An embedded grid adaptation strategy for unstructured data based finite volume computations

A grid adaptation strategy for unstructured data based codes, employing a combination of hexahedral and prismatic elements, generalizable to tetrahedral and pyramidal elements has been developed.

Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria

Most bacterial genomes harbor restriction-modification systems, encoding a REase and its cognate MTase. On attack by a foreign DNA, the REase recognizes it as nonself and subjects it to restriction. Should REases be highly specific for targeting the invading foreign DNA? It is often considered to be the case. However, when bacteria harboring a promiscuous or high-fidelity variant of the REase were challenged with bacteriophages, fitness was maximal under conditions of catalytic promiscuity. We also delineate possible mechanisms by which the REase recognizes the chromosome as self at the noncanonical sites, thereby preventing lethal dsDNA breaks. This study provides a fundamental understanding of how bacteria exploit an existing defense system to gain fitness advantage during a host-parasite coevolutionary ``arms race.''

Search on a fractal lattice using a quantum random walk

The spatial search problem on regular lattice structures in integer number of dimensions d >= 2 has been studied extensively, using both coined and coinless quantum walks. The relativistic Dirac operator has been a crucial ingredient in these studies. Here, we investigate the spatial search problem on fractals of noninteger dimensions. Although the Dirac operator cannot be defined on a fractal, we construct the quantum walk on a fractal using the flip-flop operator that incorporates a Klein-Gordon mode. We find that the scaling behavior of the spatial search is determined by the spectral (and not the fractal) dimension. Our numerical results have been obtained on the well-known Sierpinski gaskets in two and three dimensions.

Pulsed radio emission from the Fermi-LAT pulsar J1732-3131: Search and a possible detection at 34.5 MHz

We report our search for and a possible detection of periodic radio pulses at 34.5 MHz from the Fermi Large Area Telescope pulsar J1732-3131. The candidate detection has been possible in only one of the many sessions of observations made with the low-frequency array at Gauribidanur, India, when the otherwise radio weak pulsar may have apparently brightened many folds. The candidate dispersion measure along the sight line, based on the broad periodic profiles from �20min of data, is estimated to be 15.44 ± 0.32 pccc -1. We present the details of our periodic and single-pulse search, and discuss the results and their implications relevant to both, the pulsar and the intervening medium. © 2012 RAS.

Data-resolution based optimization of the data-collection strategy for near infrared diffuse optical tomography

Purpose: To optimize the data-collection strategy for diffuse optical tomography and to obtain a set of independent measurements among the total measurements using the model based data-resolution matrix characteristics. Methods: The data-resolution matrix is computed based on the sensitivity matrix and the regularization scheme used in the reconstruction procedure by matching the predicted data with the actual one. The diagonal values of data-resolution matrix show the importance of a particular measurement and the magnitude of off-diagonal entries shows the dependence among measurements. Based on the closeness of diagonal value magnitude to off-diagonal entries, the independent measurements choice is made. The reconstruction results obtained using all measurements were compared to the ones obtained using only independent measurements in both numerical and experimental phantom cases. The traditional singular value analysis was also performed to compare the results obtained using the proposed method. Results: The results indicate that choosing only independent measurements based on data-resolution matrix characteristics for the image reconstruction does not compromise the reconstructed image quality significantly, in turn reduces the data-collection time associated with the procedure. When the same number of measurements (equivalent to independent ones) are chosen at random, the reconstruction results were having poor quality with major boundary artifacts. The number of independent measurements obtained using data-resolution matrix analysis is much higher compared to that obtained using the singular value analysis. Conclusions: The data-resolution matrix analysis is able to provide the high level of optimization needed for effective data-collection in diffuse optical imaging. The analysis itself is independent of noise characteristics in the data, resulting in an universal framework to characterize and optimize a given data-collection strategy. (C) 2012 American Association of Physicists in Medicine. http://dx.doi.org/10.1118/1.4736820]

As(3)p: A Fast Algorithm to Search Structurally Similar Protiens

Protein structure comparison is essential for understanding various aspects of protein structure, function and evolution. It can be used to explore the structural diversity and evolutionary patterns of protein families. In view of the above, a new algorithm is proposed which performs faster protein structure comparison using the peptide backbone torsional angles. It is fast, robust, computationally less expensive and efficient in finding structural similarities between two different protein structures and is also capable of identifying structural repeats within the same protein molecule.

Orthogonal biofunctionalization of magnetic nanoparticles via ``clickable'' poly(ethylene glycol) silanes: a ``universal ligand'' strategy to design stealth and target-specific nanocarriers

The present work demonstrates a novel strategy to synthesize orthogonally bio-engineered magnetonanohybrids (MNPs) through the design of versatile, biocompatible linkers whose structure includes: (i) a robust anchor to bind with metal-oxide surfaces; (ii) tailored surface groups to act as spacers and (iii) a general method to implement orthogonal functionalizations of the substrate via ``click chemistry''. Ligands that possess the synthetic generality of features (i)-(iii) are categorized as ``universal ligands''. Herein, we report the synthesis of a novel, azido-terminated poly(ethylene glycol) (PEG) silane that can easily self-assemble on MNPs through hetero-condensation between surface hydroxyl groups and the silane end of the ligand, and simultaneously provide multiple clickable sites for high density, chemoselective bio-conjugation. To establish the universal-ligand-strategy, we clicked alkyl-functionalized folate onto the surface of PEGylated MNPs. By further integrating a near-infrared fluorescent (NIRF) marker (Alexa-Fluor 647) with MNPs, we demonstrated their folate-receptor mediated internalization inside cancer cells and subsequent translocation into lysosomes and mitochondria. Ex vivo NIRF imaging established that the azido-PEG-silane developed in course of the study can effectively reduce the sequestration of MNPs by macrophage organs (viz. liver and spleen). These folate-PEG-MNPs were not only stealth and noncytotoxic but their dual optical and magnetic properties aided in tracking their whereabouts through combined magnetic resonance and optical imaging. Together, these results provided a strong motivation for the future use of the ``universal ligand'' strategy towards development of ``smart'' nanohybrids for theragnostic applications.

Turning visual search time on its head

Our everyday visual experience frequently involves searching for objects in clutter. Why are some searches easy and others hard? It is generally believed that the time taken to find a target increases as it becomes similar to its surrounding distractors. Here, I show that while this is qualitatively true, the exact relationship is in fact not linear. In a simple search experiment, when subjects searched for a bar differing in orientation from its distractors, search time was inversely proportional to the angular difference in orientation. Thus, rather than taking search reaction time (RT) to be a measure of target-distractor similarity, we can literally turn search time on its head (i.e. take its reciprocal 1/RT) to obtain a measure of search dissimilarity that varies linearly over a large range of target-distractor differences. I show that this dissimilarity measure has the properties of a distance metric, and report two interesting insights come from this measure: First, for a large number of searches, search asymmetries are relatively rare and when they do occur, differ by a fixed distance. Second, search distances can be used to elucidate object representations that underlie search - for example, these representations are roughly invariant to three-dimensional view. Finally, search distance has a straightforward interpretation in the context of accumulator models of search, where it is proportional to the discriminative signal that is integrated to produce a response. This is consistent with recent studies that have linked this distance to neuronal discriminability in visual cortex. Thus, while search time remains the more direct measure of visual search, its reciprocal also has the potential for interesting and novel insights. (C) 2012 Elsevier Ltd. All rights reserved.

Inhibition of the Interaction Between NS3 Protease and HCV IRES With a Small Peptide: A Novel Therapeutic Strategy

Recently, we have demonstrated that the protease domain of NS3 alone can bind specifically to hepatitis C virus (HCV) internal ribosome entry site (IRES) near the initiator AUG, dislodges human La protein and inhibits translation in favor of viral RNA replication. Here, by using a computational approach, the contact points of the protease on the HCV IRES were putatively mapped. A 30-mer NS3 peptide was designed from the predicted RNA-binding region that retained RNA-binding ability and also inhibited IRES-mediated translation. This peptide was truncated to 15 mer and this also demonstrated ability to inhibit HCV RNA-directed translation as well as replication. More importantly, its activity was tested in an in vivo mouse model by encapsulating the peptide in Sendai virus virosomes followed by intravenous delivery. The study demonstrates for the first time that the HCV NS3-IRES RNA interaction can be selectively inhibited using a small peptide and reports a strategy to deliver the peptide into the liver.

Active Sequential Hypothesis Testing with Application to a Visual Search Problem

We consider a visual search problem studied by Sripati and Olson where the objective is to identify an oddball image embedded among multiple distractor images as quickly as possible. We model this visual search task as an active sequential hypothesis testing problem (ASHT problem). Chernoff in 1959 proposed a policy in which the expected delay to decision is asymptotically optimal. The asymptotics is under vanishing error probabilities. We first prove a stronger property on the moments of the delay until a decision, under the same asymptotics. Applying the result to the visual search problem, we then propose a ``neuronal metric'' on the measured neuronal responses that captures the discriminability between images. From empirical study we obtain a remarkable correlation (r = 0.90) between the proposed neuronal metric and speed of discrimination between the images. Although this correlation is lower than with the L-1 metric used by Sripati and Olson, this metric has the advantage of being firmly grounded in formal decision theory.

Truthful multi-armed bandit mechanisms for multi-slot sponsored search auctions

In pay-per-click sponsored search auctions which are currently extensively used by search engines, the auction for a keyword involves a certain number of advertisers (say k) competing for available slots (say m) to display their advertisements (ads for short). A sponsored search auction for a keyword is typically conducted for a number of rounds (say T). There are click probabilities mu(ij) associated with each agent slot pair (agent i and slot j). The search engine would like to maximize the social welfare of the advertisers, that is, the sum of values of the advertisers for the keyword. However, the search engine does not know the true values advertisers have for a click to their respective advertisements and also does not know the click probabilities. A key problem for the search engine therefore is to learn these click probabilities during the initial rounds of the auction and also to ensure that the auction mechanism is truthful. Mechanisms for addressing such learning and incentives issues have recently been introduced. These mechanisms, due to their connection to the multi-armed bandit problem, are aptly referred to as multi-armed bandit (MAB) mechanisms. When m = 1, exact characterizations for truthful MAB mechanisms are available in the literature. Recent work has focused on the more realistic but non-trivial general case when m > 1 and a few promising results have started appearing. In this article, we consider this general case when m > 1 and prove several interesting results. Our contributions include: (1) When, mu(ij)s are unconstrained, we prove that any truthful mechanism must satisfy strong pointwise monotonicity and show that the regret will be Theta T7) for such mechanisms. (2) When the clicks on the ads follow a certain click precedence property, we show that weak pointwise monotonicity is necessary for MAB mechanisms to be truthful. (3) If the search engine has a certain coarse pre-estimate of mu(ij) values and wishes to update them during the course of the T rounds, we show that weak pointwise monotonicity and type-I separatedness are necessary while weak pointwise monotonicity and type-II separatedness are sufficient conditions for the MAB mechanisms to be truthful. (4) If the click probabilities are separable into agent-specific and slot-specific terms, we provide a characterization of MAB mechanisms that are truthful in expectation.

Thermal oxidation strategy for the synthesis of phase-controlled GeO2 and photoluminescence characterization

We report the synthesis of trigonal and tetragonal phase GeO2 films/microrods from a Ge wafer/powder by thermal oxidation. Both trigonal and tetragonal GeO2 exhibit excitation-dependent luminescence. Trigonal GeO2 exhibits strong green luminescence while tetragonal GeO2 exhibits strong blue luminescence when excited with ultra-violet light. Yellow-red luminescence is observed when both the phases are excited with green light. The emission wavelength varies almost linearly with the excitation wavelength both for trigonal and tetragonal GeO2. The variation is significant in the case of tetragonal GeO2, indicating a potential wavelength converter material.

Similarity relations in visual search predict rapid visual categorization

How do we perform rapid visual categorization?It is widely thought that categorization involves evaluating the similarity of an object to other category items, but the underlying features and similarity relations remain unknown. Here, we hypothesized that categorization performance is based on perceived similarity relations between items within and outside the category. To this end, we measured the categorization performance of human subjects on three diverse visual categories (animals, vehicles, and tools) and across three hierarchical levels (superordinate, basic, and subordinate levels among animals). For the same subjects, we measured their perceived pair-wise similarities between objects using a visual search task. Regardless of category and hierarchical level, we found that the time taken to categorize an object could be predicted using its similarity to members within and outside its category. We were able to account for several classic categorization phenomena, such as (a) the longer times required to reject category membership; (b) the longer times to categorize atypical objects; and (c) differences in performance across tasks and across hierarchical levels. These categorization times were also accounted for by a model that extracts coarse structure from an image. The striking agreement observed between categorization and visual search suggests that these two disparate tasks depend on a shared coarse object representation.

Improving query focused summarization using look-ahead strategy

Query focused summarization is the task of producing a compressed text of original set of documents based on a query. Documents can be viewed as graph with sentences as nodes and edges can be added based on sentence similarity. Graph based ranking algorithms which use 'Biased random surfer model' like topic-sensitive LexRank have been successfully applied to query focused summarization. In these algorithms, random walk will be biased towards the sentences which contain query relevant words. Specifically, it is assumed that random surfer knows the query relevance score of the sentence to where he jumps. However, neighbourhood information of the sentence to where he jumps is completely ignored. In this paper, we propose look-ahead version of topic-sensitive LexRank. We assume that random surfer not only knows the query relevance of the sentence to where he jumps but he can also look N-step ahead from that sentence to find query relevance scores of future set of sentences. Using this look ahead information, we figure out the sentences which are indirectly related to the query by looking at number of hops to reach a sentence which has query relevant words. Then we make the random walk biased towards even to the indirect query relevant sentences along with the sentences which have query relevant words. Experimental results show 20.2% increase in ROUGE-2 score compared to topic-sensitive LexRank on DUC 2007 data set. Further, our system outperforms best systems in DUC 2006 and results are comparable to state of the art systems.