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PubMed2004

Analysis of speedup as function of block size and cluster size for parallel feed-forward neural networks on a Beowulf cluster.

The performance of feed-forward neural networks trained with the backpropagation algorithm on a dedicated Beowulf cluster is analyzed. The concept of training set parallelism is applied. A new model for run time and speedup prediction is developed. With the model the speedup and efficiency of one iteration of the neural networks can be estimated as a function of block size and cluster size. The model is applied to three example problems representing different applications and network architectures. The estimation of the model has a higher accuracy than traditional methods for run time estimation and can be efficiently calculated. Experiments show that speedup of one iteration does not necessarily translate to a shorter training time toward a given error level. To overcome this problem a heuristic extension to training set parallelism called weight averaging is developed. The results show that training in parallel should only be done on clusters with high performance network connections or a multiprocessor machine. A rule of thumb is given for how much network performance of the cluster is needed to achieve speedup of the training time for a neural network.

Cluster Analysis↗
PubMed2005

cluML: A markup language for clustering and cluster validity assessment of microarray data.

cluML is a new markup language for microarray data clustering and cluster validity assessment. The XML-based format has been designed to address some of the limitations observed in traditional formats, such as inability to store multiple clustering (including biclustering) and validation results within a dataset. cluML is an effective tool to support biomedical knowledge representation in gene expression data analysis. Although cluML was developed for DNA microarray analysis applications, it can be effectively used for the representation of clustering and for the validation of other biomedical and physical data that has no limitations.

Algorithms↗
PubMed2004

Organization of the Hox gene cluster of the silkworm, Bombyx mori: a split of the Hox cluster in a non-Drosophila insect.

A bacterial artificial chromosome (BAC) contig was constructed by chromosome walking, starting from the Hox genes of the silkworm, Bombyx mori. Bombyx orthologues of the labial (lab) and zerknult (zen) genes were newly identified. The size of the BAC contig containing the Hox gene cluster-except the lab and Hox 2 genes-was estimated to be more than 2 Mb. The Bombyx Hox cluster was mapped to linkage group (LG) 6. The lab gene was mapped on the same LG, but far apart from the cluster. Fluorescence in situ hybridization analysis confirmed that the major Hox gene cluster and lab were at different locations on the same chromosome in B. mori.

Amino Acid Sequence↗
PubMed1987

The transcriptional efficiency of clustered tRNA genes is affected by their position within the cluster.

The transcription of a mouse genomic segment containing four tRNA genes, coding for a tRNA(Ala), a tRNA(Ile), a tRNA(Pro) and a tRNA(Lys), has been studied in a HeLa cell extract, demonstrating that differences among their transcriptional efficiencies are evident using as templates either the natural cluster or an equimolecular mixture of the four isolated genes. Nevertheless, the structure of the cluster influences the transcriptional efficiency of the clustered genes. In fact, a cis-acting inhibitory sequence has been located at about 400 bp downstream of the tRNA(Pro) coding sequence. Moreover rearrangements of the reciprocal position of the various tRNA genes within the cluster results in significant changes in the transcriptional rates of the individual transcriptional units.

Animals↗
PubMed1988

Localization and physical mapping of a plasmid-borne 23-kb nif gene cluster from Enterobacter agglomerans showing homology to the entire nif gene cluster of Klebsiella pneumoniae M5a1.

A physical and genetical map of the plasmid pEA3 indigenous to Enterobacter agglomerans is presented. pEA3 is a 111-kb large plasmid containing a 23-kb large cluster of nif genes which shows extensive homology (Southern hybridization and heteroduplex analysis) to the entire nif gene cluster of Klebsiella pneumoniae (Kp) M5a1. All the nif genes on pEA3 are organized in the same manner as in K. pneumoniae, except nifJ, which is located on the left end of pEA3 nif gene cluster (near nifQB). A BamHI restriction map of pEA3 and a detailed restriction map of the 23-kb nif region on pEA3 is also presented. The nif genes of pEA3 showed a low level of acetylene reduction in Escherichia coli, demonstrating that these genes are functional and contain the whole genetic information required to fix nitrogen. The origin of vegetative replication (OriV) of pEA3 was localized about 5.5 kb from the right end of the nif gene cluster. In addition to pEA3, large plasmids from four other strains of E. agglomerans showed homology to all the Kp nif genes tested, indicating that in diazotrophic strains of E. agglomerans nif genes are usually located on plasmids. In contrast, in most of the free-living, nitrogen-fixing bacteria the nif genes are on chromosome.

DNA Restriction Enzymes↗
PubMed1992

The beta globin gene cluster of the prosimian primate Galago crassicaudatus: nucleotide sequence determination of the 41-kb cluster and comparative sequence analyses.

The nucleotide sequence of the beta globin gene cluster of the prosimian Galago crassicaudatus has been determined. A total sequence spanning 41,101 bp contains and links together previously published sequences of the five galago beta-like globin genes (5'-epsilon-gamma-psi eta-delta-beta-3'). A computer-aided search for middle interspersed repetitive sequences identified 10 LINE (L1) elements, including a 5' truncated repeat that is orthologous to the full-length L1 element found in the human epsilon-gamma intergenic region. SINE elements that were identified included one Alu type I repeat, four Alu type II repeats, and two methionine tRNA-derived Monomer (type III) elements. Alu type II and Monomer sequences are unique to the galago genome. Structural analyses of the cluster sequence reveals that it is relatively A+T rich (about 62%) and regions with high G+C content are associated primarily with globin coding regions. Comparative analyses with the beta globin cluster sequences of human, rabbit, and mouse reveal extensive sequence homologies in their genic regions, but only human, galago, and rabbit sequences share extensive intergenic sequence homologies. Divergence analyses of aligned intergenic and flanking sequences from orthologous human, galago, and rabbit sequences show a gradation in the rate of nucleotide sequence evolution along the cluster where sequences 5' of the epsilon globin gene region show the least sequence divergence and sequences just 5' of the beta globin gene region show the greatest sequence divergence.

Amino Acid Sequence↗
PubMed1995

Evidence for a mixed-ligand [4Fe-4S] cluster in the C14D mutant of PsaC. Altered reduction potentials and EPR spectral properties of the FA and FB clusters on rebinding to the P700-FX core.

PsaC-C14D (cysteine 14 replaced by aspartic acid) contains a [3Fe-4S] and a [4Fe-4S] cluster in the FB and FA sites of the free protein [Yu, L., Zhao, J., Lu, W., Bryant, D. A., & Golbeck, J. H. (1993) Biochemistry 32, 8251-8258]. When PsaC-C14D is rebound to a photosystem I (PS I) core, the g-values of 2.043, 1.939, and 1.853 appear similar to FA in a wild-type PS I complex [Zhao, J. D., Li, N., Warren, P. V., Golbeck, J. H., & Bryant, D. A. (1992) Biochemistry 31, 5093-5099]. The reconstituted PsaC-C14D-PS I complex does not contain a [3Fe-4S] cluster; rather, a set of resonances with a rhombic line shape, a gav of approximately 1.97, and broad line widths indicate the presence of a mixed-ligand [4Fe-4S] cluster, termed FB', in the aspartate site. Both FA and FB' become photoreduced at 15 K, and show an interaction spectrum when reduced within the same reaction center. An electrochemical redox study shows that FA and FB' titrate with midpoint potentials near -600 mV at pH 10.0. Single-turnover flash experiments indicate that FA and FB' function as efficient electron acceptors at room temperature, and NADP+ photoreduction rates are about 70% that of a reconstituted PsaC-PS I complex. A population of S = 3/2, [4Fe-4S] clusters was tentatively identified in the free PsaC-C14D protein by characteristic EPR resonances in the g = 5.3 region.(ABSTRACT TRUNCATED AT 250 WORDS)

Chlorophyll↗
PubMed1996

Characterization of an autoreduction pathway for the [Fe4S4]3+ cluster of mutant Chromatium vinosum high-potential iron proteins. Site-directed mutagenesis studies to probe the role of phenylalanine 66 in defining the stability of the [Fe4S4] center provide evidence for oxidative degradation via a [Fe3S4] cluster.

A number of point mutations of the conserved aromatic residue phenylalanine 66 (Phe66Tyr, -Asn, -Cys, -Ser) in Chromatium vinosum high-potential iron sulfur protein have been examined with the aim of understanding the functional role of this residue. Nonconservative replacements with polar residues have a minimal effect on the midpoint potential of the [Fe4S4]3+/2+ cluster, typically < +25 mV, with a maximum change of +40 mV for Phe66Asn. With the exception of the Phe66Tyr mutant, the oxidized state was found to be unstable relative to the recombinant native, with regeneration of the reduced state. The pathway for this transformation involves degradation of the cluster in a fraction of the sample, which provides the reducing equivalents required to bring about reduction of the remainder of the sample. This degradative reaction proceeds through a transient [Fe3S4]+ intermediate that is characterized by typical g values and power saturation behavior and is prompted by the increased solvent accessibility of the cluster core in the nonconservative Phe66 mutants as evidenced by 1H-15N HMQC NMR experiments. These results are consistent with a model where the critical role of the aromatic residues in the high-potential iron proteins is to protect the cluster from hydrolytic degradation in the oxidized state.

Bacterial Proteins↗
PubMedDate not supplied

Clustering files of chemical structures using the fuzzy k-means clustering method.

This paper evaluates the use of the fuzzy k-means clustering method for the clustering of files of 2D chemical structures. Simulated property prediction experiments with the Starlist file of logP values demonstrate that use of the fuzzy k-means method can, in some cases, yield results that are superior to those obtained with the conventional k-means method and with Ward's clustering method. Clustering of several small sets of agrochemical compounds demonstrate the ability of the fuzzy k-means method to highlight multicluster membership and to identify outlier compounds, although the former can be difficult to interpret in some cases.

Journal Article↗
PubMed2003

Nanostructured magnetic cuprate cluster: synthesis, structure, UV-Vis spectroscopy, and magnetic properties of a new copper(II) arsenate NaCuAsO4 containing discrete [Cu4O16]24- clusters.

Crystals of copper(II) arsenate NaCuAsO(4) were grown by conventional high-temperature, solid-state methods in molten-salt media. The compounds were characterized by single crystal X-ray diffraction, UV-vis spectroscopy, and magnetic susceptibility measurements. NaCuAsO(4) crystallizes in a monoclinic lattice with a = 6.002 (1) A, b = 10.853 (2) A, c = 10.373 (2) A, beta = 91.50 (3) degrees, and V = 675.4(2) A(3); P2(1)/c (No. 14); Z = 8. The newly isolated sodium copper(II) arsenate reveals a pseudo-one-dimensional channel structure where the sodium cations reside. The extended framework contains nanostructured [Cu(4)O(16)](24-) magnetic clusters that are interlinked by closed-shell, nonmagnetic AsO(4)(3-) oxy anions via sharing vertex oxygen atoms of the CuO(5) and AsO(4) polyhedral units. Each [Cu(4)O(16)](24-) cluster consists of four CuO(5) square pyramidal units in a chair configuration centered by a center of inversion. The two crystallographically independent Cu(2+) cations adopt the [4 + 1] CuO(5) Jahn-Teller distortion giving rise to an intense d-d transition in UV-vis absorption spectra. The magnetic susceptibility measurements reveal that the title compound is antiferromagnetic. At high temperatures, the data follows a pure Curie law, suggesting noninteracting spins, but with a rapid suppression of the effective spin below T = 70 K. At low temperature, the susceptibility collapses, indicating spin gap formation as the magnetic-cluster material settles into the lowest energy magnetic singlet state. The current work in the exploratory synthesis of oxy compounds containing nanostructured transition-metal-oxide magnetic clusters leads to new materials for experimental and theoretical developments of magnetic models.

Journal Article↗
PubMed2003

Magnetic and optical studies on an S = 6 ground-state cluster [Cr12O9(OH)3(O2CCMe3)15]: determination of, and the relationship between, single-ion and cluster spin Hamiltonian parameters.

The dodecametallic Cr(III) cluster [Cr(12)O(9)(OH)(3)(O(2)CCMe(3))(15)] has a ground spin state of S = 6 characterized by the spin Hamiltonian parameters g(ZZ)() = 1.965, g(XX)() = g(YY)() = 1.960, D(S=)()(6) = +0.088 cm(-)(1), and E(S=)()(6) = 0 (where D and E are the axial and rhombic zero-field splitting parameters, respectively) as determined by multifrequency EPR spectroscopy and magnetization studies. Micro-SQUID magnetization studies reveal steps due to the fine structure of the ground state, with the spacing between the steps in excellent agreement with the D(S=)()(6) value determined by EPR. Analysis of high-resolution optical data (MCD) allows us to determine the single-ion g values and D value (= -1.035 cm(-)(1)) of the constituent Cr(III) ions directly. A vector coupling analysis demonstrates that the cluster ZFS is almost entirely due to the single-ion component. Thus, the relative orientations of the local and cluster magnetic axes can lead to a cluster ZFS of opposite sign to the single-ion value, even when this is the only significant contribution.

Journal Article↗
PubMed1996

Synthetic, Structural, Spectroscopic, and Theoretical Studies of Structural Isomers of the Cluster Pt(3)(&mgr;-PPh(2))(3)Ph(PPh(3))(2). A Unique Example of Core Isomerism in Phosphine Phosphido-Rich Clusters.

Two isomers of the phosphido-bridged platinum cluster Pt(3)(&mgr;-PPh(2))(3)Ph(PPh(3))(2) (2 and 3) have been isolated, and their structures have been solved by single-crystal X-ray diffraction. Compound 2 crystallizes in the orthorhombic space group Cmc2(1) with a = 22.192(10) Å, b = 17.650(9) Å, c = 18.182(8) Å, and Z = 4. Compound 3 crystallizes with 2 molecules of dichloromethane in the monoclinic space group C2/c with a = 21.390(10) Å, b = 18.471(9) Å, c = 19.021(11) Å, beta = 105.27(5) degrees, and Z = 4. The two isomers differ essentially in their metal-metal distances and Pt-(&mgr;-PPh(2))-Pt angles. Thus 2, having an imposed C(s) symmetry, contains a bent chain of metal atoms with two short Pt-Pt distances of 2.758(3) Å and a long separation of 3.586(2) Å. In 3, which has an imposed C(2) symmetry, the metal atoms form an isosceles triangle with two Pt-Pt distances of 2.956(3) Å and one of 3.074(4) Å. These isomers can be smoothly interconverted by changing the crystallization solvents. Solution and solid-state (31)P NMR studies have been performed in order to assign the resonances of the different P nuclei and relate their chemical shifts with their structural environments. Raman spectroscopy was used to assign the nu(Pt-Pt) modes of the two structural isomers. Theoretical studies based on extended Hückel calculations and using the fragment molecular orbital approach show that the isomer with the three medium Pt-Pt distances is slightly more stable, in agreement with earlier theoretical predictions. Cluster core isomerism remains a rare phenomenon, and the present example emphasizes the role and the importance of flexible phosphido bridges in stabilizing clusters as well as the unprecedented features which can be observed in phosphine phosphido-rich metal clusters.

Journal Article↗
PubMed1996

Clusters as Ligands. 4. Synthesis, Structure, and Characterization of the Tungsten(II)-Tungsten(III) Cluster Carboxylate {[Na][W(2){OOCCCo(3)(CO)(9)}(2)(OOCCF(3))(4)(THF)(2)]}(2).

The reaction of W(2)(OOCCF(3))(4) with (CO)(9)Co(3)CCOOH and Na[OOCCF(3)] in a nonpolar solvent mixture leads to the formation of the cluster of clusters {[Na][W(2){OOCCCo(3)(CO)(9)}(2)(OOCCF(3))(4)(THF)(2)]}(2), 1, in 40% yield. The structure of 1.3C(6)H(5)CH(3) in the solid state corresponds to a dimer of W(2) dinuclear complexes (monoclinic P2(1)/c, a = 15.234(6) Å, b = 23.326(11) Å, c = 20.658(7) Å, beta = 102.46(3) degrees; V = 7,168(5) Å(3); Z = 4; R(F)() = 8.39%). Each W(2) unit is bridged by two cis cluster carboxylates, and the remaining four equatorial sites are occupied by monodentate [OOCCF(3)](-) ligands. The axial positions contain coordinated THF. The W(2) carboxylate is opened up (W-W distance of 2.449(2) Å) so that the free ends of the [OOCCF(3)](-) ligands on both W(2) carboxylate units can cooperate in chelating two Na(+) ions thereby forming a dimer of W(2) complexes. A distinctive EPR spectrum with g = 2.08 is consistent with each W(2) carboxylate being a mixed-valent W(II)-W(III) species. The reaction of W(2)(OOCCF(3))(4) with (CO)(9)Co(3)CCOOH in THF in the absence of Na[OOCCF(3)] leads to the expected diamagnetic W(II)-W(II) cluster carboxylate W(2){OOCCCo(3)(CO)(9)}(3)(OOCCF(3))(THF)(2), 3.

Journal Article↗
PubMed2005

Gold cluster carbonyls: vibrational spectroscopy of the anions and the effects of cluster size, charge, and coverage on the CO stretching frequency.

We report the vibrational spectra of the carbonyl complexes of anionic gold clusters in the range of the CO stretching frequency as measured in the gas phase using IR multiple photon dissociation spectroscopy. The investigated complexes contain between 3 and 14 Au atoms and up to 7 CO ligands. Special attention is given to the complexes that exhibit saturation CO coverage as well as to the monocarbonyl species. In conjunction with data from the corresponding cationic complexes we quantify how the CO stretching frequency varies with the charge state of the gold cluster. Our results provide a size- and charge-dependent basis to interpret values of the CO stretching frequency measured for CO on deposited gold clusters in terms of the charge states of the clusters.

Journal Article↗
PubMed2006

Relativistic DFT studies of dehydrogenation of methane by Pt cationic clusters: cooperative effect of bimetallic clusters.

The dehydrogenation reaction mechanisms of methane catalyzed by transition-metal clusters PtM(+) (M = Cu, Ag, Au) and Pt(n)(+) (n = 2-4) have been investigated theoretically. In the reactions of PtM(+) (M = Cu, Ag, Au) with CH(4), cleavage of the first C-H bond is quite facile without barrier. The second C-H bond activation and the release of H(2) from molecular complex are generally the rate-determining steps. In the reactions of platinum clusters Pt(n)()(+) (n = 2-4) with CH(4), the H(2) elimination from the dihydrogen complex is the rate-determining step. Spin crossover may occur in the reaction of Pt(2)(+) and CH(4). Pt(2)(+) and Pt(3)(+) can dehydrogenate methane efficiently due to remarkable thermodynamic stability of the products. The dehydrogenation of methane induced by Pt(4)(+) is less favored thermodynamically than Pt(n)()(+) (n = 1, 2, 3). On the basis of theoretical analyses, the differences in reactivity among the clusters and the nature of cooperative effect of the bimetallic cluster have been discussed. The calculated results provide a reasonable basis for understanding of experimental observations.

Journal Article↗
PubMed1994

The selection of antibodies for targeted therapy of small-cell lung cancer (SCLC) using a human tumour spheroid model to compare the uptake of cluster 1 and cluster w4 antibodies.

Spheroids of a small-cell lung cancer (SCLC) cell line POC were used to evaluate the uptake and penetration of two antibodies recognising different SCLC antigens. Spheroids approximately 300-400 microns in diameter were incubated with 1 microgram ml-1 125I-labelled NY.3D11, an antibody which reacts with the cluster 1 group antigen (neural cell adhesion molecule; NCAM) and [125I]SWA11, which binds to the cluster w4 antigen. The rate of uptake of both antibodies was similar; an initially rapid phase was seen during the first 8 h and maximum uptake occurred by 24 h. The mean uptake per spheroid at 24 h was 0.97 ng for [125I]NY.3D11 and 0.45 ng for [125I]SWA11. An objective measurement of antibody penetration into spheroids was developed using a computerised image analysis of immunostained sections of spheroids. The concentration of antibody and incubation times were varied. Both antibodies penetrated the spheroids to a depth of 50 microns after 30 min. This increased to about 100 microns after 4 h incubation with 1 or 100 micrograms ml-1 SWA11. The results with 1 microgram ml-1 NY.3D11 were similar, but in the presence of 100 micrograms ml-1 NY.3D11 penetration into the spheroid was deep and diffuse. These results demonstrate a major concentration-dependent difference in the uptake and penetration of cluster 1 and cluster w4 antibodies in this spheroid model and they have implications for the selection of antibodies for targeted therapy of SCLC.

Antibodies, Monoclonal↗
PubMed2004

Structure and reactivity of V(2)O(5): bulk solid, nanosized clusters, species supported on silica and alumina, cluster cations and anions.

Vanadyl bond dissociation energies are calculated by density functional theory (DFT). While the hybrid (B3LYP) functional results are close to the available reference data, gradient corrected functionals (BP86, PBE) yield large errors (about 50 to 100 kJ mol(-1)), but reproduce trends correctly. PBE calculations on a V(20)O(62)H(24) cluster model for the (001) surface of V(2)O(5) crystals virtually reproduce periodic slab calculations. The low bond dissociation energy (formation of oxygen surface defect) of 113 kJ mol(-1)(B3LYP) is due to substantial structure relaxations leading to formation of V-O-V bonds between the V(2)O(5) layers of the crystal. This relaxation cannot occur in polyhedral (V(2)O(5))(n) clusters and also not for V(2)O(5) species supported on silica or alumina (represented by cage-type models) for which bond dissociation energies of 250-300 kJ mol(-1) are calculated. The OV(OCH(3))(3) molecule and its dimer are also considered. Radical cations V(2)O(5)(+) and V(4)O(10)(+) have very low bond dissociation energies (22 and 14 kJ mol(-1), respectively), while the corresponding radical anions have higher dissociation energies (about 330 kJ mol(-1)) than the neutral clusters. The bond dissociation energies of the closed shell V(3)O(7)(+) cation (165 kJ mol(-1)) and the closed shell V(3)O(8)(-) anion (283 kJ mol(-1)) are closest to the values of the neutral clusters. This makes them suitable for gas phase studies which aim at comparisons with V(2)O(5) species on supporting oxides.

Journal Article↗
PubMed2004

New insights into catalytic hydrogenation by phosphido-substituted triruthenium clusters: confirmation of intact cluster catalysis by parahydrogen NMR.

The phosphido-substituted triruthenium cluster Ru(3)(CO)(9)(mu-H)(micro-PPh(2)) is shown to react with H(2) to form the trihydride cluster Ru(3)(CO)(9)(H)(mu-H)(2)(mu-PPh(2)), which undergoes a number of re-arrangement reactions on heating to yield other phosphido-substituted triruthenium clusters. In the presence of alkyne substrates, heating the system leads to catalytic hydrogenation via CO loss and the formation of a Ru(3)(eta(2)-PhC[double bond, length as m-dash]CHPh)(CO)(8)(micro-H)(PHPh(2)) resting state, in a reaction affected by the polarity of the solvent. No mononuclear fragments are observed in the catalytic transformation, confirming directly that the phosphido ligand is able to exert a stabilising influence on the cluster core.

Journal Article↗