CiteULike: Author De

Semiclassical Evolution of Dissipative Markovian Systems

Ozorio de Almeida — 2008-07-23T09:14:23-00:00

(29 Aug 2007)

A semiclassical approximation for an evolving density operator, driven by a "closed" hamiltonian operator and "open" markovian Lindblad operators, is obtained. The theory is based on the chord function, i.e. the Fourier transform of the Wigner function. It reduces to an exact solution of the Lindblad master equation in the case where the hamiltonian operator is a quadratic function and the Lindblad operators are linear functions of positions momenta. Initially, the semiclassical formulae for the case of hermitian Lindblad operators are reinterpreted in terms of a (real) double phase space, generated by an appropriate classical double Hamiltonian. Then, the general case of dissipative markovian evolution, that results from non-hermitian Lindblad operators, is incorporated semiclassically through an extra open term that is added to the double Hamiltonian. The particular case of generic hamiltonian operators, but linear dissipative Lindblad operators, is studied in more detail. A Liouville-type equivariance still holds for the corresponding classical evolution in double phase, but the centre subspace, which supports the Wigner function, is compressed, along with expansion of its conjugate subspace, which supports the chord function. Decoherence narrows the relevant region of double phase space to the neighborhood of a caustic for both the Wigner function and the chord function. This difficulty is avoided by a propagator in a mixed representation, so that a further "small-chord" approximation leads to a simple generalization of the quadratic theory for evolving Wigner functions.

Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways

Rajat De — 2008-07-20T06:23:44-00:00

BMC Systems Biology, Vol. 2, No. 1. (2008)

BACKGROUND:In the present article, we propose a method for determining optimal metabolic pathways in terms of the level of concentration of the enzymes catalyzing various reactions in the entire metabolic network. The method, first of all, generates data on reaction fluxes in a pathway based on steady state condition. A set of constraints is formulated incorporating weighting coefficients corresponding to concentration of enzymes catalyzing reactions in the pathway. Finally, the rate of yield of the target metabolite, starting with a given substrate, is maximized in order to identify an optimal pathway through these weighting coefficients.RESULTS:The effectiveness of the present method is demonstrated on two synthetic systems existing in the literature, two pentose phosphate, two glycolytic pathways, core carbon metabolism and a large network of carotenoid biosynthesis pathway of various organisms belonging to different phylogeny. A comparative study with the existing extreme pathway analysis also forms a part of this investigation. Biological relevance and validation of the results are provided. Finally, the impact of the method on metabolic engineering is explained with a few examples.CONCLUSIONS:The method may be viewed as determining an optimal set of enzymes that is required to get an optimal metabolic pathway. Although it is a simple one, it has been able to identify a carotenoid biosynthesis pathway and the optimal pathway of core carbon metabolic network that is closer to some earlier investigations than that obtained by the extreme pathway analysis. Moreover, the present method has identified correctly optimal pathways for pentose phosphate and glycolytic pathways. It has been mentioned using some examples how the method can suitably be used in the context of metabolic engineering.

Open Luttinger Liquids

Castro — 2008-07-17T09:56:16-00:00

Physical Review Letters, Vol. 79, No. 23. (December 1997), 4629.

Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

S De — 2006-05-11T14:25:28-00:00

BMC Struct Biol, Vol. 5 (16 August 2005)

BACKGROUND: A polypeptide chain of a protein-protein complex is said to be obligatory if it is bound to another chain throughout its functional lifetime. Such a chain might not adopt the native fold in the unbound form. A non-obligatory polypeptide chain associates with another chain and dissociates upon molecular stimulus. Although conformational changes at the interaction interface are expected, the overall 3-D structure of the non-obligatory chain is unaltered. The present study focuses on protein-protein complexes to understand further the differences between obligatory and non-obligatory interfaces. RESULTS: A non-obligatory chain in a complex of known 3-D structure is recognized by its stable existence with same fold in the bound and unbound forms. On the contrary, an obligatory chain is detected by its existence only in the bound form with no evidence for the native-like fold of the chain in the unbound form. Various interfacial properties of a large number of complexes of known 3-D structures thus classified are comparatively analyzed with an aim to identify structural descriptors that distinguish these two types of interfaces. We report that the interaction patterns across the interfaces of obligatory and non-obligatory components are different and contacts made by obligatory chains are predominantly non-polar. The obligatory chains have a higher number of contacts per interface (20 +/- 14 contacts per interface) than non-obligatory chains (13 +/- 6 contacts per interface). The involvement of main chain atoms is higher in the case of obligatory chains (16.9 %) compared to non-obligatory chains (11.2 %). The beta-sheet formation across the subunits is observed only among obligatory protein chains in the dataset. Apart from these, other features like residue preferences and interface area produce marginal differences and they may be considered collectively while distinguishing the two types of interfaces. CONCLUSION: These results can be useful in distinguishing the two types of interfaces observed in structures determined in large-scale in the structural genomics initiatives, especially for those multi-component protein assemblies for which the biochemical characterization is incomplete.

A dynamic view as a complementary perspective

De — 2008-07-01T13:10:55-00:00

Bilingualism: Language and Cognition, Vol. 10, No. 01. (2007), pp. 51-55.

A Dynamic Systems Theory approach to second language acquisition

De — 2008-07-01T13:03:11-00:00

Bilingualism: Language and Cognition, Vol. 10, No. 01. (2007), pp. 7-21.

Speeding Up Navigational Requests in a Parallel Object Database System

Jim Smith — 2008-06-07T11:57:36-00:00

Euro-Par 2002 Parallel Processing (2002), pp. 1-17.

In data intensive applications, both programming and declarative query languages have attractions, the former in comprehensiveness and the latter for ease of use. Databases sometimes support the calling of side-effect free user defined functions from within declarative queries. As well as enabling more efficient coding of computationally intensive functions, this provision not only moves computation to data in a client-server setting, but also enables speedup through data parallel execution if the server is parallel. There has been little work on the combined use of query and program based database access in the context of parallel servers. We believe Polar is the first parallel object-oriented database which supports this arbitrary navigation both in a client application and in functions (operations) which may be called from within declarative queries. This work introduces Polar’s support for navigation and for calling operations from within parallel queries and presents performance results for example navigational requests for the large OO7 benchmark.

MPI Collectives on Modern Multicore Clusters: Performance Optimizations and Communication Characteristics

Amith Mamidala — 2008-06-02T15:12:54-00:00

Cluster Computing and the Grid, 2008. CCGRID '08. 8th IEEE International Symposium on (2008), pp. 130-137.

The advances in multicore technology and modern interconnects is rapidly accelerating the number of cores deployed in today's commodity clusters. A majority of parallel applications written in MPI employ collective operations in their communication kernels. Optimization of these operations on the multicore platforms is the key to obtaining good performance speed-ups. However, designing these operations on the modern multicores is a non-trivial task. Modern multicores such as Intel's Clovertown and AMD's Opteron feature various architectural attributes resulting in interesting ramifications. For example, Clovertown deploys shared L2 caches for a pair of cores whereas in Opteron, L2 caches are exclusive to a core. Understanding the impact of these architectures on communication performance is crucial to designing efficient collective algorithms. In this paper, we systematically evaluate these architectures and use these insights to develop efficient collective operations such as MPI_Bcast, MPI_Allgather, MPI_Allreduce and MPI_Alltoall. Further, we characterize the behavior of these collective algorithms on multicores especially when concurrent network and intra-node communications occur. We also evaluate the benefits of the proposed intra-node MPI_Allreduce over Opteron multicores and compare it with Intel Clovertown systems. The optimizations proposed in this paper reduce the latency of MPI_Bcast and MPI_Allgather by 1.9 and 4.0 times, respectively on 512 cores. For MPI_Allreduce, our optimizations improve the performance by as much as 33% on the multicores. Further, we observe upto three times improvement in performance for matrix multiplication benchmark on 512 cores.

A Quantitative Analysis of Beta-Adrenergic Receptor Interactions: Resolution of High and Low Affinity States of the Receptor by Computer Modeling of Ligand Binding Data

Richard Kent — 2008-05-28T11:39:24-00:00

Mol Pharmacol, Vol. 17, No. 1. (1 January 1980), pp. 14-23.

The properties of ligand binding to the beta-adrenergic receptor have been studied using a computer modeling technique to analyze data obtained by indirect binding methods. Antagonists are shown to bind to the receptor with one homogeneous state of uniform affinity, while agonists manifest heterogeneous binding. For agonists, two distinct binding states are apparent; one of high and one of low affinity. Affinity states of the receptor are characterized by specific macroscopic dissociation constants, and the proportion of total receptors in each state can be determined. The ability of an agonist to activate adenylate cyclase (intrinsic activity) correlates closely with the amount of high affinity state formed in the presence of the agonist (p < 0.001). A similar correlation exists between adenylate cyclase activation by an agonist and the ratio of dissociation constants of the agonist for the high and low affinity states of the receptor (p < 0.001). There is an apparent impairment of high affinity state formation in membranes derived from desensitized cells. Along with a decrease in the total number of receptors, this impairment of high affinity state formation may be responsible for the decreased activation of adenylate cyclase observed after desensitization. Guanyl nucleotides mediate the transition of high affinity receptors to the low affinity state. The extent of this transition is dose dependent and is evident even at low nucleotide concentrations. Our data indicate that high and low affinity states of the beta-adrenergic receptor are interconvertible, a finding incompatible with models of ligand-receptor interaction involving independent binding sites. Computer modeling of receptor binding data significantly enhances the ability to describe the interactions for adenylate cyclase-coupled receptor systems and validates the concept and biological importance of receptor affinity states for the beta-adrenergic receptor.

High yield production of graphene by liquid phase exfoliation of graphite

Y Hernandez — 2008-05-23T08:27:28-00:00

(19 May 2008)

Graphene is at the centre of nanotechnology research. In order to fully exploit its outstanding properties, a mass production method is necessary. Two main routes are possible: large-scale growth or large-scale exfoliation. Here, we demonstrate graphene dispersions with concentrations up to ~0.01 mg/ml by dispersion and exfoliation of graphite in organic solvents such as N-methyl-pyrrolidone. This occurs because the energy required to exfoliate graphene is balanced by the solvent-graphene interaction for solvents whose surface energy matches that of graphene. We confirm the presence of individual graphene sheets with yields of up to 12% by mass, using absorption spectroscopy, transmission electron microscopy and electron diffraction. The absence of defects or oxides is confirmed by X-ray photoelectron, infra-red and Raman spectroscopies. We can produce conductive, semi-transparent films and conductive composites. Solution processing of graphene opens up a whole range of potential large-scale applications from device or sensor fabrication to liquid phase chemistry.

Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles

Anindya Bhattacharya — 2008-05-19T15:40:24-00:00

Bioinformatics, Vol. 24, No. 11. (1 June 2008), pp. 1359-1366.

Motivation: Cluster analysis (of gene-expression data) is a useful tool for identifying biologically relevant groups of genes that show similar expression patterns under multiple experimental conditions. Various methods have been proposed for clustering gene-expression data. However most of these algorithms have several shortcomings for gene-expression data clustering. In the present article, we focus on several shortcomings of conventional clustering algorithms and propose a new one that is able to produce better clustering solution than that produced by some others. Results: We present the Divisive Correlation Clustering Algorithm (DCCA) that is suitable for finding a group of genes having similar pattern of variation in their expression values. To detect clusters with high correlation and biological significance, we use the correlation clustering concept introduced by Bansal et al. Our proposed algorithm DCCA produces a clustering solution without taking number of clusters to be created as an input. DCCA uses the correlation matrix in such a way that all genes in a cluster have highest average correlation with genes in that cluster. To test the performance of the DCCA, we have applied DCCA and some well-known conventional methods to an artificial dataset, and nine gene-expression datasets, and compared the performance of the algorithms. The clustering results of the DCCA are found to be more significantly relevant to the biological annotations than those of the other methods. All these facts show the superiority of the DCCA over some others for the clustering of gene-expression data. Availability: The software has been developed using C and Visual Basic languages, and can be executed on the Microsoft Windows platforms. The software may be downloaded as a zip file from http://www.isical.ac.in/~rajat. Then it needs to be installed. Two word files (included in the zip file) need to be consulted before installation and execution of the software. Contact: rajat@isical.ac.in Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btn133

Large-Angle Electron Diffraction Structure in Laser-Induced Rescattering from Rare Gases

D Ray — 2008-05-20T14:08:25-00:00

Physical Review Letters, Vol. 100, No. 14. (2008)

We have measured full momentum images of electrons rescattered from Xe, Kr, and Ar following the liberation of the electrons from these atoms by short, intense laser pulses. At high momenta the spectra show angular structure (diffraction) which is very target dependent and in good agreement with calculated differential cross sections for the scattering of free electrons from the corresponding ionic cores.

Unbroken mirrors: challenging a theory of Autism

Victoria Southgate — 2008-05-19T17:52:28-00:00

Trends in Cognitive Sciences, Vol. In Press, Corrected Proof

The [`]broken mirror' theory of autism has received considerable attention far beyond the scientific community. This theory proposes that the varied social-cognitive difficulties characteristic of autism could be explained by dysfunction of the mirror neuron system, thought to play a role in imitation. We examine this theory and argue that explaining typical imitation behavior, and the failure to imitate in autism, requires much more than the mirror neuron system. Furthermore, evidence for the role of the mirror neuron system in autism is weak. We suggest the broken mirror theory of autism is premature and that better cognitive models of social behavior within and beyond the mirror neuron system are required to understand the causes of poor social interaction in autism.

Computation of resonant frequency of annular microstrip antenna loaded with multiple shorting posts

M Mahajan — 2008-05-09T06:48:22-00:00

Microwaves, Antennas & Propagation, IET, Vol. 2, No. 1. (2008), pp. 1-5.

Common variants near MC4R are associated with fat mass, weight and risk of obesity.

Ruth J F Loos — 2008-05-07T08:46:22-00:00

Nature genetics (4 May 2008)

To identify common variants influencing body mass index (BMI), we analyzed genome-wide association data from 16,876 individuals of European descent. After previously reported variants in FTO, the strongest association signal (rs17782313, P = 2.9 x 10(-6)) mapped 188 kb downstream of MC4R (melanocortin-4 receptor), mutations of which are the leading cause of monogenic severe childhood-onset obesity. We confirmed the BMI association in 60,352 adults (per-allele effect = 0.05 Z-score units; P = 2.8 x 10(-15)) and 5,988 children aged 7-11 (0.13 Z-score units; P = 1.5 x 10(-8)). In case-control analyses (n = 10,583), the odds for severe childhood obesity reached 1.30 (P = 8.0 x 10(-11)). Furthermore, we observed overtransmission of the risk allele to obese offspring in 660 families (P (pedigree disequilibrium test average; PDT-avg) = 2.4 x 10(-4)). The SNP location and patterns of phenotypic associations are consistent with effects mediated through altered MC4R function. Our findings establish that common variants near MC4R influence fat mass, weight and obesity risk at the population level and reinforce the need for large-scale data integration to identify variants influencing continuous biomedical traits.

Shot Boundary Detection by a Hierarchical Supervised Approach

G Camara-Chavez — 2008-04-29T14:21:47-00:00

Systems, Signals and Image Processing, 2007 and 6th EURASIP Conference focused on Speech and Image Processing, Multimedia Communications and Services. 14th International Workshop on (2007), pp. 197-200.

Video shot boundary detection plays an important role in video processing. It is the first step toward video-content analysis and content-based video retrieval. We develop a hierarchical approach for shot boundary detection based on the assumption that hierarchy helps to take decisions by reducing the amount of indeterminate transitions. Our method consists in first detecting abrupt transitions using a learning-based approach, then non-abrupt transitions are split into gradual transitions and normal frames. We describe in this paper, a machine learning system for shot boundary detection. The core of this system is a kernel-based SVM classifier. We present some results obtained for shot extraction TRECVID 2006 Task.

Thin-film hermeticity: A quantitative analysis of diamondlike carbon using variable angle spectroscopic ellipsometry

S Orzeszko — 2008-04-24T07:48:59-00:00

Journal of Applied Physics, Vol. 64, No. 8. (1988), pp. 4175-4180.

Low-energy laser therapy for prevention of oral mucositis in hematopoietic stem cell transplantation

Jaguar — 2007-10-20T18:42:58-00:00

Oral Diseases, Vol. 13, No. 6. (November 2007), pp. 538-543.

Predictive value of plant traits to grazing along a climatic gradient in the Mediterranean

De — 2005-09-29T16:52:10-00:00

Journal of Applied Ecology, Vol. 42, No. 5. (October 2005), pp. 824-833.

Op een lijn - Toekomstverkenning eerstelijnszorg 2020

Bakker De — 2008-04-06T12:44:05-00:00

This report concerns the future of primary health care in the Netherlands. With the year 2020 as time horizon, we present perspectives on demand, supply and the organization of primary care. How many caregivers will be needed, and what will the organization look like? The report offers a wealth of information about current and future primary care. Due to the many facts and figures, this report not only gives a forecast, it is also a useful reference work for everyone who is involved in primary health care. In the autumn of 2004, the Ministry of Public Health, Welfare and Sports and the parties in the field declared themselves in favor of a 'reinforcement of primary health care' as a common ambition. This study intends to provide a contribution to this goal. The report is the result of a joint project of the Netherlands Institute for Health Services Research (NIVEL) and the National Institute for Public Health and the Environment (RIVM), and it is part of the series of Public Health Status and Forecasting 2006. Dit themarapport gaat over de toekomst van de eerstelijnsgezondheidszorg in Nederland. Met het jaar 2020 als tijdshorizon worden verkenningen gepresenteerd over de zorgvraag, het zorgaanbod en de organisatie van de eerste lijn. Daarmee wordt zichtbaar welke zorgvragen in 2020 op de eerste lijn afkomen, hoeveel hulpverleners daarvoor nodig zijn en hoe de organisatie eruit kan zien. Mogelijke organisatieveranderingen worden steeds bezien vanuit de wetenschappelijke evidentie die er voor de effecten bestaat. Het rapport biedt een schat aan informatie over de huidige en toekomstige eerstelijnszorg. Door de vele feiten en cijfers is het rapport - behalve een toekomstverkenning - een nuttig naslagwerk voor allen die bij de eerstelijnszorg betrokken zijn. De veldpartijen en het Ministerie van VWS hebben zich in het najaar van 2004 uitgesproken voor 'versterking van de eerstelijnsgezondheidszorg' als een gezamenlijke ambitie. Deze studie beoogt daaraan een bijdrage te leveren. Dit rapport is het resultaat van een samenwerkingsproject van het NIVEL en het RIVM, en maakt deel uit van de reeks Volksgezondheid Toekomst Verkenningen 2006.

Modelling Complex Populations Formed by Proliferating, Quiescent and Quasi-quiescent Cells: Application to Plant Root Meristems

J Lopez-Sanchez — 2008-04-03T16:57:29-00:00

Journal of Theoretical Biology, Vol. 215, No. 2. (21 March 2002), pp. 201-213.

A proliferating population of cells may be considered complex when its proliferative or growth fractionP is lower than 1 and/or when it is formed by subpopulations with different mean cycle times. The present paper shows that in such complex populations exponential growth is consistent with a steady-state distribution of cells. Obviously, whenP =1 then cell distribution is only a function of cell age. An analytical model has been developed to study complex populations including both quiescent fractions formed by cells with unreplicated genome (G0 cells) and cells with fully duplicated chromosomes (Q2 cells). The model also considers those quasi-quiescent cells in their last transit through G1 and S (Q1 and Qs cells) before becoming quiescent. In order to solve the difficulties of a direct analysis of the whole population, its kinetic parameters have been obtained by studying the negative exponential distribution of two subpopulations: one formed by the proliferating cells and another formed by the quasi-quiescent cells. Additionally, the model could be applied when quiescence is initiated at any other cycle phase different from G1 and G2, for instance, cells in the process of replicating their DNA or being at any other mitotic phases. The utility of the method was illustrated in populations which constitute the root meristems of both Allium cepa L. and Pisum sativum L. Three facts should be stressed: (1) the method seems to be rather powerful because it can be carried out from different sets of experimentally measured parameters; (2) the rate of division and, therefore, the population doubling time can be easily estimated by this method; and (3) it also allows the determination of the amount of cells that had become quiescent either before they had replicated their DNA (G0) or after having completed their replication (Q2), as well as those quasi-quiescent cells which are progressing throughout their last pre-replicative and replicative periods (thus Q1 and Qs, respectively).

Physically realistic virtual surgery using the point-associated finite field (PAFF) approach

Suvranu De — 2008-04-03T06:51:12-00:00

Presence: Teleoper. Virtual Environ., Vol. 15, No. 3. (June 2006), pp. 294-308.

An octree partition of unity method (OctPUM) with enrichments for multiscale modeling of heterogeneous media

Michael Macri — 2008-03-14T07:43:55-00:00

Computers & Structures, Vol. 86, No. 7-8. (April 2008), pp. 780-795.

In this paper we present some enrichment techniques for the modeling of heterogeneous media in the presence of singularities such as cracks which overcome long-standing problems associated with the assumption of local periodicity in traditional asymptotic homogenization methods. An octree partition of unity method (OctPUM) is developed to solve the macroscopic problem. In this technique the geometry is discretized using hierarchical data structures known as quadtrees and octrees in two- and three-dimensions, respectively and the approximation functions, generated using the partition of unity approach, are compactly supported on n-dimensional cubes. OctPUM is in-between finite elements and meshfree methods in character and is computationally more efficient than pure meshfree techniques. Solutions near crack tips may be obtained without excessive local refinements using localized enrichment functions. In order to compute the microscopic fields near the crack edge within the macroscale computations, a structural enrichment-based homogenization method is introduced in which the approximation space of the OctPUM at the macroscopic scale is enriched by functions generated at the microscopic scale using the asymptotic homogenization technique. Several example problems in one- and two-dimensional analysis, including one involving realistic microstructures, are solved to demonstrate the effectiveness of the enrichment strategies.

Functional protein divergence in the evolution of Homo sapiens

Nuria Lopez-Bigas — 2008-02-15T13:27:09-00:00

Genome Biology, Vol. 9 (15 February 2008), R33.

Spermatogonial stem cells: characteristics and experimental possibilities

Pedro Aponte — 2006-02-18T12:23:40-00:00

Apmis, Vol. 113, No. 11-12. (November 2005), pp. 727-742.

Linear-Interval Dimension and PI Orders

Marcia Cerioli — 2008-03-10T14:00:48-00:00

Electronic Notes in Discrete Mathematics, Vol. 30 (20 February 2008), pp. 111-116.

A PI graph G is the intersection graph of a family of triangles ABC between two distinct parallel lines L1 and L2, such that A is on L1 and is on L2. We study the orders defined by transitive orientations of the complement of G, the PI orders. We describe a characterization for such orders in terms of a special order dimension called linear-interval dimension. We show that the linear-interval dimension of an order is a comparability invariant, which generalizes the well-known result that the interval dimension is a comparability invariant.

Carbon Nanotube Field-Effect Transistors for High-Performance Digital Circuits—DC Analysis and Modeling Toward Optimum Transistor Structure

A Raychowdhury — 2008-02-28T20:48:12-00:00

Electron Devices, IEEE Transactions on, Vol. 53, No. 11. (2006), pp. 2711-2717.

Scaling of silicon technology continues while a research has started in other novel materials for future technology generations beyond year 2015. Carbon nanotubes (CNTs) with their excellent carrier mobility are a promising candidate. The authors investigated different CNT-based field effect transistors (CNFETs) for an optimal switch. Schottky-barrier (SB) CNFETs, MOS CNFETs, and state-of-the-art Si MOSFETs were systematically compared from a circuit/system design perspective. The authors have performed a dc analysis and determined how noise margin and voltage swing vary as a function of tube diameter and power-supply voltage. The dc analysis of single-tube SB CNFET transistors revealed that the optimum CNT diameter for achieving the best ION-to-IOFF ratio while maintaining a good noise margin is about 1 to 1.5 nm. Despite several serious technological barriers and challenges, CNTs show a potential for future high-performance devices as they are being researched

Meshed multipath routing with selective forwarding: An efficient strategy in wireless sensor networks

S De — 2008-02-19T16:07:50-00:00

(2003)

Due to limited functionalities and potentially large number of sensors, existing routing strategies proposed for mobile ad hoc networks are not directly applicable to wireless sensor networks. In this paper, we present a meshed multipath routing (M-MPR) protocol with selective forwarding (SF) of packets and end-to-end forward error correction (FEC) coding. We also describe a meshed multipath searching scheme suitable for sensor networks, which has a reduced signaling overhead and nodal...

An improved bioluminescence resonance energy transfer strategy for imaging intracellular events in single cells and living subjects.

A De — 2007-09-23T04:42:19-00:00

Cancer Res, Vol. 67, No. 15. (1 August 2007), pp. 7175-7183.

Bioluminescence resonance energy transfer (BRET) is currently used for monitoring various intracellular events, including protein-protein interactions, in normal and aberrant signal transduction pathways. However, the BRET vectors currently used lack adequate sensitivity for imaging events of interest from both single living cells and small living subjects. Taking advantage of the critical relationship of BRET efficiency and donor quantum efficiency, we report generation of a novel BRET vector by fusing a GFP(2) acceptor protein with a novel mutant Renilla luciferase donor selected for higher quantum yield. This new BRET vector shows an overall 5.5-fold improvement in the BRET ratio, thereby greatly enhancing the dynamic range of the BRET signal. This new BRET strategy provides a unique platform to assay protein functions from both single live cells and cells located deep within small living subjects. The imaging utility of the new BRET vector is shown by constructing a sensor using two mammalian target of rapamycin pathway proteins (FKBP12 and FRB) that dimerize only in the presence of rapamycin. This new BRET vector should facilitate high-throughput sensitive BRET assays, including studies in single live cells and small living subjects. Applications will include anticancer therapy screening in cell culture and in small living animals.

Dependence of Control Coefficient Distribution on the Boundaries of a Metabolic System: A Generalized Analysis of the Effects of Additional Input and Output reactions to a Linear Pathway

P de Atauri — 2008-02-12T21:28:05-00:00

Journal of Theoretical Biology, Vol. 215, No. 2. (21 March 2002), pp. 239-251.

Both experimental and theoretical studies of metabolism are likely to relate to a segment that has been isolated for analytical purposes. In practice, it will be embedded in the whole of cellular metabolism. Thus, it is necessary to consider how conclusions about the control of an isolated pathway may be modified in this wider context where the input and output metabolites are considered as variables of cellular metabolism. Here, we analyse the effect of expanding a linear metabolic pathway by adding an extra input or an extra output. In particular, we analyse the effect of the elasticities of the extra steps on control coefficients. We derive matrix algebraic relationships for obtaining flux and concentration control coefficients from expressions depending on these extra elasticities and on parameters (elasticities and control coefficients) of the original pathway. These equations can be shown in certain cases to be generalized versions of earlier rescaling relationships and to be related to top-down analysis, but also apply where the new variable metabolite of the expanded pathway is an effector of more than one step of the original pathway. We use our relationships to analyse the dependence or independence of control coefficients upon these extra elasticities for the published analyses of the pathway of mammalian serine biosynthesis (Fell & Snell, 1988) andEscherischia coli threonine biosynthesis (Chassagnole et al., 2001). The same analysis can be applied to determine whether the transport reactions of substrates and products of a pathway in and out of a cell need to be included in estimations of the control coefficients of the enzymes.

End-to-End Flow Fairness Over IEEE 802.11-Based Wireless Mesh Networks

A Raniwala — 2008-02-11T23:41:21-00:00

INFOCOM 2007. 26th IEEE International Conference on Computer Communications. IEEE (2007), pp. 2361-2365.

Identification of Over and Under Expressed Genes Mediating Allergic Asthma

Rajat De — 2008-01-30T20:57:11-00:00

Advances in Applied Artificial Intelligence (2006), pp. 943-952.

The present article focuses on identifying some of the genes mediating the development of asthma. Here we apply a pattern recognition based approach to identify the genes those are severely over or under expressed in the allergen samples. The methodology involves clustering on gene expression and fold values followed by determining similarity/dissimilarity among various clusters, and measuring the extent of over/under expression of genes. From this analysis we have identified several genes those have significantly changed their expression values for asthmatic condition, and have reported in the present article. Some of these observations are supported by some earlier investigations. Others have been stayed unnoticed so far, but may play crucial role in mediating the development of asthma.

Thinking While Talking: Adults Fail Nonverbal False-Belief Reasoning

Newton — 2007-07-05T05:32:59-00:00

Psychological Science, Vol. 18, No. 7. (July 2007), pp. 574-579.

GPS-free coordinate assignment and routing in wireless sensor networks

A Caruso — 2007-03-10T19:45:40-00:00

(2004)

In this paper we consider the problem of constructing a coordinate system in a sensor network where location information is not available. To this purpose we introduce the Virtual Coordinate assignment protocol (VCap) which defines a virtual coordinate system based on hop distances. As compared to other approaches, VCap is simple and have very little requirements in terms of communication and memory overheads. We compare by simulations the performances of greedy routing using our virtual...

Fast Integer Multiplication using Modular Arithmetic

Anindya De — 2008-01-10T21:57:28-00:00

(9 Jan 2008)

We give an $O(N⋅ \log N⋅ 2^O(\log^*N))$ algorithm for multiplying two $N$-bit integers that improves the $O(N⋅ \log N⋅ \log\log N)$ algorithm by Schönhage-Strassen. Both these algorithms use modular arithmetic. Recently, Fürer gave an $O(N⋅ \log N⋅ 2^O(\log^*N))$ algorithm which however uses arithmetic over complex numbers as opposed to modular arithmetic. In this paper, we use multivariate polynomial multiplication along with ideas from Fürer's algorithm to achieve this improvement in the modular setting. Our algorithm can also be viewed as a $p$-adic version of Fürer's algorithm. Thus, we show that the two seemingly different approaches to integer multiplication, modular and complex arithmetic, are similar.

Logical Implementation of Uncertain Agents

De — 2008-01-08T18:50:32-00:00

Progress in Artificial Intelligence (2005), pp. 536-547.

We consider the representation and execution of agents specified using temporal logics. Previous work in this area has provided a basis for the direct execution of agent specifications, and has been extended to allow the handling of agent beliefs, deliberation and multi-agent groups. However, the key problem of uncertainty has not been tackled. Given that agents work in unknown environments, and interact with other agents that may, in turn, be unpredictable, then it is essential for any formal agent description to incorporate some mechanism for capturing this aspect. Within the framework of executable specifications, formal descriptions involving uncertainty must also be executable. The contribution of this paper is to extend executable temporal logic in order to allow the representation and execution of uncertain statements within agents. In particular, we extend the basis of the MetateM temporal framework with a probabilistic belief dimension captured by the recently introduced logic. We provide a description of the extended logic, the translation procedure for formulae in this extended logic to an executable normal form, and the execution algorithm for such formulae. We also outline technical results concerning the correctness of the translation to the normal form and the completeness of the execution mechanism.

Identifying Potential Social Impact of Collaborative Systems at Design Time

De — 2008-01-02T18:03:35-00:00

Human-Computer Interaction – INTERACT 2007 (2007), pp. 31-44.

This paper presents Manas, a Semiotic Engineering epistemic tool for the design of collaborative systems (CoSys) whose aim is to expand the designers’ knowledge and awareness of their influence on groups and group dynamics. Manas has been developed to help designers represent their conception of computer-mediated communication and reflect upon some of its potential social effects, springing from user-system interaction, as well from user-user interaction (through the system). The paper illustrates how Manas can lead designers to reflect upon both the design problem and its proposed solution(s), which allows them to make more conscious decisions. Increased knowledge and awareness should then enhance the quality of CoSys design.

Face-to-Face Sociability Signs Made Explicit in CMC

Carla Leitão — 2008-01-02T18:03:04-00:00

Human-Computer Interaction – INTERACT 2007 (2007), pp. 5-18.

This paper discusses how semiotic engineering can support the formulation of problems and solutions involved in handling face-to-face (F2F) sociability models in computer-mediated communication (CMC). Based on a case study where a group of users migrated through different types of CMC systems, we show that the designer’s model of F2F sociability is extensively signified and encoded into technology, whether they know it or not. Users are deeply affected by the designers’ F2F sociability models. Two qualitative methods of analysis are used to reveal the richness of interpretive and communicative processes in which online communities are involved, and the interplay of designers’ and users’ signs at interaction time.

Cold rolling behaviour and textural evolution in AISI 316L austenitic stainless steel

Sandip Chowdhury — 2007-12-13T00:52:42-00:00

Acta Materialia, Vol. 53, No. 14. (August 2005), pp. 3951-3959.

The present paper deals with the evolution of microstructure and texture of a 316L austenitic stainless steel during cold rolling. With increasing rolling reductions, different deformation mechanisms become active. TEM observations show the presence of deformation twinning. With increasing strain the volume fraction of twin increases. At higher degrees of reduction, there is evidence that flow localization takes place and there is formation of shear bands. The material initially shows Cu-type texture, i.e., Cu 1 1 2<1 1 1>, Bs 1 1 0<1 1 2> with a spread towards Goss 0 1 1<1 0 0>. With the progress of rolling, the Cu 1 1 2<1 1 1> component diminishes and the other two components increase their intensity during rolling. At higher strain levels, there are additional texture components, 1 1 1. The evolution of texture is correlated with the associated deformation mechanisms.

Rap1a Null Mice Have Altered Myeloid Cell Functions Suggesting Distinct Roles for the Closely Related Rap1a and 1b Proteins

Yu Li — 2007-12-03T19:17:25-00:00

J Immunol, Vol. 179, No. 12. (15 December 2007), pp. 8322-8331.

The Ras-related GTPases Rap1a and 1b have been implicated in multiple biological events including cell adhesion, free radical production, and cancer. To gain a better understanding of Rap1 function in mammalian physiology, we deleted the Rap1a gene. Although loss of Rap1a expression did not initially affect mouse size or viability, upon backcross into C57BL/6J mice some Rap1a/ embryos died in utero. T cell, B cell, or myeloid cell development was not disrupted in Rap1a / mice. However, macrophages from Rap1a null mice exhibited increased haptotaxis on fibronectin and vitronectin matrices that correlated with decreased adhesion. Chemotaxis of lymphoid and myeloid cells in response to CXCL12 or CCL21 was significantly reduced. In contrast, an increase in FcR-mediated phagocytosis was observed. Because Rap1a was previously copurified with the human neutrophil NADPH oxidase, we addressed whether GTPase loss affected superoxide production. Neutrophils from Rap1a/ mice had reduced fMLP-stimulated superoxide production as well as a weaker initial response to phorbol ester. These results suggest that, despite 95% amino acid sequence identity, similar intracellular distribution, and broad tissue distribution, Rap1a and 1b are not functionally redundant but rather differentially regulate certain cellular events.

Defensin Participation in Innate and Adaptive Immunity

Yang — 2007-10-07T05:25:02-00:00

Current Pharmaceutical Design, Vol. 13, No. 30. (October 2007), pp. 3131-3139.

Game Theory in Philosophy

Bruin — 2005-09-13T08:49:58-00:00

Topoi, Vol. 24, No. 2. (September 2005), pp. 197-208.

Pamidronate and uveitis.

S De — 2007-11-21T21:32:35-00:00

Br J Rheumatol, Vol. 34, No. 5. (May 1995)

International consensus statement on an update of the classification criteria for definite antiphospholipid syndrome (APS)

S Miyakis — 2006-01-14T07:44:52-00:00

Journal of Thrombosis and Haemostasis, Vol. 4, No. 2. (February 2006), pp. 295-306.

Nonlinear optical properties and surface-plasmon enhanced optical limiting in Ag--Cu nanoclusters co-doped in SiO[sub 2] Sol-Gel films

Prem Kiran — 2007-10-28T17:05:35-00:00

Journal of Applied Physics, Vol. 96, No. 11. (2004), pp. 6717-6723.

The nonlinear optical properties and the role of the surface-plasmon resonance (SPR) on optical limiting (OL) properties of Ag–Cu nanoclusters co-doped in SiO2 matrix prepared using the sol-gel technique with a Cu/Ag molar ratio of 1, 2 and 3, respectively, are presented. The studies were made using the second harmonic of high-power nanosecond and picosecond Nd:YAG lasers. These films show a self-defocusing nonlinearity with both nanosecond and picosecond pulses and a good nonlinear absorption behavior with the nanosecond pulse excitation. The nonlinear refractive index decreased with decreasing particle size, whereas the nonlinear absorption increased with an increase in Cu concentration. The observed nonlinear absorption is explained by taking into account the cumulative effect of both the intraband and interband mechanisms. The excitation near the SPR of Cu resulted in an enhanced OL behavior with increasing Cu concentration. No such concentration dependence is observed when the excitation is near the SPR of Ag, however, the limiting threshold is reduced approximately 10–17 times. Excitation at wavelengths far below the SPR of Ag and Cu has not shown any OL behavior. The major contribution toward OL is observed to be from the interband absorption and from a possible energy transfer within the higher unoccupied states of Cu and Ag. Although nonlinear scattering is observed at higher intensities, its contribution is found to be much less than that of the nonlinear absorption assisted by an energy transfer. ©2004 American Institute of Physics

Parameter variations and impact on circuits and microarchitecture

S Borkar — 2007-08-24T12:34:00-00:00

Design Automation Conference, 2003. Proceedings (2003), pp. 338-342.

Parameter variation in scaled technologies beyond 90nm will pose a major challenge for design of future high performance microprocessors. In this paper, we discuss process, voltage and temperature variations; and their impact on circuit and microarchitecture. Possible solutions to reduce the impact of parameter variations and to achieve higher frequency bins are also presented.

Integrated cellular and ad hoc relaying systems: iCAR

Hongyi Wu — 2007-10-14T20:54:58-00:00

Selected Areas in Communications, IEEE Journal on, Vol. 19, No. 10. (2001), pp. 2105-2115.

Integrated cellular and ad hoc relaying systems (iCAR) is a new wireless system architecture based on the integration of cellular and modern ad hoc relaying technologies. It addresses the congestion problem due to unbalanced traffic in a cellular system and provides interoperability for heterogeneous networks. The iCAR system can efficiently balance traffic loads between cells by using ad hoc relaying stations (ARS) to relay traffic from one cell to another dynamically. This not only increases the system's capacity cost effectively, but also reduces the transmission power for mobile hosts and extends system coverage. We compare the performance of the iCAR system with conventional cellular systems in terms of the call blocking/dropping probability, throughput, and signaling overhead via analysis and simulation. Our results show that with a limited number of ARSs and some increase in the signaling overhead (as well as hardware complexity), the call blocking/dropping probability in a congested cell and the overall system can be reduced

Dynamics of cell orientation

Rumi De — 2007-10-02T14:53:03-00:00

Nat Phys, Vol. 3, No. 9. (2007), pp. 655-659.

Belgium

De — 2007-09-24T20:43:16-00:00

European Journal of Political Research, Vol. 45, No. 7-8. (2006), pp. 1055-1064.

Noninvasive imaging of protein-protein interactions from live cells and living subjects using bioluminescence resonance energy transfer.

A De — 2007-09-23T04:44:01-00:00

FASEB J, Vol. 19, No. 14. (December 2005), pp. 2017-2019.

This study demonstrates a significant advancement of imaging of a distance-dependent physical process, known as the bioluminescent resonance energy transfer (BRET2) signal in living subjects, by using a cooled charge-coupled device (CCD) camera. A CCD camera-based spectral imaging strategy enables simultaneous visualization and quantitation of BRET signal from live cells and cells implanted in living mice. We used the BRET2 system, which utilizes Renilla luciferase (hRluc) protein and its substrate DeepBlueC (DBC) as an energy donor and a mutant green fluorescent protein (GFP2) as the acceptor. To accomplish this objective in this proof-of-principle study, the donor and acceptor proteins were fused to FKBP12 and FRB, respectively, which are known to interact only in the presence of the small molecule mediator rapamycin. Mammalian cells expressing these fusion constructs were imaged using a cooled-CCD camera either directly from culture dishes or by implanting them into mice. By comparing the emission photon yields in the presence and absence of rapamycin, the specific BRET signal was determined. The CCD imaging approach of BRET signal is particularly appealing due to its capacity to seamlessly bridge the gap between in vitro and in vivo studies. This work validates BRET as a powerful tool for interrogating and observing protein-protein interactions directly at limited depths in living mice.