The need for transparency and good practices in the qPCR literature

Two surveys of over 1,700 publications whose authors use quantitative real-time PCR (qPCR) reveal a lack of transparent and comprehensive reporting of essential technical information. Reporting standards are significantly improved in publications that cite the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, although such publications are still vastly outnumbered by those that do not.

Geochemical and isotopic characterization of the Bodélé Depression dust source and implications for transatlantic dust transport to the Amazon Basin

The Bodélé Depression (Chad) in the central Sahara/Sahel region of Northern Africa is the most important source of mineral dust to the atmosphere globally. The Bodélé Depression is purportedly the largest source of Saharan dust reaching the Amazon Basin by transatlantic transport. Here, we have undertaken a comprehensive study of surface sediments from the Bodélé Depression and dust deposits (Chad, Niger) in order to characterize geochemically and isotopically (Sr, Nd and Pb isotopes) this dust source, and evaluate its importance in present and past African dust records. We similarly analyzed sedimentary deposits from the Amazonian lowlands in order to assess postulated accumulation of African mineral dust in the Amazon Basin, as well as its possible impact in fertilizing the Amazon rainforest. Our results identify distinct sources of different ages and provenance in the Bodélé Depression versus the Amazon Basin, effectively ruling out an origin for the Amazonian deposits, such as the Belterra Clay Layer, by long-term deposition of Bodélé Depression material. Similarly, no evidence for contributions from other potential source areas is provided by existing isotope data (Sr, Nd) on Saharan dusts. Instead, the composition of these Amazonian deposits is entirely consistent with derivation from in-situ weathering and erosion of the Precambrian Amazonian craton, with little, if any, Andean contribution. In the Amazon Basin, the mass accumulation rate of eolian dust is only around one-third of the vertical erosion rate in shield areas, suggesting that Saharan dust is “consumed” by tropical weathering, contributing nutrients and stimulating plant growth, but never accumulates as such in the Amazon Basin. The chemical and isotope compositions found in the Bodélé Depression are varied at the local scale, and have contrasting signatures in the “silica-rich” dry lake-bed sediments and in the “calcium-rich” mixed diatomites and surrounding sand material. This unexpected finding implies that the Bodélé Depression material is not “pre-mixed” at the source to provide a homogeneous source of dust. Rather, different isotope signatures can be emitted depending on subtle vagaries of dust-producing events. Our characterization of the Bodélé Depression components indicate that the Bodélé “calcium-rich” component, identified here, is most likely released via eolian processes of sand grain saltation and abrasion and may be significant in the overall global budget of dusts carried out by the Harmattan low-level jet during the winter.

Drug-induced acute liver injury mimicking autoimmune hepatitis after intake of dietary supplements containing glucosamine and chondroitin sulfate

INTRODUCTION Herbal and dietary supplements are widely used as measures to improve and preserve health and well-being. Among the bestselling preparations are dietary supplement containing glucosamine and chondroitine sulfate taken to improve symptoms of osteoarthritis. METHODS AND RESULTS We here present a case of a male patient with biopsy-proven acute and severe autoimmune hepatitis subsequent to intake of a preparation containing glucosamine and chondroitine sulfate. Response to steroids was favorable and resulted in complete remission of the patient. Diagnostic work-up of the case revealed no other possible cause of liver injury, and causality assessment using the Roussel Uclaf Causality Assessment Method (RUCAM) resulted in a possible causal relationship between intake of glucosamine and chondroitine sulfate and the adverse hepatic reaction. CONCLUSION The present case recalls that products containing glucosamine and chondroitine sulfate can occasionally cause acute liver injury mimicking autoimmune hepatitis, and reminds of the potential dangers of compounds with poor efficacy and ill-defined safety records.

Panel report ECIS 2012: publication strategy for junior researchers: quantity vs. quality, importance of the first authorship and collaboration

The publication record is a key component of a successful academic career in IS. Despite its importance, its definition - especially for junior researchers―remains unclear. Is it better to have one A-publication or three Bpublications? Does being the third author on an A-publication carry more weight than being the first author on a Bpublication? Is it better to publish with as few co-authors as possible to demonstrate ability for independent work or is publishing with others a sign of good teamwork and academic excellence? Faced with these uncertainties, young researchers increasingly question the choices they make regarding their publication strategy. If unaddressed, these issues are bound to interfere with the quality of the IS research and scholars’ job satisfaction. This article raises these concerns associated with a publication strategy for junior researchers and reports the views voiced by five academics at a panel session at the European Conference on Information Systems 2012. In particular, the following topics are discussed: quantity vs. quality, value of the first authorship, the “optimal” number of authors, and the issues of co-authorship with an academic supervisor.

Publication trade-offs for junior scholars in IS: conjoint analysis of preferences for quality, first authorship, collaboration and time

A publication record provides evidence of research productivity and is critical for junior scholars starting their careers in academia. Publication attributes, such as level of the publication outlet, order and number of authors, are typically used to evaluate its quality. However, time spent on a publication is a limited commodity, and researchers face significant trade-offs when deciding which publications they should concentrate on. To better understand the choices made, conjoint analysis with 241 junior IS scholars was conducted. We find that when “quality vs. number of authors” and “quality vs. time” trade-offs are considered, quality is prioritized. However, the emphasis on quality is less pronounced when “rank as an author” is at stake. Especially Ph.D. students tend to choose first authorship when dealing with “quality vs. rank as an author” trade-off. Our findings provide intriguing insights into how publication attributes weigh against each other when research collaboration decisions are made.

Let’s collaborate, but I will be the first author! Exploring the importance of the first authorship for IS researchers

Collaboration among researchers is typically seen as the quintessence of academic excellence, leading to improvements in the research quality, capitalization on the diversity of perspectives and gains in productivity. Despite these benefits, many research teams find themselves torn by competition, antagonism and resentment. Desire to be the first author and resultant underperformance of non-first co-authors is often at the root of these conflicts. At the same time little is known about what motivates researchers in general and IS researchers in particular to engage as first authors. To fill this gap, this study uses survey methodology to explore the attitudes of IS researchers and their resulting behavior when it comes to authors order. Qualitative and quantitative evidence collected from 398 IS researchers is used to support our analysis. We find that researchers’ desire to be the first authors is mainly driven by such determinants as career aspirations, visibility, leadership and sense of ownership, and less so by the desire to satisfy their self-esteem and self-actualization needs. In addition, the value placed on being the first author appears to be the function of researchers’ career level, with Ph.D. students attaching significantly higher value to it than senior scholars.

Intra-annual dynamics of non-structural carbohydrates in the cambium of mature conifer trees reflects radial growth demands

The presence of soluble carbohydrates in the cambial zone, either from sugars recently produced during photosynthesis or from starch remobilized from storage organs, is necessary for radial tree growth. However, considerable uncertainties on carbohydrate dynamics and the consequences on tree productivity exist. This study aims to better understand the variation in different carbon pools at intra-annual resolution by quantifying how cambial zone sugar and starch concentrations fluctuate over the season and in relation to cambial phenology. A comparison between two physiologically different species growing at the same site, i.e., the evergreen Picea abies Karst. and the deciduous Larix decidua Mill., and between L. decidua from two contrasting elevations, is presented to identify mechanisms of growth limitation. Results indicate that the annual cycle of sugar concentration within the cambial zone is coupled to the process of wood formation. The highest sugar concentration is observed when the number of cells in secondary wall formation and lignification stages is at a maximum, subsequent to most radial growth. Starch disappears in winter, while other freeze-resistant non-structural carbohydrates (NSCs) increase. Slight differences in NSC concentration between species are consistent with the differing climate sensitivity of the evergreen and deciduous species investigated. The general absence of differences between elevations suggests that the cambial activity of trees growing at the treeline was not limited by the availability of carbohydrates at the cambial zone but instead by environmental controls on the growing season duration.

Glomerular and renal vascular structural changes in alpha8 integrin-deficient mice

Integrins are matrix receptors that regulate cell-matrix interactions during development and in adult tissue. In the adult kidney, the alpha8 chain is specifically expressed in glomerular mesangial cells and vascular smooth muscle cells. alpha8-deficient (alpha8-/-) mice demonstrate reductions in renal mass, which can range from complete renal agenesis to the development of kidneys that are only slightly smaller than wild-type kidneys. No histologic abnormalities of these kidneys have been described. However, considering the prominent expression of alpha8 in glomeruli and renal vessels, it seemed unlikely that the kidneys of alpha8-/- mice would be completely normal. Therefore, the renal phenotype of adult alpha8-/- mice was investigated, for assessment of more subtle morphologic alterations in kidney tissue. alpha8-/- mice displayed a significant reduction in nephron number and an increase in glomerular volume, compared with wild-type control animals. Albuminuria was not different in wild-type and alpha8-/- mice. Quantitative morphologic analyses revealed that the glomeruli of alpha8-/- mice were hypercellular, with an increased number of mesangial cells, compared with wild-type mice. Mesangial matrix deposition (as demonstrated for collagen IV and the alpha8 ligand fibronectin) was expanded in alpha8-/- mice, compared with wild-type mice. Collagens I and III, which are not normally present in glomeruli, were detected in the glomeruli of alpha8-/- mice. Staining for other glomerular integrins demonstrated an increased abundance of the collagen receptor alpha2 integrin in alpha8-/- mice. The glomerular capillary length density was significantly greater in alpha8-/- mice than in wild-type mice. Cortical arterial vessel walls were not altered in alpha8-/- mice, but the capillaries of the peritubular network were widened. Despite the strong mesangial and vascular expression of alpha8, glomerular and renal vascular alterations in alpha8-/- mice were relatively mild. Only aged alpha8-/- mice demonstrated increased glomerular capillary widening, compared with control animals. The results suggest that the lack of alpha8 can be largely compensated for, at least in younger alpha8-/- mice. It is not yet clear whether the occurrence of collagens that are not normally present in glomeruli and the increased abundance of the collagen receptor alpha2 contribute to maintaining the glomerular structure in alpha8-/- mice. The compensatory mechanisms involved will be the subject of future research.