Structure-function relationships of icosahedral plant viruses

X-ray diffraction studies on single crystals of a few viruses have led to the elucidation of their three dimensional structure at near atomic resolution. Both the tertiary structure of the coat protein subunit and the quaternary morganization of the icosahedral capsid in these viruses are remarkably similar. These studies have led to a critical re-examination of the structural principles in the architecture of isometric viruses and suggestions of alternative mechanisms of assembly. Apart from their role in the assembly of the virus particle, the coat proteins of certian viruses have been shown to inhibit the replication of the cognate RNA leading to cross-protection. The coat protein amino acid sequence and the genomic sequence of several spherical plant RNA viruses have been determined in the last decade. Experimental data on the mechanisms of uncoating, gene expression and replication of several classes of viruses have also become available. The function of the non-structural proteins of some viruses have been determined. This rapid progress has provided a wealth of information on several key steps in the life cycle of RNA viruses. The function of the viral coat protein, capsid architecture, assembly and disassembly and replication of isometric RNA plant viruses are discussed in the light of this accumulated knowledge.

Texts "Con and Pro" : The Early Modern Medical Controversy over Tobacco

The habit of "drinking smoke" , meaning tobacco smoking, caused a true controversy in early modern England. The new substance was used both for its alleged therapeutic properties as well as its narcotic effects. The dispute over tobacco continues the line of written controversies which were an important means of communication in the sixteenth and seventeenth century Europe. The tobacco controversy is special among medical controversies because the recreational use of tobacco soon spread and outweighed its medicinal use, ultimately causing a social and cultural crisis in England. This study examines how language is used in polemic discourse and argumentation. The material consists of medical texts arguing for and against tobacco in early modern England. The texts were compiled into an electronic corpus of tobacco texts (1577 1670) representing different genres and styles of writing. With the help of the corpus, the tobacco controversy is described and analyzed in the context of early modern medicine. A variety of methods suitable for the study of conflict discourse were used to assess internal and external text variation. The linguistic features examined include personal pronouns, intertextuality, structural components, and statistically derived keywords. A common thread in the work is persuasive language use manifested, for example, in the form of emotive adjectives and the generic use of pronouns; the latter is especially pronounced in the dichotomy between us and them. Controversies have not been studied in this manner before but the methods applied have supplemented each other and proven their suitability in the study of conflictive discourse. These methods can also be applied to present-day materials.

Bayesian Learning for Joint Sparse OFDM Channel Estimation and Data Detection

The impulse response of a typical wireless multipath channel can be modeled as a tapped delay line filter whose non-zero components are sparse relative to the channel delay spread. In this paper, a novel method of estimating such sparse multipath fading channels for OFDM systems is explored. In particular, Sparse Bayesian Learning (SBL) techniques are applied to jointly estimate the sparse channel and its second order statistics, and a new Bayesian Cramer-Rao bound is derived for the SBL algorithm. Further, in the context of OFDM channel estimation, an enhancement to the SBL algorithm is proposed, which uses an Expectation Maximization (EM) framework to jointly estimate the sparse channel, unknown data symbols and the second order statistics of the channel. The EM-SBL algorithm is able to recover the support as well as the channel taps more efficiently, and/or using fewer pilot symbols, than the SBL algorithm. To further improve the performance of the EM-SBL, a threshold-based pruning of the estimated second order statistics that are input to the algorithm is proposed, and its mean square error and symbol error rate performance is illustrated through Monte-Carlo simulations. Thus, the algorithms proposed in this paper are capable of obtaining efficient sparse channel estimates even in the presence of a small number of pilots.

Role of elasto-plastic analysis under cyclic loading in fatigue crack growth studies

Linear Elastic Fracture Mechanics (LEFM) has been widely used in the past for fatigue crack growth studies, but this is acceptable only in situations which are within small scale yielding (SSY). In many practical structural components, conditions of SSY could be violated and one has to look for fracture criteria based on elasto-plastic analysis. Crack closure phenomenon, one of the most striking discoveries based on inelastic deformations during crack growth, has significant effect on fatigue crack growth rate. Numerical simulation of this phenomenon is computationally intensive and involved but has been successfully implemented. Stress intensity factors and strain energy release rates lose their meaning, J-integral (or its incremental) values are applicable only in specific situations, whereas alternate path independent integrals have been proposed in the literature for use with elasto-plastic fracture mechanics (EPFM) based criteria. This paper presents certain salient features of two independent finite element (numerical) studies of relevance to fatigue crack growth, where elasto-plastic analysis becomes significant. These problems can only be handled in the current day computational environment, and would have been only a dream just a few years ago.

Energy absorption behaviours of CSM-based GFRC plates with hemispherical features

In the present study, the mechanical behaviour of CSM (chopped strand mat)-based GFRC (glass fibre-reinforced composite) plates with single and multiple hemispheres under compressive loads has been investigated both experimentally and numerically. The basic stress-strain behaviours arc identified with quasi-static tests on two-ply coupon laminates and short cylinders, and these are followed up with compressive tests in a UTM (universal testing machine) on single- and multiple-hemisphere plates. The ability of an explicit LS-DYNA solver in predicting the complex material behaviour of composite hemispheres, including failure, is demonstrated. The relevance and scalability of the present class of structural components as `force-multipliers' and `energy-multipliers' have been justified by virtue of findings that as the number of hemispheres in a panel increased from one to four, peak load and average absorbed energy rose by factors of approximately four and six, respectively. The performance of a composite hemisphere has been compared to similar-sized steel and aluminium hemispheres, and the former is found to be of distinctly higher specific energy than the steel specimen. A simulation-based study has also been carried out on a composite 2 x 2-hemisphere panel under impact loads and its behaviour approaching that of an ideal energy absorber has been predicted. In summary, the present investigation has established the efficacy of composite plates with hemispherical force multipliers as potential energy-absorbing countermeasures and the suitability of CAE (computer-aided engineering) for their design.

A Novel Property of DNA - As a Bioflotation Reagent in Mineral Processing

Environmental concerns regarding the use of certain chemicals in the froth flotation of minerals have led investigators to explore biological entities as potential substitutes for the reagents in vogue. Despite the fact that several microorganisms have been used for the separation of a variety of mineral systems, a detailed characterization of the biochemical molecules involved therein has not been reported so far. In this investigation, the selective flotation of sphalerite from a sphalerite-galena mineral mixture has been achieved using the cellular components of Bacillus species. The key constituent primarily responsible for the flotation of sphalerite has been identified as DNA, which functions as a bio-collector. Furthermore, using reconstitution studies, the obligatory need for the presence of non-DNA components as bio-depressants for galena has been demonstrated. A probable model involving these entities in the selective flotation of sphalerite from the mineral mixture has been discussed.

Fracture Analysis of High strength and Ultra high strength Concrete beams by using Finite Element Method

This paper presents the details of nonlinear finite element analysis (FEA) of three point bending specimens made up of high strength concrete (HSC, HSC1) and ultra high strength concrete (UHSC). Brief details about characterization and experimentation of HSC, HSC1 and UHSC have been provided. Cracking strength criterion has been used for simulation of crack propagation by conducting nonlinear FEA. The description about FEA using crack strength criterion has been outlined. Bi-linear tension softening relation has been used for modeling the cohesive stresses ahead of the crack tip. Numerical studies have been carried out on fracture analysis of three point bending specimens. It is observed from the studies that the computed values from FEA are in very good agreement with the corresponding experimental values. The computed values of stress vs crack width will be useful for evaluation of fracture energy, crack tip opening displacement and fracture toughness. Further, these values can also be used for crack growth study, remaining life assessment and residual strength evaluation of concrete structural components.

Phospholipid Mediated Activation of Calcium Dependent Protein Kinase 1 (CaCDPK1) from Chickpea: A New Paradigm of Regulation

Phospholipids, the major structural components of membranes, can also have functions in regulating signaling pathways in plants under biotic and abiotic stress. The effects of adding phospholipids on the activity of stress-induced calcium dependent protein kinase (CaCDPK1) from chickpea are reported here. Both autophosphorylation as well as phosphorylation of the added substrate were enhanced specifically by phosphatidylcholine and to a lesser extent by phosphatidic acid, but not by phosphatidylethanolamine. Diacylgylerol, the neutral lipid known to activate mammalian PKC, stimulated CaCDPK1 but at higher concentrations. Increase in V-max of the enzyme activity by these phospholipids significantly decreased the K-m indicating that phospholipids enhance the affinity towards its substrate. In the absence of calcium, addition of phospholipids had no effect on the negligible activity of the enzyme. Intrinsic fluorescence intensity of the CaCDPK1 protein was quenched on adding PA and PC. Higher binding affinity was found with PC (K-1/2 = 114 nM) compared to PA (K-1/2 = 335 nM). We also found that the concentration of PA increased in chickpea plants under salt stress. The stimulation by PA and PC suggests regulation of CaCDPK1 by these phospholipids during stress response.

Evaluation of Fracture Parameters by Double-G, Double-K Models and Crack Extension Resistance for High Strength and Ultra High Strength Concrete Beams

This paper presents the advanced analytical methodologies such as Double- G and Double - K models for fracture analysis of concrete specimens made up of high strength concrete (HSC, HSC1) and ultra high strength concrete. Brief details about characterization and experimentation of HSC, HSC1 and UHSC have been provided. Double-G model is based on energy concept and couples the Griffith's brittle fracture theory with the bridging softening property of concrete. The double-K fracture model is based on stress intensity factor approach. Various fracture parameters such as cohesive fracture toughness (4), unstable fracture toughness (K-Ic(c)), unstable fracture toughness (K-Ic(un)) and initiation fracture toughness (K-Ic(ini)) have been evaluated based on linear elastic fracture mechanics and nonlinear fracture mechanics principles. Double-G and double-K method uses the secant compliance at the peak point of measured P-CMOD curves for determining the effective crack length. Bi-linear tension softening model has been employed to account for cohesive stresses ahead of the crack tip. From the studies, it is observed that the fracture parameters obtained by using double - G and double - K models are in good agreement with each other. Crack extension resistance has been estimated by using the fracture parameters obtained through double - K model. It is observed that the values of the crack extension resistance at the critical unstable point are almost equal to the values of the unstable fracture toughness K-Ic(un) of the materials. The computed fracture parameters will be useful for crack growth study, remaining life and residual strength evaluation of concrete structural components.

OTCYMIST: Otsu-Canny minimal spanning tree for born-digital images

Text segmentation and localization algorithms are proposed for the born-digital image dataset. Binarization and edge detection are separately carried out on the three colour planes of the image. Connected components (CC's) obtained from the binarized image are thresholded based on their area and aspect ratio. CC's which contain sufficient edge pixels are retained. A novel approach is presented, where the text components are represented as nodes of a graph. Nodes correspond to the centroids of the individual CC's. Long edges are broken from the minimum spanning tree of the graph. Pair wise height ratio is also used to remove likely non-text components. A new minimum spanning tree is created from the remaining nodes. Horizontal grouping is performed on the CC's to generate bounding boxes of text strings. Overlapping bounding boxes are removed using an overlap area threshold. Non-overlapping and minimally overlapping bounding boxes are used for text segmentation. Vertical splitting is applied to generate bounding boxes at the word level. The proposed method is applied on all the images of the test dataset and values of precision, recall and H-mean are obtained using different approaches.

Guided Ultrasonic Wave Propagation through Inaccessible Damage in a Folded Plate using Sensor-Actuator Network

Rapid diagnostics and virtual imaging of damages in complex structures like folded plate can help reduce the inspection time for guided wave based NDE and integrated SHM. Folded plate or box structure is one of the major structural components for increasing the structural strength. Damage in the folded plate, mostly in the form of surface breaking cracks in the inaccessible zone is a usual problem in aerospace structures. One side of the folded plate is attached (either riveted or bonded) to adjacent structure which is not accessible for immediate inspection. The sensor-actuator network in the form of a circular array is placed on the accessible side of the folded plate. In the present work, a circular array is employed for scanning the entire folded plate type structure for damage diagnosis and wave field visualization of entire structural panel. The method employs guided wave with relatively low frequency bandwidth of 100-300 kHz. Change in the response signal with respect to a baseline signal is used to construct a quantitative relationship with damage size parameters. Detecting damage in the folded plate by using this technique has significant potential for off-line and on-line SHM technologies. By employing this technique, surface breaking cracks on inaccessible face of the folded plate are detected without disassembly of structure in a realistic environment.

Groundnut Bud Necrosis Virus Encoded NSm Associates with Membranes via Its C-Terminal Domain

Groundnut Bud Necrosis Virus (GBNV) is a tripartite ambisense RNA plant virus that belongs to serogroup IV of Tospovirus genus. Non-Structural protein-m (NSm), which functions as movement protein in tospoviruses, is encoded by the M RNA. In this communication, we demonstrate that despite the absence of any putative transmembrane domain, GBNV NSm associates with membranes when expressed in E. coli as well as in N. benthamiana. Incubation of refolded NSm with liposomes ranging in size from 200-250 nm resulted in changes in the secondary and tertiary structure of NSm. A similar behaviour was observed in the presence of anionic and zwitterionic detergents. Furthermore, the morphology of the liposomes was found to be modified in the presence of NSm. Deletion of coiled coil domain resulted in the inability of in planta expressed NSm to interact with membranes. Further, when the C-terminal coiled coil domain alone was expressed, it was found to be associated with membrane. These results demonstrate that NSm associates with membranes via the C-terminal coiled coil domain and such an association may be important for movement of viral RNA from cell to cell.

Synthesis, characterization and low temperature electrical conductivity of Polyaniline/NiFe2O4 nanocomposites

Conducting polymer/ferrite nanocomposites with an organized structure provide a new functional hybrid between organic and inorganic materials. The most popular among the conductive polymers is the polyaniline (PANI) due to its wide application in different fields. In the present work nickel ferrite (NiFe2O4) nanoparticles were prepared by sol-gel citrate-nitrate method with an average size of 21.6nm. PANI/NiFe2O4 nanoparticles were synthesized by a simple general and inexpensive in-situ polymerization in the presence of NiFe2O4 nanoparticles. The effects of NiFe2O4 nanoparticles on the dc-electrical properties of polyaniline were investigated. The structural components in the nanocomposites were identified from Fourier Transform Infrared (FTIR) spectroscopy. The crystalline phase of nanocomposites was characterized by X-Ray Diffraction (XRD). The Scanning Electron Micrograph (SEM) reveals that there was some interaction between the NiFe2O4 particles and polyaniline and the nanocomposites are composed of polycrystalline ferrite nanoparticles and PANI. The dc conductivity of polyaniline/NiFe2O4 nanocomposites have been measured as a function of temperature in the range of 80K to 300K. It is observed that the room temperature conductivity sigma(RT) decreases with increase in the relative content of NiFe2O4. The experimental data reveals that the resistivity increases for all composites with decrease of temperature exhibiting semiconductor behaviour.

GBNV encoded movement protein (NSm) remodels ER network via C-terminal coiled coil domain

Plant viruses exploit the host machinery for targeting the viral genome-movement protein complex to plasmodesmata (PD). The mechanism by which the non-structural protein m (NSm) of Groundnut bud necrosis virus (GBNV) is targeted to PD was investigated using Agrobacterium mediated transient expression of NSm and its fusion proteins in Nicotiana benthamiana. GFP:NSm formed punctuate structures that colocalized with mCherry:plasmodesmata localized protein la (PDLP la) confirming that GBNV NSm localizes to PD. Unlike in other movement proteins, the C-terminal coiled coil domain of GBNV NSm was shown to be involved in the localization of NSm to PD, as deletion of this domain resulted in the cytoplasmic localization of NSm. Treatment with Brefeldin A demonstrated the role of ER in targeting GFP NSm to PD. Furthermore, mCherry:NSm co-localized with ER-GFP (endoplasmic reticulum targeting peptide (HDEL peptide fused with GFP). Co-expression of NSm with ER-GFP showed that the ER-network was transformed into vesicles indicating that NSm interacts with ER and remodels it. Mutations in the conserved hydrophobic region of NSm (residues 130-138) did not abolish the formation of vesicles. Additionally, the conserved prolines at positions 140 and 142 were found to be essential for targeting the vesicles to the cell membrane. Further, systematic deletion of amino acid residues from N- and C-terminus demonstrated that N-terminal 203 amino acids are dispensable for the vesicle formation. On the other hand, the C-terminal coiled coil domain when expressed alone could also form vesicles. These results suggest that GBNV NSm remodels the ER network by forming vesicles via its interaction through the C-terminal coiled coil domain. Interestingly, NSm interacts with NP in vitro and coexpression of these two proteins in planta resulted in the relocalization of NP to PD and this relocalization was abolished when the N-terminal unfolded region of NSm was deleted. Thus, the NSm interacts with NP via its N-terminal unfolded region and the NSm-NP complex could in turn interact with the ER membrane via the C-terminal coiled coil domain of NSm to form vesicles that are targeted to PD and there by assist the cell to cell movement of the viral genome complex. (C) 2015 Elsevier Inc. All rights reserved.

Damage Detection Sensitivity, Specificity and Classification Data Analysis for SHM Systems Design, Verification and Validation

In this paper, we consider applying derived knowledge base regarding the sensitivity and specificity of damage(s) to be detected by an SHM system being designed and qualified. These efforts are necessary toward developing capabilities in SHM system to classify reliably various probable damages through sequence of monitoring, i.e., damage precursor identification, detection of damage and monitoring its progression. We consider the particular problem of visual and ultrasonic NDE based SHM system design requirements, where the damage detection sensitivity and specificity data definitions for a class of structural components are established. Methodologies for SHM system specification creation are discussed in details. Examples are shown to illustrate how the physics of damage detection scheme limits particular damage detection sensitivity and specificity and further how these information can be used in algorithms to combine various different NDE schemes in an SHM system to enhance efficiency and effectiveness. Statistical and data driven models to determine the sensitivity and probability of damage detection (POD) has been demonstrated for plate with varying one-sided line crack using optical and ultrasonic based inspection techniques.