Health warning: might contain multiple personalities - the problem of homonyms in Thomson Reuters Essential Science Indicators

Author name ambiguity is a crucial problem in any type of bibliometric analysis. It arises when several authors share the same name, but also when one author expresses their name in different ways. This article focuses on the former, also called the “namesake” problem. In particular, we assess the extent to which this compromises the Thomson Reuters Essential Science Indicators (ESI) ranking of the top 1% most cited authors worldwide. We show that three demographic characteristics that should be unrelated to research productivity – name origin, uniqueness of one’s family name, and the number of initials used in publishing – in fact have a very strong influence on it. In contrast to what could be expected from Web of Science publication data, researchers with Asian names – and in particular Chinese and Korean names – appear to be far more productive than researchers with Western names. Furthermore, for any country, academics with common names and fewer initials also appear to be more productive than their more uniquely named counterparts. However, this appearance of high productivity is caused purely by the fact that these “academic superstars” are in fact composites of many individual academics with the same name. We thus argue that it is high time that Thomson Reuters starts taking name disambiguation in general, and non-Anglophone names in particular, more seriously

Stabilization of the coupled oxygen and phosphorus cycles by the evolution of bioturbation

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this record Animal burrowing and sediment-mixing (bioturbation) began during the run up to the Ediacaran/Cambrian boundary, initiating a transition between the stratified Precambrian and more well-mixed Phanerozoic sedimentary records, against the backdrop of a variable global oxygen reservoir probably smaller in size than present. Phosphorus is the long-term limiting nutrient for oxygen production via burial of organic carbon, and its retention (relative to carbon) within organic matter in marine sediments is enhanced by bioturbation. Here we explore the biogeochemical implications of a bioturbation-induced organic phosphorus sink in a simple model. We show that increased bioturbation robustly triggers a net decrease in the size of the global oxygen reservoir - the magnitude of which is contingent upon the prescribed difference in carbon to phosphorus ratios between bioturbated and laminated sediments. Bioturbation also reduces steady-state marine phosphate levels, but this effect is offset by the decline in iron-adsorbed phosphate burial that results from a decrease in oxygen concentrations. The introduction of oxygen-sensitive bioturbation to dynamical model runs is sufficient to trigger a negative feedback loop: the intensity of bioturbation is limited by the oxygen decrease it initially causes. The onset of this feedback is consistent with redox variations observed during the early Cambrian rise of bioturbation, leading us to suggest that bioturbation helped to regulate early oxygen and phosphorus cycles. © 2014 Macmillan Publishers Limited. All rights reserved.Natural Environment Research Council (NERC)Inge Lehmann ScholarshipVILLUM FoundationNational Basic Research Program of ChinaNational Natural Science Foundation of ChinaDeutsche Forschungsgemeinschaft (DFG

Data Fusion of Objects Using Techniques Such as Laser Scanning, Structured Light and Photogrammetry for Cultural Heritage Applications

In this paper we present a semi-automatic 2D-3D local registration pipeline capable of coloring 3D models obtained from 3D scanners by using uncalibrated images. The proposed pipeline exploits the Structure from Motion (SfM) technique in order to reconstruct a sparse representation of the 3D object and obtain the camera parameters from image feature matches. We then coarsely register the reconstructed 3D model to the scanned one through the Scale Iterative Closest Point (SICP) algorithm. SICP provides the global scale, rotation and translation parameters, using minimal manual user intervention. In the final processing stage, a local registration refinement algorithm optimizes the color projection of the aligned photos on the 3D object removing the blurring/ghosting artefacts introduced due to small inaccuracies during the registration. The proposed pipeline is capable of handling real world cases with a range of characteristics from objects with low level geometric features to complex ones

Disorganization of the splenic microanatomy in ageing mice

The precise mechanisms responsible for immunosenescence still remain to be determined, however, considering the evidence that disruption of the organization of primary and secondary lymphoid organs results in immunodeficiency, we propose that this could be involved in the decline of immune responses with age. Therefore, we investigated the integrity of the splenic microarchitecture in mice of increasing age and its reorganization following immune challenge in young and old mice. Several differences in the anatomy of the spleen with age in both the immune and stromal cells were observed. There is an age‐related increase in the overall size of the white pulp, which occurs primarily within the T‐cell zone and is mirrored by the enlargement of the T‐cell stromal area, concurrent to the distinct boundary between T cells and B cells becoming less defined in older mice. In conjunction, there appears to be a loss of marginal zone macrophages, which is accompanied by an accumulation of fibroblasts in the spleens from older animals. Furthermore, whereas the reorganization of the white pulp is resolved after several days following antigenic challenge in young animals, it remains perturbed in older subjects. All these age‐related changes within the spleen could potentially contribute to the age‐dependent deficiencies in functional immunity

Iron Speciation in Fram Strait and Over the Northeast Greenland Shelf: An Inter-Comparison Study of Voltammetric Methods

Competitive ligand exchange - adsorptive cathodic stripping voltammetry (CLE-AdCSV) is a widely used technique to determine dissolved iron (Fe) speciation in seawater, and involves competition for Fe of a known added ligand (AL) with natural organic ligands. Three different ALs were used, 2-(2-thiazolylazo)-p-cresol (TAC), salicylaldoxime (SA) and 1-nitroso-2-napthol (NN). The total ligand concentrations ([Lt]) and conditional stability constants (log K′Fe'L) obtained using the different ALs are compared. The comparison was done on seawater samples from Fram Strait and northeast Greenland shelf region, including the Norske Trough, Nioghalvfjerdsfjorden (79N) Glacier front and Westwind Trough. Data interpretation using a one-ligand model resulted in [Lt]SA (2.72 ± 0.99 nM eq Fe) > [Lt]TAC (1.77 ± 0.57 nM eq Fe) > [Lt]NN (1.57 ± 0.58 nM eq Fe); with the mean of log K′Fe'L being the highest for TAC (log ′KFe'L(TAC) = 12.8 ± 0.5), followed by SA (log K′Fe'L(SA) = 10.9 ± 0.4) and NN (log K′Fe'L(NN) = 10.1 ± 0.6). These differences are only partly explained by the detection windows employed, and are probably due to uncertainties propagated from the calibration and the heterogeneity of the natural organic ligands. An almost constant ratio of [Lt]TAC/[Lt]SA = 0.5 - 0.6 was obtained in samples over the shelf, potentially related to contributions of humic acid-type ligands. In contrast, in Fram Strait [Lt]TAC/[Lt]SA varied considerably from 0.6 to 1, indicating the influence of other ligand types, which seemed to be detected to a different extent by the TAC and SA methods. Our results show that even though the SA, TAC and NN methods have different detection windows, the results of the one ligand model captured a similar trend in [Lt], increasing from Fram Strait to the Norske Trough to the Westwind Trough. Application of a two-ligand model confirms a previous suggestion that in Polar Surface Water and in water masses over the shelf, two ligand groups existed, a relatively strong and relatively weak ligand group. The relatively weak ligand group contributed less to the total complexation capacity, hence it could only keep part of Fe released from the 79N Glacier in the dissolved phase.This study was supported by Royal Netherland Institute for Sea Research. Collection and analysis of samples were further supported by GEOMAR Helmholtz Centre for Ocean Research (the Helmholtz Association and the German Research Foundation (DFG Award Number AC 217/1-1 to EA). IA was supported by a doctoral scholarship from Indonesia Endowment Fund for Education (LPDP), and KZ was supported by a scholarship from the China Scholarship Council

Ultrastructural and functional fate of recycled vesicles in hippocampal synapses

Efficient recycling of synaptic vesicles is thought to be critical for sustained information transfer at central terminals. However, the specific contribution that retrieved vesicles make to future transmission events remains unclear. Here we exploit fluorescence and time-stamped electron microscopy to track the functional and positional fate of vesicles endocytosed after readily releasable pool (RRP) stimulation in rat hippocampal synapses. We show that most vesicles are recovered near the active zone but subsequently take up random positions in the cluster, without preferential bias for future use. These vesicles non-selectively queue, advancing towards the release site with further stimulation in an actin-dependent manner. Nonetheless, the small subset of vesicles retrieved recently in the stimulus train persist nearer the active zone and exhibit more privileged use in the next RRP. Our findings reveal heterogeneity in vesicle fate based on nanoscale position and timing rules, providing new insights into the origins of future pool constitution

Chance-constrained optimization for pension fund portfolios in the presence of default risk

In this paper, we consider the portfolio optimization problem for a pension fund consisting of various government and corporate bonds. The aim of the problem is to maximize the fund's cash position at the end of the time horizon, while allowing for the possibility of bond defaults. We model this problem as a stochastic discrete-time optimal control problem with a chance constraint that ensures all future outgoing commitments can be met with sufficiently high probability. We then introduce a corresponding deterministic formulation that is a conservative approximation of the original stochastic optimal control problem. This approximate problem can be solved using gradient-based optimization techniques. We conclude the paper with a simulation study

Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53

Background: The availability of various "omics" datasets creates a prospect of performing the study of genome-wide genetic regulatory networks. However, one of the major challenges of using mathematical models to infer genetic regulation from microarray datasets is the lack of information for protein concentrations and activities. Most of the previous researches were based on an assumption that the mRNA levels of a gene are consistent with its protein activities, though it is not always the case. Therefore, a more sophisticated modelling framework together with the corresponding inference methods is needed to accurately estimate genetic regulation from "omics" datasets. Results: This work developed a novel approach, which is based on a nonlinear mathematical model, to infer genetic regulation from microarray gene expression data. By using the p53 network as a test system, we used the nonlinear model to estimate the activities of transcription factor (TF) p53 from the expression levels of its target genes, and to identify the activation/inhibition status of p53 to its target genes. The predicted top 317 putative p53 target genes were supported by DNA sequence analysis. A comparison between our prediction and the other published predictions of p53 targets suggests that most of putative p53 targets may share a common depleted or enriched sequence signal on their upstream non-coding region. Conclusions: The proposed quantitative model can not only be used to infer the regulatory relationship between TF and its down-stream genes, but also be applied to estimate the protein activities of TF from the expression levels of its target genes

Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history.

BACKGROUND: Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge. Here we applied BAsE-Seq, an Illumina-based single-virion sequencing technology, to eight samples from four chronic hepatitis B (CHB) patients - once before antiviral treatment and once after viral rebound due to resistance. RESULTS: With single-virion sequencing, we obtained 248-8796 single-virion sequences per sample, which allowed us to find evidence for both hard and soft selective sweeps. We were able to reconstruct population demographic history that was independently verified by clinically collected data. We further verified four of the samples independently through PacBio SMRT and Illumina Pooled deep sequencing. CONCLUSIONS: Overall, we showed that single-virion sequencing yields insight into viral evolution and population dynamics in an efficient and high throughput manner. We believe that single-virion sequencing is widely applicable to the study of viral evolution in the context of drug resistance and host adaptation, allows differentiation between soft or hard selective sweeps, and may be useful in the reconstruction of intra-host viral population demographic history

Evaluating the feasibility of using candidate DNA barcodes in discriminating species of the large Asteraceae family

<p>Abstract</p> <p>Background</p> <p>Five DNA regions, namely, <it>rbcL</it>, <it>matK</it>, ITS, ITS2, and <it>psbA-trnH</it>, have been recommended as primary DNA barcodes for plants. Studies evaluating these regions for species identification in the large plant taxon, which includes a large number of closely related species, have rarely been reported.</p> <p>Results</p> <p>The feasibility of using the five proposed DNA regions was tested for discriminating plant species within Asteraceae, the largest family of flowering plants. Among these markers, ITS2 was the most useful in terms of universality, sequence variation, and identification capability in the Asteraceae family. The species discriminating power of ITS2 was also explored in a large pool of 3,490 Asteraceae sequences that represent 2,315 species belonging to 494 different genera. The result shows that ITS2 correctly identified 76.4% and 97.4% of plant samples at the species and genus levels, respectively. In addition, ITS2 displayed a variable ability to discriminate related species within different genera.</p> <p>Conclusions</p> <p>ITS2 is the best DNA barcode for the Asteraceae family. This approach significantly broadens the application of DNA barcoding to resolve classification problems in the family Asteraceae at the genera and species levels.</p