Citation Analysis May Severely Underestimate the Impact of Clinical Research as Compared to Basic Research

Background

Citation analysis has become an important tool for research performance assessment in the medical sciences. However, different areas of medical research may have considerably different citation practices, even within the same medical field. Because of this, it is unclear to what extent citation-based bibliometric indicators allow for valid comparisons between research units active in different areas of medical research.

Methodology

A visualization methodology is introduced that reveals differences in citation practices between medical research areas. The methodology extracts terms from the titles and abstracts of a large collection of publications and uses these terms to visualize the structure of a medical field and to indicate how research areas within this field differ from each other in their average citation impact.

Results

Visualizations are provided for 32 medical fields, defined based on journal subject categories in the Web of Science database. The analysis focuses on three fields: Cardiac & cardiovascular systems, Clinical neurology, and Surgery. In each of these fields, there turn out to be large differences in citation practices between research areas. Low-impact research areas tend to focus on clinical intervention research, while high-impact research areas are often more oriented on basic and diagnostic research.

Conclusions

Popular bibliometric indicators, such as the h-index and the impact factor, do not correct for differences in citation practices between medical fields. These indicators therefore cannot be used to make accurate between-field comparisons. More sophisticated bibliometric indicators do correct for field differences but still fail to take into account within-field heterogeneity in citation practices. As a consequence, the citation impact of clinical intervention research may be substantially underestimated in comparison with basic and diagnostic research.     

Respiratory control in aquatic insects dictates their vulnerability to global warming

Forecasting species responses to climatic warming requires knowledge of how temperature impacts may be exacerbated by other environmental stressors, hypoxia being a principal example in aquatic systems. Both stressors could interact directly as temperature affects both oxygen bioavailability and ectotherm oxygen demand. Insufficient oxygen has been shown to limit thermal tolerance in several aquatic ectotherms, although, the generality of this mechanism has been challenged for tracheated arthropods. Comparing species pairs spanning four different insect orders, we demonstrate that oxygen can indeed limit thermal tolerance in tracheates. Species that were poor at regulating oxygen uptake were consistently more vulnerable to the synergistic effects of warming and hypoxia, demonstrating the importance of respiratory control in setting thermal tolerance limits.     

Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains

Background

Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers.

Results

The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping.We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population.

Conclusion

The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R package for QTL studies. Pheno2Geno is freely available on CRAN under “GNU GPL v3”. The Pheno2Geno package as well as the tutorial can also be found at: http://pheno2geno.nl.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0475-6) contains supplementary material, which is available to authorized users.     

Do restoration measures rehabilitate fauna diversity in raised bogs? A comparative study on aquatic macroinvertebrates

To assess whether raised bog restorationmeasures contribute to the conservation andrestoration of the fauna diversity,macroinvertebrate species assemblages werecompared between water bodies created byrewetting measures and water bodies whichhave not been subject to restorationmeasures, but are remnants offormer peat cuttings and trenches used forbuckwheat culture in the past.The restoration sites were inhabited bycharacteristic raised bog species and rarespecies, but their numbers were higher atthe remnant sites not affected byrestoration management. A considerablenumber of characteristic and rare faunaspecies were only found at the remnantsites. The remnant sites includedconsiderably more variation inmacroinvertebrate species assemblages andhad a higher cumulative species richness.The number of characteristicmacroinvertebrate species was not clearlyrelated to the presence of a characteristicraised bog vegetation. In restoration sitesnumbers of rare and characteristic speciesper site tended to increase with the timeelapsed after rewetting. However,restoration measures will not automaticallyresult in restoration of a more or lesscomplete macroinvertebrate speciesspectrum, as restoration measures have sofar resulted in habitats for only a limitednumber of the characteristic species.When planning restoration measures, it isrecommended to protect the populations ofrare and characteristic species present inthe area, as these populations may becomethe sources for colonization of rewettedsites. Safeguarding habitat diversityduring the restoration process andrestoration of different elements of thehabitat diversity of complete raised bogsystems will result in the characteristicfauna diversity being conserved andrestored more successfully.     

Gibberellin and phytochrome control senescence in alstroemeria leaves independently

In alstroemeria ( Alstroemeria hybrida ), leaf senescence is effectively retarded by the application of gibberellins and by low fluences of red light. In this study we examined the possible interaction of gibberellins and red light in the regulation of senescence. Determination of endogenous gibberellins revealed that leaf senescence is accompanied by significant changes in the concentrations of non‐ 13‐hydroxylated gibberellins, the onset of senescence coinciding with a dramatic drop in GA₄, whereas concentrations of 13‐hydroxylated gibberellins are far less influenced. However, no direct effect of red light on a specific GA‐metabolic step could be determined. When exogenously applied, non‐13‐hydroxylated GAs were more active than the 13‐hydroxylated GAs. It appeared that the effect of red light is additive to that of active GAs. We hypothesise that GA₄ and phytochrome control senescence in alstroemeria mainly through separate mechanisms and have independent effects and that the observed differences in gibberellin concentrations are a consequence of delayed leaf senescence rather than a cause for it.