Mode-switching: a new technique for electronically varying the agglomeration position in an acoustic particle manipulator

Acoustic radiation forces offer a means of manipulating particles within a fluid. Much interest in recent years has focussed on the use of radiation forces in microfluidic (or “lab on a chip”) devices. Such devices are well matched to the use of ultrasonic standing waves in which the resonant dimensions of the chamber are smaller than the ultrasonic wavelength in use. However, such devices have typically been limited to moving particles to one or two predetermined planes, whose positions are determined by acoustic pressure nodes/anti-nodes set up in the ultrasonic standing wave. In most cases devices have been designed to move particles to either the centre or (more recently) the side of a flow channel using ultrasonic frequencies that produce a half or quarter wavelength over the channel, respectively.It is demonstrated here that by rapidly switching back and forth between half and quarter wavelength frequencies – mode-switching – a new agglomeration position is established that permits beads to be brought to any arbitrary point between the half and quarter-wave nodes. This new agglomeration position is effectively a position of stable equilibrium. This has many potential applications, particularly in cell sorting and manipulation. It should also enable precise control of agglomeration position to be maintained regardless of manufacturing tolerances, temperature variations, fluid medium characteristics and particle concentration

Letter to the Editor: 1H, 15N, and 13C chemical shift assignments of the resuscitation promoting factor domain of Rv1009 from Mycobacterium tuberculosis

International audienceNo abstract availabl

CS AKTive Space or how we stopped worrying and learned to love the Semantic Web

The mission of the Advanced Knowledge Technologies (AKT) project is to investigate how to operationalize the knowledge management mantra of "getting the right content to the right place at the right time and in the right form." A significant result of the first three years of this six year project is CS AKTive Space (CAS), a Semantic Web application that won the 2003 Semantic Web Challenge. The challenge criteria included having to use geographically distributed, real world data that would have to be used in a context distinct from which that original data had been designed to serve. CAS is an application that, in meeting this criteria, seeks to provide the experience of an integrated information overview that allows a user to determine quickly who is doing what where in computer science research in the UK. In developing the application we have engaged a number of core Semantic Web challenges: content acquisition, ontology development to mediate heterogeneous data sources, scalable RDF storage and query facilities, and semantically directed interaction design. From our work on CAS we have begun to look at how the approaches for CAS can be generalized for the deployment of AKTive Space applications, dynamically generated from an ontology and set of services

Image annotation with Photocopain

Photo annotation is a resource-intensive task, yet is increasingly essential as image archives and personal photo collections grow in size. There is an inherent conflict in the process of describing and archiving personal experiences, because casual users are generally unwilling to expend large amounts of effort on creating the annotations which are required to organise their collections so that they can make best use of them. This paper describes the Photocopain system, a semi-automatic image annotation system which combines information about the context in which a photograph was captured with information from other readily available sources in order to generate outline annotations for that photograph that the user may further extend or amend

High-fidelity quantum state evolution in imperfect photonic integrated circuits

We propose and analyze the design of a programmable photonic integrated circuit for high-fidelity quantum computation and simulation. We demonstrate that the reconfigurability of our design allows us to overcome two major impediments to quantum optics on a chip: it removes the need for a full fabrication cycle for each experiment and allows for compensation of fabrication errors using numerical optimization techniques. Under a pessimistic fabrication model for the silicon-on-insulator process, we demonstrate a dramatic fidelity improvement for the linear optics controlled-not and controlled-phase gates and, showing the scalability of this approach, the iterative phase estimation algorithm built from individually optimized gates. We also propose and simulate an experiment that the programmability of our system would enable: a statistically robust study of the evolution of entangled photons in disordered quantum walks. Overall, our results suggest that existing fabrication processes are sufficient to build a quantum photonic processor capable of high-fidelity operation.United States. Air Force Office of Scientific Research. Multidisciplinary University Research Initiative (Grant FA9550-14-1-0052)iQuISE FellowshipNational Science Foundation (U.S.). Graduate Research Fellowship (Grant 1122374)American Society for Engineering Education. National Defense Science and Engineering Graduate FellowshipAlfred P. Sloan Foundation (Sloan Research Fellowship

Bayesian inference of ancestral dates on bacterial phylogenetic trees

The sequencing and comparative analysis of a collection of bacterial genomes from a single species or lineage of interest can lead to key insights into its evolution, ecology or epidemiology. The tool of choice for such a study is often to build a phylogenetic tree, and more specifically when possible a dated phylogeny, in which the dates of all common ancestors are estimated. Here, we propose a new Bayesian methodology to construct dated phylogenies which is specifically designed for bacterial genomics. Unlike previous Bayesian methods aimed at building dated phylogenies, we consider that the phylogenetic relationships between the genomes have been previously evaluated using a standard phylogenetic method, which makes our methodology much faster and scalable. This two-step approach also allows us to directly exploit existing phylogenetic methods that detect bacterial recombination, and therefore to account for the effect of recombination in the construction of a dated phylogeny. We analysed many simulated datasets in order to benchmark the performance of our approach in a wide range of situations. Furthermore, we present applications to three different real datasets from recent bacterial genomic studies. Our methodology is implemented in a R package called BactDating which is freely available for download at https://github.com/xavierdidelot/BactDating

Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes