Three-dimensional structure of a low-Reynolds-number turbulent boundary layer

A low-Reynolds-number zero-pressure-gradient incompressible turbulent boundary layer was investigated using a volumetric imaging technique. The Reynolds number based on momentum thickness was 700. The flow was tagged with a passive scalar from two spanwise dye slots to distinguish between fluid motions originating in the inner and outer portions of the boundary layer. The resulting volumetric scalar field was interrogated using a laser sheet scanner developed for this study. Two- and three-dimensional time-dependent visualizations of a 50 volume time series are presented (equivalent to 17δ in length). In the outer portion of the boundary layer, scalar structures were observed to lie along lines in the (x, z)-plane, inclined to the streamwise (x-)direction in the range ±50°. The ejection of brightly dyed fluid packets from the near-wall region was observed to be spatially organized, and related to the passage of the large-scale scalar structures.Carl J Delo, Richard M Kelson and Alexander J Smit

jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web

BackgroundMany software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees. Methods/Principal Findings We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels. Conclusions/Significance jsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com

How to change the oligomeric state of a circular protein assembly: switch from 11-subunit to 12-subunit TRAP suggests a general mechanism

Many critical cellular functions are performed by multisubunit circular protein oligomers whose internal geometry has evolved to meet functional requirements. The subunit number is arguably the most critical parameter of a circular protein assembly, affecting the internal and external diameters of the assembly and often impacting on the protein's function. Although accurate structural information has been obtained for several circular proteins, a lack of accurate information on alternative oligomeric states has prevented engineering such transitions. In this study we used the bacterial transcription regulator TRAP as a model system to investigate the features that define the oligomeric state of a circular protein and to question how the subunit number could be manipulated.We find that while Bacillus subtilis and Bacillus stearothermophilus TRAP form 11-subunit oligomers, the Bacillus halodurans TRAP exclusively forms 12-subunit assemblies. Significantly, the two states of TRAP are related by a simple rigid body rotation of individual subunits around inter-subunit axes. We tested if such a rotation could be induced by insertion or deletion mutations at the subunit interface. Using wild type 11-subunit TRAP, we demonstrate that removal of five C-terminal residues at the outer side of the inter-subunit axis or extension of an amino acid side chain at the opposite, inner side, increased the subunit number from 11 to 12. Our findings are supported by crystal structures of TRAP oligomers and by native mass spectrometry data.The subunit number of the TRAP oligomer can be manipulated by introducing deletion or addition mutations at the subunit interface. An analysis of available and emerging structural data on alternative oligomeric states indicates that the same principles may also apply to the subunit number of other circular assemblies suggesting that the deletion/addition approach could be used generally to engineer transitions between different oligomeric states

Two- versus three-dimensional connectivity testing of first-order queries to semi-algebraic sets

This paper addresses the question whether one can determine the connectivity of a semi-algebraic set in three dimensions by testing the connectivity of a finite number of two-dimensional ``samples'' of the set, where these samples are defined by first-order queries. The question is answered negatively for two classes of first-order queries: cartesian-product-free, and positive one-pass.Comment: corrected minor confusion in Proof of Theorem

Generalized Multivariate Extreme Value Models for Explicit Route Choice Sets

This paper analyses a class of route choice models with closed-form probability expressions, namely, Generalized Multivariate Extreme Value (GMEV) models. A large group of these models emerge from different utility formulas that combine systematic utility and random error terms. Twelve models are captured in a single discrete choice framework. The additive utility formula leads to the known logit family, being multinomial, path-size, paired combinatorial and link-nested. For the multiplicative formulation only the multinomial and path-size weibit models have been identified; this study also identifies the paired combinatorial and link-nested variations, and generalizes the path-size variant. Furthermore, a new traveller's decision rule based on the multiplicative utility formula with a reference route is presented. Here the traveller chooses exclusively based on the differences between routes. This leads to four new GMEV models. We assess the models qualitatively based on a generic structure of route utility with random foreseen travel times, for which we empirically identify that the variance of utility should be different from thus far assumed for multinomial probit and logit-kernel models. The expected travellers' behaviour and model-behaviour under simple network changes are analysed. Furthermore, all models are estimated and validated on an illustrative network example with long distance and short distance origin-destination pairs. The new multiplicative models based on differences outperform the additive models in both tests

Friction factors for smooth pipe flow

Friction factor data from two recent pipe flow experiments are combined to provide a comprehensive picture of the friction factor variation for Reynolds numbers from 10 to 36,000,000

Exploring the causes of adverse events in hospitals and potential prevention strategies

Objectives To examine the causes of adverse events (AEs) and potential prevention strategies to minimise the occurrence of AEs in hospitalised patients. Methods For the 744 AEs identified in the patient record review study in 21 Dutch hospitals, trained reviewers were asked to select all causal factors that contributed to the AE. The results were analysed together with data on preventability and consequences of AEs. In addition, the reviewers selected one or more prevention strategies for each preventable AE. The recommended prevention strategies were analysed together with four general causal categories: technical, human, organisational and patient-related factors. Results Human causes were predominantly involved in the causation of AEs (in 61% of the AEs), 61% of those being preventable and 13% leading to permanent disability. In 39% of the AEs, patient-related factors were involved, in 14% organisational factors and in 4% technical factors. Organisational causes contributed relatively often to preventable AEs (93%) and AEs resulting in permanent disability (20%). Recommended strategies to prevent AEs were quality assurance/peer review, evaluation of safety behaviour, training and procedures. For the AEs with human and patient-related causes, reviewers predominantly recommended quality assurance/peer review. AEs caused by organisational factors were considered preventable by improving procedures. Discussion Healthcare interventions directed at human causes are recommended because these play a large role in AE causation. In addition, it seems worthwhile to direct interventions on organisational causes because the AEs they cause are nearly always believed to be preventable. Organisational factors are thus relatively easy to tackle. Future research designs should allow researchers to interview healthcare providers that were involved in the event, as an additional source of information on contributing factors.

A bioinformatics approach to the development of immunoassays for specified risk material in canned meat products

A bioinformatics approach to developing antibodies to specific proteins has been evaluated for the production of antibodies to heat-processed specified risk tissues from ruminants (brain and eye tissue). The approach involved the identification of proteins specific to ruminant tissues by interrogation of the annotation fields within the Swissprot database. These protein sequences were then interrogated for peptide sequences that were unique to the protein. Peptides were selected that met these criteria as close as possible and that were also theoretically resistant to either pepsin or trypsin. The selected peptides were synthesised and used as immunogens to raise monoclonal antibodies. Antibodies specific for the synthetic peptides were raised to half of the selected peptides. These antibodies have each been incorporated into a competitive enzyme-linked immunosorbent assay (ELISA) and shown to be able to detect the heat-processed parent protein after digestion with either pepsin or trypsin. One antibody, specific for alpha crystallin peptide (from bovine eye tissue), was able to detect the peptide in canned meat products spiked with 10% eye tissue. These results, although preliminary in nature, show that bioinformatics in conjunction with enzyme digestion can be used to develop ELISA for proteins in high-temperature processed foods and demonstrate that the approach is worth further stud

The optimal schedule for pulsar timing array observations

In order to maximize the sensitivity of pulsar timing arrays to a stochastic gravitational wave background, we present computational techniques to optimize observing schedules. The techniques are applicable to both single and multi-telescope experiments. The observing schedule is optimized for each telescope by adjusting the observing time allocated to each pulsar while keeping the total amount of observing time constant. The optimized schedule depends on the timing noise characteristics of each individual pulsar as well as the performance of instrumentation. Several examples are given to illustrate the effects of different types of noise. A method to select the most suitable pulsars to be included in a pulsar timing array project is also presented.Comment: 16 pages, 6 figures, accepted by MNRA