A Refinement of some Overrelaxation Algorithms for Solving a System of Linear Equations

In this paper we propose a refinement of some successive overrelaxation methods based on the reverse Gauss–Seidel method for solving a system of linear equations Ax = b by the decomposition A = Tm − Em − Fm, where Tm is a banded matrix of bandwidth 2m + 1. We study the convergence of the methods and give software implementation of algorithms in Mathematica package with numerical examples. ACM Computing Classification System (1998): G.1.3.

Stepwise refinement of interrupt-driven real-time programs

Embedded real-time programs rely on external interrupts to respond to events in their physical environment in a timely fashion. Formal program verification theories, such as the refinement calculus, are intended for development of sequential, block-structured code and do not allow for asynchronous control constructs such as interrupt service routines. In this article we extend the refinement calculus to support formal development of interrupt-dependent programs. To do this we: use a timed semantics, to support reasoning about the occurrence of interrupts within bounded time intervals; introduce a restricted form of concurrency, to model composition of interrupt service routines with the main program they may preempt; introduce a semantics for shared variables, to model contention for variables accessed by both interrupt service routines and the main program; and use real-time scheduling theory to discharge timing requirements on interruptible program code.

An examination of the factorial invariance and refinement of the multidimensional school anger inventory for five Pacific Rim countries

The validity of the Multidimensional School Anger Inventory (MSAI) was examined with adolescents from 5 Pacific Rim countries (N ¼ 3,181 adolescents; age, M ¼ 14.8 years; 52% females). Confirmatory factor analyses examined configural invariance for the MSAI’s anger experience, hostility, destructive expression, and anger coping subscales. The model did not converge for Peruvian students. Using the top 4 loaded items for anger experience, hostility, and destructive expression configural invariance and partial metric and scalar invariances were found. Latent means analysis compared mean responses on each subscale to the U.S. sample. Students from other countries showed higher mean responses on the anger experience subscale (ds ¼ .37–.73). Australian (d ¼ .40) and Japanese students (d ¼ .21) had significantly higher mean hostility subscale scores. Australian students had higher mean scores on the destructive expression subscale (d ¼ .30), whereas Japanese students had lower mean scores (d ¼ 2.17). The largest latent mean gender differences (females lower than males) were for destructive expression among Australian (d ¼ 2.67), Guatemalan (d ¼ 2.42), and U.S. (d ¼ 2.66) students. This study supported an abbreviated, 12-item MSAI with partial invariance. Implications for the use of the MSAI in comparative research are discussed.

Selective involvement of TIMP-2 in the second activational cleavage of pro-MMP-2 : refinement of the pro-MMP-2 activation mechanism

A tissue inhibitor of metalloproteinases-2 (TIMP-2)-independent mechanism for generating the first activational cleavage of pro-matrix metalloproteinase-2 (MMP-2) was identified in membrane type-1 MMP (MT1-MMP)-transfected MCF-7 cells and confirmed in TIMP-2-deficient fibroblasts. In contrast, the second MMP-2-activational step was found to be TIMP-2 dependent in both systems. MMP-2 hemopexin C-terminal domain was found to be critical for the first step processing, confirming a need for membrane tethering. We propose that the intermediate species of MMP-2 forms the well-established trimolecular complex (MT1-MMP/TIMP-2/MMP-2) for further TIMP-2-dependent autocatalytic cleavage to the fully active species. This alternate mechanism may supplement the traditional TIMP-2-mediated first step mechanism.

The development and refinement of the practice domain framework as a conceptual tool for understanding and guiding social care practice

This study identified the common factors that influence social care practice across disciplines (such as social work and psychology), practice fields, and geographical contexts and further developed the Practice Domain Framework as an empirically-based conceptual framework to assist practitioners in understanding practice complexities. The framework has application in critical reflection, professional supervision, interdisciplinary understanding, teamwork, management, teaching and research. A mixed-methods design was used to identify the components and structure of the refined framework. Eighteen influential factors were identified and organised into eight domains: the Societal, Structural, Organisational, Practice Field, Professional Practice, Accountable Practice, Community of Place, and Personal.

Bayesian refinement of association signals for 14 loci in 3 common diseases

To further investigate susceptibility loci identified by genome-wide association studies, we genotyped 5,500 SNPs across 14 associated regions in 8,000 samples from a control group and 3 diseases: type 2 diabetes (T2D), coronary artery disease (CAD) and Graves' disease. We defined, using Bayes theorem, credible sets of SNPs that were 95% likely, based on posterior probability, to contain the causal disease-associated SNPs. In 3 of the 14 regions, TCF7L2 (T2D), CTLA4 (Graves' disease) and CDKN2A-CDKN2B (T2D), much of the posterior probability rested on a single SNP, and, in 4 other regions (CDKN2A-CDKN2B (CAD) and CDKAL1, FTO and HHEX (T2D)), the 95% sets were small, thereby excluding most SNPs as potentially causal. Very few SNPs in our credible sets had annotated functions, illustrating the limitations in understanding the mechanisms underlying susceptibility to common diseases. Our results also show the value of more detailed mapping to target sequences for functional studies. © 2012 Nature America, Inc. All rights reserved.

High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2

The X-ray structure of recombinant bovine pancreatic phospholipase A(2) (PLA2), which specifically catalyzes the cleavage of the sn-2 acylester bond of phospholipids, has been refined at 1.5 Angstrom resolution. The crystal belongs to the space group P2(1)2(1)2(1) with unit-cell parameters a = 47.12, b = 64.59 and c = 38.14 Angstrom similar to the native enzyme reported previously by Dijkstra et nl. [J. Mel. Biol. (1981), 147, 97-123]. The refinement converged to an R value of 18.4% (R-free = 22.8%) for 16 374 reflections between 10.0 and 1.5 Angstrom resolution. The surface-loop residues (60-70) art: ordered in the present orthorhombic recombinant enzyme, but disordered in the trigonal recombinant enzyme. The active-site residues, His48, Asp99, and the catalytic water superimpose well with the trigonal form. Besides the catalytic water which is hydrogen bonded to His48, it is often seen that there is a second water attached to the same N atom of His48 and simultaneously hydrogen bonded to the O atom of Asp49. It is thought that the second water facilitates the tautomerism of His48 for enzyme catalysis, The catalytic water is also hydrogen bonded to the equatorial water coordinated to the calcium ion, In addition to the equatorial water, there is also an axial calcium water and the additional structural water. These five common water molecules are hydrogen bonded to the additional 16 water molecules in the present orthorhombic structure which may further enhance the structural integrity of the active site. Besides the protein and one calcium ion, a total of 134 water molecules were located in the present high-resolution refinement.

Refinement of defection strategies stabilizes cooperation

Cooperation among unrelated individuals is an enduring evolutionary riddle and a number of possible solutions have been suggested. Most of these suggestions attempt to refine cooperative strategies, while little attention is given to the fact that novel defection strategies can also evolve in the population. Especially in the presence of punishment to the defectors and public knowledge of strategies employed by the players, a defecting strategy that avoids getting punished by selectively cooperating only with the punishers can get a selective benefit over non-conditional defectors. Furthermore, if punishment ensures cooperation from such discriminating defectors, defectors who punish other defectors can evolve as well. We show that such discriminating and punishing defectors can evolve in the population by natural selection in a Prisoner’s Dilemma game scenario, even if discrimination is a costly act. These refined defection strategies destabilize unconditional defectors. They themselves are, however, unstable in the population. Discriminating defectors give selective benefit to the punishers in the presence of non-punishers by cooperating with them and defecting with others. However, since these players also defect with other discriminators they suffer fitness loss in the pure population. Among the punishers, punishing cooperators always benefit in contrast to the punishing defectors, as the latter not only defect with other punishing defectors but also punish them and get punished. As a consequence of both these scenarios, punishing cooperators get stabilized in the population. We thus show ironically that refined defection strategies stabilize cooperation. Furthermore, cooperation stabilized by such defectors can work under a wide range of initial conditions and is robust to mistakes.

On the Fourier refinement of protein structures

The situation normally encountered in the high-resolution refinement of protein structures is one in which the inaccurate positions of P out of a total of N atoms are known whereas those of the remaining atoms are unknown. Fourier maps with coefficients (FN -- F'P) × exp (i[alpha]'P) and (mFN -- nF'P) exp (i[alpha]'P), where FN is the observed structure factor and F'P and [alpha]'P are the magnitude and the phase angle of the calculated structure factor corresponding to the inaccurate atomic positions, are often used to correct the positions of the P atoms and to determine those of the Q unknown atoms. A general theoretical approach is presented to elucidate the effect of errors in the positions of the known atoms on the corrected positions of the known atoms and the positions of the unknown atoms derived from such maps. The theory also leads to the optimal choice of parameters used in the different syntheses. When the errors in the positions of the input atoms are systematic, their effects are not taken care of automatically by the syntheses.

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of mn K-edge XANES data

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K-edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3. The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K-edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

Confirmation of linkage and refinement of the RP28 locus for autosomal recessive retinitis pigmentosa on chromosome 2p14-p15 in an Indian family

PURPOSE: To report the linkage analysis of retinitis pigmentosa (RP) in an Indian family. METHODS: Individuals were examined for symptoms of retinitis pigmentosa and their blood samples were withdrawn for genetic analysis. The disorder was tested for linkage to known 14 adRP and 22 arRP loci using microsatellite markers. RESULTS: Seventeen individuals including seven affecteds participated in the study. All affected individuals had typical RP. The age of onset of the disease ranged from 8-18 years. The disorder in this family segregated either as an autosomal recessive trait with pseudodominance or an autosomal dominant trait. Linkage to an autosomal recessive locus RP28 on chromosome 2p14-p15 was positive with a maximum two-point lod score of 3.96 at theta=0 for D2S380. All affected individuals were homozygous for alleles at D2S2320, D2S2397, D2S380, and D2S136. Recombination events placed the minimum critical region (MCR) for the RP28 gene in a 1.06 cM region between D2S2225 and D2S296. CONCLUSIONS : The present data confirmed linkage of arRP to the RP28 locus in a second Indian family. The RP28 locus was previously mapped to a 16 cM region between D2S1337 and D2S286 in a single Indian family. Haplotype analysis in this family has further narrowed the MCR for the RP28 locus to a 1.06 cM region between D2S2225 and D2S296. Of 15 genes reported in the MCR, 14 genes (KIAA0903, OTX1, MDH1, UGP2, VPS54, PELI1, HSPC159, FLJ20080, TRIP-Br2, SLC1A4, KIAA0582, RAB1A, ACTR2, and SPRED2) are either expressed in the eye or retina. Further study needs to be done to test which of these genes is mutated in patients with RP linked to the RP28 locus.