Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Clustering”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources
PubMed2004

New high-nuclearity Ni-Pt carbonyl clusters: synthesis and X-ray structure of the ordered [HNi24Pt17(CO)46]5- and the substitutionally Ni/Pt disordered [Ni32Pt24(CO)56]6- cluster anions.

Condensation between preformed Ni-Pt and Pt carbonyl clusters leads to the new [H(6-n)Ni(24)Pt(17)(CO)(46)](n-)(n= 5, 6) and the substitutionally Ni/Pt disordered [Ni(24)(Ni(12-x)Pt(x))Pt(20)(CO)(56)](6-) (x = 4) carbonyl clusters, the latter of which represents the highest nuclearity homoleptic carbonyl cluster anion so far reported.

Journal Article↗
PubMed2005

Density functional theory study of eight-atom germanium clusters: effect of electron count on cluster geometry.

Density functional theory (DFT) at the hybrid B3LYP level has been applied to the germanium clusters Ge8z(z=-6, -4, -2, 0, +2, +4) using nine initial geometries. For Ge8(2-) the D2d bisdisphenoid structure predicted by the Wade-Mingos rules is not computed to be the global minimum but instead lies 3.9 kcal mol-1 above the Td tetracapped tetrahedron global minimum predicted to exhibit spherical aromaticity. The hyperelectronic clusters Ge(8)4- and Ge8(6-) have nido B8H12 and square antiprism structures, respectively, as global minima in accord with the Wade-Mingos rules and experimental data on E(8)2+(E=Sb, Bi) cations. Hypoelectronic eight-vertex clusters isoelectronic and isolobal with Ge8, Ge8(2+) and Ge(8)4+ are not known experimentally. Their computed structures include smaller polyhedra having one or more capped triangular faces as well as more open non-polyhedral structures.

Journal Article↗
PubMed1984

Azotobacter chroococcum 7Fe ferredoxin. Two pH-dependent forms of the reduced 3Fe clusters and its conversion to a 4Fe cluster.

Ferredoxin from Azotobacter chroococcum has been studied by low-temperature magnetic-circular-dichroism and electron-paramagnetic-resonance spectroscopy. When aerobically isolated ferredoxin contains a [3Fe-4S] and [4Fe-4S] cluster. Anaerobic treatment with dithionite in the presence of ethanediol reduces the [3Fe-4S] cluster to give two spectroscopically distinct forms RI and RII which are reversibly interconvertible with a pKa approximately 7.5. The higher-pH form, RII, has a high affinity for ferrous ion and converts readily to a [4Fe-4S]1+ cluster, scavenging iron from the medium. The presence of the iron chelator EDTA inhibits this conversion.

Azotobacter↗
PubMed2004

Methane activation by nickel cluster cations, Ni+n (n=2-16): reaction mechanisms and thermochemistry of cluster-CHx (x=0-3) complexes.

The kinetic energy dependences of the reactions of Ni+(n) (n=2-16) with CD(4) are studied in a guided ion beam tandem mass spectrometer over the energy range of 0-10 eV. The main products are hydride formation Ni(n)D+, dehydrogenation to form Ni(n)CD+(2), and double dehydrogenation yielding Ni(n)C+. These primary products decompose at higher energies to form Ni(n)CD+, Ni(n-1)D+, Ni(n-1)C+, Ni(n-1)CD+, and Ni(n-1)CD+(2). Ni(n)CD(2) (+) (n=5-9) and Ni(n-1)CD(2) (+) (n > or =4) are not observed. In general, the efficiencies of the single and double dehydrogenation processes increase with cluster size. All reactions exhibit thresholds, and cross sections for the various primary and secondary reactions are analyzed to yield reaction thresholds from which bond energies for nickel cluster cations to C, CD, CD(2), and CD(3) are determined. The relative magnitudes of these bond energies are consistent with simple bond order considerations. Bond energies for larger clusters rapidly reach relatively constant values, which are used to estimate the chemisorption energies of the C, CD, CD(2), and CD(3) molecular fragments to nickel surfaces.

Journal Article↗
PubMed2005

The properties of ion-water clusters. I. The protonated 21-water cluster.

The ab initio atom-centered density-matrix propagation approach and the multistate empirical valence bond method have been employed to study the structure, dynamics, and rovibrational spectrum of a hydrated proton in the "magic" 21 water cluster. In addition to the conclusion that the hydrated proton tends to reside on the surface of the cluster, with the lone pair on the protonated oxygen pointing "outwards," it is also found that dynamical effects play an important role in determining the vibrational properties of such clusters. This result is used to analyze and complement recent experimental and theoretical studies.

Adsorption↗
PubMed2006

The structure of the Si9H12 cluster: A coupled cluster and multi-reference perturbation theory study.

Full geometry optimizations using both singles and doubles coupled cluster theory with perturbative triple excitations, CCSD(T), and second order multi-reference perturbation theory, MRMP2, have been employed to predict the structure of Si9H12, a cluster commonly used in calculations to represent the Si(100) surface. Both levels of theory predict the structure of this cluster to be symmetric (not buckled), and no evidence for a buckled (asymmetric) structure is found at either level of theory.

Journal Article↗
PubMed2006

First-principles study of intermediate size silver clusters: Shape evolution and its impact on cluster properties.

Low-energy isomers of Ag(N) clusters are studied within gradient-corrected density functional theory over the size range of N = 9-20. The candidate conformations are drawn from an extensive structural database created in a recent exploration of Cu(N) clusters [M. Yang et al., J. Chem. Phys. 124, 24308 (2006)]. Layered configurations dominate the list of the lowest-energy isomers of Ag(N) for N < 16. The most stable structures for N > 16 are compact with quasispherical shapes. The size-driven shape evolution is similar to that found earlier for Na(N) and Cu(N). The shape change has a pronounced effect on the cluster cohesive energies, ionization potentials, and polarizabilities. The properties computed for the most stable isomers of Ag(N) are in good agreement with the available experimental data.

Journal Article↗
PubMed2002

Inhibition of Fe-S cluster biosynthesis decreases mitochondrial iron export: evidence that Yfh1p affects Fe-S cluster synthesis.

Decreased expression of Yfh1p in the budding yeast, Saccharomyces cerevisiae, and the orthologous human gene frataxin results in respiratory deficiency and mitochondrial iron accumulation. The absence of Yfh1p decreases mitochondrial iron export. We demonstrate that decreased expression of Nfs1p, the yeast cysteine desulfurase that plays a central role in Fe-S cluster synthesis, also results in mitochondrial iron accumulation due to decreased export of mitochondrial iron. In the absence of Yfh1p, activity of Fe-S-containing enzymes (aconitase, succinate dehydrogenase) is decreased, whereas the activity of a non-Fe-S-containing enzyme (malate dehydrogenase) is unaffected. Aconitase protein was abundant even though the activity of aconitase was decreased in both aerobic and anaerobic conditions. These results demonstrate a direct role of Yfh1p in the formation of Fe-S clusters and indicate that mitochondrial iron export requires Fe-S cluster biosynthesis.

Aconitate Hydratase↗
PubMed1992

Analysis of gamma-ray energies for 56 excited superdeformed rotational bands of nuclei of lanthanons La to Dy and of Hg, Tl, and Pb on the basis of the two-revolving-cluster model, with evaluation of moments of inertia and radii of revolution and assignment of nucleonic compositions to the clusters and the central sphere.

Analysis of the gamma-ray energies of 28 excited superdeformed bands of lanthanon nuclei by application of the two-revolving-cluster model yields the result that the central sphere for all 28 has the semimagic-magic composition p40n50, with the range p8n12 to p14n18 for the clusters and the radius of revolution increasing from 7.31 to 7.76 fm. Similar analysis of 28 excited bands of Hg, Tl, and Pb nuclei leads to p56n82 (semimagic-magic) for the central sphere of 24 bands, p64n82 (semimagic-magic) for 2, and p64n90 (doubly semimagic) for 2, with cluster range p8n12 to p14n16 and values of the radius of revolution from 8.70 to 8.92 fm for 26 bands and 9.2 fm for 2.

Journal Article↗
PubMed1993

Analysis of the ground-state band and a closely related intercalated band of 235(92)U143 by the two-revolving-cluster model with consideration of symmetric and antisymmetric resonance of the two dissimilar clusters.

The reported ground-state band of 235(92)U143 extending from J = 7/2- to 51/2- is found to be two intercalated bands, one beginning with 7/2- and the other with 9/2-, each with DeltaJ = 2. Analysis by the two-resonating-cluster model leads to 3875 Da.fm2 for the moment of inertia for the first few levels, then increasing by centrifugal stretching. This value is interpreted by the structure p70n112 for the central sphere with clusters p11n16 and p11n15 with radius of revolution R = 8.55 fm. The major principal axis of the Poinsot ellipsoid is taken to be determined by an unquantized number K, with vector intermediate in orientation between L and J. The values of K are found by empirical analysis to equal L + 0.28, with the theory of rotation of the ellipsoid giving L + 0.28 for 7/2-, slowly decreasing to L + 0.251 for 51/2-. The 7/2- band is based on odd values of L (negative parity) and the 9/2- band on even values (positive parity). Negative parity for both bands is achieved by symmetric resonance of the two dissimilar clusters in the 7/2- band and antisymmetric resonance in the 9/2- band.

Journal Article↗
PubMed2001

Mechanism of the SDS-resistant synaptotagmin clustering mediated by the cysteine cluster at the interface between the transmembrane and spacer domains.

Synaptotagmin I (Syt I), a proposed major Ca(2+) sensor in the central nervous system, has been hypothesized as functioning in an oligomerized state during neurotransmitter release. We previously showed that Syts I, II, VII, and VIII form a stable SDS-resistant, beta-mercaptoethanol-insensitive, and Ca(2+)-independent oligomer surrounding the transmembrane domain (Fukuda, M., and Mikoshiba, K. (2000) J. Biol. Chem. 275, 28180-28185), but little is known about the molecular mechanism of the Ca(2+)-independent oligomerization by the synaptotagmin family. In this study, we analyzed the Ca(2+)-independent oligomerization properties of Syt I and found that it shows two distinct forms of self-oligomerization activity: stable SDS-resistant self-oligomerization activity and relatively unstable SDS-sensitive self-oligomerization activity. The former was found to be mediated by a post-translationally modified (i.e. fatty-acylated) cysteine (Cys) cluster (Cys-74, Cys-75, Cys-77, Cys-79, and Cys-82) at the interface between the transmembrane and spacer domains of Syt I. We also show that the number of Cys residues at the interface between the transmembrane and spacer domains determines the SDS- resistant oligomerizing capacity of each synaptotagmin isoform: Syt II, which contains seven Cys residues, showed the strongest SDS-resistant oligomerizing activity in the synaptotagmin family, whereas Syt XII, which has no Cys residues, did not form any SDS-resistant oligomers. The latter SDS-sensitive self-oligomerization of Syt I is mediated by the spacer domain, because deletion of the whole spacer domain, including the Cys cluster, abolished it, whereas a Syt I(CA) mutant carrying Cys to Ala substitutions still exhibited self-oligomerization. Based on these results, we propose that the oligomerization of the synaptotagmin family is regulated by two distinct mechanisms: the stable SDS-resistant oligomerization is mediated by the modified Cys cluster, whereas the relatively unstable (SDS-sensitive) oligomerization is mediated by the environment of the spacer domain.

Amino Acid Sequence↗
PubMed2004

Characterization of the first nonmammalian T2 cytokine gene cluster: the cluster contains functional single-copy genes for IL-3, IL-4, IL-13, and GM-CSF, a gene for IL-5 that appears to be a pseudogene, and a gene encoding another cytokinelike transcript, KK34.

A genomics approach based on the conservation of synteny was used to develop a bacterial artificial chromosome (BAC) contig across the chicken T2 cytokine gene cluster. Sequencing of representative BACs showed that the chicken genome encodes genes for the homologs of mammalian interleukin-3 (IL-3), IL-4, IL-5, IL-13, and granulocyte-macrophage colony-stimulating factor (GM-CSF). These sequences represent the first T2 cytokines found outside of mammals, and their location demonstrates that the T2 cluster is ancient (at least 300 million years old). Four of these genes (IL-3, IL-4, IL-13, and GM-CSF) are expressed at the mRNA level and can be expressed as recombinant protein. In contrast to the other four genes, the chicken IL-5 (ChIL-5) gene we sequenced lacks a recognizable promoter and regulatory sequences in the predicted 3'-untranslated region (3'-UTR). Further, there is no evidence for its expression at the mRNA level. We, therefore, hypothesize that it is a pseudogene. Genomic analysis revealed that a recently characterized cytokinelike transcript, KK34, not identified in our initial analysis of the BAC sequence, is also encoded in this cluster. This gene may represent a duplication of an ancestral IL-5 gene and may encode the functional homolog of IL-5 in the chicken.

Amino Acid Sequence↗
PubMed1996

P-fimbriae-producing septicaemic Escherichia coli from poultry possess fel-related gene clusters whereas pap-hybridizing P-fimbriae-negative strains have partial or divergent P fimbrial gene clusters.

The organization of P fimbrial gene clusters of 13 papC-hybridizing Escherichia coli strains isolated from poultry with colisepticaemia, five P-fimbriae-expressing (P-positive) and eight P-fimbriae-non-expressing (P-negative), were examined by PCR and by Southern blot hybridization using primers or gene probes specific to the I, B, A, C or G genes. The absence of P fimbrial expression was associated with lack of PCR amplification of one or more of these genes, most commonly the I gene. Restriction endonuclease EcoRI, BamHI or PstI digests of genomic DNA from all strains hybridized with each of the gene probes and demonstrated polymorphisms between P-positive and P-negative strains. PstI digests of DNA from 12 of the 13 strains, when hybridized with the A gene probe, demonstrated a 0.1 kb fragment specific to the felA gene which encodes the major structural protein of F11 fimbriae. Hence, only the P-positive strains contained complete copies of fel-related gene clusters. In contrast, most of the pap-hybridizing P-negative strains contained partial or divergent P fimbrial gene clusters, which explains the lack of P fimbrial expression by these strains.

Animals↗
PubMed2000

Structure transition in cluster-cluster aggregation under external fields

The structure transition in cluster-cluster aggregation (CCA) under different external electric fields has been investigated by computer simulations. The aggregates are generated from off-lattice CCA models involving the field-induced dipolar interactions and temperatures by means of a Metropolis algorithm. When the parameter K increases from 0 to infinity, the clusters gradually change from a diffusion-limited CCA to a chainlike pattern, where K stands for the relative strength of the field-induced dipolar interaction with thermal energy. The relation of fractal dimension D(f) to parameter K can be approximately expressed as D(f)=D(E)+(D(DLCA)-D(E))e(-betaK) with beta=0.64, where D(E) and D(DLCA) stand for the fractal dimensions of the CCA when K-->infinity and K-->0, respectively. This structure transition is a transition between a prototype disorder structure and a relative order one. The transition is attributed to the variation of the dominating interaction of systems from thermal disorder to field-induced dipolar interaction with K rising.

Journal Article↗
PubMed2001

Growth of Au clusters on amorphous Al2O3: evidence of cluster mobility above a critical size.

We study the 3D growth of clusters during the deposition of Au atoms on amorphous Al2O3. By comparing transmission electron microscopy images of the growth with Monte Carlo simulations, we show that nucleation takes place on substrate defects, but that further stages of growth imply that clusters leave the defects after they have reached a given critical size, and diffuse. An interesting consequence of this property is that, in contrast to intuition, and in a certain range of size, larger clusters are more mobile than smaller ones in this system.

Journal Article↗
PubMed1991

Colony-cluster ratio and cluster number in cultures of circulating myeloid progenitors as indicators of high-risk myelodysplasia.

Circulating myeloid progenitors were assayed in 172 normal subjects and 147 patients with myelodysplastic syndrome (MDS). Patients whose cultures had colony/cluster ratios (CCR) less than 0.3 had significantly shorter survival periods than comparable patients with CCR greater than 0.3. A second prognostic indicator, which complemented CCR, was identified in patients with less than 5% blasts. Median survival was significantly reduced in patients with greater than 15 clusters/ml blood despite colony and cluster numbers being predominantly within the normal range. Characteristic differences were found in three FAB groups large enough to allow statistical analysis. Survival amongst patients with refractory anaemia with excess of blasts (RAEB) was related to CCR and was independent of cluster number. Amongst sideroblastic patients (SA) survival related only to cluster number. Refractory anaemia (RA) patients included individuals in both high-risk groups with only three patients out of 64 showing both features. Amongst all the MDS patients, those with CCR greater than 0.3 and less than 15 clusters/ml blood formed a low-risk group (n = 60) with a relatively good prognosis of whom 85% survived the study period (median duration 938 d) including 94% of those in this group with less than 5% marrow blast cells.

Cell Aggregation↗
PubMed1979

Macrophage-lymphocyte clusters in the immune response to soluble protein antigen in vitro. IX. Antigen-pulsed macrophages as a tool for specific absorption of cluster-initiating T cells.

T-cell populations from guinea-pigs sensitized to the protein antigens purified protein derivative of Mycobacterium tuberculosis, ovalbumin, or horseradish perioxidase can be selectively depleted of cells capable of initiating antigen-specific macrophage-lymphocyte clusters in vitro. The depletion is achieved by incubating the T cells on a monolayer of antigen-pulsed macrophages in a Petri dish for some hours and then gently aspirating the cells not adhering to the bottom of the dish. When subsequently assayed, the aspirated cells were found to be depleted of cluster-initiating lymphocytes committed to horseradish peroxidase, monolayers of macrophages pulsed with that antigen must be used. The optimum time for incubation on the absorbing monolayer appears to be 4 h, and two successive incubations are more effective than one. The cell density of the absorbing monolayer and the handling of the Petri dish may be critical for effective removal of the cluster-initating lymphocytes. With optimum procedure we have achieved up to 90% depletion of specific cells with no depletion of cells committed to a control antigen.

Absorption↗
PubMed1989

19th Sir Hans Krebs lecture. Engineering of protein bound iron-sulfur clusters. A tool for the study of protein and cluster chemistry and mechanism of iron-sulfur enzymes.

An increasing number of iron-sulfur (Fe-S) proteins are found in which the Fe-S cluster is not involved in net electron transfer, as it is in the majority of Fe-S proteins. Most of the former are (de)hydratases, of which the most extensively studied is aconitase. Approaches are described and discussed by which the Fe-S cluster of this enzyme could be brought into states of different structure, ligation, oxidation and isotope composition. The species, so obtained, provided the basis for spectroscopic and chemical investigations. Results from studies by protein chemistry, EPR, Mössbauer, 1H, 2H and 57Fe electron-nuclear double resonance spectroscopy are described. Conclusions, which bear on the electronic structure of the Fe-S cluster, enzyme-substrate interaction and the enzymatic mechanism, were derived from a synopsis of the recent work described here and of previous contributions from several laboratories. These conclusions are discussed and summarized in a final section.

Aconitate Hydratase↗