Studies on the target conditioning for deposition of $LiCoO_{2}$ films

Deposition of good quality thin films of Lithium Cobalt Oxide (LiCoO2), by sputtering is preceded by target conditioning, which dictates the surface composition, morphology and electrochemical performance of the deposited film. Sputtering from a Virgin target surface, results in films with excess of the more reactive elements. The concentration of these reactive elements in the films decreases until the system reaches a steady state after sufficient sputtering from the target. This paper discusses the deposition kinetics in terms of target conditioning of LiCoO2. The composition, morphology and texturing of deposited film during various hours of sputtering were analyzed using X-ray photoelectron Spectroscopy (XPS) and Field Emission Scanning electron microscopy (FESEM). The compositional stability is not observed in the films formed during the initial hours or Sputtering from the fresh target, which becomes stable after several hours of sputtering. The Li and Co concentration in the Films deposited subsequently is found to be varying and possible causes are discussed. After the compositional stability is reached, electrochemical analysis of LiCoO2 thin films was performed, which shows a discharge capacity of 129 mu Ah/cm(2).

targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

Background: Tuberculosis still remains one of the largest killer infectious diseases, warranting the identification of newer targets and drugs. Identification and validation of appropriate targets for designing drugs are critical steps in drug discovery, which are at present major bottle-necks. A majority of drugs in current clinical use for many diseases have been designed without the knowledge of the targets, perhaps because standard methodologies to identify such targets in a high-throughput fashion do not really exist. With different kinds of 'omics' data that are now available, computational approaches can be powerful means of obtaining short-lists of possible targets for further experimental validation. Results: We report a comprehensive in silico target identification pipeline, targetTB, for Mycobacterium tuberculosis. The pipeline incorporates a network analysis of the protein-protein interactome, a flux balance analysis of the reactome, experimentally derived phenotype essentiality data, sequence analyses and a structural assessment of targetability, using novel algorithms recently developed by us. Using flux balance analysis and network analysis, proteins critical for survival of M. tuberculosis are first identified, followed by comparative genomics with the host, finally incorporating a novel structural analysis of the binding sites to assess the feasibility of a protein as a target. Further analyses include correlation with expression data and non-similarity to gut flora proteins as well as 'anti-targets' in the host, leading to the identification of 451 high-confidence targets. Through phylogenetic profiling against 228 pathogen genomes, shortlisted targets have been further explored to identify broad-spectrum antibiotic targets, while also identifying those specific to tuberculosis. Targets that address mycobacterial persistence and drug resistance mechanisms are also analysed. Conclusion: The pipeline developed provides rational schema for drug target identification that are likely to have high rates of success, which is expected to save enormous amounts of money, resources and time in the drug discovery process. A thorough comparison with previously suggested targets in the literature demonstrates the usefulness of the integrated approach used in our study, highlighting the importance of systems-level analyses in particular. The method has the potential to be used as a general strategy for target identification and validation and hence significantly impact most drug discovery programmes.

An Algorithm for Tracking a Maneuvering Target in Clutter

We consider the problem of tracking a maneuvering target in clutter. In such an environment, missed detections and false alarms make it impossible to decide, with certainty, the origin of received echoes. Processing radar returns in cluttered environments consists of three functions: 1) target detection and plot formation, 2) plot-to-track association, and 3) track updating. Two inadequacies of the present approaches are 1) Optimization of detection characteristics have not been considered and 2) features that can be used in the plot-to-track correlation process are restricted to a specific class. This paper presents a new approach to overcome these limitations. This approach facilitates tracking of a maneuvering target in clutter and improves tracking performance for weak targets.

Launch Envelope Optimization of Virtual Sliding Target Guidance Scheme

This paper presents an optimization of the performance of a recently proposed virtual sliding target (VST) guidance scheme in terms of maximization of its launch envelope for three- dimensional (3-D) engagements. The objective is to obtain the launch envelope of the missile using the VST guidance scheme for different lateral launch angles with respect to the line of sight (LOS) and demonstrate its superiority over kinematics-based guidance laws like proportional navigation (PN). The VST scheme uses PN as its basic guidance scheme and exploits the relation between the atmospheric properties, missile aerodynamic characteristics, and the optimal trajectory of the missile. The missile trajectory is shaped by controlling the instantaneous position and the speed of a virtual target which the missile pursues during the midcourse phase. In the proposed method it is shown that an appropriate value of initial position for the virtual target in 3-D, combined with optimized virtual target parameters, can significantly improve the launch envelope performance. The paper presents the formulation of the optimization problem, obtains the approximate models used to make the optimization problem more tractable, and finally presents the optimized performance of the missile in terms of launch envelope and shows significant improvement over kinematic-based guidance laws. The paper also proposes modification to the basic VST scheme. Some simulations using the full-fledged six degrees-of-freedom (6-DOF) models are also presented to validate the models and technique used.

Computational systems approach for drug target discovery

Importance of the field: The shift in focus from ligand based design approaches to target based discovery over the last two to three decades has been a major milestone in drug discovery research. Currently, it is witnessing another major paradigm shift by leaning towards the holistic systems based approaches rather the reductionist single molecule based methods. The effect of this new trend is likely to be felt strongly in terms of new strategies for therapeutic intervention, new targets individually and in combinations, and design of specific and safer drugs. Computational modeling and simulation form important constituents of new-age biology because they are essential to comprehend the large-scale data generated by high-throughput experiments and to generate hypotheses, which are typically iterated with experimental validation. Areas covered in this review: This review focuses on the repertoire of systems-level computational approaches currently available for target identification. The review starts with a discussion on levels of abstraction of biological systems and describes different modeling methodologies that are available for this purpose. The review then focuses on how such modeling and simulations can be applied for drug target discovery. Finally, it discusses methods for studying other important issues such as understanding targetability, identifying target combinations and predicting drug resistance, and considering them during the target identification stage itself. What the reader will gain: The reader will get an account of the various approaches for target discovery and the need for systems approaches, followed by an overview of the different modeling and simulation approaches that have been developed. An idea of the promise and limitations of the various approaches and perspectives for future development will also be obtained. Take home message: Systems thinking has now come of age enabling a `bird's eye view' of the biological systems under study, at the same time allowing us to `zoom in', where necessary, for a detailed description of individual components. A number of different methods available for computational modeling and simulation of biological systems can be used effectively for drug target discovery.

Target reliability based design optimization of anchored cantilever sheet pile walls

In this study, the stability of anchored cantilever sheet pile wall in sandy soils is investigated using reliability analysis. Targeted stability is formulated as an optimization problem in the framework of an inverse first order reliability method. A sensitivity analysis is conducted to investigate the effect of parameters influencing the stability of sheet pile wall. Backfill soil properties, soil - steel pile interface friction angle, depth of the water table from the top of the sheet pile wall, total depth of embedment below the dredge line, yield strength of steel, section modulus of steel sheet pile, and anchor pull are all treated as random variables. The sheet pile wall system is modeled as a series of failure mode combination. Penetration depth, anchor pull, and section modulus are calculated for various target component and system reliability indices based on three limit states. These are: rotational failure about the position of the anchor rod, expressed in terms of moment ratio; sliding failure mode, expressed in terms of force ratio; and flexural failure of the steel sheet pile wall, expressed in terms of the section modulus ratio. An attempt is made to propose reliability based design charts considering the failure criteria as well as the variability in the parameters. The results of the study are compared with studies in the literature.

Diversity of DNA methyltransferases that recognize asymmetric target sequences

DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases usually recognize palindromic DNA sequences and add a methyl group to the target base (either adenine or cytosine) on both strands. However, there are a number of MTases that recognize asymmetric target sequences and differ in their subunit organization. In a bacterial cell, after each round of replication, the substrate for any MTase is hemimethylated DNA, and it therefore needs only a single methylation event to restore the fully methylated state. This is in consistent with the fact that most of the DNA MTases studied exist as monomers in solution. Multiple lines of evidence suggest that some DNA MTases function as dimers. Further, functional analysis of many restriction-modification systems showed the presence of more than one or fused MTase genes. It was proposed that presence of two MTases responsible for the recognition and methylation of asymmetric sequences would protect the nascent strands generated during DNA replication from cognate restriction endonuclease. In this review, MTases recognizing asymmetric sequences have been grouped into different subgroups based on their unique properties. Detailed characterization of these unusual MTases would help in better understanding of their specific biological roles and mechanisms of action. The rapid progress made by the genome sequencing of bacteria and archaea may accelerate the identification and study of species- and strain-specific MTases of host-adapted bacteria and their roles in pathogenic mechanisms.

Diversity of DNA methyltransferases that recognize asymmetric target sequences

DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases usually recognize palindromic DNA sequences and add a methyl group to the target base (either adenine or cytosine) on both strands. However, there are a number of MTases that recognize asymmetric target sequences and differ in their subunit organization. In a bacterial cell, after each round of replication, the substrate for any MTase is hemimethylated DNA, and it therefore needs only a single methylation event to restore the fully methylated state. This is in consistent with the fact that most of the DNA MTases studied exist as monomers in solution. Multiple lines of evidence suggest that some DNA MTases function as dimers. Further, functional analysis of many restriction-modification systems showed the presence of more than one or fused MTase genes. It was proposed that presence of two MTases responsible for the recognition and methylation of asymmetric sequences would protect the nascent strands generated during DNA replication from cognate restriction endonuclease. In this review, MTases recognizing asymmetric sequences have been grouped into different subgroups based on their unique properties. Detailed characterization of these unusual MTases would help in better understanding of their specific biological roles and mechanisms of action. The rapid progress made by the genome sequencing of bacteria and archaea may accelerate the identification and study of species- and strain-specific MTases of host-adapted bacteria and their roles in pathogenic mechanisms.

Source and target enzyme signature in serine protease inhibitor active site sequences

Amino acid sequences of proteinaceous proteinase inhibitors have been extensively analysed for deriving information regarding the molecular evolution and functional relationship of these proteins. These sequences have been grouped into several well defined families. It was found that the phylogeny constructed with the sequences corresponding to the exposed loop responsible for inhibition has several branches that resemble those obtained from comparisons using the entire sequence. The major branches of the unrooted tree corresponded to the families to which the inhibitors belonged. Further branching is related to the enzyme specificity of the inhibitor. Examination of the active site loop sequences of trypsin inhibitors revealed that there are strong preferences for specific amino acids at different positions of the loop. These preferences are inhibitor class specific. Inhibitors active against more than one enzyme occur within a class and confirm to class specific sequence in their loops. Hence, only a few positions in the loop seem to determine the specificity. The ability to inhibit the same enzyme by inhibitors that belong to different classes appears to be a result of convergent evolution

Heat Shock Protein 90 as a Drug Target against Protozoan Infections Biochemical characterization of HSP90 From plasmodium falciparum and trypanosoma evansi and evaluation of its inhibitor as a candidate drug

Using a pharmacological inhibitor of Hsp90 in cultured malarial parasite, we have previously implicated Plasmodium falciparum Hsp90 (PfHsp90) as a drug target against malaria. In this study, we have biochemically characterized PfHsp90 in terms of its ATPase activity and interaction with its inhibitor geldanamycin (GA) and evaluated its potential as a drug target in a preclinical mouse model of malaria. In addition, we have explored the potential of Hsp90 inhibitors as drugs for the treatment of Trypanosoma infection in animals. Our studies with full-length PfHsp90 showed it to have the highest ATPase activity of all known Hsp90s; its ATPase activity was 6 times higher than that of human Hsp90. Also, GA brought about more robust inhibition of PfHsp90 ATPase activity as compared with human Hsp90. Mass spectrometric analysis of PfHsp90 expressed in P. falciparum identified a site of acetylation that overlapped with Aha1 and p23 binding domain, suggesting its role in modulating Hsp90 multichaperone complex assembly. Indeed, treatment of P. falciparum cultures with a histone deacetylase inhibitor resulted in a partial dissociation of PfHsp90 complex. Furthermore, we found a well known, semisynthetic Hsp90 inhibitor, namely 17-(allylamino)-17-demethoxygeldanamycin, to be effective in attenuating parasite growth and prolonging survival in a mouse model of malaria. We also characterized GA binding to Hsp90 from another protozoan parasite, namely Trypanosoma evansi. We found 17-(allylamino)-17-demethoxygeldanamycin to potently inhibit T. evansi growth in a mouse model of trypanosomiasis. In all, our biochemical characterization, drug interaction, and animal studies supported Hsp90 as a drug target and its inhibitor as a potential drug against protozoan diseases.

devovo biosynthesis of heme offers a new chemotherapeutic target in the human malarial parasite

The human malarial parasite, Image , has been found to synthesize heme Image , despite the accumulation of large quantities of polymeric heme derived from the hemoglobin of the red cell host. The parasite δ-aminolevulinate dehydrase level is significantly lower than that of the host and its inhibition by succinylacetone leads to inhibition of parasite protein synthesis and viability.

Determination of rational strategies for players in two-target games

This paper addresses some of the basic issues involved in the determination of rational strategies for players in two-target games. We show that unlike single-target games where the task of role assignment and selection of strategies is conceptually straightforward, in two-target games, many factors like the preference ordering of outcomes by players, the relative configuration of the target sets and secured outcome regions, the uncertainty about the parameters of the game, etc., also influence the rational selection of strategies by players. The importance of these issues is illustrated through appropriate examples.

Model Based Target Tracking in a Wireless Network of Passive Infrared Sensor Nodes

We consider the problem of tracking an intruder in a plane region by using a wireless sensor network comprising motes equipped with passive infrared (PIR) sensors deployed over the region. An input-output model for the PIR sensor and a method to estimate the angular speed of the target from the sensor output are proposed. With the measurement model so obtained, we study the centralized and decentralized tracking performance using the extended Kalman filter.

Cytotoxic T lymphocytes raised against Japanese encephalitis virus: effector cell phenotype, target specificity and in vitro virus clearance.

Several H-2 defined cell lines were examined for their ability to support infection and replication of Japanese encephalitis virus (JEV) before their use in in vitro and in vivo stimulation protocols for generating cytotoxic T lymphocytes (CTLs) against JEV. Among II different cell lines tested, two H-2(d) macrophage tumour lines (P388D1, RAW 264.7), an H-2(d) hybridoma (Sp2/0), an H-2K(k)D(d) neuroblastoma (Neuro 2a), and H-2(k) fibroblast cell line (L929) were found to support JEV infection and replication. These cell lines were used to generate anti-JEV CTLs by using in vivo immunization followed by in vitro stimulation of BALB/c mice. We observed that not only syngeneic and allogeneic infected cells but also JEV-infected xenogeneic cells could prime BALB/c mice for the generation of JEV-specific CTLs upon subsequent in vitro stimulation of splenocytes with JEV-infected syngeneic cells. Although infected xenogeneic cells were used for immunization, the anti-JEV effecters that were generated lysed infected syngeneic targets but not JEV-infected xenogeneic or allogeneic target cells in a 5h Cr-51 release assay. These anti-JEV effecters recognized syngeneic target cells infected with West Nile virus to a lesser extent and were shown to be Lyt-2.2(+) T cells. The results of unlabelled cold target competition studies suggested alterations in the cell surface expression of viral antigenic determinants recognized by these CTLs. We further demonstrate that the JEV-specific CTLs generated could virtually block the release of infectious virus particles from infected P388D1 and Neuro 2a cells in vitro.

Target space of an asymmetric chiral gauged wzw model

It is shown that the asymmetric chiral gauging of the WZW models give rise to consistent string backgrounds. The target space structure of the chiral gauged SL(2,R) WZW model, with the gauging of subgroups SO(1, 1) in the left and U(1) in the right moving sector, is obtained. We then analyze the symmetries of the background and show the presence of a non-trivial isometry in the canonical parametrization of the WZW model. Using these results, the equivalence of the asymmetric models with the symmetric ones is demonstrated.