Successful data recovery from oscillation photographs containing strong polycrystalline diffraction rings from an unknown small-molecule contaminant: preliminary structure solution of Salmonella typhimurium pyridoxal kinase (PdxK)

Pyridoxal kinase (PdxK; EC 2.7.1.35) belongs to the phosphotransferase family of enzymes and catalyzes the conversion of the three active forms of vitamin B-6, pyridoxine, pyridoxal and pyridoxamine, to their phosphorylated forms and thereby plays a key role in pyridoxal 5 `-phosphate salvage. In the present study, pyridoxal kinase from Salmonella typhimurium was cloned and overexpressed in Escherichia coli, purified using Ni-NTA affinity chromatography and crystallized. X-ray diffraction data were collected to 2.6 angstrom resolution at 100 K. The crystal belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unitcell parameters a = 65.11, b = 72.89, c = 107.52 angstrom. The data quality obtained by routine processing was poor owing to the presence of strong diffraction rings caused by a polycrystalline material of an unknown small molecule in all oscillation images. Excluding the reflections close to powder/polycrystalline rings provided data of sufficient quality for structure determination. A preliminary structure solution has been obtained by molecular replacement with the Phaser program in the CCP4 suite using E. coli pyridoxal kinase (PDB entry 2ddm) as the phasing model. Further refinement and analysis of the structure are likely to provide valuable insights into catalysis by pyridoxal kinases.

A Modified Fluorimetric Method for Determination of Hydrogen Peroxide Using Homovanillic Acid Oxidation Principle

Hydrogen peroxide (H2O2) level in biological samples is used as an important index in various studies. Quantification of H2O2 level in tissue fractions in presence of H2O2 metabolizing enzymes may always provide an incorrect result. A modification is proposed for the spectrofluorimetric determination of H2O2 in homovanillic acid (HVA) oxidation method. The modification was included to precipitate biological samples with cold trichloroacetic acid (TCA, 5% w/v) followed by its neutralization with K2HPO4 before the fluorimetric estimation of H2O2 is performed. TCA was used to precipitate the protein portions contained in the tissue fractions. After employing the above modification, it was observed that H2O2 content in tissue samples was >= 2 fold higher than the content observed in unmodified method. Minimum 2 h incubation of samples in reaction mixture was required for completion of the reaction. The stability of the HVA dimer as reaction product was found to be > 12 h. The method was validated by using known concentrations of H2O2 and catalase enzyme that quenches H2O2 as substrate. This method can be used efficiently to determine more accurate tissue H2O2 level without using internal standard and multiple samples can be processed at a time with additional low cost reagents such as TCA and K2HPO4.

De novo inference of protein function from coarse-grained dynamics

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 mu s coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. (C) 2014 Wiley Periodicals, Inc.

On the Two-Step Mechanism for Synthesis of Transition-Metal Nanoparticles

The two-step particle synthesis mechanism, also known as the Finke-Watzky (1997) mechanism, has emerged as a significant development in the field of nanoparticle synthesis. It explains a characteristic feature of the synthesis of transition metal nanoparticles, an induction period in precursor concentration followed by its rapid sigmoidal decrease. The classical LaMer theory (1950) of particle formation fails to capture this behavior. The two-step mechanism considers slow continuous nucleation and autocatalytic growth of particles directly from precursor as its two kinetic steps. In the present work, we test the two-step mechanism rigorously using population balance models. We find that it explains precursor consumption very well, but fails to explain particle synthesis. The effect of continued nucleation on particle synthesis is not suppressed sufficiently by the rapid autocatalytic growth of particles. The nucleation continues to increase breadth of size distributions to unexpectedly large values as compared to those observed experimentally. A number of variations of the original mechanism with additional reaction steps are investigated next. The simulations show that continued nucleation from the beginning of the synthesis leads to formation of highly polydisperse particles in all of the tested cases. A short nucleation window, realized with delayed onset of nucleation and its suppression soon after in one of the variations, appears as one way to explain all of the known experimental observations. The present investigations clearly establish the need to revisit the two-step particle synthesis mechanism.

Experimental determination and theoretical correlation for the solubilities of dicarboxylic acid esters in supercritical carbon dioxide

The synthesis of high molecular weight esters such as bis (2-ethylhexyl) sebacate is of significance for its use as a lubricant. This ester is synthesized by the transesterification of dimethyl sebacate with 2-ethylhexanol. Therefore, the solubilities of bis (2-ethylhexyl) sebacate and dimethyl sebacate were determined at 308-328 K at pressures of 10-18 MPa in supercritical carbon dioxide. The solubility of dimethyl sebacate was always higher than bis (2-ethylhexyl) sebacate at a given temperature and pressure. The Mendez-Teja model was used to verify the self-consistency of data. Further, a new semi-empirical model with three parameters was developed using the solution theory coupled with Wilson activity coefficient. This model was used to correlate the experimental data of this work and solubilities of many high molecular weight esters reported in the literature. (C) 2015 Elsevier B.V. All rights reserved.

Construction of Singer Subgroup Orbit Codes Based on Cyclic Difference Sets

A recent approach for the construction of constant dimension subspace codes, designed for error correction in random networks, is to consider the codes as orbits of suitable subgroups of the general linear group. In particular, a cyclic orbit code is the orbit of a cyclic subgroup. Hence a possible method to construct large cyclic orbit codes with a given minimum subspace distance is to select a subspace such that the orbit of the Singer subgroup satisfies the distance constraint. In this paper we propose a method where some basic properties of difference sets are employed to select such a subspace, thereby providing a systematic way of constructing cyclic orbit codes with specified parameters. We also present an explicit example of such a construction.

Experimental and numerical studies on protection of buried pipelines and underground utilities using geocells

This paper presents the results of the laboratory model tests and the numerical studies conducted on small diameter PVC pipes, buried in geocell reinforced sand beds. The aim of the study was to evaluate the suitability of the geocell reinforcement in protecting the underground utilities and buried pipelines. In addition to geocells, the efficacy of only geogrid and geocell with additional basal geogrid cases were also studied. A PVC (Poly Vinyl Chloride) pipe with external diameter 75 mm and thickness 1.4 mm was used in the experiments. The vehicle tire contact pressure was simulated by applying the pressure on the top of the bed with the help of a steel plate. Results suggest that the use of geocells with additional basal geogrid considerably reduces the deformation of the pipe as compared to other types of reinforcements. Further, the depth of placement of pipe was also varied between 1B to 2B (B is the width of loading plate) below the plate in the presence of geocell with additional basal geogrid. More than 50% reduction in the pressure and more than 40% reduction in the strain values were observed in the presence of reinforcements at different depths as compared to the unreinforced beds. Conversely, the performance of the subgrade soil was also found to be marginally influenced by the position of the pipe, even in the presence of the relatively stiff reinforcement system. Further, experimental results were validated with 3-dimensional numerical studies using FLAC(3D) (Fast Lagrangian Analysis of Continua in 3D). A good agreement in the measured pipe stain values were observed between the experimental and numerical studies. Numerical studies revealed that the geocells distribute the stresses in the lateral direction and thus reduce the pressure on the pipe. In addition, the results of the 1-g model tests were scaled up to the prototype case of the shallow buried pipeline below the pavement using the appropriate scaling laws. (C) 2015 Elsevier Ltd. All rights reserved.

Three-dimensional numerical analysis of geocell-reinforced soft clay beds by considering the actual geometry of geocell pockets

Due to its complex honeycomb structure, the numerical modeling of the geocell has always been a big challenge. Generally, the equivalent composite approach is used to model the geocells. In the equivalent composite approach, the geocellsoil composite is treated as the soil layer with improved strength and stiffness values. Though this approach is very simple, it is unrealistic to model the geocells as the soil layer. This paper presents a more realistic approach of modeling the geocells in three-dimensional (3D) framework by considering the actual curvature of the geocell pocket. A square footing resting on geocell reinforced soft clay bed was modeled using the ``fast Lagrangian analysis of continua in 3D'' (FLAC(3D)) finite difference package. Three different material models, namely modified Cam-clay, Mohr-Coulomb, and linear elastic were used to simulate the behaviour of foundation soil, infill soil and the geocell, respectively. It was found that the geocells distribute the load laterally to the wider area below the footing as compared to the unreinforced case. More than 50% reduction in the stress was observed in the clay bed in the presence of geocells. In addition to geocells, two other cases, namely, only geogrid and geocell with additional basal geogrid cases were also simulated. The numerical model was systematically validated with the results of the physical model tests. Using the validated numerical model, parametric studies were conducted to evaluate the influence of various geocell properties on the performance of reinforced clay beds.

Vacancy mediated clipping of multi-layered graphene: A precursor for 1, 2 and 3D carbon structures

Using first principles calculations, we show that the overlapping defects in bi-layer graphene (both AA-and AB-stacked) interact forming inter-layer covalent bonds, giving rise to two-dimensional (2D) clipped structures, without explicit use of functional groups. These clipped structures can be transformed into one-dimensional (1D) double wall nanotubes (DWCNT) or multi-layered three dimensional (3D) bulk structures. These clipped structures show good mechanical strength due to covalent bonding between multi-layers. Clipping also provides a unique way to simultaneously harness the conductivity of both walls of a double wall nanotube through covalently bonded scattering junctions. With additional conducting channels and improved mechanical stability, these clipped structures can lead to a myriad of applications in novel devices. (C) 2015 Elsevier Ltd. All rights reserved.

A survey on compressed domain video analysis techniques

Image and video analysis requires rich features that can characterize various aspects of visual information. These rich features are typically extracted from the pixel values of the images and videos, which require huge amount of computation and seldom useful for real-time analysis. On the contrary, the compressed domain analysis offers relevant information pertaining to the visual content in the form of transform coefficients, motion vectors, quantization steps, coded block patterns with minimal computational burden. The quantum of work done in compressed domain is relatively much less compared to pixel domain. This paper aims to survey various video analysis efforts published during the last decade across the spectrum of video compression standards. In this survey, we have included only the analysis part, excluding the processing aspect of compressed domain. This analysis spans through various computer vision applications such as moving object segmentation, human action recognition, indexing, retrieval, face detection, video classification and object tracking in compressed videos.

Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1

Following transmission, HIV-1 adapts in the new host by acquiring mutations that allow it to escape from the host immune response at multiple epitopes. It also reverts mutations associated with epitopes targeted in the transmitting host but not in the new host. Moreover, escape mutations are often associated with additional compensatory mutations that partially recover fitness costs. It is unclear whether recombination expedites this process of multi-locus adaptation. To elucidate the role of recombination, we constructed a detailed population dynamics model that integrates viral dynamics, host immune response at multiple epitopes through cytotoxic T lymphocytes, and viral evolution driven by mutation, recombination, and selection. Using this model, we compute the expected waiting time until the emergence of the strain that has gained escape and compensatory mutations against the new host's immune response, and reverted these mutations at epitopes no longer targeted. We find that depending on the underlying fitness landscape, shaped by both costs and benefits of mutations, adaptation proceeds via distinct dominant pathways with different effects of recombination, in particular distinguishing escape and reversion. When adaptation at a single epitope is involved, recombination can substantially accelerate immune escape but minimally affects reversion. When multiple epitopes are involved, recombination can accelerate or inhibit adaptation depending on the fitness landscape. Specifically, recombination tends to delay adaptation when a purely uphill fitness landscape is accessible at each epitope, and accelerate it when a fitness valley is associated with each epitope. Our study points to the importance of recombination in shaping the adaptation of HIV-1 following its transmission to new hosts, a process central to T cell-based vaccine strategies. (C) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license.

Future collider signatures of the possible 750 GeV state

If the recent indications of a possible state I broken vertical bar with mass similar to 750 GeV decaying into two photons reported by ATLAS and CMS in LHC collisions at 13 TeV were to become confirmed, the prospects for future collider physics at the LHC and beyond would be affected radically, as we explore in this paper. Even minimal scenarios for the I broken vertical bar resonance and its gamma gamma decays require additional particles with masses . We consider here two benchmark scenarios that exemplify the range of possibilities: one in which I broken vertical bar is a singlet scalar or pseudoscalar boson whose production and gamma gamma decays are due to loops of coloured and charged fermions, and another benchmark scenario in which I broken vertical bar is a superposition of (nearly) degenerate CP-even and CP-odd Higgs bosons in a (possibly supersymmetric) two-Higgs doublet model also with additional fermions to account for the gamma gamma decay rate. We explore the implications of these benchmark scenarios for the production of I broken vertical bar and its new partners at colliders in future runs of the LHC and beyond, at higher-energy pp colliders and at e (+) e (-) and gamma gamma colliders, with emphasis on the bosonic partners expected in the doublet scenario and the fermionic partners expected in both scenarios.

PIB: Profiling Influential Blogger in Online Social Networks, A Knowledge Driven Data Mining Approach

Online Social Networks (OSNs) facilitate to create and spread information easily and rapidly, influencing others to participate and propagandize. This work proposes a novel method of profiling Influential Blogger (IB) based on the activities performed on one's blog documents who influences various other bloggers in Social Blog Network (SBN). After constructing a social blogging site, a SBN is analyzed with appropriate parameters to get the Influential Blog Power (IBP) of each blogger in the network and demonstrate that profiling IB is adequate and accurate. The proposed Profiling Influential Blogger (PIB) Algorithm survival rate of IB is high and stable. (C) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Flood Routing Models in Confluent and Dividing Channels

By introducing a water depth connecting formula, the hydraulic equations in the dividing channel system were coupled and the relation of discharge distribution between the branches of the dividing channels can be yielded. In this manner, a numerical model for the confluent channels was established to study the variation of backwater effects with the parameters in the channel junction. The meeting of flood peaks in the mainstream and tributary can be analyzed with this model. The flood peak meeting is found to be a major factor for the extremely high water level in the mainstream during the 1998 Yangtze River flood. Subsequently the variations of discharge distribution and water level with channel parameters between each branch in this system were studied as well. As a result, flood evolution caused by Jingjiang River shortcut and sediment deposition in the entrance of dividing channels of the Yangtze River may be qualitatively elucidated. It is suggested to be an effective measure for flood mitigation to enhance regulation capability of reservoirs available upstream of the tributaries and harness branch entrance channels.

A constitutive model for transversely isotropic foams, and its application to the indentation of balsa wood

An elastic-plastic constitutive model for transversely isotropic compressible solids (foams) has been developed. A quadratic yield surface with four parameters and one hardening function is proposed. Associated plastic flow is assumed and the yield surface evolves in a self-similar manner calibrated by the uniaxial compressive (or tensile) response of the cellular solid in the axial direction. All material constants in the model (elastic and plastic) can be determined from a combination of a total of four uniaxial and shear tests. The model is used to predict the indentation response of balsa wood to a conical indenter. For the three cone angles considered in this study, very good agreement is found between the experimental measurements and the finite element (FE) predictions of the transversely isotropic cellular solid model. On the other hand, an isotropic foam model is shown to be inadequate to capture the indentation response. © 2005 Elsevier Ltd. All rights reserved.