Image reconstruction using iterative transpose algorithm for optical tomography

This paper describes a transpose algorithm for use with an optical tomography system. The measurement system consisted of two orthogonal arrays, each having ten parallel views, resulting in a total of twenty sensors. The measurement section is divided into hundred equi-sized pixels. The forward problem is modelled by allocating an optical attenuation coefficient to each pixel. The attenuation of incident collimated light beams is then modelled using the Lambert-Beer law. The inverse problem is defined and the transpose of the sensitivity matrix is used to obtain an estimate of the attenuation coefficients in each pixel. The iterative method is investigated as a means of improving reconstructed image qualit

A Muslim Seletar family in Malaysia: Negotiating a liminal religious and ethnic identity

This article is drawn from ethnographic research undertaken in Johor state in Malaysia, referring also to related historical, theoretical and anthropological literature. I make some key observations about the modern practices and identity of a group of Muslims in Malaysia who can be seen to form a particular subset of their Seletar ethnic group. This is discussed in the context of the ongoing debate and contestation of Muslim / Malay and bumiputera identity and status. The article examines how these Muslim Orang Asli appear to negotiate their Muslim identity in relation to their Seletar identity and how they still subscribe to being Seletar in terms of language and specific aspects of culture which remain important to them. The research draws conclusions about how their agency in their chosen hybridity of cultural practice and religion provides a kind of emblematic model highlighting the potential multiplicity in Malaysian bumiputera indigineity (or Malayness)

An isoparametric approach to high-order curvilinear boundary-layer meshing

This is the final version of the article. Available from Elsevier via the DOI in this record.The generation of high-order curvilinear meshes for complex three-dimensional geometries is presently a challenging topic, particularly for meshes used in simulations at high Reynolds numbers where a thin boundary layer exists near walls and elements are highly stretched in the direction normal to flow. In this paper, we present a conceptually simple but very effective and modular method to address this issue. We propose an isoparametric approach, whereby a mesh containing a valid coarse discretization comprising of high-order triangular prisms near walls is refined to obtain a finer prismatic or tetrahedral boundary-layer mesh. The validity of the prismatic mesh provides a suitable mapping that allows one to obtain very fine mesh resolutions across the thickness of the boundary layer. We describe the method in detail for a high-order approximation using modal basis functions, discuss the requirements for the splitting method to produce valid prismatic and tetrahedral meshes and provide a sufficient criterion of validity in both cases. By considering two complex aeronautical configurations, we demonstrate how highly stretched meshes with sufficient resolution within the laminar sublayer can be generated to enable the simulation of flows with Reynolds numbers of 106 and above.This work was partly supported by EU Grant No. 265780 as part of the EU FP7 project “IDIHOM: Industrialization of High-Order Methods — A Top-Down Approach”. We would like to thank Dr. Tobias Leicht of DLR for asking a very pertinent question concerning the validity of the generated high-order mesh that we believe to have answered in this article. We also thank Jean-Eloi Lombard for his assistance in generating the mesh for Fig. 15

Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics

Background
High throughput yeast functional genomics experiments are revealing associations among tens to hundreds of genes using numerous experimental conditions. To fully understand how the identified genes might be involved in the observed system, it is essential to consider the widest range of biological annotation possible. Biologists often start their search by collating the annotation provided for each protein within databases such as the Saccharomyces Genome Database, manually comparing them for similar features, and empirically assessing their significance. Such tasks can be automated, and more precise calculations of the significance can be determined using established probability measures. 
Results
We developed Yeast Features, an intuitive online tool to help establish the significance of finding a diverse set of shared features among a collection of yeast proteins. A total of 18,786 features from the Saccharomyces Genome Database are considered, including annotation based on the Gene Ontology’s molecular function, biological process and cellular compartment, as well as conserved domains, protein-protein and genetic interactions, complexes, metabolic pathways, phenotypes and publications. The significance of shared features is estimated using a hypergeometric probability, but novel options exist to improve the significance by adding background knowledge of the experimental system. For instance, increased statistical significance is achieved in gene deletion experiments because interactions with essential genes will never be observed. We further demonstrate the utility by suggesting the functional roles of the indirect targets of an aminoglycoside with a known mechanism of action, and also the targets of an herbal extract with a previously unknown mode of action. The identification of shared functional features may also be used to propose novel roles for proteins of unknown function, including a role in protein synthesis for YKL075C.
Conclusions
Yeast Features (YF) is an easy to use web-based application (http://software.dumontierlab.com/yeastfeatures/) which can identify and prioritize features that are shared among a set of yeast proteins. This approach is shown to be valuable in the analysis of complex data sets, in which the extracted associations revealed significant functional relationships among the gene products.
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Analysis of dielectrophoresis AC electrokinetic in equilibrium using MATLAB

This paper presents an ideal case for dielectrophoretic (DEP) occurrence to separate a mixture of two sizes of particles in microchannel analysed with DEP 3D equation using Matlab. The analysis was done on the particles mobility changes when the medium conductivity varied. The analysis was also done when the particles suspended in different mediums conductivity. The effect of dielectrophoresis on the velocity of the particle when the frequency increased has been successfully discovered

Process for the determination of thickness of polymeric microchannels for microfluidic applications

We have developed a technique of fabricating device channels for microfludics system by using high performance epoxy polymeric based dry film resists (DFRs). We will use the fabrication method originated in silicon microelectronics fabrication industry. This is because the interest in this industry has made the current microfluidic devices fabricated not only from silicon substrate but also to a range of polymers and glasses. Our observations are made on the effect of the thickness before and after curing and bonding mechanism of DFR on glass substrate. Therefore the thickness of the channels is recorded. The outcomes of the bonding procedure are captured. These channels are patterned and sandwiched in between two glass substrates. They can be used for handling continuous fluid flow and particle. In our advance, the channel was formed for dielectrophoretic (DEP) colloidal particle separation systems

Impact of commonly prescribed exercise interventions on platelet activation in physically inactive and overweight men.

The exercise paradox infers that, despite the well-established cardioprotective effects of repeated episodic exercise (training), the risk of acute atherothrombotic events may be transiently increased during and soon after an exercise bout. However, the acute impact of different exercise modalities on platelet function has not previously been addressed. We hypothesized that distinct modalities of exercise would have differing effects on in vivo platelet activation and reactivity to agonists which induce monocyte-platelet aggregate (MPA) formation. Eight middle-aged (53.5 ± 1.6 years) male participants took part in four 30 min experimental interventions (aerobic AE, resistance RE, combined aerobic/resistance exercise CARE, or no-exercise NE), in random order. Blood samples were collected before, immediately after, and 1 h after each intervention, and incubated with one of three agonists of physiologically/clinically relevant pathways of platelet activation (thrombin receptor activating peptide-6 TRAP, arachidonic acid AA, and cross-linked collagen-related peptide xCRP). In the presence of AA, TRAP, and xCRP, both RE and CARE evoked increases in MPAs immediately post-exercise (P < 0.01), whereas only AA significantly increased MPAs immediately after AE (P < 0.01). These increases in platelet activation post-exercise were transient, as responses approached pre-exercise levels by 1 h. These are the first data to suggest that exercise involving a resistance component in humans may transiently increase platelet-mediated thrombotic risk more than aerobic modalities

Continuing mortality of vultures in India associated with illegal veterinary use of diclofenac and a potential threat from nimesulide

AbstractThe collapse of South Asia's Gyps vulture populations is attributable to the veterinary use of the non-steroidal anti-inflammatory drug (NSAID) diclofenac. Vultures died after feeding on carcasses of recently-medicated animals. The governments of India, Nepal and Pakistan banned the veterinary use of diclofenac in 2006. We analysed results of 62 necropsies and 48 NSAID assays of liver and/or kidney for vultures of five species found dead in India between 2000 and 2012. Visceral gout and diclofenac were detected in vultures from nine states and three species: Gyps bengalensis, Gyps indicus and Gyps himalayensis. Visceral gout was found in every vulture carcass in which a measurable level of diclofenac was detected. Meloxicam, an NSAID of low toxicity to vultures, was found in two vultures and nimesulide in five vultures. Nimesulide at elevated tissue concentrations was associated with visceral gout in four of these cases, always without diclofenac, suggesting that nimesulide may have similar toxic effects to those of diclofenac. Residues of meloxicam on its own were never associated with visceral gout. The proportion of Gyps vultures found dead in the wild in India with measurable levels of diclofenac in their tissues showed a modest and non-significant decline since the ban on the veterinary use of diclofenac. The prevalence of visceral gout declined less, probably because some cases of visceral gout from 2008 onwards were associated with nimesulide rather than diclofenac. Veterinary use of nimesulide is a potential threat to the recovery of vulture populations.Financial support and assistance for the project from the Director, Indian Veterinary Research Institute (IVRI), the UK Government’s Darwin Initiative and the Royal Society for the Protection of Birds is gratefully acknowledged.This is the accepted manuscript. The final version is available from Cambridge University Press via http://dx.doi.org/10.1017/S003060531500037

Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations.

Understanding gene regulation requires knowledge of changes in transcription factor (TF) activities. Simultaneous direct measurement of numerous TF activities is currently impossible. Nevertheless, statistical approaches to infer TF activities have yielded non-trivial and verifiable predictions for individual TFs. Here, global statistical modelling identifies changes in TF activities from transcript profiles of Escherichia coli growing in stable (fixed oxygen availabilities) and dynamic (changing oxygen availability) environments. A core oxygen-responsive TF network, supplemented by additional TFs acting under specific conditions, was identified. The activities of the cytoplasmic oxygen-responsive TF, FNR, and the membrane-bound terminal oxidases implied that, even on the scale of the bacterial cell, spatial effects significantly influence oxygen-sensing. Several transcripts exhibited asymmetrical patterns of abundance in aerobic to anaerobic and anaerobic to aerobic transitions. One of these transcripts, ndh, encodes a major component of the aerobic respiratory chain and is regulated by oxygen-responsive TFs ArcA and FNR. Kinetic modelling indicated that ArcA and FNR behaviour could not explain the ndh transcript profile, leading to the identification of another TF, PdhR, as the source of the asymmetry. Thus, this approach illustrates how systematic examination of regulatory responses in stable and dynamic environments yields new mechanistic insights into adaptive processes