COX24 codes for a mitochondrial protein required for processing of the COX1 transcript

In most strains of Saccharomyces cerevisiae the mitochondrial gene COX1, for subunit 1 of cytochrome oxidase, contains multiple exons and introns. Processing of COX1 primary transcript requires accessory proteins factors, some of which are encoded by nuclear genes and others by reading frames residing in some of the introns of the COX1 and COB genes. Here we show that the low molecular weight protein product of open reading frame YLR204W, for which we propose the name COX24, is also involved in processing of COX1 RNA intermediates. The growth defect of cox24 mutants is partially rescued in strains harboring mitochondrial DNA lacking introns. Northern blot analyses of mitochondrial transcripts indicate cox24 null mutants to be blocked in processing of introns aI2 and aI3. The dependence of intron aI3 excision on Cox24p is also supported by the growth properties of the cox24 mutant harboring mitochondrial DNA with different intron compositions. The intermediate phenotype of the cox24 mutant in the background of intronless mitochondrial DNA, however, suggests that in addition to its role in splicing of the COX1 pre-mRNA, Cox24p still has another function. Based on the analysis of a cox14-cox24 double mutant, we propose that the other function of Cox24p is related to translation of the COX1 mRNA. © 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

The Rv1712 locus from Mycobacterium tuberculosis H37Rv codes for a functional CMP kinase that preferentially Phosphorylates dCMP

The Mycobacterium tuberculosis cmk gene, predicted to encode a CMP kinase (CMK), was cloned and expressed, and its product was purified to homogeneity. Steady-state kinetics confirmed that M. tuberculosis CMK is a monomer that preferentially phosphorylates CMP and dCMP by a sequential mechanism. A plausible role for CMK is discussed. Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Encoding through generalized polynomial codes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Integrating open source codes for solid modeling and automatic mesh generation in FEM applications

The applications of the Finite Element Method (FEM) for three-dimensional domains are already well documented in the framework of Computational Electromagnetics. However, despite the power and reliability of this technique for solving partial differential equations, there are only a few examples of open source codes available and dedicated to the solid modeling and automatic constrained tetrahedralization, which are the most time consuming steps in a typical three-dimensional FEM simulation. Besides, these open source codes are usually developed separately by distinct software teams, and even under conflicting specifications. In this paper, we describe an experiment of open source code integration for solid modeling and automatic mesh generation. The integration strategy and techniques are discussed, and examples and performance results are given, specially for complicated and irregular volumes which are not simply connected. © 2011 IEEE.

Construction of perfect space-time codes

In this work, we propose an innovative methodology to extend the construction of minimum and non-minimum delay perfect codes as a subset of cyclic division algebras over ℚ(ζ3), where the signal constellations are isomorphic to the hexagonal An 2 -rotated lattice, for any channel of any dimension n such that gcd{n, 3) = 1.

Commutative group codes in R4, R6, R8 and R16-Approaching the bound

Spherical codes in even dimensions n = 2m generated by a commutative group of orthogonal matrices can be determined by a quotient of m-dimensional lattices when the sublattice has an orthogonal basis. We discuss here the existence of orthogonal sublattices of the lattices A2, D3, D4 and E8, which have the best packing density in their dimensions, in order to generate families of commutative group codes approaching the bound presented in Siqueira and Costa (2008) [14]. © 2013 Elsevier B.V. All rights reserved.

Delaunay Tetrahedralization of the Heart Based on Integration of Open Source Codes

The Finite Element Method (FEM) is a way of numerical solution applied in different areas, as simulations used in studies to improve cardiac ablation procedures. For this purpose, the meshes should have the same size and histological features of the focused structures. Some methods and tools used to generate tetrahedral meshes are limited mainly by the use conditions. In this paper, the integration of Open Source Softwares is presented as an alternative to solid modeling and automatic mesh generation. To demonstrate its efficiency, the cardiac structures were considered as a first application context: atriums, ventricles, valves, arteries and pericardium. The proposed method is feasible to obtain refined meshes in an acceptable time and with the required quality for simulations using FEM.

Spectrum Distribution in Cognitive Radio: Error Correcting Codes Perspective

Cognitive radio is a growing zone in wireless communication which offers an opening in complete utilization of incompetently used frequency spectrum: deprived of crafting interference for the primary (authorized) user, the secondary user is indorsed to use the frequency band. Though, scheming a model with the least interference produced by the secondary user for primary user is a perplexing job. In this study we proposed a transmission model based on error correcting codes dealing with a countable number of pairs of primary and secondary users. However, we obtain an effective utilization of spectrum by the transmission of the pairs of primary and secondary users' data through the linear codes with different given lengths. Due to the techniques of error correcting codes we developed a number of schemes regarding an appropriate bandwidth distribution in cognitive radio.

A BCH code and a sequence of cyclic codes

This study establishes that for a given binary BCH code C0 n of length n generated by a polynomial g(x) ∈ F2[x] of degree r there exists a family of binary cyclic codes {Cm 2m−1(n+1)n}m≥1 such that for each m ≥ 1, the binary cyclic code Cm 2m−1(n+1)n has length 2m−1(n + 1)n and is generated by a generalized polynomial g(x 1 2m ) ∈ F2[x, 1 2m Z≥0] of degree 2mr. Furthermore, C0 n is embedded in Cm 2m−1(n+1)n and Cm 2m−1(n+1)n is embedded in Cm+1 2m(n+1)n for each m ≥ 1. By a newly proposed algorithm, codewords of the binary BCH code C0 n can be transmitted with high code rate and decoded by the decoder of any member of the family {Cm 2m−1(n+1)n}m≥1 of binary cyclic codes, having the same code rate.

Construction and decoding of BCH codes over chain of commutative rings

In this paper, we present a new construction and decoding of BCH codes over certain rings. Thus, for a nonnegative integer t, let A0 ⊂ A1 ⊂···⊂ At−1 ⊂ At be a chain of unitary commutative rings, where each Ai is constructed by the direct product of appropriate Galois rings, and its projection to the fields is K0 ⊂ K1 ⊂···⊂ Kt−1 ⊂ Kt (another chain of unitary commutative rings), where each Ki is made by the direct product of corresponding residue fields of given Galois rings. Also, A∗ i and K∗ i are the groups of units of Ai and Ki, respectively. This correspondence presents a construction technique of generator polynomials of the sequence of Bose, Chaudhuri, and Hocquenghem (BCH) codes possessing entries from A∗ i and K∗ i for each i, where 0 ≤ i ≤ t. By the construction of BCH codes, we are confined to get the best code rate and error correction capability; however, the proposed contribution offers a choice to opt a worthy BCH code concerning code rate and error correction capability. In the second phase, we extend the modified Berlekamp-Massey algorithm for the above chains of unitary commutative local rings in such a way that the error will be corrected of the sequences of codewords from the sequences of BCH codes at once. This process is not much different than the original one, but it deals a sequence of codewords from the sequence of codes over the chain of Galois rings.

Goppa codes through polynomials of B[X;(1/2^2)Z_0] and its decoding principle

In this paper, we present a decoding principle for Goppa codes constructed by generalized polynomials, which is based on modified Berlekamp-Massey algorithm. This algorithm corrects all errors up to the Hamming weight $t\leq 2r$, i.e., whose minimum Hamming distance is $2^{2}r+1$.

Linear codes over finite local rings in a chain

For a positive integer $t$, let \begin{equation*} \begin{array}{ccccccccc} (\mathcal{A}_{0},\mathcal{M}_{0}) & \subseteq & (\mathcal{A}_{1},\mathcal{M}_{1}) & \subseteq & & \subseteq & (\mathcal{A}_{t-1},\mathcal{M}_{t-1}) & \subseteq & (\mathcal{A},\mathcal{M}) \\ \cap & & \cap & & & & \cap & & \cap \\ (\mathcal{R}_{0},\mathcal{M}_{0}^{2}) & & (\mathcal{R}_{1},\mathcal{M}_{1}^{2}) & & & & (\mathcal{R}_{t-1},\mathcal{M}_{t-1}^{2}) & & (\mathcal{R},\mathcal{M}^{2}) \end{array} \end{equation*} be a chain of unitary local commutative rings $(\mathcal{A}_{i},\mathcal{M}_{i})$ with their corresponding Galois ring extensions $(\mathcal{R}_{i},\mathcal{M}_{i}^{2})$, for $i=0,1,\cdots,t$. In this paper, we have given a construction technique of the cyclic, BCH, alternant, Goppa and Srivastava codes over these rings. Though, initially in \cite{AP} it is for local ring $(\mathcal{A},\mathcal{M})$, in this paper, this new approach have given a choice in selection of most suitable code in error corrections and code rate perspectives.

Goppa codes over certain semigroups

A Goppa code is described in terms of a polynomial, known as Goppa polynomial, and in contrast to cyclic codes, where it is difficult to estimate the minimum Hamming distance d from the generator polynomial. Furthermore, a Goppa code has the property that d ≥ deg(h(X))+1, where h(X) is a Goppa polynomial. In this paper, we present a decoding principle for Goppa codes constructed by generalized polynomials, which is based on modified Berlekamp-Massey algorithm.