Research letter: How should abridged scientific articles be presented in journals? A survey of readers and authors

SEVERAL SCIENTIFIC AND GENERAL MEDICAL JOURNALS publish full-length articles on their Web sites and abridged versions in their print journals. We surveyed a stratified random sample of BMJ readers and authors to elicit their preferred format for the abridged print version. Each participant received a research paper abridged in 3 different formats: conventional abridged version, journalistic version and enhanced-abstract version. Overall, 45% (95% confidence interval [CI] 42%–48%) of the respondents said they liked the conventional version most, 31% (95% CI 28%–34%) preferred the journalistic version and 25% (95% CI 22%–27%) preferred the enhanced-abstract version. Twenty-eight percent (95% CI 25%–32%) indicated that use of the journalistic format for abridged articles would very likely stop them from submitting papers to BMJ, and 13% (95% CI 11%–16%) said the use of the enhanced-abstract version would stop them from submitting to BMJ. Publishers of general medical journals who publish shortened articles should consider that authors and readers prefer a more conventional style of abridged papers.To allow critical appraisal of a scientific paper, a certain amount of space is needed to describe the methods and results. Editorial space is scarce, however, and editors struggle to meet the expectations of both authors and readers. Moreover, it seems that many readers read only parts of scientific papers. Now that electronic publishing is available, several scientific and general medical journals have adopted strategies to publish detailed articles on their Web sites, often in advance of the print journal publication, with a more concise presentation appearing in the print journal.Since 2000 most papers in BMJ have been published in their full-length form on the journal''s Web site and in an abridged form in the print journal.¹ Currently the abridgement is simply a condensed version of the full-length paper (about 30%–50% shorter). The conventional structure of scientific papers is maintained, and the original wording is hardly altered.There are many alternative forms of presenting abridged scientific information. “Serious” magazines such as The Economist use a journalistic approach, presenting the salient information at the beginning and more technical details later in the text. Medical journals such as Evidence-Based Medicine use enhanced abstracts, in which details of the results are presented (including a table or figure), and the main text — if there is any — provides context and interpretation. We performed a survey to find which format of short version — the conventional approach, a journalistic version or a version with an enhanced abstract — of scientific articles is preferred by readers and authors. We randomly sampled 2 papers each of 6 study designs (randomized controlled trial, systematic review, meta-analysis, cohort study, case–control study and qualitative study) published in conventional abridged form^2,3 in BMJ between January 2000 and June 2002. The conventional format is a condensed version of the full-length paper and contains 1300–1500 words; the structure of the paper (Introduction, Methods, Results, Discussion) is retained.³ For each paper we prepared 2 additional abridged formats: a journalistic version⁴ and an enhanced-abstract version (see the online appendix at www.cmaj.ca/cgi/content/full/172/2/203/DC1 for a sample of 3 abridgements of 1 paper). The journalistic version was based on a style typically used by “serious” newspapers, with the following subheadings: “Why we carried out this study,” “The background,” “What were the main findings?,” “How did we perform the study?” and “Why are these results important?” This format had no abstract, the paper starting instead with the main findings and conclusions in the first paragraph, followed by less salient details. The enhanced-abstract version provided detailed results in the abstract (including a table or figure), and the main body of the text was explanatory, focusing on the context and discussion.We drew a stratified random sample from 1728 UK and non-UK readers and 360 corresponding authors of a research paper published in BMJ between January 2000 and June 2002. Each participant received all 3 abridged versions of 1 of 12 research papers. The study design of the paper and the order of versions were allocated randomly to each participant.We asked the respondents to rank the 3 versions in order of preference and to indicate how strongly they felt about their preference. We also asked participants whether use of either of the journalistic or enhanced-abstract formats instead of the conventional format would prevent them from submitting papers to BMJ in the future. We offered a book voucher as an incentive and sent 2 reminders to nonrespondents.⁴Of the sample of 2088 respondents, 55 were excluded (43 had incorrect mailing addresses, and 12, being both readers and authors, were selected more than once because of overlap in the databases). Of the 2033 eligible participants, 1002 (49%) responded. The response rate was higher for authors (220/321 [68%]) than readers (782/1712 [46%]). Item nonresponse was minimal.A total of 45% (95% confidence interval [CI] 42%–48%) of the respondents (446/997) (42% of readers and 56% of authors) said that they liked the conventional abridged version most (Fig. 1). The next most preferred format was the journalistic version (31% [95% CI 28%–34%] [306/997]), followed by the enhanced-abstract version (25% [95% CI 22%–27%] [245/997]). When we stratified for location (UK v. non-UK) and audience (reader v. author), the conventional abridged version remained the preferred version, except among UK readers, who gave the 3 versions similar rankings (Fig. 1).Open in a separate windowFig. 1: Type of short version of scientific article most preferred by BMJ authors and readers, stratified for audience (authors v. readers) and geographic location (UK v. non-UK). Error bars represent the 95% confidence interval.Most respondents (87% [95% CI 85%–89%] [863/994]) liked their first choice “a lot.” Thirteen percent (95% CI 11%–15%) (127/994) liked their first choice only “a little,” and none said they “don''t like it at all.” Four respondents (0.4%) did not have an opinion.A total of 268 respondents said they were unlikely to submit a paper to BMJ in the future. Of the remaining 734 respondents, 28% (95% CI 25%–32%) indicated that use of the journalistic format for abridgement would very likely stop them from submitting papers to BMJ, and 13% (95% CI 11%–16%) said that use of the enhanced-abstract format as abridgement would.Our findings that a conventional abridged version was preferred by BMJ authors and readers and that many respondents indicated that use of journalistic and enhanced-abstract formats would prevent them from submitting future papers to the journal are important signals for editors. They indicate that contributors'' opinions should be considered when planning major changes for the presentational style of scientific papers.The main limitation of our study is the low response rate for readers (46%), despite strategies to optimize response rates.⁴ However, we believe that the information we received from readers is still useful, since we have no reason to believe that any particular selection mechanism is active other than lack of interest in the presentation of research papers.Publishers of scientific and general medical journals who use or are considering using abridgements of scientific articles should bear in mind that a conventional format of abridged papers may be the choice most likely to satisfy both readers and authors.     

Nitrogen supply affects arbuscular mycorrhizal colonization of Artemisia vulgaris in a phosphate-polluted field site

Root colonization by arbuscular mycorrhizal fungi (AMF) was investigated in industrially polluted grassland characterized by exceptionally high phosphorus levels (up to 120 g kg(-1) soil). Along a pollution-induced nitrogen gradient, soil and tissue element concentrations of Artemisia vulgaris plants and their mycorrhizal status were determined. Additionally, we compared mycorrhization rates and above-ground biomass of A. vulgaris at N-fertilized and control plots in the N-poor area. Despite high soil and tissue P concentrations, plants from N-deficient plots, which were characterized by low tissue N concentrations and N : P ratios, were strongly colonized by AMF, whereas at a plot with comparable P levels, but higher soil and plant N concentrations and N : P ratios, mycorrhization rates were significantly lower. Correlation analyses revealed a negative relationship between percentage root colonization of A. vulgaris by AMF and both tissue N concentration and N : P ratio. Accordingly, in the fertilization experiment, control plants had higher mycorrhization rates than N-fertilized plants, whereas the species attained higher biomass at N-fertilized plots. The results suggest that N deficiency stimulates root colonization by AMF in this extraordinarily P-rich field site.     

Molecular mass, stoichiometry, and assembly of 20 S particles

N-Ethylmaleimide-sensitive factor (NSF), soluble NSF attachment proteins (SNAPs), and SNAP receptor (neuronal SNARE) complexes form 20 S particles with a mass of 788 +/- 122 kDa as judged by scanning transmission electron microscopy. A single NSF hexamer and three alpha SNAP monomers reside within a 20 S particle as determined by quantitative amino acid analysis. In order to study the binding of alpha SNAP and NSF in solution, to define their binding domains, and to specify the role of oligomerization in their interaction, we fused domains of alpha SNAP and NSF to oligomerization modules derived from thrombospondin-1, a trimer, and cartilage oligomeric matrix protein, a pentamer, respectively. Binding studies with these fusion proteins reproduced the interaction of alpha SNAP and NSF N domains in the absence of the hexamerization domain of NSF (D2). Trimeric alpha SNAP (or its C-terminal half) is sufficient to recruit NSF even in the absence of SNARE complexes. Furthermore, pentameric NSF N domains are able to bind alpha SNAP in complex with SNAREs, whereas monomeric N domains do not. Our results demonstrate that the oligomerization of both NSF N domains and alpha SNAP provides a critical driving force for their interaction and the assembly of 20 S particles.     

Modulation of CpG oligodeoxynucleotide-mediated immune stimulation by locked nucleic acid (LNA)

Locked nucleic acid (LNA) is an RNA derivative that when introduced into oligodeoxynucleotides (ODN), mediates high efficacy and stability. CpG ODNs are potent immune stimulators and are recognized by toll-like receptor-9 (TLR9). Some phosphorothioate antisense ODNs bearing CpG dinucleotides have been shown to possess immune modulatory capacities. We investigated the effects of LNA substitutions on immune stimulation mediated by antisense ODN G3139 or CpG ODN 2006. LNA ODNs were tested for their ability to stimulate cytokine secretion from human immune cells or TLR9-dependent signaling. Phosphorothioate chimeric LNA/DNA antisense ODNs with phosphodiester-linked LNA nucleobases at both ends showed a marked decrease of immune modulation with an increasing number of 3' and 5' LNA bases. In addition, guanosine-LNA and cytosine-LNA or simply cytosine-LNA substitutions in the CpG dinucleotides of ODN 2006 led to strong decrease or near complete loss of immune modulation. TLR9-mediated signaling was similarly affected. These data indicate that increasing amounts of LNA residues in the flanks or substitutions of CpG nucleobases with LNA reduce or eliminate the immune stimulatory effects of CpG-containing phosphorothioate ODN.     

Extensive linkage disequilibrium in small human populations in Eurasia

The extent of linkage disequilibrium (LD) was studied in two small food-gathering populations—Evenki and Saami—and two larger food-producing populations—Finns and Swedes—in northern Eurasia. In total, 50 single-nucleotide polymorphisms (SNPs) from five genes were genotyped using real-time pyrophosphate DNA sequencing, whereas 14 microsatellites were genotyped in two X-chromosomal regions. In addition, hypervariable region I of the mtDNA was sequenced to shed light on the demographic history of the populations. The SNP data, as well as the microsatellite data, reveal extensive levels of LD in Evenki and Saami when compared to Finns and Swedes. mtDNA-sequence variation is compatible with constant population size over time in Evenki and Saami but indicates population expansion in Finns and Swedes. Furthermore, the similarity between Finns and Swedes in SNP allele- and haplotype-frequency distributions indicate that these two populations may share a recent common origin. These findings suggest that populations such as the Evenki and the Saami, rather than the Finns, may be particularly suited for the initial coarse mapping of common complex diseases.     

Regulation of ferritin mRNA translation in primary erythroblasts: exogenous c-Kit plus EpoR signaling mimics v-ErbA oncoprotein activity

In general, translation efficiency of ferritin mRNAs is modulated by variations in iron supply. In primary avian erythroblasts undergoing short-term proliferation, however, ferritin heavy chain (ferH) mRNA is repressed at all iron levels. Yet, expression of v-ErbA oncoprotein is sufficient to reinduce ferH mRNA utilization at physiological iron concentrations. Since overexpression of the receptor tyrosine kinase c-Kit and erythropoietin receptor (EpoR) stimulates long-term proliferation of primary erythroblasts like v-ErbA, we analyzed the impact of cooperation between c-Kit and EpoR on the regulation of iron storage. Whereas endogenous c-Kit in combination with exogenous EpoR had no significant effect, ectopic overexpression of both receptors abolished translational repression of ferH mRNA upon iron administration. Thus, high-intensity signaling through c-Kit plus EpoR pathways mimics the v-ErbA-mediated regulatory phenotype.     

Serological Differentiation between HCV Subtypes 1a and 1b by a Recombinant Immunoblot Assay

Until now, no serological assay has been available for the differentiation of HCV subtypes. Since there is evidence that the subtypes differently influence the clinical course of HCV infection and the outcome of interferon therapy, we established a strip immunoblot assay (NS-4 IBA) with recombinant HCV proteins of the nonstructural 4 (NS-4) region propagated in Escherichia coli. Using this NS-4 IBA, we were able to distinguish HCV subtypes la and 1b, which are the most prevalent subtypes in Europe and the U.S.A. The results of the serotyping assay were compared with those obtained by nucleotide sequencing from the NS-5 region. Concordant results were observed to match 94.9% (n = 100) by the NS-4 IBA and nucleotide sequencing. Discrepant results were obtained in only 5.1% (n = 6). These data indicate that HCV subtypes can be serologically distinguished, providing the possibility for easier identification of infection with different KCV subtypes.     

Evaluation of a 345 nm Femtosecond Laser for Corneal Surgery with Respect to Intraocular Radiation Hazard

Purpose

We report our findings from a preclinical safety study designed to assess potential side effects of corneal ultraviolet femtosecond laser treatment on lens and retina.

Methods

Refractive lenticules (-5 dpt) with a diameter of 6 mm were created in the right cornea of eight Dutch Belted rabbits. Radiant exposure was 0.5 J/cm² in two animals and 18 J/cm² in six animals. The presence of lens opacities was assessed prior to and up to six months following laser application using Scheimpflug images (Pentacam, Oculus) and backscatter analysis (Opacity Lensmeter 702, Interzeag). Ganzfeld flash and flicker electroretinogram (ERG) recordings were obtained from both eyes prior to and up to six weeks following laser application. At the study endpoint, retinas were examined by light microscopy.

Results

Independent of energy dose applied, no cataract formation could be observed clinically or with either of the two objective methods used. No changes in ERG recordings over time and no difference between treated and untreated eye were detected. Histologically, retinal morphology was preserved and retinal pigment epithelium as well as photoreceptor inner and outer segments appeared undamaged. Quantitative digital image analysis did not reveal cell loss in inner or outer nuclear layers.

Conclusions

Our analysis confirms theoretical considerations suggesting that ultraviolet femtosecond laser treatment of the cornea is safe for intraocular tissues. Transmitted light including stray light induces no photochemical effects in lens or retina at energy levels much higher than required for the clinical purpose. These conclusions cannot be applied to eyes with pre-existing retinal damage, as these may be more vulnerable to light.     

Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes

Although a highly heritable and disabling disease, bipolar disorder''s (BD) genetic variants have been challenging to identify. We present new genotype data for 1,190 cases and 401 controls and perform a genome-wide association study including additional samples for a total of 2,191 cases and 1,434 controls. We do not detect genome-wide significant associations for individual loci; however, across all SNPs, we show an association between the power to detect effects calculated from a previous genome-wide association study and evidence for replication (P = 1.5×10⁻⁷). To demonstrate that this result is not likely to be a false positive, we analyze replication rates in a large meta-analysis of height and show that, in a large enough study, associations replicate as a function of power, approaching a linear relationship. Within BD, SNPs near exons exhibit a greater probability of replication, supporting an enrichment of reproducible associations near functional regions of genes. These results indicate that there is likely common genetic variation associated with BD near exons (±10 kb) that could be identified in larger studies and, further, provide a framework for assessing the potential for replication when combining results from multiple studies.     

Zooplankton interactions in an enclosure experiment: insights from stable isotope analyses

1. Density gradients of cladocerans and copepods were generated in an enclosure experiment to compare the impact on the plankton of a filter feeder (Daphnia hyalina × galeata) with that of more selective feeders (calanoid and cyclopoid copepods). The experiment was conducted in situ over 25 days during spring in a mesotrophic lake, Schöhsee, Germany. 2. The plankton community was monitored regularly. Daphniids were able to graze on the phytoplankton present, which mainly consisted of small (<1000 μm³) species, whereas copepods did not show any impact on algae. 3. At the end of the experiment, Daphnia and remaining cyclopoid copepods were harvested and sorted manually, prior to analyses for stable isotopes of carbon and nitrogen. Daphniids from mesocosms stocked purely with differing densities of Daphnia showed little variability in stable isotope values, whereas those that thrived in enclosure bags together with copepods exhibited lower δ¹³C values. 4. The change in Daphniaδ¹³C indicates a change of food sources, modified by the presence of the copepods: the higher the mean abundance of copepods in the enclosures, the more ¹³C‐depleted the daphniids. Increasing abundance of high nucleic acid (HNA) bacteria in the copepod bags may account for the trend in Daphniaδ¹³C via increased grazing on the bacteria themselves, or via grazing on phytoplankton utilising isotopically light CO₂ from respiratory release. 5. Cyclopoid copepod stable isotope signatures were related to Daphnia and copepod abundances in copepod bags, suggesting that cyclopoids preyed on the available zooplankton.