B mu G@Sbase - a microarray database and analysis tool

The manufacture and use of a whole-genome microarray is a complex process and it is essential that all data surrounding the process is stored, is accessible and can be easily associated with the data generated following hybridization and scanning. As part of a program funded by the Wellcome Trust, the Bacterial Microarray Group at St. George's Hospital Medical School (BμG@S) will generate whole-genome microarrays for 12 bacterial pathogens for use in collaboration with specialist research groups. BμG@S will collaborate with these groups at all levels, including the experimental design, methodology and analysis. In addition, we will provide informatic support in the form of a database system (BμG@Sbase). BμG@Sbase will provide access through a web interface to the microarray design data and will allow individual users to store their data in a searchable, secure manner. Tools developed by BμG@S in collaboration with specific research groups investigating analysis methodology will also be made available to those groups using the arrays and submitting data to BμG@Sbase

Equivalent air spring suspension model for quarter-passive model of passenger vehicles

This paper investigates the GENSIS air spring suspension system equivalence to a passive suspension system. The SIMULINK simulation together with the OptiY optimization is used to obtain the air spring suspension model equivalent to passive suspension system, where the car body response difference from both systems with the same road profile inputs is used as the objective function for optimization (OptiY program). The parameters of air spring system such as initial pressure, volume of bag, length of surge pipe, diameter of surge pipe, and volume of reservoir are obtained from optimization. The simulation results show that the air spring suspension equivalent system can produce responses very close to the passive suspension system

Coverage, Matching, and Beyond: New Results on Budgeted Mechanism Design

We study a type of reverse (procurement) auction problems in the presence of budget constraints. The general algorithmic problem is to purchase a set of resources, which come at a cost, so as not to exceed a given budget and at the same time maximize a given valuation function. This framework captures the budgeted version of several well known optimization problems, and when the resources are owned by strategic agents the goal is to design truthful and budget feasible mechanisms, i.e. elicit the true cost of the resources and ensure the payments of the mechanism do not exceed the budget. Budget feasibility introduces more challenges in mechanism design, and we study instantiations of this problem for certain classes of submodular and XOS valuation functions. We first obtain mechanisms with an improved approximation ratio for weighted coverage valuations, a special class of submodular functions that has already attracted attention in previous works. We then provide a general scheme for designing randomized and deterministic polynomial time mechanisms for a class of XOS problems. This class contains problems whose feasible set forms an independence system (a more general structure than matroids), and some representative problems include, among others, finding maximum weighted matchings, maximum weighted matroid members, and maximum weighted 3D-matchings. For most of these problems, only randomized mechanisms with very high approximation ratios were known prior to our results

Multiscale molecular simulations of the formation and structure of polyamide membranes created by interfacial polymerization

Large scale molecular simu lations to model the formation of polyamide membranes have been carried out using a procedure that mimics experimental interfacial polymerization of trimesoyl chloride (TMC) and metaphenylene diamine (MPD) monomers. A coarse - grained representation of the m onomers has been developed to facilitate these simulations, which captures essential features of the stereochemistry of the monomers and of amide bonding between them. Atomic models of the membranes are recreated from the final coarse - grained representatio ns. Consistent with earlier treatments, membranes are formed through the growth and aggregation of oligomer clusters. The membranes are inhomogeneous, displaying opposing gradients of trapped carboxyl and amine side groups, local density variations, and r egions where the density of amide bonding is reduced as a result of the aggregation process. We observe the interfacial polymerization reaction is self - limiting and the simulated membranes display a thickness of 5 – 10 nm. They also display a surface roughn ess of 1 – 4 nm. Comparisons are made with recently published experimental results on the structure and chemistry of these membranes and some interesting similarities and differences are found

New Neighbours: Modelling the Growing Population of Gamma-ray Millisecond Pulsars

The Fermi Large Area Telescope, in collaboration with several groups from the radio community, have had marvellous success at uncovering new gamma-ray millisecond pulsars (MSPs). In fact, MSPs now make up a sizable fraction of the total number of known gamma-ray pulsars. The MSP population is characterized by a variety of pulse profile shapes, peak separations, and radio-to-gamma phase lags, with some members exhibiting nearly phase-aligned radio and gamma-ray light curves (LCs). The MSPs' short spin periods underline the importance of including special relativistic effects in LC calculations, even for emission originating from near the stellar surface. We present results on modelling and classification of MSP LCs using standard pulsar model geometries.Comment: 4 pages, 2 figures, proceedings of the ICREA Workshop on The High-Energy Emission from Pulsars and their Systems (HEEPS), Sant Cugat, Spai

Incidence and mechanism of the pivot shift. An in vitro study.

Accepted versio

Helicity at Photospheric and Chromospheric Heights

In the solar atmosphere the twist parameter $\alpha$ has the same sign as magnetic helicity. It has been observed using photospheric vector magnetograms that negative/positive helicity is dominant in the northern/southern hemisphere of the Sun. Chromospheric features show dextral/sinistral dominance in the northern/southern hemisphere and sigmoids observed in X-rays also have a dominant sense of reverse-S/forward-S in the northern/southern hemisphere. It is of interest whether individual features have one-to-one correspondence in terms of helicity at different atmospheric heights. We use UBF \Halpha images from the Dunn Solar Telescope (DST) and other \Halpha data from Udaipur Solar Observatory and Big Bear Solar Observatory. Near-simultaneous vector magnetograms from the DST are used to establish one-to-one correspondence of helicity at photospheric and chromospheric heights. We plan to extend this investigation with more data including coronal intensities.Comment: 5 pages, 1 figure, 1 table To appear in "Magnetic Coupling between the Interior and the Atmosphere of the Sun", eds. S.S. Hasan and R.J. Rutten, Astrophysics and Space Science Proceedings, Springer-Verlag, Heidelberg, Berlin, 200

Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis

The aryl hydrocarbon receptor (AhR) is a ligand-dependent, basic helix-loop-helix Per-Arnt-Sim (PAS)-containing transcription factor that can bind and be activated by structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Our previous three-dimensional homology model of the mouse AhR (mAhR) PAS B ligand binding domain allowed identification of the binding site and its experimental validation. We have extended this analysis by conducting comparative structural modeling studies of the ligand binding domains of six additional highaffinity mammalian AhRs. These results, coupled with site-directed mutagenesis and AhR functional analysis, have allowed detection of the "TCDD binding-fingerprint" of conserved residues within the ligand binding cavity necessary for high-affinity TCDD binding and TCDD-dependent AhR transformation DNA binding. The essential role of selected residues was further evaluated using molecular docking simulations of TCDD with both wild-type and mutant mAhRs. Taken together, our results dramatically improve our understanding of the molecular determinants of TCDD binding and provide a basis for future studies directed toward rationalizing the observed species differences in AhR sensitivity to TCDD and understanding the mechanistic basis for the dramatic diversity in AhR ligand structure. © 2009 American Chemical Society