Design and performance evaluation of a systolic architecture for hidden-surface removal

In this paper, we propose a systolic architecture for hidden-surface removal. Systolic architecture is a kind of parallel architecture best known for its easy VLSI implementability. After discussing the design details of the architecture, we present the results of the simulation experiments conducted in order to evaluate the performance of the architecture.

Splittings of free groups, normal forms and partitions of ends

Splittings of a free group correspond to embedded spheres in the 3-manifold M = # (k) S (2) x S (1). These can be represented in a normal form due to Hatcher. In this paper, we determine the normal form in terms of crossings of partitions of ends corresponding to normal spheres, using a graph of trees representation for normal forms. In particular, we give a constructive proof of a criterion determining when a conjugacy class in pi (2)(M) can be represented by an embedded sphere.

Vitamin A and thyroxine carrier proteins in chicken plasma Steady-state control of the plasma level of free retinol-binding protein and free thyroxine

1. 1. The binding parameters of prealbumin-2 with retinol-binding protein and thyroxine (T4) revealed the existence of distinct and multiple sites for both retinol-binding protein and T4. 2. 2. From the analysis of binding parameters of retinol-binding protein with prealbumin-2 it is clear that under steady-state conditions about 99% of the holo-retinol-binding protein remains bound to prealbumin-2. 3. 3. Equilibrium dialysis studies on binding properties of thyroid hormones with prealbumin-2 revealed that it has a single high affinity site and three low affinity sites. 4. 4. The occurrence of three carrier proteins for thyroid hormones, thyroxine-binding globulin, prealbumin-2 and albumin has been demonstrated. However, the chicken thyroxine-binding globulin differs from human thyroxine-binding globulin by being relatively less acidic and occuring at a two-fold lower concentration. But the thyroid hormone binding parameters are comparable. 5. 5. Highly sensitive methods were developed for determination of T4 binding capacities of the various proteins and plasma level of total T4 by fractionation of carrier proteins and further quantitatively employing in electrophoresis and equilibrium dialysis. 6. 6. The thyroxine-binding proteins were found to be two types, one (viz., thyroxine-binding globulin) of great affinity but of low binding capacity, which mainly acts as reservoir of T4, and another (viz.,prealbumin-2) of low affinity but of high binding capacity, which can participate predominantly in the control of the free T4 pool.

Free vibration of circular plates of arbitrary thickness

Free vibration of circular plates of arbitrary thickness is investigated using the method of initial functions. State-space approach is used to derive the governing equations of the above method. The formulation is such that theories of any desired order can be obtained by deleting higher terms in the infinite-order differential equations. Numerical results are obtained for flexural and extensional vibration of circular plates. Results are also computed using Mindlin's theory and they are in agreement with the present analysis.

Integration-free algorithms for fixed end-point regulator problems

A new formulation is suggested for the fixed end-point regulator problem, which, in conjunction with the recently developed integration-free algorithms, provides an efficient means of obtaining numerical solutions to such problems.

Chemical approaches of penicillin allergy—III Isolation of the penicillin-free carrier receptor protein (CRP) on a polymeric 7-deoxy penicillin analogue template and its role in penicillin immunogeneses in rabbit and man

Specific penicillin-carrier receptor proteins (CRP) have been isolated from the sera of penicillin allergic rabbits and human subjects in the unconjugated native state in electrophoretically homogeneous form by employing a synthetic polymeric affinity template containing the 7-deoxy analogue of penicillin G. The synthesis of the 7-deoxy analogue has been described. In this affinity system the antipenicillin-antibody is desorbed by 0·9M thiourea and the CRP in 8M urea. The CRP after incubation with penicillin is converted into the full-fledged antigen. Studies on the origin of CRP and the nature of antibody as well as comparative studies on the properties of the rabbit antibody and those of antibodies elicited by a BSA-BPO conjugate are reported.

Transformations of acetates of citronellol, geraniol, and linalool by Aspergillus niger: regiospecific hydroxylation of citronellol by a cell-free system

Incubation of acetates of geraniol, citronellol and linalool with Aspergillus niger resulted in their hydrolysis to corresponding alcohols which were further hydroxylated to their respective 8-hydroxy derivatives. In the case of linalyl acetate, besides linalool and 8-hydroxylinalool, small amounts of geraniol and agr-terpineol were also formed. Microsomes (105 000xg sediment) prepared from induced cells of A. niger were found to convert (1-3H)citronellol to 8-hydroxy citronellol in the presence of NADPH and O2. The pH optimum for the hydroxylase was found to be 7.6.

Enantioselective and Protecting Group-Free Synthesis of 1-Deoxythionojirimycin, 1-Deoxythiomannojirimycin, and 1-Deoxythiotalonojirimycin

1-Deoxythioglyconojirimycins were synthesized by using a protecting group-free strategy, starting from readily available carbohydrates, in good overall yield. Use of benzyl-triethylammonium tetrathiomolybdate, BnEt3N](2)MoS4, as a sulfur transfer reagent and borohydride exchange resin (BER) reduction of a lactone enabled the efficient synthesis of the title compounds.

Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Background: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multidomain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. Methodology: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. Conclusions: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multidomain architecture.

Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

Background: One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results: In this study, we have explored the ligand induced conformational changes in H. pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione) for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H. pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions: In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in any protein of known structure.