Noniterative inversion strategy for photoacoustic tomography: recovery of absorbed energy map from boundary pressure measurements

The inverse problem in photoacoustic tomography (PAT) seeks to obtain the absorbed energy map from the boundary pressure measurements for which computationally intensive iterative algorithms exist. The computational challenge is heightened when the reconstruction is done using boundary data split into its frequency spectrum to improve source localization and conditioning of the inverse problem. The key idea of this work is to modify the update equation wherein the Jacobian and the perturbation in data are summed over all wave numbers, k, and inverted only once to recover the absorbed energy map. This leads to a considerable reduction in the overall computation time. The results obtained using simulated data, demonstrates the efficiency of the proposed scheme without compromising the accuracy of reconstruction.

The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence

While phosphotyrosine modification is an established regulatory mechanism in eukaryotes, it is less well characterized in bacteria due to low prevalence. To gain insight into the extent and biological importance of tyrosine phosphorylation in Escherichia coli, we used immunoaffinity-based phosphotyrosine peptide enrichment combined with high resolution mass spectrometry analysis to comprehensively identify tyrosine phosphorylated proteins and accurately map phosphotyrosine sites. We identified a total of 512 unique phosphotyrosine sites on 342 proteins in E. coli K12 and the human pathogen enterohemorrhagic E. coli (EHEC) O157:H7, representing the largest phosphotyrosine proteome reported to date in bacteria. This large number of tyrosine phosphorylation sites allowed us to define five phosphotyrosine site motifs. Tyrosine phosphorylated proteins belong to various functional classes such as metabolism, gene expression and virulence. We demonstrate for the first time that proteins of a type III secretion system (T3SS), required for the attaching and effacing (A/E) lesion phenotype characteristic for intestinal colonization by certain EHEC strains, are tyrosine phosphorylated by bacterial kinases. Yet, A/E lesion and metabolic phenotypes were unaffected by the mutation of the two currently known tyrosine kinases, Etk and Wzc. Substantial residual tyrosine phosphorylation present in an etk wzc double mutant strongly indicated the presence of hitherto unknown tyrosine kinases in E. coli. We assess the functional importance of tyrosine phosphorylation and demonstrate that the phosphorylated tyrosine residue of the regulator SspA positively affects expression and secretion of T3SS proteins and formation of A/E lesions. Altogether, our study reveals that tyrosine phosphorylation in bacteria is more prevalent than previously recognized, and suggests the involvement of phosphotyrosine-mediated signaling in a broad range of cellular functions and virulence.

Higher-Dimensional Analogues of the Map Coloring Problem

After a brief discussion of the history of the problem, we propose a generalization of the map coloring problem to higher dimensions.

A Multicast Authentication Protocol (MAP) for Dynamic Multicast Groups in Wireless Networks

In this paper, we have proposed a centralized multicast authentication protocol (MAP) for dynamic multicast groups in wireless networks. In our protocol, a multicast group is defined only at the time of the multicasting. The authentication server (AS) in the network generates a session key and authenticates it to each of the members of a multicast group using the computationally inexpensive least common multiple (LCM) method. In addition, a pseudo random function (PRF) is used to bind the secret keys of the network members with their identities. By doing this, the AS is relieved from storing per member secrets in its memory, making the scheme completely storage scalable. The protocol minimizes the load on the network members by shifting the computational tasks towards the AS node as far as possible. The protocol possesses a membership revocation mechanism and is protected against replay attack and brute force attack. Analytical and simulation results confirm the effectiveness of the proposed protocol.

Incorporation of Interfacial Intermetallic Morphology in Fracture Mechanism Map for Sn-Ag-Cu Solder Joints

A fracture mechanism map (FMM) is a powerful tool which correlates the fracture behavior of a material to its microstructural characteristics in an explicit and convenient way. In the FMM for solder joints, an effective thickness of the interfacial intermetallic compound (IMC) layer (t (eff)) and the solder yield strength (sigma (ys,eff)) are used as abscissa and ordinate axes, respectively, as these two predominantly affect the fracture behavior of solder joints. Earlier, a definition of t (eff), based on the uniform thickness of IMC (t (u)) and the average height of the IMC scallops (t (s)), was proposed and shown to aptly explain the fracture behavior of solder joints on Cu. This paper presents a more general definition of t (eff) that is more widely applicable to a range of metallizations, including Cu and electroless nickel immersion gold (ENIG). Using this new definition of t (eff), mode I FMM for SAC387/Cu joints has been updated and its validity was confirmed. A preliminary FMM for SAC387/Cu joints with ENIG metallization is also presented.

Imaging cellular signalling: many `moving tales' in MAP kinase odyssey

Cellular signalling events are at the core of every adaptive response. Signalling events link environmental changes to physiological responses, consequently allowing cellular and organismal sustenance and survival. Classical approaches to study cellular signalling have relied on a variety of cell disruptive techniques which yield limited kinetic information, while the underlying events are much more complex. In this article, we discuss how modern live cell imaging microscopy has found increasing utilization in revealing spatio temporal dynamics of various signalling pathways. Utilizing the well studied mitogen-activated protein kinase (MAPK) signalling cascade as a template, the design, construction and utilization of `mobile' (translocation proficient) biosensors, suitable for studying MAPK signalling in living cells are described in detail. Experimental setup and results obtained from these biosensors, based on different proteins involved in the MAPK signalling cascade, have been described along with the setup of a microscope optimal for live cell imaging applications. Utilizing the ability to activate or deactivate signalling pathways using defined activators and specific pharmacological inhibitors, we also show how these sensors can yield unique spatial and temporal kinetic information of signalling in living cells.

Representative seismic hazard map of Coimbatore, India

The seismic hazard value of any region depends upon three important components such as probable earthquake location, maximum earthquake magnitude and the attenuation equation. This paper presents a representative way of estimating these three important components considering region specific seismotectonic features. Rupture Based Seismic Hazard Analysis (RBSHA) given by Anbazhagan et al. (2011) is used to determine the probable future earthquake locations. This approach is verified on the earthquake data of Bhuj region. The probable earthquake location for this region is identified considering earthquake data till the year 2000. These identified locations match well with the reported locations after 2000. The further Coimbatore City is selected as the study area to develop a representative seismic hazard map using RBSHA approach and to compare with deterministic seismic hazard analysis. Probable future earthquake zones for Coimbatore are located considering the rupture phenomenon as per energy release theory discussed by Anbazhagan et at (2011). Rupture character of the region has been established by estimating the subsurface rupture length of each source and normalized with respect to the length of the source. Average rupture length of the source with respect to its total length is found to be similar for most of the sources in the region, which is called as the rupture character of the region. Maximum magnitudes of probable zones are estimated considering seismic sources close by and regional rupture character established. Representative GMPEs for the study area have been selected by carrying out efficacy test through an average log likelihood value (LLH) as ranking estimator and considering the Isoseismal map. New seismic hazard map of Coimbatore has been developed using the above regional representative parameters of probable earthquake locations, maximum earthquake magnitude and best suitable GMPEs. The new hazard map gives acceleration values at bedrock for maximum possible earthquakes. These results are compared with deterministic seismic hazard map and recently published probabilistic seismic hazard values. (C) 2014 Elsevier B.V. All rights reserved.

NON-GLYCINE RESIDUES IN THE DISALLOWED REGIONS OF THE RAMACHANDRAN MAP AND THEIR NEIGHBORHOOD PREFERENCES

The allowed and the ``disallowed'' regions in the celebrated Ramachandran map (phi-psi] map) was elegantly deduced by Ramachandran, Ramakrishnan and Sasisekharan even before the protein crystal structures became available. This powerful map was derived based on rigid geometry of the peptide group and later several investigations on protein crystal structures reported the occurrence of a small fraction of the phi-psi] torsion angles in the disallowed region. The question is what factors make these residues adopt disallowed conformations? Is it driven by the necessity to maintain the overall topology or is it associated with function or is it just that the disallowed conformations are extreme limits of the allowed conformations? Today, with the availability of a large number of high resolution crystal structures, we have revisited this problem. Apart from validating some of the earlier findings such as residue propensities, preferred location in the secondary structure, we have explored their spatial neighborhood preferences using the protein structure network PSN] approach developed in our lab. Finally, the structural and functional implications of the disallowed conformations are examined.

PROPENSITIES OF AMINO ACID RESIDUES IN PROTEINS FOR DIFFERENT REGIONS OF THE RAMACHANDRAN MAP

Using a dataset of 1164 crystal structures of largely non-homologous proteins defined at a resolution of 1.5 angstrom or better, we have investigated the (phi,psi) preferences of 20 residue types by considering the residues which occur in loops. Propensities of residue types to occur in the loops with (phi,psi) values in the aa region of the Ramachandran map has a poor correlation coefficient of 0.48 to the Chou-Fasman propensities of the residue types to occur in the a-helical segments. However the correlation coefficient between propensities of residues in loops to adopt beta conformations and those in beta-sheet is much higher (0.95). These observations suggest that a-helix formation is well influenced by the local amino acid sequence while intrinsic preference of residue types for beta-sheet plays a major role in the formation of beta-sheet. The main chain polar groups of residues in loops, that can affect the (phi,psi) values, can be involved in intra-molecular hydrogen bonding. Therefore we investigated further by considering subset of residues in loops with low (0 to 2) number of intra-molecular hydrogen bonds per residue involving main chain polar atoms. For this subset, the correlation coefficients between propensities for alpha-helix and alpha(R) region and between beta-sheet and beta-region are 0.26 and 0.64 respectively. This reiterates higher intrinsic tendency of beta-region favouring residues to adopt beta-sheet than alpha(R) region favouring residues to adopt alpha-helical structure.

HupB, a Nucleoid-Associated Protein of Mycobacterium tuberculosis, Is Modified by Serine/Threonine Protein Kinases In Vivo

HU, a widely conserved bacterial histone-like protein, regulates many genes, including those involved in stress response and virulence. Whereas ample data are available on HU-DNA communication, the knowledge on how HU perceives a signal and transmit it to DNA remains limited. In this study, we identify HupB, the HU homolog of the human pathogen Mycobacterium tuberculosis, as a component of serine/threonine protein kinase (STPK) signaling. HupB is extracted in its native state from the exponentially growing cells of M. tuberculosis H37Ra and is shown to be phosphorylated on both serine and threonine residues. The STPKs capable of modifying HupB are determined in vitro and the residues modified by the STPKs are identified for both in vivo and the in vitro proteins through mass spectrometry. Of the identified phosphosites, Thr(65) and Thr(74) in the DNA-embracing beta-strand of the N-terminal domain of HupB (N-HupB) are shown to be crucial for its interaction with DNA. In addition, Arg(55) is also identified as an important residue for N-HupB-DNA interaction. N-HupB is shown to have a diminished interaction with DNA after phosphorylation. Furthermore, hupB is shown to be maximally expressed during the stationary phase in M. tuberculosis H37Ra, while HupB kinases were found to be constitutively expressed (PknE and PknF) or most abundant during the exponential phase (PknB). In conclusion, HupB, a DNA-binding protein, with an ability to modulate chromatin structure is proposed to work in a growth-phase-dependent manner through its phosphorylation carried out by the mycobacterial STPKs.

Hot deformation behavior of Ni-Fe-Ga-based ferromagnetic shape memory alloy - A study using processing map

Ni-Fe-Ga-based alloys form a new class of ferromagnetic shape memory alloys (FSMAs) that show considerable formability because of the presence of a disordered fcc gamma-phase. The current study explores the deformation processing of this alloy using an off-stoichiometric Ni55Fe59Ga26 alloy that contains the ductile gamma-phase. The hot deformation behavior of this alloy has been characterized on the basis of its flow stress variation obtained by isothermal constant true strain rate compression tests in the 1123-1323 K temperature range and strain rate range of 10(-3)-10 s(-1) and using a combination of constitutive modeling and processing map. The dynamic recrystallization (DRX) regime for thermomechanical processing has been identified for this Heusler alloy on the basis of the processing maps and the deformed microstructures. This alloy also shows evidence of dynamic strain-aging (DSA) effect which has not been reported so far for any Heusler FSMAs. Similar effect is also noticed in a Ni-Mn-Ga-based Heusler alloy which is devoid of any gamma-phase. (C) 2014 Elsevier Ltd. All rights reserved.

Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes

The highly modular nature of protein kinases generates diverse functional roles mediated by evolutionary events such as domain recombination, insertion and deletion of domains. Usually domain architecture of a kinase is related to the subfamily to which the kinase catalytic domain belongs. However outlier kinases with unusual domain architectures serve in the expansion of the functional space of the protein kinase family. For example, Src kinases are made-up of SH2 and SH3 domains in addition to the kinase catalytic domain. A kinase which lacks these two domains but retains sequence characteristics within the kinase catalytic domain is an outlier that is likely to have modes of regulation different from classical src kinases. This study defines two types of outlier kinases: hybrids and rogues depending on the nature of domain recombination. Hybrid kinases are those where the catalytic kinase domain belongs to a kinase subfamily but the domain architecture is typical of another kinase subfamily. Rogue kinases are those with kinase catalytic domain characteristic of a kinase subfamily but the domain architecture is typical of neither that subfamily nor any other kinase subfamily. This report provides a consolidated set of such hybrid and rogue kinases gleaned from six eukaryotic genomes-S. cerevisiae, D. melanogaster, C. elegans, M. musculus, T. rubripes and H. sapiens-and discusses their functions. The presence of such kinases necessitates a revisiting of the classification scheme of the protein kinase family using full length sequences apart from classical classification using solely the sequences of kinase catalytic domains. The study of these kinases provides a good insight in engineering signalling pathways for a desired output. Lastly, identification of hybrids and rogues in pathogenic protozoa such as P. falciparum sheds light on possible strategies in host-pathogen interactions.

Development of a global inundation map at high spatial resolution from topographic downscaling of coarse-scale remote sensing data

Large-scale estimates of the area of terrestrial surface waters have greatly improved over time, in particular through the development of multi-satellite methodologies, but the generally coarse spatial resolution (tens of kms) of global observations is still inadequate for many ecological applications. The goal of this study is to introduce a new, globally applicable downscaling method and to demonstrate its applicability to derive fine resolution results from coarse global inundation estimates. The downscaling procedure predicts the location of surface water cover with an inundation probability map that was generated by bagged derision trees using globally available topographic and hydrographic information from the SRTM-derived HydroSHEDS database and trained on the wetland extent of the GLC2000 global land cover map. We applied the downscaling technique to the Global Inundation Extent from Multi-Satellites (GIEMS) dataset to produce a new high-resolution inundation map at a pixel size of 15 arc-seconds, termed GIEMS-D15. GIEMS-D15 represents three states of land surface inundation extents: mean annual minimum (total area, 6.5 x 10(6) km(2)), mean annual maximum (12.1 x 10(6) km(2)), and long-term maximum (173 x 10(6) km(2)); the latter depicts the largest surface water area of any global map to date. While the accuracy of GIEMS-D15 reflects distribution errors introduced by the downscaling process as well as errors from the original satellite estimates, overall accuracy is good yet spatially variable. A comparison against regional wetland cover maps generated by independent observations shows that the results adequately represent large floodplains and wetlands. GIEMS-D15 offers a higher resolution delineation of inundated areas than previously available for the assessment of global freshwater resources and the study of large floodplain and wetland ecosystems. The technique of applying inundation probabilities also allows for coupling with coarse-scale hydro-climatological model simulations. (C) 2014 Elsevier Inc All rights reserved.

High-Temperature Deformation Processing Map Approach for Obtaining the Desired Microstructure in a Multi-component (Ni-Ti-Cu-Fe) Alloy

An equiatomic NiTiCuFe multi-component alloy with simple body-centered cubic (bcc) and face-centered cubic solid-solution phases in the microstructure was processed by vacuum induction melting furnace under dynamic Ar atmosphere. High-temperature uniaxial compression experiments were conducted on it in the temperature range of 1073 K to 1303 K (800 degrees C to 1030 degrees C) and strain rate range of 10(-3) to 10(-1) s(-1). The data generated were analyzed with the aid of the dynamic materials model through which power dissipation efficiency and instability maps were generated so as to identify the governing deformation mechanisms that are operative in different temperature-strain rate regimes with the aid of complementary microstructural analysis of the deformed specimens. Results indicate that the stable domain for the high temperature deformation of the multi-component alloy occurs in the temperature range of 1173 K to 1303 K (900 degrees C to 1030 degrees C) and (epsilon) over dot range of 10(-3) to 10(-1.2) s(-1), and the deformation is unstable at T = 1073 K to 1153 K (800 degrees C to 880 degrees C) and (epsilon) over dot = 10(-3) to 10(-1.4) s(-1) as well as T = 1223 K to 1293 K (950 degrees C to 1020 degrees C) and (epsilon) over dot = 10(-1.4) to 10(-1) s(-1), with adiabatic shear banding, localized plastic flow, or cracking being the unstable mechanisms. A constitutive equation that describes the flow stress of NiTiCuFe multi-component alloy as a function of strain rate and deformation temperature was also determined. (C) The Minerals, Metals & Materials Society and ASM International 2015

A Gaussian network model study suggests that structural fluctuations are higher for inactive states than active states of protein kinases

We performed Gaussian network model based normal mode analysis of 3-dimensional structures of multiple active and inactive forms of protein kinases. In 14 different kinases, a more number of residues (1095) show higher structural fluctuations in inactive states than those in active states (525), suggesting that, in general, mobility of inactive states is higher than active states. This statistically significant difference is consistent with higher crystallographic B-factors and conformational energies for inactive than active states, suggesting lower stability of inactive forms. Only a small number of inactive conformations with the DFG motif in the ``in'' state were found to have fluctuation magnitudes comparable to the active conformation. Therefore our study reports for the first time, intrinsic higher structural fluctuation for almost all inactive conformations compared to the active forms. Regions with higher fluctuations in the inactive states are often localized to the aC-helix, aG-helix and activation loop which are involved in the regulation and/or in structural transitions between active and inactive states. Further analysis of 476 kinase structures involved in interactions with another domain/protein showed that many of the regions with higher inactive-state fluctuation correspond to contact interfaces. We also performed extensive GNM analysis of (i) insulin receptor kinase bound to another protein and (ii) holo and apo forms of active and inactive conformations followed by multi-factor analysis of variance. We conclude that binding of small molecules or other domains/proteins reduce the extent of fluctuation irrespective of active or inactive forms. Finally, we show that the perceived fluctuations serve as a useful input to predict the functional state of a kinase.