Education and taxonomy: the role of the Field Studies Council and AIDGAP

The taxonomic disciplines, classification and identification, are fundamental to most biological sciences. Yet, taxonomic teaching and research have declined to a level where adequate support for the other sciences can no longer be sustained. New teaching initiatives are needed, combined with the provision of suitable resource materials and identification guides. Bodies such as the Field Studies Council and the Linnean Society have a tradition of publishing identification keys, but the experience of the AIDGAP project, first started in 1976, shows that considerable thought must be given to content and presentation. Testing prior to publication is vital.     

Style Guide and Information for Authors

The following specifications aim at speeding publication and minimizing editorial changes and retyping. The details of the American Anthropologist style as specified here are in part a codification of past practices and in part changes from them. Therefore, authors are urged to follow this guide carefully instead of relying on past issues.     

A Matter of Contrast: Yellow Flower Colour Constrains Style Length in Crocus species

Most flowers display distinct colour patterns comprising two different areas. The peripheral large-area component of floral colour patterns attracts flower visitors from some distance and the central small-area component guides flower visitors towards landing sites. Whereas the peripheral colour is largely variable among species, the central colour, produced mostly by anthers and pollen or pollen mimicking floral guides, is predominantly yellow and UV-absorbing. This holds also for yellow flowers that regularly display a UV bull’s eye pattern. Here we show that yellow-flowering Crocus species are a noticeable exception, since yellow-flowering Crocus species–being entirely UV-absorbing–exhibit low colour contrast between yellow reproductive organs and yellow tepals. The elongated yellow or orange-yellow style of Crocus flowers is a stamen-mimicking structure promoting cross-pollination by facilitating flower visitors’ contact with the apical stigma before the flower visitors are touching the anthers. Since Crocus species possess either yellow, violet or white tepals, the colour contrast between the stamen-mimicking style and the tepals varies among species. In this study comprising 106 Crocus species, it was tested whether the style length of Crocus flowers is dependent on the corolla colour. The results show that members of the genus Crocus with yellow tepals have evolved independently up to twelve times in the genus Crocus and that yellow-flowering Crocus species possess shorter styles as compared to violet- and white-flowering ones. The manipulation of flower visitors by anther-mimicking elongated styles in Crocus flowers is discussed.     

The European antibody network's practical guide to finding and validating suitable antibodies for research

Antibodies are widely exploited as research/diagnostic tools and therapeutics. Despite providing exciting research opportunities, the multitude of available antibodies also offers a bewildering array of choice. Importantly, not all companies comply with the highest standards, and thus many reagents fail basic validation tests. The responsibility for antibodies being fit for purpose rests, surprisingly, with their user. This paper condenses the extensive experience of the European Monoclonal Antibody Network to help researchers identify antibodies specific for their target antigen. A stepwise strategy is provided for prioritising antibodies and making informed decisions regarding further essential validation requirements. Web-based antibody validation guides provide practical approaches for testing antibody activity and specificity. We aim to enable researchers with little or no prior experience of antibody characterization to understand how to determine the suitability of their antibody for its intended purpose, enabling both time and cost effective generation of high quality antibody-based data fit for publication.     

VennDIS: A JavaFX‐based Venn and Euler diagram software to generate publication quality figures

Venn diagrams are graphical representations of the relationships among multiple sets of objects and are often used to illustrate similarities and differences among genomic and proteomic datasets. All currently existing tools for producing Venn diagrams evince one of two traits; they require expertise in specific statistical software packages (such as R), or lack the flexibility required to produce publication‐quality figures. We describe a simple tool that addresses both shortcomings, Venn Diagram Interactive Software (VennDIS), a JavaFX‐based solution for producing highly customizable, publication‐quality Venn, and Euler diagrams of up to five sets. The strengths of VennDIS are its simple graphical user interface and its large array of customization options, including the ability to modify attributes such as font, style and position of the labels, background color, size of the circle/ellipse, and outline color. It is platform independent and provides real‐time visualization of figure modifications. The created figures can be saved as XML files for future modification or exported as high‐resolution images for direct use in publications.     

Reanalysis of epidemiological evidence on lung cancer and passive smoking

ObjectiveTo assess the epidemiological evidence for an increase in the risk of lung cancer resulting from exposure to environmental tobacco smoke.DesignReanalysis of 37 published epidemiological studies previously included in a meta-analysis allowing for the possibility of publication bias.ResultsIf it is assumed that all studies that have ever been carried out are included, or that those selected for review are truly representative of all such studies, then the estimated excess risk of lung cancer is 24%, as previously reported (95% confidence interval 13% to 36%, P<0.001). However, a significant correlation between study outcome and study size suggests the presence of publication bias. Adjustment for such bias implies that the risk has been overestimated. For example, if only 60% of studies have been included, the estimate of excess risk falls from 24% to 15%.ConclusionA modest degree of publication bias leads to a substantial reduction in the relative risk and to a weaker level of significance, suggesting that the published estimate of the increased risk of lung cancer associated with environmental tobacco smoke needs to be interpreted with caution.

Key messages

• A systematic review of epidemiological studies on passive smoking estimated the increased risk of lung cancer as 24%
• There is clear evidence of publication bias in these studies
• Reanalysis of the data allowing for the possibility of publication bias substantially lowers the estimate of relative risk

     

Floral signposts: testing the significance of visual 'nectar guides' for pollinator behaviour and plant fitness

Nectar guides, contrasting patterns on flowers that supposedly direct pollinators towards a concealed nectar reward, are taxonomically widespread. However, there have been few studies of their functional significance and effects on plant fitness. Most previous studies focused on pollinator behaviour and used artificial flowers in laboratory settings. We experimentally investigated the role of putative nectar guides in a natural system: the South African iris Lapeirousia oreogena, whose flowers have a clearly visible pattern of six white arrow-markings pointing towards the narrow entrance of the long corolla tube, and its sole pollinator, a long-proboscid nemestrinid fly. We painted over none, some or all of the white arrow-markings with ink that matched the colour of the corolla background. Although arrow-marking removal had little effect on the approaches by flies to flowers from a distance, it dramatically reduced the likelihood of proboscis insertion. Export of pollen dye analogue (an estimate of male fitness) was reduced to almost zero in flowers from which all nectar guides had been removed, and fruit set (a measure of female fitness) was also significantly reduced. Our results confirm that the markings on L. oreogena flowers serve as nectar guides and suggest that they are under strong selective maintenance through both male and female fitness components in this pollination system.     

Interactive microbial genome visualization with GView

SUMMARY: GView is a Java application for viewing and examining prokaryotic genomes in a circular or linear context. It accepts standard sequence file formats and an optional style specification file to generate customizable, publication quality genome maps in bitmap and scalable vector graphics formats. GView features an interactive pan-and-zoom interface, a command-line interface for incorporation in genome analysis pipelines, and a public Application Programming Interface for incorporation in other Java applications. AVAILABILITY: GView is a freely available application licensed under the GNU Public License. The application, source code, documentation, file specifications, tutorials and image galleries are available at http://gview.ca.     

The Kardashian index: a measure of discrepant social media profile for scientists

In the era of social media there are now many different ways that a scientist can build their public profile; the publication of high-quality scientific papers being just one. While social media is a valuable tool for outreach and the sharing of ideas, there is a danger that this form of communication is gaining too high a value and that we are losing sight of key metrics of scientific value, such as citation indices. To help quantify this, I propose the ‘Kardashian Index’, a measure of discrepancy between a scientist’s social media profile and publication record based on the direct comparison of numbers of citations and Twitter followers.     

Towards a reduction in publication bias.

Current practice results in the publication of many research studies in medical and related disciplines which may be criticised on the grounds of inadequate sample size and statistical power. Small studies continue to be carried out with little more than a blind hope of showing the desired effect. Nevertheless, papers based on such work are submitted for publication, especially if the results turn out to be statistically significant. There is confusion about what makes a result suitable for publication. Often there is a preference for statistically significant results at the peer review stage. Consequently published reports of small studies tend to contain too many false positive results and to exaggerate the true effects. The use of a criterion of a posteriori power does not eliminate the bias; a priori power is the criterion of choice. This could be implemented by peer review of study protocols at the planning stage by funding bodies and journals.     

Management planning guidance for protected sites in the UK; a comparison of decision-making processes in nine guides

The processes for making decisions on objectives and management actions were identified in nine easily available management planning guides, all aimed at UK protected sites (Sites of Special Scientific Interest, Natura 2000, Ramsar, etc), and compared. They varied considerably between guides, to the extent that no two guides recommend identical processes. Processes were sometimes entirely absent, and usually incomplete. Poor guidance on decision-making may result in plans that are ineffective or damaging to the conservation of sites. The reasons for inconsistency are explored, suggestions are made for improving and testing of management planning guidance, and questions are raised about best practice and the value of a standard approach in planning the management of sites.     

ASTHMA AND CARDIAC DYSPNEA—A DIFFERENTIAL DIAGNOSIS

There appear to be no infallible guides by which to differentiate between cardiac insufficiency and asthma as a cause of dyspnea, wheezing and coughing in elderly patients. Many of the symptoms of one condition are also symptoms of the other. Even the results of therapeutic trial cannot be relied upon to establish diagnosis, for drugs effective in treatment of heart disease may also help relieve asthma, and vice versa.Although there is no single factor that can be considered pathognomonic, there are certain symptoms and results of tests which are more strongly indicative of one condition than of the other. Careful evaluation of all factors, while it may not serve to establish unequivocal diagnosis, will provide a basis for judicious treatment of the patient.     

Physical and biological performance of a novel block copolymer nerve guide

Although the ability to regenerate is evident in the nervous system, lesioned neurites are unable to cross gaps in neuronal pathways. In order to bridge gaps, guiding cues are essential to direct neurite regrowth. To overcome many of the shortcomings of polymer-based nerve guides, we developed a bioresorbable nerve guide composed of a novel trimethylene carbonate-caprolacton block copolymer (TMC-CL). Pore formation was controlled by using special solvent/precipitation media compositions in combination with the pore forming agent poly ethylene glycol (PEG). NMR spectroscopy, shear force-, compression-, and permeation assays were used for conduit characterization. The polymer conduit has a semipermeable wall with submicron pores to allow free metabolite/drug exchange. In order to investigate the principle of temporally controlled expression of therapeutic proteins in nerve guides, Neuro-2a cells were genetically engineered to express the reporter gene product green fluorescent protein (GFP) under the control of the Tet-On system. When these transduced cells were encapsulated in nerve guides, GFP expression could be induced for days by adding the antibiotic tetracycline derivative doxycycline to the nerve guide environment. Furthermore, encapsulated dorsal root ganglia (DRG) produced long neurites in vitro. In subsequent in vivo experiments, nerve guides filled with Schwann cells (SC) were implanted into lesioned spinal cords of adult rats. Regeneration of spinal cord axons into nerve guides was promoted by co-implanted Schwann cells. The data suggest that the novel TMC-CL nerve guides provide a promising tool for neuroregeneration.     

Stability and Longevity in the Publication Careers of U.S. Doctorate Recipients

Since the 1950s, the number of doctorate recipients has risen dramatically in the United States. In this paper, we investigate whether the longevity of doctorate recipients’ publication careers has changed. This is achieved by matching 1951–2010 doctorate recipients with rare names in astrophysics, chemistry, economics, genetics and psychology in the dissertation database ProQuest to their publications in the publication database Web of Science. Our study shows that pre-PhD publication careers have changed: the median year of first publication has shifted from after the PhD to several years before PhD in most of the studied fields. In contrast, post-PhD publication career spans have not changed much in most fields. The share of doctorate recipients who have published for more than twenty years has remained stable over time; the shares of doctorate recipients publishing for shorter periods also remained almost unchanged. Thus, though there have been changes in pre-PhD publication careers, post-PhD career spans remained quite stable.     

Asthma and cardiac dyspnea; a differential diagnosis

There appear to be no infallible guides by which to differentiate between cardiac insufficiency and asthma as a cause of dyspnea, wheezing and coughing in elderly patients. Many of the symptoms of one condition are also symptoms of the other. Even the results of therapeutic trial cannot be relied upon to establish diagnosis, for drugs effective in treatment of heart disease may also help relieve asthma, and vice versa. Although there is no single factor that can be considered pathognomonic, there are certain symptoms and results of tests which are more strongly indicative of one condition than of the other. Careful evaluation of all factors, while it may not serve to establish unequivocal diagnosis, will provide a basis for judicious treatment of the patient.     

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.     

Teaching the tourists in Galápagos: what do Galápagos National Park guides know,think, and teach tourists about evolution?

Background

Evolution is everywhere in Galápagos, especially regarding the role the islands have played in the history of evolutionary thought. In turn, the Galápagos National Park guides are in a unique position as informal science educators, as they are the primary points-of-contact for the islands’ ~ 200,000 tourists per year. Our goal was to assess the guides’ knowledge and acceptance of the theory of evolution, in addition to learning more about their perceptions of the connection between the islands and evolution.

Methods

We surveyed 63 guides in three towns on three of the archipelago’s populated islands. Surveys included items targeting the guides knowledge of evolution (via the Knowledge of Evolution Exam, or the KEE) and acceptance of the theory of evolution (via the Measure of Acceptance of the Theory of Evolution, or the MATE). Additional, novel items gauged the guides’ perceptions of the islands, insofar as Galápagos is connected to evolution and the history of evolutionary thought.

Results

Although acceptance of evolution was high, knowledge was relatively low. However, the guides are proud of the islands’ association with the history of evolutionary thought, and enjoy talking about evolution while giving tours. On open-ended responses, guides claimed to especially enjoy talking with tourists about geology and island culture, and a few voiced concerns about the conflict between evolution and religion. Finally, the overwhelming majority of the guides agreed or strongly agreed with the statement, “I would like to learn more about Galápagos and the history of evolutionary thought.”

Conclusions

Galápagos guides display a disconnect between what is felt about evolution, and what is known about how evolution actually works. We can probably trace their fondness for, and acceptance of, evolution to the clear connection between evolution, tourism, and the guides’ livelihoods. We can trace their lack of knowledge to their schooling, as prior work detected similarly low knowledge of evolution in the islands’ schoolteachers. However, the guides are a receptive audience for professional development pertaining to our contemporary understanding of the mechanics of biological evolution. Improving guides’ understanding of biological evolution could, in turn, inform the evolutionary understanding of thousands of tourists each year.