GeneMCL in microarray analysis

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms. (c) 2005 Elsevier Ltd. All rights reserved.

The syntheses, structures and redox properties of phosphine-gold(I) and triruthenium-carbonyl cluster derivatives of tolans

The syntheses of several ethynyl-gold(I) phosphine substituted tolans (1,2-diaryl acetylenes) of general form [Au(C=CC6H4C=CC6H4X)(PPh3)] are described [X = Me (2a), OMe (2b), CO2Me (2c), NO2 (2d), CN (2e)]. These complexes react readily with [Ru-3(CO) 10(mu-dppm)] to give the heterometallic clusters [Ru3(mu-AuPPh3)(mu-eta(1), eta(2)-C2C6H4C, CC6H4X)(CO)(7)(mu-dppm)] (3a-e). The crystallographically determined molecular structures of 2b, 2d, 2e and 3a-e are reported here, that of 2a having been described on a previous occasion. Structural, spectroscopic and electrochemical studies were conducted and have revealed little electronic interaction between the remote substituent and the organometallic end-caps. (C) 2007 Elsevier B. V. All rights reserved.

Synthesis of a Mn-6 cluster and its self-assembly of an azido-bridged polymer

A rare mu(6)-oxo-centered Mn-6 mixed-valent cluster (1) is prepared and used as a secondary building unit for the self-assembly of its azido-bridged polymeric analogue (2) in a systematic way with the retention of the Mn-6 core of (1). Both complexes are characterized by X-ray single-crystal structure determination. The complex 1 was crystallized in a monoclinic system, space group P2(1), a = 11.252(5) A, b = 20.893(9) A, c = 12.301(6) A, and beta = 115.853(7)degrees, whereas the polymeric analogue was crystallized in an orthorhombic system, space group P2(1)2(1)2(1), a = 13.1941(8) A, b = 14.9897(9) A, and c = 27.8746(14) A. Variable-temperature magnetic behavior showed the presence of strong antiferromagnetic interaction in both cases.

A new tetrameric Cu-II cluster with square topology exhibiting ferro- and antiferromagnetic magnetic pathways: which is which?

[Cu4L2(bpy)(4)(H2O)(3)](ClO4)(4).2.5H(2)O, 1, a new tetranuclear Cu-II cluster showing square planar geometry, formed with aspartate bridging ligand (L) has been synthesized. The global magnetic coupling is ferromagnetic but theoretical DFT/B3LYP calculations are necessary to assign which Cu-L-Cu side is ferro or antiferromagnetically coupled.

Building cluster and shading in urban canyon for hot dry climate - Part 1: Air and surface temperature measurements

Under low latitude conditions, minimization of solar radiation within the urban environment may often be a desirable criterion in urban design. The dominance of the direct component of the global solar irradiance under clear high sun conditions requires that the street solar access must be small. It is well known that the size and proportion of open spaces has a great influence on the urban microclimate This paper is directed towards finding the interaction between urban canyon geometry and incident solar radiation. The effect of building height and street width on the shading of the street surfaces and ground for different orientations have been examined and evaluated. It is aimed to explore the extent to which these parameters affect the temperature in the street. This work is based on air and surface temperature measurements taken in different urban street canyons in EL-Oued City (hot and and climate), Algeria. In general, the results show that there are less air temperature variations compared to the surface temperature which really depends on the street geometry and sky view factor. In other words, there is a big correlation between the street geometry, sky view factor and surface temperatures.

Building cluster and shading in urban canyon for hot dry climate Part 2: Shading simulations

Under low latitude conditions, minimisation of solar irradiance within the urban environment may often be an important criterion in urban design. This can be achieved when the obstruction angle is large (high H/W ratio, H = height, W = width). Solar access to streets can always be decreased by increasing H/W to larger values. It is shown in this paper that the street canyon orientation (and not only the H/W ratio) has a considerable effect on solar shading and urban microclimate. The paper demonstrates through a series of shading simulation and temperature measurements that a number of useful relationships can be developed between the geometry and the microclimate of urban street canyons. These relationships are potentially helpful to assist in the formulation of urban design guidelines governing street dimensions and orientations for use by urban designers.

Protocol for the PINCER trial: a cluster randomised trial comparing the effectiveness of a pharmacist-led IT-based intervention with simple feedback in reducing rates of clinically important errors in medicines management in general practices

Background: Medication errors are an important cause of morbidity and mortality in primary care. The aims of this study are to determine the effectiveness, cost effectiveness and acceptability of a pharmacist-led information-technology-based complex intervention compared with simple feedback in reducing proportions of patients at risk from potentially hazardous prescribing and medicines management in general (family) practice. Methods: Research subject group: "At-risk" patients registered with computerised general practices in two geographical regions in England. Design: Parallel group pragmatic cluster randomised trial. Interventions: Practices will be randomised to either: (i) Computer-generated feedback; or (ii) Pharmacist-led intervention comprising of computer-generated feedback, educational outreach and dedicated support. Primary outcome measures: The proportion of patients in each practice at six and 12 months post intervention: - with a computer-recorded history of peptic ulcer being prescribed non-selective non-steroidal anti-inflammatory drugs - with a computer-recorded diagnosis of asthma being prescribed beta-blockers - aged 75 years and older receiving long-term prescriptions for angiotensin converting enzyme inhibitors or loop diuretics without a recorded assessment of renal function and electrolytes in the preceding 15 months. Secondary outcome measures; These relate to a number of other examples of potentially hazardous prescribing and medicines management. Economic analysis: An economic evaluation will be done of the cost per error avoided, from the perspective of the UK National Health Service (NHS), comparing the pharmacist-led intervention with simple feedback. Qualitative analysis: A qualitative study will be conducted to explore the views and experiences of health care professionals and NHS managers concerning the interventions, and investigate possible reasons why the interventions prove effective, or conversely prove ineffective. Sample size: 34 practices in each of the two treatment arms would provide at least 80% power (two-tailed alpha of 0.05) to demonstrate a 50% reduction in error rates for each of the three primary outcome measures in the pharmacist-led intervention arm compared with a 11% reduction in the simple feedback arm. Discussion: At the time of submission of this article, 72 general practices have been recruited (36 in each arm of the trial) and the interventions have been delivered. Analysis has not yet been undertaken.

Advanced scalable algorithms for advanced architectures

With the latest advances in the area of advanced computer architectures we are seeing already large scale machines at petascale level and we are discussing exascale computing. All these require efficient scalable algorithms in order to bridge the performance gap. In this paper examples of various approaches of designing scalable algorithms for such advanced architectures will be given and the corresponding properties of these algorithms will be outlined and discussed. Examples will outline such scalable algorithms applied to large scale problems in the area Computational Biology, Environmental Modelling etc. The key properties of such advanced and scalable algorithms will be outlined.

Economic models and algorithms for distributed systems

Distributed computing paradigms for sharing resources such as Clouds, Grids, Peer-to-Peer systems, or voluntary computing are becoming increasingly popular. While there are some success stories such as PlanetLab, OneLab, BOINC, BitTorrent, and SETI@home, a widespread use of these technologies for business applications has not yet been achieved. In a business environment, mechanisms are needed to provide incentives to potential users for participating in such networks. These mechanisms may range from simple non-monetary access rights, monetary payments to specific policies for sharing. Although a few models for a framework have been discussed (in the general area of a "Grid Economy"), none of these models has yet been realised in practice. This book attempts to fill this gap by discussing the reasons for such limited take-up and exploring incentive mechanisms for resource sharing in distributed systems. The purpose of this book is to identify research challenges in successfully using and deploying resource sharing strategies in open-source and commercial distributed systems.

An analysis of real time implementation of Fourier transform-based frequency recognition algorithms

Frequency recognition is an important task in many engineering fields such as audio signal processing and telecommunications engineering, for example in applications like Dual-Tone Multi-Frequency (DTMF) detection or the recognition of the carrier frequency of a Global Positioning, System (GPS) signal. This paper will present results of investigations on several common Fourier Transform-based frequency recognition algorithms implemented in real time on a Texas Instruments (TI) TMS320C6713 Digital Signal Processor (DSP) core. In addition, suitable metrics are going to be evaluated in order to ascertain which of these selected algorithms is appropriate for audio signal processing(1).

Pulse shaping using state space algorithms

We discuss the use of pulse shaping for optimal excitation of samples in time-domain THz spectroscopy. Pulse shaping can be performed in a 4f optical system to specifications from state space models of the system's dynamics. Subspace algorithms may be used for the identification of the state space models.

Suboptimal system recovery from communication loss in a multi-robot localization scenario using EKF algorithms

This paper describes a multi-robot localization scenario where, for a period of time, the robot team loses communication with one of the robots due to system error. In this novel approach, extended Kalman filter (EKF) algorithms utilize relative measurements to localize the robots in space. These measurements are used to reliably compensate "dead-com" periods were no information can be exchanged between the members of the robot group.