Full publication of papers presented at the 1995 through 1999 European Association of Plastic Surgeons annual scientific meetings: a systemic bibliometric analysis

From the multitude of oral presentations at major medical meetings, the most informative and highest-quality studies make it to full publication in peer-reviewed journals. The rate of publication may be regarded as an indicator of the scientific level of the meeting. Study of the publication rates of consecutive annual meetings allows for the evaluation of the consistency of the scientific level of these meetings and for comparison with publication rates of other meetings in the same field of interest. To grade how useful any publication is to other authors, one can furthermore measure how frequently they cite it in their own publications. Finally, the time lag between oral presentation and full publication is of importance to both its authors and the audience at the meeting. The main objectives of this study were to determine the publication rate of papers of various fields of interest as presented at five consecutive annual meetings of the European Association of Plastic Surgeons (EURAPS) and the time lag between these presentations and their publication. The authors compared their overall findings to those reported for other surgical specialties. Moreover, they identified and classified the journals in which the full publications appeared as an indicator of the scientific value of the meeting. They conclude that a greater than average number of papers presented at the 1995 through 1999 annual EURAPS meetings went on to full publication in peer-reviewed journals. Among these journals, Plastic and Reconstructive Surgery was the best source for information presented at the meetings. Although approximately 90 percent of the publications appeared before 3 years had passed after a meeting, additional publications may be expected to appear even more than 6 years after the meeting. Given the high publication rate and the high average normalized impact factor of the journals in which the presentations appeared, the five studied EURAPS meetings overall had high scientific value.     

Rising Publication Delays Inflate Journal Impact Factors

Journal impact factors have become an important criterion to judge the quality of scientific publications over the years, influencing the evaluation of institutions and individual researchers worldwide. However, they are also subject to a number of criticisms. Here we point out that the calculation of a journal’s impact factor is mainly based on the date of publication of its articles in print form, despite the fact that most journals now make their articles available online before that date. We analyze 61 neuroscience journals and show that delays between online and print publication of articles increased steadily over the last decade. Importantly, such a practice varies widely among journals, as some of them have no delays, while for others this period is longer than a year. Using a modified impact factor based on online rather than print publication dates, we demonstrate that online-to-print delays can artificially raise a journal’s impact factor, and that this inflation is greater for longer publication lags. We also show that correcting the effect of publication delay on impact factors changes journal rankings based on this metric. We thus suggest that indexing of articles in citation databases and calculation of citation metrics should be based on the date of an article’s online appearance, rather than on that of its publication in print.     

Amendment of Articles 8, 9, 10, 21 and 78 of the International Code of Zoological Nomenclature to expand and refine methods of publication

The International Commission on Zoological Nomenclature has voted in favour of a revised version of the amendment to the International Code of Zoological Nomenclature that was proposed in 2008. The purpose of the amendment is to expand and refine the methods of publication allowed by the Code, particularly in relation to electronic publication. The amendment establishes an Official Register of Zoological Nomenclature (with ZooBank as its online version), allows electronic publication after 2011 under certain conditions, and disallows publication on optical discs after 2012. The requirements for electronic publications are that the work be registered in ZooBank before it is published, that the work itself state the date of publication and contain evidence that registration has occurred, and that the ZooBank registration state both the name of an electronic archive intended to preserve the work and the ISSN or ISBN associated with the work. Registration of new scientific names and nomenclatural acts is not required. The Commission has confirmed that ZooBank is ready to handle the requirements of the amendment.     

MIQE précis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments

The conclusions of thousands of peer-reviewed publications rely on data obtained using fluorescence-based quantitative real-time PCR technology. However, the inadequate reporting of experimental detail, combined with the frequent use of flawed protocols is leading to the publication of papers that may not be technically appropriate. We take the view that this problem requires the delineation of a more transparent and comprehensive reporting policy from scientific journals. This editorial aims to provide practical guidance for the incorporation of absolute minimum standards encompassing the key assay parameters for accurate design, documentation and reporting of qPCR experiments (MIQE précis) and guidance on the publication of pure 'reference gene' articles.     

MedScan,a natural language processing engine for MEDLINE abstracts

MOTIVATION: The importance of extracting biomedical information from scientific publications is well recognized. A number of information extraction systems for the biomedical domain have been reported, but none of them have become widely used in practical applications. Most proposals to date make rather simplistic assumptions about the syntactic aspect of natural language. There is an urgent need for a system that has broad coverage and performs well in real-text applications. RESULTS: We present a general biomedical domain-oriented NLP engine called MedScan that efficiently processes sentences from MEDLINE abstracts and produces a set of regularized logical structures representing the meaning of each sentence. The engine utilizes a specially developed context-free grammar and lexicon. Preliminary evaluation of the system's performance, accuracy, and coverage exhibited encouraging results. Further approaches for increasing the coverage and reducing parsing ambiguity of the engine, as well as its application for information extraction are discussed.     

Reliable structural interpretation of small-angle scattering data from bio-molecules in solution - the importance of quality control and a standard reporting framework

Small-angle scattering is becoming an increasingly popular tool for the study of bio-molecular structures in solution. The large number of publications with 3D-structural models generated from small-angle solution scattering data has led to a growing consensus for the need to establish a standard reporting framework for their publication. The International Union of Crystallography recently established a set of guidelines for the necessary information required for the publication of such structural models. Here we describe the rationale for these guidelines and the importance of standardising the way in which small-angle scattering data from bio-molecules and associated structural interpretations are reported.     

T. R. R. Stebbing:A bibliography with biographic notes

T. R. R. Stebbing (1835–1926), a specialist on the systematics of amphipod Crustacea, was raised in London in a literary family and studied classics, law and history at Oxford. After his ordination as a priest in 1859 he was a schoolmaster, then, after he married, a private tutor at Torquay. About 1863 he read Darwin's Origin of species and was convinced by it; by 1868 he had become a naturalist and systematist. In 1877 he moved to Tunbridge Wells where he spent the rest of his life studying Crustacea, active in scientific societies, and writing essays and reviews.
Stebbing's Darwinism was not particularly original, though he marshalled some good examples from the invertebrates to indicate the importance of variation within and between species. He regarded natural selection as a directing force by which God's plan for organisms was being worked out, and credited it with the origin of language, morality and religion. In taxonomic practice, Stebbing advocated priority of names, simple rules of transliteration and gender, and publication of new names only in a few easily-accessible journals. After the publication of the Regies internationales de la nomenclature zoologique in 1905 his writings on taxonomic practice were confined to minor issues.
A bibliography of Stebbing's 242 publications concerned with carcinology, Darwinism, nomenclature and miscellaneous subjects has been compiled.     

Alpha omega alpha election and medical school thesis publication: relationship to subsequent publication rate over a twenty-year period.

To determine the importance of academic and research success during medical school upon subsequent academic activity, a computerized literature search was performed using the names of the 79 surviving members of the Yale Medical School Class of 1970. Individuals elected to Alpha Omega Alpha (AOA) during the third year of school had significantly more publications (mean 101.7 +/- 69.6) between 1970 and 1990 than those elected during the fourth year (mean 28.3 +/- 48.0, p = 0.01). Both had significantly more publications than non-AOA members (mean 11.1 +/- 19.4, p = 0.02). Publication of the student''s medical school thesis was also associated with a greater number of publications than thesis non-publication (mean 22.1 +/- 37.5 vs 14.4 +/- 30.0, p = 0.005). These studies demonstrate that, at least at the institution studied, election to AOA and publication of the results of a research project were associated with increased publication rates in the medical field over the 20-year period following medical school graduation.     

The taxonomist - an endangered race. A practical proposal for its survival

Background

Taxonomy or biological systematics is the basic scientific discipline of biology, postulating hypotheses of identity and relationships, on which all other natural sciences dealing with organisms relies. However, the scientific contributions of taxonomists have been largely neglected when using species names in scientific publications by not citing the authority on which they are based.

Discussion

Consequences of this neglect is reduced recognition of the importance of taxonomy, which in turn results in diminished funding, lower interest from journals in publishing taxonomic research, and a reduced number of young scientists entering the field. This has lead to the so-called taxonomic impediment at a time when biodiversity studies are of critical importance. Here we emphasize a practical and obvious solution to this dilemma. We propose that whenever a species name is used, the author(s) of the species hypothesis be included and the original literature source cited, including taxonomic revisions and identification literature - nothing more than what is done for every other hypothesis or assumption included in a scientific publication. In addition, we postulate that journals primarily publishing taxonomic studies should be indexed in ISI^SM.

Summary

The proposal outlined above would make visible the true contribution of taxonomists within the scientific community, and would provide a more accurate assessment for funding agencies impact and importance of taxonomy, and help in the recruitment of young scientists into the field, thus helping to alleviate the taxonomic impediment. In addition, it would also make much of the biological literature more robust by reducing or alleviating taxonomic uncertainty.     

Evidence-based palaeopathology: Meta-analysis of PubMed-listed scientific studies on ancient Egyptian mummies

There is a plethora of published scientific studies on ancient Egyptian mummies. Surprisingly, hitherto there is no systematic review of this research, which would help to assess the quality of this vast body of published literature and thus to increase “evidence” in palaeopathological research. The aim of this study was to review all PubMed-listed scientific studies performed on Ancient Egyptian mummies. A total of 131 studies were found in the database for the selected time period, 1977-2005. Our “meta-analysis” showed that the number of publications per year varies enormously. The majority of mummies examined date to the third intermediate and Ptolemaic periods; data from other time periods were lacking. Identification of the cause of death and ¹⁴C-dating of the mummy or funeral goods were rarely addressed. There was a tendency towards an increased use of non-invasive examination methods in more modern times. Our meta-analysis addressed both scientific content (e.g. palaeopathological findings/examination methods) and publication issues (e.g. location of the first author or year of publication) in these studies. Based on our experience, we recommend some minimum publication standards for palaeopathologic studies on ancient mummies, which shall improve evidence-based research in palaeopathology in general.     

LitDB - Keeping Track of Research Papers From Your Institute Made Simple

Background

In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their scientific publications. However, in most institutions and universities articles are often managed in a redundant file-based and non-central way. Whereas excellent reference management software packages such as Zotero, Endnote or Mendeley exist to manage bibliographies and references when writing scientific articles, we are not aware of any open source database solution keeping track of publication records from large scientific groups, entire institutions and/or universities.

Results

We here describe LitDB, a novel open source literature database solution for easy maintenance of publication lists assigned to various topics. In the last 2 years more than 50 users have been using LitDB at our research institute. The LitDB system is accessed via a web browser. Publications can be uploaded through direct exports from reference manager libraries or by entering PubMed IDs. Single users or user groups can track their citation counts, h-index and impact factor statistics and gain insights into the publication records of other users. It offers various visualization functions like coauthor networks and provides ways to organize publications from dedicated projects and user groups. The latter is in particular beneficial to manage publication lists of large research groups and research initiatives through a “crowd-sourcing” effort.

Conclusions

Keeping track of papers authored and published by a research group, institute or university is an important and non-trivial task. By using a centralized web-based platform for publication management such as LitDB the compilation of project- and group-related publication lists becomes easily manageable and it is less likely that papers are forgotten along the way.

     

The scientific value of Amazonian protected areas

Protected areas (PAs) are under increasing pressure to demonstrate their broader value and contribution to society. Scientific research and associated knowledge production comprise one such value, which has received relatively little attention in the academic literature. Here, we use the Amazon region as a case study to quantify scientific knowledge production (as measured by scientific publications in peer-reviewed journals) in PAs and identify the main biophysical, geographical and social characteristics that influence such production. We adopt a multi-model inference approach with an innovative hurdle regression model to independently assess the factors influencing the presence of research and the number of studies in PAs. Our results indicate a highly skewed pattern of scientific production, with many PAs with few or no associated scientific articles. Larger, older and more highly protected PAs in Ecuador and Peru were most likely to have scientific production, while time since first publication was most strongly associated with the number of publications from a PA. These findings provide important insights that could be used to support and strengthen policy aimed at increasing the value of Amazonian protected areas for scientific research.     

Analysis of acanthocephalan literature published since 1900.

The data for this study are based on more than 6000 articles that mention Acanthocephala. The results indicate: (1) the difficulty in being current on world literature. It took about 3 years beyond the date of publication to discover many articles. (2) Except for World Wars I and II there has been a sustained increase in the number of articles. At present this rate exceeds 1000 titles per 5-year period. (3) Investigator interest, as measured by multiple publications by a given author, has remained very small. (4) Most publications have originated in the U.S.S.R. and U.S.A. followed by Great Britain and Germany. (5) Number of authors per title has increased dramatically. Currently, there are more four-author than single-author articles. (6) Fish are host animals most likely to be mentioned as containing acanthocephalans.     

Research Trends in Evidence-Based Medicine: A Joinpoint Regression Analysis of More than 50 Years of Publication Data

Background

Evidence-based medicine (EBM) has developed as the dominant paradigm of assessment of evidence that is used in clinical practice. Since its development, EBM has been applied to integrate the best available research into diagnosis and treatment with the purpose of improving patient care. In the EBM era, a hierarchy of evidence has been proposed, including various types of research methods, such as meta-analysis (MA), systematic review (SRV), randomized controlled trial (RCT), case report (CR), practice guideline (PGL), and so on. Although there are numerous studies examining the impact and importance of specific cases of EBM in clinical practice, there is a lack of research quantitatively measuring publication trends in the growth and development of EBM. Therefore, a bibliometric analysis was constructed to determine the scientific productivity of EBM research over decades.

Methods

NCBI PubMed database was used to search, retrieve and classify publications according to research method and year of publication. Joinpoint regression analysis was undertaken to analyze trends in research productivity and the prevalence of individual research methods.

Findings

Analysis indicates that MA and SRV, which are classified as the highest ranking of evidence in the EBM, accounted for a relatively small but auspicious number of publications. For most research methods, the annual percent change (APC) indicates a consistent increase in publication frequency. MA, SRV and RCT show the highest rate of publication growth in the past twenty years. Only controlled clinical trials (CCT) shows a non-significant reduction in publications over the past ten years.

Conclusions

Higher quality research methods, such as MA, SRV and RCT, are showing continuous publication growth, which suggests an acknowledgement of the value of these methods. This study provides the first quantitative assessment of research method publication trends in EBM.     

Indian publishing: enduring the boom

There has been a boom in the publication of Indian plant science research in recent years, defying national trends in other sciences and outperforming the international trends in plant science publications. This boom augurs well for India considering the importance of agriculture to her economy and the crucial need for science-based solutions to break the yield barriers. However, sustaining it requires tackling the problems of funding, infrastructure, manpower and other policy issues.     

The correlates of research success.

A survey was carried out of the undergraduate backgrounds and research achievements of 885 (94.1%) of all 940 medically qualified professors and readers in medical faculties in the United Kingdom. A total of 217 (24.5%) of the graduates in these senior academic positions had graduated from Oxford or Cambridge and 137 (15.5%) had an intercalated BSc. The corresponding figures for a control group matched for sex and date of graduation were 118 (13.3%) for Oxford and Cambridge (academic to control odds ratio 2.11:1) and 34 (3.8%) for the BSc (odds ratio 4.58:1). Those with an intercalated BSc in the clinical specialties raised substantially more research grants from the Medical Research Council than their peers from Oxford and Cambridge or those without a BSc. The Oxford and Cambridge group raised more grants in the non-clinical specialties. Bibliometric analysis was carried out on the United Kingdom graduates within the broad specialty of medicine (n = 218) matched for date of graduation. Academics with a BSc had a better publication record over 10 years (median number of original publications 72) than the Oxford and Cambridge group (median 59) and a substantially better record than those from other schools without a BSc (median 46). Citation analysis was carried out on subsets of the above sample matched for date of graduation and frequency of publication. Those with an intercalated BSc were cited more often (8.04 citations/paper) than the Oxford and Cambridge graduates (7.63) and substantially more than their peers without a BSc (4.16). These data show very clearly that research training or experience, or both, as an undergraduate has a substantial influence on career development and correlates positively with subsequent research performance many years later.     

Prioritizing key resilience indicators to support coral reef management in a changing climate

Managing coral reefs for resilience to climate change is a popular concept but has been difficult to implement because the empirical scientific evidence has either not been evaluated or is sometimes unsupportive of theory, which leads to uncertainty when considering methods and identifying priority reefs. We asked experts and reviewed the scientific literature for guidance on the multiple physical and biological factors that affect the ability of coral reefs to resist and recover from climate disturbance. Eleven key factors to inform decisions based on scaling scientific evidence and the achievability of quantifying the factors were identified. Factors important to resistance and recovery, which are important components of resilience, were not strongly related, and should be assessed independently. The abundance of resistant (heat-tolerant) coral species and past temperature variability were perceived to provide the greatest resistance to climate change, while coral recruitment rates, and macroalgae abundance were most influential in the recovery process. Based on the 11 key factors, we tested an evidence-based framework for climate change resilience in an Indonesian marine protected area. The results suggest our evidence-weighted framework improved upon existing un-weighted methods in terms of characterizing resilience and distinguishing priority sites. The evaluation supports the concept that, despite high ecological complexity, relatively few strong variables can be important in influencing ecosystem dynamics. This is the first rigorous assessment of factors promoting coral reef resilience based on their perceived importance, empirical evidence, and feasibility of measurement. There were few differences between scientists' perceptions of factor importance and the scientific evidence found in journal publications but more before and after impact studies will be required to fully test the validity of all the factors. The methods here will increase the feasibility and defensibility of including key resilience metrics in evaluations of coral reefs, as well as reduce costs. Adaptation, marine protected areas, priority setting, resistance, recovery.     

Looking for Landmarks: The Role of Expert Review and Bibliometric Analysis in Evaluating Scientific Publication Outputs

Objective

To compare expert assessment with bibliometric indicators as tools to assess the quality and importance of scientific research papers.

Methods and Materials

Shortly after their publication in 2005, the quality and importance of a cohort of nearly 700 Wellcome Trust (WT) associated research papers were assessed by expert reviewers; each paper was reviewed by two WT expert reviewers. After 3 years, we compared this initial assessment with other measures of paper impact.

Results

Shortly after publication, 62 (9%) of the 687 research papers were determined to describe at least a ‘major addition to knowledge’ –6 were thought to be ‘landmark’ papers. At an aggregate level, after 3 years, there was a strong positive association between expert assessment and impact as measured by number of citations and F1000 rating. However, there were some important exceptions indicating that bibliometric measures may not be sufficient in isolation as measures of research quality and importance, and especially not for assessing single papers or small groups of research publications.

Conclusion

When attempting to assess the quality and importance of research papers, we found that sole reliance on bibliometric indicators would have led us to miss papers containing important results as judged by expert review. In particular, some papers that were highly rated by experts were not highly cited during the first three years after publication. Tools that link expert peer reviews of research paper quality and importance to more quantitative indicators, such as citation analysis would be valuable additions to the field of research assessment and evaluation.