Search tips
Search criteria

Results 1-25 (940205)

Clipboard (0)

Related Articles

1.  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 
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.
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.
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.
Classification of editorial discourse provides insight into editorial decision making and concepts that need exploration in future studies.
PMCID: PMC2121101  PMID: 17894854
2.  Letter to the editor for the article "Auto-injector needle length may be inadequate to deliver epinephrine intramuscularly in women with confirmed food allergy" 
Letter to the Editor for "Auto-injector needle length may be inadequate to deliver epinephrine intramuscularly in women with confirmed food allergy" by Tsai et al. There are limitations of this study note mentioning such as method of compression, role of propulsion, defining those patients who are at risk of prophylaxis and future studies.
PMCID: PMC4326436
Anaphylaxis; Epinephrine; Auto-injector; Needle length
3.  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 This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC2844992  PMID: 20147306
4.  An editor for pathway drawing and data visualization in the Biopathways Workbench 
BMC Systems Biology  2009;3:99.
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.
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.
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.
PMCID: PMC2763869  PMID: 19799790
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.  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.
PMCID: PMC3168350  PMID: 21957412
Plagiarism; editors; authors
7.  Avogadro: an advanced semantic chemical editor, visualization, and analysis platform 
The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types.
The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here.
Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from
PMCID: PMC3542060  PMID: 22889332
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.
PMCID: PMC3622511  PMID: 23580911
blood vessels; dermatoscopy; dermoscopy; pityriasis rubra pilaris; psoriasis
9.  “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.
PMCID: PMC3805489  PMID: 24014339
10.  Evaluating adherence to the International Committee of Medical Journal Editors’ policy of mandatory, timely clinical trial registration 
To determine whether two specific criteria in Uniform Requirements for Manuscripts (URM) created by the International Committee of Medical Journal Editors (ICMJE)—namely, including the trial ID registration within manuscripts and timely registration of trials, are being followed.
Materials and methods
Observational study using computerized analysis of publicly available Medline article data and clinical trial registry data. We analyzed a purposive set of five ICMJE founding journals looking at all trial articles published in those journals during 2010–2011, and data from the (CTG) trial registry. We measured adherence to trial ID inclusion policy as the percentage of trial journal articles that contained a valid trial ID within the article (journal-based sample). Adherence to timely registration was measured as the percentage of trials that registered the trial before enrolling the first participant within a 60-day grace period. We also examined timely registration rates by year of all phase II and higher interventional trials in CTG (registry-based sample).
To determine trial ID inclusion, we analyzed 698 clinical trial articles in five journals. A total of 95.8% (661/690) of trial journal articles included the trial ID. In 88.3% the trial-article link is stored within a structured Medline field. To evaluate timely registration, we analyzed trials referenced by 451 articles from the selected five journals. A total of 60% (272/451) of articles were registered in a timely manner with an improving trend for trials initiated in later years (eg, 89% of trials that began in 2008 were registered in a timely manner). In the registry-based sample, the timely registration rates ranged from 56% for trials registered in 2006 to 72% for trials registered in 2011.
Adherence to URM requirements for registration and trial ID inclusion increases the utility of PubMed and links it in an important way to clinical trial repositories. This new integrated knowledge source can facilitate research prioritization, clinical guidelines creation, and precision medicine.
The five selected journals adhere well to the policy of mandatory trial registration and also outperform the registry in adherence to timely registration. ICMJE's URM policy represents a unique international mandate that may be providing a powerful incentive for sponsors and investigators to document clinical trials and trial result publications and thus fulfill important obligations to trial participants and society.
PMCID: PMC3715364  PMID: 23396544
clinical trials as topic/legislation; registries; cross-sectional analysis; Databases; publication policy; trial registration
11.  PREP-Mt: predictive RNA editor for plant mitochondrial genes 
BMC Bioinformatics  2005;6:96.
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.
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.
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.
PMCID: PMC1087475  PMID: 15826309
12.  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.
PMCID: PMC416596  PMID: 15059851
13.  Do Author-Suggested Reviewers Rate Submissions More Favorably than Editor-Suggested Reviewers? A Study on Atmospheric Chemistry and Physics 
PLoS ONE  2010;5(10):e13345.
Ratings in journal peer review can be affected by sources of bias. The bias variable investigated here was the information on whether authors had suggested a possible reviewer for their manuscript, and whether the editor had taken up that suggestion or had chosen a reviewer that had not been suggested by the authors. Studies have shown that author-suggested reviewers rate manuscripts more favorably than editor-suggested reviewers do.
Methodology/Principal Findings
Reviewers' ratings on three evaluation criteria and the reviewers' final publication recommendations were available for 552 manuscripts (in total 1145 reviews) that were submitted to Atmospheric Chemistry and Physics, an interactive open access journal using public peer review (authors' and reviewers' comments are publicly exchanged). Public peer review is supposed to bring a new openness to the reviewing process that will enhance its objectivity. In the statistical analysis the quality of a manuscript was controlled for to prevent favorable reviewers' ratings from being attributable to quality instead of to the bias variable.
Our results agree with those from other studies that editor-suggested reviewers rated manuscripts between 30% and 42% less favorably than author-suggested reviewers. Against this backdrop journal editors should consider either doing without the use of author-suggested reviewers or, if they are used, bringing in more than one editor-suggested reviewer for the review process (so that the review by author-suggested reviewers can be put in perspective).
PMCID: PMC2954795  PMID: 20976226
14.  Guidelines, Editors, Pharma And The Biological Paradigm Shift 
Mens Sana Monographs  2007;5(1):27-30.
Private investment in biomedical research has increased over the last few decades. At most places it has been welcomed as the next best thing to technology itself. Much of the intellectual talent from academic institutions is getting absorbed in lucrative positions in industry. Applied research finds willing collaborators in venture capital funded industry, so a symbiotic growth is ensured for both.
There are significant costs involved too. As academia interacts with industry, major areas of conflict of interest especially applicable to biomedical research have arisen. They are related to disputes over patents and royalty, hostile encounters between academia and industry, as also between public and private enterprise, legal tangles, research misconduct of various types, antagonistic press and patient-advocate lobbies and a general atmosphere in which commercial interest get precedence over patient welfare.
Pharma image stinks because of a number of errors of omission and commission. A recent example is suppression of negative findings about Bayer's Trasylol (Aprotinin) and the marketing maneuvers of Eli Lilly's Xigris (rhAPC). Whenever there is a conflict between patient vulnerability and profit motives, pharma often tends to tilt towards the latter. Moreover there are documents that bring to light how companies frequently cross the line between patient welfare and profit seeking behaviour.
A voluntary moratorium over pharma spending to pamper drug prescribers is necessary. A code of conduct adopted recently by OPPI in India to limit pharma company expenses over junkets and trinkets is a welcome step.
Clinical practice guidelines (CPG) are considered important as they guide the diagnostic/therapeutic regimen of a large number of medical professionals and hospitals and provide recommendations on drugs, their dosages and criteria for selection. Along with clinical trials, they are another area of growing influence by the pharmaceutical industry. For example, in a relatively recent survey of 2002, it was found that about 60% of 192 authors of clinical practice guidelines reported they had financial connections with the companies whose drugs were under consideration. There is a strong case for making CPGs based not just on effectivity but cost effectivity. The various ramifications of this need to be spelt out. Work of bodies like the Appraisal of Guidelines Research and Evaluation (AGREE) Collaboration and Guidelines Advisory Committee (GAC) are also worth a close look.
Even the actions of Foundations that work for disease amelioration have come under scrutiny. The process of setting up ‘Best Practices’ Guidelines for interactions between the pharmaceutical industry and clinicians has already begun and can have important consequences for patient care. Similarly, Good Publication Practice (GPP) for pharmaceutical companies have also been set up aimed at improving the behaviour of drug companies while reporting drug trials
The rapidly increasing trend toward influence and control by industry has become a concern for many. It is of such importance that the Association of American Medical Colleges has issued two relatively new documents - one, in 2001, on how to deal with individual conflicts of interest; and the other, in 2002, on how to deal with institutional conflicts of interest in the conduct of clinical research. Academic Medical Centers (AMCs), as also medical education and research institutions at other places, have to adopt means that minimize their conflicts of interest.
Both medical associations and research journal editors are getting concerned with individual and institutional conflicts of interest in the conduct of clinical research and documents are now available which address these issues. The 2001 ICMJE revision calls for full disclosure of the sponsor's role in research, as well as assurance that the investigators are independent of the sponsor, are fully accountable for the design and conduct of the trial, have independent access to all trial data and control all editorial and publication decisions. However the findings of a 2002 study suggest that academic institutions routinely participate in clinical research that does not adhere to ICMJE standards of accountability, access to data and control of publication.
There is an inevitable slant to produce not necessarily useful but marketable products which ensure the profitability of industry and research grants outflow to academia. Industry supports new, not traditional, therapies, irrespective of what is effective. Whatever traditional therapy is supported is most probably because the company concerned has a product with a big stake there, which has remained a ‘gold standard’ or which that player thinks has still some ‘juice’ left.
Industry sponsorship is mainly for potential medications, not for trying to determine whether there may be non-pharmacological interventions that may be equally good, if not better. In the paradigm shift towards biological psychiatry, the role of industry sponsorship is not overt but probably more pervasive than many have realised, or the right thinking may consider good, for the health of the branch in the long run.
An issue of major concern is protection of the interests of research subjects. Patients agree to become research subjects not only for personal medical benefit but, as an extension, to benefit the rest of the patient population and also advance medical research.
We all accept that industry profits have to be made, and investment in research and development by the pharma industry is massive. However, we must also accept there is a fundamental difference between marketing strategies for other entities and those for drugs.
The ultimate barometer is patient welfare and no drug that compromises it can stand the test of time. So, how does it make even commercial sense in the long term to market substandard products? The greatest mistake long-term players in industry may make is try to adopt the shady techniques of the upstart new entrant. Secrecy of marketing/sales tactics, of the process of manufacture, of other strategies and plans of business expansion, of strategies to tackle competition are fine business tactics. But it is critical that secrecy as a tactic not extend to reporting of research findings, especially those contrary to one's product.
Pharma has no option but to make a quality product, do comprehensive adverse reaction profiles, and market it only if it passes both tests.
Why does pharma adopt questionable tactics? The reasons are essentially two:
What with all the constraints, a drug comes to the pharmacy after huge investments. There are crippling overheads and infrastructure costs to be recovered. And there are massive profit margins to be maintained. If these were to be dependent only on genuine drug discoveries, that would be taking too great a risk.Industry players have to strike the right balance between profit making and credibility. In profit making, the marketing champions play their role. In credibility ratings, researchers and paid spokes-persons play their role. All is hunky dory till marketing is based on credibility. When there is nothing available to make for credibility, something is projected as one and marketing carried out, in the calculated hope that profits can accrue, since profit making must continue endlessly. That is what makes pharma adopt even questionable means to make profits.
Essentially, there are four types of drugs. First, drugs that work and have minimal side-effects; second, drugs which work but have serious side-effects; third, drugs that do not work and have minimal side-effects; and fourth, drugs which work minimally but have serious side-effects. It is the second and fourth types that create major hassles for industry. Often, industry may try to project the fourth type as the second to escape censure.
The major cat and mouse game being played by conscientious researchers is in exposing the third and fourth for what they are and not allowing industry to palm them off as the first and second type respectively. The other major game is in preventing the second type from being projected as the first. The third type are essentially harmless, so they attract censure all right and some merriment at the antics to market them. But they escape anything more than a light rap on the knuckles, except when they are projected as the first type.
What is necessary for industry captains and long-term players is to realise:
Their major propelling force can only be producing the first type. 2. They accept the second type only till they can lay their hands on the first. 3. The third type can be occasionally played around with to shore up profits, but never by projecting them as the first type. 4. The fourth type are the laggards, real threat to credibility and therefore do not deserve any market hype or promotion.
In finding out why most pharma indulges in questionable tactics, we are lead to some interesting solutions to prevent such tactics with the least amount of hassles for all concerned, even as both profits and credibility are kept intact.
PMCID: PMC3192391  PMID: 22058616
Academia; Pharmaceutical Industry; Clinical Practice Guidelines; Best Practice Guidelines; Academic Medical Centers; Medical Associations; Research Journals; Clinical Research; Public Welfare; Pharma Image; Corporate Welfare; Biological Psychiatry; Law Suits Against Industry
15.  The publication of ethically uncertain research: attitudes and practices of journal editors 
BMC Medical Ethics  2012;13:4.
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.
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.
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.
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.
PMCID: PMC3378458  PMID: 22494972
Editors; Ethics; Publication ethics
16.  Can a core outcome set improve the quality of systematic reviews? – a survey of the Co-ordinating Editors of Cochrane review groups 
Trials  2013;14:21.
Missing outcome data or the inconsistent reporting of outcome data in clinical research can affect the quality of evidence within a systematic review. A potential solution is an agreed standardized set of outcomes known as a core outcome set (COS) to be measured in all studies for a specific condition. We investigated the amount of missing patient data for primary outcomes in Cochrane systematic reviews, and surveyed the Co-ordinating Editors of Cochrane Review Groups (CRGs) on issues related to the standardization of outcomes in their CRG’s reviews. These groups are responsible for the more than 7,000 protocols and full versions of Cochrane Reviews that are currently available, and the several hundred new reviews published each year, presenting the world’s largest collection of standardized systematic reviews in health care.
Using an unselected cohort of Cochrane Reviews, we calculated and presented the percentage of missing patient data for the primary outcome measure chosen for each review published by each CRG. We also surveyed the CRG Co-ordinating Editors to see what their policies are with regards to outcome selection and outcomes to include in the Summary of Finding (SoF) tables in their Cochrane Reviews. They were also asked to list the main advantages and challenges of standardizing outcomes across all reviews within their CRG.
In one fifth of the 283 reviews in the sample, more than 50% of the patient data for the primary outcome was missing. Responses to the survey were received from 90% of Co-ordinating Editors. Thirty-six percent of CRGs have a centralized policy regarding which outcomes to include in the SoF table and 73% of Co-ordinating Editors thought that a COS for effectiveness trials should be used routinely for a SoF table.
The reliability of systematic reviews, in particular meta-analyses they contain, can be improved if more attention is paid to missing outcome data. The availability of COSs for specific health conditions might help with this and the concept has support from the majority of Co-ordinating Editors in CRGs.
PMCID: PMC3575292  PMID: 23339751
COMET; Cochrane review groups; Co-ordinating editors; Core outcome set; ORBIT; Systematic reviews; Survey
17.  What do letters to the editor publish about randomized controlled trials? A cross-sectional study 
BMC Research Notes  2013;6:414.
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.
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).
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.
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.
PMCID: PMC3852599  PMID: 24124753
Letters to the editor; Randomized controlled trials; Journalogy
18.  Conflicts of interest in biomedical publications: considerations for authors, peer reviewers, and editors 
Croatian Medical Journal  2013;54(6):600-608.
This article overviews evidence on common instances of conflict of interest (COI) in research publications from general and specialized fields of biomedicine. Financial COIs are viewed as the most powerful source of bias, which may even distort citation outcomes of sponsored publications. The urge to boost journal citation indicators by stakeholders of science communication is viewed as a new secondary interest, which may compromize the interaction between authors, peer reviewers, and editors. Comprehensive policies on disclosure of financial and non-financial COIs in scholarly journals are presented as proxies of their indexing in evidence-based databases, and examples of successful medical journals are discussed in detail. Reports on clinical trials, systematic reviews, meta-analyses, and clinical practice guidelines may be unduly influenced by author-pharmaceutical industry relations, but these publications do not always contain explicit disclosures to allow the readers to judge the reliability of the published conclusions and practice-changing recommendations. The article emphasizes the importance of adhering to the guidance on COI from learned associations such as the International Committee of Medical Journal Editors (ICMJE). It also considers joint efforts of authors, peer reviewers, and editors as a foundation for appropriately defining and disclosing potential COIs.
PMCID: PMC3893982  PMID: 24382859
19.  Photoletter to the editor: Acquired idiopathic generalized anhidrosis 
Anhidrosis is a failure in sweat production in response to physiological thermal or chemical stimuli. Acquired idiopathic generalized anhidrosis is a rare disorder without sweat gland pathology and without neurologic symptoms. Most cases have been reported from Far East. We report a case of a 58-year-old Caucasian male who suffered from heat intolerance, heat-induced cutaneous burning and failed to sweat even in sauna for five years. A skin biopsy disclosed no pathologies. He had no neurologic disorders. The diagnosis of acquired idiopathic generalized anhidrosis was confirmed and treatment with methylprednisolone initiated. This led to improvement of heat tolerance, remission of burning and partial remission of sweating.
PMCID: PMC4299708  PMID: 25621094
acquired anhidrosis; minor starch test; eccrine sweat glands; corticosteroids
20.  FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data 
BMC Systems Biology  2009;3:26.
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.
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.
We have created an open source software tool called FORG3D that can be used for visualizing and exploring integrated genome scale data.
PMCID: PMC2651117  PMID: 19239683
21.  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
PMCID: PMC2672624  PMID: 19151095
22.  JSME: a free molecule editor in JavaScript 
A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript.
The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages.
A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page
PMCID: PMC3662632  PMID: 23694746
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.
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

Results 1-25 (940205)