Beta-hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease

Refolding of staphylococcal nuclease has been studied recently by hydrogen-deuterium exchange and NMR spectroscopy. These studies infer that beta-hairpin formed by strand 2 and strand 3 connected by reverse turn forms early during the refolding of nuclease. Typically, hydrogen-deuterium exchange NMR techniques are usually carried out on a time scale of milliseconds whereas beta-hairpins are known to fold on a much shorter time scale. It follows that in the experiments, the hydrogen-deuterium exchange protection patterns could be arising from a significant population of fully formed hairpins. In order to demonstrate it is the fully formed hairpins which gives rise to the hydrogen-deuterium exchange protection patterns, we have considered molecular dynamics simulation of the peptide (21)DTVKLMYKGQPMTFR(35) from staphylococcal nuclease corresponding to the beta-hairpin region, using GROMOS96 force field under NVT conditions. Starting from unfolded conformational states, the peptide folds into hairpin conformations with native-like and non-native hydrogen bonding patterns. Subsequent to folding, equilibrium conditions prevail. The computed protection factors and atom depth values, at equilibrium, of the various amide protons agree qualitatively with experimental observations. A collection of molecules following the trajectories observed in the simulations can account for experimental observations. These simulations provide a molecular picture of the formed hairpins and their conformational features during the refolding experiments on nuclease, monitored by hydrogen-deuterium exchange.     

Effect of impurities (graphite) on the high-temperature creep properties of NiAl

Previous high-temperature compression creep studies of NiAl have shown peculiar behaviour in the temperature range 700 to 900° C, which was perhaps due to precipitation of impurities in the matrix. To isolate the impurity effect, high-purity NiAl samples with 0.15 at% and 0.20 at% carbon (graphite) additions have been creep tested at four temperatures between 700 and 850° C. Addition of graphite has been shown to produce a significant reduction in the creep strength of the alloyS. However, alloys with higher graphite concentrations have shown better creep resistance than those with lower graphite concentrations. Transmission electron microscopy indicates the presence of competing softening and hardening mechanisms in the alloys. Softening is due to the graphite particles acting as a dislocation source. Hardening results from a grain-boundary hardening mechanism due to the graphite particles segregating at grain boundaries and a dislocation-impurity (fine graphite) interaction, developing a Cottrell-like atmosphere.     

A framework for joint community detection across multiple related networks

Community detection in networks is an active area of research with many practical applications. However, most of the early work in this area has focused on partitioning a single network or a bipartite graph into clusters/communities. With the rapid proliferation of online social media, it has become increasingly common for web users to have noticeable presence across multiple web sites. This raises the question whether it is possible to combine information from several networks to improve community detection. In this paper, we present a framework that identifies communities simultaneously across different networks and learns the correspondences between them. The framework is applicable to networks generated from multiple web sites as well as to those derived from heterogeneous nodes of the same web site. It also allows the incorporation of prior information about the potential relationships between the communities in different networks. Extensive experiments have been performed on both synthetic and real-life data sets to evaluate the effectiveness of our framework. Our results show superior performance of simultaneous community detection over three alternative methods, including normalized cut and matrix factorization on a single network or a bipartite graph.     

Evaluation of hot corrosion resistance of HVOF coatings on a Ni-based superalloy in molten salt environment

High-velocity oxy-fuel (HVOF) has the advantage of being a continuous and most convenient process for applying coatings to industrial installations at site. In this study, Cr₃C₂–NiCr, NiCrBSi, Stellite-6 and Ni–20Cr coatings were deposited on a Ni-based superalloy (19.5Cr–3Fe–0.3Ti–0.1C–balance Ni) using an HVOF process. Hot corrosion studies were performed on bare as well as coated superalloy specimens after exposure to a molten salt environment at 900 °C under cyclic conditions. The thermogravimetric technique was used to establish the kinetics of corrosion. XRD, SEM/EDAX and EPMA techniques were used to analyse the corrosion products. The hot corrosion resistance of all the coatings were superior to bare superalloy. Among the coatings studied, the Ni–20Cr coated superalloy imparted maximum hot corrosion resistance, whereas the Stellite-6 coated indicated minimum resistance. The hot corrosion resistance of all coatings may be attributed to the formation of oxides and spinels of nickel, chromium or cobalt.     

Designing communication strategies for heterogeneous parallel systems

This paper explores the suitability of the emerging passive star-coupled optical interconnection using wavelength division multiplexing as the system interconnect to provide high bandwidth (Gbits/sec) communication demanded by heterogeneous systems. Several different communication strategies (combinations of communication topologies and protocols) are investigated under a representative master-slave computational model. The interplay between system speed, network speed, task granularity, and degree of parallelism is studied using both analytical modeling and simulations. It is shown that a hierarchical ALOHA-based communication strategy between the master and the slaves, implemented on top of the passive star-coupled network, leads to a considerable reduction in channel contention and provides 50–80% reduction in task completion time for applications with medium to high degrees of coarse grain parallelism. Comparable reduction in channel contention is also shown to be achieved by using tunable acoustooptic filters at master nodes.     

Effect of solid polymer electrolyte on the sensitization of photocurrents in solid-state electrochemical cells using conducting polypyrrole

The effect of small concentration of methylene blue dye on photocurrents was studied in the solid-state photoelectrochemical cells fabricated using conducting polypyrrole-coated electrodes sandwiched with solid-polymer electrolyte, namely, polyvinylpyrrolidone with phosphoric acid. A maximum photosensitivity factor (S=I _l/I _d, where I _l is the photocurrent and I _d is the dark current) of the order of 5 is observed. The current–voltage (I–V) characteristics in such cells reveal that charge transport is mainly governed by the space charge effect. Comparison of the results presented in this paper with the ones we reported earlier [23] indicates that the matrix in which dye has been incorporated plays an important role in such sensitization processes. A matrix that can efficiently transport the photogenerated charge carriers is observed to be more suitable for such dye-sensitized devices.     

FRAPP: a framework for high-accuracy privacy-preserving mining

To preserve client privacy in the data mining process, a variety of techniques based on random perturbation of individual data records have been proposed recently. In this paper, we present FRAPP, a generalized matrix-theoretic framework of random perturbation, which facilitates a systematic approach to the design of perturbation mechanisms for privacy-preserving mining. Specifically, FRAPP is used to demonstrate that (a) the prior techniques differ only in their choices for the perturbation matrix elements, and (b) a symmetric positive-definite perturbation matrix with minimal condition number can be identified, substantially enhancing the accuracy even under strict privacy requirements. We also propose a novel perturbation mechanism wherein the matrix elements are themselves characterized as random variables, and demonstrate that this feature provides significant improvements in privacy at only a marginal reduction in accuracy. The quantitative utility of FRAPP, which is a general-purpose random-perturbation-based privacy-preserving mining technique, is evaluated specifically with regard to association and classification rule mining on a variety of real datasets. Our experimental results indicate that, for a given privacy requirement, either substantially lower modeling errors are incurred as compared to the prior techniques, or the errors are comparable to those of direct mining on the true database. A partial and preliminary version of this paper appeared in the Proc. of the 21st IEEE Intl. Conf. on Data Engineering (ICDE), Tokyo, Japan, 2005, pgs. 193–204.     

Truncated O-Glycan-Bearing MUC16 Enhances Pancreatic Cancer Cells Aggressiveness via α4β1 Integrin Complexes and FAK Signaling

Elevated levels of Mucin-16 (MUC16) in conjunction with a high expression of truncated O-glycans is implicated in playing crucial roles in the malignancy of pancreatic ductal adenocarcinoma (PDAC). However, the mechanisms by which such aberrant glycoforms present on MUC16 itself promote an increased disease burden in PDAC are yet to be elucidated. This study demonstrates that the CRISPR/Cas9-mediated genetic deletion of MUC16 in PDAC cells decreases tumor cell migration. We found that MUC16 enhances tumor malignancy by activating the integrin-linked kinase and focal adhesion kinase (ILK/FAK)-signaling axis. These findings are especially noteworthy in truncated O-glycan (Tn and STn antigen)-expressing PDAC cells. Activation of these oncogenic-signaling pathways resulted in part from interactions between MUC16 and integrin complexes (α4β1), which showed a stronger association with aberrant glycoforms of MUC16. Using a monoclonal antibody to functionally hinder MUC16 significantly reduced the migratory cascades in our model. Together, these findings suggest that truncated O-glycan containing MUC16 exacerbates malignancy in PDAC by activating FAK signaling through specific interactions with α4 and β1 integrin complexes on cancer cell membranes. Targeting these aberrant glycoforms of MUC16 can aid in the development of a novel platform to study and treat metastatic pancreatic cancer.     

Binning algorithm for high-resolution IRS-P4 OCM chlorophyll image

Daily chlorophyll-a concentration from the Ocean Colour Monitor (OCM) sensor onboard the Indian Remote Sensing satellite (IRS-P4) is used to make weekly and monthly chlorophyll-a concentration maps. The pathwise swath data at 12 noon for every alternate day over the north Indian Ocean (NIO) during February 2004 and February 2005 were used to compare the existing algorithms for binning the data. Atmospherically corrected and geocorrected OCM data were used in the comparative study of three averaging algorithms – arithmetic mean (AVG), geometric mean (GEO) and maximum likelihood estimator (MLE). The analysis shows that the AVG algorithm is best suited when compared with the two other algorithms. However, for case 1 water, MLE gives nearly the same value as AVG. Based on this result, AVG was selected for operational weekly and monthly averaging of OCM data over the NIO. These high-resolution-derived chlorophyll-a weekly and monthly products will be useful to resolve inter-annual-to-decadal changes in chlorophyll-a concentration over the NIO.