Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations

Background: Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation in the regulation of kinases leads to malignancy. We have identified and analysed putative protein kinases encoded in the genome of chimpanzee which is a close evolutionary relative of human. Result: The shared core biology between chimpanzee and human is characterized by many orthologous protein kinases which are involved in conserved pathways. Domain architectures specific to chimp/human kinases have been observed. Chimp kinases with unique domain architectures are characterized by deletion of one or more non-kinase domains in the human kinases. Interestingly, counterparts of some of the multi-domain human kinases in chimp are characterized by identical domain architectures but with kinase-like non-kinase domain. Remarkably, out of 587 chimpanzee kinases no human orthologue with greater than 95% sequence identity could be identified for 160 kinases. Variations in chimpanzee kinases compared to human kinases are brought about also by differences in functions of domains tethered to the catalytic kinase domain. For example, the heterodimer forming PB1 domain related to the fold of ubiquitin/Ras-binding domain is seen uniquely tethered to PKC-like chimpanzee kinase. Conclusion: Though the chimpanzee and human are evolutionary very close, there are chimpanzee kinases with no close counterpart in the human suggesting differences in their functions. This analysis provides a direction for experimental analysis of human and chimpanzee protein kinases in order to enhance our understanding on their specific biological roles.

Selective dissemination of XML documents based on genetically learned user model and Support Vector Machines

Extensible Markup Language ( XML) has emerged as a medium for interoperability over the Internet. As the number of documents published in the form of XML is increasing, there is a need for selective dissemination of XML documents based on user interests. In the proposed technique, a combination of Adaptive Genetic Algorithms and multi class Support Vector Machine ( SVM) is used to learn a user model. Based on the feedback from the users, the system automatically adapts to the user's preference and interests. The user model and a similarity metric are used for selective dissemination of a continuous stream of XML documents. Experimental evaluations performed over a wide range of XML documents, indicate that the proposed approach significantly improves the performance of the selective dissemination task, with respect to accuracy and efficiency.

Selective dissemination of XML documents based on genetically learned user model and Support Vector Machines

Extensible Markup Language ( XML) has emerged as a medium for interoperability over the Internet. As the number of documents published in the form of XML is increasing, there is a need for selective dissemination of XML documents based on user interests. In the proposed technique, a combination of Adaptive Genetic Algorithms and multi class Support Vector Machine ( SVM) is used to learn a user model. Based on the feedback from the users, the system automatically adapts to the user's preference and interests. The user model and a similarity metric are used for selective dissemination of a continuous stream of XML documents. Experimental evaluations performed over a wide range of XML documents, indicate that the proposed approach significantly improves the performance of the selective dissemination task, with respect to accuracy and efficiency.

Discovering user preferences by using time entries in click-through data to improve search engine results

The search engine log files have been used to gather direct user feedback on the relevancy of the documents presented in the results page. Typically the relative position of the clicks gathered from the log files is used a proxy for the direct user feedback. In this paper we identify reasons for the incompleteness of the relative position of clicks for deciphering the user preferences. Hence, we propose the use of time spent by the user in reading through the document as indicative of user preference for a document with respect to a query. Also, we identify the issues involved in using the time measure and propose means to address them.

Flow Generated By Pitched Blade Turbines Ii: Simulation Using Κ-Ε Model

Experimental data on average velocity and turbulence intensity generated by pitched blade downflow turbines (PTD) were presented in Part I of this paper. Part II presents the results of the simulation of flow generated by PTD The standard κ-ε model along with the boundary conditions developed in the Part 1 have been employed to predict the flow generated by PTD in cylindrical baffled vessel. This part describes the new software FIAT (Flow In Agitated Tanks) for the prediction of three dimensional flow in stirred tanks. The basis of this software has been described adequately. The influence of grid size, impeller boundary conditions and values of model parameters on the predicted flow have been analysed. The model predictions successfully reproduce the three dimensionality and the other essential characteristics of the flow. The model can be used to improve the overall understanding about the relative distribution of turbulence by PTD in the agitated tank

Characterization of oxygen free radicals generated during vanadate-stimulated NADH oxidation

The oxidation of NADH and accompanying reduction of oxygen to H2O2 stimulated by polyvanadate was markedly inhibited by SOD and cytochrome c. The presence of decavanadate, the polymeric form, is necessary for obtaining the microsomal enzyme-catalyzed activity. The accompanying activity of reduction of cytochrome c was found to be SOD-insensitive and therefore does not represent superoxide formation. The reduction of cytochrome c by vanadyl sulfate was also SOD-insensitive. In the presence of H2O2 all the forms of vanadate were able to oxidize reduced cytochrome c, which was sensitive to mannitol, tris and also catalase, indicating H202-dependent generation of hydroxyl radicals. Using ESR and spin trapping technique only hydroxyl radicals, but not superoxide anion radicals, were detected during polyvanadate-dependent NADH oxidation.

On infinitesimal σ-fields generated by random processes

It is proved that the infinitesimal look-ahead and look-back σ-fields of a random process disagree at atmost countably many time instants.

Modelling, simulation, and graphical user interface for industrial gas carburising process

A mathematical model has been developed for the gas carburising (diffusion) process using finite volume method. The computer simulation has been carried out for an industrial gas carburising process. The model's predictions are in good agreement with industrial experimental data and with data collected from the literature. A study of various mass transfer and diffusion coefficients has been carried out in order to suggest which correlations should be used for the gas carburising process. The model has been interfaced in a Windows environment using a graphical user interface. In this way, the model is extremely user friendly. The sensitivity analysis of various parameters such as initial carbon concentration in the specimen, carbon potential of the atmosphere, temperature of the process, etc. has been carried out using the model.

Aromatic, microporous polymer networks with high surface area generated in Friedel-Crafts-type polycondensations

A series of novel, microporous polymer networks (MPNs) have been generated in a simple, acid catalysed Friedel-Crafts-type self-condensation of A(2)B(2)- and A(2)B(4)-type fluorenone monomers. Two A2B4-type monomers with 2,7-bis(N, N-diphenylamino) A or 2,7-bis [4-(N, N-diphenylamino) phenyl] D substitution of the fluorenone cores lead to MPNs with high S(BET) surface areas of up to 1400 m(2) g(-1). Two MPNs made of binary monomer mixtures showed the highest Brunauer-Emmett-Teller (BET) surface areas S(BET) of our series (SBET of up to 1800 m(2) g(-1)) after washing the powdery samples with supercritical carbon dioxide. Total pore volumes of up to 1.6 cm(3) g(-1) have been detected. It is observed that the substitution pattern of the monomers is strongly influencing the resulting physicochemical properties of the microporous polymer networks (MPNs).

Relationship Between Physical Structure and Tribology of Single Soot Particles Generated by Burning Ethylene

Ethylene gas is burnt and the soot generated is sampled thermophoretically at different heights along the flame axis starting from a region close to the root of the flame. The morphology and crystallinity of the particle are recorded using high resolution transmission electron microscopes. The hardness of a single particle is measured using a nanoindenter. The frictional resistance and material removal of a particle are measured using an atomic force microscope. The particles present in the mid-flame region are found to have a crystalline shell. The ones at the flame root are found to be highly disordered and the ones at the flame tip and above have randomly distributed pockets of short range order. The physical state of a particle is found to relate, but not very strongly, with the mechanical and tribological properties of the particles.

Setting up Multilingual Information Repository: A case Study with EPrints.org Software

Today 80 % of the content on the Web is in English, which is spoken by only 8% of the World population and 5% of Indian population. There is wealth of useful content in the various languages of the world other than English, which can be made available on the Internet. But, to date, for various reasons most of it is not yet available on the Internet. India itself has 18 officially recognized languages and scores of dialects. Although the medium of instruction for most of the higher education and research in India is English, substantial amount of literature by way of novels, textbooks, scholarly information are being generated in the other languages in the country. Many of the e-governance initiatives are in the respective state languages. In the past, support for different languages by the operating systems and the software packages were not very encouraging. However, with the advent of Unicode technology, operating systems and software packages are supporting almost all the major languages of the world that have scripts. In the work reported in this paper, we have explained the configuration changes that are needed for Eprints.org software to store multilingual content and to create a multilingual user interface.

Virtually cool ternary content addressable memory

Fast content addressable data access mechanisms have compelling applications in today's systems. Many of these exploit the powerful wildcard matching capabilities provided by ternary content addressable memories. For example, TCAM based implementations of important algorithms in data mining been developed in recent years; these achieve an an order of magnitude speedup over prevalent techniques. However, large hardware TCAMs are still prohibitively expensive in terms of power consumption and cost per bit. This has been a barrier to extending their exploitation beyond niche and special purpose systems. We propose an approach to overcome this barrier by extending the traditional virtual memory hierarchy to scale up the user visible capacity of TCAMs while mitigating the power consumption overhead. By exploiting the notion of content locality (as opposed to spatial locality), we devise a novel combination of software and hardware techniques to provide an abstraction of a large virtual ternary content addressable space. In the long run, such abstractions enable applications to disassociate considerations of spatial locality and contiguity from the way data is referenced. If successful, ideas for making content addressability a first class abstraction in computing systems can open up a radical shift in the way applications are optimized for memory locality, just as storage class memories are soon expected to shift away from the way in which applications are typically optimized for disk access locality.

A non-isothiocyanate route to synthesize trisubstituted thioureas of arylamines using in situ generated dithiocarbamates

A novel, user-friendly, and convenient method for the synthesis of trisubstituted thioureas of arylamines is presented, for the first time, using in situ generated dithiocarbamates of secondary amines. This strategy provides an excellent opportunity to access thioureas containing primary aryl amines. A non-isothiocyanate route to obtain thioureas is the advantage of this strategy, which may provide a useful route to synthesize a variety of biologically active derivatives of thioureas.

NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection

NrichD content content-type=''no-hyphen'' xlink:type=''simple''>( ext-link-type=''uri'' xlink:href=''http://proline.biochem.iisc.ernet.in/NRICHD/'' xlink:type=''simple''>http://proline.biochem.iisc.ernet.in/NRICHD/)< /named-content> is a database of computationally designed protein-like sequences, augmented into natural sequence databases that can perform hops in protein sequence space to assist in the detection of remote relationships. Establishing protein relationships in the absence of structural evidence or natural `intermediately related sequences' is a challenging task. Recently, we have demonstrated that the computational design of artificial intermediary sequences/linkers is an effective approach to fill naturally occurring voids in protein sequence space. Through a large-scale assessment we have demonstrated that such sequences can be plugged into commonly employed search databases to improve the performance of routinely used sequence search methods in detecting remote relationships. Since it is anticipated that such data sets will be employed to establish protein relationships, two databases that have already captured these relationships at the structural and functional domain level, namely, the SCOP database and the Pfam database, have been `enriched' with these artificial intermediary sequences. NrichD database currently contains 3 611 010 artificial sequences that have been generated between 27 882 pairs of families from 374 SCOP folds. The data sets are freely available for download. Additional features include the design of artificial sequences between any two protein families of interest to the user.

Thermoelectric properties of Pb0.75-xMnxSn0.25Te alloys with variable manganese content

Lead tin telluride is one of the well-established thermoelectric materials in the temperature range 350-750 K. In the present study, Pb0.75-xMnxSn0.25Te1.00 alloys with variable manganese (Mn) content were prepared by solid state synthesis and the thermoelectric properties were studied. X-ray diffraction, (XRD) showed that the samples followed Vegard's law, indicating solid solution formation and substitution of Mn at the Pb site. Scanning Electron Microscopy (SEM) showed that the grain sizes varied from <1 mu m to more than 10 mu m and MnTe rich phase was present for higher Mn content. Seebeck coefficient, electrical resistivity and thermal conductivity were measured from room temperature to 720 K. At 300 K, large Seebeck values were obtained, possibly due to increased effective mass on Mn substitution and low carrier concentration of the samples. At higher temperatures, transition from n-type to p-type indicated the presence of thermally generated carriers. Temperature dependent electrical resistivity showed the transition from degenerate to non-degenerate behavior. For thermal conductivity, low values (similar to 1 W/m-K at 300 K) were obtained. At higher temperatures bipolar conduction was observed, in agreement with the Seebeck and resistivity data. Due to low power factor, the maximum thermoelectric figure of merit (zT) was limited to 0.23 at 329 K for the sample with lowest Mn content (x=0.03). (C) 2015 Elsevier Ltd. All rights reserved.