Interaction of metal ions with 6-oxopurine nucleotides. Part 2. X-Ray structures of ternary nickel(II) complexes with 2'-deoxyguanosine 5'-monophosphate or guanosine 5'-monophosphate

The ternary metal nucleotide complexes [Ni(en)1.3(H2O)1.4(H2O)2][Ni(5?-dGMP)2(en)0.7-(H2O)0.6(H2O)2]·7H2O (1) and [Ni(en)2(H2O)2][Ni(5?-GMP)2(H2O)4]·6H2O (2)(en = ethylenediamine, 5?-dGMP = 2?-deoxyguanosine 5?-monophosphate, 5?-GMP = guanosine 5?-monophosphate) have been prepared and their structures analyzed by X-ray diffraction methods. Both compounds crystallise in the space group C2221 with a= 8.810(1), b= 25.090(4), c= 21.084(1)Å, and Z= 4 for (1) and a= 8.730(1), b= 25.691(4), c= 21.313(5)Å, and Z= 4 for (2). The structures were deduced from the analogous CoIII complexes and refined by full-matrix least-squares methods to final R values of 0.087 and 0.131 for 1 211 and 954 reflections for (1) and (2) respectively. An interesting feature of the deoxyribonucleotide complex (1) is that en is not totally labilized from the metal centre on nucleotide co-ordination, as observed in corresponding ribonucleotide complexes. Apart from extensive intra- and inter-molecular hydrogen bonding, the structures are stabilized by significant intracomplex base�base and base�sugar interactions. The nucleotides in both complexes have an anti base, C(2?)-endo sugar pucker, and gauche�gauche conformation about the C(4?)�C(5?) bond.

How to deal with sparse macroseismic data

This study discusses the scope of historical earthquake analysis in low-seismicity regions. Examples of non-damaging earthquake reports are given from the Eastern Baltic (Fennoscandian) Shield in north-eastern Europe from the 16th to the 19th centuries. The information available for past earthquakes in the region is typically sparse and cannot be increased through a careful search of the archives. This study applies recommended rigorous methodologies of historical seismology developed using ample data to the sparse reports from the Eastern Baltic Shield. Attention is paid to the context of reporting, the identity and role of the authors, the circumstances of the reporting, and the opportunity to verify the available information by collating the sources. We evaluate the reliability of oral earthquake recollections and develop criteria for cases when a historical earthquake is attested to by a single source. We propose parametric earthquake scenarios as a way to deal with sparse macroseismic reports and as an improvement to existing databases.

Simulation and graph mining tools for improving gene mapping efficiency

Gene mapping is a systematic search for genes that affect observable characteristics of an organism. In this thesis we offer computational tools to improve the efficiency of (disease) gene-mapping efforts. In the first part of the thesis we propose an efficient simulation procedure for generating realistic genetical data from isolated populations. Simulated data is useful for evaluating hypothesised gene-mapping study designs and computational analysis tools. As an example of such evaluation, we demonstrate how a population-based study design can be a powerful alternative to traditional family-based designs in association-based gene-mapping projects. In the second part of the thesis we consider a prioritisation of a (typically large) set of putative disease-associated genes acquired from an initial gene-mapping analysis. Prioritisation is necessary to be able to focus on the most promising candidates. We show how to harness the current biomedical knowledge for the prioritisation task by integrating various publicly available biological databases into a weighted biological graph. We then demonstrate how to find and evaluate connections between entities, such as genes and diseases, from this unified schema by graph mining techniques. Finally, in the last part of the thesis, we define the concept of reliable subgraph and the corresponding subgraph extraction problem. Reliable subgraphs concisely describe strong and independent connections between two given vertices in a random graph, and hence they are especially useful for visualising such connections. We propose novel algorithms for extracting reliable subgraphs from large random graphs. The efficiency and scalability of the proposed graph mining methods are backed by extensive experiments on real data. While our application focus is in genetics, the concepts and algorithms can be applied to other domains as well. We demonstrate this generality by considering coauthor graphs in addition to biological graphs in the experiments.

A standard reference frame for the description of Nucleic Acid Base-Pair Geometry

A common point of reference is needed to describe the three-dimensional arrangements of bases and base-pairs in nucleic acid structures. The different standards used in computer programs created for this purpose give rise to con¯icting interpretations of the same structure.1 For example, parts of a structure that appear ``normal'' according to one computational scheme may be highly unusual according to another and vice versa. It is thus dif®cult to carry out comprehensive comparisons of nucleic acid structures and to pinpoint unique conformational features in individual structures

Error-free matrix symmetrizers and equivalent symmetric matrices

A symmetrizer of the matrix A is a symmetric solution X that satisfies the matrix equation XA=AprimeX. An exact matrix symmetrizer is computed by obtaining a general algorithm and superimposing a modified multiple modulus residue arithmetic on this algorithm. A procedure based on computing a symmetrizer to obtain a symmetric matrix, called here an equivalent symmetric matrix, whose eigenvalues are the same as those of a given real nonsymmetric matrix is presented.

Fracture Properties of Concrete-Concrete Interfaces Using Digital Image Correlation

The mode I and mode II fracture toughness and the critical strain energy release rate for different concrete-concrete jointed interfaces are experimentally determined using the Digital Image Correlation technique. Concrete beams having different compressive strength materials on either side of a centrally placed vertical interface are prepared and tested under three-point bending in a closed loop servo-controlled testing machine under crack mouth opening displacement control. Digital images are captured before loading (undeformed state) and at different instances of loading. These images are analyzed using correlation techniques to compute the surface displacements, strain components, crack opening and sliding displacements, load-point displacement, crack length and crack tip location. It is seen that the CMOD and vertical load-point displacement computed using DIC analysis matches well with those measured experimentally.

Electrical Relaxation and Transport in 0.5Cs(2)O-0.5Li(2)O-3B(2)O(3) Glasses

The frequency and temperature dependence of the dielectric constant and the electrical conductivity of the transparent glasses in the composition 0.5Cs(2)O-0.5Li(2)O-3B(2)O(3) (CLBO) were investigated in the 100 Hz - 10 MHz frequency range. The dielectric constant for the as-quenched glass increased with increasing temperature, exhibiting anomalies in the vicinity of the glass transition and crystallization temperatures. The temperature coefficient of dielectric constant was estimated (35 +/- 2 ppm. K-1) using Havinga's formula. The dielectric loss at 313 K is 0.005 +/- 0.0005 at all the frequencies understudy. The activation energy associated with the electrical relaxation determined from the electric modulus spectra was found to be 1.73 +/- 0.05 eV, close to that of the activation energy obtained for DC conductivity (1.6 +/- 0.06 eV). The frequency dependent electrical conductivity was analyzed using Jonscher's power law. The combination of these dielectric characteristics suggests that these are good candidates for electrical energy storage device applications.

Unsteady free convection flow under the influence of a magnetic field

The unsteady free convection boundary layer at the stagnation point of a two-dimensional body and an axisymmetric body with prescribed surface heat flux or temperature has been studied. The magnetic field is applied parallel to the surface and the effect of induced magnetic field has been considered. It is found that for certain powerlaw distribution of surface heat flux or temperature and magnetic field with time, the governing boundary layer equations admit a self-similar solution locally. The resulting nonlinear ordinary differential equations have been solved using a finite element method and a shooting method with Newton's corrections for missing initial conditions. The results show that the skin friction and heat transfer coefficients, and x-component of the induced magnetic field on the surface increase with the applied magnetic field. In general, the skin friction, heat transfer and x-component of the induced magnetic field for axisymmetric case are more than those of the two-dimensional case. Also they change more when the surface heat flux or temperature decreases with time than when it increases with time. The skin friction, heat transfer and x-component of the induced magnetic field are significantly affected by the magnetic Prandtl number and they increase as the magnetic Prandtl number decreases. The skin friction and x-component of the magnetic field increase with the dissipation parameter, but heat transfer decreases.

Iron, cobalt and nickel nanoparticles encapsulated in carbon obtained by the arc evaporation of graphite with the metals

Are evaporation of graphite with Fe, Co and Ni yields two distinct types of metal nanoparticles, wrapped in graphitic layers and highly resistant to oxidation. Electron microscopy shows that the metal particles (10-40 nm) in the stub region are encapsulated in carbon onions, the particles in the soot being considerably smaller (2-15 nm). The metal particles in the soot are either ferromagnetic with lowered Curie temperatures or superparamagnetic.

Joining of dissimilar metals: issues and modelling techniques

Joining of dissimilar metals involves a number of scientific issues, the modelling of which offers unique challenges. This review discusses the complexities in different joining processes and dissimilar combinations, and the corresponding computational techniques that have the potential to address the same. Future directions in modelling at both macroscopic and microscopic scales are also suggested.

Solubilities of Benzene Derivatives in Supercritical Carbon Dioxide

The solubilities of benzene derivatives in supercritical carbon dioxide was determined by the saturation method over the pressure range (9.5 to 14.5) MPa. The solubilities were determined at (308 and 313) K for 1-chloro-2,4-dinitrobenzene and (308, 318, and 328) K for m-dinitrobenzene. At 308K, the solubility (in mole fraction) of 1-chloro-2,4-dinitrobenzene varied from (2.83 to 5.88).10(-3) while the solubility of m-dinitrobenzene increased from (2.05 to 5.54).10(-3) as the pressure increased from (9.5 to 14.5) MPa. However, the solubilities of both compounds decreased with increasing temperature. Models based on the solubility parameter and semiempirical models such as the Mendez-Santiago-Teja model, the Gordillo model, and the association model, were used to correlate the experimental solubility data for the benzene derivatives.

Comparative Nucleotide and Amino Acid Sequence Analysis of the Sequence-Specific RNA-Binding Rotavirus Nonstructural Protein NSP3

NSP3, an acidic nonstructural protein, encoded by gene 7 has been implicated as the key player in the assembly of the 11 viral plus-strand RNAs into the early replication intermediates during rotavirus morphogenesis. To date, the sequence or NSP3 from only three animal rotaviruses (SA11, SA114F, and bovine UK) has been determined and that from a human strain has not been reported. To determine the genetic diversity among gene 7 alleles from group A rotaviruses, the nucleotide sequence of the NSP3 gene from 13 strains belonging to nine different G serotypes, from both humans and animals, has been determined. Based on the amino acid sequence identity as well as phylogenetic analysis, NSP3 from group A rotaviruses falls into three evolutionarily related groups, i.e., the SA11 group, the Wa group, and the S2 group. The SA 11/SA114F gene appears to have a distant ancestral origin from that of the others and codes for a polypeptide of 315 amino acids (aa) in length. NSP3 from all other group A rotaviruses is only 313 aa in length because of a 2-amino-acid deletion near the carboxy-terminus, While the SA114F gene has the longest 3' untranslated region (UTR) of 132 nucleotides, that from other strains suffered deletions of varying lengths at two positions downstream of the translational termination codon. In spite of the divergence of the nucleotide (nt) sequence in the protein coding region, a stretch of about 80 nt in the 3' UTR is highly conserved in the NSP3 gene from all the strains. This conserved sequence in the 3' UTR might play an important role in the regulation of expression of the NSP3 gene. (C) 1995 Academic Press, Inc.

Structure of 9[alpha],19-dihydroxy-4-androstene-3,17-dione

C19H26O4, M(r) = 318.41, orthorhombic, P2(1)2(1)2(1), a = 10.591 (1), b = 11.133 (1), c = 13.657 (2) angstrom, V = 1610.29 angstrom 3, Z = 4, D(m) (flotation in KI) = 1.301, D(x) = 1.313 g cm-3, Mo K-alpha, lambda = 0.7107 angstrom, mu = 0.85 cm-1, F(000) = 688, T = 293 K, R = 0.057 for 1253 significant reflections. The A ring is disordered with atoms C(2) and O(19) occupying two possible sites. The molecules are held together by a hydrogen bond [O(9)...O(17) = 2.89 angstrom].