Formal Verification of Full-Wave Rectifier: A Case Study

We present a case study of formal verification of full-wave rectifier for analog and mixed signal designs. We have used the Checkmate tool from CMU [1], which is a public domain formal verification tool for hybrid systems. Due to the restriction imposed by Checkmate it necessitates to make the changes in the Checkmate implementation to implement the complex and non-linear system. Full-wave rectifier has been implemented by using the Checkmate custom blocks and the Simulink blocks from MATLAB from Math works. After establishing the required changes in the Checkmate implementation we are able to efficiently verify the safety properties of the full-wave rectifier.Comment: The IEEE 8th International Conference on ASIC (IEEE ASICON 2009), October 20-23 2009, Changsha, Chin

CytoPred: a server for prediction and classification of cytokines

Cytokines are messengers of immune system. They are small secreted proteins that mediate and regulate the immune system, inflammation and hematopoiesis. Recent studies have revealed important roles played by the cytokines in adjuvants as therapeutic targets and in cancer therapy. In this paper, an attempt has been made to predict this important class of proteins and classify further them into families and subfamilies. A PSI-BLAST+Support Vector Machine-based hybrid approach is adopted to develop the prediction methods. CytoPred is capable of predicting cytokines with an accuracy of 98.29%. The overall accuracy of classification of cytokines into four families and further classification into seven subfamilies is 99.77 and 97.24%, respectively. It has been shown by comparison that CytoPred performs better than the already existing CTKPred. A user-friendly server CytoPred has been developed and available at http://www.imtech.res.in/raghava/cytopred

Prediction and classification of chemokines and their receptors

Chemokines are low molecular mass cytokine-like proteins that orchestrate myriads of immune functions like leukocyte trafficking, T cell differentiation, angiogenesis, hematopeosis and mast cell degranulation. Chemokines also play a role as HIV-1 inhibitor and act as potent natural adjuvant in antitumor immunotherapy. Receptors for these molecules are all seven-pass transmembrane G-protein-coupled receptors that are intimately involved with chemokines in a wide array of physiological and pathological conditions. These receptors also have a major role as co-receptors for HIV-1 entry into target cells. Therefore, chemokine receptors have proven to be excellent targets for small molecule in pharmaceutical industry. The immense importance of chemokines and their receptors motivated us to develop a support vector machine-based method ChemoPred to predict this important class of proteins and further classify them into subfamilies. ChemoPred is capable of predicting chemokines and chemokine receptors with an accuracy of 95.08% and 92.19%, respectively. The overall accuracy of classification of chemokines into three subfamilies was 96.00% and that of chemokine receptors into three families was 92.87%. The server ChemoPred is freely available at www.imtech.res.in/raghava/chemopred

PRRDB: A comprehensive database of Pattern-Recognition Receptors and their ligands

<p>Abstract</p> <p>Background</p> <p>Recently in a number of studies, it has been demonstrated that the innate immune system doesn't merely acts as the first line of defense but provides critical signals for the development of specific adaptive immune response. Innate immune system employs a set of receptors called pattern recognition receptors (PRRs) that recognize evolutionarily conserved patterns from pathogens called pathogen associated molecular patterns (PAMPs). In order to assist scientific community, a database PRRDB has been developed that provides extensive information about pattern recognition receptors and their ligands.</p> <p>Results</p> <p>The current version of database contains around 500 patterns recognizing receptors from 77 distinct organisms ranging from insects to human. This includes 177 Toll-like receptors, 124 are Scavenger receptors and 67 are Nucleotide Binding Site-Leucine repeats rich receptors. The database also provides information about 266 ligands that includes carbohydrates, proteins, nucleic acids, glycolipids, glycoproteins, lipopeptides. A number of web tools have been integrated in PRRDB in order to provide following services: i) searching on any field; ii) database browsing; and iii) BLAST search against the pattern-recognition receptors. PRRDB also provides external links to standard databases like Swiss-Prot and Pubmed.</p> <p>Conclusion</p> <p>PRRDB is a unique database of its kind, which provides comprehensive information about innate immunity. This database will be very useful in designing effective adjuvant for subunit vaccine and in understanding role of innate immunity. The database is available from the URL's in the Availabiltiy and requirements section.</p

Monitoring and Assessment of Soil Quality near Kashlog Limestone mine at Darlaghat District Solan, Himachal Pradesh, India

Limestone mining for an area is an economic activity but may lead to degradation of soil quality. Opencast mining operations involved displacement of large amount of overburden/rock mass materials to excavate the limestone for many purposes. In mining areas the soils are affected by various mining operations i.e blasting, drilling and storage of overburden dump materials, clearing of land, construction of ancillary facilities and movement of vehicles.  It is essential to determine the potential of soil in the area and identify the impacts of urbanization, industrialization and mining on soil quality. Present study is carried out to determine the soil characteristics, Impact of mining, industrialization and more importantly from agricultural point of view. Soil samples collected from ten locations were analyzed for physic- chemical characteristics. From the data it is observed that the concentration of total iron in 2 samples were above the permissible limit of 5.77%. Potassium levels were under the category very high whereas the levels of Phosphorus were reported to be in the category of less to medium. Higher potassium content of all the samples may be due to using fertilizers containing potassium. Cacium and magnesium levels are also higher than the prescribed safe limit in few samples. Key Words: Pollution, urbanization, industrialization, mining and fertilizer

Crystallization of Simple Fluids: Relative Stability of f.c.c. and b.c.c Structures

A free-energy functional for a crystal that contains both the symmetry conserved and symmetry broken parts of the direct pair correlation function is developed. The free-energy functional is used to investigate the crystallization of fluids interacting via the inverse power potential ; $u(r)=\epsilon {(\sigma/r)}^n$. In agreement with simulation results we find that for $n=12$ the freezing is into close packed f.c.c structure while for soft repulsions $(n\leq 6)$ b.c.c phase is more stable.Comment: 9 pages, 2 figure