Cloning and functional expression of venom prothrombin activator protease from Pseudonaja textilis with whole blood procoagulant activity

The snake venom group C prothrombin activators contain a number of components that enhance the rate of prothrombin activation. The cloning and expression of full-length cDNA for one of these components, an activated factor X (factor Xa)-like protease from Pseudonaja textilis as well as the generation of functional chimeric constructs with procoagulant activity were described. The complete cDNA codes for a propeptide, light chain, activation peptide (AP) and heavy chain related in sequence to mammalian factor X. Efficient expression of the protease was achieved with constructs where the AP was deleted and the cleavage sites between the heavy and light chains modified, or where the AP was replaced with a peptide involved in insulin receptor processing. In human kidney cells (H293F) transfected with these constructs, up to 80% of the pro-form was processed to heavy and light chains. Binding of the protease to barium citrate and use of specific antibodies demonstrated that gamma-carboxylation of glutamic acid residues had occurred on the light chain in both cases, as observed in human factor Xa and the native P. textilis protease. The recombinant protease caused efficient coagulation of whole citrated blood and citrated plasma that was enhanced by the presence of Ca2+. This study identified the complete cDNA sequence of a factor Xa-like protease from P. textilis and demonstrated for the first time the expression of a recombinant form of P. textilis protease capable of blood coagulation.

Strength analysis of steel-concrete composite beams in combined bending and shear

Despite experimental evidences, the contributions of the concrete slab and composite action to the vertical shear strength of simply supported steel-concrete composite beams are not considered in current design codes, which lead to conservative designs. In this paper, the finite element method is used to investigate the flexural and shear strengths of simply supported composite beams under combined bending and shear. A three-dimensional finite element model has been developed to account for geometric and material nonlinear behavior of composite beams, and verified by experimental results. The verified finite element model is than employed to quantify the contributions of the concrete slab and composite action to the moment and shear capacities of composite beams. The effect of the degree of shear connection on the vertical shear strength of deep composite beams loaded in shear is studied. Design models for vertical shear strength including contributions from the concrete slab and composite action and for the ultimate moment-shear interaction ate proposed for the design of simply supported composite beams in combined bending and shear. The proposed design models provide a consistent and economical design procedure for simply supported composite beams.

Theory of strongly correlated electron systems. I. Intersite coulomb interaction and the approximation of renormalized fermions in total energy calculations

The diagrammatic strong-coupling perturbation theory (SCPT) for correlated electron systems is developed for intersite Coulomb interaction and for a nonorthogonal basis set. The construction is based on iterations of exact closed equations for many - electron Green functions (GFs) for Hubbard operators in terms of functional derivatives with respect to external sources. The graphs, which do not contain the contributions from the fluctuations of the local population numbers of the ion states, play a special role: a one-to-one correspondence is found between the subset of such graphs for the many - electron GFs and the complete set of Feynman graphs of weak-coupling perturbation theory (WCPT) for single-electron GFs. This fact is used for formulation of the approximation of renormalized Fermions (ARF) in which the many-electron quasi-particles behave analogously to normal Fermions. Then, by analyzing: (a) Sham's equation, which connects the self-energy and the exchange- correlation potential in density functional theory (DFT); and (b) the Galitskii and Migdal expressions for the total energy, written within WCPT and within ARF SCPT, a way we suggest a method to improve the description of the systems with correlated electrons within the local density approximation (LDA) to DFT. The formulation, in terms of renormalized Fermions LIDA (RF LDA), is obtained by introducing the spectral weights of the many electron GFs into the definitions of the charge density, the overlap matrices, effective mixing and hopping matrix elements, into existing electronic structure codes, whereas the weights themselves have to be found from an additional set of equations. Compared with LDA+U and self-interaction correction (SIC) methods, RF LDA has the advantage of taking into account the transfer of spectral weights, and, when formulated in terms of GFs, also allows for consideration of excitations and nonzero temperature. Going beyond the ARF SCPT, as well as RF LIDA, and taking into account the fluctuations of ion population numbers would require writing completely new codes for ab initio calculations. The application of RF LDA for ab initio band structure calculations for rare earth metals is presented in part 11 of this study (this issue). (c) 2005 Wiley Periodicals, Inc.

Statistical mechanics of error-correcting codes

We investigate the performance of error-correcting codes, where the code word comprises products of K bits selected from the original message and decoding is carried out utilizing a connectivity tensor with C connections per index. Shannon's bound for the channel capacity is recovered for large K and zero temperature when the code rate K/C is finite. Close to optimal error-correcting capability is obtained for finite K and C. We examine the finite-temperature case to assess the use of simulated annealing for decoding and extend the analysis to accommodate other types of noisy channels.

Finite connectivity systems as error-correcting codes

We investigate the performance of parity check codes using the mapping onto spin glasses proposed by Sourlas. We study codes where each parity check comprises products of K bits selected from the original digital message with exactly C parity checks per message bit. We show, using the replica method, that these codes saturate Shannon's coding bound for K?8 when the code rate K/C is finite. We then examine the finite temperature case to asses the use of simulated annealing methods for decoding, study the performance of the finite K case and extend the analysis to accommodate different types of noisy channels. The analogy between statistical physics methods and decoding by belief propagation is also discussed.

Simple Gallager codes for BSC

We investigate the performance of Gallager type error- correcting codes for Binary Symmetric Channels, where the code word comprises products of K bits selected from the original message and decoding is carried out utilizing a connectivity tensor with C connections per index. Shannon's bound for the channel capacity is recovered for large K and zero temperature when the code rate K/C is finite. Close to optimal error-correcting capability, with improved decoding properties is obtained for finite K and C.

Error-correcting codes that nearly saturate Shannon's bound

Gallager-type error-correcting codes that nearly saturate Shannon's bound are constructed using insight gained from mapping the problem onto that of an Ising spin system. The performance of the suggested codes is evaluated for different code rates in both finite and infinite message length.

Typical performance of gallager-type error-correcting codes

The performance of Gallager's error-correcting code is investigated via methods of statistical physics. In this method, the transmitted codeword comprises products of the original message bits selected by two randomly-constructed sparse matrices; the number of non-zero row/column elements in these matrices constitutes a family of codes. We show that Shannon's channel capacity is saturated for many of the codes while slightly lower performance is obtained for others which may be of higher practical relevance. Decoding aspects are considered by employing the TAP approach which is identical to the commonly used belief-propagation-based decoding.

Statistical physics of irregular low-density parity-check codes

Low-density parity-check codes with irregular constructions have recently been shown to outperform the most advanced error-correcting codes to date. In this paper we apply methods of statistical physics to study the typical properties of simple irregular codes. We use the replica method to find a phase transition which coincides with Shannon's coding bound when appropriate parameters are chosen. The decoding by belief propagation is also studied using statistical physics arguments; the theoretical solutions obtained are in good agreement with simulation results. We compare the performance of irregular codes with that of regular codes and discuss the factors that contribute to the improvement in performance.

TAP for parity check error correcting codes

We employ the methods presented in the previous chapter for decoding corrupted codewords, encoded using sparse parity check error correcting codes. We show the similarity between the equations derived from the TAP approach and those obtained from belief propagation, and examine their performance as practical decoding methods.

Statistical mechanics of low-density parity check error-correcting codes over Galois fields

A variation of low-density parity check (LDPC) error-correcting codes defined over Galois fields (GF(q)) is investigated using statistical physics. A code of this type is characterised by a sparse random parity check matrix composed of C non-zero elements per column. We examine the dependence of the code performance on the value of q, for finite and infinite C values, both in terms of the thermodynamical transition point and the practical decoding phase characterised by the existence of a unique (ferromagnetic) solution. We find different q-dependence in the cases of C = 2 and C ≥ 3; the analytical solutions are in agreement with simulation results, providing a quantitative measure to the improvement in performance obtained using non-binary alphabets.

Error-correcting codes on a Bethe-like lattice

We analyse Gallager codes by employing a simple mean-field approximation that distorts the model geometry and preserves important interactions between sites. The method naturally recovers the probability propagation decoding algorithm as a minimization of a proper free-energy. We find a thermodynamical phase transition that coincides with information theoretical upper-bounds and explain the practical code performance in terms of the free-energy landscape.

Weight vs magnetization enumerator for Gallager codes

We propose a method to determine the critical noise level for decoding Gallager type low density parity check error correcting codes. The method is based on the magnetization enumerator (¸M), rather than on the weight enumerator (¸W) presented recently in the information theory literature. The interpretation of our method is appealingly simple, and the relation between the different decoding schemes such as typical pairs decoding, MAP, and finite temperature decoding (MPM) becomes clear. Our results are more optimistic than those derived via the methods of information theory and are in excellent agreement with recent results from another statistical physics approach.