles, respectively.
Conclusion Current collaborations should be transformed into research partnerships, with the goals of mutual learning and institutional capacity strengthening in the developing world.
doi:10.1136/bmj.38069.518137.F6
PMCID: PMC416596  PMID: 15059851
20.  Consensus and contention regarding redundant publications in clinical research: cross-sectional survey of editors and authors 
Journal of Medical Ethics  2003;29(2):109-114.
Objectives: To examine the perspectives of journal editors and authors on overlapping and redundant publications in clinical research.
Design: Pretested cross-sectional survey, containing both forced choice and open ended questions, administered by mail to the senior editors (N=99) and one randomly selected author (N=99) from all journals in the Abridged Index Medicus (1996) that published clinical research.
Main measurements: The views of editors and authors about the extent of redundant publications, why they occur, how to prevent and respond to cases, and when the publication of overlapping manuscripts is justified.
Results: Seventy two per cent (N=71) of editors and 65% (N=64) of authors completed the survey. There was consensus between both groups that redundant publications occur because authors feel the pressure to publish and journals do not do enough to publicise, criticise, and punish cases, and that the publication of most types of overlapping articles is unacceptable. Sixty seven per cent of authors but only 31% of editors felt, however, that it was justified to publish an overlapping article in a non-peer reviewed symposium supplement, and 68% of editors but 39% of authors supported imposing restrictions on guilty authors' future submissions. In written comments, 15% to 30% of both groups emphasised that it was justified to publish overlapping articles when there were different or non-English-speaking audiences, new data, strengthened methods, or disputed findings.
Conclusions: Editors, authors, and other academic leaders should together develop explicit guidelines that clarify points of contention and ambiguity regarding overlapping manuscripts.
doi:10.1136/jme.29.2.109
PMCID: PMC1733707  PMID: 12672892
21.  The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments 
Nucleic Acids Research  2009;37(Web Server issue):W253-W259.
RNA editing alters plant mitochondrial and chloroplast transcripts by converting specific cytidines to uridines, which usually results in a change in the amino acid sequence of the translated protein. Systematic studies have experimentally identified sites of RNA editing in organellar transcriptomes from several species, but these analyses have not kept pace with rate of genome sequencing. The PREP (predictive RNA editors for plants) suite was developed to computationally predict sites of RNA editing based on the well-known principle that editing in plant organelles increases the conservation of proteins across species. The PREP suite provides predictive RNA editors for plant mitochondrial genes (PREP-Mt), for chloroplast genes (PREP-Cp), and for alignments submitted by the user (PREP-Aln). These servers require minimal input, are very fast, and are highly accurate on all seed plants examined to date. PREP-Mt has proved useful in several research studies and the newly developed PREP-Cp and PREP-Aln servers should be of further assistance for analyses that require knowledge of the location of sites of RNA editing. The PREP suite is freely available at http://prep.unl.edu/.
doi:10.1093/nar/gkp337
PMCID: PMC2703948  PMID: 19433507
22.  US health journal editors' opinions and policies on research in race, ethnicity, and health. 
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.
PMCID: PMC2608355  PMID: 9685775
23.  More on Lexical Bias: How Efficient Can a “Lexical Editor” Be? 
The lexical bias effect (the tendency for phonological speech errors to create words more often than nonwords) has been debated for over 30 years. One account attributes the effect to a lexical editor, a strategic component of the production system that examines each planned phonological string, and suppresses it if it is a nonword. The alternative explanation is that the effect occurs automatically as a result of phonological-lexical feedback. Using a new paradigm, we explicitly asked participants to do lexical editing on their planned speech and compared performance on this inner lexical decision task to results obtained from the standard lexical decision task in three subsequent experiments. Our experimentally created “lexical editor” needed 300 ms to recognize and suppress nonwords, as determined by comparing reaction times when editing was and was not required. Therefore, we concluded that even though strategic lexical editing can be done, any such editing that occurs in daily speech occurs sporadically, if at all.
doi:10.1016/j.jml.2008.09.006
PMCID: PMC2746698  PMID: 20126302
lexical bias; self-monitoring; speech errors; feedback
24.  Challenges in implementing a knowledge editor for the Arden Syntax: knowledge base maintenance and standardization of database linkages. 
CONTEXT: Incorporation of research findings into clinical practice lags behind their dissemination in the medical literature. Arden Syntax is a standard that could be used to encode evidence in a clinical decision support system (CDSS). However, dissemination of knowledge is hampered by lack of standard linkages to clinical databases. OBJECTIVE: To create a knowledge editor that facilitates transfer of knowledge from the medical literature to clinical practice via a CDSS. METHODS: Using a Web browser-based application, we implemented linkages to MEDLINE to permit queries on demand and registration of queries to be executed periodically, with results copied into Arden Medical Logic Modules (MLMs). To facilitate standardization of MLMs, database linkages are encoded using emerging HL7 standards such as a data model (virtual medical record). CONCLUSIONS: A Web-based application can facilitate transfer of knowledge into clinical practice and knowledge base maintenance through periodic queries and deployment of standards for knowledge representation.
PMCID: PMC2244416  PMID: 12463846
25.  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).
PMCID: PMC2232101  PMID: 9929265

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