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Sample records for clustered functional pseudogenes

  1. Functional redundancy and/or ongoing pseudogenization among F-box protein genes expressed in Arabidopsis male gametophyte.

    Science.gov (United States)

    Ikram, Sobia; Durandet, Monique; Vesa, Simona; Pereira, Serge; Guerche, Philippe; Bonhomme, Sandrine

    2014-06-01

    F-box protein genes family is one of the largest gene families in plants, with almost 700 predicted genes in the model plant Arabidopsis. F-box proteins are key components of the ubiquitin proteasome system that allows targeted protein degradation. Transcriptome analyses indicate that half of these F-box protein genes are found expressed in microspore and/or pollen, i.e., during male gametogenesis. To assess the role of F-box protein genes during this crucial developmental step, we selected 34 F-box protein genes recorded as highly and specifically expressed in pollen and isolated corresponding insertion mutants. We checked the expression level of each selected gene by RT-PCR and confirmed pollen expression for 25 genes, but specific expression for only 10 of the 34 F-box protein genes. In addition, we tested the expression level of selected F-box protein genes in 24 mutant lines and showed that 11 of them were null mutants. Transmission analysis of the mutations to the progeny showed that none of the single mutations was gametophytic lethal. These unaffected transmission efficiencies suggested leaky mutations or functional redundancy among F-box protein genes. Cytological observation of the gametophytes in the mutants confirmed these results. Combinations of mutations in F-box protein genes from the same subfamily did not lead to transmission defect either, further highlighting functional redundancy and/or a high proportion of pseudogenes among these F-box protein genes.

  2. Pervasive survival of expressed mitochondrial rps14 pseudogenes in grasses and their relatives for 80 million years following three functional transfers to the nucleus

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    Palmer Jeffrey D

    2006-07-01

    Full Text Available Abstract Background Many mitochondrial genes, especially ribosomal protein genes, have been frequently transferred as functional entities to the nucleus during plant evolution, often by an RNA-mediated process. A notable case of transfer involves the rps14 gene of three grasses (rice, maize, and wheat, which has been relocated to the intron of the nuclear sdh2 gene and which is expressed and targeted to the mitochondrion via alternative splicing and usage of the sdh2 targeting peptide. Although this transfer occurred at least 50 million years ago, i.e., in a common ancestor of these three grasses, it is striking that expressed, nearly intact pseudogenes of rps14 are retained in the mitochondrial genomes of both rice and wheat. To determine how ancient this transfer is, the extent to which mitochondrial rps14 has been retained and is expressed in grasses, and whether other transfers of rps14 have occurred in grasses and their relatives, we investigated the structure, expression, and phylogeny of mitochondrial and nuclear rps14 genes from 32 additional genera of grasses and from 9 other members of the Poales. Results Filter hybridization experiments showed that rps14 sequences are present in the mitochondrial genomes of all examined Poales except for members of the grass subfamily Panicoideae (to which maize belongs. However, PCR amplification and sequencing revealed that the mitochondrial rps14 genes of all examined grasses (Poaceae, Cyperaceae, and Joinvilleaceae are pseudogenes, with all those from the Poaceae sharing two 4-NT frameshift deletions and all those from the Cyperaceae sharing a 5-NT insertion (only one member of the Joinvilleaceae was examined. cDNA analysis showed that all mitochondrial pseudogenes examined (from all three families are transcribed, that most are RNA edited, and that surprisingly many of the edits are reverse (U→C edits. Putatively nuclear copies of rps14 were isolated from one to several members of each of these

  3. The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes

    DEFF Research Database (Denmark)

    Pantano, Lorena; Jodar, Meritxell; Bak, Mads

    2015-01-01

    -specific genes. The most abundant class of small noncoding RNAs in sperm are PIWI-interacting RNAs (piRNAs). Surprisingly, we found that human sperm cells contain piRNAs processed from pseudogenes. Clusters of piRNAs from human testes contain pseudogenes transcribed in the antisense strand and processed...... into small RNAs. Several human protein-coding genes contain antisense predicted targets of pseudogene-derived piRNAs in the male germline and these piRNAs are still found in mature sperm. Our study provides the most extensive data set and annotation of human sperm small RNAs to date and is a resource...... for further functional studies on the roles of sperm small RNAs. In addition, we propose that some of the pseudogene-derived human piRNAs may regulate expression of their parent gene in the male germline....

  4. Differentially-Expressed Pseudogenes in HIV-1 Infection.

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    Gupta, Aditi; Brown, C Titus; Zheng, Yong-Hui; Adami, Christoph

    2015-09-29

    Not all pseudogenes are transcriptionally silent as previously thought. Pseudogene transcripts, although not translated, contribute to the non-coding RNA pool of the cell that regulates the expression of other genes. Pseudogene transcripts can also directly compete with the parent gene transcripts for mRNA stability and other cell factors, modulating their expression levels. Tissue-specific and cancer-specific differential expression of these "functional" pseudogenes has been reported. To ascertain potential pseudogene:gene interactions in HIV-1 infection, we analyzed transcriptomes from infected and uninfected T-cells and found that 21 pseudogenes are differentially expressed in HIV-1 infection. This is interesting because parent genes of one-third of these differentially-expressed pseudogenes are implicated in HIV-1 life cycle, and parent genes of half of these pseudogenes are involved in different viral infections. Our bioinformatics analysis identifies candidate pseudogene:gene interactions that may be of significance in HIV-1 infection. Experimental validation of these interactions would establish that retroviruses exploit this newly-discovered layer of host gene expression regulation for their own benefit.

  5. Differential Retention of Gene Functions in a Secondary Metabolite Cluster.

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    Reynolds, Hannah T; Slot, Jason C; Divon, Hege H; Lysøe, Erik; Proctor, Robert H; Brown, Daren W

    2017-08-01

    In fungi, distribution of secondary metabolite (SM) gene clusters is often associated with host- or environment-specific benefits provided by SMs. In the plant pathogen Alternaria brassicicola (Dothideomycetes), the DEP cluster confers an ability to synthesize the SM depudecin, a histone deacetylase inhibitor that contributes weakly to virulence. The DEP cluster includes genes encoding enzymes, a transporter, and a transcription regulator. We investigated the distribution and evolution of the DEP cluster in 585 fungal genomes and found a wide but sporadic distribution among Dothideomycetes, Sordariomycetes, and Eurotiomycetes. We confirmed DEP gene expression and depudecin production in one fungus, Fusarium langsethiae. Phylogenetic analyses suggested 6-10 horizontal gene transfers (HGTs) of the cluster, including a transfer that led to the presence of closely related cluster homologs in Alternaria and Fusarium. The analyses also indicated that HGTs were frequently followed by loss/pseudogenization of one or more DEP genes. Independent cluster inactivation was inferred in at least four fungal classes. Analyses of transitions among functional, pseudogenized, and absent states of DEP genes among Fusarium species suggest enzyme-encoding genes are lost at higher rates than the transporter (DEP3) and regulatory (DEP6) genes. The phenotype of an experimentally-induced DEP3 mutant of Fusarium did not support the hypothesis that selective retention of DEP3 and DEP6 protects fungi from exogenous depudecin. Together, the results suggest that HGT and gene loss have contributed significantly to DEP cluster distribution, and that some DEP genes provide a greater fitness benefit possibly due to a differential tendency to form network connections. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2017. This work is written by US Government employees and is in the public domain in the US.

  6. Functional PMS2 hybrid alleles containing a pseudogene-specific missense variant trace back to a single ancient intrachromosomal recombination event.

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    Ganster, Christina; Wernstedt, Annekatrin; Kehrer-Sawatzki, Hildegard; Messiaen, Ludwine; Schmidt, Konrad; Rahner, Nils; Heinimann, Karl; Fonatsch, Christa; Zschocke, Johannes; Wimmer, Katharina

    2010-05-01

    Sequence exchange between PMS2 and its pseudogene PMS2CL, embedded in an inverted duplication on chromosome 7p22, has been reported to be an ongoing process that leads to functional PMS2 hybrid alleles containing PMS2- and PMS2CL-specific sequence variants at the 5'-and the 3'-end, respectively. The frequency of PMS2 hybrid alleles, their biological significance, and the mechanisms underlying their formation are largely unknown. Here we show that overall hybrid alleles account for one-third of 384 PMS2 alleles analyzed in individuals of different ethnic backgrounds. Depending on the population, 14-60% of hybrid alleles carry PMS2CL-specific sequences in exons 13-15, the remainder only in exon 15. We show that exons 13-15 hybrid alleles, named H1 hybrid alleles, constitute different haplotypes but trace back to a single ancient intrachromosomal recombination event with crossover. Taking advantage of an ancestral sequence variant specific for all H1 alleles we developed a simple gDNA-based polymerase chain reaction (PCR) assay that can be used to identify H1-allele carriers with high sensitivity and specificity (100 and 99%, respectively). Because H1 hybrid alleles harbor missense variant p.N775S of so far unknown functional significance, we assessed the H1-carrier frequency in 164 colorectal cancer patients. So far, we found no indication that the variant plays a major role with regard to cancer susceptibility. (c) 2010 Wiley-Liss, Inc.

  7. Evolution of a pseudogene: exclusive survival of a functional mitochondrial nad7 gene supports Haplomitrium as the earliest liverwort lineage and proposes a secondary loss of RNA editing in Marchantiidae.

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    Groth-Malonek, Milena; Wahrmund, Ute; Polsakiewicz, Monika; Knoop, Volker

    2007-04-01

    Gene transfer from the mitochondrion into the nucleus is a corollary of the endosymbiont hypothesis. The frequent and independent transfer of genes for mitochondrial ribosomal proteins is well documented with many examples in angiosperms, whereas transfer of genes for components of the respiratory chain is a rarity. A notable exception is the nad7 gene, encoding subunit 7 of complex I, in the liverwort Marchantia polymorpha, which resides as a full-length, intron-carrying and transcribed, but nonspliced pseudogene in the chondriome, whereas its functional counterpart is nuclear encoded. To elucidate the patterns of pseudogene degeneration, we have investigated the mitochondrial nad7 locus in 12 other liverworts of broad phylogenetic distribution. We find that the mitochondrial nad7 gene is nonfunctional in 11 of them. However, the modes of pseudogene degeneration vary: whereas point mutations, accompanied by single-nucleotide indels, predominantly introduce stop codons into the reading frame in marchantiid liverworts, larger indels introduce frameshifts in the simple thalloid and leafy jungermanniid taxa. Most notably, however, the mitochondrial nad7 reading frame appears to be intact in the isolated liverwort genus Haplomitrium. Its functional expression is shown by cDNA analysis identifying typical RNA-editing events to reconstitute conserved codon identities and also confirming functional splicing of the 2 liverwort-specific group II introns. We interpret our results 1) to indicate the presence of a functional mitochondrial nad7 gene in the earliest land plants and strongly supporting a basal placement of Haplomitrium among the liverworts, 2) to indicate different modes of pseudogene degeneration and chondriome evolution in the later branching liverwort clades, 3) to suggest a surprisingly long maintenance of a nonfunctional gene in the presumed oldest group of land plants, and 4) to support the model of a secondary loss of RNA-editing activity in marchantiid

  8. The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes

    Science.gov (United States)

    Pantano, Lorena; Jodar, Meritxell; Bak, Mads; Ballescà, Josep Lluís; Tommerup, Niels; Oliva, Rafael; Vavouri, Tanya

    2015-01-01

    At the end of mammalian sperm development, sperm cells expel most of their cytoplasm and dispose of the majority of their RNA. Yet, hundreds of RNA molecules remain in mature sperm. The biological significance of the vast majority of these molecules is unclear. To better understand the processes that generate sperm small RNAs and what roles they may have, we sequenced and characterized the small RNA content of sperm samples from two human fertile individuals. We detected 182 microRNAs, some of which are highly abundant. The most abundant microRNA in sperm is miR-1246 with predicted targets among sperm-specific genes. The most abundant class of small noncoding RNAs in sperm are PIWI-interacting RNAs (piRNAs). Surprisingly, we found that human sperm cells contain piRNAs processed from pseudogenes. Clusters of piRNAs from human testes contain pseudogenes transcribed in the antisense strand and processed into small RNAs. Several human protein-coding genes contain antisense predicted targets of pseudogene-derived piRNAs in the male germline and these piRNAs are still found in mature sperm. Our study provides the most extensive data set and annotation of human sperm small RNAs to date and is a resource for further functional studies on the roles of sperm small RNAs. In addition, we propose that some of the pseudogene-derived human piRNAs may regulate expression of their parent gene in the male germline. PMID:25904136

  9. The PCNA pseudogenes in the human genome

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    Stoimenov Ivaylo

    2012-02-01

    Full Text Available Abstract Background The proliferating cell nuclear antigen (PCNA is a key protein in the eukaryotic DNA replication and cell proliferation. Following the cloning and characterisation of the human PCNA gene, the question of the existence of pseudogenes in the human genome was raised. Findings In this short communication we summarise the existing information about the PCNA pseudogenes and critically assess their status. Conclusions We propose the existence of at least four valid PCNA pseudogenes, PCNAP1, PCNAP2, LOC392454 and LOC390102. We would like to recommend assignment of a name for LOC392454 as "proliferating cell nuclear antigen pseudogene 3" (alias PCNAP3 and a name for LOC390102 as "proliferating cell nuclear antigen pseudogene 4" (alias PCNAP4. We prompt for more critical evaluation of the existence of a PCNA pseudogene, designated as PCNAP.

  10. Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

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    White Brian

    2009-01-01

    important mechanisms of genetic convergence between Paratyphi A and Typhi, with most pseudogenes arising independently after extensive recombination between the serovars. The recombination events, along with divergence of and within each serovar, provide a relative time scale for pseudogene-forming mutations, affording rare insights into the progression of functional gene loss associated with host adaptation in Salmonella.

  11. Evolution of the NANOG pseudogene family in the human and chimpanzee genomes

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    Maughan Peter J

    2006-02-01

    Full Text Available Abstract Background The NANOG gene is expressed in mammalian embryonic stem cells where it maintains cellular pluripotency. An unusually large family of pseudogenes arose from it with one unprocessed and ten processed pseudogenes in the human genome. This article compares the NANOG gene and its pseudogenes in the human and chimpanzee genomes and derives an evolutionary history of this pseudogene family. Results The NANOG gene and all pseudogenes except NANOGP8 are present at their expected orthologous chromosomal positions in the chimpanzee genome when compared to the human genome, indicating that their origins predate the human-chimpanzee divergence. Analysis of flanking DNA sequences demonstrates that NANOGP8 is absent from the chimpanzee genome. Conclusion Based on the most parsimonious ordering of inferred source-gene mutations, the deduced evolutionary origins for the NANOG pseudogene family in the human and chimpanzee genomes, in order of most ancient to most recent, are NANOGP6, NANOGP5, NANOGP3, NANOGP10, NANOGP2, NANOGP9, NANOGP7, NANOGP1, and NANOGP4. All of these pseudogenes were fixed in the genome of the human-chimpanzee common ancestor. NANOGP8 is the most recent pseudogene and it originated exclusively in the human lineage after the human-chimpanzee divergence. NANOGP1 is apparently an unprocessed pseudogene. Comparison of its sequence to the functional NANOG gene's reading frame suggests that this apparent pseudogene remained functional after duplication and, therefore, was subject to selection-driven conservation of its reading frame, and that it may retain some functionality or that its loss of function may be evolutionarily recent.

  12. Isolation and characterization of the human homologue of rig and its pseudogenes: The functional gene has features characteristic of housekeeping genes

    International Nuclear Information System (INIS)

    Shiga, Kiyoto; Yamamoto, Hiroshi; Okamoto, Hiroshi

    1990-01-01

    Rig (rat insulinoma gene) was first isolated from a cDNA library of rat insulinomas and has been found to be activated in various human tumors such as insulinomas, esophageal cancers, and colon cancers. Here the authors isolated the human homologue of rig from a genomic DNA library constructed from a human esophageal carcinoma and determined its complete nucleotide sequence. The gene is composed of about 3,000 nucleotides and divided into four exons separated by three introns: exon 3 encodes the nuclear location signal and the DNA-binding domain of the RIG protein. The transcription initiation site was located at -46 base pairs upstream from the first ATG codon. The 5'-flanking region of the gene has no apparent TATA-box or CAAT-box sequence. However, two GC boxes are found at -189 and -30 base pairs upstream from the transcription initiation site and five GC boxes are also found in introns 1 and 2. The gene is bounded in the 5' region by CpG islands, regions of DNA with a high GC content and a high frequency of CpG dinucleotides relative to the bulk genome. Furthermore, the human genome contains at least six copies of RIG pseudogenes, and four of them have the characteristics of processed pseudogenes. From these results together with the finding that RIG is expressed in a wide variety of tissues and cells, they speculate that RIG belongs to the class of housekeeping genes, whose products are necessary for the growth of all cell types

  13. Characterization of the ovine ribosomal protein SA gene and its pseudogenes

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    Van Zeveren Alex

    2010-03-01

    Full Text Available Abstract Background The ribosomal protein SA (RPSA, previously named 37-kDa laminin receptor precursor/67-kDa laminin receptor (LRP/LR is a multifunctional protein that plays a role in a number of pathological processes, such as cancer and prion diseases. In all investigated species, RPSA is a member of a multicopy gene family consisting of one full length functional gene and several pseudogenes. Therefore, for studies on RPSA related pathways/pathologies, it is important to characterize the whole family and to address the possible function of the other RPSA family members. The present work aims at deciphering the RPSA family in sheep. Results In addition to the full length functional ovine RPSA gene, 11 other members of this multicopy gene family, all processed pseudogenes, were identified. Comparison between the RPSA transcript and these pseudogenes shows a large variety in sequence identities ranging from 99% to 74%. Only one of the 11 pseudogenes, i.e. RPSAP7, shares the same open reading frame (ORF of 295 amino acids with the RPSA gene, differing in only one amino acid. All members of the RPSA family were annotated by comparative mapping and fluorescence in situ hybridization (FISH localization. Transcription was investigated in the cerebrum, cerebellum, spleen, muscle, lymph node, duodenum and blood, and transcripts were detected for 6 of the 11 pseudogenes in some of these tissues. Conclusions In the present work we have characterized the ovine RPSA family. Our results have revealed the existence of 11 ovine RPSA pseudogenes and provide new data on their structure and sequence. Such information will facilitate molecular studies of the functional RPSA gene taking into account the existence of these pseudogenes in the design of experiments. It remains to be investigated if the transcribed members are functional as regulatory non-coding RNA or as functional proteins.

  14. Mycobacterium leprae: genes, pseudogenes and genetic diversity

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    Singh, Pushpendra; Cole, Stewart T

    2011-01-01

    Leprosy, which has afflicted human populations for millenia, results from infection with Mycobacterium leprae, an unculturable pathogen with an exceptionally long generation time. Considerable insight into the biology and drug resistance of the leprosy bacillus has been obtained from genomics. M. leprae has undergone reductive evolution and pseudogenes now occupy half of its genome. Comparative genomics of four different strains revealed remarkable conservation of the genome (99.995% identity) yet uncovered 215 polymorphic sites, mainly single nucleotide polymorphisms, and a handful of new pseudogenes. Mapping these polymorphisms in a large panel of strains defined 16 single nucleotide polymorphism-subtypes that showed strong geographical associations and helped retrace the evolution of M. leprae. PMID:21162636

  15. PMS2 gene mutational analysis: direct cDNA sequencing to circumvent pseudogene interference.

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    Wimmer, Katharina; Wernstedt, Annekatrin

    2014-01-01

    The presence of highly homologous pseudocopies can compromise the mutation analysis of a gene of interest. In particular, when using PCR-based strategies, pseudogene co-amplification has to be effectively prevented. This is often achieved by using primers designed to be parental gene specific according to the reference sequence and by applying stringent PCR conditions. However, there are cases in which this approach is of limited utility. For example, it has been shown that the PMS2 gene exchanges sequences with one of its pseudogenes, named PMS2CL. This results in functional PMS2 alleles containing pseudogene-derived sequences at their 3'-end and in nonfunctional PMS2CL pseudogene alleles that contain gene-derived sequences. Hence, the paralogues cannot be distinguished according to the reference sequence. This shortcoming can be effectively circumvented by using direct cDNA sequencing. This approach is based on the selective amplification of PMS2 transcripts in two overlapping 1.6-kb RT-PCR products. In addition to avoiding pseudogene co-amplification and allele dropout, this method has also the advantage that it allows to effectively identify deletions, splice mutations, and de novo retrotransposon insertions that escape the detection of most DNA-based mutation analysis protocols.

  16. Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda

    KAUST Repository

    Nozawa, Masafumi

    2016-11-29

    Y chromosomes often degenerate via the accumulation of pseudogenes and transposable elements. By contrast, little is known about X-chromosome degeneration. Here we compare the pseudogenization process between genes on the neo-sex chromosomes in Drosophila miranda and their autosomal orthologues in closely related species. The pseudogenization rate on the neo-X is much lower than the rate on the neo-Y, but appears to be higher than the rate on the orthologous autosome in D. pseudoobscura. Genes under less functional constraint and/or genes with male-biased expression tend to become pseudogenes on the neo-X, indicating the accumulation of slightly deleterious mutations and the feminization of the neo-X. We also find a weak trend that the genes with female-benefit/male-detriment effects identified in D. melanogaster are pseudogenized on the neo-X, implying the masculinization of the neo-X. These observations suggest that both X and Y chromosomes can degenerate due to a complex suite of evolutionary forces.

  17. Clustering aspects in nuclear structure functions

    International Nuclear Information System (INIS)

    Hirai, M.; Saito, K.; Watanabe, T.; Kumano, S.

    2011-01-01

    For understanding an anomalous nuclear effect experimentally observed for the beryllium-9 nucleus at the Thomas Jefferson National Accelerator Facility, clustering aspects are studied in structure functions of deep inelastic lepton-nucleus scattering by using momentum distributions calculated in antisymmetrized (or fermionic) molecular dynamics (AMD) and also in a simple shell model for comparison. According to AMD, the 9 Be nucleus consists of two α-like clusters with a surrounding neutron. The clustering produces high-momentum components in nuclear wave functions, which affects nuclear modifications of the structure functions. We investigated whether clustering features could appear in the structure function F 2 of 9 Be along with studies for other light nuclei. We found that nuclear modifications of F 2 are similar in both AMD and shell models within our simple convolution description although there are slight differences in 9 Be. It indicates that the anomalous 9 Be result should be explained by a different mechanism from the nuclear binding and Fermi motion. If nuclear-modification slopes d(F 2 A /F 2 D )/dx are shown by the maximum local densities, the 9 Be anomaly can be explained by the AMD picture, namely by the clustering structure, whereas it certainly cannot be described in the simple shell model. This fact suggests that the large nuclear modification in 9 Be should be explained by large densities in the clusters. For example, internal nucleon structure could be modified in the high-density clusters. The clustering aspect of nuclear structure functions is an unexplored topic which is interesting for future investigations.

  18. Cranked cluster wave function for molecular states

    International Nuclear Information System (INIS)

    Horiuchi, Hisashi; Yabana, Kazuhiro; Wada, Takahiro.

    1986-01-01

    Construction of the cranked cluster wave function is discussed by focussing on three problems; the self-consistency between the potential and the density distribution, the properties of the rotational angular frequency which is strongly influenced by the inter-cluster Pauli principle and by the parity projection, and the spin alignment along the rotation axis with the resulting structure-change of the molecular state. (author)

  19. Noise-induced multistability in the regulation of cancer by genes and pseudogenes

    Energy Technology Data Exchange (ETDEWEB)

    Petrosyan, K. G., E-mail: pkaren@phys.sinica.edu.tw [Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan (China); Hu, Chin-Kun, E-mail: huck@phys.sinica.edu.tw [Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan (China); National Center for Theoretical Sciences, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Business School, University of Shanghai for Science and Technology, Shanghai 200093 (China)

    2016-07-28

    We extend a previously introduced model of stochastic gene regulation of cancer to a nonlinear case having both gene and pseudogene messenger RNAs (mRNAs) self-regulated. The model consists of stochastic Boolean genetic elements and possesses noise-induced multistability (multimodality). We obtain analytical expressions for probabilities for the case of constant but finite number of microRNA molecules which act as a noise source for the competing gene and pseudogene mRNAs. The probability distribution functions display both the global bistability regime as well as even-odd number oscillations for a certain range of model parameters. Statistical characteristics of the mRNA’s level fluctuations are evaluated. The obtained results of the extended model advance our understanding of the process of stochastic gene and pseudogene expressions that is crucial in regulation of cancer.

  20. A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease

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    María Angeles Zuriaga

    2015-05-01

    Full Text Available A pseudogene, designated as "ps(5.8S+ITS-2", paralogous to the 5.8S gene and internal transcribed spacer (ITS-2 of the nuclear ribosomal DNA (rDNA, has been recently found in many triatomine species distributed throughout North America, Central America and northern South America. Among characteristics used as criteria for pseudogene verification, secondary structures and free energy are highlighted, showing a lower fit between minimum free energy, partition function and centroid structures, although in given cases the fit only appeared to be slightly lower. The unique characteristics of "ps(5.8S+ITS-2" as a processed or retrotransposed pseudogenic unit of the ghost type are reviewed, with emphasis on its potential functionality compared to the functionality of genes and spacers of the normal rDNA operon. Besides the technical problem of the risk for erroneous sequence results, the usefulness of "ps(5.8S+ITS-2" for specimen classification, phylogenetic analyses and systematic/taxonomic studies should be highlighted, based on consistence and retention index values, which in pseudogenic sequence trees were higher than in functional sequence trees. Additionally, intraindividual, interpopulational and interspecific differences in pseudogene amount and the fact that it is a pseudogene in the nuclear rDNA suggests a potential relationships with fitness, behaviour and adaptability of triatomine vectors and consequently its potential utility in Chagas disease epidemiology and control.

  1. A genomic perspective on protein tyrosine phosphatases: gene structure, pseudogenes, and genetic disease linkage

    DEFF Research Database (Denmark)

    Andersen, Jannik N; Jansen, Peter G; Echwald, Søren M

    2004-01-01

    sequence databases, we discovered one novel human PTP gene and defined chromosomal loci and exon structure of the additional 37 genes encoding known PTP transcripts. Direct orthologs were present in the mouse genome for all 38 human PTP genes. In addition, we identified 12 PTP pseudogenes unique to humans...... that have probably contaminated previous bioinformatics analysis of this gene family. PCR amplification and transcript sequencing indicate that some PTP pseudogenes are expressed, but their function (if any) is unknown. Furthermore, we analyzed the enhanced diversity generated by alternative splicing...

  2. Recombination among multiple mitochondrial pseudogenes from a passerine genus

    DEFF Research Database (Denmark)

    Nielsen, Kirstine Klitgaard; Arctander, P.

    2001-01-01

    to the observed differences in substitution patterns 58% of the cloned sequences were identified as pseudogenes. Recombination could be traced in 19% of the inferred nuclear pseudogenes, but this figure probably represents a Significant underestimation of the factual recombination events. The nonrecombined...... pseudogenes consisted of multiple haplotypes found to diverge from 1 to 16% from the mitochondrial gene. The number of mitochondrial nuclear copies and their apparent frequent recombination suggest that pseudogenes constitute a serious potential risk in confounding phylogenetic studies and population genetic...

  3. Differentially-Expressed Pseudogenes in HIV-1 Infection

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    Aditi Gupta

    2015-09-01

    Full Text Available Not all pseudogenes are transcriptionally silent as previously thought. Pseudogene transcripts, although not translated, contribute to the non-coding RNA pool of the cell that regulates the expression of other genes. Pseudogene transcripts can also directly compete with the parent gene transcripts for mRNA stability and other cell factors, modulating their expression levels. Tissue-specific and cancer-specific differential expression of these “functional” pseudogenes has been reported. To ascertain potential pseudogene:gene interactions in HIV-1 infection, we analyzed transcriptomes from infected and uninfected T-cells and found that 21 pseudogenes are differentially expressed in HIV-1 infection. This is interesting because parent genes of one-third of these differentially-expressed pseudogenes are implicated in HIV-1 life cycle, and parent genes of half of these pseudogenes are involved in different viral infections. Our bioinformatics analysis identifies candidate pseudogene:gene interactions that may be of significance in HIV-1 infection. Experimental validation of these interactions would establish that retroviruses exploit this newly-discovered layer of host gene expression regulation for their own benefit.

  4. The correlation functions for the clustering of galaxies and Abell clusters

    International Nuclear Information System (INIS)

    Jones, B.J.T.; Jones, J.E.; Copenhagen Univ.

    1985-01-01

    The difference in amplitudes between the galaxy-galaxy correlation function and the correlation function between Abell clusters is a consequence of two facts. Firstly, most Abell clusters with z<0.08 lie in a relatively small volume of the sampled space, and secondly, the fraction of galaxies lying in Abell clusters differs considerably inside and outside of this volume. (The Abell clusters are confined to a smaller volume of space than are the galaxies.) We discuss the implications of this interpretation of the clustering correlation functions and present a simple model showing how such a situation may arise quite naturally in standard theories for galaxy formation. (orig.)

  5. Improved Density Functional Tight Binding Potentials for Metalloid Aluminum Clusters

    Science.gov (United States)

    2016-06-01

    unlimited IMPROVED DENSITY-FUNCTIONAL TIGHT BINDING POTENTIALS FOR METALLOID ALUMINUM CLUSTERS by Joon H. Kim June 2016 Thesis Advisor...DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE IMPROVED DENSITY-FUNCTIONAL TIGHT BINDING POTENTIALS FOR METALLOID ALUMINUM CLUSTERS 5. FUNDING...repulsive potentials for use in density-functional tight binding (DFTB) simulations of low-valence aluminum metalloid clusters . These systems are under

  6. Mass functions for eight galactic clusters in the solar neighborhood

    International Nuclear Information System (INIS)

    Francic, S.P.

    1989-01-01

    Mass functions for eight galactic clusters in the solar neighborhood have been obtained. The mass functions have been determined from proper motion membership probabilities and unlike similar investigations, corrected for outlying cluster stars. The membership probabilities have been determined from the joint proper motion and surface density distributions for the field and clusters stars. They have also been corrected for any magnitude dependences. Comparison of the mass functions with the Salpeter IMF shows that the older clusters tend to be deficient in the number of low mass stars, while the younger clusters tend to have more. Analysis of the relaxation times shows that the deficiency of faint stars in the older clusters is likely due to their evaporation from the cluster. The combined mass function for six of the cluster results in a power law with a power law index of -1.97 ± 0.17 for 1.1 < M/Mass of sun < 2.5. This agrees with a recent determination of the field star IMF where the power law index is -2.00 ± 0.18 for 0.8 < M/Mass of sun < 18. If the older clusters are not considered, then comparison of the combined mass function with the individual cluster mass functions shows that the universality hypothesis cannot be denied

  7. Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda

    KAUST Repository

    Nozawa, Masafumi; Onizuka, Kanako; Fujimi, Mai; Ikeo, Kazuho; Gojobori, Takashi

    2016-01-01

    Y chromosomes often degenerate via the accumulation of pseudogenes and transposable elements. By contrast, little is known about X-chromosome degeneration. Here we compare the pseudogenization process between genes on the neo-sex chromosomes

  8. Pseudogene accumulation might promote the adaptive microevolution of Yersinia pestis

    DEFF Research Database (Denmark)

    Tong, Zongzhong; Zhou, Dongsheng; Song, Yajun

    2005-01-01

    . pestis from different natural plague foci in China based on pseudogene profiles. Twenty-four mutations that led to inactivation in the corresponding genes were analysed, and a PCR-based screening method was employed to investigate the distribution of these mutations among Y. pestis isolates from...

  9. Pseudogenes regulate parental gene expression via ceRNA network.

    Science.gov (United States)

    An, Yang; Furber, Kendra L; Ji, Shaoping

    2017-01-01

    The concept of competitive endogenous RNA (ceRNA) was first proposed by Salmena and colleagues. Evidence suggests that pseudogene RNAs can act as a 'sponge' through competitive binding of common miRNA, releasing or attenuating repression through sequestering miRNAs away from parental mRNA. In theory, ceRNAs refer to all transcripts such as mRNA, tRNA, rRNA, long non-coding RNA, pseudogene RNA and circular RNA, because all of them may become the targets of miRNA depending on spatiotemporal situation. As binding of miRNA to the target RNA is not 100% complementary, it is possible that one miRNA can bind to multiple target RNAs and vice versa. All RNAs crosstalk through competitively binding to miRNAvia miRNA response elements (MREs) contained within the RNA sequences, thus forming a complex regulatory network. The ratio of a subset of miRNAs to the corresponding number of MREs determines repression strength on a given mRNA translation or stability. An increase in pseudogene RNA level can sequester miRNA and release repression on the parental gene, leading to an increase in parental gene expression. A massive number of transcripts constitute a complicated network that regulates each other through this proposed mechanism, though some regulatory significance may be mild or even undetectable. It is possible that the regulation of gene and pseudogene expression occurring in this manor involves all RNAs bearing common MREs. In this review, we will primarily discuss how pseudogene transcripts regulate expression of parental genes via ceRNA network and biological significance of regulation. © 2016 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  10. Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in Chlamydia trachomatis serovar L2 and D strains

    Directory of Open Access Journals (Sweden)

    Graham David E

    2009-07-01

    Full Text Available Abstract Background Chlamydia have reduced genomes that reflect their obligately parasitic lifestyle. Despite their different tissue tropisms, chlamydial strains share a large number of common genes and have few recognized pseudogenes, indicating genomic stability. All of the Chlamydiaceae have homologs of the aaxABC gene cluster that encodes a functional arginine:agmatine exchange system in Chlamydia (Chlamydophilapneumoniae. However, Chlamydia trachomatis serovar L2 strains have a nonsense mutation in their aaxB genes, and C. trachomatis serovar A and B strains have frameshift mutations in their aaxC homologs, suggesting that relaxed selection may have enabled the evolution of aax pseudogenes. Biochemical experiments were performed to determine whether the aaxABC genes from C. trachomatis strains were transcribed, and mutagenesis was used to identify nucleotide substitutions that prevent protein maturation and activity. Molecular evolution techniques were applied to determine the relaxation of selection and the scope of aax gene inactivation in the Chlamydiales. Results The aaxABC genes were co-transcribed in C. trachomatis L2/434, during the mid-late stage of cellular infection. However, a stop codon in the aaxB gene from this strain prevented the heterologous production of an active pyruvoyl-dependent arginine decarboxylase. Replacing that ochre codon with its ancestral tryptophan codon rescued the activity of this self-cleaving enzyme. The aaxB gene from C. trachomatis D/UW-3 was heterologously expressed as a proenzyme that failed to cleave and form the catalytic pyruvoyl cofactor. This inactive protein could be rescued by replacing the arginine-115 codon with an ancestral glycine codon. The aaxC gene from the D/UW-3 strain encoded an active arginine:agmatine antiporter protein, while the L2/434 homolog was unexpectedly inactive. Yet the frequencies of nonsynonymous versus synonymous nucleotide substitutions show no signs of relaxed

  11. Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions.

    Science.gov (United States)

    Harpke, Doerte; Peterson, Angela

    2008-05-01

    The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, ITS2) represents the most widely applied nuclear marker in eukaryotic phylogenetics. Although this region has been assumed to evolve in concert, the number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenes has risen. The 5.8S rDNA is the most important diagnostic marker for functionality of the ITS region. In Mammillaria, intra-individual 5.8S rDNA polymorphisms of up to 36% and up to nine different types have been found. Twenty-eight of 30 cloned genomic Mammillaria sequences were identified as putative pseudogenes. For the identification of pseudogenic ITS regions, in addition to formal tests based on substitution rates, we attempted to focus on functional features of the 5.8S rDNA (5.8S motif, secondary structure). The importance of functional data for the identification of pseudogenes is outlined and discussed. The identification of pseudogenes is essential, because they may cause erroneous phylogenies and taxonomic problems.

  12. Lithuanian medical tourism cluster: conditions and background for functioning

    Directory of Open Access Journals (Sweden)

    Korol A. N.

    2017-10-01

    Full Text Available as the global economy develops, more and more attention is paid to the creation of tourist clusters, which are extremely important for the economy and national competitiveness. This article analyzes the cluster of medical tourism in Lithuania, and explores the conditions for its successful functioning. The creation of the medical tourism cluster is highly influenced by a number of factors: the regulation of tourist and medical services, the level of entrepreneurial activity, human resources, the experience of partnership. In addition, the article analyzes the structure of the medical tourism cluster, determines the prerequisites for the functioning of the Lithuanian medical tourism cluster, including a wide range of services, European standards for the provision of medical services, high qualification of specialists, etc. When writing the article, the methods of systematic and logical analysis of scientific literature were used.

  13. A recombination point is conserved in the mitochondrial genome of higher plant species and located downstream from the cox2 pseudogene in Solanum tuberosum L.

    Directory of Open Access Journals (Sweden)

    Susely F.S. Tada

    2006-01-01

    Full Text Available The potato (Solanum tuberosum L. mitochondrial cox3/sdh4/pseudo-cox2 gene cluster has previously been identified by heterologous hybridization using a Marchantia polymorpha sdh4 probe. In our present study we used Southern blotting using sdh4 and cox2 probes to show that the sdh4 and cox2 genes are clustered in the mitochondria of potato, soybean and pea. Northern blotting revealed cotranscription of sdh4 and cox2 in potato but not in cauliflower, indicating that these genes are not clustered in cauliflower. A putative recombination point was detected downstream of the cox2 pseudogene (pseudo-cox2 in potato mitochondrial DNA (mtDNA. This sequence corresponds to a 32 bp sequence which appears to be well-conserved and is adjacent to the terminals of some mitochondrial genes in Citrullus lanatus, Beta vulgaris and Arabidopsis thaliana and is probably involved in the genic rearrangements. It is possible the potato mtDNA pseudo-cox2 gene was generated by recombination during evolution in the same way as that of several other mitochondrial genes and remains as an inactive partial copy of the functional cox2 which was also detected in potato mtDNA.

  14. Evolution of the cluster X-ray luminosity function

    DEFF Research Database (Denmark)

    Mullis, C.R.; Vikhlinin, A.; Henry, J.P.

    2004-01-01

    We report measurements of the cluster X-ray luminosity function out to z = 0.8 based on the final sample of 201 galaxy systems from the 160 Square Degree ROSAT Cluster Survey. There is little evidence for any measurable change in cluster abundance out to z similar to 0.6 at luminosities of less...... than a few times 10(44) h(50)(-2) ergs s(-1) (0.5 - 2.0 keV). However, for 0.6 cluster deficit using integrated number counts...... independently confirm the presence of evolution. Whereas the bulk of the cluster population does not evolve, the most luminous and presumably most massive structures evolve appreciably between z = 0.8 and the present. Interpreted in the context of hierarchical structure formation, we are probing sufficiently...

  15. Functionalization of carbon nanotubes with silver clusters

    International Nuclear Information System (INIS)

    Cveticanin, Jelena; Krkljes, Aleksandra; Kacarevic-Popovic, Zorica; Mitric, Miodrag; Rakocevic, Zlatko; Trpkov, Djordje; Neskovic, Olivera

    2010-01-01

    In this paper, an advanced method of one-step functionalization of single and multi walled carbon nanotubes (SWCNTs and MWCNTs) using γ-irradiation was described. Two synthesis procedures, related with different reduction species, were employed. For the first time, poly(vinyl alcohol) PVA is successfully utilized as a source to reduce silver (Ag) metal ions without having any additional reducing agents to obtain Ag nanoparticles on CNTs. The decoration of carbon nanotubes with Ag nanoparticles takes place through anchoring of (PVA) on nanotube's surface. Optical properties of as-prepared samples and mechanism responsible for the functionalization of carbon nanotubes were investigated using UV-vis and FTIR spectroscopy, respectively. Decorated carbon nanotubes were visualized using microscopic techniques: transmission electron microscopy and scanning tunneling microscopy. Also, the presence of Ag on the nanotubes was confirmed using energy dispersive X-ray spectroscopy. This simple and effective method of making a carbon nanotube type of composites is of interest not only for an application in various areas of technology and biology, but for investigation of the potential of radiation technology for nanoengineering of materials.

  16. Loss of Octarepeats in Two Processed Prion Pseudogenes in the Red Squirrel, Sciurus vulgaris

    Science.gov (United States)

    Kortum, Timothy T.; Hupkes, Marlinda; Kohlen, Wouter; van Rheede, Teun; de Jong, Wilfried W.

    2010-01-01

    The N-terminal region of the mammalian prion protein (PrP) contains an ‘octapeptide’ repeat which is involved in copper binding. This eight- or nine-residue peptide is repeated four to seven times, depending on the species, and polymorphisms in repeat number do occur. Alleles with three repeats are very rare in humans and goats, and deduced PrP sequences with two repeats have only been reported in two lemur species and in the red squirrel, Sciurus vulgaris. We here describe that the red squirrel two-repeat PrP sequence actually represents a retroposed pseudogene, and that an additional and older processed pseudogene with three repeats also occurs in this species as well as in ground squirrels. We argue that repeat numbers may tend to contract rather than expand in prion retropseudogenes, and that functional prion genes with two repeats may not be viable. Electronic supplementary material The online version of this article (doi:10.1007/s00239-010-9390-7) contains supplementary material, which is available to authorized users. PMID:20878152

  17. Topological defect clustering and plastic deformation mechanisms in functionalized graphene

    Science.gov (United States)

    Nunes, Ricardo; Araujo, Joice; Chacham, Helio

    2011-03-01

    We present ab initio results suggesting that strain plays a central role in the clustering of topological defects in strained and functionalized graphene models. We apply strain onto the topological-defect graphene networks from our previous work, and obtain topological-defect clustering patterns which are in excellent agreement with recent observations in samples of reduced graphene oxide. In our models, the graphene layer, containing an initial concentration of isolated topological defects, is covered by hydrogen or hydroxyl groups. Our results also suggest a rich variety of plastic deformation mechanism in functionalized graphene systems. We acknowledge support from the Brazilian agencies: CNPq, Fapemig, and INCT-Materiais de Carbono.

  18. clusters

    Indian Academy of Sciences (India)

    2017-09-27

    Sep 27, 2017 ... Author for correspondence (zh4403701@126.com). MS received 15 ... lic clusters using density functional theory (DFT)-GGA of the DMOL3 package. ... In the process of geometric optimization, con- vergence thresholds ..... and Postgraduate Research & Practice Innovation Program of. Jiangsu Province ...

  19. Evolution of the cluster x-ray luminosity function slope

    International Nuclear Information System (INIS)

    Henry, J.P.; Soltan, A.; Briel, U.; Gunn, J.E.

    1982-01-01

    We report the results of an X-ray survey of 58 clusters of galaxies at moderate and high redshifts. Using a luminosity-limited subsample of 25 objects, we find that to a redshift of 0.5 the slope (i.e., power-law index) of the luminosity function of distant clusters is independent of redshift and consistent with that of nearby clusters. The time scale for change in the slope must be greater than 9 billion years. We cannot measure the normalization of the luminosity function because our sample is not complete. We discuss the implications of our data for theoretical models. In particular, Perrenod's models with high Ω are excluded by the present data

  20. Photometric studies of globular clusters in the Andromeda Nebula. Luminosity function for old globular clusters

    International Nuclear Information System (INIS)

    Sharov, A.S.; Lyutyj, V.M.

    1989-01-01

    The luminosity function for old globular clusters in M 31 is presented. The objects were selected according to their structural and photometric properties. At the usually accepted normal (Gaussian) distribution, the luminosity function is characterized by the following parameters: the mean magnitude, corrected for the extinction inside M 31, V-bar 0 =16 m ,38±0 m .08, and the absolute magnitude M-bar v =-8 m .29 assuming )m-M) v =23 m .67, standard deviation σ M v =1 m .16±0 m .08 and total object number N=300±17. Old globular clusters in M 31 are in the average about one magnitude more luminous then those in our Galaxy (M v ≅ -7 m .3). Intrinsic luminosity dispersions of globular clusters are nearly the same in both galaxies. Available data on globular clusters in the Local Group galaxies against the universality of globular luminosity function with identical parameters M v and σ M v

  1. Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae

    DEFF Research Database (Denmark)

    Haugen, P; Huss, V A; Nielsen, Henrik

    1999-01-01

    on the complementary strand. A comparison between related group-I introns in the Bangiophyceae revealed homing-endonuclease-like pseudogenes due to frame-shifts and deletions in Porphyra and Bangia. The Scenedesmus and Porphyra introns provide new insights into the evolution and possible novel functions of nuclear...

  2. The food, GI tract functionality and human health cluster

    NARCIS (Netherlands)

    Mattila-Sandholm, T.; Blaut, M.; Daly, C.; Vuyst, de L.; Dore, J.; Gibson, G.; Goossens, H.; Knorr, D.; Lucas, J.; Lahteenmaki, L.; Mercenier, A.M.E.; Saarela, M.; Shanahan, F.; Vos, de W.M.

    2002-01-01

    The Food, GI-tract Functionality and Human Health (PROEUHEALTH) Cluster brings together eight complementary, multicentre interdisciplinary research projects. All have the common aim of improving the health and quality of life of European comsumers. The collaboration involves 64 different research

  3. Structure of gene and pseudogenes of human apoferritin H

    Energy Technology Data Exchange (ETDEWEB)

    Costanzo, F; Colombo, M; Staempfli, S; Santoro, C; Marone, M; Frank, K; Delius, H; Cortese, R

    1986-01-24

    Ferritin is composed of two subunits, H and L. cDNA's coding for these proteins from human liver, lymphocytes and from the monocyte-like cell line U937 have been cloned and sequenced. Southern blot analysis on total human DNA reveals that there are many DNA segments hybridizing to the apoferritin H and L cDNA probes. In view of the tissue heterogeneity of ferritin molecules, it appeared possible that apoferritin molecules could be coded by a family of genes differentially expressed in various tissues. In this paper, the authors describe the cloning and sequencing of the gene coding for human apoferritin H. This gene has three introns; the exon sequence is identical to that of cDNAs isolated from human liver, lymphocytes, HeLa cells and endothelial cells. In addition they show that at least 15 intronless pseudogenes exist, with features suggesting that there were originated by reverse transcription and insertion. On the basis of these results they conclude that only one gene is responsible for the synthesis of the majority of apoferritin H mRNA in various tissues examined, and that probably all the other DNA segments hybridizing with apoferritin cDNA are pseudogenes.

  4. Isomers of Cu6 cluster: a density function theory study

    International Nuclear Information System (INIS)

    Jia Yanhui; Wang Shanshan; Li Gongping

    2008-01-01

    The possible structure of Cu 6 cluster has been given with the GaussView that is a graphical user interface software. The structure optimization was performed on the B3LYP functional and SDD basic set of the quantum computational software of Gaussian03. And eight isomers of Cu 6 cluster were calculated. The binding energy and the structure of eight isomers have been investigated in detail. The result showed that the value of the binding energy was in reasonable agreement with available experimental data, as well as with other theoretical results, and the most stable structure was the triangle of plane. Three new isomers of the Cu 6 cluster have been got in our work, which would be the valuable data for the further theoretical and experimental study. (authors)

  5. Ribosomal RNA Genes Contribute to the Formation of Pseudogenes and Junk DNA in the Human Genome.

    Science.gov (United States)

    Robicheau, Brent M; Susko, Edward; Harrigan, Amye M; Snyder, Marlene

    2017-02-01

    Approximately 35% of the human genome can be identified as sequence devoid of a selected-effect function, and not derived from transposable elements or repeated sequences. We provide evidence supporting a known origin for a fraction of this sequence. We show that: 1) highly degraded, but near full length, ribosomal DNA (rDNA) units, including both 45S and Intergenic Spacer (IGS), can be found at multiple sites in the human genome on chromosomes without rDNA arrays, 2) that these rDNA sequences have a propensity for being centromere proximal, and 3) that sequence at all human functional rDNA array ends is divergent from canonical rDNA to the point that it is pseudogenic. We also show that small sequence strings of rDNA (from 45S + IGS) can be found distributed throughout the genome and are identifiable as an "rDNA-like signal", representing 0.26% of the q-arm of HSA21 and ∼2% of the total sequence of other regions tested. The size of sequence strings found in the rDNA-like signal intergrade into the size of sequence strings that make up the full-length degrading rDNA units found scattered throughout the genome. We conclude that the displaced and degrading rDNA sequences are likely of a similar origin but represent different stages in their evolution towards random sequence. Collectively, our data suggests that over vast evolutionary time, rDNA arrays contribute to the production of junk DNA. The concept that the production of rDNA pseudogenes is a by-product of concerted evolution represents a previously under-appreciated process; we demonstrate here its importance. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Theoretical stellar luminosity functions and globular cluster ages and compositions

    International Nuclear Information System (INIS)

    Ratcliff, S.J.

    1985-01-01

    The ages and chemical compositions of the stars in globular clusters are of great interest, particularly because age estimates from the well-known exercise of fitting observed color-magnitude diagrams to theoretical predictions tend to yield ages in excess of the Hubble time (an estimate to the age of the Universe) in standard cosmological models, for currently proposed high values of Hubble's constant (VandenBerg 1983). Relatively little use has been made of stellar luminosity functions of the globular clusters, for which reliable observations are now becoming available, to constrain the ages or compositions. The comparison of observed luminosity functions to theoretical ones allows one to take advantage of information not usually used, and has the advantage of being relatively insensitive to our lack of knowledge of the detailed structure of stellar envelopes and atmospheres. A computer program was developed to apply standard stellar evolutionary theory, using the most recently available input physics (opacities, nuclear reaction rates), to the calculation of the evolution of low-mass Population II stars. An algorithm for computing luminosity functions from the evolutionary tracks was applied to sets of tracks covering a broad range of chemical compositions and ages, such as may be expected for globular clusters

  7. Functional Analysis of the Chaperone-Usher Fimbrial Gene Clusters of Salmonella enterica serovar Typhi.

    Science.gov (United States)

    Dufresne, Karine; Saulnier-Bellemare, Julie; Daigle, France

    2018-01-01

    The human-specific pathogen Salmonella enterica serovar Typhi causes typhoid, a major public health issue in developing countries. Several aspects of its pathogenesis are still poorly understood. S . Typhi possesses 14 fimbrial gene clusters including 12 chaperone-usher fimbriae ( stg, sth, bcf , fim, saf , sef , sta, stb, stc, std, ste , and tcf ). These fimbriae are weakly expressed in laboratory conditions and only a few are actually characterized. In this study, expression of all S . Typhi chaperone-usher fimbriae and their potential roles in pathogenesis such as interaction with host cells, motility, or biofilm formation were assessed. All S . Typhi fimbriae were better expressed in minimal broth. Each system was overexpressed and only the fimbrial gene clusters without pseudogenes demonstrated a putative major subunits of about 17 kDa on SDS-PAGE. Six of these (Fim, Saf, Sta, Stb, Std, and Tcf) also show extracellular structure by electron microscopy. The impact of fimbrial deletion in a wild-type strain or addition of each individual fimbrial system to an S . Typhi afimbrial strain were tested for interactions with host cells, biofilm formation and motility. Several fimbriae modified bacterial interactions with human cells (THP-1 and INT-407) and biofilm formation. However, only Fim fimbriae had a deleterious effect on motility when overexpressed. Overall, chaperone-usher fimbriae seem to be an important part of the balance between the different steps (motility, adhesion, host invasion and persistence) of S . Typhi pathogenesis.

  8. Density functional study of the bonding in small silicon clusters

    International Nuclear Information System (INIS)

    Fournier, R.; Sinnott, S.B.; DePristo, A.E.

    1992-01-01

    We report the ground electronic state, equilibrium geometry, vibrational frequencies, and binding energy for various isomers of Si n (n = 2--8) obtained with the linear combination of atomic orbitals-density functional method. We used both a local density approximation approach and one with gradient corrections. Our local density approximation results concerning the relative stability of electronic states and isomers are in agreement with Hartree--Fock and Moller--Plesset (MP2) calculations [K. Raghavachari and C. M. Rohlfing, J. Chem. Phys. 89, 2219 (1988)]. The binding energies calculated with the gradient corrected functional are in good agreement with experiment (Si 2 and Si 3 ) and with the best theoretical estimates. Our analysis of the bonding reveals two limiting modes of bonding and classes of silicon clusters. One class of clusters is characterized by relatively large s atomic populations and a large number of weak bonds, while the other class of clusters is characterized by relatively small s atomic populations and a small number of strong bonds

  9. Dyadic Green's function of a cluster of spheres.

    Science.gov (United States)

    Moneda, Angela P; Chrissoulidis, Dimitrios P

    2007-11-01

    The electric dyadic Green's function (dGf) of a cluster of spheres is obtained by application of the superposition principle, dyadic algebra, and the indirect mode-matching method. The analysis results in a set of linear equations for the unknown, vector, wave amplitudes of the dGf; that set is solved by truncation and matrix inversion. The theory is exact in the sense that no simplifying assumptions are made in the analytical steps leading to the dGf, and it is general in the sense that any number, position, size and electrical properties can be considered for the spheres that cluster together. The point source can be anywhere, even within one of the spheres. Energy conservation, reciprocity, and other tests prove that this solution is correct. Numerical results are presented for an electric Hertz dipole radiating in the presence of an array of rexolite spheres, which manifests lensing and beam-forming capabilities.

  10. Anchoring selenido-carbonyl ruthenium clusters to functionalized silica xerogels

    International Nuclear Information System (INIS)

    Cauzzi, Daniele; Graiff, Claudia; Pattacini, Roberto; Predieri, Giovanni; Tiripicchio, Antonio

    2003-01-01

    Silica Xerogels containing carbonyl Ru 3 Se 2 nido clusters were prepared in three different ways. The simple dispersion of [Ru 3 (μ 3 -Se) 2 (CO) 7 (PPh 3 ) 2 ] via sol gel process produces an inhomogeneous material; by contrast, homogeneous xerogels were obtained by reaction of [Ru 3 (μ 3 -Se) 2 (CO) 8 (PPh 3 )] with functionalized xerogels containing grafted diphenylphosphine moieties and by reaction of [Ru 3 (CO) 12 ] with a xerogel containing grafted phosphine-selenide groups. The reaction between [Ru 3 (CO) 12 ] and dodecyl diphenylphosphine selenide led to the formation of four selenido carbonyl clusters, which are soluble in hydrocarbon solvents and can be deposited as thin films from their solution by slow evaporation. (author)

  11. Pseudogenization of the MCP-2/CCL8 chemokine gene in European rabbit (genus Oryctolagus, but not in species of Cottontail rabbit (Sylvilagus and Hare (Lepus

    Directory of Open Access Journals (Sweden)

    van der Loo Wessel

    2012-08-01

    Full Text Available Abstract Background Recent studies in human have highlighted the importance of the monocyte chemotactic proteins (MCP in leukocyte trafficking and their effects in inflammatory processes, tumor progression, and HIV-1 infection. In European rabbit (Oryctolagus cuniculus one of the prime MCP targets, the chemokine receptor CCR5 underwent a unique structural alteration. Until now, no homologue of MCP-2/CCL8a, MCP-3/CCL7 or MCP-4/CCL13 genes have been reported for this species. This is interesting, because at least the first two genes are expressed in most, if not all, mammals studied, and appear to be implicated in a variety of important chemokine ligand-receptor interactions. By assessing the Rabbit Whole Genome Sequence (WGS data we have searched for orthologs of the mammalian genes of the MCP-Eotaxin cluster. Results We have localized the orthologs of these chemokine genes in the genome of European rabbit and compared them to those of leporid genera which do (i.e. Oryctolagus and Bunolagus or do not share the CCR5 alteration with European rabbit (i.e. Lepus and Sylvilagus. Of the Rabbit orthologs of the CCL8, CCL7, and CCL13 genes only the last two were potentially functional, although showing some structural anomalies at the protein level. The ortholog of MCP-2/CCL8 appeared to be pseudogenized by deleterious nucleotide substitutions affecting exon1 and exon2. By analyzing both genomic and cDNA products, these studies were extended to wild specimens of four genera of the Leporidae family: Oryctolagus, Bunolagus, Lepus, and Sylvilagus. It appeared that the anomalies of the MCP-3/CCL7 and MCP-4/CCL13 proteins are shared among the different species of leporids. In contrast, whereas MCP-2/CCL8 was pseudogenized in every studied specimen of the Oryctolagus - Bunolagus lineage, this gene was intact in species of the Lepus - Sylvilagus lineage, and was, at least in Lepus, correctly transcribed. Conclusion The biological function of a gene was often

  12. The luminosity function for globular clusters, 4: M3

    International Nuclear Information System (INIS)

    Simoda, Mahiro; Fukuoka, Takashi

    1976-01-01

    The subgiant-turnoff portion (V = 17.2 - 20.0 mag) of the luminosity function for the globular cluster M3 has been determined from photometry of the stars within the annuli 3'-8' and 6'-8' for V = 17.2 - 19.0 mag and 19.0 - 20.0 mag, respectively, by using plates taken with the Kitt Peak 2.1-m reflector. Our result shows that the luminosity function for M3 has a similar steep rise in the subgiant portion as other clusters so far studied (M5, M13, and M92), in direct conflict with the result by SANDAGE (1954, 1957). A probable cause of this discrepancy is given. Comparison with theoretical luminosity functions by SIMODA and IBEN (1970) suggests that theory and observation are not inconsistent if the initial helium abundance of M3 stars is taken to be about 20 percent. It is suggested that M13 has a larger helium abundance than M3 and M92 from the intercomparison of their luminosity functions and color-magnitude diagrams. (auth.)

  13. Derivation of the density functional theory from the cluster expansion.

    Science.gov (United States)

    Hsu, J Y

    2003-09-26

    The density functional theory is derived from a cluster expansion by truncating the higher-order correlations in one and only one term in the kinetic energy. The formulation allows self-consistent calculation of the exchange correlation effect without imposing additional assumptions to generalize the local density approximation. The pair correlation is described as a two-body collision of bound-state electrons, and modifies the electron- electron interaction energy as well as the kinetic energy. The theory admits excited states, and has no self-interaction energy.

  14. Clustering of near clusters versus cluster compactness

    International Nuclear Information System (INIS)

    Yu Gao; Yipeng Jing

    1989-01-01

    The clustering properties of near Zwicky clusters are studied by using the two-point angular correlation function. The angular correlation functions for compact and medium compact clusters, for open clusters, and for all near Zwicky clusters are estimated. The results show much stronger clustering for compact and medium compact clusters than for open clusters, and that open clusters have nearly the same clustering strength as galaxies. A detailed study of the compactness-dependence of correlation function strength is worth investigating. (author)

  15. Functional clustering in hippocampal cultures: relating network structure and dynamics

    International Nuclear Information System (INIS)

    Feldt, S; Dzakpasu, R; Olariu, E; Żochowski, M; Wang, J X; Shtrahman, E

    2010-01-01

    In this work we investigate the relationship between gross anatomic structural network properties, neuronal dynamics and the resultant functional structure in dissociated rat hippocampal cultures. Specifically, we studied cultures as they developed under two conditions: the first supporting glial cell growth (high glial group), and the second one inhibiting it (low glial group). We then compared structural network properties and the spatio-temporal activity patterns of the neurons. Differences in dynamics between the two groups could be linked to the impact of the glial network on the neuronal network as the cultures developed. We also implemented a recently developed algorithm called the functional clustering algorithm (FCA) to obtain the resulting functional network structure. We show that this new algorithm is useful for capturing changes in functional network structure as the networks evolve over time. The FCA detects changes in functional structure that are consistent with expected dynamical differences due to the impact of the glial network. Cultures in the high glial group show an increase in global synchronization as the cultures age, while those in the low glial group remain locally synchronized. We additionally use the FCA to quantify the amount of synchronization present in the cultures and show that the total level of synchronization in the high glial group is stronger than in the low glial group. These results indicate an interdependence between the glial and neuronal networks present in dissociated cultures

  16. Diagnostics of subtropical plants functional state by cluster analysis

    Directory of Open Access Journals (Sweden)

    Oksana Belous

    2016-05-01

    Full Text Available The article presents an application example of statistical methods for data analysis on diagnosis of the adaptive capacity of subtropical plants varieties. We depicted selection indicators and basic physiological parameters that were defined as diagnostic. We used evaluation on a set of parameters of water regime, there are: determination of water deficit of the leaves, determining the fractional composition of water and detection parameters of the concentration of cell sap (CCS (for tea culture flushes. These settings are characterized by high liability and high responsiveness to the effects of many abiotic factors that determined the particular care in the selection of plant material for analysis and consideration of the impact on sustainability. On the basis of the experimental data calculated the coefficients of pair correlation between climatic factors and used physiological indicators. The result was a selection of physiological and biochemical indicators proposed to assess the adaptability and included in the basis of methodical recommendations on diagnostics of the functional state of the studied cultures. Analysis of complex studies involving a large number of indicators is quite difficult, especially does not allow to quickly identify the similarity of new varieties for their adaptive responses to adverse factors, and, therefore, to set general requirements to conditions of cultivation. Use of cluster analysis suggests that in the analysis of only quantitative data; define a set of variables used to assess varieties (and the more sampling, the more accurate the clustering will happen, be sure to ascertain the measure of similarity (or difference between objects. It is shown that the identification of diagnostic features, which are subjected to statistical processing, impact the accuracy of the varieties classification. Selection in result of the mono-clusters analysis (variety tea Kolhida; hazelnut Lombardsky red; variety kiwi Monty

  17. Relativistic form factors for clusters with nonrelativistic wave functions

    International Nuclear Information System (INIS)

    Mitra, A.N.; Kumari, I.

    1977-01-01

    Using a simple variant of an argument employed by Licht and Pagnamenta (LP) on the effect of Lorentz contraction on the elastic form factors of clusters with nonrelativistic wave functions, it is shown how their result can be generalized to inelastic form factors so as to produce (i) a symmetrical appearance of Lorentz contraction effects in the initial and final states, and (ii) asymptotic behavior in accord with dimensional scaling theories. A comparison of this result with a closely analogous parametric form obtained by Brodsky and Chertok from a propagator chain model leads, with plausible arguments, to the conclusion of an effective mass M for the cluster, with M 2 varying as the number n of the quark constituents, instead of as n 2 . A further generalization of the LP formula is obtained for an arbitrary duality-diagram vertex, again with asymptotic behavior in conformity with dimensional scaling. The practical usefulness of this approach is emphasized as a complementary tool to those of high-energy physics for phenomenological fits to data up to moderate values of q 2

  18. Structure and Stability of GeAun, n = 1-10 clusters: A Density Functional Study

    International Nuclear Information System (INIS)

    Priyanka,; Dharamvir, Keya; Sharma, Hitesh

    2011-01-01

    The structures of Germanium doped gold clusters GeAu n (n = 1-10) have been investigated using ab initio calculations based on density functional theory (DFT). We have obtained ground state geometries of GeAu n clusters and have it compared with Silicon doped gold clusters and pure gold clusters. The ground state geometries of the GeAu n clusters show patterns similar to silicon doped gold clusters except for n = 5, 6 and 9. The introduction of germanium atom increases the binding energy of gold clusters. The binding energy per atom of germanium doped cluster is smaller than the corresponding silicon doped gold cluster. The HUMO-LOMO gap for Au n Ge clusters have been found to vary between 0.46 eV-2.09 eV. The mullikan charge analysis indicates that charge of order of 0.1e always transfers from germanium atom to gold atom.

  19. Pseudogenes and DNA-based diet analyses: A cautionary tale from a relatively well sampled predator-prey system

    DEFF Research Database (Denmark)

    Dunshea, G.; Barros, N. B.; Wells, R. S.

    2008-01-01

    Mitochondrial ribosomal DNA is commonly used in DNA-based dietary analyses. In such studies, these sequences are generally assumed to be the only version present in DNA of the organism of interest. However, nuclear pseudogenes that display variable similarity to the mitochondrial versions...... are common in many taxa. The presence of nuclear pseudogenes that co-amplify with their mitochondrial paralogues can lead to several possible confounding interpretations when applied to estimating animal diet. Here, we investigate the occurrence of nuclear pseudogenes in fecal samples taken from bottlenose...... dolphins (Tursiops truncatus) that were assayed for prey DNA with a universal primer technique. We found pseudogenes in 13 of 15 samples and 1-5 pseudogene haplotypes per sample representing 5-100% of all amplicons produced. The proportion of amplicons that were pseudogenes and the diversity of prey DNA...

  20. Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome

    Directory of Open Access Journals (Sweden)

    Michael John Milligan

    2016-03-01

    Full Text Available Pseudogenes are abundant in the human genome and had long been thought of purely as nonfunctional gene fossils. Recent observations point to a role for pseudogenes in regulating genes transcriptionally and post-transcriptionally in human cells. To computationally interrogate the network space of integrated pseudogene and long non-coding RNA regulation in the human transcriptome, we developed and implemented an algorithm to identify all long non-coding RNA (lncRNA transcripts that overlap the genomic spans, and specifically the exons, of any human pseudogenes in either sense or antisense orientation. As inputs to our algorithm, we imported three public repositories of pseudogenes: GENCODE v17 (processed and unprocessed, Ensembl 72; Retroposed Pseudogenes V5 (processed only and Yale Pseudo60 (processed and unprocessed, Ensembl 60; two public lncRNA catalogs: Broad Institute, GENCODE v17; NCBI annotated piRNAs; and NHGRI clinical variants. The data sets were retrieved from the UCSC Genome Database using the UCSC Table Browser. We identified 2277 loci containing exon-to-exon overlaps between pseudogenes, both processed and unprocessed, and long non-coding RNA genes. Of these loci we identified 1167 with Genbank EST and full-length cDNA support providing direct evidence of transcription on one or both strands with exon-to-exon overlaps. The analysis converged on 313 pseudogene-lncRNA exon-to-exon overlaps that were bidirectionally supported by both full-length cDNAs and ESTs. In the process of identifying transcribed pseudogenes, we generated a comprehensive, positionally non-redundant encyclopedia of human pseudogenes, drawing upon multiple, and formerly disparate public pseudogene repositories. Collectively, these observations suggest that pseudogenes are pervasively transcribed on both strands and are common drivers of gene regulation.

  1. Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P

    Directory of Open Access Journals (Sweden)

    Lahey Cora

    2006-08-01

    Full Text Available Abstract Background Gaucher disease is a potentially severe lysosomal storage disorder caused by mutations in the human glucocerebrosidase gene (GBA. We have developed a multiplexed genetic assay for eight diseases prevalent in the Ashkenazi population: Tay-Sachs, Gaucher type I, Niemann-Pick types A and B, mucolipidosis type IV, familial dysautonomia, Canavan, Bloom syndrome, and Fanconi anemia type C. This assay includes an allelic determination for GBA allele c.1448T>C (L444P. The goal of this study was to clinically evaluate this assay. Methods Biotinylated, multiplex PCR products were directly hybridized to capture probes immobilized on fluorescently addressed microspheres. After incubation with streptavidin-conjugated fluorophore, the reactions were analyzed by Luminex IS100. Clinical evaluations were conducted using de-identified patient DNA samples. Results We evaluated a multiplexed suspension array assay that includes wild-type and mutant genetic determinations for Gaucher disease allele c.1448T>C. Two percent of samples reported to be wild-type by conventional methods were observed to be c.1448T>C heterozygous using our assay. Sequence analysis suggested that this phenomenon was due to co-amplification of the functional gene and a paralogous pseudogene (ΨGBA due to a polymorphism in the primer-binding site of the latter. Primers for the amplification of this allele were then repositioned to span an upstream deletion in the pseudogene, yielding a much longer amplicon. Although it is widely reported that long amplicons negatively impact amplification or detection efficiency in recently adopted multiplex techniques, this assay design functioned properly and resolved the occurrence of false heterozygosity. Conclusion Although previously available sequence information suggested GBA gene/pseudogene discrimination capabilities with a short amplified product, we identified common single-nucleotide polymorphisms in the pseudogene that

  2. Estimation of cluster stability using the theory of electron density functional

    International Nuclear Information System (INIS)

    Borisov, Yu.A.

    1985-01-01

    Prospects of using simple versions of the electron density functional for studying the energy characteristics of cluster compounds Was discussed. These types of cluster compounds were considered: clusters of Cs, Be, B, Sr, Cd, Sc, In, V, Tl, I elements as intermediate form between molecule and solid body, metalloorganic Mo, W, Tc, Re, Rn clusters and elementoorganic compounds of nido-cluster type. The problem concerning changes in the binding energy of homoatomic clusters depending on their size and three-dimensional structure was analysed

  3. Cluster-cluster clustering

    International Nuclear Information System (INIS)

    Barnes, J.; Dekel, A.; Efstathiou, G.; Frenk, C.S.; Yale Univ., New Haven, CT; California Univ., Santa Barbara; Cambridge Univ., England; Sussex Univ., Brighton, England)

    1985-01-01

    The cluster correlation function xi sub c(r) is compared with the particle correlation function, xi(r) in cosmological N-body simulations with a wide range of initial conditions. The experiments include scale-free initial conditions, pancake models with a coherence length in the initial density field, and hybrid models. Three N-body techniques and two cluster-finding algorithms are used. In scale-free models with white noise initial conditions, xi sub c and xi are essentially identical. In scale-free models with more power on large scales, it is found that the amplitude of xi sub c increases with cluster richness; in this case the clusters give a biased estimate of the particle correlations. In the pancake and hybrid models (with n = 0 or 1), xi sub c is steeper than xi, but the cluster correlation length exceeds that of the points by less than a factor of 2, independent of cluster richness. Thus the high amplitude of xi sub c found in studies of rich clusters of galaxies is inconsistent with white noise and pancake models and may indicate a primordial fluctuation spectrum with substantial power on large scales. 30 references

  4. Pseudogene PHBP1 promotes esophageal squamous cell carcinoma proliferation by increasing its cognate gene PHB expression.

    Science.gov (United States)

    Feng, Feiyue; Qiu, Bin; Zang, Ruochuan; Song, Peng; Gao, Shugeng

    2017-04-25

    Natural antisense transcripts (NATs) as one of the most diverse classes of long noncoding RNAs (lncRNAs), have been demonstrated involved in fundamental biological processes in human. Here, we reported that human prohibitin gene pseudogene 1 (PHBP1) was upregulated in ESCC, and increased PHBP1 expression in ESCC was associated with clinical advanced stage. Functional experiments showed that PHBP1 knockdown inhibited ESCC cells proliferation, colony formation and xenograft tumor growth in vitro and in vivo by causing cell-cycle arrest at the G1-G0 phase. Mechanisms analysis revealed that PHBP1 transcript as an antisense transcript of PHB is partially complementary to PHB mRNA and formed an RNA-RNA hybrid with PHB, consequently inducing an increase of PHB expression at both the mRNA and protein levels. Furthermore, PHBP1 expression is strongly correlated with PHB expression in ESCC tissues. Collectively, this study elucidates an important role of PHBP1 in promoting ESCC partly via increasing PHB expression.

  5. Mathematical model for research and analyze relations and functions between enterprises, members of cluster

    Science.gov (United States)

    Angelov, Kiril; Kaynakchieva, Vesela

    2017-12-01

    The aim of the current study is to research and analyze Mathematical model for research and analyze of relations and functions between enterprises, members of cluster, and its approbation in given cluster. Subject of the study are theoretical mechanisms for the definition of mathematical models for research and analyze of relations and functions between enterprises, members of cluster. Object of the study are production enterprises, members of cluster. Results of this study show that described theoretical mathematical model is applicable for research and analyze of functions and relations between enterprises, members of cluster from different industrial sectors. This circumstance creates alternatives for election of cluster, where is experimented this model for interaction improvement between enterprises, members of cluster.

  6. Integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A hypothesis.

    Science.gov (United States)

    Gunbin, Konstantin; Peshkin, Leonid; Popadin, Konstantin; Annis, Sofia; Ackermann, Rebecca R; Khrapko, Konstantin

    2017-05-01

    Fragments of mitochondrial DNA are known to get inserted into nuclear DNA to form NUMTs, i.e. nuclear pseudogenes of the mtDNA. The insertion of a NUMT is a rare event. Hundreds of pseudogenes have been cataloged in the human genome. NUMTs are, in essence, a special type of mutation with their own internal timer, which is synchronized with an established molecular clock, the mtDNA. Thus insertion of NUMTs can be timed with respect to evolution milestones such as the emergence of new species. We asked whether NUMTs were inserted uniformly over time or preferentially during certain periods of evolution, as implied by the "punctuated evolution" model. To our surprise, the NUMT insertion times do appear nonrandom with at least one cluster positioned at around 2.8 million years ago (Ma). Interestingly, 2.8Ma closely corresponds to the time of emergence of the genus Homo, and to a well-documented period of major climate change ca. 2.9-2.5Ma. It is tempting to hypothesize that the insertion of NUMTs is related to the speciation process. NUMTs could be either "riders", i.e., their insertion could be facilitated by the overall higher genome rearrangement activity during speciation, or "drivers", i.e. they may more readily get fixed in the population due to positive selection associated with speciation. If correct, the hypothesis would support the idea that evolution of our genus may have happened in a rapid, punctuated manner. Copyright © 2016 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  7. How many 5S rRNA genes and pseudogenes are there in ''Aspergillus nidulans''?

    International Nuclear Information System (INIS)

    Pelczar, P.; Fiett, J.; Bartnik, E.

    1994-01-01

    We have estimated the number of 5S rRNA genes in ''Aspergillus nidulans'' using two-dimensional agarose gel electrophoresis and hybridization to appropriate probes, representing the 5'-halves, the 3'-halves of the 5S rRNA sequence and a sequence found at the 3'-end of all known. ''A. nidulans'' pseudogenes (block C). We have found 23 5S rRNA genes, 15 pseudogenes consisting of the 5'-half of the 5S rRNA sequence (of which 3 are flanked by block C) and 12 copies of block C which do not seem to be in the vicinity of 5S rRNA sequences. This number of genes is much lower than our earlier estimates, and makes our previously analyzed sample of 9 sequenced genes and 3 pseudogenes much more representative. (author). 7 refs, 1 fig

  8. U1 snDNA clusters in grasshoppers: chromosomal dynamics and genomic organization

    Science.gov (United States)

    Anjos, A; Ruiz-Ruano, F J; Camacho, J P M; Loreto, V; Cabrero, J; de Souza, M J; Cabral-de-Mello, D C

    2015-01-01

    The spliceosome, constituted by a protein set associated with small nuclear RNA (snRNA), is responsible for mRNA maturation through intron removal. Among snRNA genes, U1 is generally a conserved repetitive sequence. To unveil the chromosomal/genomic dynamics of this multigene family in grasshoppers, we mapped U1 genes by fluorescence in situ hybridization in 70 species belonging to the families Proscopiidae, Pyrgomorphidae, Ommexechidae, Romaleidae and Acrididae. Evident clusters were observed in all species, indicating that, at least, some U1 repeats are tandemly arrayed. High conservation was observed in the first four families, with most species carrying a single U1 cluster, frequently located in the third or fourth longest autosome. By contrast, extensive variation was observed among Acrididae, from a single chromosome pair carrying U1 to all chromosome pairs carrying it, with occasional occurrence of two or more clusters in the same chromosome. DNA sequence analysis in Eyprepocnemis plorans (species carrying U1 clusters on seven different chromosome pairs) and Locusta migratoria (carrying U1 in a single chromosome pair) supported the coexistence of functional and pseudogenic lineages. One of these pseudogenic lineages was truncated in the same nucleotide position in both species, suggesting that it was present in a common ancestor to both species. At least in E. plorans, this U1 snDNA pseudogenic lineage was associated with 5S rDNA and short interspersed elements (SINE)-like mobile elements. Given that we conclude in grasshoppers that the U1 snDNA had evolved under the birth-and-death model and that its intragenomic spread might be related with mobile elements. PMID:25248465

  9. Comparative genomic analysis of the arthropod muscle myosin heavy chain genes allows ancestral gene reconstruction and reveals a new type of 'partially' processed pseudogene

    Directory of Open Access Journals (Sweden)

    Kollmar Martin

    2008-02-01

    Full Text Available Abstract Background Alternative splicing of mutually exclusive exons is an important mechanism for increasing protein diversity in eukaryotes. The insect Mhc (myosin heavy chain gene produces all different muscle myosins as a result of alternative splicing in contrast to most other organisms of the Metazoa lineage, that have a family of muscle genes with each gene coding for a protein specialized for a functional niche. Results The muscle myosin heavy chain genes of 22 species of the Arthropoda ranging from the waterflea to wasp and Drosophila have been annotated. The analysis of the gene structures allowed the reconstruction of an ancient muscle myosin heavy chain gene and showed that during evolution of the arthropods introns have mainly been lost in these genes although intron gain might have happened in a few cases. Surprisingly, the genome of Aedes aegypti contains another and that of Culex pipiens quinquefasciatus two further muscle myosin heavy chain genes, called Mhc3 and Mhc4, that contain only one variant of the corresponding alternative exons of the Mhc1 gene. Mhc3 transcription in Aedes aegypti is documented by EST data. Mhc3 and Mhc4 inserted in the Aedes and Culex genomes either by gene duplication followed by the loss of all but one variant of the alternative exons, or by incorporation of a transcript of which all other variants have been spliced out retaining the exon-intron structure. The second and more likely possibility represents a new type of a 'partially' processed pseudogene. Conclusion Based on the comparative genomic analysis of the alternatively spliced arthropod muscle myosin heavy chain genes we propose that the splicing process operates sequentially on the transcript. The process consists of the splicing of the mutually exclusive exons until one exon out of the cluster remains while retaining surrounding intronic sequence. In a second step splicing of introns takes place. A related mechanism could be responsible for

  10. Antisymmetrized four-body wave function and coexistence of single particle and cluster structures

    International Nuclear Information System (INIS)

    Sasakawa, T.

    1979-01-01

    It is shown that each Yakubovski component of the totally antisymmetric four-body wave function satisfies the same equation as the unantisymmetric wave function. In the antisymmetric total wave function, the wave functions belonging to the same kind of partition are totally antisymmetric among themselves. This leads to the coexistence of cluster models, including the single particle model as a special case of the cluster model, as a sum

  11. clusters

    Indian Academy of Sciences (India)

    environmental as well as technical problems during fuel gas utilization. ... adsorption on some alloys of Pd, namely PdAu, PdAg ... ried out on small neutral and charged Au24,26,27, Cu,28 ... study of Zanti et al.29 on Pdn (n = 1–9) clusters.

  12. FTH1P3, a Novel H-Ferritin Pseudogene Transcriptionally Active, Is Ubiquitously Expressed and Regulated during Cell Differentiation.

    Directory of Open Access Journals (Sweden)

    Maddalena Di Sanzo

    Full Text Available Ferritin, the major iron storage protein, performs its essential functions in the cytoplasm, nucleus and mitochondria. The variable assembly of 24 subunits of the Heavy (H and Light (L type composes the cytoplasmic molecule. In humans, two distinct genes code these subunits, both belonging to complex multigene families. Until now, one H gene has been identified with the coding sequence interrupted by three introns and more than 20 intronless copies widely dispersed on different chromosomes. Two of the intronless genes are actively transcribed in a tissue-specific manner. Herein, we report that FTH1P3, another intronless pseudogene, is transcribed. FTH1P3 transcript was detected in several cell lines and tissues, suggesting that its transcription is ubiquitary, as it happens for the parental ferritin H gene. Moreover, FTH1P3 expression is positively regulated during the cell differentiation process.

  13. Monoxides of small terbium clusters: A density functional theory investigation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, G. L.; Yuan, H. K., E-mail: yhk10@swu.edu.cn; Chen, H.; Kuang, A. L.; Li, Y.; Wang, J. Z.; Chen, J. [School of Physical Science and Technology, Southwest University, Chongqing 400715 (China)

    2014-12-28

    To investigate the effect of oxygen atom on the geometrical structures, electronic, and magnetic properties of small terbium clusters, we carried out the first-principles calculations on Tb{sub n}O (n = 1-14) clusters. The capping of an oxygen atom on one trigonal-facet of Tb{sub n} structures is always favored energetically, which can significantly improve the structural stability. The far-infrared vibrational spectroscopies are found to be different from those of corresponding bare clusters, providing a distinct signal to detect the characteristic structures of Tb{sub n}O clusters. The primary effect of oxygen atom on magnetic properties is to change the magnetic orderings among Tb atoms and to reduce small of local magnetic moments of the O-coordinated Tb atoms, both of which serve as the key reasons for the experimental magnetic evolution of an oscillating behavior. These calculations are consistent with, and help to account for, the experimentally observed magnetic properties of monoxide Tb{sub n}O clusters [C. N. Van Dijk et al., J. Appl. Phys. 107, 09B526 (2010)].

  14. Is prnt a pseudogene? Identification of ram Prt in testis and ejaculated spermatozoa.

    Directory of Open Access Journals (Sweden)

    Jorge Pimenta

    Full Text Available A hallmark of prion diseases or transmissible spongiform encephalopaties is the conversion of the cellular prion protein (PrP(C, expressed by the prion gene (prnp, into an abnormally folded isoform (PrP(Sc with amyloid-like features that causes scrapie in sheep among other diseases. prnp together with prnd (which encodes a prion-like protein designated as Doppel, and prnt (that encodes the prion protein testis specific--Prt with sprn (shadow of prion protein gene, that encodes Shadoo or Sho genes, constitute the "prion gene complex". Whereas a role for prnd in the proper functioning of male reproductive system has been confirmed, the function of prnt, a recently discovered prion family gene, comprises a conundrum leading to the assumption that ruminant prnt is a pseudogene with no protein expression. The main objective of the present study was to identify Prt localization in the ram reproductive system and simultaneously to elucidate if ovine prnt gene is transcribed into protein-coding RNA. Moreover, as Prt is a prnp-related protein, the amyloid propensity was also tested for ovine and caprine Prt. Recombinant Prt was used to immunize BALB/c mice, and the anti-Prt polyclonal antibody (APPA immune response was evaluated by ELISA and Western Blot. When tested by indirect immunofluorescence, APPA showed high avidity to the ram sperm head apical ridge subdomain, before and after induced capacitation, but did not show the same behavior against goat spermatozoa, suggesting high antibody specificity against ovine-Prt. Prt was also found in the testis when assayed by immunohistochemistry during ram spermatogenesis, where spermatogonia, spermatocytes, spermatids and spermatozoa, stained positive. These observations strongly suggest ovine prnt to be a translated protein-coding gene, pointing to a role for Prt protein in the ram reproductive physiology. Besides, caprine Prt appears to exhibit a higher amyloid propensity than ovine Prt, mostly associated

  15. First evidence of independent pseudogenization of Toll-like receptor 5 in passerine birds

    Czech Academy of Sciences Publication Activity Database

    Bainová, H.; Králová, Tereza; Bryjová, Anna; Albrecht, Tomáš; Bryja, Josef; Vinkler, M.

    2014-01-01

    Roč. 45, č. 1 (2014), s. 151-155 ISSN 0145-305X R&D Projects: GA ČR GAP505/10/1871 Institutional support: RVO:68081766 Keywords : Birds * Expression * Innate immunity * Toll-like receptor 5 * Pseudogene * Flagellin Subject RIV: EG - Zoology Impact factor: 2.815, year: 2014

  16. Avoidance of pseudogene interference in the detection of 3' deletions in PMS2.

    Science.gov (United States)

    Vaughn, Cecily P; Hart, Kimberly J; Samowitz, Wade S; Swensen, Jeffrey J

    2011-09-01

    Lynch syndrome is characterized by mutations in the mismatch repair genes MLH1, MSH2, MSH6, and PMS2. In PMS2, detection of mutations is confounded by numerous pseudogenes. Detection of 3' deletions is particularly complicated by the pseudogene PMS2CL, which has strong similarity to PMS2 exons 9 and 11-15, due to extensive gene conversion. A newly designed multiplex ligation-dependent probe amplification (MLPA) kit incorporates probes for variants found in both PMS2 and PMS2CL. This provides detection of deletions, but does not allow localization of deletions to the gene or pseudogene. To address this, we have developed a methodology incorporating reference samples with known copy numbers of variants, and paired MLPA results with sequencing of PMS2 and PMS2CL. We tested a subset of clinically indicated samples for which mutations were either unidentified or not fully characterized using existing methods. We identified eight unrelated patients with deletions encompassing exons 9-15, 11-15, 13-15, 14-15, and 15. By incorporating specific, characterized reference samples and sequencing the gene and pseudogene it is possible to identify deletions in this region of PMS2 and provide clinically relevant results. This methodology represents a significant advance in the diagnosis of patients with Lynch syndrome caused by PMS2 mutations. © 2011 Wiley-Liss, Inc.

  17. The ergot alkaloid gene cluster: Functional analyses and evolutionary aspects

    Czech Academy of Sciences Publication Activity Database

    Lorenz, N.; Haarmann, T.; Pažoutová, Sylvie; Jung, M.; Tudzynski, P.

    2009-01-01

    Roč. 70, 15-16 (2009), s. 1822-1832 ISSN 0031-9422 Institutional research plan: CEZ:AV0Z50200510 Keywords : Claviceps purpurea * Ergot fungus * Ergot alkaloid gene cluster Subject RIV: EE - Microbiology, Virology Impact factor: 3.104, year: 2009

  18. Cluster size statistic and cluster mass statistic: two novel methods for identifying changes in functional connectivity between groups or conditions.

    Science.gov (United States)

    Ing, Alex; Schwarzbauer, Christian

    2014-01-01

    Functional connectivity has become an increasingly important area of research in recent years. At a typical spatial resolution, approximately 300 million connections link each voxel in the brain with every other. This pattern of connectivity is known as the functional connectome. Connectivity is often compared between experimental groups and conditions. Standard methods used to control the type 1 error rate are likely to be insensitive when comparisons are carried out across the whole connectome, due to the huge number of statistical tests involved. To address this problem, two new cluster based methods--the cluster size statistic (CSS) and cluster mass statistic (CMS)--are introduced to control the family wise error rate across all connectivity values. These methods operate within a statistical framework similar to the cluster based methods used in conventional task based fMRI. Both methods are data driven, permutation based and require minimal statistical assumptions. Here, the performance of each procedure is evaluated in a receiver operator characteristic (ROC) analysis, utilising a simulated dataset. The relative sensitivity of each method is also tested on real data: BOLD (blood oxygen level dependent) fMRI scans were carried out on twelve subjects under normal conditions and during the hypercapnic state (induced through the inhalation of 6% CO2 in 21% O2 and 73%N2). Both CSS and CMS detected significant changes in connectivity between normal and hypercapnic states. A family wise error correction carried out at the individual connection level exhibited no significant changes in connectivity.

  19. The evolution of the global stellar mass function of star clusters: an analytic description

    NARCIS (Netherlands)

    Lamers, H.J.G.L.M.; Baumgardt, H.; Gieles, M.

    2013-01-01

    The evolution of the global stellar mass function of star clusters is studied based on a large set of N-body simulations of clusters with a range of initial masses, initial concentrations, in circular or elliptical orbits in different tidal environments. Models with and without initial mass

  20. A Comparison between Standard and Functional Clustering Methodologies: Application to Agricultural Fields for Yield Pattern Assessment

    Directory of Open Access Journals (Sweden)

    Simone Pascucci

    2018-04-01

    Full Text Available The recognition of spatial patterns within agricultural fields, presenting similar yield potential areas, stable through time, is very important for optimizing agricultural practices. This study proposes the evaluation of different clustering methodologies applied to multispectral satellite time series for retrieving temporally stable (constant patterns in agricultural fields, related to within-field yield spatial distribution. The ability of different clustering procedures for the recognition and mapping of constant patterns in fields of cereal crops was assessed. Crop vigor patterns, considered to be related to soils characteristics, and possibly indicative of yield potential, were derived by applying the different clustering algorithms to time series of Landsat images acquired on 94 agricultural fields near Rome (Italy. Two different approaches were applied and validated using Landsat 7 and 8 archived imagery. The first approach automatically extracts and calculates for each field of interest (FOI the Normalized Difference Vegetation Index (NDVI, then exploits the standard K-means clustering algorithm to derive constant patterns at the field level. The second approach applies novel clustering procedures directly to spectral reflectance time series, in particular: (1 standard K-means; (2 functional K-means; (3 multivariate functional principal components clustering analysis; (4 hierarchical clustering. The different approaches were validated through cluster accuracy estimates on a reference set of FOIs for which yield maps were available for some years. Results show that multivariate functional principal components clustering, with an a priori determination of the optimal number of classes for each FOI, provides a better accuracy than those of standard clustering algorithms. The proposed novel functional clustering methodologies are effective and efficient for constant pattern retrieval and can be used for a sustainable management of

  1. Cluster pair correlation function of simple fluids: energetic connectivity criteria

    OpenAIRE

    Pugnaloni, Luis A.; Zarragoicoechea, Guillermo J.; Vericat, Fernando

    2006-01-01

    We consider the clustering of Lennard-Jones particles by using an energetic connectivity criterion proposed long ago by T.L. Hill [J. Chem. Phys. 32, 617 (1955)] for the bond between pairs of particles. The criterion establishes that two particles are bonded (directly connected) if their relative kinetic energy is less than minus their relative potential energy. Thus, in general, it depends on the direction as well as on the magnitude of the velocities and positions of the particles. An integ...

  2. A density functional study of carbon monoxide adsorption on small cationic, neutral, and anionic gold clusters

    Science.gov (United States)

    Wu, X.; Senapati, L.; Nayak, S. K.; Selloni, A.; Hajaligol, M.

    2002-08-01

    CO adsorption on small cationic, neutral, and anionic Aun (n=1-6) clusters has been investigated using density functional theory in the generalized gradient approximation. Among various possible CO adsorption sites, the on-top (one-fold coordinated) is found to be the most favorable one, irrespective of the charge state of the cluster. In addition, planar structures are preferred by both the bare and the CO-adsorbed clusters. The adsorption energies of CO on the cationic clusters are generally greater than those on the neutral and anionic complexes, and decrease with size. The adsorption energies on the anions, instead, increase with cluster size and reach a local maximum at Au5CO-, in agreement with recent experiment. The differences in adsorption energies for the different charge states decrease with increasing cluster size.

  3. Spectroscopic constraints on the form of the stellar cluster mass function

    Science.gov (United States)

    Bastian, N.; Konstantopoulos, I. S.; Trancho, G.; Weisz, D. R.; Larsen, S. S.; Fouesneau, M.; Kaschinski, C. B.; Gieles, M.

    2012-05-01

    This contribution addresses the question of whether the initial cluster mass function (ICMF) has a fundamental limit (or truncation) at high masses. The shape of the ICMF at high masses can be studied using the most massive young (advantages are that more clusters can be used and that the ICMF leaves a distinct pattern on the global relation between the cluster luminosity and median age within a population. If a truncation is present, a generic prediction (nearly independent of the cluster disruption law adopted) is that the median age of bright clusters should be younger than that of fainter clusters. In the case of an non-truncated ICMF, the median age should be independent of cluster luminosity. Here, we present optical spectroscopy of twelve young stellar clusters in the face-on spiral galaxy NGC 2997. The spectra are used to estimate the age of each cluster, and the brightness of the clusters is taken from the literature. The observations are compared with the model expectations of Larsen (2009, A&A, 494, 539) for various ICMF forms and both mass dependent and mass independent cluster disruption. While there exists some degeneracy between the truncation mass and the amount of mass independent disruption, the observations favour a truncated ICMF. For low or modest amounts of mass independent disruption, a truncation mass of 5-6 × 105 M⊙ is estimated, consistent with previous determinations. Additionally, we investigate possible truncations in the ICMF in the spiral galaxy M 83, the interacting Antennae galaxies, and the collection of spiral and dwarf galaxies present in Larsen (2009, A&A, 494, 539) based on photometric catalogues taken from the literature, and find that all catalogues are consistent with having a truncation in the cluster mass functions. However for the case of the Antennae, we find a truncation mass of a few × 106M⊙ , suggesting a dependence on the environment, as has been previously suggested.

  4. Functional clustering of time series gene expression data by Granger causality

    Science.gov (United States)

    2012-01-01

    Background A common approach for time series gene expression data analysis includes the clustering of genes with similar expression patterns throughout time. Clustered gene expression profiles point to the joint contribution of groups of genes to a particular cellular process. However, since genes belong to intricate networks, other features, besides comparable expression patterns, should provide additional information for the identification of functionally similar genes. Results In this study we perform gene clustering through the identification of Granger causality between and within sets of time series gene expression data. Granger causality is based on the idea that the cause of an event cannot come after its consequence. Conclusions This kind of analysis can be used as a complementary approach for functional clustering, wherein genes would be clustered not solely based on their expression similarity but on their topological proximity built according to the intensity of Granger causality among them. PMID:23107425

  5. Photoluminescence quenching of chemically functionalized porous silicon by a ruthenium cluster

    Energy Technology Data Exchange (ETDEWEB)

    Boukherroub, R.; Wayner, D.D.M. [Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario (Canada); Lockwood, D.J. [Institute for Microstructural Sciences, National Research Council of Canada, Ottawa, Ontario (Canada); Zargarian, D. [Chemistry Department, University of Montreal, C.P. 6128, succursale, Centre-ville, Montreal QC (Canada)

    2003-05-01

    This paper describes photoluminescence (PL) quenching of hydrogen-terminated and chemically derivatized porous silicon (PSi) nanostructures by a green ruthenium cluster (I). Chemisorption of freshly prepared PSi surfaces in a hexane solution of the Ru cluster for several days at room temperature led to a complete quenching of the PSi PL. The only visible PL was due to the original PL of the cluster. When the PSi surface functionalized with undecylenic acid was immersed in the same hexane solution of (I), the PSi PL was completely quenched and accompanied with a shift to a lower energy of the cluster PL. This shift was assigned to the formation of an ester linkage resulting from the nucleophilic attack of the PO anion of the cluster on the terminal acid functional group. (Abstract Copyright [2003], Wiley Periodicals, Inc.)

  6. Photoluminescence quenching of chemically functionalized porous silicon by a ruthenium cluster

    Science.gov (United States)

    Boukherroub, R.; Wayner, D. D. M.; Lockwood, D. J.; Zargarian, D.

    2003-05-01

    This paper describes photoluminescence (PL) quenching of hydrogen-terminated and chemically derivatized porous silicon (PSi) nanostructures by a green ruthenium cluster (I). Chemisorption of freshly prepared PSi surfaces in a hexane solution of the Ru cluster for several days at room temperature led to a complete quenching of the PSi PL. The only visible PL was due to the original PL of the cluster. When the PSi surface functionalized with undecylenic acid was immersed in the same hexane solution of (I), the PSi PL was completely quenched and accompanied with a shift to a lower energy of the cluster PL. This shift was assigned to the formation of an ester linkage resulting from the nucleophilic attack of the PO anion of the cluster on the terminal acid functional group.

  7. Functional Interference Clusters in Cancer Patients With Bone Metastases: A Secondary Analysis of RTOG 9714

    International Nuclear Information System (INIS)

    Chow, Edward; James, Jennifer; Barsevick, Andrea; Hartsell, William; Ratcliffe, Sarah; Scarantino, Charles; Ivker, Robert; Roach, Mack; Suh, John; Petersen, Ivy; Konski, Andre; Demas, William; Bruner, Deborah

    2010-01-01

    Purpose: To explore the relationships (clusters) among the functional interference items in the Brief Pain Inventory (BPI) in patients with bone metastases. Methods: Patients enrolled in the Radiation Therapy Oncology Group (RTOG) 9714 bone metastases study were eligible. Patients were assessed at baseline and 4, 8, and 12 weeks after randomization for the palliative radiotherapy with the BPI, which consists of seven functional items: general activity, mood, walking ability, normal work, relations with others, sleep, and enjoyment of life. Principal component analysis with varimax rotation was used to determine the clusters between the functional items at baseline and the follow-up. Cronbach's alpha was used to determine the consistency and reliability of each cluster at baseline and follow-up. Results: There were 448 male and 461 female patients, with a median age of 67 years. There were two functional interference clusters at baseline, which accounted for 71% of the total variance. The first cluster (physical interference) included normal work and walking ability, which accounted for 58% of the total variance. The second cluster (psychosocial interference) included relations with others and sleep, which accounted for 13% of the total variance. The Cronbach's alpha statistics were 0.83 and 0.80, respectively. The functional clusters changed at week 12 in responders but persisted through week 12 in nonresponders. Conclusion: Palliative radiotherapy is effective in reducing bone pain. Functional interference component clusters exist in patients treated for bone metastases. These clusters changed over time in this study, possibly attributable to treatment. Further research is needed to examine these effects.

  8. Pseudogenization of a sweet-receptor gene accounts for cats' indifference toward sugar.

    Directory of Open Access Journals (Sweden)

    Xia Li

    2005-07-01

    Full Text Available Although domestic cats (Felis silvestris catus possess an otherwise functional sense of taste, they, unlike most mammals, do not prefer and may be unable to detect the sweetness of sugars. One possible explanation for this behavior is that cats lack the sensory system to taste sugars and therefore are indifferent to them. Drawing on work in mice, demonstrating that alleles of sweet-receptor genes predict low sugar intake, we examined the possibility that genes involved in the initial transduction of sweet perception might account for the indifference to sweet-tasting foods by cats. We characterized the sweet-receptor genes of domestic cats as well as those of other members of the Felidae family of obligate carnivores, tiger and cheetah. Because the mammalian sweet-taste receptor is formed by the dimerization of two proteins (T1R2 and T1R3; gene symbols Tas1r2 and Tas1r3, we identified and sequenced both genes in the cat by screening a feline genomic BAC library and by performing PCR with degenerate primers on cat genomic DNA. Gene expression was assessed by RT-PCR of taste tissue, in situ hybridization, and immunohistochemistry. The cat Tas1r3 gene shows high sequence similarity with functional Tas1r3 genes of other species. Message from Tas1r3 was detected by RT-PCR of taste tissue. In situ hybridization and immunohistochemical studies demonstrate that Tas1r3 is expressed, as expected, in taste buds. However, the cat Tas1r2 gene shows a 247-base pair microdeletion in exon 3 and stop codons in exons 4 and 6. There was no evidence of detectable mRNA from cat Tas1r2 by RT-PCR or in situ hybridization, and no evidence of protein expression by immunohistochemistry. Tas1r2 in tiger and cheetah and in six healthy adult domestic cats all show the similar deletion and stop codons. We conclude that cat Tas1r3 is an apparently functional and expressed receptor but that cat Tas1r2 is an unexpressed pseudogene. A functional sweet-taste receptor heteromer

  9. Pseudogenization of a Sweet-Receptor Gene Accounts for Cats' Indifference toward Sugar.

    Directory of Open Access Journals (Sweden)

    2005-07-01

    Full Text Available Although domestic cats (Felis silvestris catus possess an otherwise functional sense of taste, they, unlike most mammals, do not prefer and may be unable to detect the sweetness of sugars. One possible explanation for this behavior is that cats lack the sensory system to taste sugars and therefore are indifferent to them. Drawing on work in mice, demonstrating that alleles of sweet-receptor genes predict low sugar intake, we examined the possibility that genes involved in the initial transduction of sweet perception might account for the indifference to sweet-tasting foods by cats. We characterized the sweet-receptor genes of domestic cats as well as those of other members of the Felidae family of obligate carnivores, tiger and cheetah. Because the mammalian sweet-taste receptor is formed by the dimerization of two proteins (T1R2 and T1R3; gene symbols Tas1r2 and Tas1r3, we identified and sequenced both genes in the cat by screening a feline genomic BAC library and by performing PCR with degenerate primers on cat genomic DNA. Gene expression was assessed by RT-PCR of taste tissue, in situ hybridization, and immunohistochemistry. The cat Tas1r3 gene shows high sequence similarity with functional Tas1r3 genes of other species. Message from Tas1r3 was detected by RT-PCR of taste tissue. In situ hybridization and immunohistochemical studies demonstrate that Tas1r3 is expressed, as expected, in taste buds. However, the cat Tas1r2 gene shows a 247-base pair microdeletion in exon 3 and stop codons in exons 4 and 6. There was no evidence of detectable mRNA from cat Tas1r2 by RT-PCR or in situ hybridization, and no evidence of protein expression by immunohistochemistry. Tas1r2 in tiger and cheetah and in six healthy adult domestic cats all show the similar deletion and stop codons. We conclude that cat Tas1r3 is an apparently functional and expressed receptor but that cat Tas1r2 is an unexpressed pseudogene. A functional sweet-taste receptor heteromer

  10. Inelastic electron scattering as an indicator of clustering in wave functions

    International Nuclear Information System (INIS)

    1998-01-01

    While the shell model is the most fundamental of nuclear structure models, states in light nuclei also have been described successfully in terms of clusters. Indeed, Wildemuth and Tang have shown a correspondence between the cluster and shell models, the clusters arising naturally as correlations out of the shell model Hamiltonian. For light nuclei, the cluster model reduces the many-body problem to a few-body one, with interactions occurring between the clusters. These interactions involve particle exchanges, since the nucleons may still be considered somewhat freely moving, with their motion not strictly confined to the clusters themselves. Such is the relation of the cluster model to the shell model. For a realistic shell model then, one may expect some evidence of clustering in the wave functions for those systems in which the cluster model is valid. The results obtained using the multi-ℎωshell model wave functions are closer in agreement with experiment than the results obtained using the 0ℎωwave functions. Yet in all cases, that level of agreement is not good, with the calculations underpredicting the measured values by at least a factor of two. This indicates that the shell model wave functions do not exhibit clustering behavior, which is expected to manifest itself at small momentum transfer. The exception is the transition to the 7 - /2 state in 7 Li, for which the value obtained from the γ-decay width is in agreement with the value obtained from the MK3W and (0 + 2 + 4)ℎωshell model calculations

  11. Inelastic electron scattering as an indicator of clustering in wave functions

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-09-01

    While the shell model is the most fundamental of nuclear structure models, states in light nuclei also have been described successfully in terms of clusters. Indeed, Wildemuth and Tang have shown a correspondence between the cluster and shell models, the clusters arising naturally as correlations out of the shell model Hamiltonian. For light nuclei, the cluster model reduces the many-body problem to a few-body one, with interactions occurring between the clusters. These interactions involve particle exchanges, since the nucleons may still be considered somewhat freely moving, with their motion not strictly confined to the clusters themselves. Such is the relation of the cluster model to the shell model. For a realistic shell model then, one may expect some evidence of clustering in the wave functions for those systems in which the cluster model is valid. The results obtained using the multi-{Dirac_h}{omega}shell model wave functions are closer in agreement with experiment than the results obtained using the 0{Dirac_h}{omega}wave functions. Yet in all cases, that level of agreement is not good, with the calculations underpredicting the measured values by at least a factor of two. This indicates that the shell model wave functions do not exhibit clustering behavior, which is expected to manifest itself at small momentum transfer. The exception is the transition to the 7{sup -}/2 state in {sup 7}Li, for which the value obtained from the {gamma}-decay width is in agreement with the value obtained from the MK3W and (0 + 2 + 4){Dirac_h}{omega}shell model calculations 17 refs., 1 tab., 2 figs.

  12. The externally corrected coupled cluster approach with four- and five-body clusters from the CASSCF wave function.

    Science.gov (United States)

    Xu, Enhua; Li, Shuhua

    2015-03-07

    An externally corrected CCSDt (coupled cluster with singles, doubles, and active triples) approach employing four- and five-body clusters from the complete active space self-consistent field (CASSCF) wave function (denoted as ecCCSDt-CASSCF) is presented. The quadruple and quintuple excitation amplitudes within the active space are extracted from the CASSCF wave function and then fed into the CCSDt-like equations, which can be solved in an iterative way as the standard CCSDt equations. With a size-extensive CASSCF reference function, the ecCCSDt-CASSCF method is size-extensive. When the CASSCF wave function is readily available, the computational cost of the ecCCSDt-CASSCF method scales as the popular CCSD method (if the number of active orbitals is small compared to the total number of orbitals). The ecCCSDt-CASSCF approach has been applied to investigate the potential energy surface for the simultaneous dissociation of two O-H bonds in H2O, the equilibrium distances and spectroscopic constants of 4 diatomic molecules (F2(+), O2(+), Be2, and NiC), and the reaction barriers for the automerization reaction of cyclobutadiene and the Cl + O3 → ClO + O2 reaction. In most cases, the ecCCSDt-CASSCF approach can provide better results than the CASPT2 (second order perturbation theory with a CASSCF reference function) and CCSDT methods.

  13. H2A/K pseudogene mutation may promote cell proliferation

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Jisheng; Jing, Ruirui; Lv, Xin; Wang, Xiaoyue; Li, Junqiang; Li, Lin; Li, Cuiling; Wang, Daoguang; Bi, Baibing; Chen, Xinjun [Cancer Research Center, Shandong University School of Medicine, Jinan 250012 (China); Yang, Jing-Hua, E-mail: sdu_crc_group1@126.com [Cancer Research Center, Shandong University School of Medicine, Jinan 250012 (China); Department of Surgery, VA Boston Healthcare System, Boston University School of Medicine, Boston 510660, MA (United States)

    2016-05-15

    Highlights: • The mutant H2A/K pseudogene is active. • The mutant H2A/K pseudogene can promote cell proliferation. - Abstract: Little attention has been paid to the histone H2A/K pseudogene. Results from our laboratory showed that 7 of 10 kidney cancer patients carried a mutant H2A/K pseudogene; therefore, we were interested in determining the relationship between mutant H2A/K and cell proliferation. We used shotgun and label-free proteomics methods to study whether mutant H2A/K lncRNAs affected cell proliferation. Quantitative proteomic analysis indicated that the expression of mutant H2A/K lncRNAs resulted in the upregulation of many oncogenes, which promoted cell proliferation. Further interaction analyses revealed that a proliferating cell nuclear antigen (PCNA)-protein interaction network, with PCNA in the center, contributes to cell proliferation in cells expressing the mutant H2A/K lncRNAs. Western blotting confirmed the critical upregulation of PCNA by mutant H2A/K lncRNA expression. Finally, the promotion of cell proliferation by mutant H2A/K lncRNAs (C290T, C228A and A45G) was confirmed using cell proliferation assays. Although we did not determine the exact mechanism by which the oncogenes were upregulated by the mutant H2A/K lncRNAs, we confirmed that the mutant H2A/K lncRNAs promoted cell proliferation by upregulating PCNA and other oncogenes. The hypothesis that cell proliferation is promoted by the mutant H2A/K lncRNAs was supported by the protein expression and cell proliferation assay results. Therefore, mutant H2A/K lncRNAs may be a new factor in renal carcinogenesis.

  14. Statistical indicators of collective behavior and functional clusters in gene networks of yeast

    Science.gov (United States)

    Živković, J.; Tadić, B.; Wick, N.; Thurner, S.

    2006-03-01

    We analyze gene expression time-series data of yeast (S. cerevisiae) measured along two full cell-cycles. We quantify these data by using q-exponentials, gene expression ranking and a temporal mean-variance analysis. We construct gene interaction networks based on correlation coefficients and study the formation of the corresponding giant components and minimum spanning trees. By coloring genes according to their cell function we find functional clusters in the correlation networks and functional branches in the associated trees. Our results suggest that a percolation point of functional clusters can be identified on these gene expression correlation networks.

  15. Comparison of two schemes for automatic keyword extraction from MEDLINE for functional gene clustering.

    Science.gov (United States)

    Liu, Ying; Ciliax, Brian J; Borges, Karin; Dasigi, Venu; Ram, Ashwin; Navathe, Shamkant B; Dingledine, Ray

    2004-01-01

    One of the key challenges of microarray studies is to derive biological insights from the unprecedented quatities of data on gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the nature of the functional links among genes within the derived clusters. However, the quality of the keyword lists extracted from biomedical literature for each gene significantly affects the clustering results. We extracted keywords from MEDLINE that describes the most prominent functions of the genes, and used the resulting weights of the keywords as feature vectors for gene clustering. By analyzing the resulting cluster quality, we compared two keyword weighting schemes: normalized z-score and term frequency-inverse document frequency (TFIDF). The best combination of background comparison set, stop list and stemming algorithm was selected based on precision and recall metrics. In a test set of four known gene groups, a hierarchical algorithm correctly assigned 25 of 26 genes to the appropriate clusters based on keywords extracted by the TDFIDF weighting scheme, but only 23 og 26 with the z-score method. To evaluate the effectiveness of the weighting schemes for keyword extraction for gene clusters from microarray profiles, 44 yeast genes that are differentially expressed during the cell cycle were used as a second test set. Using established measures of cluster quality, the results produced from TFIDF-weighted keywords had higher purity, lower entropy, and higher mutual information than those produced from normalized z-score weighted keywords. The optimized algorithms should be useful for sorting genes from microarray lists into functionally discrete clusters.

  16. Clinical analysis of PMS2: mutation detection and avoidance of pseudogenes.

    Science.gov (United States)

    Vaughn, Cecily P; Robles, Jorge; Swensen, Jeffrey J; Miller, Christine E; Lyon, Elaine; Mao, Rong; Bayrak-Toydemir, Pinar; Samowitz, Wade S

    2010-05-01

    Germline mutation detection in PMS2, one of four mismatch repair genes associated with Lynch syndrome, is greatly complicated by the presence of numerous pseudogenes. We used a modification of a long-range PCR method to evaluate PMS2 in 145 clinical samples. This modification avoids potential interference from the pseudogene PMS2CL by utilizing a long-range product spanning exons 11-15, with the forward primer anchored in exon 10, an exon not shared by PMS2CL. Large deletions were identified by MLPA. Pathogenic PMS2 mutations were identified in 22 of 59 patients whose tumors showed isolated loss of PMS2 by immunohistochemistry (IHC), the IHC profile most commonly associated with a germline PMS2 mutation. Three additional patients with pathogenic mutations were identified from 53 samples without IHC data. Thirty-seven percent of the identified mutations were large deletions encompassing one or more exons. In 27 patients whose tumors showed absence of either another protein or combination of proteins, no pathogenic mutations were identified. We conclude that modified long-range PCR can be used to preferentially amplify the PMS2 gene and avoid pseudogene interference, thus providing a clinically useful germline analysis of PMS2. Our data also support the use of IHC screening to direct germline testing of PMS2. (c) 2010 Wiley-Liss, Inc.

  17. Human Nanog pseudogene8 promotes the proliferation of gastrointestinal cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Uchino, Keita, E-mail: uchino13@intmed1.med.kyushu-u.ac.jp [Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Hirano, Gen [Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Hirahashi, Minako [Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Isobe, Taichi; Shirakawa, Tsuyoshi; Kusaba, Hitoshi; Baba, Eishi [Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Tsuneyoshi, Masazumi [Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Akashi, Koichi [Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan)

    2012-09-10

    There is emerging evidence that human solid tumor cells originate from cancer stem cells (CSCs). In cancer cell lines, tumor-initiating CSCs are mainly found in the side population (SP) that has the capacity to extrude dyes such as Hoechst 33342. We found that Nanog is expressed specifically in SP cells of human gastrointestinal (GI) cancer cells. Nucleotide sequencing revealed that NanogP8 but not Nanog was expressed in GI cancer cells. Transfection of NanogP8 into GI cancer cell lines promoted cell proliferation, while its inhibition by anti-Nanog siRNA suppressed the proliferation. Immunohistochemical staining of primary GI cancer tissues revealed NanogP8 protein to be strongly expressed in 3 out of 60 cases. In these cases, NanogP8 was found especially in an infiltrative part of the tumor, in proliferating cells with Ki67 expression. These data suggest that NanogP8 is involved in GI cancer development in a fraction of patients, in whom it presumably acts by supporting CSC proliferation. -- Highlights: Black-Right-Pointing-Pointer Nanog maintains pluripotency by regulating embryonic stem cells differentiation. Black-Right-Pointing-Pointer Nanog is expressed in cancer stem cells of human gastrointestinal cancer cells. Black-Right-Pointing-Pointer Nucleotide sequencing revealed that Nanog pseudogene8 but not Nanog was expressed. Black-Right-Pointing-Pointer Nanog pseudogene8 promotes cancer stem cells proliferation. Black-Right-Pointing-Pointer Nanog pseudogene8 is involved in gastrointestinal cancer development.

  18. Human Nanog pseudogene8 promotes the proliferation of gastrointestinal cancer cells

    International Nuclear Information System (INIS)

    Uchino, Keita; Hirano, Gen; Hirahashi, Minako; Isobe, Taichi; Shirakawa, Tsuyoshi; Kusaba, Hitoshi; Baba, Eishi; Tsuneyoshi, Masazumi; Akashi, Koichi

    2012-01-01

    There is emerging evidence that human solid tumor cells originate from cancer stem cells (CSCs). In cancer cell lines, tumor-initiating CSCs are mainly found in the side population (SP) that has the capacity to extrude dyes such as Hoechst 33342. We found that Nanog is expressed specifically in SP cells of human gastrointestinal (GI) cancer cells. Nucleotide sequencing revealed that NanogP8 but not Nanog was expressed in GI cancer cells. Transfection of NanogP8 into GI cancer cell lines promoted cell proliferation, while its inhibition by anti-Nanog siRNA suppressed the proliferation. Immunohistochemical staining of primary GI cancer tissues revealed NanogP8 protein to be strongly expressed in 3 out of 60 cases. In these cases, NanogP8 was found especially in an infiltrative part of the tumor, in proliferating cells with Ki67 expression. These data suggest that NanogP8 is involved in GI cancer development in a fraction of patients, in whom it presumably acts by supporting CSC proliferation. -- Highlights: ► Nanog maintains pluripotency by regulating embryonic stem cells differentiation. ► Nanog is expressed in cancer stem cells of human gastrointestinal cancer cells. ► Nucleotide sequencing revealed that Nanog pseudogene8 but not Nanog was expressed. ► Nanog pseudogene8 promotes cancer stem cells proliferation. ► Nanog pseudogene8 is involved in gastrointestinal cancer development.

  19. Density functional calculations on 13-atom Pd12M (M = Sc—Ni) bimetallic clusters

    International Nuclear Information System (INIS)

    Tang Chun-Mei; Chen Sheng-Wei; Zhu Wei-Hua; Tao Cheng-Jun; Zhang Ai-Mei; Gong Jiang-Feng; Zou Hua; Liu Ming-Yi; Zhu Feng

    2012-01-01

    The geometric structures, electronic and magnetic properties of the 3d transition metal doped clusters Pd 12 M (M = Sc—Ni) are studied using the semi-core pseudopots density functional theory. The groundstate geometric structure of the Pd 12 M cluster is probably of pseudoicosahedron. The I h -Pd 12 M cluster has the most thermodynamic stability in five different symmetric isomers. The energy gap shows that Pd 12 M cluster is partly metallic. Both the absolutely predominant metal bond and very weak covalent bond might exist in the Pd 12 M cluster. The magnetic moment of Pd 12 M varies from 0 to 5 μ B , implying that it has a potential application in new nanomaterials with tunable magnetic properties

  20. Density functional study of carbon monoxide adsorption on small cationic, neutral, and anionic aluminum nitride clusters

    Science.gov (United States)

    Guo, Ling

    CO adsorption on small cationic, neutral, and anionic (AlN)n (n = 1-6) clusters has been investigated using density functional theory in the generalized gradient approximation. Among various possible CO adsorption sites, an N on-top (onefold coordinated) site is found to be the most favorable one, irrespective of the charge state of the clusters. The adsorption energies of CO on the anionic (AlN)nCO (n = 2-4) clusters are greater than those on the neutral and cationic complexes. The adsorption energies on the cationic and neutral complexes reflect the odd-even oscillations, and the adsorption energies of CO on the cationic (AlN)nCO (n = 5, 6) clusters are greater than those on the neutral and anionic complexes. The adsorption energies for the different charge states decrease with increasing cluster size.

  1. Constraints on Ωm and σ8 from the potential-based cluster temperature function

    Science.gov (United States)

    Angrick, Christian; Pace, Francesco; Bartelmann, Matthias; Roncarelli, Mauro

    2015-12-01

    The abundance of galaxy clusters is in principle a powerful tool to constrain cosmological parameters, especially Ωm and σ8, due to the exponential dependence in the high-mass regime. While the best observables are the X-ray temperature and luminosity, the abundance of galaxy clusters, however, is conventionally predicted as a function of mass. Hence, the intrinsic scatter and the uncertainties in the scaling relations between mass and either temperature or luminosity lower the reliability of galaxy clusters to constrain cosmological parameters. In this article, we further refine the X-ray temperature function for galaxy clusters by Angrick et al., which is based on the statistics of perturbations in the cosmic gravitational potential and proposed to replace the classical mass-based temperature function, by including a refined analytic merger model and compare the theoretical prediction to results from a cosmological hydrodynamical simulation. Although we find already a good agreement if we compare with a cluster temperature function based on the mass-weighted temperature, including a redshift-dependent scaling between mass-based and spectroscopic temperature yields even better agreement between theoretical model and numerical results. As a proof of concept, incorporating this additional scaling in our model, we constrain the cosmological parameters Ωm and σ8 from an X-ray sample of galaxy clusters and tentatively find agreement with the recent cosmic microwave background based results from the Planck mission at 1σ-level.

  2. Modulated modularity clustering as an exploratory tool for functional genomic inference.

    Directory of Open Access Journals (Sweden)

    Eric A Stone

    2009-05-01

    Full Text Available In recent years, the advent of high-throughput assays, coupled with their diminishing cost, has facilitated a systems approach to biology. As a consequence, massive amounts of data are currently being generated, requiring efficient methodology aimed at the reduction of scale. Whole-genome transcriptional profiling is a standard component of systems-level analyses, and to reduce scale and improve inference clustering genes is common. Since clustering is often the first step toward generating hypotheses, cluster quality is critical. Conversely, because the validation of cluster-driven hypotheses is indirect, it is critical that quality clusters not be obtained by subjective means. In this paper, we present a new objective-based clustering method and demonstrate that it yields high-quality results. Our method, modulated modularity clustering (MMC, seeks community structure in graphical data. MMC modulates the connection strengths of edges in a weighted graph to maximize an objective function (called modularity that quantifies community structure. The result of this maximization is a clustering through which tightly-connected groups of vertices emerge. Our application is to systems genetics, and we quantitatively compare MMC both to the hierarchical clustering method most commonly employed and to three popular spectral clustering approaches. We further validate MMC through analyses of human and Drosophila melanogaster expression data, demonstrating that the clusters we obtain are biologically meaningful. We show MMC to be effective and suitable to applications of large scale. In light of these features, we advocate MMC as a standard tool for exploration and hypothesis generation.

  3. Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: Application to polycyclic aromatic hydrocarbon clusters

    Science.gov (United States)

    Rapacioli, Mathias; Spiegelman, Fernand; Talbi, Dahbia; Mineva, Tzonka; Goursot, Annick; Heine, Thomas; Seifert, Gotthard

    2009-06-01

    The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.

  4. Novel Functions of MicroRNA-17-92 Cluster in the Endocrine System.

    Science.gov (United States)

    Wan, Shan; Chen, Xiang; He, Yuedong; Yu, Xijie

    2018-01-01

    MiR-17-92 cluster is coded by MIR17HG in chromosome 13, which is highly conserved in vertebrates. Published literatures have proved that miR-17-92 cluster critically regulates tumorigenesis and metastasis. Recent researches showed that the miR-17-92 cluster also plays novel functions in the endocrine system. To summarize recent findings on the physiological and pathological roles of miR-17-92 cluster in bone, lipid and glucose metabolisms. MiR-17-92 cluster plays significant regulatory roles in bone development and metabolism through regulating the differentiation and function of osteoblasts and osteoclasts. In addition, miR-17- 92 cluster is nearly involved in every aspect of lipid metabolism. Last but not the least, the miR-17-92 cluster is closely bound up with pancreatic beta cell function, development of type 1 diabetes and insulin resistance. However, whether miR-17-92 cluster is involved in the communication among bone, fat and glucose metabolisms remains unknown. Growing evidence indicates that miR-17-92 cluster plays significant roles in bone, lipid and glucose metabolisms through a variety of signaling pathways. Fully understanding its modulating mechanisms may necessarily facilitate to comprehend the clinical and molecule features of some metabolic disorders such as osteoporosis, arthrosclerosis and diabetes mellitus. It may provide new drug targets to prevent and cure these disorders. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  5. Minkowski Functionals and Cluster Analysis for CMB Maps

    Science.gov (United States)

    Novikov, D.; Feldman, Hume A.; Shandarin, Sergei F.

    We suggest novel statistics for the CMB maps that are sensitive to non-Gaussian features. These statistics are natural generalizations of the geometrical and topological methods that have been already used in cosmology such as the cumulative distribution function and genus. We compute the distribution functions of the Partial Minkowski Functionals for the excursion set above or bellow a constant temperature threshold. Minkowski Functionals are additive and are translationally and rotationally invariant. Thus, they can be used for patchy and/or incomplete coverage. The technique is highly efficient computationally (it requires only O(N) operations, where N is the number of pixels per one threshold level). Further, the procedure makes it possible to split large data sets into smaller subsets. The full advantage of these statistics can be obtained only on very large data sets. We apply it to the 4-year DMR COBE data corrected for the Galaxy contamination as an illustration of the technique.

  6. A Clustering-Based Automatic Transfer Function Design for Volume Visualization

    Directory of Open Access Journals (Sweden)

    Tianjin Zhang

    2016-01-01

    Full Text Available The two-dimensional transfer functions (TFs designed based on intensity-gradient magnitude (IGM histogram are effective tools for the visualization and exploration of 3D volume data. However, traditional design methods usually depend on multiple times of trial-and-error. We propose a novel method for the automatic generation of transfer functions by performing the affinity propagation (AP clustering algorithm on the IGM histogram. Compared with previous clustering algorithms that were employed in volume visualization, the AP clustering algorithm has much faster convergence speed and can achieve more accurate clustering results. In order to obtain meaningful clustering results, we introduce two similarity measurements: IGM similarity and spatial similarity. These two similarity measurements can effectively bring the voxels of the same tissue together and differentiate the voxels of different tissues so that the generated TFs can assign different optical properties to different tissues. Before performing the clustering algorithm on the IGM histogram, we propose to remove noisy voxels based on the spatial information of voxels. Our method does not require users to input the number of clusters, and the classification and visualization process is automatic and efficient. Experiments on various datasets demonstrate the effectiveness of the proposed method.

  7. Functional Principal Component Analysis and Randomized Sparse Clustering Algorithm for Medical Image Analysis

    Science.gov (United States)

    Lin, Nan; Jiang, Junhai; Guo, Shicheng; Xiong, Momiao

    2015-01-01

    Due to the advancement in sensor technology, the growing large medical image data have the ability to visualize the anatomical changes in biological tissues. As a consequence, the medical images have the potential to enhance the diagnosis of disease, the prediction of clinical outcomes and the characterization of disease progression. But in the meantime, the growing data dimensions pose great methodological and computational challenges for the representation and selection of features in image cluster analysis. To address these challenges, we first extend the functional principal component analysis (FPCA) from one dimension to two dimensions to fully capture the space variation of image the signals. The image signals contain a large number of redundant features which provide no additional information for clustering analysis. The widely used methods for removing the irrelevant features are sparse clustering algorithms using a lasso-type penalty to select the features. However, the accuracy of clustering using a lasso-type penalty depends on the selection of the penalty parameters and the threshold value. In practice, they are difficult to determine. Recently, randomized algorithms have received a great deal of attentions in big data analysis. This paper presents a randomized algorithm for accurate feature selection in image clustering analysis. The proposed method is applied to both the liver and kidney cancer histology image data from the TCGA database. The results demonstrate that the randomized feature selection method coupled with functional principal component analysis substantially outperforms the current sparse clustering algorithms in image cluster analysis. PMID:26196383

  8. The Mass Function of Young Star Clusters in the "Antennae" Galaxies.

    Science.gov (United States)

    Zhang; Fall

    1999-12-20

    We determine the mass function of young star clusters in the merging galaxies known as the "Antennae" (NGC 4038/9) from deep images taken with the Wide Field Planetary Camera 2 on the refurbished Hubble Space Telescope. This is accomplished by means of reddening-free parameters and a comparison with stellar population synthesis tracks to estimate the intrinsic luminosity and age, and hence the mass, of each cluster. We find that the mass function of the young star clusters (with ages less, similar160 Myr) is well represented by a power law of the form psi&parl0;M&parr0;~M-2 over the range 104 less, similarM less, similar106 M middle dot in circle. This result may have important implications for our understanding of the origin of globular clusters during the early phases of galactic evolution.

  9. The Luminosity Functions of Old and Intermediate-Age Globular Clusters in NGC 3610

    OpenAIRE

    Whitmore, B. C.; Schweizer, F.; Kundu, A.; Miller, B. W.

    2002-01-01

    The WFPC2 Camera on board HST has been used to obtain high-resolution images of NGC 3610, a dynamically young elliptical galaxy. These observations supersede shorter, undithered HST observations where an intermediate-age population of globular clusters was first discovered. The new observations show the bimodal color distribution of globular clusters more clearly, with peaks at (V-I)o = 0.95 and 1.17. The luminosity function (LF) of the blue, metal-poor population of clusters in NGC 3610 turn...

  10. A-dependence of structure functions and multiquark clusters in nuclei

    International Nuclear Information System (INIS)

    Kondratyuk, L.; Shmatikov, M.

    1984-01-01

    Assuming existence of 12q-clusters (bags) in nuclei the structure functions of deep inelastic scattering of leptons on nuclei are discussed. Universal momentum distribution of quarks in a multiquark cluster is used with high-momentum component falling exponentially PHIsub(q)sup(2)(k) approximately esup(-k/ksub(0)) with k 0 approximately equal to 50-60 MeV/c. The admixture of 12q-cluster W required for the description of SLAG data increases from 10% for 4 He to 30% for Au. The A-dependence of W agrees well with the A-dependence of cumulative particle spectra

  11. Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters using Density Functional Theory

    Science.gov (United States)

    2017-05-05

    Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6390--17-9724 Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters...TELEPHONE NUMBER (include area code) b. ABSTRACT c. THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Equilibrium Structures and Absorption...and electronic excited-state absorption spectra for eqilibrium structures of SixOy molecular clusters using density function theory (DFT) and time

  12. Effect of functionalization of boron nitride flakes by main group metal clusters on their optoelectronic properties

    Science.gov (United States)

    Chakraborty, Debdutta; Chattaraj, Pratim Kumar

    2017-10-01

    The possibility of functionalizing boron nitride flakes (BNFs) with some selected main group metal clusters, viz. OLi4, NLi5, CLi6, BLI7 and Al12Be, has been analyzed with the aid of density functional theory (DFT) based computations. Thermochemical as well as energetic considerations suggest that all the metal clusters interact with the BNF moiety in a favorable fashion. As a result of functionalization, the static (first) hyperpolarizability (β ) values of the metal cluster supported BNF moieties increase quite significantly as compared to that in the case of pristine BNF. Time dependent DFT analysis reveals that the metal clusters can lower the transition energies associated with the dominant electronic transitions quite significantly thereby enabling the metal cluster supported BNF moieties to exhibit significant non-linear optical activity. Moreover, the studied systems demonstrate broad band absorption capability spanning the UV-visible as well as infra-red domains. Energy decomposition analysis reveals that the electrostatic interactions principally stabilize the metal cluster supported BNF moieties.

  13. The galaxy cluster mid-infrared luminosity function at 1.3 < z < 3.2

    Energy Technology Data Exchange (ETDEWEB)

    Wylezalek, Dominika; Vernet, Joël; De Breuck, Carlos [European Southern Observatory, Karl-Schwarzschildstr.2, D-85748 Garching bei München (Germany); Stern, Daniel [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Brodwin, Mark [Department of Physics and Astronomy, University of Missouri, 5110 Rockhill Road, Kansas City, MO 64110 (United States); Galametz, Audrey [INAF-Osservatorio di Roma, Via Frascati 33, I-00040, Monteporzio (Italy); Gonzalez, Anthony H. [Department of Astronomy, University of Florida, Gainesville, FL 32611 (United States); Jarvis, Matt [Astrophysics, Department of Physics, Keble Road, Oxford OX1 3RH (United Kingdom); Hatch, Nina [School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD (United Kingdom); Seymour, Nick [CASS, P.O. Box 76, Epping, NSW, 1710 (Australia); Stanford, Spencer A. [Physics Department, University of California, Davis, CA 95616 (United States)

    2014-05-01

    We present 4.5 μm luminosity functions for galaxies identified in 178 candidate galaxy clusters at 1.3 < z < 3.2. The clusters were identified as Spitzer/Infrared Array Camera (IRAC) color-selected overdensities in the Clusters Around Radio-Loud AGN project, which imaged 420 powerful radio-loud active galactic nuclei (RLAGNs) at z > 1.3. The luminosity functions are derived for different redshift and richness bins, and the IRAC imaging reaches depths of m* + 2, allowing us to measure the faint end slopes of the luminosity functions. We find that α = –1 describes the luminosity function very well in all redshift bins and does not evolve significantly. This provides evidence that the rate at which the low mass galaxy population grows through star formation gets quenched and is replenished by in-falling field galaxies does not have a major net effect on the shape of the luminosity function. Our measurements for m* are consistent with passive evolution models and high formation redshifts (z{sub f} ∼ 3). We find a slight trend toward fainter m* for the richest clusters, implying that the most massive clusters in our sample could contain older stellar populations, yet another example of cosmic downsizing. Modeling shows that a contribution of a star-forming population of up to 40% cannot be ruled out. This value, found from our targeted survey, is significantly lower than the values found for slightly lower redshift, z ∼ 1, clusters found in wide-field surveys. The results are consistent with cosmic downsizing, as the clusters studied here were all found in the vicinity of RLAGNs—which have proven to be preferentially located in massive dark matter halos in the richest environments at high redshift—and they may therefore be older and more evolved systems than the general protocluster population.

  14. The galaxy cluster mid-infrared luminosity function at 1.3 < z < 3.2

    International Nuclear Information System (INIS)

    Wylezalek, Dominika; Vernet, Joël; De Breuck, Carlos; Stern, Daniel; Brodwin, Mark; Galametz, Audrey; Gonzalez, Anthony H.; Jarvis, Matt; Hatch, Nina; Seymour, Nick; Stanford, Spencer A.

    2014-01-01

    We present 4.5 μm luminosity functions for galaxies identified in 178 candidate galaxy clusters at 1.3 < z < 3.2. The clusters were identified as Spitzer/Infrared Array Camera (IRAC) color-selected overdensities in the Clusters Around Radio-Loud AGN project, which imaged 420 powerful radio-loud active galactic nuclei (RLAGNs) at z > 1.3. The luminosity functions are derived for different redshift and richness bins, and the IRAC imaging reaches depths of m* + 2, allowing us to measure the faint end slopes of the luminosity functions. We find that α = –1 describes the luminosity function very well in all redshift bins and does not evolve significantly. This provides evidence that the rate at which the low mass galaxy population grows through star formation gets quenched and is replenished by in-falling field galaxies does not have a major net effect on the shape of the luminosity function. Our measurements for m* are consistent with passive evolution models and high formation redshifts (z f ∼ 3). We find a slight trend toward fainter m* for the richest clusters, implying that the most massive clusters in our sample could contain older stellar populations, yet another example of cosmic downsizing. Modeling shows that a contribution of a star-forming population of up to 40% cannot be ruled out. This value, found from our targeted survey, is significantly lower than the values found for slightly lower redshift, z ∼ 1, clusters found in wide-field surveys. The results are consistent with cosmic downsizing, as the clusters studied here were all found in the vicinity of RLAGNs—which have proven to be preferentially located in massive dark matter halos in the richest environments at high redshift—and they may therefore be older and more evolved systems than the general protocluster population.

  15. THE REST-FRAME OPTICAL LUMINOSITY FUNCTION OF CLUSTER GALAXIES AT z < 0.8 AND THE ASSEMBLY OF THE CLUSTER RED SEQUENCE

    International Nuclear Information System (INIS)

    Rudnick, Gregory; Von der Linden, Anja; De Lucia, Gabriella; White, Simon; Pello, Roser; Aragon-Salamanca, Alfonso; Marchesini, Danilo; Clowe, Douglas; Halliday, Claire; Jablonka, Pascale; Milvang-Jensen, Bo; Poggianti, Bianca; Saglia, Roberto; Simard, Luc; Zaritsky, Dennis

    2009-01-01

    We present the rest-frame optical luminosity function (LF) of red-sequence galaxies in 16 clusters at 0.4 < z < 0.8 drawn from the ESO Distant Cluster Survey (EDisCS). We compare our clusters to an analogous sample from the Sloan Digital Sky Survey (SDSS) and match the EDisCS clusters to their most likely descendants. We measure all LFs down to M ∼ M * + (2.5-3.5). At z < 0.8, the bright end of the LF is consistent with passive evolution but there is a significant buildup of the faint end of the red sequence toward lower redshift. There is a weak dependence of the LF on cluster velocity dispersion for EDisCS but no such dependence for the SDSS clusters. We find tentative evidence that red-sequence galaxies brighter than a threshold magnitude are already in place, and that this threshold evolves to fainter magnitudes toward lower redshifts. We compare the EDisCS LFs with the LF of coeval red-sequence galaxies in the field and find that the bright end of the LFs agree. However, relative to the number of bright red galaxies, the field has more faint red galaxies than clusters at 0.6 < z < 0.8 but fewer at 0.4 < z < 0.6, implying differential evolution. We compare the total light in the EDisCS cluster red sequences to the total red-sequence light in our SDSS cluster sample. Clusters at 0.4 < z < 0.8 must increase their luminosity on the red sequence (and therefore stellar mass in red galaxies) by a factor of 1-3 by z = 0. The necessary processes that add mass to the red sequence in clusters predict local clusters that are overluminous as compared to those observed in the SDSS. The predicted cluster luminosities can be reconciled with observed local cluster luminosities by combining multiple previously known effects.

  16. MHCcluster, a method for functional clustering of MHC molecules

    DEFF Research Database (Denmark)

    Thomsen, Martin Christen Frølund; Lundegaard, Claus; Buus, Søren

    2013-01-01

    The identification of peptides binding to major histocompatibility complexes (MHC) is a critical step in the understanding of T cell immune responses. The human MHC genomic region (HLA) is extremely polymorphic comprising several thousand alleles, many encoding a distinct molecule. The potentially...... binding specificity. The method has a flexible web interface that allows the user to include any MHC of interest in the analysis. The output consists of a static heat map and graphical tree-based visualizations of the functional relationship between MHC variants and a dynamic TreeViewer interface where...

  17. A spectral scheme for Kohn–Sham density functional theory of clusters

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, Amartya S., E-mail: baner041@umn.edu; Elliott, Ryan S., E-mail: relliott@umn.edu; James, Richard D., E-mail: james@umn.edu

    2015-04-15

    Starting from the observation that one of the most successful methods for solving the Kohn–Sham equations for periodic systems – the plane-wave method – is a spectral method based on eigenfunction expansion, we formulate a spectral method designed towards solving the Kohn–Sham equations for clusters. This allows for efficient calculation of the electronic structure of clusters (and molecules) with high accuracy and systematic convergence properties without the need for any artificial periodicity. The basis functions in this method form a complete orthonormal set and are expressible in terms of spherical harmonics and spherical Bessel functions. Computation of the occupied eigenstates of the discretized Kohn–Sham Hamiltonian is carried out using a combination of preconditioned block eigensolvers and Chebyshev polynomial filter accelerated subspace iterations. Several algorithmic and computational aspects of the method, including computation of the electrostatics terms and parallelization are discussed. We have implemented these methods and algorithms into an efficient and reliable package called ClusterES (Cluster Electronic Structure). A variety of benchmark calculations employing local and non-local pseudopotentials are carried out using our package and the results are compared to the literature. Convergence properties of the basis set are discussed through numerical examples. Computations involving large systems that contain thousands of electrons are demonstrated to highlight the efficacy of our methodology. The use of our method to study clusters with arbitrary point group symmetries is briefly discussed.

  18. A spectral scheme for Kohn-Sham density functional theory of clusters

    Science.gov (United States)

    Banerjee, Amartya S.; Elliott, Ryan S.; James, Richard D.

    2015-04-01

    Starting from the observation that one of the most successful methods for solving the Kohn-Sham equations for periodic systems - the plane-wave method - is a spectral method based on eigenfunction expansion, we formulate a spectral method designed towards solving the Kohn-Sham equations for clusters. This allows for efficient calculation of the electronic structure of clusters (and molecules) with high accuracy and systematic convergence properties without the need for any artificial periodicity. The basis functions in this method form a complete orthonormal set and are expressible in terms of spherical harmonics and spherical Bessel functions. Computation of the occupied eigenstates of the discretized Kohn-Sham Hamiltonian is carried out using a combination of preconditioned block eigensolvers and Chebyshev polynomial filter accelerated subspace iterations. Several algorithmic and computational aspects of the method, including computation of the electrostatics terms and parallelization are discussed. We have implemented these methods and algorithms into an efficient and reliable package called ClusterES (Cluster Electronic Structure). A variety of benchmark calculations employing local and non-local pseudopotentials are carried out using our package and the results are compared to the literature. Convergence properties of the basis set are discussed through numerical examples. Computations involving large systems that contain thousands of electrons are demonstrated to highlight the efficacy of our methodology. The use of our method to study clusters with arbitrary point group symmetries is briefly discussed.

  19. A spectral scheme for Kohn–Sham density functional theory of clusters

    International Nuclear Information System (INIS)

    Banerjee, Amartya S.; Elliott, Ryan S.; James, Richard D.

    2015-01-01

    Starting from the observation that one of the most successful methods for solving the Kohn–Sham equations for periodic systems – the plane-wave method – is a spectral method based on eigenfunction expansion, we formulate a spectral method designed towards solving the Kohn–Sham equations for clusters. This allows for efficient calculation of the electronic structure of clusters (and molecules) with high accuracy and systematic convergence properties without the need for any artificial periodicity. The basis functions in this method form a complete orthonormal set and are expressible in terms of spherical harmonics and spherical Bessel functions. Computation of the occupied eigenstates of the discretized Kohn–Sham Hamiltonian is carried out using a combination of preconditioned block eigensolvers and Chebyshev polynomial filter accelerated subspace iterations. Several algorithmic and computational aspects of the method, including computation of the electrostatics terms and parallelization are discussed. We have implemented these methods and algorithms into an efficient and reliable package called ClusterES (Cluster Electronic Structure). A variety of benchmark calculations employing local and non-local pseudopotentials are carried out using our package and the results are compared to the literature. Convergence properties of the basis set are discussed through numerical examples. Computations involving large systems that contain thousands of electrons are demonstrated to highlight the efficacy of our methodology. The use of our method to study clusters with arbitrary point group symmetries is briefly discussed

  20. A theoretical study of lithium-doped gallium clusters by density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Sentuerk, Suekrue; Ekincioglu, Yavuz [Dumlupinar Univ., Kutahya (Turkey). Dept. of Physics

    2012-05-15

    The geometrical structures, stabilities, and electronic properties of Ga{sub n}Li (n = 1-13) clusters were investigated within the density functional theory (DFT). The impurity lithium atom enhances the stability of Ga{sub n}Li (n = 1-13) clusters, especially Ga{sub n}Li (n = 9-13) compared to Ga{sub n} (n = 9-14), that is at either apex position or side position. The dissociation energy, second-order energy differences, and the energy gaps between highest occupied and lowest unoccupied molecular orbital (HOMO-LUMO) indicate that the Ga{sub 7}Li, Ga{sub 9}Li, and Ga{sub 11}Li clusters are more stable within the studied cluster range. Moreover, the variation of the average bond length of Ga - Li is due to the surface effect, and the binding strength increases resulting from the increase of charge amount. (orig.)

  1. RNA editing makes mistakes in plant mitochondria: editing loses sense in transcripts of a rps19 pseudogene and in creating stop codons in coxI and rps3 mRNAs of Oenothera.

    Science.gov (United States)

    Schuster, W; Brennicke, A

    1991-01-01

    An intact gene for the ribosomal protein S19 (rps19) is absent from Oenothera mitochondria. The conserved rps19 reading frame found in the mitochondrial genome is interrupted by a termination codon. This rps19 pseudogene is cotranscribed with the downstream rps3 gene and is edited on both sides of the translational stop. Editing, however, changes the amino acid sequence at positions that were well conserved before editing. Other strange editings create translational stops in open reading frames coding for functional proteins. In coxI and rps3 mRNAs CGA codons are edited to UGA stop codons only five and three codons, respectively, downstream to the initiation codon. These aberrant editings in essential open reading frames and in the rps19 pseudogene appear to have been shifted to these positions from other editing sites. These observations suggest a requirement for a continuous evolutionary constraint on the editing specificities in plant mitochondria. Images PMID:1762921

  2. Density functional calculations for atoms, molecules and clusters

    International Nuclear Information System (INIS)

    Gunnarsson, O.; Jones, R.O.

    1980-01-01

    The density functional formalism provides a framework for including exchange and correlation effects in the calculation of ground state properties of many-electron systems. The reduction of the problem to the solution of single-particle equations leads to important numerical advantages over other ab initio methods of incorporating correlation effects. The essential features of the scheme are outlined and results obtained for atomic and molecular systems are surveyed. The local spin density (LSD) approximation gives generally good results for systems where the bonding involves s and p electrons, but results are less satisfactory for d-bonded systems. Non-local modifications to the LSD approximation have been tested on atomic systems yielding much improved total energies. (Auth.)

  3. The Seven Sisters DANCe. I. Empirical isochrones, luminosity, and mass functions of the Pleiades cluster

    Science.gov (United States)

    Bouy, H.; Bertin, E.; Sarro, L. M.; Barrado, D.; Moraux, E.; Bouvier, J.; Cuillandre, J.-C.; Berihuete, A.; Olivares, J.; Beletsky, Y.

    2015-05-01

    Context. The DANCe survey provides photometric and astrometric (position and proper motion) measurements for approximately 2 million unique sources in a region encompassing ~80 deg2 centered on the Pleiades cluster. Aims: We aim at deriving a complete census of the Pleiades and measure the mass and luminosity functions of the cluster. Methods: Using the probabilistic selection method previously described, we identified high probability members in the DANCe (i ≥ 14 mag) and Tycho-2 (V ≲ 12 mag) catalogues and studied the properties of the cluster over the corresponding luminosity range. Results: We find a total of 2109 high-probability members, of which 812 are new, making it the most extensive and complete census of the cluster to date. The luminosity and mass functions of the cluster are computed from the most massive members down to ~0.025 M⊙. The size, sensitivity, and quality of the sample result in the most precise luminosity and mass functions observed to date for a cluster. Conclusions: Our census supersedes previous studies of the Pleiades cluster populations, in terms of both sensitivity and accuracy. Based on service observations made with the William Herschel Telescope operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofísica de Canarias.Table 1 and Appendices are available in electronic form at http://www.aanda.orgDANCe catalogs (Tables 6 and 7) and full Tables 2-5 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/577/A148

  4. Acyl-CoA-binding protein/diazepam-binding inhibitor gene and pseudogenes

    DEFF Research Database (Denmark)

    Mandrup, S; Hummel, R; Ravn, S

    1992-01-01

    Acyl-CoA-binding protein (ACBP) is a 10 kDa protein isolated from bovine liver by virtue of its ability to bind and induce the synthesis of medium-chain acyl-CoA esters. Surprisingly, it turned out to be identical to a protein named diazepam-binding Inhibitor (DBI) claimed to be an endogenous mod...... have molecularly cloned and characterized the ACBP/DBI gene family in rat. The rat ACBP/DBI gene family comprises one expressed gene and four processed pseudogenes of which one was shown to exist in two allelic forms. The expressed gene is organized into four exons and three introns...

  5. Perceptions of firms within a cluster regarding the cluster's function and success: Amish furniture manufacturing in Ohio

    Science.gov (United States)

    Matthew S. Bumgardner; Gary W. Graham; P. Charles Goebel; Robert L. Romig

    2011-01-01

    The Amish-based furniture manufacturing cluster in and around Holmes County, OH, is home to some 400 shops and has become an important regional driver of demand for hardwood products. The cluster has expanded even as the broader domestic furniture industry has declined. Clustering dynamics are seen as important to the success, but little information has been available...

  6. Density-functional investigations on the neutral and charged Cun (n = 2 ∼ 12) clusters

    International Nuclear Information System (INIS)

    Jiang Yuanqi; Duan Haiming

    2011-01-01

    Combined with the semi-empirical inter-atomic potential, the geometrical and electronic properties of the ground- and low-lying states of Cu n (n = 2 ∼ 12) and Cu n ± (n = 2 ∼ 12) clusters are investigated systematically by density-functional calculations. Our results show that: the ground-state geometries prefer to linear or planar structures for the Cu n (n = 2 ∼ 6) and Cu n ± (n = 2 ∼ 5) clusters and the planar structures are all base on triangles, while for the larger clusters, the pentagonal bi-pyramids are the basic units to form the ground-state geometries, and the traditional high-symmetric structures do not dominate to the ground-states for these small copper clusters. The calculated binding energies of Cu n (n = 2 ∼ 12) clusters are in very good agreement with the experimental results, and the obtained ionization potentials (IPs) and electron affinities (EAs) are also in agreement with the observations; Several electronic properties (such as the IPs, EAs and the second-order energy differences) all exhibit oscillations, which can be due to the relatively high stabilities of the copper clusters containing even number electrons. (authors)

  7. Analysis and comparison of very large metagenomes with fast clustering and functional annotation

    Directory of Open Access Journals (Sweden)

    Li Weizhong

    2009-10-01

    Full Text Available Abstract Background The remarkable advance of metagenomics presents significant new challenges in data analysis. Metagenomic datasets (metagenomes are large collections of sequencing reads from anonymous species within particular environments. Computational analyses for very large metagenomes are extremely time-consuming, and there are often many novel sequences in these metagenomes that are not fully utilized. The number of available metagenomes is rapidly increasing, so fast and efficient metagenome comparison methods are in great demand. Results The new metagenomic data analysis method Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline (RAMMCAP was developed using an ultra-fast sequence clustering algorithm, fast protein family annotation tools, and a novel statistical metagenome comparison method that employs a unique graphic interface. RAMMCAP processes extremely large datasets with only moderate computational effort. It identifies raw read clusters and protein clusters that may include novel gene families, and compares metagenomes using clusters or functional annotations calculated by RAMMCAP. In this study, RAMMCAP was applied to the two largest available metagenomic collections, the "Global Ocean Sampling" and the "Metagenomic Profiling of Nine Biomes". Conclusion RAMMCAP is a very fast method that can cluster and annotate one million metagenomic reads in only hundreds of CPU hours. It is available from http://tools.camera.calit2.net/camera/rammcap/.

  8. PRIMUS: Galaxy clustering as a function of luminosity and color at 0.2 < z < 1

    Energy Technology Data Exchange (ETDEWEB)

    Skibba, Ramin A.; Smith, M. Stephen M.; Coil, Alison L.; Mendez, Alexander J. [Department of Physics, Center for Astrophysics and Space Sciences, University of California, 9500 Gilman Drive, La Jolla, San Diego, CA 92093 (United States); Moustakas, John [Department of Physics and Astronomy, Siena College, 515 Loudon Road, Loudonville, NY 12211 (United States); Aird, James [Department of Physics, Durham University, Durham DH1 3LE (United Kingdom); Blanton, Michael R. [Center for Cosmology and Particle Physics, Department of Physics, New York University, 4 Washington Place, New York, NY 10003 (United States); Bray, Aaron D.; Eisenstein, Daniel J. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Cool, Richard J. [MMT Observatory, 1540 E Second Street, University of Arizona, Tucson, AZ 85721 (United States); Wong, Kenneth C. [Steward Observatory, The University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Zhu, Guangtun, E-mail: rskibba@ucsd.edu [Department of Physics and Astronomy, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States)

    2014-04-01

    We present measurements of the luminosity and color-dependence of galaxy clustering at 0.2 < z < 1.0 in the Prism Multi-object Survey. We quantify the clustering with the redshift-space and projected two-point correlation functions, ξ(r{sub p} , π) and w{sub p} (r{sub p} ), using volume-limited samples constructed from a parent sample of over ∼130, 000 galaxies with robust redshifts in seven independent fields covering 9 deg{sup 2} of sky. We quantify how the scale-dependent clustering amplitude increases with increasing luminosity and redder color, with relatively small errors over large volumes. We find that red galaxies have stronger small-scale (0.1 Mpc h {sup –1} < r{sub p} < 1 Mpc h {sup –1}) clustering and steeper correlation functions compared to blue galaxies, as well as a strong color dependent clustering within the red sequence alone. We interpret our measured clustering trends in terms of galaxy bias and obtain values of b {sub gal} ≈ 0.9-2.5, quantifying how galaxies are biased tracers of dark matter depending on their luminosity and color. We also interpret the color dependence with mock catalogs, and find that the clustering of blue galaxies is nearly constant with color, while redder galaxies have stronger clustering in the one-halo term due to a higher satellite galaxy fraction. In addition, we measure the evolution of the clustering strength and bias, and we do not detect statistically significant departures from passive evolution. We argue that the luminosity- and color-environment (or halo mass) relations of galaxies have not significantly evolved since z ∼ 1. Finally, using jackknife subsampling methods, we find that sampling fluctuations are important and that the COSMOS field is generally an outlier, due to having more overdense structures than other fields; we find that 'cosmic variance' can be a significant source of uncertainty for high-redshift clustering measurements.

  9. Clusters of Insomnia Disorder: An Exploratory Cluster Analysis of Objective Sleep Parameters Reveals Differences in Neurocognitive Functioning, Quantitative EEG, and Heart Rate Variability

    Science.gov (United States)

    Miller, Christopher B.; Bartlett, Delwyn J.; Mullins, Anna E.; Dodds, Kirsty L.; Gordon, Christopher J.; Kyle, Simon D.; Kim, Jong Won; D'Rozario, Angela L.; Lee, Rico S.C.; Comas, Maria; Marshall, Nathaniel S.; Yee, Brendon J.; Espie, Colin A.; Grunstein, Ronald R.

    2016-01-01

    Study Objectives: To empirically derive and evaluate potential clusters of Insomnia Disorder through cluster analysis from polysomnography (PSG). We hypothesized that clusters would differ on neurocognitive performance, sleep-onset measures of quantitative (q)-EEG and heart rate variability (HRV). Methods: Research volunteers with Insomnia Disorder (DSM-5) completed a neurocognitive assessment and overnight PSG measures of total sleep time (TST), wake time after sleep onset (WASO), and sleep onset latency (SOL) were used to determine clusters. Results: From 96 volunteers with Insomnia Disorder, cluster analysis derived at least two clusters from objective sleep parameters: Insomnia with normal objective sleep duration (I-NSD: n = 53) and Insomnia with short sleep duration (I-SSD: n = 43). At sleep onset, differences in HRV between I-NSD and I-SSD clusters suggest attenuated parasympathetic activity in I-SSD (P insomnia clusters derived from cluster analysis differ in sleep onset HRV. Preliminary data suggest evidence for three clusters in insomnia with differences for sustained attention and sleep-onset q-EEG. Clinical Trial Registration: Insomnia 100 sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR) identification number 12612000049875. URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=347742. Citation: Miller CB, Bartlett DJ, Mullins AE, Dodds KL, Gordon CJ, Kyle SD, Kim JW, D'Rozario AL, Lee RS, Comas M, Marshall NS, Yee BJ, Espie CA, Grunstein RR. Clusters of Insomnia Disorder: an exploratory cluster analysis of objective sleep parameters reveals differences in neurocognitive functioning, quantitative EEG, and heart rate variability. SLEEP 2016;39(11):1993–2004. PMID:27568796

  10. A gonococcal homologue of meningococcal γ-glutamyl transpeptidase gene is a new type of bacterial pseudogene that is transcriptionally active but phenotypically silent

    Directory of Open Access Journals (Sweden)

    Watanabe Haruo

    2005-10-01

    Full Text Available Abstract Background It has been speculated that the γ-glutamyl transpeptidase (ggt gene is present only in Neisseria meningitidis and not among related species such as Neisseria gonorrhoeae and Neisseria lactamica, because N. meningitidis is the only bacterium with GGT activity. However, nucleotide sequences highly homologous to the meningococcal ggt gene were found in the genomes of N. gonorrhoeae isolates. Results The gonococcal homologue (ggt gonococcal homologue; ggh was analyzed. The nucleotide sequence of the ggh gene was approximately 95 % identical to that of the meningococcal ggt gene. An open reading frame in the ggh gene was disrupted by an ochre mutation and frameshift mutations induced by a 7-base deletion, but the amino acid sequences deduced from the artificially corrected ggh nucleotide sequences were approximately 97 % identical to that of the meningococcal ggt gene. The analyses of the sequences flanking the ggt and ggh genes revealed that both genes were localized in a common DNA region containing the fbp-ggt (or ggh-glyA-opcA-dedA-abcZ gene cluster. The expression of the ggh RNA could be detected by dot blot, RT-PCR and primer extension analyses. Moreover, the truncated form of ggh-translational product was also found in some of the gonococcal isolates. Conclusion This study has shown that the gonococcal ggh gene is a pseudogene of the meningococcal ggt gene, which can also be designated as Ψggt. The gonococcal ggh (Ψggt gene is the first identified bacterial pseudogene that is transcriptionally active but phenotypically silent.

  11. The Magellanic Bridge Cluster NGC 796: Deep Optical AO Imaging Reveals the Stellar Content and Initial Mass Function of a Massive Open Cluster

    Science.gov (United States)

    Kalari, Venu M.; Carraro, Giovanni; Evans, Christopher J.; Rubio, Monica

    2018-04-01

    NGC 796 is a massive young cluster located 59 kpc from us in the diffuse intergalactic medium of the 1/5–1/10 Z⊙ Magellanic Bridge, allowing us to probe variations in star formation and stellar evolution processes as a function of metallicity in a resolved fashion, and providing a link between resolved studies of nearby solar-metallicity and unresolved distant metal-poor clusters located in high-redshift galaxies. In this paper, we present adaptive optics griHα imaging of NGC 796 (at 0.″5, which is ∼0.14 pc at the cluster distance) along with optical spectroscopy of two bright members to quantify the cluster properties. Our aim is to explore whether star formation and stellar evolution vary as a function of metallicity by comparing the properties of NGC 796 to higher-metallicity clusters. We find an age of {20}-5+12 Myr from isochronal fitting of the cluster main sequence in the color–magnitude diagram. Based on the cluster luminosity function, we derive a top-heavy stellar initial mass function (IMF) with a slope α = 1.99 ± 0.2, hinting at a metallicity and/or environmental dependence of the IMF, which may lead to a top-heavy IMF in the early universe. Study of the Hα emission-line stars reveals that classical Be stars constitute a higher fraction of the total B-type stars when compared with similar clusters at greater metallicity, providing some support to the chemically homogeneous theory of stellar evolution. Overall, NGC 796 has a total estimated mass of 990 ± 200 M⊙, and a core radius of 1.4 ± 0.3 pc, which classifies it as a massive young open cluster, unique in the diffuse interstellar medium of the Magellanic Bridge.

  12. Self Organizing Maps to efficiently cluster and functionally interpret protein conformational ensembles

    Directory of Open Access Journals (Sweden)

    Fabio Stella

    2013-09-01

    Full Text Available An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the original ensembles can be summarized by using only the representative conformations of the clusters obtained. In addition the network components analysis allows to discover and interpret the dynamic behavior of the conformations won by each neuron. The results showed the ability of this approach to efficiently derive a functional interpretation of the protein dynamics described by the original conformational ensemble, highlighting its potential as a support for protein engineering.

  13. Accurate Energies and Structures for Large Water Clusters Using the X3LYP Hybrid Density Functional

    OpenAIRE

    Su, Julius T.; Xu, Xin; Goddard, William A., III

    2004-01-01

    We predict structures and energies of water clusters containing up to 19 waters with X3LYP, an extended hybrid density functional designed to describe noncovalently bound systems as accurately as covalent systems. Our work establishes X3LYP as the most practical ab initio method today for calculating accurate water cluster structures and energies. We compare X3LYP/aug-cc-pVTZ energies to the most accurate theoretical values available (n = 2−6, 8), MP2 with basis set superposition error (BSSE)...

  14. Identification of alterations associated with age in the clustering structure of functional brain networks.

    Science.gov (United States)

    Guzman, Grover E C; Sato, Joao R; Vidal, Maciel C; Fujita, Andre

    2018-01-01

    Initial studies using resting-state functional magnetic resonance imaging on the trajectories of the brain network from childhood to adulthood found evidence of functional integration and segregation over time. The comprehension of how healthy individuals' functional integration and segregation occur is crucial to enhance our understanding of possible deviations that may lead to brain disorders. Recent approaches have focused on the framework wherein the functional brain network is organized into spatially distributed modules that have been associated with specific cognitive functions. Here, we tested the hypothesis that the clustering structure of brain networks evolves during development. To address this hypothesis, we defined a measure of how well a brain region is clustered (network fitness index), and developed a method to evaluate its association with age. Then, we applied this method to a functional magnetic resonance imaging data set composed of 397 males under 31 years of age collected as part of the Autism Brain Imaging Data Exchange Consortium. As results, we identified two brain regions for which the clustering change over time, namely, the left middle temporal gyrus and the left putamen. Since the network fitness index is associated with both integration and segregation, our finding suggests that the identified brain region plays a role in the development of brain systems.

  15. Mapping of the mouse actin capping protein {alpha} subunit genes and pseudogenes

    Energy Technology Data Exchange (ETDEWEB)

    Hart, M.C.; Korshunova, Y.O.; Cooper, J.A. [Washington Univ. School of Medicine, St. Louis, MO (United States)

    1997-02-01

    Capping protein (CP), a heterodimer of {alpha} and {beta} subunits, is found in all eukaryotes. CP binds to the barbed ends of actin filaments in vitro and controls actin assembly and cell motility in vivo. Vertebrates have three {alpha} isoforms ({alpha}1, {alpha}2, {alpha}3) produced from different genes, whereas lower organisms have only one gene and one isoform. We isolated genomic clones corresponding to the a subunits of mouse CP and found three {alpha}1 genes, two of which are pseudogenes, and a single gene for both {alpha}2 and {alpha}3. Their chromosomal locations were identified by interspecies backcross mapping. The {alpha}1 gene (Cappa1) mapped to Chromosome 3 between D3Mit11 and D3Mit13. The {alpha}1 pseudogenes (Cappa1-ps1 and Cappa1-ps2) mapped to Chromosomes 1 and 9, respectively. The {alpha}2 gene (Cappa2) mapped to Chromosome 6 near Ptn. The {alpha}3 gene (Cappa3) also mapped to Chromosome 6, approximately 68 cM distal from Cappa2 near Kras2. One mouse mutation, de, maps in the vicinity of the {alpha}1 gene. No known mouse mutations map to regions near the {alpha}2 or {alpha}3 genes. 29 refs., 3 figs., 1 tab.

  16. Density functional studies: First principles and semiempirical calculations of clusters and surfaces

    International Nuclear Information System (INIS)

    Sinnott, S.B.

    1993-01-01

    In the research presented here, various theoretical electronic structure techniques are utilized to analyze widely different systems from silicon clusters to transition metal solids and surfaces. For the silicon clusters, first principles density functional methods are used to investigate Si N for N = 2-8. The goal is to understand the different types of bonding that can occur in such small clusters where the coordination of the atoms differs substantially from that of the stable bulk tetrahedral bonding. Such uncoordinated structures can provide a good test of more approximate theories that can be used eventually to model silicon surfaces, of obvious technological importance. For the transition metal systems, non-self-consistent electronic structure methods are used to provide an understanding of the driving force for surface relaxations. An in-depth analysis of the results is presented and the physical basis of surface relaxation within the theory is discussed. In addition, the limitations inherent in calculations of metal surface relaxation are addressed. Finally, in an effort to increase understanding of approximate methods, a novel non-self-consistent density functional electronic structure method is developed that is ∼1000 times faster computationally than more sophisticated methods. This new method is tested for a variety of systems including diatomics, mixed clusters, surfaces and bulk lattices. The strengths and weaknesses of the new theory are discussed in detail, leading to greater understanding of non-self-consistent density functional theories as a whole

  17. Low-mass stars in globular clusters. III. The mass function of 47 Tucanae.

    Science.gov (United States)

    de Marchi, G.; Paresce, F.

    1995-12-01

    We have used the WFPC2 on board HST to investigate the stellar population in a field located 4'6 E of the center of the globular cluster 47 Tuc (NGC 104), close to the half-mass radius, through wide band imaging at 606 and 812nm. A total of ~3000 stars are accurately classified by two-color photometry to form a color-magnitude diagram extending down to a limiting magnitude m_814_=~m_I_=~24. A rich cluster main sequence is detected spanning the range from m_814_=~18 through m_814_=~23, where it spreads considerably due to the increasing photometric uncertainty and galaxy contamination. A secondary sequence of objects is also detected, parallel to the main sequence, as expected for a population of binary stars. The measured binary fraction in the range 195%. The main sequence luminosity function obtained from the observed CMD increases with decreasing luminosity following a power-law trend with index α=~0.15 in the range 5crowding. On the basis of the available mass-luminosity relation for this metallicity, the resultant mass function shows a power-law increase in numbers for decreasing masses in the range 0.8-0.3Msun_ with a slope α=~1.5, but then flattens out in the 0.3-0.15Msun_ range. The comparison of the mass function of 47 Tuc with that of NGC 6397 (Paper I) and of M 15 (Paper II), previously investigated with the same instrumentation, suggests that the stellar population near the half-mass radius of these clusters should not be very sensitive to either internal or externally-driven dynamical processes. The difference between their mass functions could then be attributed to metallicity, reflecting an intrinsic difference in their initial mass functions, unless mass-segregation is stronger in 47 Tuc than in the other two clusters. This latter circumstance could be due, for instance, to the large number of binaries discovered in 47 Tuc. In all cases, however, the mass function is found to flatten below 0.3Msun_ and the flattening is most likely an intrinsic

  18. Density functional theory and surface reactivity study of bimetallic AgnYm (n+m = 10) clusters

    Science.gov (United States)

    Hussain, Riaz; Hussain, Abdullah Ijaz; Chatha, Shahzad Ali Shahid; Hussain, Riaz; Hanif, Usman; Ayub, Khurshid

    2018-06-01

    Density functional theory calculations have been performed on pure silver (Agn), yttrium (Ym) and bimetallic silver yttrium clusters AgnYm (n + m = 2-10) for reactivity descriptors in order to realize sites for nucleophilic and electrophilic attack. The reactivity descriptors of the clusters, studied as a function of cluster size and shape, reveal the presence of different type of reactive sites in a cluster. The size and shape of the pure silver, yttrium and bimetallic silver yttrium cluster (n = 2-10) strongly influences the number and position of active sites for an electrophilic and/or nucleophilic attack. The trends of reactivities through reactivity descriptors are confirmed through comparison with experimental data for CO binding with silver clusters. Moreover, the adsorption of CO on bimetallic silver yttrium clusters is also evaluated. The trends of binding energies support the reactivity descriptors values. Doping of pure cluster with the other element also influence the hardness, softness and chemical reactivity of the clusters. The softness increases as we increase the number of silver atoms in the cluster, whereas the hardness decreases. The chemical reactivity increases with silver doping whereas it decreases by increasing yttrium concentration. Silver atoms are nucleophilic in small clusters but changed to electrophilic in large clusters.

  19. Machine learning etudes in astrophysics: selection functions for mock cluster catalogs

    International Nuclear Information System (INIS)

    Hajian, Amir; Alvarez, Marcelo A.; Bond, J. Richard

    2015-01-01

    Making mock simulated catalogs is an important component of astrophysical data analysis. Selection criteria for observed astronomical objects are often too complicated to be derived from first principles. However the existence of an observed group of objects is a well-suited problem for machine learning classification. In this paper we use one-class classifiers to learn the properties of an observed catalog of clusters of galaxies from ROSAT and to pick clusters from mock simulations that resemble the observed ROSAT catalog. We show how this method can be used to study the cross-correlations of thermal Sunya'ev-Zeldovich signals with number density maps of X-ray selected cluster catalogs. The method reduces the bias due to hand-tuning the selection function and is readily scalable to large catalogs with a high-dimensional space of astrophysical features

  20. Machine learning etudes in astrophysics: selection functions for mock cluster catalogs

    Energy Technology Data Exchange (ETDEWEB)

    Hajian, Amir; Alvarez, Marcelo A.; Bond, J. Richard, E-mail: ahajian@cita.utoronto.ca, E-mail: malvarez@cita.utoronto.ca, E-mail: bond@cita.utoronto.ca [Canadian Institute for Theoretical Astrophysics, University of Toronto, Toronto, ON M5S 3H8 (Canada)

    2015-01-01

    Making mock simulated catalogs is an important component of astrophysical data analysis. Selection criteria for observed astronomical objects are often too complicated to be derived from first principles. However the existence of an observed group of objects is a well-suited problem for machine learning classification. In this paper we use one-class classifiers to learn the properties of an observed catalog of clusters of galaxies from ROSAT and to pick clusters from mock simulations that resemble the observed ROSAT catalog. We show how this method can be used to study the cross-correlations of thermal Sunya'ev-Zeldovich signals with number density maps of X-ray selected cluster catalogs. The method reduces the bias due to hand-tuning the selection function and is readily scalable to large catalogs with a high-dimensional space of astrophysical features.

  1. A density functional study of structures and stability of SinCN clusters

    International Nuclear Information System (INIS)

    Gai Zhigang; Yang Li; Zhao Jie; Chu Shibo

    2011-01-01

    In this paper, density functional theory (DFT) B3LYP method with 6-311G * basis set has been used to investigate geometric configurations, vibrational frequencies and ground state energies of Si n CN (n = 2 ∼ 6) clusters. The energies and spin multiplicities of ground states and substable states have been discussed, respectively. Harmonic frequencies and infrared spectra intensity for these clusters are given in order to aid in the characterization of the stable structures. The results show that the zero point energy (ZPE), thermocapacity and entropies are nearly in proportion to increased n, whose average enhancement are 0.80 kcal/mol, 5.20 cal/mol · K and 12.72 cal/ mol · K, respectively. The stability of Si n CN (n = 2 ∼ 6) clusters with even n are greater than that with odd n. (authors)

  2. A Proteomic Approach to Investigating Gene Cluster Expression and Secondary Metabolite Functionality in Aspergillus fumigatus

    Science.gov (United States)

    Owens, Rebecca A.; Hammel, Stephen; Sheridan, Kevin J.; Jones, Gary W.; Doyle, Sean

    2014-01-01

    A combined proteomics and metabolomics approach was utilised to advance the identification and characterisation of secondary metabolites in Aspergillus fumigatus. Here, implementation of a shotgun proteomic strategy led to the identification of non-redundant mycelial proteins (n = 414) from A. fumigatus including proteins typically under-represented in 2-D proteome maps: proteins with multiple transmembrane regions, hydrophobic proteins and proteins with extremes of molecular mass and pI. Indirect identification of secondary metabolite cluster expression was also achieved, with proteins (n = 18) from LaeA-regulated clusters detected, including GliT encoded within the gliotoxin biosynthetic cluster. Biochemical analysis then revealed that gliotoxin significantly attenuates H2O2-induced oxidative stress in A. fumigatus (p>0.0001), confirming observations from proteomics data. A complementary 2-D/LC-MS/MS approach further elucidated significantly increased abundance (pproteome and experimental strategies, plus mechanistic data pertaining to gliotoxin functionality in the organism. PMID:25198175

  3. Filling- and interaction-driven Mott transition. Quantum cluster calculations within self-energy-functional theory

    International Nuclear Information System (INIS)

    Balzer, Matthias

    2008-01-01

    The central goal of this thesis is the examination of strongly correlated electron systems on the basis of the two-dimensional Hubbard model. We analyze how the properties of the Mott insulator change upon doping and with interaction strength. The numerical evaluation is done using quantum cluster approximations, which allow for a thermodynamically consistent description of the ground state properties. The framework of self-energy-functional theory offers great flexibility for the construction of cluster approximations. A detailed analysis sheds light on the quality and the convergence properties of different cluster approximations within the self-energy-functional theory. We use the one-dimensional Hubbard model for these examinations and compare our results with the exact solution. In two dimensions the ground state of the particle-hole symmetric model at half-filling is an antiferromagnetic insulator, independent of the interaction strength. The inclusion of short-range spatial correlations by our cluster approach leads to a considerable improvement of the antiferromagnetic order parameter as compared to dynamical mean-field theory. In the paramagnetic phase we furthermore observe a metal-insulator transition as a function of the interaction strength, which qualitatively differs from the pure mean-field scenario. Starting from the antiferromagnetic Mott insulator a filling-controlled metal-insulator transition in a paramagnetic metallic phase can be observed. Depending on the cluster approximation used an antiferromagnetic metallic phase may occur at first. In addition to long-range antiferromagnetic order, we also considered superconductivity in our calculations. The superconducting order parameter as a function of doping is in good agreement with other numerical methods, as well as with experimental results. (orig.)

  4. From the Cluster Temperature Function to the Mass Function at Low Z

    Science.gov (United States)

    Mushotzky, Richard (Technical Monitor); Markevitch, Maxim

    2004-01-01

    This XMM project consisted of three observations of the nearby, hot galaxy cluster Triangulum Australis, one of the cluster center and two offsets. The goal was to measure the radial gas temperature profile out to large radii and derive the total gravitating mass within the radius of average mass overdensity 500. The central pointing also provides data for a detailed two-dimensional gas temperature map of this interesting cluster. We have analyzed all three observations. The derivation of the temperature map using the central pointing is complete, and the paper is soon to be submitted. During the course of this study and of the analysis of archival XMM cluster observations, it became apparent that the commonly used XMM background flare screening techniques are often not accurate enough for studies of the cluster outer regions. The information on the cluster's total masses is contained at large off-center distances, and it is precisely the temperatures for those low-brightness regions that are most affected by the detector background anomalies. In particular, our two offset observations of the Triangulum have been contaminated by the background flares ("bad cosmic weather") to a degree where they could not be used for accurate spectral analysis. This forced us to expand the scope of our project. We needed to devise a more accurate method of screening and modeling the background flares, and to evaluate the uncertainty of the XMM background modeling. To do this, we have analyzed a large number of archival EPIC blank-field and closed-cover observations. As a result, we have derived stricter background screening criteria. It also turned out that mild flares affecting EPIC-pn can be modeled with an adequate accuracy. Such modeling has been used to derive our Triangulum temperature map. The results of our XMM background analysis, including the modeling recipes, are presented in a paper which is in final preparation and will be submitted soon. It will be useful not only

  5. WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results.

    Science.gov (United States)

    Joshi, Vineet K; Freudenberg, Johannes M; Hu, Zhen; Medvedovic, Mario

    2011-01-17

    Cluster analysis methods have been extensively researched, but the adoption of new methods is often hindered by technical barriers in their implementation and use. WebGimm is a free cluster analysis web-service, and an open source general purpose clustering web-server infrastructure designed to facilitate easy deployment of integrated cluster analysis servers based on clustering and functional annotation algorithms implemented in R. Integrated functional analyses and interactive browsing of both, clustering structure and functional annotations provides a complete analytical environment for cluster analysis and interpretation of results. The Java Web Start client-based interface is modeled after the familiar cluster/treeview packages making its use intuitive to a wide array of biomedical researchers. For biomedical researchers, WebGimm provides an avenue to access state of the art clustering procedures. For Bioinformatics methods developers, WebGimm offers a convenient avenue to deploy their newly developed clustering methods. WebGimm server, software and manuals can be freely accessed at http://ClusterAnalysis.org/.

  6. Density functional study of structural and electronic properties of bimetallic silver-gold clusters: Comparison with pure gold and silver clusters

    Science.gov (United States)

    Bonacic-Koutecky, Vlasta; Burda, Jaroslav; Mitric, Roland; Ge, Maofa; Zampella, Giuseppe; Fantucci, Piercarlo

    2002-08-01

    Bimetallic silver-gold clusters offer an excellent opportunity to study changes in metallic versus "ionic" properties involving charge transfer as a function of the size and the composition, particularly when compared to pure silver and gold clusters. We have determined structures, ionization potentials, and vertical detachment energies for neutral and charged bimetallic AgmAun 3[less-than-or-equal](m+n)[less-than-or-equal]5 clusters. Calculated VDE values compare well with available experimental data. In the stable structures of these clusters Au atoms assume positions which favor the charge transfer from Ag atoms. Heteronuclear bonding is usually preferred to homonuclear bonding in clusters with equal numbers of hetero atoms. In fact, stable structures of neutral Ag2Au2, Ag3Au3, and Ag4Au4 clusters are characterized by the maximum number of hetero bonds and peripheral positions of Au atoms. Bimetallic tetramer as well as hexamer are planar and have common structural properties with corresponding one-component systems, while Ag4Au4 and Ag8 have 3D forms in contrast to Au8 which assumes planar structure. At the density functional level of theory we have shown that this is due to participation of d electrons in bonding of pure Aun clusters while s electrons dominate bonding in pure Agm as well as in bimetallic clusters. In fact, Aun clusters remain planar for larger sizes than Agm and AgnAun clusters. Segregation between two components in bimetallic systems is not favorable, as shown in the example of Ag5Au5 cluster. We have found that the structures of bimetallic clusters with 20 atoms Ag10Au10 and Ag12Au8 are characterized by negatively charged Au subunits embedded in Ag environment. In the latter case, the shape of Au8 is related to a pentagonal bipyramid capped by one atom and contains three exposed negatively charged Au atoms. They might be suitable for activating reactions relevant to catalysis. According to our findings the charge transfer in bimetallic

  7. Synthesis and Characterization of Rh-Co Butterfly Clusters Capped by Functionally Substituted 1-Alkynes

    Institute of Scientific and Technical Information of China (English)

    朱保华; 胡斌; 张伟强; 边治国; 赵全义; 殷元骐; 孙杰

    2003-01-01

    By the reactions of [Rh2Co2(CO)12] 1 with functionally substituted alkyne ligands HC≡CR 2 (R = FeCp2) and 3 (R = 2-OH-C6H4COOCH2), respectively in n-hexane at room temperature, two new cluster derivatives [Rh2Co2(CO)6(μ-CO)4(μ4, η2-HC≡CR)] 4 (R = FeCp2) and 5 (R = 2-OH-C6H4COOCH2) were obtained respectively. The alkyne was inserted into the Co-Co bond of cluster 1 to give two butterfly clusters. Cluster 4 has been determined by single-crystal X-ray diffraction. Crystallographic data: C22H10Co2FeO10Rh2, Mr = 813.83, orthorhombic, space group P212121, a = 11.5318(7), b = 12.6572(7), c = 17.018(1) A。, V = 2483.9(3) A。3, Z = 4, Dc = 2.176 g/cm3, F(000) = 1568, μ = 3.233 mm-1, the final R = 0.0366 and wR = 0.0899 for 5367 observed reflections with I > 2σ(I). The two clusters have also been characterized by elemental analysis, IR and 1H-NMR spectroscopy.

  8. Diffusion Geometry Unravels the Emergence of Functional Clusters in Collective Phenomena

    Science.gov (United States)

    De Domenico, Manlio

    2017-04-01

    Collective phenomena emerge from the interaction of natural or artificial units with a complex organization. The interplay between structural patterns and dynamics might induce functional clusters that, in general, are different from topological ones. In biological systems, like the human brain, the overall functionality is often favored by the interplay between connectivity and synchronization dynamics, with functional clusters that do not coincide with anatomical modules in most cases. In social, sociotechnical, and engineering systems, the quest for consensus favors the emergence of clusters. Despite the unquestionable evidence for mesoscale organization of many complex systems and the heterogeneity of their interconnectivity, a way to predict and identify the emergence of functional modules in collective phenomena continues to elude us. Here, we propose an approach based on random walk dynamics to define the diffusion distance between any pair of units in a networked system. Such a metric allows us to exploit the underlying diffusion geometry to provide a unifying framework for the intimate relationship between metastable synchronization, consensus, and random search dynamics in complex networks, pinpointing the functional mesoscale organization of synthetic and biological systems.

  9. Information processing architecture of functionally defined clusters in the macaque cortex.

    Science.gov (United States)

    Shen, Kelly; Bezgin, Gleb; Hutchison, R Matthew; Gati, Joseph S; Menon, Ravi S; Everling, Stefan; McIntosh, Anthony R

    2012-11-28

    Computational and empirical neuroimaging studies have suggested that the anatomical connections between brain regions primarily constrain their functional interactions. Given that the large-scale organization of functional networks is determined by the temporal relationships between brain regions, the structural limitations may extend to the global characteristics of functional networks. Here, we explored the extent to which the functional network community structure is determined by the underlying anatomical architecture. We directly compared macaque (Macaca fascicularis) functional connectivity (FC) assessed using spontaneous blood oxygen level-dependent functional magnetic resonance imaging (BOLD-fMRI) to directed anatomical connectivity derived from macaque axonal tract tracing studies. Consistent with previous reports, FC increased with increasing strength of anatomical connection, and FC was also present between regions that had no direct anatomical connection. We observed moderate similarity between the FC of each region and its anatomical connectivity. Notably, anatomical connectivity patterns, as described by structural motifs, were different within and across functional modules: partitioning of the functional network was supported by dense bidirectional anatomical connections within clusters and unidirectional connections between clusters. Together, our data directly demonstrate that the FC patterns observed in resting-state BOLD-fMRI are dictated by the underlying neuroanatomical architecture. Importantly, we show how this architecture contributes to the global organizational principles of both functional specialization and integration.

  10. Approximation Of Multi-Valued Inverse Functions Using Clustering And Sugeno Fuzzy Inference

    Science.gov (United States)

    Walden, Maria A.; Bikdash, Marwan; Homaifar, Abdollah

    1998-01-01

    Finding the inverse of a continuous function can be challenging and computationally expensive when the inverse function is multi-valued. Difficulties may be compounded when the function itself is difficult to evaluate. We show that we can use fuzzy-logic approximators such as Sugeno inference systems to compute the inverse on-line. To do so, a fuzzy clustering algorithm can be used in conjunction with a discriminating function to split the function data into branches for the different values of the forward function. These data sets are then fed into a recursive least-squares learning algorithm that finds the proper coefficients of the Sugeno approximators; each Sugeno approximator finds one value of the inverse function. Discussions about the accuracy of the approximation will be included.

  11. Covalent functionalization of octagraphene with magnetic octahedral B6- and non-planar C6- clusters

    Science.gov (United States)

    Chigo-Anota, E.; Cárdenas-Jirón, G.; Salazar Villanueva, M.; Bautista Hernández, A.; Castro, M.

    2017-10-01

    The interaction between the magnetic boron octahedral (B6-) and non-planar (C6-) carbon clusters with semimetal nano-sheet of octa-graphene (C64H24) in the gas phase is studied by means of DFT calculations. These results reveal that non-planar-1 (anion) carbon cluster exhibits structural stability, low chemical reactivity, magnetic (1.0 magneton bohr) and semiconductor behavior. On the other hand, there is chemisorption phenomena when the stable B6- and C6- clusters are absorbed on octa-graphene nanosheets. Such absorption generates high polarity and the low-reactivity remains as on the individual pristine cases. Electronic charge transference occurs from the clusters toward the nanosheets, producing a reduction of the work function for the complexes and also induces a magnetic behavior on the functionalized sheets. The quantum descriptors obtained for these systems reveal that they are feasible candidates for the design of molecular circuits, magnetic devices, and nano-vehicles for drug delivery.

  12. Defective functional connectivity between posterior hypothalamus and regions of the diencephalic-mesencephalic junction in chronic cluster headache.

    Science.gov (United States)

    Ferraro, Stefania; Nigri, Anna; Bruzzone, Maria Grazia; Brivio, Luca; Proietti Cecchini, Alberto; Verri, Mattia; Chiapparini, Luisa; Leone, Massimo

    2018-01-01

    Objective We tested the hypothesis of a defective functional connectivity between the posterior hypothalamus and diencephalic-mesencephalic regions in chronic cluster headache based on: a) clinical and neuro-endocrinological findings in cluster headache patients; b) neuroimaging findings during cluster headache attacks; c) neuroimaging findings in drug-refractory chronic cluster headache patients improved after successful deep brain stimulation. Methods Resting state functional magnetic resonance imaging, associated with a seed-based approach, was employed to investigate the functional connectivity of the posterior hypothalamus in chronic cluster headache patients (n = 17) compared to age and sex-matched healthy subjects (n = 16). Random-effect analyses were performed to study differences between patients and controls in ipsilateral and contralateral-to-the-pain posterior hypothalamus functional connectivity. Results Cluster headache patients showed an increased functional connectivity between the ipsilateral posterior hypothalamus and a number of diencephalic-mesencephalic structures, comprising ventral tegmental area, dorsal nuclei of raphe, and bilateral substantia nigra, sub-thalamic nucleus, and red nucleus ( p cluster headache patients mainly involves structures that are part of (i.e. ventral tegmental area, substantia nigra) or modulate (dorsal nuclei of raphe, sub-thalamic nucleus) the midbrain dopaminergic systems. The midbrain dopaminergic systems could play a role in cluster headache pathophysiology and in particular in the chronicization process. Future studies are needed to better clarify if this finding is specific to cluster headache or if it represents an unspecific response to chronic pain.

  13. Evolution of the stellar mass function in multiple-population globular clusters

    Science.gov (United States)

    Vesperini, Enrico; Hong, Jongsuk; Webb, Jeremy J.; D'Antona, Franca; D'Ercole, Annibale

    2018-05-01

    We present the results of a survey of N-body simulations aimed at studying the effects of the long-term dynamical evolution on the stellar mass function (MF) of multiple stellar populations in globular clusters. Our simulations show that if first-(1G) and second-generation (2G) stars have the same initial MF (IMF), the global MFs of the two populations are affected similarly by dynamical evolution and no significant differences between the 1G and 2G MFs arise during the cluster's evolution. If the two populations have different IMFs, dynamical effects do not completely erase memory of the initial differences. Should observations find differences between the global 1G and 2G MFs, these would reveal the fingerprints of differences in their IMFs. Irrespective of whether the 1G and 2G populations have the same global IMF or not, dynamical effects can produce differences between the local (measured at various distances from the cluster centre) 1G and 2G MFs; these differences are a manifestation of the process of mass segregation in populations with different initial structural properties. In dynamically old and spatially mixed clusters, however, differences between the local 1G and 2G MFs can reveal differences between the 1G and 2G global MFs. In general, for clusters with any dynamical age, large differences between the local 1G and 2G MFs are more likely to be associated with differences in the global MF. Our study also reveals a dependence of the spatial mixing rate on the stellar mass, another dynamical consequence of the multiscale nature of multiple-population clusters.

  14. Evolution of the Black Hole Mass Function in Star Clusters from Multiple Mergers

    Science.gov (United States)

    Christian, Pierre; Mocz, Philip; Loeb, Abraham

    2018-05-01

    We investigate the effects of black hole (BH) mergers in star clusters on the black hole mass function (BHMF). As BHs are not produced in pair-instability supernovae, it is suggested that there is a dearth of high-mass stellar BHs. This dearth generates a gap in the upper end of the BHMF. Meanwhile, parameter fitting of X-ray binaries suggests the existence of a gap in the mass function under 5 solar masses. We show, through evolving a coagulation equation, that BH mergers can appreciably fill the upper mass gap, and that the lower mass gap generates potentially observable features at larger mass scales. We also explore the importance of ejections in such systems and whether dynamical clusters can be formation sites of intermediate-mass BH seeds.

  15. Independent pseudogenization of CYP2J19 in penguins, owls and kiwis implicates gene in red carotenoid synthesis.

    Science.gov (United States)

    Emerling, Christopher A

    2018-01-01

    Carotenoids have important roles in bird behavior, including pigmentation for sexual signaling and improving color vision via retinal oil droplets. Yellow carotenoids are diet-derived, but red carotenoids (ketocarotenoids) are typically synthesized from yellow precursors via a carotenoid ketolase. Recent research on passerines has provided evidence that a cytochrome p450 enzyme, CYP2J19, is responsible for this reaction, though it is unclear if this function is phylogenetically restricted. Here I provide evidence that CYP2J19 is the carotenoid ketolase common to Aves using the genomes of 65 birds and the retinal transcriptomes of 15 avian taxa. CYP2J19 is functionally intact and robustly transcribed in all taxa except for several species adapted to foraging in dim light conditions. Two penguins, an owl and a kiwi show evidence of genetic lesions and relaxed selection in their genomic copy of CYP2J19, and six owls show evidence of marked reduction in CYP2J19 retinal transcription compared to nine diurnal avian taxa. Furthermore, one of the owls appears to transcribe a CYP2J19 pseudogene. Notably, none of these taxa are known to use red carotenoids for sexual signaling and several species of owls and penguins represent the only birds known to completely lack red retinal oil droplets. The remaining avian taxa belong to groups known to possess red oil droplets, are known or expected to deposit red carotenoids in skin and/or plumage, and/or frequently forage in bright light. The loss and reduced expression of CYP2J19 is likely an adaptation to maximize retinal sensitivity, given that oil droplets reduce the amount of light available to the retina. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Parallel origins of duplications and the formation of pseudogenes in mitochondrial DNA from parthenogenetic lizards (Heteronotia binoei; Gekkonidae).

    Science.gov (United States)

    Zevering, C E; Moritz, C; Heideman, A; Sturm, R A

    1991-11-01

    Analysis of mitochondrial DNAs (mtDNAs) from parthenogenetic lizards of the Heteronotia binoei complex with restriction enzymes revealed an approximately 5-kb addition present in all 77 individuals. Cleavage site mapping suggested the presence of a direct tandem duplication spanning the 16S and 12S rRNA genes, the control region and most, if not all, of the gene for the subunit 1 of NADH dehydrogenase (ND1). The location of the duplication was confirmed by Southern hybridization. A restriction enzyme survey provided evidence for modifications to each copy of the duplicated sequence, including four large deletions. Each gene affected by a deletion was complemented by an intact version in the other copy of the sequence, although for one gene the functional copy was heteroplasmic for another deletion. Sequencing of a fragment from one copy of the duplication which encompassed the tRNA(leu)(UUR) and parts of the 16S rRNA and ND1 genes, revealed mutations expected to disrupt function. Thus, evolution subsequent to the duplication event has resulted in mitochondrial pseudogenes. The presence of duplications in all of these parthenogens, but not among representatives of their maternal sexual ancestors, suggests that the duplications arose in the parthenogenetic form. This provides the second instance in H. binoei of mtDNA duplication associated with the transition from sexual to parthenogenetic reproduction. The increased incidence of duplications in parthenogenetic lizards may be caused by errors in mtDNA replication due to either polyploidy or hybridity of their nuclear genomes.

  17. [Clustered regularly interspaced short palindromic repeats: structure, function and application--a review].

    Science.gov (United States)

    Cui, Yujun; Li, Yanjun; Yan, Yanfeng; Yang, Ruifu

    2008-11-01

    CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats), the basis of spoligotyping technology, can provide prokaryotes with heritable adaptive immunity against phages' invasion. Studies on CRISPR loci and their associated elements, including various CAS (CRISPR-associated) proteins and leader sequences, are still in its infant period. We introduce the brief history', structure, function, bioinformatics research and application of this amazing immunity system in prokaryotic organism for inspiring more scientists to find their interest in this developing topic.

  18. Why do ultrasoft repulsive particles cluster and crystallize? Analytical results from density-functional theory.

    Science.gov (United States)

    Likos, Christos N; Mladek, Bianca M; Gottwald, Dieter; Kahl, Gerhard

    2007-06-14

    We demonstrate the accuracy of the hypernetted chain closure and of the mean-field approximation for the calculation of the fluid-state properties of systems interacting by means of bounded and positive pair potentials with oscillating Fourier transforms. Subsequently, we prove the validity of a bilinear, random-phase density functional for arbitrary inhomogeneous phases of the same systems. On the basis of this functional, we calculate analytically the freezing parameters of the latter. We demonstrate explicitly that the stable crystals feature a lattice constant that is independent of density and whose value is dictated by the position of the negative minimum of the Fourier transform of the pair potential. This property is equivalent with the existence of clusters, whose population scales proportionally to the density. We establish that regardless of the form of the interaction potential and of the location on the freezing line, all cluster crystals have a universal Lindemann ratio Lf=0.189 at freezing. We further make an explicit link between the aforementioned density functional and the harmonic theory of crystals. This allows us to establish an equivalence between the emergence of clusters and the existence of negative Fourier components of the interaction potential. Finally, we make a connection between the class of models at hand and the system of infinite-dimensional hard spheres, when the limits of interaction steepness and space dimension are both taken to infinity in a particularly described fashion.

  19. The stellar and substellar mass function in central region of the old open cluster Praesepe from deep LBT observations

    Directory of Open Access Journals (Sweden)

    Goldman B.

    2011-07-01

    Full Text Available Studies of the mass function of open clusters of different ages allow us to study the efficiency with which brown dwarfs are evaporated from clusters to populate the field. Surveys in relatively old clusters (age ≳100 Myr do not suffer from problems found in young clusters, such as intra-cluster extinction and large uncertainties in brown dwarf models. In this paper, we present the results of a photometric survey to study the mass function of the old open cluster Praesepe (age of ~590 Myr and distance of ~190 pc, down to the substellar regime. We have performed optical (riz and Y-band photometric survey of Praesepe with the Large Binocular Telescope Camera, for a spatial coverage of 0.61 deg2 from ~90 MJ down to a 5σ detection limit at 40 MJ.

  20. Guided basin-hopping search of small boron clusters with density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Ng, Wei Chun; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melacca Campus, 75450 Melaka (Malaysia)

    2015-04-24

    The search for the ground state structures of Boron clusters has been a difficult computational task due to the unique metalloid nature of Boron atom. Previous research works had overcome the problem in the search of the Boron ground-state structures by adding symmetry constraints prior to the process of locating the local minima in the potential energy surface (PES) of the Boron clusters. In this work, we shown that, with the deployment of a novel computational approach that incorporates density functional theory (DFT) into a guided global optimization search algorithm based on basin-hopping, it is possible to directly locate the local minima of small Boron clusters in the PES at the DFT level. The ground-state structures search algorithm as proposed in this work is initiated randomly and needs not a priori symmetry constraint artificially imposed throughout the search process. Small sized Boron clusters so obtained compare well to the results obtained by similar calculations in the literature. The electronic properties of each structures obtained are calculated within the DFT framework.

  1. Direct atomic imaging and density functional theory study of the Au24Pd1 cluster catalyst.

    Science.gov (United States)

    Bruma, A; Negreiros, F R; Xie, S; Tsukuda, T; Johnston, R L; Fortunelli, A; Li, Z Y

    2013-10-21

    In this study we report a direct, atomic-resolution imaging of calcined Au24Pd1 clusters supported on multiwall carbon nanotubes by employing aberration-corrected scanning transmission electron microscopy. Using gold atoms as mass standards, we confirm the cluster size to be 25 ± 2, in agreement with the Au24Pd1(SR)18 precursor used in the synthesis. Concurrently, a Density-Functional/Basin-Hopping computational algorithm is employed to locate the low-energy configurations of free Au24Pd1 cluster. Cage structures surrounding a single core atom are found to be favored, with a slight preference for Pd to occupy the core site. The cluster shows a tendency toward elongated arrangements, consistent with experimental data. The degree of electron transfer from the Pd dopant to Au is quantified through a Löwdin charge analysis, suggesting that Pd may act as an electron promoter to the surrounding Au atoms when they are involved in catalytic reactions.

  2. Guided basin-hopping search of small boron clusters with density functional theory

    International Nuclear Information System (INIS)

    Ng, Wei Chun; Yoon, Tiem Leong; Lim, Thong Leng

    2015-01-01

    The search for the ground state structures of Boron clusters has been a difficult computational task due to the unique metalloid nature of Boron atom. Previous research works had overcome the problem in the search of the Boron ground-state structures by adding symmetry constraints prior to the process of locating the local minima in the potential energy surface (PES) of the Boron clusters. In this work, we shown that, with the deployment of a novel computational approach that incorporates density functional theory (DFT) into a guided global optimization search algorithm based on basin-hopping, it is possible to directly locate the local minima of small Boron clusters in the PES at the DFT level. The ground-state structures search algorithm as proposed in this work is initiated randomly and needs not a priori symmetry constraint artificially imposed throughout the search process. Small sized Boron clusters so obtained compare well to the results obtained by similar calculations in the literature. The electronic properties of each structures obtained are calculated within the DFT framework

  3. Accurate density-functional calculations on large systems: Fullerenes and magnetic clusters

    International Nuclear Information System (INIS)

    Dunlap, B.I.

    1996-01-01

    Efforts to accurately compute all-electron density-functional energies for large molecules and clusters using Gaussian basis sets will be reviewed. The foundation of this effort, variational fitting, will be described and followed by three applications of the method. The first application concerns fullerenes. When first discovered, C 60 is quite unstable relative to the higher fullerenes. In addition, to raising questions about the relative abundance of the various fullerenes, this work conflicted with the then state-of-the art density-funcitonal calculations on crystalline graphite. Now high accuracy molecular and band structure calculations are in fairly good agreement. Second, we have used these methods to design transition metal clusters having the highest magnetic moment by maximizing the symmetry-required degeneracy of the one-electron orbitals. Most recently, we have developed accurate, variational generalized-gradient approximation (GGA) forces for use in geometry optimization of clusters and in molecular-dynamics simulations of friction. The GGA optimized geometries of a number of large clusters will be given

  4. The Impact of Multipollutant Clusters on the Association Between Fine Particulate Air Pollution and Microvascular Function.

    Science.gov (United States)

    Ljungman, Petter L; Wilker, Elissa H; Rice, Mary B; Austin, Elena; Schwartz, Joel; Gold, Diane R; Koutrakis, Petros; Benjamin, Emelia J; Vita, Joseph A; Mitchell, Gary F; Vasan, Ramachandran S; Hamburg, Naomi M; Mittleman, Murray A

    2016-03-01

    Prior studies including the Framingham Heart Study have suggested associations between single components of air pollution and vascular function; however, underlying mixtures of air pollution may have distinct associations with vascular function. We used a k-means approach to construct five distinct pollution mixtures from elemental analyses of particle filters, air pollution monitoring data, and meteorology. Exposure was modeled as an interaction between fine particle mass (PM2.5), and concurrent pollution cluster. Outcome variables were two measures of microvascular function in the fingertip in the Framingham Offspring and Third Generation cohorts from 2003 to 2008. In 1,720 participants, associations between PM2.5 and baseline pulse amplitude tonometry differed by air pollution cluster (interaction P value 0.009). Higher PM2.5 on days with low mass concentrations but high proportion of ultrafine particles from traffic was associated with 18% (95% confidence interval: 4.6%, 33%) higher baseline pulse amplitude per 5 μg/m and days with high contributions of oil and wood combustion with 16% (95% confidence interval: 0.2%, 34%) higher baseline pulse amplitude. We observed no variation in associations of PM2.5 with hyperemic response to ischemia observed across air pollution clusters. PM2.5 exposure from air pollution mixtures with large contributions of local ultrafine particles from traffic, heating oil, and wood combustion was associated with higher baseline pulse amplitude but not hyperemic response. Our findings suggest little association between acute exposure to air pollution clusters reflective of select sources and hyperemic response to ischemia, but possible associations with excessive small artery pulsatility with potentially deleterious microvascular consequences.

  5. Deep UV Luminosity Functions at the Infall Region of the Coma Cluster

    Science.gov (United States)

    Hammer, D. M.; Hornschemeier, A. E.; Salim, S.; Smith, R.; Jenkins, L.; Mobasher, B.; Miller, N.; Ferguson, H.

    2011-01-01

    We have used deep GALEX observations at the infall region of the Coma cluster to measure the faintest UV luminosity functions (LFs) presented for a rich galaxy cluster thus far. The Coma UV LFs are measured to M(sub uv) = -10.5 in the GALEX FUV and NUV bands, or 3.5 mag fainter than previous studies, and reach the dwarf early-type galaxy population in Coma for the first time. The Schechter faint-end slopes (alpha approximately equal to -1.39 in both GALEX bands) are shallower than reported in previous Coma UV LF studies owing to a flatter LF at faint magnitudes. A Gaussian-plus-Schechter model provides a slightly better parametrization of the UV LFs resulting in a faint-end slope of alpha approximately equal to -1.15 in both GALEX bands. The two-component model gives faint-end slopes shallower than alpha = -1 (a turnover) for the LFs constructed separately for passive and star forming galaxies. The UV LFs for star forming galaxies show a turnover at M(sub UV) approximately equal to -14 owing to a deficit of dwarf star forming galaxies in Coma with stellar masses below M(sub *) = 10(sup 8) solar mass. A similar turnover is identified in recent UV LFs measured for the Virgo cluster suggesting this may be a common feature of local galaxy clusters, whereas the field UV LFs continue to rise at faint magnitudes. We did not identify an excess of passive galaxies as would be expected if the missing dwarf star forming galaxies were quenched inside the cluster. In fact, the LFs for both dwarf passive and star forming galaxies show the same turnover at faint magnitudes. We discuss the possible origin of the missing dwarf star forming galaxies in Coma and their expected properties based on comparisons to local field galaxies.

  6. DEEP ULTRAVIOLET LUMINOSITY FUNCTIONS AT THE INFALL REGION OF THE COMA CLUSTER

    International Nuclear Information System (INIS)

    Hammer, D. M.; Hornschemeier, A. E.; Jenkins, L.; Salim, S.; Smith, R.; Mobasher, B.; Miller, N.; Ferguson, H.

    2012-01-01

    We have used deep GALEX observations at the infall region of the Coma cluster to measure the faintest ultraviolet (UV) luminosity functions (LFs) presented for a rich galaxy cluster thus far. The Coma UV LFs are measured to M UV = –10.5 in the GALEX FUV and NUV bands, or 3.5 mag fainter than previous studies, and reach the dwarf early-type galaxy population in Coma for the first time. The Schechter faint-end slopes (α ≈ –1.39 in both GALEX bands) are shallower than reported in previous Coma UV LF studies owing to a flatter LF at faint magnitudes. A Gaussian-plus-Schechter model provides a slightly better parameterization of the UV LFs resulting in a faint-end slope of α ≈ –1.15 in both GALEX bands. The two-component model gives faint-end slopes shallower than α = –1 (a turnover) for the LFs constructed separately for passive and star-forming galaxies. The UV LFs for star-forming galaxies show a turnover at M UV ≈ –14 owing to a deficit of dwarf star-forming galaxies in Coma with stellar masses below M * = 10 8 M ☉ . A similar turnover is identified in recent UV LFs measured for the Virgo cluster suggesting this may be a common feature of local galaxy clusters, whereas the field UV LFs continue to rise at faint magnitudes. We did not identify an excess of passive galaxies as would be expected if the missing dwarf star-forming galaxies were quenched inside the cluster. In fact, the LFs for both dwarf passive and star-forming galaxies show the same turnover at faint magnitudes. We discuss the possible origin of the missing dwarf star-forming galaxies in Coma and their expected properties based on comparisons to local field galaxies.

  7. UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.

    Science.gov (United States)

    Lua, Rhonald C; Wilson, Stephen J; Konecki, Daniel M; Wilkins, Angela D; Venner, Eric; Morgan, Daniel H; Lichtarge, Olivier

    2016-01-04

    The structure and function of proteins underlie most aspects of biology and their mutational perturbations often cause disease. To identify the molecular determinants of function as well as targets for drugs, it is central to characterize the important residues and how they cluster to form functional sites. The Evolutionary Trace (ET) achieves this by ranking the functional and structural importance of the protein sequence positions. ET uses evolutionary distances to estimate functional distances and correlates genotype variations with those in the fitness phenotype. Thus, ET ranks are worse for sequence positions that vary among evolutionarily closer homologs but better for positions that vary mostly among distant homologs. This approach identifies functional determinants, predicts function, guides the mutational redesign of functional and allosteric specificity, and interprets the action of coding sequence variations in proteins, people and populations. Now, the UET database offers pre-computed ET analyses for the protein structure databank, and on-the-fly analysis of any protein sequence. A web interface retrieves ET rankings of sequence positions and maps results to a structure to identify functionally important regions. This UET database integrates several ways of viewing the results on the protein sequence or structure and can be found at http://mammoth.bcm.tmc.edu/uet/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

    Directory of Open Access Journals (Sweden)

    Vassilev Boris

    2010-04-01

    Full Text Available Abstract Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94% appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1 a dimer interface motif found in voltage-gated chloride channels, (2 a proton transfer motif found in heme-copper oxidases, and (3 a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

  9. Determination of the structures of small gold clusters on stepped magnesia by density functional calculations.

    Science.gov (United States)

    Damianos, Konstantina; Ferrando, Riccardo

    2012-02-21

    The structural modifications of small supported gold clusters caused by realistic surface defects (steps) in the MgO(001) support are investigated by computational methods. The most stable gold cluster structures on a stepped MgO(001) surface are searched for in the size range up to 24 Au atoms, and locally optimized by density-functional calculations. Several structural motifs are found within energy differences of 1 eV: inclined leaflets, arched leaflets, pyramidal hollow cages and compact structures. We show that the interaction with the step clearly modifies the structures with respect to adsorption on the flat defect-free surface. We find that leaflet structures clearly dominate for smaller sizes. These leaflets are either inclined and quasi-horizontal, or arched, at variance with the case of the flat surface in which vertical leaflets prevail. With increasing cluster size pyramidal hollow cages begin to compete against leaflet structures. Cage structures become more and more favourable as size increases. The only exception is size 20, at which the tetrahedron is found as the most stable isomer. This tetrahedron is however quite distorted. The comparison of two different exchange-correlation functionals (Perdew-Burke-Ernzerhof and local density approximation) show the same qualitative trends. This journal is © The Royal Society of Chemistry 2012

  10. Which Density Functional Should Be Used to Describe Protonated Water Clusters?

    Science.gov (United States)

    Shi, Ruili; Huang, Xiaoming; Su, Yan; Lu, Hai-Gang; Li, Si-Dian; Tang, Lingli; Zhao, Jijun

    2017-04-27

    Protonated water cluster is one of the most important hydrogen-bond network systems. Finding an appropriate DFT method to study the properties of protonated water clusters can substantially improve the economy in computational resources without sacrificing the accuracy compared to high-level methods. Using high-level MP2 and CCSD(T) methods as well as experimental results as benchmark, we systematically examined the effect of seven exchange-correlation GGA functionals (with BLYP, B3LYP, X3LYP, PBE0, PBE1W, M05-2X, and B97-D parametrizations) in describing the geometric parameters, interaction energies, dipole moments, and vibrational properties of protonated water clusters H + (H 2 O) 2-9,12 . The overall performance of all these functionals is acceptable, and each of them has its advantage in certain aspects. X3LYP is the best to describe the interaction energies, and PBE0 and M05-2X are also recommended to investigate interaction energies. PBE0 gives the best anharmonic frequencies, followed by PBE1W, B97-D and BLYP methods. PBE1W, B3LYP, B97-D, and X3LYP can yield better geometries. The capability of B97-D to distinguish the relative energies between isomers is the best among all the seven methods, followed by M05-2X and PBE0.

  11. The effectiveness of Cluster Organization Functions from a Member Company Perspective: The Case of Food Valley Organization

    NARCIS (Netherlands)

    Omta, S.W.F.; Fortuin, F.T.J.M.

    2011-01-01

    This paper aims to analyze the effectiveness of the different cluster organization functions (services, activities and information sources) of Food Valley Organization in the Dutch agifood innovation system, as evaluated by its member companies. It is concluded that, in accordance with cluster

  12. Intron-exon organization of the active human protein S gene PS. alpha. and its pseudogene PS. beta. : Duplication and silencing during primate evolution

    Energy Technology Data Exchange (ETDEWEB)

    Ploos van Amstel, H.; Reitsma, P.H.; van der Logt, C.P.; Bertina, R.M. (University Hospital, Leiden (Netherlands))

    1990-08-28

    The human protein S locus on chromosome 3 consists of two protein S genes, PS{alpha} and PS{beta}. Here the authors report the cloning and characterization of both genes. Fifteen exons of the PS{alpha} gene were identified that together code for protein S mRNA as derived from the reported protein S cDNAs. Analysis by primer extension of liver protein S mRNA, however, reveals the presence of two mRNA forms that differ in the length of their 5{prime}-noncoding region. Both transcripts contain a 5{prime}-noncoding region longer than found in the protein S cDNAs. The two products may arise from alternative splicing of an additional intron in this region or from the usage of two start sites for transcription. The intron-exon organization of the PS{alpha} gene fully supports the hypothesis that the protein S gene is the product of an evolutional assembling process in which gene modules coding for structural/functional protein units also found in other coagulation proteins have been put upstream of the ancestral gene of a steroid hormone binding protein. The PS{beta} gene is identified as a pseudogene. It contains a large variety of detrimental aberrations, viz., the absence of exon I, a splice site mutation, three stop codons, and a frame shift mutation. Overall the two genes PS{alpha} and PS{beta} show between their exonic sequences 96.5% homology. Southern analysis of primate DNA showed that the duplication of the ancestral protein S gene has occurred after the branching of the orangutan from the African apes. A nonsense mutation that is present in the pseudogene of man also could be identified in one of the two protein S genes of both chimpanzee and gorilla. This implicates that silencing of one of the two protein S genes must have taken place before the divergence of the three African apes.

  13. Function analysis of 5'-UTR of the cellulosomal xyl-doc cluster in Clostridium papyrosolvens.

    Science.gov (United States)

    Zou, Xia; Ren, Zhenxing; Wang, Na; Cheng, Yin; Jiang, Yuanyuan; Wang, Yan; Xu, Chenggang

    2018-01-01

    Anaerobic, mesophilic, and cellulolytic Clostridium papyrosolvens produces an efficient cellulolytic extracellular complex named cellulosome that hydrolyzes plant cell wall polysaccharides into simple sugars. Its genome harbors two long cellulosomal clusters: cip - cel operon encoding major cellulosome components (including scaffolding) and xyl - doc gene cluster encoding hemicellulases. Compared with works on cip - cel operon, there are much fewer studies on xyl - doc mainly due to its rare location in cellulolytic clostridia. Sequence analysis of xyl - doc revealed that it harbors a 5' untranslated region (5'-UTR) which potentially plays a role in the regulation of downstream gene expression. Here, we analyzed the function of 5'-UTR of xyl - doc cluster in C. papyrosolvens in vivo via transformation technology developed in this study. In this study, we firstly developed an electrotransformation method for C. papyrosolvens DSM 2782 before the analysis of 5'-UTR of xyl - doc cluster. In the optimized condition, a field with an intensity of 7.5-9.0 kV/cm was applied to a cuvette (0.2 cm gap) containing a mixture of plasmid and late cell suspended in exponential phase to form a 5 ms pulse in a sucrose-containing buffer. Afterwards, the putative promoter and the 5'-UTR of xyl - doc cluster were determined by sequence alignment. It is indicated that xyl - doc possesses a long conservative 5'-UTR with a complex secondary structure encompassing at least two perfect stem-loops which are potential candidates for controlling the transcriptional termination. In the last step, we employed an oxygen-independent flavin-based fluorescent protein (FbFP) as a quantitative reporter to analyze promoter activity and 5'-UTR function in vivo. It revealed that 5'-UTR significantly blocked transcription of downstream genes, but corn stover can relieve its suppression. In the present study, our results demonstrated that 5'-UTR of the cellulosomal xyl - doc cluster blocks the

  14. Multiple cluster axis II comorbidity and functional outcome in severe patients with borderline personality disorder.

    Science.gov (United States)

    Palomares, Nerea; McMaster, Antonia; Díaz-Marsá, Marina; de la Vega, Irene; Montes, Ana; Carrasco, José Luis

    2016-11-01

    Current literature suggests that personality disorder comorbidity negatively contributes to both the severity and prognosis of other disorders; however, little literature has been devoted to its influence on borderline personality disorder (BPD). The objective of the present work is to study comorbidity with other personality disorders in a severe clinical sample of patients with BPD, and its relationship with global functionality. A sample of 65 patients with severe borderline personality disorder was included in the study. Clinical and functionality measures were applied in order to study comorbidity of BPD with other disorders and its relationship with functionality. Associations with other comorbid PDs were analyzed with t-tests and linear correlations. Most patients (87%) presented comorbidity with other PDs. Almost half of the sample (42%) presented more than two PDs, and cluster A (paranoid) and C (obsessive and avoidant) PD were more frequent than cluster B (histrionic and antisocial). Only the presence of avoidant PD predicted a worse functional outcome in the long term (U Mann Withney ppersonality disorder might negatively predict for prognosis.

  15. Identification of Flood Reactivity Regions via the Functional Clustering of Hydrographs

    Science.gov (United States)

    Brunner, Manuela I.; Viviroli, Daniel; Furrer, Reinhard; Seibert, Jan; Favre, Anne-Catherine

    2018-03-01

    Flood hydrograph shapes contain valuable information on the flood-generation mechanisms of a catchment. To make good use of this information, we express flood hydrograph shapes as continuous functions using a functional data approach. We propose a clustering approach based on functional data for flood hydrograph shapes to identify a set of representative hydrograph shapes on a catchment scale and use these catchment-specific sets of representative hydrographs to establish regions of catchments with similar flood reactivity on a regional scale. We applied this approach to flood samples of 163 medium-size Swiss catchments. The results indicate that three representative hydrograph shapes sufficiently describe the hydrograph shape variability within a catchment and therefore can be used as a proxy for the flood behavior of a catchment. These catchment-specific sets of three hydrographs were used to group the catchments into three reactivity regions of similar flood behavior. These regions were not only characterized by similar hydrograph shapes and reactivity but also by event magnitudes and triggering event conditions. We envision these regions to be useful in regionalization studies, regional flood frequency analyses, and to allow for the construction of synthetic design hydrographs in ungauged catchments. The clustering approach based on functional data which establish these regions is very flexible and has the potential to be extended to other geographical regions or toward the use in climate impact studies.

  16. Analysis of the Structures and Properties of (GaSb)n (n = 4-9) Clusters through Density Functional Theory.

    Science.gov (United States)

    Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De; Wan, Jian Guo

    2016-07-07

    An optimization strategy combining global semiempirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (GaSb)n clusters up to n = 9. The growth pattern of the clusters differed from those of previously reported group III-V binary clusters. A cagelike configuration was found for cluster sizes n ≤ 7. The structure of (GaSb)6 deviated from that of other III-V clusters. Competition existed between core-shell and hollow cage structures of (GaSb)7. Novel noncagelike structures were energetically preferred over the cages for the (GaSb)8 and (GaSb)9 clusters. Electronic properties, such as vertical ionization potential, adiabatic electron affinities, HOMO-LUMO gaps, and average on-site charges on Ga or Sb atoms, as well as binding energies, were computed.

  17. DATA CLASSIFICATION WITH NEURAL CLASSIFIER USING RADIAL BASIS FUNCTION WITH DATA REDUCTION USING HIERARCHICAL CLUSTERING

    Directory of Open Access Journals (Sweden)

    M. Safish Mary

    2012-04-01

    Full Text Available Classification of large amount of data is a time consuming process but crucial for analysis and decision making. Radial Basis Function networks are widely used for classification and regression analysis. In this paper, we have studied the performance of RBF neural networks to classify the sales of cars based on the demand, using kernel density estimation algorithm which produces classification accuracy comparable to data classification accuracy provided by support vector machines. In this paper, we have proposed a new instance based data selection method where redundant instances are removed with help of a threshold thus improving the time complexity with improved classification accuracy. The instance based selection of the data set will help reduce the number of clusters formed thereby reduces the number of centers considered for building the RBF network. Further the efficiency of the training is improved by applying a hierarchical clustering technique to reduce the number of clusters formed at every step. The paper explains the algorithm used for classification and for conditioning the data. It also explains the complexities involved in classification of sales data for analysis and decision-making.

  18. Symmetrized partial-wave method for density-functional cluster calculations

    International Nuclear Information System (INIS)

    Averill, F.W.; Painter, G.S.

    1994-01-01

    The computational advantage and accuracy of the Harris method is linked to the simplicity and adequacy of the reference-density model. In an earlier paper, we investigated one way the Harris functional could be extended to systems outside the limits of weakly interacting atoms by making the charge density of the interacting atoms self-consistent within the constraints of overlapping spherical atomic densities. In the present study, a method is presented for augmenting the interacting atom charge densities with symmetrized partial-wave expansions on each atomic site. The added variational freedom of the partial waves leads to a scheme capable of giving exact results within a given exchange-correlation approximation while maintaining many of the desirable convergence and stability properties of the original Harris method. Incorporation of the symmetry of the cluster in the partial-wave construction further reduces the level of computational effort. This partial-wave cluster method is illustrated by its application to the dimer C 2 , the hypothetical atomic cluster Fe 6 Al 8 , and the benzene molecule

  19. Automatic detection of arterial input function in dynamic contrast enhanced MRI based on affinity propagation clustering.

    Science.gov (United States)

    Shi, Lin; Wang, Defeng; Liu, Wen; Fang, Kui; Wang, Yi-Xiang J; Huang, Wenhua; King, Ann D; Heng, Pheng Ann; Ahuja, Anil T

    2014-05-01

    To automatically and robustly detect the arterial input function (AIF) with high detection accuracy and low computational cost in dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). In this study, we developed an automatic AIF detection method using an accelerated version (Fast-AP) of affinity propagation (AP) clustering. The validity of this Fast-AP-based method was proved on two DCE-MRI datasets, i.e., rat kidney and human head and neck. The detailed AIF detection performance of this proposed method was assessed in comparison with other clustering-based methods, namely original AP and K-means, as well as the manual AIF detection method. Both the automatic AP- and Fast-AP-based methods achieved satisfactory AIF detection accuracy, but the computational cost of Fast-AP could be reduced by 64.37-92.10% on rat dataset and 73.18-90.18% on human dataset compared with the cost of AP. The K-means yielded the lowest computational cost, but resulted in the lowest AIF detection accuracy. The experimental results demonstrated that both the AP- and Fast-AP-based methods were insensitive to the initialization of cluster centers, and had superior robustness compared with K-means method. The Fast-AP-based method enables automatic AIF detection with high accuracy and efficiency. Copyright © 2013 Wiley Periodicals, Inc.

  20. Transcriptional interference networks coordinate the expression of functionally related genes clustered in the same genomic loci.

    Science.gov (United States)

    Boldogköi, Zsolt

    2012-01-01

    The regulation of gene expression is essential for normal functioning of biological systems in every form of life. Gene expression is primarily controlled at the level of transcription, especially at the phase of initiation. Non-coding RNAs are one of the major players at every level of genetic regulation, including the control of chromatin organization, transcription, various post-transcriptional processes, and translation. In this study, the Transcriptional Interference Network (TIN) hypothesis was put forward in an attempt to explain the global expression of antisense RNAs and the overall occurrence of tandem gene clusters in the genomes of various biological systems ranging from viruses to mammalian cells. The TIN hypothesis suggests the existence of a novel layer of genetic regulation, based on the interactions between the transcriptional machineries of neighboring genes at their overlapping regions, which are assumed to play a fundamental role in coordinating gene expression within a cluster of functionally linked genes. It is claimed that the transcriptional overlaps between adjacent genes are much more widespread in genomes than is thought today. The Waterfall model of the TIN hypothesis postulates a unidirectional effect of upstream genes on the transcription of downstream genes within a cluster of tandemly arrayed genes, while the Seesaw model proposes a mutual interdependence of gene expression between the oppositely oriented genes. The TIN represents an auto-regulatory system with an exquisitely timed and highly synchronized cascade of gene expression in functionally linked genes located in close physical proximity to each other. In this study, we focused on herpesviruses. The reason for this lies in the compressed nature of viral genes, which allows a tight regulation and an easier investigation of the transcriptional interactions between genes. However, I believe that the same or similar principles can be applied to cellular organisms too.

  1. Gender differences in associations between DSM-5 posttraumatic stress disorder symptom clusters and functional impairment in war veterans.

    Science.gov (United States)

    Meyer, Eric C; Konecky, Brian; Kimbrel, Nathan A; DeBeer, Bryann B; Marx, Brian P; Schumm, Jeremiah; Penk, Walter E; Gulliver, Suzy Bird; Morissette, Sandra B

    2018-05-01

    Understanding the links between posttraumatic stress disorder (PTSD) symptoms and functional impairment is essential for assisting veterans in transitioning to civilian life. Moreover, there may be differences between men and women in the relationships between PTSD symptoms and functional impairment. However, no prior studies have examined the links between functional impairment and the revised symptom clusters as defined in the Diagnostic and Statistical Manual of Mental Disorders, 5th ed. (DSM-5; American Psychiatric Association, 2013) or whether the associations between PTSD symptom clusters and functional impairment differ by gender. We examined the associations between the DSM-5 PTSD symptom clusters and functional impairment in 252 trauma-exposed Iraq and Afghanistan war veterans (79 females). Regression analyses included demographic factors and exposure to both combat and military sexual trauma as covariates. In the total sample, both the intrusions cluster (β = .18, p = .045) and the negative alterations in cognition and mood cluster (β = .45, p < .001) were associated with global functional impairment. Among male veterans, global functional impairment was associated only with negative alterations in cognition and mood (β = .52, p < .001). However, by contrast, among female veterans, only marked alterations in arousal and reactivity were associated with global functional impairment (β = .35, p = .027). These findings suggest that there may be important gender differences with respect to the relationship between PTSD symptoms and functional impairment. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  2. A comparison of density functional theory and coupled cluster methods for the calculation of electric dipole polarizability gradients of methane

    DEFF Research Database (Denmark)

    Paidarová, Ivana; Sauer, Stephan P. A.

    2012-01-01

    We have compared the performance of density functional theory (DFT) using five different exchange-correlation functionals with four coupled cluster theory based wave function methods in the calculation of geometrical derivatives of the polarizability tensor of methane. The polarizability gradient...

  3. One- and two-particle correlation functions in the dynamical quantum cluster approach

    International Nuclear Information System (INIS)

    Hochkeppel, Stephan

    2008-01-01

    This thesis is dedicated to a theoretical study of the 1-band Hubbard model in the strong coupling limit. The investigation is based on the Dynamical Cluster Approximation (DCA) which systematically restores non-local corrections to the Dynamical Mean Field approximation (DMFA). The DCA is formulated in momentum space and is characterised by a patching of the Brillouin zone where momentum conservation is only recovered between two patches. The approximation works well if k-space correlation functions show a weak momentum dependence. In order to study the temperature and doping dependence of the spin- and charge excitation spectra, we explicitly extend the Dynamical Cluster Approximation to two-particle response functions. The full irreducible two-particle vertex with three momenta and frequencies is approximated by an effective vertex dependent on the momentum and frequency of the spin and/or charge excitations. The effective vertex is calculated by using the Quantum Monte Carlo method on the finite cluster whereas the analytical continuation of dynamical quantities is performed by a stochastic version of the maximum entropy method. A comparison with high temperature auxiliary field quantum Monte Carlo data serves as a benchmark for our approach to two-particle correlation functions. Our method can reproduce basic characteristics of the spin- and charge excitation spectrum. Near and beyond optimal doping, our results provide a consistent overall picture of the interplay between charge, spin and single-particle excitations: a collective spin mode emerges at optimal doping and sufficiently low temperatures in the spin response spectrum and exhibits the energy scale of the magnetic exchange interaction J. Simultaneously, the low energy single-particle excitations are characterised by a coherent quasiparticle with bandwidth J. The origin of the quasiparticle can be quite well understood in a picture of a more or less antiferromagnetic ordered background in which holes

  4. Spectroscopic and functional characterization of iron-sulfur cluster-bound forms of Azotobacter vinelandii (Nif)IscA.

    Science.gov (United States)

    Mapolelo, Daphne T; Zhang, Bo; Naik, Sunil G; Huynh, Boi Hanh; Johnson, Michael K

    2012-10-16

    The mechanism of [4Fe-4S] cluster assembly on A-type Fe-S cluster assembly proteins, in general, and the specific role of (Nif)IscA in the maturation of nitrogen fixation proteins are currently unknown. To address these questions, in vitro spectroscopic studies (UV-visible absorption/CD, resonance Raman and Mössbauer) have been used to investigate the mechanism of [4Fe-4S] cluster assembly on Azotobacter vinelandii(Nif)IscA, and the ability of (Nif)IscA to accept clusters from NifU and to donate clusters to the apo form of the nitrogenase Fe-protein. The results show that (Nif)IscA can rapidly and reversibly cycle between forms containing one [2Fe-2S](2+) and one [4Fe-4S](2+) cluster per homodimer via DTT-induced two-electron reductive coupling of two [2Fe-2S](2+) clusters and O(2)-induced [4Fe-4S](2+) oxidative cleavage. This unique type of cluster interconversion in response to cellular redox status and oxygen levels is likely to be important for the specific role of A-type proteins in the maturation of [4Fe-4S] cluster-containing proteins under aerobic growth or oxidative stress conditions. Only the [4Fe-4S](2+)-(Nif)IscA was competent for rapid activation of apo-nitrogenase Fe protein under anaerobic conditions. Apo-(Nif)IscA was shown to accept clusters from [4Fe-4S] cluster-bound NifU via rapid intact cluster transfer, indicating a potential role as a cluster carrier for delivery of clusters assembled on NifU. Overall the results support the proposal that A-type proteins can function as carrier proteins for clusters assembled on U-type proteins and suggest that they are likely to supply [2Fe-2S] clusters rather than [4Fe-4S] for the maturation of [4Fe-4S] cluster-containing proteins under aerobic or oxidative stress growth conditions.

  5. Defining functioning levels in patients with schizophrenia: A combination of a novel clustering method and brain SPECT analysis.

    Science.gov (United States)

    Catherine, Faget-Agius; Aurélie, Vincenti; Eric, Guedj; Pierre, Michel; Raphaëlle, Richieri; Marine, Alessandrini; Pascal, Auquier; Christophe, Lançon; Laurent, Boyer

    2017-12-30

    This study aims to define functioning levels of patients with schizophrenia by using a method of interpretable clustering based on a specific functioning scale, the Functional Remission Of General Schizophrenia (FROGS) scale, and to test their validity regarding clinical and neuroimaging characterization. In this observational study, patients with schizophrenia have been classified using a hierarchical top-down method called clustering using unsupervised binary trees (CUBT). Socio-demographic, clinical, and neuroimaging SPECT perfusion data were compared between the different clusters to ensure their clinical relevance. A total of 242 patients were analyzed. A four-group functioning level structure has been identified: 54 are classified as "minimal", 81 as "low", 64 as "moderate", and 43 as "high". The clustering shows satisfactory statistical properties, including reproducibility and discriminancy. The 4 clusters consistently differentiate patients. "High" functioning level patients reported significantly the lowest scores on the PANSS and the CDSS, and the highest scores on the GAF, the MARS and S-QoL 18. Functioning levels were significantly associated with cerebral perfusion of two relevant areas: the left inferior parietal cortex and the anterior cingulate. Our study provides relevant functioning levels in schizophrenia, and may enhance the use of functioning scale. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Coupled-cluster representation of Green function employing modified spectral resolutions of similarity transformed Hamiltonians

    Energy Technology Data Exchange (ETDEWEB)

    Kowalski, K., E-mail: karol.kowalski@pnnl.gov; Bhaskaran-Nair, K.; Shelton, W. A. [William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352 (United States)

    2014-09-07

    In this paper we discuss a new formalism for producing an analytic coupled-cluster (CC) Green's function for an N-electron system by shifting the poles of similarity transformed Hamiltonians represented in N − 1 and N + 1 electron Hilbert spaces. Simple criteria are derived for the states in N − 1 and N + 1 electron spaces that are then corrected in the spectral resolution of the corresponding matrix representations of the similarity transformed Hamiltonian. The accurate description of excited state processes within a Green's function formalism would be of significant importance to a number of scientific communities ranging from physics and chemistry to engineering and the biological sciences. This is because the Green's function methodology provides a direct path for not only calculating properties whose underlying origins come from coupled many-body interactions but also provides a straightforward path for calculating electron transport, response, and correlation functions that allows for a direct link with experiment. As a special case of this general formulation, we discuss the application of this technique for Green's function defined by the CC with singles and doubles representation of the ground-state wave function.

  7. Coupled-cluster representation of Green function employing modified spectral resolutions of similarity transformed Hamiltonians

    Energy Technology Data Exchange (ETDEWEB)

    Kowalski, K. [William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA; Bhaskaran-Nair, K. [William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA; Shelton, W. A. [William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA

    2014-09-07

    In this paper we discuss a new formalism for producing an analytic coupled-cluster (CC) Green's function for an N-electron system by shifting the poles of similarity transformed Hamiltonians represented in N - 1 and N + 1 electron Hilbert spaces. Simple criteria are derived for the states in N - 1 and N + 1 electron spaces that are then corrected in the spectral resolution of the corresponding matrix representations of the similarity transformed Hamiltonian. The accurate description of excited state processes within a Green's function formalism would be of significant importance to a number of scientific communities ranging from physics and chemistry to engineering and the biological sciences. This is because the Green's function methodology provides a direct path for not only calculating properties whose underlying origins come from coupled many-body interactions but also provides a straightforward path for calculating electron transport, response, and correlation functions that allows for a direct link with experiment. Finally, as a special case of this general formulation, we discuss the application of this technique for Green's function defined by the CC with singles and doubles representation of the ground-state wave function.

  8. Coupled-cluster representation of Green function employing modified spectral resolutions of similarity transformed Hamiltonians

    International Nuclear Information System (INIS)

    Kowalski, K.; Bhaskaran-Nair, K.; Shelton, W. A.

    2014-01-01

    In this paper we discuss a new formalism for producing an analytic coupled-cluster (CC) Green's function for an N-electron system by shifting the poles of similarity transformed Hamiltonians represented in N − 1 and N + 1 electron Hilbert spaces. Simple criteria are derived for the states in N − 1 and N + 1 electron spaces that are then corrected in the spectral resolution of the corresponding matrix representations of the similarity transformed Hamiltonian. The accurate description of excited state processes within a Green's function formalism would be of significant importance to a number of scientific communities ranging from physics and chemistry to engineering and the biological sciences. This is because the Green's function methodology provides a direct path for not only calculating properties whose underlying origins come from coupled many-body interactions but also provides a straightforward path for calculating electron transport, response, and correlation functions that allows for a direct link with experiment. As a special case of this general formulation, we discuss the application of this technique for Green's function defined by the CC with singles and doubles representation of the ground-state wave function

  9. Dietary Patterns Derived by Cluster Analysis are Associated with Cognitive Function among Korean Older Adults.

    Science.gov (United States)

    Kim, Jihye; Yu, Areum; Choi, Bo Youl; Nam, Jung Hyun; Kim, Mi Kyung; Oh, Dong Hoon; Yang, Yoon Jung

    2015-05-29

    The objective of this study was to investigate major dietary patterns among older Korean adults through cluster analysis and to determine an association between dietary patterns and cognitive function. This is a cross-sectional study. The data from the Korean Multi-Rural Communities Cohort Study was used. Participants included 765 participants aged 60 years and over. A quantitative food frequency questionnaire with 106 items was used to investigate dietary intake. The Korean version of the MMSE-KC (Mini-Mental Status Examination-Korean version) was used to assess cognitive function. Two major dietary patterns were identified using K-means cluster analysis. The "MFDF" dietary pattern indicated high consumption of Multigrain rice, Fish, Dairy products, Fruits and fruit juices, while the "WNC" dietary pattern referred to higher intakes of White rice, Noodles, and Coffee. Means of the total MMSE-KC and orientation score of the participants in the MFDF dietary pattern were higher than those of the WNC dietary pattern. Compared with the WNC dietary pattern, the MFDF dietary pattern showed a lower risk of cognitive impairment after adjusting for covariates (OR 0.64, 95% CI 0.44-0.94). The MFDF dietary pattern, with high consumption of multigrain rice, fish, dairy products, and fruits may be related to better cognition among Korean older adults.

  10. Dietary Patterns Derived by Cluster Analysis are Associated with Cognitive Function among Korean Older Adults

    Directory of Open Access Journals (Sweden)

    Jihye Kim

    2015-05-01

    Full Text Available The objective of this study was to investigate major dietary patterns among older Korean adults through cluster analysis and to determine an association between dietary patterns and cognitive function. This is a cross-sectional study. The data from the Korean Multi-Rural Communities Cohort Study was used. Participants included 765 participants aged 60 years and over. A quantitative food frequency questionnaire with 106 items was used to investigate dietary intake. The Korean version of the MMSE-KC (Mini-Mental Status Examination–Korean version was used to assess cognitive function. Two major dietary patterns were identified using K-means cluster analysis. The “MFDF” dietary pattern indicated high consumption of Multigrain rice, Fish, Dairy products, Fruits and fruit juices, while the “WNC” dietary pattern referred to higher intakes of White rice, Noodles, and Coffee. Means of the total MMSE-KC and orientation score of the participants in the MFDF dietary pattern were higher than those of the WNC dietary pattern. Compared with the WNC dietary pattern, the MFDF dietary pattern showed a lower risk of cognitive impairment after adjusting for covariates (OR 0.64, 95% CI 0.44–0.94. The MFDF dietary pattern, with high consumption of multigrain rice, fish, dairy products, and fruits may be related to better cognition among Korean older adults.

  11. Determination of spectral, structural and energetic properties of small lithium clusters, within the density functional theory formalism

    International Nuclear Information System (INIS)

    Gardet, G.

    1995-01-01

    A systematic study of small lithium clusters (with size less than 19), within the Density Functional Theory (DFT) formalism is presented. We examine structural properties of the so called local level of approximation. For clusters with size smaller than 8, the conformations are well known from ab initio calculations and are found here at much lower computational cost, with only small differences. For bigger clusters, two growth pattern have been used, based upon the increase of the number of pentagonal subunits in the clusters by absorption of one or two Li atoms. Several new stable structures are proposed. Then DFT gradient-corrected functionals have been used for relative stability determination of these clusters. Ionisation potentials and binding energies are also investigated in regard to clusters size and geometry. Calculations of excited states of lithium clusters (with size less than 9) have been performed within two different approaches. Using a set of Kohn-Sham orbitals to construct wave functions, oscillator strengths calculation of the electric dipole transitions is performed. Transition energies, oscillator strengths and optical absorption presented here are generally in reasonable agreement with the experimental data and the Configuration Interaction calculations. (author)

  12. Synergy between pair coupled cluster doubles and pair density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Garza, Alejandro J.; Bulik, Ireneusz W. [Department of Chemistry, Rice University, Houston, Texas 77251-1892 (United States); Henderson, Thomas M. [Department of Chemistry and Department of Physics and Astronomy, Rice University, Houston, Texas 77251-1892 (United States); Scuseria, Gustavo E. [Department of Chemistry and Department of Physics and Astronomy, Rice University, Houston, Texas 77251-1892 (United States); Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589 (Saudi Arabia)

    2015-01-28

    Pair coupled cluster doubles (pCCD) has been recently studied as a method capable of accounting for static correlation with low polynomial cost. We present three combinations of pCCD with Kohn–Sham functionals of the density and on-top pair density (the probability of finding two electrons on top of each other) to add dynamic correlation to pCCD without double counting. With a negligible increase in computational cost, these pCCD+DFT blends greatly improve upon pCCD in the description of typical problems where static and dynamic correlations are both important. We argue that—as a black-box method with low scaling, size-extensivity, size-consistency, and a simple quasidiagonal two-particle density matrix—pCCD is an excellent match for pair density functionals in this type of fusion of multireference wavefunctions with DFT.

  13. Resonance chains in open systems, generalized zeta functions and clustering of the length spectrum

    International Nuclear Information System (INIS)

    Barkhofen, S; Faure, F; Weich, T

    2014-01-01

    In many non-integrable open systems in physics and mathematics, resonances have been found to be surprisingly ordered along curved lines in the complex plane. In this article we provide a unifying approach to these resonance chains by generalizing dynamical zeta functions. By means of a detailed numerical study we show that these generalized zeta functions explain the mechanism that creates the chains of quantum resonance and classical Ruelle resonances for three-disk systems as well as geometric resonances on Schottky surfaces. We also present a direct system-intrinsic definition of the continuous lines on which the resonances are strung together as a projection of an analytic variety. Additionally, this approach shows that the existence of resonance chains is directly related to a clustering of the classical length spectrum on multiples of a base length. Finally, this link is used to construct new examples where several different structures of resonance chains coexist. (paper)

  14. Mean Occupation Function of High-redshift Quasars from the Planck Cluster Catalog

    Science.gov (United States)

    Chakraborty, Priyanka; Chatterjee, Suchetana; Dutta, Alankar; Myers, Adam D.

    2018-06-01

    We characterize the distribution of quasars within dark matter halos using a direct measurement technique for the first time at redshifts as high as z ∼ 1. Using the Planck Sunyaev-Zeldovich (SZ) catalog for galaxy groups and the Sloan Digital Sky Survey (SDSS) DR12 quasar data set, we assign host clusters/groups to the quasars and make a measurement of the mean number of quasars within dark matter halos as a function of halo mass. We find that a simple power-law fit of {log} =(2.11+/- 0.01) {log}(M)-(32.77+/- 0.11) can be used to model the quasar fraction in dark matter halos. This suggests that the quasar fraction increases monotonically as a function of halo mass even to redshifts as high as z ∼ 1.

  15. Generation and reactivation of T-cell receptor A joining region pseudogenes in primates

    Energy Technology Data Exchange (ETDEWEB)

    Thiel, C.; Lanchbury, J.S. [Guy`s Hospital, London (United Kingdom); Otting, N. [Biomedical Primate Research Centre, Rijswijk (Netherlands)] [and others

    1996-06-01

    Tandemly duplicated T-cell receptor (Tcr) AJ (J{alpha}) segments contribute significantly to TCRA chain junctional region diversity in mammals. Since only limited data exists on TCRA diversity in nonhuman primates, we examined the TCRAJ regions of 37 chimpanzee and 71 rhesus macaque TCRA cDNA clones derived from inverse polymerase chain reaction on peripheral blood mononuclear cell cDNA of healthy animals. Twenty-five different TCRAJ regions were characterized in the chimpanzee and 36 in the rhesus macaque. Each bears a close structural relationship to an equivalent human TCRAJ region. Conserved amino acid motifs are shared between all three species. There are indications that differences between nonhuman primates and humans exist in the generation of TCRAJ pseudogenes. The nucleotide and amino acid sequences of the various characterized TCRAJ of each species are reported and we compare our results to the available information on human genomic sequences. Although we provide evidence of dynamic processes modifying TCRAJ segments during primate evolution, their repertoire and primary structure appears to be relatively conserved. 21 refs., 2 figs.

  16. Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes.

    Directory of Open Access Journals (Sweden)

    Irene Keller

    2007-02-01

    Full Text Available Comparisons of the DNA sequences of metazoa show an excess of transitional over transversional substitutions. Part of this bias is due to the relatively high rate of mutation of methylated cytosines to thymine. Postmutation processes also introduce a bias, particularly selection for codon-usage bias in coding regions. It is generally assumed, however, that there is a universal bias in favour of transitions over transversions, possibly as a result of the underlying chemistry of mutation. Surprisingly, this underlying trend has been evaluated only in two types of metazoan, namely Drosophila and the Mammalia. Here, we investigate a third group, and find no such bias. We characterize the point substitution spectrum in Podisma pedestris, a grasshopper species with a very large genome. The accumulation of mutations was surveyed in two pseudogene families, nuclear mitochondrial and ribosomal DNA sequences. The cytosine-guanine (CpG dinucleotides exhibit the high transition frequencies expected of methylated sites. The transition rate at other cytosine residues is significantly lower. After accounting for this methylation effect, there is no significant difference between transition and transversion rates. These results contrast with reports from other taxa and lead us to reject the hypothesis of a universal transition/transversion bias. Instead we suggest fundamental interspecific differences in point substitution processes.

  17. Heterogeneity of Human Neutrophil CD177 Expression Results from CD177P1 Pseudogene Conversion.

    Directory of Open Access Journals (Sweden)

    Zuopeng Wu

    2016-05-01

    Full Text Available Most humans harbor both CD177neg and CD177pos neutrophils but 1-10% of people are CD177null, placing them at risk for formation of anti-neutrophil antibodies that can cause transfusion-related acute lung injury and neonatal alloimmune neutropenia. By deep sequencing the CD177 locus, we catalogued CD177 single nucleotide variants and identified a novel stop codon in CD177null individuals arising from a single base substitution in exon 7. This is not a mutation in CD177 itself, rather the CD177null phenotype arises when exon 7 of CD177 is supplied entirely by the CD177 pseudogene (CD177P1, which appears to have resulted from allelic gene conversion. In CD177 expressing individuals the CD177 locus contains both CD177P1 and CD177 sequences. The proportion of CD177hi neutrophils in the blood is a heritable trait. Abundance of CD177hi neutrophils correlates with homozygosity for CD177 reference allele, while heterozygosity for ectopic CD177P1 gene conversion correlates with increased CD177neg neutrophils, in which both CD177P1 partially incorporated allele and paired intact CD177 allele are transcribed. Human neutrophil heterogeneity for CD177 expression arises by ectopic allelic conversion. Resolution of the genetic basis of CD177null phenotype identifies a method for screening for individuals at risk of CD177 isoimmunisation.

  18. A numerical study of spin-dependent organization of alkali-metal atomic clusters using density-functional method

    International Nuclear Information System (INIS)

    Liu Xuan; Ito, Haruhiko; Torikai, Eiko

    2012-01-01

    We calculate the different geometric isomers of spin clusters composed of a small number of alkali-metal atoms using the UB3LYP density-functional method. The electron density distribution of clusters changes according to the value of total spin. Steric structures as well as planar structures arise when the number of atoms increases. The lowest spin state is the most stable and Li n , Na n , K n , Rb n , and Cs n with n = 2–8 can be formed in higher spin states. In the highest spin state, the preparation of clusters depends on the kind and the number of constituent atoms. The interaction energy between alkali-metal atoms and rare-gas atoms is smaller than the binding energy of spin clusters. Consequently, it is possible to self-organize the alkali-metal-atom clusters on a non-wetting substrate coated with rare-gas atoms.

  19. On the luminosity function, lifetimes, and origin of blue stragglers in globular clusters

    Science.gov (United States)

    Bailyn, Charles D.; Pinsonneault, Marc H.

    1995-01-01

    We compute theoretical evolutionary tracks of blue stragglers created by mergers. Two formation scenarios are considered: mergers of primordial binaries, and stellar collisions. These two scenarios predict strikingly different luminosity functions, which are potentially distinguishable observationally. Tabulated theoretical luminosity functions and lifetimes are presented for blue stragglers formed under a variety of input conditions. We compare our results with observations of the blue straggler sequences in 47 Tucanae and M3. In the case of 47 Tuc, the luminosity function and the formation rate are compatible with the hypothesis that the blue stragglers formed through the collision of single stars. Mergers of primordial binaries are only marginally cosistent with the data, and a significant enhancement of the collision cross section by binary-single-star encounters appears to be ruled out. In the case of M3, we find that the innermost blue stragglers have a luminosity function significantly different from that of the outer stragglers, thus confirming earlier suggestions that there are two distinct populations of blue stragglers in this cluster. The inner stragglers are preferentially brighter and bluer, as would be expected if they were made by collisions, but there are so many of them that the collision rate would need to be enhanced by interactions involving wide binaries. The luminosity function of the outer stragglers is almost identical to the predictions of mergers from primordial binaries and is inconsistent with the collision hypothesis.

  20. Spherical Harmonic Analysis of Particle Velocity Distribution Function: Comparison of Moments and Anisotropies using Cluster Data

    Science.gov (United States)

    Gurgiolo, Chris; Vinas, Adolfo F.

    2009-01-01

    This paper presents a spherical harmonic analysis of the plasma velocity distribution function using high-angular, energy, and time resolution Cluster data obtained from the PEACE spectrometer instrument to demonstrate how this analysis models the particle distribution function and its moments and anisotropies. The results show that spherical harmonic analysis produced a robust physical representation model of the velocity distribution function, resolving the main features of the measured distributions. From the spherical harmonic analysis, a minimum set of nine spectral coefficients was obtained from which the moment (up to the heat flux), anisotropy, and asymmetry calculations of the velocity distribution function were obtained. The spherical harmonic method provides a potentially effective "compression" technique that can be easily carried out onboard a spacecraft to determine the moments and anisotropies of the particle velocity distribution function for any species. These calculations were implemented using three different approaches, namely, the standard traditional integration, the spherical harmonic (SPH) spectral coefficients integration, and the singular value decomposition (SVD) on the spherical harmonic methods. A comparison among the various methods shows that both SPH and SVD approaches provide remarkable agreement with the standard moment integration method.

  1. Structural, electronic, and magnetic properties of Y(n)O (n=2-14) clusters: Density functional study.

    Science.gov (United States)

    Yang, Zhi; Xiong, Shi-Jie

    2008-09-28

    The geometries stability, electronic properties, and magnetism of Y(n)O clusters up to n=14 are systematically studied with density functional theory. In the lowest-energy structures of Y(n)O clusters, the equilibrium site of the oxygen atom gradually moves from an outer site of the cluster, via a surface site, and finally, to an interior site as the number of the Y atoms increases from 2 to 14. Starting from n=12, the O atom falls into the center of the cluster with the Y atoms forming the outer frame. The results show that clusters with n=2, 4, 8, and 12 are more stable than their respective neighbors, and that the total magnetic moments of Y(n)O clusters are all quite small except Y(12)O cluster. The lowest-energy structure of Y(12)O cluster is a perfect icosahedron with a large magnetic moment 6mu(B). In addition, we find that the total magnetic moments are quenched for n=2, 6, and 8 due to the closed-shell electronic configuration. The calculated ionization potentials and electron affinities are in good agreement with the experimental results, which imply that the present theoretical treatments are satisfactory.

  2. Cluster synchronization in networks of identical oscillators with α-function pulse coupling.

    Science.gov (United States)

    Chen, Bolun; Engelbrecht, Jan R; Mirollo, Renato

    2017-02-01

    We study a network of N identical leaky integrate-and-fire model neurons coupled by α-function pulses, weighted by a coupling parameter K. Studies of the dynamics of this system have mostly focused on the stability of the fully synchronized and the fully asynchronous splay states, which naturally depends on the sign of K, i.e., excitation vs inhibition. We find that there is also a rich set of attractors consisting of clusters of fully synchronized oscillators, such as fixed (N-1,1) states, which have synchronized clusters of sizes N-1 and 1, as well as splay states of clusters with equal sizes greater than 1. Additionally, we find limit cycles that clarify the stability of previously observed quasiperiodic behavior. Our framework exploits the neutrality of the dynamics for K=0 which allows us to implement a dimensional reduction strategy that simplifies the dynamics to a continuous flow on a codimension 3 subspace with the sign of K determining the flow direction. This reduction framework naturally incorporates a hierarchy of partially synchronized subspaces in which the new attracting states lie. Using high-precision numerical simulations, we describe completely the sequence of bifurcations and the stability of all fixed points and limit cycles for N=2-4. The set of possible attracting states can be used to distinguish different classes of neuron models. For instance from our previous work [Chaos 24, 013114 (2014)CHAOEH1054-150010.1063/1.4858458] we know that of the types of partially synchronized states discussed here, only the (N-1,1) states can be stable in systems of identical coupled sinusoidal (i.e., Kuramoto type) oscillators, such as θ-neuron models. Upon introducing a small variation in individual neuron parameters, the attracting fixed points we discuss here generalize to equivalent fixed points in which neurons need not fire coincidently.

  3. A proteomic approach to investigating gene cluster expression and secondary metabolite functionality in Aspergillus fumigatus.

    Directory of Open Access Journals (Sweden)

    Rebecca A Owens

    Full Text Available A combined proteomics and metabolomics approach was utilised to advance the identification and characterisation of secondary metabolites in Aspergillus fumigatus. Here, implementation of a shotgun proteomic strategy led to the identification of non-redundant mycelial proteins (n = 414 from A. fumigatus including proteins typically under-represented in 2-D proteome maps: proteins with multiple transmembrane regions, hydrophobic proteins and proteins with extremes of molecular mass and pI. Indirect identification of secondary metabolite cluster expression was also achieved, with proteins (n = 18 from LaeA-regulated clusters detected, including GliT encoded within the gliotoxin biosynthetic cluster. Biochemical analysis then revealed that gliotoxin significantly attenuates H2O2-induced oxidative stress in A. fumigatus (p>0.0001, confirming observations from proteomics data. A complementary 2-D/LC-MS/MS approach further elucidated significantly increased abundance (p<0.05 of proliferating cell nuclear antigen (PCNA, NADH-quinone oxidoreductase and the gliotoxin oxidoreductase GliT, along with significantly attenuated abundance (p<0.05 of a heat shock protein, an oxidative stress protein and an autolysis-associated chitinase, when gliotoxin and H2O2 were present, compared to H2O2 alone. Moreover, gliotoxin exposure significantly reduced the abundance of selected proteins (p<0.05 involved in de novo purine biosynthesis. Significantly elevated abundance (p<0.05 of a key enzyme, xanthine-guanine phosphoribosyl transferase Xpt1, utilised in purine salvage, was observed in the presence of H2O2 and gliotoxin. This work provides new insights into the A. fumigatus proteome and experimental strategies, plus mechanistic data pertaining to gliotoxin functionality in the organism.

  4. Cluster management.

    Science.gov (United States)

    Katz, R

    1992-11-01

    Cluster management is a management model that fosters decentralization of management, develops leadership potential of staff, and creates ownership of unit-based goals. Unlike shared governance models, there is no formal structure created by committees and it is less threatening for managers. There are two parts to the cluster management model. One is the formation of cluster groups, consisting of all staff and facilitated by a cluster leader. The cluster groups function for communication and problem-solving. The second part of the cluster management model is the creation of task forces. These task forces are designed to work on short-term goals, usually in response to solving one of the unit's goals. Sometimes the task forces are used for quality improvement or system problems. Clusters are groups of not more than five or six staff members, facilitated by a cluster leader. A cluster is made up of individuals who work the same shift. For example, people with job titles who work days would be in a cluster. There would be registered nurses, licensed practical nurses, nursing assistants, and unit clerks in the cluster. The cluster leader is chosen by the manager based on certain criteria and is trained for this specialized role. The concept of cluster management, criteria for choosing leaders, training for leaders, using cluster groups to solve quality improvement issues, and the learning process necessary for manager support are described.

  5. The cluster index of regularly varying sequences with applications to limit theory for functions of multivariate Markov chains

    DEFF Research Database (Denmark)

    Mikosch, Thomas Valentin; Wintenberger, Olivier

    2014-01-01

    We introduce the cluster index of a multivariate stationary sequence and characterize the index in terms of the spectral tail process. This index plays a major role in limit theory for partial sums of sequences. We illustrate the use of the cluster index by characterizing infinite variance stable...... limit distributions and precise large deviation results for sums of multivariate functions acting on a stationary Markov chain under a drift condition....

  6. Genomic organization, tissue distribution and functional characterization of the rat Pate gene cluster.

    Directory of Open Access Journals (Sweden)

    Angireddy Rajesh

    Full Text Available The cysteine rich prostate and testis expressed (Pate proteins identified till date are thought to resemble the three fingered protein/urokinase-type plasminogen activator receptor proteins. In this study, for the first time, we report the identification, cloning and characterization of rat Pate gene cluster and also determine the expression pattern. The rat Pate genes are clustered on chromosome 8 and their predicted proteins retained the ten cysteine signature characteristic to TFP/Ly-6 protein family. PATE and PATE-F three dimensional protein structure was found to be similar to that of the toxin bucandin. Though Pate gene expression is thought to be prostate and testis specific, we observed that rat Pate genes are also expressed in seminal vesicle and epididymis and in tissues beyond the male reproductive tract. In the developing rats (20-60 day old, expression of Pate genes seem to be androgen dependent in the epididymis and testis. In the adult rat, androgen ablation resulted in down regulation of the majority of Pate genes in the epididymides. PATE and PATE-F proteins were found to be expressed abundantly in the male reproductive tract of rats and on the sperm. Recombinant PATE protein exhibited potent antibacterial activity, whereas PATE-F did not exhibit any antibacterial activity. Pate expression was induced in the epididymides when challenged with LPS. Based on our results, we conclude that rat PATE proteins may contribute to the reproductive and defense functions.

  7. Carbon Isotopes in Globular Clusters Down to the Bump in the Luminosity Function

    Science.gov (United States)

    Shetrone, Matthew D.

    2003-03-01

    We find that the 12C/13C ratio evolves from high values (>20) below the bump in the luminosity function (BLF) to near the equilibrium value of the CNO cycle above the BLF in the globular clusters (GCs) NGC 6528 and M4. This is the first time that the predicted decline of the 12C/13C ratios due to the extra mixing at the BLF is detected in a GC. In M4, a slight decline from 12C/13C = 10 just above the BLF at MV=+0.5 to 12C/13C = 4 at MV=-0.6 is detected, suggesting that some additional mixing may occur beyond the BLF in this cluster. Isotope ratios are measured and found to be constant in the GCs NGC 6553 and 47 Tucanae down to just above the BLF of those GCs. Based on observations made in part at the W. M. Keck Observatory by the Gemini staff, supported by the Gemini Observatory, which is operated by the Association of Universities of Research in Astronomy, Inc., on behalf of the international Gemini partnership of Argentina, Australia, Brazil, Canada, Chile, the UK, and the US. The W. M. Keck Observatory is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation.

  8. Genetic interrelations in the actinomycin biosynthetic gene clusters of Streptomyces antibioticus IMRU 3720 and Streptomyces chrysomallus ATCC11523, producers of actinomycin X and actinomycin C

    Science.gov (United States)

    Crnovčić, Ivana; Rückert, Christian; Semsary, Siamak; Lang, Manuel; Kalinowski, Jörn; Keller, Ullrich

    2017-01-01

    Sequencing the actinomycin (acm) biosynthetic gene cluster of Streptomyces antibioticus IMRU 3720, which produces actinomycin X (Acm X), revealed 20 genes organized into a highly similar framework as in the bi-armed acm C biosynthetic gene cluster of Streptomyces chrysomallus but without an attached additional extra arm of orthologues as in the latter. Curiously, the extra arm of the S. chrysomallus gene cluster turned out to perfectly match the single arm of the S. antibioticus gene cluster in the same order of orthologues including the the presence of two pseudogenes, scacmM and scacmN, encoding a cytochrome P450 and its ferredoxin, respectively. Orthologues of the latter genes were both missing in the principal arm of the S. chrysomallus acm C gene cluster. All orthologues of the extra arm showed a G +C-contents different from that of their counterparts in the principal arm. Moreover, the similarities of translation products from the extra arm were all higher to the corresponding translation products of orthologue genes from the S. antibioticus acm X gene cluster than to those encoded by the principal arm of their own gene cluster. This suggests that the duplicated structure of the S. chrysomallus acm C biosynthetic gene cluster evolved from previous fusion between two one-armed acm gene clusters each from a different genetic background. However, while scacmM and scacmN in the extra arm of the S. chrysomallus acm C gene cluster are mutated and therefore are non-functional, their orthologues saacmM and saacmN in the S. antibioticus acm C gene cluster show no defects seemingly encoding active enzymes with functions specific for Acm X biosynthesis. Both acm biosynthetic gene clusters lack a kynurenine-3-monooxygenase gene necessary for biosynthesis of 3-hydroxy-4-methylanthranilic acid, the building block of the Acm chromophore, which suggests participation of a genome-encoded relevant monooxygenase during Acm biosynthesis in both S. chrysomallus and S

  9. Clustering of Midlife Lifestyle Behaviors and Subsequent Cognitive Function: A Longitudinal Study

    Science.gov (United States)

    Andreeva, Valentina A.; Lassale, Camille; Hercberg, Serge; Galan, Pilar

    2014-01-01

    Objectives. We examined the association between individual and clustered lifestyle behaviors in middle age and later in cognitive functioning. Methods. Middle-aged participants (n = 2430) in the Supplémentation en Vitamines et Minéraux Antioxydant study self-reported their low physical activity, sedentary behavior, alcohol use, smoking, low fruit and vegetable consumption, and low fish consumption. We assessed cognition 13 years later via 6 neuropsychological tests. After standardization, we summed the scores for a composite cognitive measure. We estimated executive functioning and verbal memory scores using principal component analysis. We estimated the mean differences (95% confidence intervals [CIs]) in cognitive performance by the number of unhealthy behaviors using analysis of covariance. We identified latent unhealthy behavior factor via structural equation modeling. Results. Global cognitive function and verbal memory were linearly, negatively associated with the number of unhealthy behaviors: adjusted mean differences = −0.36 (95% CI = −0.69, −0.03) and −0.46 (95% CI = −0.80, −0.11), respectively, per unit increase in the number of unhealthy behaviors. The latent unhealthy behavior factor with low fruit and vegetable consumption and low physical activity as main contributors was associated with reduced verbal memory (RMSEA = 0.02; CFI = 0.96; P = .004). No association was found with executive functioning. Conclusions. Comprehensive public health strategies promoting healthy lifestyles might help deter cognitive aging. PMID:25211733

  10. Multivariate spatial Gaussian mixture modeling for statistical clustering of hemodynamic parameters in functional MRI

    International Nuclear Information System (INIS)

    Fouque, A.L.; Ciuciu, Ph.; Risser, L.; Fouque, A.L.; Ciuciu, Ph.; Risser, L.

    2009-01-01

    In this paper, a novel statistical parcellation of intra-subject functional MRI (fMRI) data is proposed. The key idea is to identify functionally homogenous regions of interest from their hemodynamic parameters. To this end, a non-parametric voxel-based estimation of hemodynamic response function is performed as a prerequisite. Then, the extracted hemodynamic features are entered as the input data of a Multivariate Spatial Gaussian Mixture Model (MSGMM) to be fitted. The goal of the spatial aspect is to favor the recovery of connected components in the mixture. Our statistical clustering approach is original in the sense that it extends existing works done on univariate spatially regularized Gaussian mixtures. A specific Gibbs sampler is derived to account for different covariance structures in the feature space. On realistic artificial fMRI datasets, it is shown that our algorithm is helpful for identifying a parsimonious functional parcellation required in the context of joint detection estimation of brain activity. This allows us to overcome the classical assumption of spatial stationarity of the BOLD signal model. (authors)

  11. Si clusters/defective graphene composites as Li-ion batteries anode materials: A density functional study

    International Nuclear Information System (INIS)

    Li, Meng; Liu, Yue-Jie; Zhao, Jing-xiang; Wang, Xiao-guang

    2015-01-01

    Highlights: • We study the interaction between Si clusters with pristine and defective graphene. • We find that the binding strength of Si clusters on graphene can be enhanced to different degrees after introducing various defects. • It is found that both graphene and Si cluster in the Si/graphene composites can preserve their Li uptake ability. - Abstract: Recently, the Si/graphene hybrid composites have attracted considerable attention due to their potential application for Li-ion batteries. How to effectively anchor Si clusters to graphene substrates to ensure their stability is an important factor to determine their performance for Li-ion batteries. In the present work, we have performed comprehensive density functional theory (DFT) calculations to investigate the geometric structures, stability, and electronic properties of the deposited Si clusters on defective graphenes as well as their potential applications for Li-ion batteries. The results indicate that the interfacial bonding between these Si clusters with the pristine graphene is quietly weak with a small adsorption energy (<−0.21 eV). Due to the presence of vacancy site, the binding strength of Si clusters on defective graphene is much stronger than that of pristine one, accompanying with a certain amount of charge transfer from Si clusters to graphene substrates. Moreover, the ability of Si/graphene hybrids for Li uptake is studied by calculating the adsorption of Li atoms. We find that both graphenes and Si clusters in the Si/graphene composites preserve their Li uptake ability, indicating that graphenes not only server as buffer materials for accommodating the expansion of Si cluster, but also provide additional intercalation sites for Li

  12. Actinide chemistry using singlet-paired coupled cluster and its combinations with density functionals

    Science.gov (United States)

    Garza, Alejandro J.; Sousa Alencar, Ana G.; Scuseria, Gustavo E.

    2015-12-01

    Singlet-paired coupled cluster doubles (CCD0) is a simplification of CCD that relinquishes a fraction of dynamic correlation in order to be able to describe static correlation. Combinations of CCD0 with density functionals that recover specifically the dynamic correlation missing in the former have also been developed recently. Here, we assess the accuracy of CCD0 and CCD0+DFT (and variants of these using Brueckner orbitals) as compared to well-established quantum chemical methods for describing ground-state properties of singlet actinide molecules. The f0 actinyl series (UO22+, NpO23+, PuO24+), the isoelectronic NUN, and thorium (ThO, ThO2+) and nobelium (NoO, NoO2) oxides are studied.

  13. Functional and immunohistochemical evaluation of porcine neonatal islet-like cell clusters

    DEFF Research Database (Denmark)

    Nielsen, T B; Yderstraede, K B; Schrøder, H D

    2003-01-01

    Porcine neonatal islet-like cell clusters (NICCs) may be an attractive source of insulin-producing tissue for xenotransplantation in type I diabetic patients. We examined the functional and immunohistochemical outcome of the islet grafts in vitro during long-term culture and in vivo after...... transplantation to athymic nude mice. On average we obtained 29,000 NICCs from each pancreas. In a perifusion system, NICCs responded poorly to a glucose challenge alone, but 10 mmol/L arginine elicited a fourfold increase in insulin secretion and 16.7 mmol/L glucose + 10 mmol/L arginine caused a sevenfold...... co-stained for proliferation. However no co-staining was observed between insulin- and glucagon-positive cells or between hormone-and CK-positive cells. Following transplantation of 2000 NICCs under the renal capsule of diabetic nude mice, BG levels were normalized within an average of 13 weeks. Oral...

  14. Diagonal Born-Oppenheimer correction for coupled-cluster wave-functions

    Science.gov (United States)

    Shamasundar, K. R.

    2018-06-01

    We examine how geometry-dependent normalisation freedom of electronic wave-functions affects extraction of a meaningful diagonal Born-Oppenheimer correction (DBOC) to the ground-state Born-Oppenheimer potential energy surface (PES). By viewing this freedom as a kind of gauge-freedom, it is shown that DBOC and the resulting associated mass-dependent adiabatic PES are gauge-invariant quantities. A sum-over-states (SOS) formula for DBOC which explicitly exhibits this invariance is derived. A biorthogonal formulation suitable for DBOC computations using standard unnormalised coupled-cluster (CC) wave-functions is presented. This is shown to lead to a biorthogonal version of SOS formula with similar properties. On this basis, different computational schemes for evaluating DBOC using approximate CC wave-functions are derived. One of this agrees with the formula used in the current literature. The connection to adiabatic-to-diabatic transformations in non-adiabatic dynamics is explored and complications arising from biorthogonal nature of CC theory are identified.

  15. Structures, stability, magnetic moments and growth strategies of the Fe_nN (n = 1–7) clusters: All-electron density functional theory calculations

    International Nuclear Information System (INIS)

    Li, Zhi; Zhao, Zhen

    2017-01-01

    The geometries, electronic properties, magnetic moments and growth strategies of the Fe_nN (n = 1–7) clusters are investigated using all-electron density functional theory. The results show that N doping significantly distorts the Fe_n clusters. Fe_4N and Fe_6N clusters are more stable structures than other considered Fe_nN clusters. Local peaks of HOMO-LUMO gap curve are found at n = 3, 7, implying that the chemical stability of the Fe_3N and Fe_7N clusters is higher. Fe_2N, Fe_4N and Fe_6N clusters have larger magnetic moments compared to other considered Fe_nN (n = 1–7) clusters. It can be seen that the Fe_5 clusters are easier to adsorb a Fe atom while the Fe_4 clusters are easier to adsorb a N atom. The considered Fe_mN clusters prefer to adsorb a Fe atom and larger Fe_mN clusters are easier to grow. - Highlights: • The structural stability of the Fe_4N and Fe_6N clusters is higher. • The chemical stability of the Fe_3N and Fe_7N clusters is higher. • Fe_5 clusters are easier to adsorb a Fe atom while Fe_4 clusters are easier to adsorb a N atom. • Fe_nN clusters prefer to adsorb a Fe atom.

  16. The Excursion Set Theory of Halo Mass Functions, Halo Clustering, and Halo Growth

    Science.gov (United States)

    Zentner, Andrew R.

    I review the excursion set theory with particular attention toward applications to cold dark matter halo formation and growth, halo abundance, and halo clustering. After a brief introduction to notation and conventions, I begin by recounting the heuristic argument leading to the mass function of bound objects given by Press and Schechter. I then review the more formal derivation of the Press-Schechter halo mass function that makes use of excursion sets of the density field. The excursion set formalism is powerful and can be applied to numerous other problems. I review the excursion set formalism for describing both halo clustering and bias and the properties of void regions. As one of the most enduring legacies of the excursion set approach and one of its most common applications, I spend considerable time reviewing the excursion set theory of halo growth. This section of the review culminates with the description of two Monte Carlo methods for generating ensembles of halo mass accretion histories. In the last section, I emphasize that the standard excursion set approach is the result of several simplifying assumptions. Dropping these assumptions can lead to more faithful predictions and open excursion set theory to new applications. One such assumption is that the height of the barriers that define collapsed objects is a constant function of scale. I illustrate the implementation of the excursion set approach for barriers of arbitrary shape. One such application is the now well-known improvement of the excursion set mass function derived from the "moving" barrier for ellipsoidal collapse. I also emphasize that the statement that halo accretion histories are independent of halo environment in the excursion set approach is not a general prediction of the theory. It is a simplifying assumption. I review the method for constructing correlated random walks of the density field in the more general case. I construct a simple toy model to illustrate that excursion set

  17. Structures, electronic properties and magnetisms of FeBN (N ≤ 15) clusters: density functional theory investigations

    International Nuclear Information System (INIS)

    Liu Huoyan; Lel Xueling; Chen Hang; Liu Zhifeng; Liu Liren; Zhu Hengjiang

    2011-01-01

    The equilibrium structures, electronic properties and magnetisms of FeB N (N ≤ 15) clusters have been investigated by generalized gradient approximation (GGA) of density functional theory at different spin multiplicities. The average atomic binding energies, second-order energy differences and gaps of ground-state structures are calculated and discussed. The results show that FeB 3 , FeB 8 , FeB 12 and FeB 14 possess relatively higher stabilities. Moreover, there is a distinct hybridization between the d orbital of Fe and the p orbital of B for the ground-state cluster. The total magnetic moment for groundstate cluster is mainly provided by 3 d orbital of Fe atom, and exhibits the odd-even oscillation tendency with the increasing of cluster size. (authors)

  18. On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit

    Science.gov (United States)

    Santra, Biswajit; Michaelides, Angelos; Scheffler, Matthias

    2007-11-01

    The ability of several density-functional theory (DFT) exchange-correlation functionals to describe hydrogen bonds in small water clusters (dimer to pentamer) in their global minimum energy structures is evaluated with reference to second order Møller-Plesset perturbation theory (MP2). Errors from basis set incompleteness have been minimized in both the MP2 reference data and the DFT calculations, thus enabling a consistent systematic evaluation of the true performance of the tested functionals. Among all the functionals considered, the hybrid X3LYP and PBE0 functionals offer the best performance and among the nonhybrid generalized gradient approximation functionals, mPWLYP and PBE1W perform best. The popular BLYP and B3LYP functionals consistently underbind and PBE and PW91 display rather variable performance with cluster size.

  19. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

    Directory of Open Access Journals (Sweden)

    Angela F Harper

    2017-02-01

    Full Text Available Peroxiredoxins (Prxs or Prdxs are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx superfamily identified using a novel method called MISST (Multi-level Iterative Sequence Searching Technique. MISST is an iterative search process developed to be both agglomerative, to add sequences containing similar functional site features, and divisive, to split groups when functional site features suggest distinct functionally-relevant clusters. Superfamily members need not be identified initially-MISST begins with a minimal representative set of known structures and searches GenBank iteratively. Further, the method's novelty lies in the manner in which isofunctional groups are selected; rather than use a single or shifting threshold to identify clusters, the groups are deemed isofunctional when they pass a self-identification criterion, such that the group identifies itself and nothing else in a search of GenBank. The method was preliminarily validated on the Prxs, as the Prxs presented challenges of both agglomeration and division. For example, previous sequence analysis clustered the Prx functional families Prx1 and Prx6 into one group. Subsequent expert analysis clearly identified Prx6 as a distinct functionally relevant group. The MISST process distinguishes these two closely related, though functionally distinct, families. Through MISST search iterations, over 38,000 Prx sequences were identified, which the method divided into six isofunctional clusters, consistent with previous expert analysis. The results represent the most complete computational functional analysis of proteins comprising the Prx superfamily. The feasibility of this novel method is

  20. Functional dissection of HOXD cluster genes in regulation of neuroblastoma cell proliferation and differentiation.

    Directory of Open Access Journals (Sweden)

    Yunhong Zha

    Full Text Available Retinoic acid (RA can induce growth arrest and neuronal differentiation of neuroblastoma cells and has been used in clinic for treatment of neuroblastoma. It has been reported that RA induces the expression of several HOXD genes in human neuroblastoma cell lines, but their roles in RA action are largely unknown. The HOXD cluster contains nine genes (HOXD1, HOXD3, HOXD4, and HOXD8-13 that are positioned sequentially from 3' to 5', with HOXD1 at the 3' end and HOXD13 the 5' end. Here we show that all HOXD genes are induced by RA in the human neuroblastoma BE(2-C cells, with the genes located at the 3' end being activated generally earlier than those positioned more 5' within the cluster. Individual induction of HOXD8, HOXD9, HOXD10 or HOXD12 is sufficient to induce both growth arrest and neuronal differentiation, which is associated with downregulation of cell cycle-promoting genes and upregulation of neuronal differentiation genes. However, induction of other HOXD genes either has no effect (HOXD1 or has partial effects (HOXD3, HOXD4, HOXD11 and HOXD13 on BE(2-C cell proliferation or differentiation. We further show that knockdown of HOXD8 expression, but not that of HOXD9 expression, significantly inhibits the differentiation-inducing activity of RA. HOXD8 directly activates the transcription of HOXC9, a key effector of RA action in neuroblastoma cells. These findings highlight the distinct functions of HOXD genes in RA induction of neuroblastoma cell differentiation.

  1. Benchmark CCSD(T) and DFT study of binding energies in Be7 - 12: in search of reliable DFT functional for beryllium clusters

    Science.gov (United States)

    Labanc, Daniel; Šulka, Martin; Pitoňák, Michal; Černušák, Ivan; Urban, Miroslav; Neogrády, Pavel

    2018-05-01

    We present a computational study of the stability of small homonuclear beryllium clusters Be7 - 12 in singlet electronic states. Our predictions are based on highly correlated CCSD(T) coupled cluster calculations. Basis set convergence towards the complete basis set limit as well as the role of the 1s core electron correlation are carefully examined. Our CCSD(T) data for binding energies of Be7 - 12 clusters serve as a benchmark for performance assessment of several density functional theory (DFT) methods frequently used in beryllium cluster chemistry. We observe that, from Be10 clusters on, the deviation from CCSD(T) benchmarks is stable with respect to size, and fluctuating within 0.02 eV error bar for most examined functionals. This opens up the possibility of scaling the DFT binding energies for large Be clusters using CCSD(T) benchmark values for smaller clusters. We also tried to find analogies between the performance of DFT functionals for Be clusters and for the valence-isoelectronic Mg clusters investigated recently in Truhlar's group. We conclude that it is difficult to find DFT functionals that perform reasonably well for both beryllium and magnesium clusters. Out of 12 functionals examined, only the M06-2X functional gives reasonably accurate and balanced binding energies for both Be and Mg clusters.

  2. Enhanced Cell Capture on Functionalized Graphene Oxide Nanosheets through Oxygen Clustering.

    Science.gov (United States)

    Bardhan, Neelkanth M; Kumar, Priyank V; Li, Zeyang; Ploegh, Hidde L; Grossman, Jeffrey C; Belcher, Angela M; Chen, Guan-Yu

    2017-02-28

    With the global rise in incidence of cancer and infectious diseases, there is a need for the development of techniques to diagnose, treat, and monitor these conditions. The ability to efficiently capture and isolate cells and other biomolecules from peripheral whole blood for downstream analyses is a necessary requirement. Graphene oxide (GO) is an attractive template nanomaterial for such biosensing applications. Favorable properties include its two-dimensional architecture and wide range of functionalization chemistries, offering significant potential to tailor affinity toward aromatic functional groups expressed in biomolecules of interest. However, a limitation of current techniques is that as-synthesized GO nanosheets are used directly in sensing applications, and the benefits of their structural modification on the device performance have remained unexplored. Here, we report a microfluidic-free, sensitive, planar device on treated GO substrates to enable quick and efficient capture of Class-II MHC-positive cells from murine whole blood. We achieve this by using a mild thermal annealing treatment on the GO substrates, which drives a phase transformation through oxygen clustering. Using a combination of experimental observations and MD simulations, we demonstrate that this process leads to improved reactivity and density of functionalization of cell capture agents, resulting in an enhanced cell capture efficiency of 92 ± 7% at room temperature, almost double the efficiency afforded by devices made using as-synthesized GO (54 ± 3%). Our work highlights a scalable, cost-effective, general approach to improve the functionalization of GO, which creates diverse opportunities for various next-generation device applications.

  3. Cluster abundance in chameleon f ( R ) gravity I: toward an accurate halo mass function prediction

    Energy Technology Data Exchange (ETDEWEB)

    Cataneo, Matteo; Rapetti, David [Dark Cosmology Centre, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, 2100 Copenhagen (Denmark); Lombriser, Lucas [Institute for Astronomy, University of Edinburgh, Royal Observatory, Blackford Hill, Edinburgh, EH9 3HJ (United Kingdom); Li, Baojiu, E-mail: matteoc@dark-cosmology.dk, E-mail: drapetti@dark-cosmology.dk, E-mail: llo@roe.ac.uk, E-mail: baojiu.li@durham.ac.uk [Institute for Computational Cosmology, Department of Physics, Durham University, South Road, Durham DH1 3LE (United Kingdom)

    2016-12-01

    We refine the mass and environment dependent spherical collapse model of chameleon f ( R ) gravity by calibrating a phenomenological correction inspired by the parameterized post-Friedmann framework against high-resolution N -body simulations. We employ our method to predict the corresponding modified halo mass function, and provide fitting formulas to calculate the enhancement of the f ( R ) halo abundance with respect to that of General Relativity (GR) within a precision of ∼< 5% from the results obtained in the simulations. Similar accuracy can be achieved for the full f ( R ) mass function on the condition that the modeling of the reference GR abundance of halos is accurate at the percent level. We use our fits to forecast constraints on the additional scalar degree of freedom of the theory, finding that upper bounds competitive with current Solar System tests are within reach of cluster number count analyses from ongoing and upcoming surveys at much larger scales. Importantly, the flexibility of our method allows also for this to be applied to other scalar-tensor theories characterized by a mass and environment dependent spherical collapse.

  4. Cluster evolution

    International Nuclear Information System (INIS)

    Schaeffer, R.

    1987-01-01

    The galaxy and cluster luminosity functions are constructed from a model of the mass distribution based on hierarchical clustering at an epoch where the matter distribution is non-linear. These luminosity functions are seen to reproduce the present distribution of objects as can be inferred from the observations. They can be used to deduce the redshift dependence of the cluster distribution and to extrapolate the observations towards the past. The predicted evolution of the cluster distribution is quite strong, although somewhat less rapid than predicted by the linear theory

  5. The HMGA1 Pseudogene 7 Induces miR-483 and miR-675 Upregulation by Activating Egr1 through a ceRNA Mechanism

    Directory of Open Access Journals (Sweden)

    Marco De Martino

    2017-11-01

    Full Text Available Several studies have established that pseudogene mRNAs can work as competing endogenous RNAs and, when deregulated, play a key role in the onset of human neoplasias. Recently, we have isolated two HMGA1 pseudogenes, HMGA1P6 and HMGA1P7. These pseudogenes have a critical role in cancer progression, acting as micro RNA (miRNA sponges for HMGA1 and other cancer-related genes. HMGA1 pseudogenes were found overexpressed in several human carcinomas, and their expression levels positively correlate with an advanced cancer stage and a poor prognosis. In order to investigate the molecular alterations following HMGA1 pseudogene 7 overexpression, we carried out miRNA sequencing analysis on HMGA1P7 overexpressing mouse embryonic fibroblasts. Intriguingly, the most upregulated miRNAs were miR-483 and miR-675 that have been described as key regulators in cancer progression. Here, we report that HMGA1P7 upregulates miR-483 and miR-675 through a competing endogenous RNA mechanism with Egr1, a transcriptional factor that positively regulates miR-483 and miR-675 expression.

  6. Identification of Mycobacterium tuberculosis complex based on amplification and sequencing of the oxyR pseudogene from stored Ziehl-Neelsen-stained sputum smears in Brazil

    Directory of Open Access Journals (Sweden)

    Marcio Roberto Silva

    2011-02-01

    Full Text Available A cross-sectional analysis of stored Ziehl-Neelsen (ZN-stained sputum smear slides (SSS obtained from two public tuberculosis referral laboratories located in Juiz de Fora, Minas Gerais, was carried out to distinguish Mycobacterium bovis from other members of the Mycobacterium tuberculosis complex (MTC. A two-step approach was used to distinguish M. bovis from other members of MTC: (i oxyR pseudogene amplification to detect MTC and, subsequently, (ii allele-specific sequencing based on the polymorphism at position 285 of this gene. The oxyR pseudogene was successfully amplified in 100 of 177 (56.5% SSS available from 99 individuals. No molecular profile of M. bovis was found. Multivariate analysis indicated that acid-fast bacilli (AFB results and the source laboratory were associated (p < 0.05 with oxyR pseudogene amplification. SSS that were AFB++ SSS showed more oxyR pseudogene amplification than those with AFB0, possibly due to the amount of DNA. One of the two source laboratories presented a greater chance of oxyR pseudogene amplification, suggesting that differences in sputum conservation between laboratories could have influenced the preservation of DNA. This study provides evidence that stored ZN-SSS can be used for the molecular detection of MTC.

  7. Cosmological constraints from the evolution of the cluster baryon mass function at z similar to 0.5

    DEFF Research Database (Denmark)

    Vikhlinin, A.; Voevodkin, A.; Mullis, C.R.

    2003-01-01

    measurements of the gas masses for distant clusters, we find strong evolution of the baryon mass function between z > 0.4 and the present. The observed evolution defines a narrow band in the Omega(m)-Lambda plane, Omega(m) + 0.23Lambda = 0.41 +/- 0.10 at 68% confidence, which intersects with constraints from...

  8. Bivariate functional data clustering: grouping streams based on a varying coefficient model of the stream water and air temperature relationship

    Science.gov (United States)

    H. Li; X. Deng; Andy Dolloff; E. P. Smith

    2015-01-01

    A novel clustering method for bivariate functional data is proposed to group streams based on their water–air temperature relationship. A distance measure is developed for bivariate curves by using a time-varying coefficient model and a weighting scheme. This distance is also adjusted by spatial correlation of streams via the variogram. Therefore, the proposed...

  9. Subaru weak-lensing survey of dark matter subhalos in the Coma cluster: Subhalo mass function and statistical properties

    International Nuclear Information System (INIS)

    Okabe, Nobuhiro; Futamase, Toshifumi; Kuroshima, Risa; Kajisawa, Masaru

    2014-01-01

    We present a 4 deg 2 weak gravitational lensing survey of subhalos in the very nearby Coma cluster using the Subaru/Suprime-Cam. The large apparent size of cluster subhalos allows us to measure the mass of 32 subhalos detected in a model-independent manner, down to the order of 10 –3 of the virial mass of the cluster. Weak-lensing mass measurements of these shear-selected subhalos enable us to investigate subhalo properties and the correlation between subhalo masses and galaxy luminosities for the first time. The mean distortion profiles stacked over subhalos show a sharply truncated feature which is well-fitted by a Navarro-Frenk-White (NFW) mass model with the truncation radius, as expected due to tidal destruction by the main cluster. We also found that subhalo masses, truncation radii, and mass-to-light ratios decrease toward the cluster center. The subhalo mass function, dn/dln M sub , in the range of 2 orders of magnitude in mass, is well described by a single power law or a Schechter function. Best-fit power indices of 1.09 −0.32 +0.42 for the former model and 0.99 −0.23 +0.34 for the latter, are in remarkable agreement with slopes of ∼0.9-1.0 predicted by the cold dark matter paradigm. The tangential distortion signals in the radial range of 0.02-2 h –1 Mpc from the cluster center show a complex structure which is well described by a composition of three mass components of subhalos, the NFW mass distribution as a smooth component of the main cluster, and a lensing model from a large scale structure behind the cluster. Although the lensing signals are 1 order of magnitude lower than those for clusters at z ∼ 0.2, the total signal-to-noise ratio, S/N = 13.3, is comparable, or higher, because the enormous number of background source galaxies compensates for the low lensing efficiency of the nearby cluster.

  10. Subaru Weak-lensing Survey of Dark Matter Subhalos in the Coma Cluster: Subhalo Mass Function and Statistical Properties

    Science.gov (United States)

    Okabe, Nobuhiro; Futamase, Toshifumi; Kajisawa, Masaru; Kuroshima, Risa

    2014-04-01

    We present a 4 deg2 weak gravitational lensing survey of subhalos in the very nearby Coma cluster using the Subaru/Suprime-Cam. The large apparent size of cluster subhalos allows us to measure the mass of 32 subhalos detected in a model-independent manner, down to the order of 10-3 of the virial mass of the cluster. Weak-lensing mass measurements of these shear-selected subhalos enable us to investigate subhalo properties and the correlation between subhalo masses and galaxy luminosities for the first time. The mean distortion profiles stacked over subhalos show a sharply truncated feature which is well-fitted by a Navarro-Frenk-White (NFW) mass model with the truncation radius, as expected due to tidal destruction by the main cluster. We also found that subhalo masses, truncation radii, and mass-to-light ratios decrease toward the cluster center. The subhalo mass function, dn/dln M sub, in the range of 2 orders of magnitude in mass, is well described by a single power law or a Schechter function. Best-fit power indices of 1.09^{+0.42}_{-0.32} for the former model and 0.99_{-0.23}^{+0.34} for the latter, are in remarkable agreement with slopes of ~0.9-1.0 predicted by the cold dark matter paradigm. The tangential distortion signals in the radial range of 0.02-2 h -1 Mpc from the cluster center show a complex structure which is well described by a composition of three mass components of subhalos, the NFW mass distribution as a smooth component of the main cluster, and a lensing model from a large scale structure behind the cluster. Although the lensing signals are 1 order of magnitude lower than those for clusters at z ~ 0.2, the total signal-to-noise ratio, S/N = 13.3, is comparable, or higher, because the enormous number of background source galaxies compensates for the low lensing efficiency of the nearby cluster. Based on data collected from the Subaru Telescope and obtained from SMOKA, operated by the Astronomy Data Center, National Astronomical Observatory of

  11. The cylindrical K-function and Poisson line cluster point processes

    DEFF Research Database (Denmark)

    Møller, Jesper; Safavimanesh, Farzaneh; Rasmussen, Jakob G.

    Poisson line cluster point processes, is also introduced. Parameter estimation based on moment methods or Bayesian inference for this model is discussed when the underlying Poisson line process and the cluster memberships are treated as hidden processes. To illustrate the methodologies, we analyze two...

  12. Reactions of ruthenium and osmium cluster carbonyls with heteroatom-substituted and functionalized alkynes

    International Nuclear Information System (INIS)

    Koridze, A.A.

    2000-01-01

    The results of studies of the reactions of ruthenium and osmium cluster carbonyls with metal (M = Re, Mn, Fe) alkynes, silylalkynes, propargyl alcohols and their derivatives, diynes, enynes, and ferrocenylacetylene are summarized. Intramolecular rearrangements in the cluster complexes including migrations of carbonyl, hydride, and hydrocarbon ligands and the metal core reorganization are considered [ru

  13. Evolution of the cluster optical galaxy luminosity function in the CFHTLS: breaking the degeneracy between mass and redshift

    Science.gov (United States)

    Sarron, F.; Martinet, N.; Durret, F.; Adami, C.

    2018-06-01

    Obtaining large samples of galaxy clusters is important for cosmology: cluster counts as a function of redshift and mass can constrain the parameters of our Universe. They are also useful in order to understand the formation and evolution of clusters. We develop an improved version of the Adami & MAzure Cluster FInder (AMACFI), now the Adami, MAzure & Sarron Cluster FInder (AMASCFI), and apply it to the 154 deg2 of the Canada-France-Hawaii Telescope Legacy Survey (CFHTLS) to obtain a large catalogue of 1371 cluster candidates with mass M200 > 1014 M⊙ and redshift z ≤ 0.7. We derive the selection function of the algorithm from the Millennium simulation, and cluster masses from a richness-mass scaling relation built from matching our candidates with X-ray detections. We study the evolution of these clusters with mass and redshift by computing the i'-band galaxy luminosity functions (GLFs) for the early-type (ETGs) and late-type galaxies (LTGs). This sample is 90% pure and 70% complete, and therefore our results are representative of a large fraction of the cluster population in these redshift and mass ranges. We find an increase in both the ETG and LTG faint populations with decreasing redshift (with Schechter slopes αETG = -0.65 ± 0.03 and αLTG = -0.95 ± 0.04 at z = 0.6, and αETG = -0.79 ± 0.02 and αLTG = -1.26 ± 0.03 at z = 0.2) and also a decrease in the LTG (but not the ETG) bright end. Our large sample allows us to break the degeneracy between mass and redshift, finding that the redshift evolution is more pronounced in high-mass clusters, but that there is no significant dependence of the faint end on mass for a given redshift. These results show that the cluster red sequence is mainly formed at redshift z > 0.7, and that faint ETGs continue to enrich the red sequence through quenching of brighter LTGs at z ≤ 0.7. The efficiency of this quenching is higher in large-mass clusters, while the accretion rate of faint LTGs is lower as the more massive

  14. Functional organization of a single nif cluster in the mesophilic archaeon Methanosarcina mazei strain Gö1

    Directory of Open Access Journals (Sweden)

    Claudia Ehlers

    2002-01-01

    Full Text Available The mesophilic methanogenic archaeon Methanosarcina mazei strain Gö1 is able to utilize molecular nitrogen (N2 as its sole nitrogen source. We have identified and characterized a single nitrogen fixation (nif gene cluster in M. mazei Gö1 with an approximate length of 9 kbp. Sequence analysis revealed seven genes with sequence similarities to nifH, nifI1, nifI2, nifD, nifK, nifE and nifN, similar to other diazotrophic methanogens and certain bacteria such as Clostridium acetobutylicum, with the two glnB-like genes (nifI1 and nifI2 located between nifH and nifD. Phylogenetic analysis of deduced amino acid sequences for the nitrogenase structural genes of M. mazei Gö1 showed that they are most closely related to Methanosarcina barkeri nif2 genes, and also closely resemble those for the corresponding nif products of the gram-positive bacterium C. acetobutylicum. Northern blot analysis and reverse transcription PCR analysis demonstrated that the M. mazei nif genes constitute an operon transcribed only under nitrogen starvation as a single 8 kb transcript. Sequence analysis revealed a palindromic sequence at the transcriptional start site in front of the M. mazei nifH gene, which may have a function in transcriptional regulation of the nif operon.

  15. Structural, Functional, and Clinical Characterization of a Novel PTPN11 Mutation Cluster Underlying Noonan Syndrome.

    Science.gov (United States)

    Pannone, Luca; Bocchinfuso, Gianfranco; Flex, Elisabetta; Rossi, Cesare; Baldassarre, Giuseppina; Lissewski, Christina; Pantaleoni, Francesca; Consoli, Federica; Lepri, Francesca; Magliozzi, Monia; Anselmi, Massimiliano; Delle Vigne, Silvia; Sorge, Giovanni; Karaer, Kadri; Cuturilo, Goran; Sartorio, Alessandro; Tinschert, Sigrid; Accadia, Maria; Digilio, Maria C; Zampino, Giuseppe; De Luca, Alessandro; Cavé, Hélène; Zenker, Martin; Gelb, Bruce D; Dallapiccola, Bruno; Stella, Lorenzo; Ferrero, Giovanni B; Martinelli, Simone; Tartaglia, Marco

    2017-04-01

    Germline mutations in PTPN11, the gene encoding the Src-homology 2 (SH2) domain-containing protein tyrosine phosphatase (SHP2), cause Noonan syndrome (NS), a relatively common, clinically variable, multisystem disorder. Here, we report on the identification of five different PTPN11 missense changes affecting residues Leu 261 , Leu 262 , and Arg 265 in 16 unrelated individuals with clinical diagnosis of NS or with features suggestive for this disorder, specifying a novel disease-causing mutation cluster. Expression of the mutant proteins in HEK293T cells documented their activating role on MAPK signaling. Structural data predicted a gain-of-function role of substitutions at residues Leu 262 and Arg 265 exerted by disruption of the N-SH2/PTP autoinhibitory interaction. Molecular dynamics simulations suggested a more complex behavior for changes affecting Leu 261 , with possible impact on SHP2's catalytic activity/selectivity and proper interaction of the PTP domain with the regulatory SH2 domains. Consistent with that, biochemical data indicated that substitutions at codons 262 and 265 increased the catalytic activity of the phosphatase, while those affecting codon 261 were only moderately activating but impacted substrate specificity. Remarkably, these mutations underlie a relatively mild form of NS characterized by low prevalence of cardiac defects, short stature, and cognitive and behavioral issues, as well as less evident typical facial features. © 2017 WILEY PERIODICALS, INC.

  16. The Low-mass Population in the Young Cluster Stock 8: Stellar Properties and Initial Mass Function

    Energy Technology Data Exchange (ETDEWEB)

    Jose, Jessy; Herczeg, Gregory J.; Fang, Qiliang [Kavli Institute for Astronomy and Astrophysics, Peking University, Yi He Yuan Lu 5, Haidian Qu, Beijing 100871 (China); Samal, Manash R. [Graduate Institute of Astronomy, National Central University 300, Jhongli City, Taoyuan County 32001, Taiwan (China); Panwar, Neelam, E-mail: jessyvjose1@gmail.com [Department of Physics and Astrophysics, University of Delhi, Delhi 110007 (India)

    2017-02-10

    The evolution of H ii regions/supershells can trigger a new generation of stars/clusters at their peripheries, with environmental conditions that may affect the initial mass function, disk evolution, and star formation efficiency. In this paper we study the stellar content and star formation processes in the young cluster Stock 8, which itself is thought to be formed during the expansion of a supershell. We present deep optical photometry along with JHK and 3.6 and 4.5 μ m photometry from UKIDSS and Spitzer -IRAC. We use multicolor criteria to identify the candidate young stellar objects in the region. Using evolutionary models, we obtain a median log(age) of ∼6.5 (∼3.0 Myr) with an observed age spread of ∼0.25 dex for the cluster. Monte Carlo simulations of the population of Stock 8, based on estimates for the photometric uncertainty, differential reddening, binarity, and variability, indicate that these uncertainties introduce an age spread of ∼0.15 dex. The intrinsic age spread in the cluster is ∼0.2 dex. The fraction of young stellar objects surrounded by disks is ∼35%. The K -band luminosity function of Stock 8 is similar to that of the Trapezium cluster. The initial mass function (IMF) of Stock 8 has a Salpeter-like slope at >0.5 M {sub ⊙} and flattens and peaks at ∼0.4 M {sub ⊙}, below which it declines into the substellar regime. Although Stock 8 is surrounded by several massive stars, there seems to be no severe environmental effect in the form of the IMF due to the proximity of massive stars around the cluster.

  17. The function of Shp2 tyrosine phosphatase in the dispersal of acetylcholine receptor clusters

    Directory of Open Access Journals (Sweden)

    Madhavan Raghavan

    2008-07-01

    Full Text Available Abstract Background A crucial event in the development of the vertebrate neuromuscular junction (NMJ is the postsynaptic enrichment of muscle acetylcholine (ACh receptors (AChRs. This process involves two distinct steps: the local clustering of AChRs at synapses, which depends on the activation of the muscle-specific receptor tyrosine kinase MuSK by neural agrin, and the global dispersal of aneural or "pre-patterned" AChR aggregates, which is triggered by ACh or by synaptogenic stimuli. We and others have previously shown that tyrosine phosphatases, such as the SH2 domain-containing phosphatase Shp2, regulate AChR cluster formation in muscle cells, and that tyrosine phosphatases also mediate the dispersal of pre-patterned AChR clusters by synaptogenic stimuli, although the specific phosphatases involved in this latter step remain unknown. Results Using an assay system that allows AChR cluster assembly and disassembly to be studied separately and quantitatively, we describe a previously unrecognized role of the tyrosine phosphatase Shp2 in AChR cluster disassembly. Shp2 was robustly expressed in embryonic Xenopus muscle in vivo and in cultured myotomal muscle cells, and treatment of the muscle cultures with an inhibitor of Shp2 (NSC-87877 blocked the dispersal of pre-patterned AChR clusters by synaptogenic stimuli. In contrast, over-expression in muscle cells of either wild-type or constitutively active Shp2 accelerated cluster dispersal. Significantly, forced expression in muscle of the Shp2-activator SIRPα1 (signal regulatory protein α1 also enhanced the disassembly of AChR clusters, whereas the expression of a truncated SIRPα1 mutant that suppresses Shp2 signaling inhibited cluster disassembly. Conclusion Our results suggest that Shp2 activation by synaptogenic stimuli, through signaling intermediates such as SIRPα1, promotes the dispersal of pre-patterned AChR clusters to facilitate the selective accumulation of AChRs at developing NMJs.

  18. A Resting-State Brain Functional Network Study in MDD Based on Minimum Spanning Tree Analysis and the Hierarchical Clustering

    Directory of Open Access Journals (Sweden)

    Xiaowei Li

    2017-01-01

    Full Text Available A large number of studies demonstrated that major depressive disorder (MDD is characterized by the alterations in brain functional connections which is also identifiable during the brain’s “resting-state.” But, in the present study, the approach of constructing functional connectivity is often biased by the choice of the threshold. Besides, more attention was paid to the number and length of links in brain networks, and the clustering partitioning of nodes was unclear. Therefore, minimum spanning tree (MST analysis and the hierarchical clustering were first used for the depression disease in this study. Resting-state electroencephalogram (EEG sources were assessed from 15 healthy and 23 major depressive subjects. Then the coherence, MST, and the hierarchical clustering were obtained. In the theta band, coherence analysis showed that the EEG coherence of the MDD patients was significantly higher than that of the healthy controls especially in the left temporal region. The MST results indicated the higher leaf fraction in the depressed group. Compared with the normal group, the major depressive patients lost clustering in frontal regions. Our findings suggested that there was a stronger brain interaction in the MDD group and a left-right functional imbalance in the frontal regions for MDD controls.

  19. Functional Clustering of the Human Inferior Parietal Lobule by Whole-Brain Connectivity Mapping of Resting-State Functional Magnetic Resonance Imaging Signals

    Science.gov (United States)

    Li, Chiang-Shan R.

    2014-01-01

    Abstract The human inferior parietal lobule (IPL) comprised the lateral bank of the intraparietal sulcus, angular gyrus, and supramarginal gyrus, defined on the basis of anatomical landmarks and cytoarchitectural organization of neurons. However, it is not clear as to whether the three areas represent functional subregions within the IPL. For instance, imaging studies frequently identified clusters of activities that cut across areal boundaries. Here, we used resting-state functional magnetic resonance imaging (fMRI) data to examine how individual voxels within the IPL are best clustered according to their connectivity to the whole brain. The results identified a best estimate of seven clusters that are hierarchically arranged as the anterior, middle, and posterior subregions. The anterior, middle, and posterior IPL are each significantly connected to the somatomotor areas, superior/middle/inferior frontal gyri, and regions of the default mode network. This functional segregation is supported by recent cytoarchitechtonics and tractography studies. IPL showed hemispheric differences in connectivity that accord with a predominantly left parietal role in tool use and language processing and a right parietal role in spatial attention and mathematical cognition. The functional clusters may also provide a more parsimonious and perhaps even accurate account of regional activations of the IPL during a variety of cognitive challenges, as reported in earlier fMRI studies. PMID:24308753

  20. The luminosity function of star clusters in 20 star-forming galaxies based on Hubble legacy archive photometry

    International Nuclear Information System (INIS)

    Whitmore, Bradley C.; Bowers, Ariel S.; Lindsay, Kevin; Ansari, Asna; Evans, Jessica; Chandar, Rupali; Larsen, Soeren

    2014-01-01

    Luminosity functions (LFs) have been determined for star cluster populations in 20 nearby (4-30 Mpc), star-forming galaxies based on Advanced Camera for Surveys source lists generated by the Hubble Legacy Archive (HLA). These cluster catalogs provide one of the largest sets of uniform, automatically generated cluster candidates available in the literature at present. Comparisons are made with other recently generated cluster catalogs demonstrating that the HLA-generated catalogs are of similar quality, but in general do not go as deep. A typical cluster LF can be approximated by a power law, dN/dL∝L α , with an average value for α of –2.37 and rms scatter = 0.18 when using the F814W ('I') band. A comparison of fitting results based on methods that use binned and unbinned data shows good agreement, although there may be a systematic tendency for the unbinned (maximum likelihood) method to give slightly more negative values of α for galaxies with steeper LFs. We find that galaxies with high rates of star formation (or equivalently, with the brightest or largest numbers of clusters) have a slight tendency to have shallower values of α. In particular, the Antennae galaxy (NGC 4038/39), a merging system with a relatively high star formation rate (SFR), has the second flattest LF in the sample. A tentative correlation may also be present between Hubble type and values of α, in the sense that later type galaxies (i.e., Sd and Sm) appear to have flatter LFs. Hence, while there do appear to be some weak correlations, the relative similarity in the values of α for a large number of star-forming galaxies suggests that, to first order, the LFs are fairly universal. We examine the bright end of the LFs and find evidence for a downturn, although it only pertains to about 1% of the clusters. Our uniform database results in a small scatter (≈0.4 to 0.5 mag) in the correlation between the magnitude of the brightest cluster (M brightest ) and log of the number

  1. Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss.

    Science.gov (United States)

    Zhu, Tao; Niu, Deng-Ke

    2013-03-05

    Although intron loss in evolution has been described, the mechanism involved is still unclear. Three models have been proposed, the reverse transcriptase (RT) model, genomic deletion model and double-strand-break repair model. The RT model, also termed mRNA-mediated intron loss, suggests that cDNA molecules reverse transcribed from spliced mRNA recombine with genomic DNA causing intron loss. Many studies have attempted to test this model based on its predictions, such as simultaneous loss of adjacent introns, 3'-side bias of intron loss, and germline expression of intron-lost genes. Evidence either supporting or opposing the model has been reported. The mechanism of intron loss proposed in the RT model shares the process of reverse transcription with the formation of processed pseudogenes. If the RT model is correct, genes that have produced more processed pseudogenes are more likely to undergo intron loss. In the present study, we observed that the frequency of intron loss is correlated with processed pseudogene abundance by analyzing a new dataset of intron loss obtained in mice and rats. Furthermore, we found that mRNA molecules of intron-lost genes are mostly translated on free cytoplasmic ribosomes, a feature shared by mRNA molecules of the parental genes of processed pseudogenes and long interspersed elements. This feature is likely convenient for intron-lost gene mRNA molecules to be reverse transcribed. Analyses of adjacent intron loss, 3'-side bias of intron loss, and germline expression of intron-lost genes also support the RT model. Compared with previous evidence, the correlation between the abundance of processed pseudogenes and intron loss frequency more directly supports the RT model of intron loss. Exploring such a correlation is a new strategy to test the RT model in organisms with abundant processed pseudogenes.

  2. A functional bikaverin biosynthesis gene cluster in rare strains of Botrytis cinerea is positively controlled by VELVET.

    Directory of Open Access Journals (Sweden)

    Julia Schumacher

    Full Text Available The gene cluster responsible for the biosynthesis of the red polyketidic pigment bikaverin has only been characterized in Fusarium ssp. so far. Recently, a highly homologous but incomplete and nonfunctional bikaverin cluster has been found in the genome of the unrelated phytopathogenic fungus Botrytis cinerea. In this study, we provided evidence that rare B. cinerea strains such as 1750 have a complete and functional cluster comprising the six genes orthologous to Fusarium fujikuroi ffbik1-ffbik6 and do produce bikaverin. Phylogenetic analysis confirmed that the whole cluster was acquired from Fusarium through a horizontal gene transfer (HGT. In the bikaverin-nonproducing strain B05.10, the genes encoding bikaverin biosynthesis enzymes are nonfunctional due to deleterious mutations (bcbik2-3 or missing (bcbik1 but interestingly, the genes encoding the regulatory proteins BcBIK4 and BcBIK5 do not harbor deleterious mutations which suggests that they may still be functional. Heterologous complementation of the F. fujikuroi Δffbik4 mutant confirmed that bcbik4 of strain B05.10 is indeed fully functional. Deletion of bcvel1 in the pink strain 1750 resulted in loss of bikaverin and overproduction of melanin indicating that the VELVET protein BcVEL1 regulates the biosynthesis of the two pigments in an opposite manner. Although strain 1750 itself expresses a truncated BcVEL1 protein (100 instead of 575 aa that is nonfunctional with regard to sclerotia formation, virulence and oxalic acid formation, it is sufficient to regulate pigment biosynthesis (bikaverin and melanin and fenhexamid HydR2 type of resistance. Finally, a genetic cross between strain 1750 and a bikaverin-nonproducing strain sensitive to fenhexamid revealed that the functional bikaverin cluster is genetically linked to the HydR2 locus.

  3. Of the Nine Cytidine Deaminase-Like Genes in Arabidopsis, Eight Are Pseudogenes and Only One Is Required to Maintain Pyrimidine Homeostasis in Vivo.

    Science.gov (United States)

    Chen, Mingjia; Herde, Marco; Witte, Claus-Peter

    2016-06-01

    CYTIDINE DEAMINASE (CDA) catalyzes the deamination of cytidine to uridine and ammonia in the catabolic route of C nucleotides. The Arabidopsis (Arabidopsis thaliana) CDA gene family comprises nine members, one of which (AtCDA) was shown previously in vitro to encode an active CDA. A possible role in C-to-U RNA editing or in antiviral defense has been discussed for other members. A comprehensive bioinformatic analysis of plant CDA sequences, combined with biochemical functionality tests, strongly suggests that all Arabidopsis CDA family members except AtCDA are pseudogenes and that most plants only require a single CDA gene. Soybean (Glycine max) possesses three CDA genes, but only two encode functional enzymes and just one has very high catalytic efficiency. AtCDA and soybean CDAs are located in the cytosol. The functionality of AtCDA in vivo was demonstrated with loss-of-function mutants accumulating high amounts of cytidine but also CMP, cytosine, and some uridine in seeds. Cytidine hydrolysis in cda mutants is likely caused by NUCLEOSIDE HYDROLASE1 (NSH1) because cytosine accumulation is strongly reduced in a cda nsh1 double mutant. Altered responses of the cda mutants to fluorocytidine and fluorouridine indicate that a dual specific nucleoside kinase is involved in cytidine as well as uridine salvage. CDA mutants display a reduction in rosette size and have fewer leaves compared with the wild type, which is probably not caused by defective pyrimidine catabolism but by the accumulation of pyrimidine catabolism intermediates reaching toxic concentrations. © 2016 American Society of Plant Biologists. All Rights Reserved.

  4. Density functional study of TaSin (n = 1-3, 12) clusters adsorbed to graphene surface

    International Nuclear Information System (INIS)

    Guo Ping; Zheng Lin; Zheng Jiming; Zhang Ruizhi; Yang Luna; Ren, Zhaoyu

    2011-01-01

    A plane-wave density functional theory (DFT) calculations have been performed to investigate structural and electronic properties of TaSi n (n = 1-3, 12) clusters supported by graphene surface. The resulting adsorption structures are described and discussed in terms of stability, bonding, and electron transfer between the cluster and the graphene. The TaSi n clusters on graphene surface favor their free-standing ground-state structures. Especially in the cases of the linear TaSi 2 and the planar TaSi 3 , the graphene surface may catalyze the transition of the TaSi n clusters from an isomer of lower dimensionality into the ground-state structure. The adsorption site and configuration of TaSi n on graphene surface are dominated by the interaction between Ta atom and graphene. Ta atom prefers to adsorb on the hollow site of graphene, and Si atoms tend to locate on the bridge site. Further, the electron transfer is found to proceed from the cluster to the surface for n = 1 and 2, while its direction reverses as n > 2. For the case of TaSi, chemisorption is shown to prevail over physisorption as the dominant mode of surface-adsorbate interaction by charge density analysis.

  5. A numerical study of spin-dependent organization of alkali-metal atomic clusters using density-functional method

    Energy Technology Data Exchange (ETDEWEB)

    Liu Xuan, E-mail: liu.x.ad@m.titech.ac.jp; Ito, Haruhiko [Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology (Japan); Torikai, Eiko [Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi (Japan)

    2012-08-15

    We calculate the different geometric isomers of spin clusters composed of a small number of alkali-metal atoms using the UB3LYP density-functional method. The electron density distribution of clusters changes according to the value of total spin. Steric structures as well as planar structures arise when the number of atoms increases. The lowest spin state is the most stable and Li{sub n}, Na{sub n}, K{sub n}, Rb{sub n}, and Cs{sub n} with n = 2-8 can be formed in higher spin states. In the highest spin state, the preparation of clusters depends on the kind and the number of constituent atoms. The interaction energy between alkali-metal atoms and rare-gas atoms is smaller than the binding energy of spin clusters. Consequently, it is possible to self-organize the alkali-metal-atom clusters on a non-wetting substrate coated with rare-gas atoms.

  6. Nanomanufacturing of titania interfaces with controlled structural and functional properties by supersonic cluster beam deposition

    Energy Technology Data Exchange (ETDEWEB)

    Podestà, Alessandro, E-mail: alessandro.podesta@mi.infn.it, E-mail: pmilani@mi.infn.it; Borghi, Francesca; Indrieri, Marco; Bovio, Simone; Piazzoni, Claudio; Milani, Paolo, E-mail: alessandro.podesta@mi.infn.it, E-mail: pmilani@mi.infn.it [Centro Interdisciplinare Materiali e Interfacce Nanostrutturati (C.I.Ma.I.Na.), Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy)

    2015-12-21

    Great emphasis is placed on the development of integrated approaches for the synthesis and the characterization of ad hoc nanostructured platforms, to be used as templates with controlled morphology and chemical properties for the investigation of specific phenomena of great relevance in interdisciplinary fields such as biotechnology, medicine, and advanced materials. Here, we discuss the crucial role and the advantages of thin film deposition strategies based on cluster-assembling from supersonic cluster beams. We select cluster-assembled nanostructured titania (ns-TiO{sub 2}) as a case study to demonstrate that accurate control over morphological parameters can be routinely achieved, and consequently, over several relevant interfacial properties and phenomena, like surface charging in a liquid electrolyte, and proteins and nanoparticles adsorption. In particular, we show that the very good control of nanoscale morphology is obtained by taking advantage of simple scaling laws governing the ballistic deposition regime of low-energy, mass-dispersed clusters with reduced surface mobility.

  7. Nanomanufacturing of titania interfaces with controlled structural and functional properties by supersonic cluster beam deposition

    International Nuclear Information System (INIS)

    Podestà, Alessandro; Borghi, Francesca; Indrieri, Marco; Bovio, Simone; Piazzoni, Claudio; Milani, Paolo

    2015-01-01

    Great emphasis is placed on the development of integrated approaches for the synthesis and the characterization of ad hoc nanostructured platforms, to be used as templates with controlled morphology and chemical properties for the investigation of specific phenomena of great relevance in interdisciplinary fields such as biotechnology, medicine, and advanced materials. Here, we discuss the crucial role and the advantages of thin film deposition strategies based on cluster-assembling from supersonic cluster beams. We select cluster-assembled nanostructured titania (ns-TiO 2 ) as a case study to demonstrate that accurate control over morphological parameters can be routinely achieved, and consequently, over several relevant interfacial properties and phenomena, like surface charging in a liquid electrolyte, and proteins and nanoparticles adsorption. In particular, we show that the very good control of nanoscale morphology is obtained by taking advantage of simple scaling laws governing the ballistic deposition regime of low-energy, mass-dispersed clusters with reduced surface mobility

  8. Nanomanufacturing of titania interfaces with controlled structural and functional properties by supersonic cluster beam deposition

    Science.gov (United States)

    Podestà, Alessandro; Borghi, Francesca; Indrieri, Marco; Bovio, Simone; Piazzoni, Claudio; Milani, Paolo

    2015-12-01

    Great emphasis is placed on the development of integrated approaches for the synthesis and the characterization of ad hoc nanostructured platforms, to be used as templates with controlled morphology and chemical properties for the investigation of specific phenomena of great relevance in interdisciplinary fields such as biotechnology, medicine, and advanced materials. Here, we discuss the crucial role and the advantages of thin film deposition strategies based on cluster-assembling from supersonic cluster beams. We select cluster-assembled nanostructured titania (ns-TiO2) as a case study to demonstrate that accurate control over morphological parameters can be routinely achieved, and consequently, over several relevant interfacial properties and phenomena, like surface charging in a liquid electrolyte, and proteins and nanoparticles adsorption. In particular, we show that the very good control of nanoscale morphology is obtained by taking advantage of simple scaling laws governing the ballistic deposition regime of low-energy, mass-dispersed clusters with reduced surface mobility.

  9. Grupos funcionais de gramíneas forrageiras tropicais Functional clusters of tropical forage grasses

    Directory of Open Access Journals (Sweden)

    Carlindo Santos Rodrigues

    2012-06-01

    were submitted to cluster analysis by Tocher's optimization by adopting the mean Euclidean distance as a basic measure of dissimilarity. Grasses were grouped as follows: Summer - the group I (Xaraés, Massai, Mombaca and Marandu; group II (Molassa and Aruana; and group III (Jaraguagrass. Fall - group I (Mombaca, Massai, Xaraés, Marandu and Molassa; group II - (Jaraguagrass; and group III (Aruana. Possibly, the greater role of the tiller mortality factor in the formation of groups in the fall influenced the reorganization of the groups. The patterns of mass development of the different groups of grasses differ from each other as for the means of utilizing the resources available. There was a change in the scores of all factors with the change of the period from summer to Fall. The functional clustering of grasses demonstrates that gender and/or different species can be placed in the same group.

  10. 25. Steenbock symposium -- Biosynthesis and function of metal clusters for enzymes: Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-31

    This symposium was held June 10--14, 1997 in Madison, Wisconsin. The purpose of this conference was to provide a multidisciplinary forum for exchange of state-of-the-art information on biochemistry of enzymes that have an affinity for metal clusters. Attention is focused on the following: metal clusters involved in energy conservation and remediation; tungsten, molybdenum, and cobalt-containing enzymes; Fe proteins, and Mo-binding proteins; nickel enzymes; and nitrogenase.

  11. Benchmarking density-functional-theory calculations of rotational g tensors and magnetizabilities using accurate coupled-cluster calculations.

    Science.gov (United States)

    Lutnaes, Ola B; Teale, Andrew M; Helgaker, Trygve; Tozer, David J; Ruud, Kenneth; Gauss, Jürgen

    2009-10-14

    An accurate set of benchmark rotational g tensors and magnetizabilities are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster single-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the results obtained is established for the rotational g tensors by careful comparison with experimental data, taking into account zero-point vibrational corrections. After an analysis of the basis sets employed, extrapolation techniques are used to provide estimates of the basis-set-limit quantities, thereby establishing an accurate benchmark data set. The utility of the data set is demonstrated by examining a wide variety of density functionals for the calculation of these properties. None of the density-functional methods are competitive with the CCSD or CCSD(T) methods. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of density-functional calculations constrained to give the same electronic density. The importance of current dependence in exchange-correlation functionals is discussed in light of this comparison.

  12. Structures, stability, magnetic moments and growth strategies of the Fe{sub n}N (n = 1–7) clusters: All-electron density functional theory calculations

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhi, E-mail: lizhi81723700@163.com [School of Materials and Metallurgy, University of Science and Technology Liaoning, Anshan, 114051 (China); Zhao, Zhen [School of Chemistry and Life Science, Anshan Normal University, Anshan, 114007 (China)

    2017-02-01

    The geometries, electronic properties, magnetic moments and growth strategies of the Fe{sub n}N (n = 1–7) clusters are investigated using all-electron density functional theory. The results show that N doping significantly distorts the Fe{sub n} clusters. Fe{sub 4}N and Fe{sub 6}N clusters are more stable structures than other considered Fe{sub n}N clusters. Local peaks of HOMO-LUMO gap curve are found at n = 3, 7, implying that the chemical stability of the Fe{sub 3}N and Fe{sub 7}N clusters is higher. Fe{sub 2}N, Fe{sub 4}N and Fe{sub 6}N clusters have larger magnetic moments compared to other considered Fe{sub n}N (n = 1–7) clusters. It can be seen that the Fe{sub 5} clusters are easier to adsorb a Fe atom while the Fe{sub 4} clusters are easier to adsorb a N atom. The considered Fe{sub m}N clusters prefer to adsorb a Fe atom and larger Fe{sub m}N clusters are easier to grow. - Highlights: • The structural stability of the Fe{sub 4}N and Fe{sub 6}N clusters is higher. • The chemical stability of the Fe{sub 3}N and Fe{sub 7}N clusters is higher. • Fe{sub 5} clusters are easier to adsorb a Fe atom while Fe{sub 4} clusters are easier to adsorb a N atom. • Fe{sub n}N clusters prefer to adsorb a Fe atom.

  13. Quantum size correction to the work function and the centroid of excess charge in positively ionized simple metal clusters

    Directory of Open Access Journals (Sweden)

    M. Payami

    2003-12-01

    Full Text Available  In this work, we have shown the important role of the finite-size correction to the work function in predicting the correct position of the centroid of excess charge in positively charged simple metal clusters with different values . For this purpose, firstly we have calculated the self-consistent Kohn-Sham energies of neutral and singly-ionized clusters with sizes in the framework of local spin-density approximation and stabilized jellium model (SJM as well as simple jellium model (JM with rigid jellium. Secondly, we have fitted our results to the asymptotic ionization formulas both with and without the size correction to the work function. The results of fittings show that the formula containing the size correction predict a correct position of the centroid inside the jellium while the other predicts a false position, outside the jellium sphere.

  14. Density functional study of photoabsorption in metallic clusters using an exchange-correlation potential with correct long-range behaviour

    Energy Technology Data Exchange (ETDEWEB)

    Torres, M.B. [Dpto. de Matematicas y Computacion, Universidad de Burgos, Burgos (Spain); Balbas, L.C. [Dpto. de Fisica Teorica, Universidad de Valladolid, Valladolid (Spain)

    2002-06-17

    The atomic exchange-correlation (xc) potential with the correct -1/r asymptotic behaviour constructed by Parr and Ghosh (Parr R G and Ghosh S K 1995 Phys. Rev. A 51 3564) is adapted here to study, within time density functional theory, the linear response to external fields of (i) neutral and charged sodium clusters, and (ii) doped clusters of the type Na{sub n}Pb (n=4, 6, 16). The resulting photoabsorption cross sections are compared to experimental results, when available, and to results from previous calculations using local and non-local xc functionals. The calculated static polarizabilities and plasmon frequencies are closer to the experimental values than previous results. (author)

  15. Quantum size correction to the work function and centroid of excess charge in positively ionized simple metal clusters

    International Nuclear Information System (INIS)

    Payami, M.

    2004-01-01

    In this work, we have shown the important role of the finite-size correction to the work function in predicting the correct position of the centroid of excess charge in positively charged simple metal clusters with different r s values (2≤ r s ≥ 7). For this purpose, firstly we have calculated the self-consistent Kohn-Sham energies of neutral and singly-ionized clusters with sizes 2≤ N ≥100 in the framework of local spin-density approximation and stabilized jellium model as well as simple jellium model with rigid jellium. Secondly, we have fitted our results to the asymptotic ionization formulas both with and without the size correction to the work function. The results of fittings show that the formula containing the size correction predict a correct position of the centroid inside the jellium while the other predicts a false position, outside the jellium sphere

  16. Phylogenetic relationships among Brazilian howler monkeys, genus Alouatta (Platyrrhini, Atelidae, based on g1-globin pseudogene sequences

    Directory of Open Access Journals (Sweden)

    Carla Maria Meireles

    1999-09-01

    Full Text Available The genus Alouatta (howler monkeys is the most widely distributed of New World primates, and has been arranged in three species groups: the Central American Alouatta palliata group and the South American Alouatta seniculus and Alouatta caraya groups. While the latter is monotypic, the A. seniculus group encompasses at least three species (A. seniculus, A. belzebul and A. fusca. In the present study, approximately 600 base pairs of the g1-globin pseudogene were sequenced in the four Brazilian species (A. seniculus, A. belzebul, A. fusca and A. caraya. Maximum parsimony and maximum likelihood methods yielded phylogenetic trees with the same arrangement: {A. caraya [A. seniculus (A. fusca, A. belzebul]}. The most parsimonious tree had bootstrap values greater than 82% for all groupings, and strength of grouping values of at least 2, supporting the sister clade of A. fusca and A. belzebul. The study also confirmed the presence of a 150-base pair Alu insertion element and a 1.8-kb deletion in the g1-globin pseudogene in A. fusca, features found previously in the remaining three species. The cladistic classification based on molecular data agrees with those of morphological studies, with the monospecific A. caraya group being clearly differentiated from the A. seniculus group.Os guaribas, do gênero Alouatta, que são os primatas do Novo Mundo com maior distribuição geográfica, têm sido colocados em três grupos de espécies: o grupo Alouatta palliata da América central, e os grupos sulamericanos Alouatta seniculus e Alouatta caraya. Este último é monotípico, mas o grupo A. seniculus inclui pelo menos três espécies (A. seniculus, A. belzebul e A. fusca. Neste estudo, foram seqüenciados aproximadamente 600 pares de base do pseudogene globina g1 nas quatro espécies brasileiras (A. seniculus, A. belzebul, A. fusca e A. caraya. Os métodos de máxima parcimônia e máxima verossimilhança produziram árvores filogenéticas com o mesmo arranjo

  17. RFLPs for ATP1BL1 (. beta. subunit Na sup + /K sup + ATPase pseudogene) on chromosome 4

    Energy Technology Data Exchange (ETDEWEB)

    Georgiou, C.; Shull, M. (Univ. of Iowa Hospitals, Iowa City (USA)); Lingrel, J.B.; Murray, J.C.; Lane, L.K. (Univ. of Cincinnati College of Medicine, OH (USA))

    1989-11-11

    {beta}51-1(1.4) contains a 1.4kb EcoRI fragment, free of repetitive elements, from the {beta} subunit Na{sup +}/K{sup +} ATPase pseudogene (ATP1BL1). The vector is pUG18. EcoRI identifies 2 allelic bands of 7.0 and 14.0 kb. KpnI identifies 2 allelic bands of 19.0 and 23.0 kb. The probe was localized to chromosome 4 by linkage to chromosome 4 markers (D4S35, KIT) and somatic cell hybrid analysis. Co-dominant segregation was shown in 32 and 16 CEPH families for EcoRI and KpnI respectively.

  18. Studying the varied shapes of gold clusters by an elegant optimization algorithm that hybridizes the density functional tight-binding theory and the density functional theory

    Science.gov (United States)

    Yen, Tsung-Wen; Lim, Thong-Leng; Yoon, Tiem-Leong; Lai, S. K.

    2017-11-01

    We combined a new parametrized density functional tight-binding (DFTB) theory (Fihey et al. 2015) with an unbiased modified basin hopping (MBH) optimization algorithm (Yen and Lai 2015) and applied it to calculate the lowest energy structures of Au clusters. From the calculated topologies and their conformational changes, we find that this DFTB/MBH method is a necessary procedure for a systematic study of the structural development of Au clusters but is somewhat insufficient for a quantitative study. As a result, we propose an extended hybridized algorithm. This improved algorithm proceeds in two steps. In the first step, the DFTB theory is employed to calculate the total energy of the cluster and this step (through running DFTB/MBH optimization for given Monte-Carlo steps) is meant to efficiently bring the Au cluster near to the region of the lowest energy minimum since the cluster as a whole has explicitly considered the interactions of valence electrons with ions, albeit semi-quantitatively. Then, in the second succeeding step, the energy-minimum searching process will continue with a skilledly replacement of the energy function calculated by the DFTB theory in the first step by one calculated in the full density functional theory (DFT). In these subsequent calculations, we couple the DFT energy also with the MBH strategy and proceed with the DFT/MBH optimization until the lowest energy value is found. We checked that this extended hybridized algorithm successfully predicts the twisted pyramidal structure for the Au40 cluster and correctly confirms also the linear shape of C8 which our previous DFTB/MBH method failed to do so. Perhaps more remarkable is the topological growth of Aun: it changes from a planar (n =3-11) → an oblate-like cage (n =12-15) → a hollow-shape cage (n =16-18) and finally a pyramidal-like cage (n =19, 20). These varied forms of the cluster's shapes are consistent with those reported in the literature.

  19. Density functional study of structural and catalytic properties of free and supported metal nano cluster; Dichtefunktionalstudie der strukturellen und katalytischen Eigenschaften freier und getraegerter Metallnanocluster

    Energy Technology Data Exchange (ETDEWEB)

    Huber, B.

    2007-04-11

    The structural and catalytic properties of metal clusters were determined in the framework of density functional theory. The first part of this work investigates the electronic and geometrical structure of sodium clusters with up to 309 atoms. The ground-state structures of the clusters are determined and the corresponding electronic density of states is compared to experimental photoelectron spectras. The excellent agreement to the experimental results indicates that the correct growth motive of the sodium clusters was found. Small clusters from Na{sup -}{sub 20} to Na{sup -}{sub 42} prefer pentagonal and icosahedral structures with anti-Mackay overlayers, while clusters larger than Na{sup -}{sub 50} prefer icosahedral structures with Mackay overlayers. Clusters between the closed-shell Mackay Clusters often exhibit a twist deformation with respect to the regular Mackay positions. The second part of this work investigates the catalytic properties of free and supported palladium clusters. For both cases the oxidation of small Pd{sub N} clusters (N {<=} 9) was studied. It turned out that MgO supported Pd-clusters dissociate oxygen with a significant lower reaction energy than free clusters or supported systems with particles consisting of several thousands of atoms. The reaction with oxygen transforms the non-crystalline Pd-clusters into crystalline Pd{sub x}O{sub y} nano-oxide clusters that are in epitaxy with the underlying support. Simulations of the CO oxidation on the Pd{sub x}O{sub y} cluster predict a low-temperature reaction mechanism. By calculating the electronic density of states and CO stretch frequencies, different ways of verifying the results experimentally are discussed. (orig.)

  20. RNA-based mutation analysis identifies an unusual MSH6 splicing defect and circumvents PMS2 pseudogene interference.

    Science.gov (United States)

    Etzler, J; Peyrl, A; Zatkova, A; Schildhaus, H-U; Ficek, A; Merkelbach-Bruse, S; Kratz, C P; Attarbaschi, A; Hainfellner, J A; Yao, S; Messiaen, L; Slavc, I; Wimmer, K

    2008-02-01

    Heterozygous germline mutations in one of the mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2 cause hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch syndrome, a dominantly inherited cancer susceptibility syndrome. Recent reports provide evidence for a novel recessively inherited cancer syndrome with constitutive MMR deficiency due to biallelic germline mutations in one of the MMR genes. MMR-deficiency (MMR-D) syndrome is characterized by childhood brain tumors, hematological and/or gastrointestinal malignancies, and signs of neurofibromatosis type 1 (NF1). We established an RNA-based mutation detection assay for the four MMR genes, since 1) a number of splicing defects may escape detection by the analysis of genomic DNA, and 2) DNA-based mutation detection in the PMS2 gene is severely hampered by the presence of multiple highly similar pseudogenes, including PMS2CL. Using this assay, which is based on direct cDNA sequencing of RT-PCR products, we investigated two families with children suspected to suffer from MMR-D syndrome. We identified a homozygous complex MSH6 splicing alteration in the index patients of the first family and a novel homozygous PMS2 mutation (c.182delA) in the index patient of the second family. Furthermore, we demonstrate, by the analysis of a PMS2/PMS2CL "hybrid" allele carrier, that RNA-based PMS2 testing effectively avoids the caveats of genomic DNA amplification approaches; i.e., pseudogene coamplification as well as allelic dropout, and will, thus, allow more sensitive mutation analysis in MMR deficiency and in HNPCC patients with PMS2 defects. (c) 2007 Wiley-Liss, Inc.

  1. The Impact of Multi-pollutant Clusters on the Association between Fine Particulate Air Pollution and Microvascular Function

    Science.gov (United States)

    Ljungman, Petter L.; Wilker, Elissa H.; Rice, Mary B.; Austin, Elena; Schwartz, Joel; Gold, Diane R.; Koutrakis, Petros; Benjamin, Emelia J.; Vita, Joseph A.; Mitchell, Gary F.; Vasan, Ramachandran S.

    2016-01-01

    Background Prior studies including the Framingham Heart Study have suggested associations between single components of air pollution and vascular function; however, underlying mixtures of air pollution may have distinct associations with vascular function. Methods We used a k-means approach to construct five distinct pollution mixtures from elemental analyses of particle filters, air pollution monitoring data, and meteorology. Exposure was modeled as an interaction between fine particle mass (PM2.5), and concurrent pollution cluster. Outcome variables were two measures of microvascular function in the fingertip in the Framingham Offspring and Third Generation cohorts from 2003-2008. Results In 1,720 participants, associations between PM2.5 and baseline pulse amplitude tonometry differed by air pollution cluster (interaction p value 0.009). Higher PM2.5 on days with low mass concentrations but high proportion of ultrafine particles from traffic was associated with 18% (95% CI 4.6%; 33%) higher baseline pulse amplitude per 5 μg/m3 and days with high contributions of oil and wood combustion with 16% (95% CI 0.2%; 34%) higher baseline pulse amplitude. We observed no variation in associations of PM2.5 with hyperemic response to ischemia observed across air pollution clusters. Conclusions PM2.5 exposure from air pollution mixtures with large contributions of local ultrafine particles from traffic, heating oil and wood combustion was associated with higher baseline pulse amplitude but not PAT ratio. Our findings suggest little association between acute exposure to air pollution clusters reflective of select sources and hyperemic response to ischemia, but possible associations with excessive small artery pulsatility with potentially deleterious microvascular consequences. PMID:26562062

  2. Clusters of Insomnia Disorder: An Exploratory Cluster Analysis of Objective Sleep Parameters Reveals Differences in Neurocognitive Functioning, Quantitative EEG, and Heart Rate Variability.

    Science.gov (United States)

    Miller, Christopher B; Bartlett, Delwyn J; Mullins, Anna E; Dodds, Kirsty L; Gordon, Christopher J; Kyle, Simon D; Kim, Jong Won; D'Rozario, Angela L; Lee, Rico S C; Comas, Maria; Marshall, Nathaniel S; Yee, Brendon J; Espie, Colin A; Grunstein, Ronald R

    2016-11-01

    To empirically derive and evaluate potential clusters of Insomnia Disorder through cluster analysis from polysomnography (PSG). We hypothesized that clusters would differ on neurocognitive performance, sleep-onset measures of quantitative ( q )-EEG and heart rate variability (HRV). Research volunteers with Insomnia Disorder (DSM-5) completed a neurocognitive assessment and overnight PSG measures of total sleep time (TST), wake time after sleep onset (WASO), and sleep onset latency (SOL) were used to determine clusters. From 96 volunteers with Insomnia Disorder, cluster analysis derived at least two clusters from objective sleep parameters: Insomnia with normal objective sleep duration (I-NSD: n = 53) and Insomnia with short sleep duration (I-SSD: n = 43). At sleep onset, differences in HRV between I-NSD and I-SSD clusters suggest attenuated parasympathetic activity in I-SSD (P insomnia clusters derived from cluster analysis differ in sleep onset HRV. Preliminary data suggest evidence for three clusters in insomnia with differences for sustained attention and sleep-onset q -EEG. Insomnia 100 sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR) identification number 12612000049875. URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=347742. © 2016 Associated Professional Sleep Societies, LLC.

  3. Unraveling the hidden heterogeneities of breast cancer based on functional miRNA cluster.

    Directory of Open Access Journals (Sweden)

    Li Li

    Full Text Available It has become increasingly clear that the current taxonomy of clinical phenotypes is mixed with molecular heterogeneity, which potentially affects the treatment effect for involved patients. Defining the hidden molecular-distinct diseases using modern large-scale genomic approaches is therefore useful for refining clinical practice and improving intervention strategies. Given that microRNA expression profiling has provided a powerful way to dissect hidden genetic heterogeneity for complex diseases, the aim of the study was to develop a bioinformatics approach that identifies microRNA features leading to the hidden subtyping of complex clinical phenotypes. The basic strategy of the proposed method was to identify optimal miRNA clusters by iteratively partitioning the sample and feature space using the two-ways super-paramagnetic clustering technique. We evaluated the obtained optimal miRNA cluster by determining the consistency of co-expression and the chromosome location among the within-cluster microRNAs, and concluded that the optimal miRNA cluster could lead to a natural partition of disease samples. We applied the proposed method to a publicly available microarray dataset of breast cancer patients that have notoriously heterogeneous phenotypes. We obtained a feature subset of 13 microRNAs that could classify the 71 breast cancer patients into five subtypes with significantly different five-year overall survival rates (45%, 82.4%, 70.6%, 100% and 60% respectively; p = 0.008. By building a multivariate Cox proportional-hazards prediction model for the feature subset, we identified has-miR-146b as one of the most significant predictor (p = 0.045; hazard ratios = 0.39. The proposed algorithm is a promising computational strategy for dissecting hidden genetic heterogeneity for complex diseases, and will be of value for improving cancer diagnosis and treatment.

  4. Data Clustering

    Science.gov (United States)

    Wagstaff, Kiri L.

    2012-03-01

    clustering, in which some partial information about item assignments or other components of the resulting output are already known and must be accommodated by the solution. Some algorithms seek a partition of the data set into distinct clusters, while others build a hierarchy of nested clusters that can capture taxonomic relationships. Some produce a single optimal solution, while others construct a probabilistic model of cluster membership. More formally, clustering algorithms operate on a data set X composed of items represented by one or more features (dimensions). These could include physical location, such as right ascension and declination, as well as other properties such as brightness, color, temporal change, size, texture, and so on. Let D be the number of dimensions used to represent each item, xi ∈ RD. The clustering goal is to produce an organization P of the items in X that optimizes an objective function f : P -> R, which quantifies the quality of solution P. Often f is defined so as to maximize similarity within a cluster and minimize similarity between clusters. To that end, many algorithms make use of a measure d : X x X -> R of the distance between two items. A partitioning algorithm produces a set of clusters P = {c1, . . . , ck} such that the clusters are nonoverlapping (c_i intersected with c_j = empty set, i != j) subsets of the data set (Union_i c_i=X). Hierarchical algorithms produce a series of partitions P = {p1, . . . , pn }. For a complete hierarchy, the number of partitions n’= n, the number of items in the data set; the top partition is a single cluster containing all items, and the bottom partition contains n clusters, each containing a single item. For model-based clustering, each cluster c_j is represented by a model m_j , such as the cluster center or a Gaussian distribution. The wide array of available clustering algorithms may seem bewildering, and covering all of them is beyond the scope of this chapter. Choosing among them for a

  5. Rapid differentiation of Staphylococcus aureus isolates harbouring egc loci with pseudogenes psient1 and psient2 and the selu or seluv gene using PCR-RFLP.

    Science.gov (United States)

    Collery, Mark M; Smyth, Cyril J

    2007-02-01

    The egc locus of Staphylococus aureus harbours two enterotoxin genes (seg and sei) and three enterotoxin-like genes (selm, seln and selo). Between the sei and seln genes are located two pseudogenes, psient1 and psient2, or the selu or seluv gene. While these two alternative sei-seln intergenic regions can be distinguished by PCR, to date, DNA sequencing has been the only confirmatory option because of the very high degree of sequence similarity between egc loci bearing the pseudogenes and the selu or seluv gene. In silico restriction enzyme digestion of genomic regions encompassing the egc locus from the 3' end of the sei gene through the 5' first quarter of the seln gene allowed pseudogene- and selu- or seluv-bearing egc loci to be distinguished by PCR-RFLP. Experimental application of these findings demonstrated that endonuclease HindIII cleaved PCR amplimers bearing pseudogenes but not those with a selu or seluv gene, while selu- or seluv-bearing amplimers were susceptible to cleavage by endonuclease HphI, but not by endonuclease HindIII. The restriction enzyme BccI cleaved selu- or seluv-harbouring amplimers at a unique restriction site created by their signature 15 bp insertion compared with pseudogene-bearing amplimers, thereby allowing distinction of these egc loci. PCR-RFLP analysis using these restriction enzymes provides a rapid, easy to interpret alternative to DNA sequencing for verification of PCR findings on the nature of an egc locus type, and can also be used for the primary identification of the intergenic sei-seln egc locus type.

  6. Ensemble averaged structure–function relationship for nanocrystals: effective superparamagnetic Fe clusters with catalytically active Pt skin [Ensemble averaged structure-function relationship for composite nanocrystals: magnetic bcc Fe clusters with catalytically active fcc Pt skin

    Energy Technology Data Exchange (ETDEWEB)

    Petkov, Valeri [Central Michigan University, Mt. Pleasant, MI (United States); Prasai, Binay [Central Michigan University, Mt. Pleasant, MI (United States); Shastri, Sarvjit [Argonne National Lab. (ANL), Argonne, IL (United States). X-ray Science Division; Park, Hyun-Uk [Sungkyunkwan University, Suwon (Korea). Department of Chemistry; Kwon, Young-Uk [Sungkyunkwan University, Suwon (Korea). Department of Chemistry; Skumryev, Vassil [Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona (Spain); Universitat Autònoma de Barcelona (Spain). Department of Physics

    2017-09-12

    Practical applications require the production and usage of metallic nanocrystals (NCs) in large ensembles. Besides, due to their cluster-bulk solid duality, metallic NCs exhibit a large degree of structural diversity. This poses the question as to what atomic-scale basis is to be used when the structure–function relationship for metallic NCs is to be quantified precisely. In this paper, we address the question by studying bi-functional Fe core-Pt skin type NCs optimized for practical applications. In particular, the cluster-like Fe core and skin-like Pt surface of the NCs exhibit superparamagnetic properties and a superb catalytic activity for the oxygen reduction reaction, respectively. We determine the atomic-scale structure of the NCs by non-traditional resonant high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Using the experimental structure data we explain the observed magnetic and catalytic behavior of the NCs in a quantitative manner. Lastly, we demonstrate that NC ensemble-averaged 3D positions of atoms obtained by advanced X-ray scattering techniques are a very proper basis for not only establishing but also quantifying the structure–function relationship for the increasingly complex metallic NCs explored for practical applications.

  7. Identification of Voxels Confounded by Venous Signals Using Resting-State fMRI Functional Connectivity Graph Clustering

    Directory of Open Access Journals (Sweden)

    Klaudius eKalcher

    2015-12-01

    Full Text Available Identifying venous voxels in fMRI datasets is important to increase the specificity of fMRI analyses to microvasculature in the vicinity of the neural processes triggering the BOLD response. This is, however, difficult to achieve in particular in typical studies where magnitude images of BOLD EPI are the only data available. In this study, voxelwise functional connectivity graphs were computed on minimally preprocessed low TR (333 ms multiband resting-state fMRI data, using both high positive and negative correlations to define edges between nodes (voxels. A high correlation threshold for binarization ensures that most edges in the resulting sparse graph reflect the high coherence of signals in medium to large veins. Graph clustering based on the optimization of modularity was then employed to identify clusters of coherent voxels in this graph, and all clusters of 50 or more voxels were then interpreted as corresponding to medium to large veins. Indeed, a comparison with SWI reveals that 75.6 ± 5.9% of voxels within these large clusters overlap with veins visible in the SWI image or lie outside the brain parenchyma. Some of the remainingdifferences between the two modalities can be explained by imperfect alignment or geometric distortions between the two images. Overall, the graph clustering based method for identifying venous voxels has a high specificity as well as the additional advantages of being computed in the same voxel grid as the fMRI dataset itself and not needingany additional data beyond what is usually acquired (and exported in standard fMRI experiments.

  8. Bacterial xylose isomerases from the mammal gut Bacteroidetes cluster function in Saccharomyces cerevisiae for effective xylose fermentation.

    Science.gov (United States)

    Peng, Bingyin; Huang, Shuangcheng; Liu, Tingting; Geng, Anli

    2015-05-17

    Xylose isomerase (XI) catalyzes the conversion of xylose to xylulose, which is the key step for anaerobic ethanolic fermentation of xylose. Very few bacterial XIs can function actively in Saccharomyces cerevisiae. Here, we illustrate a group of XIs that would function for xylose fermentation in S. cerevisiae through phylogenetic analysis, recombinant yeast strain construction, and xylose fermentation. Phylogenetic analysis of deposited XI sequences showed that XI evolutionary relationship was highly consistent with the bacterial taxonomic orders and quite a few functional XIs in S. cerevisiae were clustered with XIs from mammal gut Bacteroidetes group. An XI from Bacteroides valgutus in this cluster was actively expressed in S. cerevisiae with an activity comparable to the fungal XI from Piromyces sp. Two XI genes were isolated from the environmental metagenome and they were clustered with XIs from environmental Bacteroidetes group. These two XIs could not be expressed in yeast with activity. With the XI from B. valgutus expressed in S. cerevisiae, background yeast strains were optimized by pentose metabolizing pathway enhancement and adaptive evolution in xylose medium. Afterwards, more XIs from the mammal gut Bacteroidetes group, including those from B. vulgatus, Tannerella sp. 6_1_58FAA_CT1, Paraprevotella xylaniphila and Alistipes sp. HGB5, were individually transformed into S. cerevisiae. The known functional XI from Orpinomyces sp. ukk1, a mammal gut fungus, was used as the control. All the resulting recombinant yeast strains were able to ferment xylose. The respiration-deficient strains harboring B. vulgatus and Alistipes sp. HGB5 XI genes respectively obtained specific xylose consumption rate of 0.662 and 0.704 g xylose gcdw(-1) h(-1), and ethanol specific productivity of 0.277 and 0.283 g ethanol gcdw(-1) h(-1), much comparable to those obtained by the control strain carrying Orpinomyces sp. ukk1 XI gene. This study demonstrated that XIs clustered in the

  9. Magnetism, structures and stabilities of cluster assembled TM@Si nanotubes (TM = Cr, Mn and Fe): a density functional study.

    Science.gov (United States)

    Dhaka, Kapil; Bandyopadhyay, Debashis

    2016-08-02

    The present study reports transition metal (TM = Cr, Mn and Fe) doped silicon nanotubes with tunable band structures and magnetic properties by careful selection of cluster assemblies as building blocks using the first-principles density functional theory. We found that the transition metal doping and in addition, the hydrogen termination process can stabilize the pure silicon nanoclusters or cluster assemblies and then it could be extended as magnetic nanotubes with finite magnetic moments. Study of the band structures and density of states (DOS) of different empty and TM doped nanotubes (Type 1 to Type 4) show that these nanotubes are useful as metals, semiconductors, semi-metals and half-metals. These designer magnetic materials could be useful in spintronics and magnetic devices of nanoscale order.

  10. Functional characterization of KanP, a methyltransferase from the kanamycin biosynthetic gene cluster of Streptomyces kanamyceticus.

    Science.gov (United States)

    Nepal, Keshav Kumar; Yoo, Jin Cheol; Sohng, Jae Kyung

    2010-09-20

    KanP, a putative methyltransferase, is located in the kanamycin biosynthetic gene cluster of Streptomyces kanamyceticus ATCC12853. Amino acid sequence analysis of KanP revealed the presence of S-adenosyl-L-methionine binding motifs, which are present in other O-methyltransferases. The kanP gene was expressed in Escherichia coli BL21 (DE3) to generate the E. coli KANP recombinant strain. The conversion of external quercetin to methylated quercetin in the culture extract of E. coli KANP proved the function of kanP as S-adenosyl-L-methionine-dependent methyltransferase. This is the first report concerning the identification of an O-methyltransferase gene from the kanamycin gene cluster. The resistant activity assay and RT-PCR analysis demonstrated the leeway for obtaining methylated kanamycin derivatives from the wild-type strain of kanamycin producer. 2009 Elsevier GmbH. All rights reserved.

  11. Hybrid RPA-cluster model for the dipole strength function of sup(11)Li

    International Nuclear Information System (INIS)

    Teruya, N.; Bertulani, C.A.; Krewald, S.

    1990-09-01

    A hybrid RPA-cluster model is developed and applied to the calculation of the dipole response of sup(11)L1. A strong collective state at 1.81 MeV is found. Its width is predicted to be 4.0 MeV. The electromagnetic excitation cross section was found to be 700 mb for sup(11)L1 + sup(208)Pb (E = 800 MeV/n), close to the experimental result. (author)

  12. Density-functional theory study of ionic inhomogeneity in metal clusters using SC-ISJM

    Science.gov (United States)

    Payami, Mahmoud; Mahmoodi, Tahereh

    2017-12-01

    In this work we have applied the recently formulated self-compressed inhomogeneous stabilized jellium model [51] to describe the equilibrium electronic and geometric properties of atomic-closed-shell simple metal clusters of AlN (N = 13, 19, 43, 55, 79, 87, 135, 141), NaN, and CsN (N = 9, 15, 27, 51, 59, 65, 89, 113). To validate the results, we have also performed first-principles pseudo-potential calculations and used them as our reference. In the model, we have considered two regions consisting of ;surface; and ;inner; ones, the border separating them being sharp. This generalization makes possible to decouple the relaxations of different parts of the system. The results show that the present model correctly predicts the size reductions seen in most of the clusters. It also predicts increase in size of some clusters, as observed from first-principles results. Moreover, the changes in inter-layer distances, being as contractions or expansions, are in good agreement with the atomic simulation results. For a more realistic description of the properties, it is possible to improve the method of choosing the surface thicknesses or generalize the model to include more regions than just two.

  13. Effects of Galaxy collisions on the structure and evolution of Galaxy clusters. I. Mass and luminosity functions and background light

    International Nuclear Information System (INIS)

    Miller, G.E.; Department of Astronomy, University of Texas at Austin)

    1983-01-01

    The role of galaxy collisions in controlling the form of the galaxy mass and luminosity functions and in creating a diffuse background light is investigated by means of a direct computer simulation. Galaxy collisions are treated in a realistic manner, including both galaxy mergers and tidal encounters. A large number of theoretical studies of a galaxy collisions were consulted to formulate the basic input physics of collision cross sections. Despite this large number of studies, there remains considerable uncertainty in the effects of a collision on a galaxy due mainly to our lack of knowledge of the orbital distribution of matter in galaxies. To improve this situation, some methods of semiempirical calibration are suggested: for example, a survey of background light in clusters of different richness and morphological classes. If real galaxies are represented by galaxy models where the bulk of the matter is on radial, rather than circular, orbits, then tidal collisions are more damaging and there are a number of interesting effects: Repeated tidal encounters lead to galaxy mass and luminosity functions which are largely independent of model parameters and the initial galaxy mass function. It appears unlikely that the form of the average present-day luminosity function characteristic of both field and cluster galaxies is due to collisions, but certain observed deviations from the average found by Heiligman and Turner and by Dressler may be a signature of collisions, in particular a flat faint-end slope. The amount of luminous matter stripped from the galaxies in the simulations agrees with the amount of diffuse background light seen in the Coma Cluster

  14. Enhancing Executive Functions Among Dutch Elementary School Children Using the Train Your Mind Program: Protocol for a Cluster Randomized Trial.

    Science.gov (United States)

    Bervoets, Joachim; Jonkman, Lisa M; Mulkens, Sandra; de Vries, Hein; Kok, Gerjo

    2018-06-07

    Executive functions are higher cognitive control functions, which are essential to physical and psychological well-being, academic performance, and healthy social relationships. Executive functions can be trained, albeit without broad transfer, to this date. Broad transfer entails the translation of improved cognitive functions to daily life (behaviors). The intervention Train your Mind was designed to train executive functions among elementary school children aged 9 to 11 years, and obtain broad transfer in terms of enhanced physical activity, healthy eating, and socioemotional regulation. This paper aims to describe the cluster randomized trial to test the effectiveness of the Train your Mind intervention. Train your Mind was integrated into the existing school curriculum for 8 months (25 weeks excluding holidays). The effectiveness of the intervention was tested in a cluster randomized trial comprising 13 schools, 34 groups (school classes), and 800 children, using a battery of 6 computer tasks at pre- and postmeasurement. Each of the 3 core executive functions was measured by 2 tasks (Flanker and Go/No-Go; N-Back and Running Span; Attention Switching Task and Dots/Triangles). Moreover, we administered questionnaires that measure emotion-regulation, cognitive errors, physical activity, dietary habits, and the psycho-social determinants of diet and physical activity. Body mass index was also measured. Multilevel analyses will account for clustering at the school and group levels, and randomization took place at the school level. Results are currently being analyzed. The main purpose of this study is to test Train your Mind's effectiveness in enhancing executive functions. Second, we investigate whether increased executive functions lead to improved physical activity and healthy eating. If found effective, executive function training could easily be integrated into school curricula everywhere, and as such, boost health, academic performance, and emotion

  15. Analysis of NFU-1 metallocofactor binding-site substitutions-impacts on iron-sulfur cluster coordination and protein structure and function.

    Science.gov (United States)

    Wesley, Nathaniel A; Wachnowsky, Christine; Fidai, Insiya; Cowan, J A

    2017-11-01

    Iron-sulfur (Fe/S) clusters are ancient prosthetic groups found in numerous metalloproteins and are conserved across all kingdoms of life due to their diverse, yet essential functional roles. Genetic mutations to a specific subset of mitochondrial Fe/S cluster delivery proteins are broadly categorized as disease-related under multiple mitochondrial dysfunction syndrome (MMDS), with symptoms indicative of a general failure of the metabolic system. Multiple mitochondrial dysfunction syndrome 1 (MMDS1) arises as a result of the missense mutation in NFU1, an Fe/S cluster scaffold protein, which substitutes a glycine near the Fe/S cluster-binding pocket to a cysteine (p.Gly208Cys). This substitution has been shown to promote protein dimerization such that cluster delivery to NFU1 is blocked, preventing downstream cluster trafficking. However, the possibility of this additional cysteine, located adjacent to the cluster-binding site, serving as an Fe/S cluster ligand has not yet been explored. To fully understand the consequences of this Gly208Cys replacement, complementary substitutions at the Fe/S cluster-binding pocket for native and Gly208Cys NFU1 were made, along with six other variants. Herein, we report the results of an investigation on the effect of these substitutions on both cluster coordination and NFU1 structure and function. The data suggest that the G208C substitution does not contribute to cluster binding. Rather, replacement of the glycine at position 208 changes the oligomerization state as a result of global structural alterations that result in the downstream effects manifest as MMDS1, but does not perturb the coordination chemistry of the Fe-S cluster. © 2017 Federation of European Biochemical Societies.

  16. Diversity, evolution, and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora.

    Science.gov (United States)

    Rezzonico, Fabio; Smits, Theo H M; Duffy, Brion

    2011-06-01

    The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system confers acquired heritable immunity against mobile nucleic acid elements in prokaryotes, limiting phage infection and horizontal gene transfer of plasmids. In CRISPR arrays, characteristic repeats are interspersed with similarly sized nonrepetitive spacers derived from transmissible genetic elements and acquired when the cell is challenged with foreign DNA. New spacers are added sequentially and the number and type of CRISPR units can differ among strains, providing a record of phage/plasmid exposure within a species and giving a valuable typing tool. The aim of this work was to investigate CRISPR diversity in the highly homogeneous species Erwinia amylovora, the causal agent of fire blight. A total of 18 CRISPR genotypes were defined within a collection of 37 cosmopolitan strains. Strains from Spiraeoideae plants clustered in three major groups: groups II and III were composed exclusively of bacteria originating from the United States, whereas group I generally contained strains of more recent dissemination obtained in Europe, New Zealand, and the Middle East. Strains from Rosoideae and Indian hawthorn (Rhaphiolepis indica) clustered separately and displayed a higher intrinsic diversity than that of isolates from Spiraeoideae plants. Reciprocal exclusion was generally observed between plasmid content and cognate spacer sequences, supporting the role of the CRISPR/Cas system in protecting against foreign DNA elements. However, in several group III strains, retention of plasmid pEU30 is inconsistent with a functional CRISPR/Cas system.

  17. Transcriptional interference networks coordinate the expression of functionally-related genes clustered in the same genomic loci

    Directory of Open Access Journals (Sweden)

    Zsolt eBoldogkoi

    2012-07-01

    Full Text Available The regulation of gene expression is essential for normal functioning of biological systems in every form of life. Gene expression is primarily controlled at the level of transcription, especially at the phase of initiation. Non-coding RNAs are one of the major players at every level of genetic regulation, including the control of chromatin organisation, transcription, various post-transcriptional processes and translation. In this study, the Transcriptional Interference Network (TIN hypothesis was put forward in an attempt to explain the global expression of antisense RNAs and the overall occurrence of tandem gene clusters in the genomes of various biological systems ranging from viruses to mammalian cells. The TIN hypothesis suggests the existence of a novel layer of genetic regulation, based on the interactions between the transcriptional machineries of neighbouring genes at their overlapping regions, which are assumed to play a fundamental role in coordinating gene expression within a cluster of functionally-linked genes. It is claimed that the transcriptional overlaps between adjacent genes are much more widespread in genomes than is thought today. The Waterfall model of the TIN hypothesis postulates a unidirectional effect of upstream genes on the transcription of downstream genes within a cluster of tandemly-arrayed genes, while the Seesaw model proposes a mutual interdependence of gene expression between the oppositely-oriented genes. The TIN represents an auto-regulatory system with an exquisitely timed and highly synchronised cascade of gene expression in functionally-linked genes located in close physical proximity to each other. In this study, we focused on herpesviruses. The reason for this lies in the compressed nature of viral genes, which allows a tight regulation and an easier investigation of the transcriptional interactions between genes. However, I believe that the same or similar principles can be applied to cellular

  18. The Effect of Scalp Point Cluster-Needling on Learning and Memory Function and Neurotransmitter Levels in Rats with Vascular Dementia

    OpenAIRE

    Yang, Junli; Litscher, Gerhard; Li, Haitao; Guo, Wenhai; Liang, Zhang; Zhang, Ting; Wang, Weihua; Li, Xiaoyan; Zhou, Yao; Zhao, Bing; Rong, Qi; Sheng, Zemin; Gaischek, Ingrid; Litscher, Daniela; Wang, Lu

    2014-01-01

    We observed the effect of scalp point cluster-needling treatment on learning and memory function and neurotransmitter levels in rats with vascular dementia (VD). Permanent ligation of the bilateral carotid arteries was used to create the VD rat model. A Morris water maze was used to measure the rats' learning and memory function, and the changes in neurotransmitter levels in the rats' hippocampus were analyzed. The results show that scalp point cluster-needling can increase the VD rat model's...

  19. A First Estimate of the X-Ray Binary Frequency as a Function of Star Cluster Mass in a Single Galactic System

    Science.gov (United States)

    Clark, D. M.; Eikenberry, S. S.; Brandl, B. R.; Wilson, J. C.; Carson, J. C.; Henderson, C. P.; Hayward, T. L.; Barry, D. J.; Ptak, A. F.; Colbert, E. J. M.

    2008-05-01

    We use the previously identified 15 infrared star cluster counterparts to X-ray point sources in the interacting galaxies NGC 4038/4039 (the Antennae) to study the relationship between total cluster mass and X-ray binary number. This significant population of X-Ray/IR associations allows us to perform, for the first time, a statistical study of X-ray point sources and their environments. We define a quantity, η, relating the fraction of X-ray sources per unit mass as a function of cluster mass in the Antennae. We compute cluster mass by fitting spectral evolutionary models to Ks luminosity. Considering that this method depends on cluster age, we use four different age distributions to explore the effects of cluster age on the value of η and find it varies by less than a factor of 4. We find a mean value of η for these different distributions of η = 1.7 × 10-8 M-1⊙ with ση = 1.2 × 10-8 M-1⊙. Performing a χ2 test, we demonstrate η could exhibit a positive slope, but that it depends on the assumed distribution in cluster ages. While the estimated uncertainties in η are factors of a few, we believe this is the first estimate made of this quantity to "order of magnitude" accuracy. We also compare our findings to theoretical models of open and globular cluster evolution, incorporating the X-ray binary fraction per cluster.

  20. Genetic interrelations in the actinomycin biosynthetic gene clusters of Streptomyces antibioticus IMRU 3720 and Streptomyces chrysomallus ATCC11523, producers of actinomycin X and actinomycin C

    Directory of Open Access Journals (Sweden)

    Crnovčić I

    2017-04-01

    Full Text Available Ivana Crnovčić,1 Christian Rückert,2 Siamak Semsary,1 Manuel Lang,1 Jörn Kalinowski,2 Ullrich Keller1 1Institut für Chemie, Technische Universität Berlin, Berlin-Charlottenburg, 2Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany Abstract: Sequencing the actinomycin (acm biosynthetic gene cluster of Streptomyces antibioticus IMRU 3720, which produces actinomycin X (Acm X, revealed 20 genes organized into a highly similar framework as in the bi-armed acm C biosynthetic gene cluster of Streptomyces chrysomallus but without an attached additional extra arm of orthologues as in the latter. Curiously, the extra arm of the S. chrysomallus gene cluster turned out to perfectly match the single arm of the S. antibioticus gene cluster in the same order of orthologues including the the presence of two pseudogenes, scacmM and scacmN, encoding a cytochrome P450 and its ferredoxin, respectively. Orthologues of the latter genes were both missing in the principal arm of the S. chrysomallus acm C gene cluster. All orthologues of the extra arm showed a G +C-contents different from that of their counterparts in the principal arm. Moreover, the similarities of translation products from the extra arm were all higher to the corresponding translation products of orthologue genes from the S. antibioticus acm X gene cluster than to those encoded by the principal arm of their own gene cluster. This suggests that the duplicated structure of the S. chrysomallus acm C biosynthetic gene cluster evolved from previous fusion between two one-armed acm gene clusters each from a different genetic background. However, while scacmM and scacmN in the extra arm of the S. chrysomallus acm C gene cluster are mutated and therefore are non-functional, their orthologues saacmM and saacmN in the S. antibioticus acm C gene cluster show no defects seemingly encoding active enzymes with functions specific for Acm X biosynthesis. Both acm

  1. Distinct functional domains within the acidic cluster of tegument protein pp28 required for trafficking and cytoplasmic envelopment of human cytomegalovirus.

    Science.gov (United States)

    Seo, Jun-Young; Jeon, Hyejin; Hong, Sookyung; Britt, William J

    2016-10-01

    Human cytomegalovirus UL99-encoded tegument protein pp28 contains a 16 aa acidic cluster that is required for pp28 trafficking to the assembly compartment (AC) and the virus assembly. However, functional signals within the acidic cluster of pp28 remain undefined. Here, we demonstrated that an acidic cluster rather than specific sorting signals was required for trafficking to the AC. Recombinant viruses with chimeric pp28 proteins expressing non-native acidic clusters exhibited delayed viral growth kinetics and decreased production of infectious virus, indicating that the native acidic cluster of pp28 was essential for wild-type virus assembly. These results suggested that the acidic cluster of pp28 has distinct functional domains required for trafficking and for efficient virus assembly. The first half (aa 44-50) of the acidic cluster was sufficient for pp28 trafficking, whereas the native acidic cluster consisting of aa 51-59 was required for the assembly of wild-type levels of infectious virus.

  2. Benchmark calculations of excess electrons in water cluster cavities: balancing the addition of atom-centered diffuse functions versus floating diffuse functions.

    Science.gov (United States)

    Zhang, Changzhe; Bu, Yuxiang

    2016-09-14

    Diffuse functions have been proved to be especially crucial for the accurate characterization of excess electrons which are usually bound weakly in intermolecular zones far away from the nuclei. To examine the effects of diffuse functions on the nature of the cavity-shaped excess electrons in water cluster surroundings, both the HOMO and LUMO distributions, vertical detachment energies (VDEs) and visible absorption spectra of two selected (H2O)24(-) isomers are investigated in the present work. Two main types of diffuse functions are considered in calculations including the Pople-style atom-centered diffuse functions and the ghost-atom-based floating diffuse functions. It is found that augmentation of atom-centered diffuse functions contributes to a better description of the HOMO (corresponding to the VDE convergence), in agreement with previous studies, but also leads to unreasonable diffuse characters of the LUMO with significant red-shifts in the visible spectra, which is against the conventional point of view that the more the diffuse functions, the better the results. The issue of designing extra floating functions for excess electrons has also been systematically discussed, which indicates that the floating diffuse functions are necessary not only for reducing the computational cost but also for improving both the HOMO and LUMO accuracy. Thus, the basis sets with a combination of partial atom-centered diffuse functions and floating diffuse functions are recommended for a reliable description of the weakly bound electrons. This work presents an efficient way for characterizing the electronic properties of weakly bound electrons accurately by balancing the addition of atom-centered diffuse functions and floating diffuse functions and also by balancing the computational cost and accuracy of the calculated results, and thus is very useful in the relevant calculations of various solvated electron systems and weakly bound anionic systems.

  3. Characterization of the human laminin beta2 chain locus (LAMB2): linkage to a gene containing a nonprocessed, transcribed LAMB2-like pseudogene (LAMB2L) and to the gene encoding glutaminyl tRNA synthetase (QARS)

    DEFF Research Database (Denmark)

    Durkin, M E; Jäger, A C; Khurana, T S

    1999-01-01

    The laminin beta2 chain is an important constituent of certain kidney and muscle basement membranes. We have generated a detailed physical map of a 110-kb genomic DNA segment surrounding the human laminin beta2 chain gene (LAMB2) on chromosome 3p21.3-->p21.2, a region paralogous with the chromosome...... 7q22-->q31 region that contains the laminin beta1 chain gene locus (LAMB1). Several CpG islands and a novel polymorphic microsatellite marker (D3S4594) were identified. The 3' end of LAMB2 lies 16 kb from the 5' end of the glutaminyl tRNA synthetase gene (QARS). About 20 kb upstream of LAMB2 we...... found a gene encoding a transcribed, non-processed LAMB2-like pseudogene (LAMB2L). The sequence of 1.75 kb of genomic DNA at the 3' end of LAMB2L was similar to exons 8-12 of the laminin beta2 chain gene. The LAMB2L-LAMB2-QARS cluster lies telomeric to the gene encoding the laminin-binding protein...

  4. Multiple populations within globular clusters in Early-type galaxies Exploring their effect on stellar initial mass function estimates

    Science.gov (United States)

    Chantereau, W.; Usher, C.; Bastian, N.

    2018-05-01

    It is now well-established that most (if not all) ancient globular clusters host multiple populations, that are characterised by distinct chemical features such as helium abundance variations along with N-C and Na-O anti-correlations, at fixed [Fe/H]. These very distinct chemical features are similar to what is found in the centres of the massive early-type galaxies and may influence measurements of the global properties of the galaxies. Additionally, recent results have suggested that M/L variations found in the centres of massive early-type galaxies might be due to a bottom-heavy stellar initial mass function. We present an analysis of the effects of globular cluster-like multiple populations on the integrated properties of early-type galaxies. In particular, we focus on spectral features in the integrated optical spectrum and the global mass-to-light ratio that have been used to infer variations in the stellar initial mass function. To achieve this we develop appropriate stellar population synthesis models and take into account, for the first time, an initial-final mass relation which takes into consideration a varying He abundance. We conclude that while the multiple populations may be present in massive early-type galaxies, they are likely not responsible for the observed variations in the mass-to-light ratio and IMF sensitive line strengths. Finally, we estimate the fraction of stars with multiple populations chemistry that come from disrupted globular clusters within massive ellipticals and find that they may explain some of the observed chemical patterns in the centres of these galaxies.

  5. Viral unmasking of cellular 5S rRNA pseudogene transcripts induces RIG-I-mediated immunity.

    Science.gov (United States)

    Chiang, Jessica J; Sparrer, Konstantin M J; van Gent, Michiel; Lässig, Charlotte; Huang, Teng; Osterrieder, Nikolaus; Hopfner, Karl-Peter; Gack, Michaela U

    2018-01-01

    The sensor RIG-I detects double-stranded RNA derived from RNA viruses. Although RIG-I is also known to have a role in the antiviral response to DNA viruses, physiological RNA species recognized by RIG-I during infection with a DNA virus are largely unknown. Using next-generation RNA sequencing (RNAseq), we found that host-derived RNAs, most prominently 5S ribosomal RNA pseudogene 141 (RNA5SP141), bound to RIG-I during infection with herpes simplex virus 1 (HSV-1). Infection with HSV-1 induced relocalization of RNA5SP141 from the nucleus to the cytoplasm, and virus-induced shutoff of host protein synthesis downregulated the abundance of RNA5SP141-interacting proteins, which allowed RNA5SP141 to bind RIG-I and induce the expression of type I interferons. Silencing of RNA5SP141 strongly dampened the antiviral response to HSV-1 and the related virus Epstein-Barr virus (EBV), as well as influenza A virus (IAV). Our findings reveal that antiviral immunity can be triggered by host RNAs that are unshielded following depletion of their respective binding proteins by the virus.

  6. Computational Investigation of the Geometrical and Electronic Structures of VGen-/0 (n = 1-4) Clusters by Density Functional Theory and Multiconfigurational CASSCF/CASPT2 Method.

    Science.gov (United States)

    Tran, Van Tan; Nguyen, Minh Thao; Tran, Quoc Tri

    2017-10-12

    Density functional theory and the multiconfigurational CASSCF/CASPT2 method have been employed to study the low-lying states of VGe n -/0 (n = 1-4) clusters. For VGe -/0 and VGe 2 -/0 clusters, the relative energies and geometrical structures of the low-lying states are reported at the CASSCF/CASPT2 level. For the VGe 3 -/0 and VGe 4 -/0 clusters, the computational results show that due to the large contribution of the Hartree-Fock exact exchange, the hybrid B3LYP, B3PW91, and PBE0 functionals overestimate the energies of the high-spin states as compared to the pure GGA BP86 and PBE functionals and the CASPT2 method. On the basis of the pure GGA BP86 and PBE functionals and the CASSCF/CASPT2 results, the ground states of anionic and neutral clusters are defined, the relative energies of the excited states are computed, and the electron detachment energies of the anionic clusters are evaluated. The computational results are employed to give new assignments for all features in the photoelectron spectra of VGe 3 - and VGe 4 - clusters.

  7. Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function.

    Science.gov (United States)

    Goad, David M; Zhu, Chuanmei; Kellogg, Elizabeth A

    2017-10-01

    CLV3/ESR (CLE) proteins are important signaling peptides in plants. The short CLE peptide (12-13 amino acids) is cleaved from a larger pre-propeptide and functions as an extracellular ligand. The CLE family is large and has resisted attempts at classification because the CLE domain is too short for reliable phylogenetic analysis and the pre-propeptide is too variable. We used a model-based search for CLE domains from 57 plant genomes and used the entire pre-propeptide for comprehensive clustering analysis. In total, 1628 CLE genes were identified in land plants, with none recognizable from green algae. These CLEs form 12 groups within which CLE domains are largely conserved and pre-propeptides can be aligned. Most clusters contain sequences from monocots, eudicots and Amborella trichopoda, with sequences from Picea abies, Selaginella moellendorffii and Physcomitrella patens scattered in some clusters. We easily identified previously known clusters involved in vascular differentiation and nodulation. In addition, we found a number of discrete groups whose function remains poorly characterized. Available data indicate that CLE proteins within a cluster are likely to share function, whereas those from different clusters play at least partially different roles. Our analysis provides a foundation for future evolutionary and functional studies. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  8. Structural and functional organization of the HF.10 human zinc finger gene (ZNF35) located on chromosome 3p21-p22

    DEFF Research Database (Denmark)

    Lanfrancone, L; Pengue, G; Pandolfi, P P

    1992-01-01

    We report the structural and functional characterization of the HF.10 zinc finger gene (ZNF35) in normal human cells, as well as a processed pseudogene. The HF.10 gene spans about 13 kb and it is interrupted by three introns. All 11 zinc finger DNA-binding domains are contiguously encoded within...... and partial nucleotide sequencing of the HF.10 pseudogene indicated that it has arisen by retroposition of spliced HF.10 mRNA. In situ hybridization experiments revealed that both the functional locus and the pseudogene map to chromosome 3p21p22, a region that is frequently deleted in small cell lung...... and renal carcinomas. Hybridization of the HF.10 gene and the HF.10 pseudogene DNA probes to metaphases from a small cell lung carcinoma cell line with the 3p deletion revealed that both loci are part of the deleted chromosome region....

  9. Effects of shape and dopant on structural, optical absorption, Raman, and vibrational properties of silver and copper quantum clusters: A density functional theory study

    International Nuclear Information System (INIS)

    Li Wei-Yin; Chen Fu-Yi

    2014-01-01

    We investigate the effects of shape and single-atom doping on the structural, optical absorption, Raman, and vibrational properties of Ag 13 , Ag 12 Cu 1 , Cu 13 , and Cu 12 Ag 1 clusters by using the (time-dependent) density functional theory. The results show that the most stable structures are cuboctahedron (COh) for Ag 13 and icosahedron (Ih) for Cu 13 , Ag 12 Cu 1core , and Cu 12 Ag 1sur . In the visible—near infrared optical absorption, the transitions consist of the interband and the intraband transitions. Moreover, red shifts are observed as follows: 1) clusters change from Ag 12 Cu 1core to Ag 13 to Ag 12 Cu 1sur with the same motifs, 2) the shapes of pure Ag 13 and Ag 12 Cu 1core clusters change from COh to Ih to decahedron (Dh), 3) the shape of Ag 12 Cu 1sur clusters changes from Ih to COh to Dh, and 4) the shapes of pure Cu 13 and Cu 12 Ag 1 clusters change from Ih to Dh to COh. All of the Raman and vibrational spectra exhibit many significant vibrational modes related to the shapes and the compositions of the clusters. The ranges of vibrational spectra of Ag 13 , Ag 12 Cu 1 or Cu 13 , and Cu 12 Ag 1 clusters become narrower and the vibrational intensities increase as the shape of the clusters changes from Ih to Dh to COh. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  10. Energy landscapes of nucleophilic substitution reactions: a comparison of density functional theory and coupled cluster methods

    NARCIS (Netherlands)

    Swart, M.; Sola, M.; Bickelhaupt, F.M.

    2007-01-01

    We have carried out a detailed evaluation of the performance of all classes of density functional theory (DFT) for describing the potential energy surface (PES) of a wide range of nucleophilic substitution (S

  11. Function and Regulation of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR / CRISPR Associated (Cas Systems

    Directory of Open Access Journals (Sweden)

    Peter C. Fineran

    2012-10-01

    Full Text Available Phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. Thus, bacteria have evolved numerous ‘innate’ mechanisms of defense against phage, such as abortive infection or restriction/modification systems. In contrast, the clustered regularly interspaced short palindromic repeats (CRISPR systems provide acquired, yet heritable, sequence-specific ‘adaptive’ immunity against phage and other horizontally-acquired elements, such as plasmids. Resistance is acquired following viral infection or plasmid uptake when a short sequence of the foreign genome is added to the CRISPR array. CRISPRs are then transcribed and processed, generally by CRISPR associated (Cas proteins, into short interfering RNAs (crRNAs, which form part of a ribonucleoprotein complex. This complex guides the crRNA to the complementary invading nucleic acid and targets this for degradation. Recently, there have been rapid advances in our understanding of CRISPR/Cas systems. In this review, we will present the current model(s of the molecular events involved in both the acquisition of immunity and interference stages and will also address recent progress in our knowledge of the regulation of CRISPR/Cas systems.

  12. OPTIMAL MODEL OF FUNCTIONING OF OLERICULTURE: VERTICAL INTEGRATION, AGRICULTURAL FILIERES, CLUSTERS

    Directory of Open Access Journals (Sweden)

    Y. B. Mindlin

    2016-01-01

    Full Text Available The goal of the present paper is to identify the optimal strategy of development of the Russian olericulture in order to substitute imported products and to build up logistic and transport infrastructure. Existing problems of the Russian olericulture are described. It is demonstrated that these problems can be solved on the basis of big integrated structures. Formation of these structures can be based on hierarchical (vertical  integration or networking (agricultural filieres or clusters models. A comparative analysis of these models of development of olericulture is made. Advantages and inconveniences of each model are described. It is demonstrated that sustainable development of the Russian olericulture can be insured only by a combination of hierarchical and networking tools. Vertical integration will help to reach quick increase of production, while networking models are necessary for inclusion of small producers into production chains, development of product range and development of supporting industries. Networking models are also necessary for social tasks. It means that the optimal strategy of development of the  Russian olericulture should be based on a combination of networking and hierarchical tools. This combination is necessary for agricultural corporation as well as for the Russian olericulture in general.

  13. Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR associated (Cas) systems.

    Science.gov (United States)

    Richter, Corinna; Chang, James T; Fineran, Peter C

    2012-10-19

    Phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. Thus, bacteria have evolved numerous 'innate' mechanisms of defense against phage, such as abortive infection or restriction/modification systems. In contrast, the clustered regularly interspaced short palindromic repeats (CRISPR) systems provide acquired, yet heritable, sequence-specific 'adaptive' immunity against phage and other horizontally-acquired elements, such as plasmids. Resistance is acquired following viral infection or plasmid uptake when a short sequence of the foreign genome is added to the CRISPR array. CRISPRs are then transcribed and processed, generally by CRISPR associated (Cas) proteins, into short interfering RNAs (crRNAs), which form part of a ribonucleoprotein complex. This complex guides the crRNA to the complementary invading nucleic acid and targets this for degradation. Recently, there have been rapid advances in our understanding of CRISPR/Cas systems. In this review, we will present the current model(s) of the molecular events involved in both the acquisition of immunity and interference stages and will also address recent progress in our knowledge of the regulation of CRISPR/Cas systems.

  14. Reactions of mixed silver-gold cluster cations AgmAun+ (m+n=4,5,6) with CO: Radiative association kinetics and density functional theory computations

    International Nuclear Information System (INIS)

    Neumaier, Marco; Weigend, Florian; Hampe, Oliver; Kappes, Manfred M.

    2006-01-01

    Near thermal energy reactive collisions of small mixed metal cluster cations Ag m Au n + (m+n=4, 5, and 6) with carbon monoxide have been studied in the room temperature Penning trap of a Fourier transform ion-cyclotron-resonance mass spectrometer as a function of cluster size and composition. The tetrameric species AgAu 3 + and Ag 2 Au 2 + are found to react dissociatively by way of Au or Ag atom loss, respectively, to form the cluster carbonyl AgAu 2 CO + . In contrast, measurements on a selection of pentamers and hexamers show that CO is added with absolute rate constants that decrease with increasing silver content. Experimentally determined absolute rate constants for CO adsorption were analyzed using the radiative association kinetics model to obtain cluster cation-CO binding energies ranging from 0.77 to 1.09 eV. High-level ab initio density functional theory (DFT) computations identifying the lowest-energy cluster isomers and the respective CO adsorption energies are in good agreement with the experimental findings clearly showing that CO binds in a ''head-on'' fashion to a gold atom in the mixed clusters. DFT exploration of reaction pathways in the case of Ag 2 Au 2 + suggests that exoergicities are high enough to access the minimum energy products for all reactive clusters probed

  15. Reactions of mixed silver-gold cluster cations AgmAun+ (m+n=4,5,6) with CO: Radiative association kinetics and density functional theory computations

    Science.gov (United States)

    Neumaier, Marco; Weigend, Florian; Hampe, Oliver; Kappes, Manfred M.

    2006-09-01

    Near thermal energy reactive collisions of small mixed metal cluster cations AgmAun+ (m +n=4, 5, and 6) with carbon monoxide have been studied in the room temperature Penning trap of a Fourier transform ion-cyclotron-resonance mass spectrometer as a function of cluster size and composition. The tetrameric species AgAu3+ and Ag2Au2+ are found to react dissociatively by way of Au or Ag atom loss, respectively, to form the cluster carbonyl AgAu2CO+. In contrast, measurements on a selection of pentamers and hexamers show that CO is added with absolute rate constants that decrease with increasing silver content. Experimentally determined absolute rate constants for CO adsorption were analyzed using the radiative association kinetics model to obtain cluster cation-CO binding energies ranging from 0.77to1.09eV. High-level ab initio density functional theory (DFT) computations identifying the lowest-energy cluster isomers and the respective CO adsorption energies are in good agreement with the experimental findings clearly showing that CO binds in a "head-on" fashion to a gold atom in the mixed clusters. DFT exploration of reaction pathways in the case of Ag2Au2+ suggests that exoergicities are high enough to access the minimum energy products for all reactive clusters probed.

  16. A density functional theory study on structures, stabilities, and electronic and magnetic properties of Au{sub n}C (n = 1–9) clusters

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Xiao-Fei; Yan, Li-Li; Huang, Teng; Hong, Yu; Miao, Shou-Kui [Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); Peng, Xiu-Qiu [School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China); Liu, Yi-Rong, E-mail: liuyirong@aiofm.ac.cn [Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); Huang, Wei, E-mail: huangwei6@ustc.edu.cn [Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2016-06-15

    The equilibrium geometric structures, relative stabilities, electronic stabilities, and electronic and magnetic properties of the Au{sub n}C and Au{sub n+1} (n = 1–9) clusters are systematically investigated using density functional theory (DFT) with hyper-generalized gradient approximation (GGA). The optimized geometries show that one Au atom added to the Au{sub n−1}C cluster is the dominant growth pattern for the Au{sub n}C clusters. In contrast to the pure gold clusters, the Au{sub n}C clusters are most stable in a quasi-planar or three-dimensional (3D) structure because the C dopant induces the local non-planarity, with exceptions of the Au{sub 6,8}C clusters who have 2D structures. The analysis of the relative and electronic stabilities reveals that the Au{sub 4}C and Au{sub 6} clusters are the most stable in the series of studied clusters, respectively. In addition, a natural bond orbital (NBO) analysis shows that the charges in the Au{sub n}C clusters transfer from the Au{sub n} host to the C atom. Moreover, the Au and C atoms interact with each other mostly via covalent bond rather than ionic bond, which can be confirmed through the average ionic character of the Au–C bond. Meanwhile, the charges mainly transfer between 2s and 2p orbitals within the C atom, and among 5d, 6s, and 6p orbitals within the Au atom for the Au{sub n}C clusters. As for the magnetic properties of the Au{sub n}C clusters, the total magnetic moments are 1 μ{sub B} for n = odd clusters, with the total magnetic moments mainly locating on the C atoms for Au{sub 1,3,9}C and on the Au{sub n} host for Au{sub 5,7}C clusters. However, the total magnetic moments of the Au{sub n}C clusters are zero for n = even clusters. Simultaneously, the magnetic moments mainly locate on the 2p orbital within the C atom and on the 5d, 6s orbitals within the Au atom.

  17. Investigation of the electronic structure of the BiSBr and BiSeBr clusters by density functional method

    International Nuclear Information System (INIS)

    Audzijonis, A.; Gaigalas, G.; Zigas, L.; Pauliukas, A.; Zaltauskas, R.; Kvedaravicius, A.; Cerskus, A.

    2008-01-01

    The energy levels of valence bands (VB) of the BiSBr and BiSeBr crystals have been calculated for investigation of the photoelectron emission spectra of BiSBr, BiSeBr and BiSI crystals. The molecular model of this crystal has been used for the calculation of VB by the Density Functional Theory (DFT) method. The molecular cluster, consisting of 20 molecules of BiSBr, BiSeBr, has been used for calculations of averaged total density of states, including atom vibrations. The spectra of the averaged total density of states from VB of BiSBr and BiSeBr clusters have been compared with the experimental photoelectron emission spectra from VB of BiSI crystals. The results clarify that the atomic vibrations in A 5 B 6 C 7 type crystals with chain structure create a smoother appearance of the averaged total density of state spectrum and the experimental X-ray photoemission spectra (XPS)

  18. Elucidating the role of surface passivating ligand structural parameters in hole wave function delocalization in semiconductor cluster molecules.

    Science.gov (United States)

    Teunis, Meghan B; Nagaraju, Mulpuri; Dutta, Poulami; Pu, Jingzhi; Muhoberac, Barry B; Sardar, Rajesh; Agarwal, Mangilal

    2017-09-28

    This article describes the mechanisms underlying electronic interactions between surface passivating ligands and (CdSe) 34 semiconductor cluster molecules (SCMs) that facilitate band-gap engineering through the delocalization of hole wave functions without altering their inorganic core. We show here both experimentally and through density functional theory calculations that the expansion of the hole wave function beyond the SCM boundary into the ligand monolayer depends not only on the pre-binding energetic alignment of interfacial orbitals between the SCM and surface passivating ligands but is also strongly influenced by definable ligand structural parameters such as the extent of their π-conjugation [π-delocalization energy; pyrene (Py), anthracene (Anth), naphthalene (Naph), and phenyl (Ph)], binding mode [dithiocarbamate (DTC, -NH-CS 2 - ), carboxylate (-COO - ), and amine (-NH 2 )], and binding head group [-SH, -SeH, and -TeH]. We observe an unprecedentedly large ∼650 meV red-shift in the lowest energy optical absorption band of (CdSe) 34 SCMs upon passivating their surface with Py-DTC ligands and the trend is found to be Ph- wave function delocalization rather than carrier trapping and/or phonon-mediated relaxation. Taken together, knowledge of how ligands electronically interact with the SCM surface is crucial to semiconductor nanomaterial research in general because it allows the tuning of electronic properties of nanomaterials for better charge separation and enhanced charge transfer, which in turn will increase optoelectronic device and photocatalytic efficiencies.

  19. GRIN2B encephalopathy : Novel findings on phenotype, variant clustering, functional consequences and treatment aspects

    NARCIS (Netherlands)

    Platzer, Konrad; Yuan, Hongjie; Schütz, Hannah; Winschel, Alexander; Chen, Wenjuan; Hu, Chun; Kusumoto, Hirofumi; Heyne, Henrike O; Helbig, Katherine L; Tang, Sha; Willing, Marcia C; Tinkle, Brad T; Adams, Darius J; Depienne, Christel; Keren, Boris; Mignot, Cyril; Frengen, Eirik; Strømme, Petter; Biskup, Saskia; Döcker, Dennis; Strom, Tim M.; Mefford, Heather C.; Myers, Candace T.; Muir, Alison M; LaCroix, Amy; Sadleir, Lynette G.; Scheffer, Ingrid E.; Brilstra, Eva; van Haelst, Mieke M.; van der Smagt, Jasper J.; Bok, Levinus A; Møller, Rikke S.; Jensen, Uffe Birk; Millichap, John J; Berg, Anne T; Goldberg, Ethan M; De Bie, Isabelle; Fox, Stephanie; Major, Philippe; Jones, Julie R; Zackai, Elaine H.; Abou Jamra, Rami; Rolfs, Arndt; Leventer, Richard J; Lawson, John A; Roscioli, Tony; Jansen, Floor E.; Ranza, Emmanuelle; Korff, Christian M; Lehesjoki, Anna-Elina; Courage, Carolina; Linnankivi, Tarja; Smith, Douglas R; Stanley, Christine; Mintz, Mark; McKnight, Dianalee; Decker, Amy; Tan, Wen-Hann; Tarnopolsky, Mark A; Brady, Lauren I; Wolff, Markus; Dondit, Lutz; Pedro, Helio F; Parisotto, Sarah E; Jones, Kelly L; Patel, Anup D; Franz, David N; Vanzo, Rena; Marco, Elysa; Ranells, Judith D; Di Donato, Nataliya; Dobyns, William B.; Laube, Bodo; Traynelis, Stephen F; Lemke, Johannes R.

    2017-01-01

    Background: We aimed for a comprehensive delineation of genetic, functional and phenotypic aspects of GRIN2B encephalopathy and explored potential prospects of personalised medicine. Methods: Data of 48 individuals with de novo GRIN2B variants were collected from several diagnostic and research

  20. Multicomponent Program to Reduce Functional Decline in Frail Elderly People : A Cluster Controlled Trial

    NARCIS (Netherlands)

    Ruikes, Franca G. H.; Zuidema, Sytse U.; Akkermans, Reinier P.; Assendelft, Willem J. J.; Schers, Henk J.; Koopmans, Raymond T. C. M.

    2016-01-01

    Background: The increasing number of community-dwelling frail elderly people poses a challenge to general practice. We evaluated the effectiveness of a general practitioner-led extensive, multicomponent program integrating cure, care, and welfare for the prevention of functional decline. Methods: We

  1. Multicomponent Program to Reduce Functional Decline in Frail Elderly People: A Cluster Controlled Trial

    NARCIS (Netherlands)

    Ruikes, F.G.; Zuidema, S.U.; Akkermans, R.P.; Assendelft, W.J.; Schers, H.J.; Koopmans, R.T.

    2016-01-01

    BACKGROUND: The increasing number of community-dwelling frail elderly people poses a challenge to general practice. We evaluated the effectiveness of a general practitioner-led extensive, multicomponent program integrating cure, care, and welfare for the prevention of functional decline. METHODS: We

  2. Filling- and interaction-driven Mott transition. Quantum cluster calculations within self-energy-functional theory; Fuellungs- und wechselwirkungsabhaengiger Mott-Uebergang. Quanten-Cluster-Rechnungen im Rahmen der Selbstenergiefunktional-Theorie

    Energy Technology Data Exchange (ETDEWEB)

    Balzer, Matthias

    2008-07-01

    The central goal of this thesis is the examination of strongly correlated electron systems on the basis of the two-dimensional Hubbard model. We analyze how the properties of the Mott insulator change upon doping and with interaction strength. The numerical evaluation is done using quantum cluster approximations, which allow for a thermodynamically consistent description of the ground state properties. The framework of self-energy-functional theory offers great flexibility for the construction of cluster approximations. A detailed analysis sheds light on the quality and the convergence properties of different cluster approximations within the self-energy-functional theory. We use the one-dimensional Hubbard model for these examinations and compare our results with the exact solution. In two dimensions the ground state of the particle-hole symmetric model at half-filling is an antiferromagnetic insulator, independent of the interaction strength. The inclusion of short-range spatial correlations by our cluster approach leads to a considerable improvement of the antiferromagnetic order parameter as compared to dynamical mean-field theory. In the paramagnetic phase we furthermore observe a metal-insulator transition as a function of the interaction strength, which qualitatively differs from the pure mean-field scenario. Starting from the antiferromagnetic Mott insulator a filling-controlled metal-insulator transition in a paramagnetic metallic phase can be observed. Depending on the cluster approximation used an antiferromagnetic metallic phase may occur at first. In addition to long-range antiferromagnetic order, we also considered superconductivity in our calculations. The superconducting order parameter as a function of doping is in good agreement with other numerical methods, as well as with experimental results. (orig.)

  3. Identification of Functional Clusters in the Striatum Using Infinite Relational Modeling

    DEFF Research Database (Denmark)

    Andersen, Kasper Winther; Madsen, Kristoffer Hougaard; Siebner, Hartwig

    2011-01-01

    In this paper we investigate how the Infinite Relational Model can be used to infer functional groupings of the human striatum using resting state fMRI data from 30 healthy subjects. The Infinite Relational Model is a non-parametric Bayesian method for infering community structure in complex netw...... and non-links in the graphs as missing. We find that the model is performing well above chance for all subjects....

  4. Deficits of entropy modulation in schizophrenia are predicted by functional connectivity strength in the theta band and structural clustering.

    Science.gov (United States)

    Gomez-Pilar, Javier; de Luis-García, Rodrigo; Lubeiro, Alba; de Uribe, Nieves; Poza, Jesús; Núñez, Pablo; Ayuso, Marta; Hornero, Roberto; Molina, Vicente

    2018-01-01

    Spectral entropy (SE) allows comparing task-related modulation of electroencephalogram (EEG) between patients and controls, i.e. spectral changes of the EEG associated to task performance. A SE modulation deficit has been replicated in different schizophrenia samples. To investigate the underpinnings of SE modulation deficits in schizophrenia, we applied graph-theory to EEG recordings during a P300 task and fractional anisotropy (FA) data from diffusion tensor imaging in 48 patients (23 first episodes) and 87 healthy controls. Functional connectivity was assessed from phase-locking values among sensors in the theta band, and structural connectivity was based on FA values for the tracts connecting pairs of regions. From those data, averaged clustering coefficient (CLC), characteristic path-length (PL) and connectivity strength (CS, also known as density) were calculated for both functional and structural networks. The corresponding functional modulation values were calculated as the difference in SE and CLC, PL and CS between the pre-stimulus and response windows during the task. The results revealed a higher functional CS in the pre-stimulus window in patients, predictive of smaller modulation of SE in this group. The amount of increase in theta CS from pre-stimulus to response related to SE modulation in patients and controls. Structural CLC was associated with SE modulation in the patients. SE modulation was predictive of negative symptoms, whereas CLC and PL modulation was associated with cognitive performance in the patients. These results support that a hyperactive functional connectivity and/or structural connective deficits in the patients hamper the dynamical modulation of connectivity underlying cognition.

  5. CLASH-VLT: The stellar mass function and stellar mass density profile of the z=0.44 cluster of galaxies MACS J1206.2-0847

    CERN Document Server

    Annunziatella, M; Mercurio, A.; Nonino, M.; Rosati, P.; Balestra, I.; Presotto, V.; Girardi, M.; Gobat, R.; Grillo, C.; Medezinski, E.; Kelson, D.; Postman, M.; Scodeggio, M.; Brescia, M.; Sartoris, B.; Demarco, R.; Fritz, A.; Koekemoer, A.; Lemze, D.; Lombardi, M.; Bradley, L.; Coe, D.; Donahue, M.; Regös, E.; Umetsu, K.; Vanzella, E.; Infante, L.; Kuchner, U.; Maier, C.; Verdugo, M.; Ziegler, B.

    2014-01-01

    Context. The study of the galaxy stellar mass function (SMF) in relation to the galaxy environment and the stellar mass density profile, rho(r), is a powerful tool to constrain models of galaxy evolution. Aims. We determine the SMF of the z=0.44 cluster of galaxies MACS J1206.2-0847 separately for passive and star-forming (SF) galaxies, in different regions of the cluster, from the center out to approximately 2 virial radii. We also determine rho(r) to compare it to the number density and total mass density profiles. Methods. We use the dataset from the CLASH-VLT survey. Stellar masses are obtained by SED fitting on 5-band photometric data obtained at the Subaru telescope. We identify 1363 cluster members down to a stellar mass of 10^9.5 Msolar. Results. The whole cluster SMF is well fitted by a double Schechter function. The SMFs of cluster SF and passive galaxies are statistically different. The SMF of the SF cluster galaxies does not depend on the environment. The SMF of the passive population has a signif...

  6. Photodissociation of hydrogen iodide on the surface of large argon clusters: The orientation of the librational wave function and the scattering from the cluster cage

    International Nuclear Information System (INIS)

    Slavicek, Petr; Jungwirth, Pavel; Lewerenz, Marius; Nahler, N. Hendrik; Farnik, Michal; Buck, Udo

    2004-01-01

    A set of photodissociation experiments and simulations of hydrogen iodide (HI) on Ar n clusters, with an average size =139, has been carried out for different laser polarizations. The doped clusters are prepared by a pick-up process. The HI molecule is then photodissociated by a UV laser pulse and the outgoing H fragment is ionized by resonance enhanced multiphoton ionization in a (2+1) excitation scheme within the same laser pulse at the wavelength of 243 nm. The measured time-of-flight spectra are transformed into hydrogen kinetic energy distributions. They exhibit a strong fraction of caged H atoms at zero-kinetic energy and peaks at the unperturbed cage exit for both spin-orbit channels nearly independent of the polarization. At this dissociation wavelength, the bare HI molecule exhibits a strict state separation, with a parallel transition to the spin-orbit excited state and perpendicular transitions to the ground state. The experimental results have been reproduced using molecular simulation techniques. Classical molecular dynamics was used to estimate the HI dopant distribution after the pick-up procedure. Subsequently, quasi-classical molecular dynamics (Wigner trajectories approach) has been applied for the photodissociation dynamics. The following main results have been obtained: (i) The HI dopant lands on the surface of the argon cluster during the pick-up process, (ii) zero-point energy plays a dominant role for the hydrogen orientation in the ground state of HI-Ar n surface clusters, qualitatively changing the result of the photodissociation experiment upon increasing the number of argon atoms, and, finally, (iii) the scattering of hydrogen atoms from the cage which originate from different dissociation states seriously affects the experimentally measured kinetic energy distributions

  7. IR + VUV double resonance spectroscopy and extended density functional theory studies of ketone solvation by alcohol: 2-butanone·(methanol)n, n = 1-4 clusters.

    Science.gov (United States)

    Shin, Joong-Won; Bernstein, Elliot R

    2017-09-28

    Infrared plus vacuum ultraviolet (IR + VUV) photoionization vibrational spectroscopy of 2-butanone/methanol clusters [MEK·(MeOH) n , n = 1-4] is performed to explore structures associated with hydrogen bonding of MeOH molecules to the carbonyl functional group of the ketone. IR spectra and X3LYP/6-31++G(d,p) calculations show that multiple isomers of MEK·(MeOH) n are generated in the molecular beam as a result of several hydrogen bonding sites available to the clusters throughout the size range investigated. Isomer interconversion involving solvating MeOH rearrangement should probably occur for n = 1 and 2. The mode energy for a hydrogen bonded OH stretching transition gradually redshifts as the cluster size increases. Calculations suggest that the n = 3 cluster isomers adopt structures in which the MEK molecule is inserted into the cyclic MeOH hydrogen bond network. In larger structures, the cyclic network may be preserved.

  8. Simulation of resonance hyper-Rayleigh scattering of molecules and metal clusters using a time-dependent density functional theory approach.

    Science.gov (United States)

    Hu, Zhongwei; Autschbach, Jochen; Jensen, Lasse

    2014-09-28

    Resonance hyper-Rayleigh scattering (HRS) of molecules and metal clusters have been simulated based on a time-dependent density functional theory approach. The resonance first-order hyperpolarizability (β) is obtained by implementing damped quadratic response theory using the (2n + 1) rule. To test this implementation, the prototypical dipolar molecule para-nitroaniline (p-NA) and the octupolar molecule crystal violet are used as benchmark systems. Moreover, small silver clusters Ag 8 and Ag 20 are tested with a focus on determining the two-photon resonant enhancement arising from the strong metal transition. Our results show that, on a per atom basis, the small silver clusters possess two-photon enhanced HRS comparable to that of larger nanoparticles. This finding indicates the potential interest of using small metal clusters for designing new nonlinear optical materials.

  9. Photoelectron Spectroscopy and Density Functional Theory Studies of Iron Sulfur (FeS)m- (m = 2-8) Cluster Anions: Coexisting Multiple Spin States.

    Science.gov (United States)

    Yin, Shi; Bernstein, Elliot R

    2017-10-05

    Iron sulfur cluster anions (FeS) m - (m = 2-8) are studied by photoelectron spectroscopy (PES) at 3.492 eV (355 nm) and 4.661 eV (266 nm) photon energies, and by density functional theory (DFT) calculations. The most probable structures and ground state spin multiplicities for (FeS) m - (m = 2-8) clusters are tentatively assigned through a comparison of their theoretical and experiment first vertical detachment energy (VDE) values. Many spin states lie within 0.5 eV of the ground spin state for the larger (FeS) m - (m ≥ 4) clusters. Theoretical VDEs of these low lying spin states are in good agreement with the experimental VDE values. Therefore, multiple spin states of each of these iron sulfur cluster anions probably coexist under the current experimental conditions. Such available multiple spin states must be considered when evaluating the properties and behavior of these iron sulfur clusters in real chemical and biological systems. The experimental first VDEs of (FeS) m - (m = 1-8) clusters are observed to change with the cluster size (number m). The first VDE trends noted can be related to the different properties of the highest singly occupied molecular orbitals (NBO, HSOMOs) of each cluster anion. The changing nature of the NBO/HSOMO of these (FeS) m - (m = 1-8) clusters from a p orbital on S, to a d orbital on Fe, and to an Fe-Fe bonding orbital is probably responsible for the observed increasing trend for their first VDEs with respect to m.

  10. Range-clustering queries

    NARCIS (Netherlands)

    Abrahamsen, M.; de Berg, M.T.; Buchin, K.A.; Mehr, M.; Mehrabi, A.D.

    2017-01-01

    In a geometric k -clustering problem the goal is to partition a set of points in R d into k subsets such that a certain cost function of the clustering is minimized. We present data structures for orthogonal range-clustering queries on a point set S : given a query box Q and an integer k>2 , compute

  11. Structure and Electronic Properties of Neutral and Negatively Charged RhBn Clusters (n = 3-10): A Density Functional Theory Study.

    Science.gov (United States)

    Li, Peifang; Mei, Tingting; Lv, Linxia; Lu, Cheng; Wang, Weihua; Bao, Gang; Gutsev, Gennady L

    2017-08-31

    The geometrical structure and electronic properties of the neutral RhB n and singly negatively charged RhB n - clusters are obtained in the range of 3 ≤ n ≤ 10 using the unbiased CALYPSO structure search method and density functional theory (DFT). A combination of the PBE0 functional and the def2-TZVP basis set is used for determining global minima on potential energy surfaces of the Rh-doped B n clusters. The photoelectron spectra of the anions are simulated using the time-dependent density functional theory (TD-DFT) method. Good agreement between our simulated and experimentally obtained photoelectron spectra for RhB 9 - provides support to the validity of our theoretical method. The relative stabilities of the ground-state RhB n and RhB n - clusters are estimated using the calculated binding energies, second-order total energy differences, and HOMO-LUMO gaps. It is found that RhB 7 and RhB 8 - are the most stable species in the neutral and anionic series, respectively. The chemical bonding analysis reveals that the RhB 8 - cluster possesses two sets of delocalized σ and π bonds. In both cases, the Hückel 4N + 2 rule is fulfilled and this cluster possesses both σ and π aromaticities.

  12. Van der Waals potentials between metal clusters and helium atoms obtained with density functional theory and linear response methods

    International Nuclear Information System (INIS)

    Liebrecht, M.

    2014-01-01

    The importance of van der Waals interactions in many diverse research fields such as, e. g., polymer science, nano--materials, structural biology, surface science and condensed matter physics created a high demand for efficient and accurate methods that can describe van der Waals interactions from first principles. These methods should be able to deal with large and complex systems to predict functions and properties of materials that are technologically and biologically relevant. Van der Waals interactions arise due to quantum mechanical correlation effects and finding appropriate models an numerical techniques to describe this type of interaction is still an ongoing challenge in electronic structure and condensed matter theory. This thesis introduces a new variational approach to obtain intermolecular interaction potentials between clusters and helium atoms by means of density functional theory and linear response methods. It scales almost linearly with the number of electrons and can therefore be applied to much larger systems than standard quantum chemistry techniques. The main focus of this work is the development of an ab-initio method to account for London dispersion forces, which are purely attractive and dominate the interaction of non--polar atoms and molecules at large distances. (author) [de

  13. Structured functional assessments in general practice increased the use of part-time sick leave: a cluster randomised controlled trial.

    Science.gov (United States)

    Osterås, Nina; Gulbrandsen, Pål; Kann, Inger Cathrine; Brage, Søren

    2010-03-01

    A method for structured functional assessments of persons with long-term sick leave was implemented in a cluster randomised controlled trial in general practice. The aim was to analyse intervention effects on general practitioner (GP) sick-listing practice and patient sick leave. 57 GPs were randomly assigned to an intervention or a control group. The intervention group GPs learned the method at a 1-day workshop including teamwork and role-playing. The control group GPs were requested to assess functional ability as usual during the 8 months intervention period in 2005. Outcome measures included duration of patient sick leave episodes, GP prescription of part-time sick leave, active sick leave, and vocational rehabilitation. This data was extracted from a national register. The GPs in the intervention group prescribed part-time sick leave more often (p part-time and less active sick leave compared to the control group GPs. As a result, more intervention GP patients returned to part-time work compared to control GP patients. No intervention effect was seen on duration of patient sick leave episodes or on prescription of vocational rehabilitation.

  14. In planta functions of cytochrome P450 monooxygenase genes in the phytocassane biosynthetic gene cluster on rice chromosome 2.

    Science.gov (United States)

    Ye, Zhongfeng; Yamazaki, Kohei; Minoda, Hiromi; Miyamoto, Koji; Miyazaki, Sho; Kawaide, Hiroshi; Yajima, Arata; Nojiri, Hideaki; Yamane, Hisakazu; Okada, Kazunori

    2018-06-01

    In response to environmental stressors such as blast fungal infections, rice produces phytoalexins, an antimicrobial diterpenoid compound. Together with momilactones, phytocassanes are among the major diterpenoid phytoalexins. The biosynthetic genes of diterpenoid phytoalexin are organized on the chromosome in functional gene clusters, comprising diterpene cyclase, dehydrogenase, and cytochrome P450 monooxygenase genes. Their functions have been studied extensively using in vitro enzyme assay systems. Specifically, P450 genes (CYP71Z6, Z7; CYP76M5, M6, M7, M8) on rice chromosome 2 have multifunctional activities associated with ent-copalyl diphosphate-related diterpene hydrocarbons, but the in planta contribution of these genes to diterpenoid phytoalexin production remains unknown. Here, we characterized cyp71z7 T-DNA mutant and CYP76M7/M8 RNAi lines to find that potential phytoalexin intermediates accumulated in these P450-suppressed rice plants. The results suggested that in planta, CYP71Z7 is responsible for C2-hydroxylation of phytocassanes and that CYP76M7/M8 is involved in C11α-hydroxylation of 3-hydroxy-cassadiene. Based on these results, we proposed potential routes of phytocassane biosynthesis in planta.

  15. Classifying human operator functional state based on electrophysiological and performance measures and fuzzy clustering method.

    Science.gov (United States)

    Zhang, Jian-Hua; Peng, Xiao-Di; Liu, Hua; Raisch, Jörg; Wang, Ru-Bin

    2013-12-01

    The human operator's ability to perform their tasks can fluctuate over time. Because the cognitive demands of the task can also vary it is possible that the capabilities of the operator are not sufficient to satisfy the job demands. This can lead to serious errors when the operator is overwhelmed by the task demands. Psychophysiological measures, such as heart rate and brain activity, can be used to monitor operator cognitive workload. In this paper, the most influential psychophysiological measures are extracted to characterize Operator Functional State (OFS) in automated tasks under a complex form of human-automation interaction. The fuzzy c-mean (FCM) algorithm is used and tested for its OFS classification performance. The results obtained have shown the feasibility and effectiveness of the FCM algorithm as well as the utility of the selected input features for OFS classification. Besides being able to cope with nonlinearity and fuzzy uncertainty in the psychophysiological data it can provide information about the relative importance of the input features as well as the confidence estimate of the classification results. The OFS pattern classification method developed can be incorporated into an adaptive aiding system in order to enhance the overall performance of a large class of safety-critical human-machine cooperative systems.

  16. From Lipid Homeostasis to Differentiation: Old and New Functions of the Zinc Cluster Proteins Ecm22, Upc2, Sut1 and Sut2

    Directory of Open Access Journals (Sweden)

    Ifeoluwapo Matthew Joshua

    2017-04-01

    Full Text Available Zinc cluster proteins are a large family of transcriptional regulators with a wide range of biological functions. The zinc cluster proteins Ecm22, Upc2, Sut1 and Sut2 have initially been identified as regulators of sterol import in the budding yeast Saccharomyces cerevisiae. These proteins also control adaptations to anaerobic growth, sterol biosynthesis as well as filamentation and mating. Orthologs of these zinc cluster proteins have been identified in several species of Candida. Upc2 plays a critical role in antifungal resistance in these important human fungal pathogens. Upc2 is therefore an interesting potential target for novel antifungals. In this review we discuss the functions, mode of actions and regulation of Ecm22, Upc2, Sut1 and Sut2 in budding yeast and Candida.

  17. Structures and Spectroscopic Properties of F-(H2O) n with n = 1-10 Clusters from a Global Search Based On Density Functional Theory.

    Science.gov (United States)

    Shi, Ruili; Wang, Pengju; Tang, Lingli; Huang, Xiaoming; Chen, Yonggang; Su, Yan; Zhao, Jijun

    2018-04-05

    Using a genetic algorithm incorporated in density functional theory, we explore the ground state structures of fluoride anion-water clusters F - (H 2 O) n with n = 1-10. The F - (H 2 O) n clusters prefer structures in which the F - anion remains at the surface of the structure and coordinates with four water molecules, as the F - (H 2 O) n clusters have strong F - -H 2 O interactions as well as strong hydrogen bonds between H 2 O molecules. The strong interaction between the F - anion and adjacent H 2 O molecule leads to a longer O-H distance in the adjacent molecule than in an individual water molecule. The simulated infrared (IR) spectra of the F - (H 2 O) 1-5 clusters obtained via second-order vibrational perturbation theory (VPT2) and including anharmonic effects reproduce the experimental results quite well. The strong interaction between the F - anion and water molecules results in a large redshift (600-2300 cm -1 ) of the adjacent O-H stretching mode. Natural bond orbital (NBO) analysis of the lowest-energy structures of the F - (H 2 O) 1-10 clusters illustrates that charge transfer from the lone pair electron orbital of F - to the antibonding orbital of the adjacent O-H is mainly responsible for the strong interaction between the F - anion and water molecules, which leads to distinctly different geometric and vibrational properties compared with neutral water clusters.

  18. Functional Genome Mining for Metabolites Encoded by Large Gene Clusters through Heterologous Expression of a Whole-Genome Bacterial Artificial Chromosome Library in Streptomyces spp.

    Science.gov (United States)

    Xu, Min; Wang, Yemin; Zhao, Zhilong; Gao, Guixi; Huang, Sheng-Xiong; Kang, Qianjin; He, Xinyi; Lin, Shuangjun; Pang, Xiuhua; Deng, Zixin

    2016-01-01

    ABSTRACT Genome sequencing projects in the last decade revealed numerous cryptic biosynthetic pathways for unknown secondary metabolites in microbes, revitalizing drug discovery from microbial metabolites by approaches called genome mining. In this work, we developed a heterologous expression and functional screening approach for genome mining from genomic bacterial artificial chromosome (BAC) libraries in Streptomyces spp. We demonstrate mining from a strain of Streptomyces rochei, which is known to produce streptothricins and borrelidin, by expressing its BAC library in the surrogate host Streptomyces lividans SBT5, and screening for antimicrobial activity. In addition to the successful capture of the streptothricin and borrelidin biosynthetic gene clusters, we discovered two novel linear lipopeptides and their corresponding biosynthetic gene cluster, as well as a novel cryptic gene cluster for an unknown antibiotic from S. rochei. This high-throughput functional genome mining approach can be easily applied to other streptomycetes, and it is very suitable for the large-scale screening of genomic BAC libraries for bioactive natural products and the corresponding biosynthetic pathways. IMPORTANCE Microbial genomes encode numerous cryptic biosynthetic gene clusters for unknown small metabolites with potential biological activities. Several genome mining approaches have been developed to activate and bring these cryptic metabolites to biological tests for future drug discovery. Previous sequence-guided procedures relied on bioinformatic analysis to predict potentially interesting biosynthetic gene clusters. In this study, we describe an efficient approach based on heterologous expression and functional screening of a whole-genome library for the mining of bioactive metabolites from Streptomyces. The usefulness of this function-driven approach was demonstrated by the capture of four large biosynthetic gene clusters for metabolites of various chemical types, including

  19. divergence, pseudogenes, and

    Indian Academy of Sciences (India)

    Ribosomal internal transcribed spacer (ITS) sequences are commonly used for phylogenetic reconstruction because they are highly reiterated as components of rDNA repeats, and hence are often subject to rapid homogenization through concerted evolution. Concerted evolution leads to intragenomic uniformity of repeats ...

  20. A CONSTRAINT ON BROWN DWARF FORMATION VIA EJECTION: RADIAL VARIATION OF THE STELLAR AND SUBSTELLAR MASS FUNCTION OF THE YOUNG OPEN CLUSTER IC 2391

    International Nuclear Information System (INIS)

    Boudreault, S.; Bailer-Jones, C. A. L.

    2009-01-01

    We present the stellar and substellar mass function (MF) of the open cluster IC 2391, plus its radial dependence, and use this to put constraints on the formation mechanism of brown dwarfs (BDs). Our multi-band optical and infrared photometric survey with spectroscopic follow-up covers 11 deg 2 , making it the largest survey of this cluster to date. We observe a radial variation in the MF over the range 0.072-0.3 M sun , but no significant variation in the MF below the substellar boundary at the three cluster radius intervals is analyzed. This lack of radial variation for low masses is what we would expect with the ejection scenario for BD formation, although considering that IC 2391 has an age about three times older than its crossing time, we expect that BDs with a velocity greater than the escape velocity have already escaped the cluster. Alternatively, the variation in the MF of the stellar objects could be an indication that they have undergone mass segregation via dynamical evolution. We also observe a significant variation across the cluster in the color of the (background) field star locus in color-magnitude diagrams and conclude that this is due to variable background extinction in the Galactic plane. From our preliminary spectroscopic follow-up, to confirm BD status and cluster membership, we find that all candidates are M dwarfs (in either the field or the cluster), demonstrating the efficiency of our photometric selection method in avoiding contaminants (e.g., red giants). About half of our photometric candidates for which we have spectra are spectroscopically confirmed as cluster members; two are new spectroscopically confirmed BD members of IC 2391.

  1. The experience of functioning of the dairy cluster of the Voronezh region in the aspect of observing the criteria of economic efficiency

    Directory of Open Access Journals (Sweden)

    A. V. Kotarev

    2018-01-01

    Full Text Available In the article the analysis of tendencies of development of sector of dairy animal industries on the basis of formation of a dairy cluster is given. It is shown that the structure of dairy cattle breeding in the Voronezh region is built in the form of a milk cluster, in the functioning of which most of the existing enterprises of the dairy industry take part. The largest participants of the dairy cluster are: EkoNivaAgro LLC, GK Molvest, Agroholding Don-Agro. In the cluster, all the operations of the whole milk production process are carried out, starting from the production of feed and breeding of breeding animals and ending with the delivery of finished products to the end users. Also, the cluster included auxiliary organizations that carry out scientific, educational, research and veterinary support of the entire production chain. Within the framework of the cluster, effective interaction of all its participants is established, which is necessary for obtaining high quality milk and dairy products. The advantage of a dairy cluster in the Voronezh region is the opportunity to provide targeted benefits to organizations that are important for the economy of the region, and the state gets the opportunity to regulate innovation, investment flows and evaluate the effectiveness of financial investments. The implementation of investment projects in animal husbandry in the medium term (for the period until 2020 will increase milk production by 30%. The economic efficiency of dairy cattle is a cumulative category that reflects the impact of technological, economic, social and environmental factors on the productivity of production. Cluster development of the dairy cattle breeding industry in the Voronezh Region allows obtaining a positive synergistic effect, reducing transaction costs, and increasing the genetic potential of dairy cattle.

  2. Are pelvic adhesions associated with pain, physical, emotional and functional characteristics of women presenting with chronic pelvic pain? A cluster analysis.

    Science.gov (United States)

    Cheong, Ying; Saran, Mili; Hounslow, James William; Reading, Isabel Claire

    2018-01-08

    Chronic pelvic pain is a debilitating condition. It is unknown if there is a clinical phenotype for adhesive disorders. This study aimed to determine if the presence or absence, nature, severity and extent of adhesions correlated with demographic and patient reported clinical characteristics of women presenting with CPP. Women undergoing a laparoscopy for the investigation of chronic pelvic pain were recruited prospectively; their pain and phenotypic characteristics were entered into a hierarchical cluster analysis. The groups with differing baseline clinical and operative characteristics in terms of adhesions involvement were analyzed. Sixty two women were recruited where 37 had adhesions. A low correlation was found between women's reported current pain scores and that of most severe (r = 0.34) or average pain experienced (r = 0.44) in the last 6 months. Three main groups of women with CPP were identified: Cluster 1 (n = 35) had moderate severity of pain, with poor average and present pain intensity; Cluster 2 (n = 14) had a long duration of symptoms/diagnosis, the worst current pain and worst physical, emotional and social functions; Cluster 3 (n = 11) had the shortest duration of pain and showed the best evidence of coping with low (good) physical, social and emotional scores. This cluster also had the highest proportion of women with adhesions (82%) compared to 51% in Cluster 1 and 71% in Cluster 2. In this study, we found that there is little or no correlation between patient-reported pain, physical, emotional and functional characteristics scores with the presence or absence of intra-abdominal/pelvic adhesions found during investigative laparoscopy. Most women who had adhesions had the lowest reported current pain scores.

  3. Systematic Study of Au6 to Au12 Gold Clusters on MgO(100) F Centers Using Density-Functional Theory

    DEFF Research Database (Denmark)

    Vilhelmsen, Lasse; Hammer, Bjørk

    2012-01-01

    We present an optimized genetic algorithm used in conjunction with density-functional theory in the search for stable gold clusters and O2 adsorption ensembles in F centers at MgO(100). For Au8 the method recovers known structures and identifies several more stable ones. When O2 adsorption...

  4. Predicting the mean cycle time as a function of throughput and product mix for cluster tool workstations using EPT-based aggregate modeling

    NARCIS (Netherlands)

    Veeger, C.P.L.; Etman, L.F.P.; Herk, van J.; Rooda, J.E.

    2009-01-01

    Predicting the mean cycle time as a function of throughput and product mix is helpful in making the production planning for cluster tools. To predict the mean cycle time, detailed simulation models may be used. However, detailed models require much development time, and it may not be possible to

  5. Subphenotypes of mild-to-moderate COPD by factor and cluster analysis of pulmonary function, CT imaging and breathomics in a population-based survey

    NARCIS (Netherlands)

    Fens, Niki; van Rossum, Annelot G. J.; Zanen, Pieter; van Ginneken, Bram; van Klaveren, Rob J.; Zwinderman, Aeilko H.; Sterk, Peter J.

    2013-01-01

    Classification of COPD is currently based on the presence and severity of airways obstruction. However, this may not fully reflect the phenotypic heterogeneity of COPD in the (ex-) smoking community. We hypothesized that factor analysis followed by cluster analysis of functional, clinical,

  6. Electrons as probes of dynamics in molecules and clusters: A contribution from Time Dependent Density Functional Theory

    International Nuclear Information System (INIS)

    Wopperer, P.; Dinh, P.M.; Reinhard, P.-G.; Suraud, E.

    2015-01-01

    There are various ways to analyze the dynamical response of clusters and molecules to electromagnetic perturbations. Particularly rich information can be obtained from measuring the properties of electrons emitted in the course of the excitation dynamics. Such an analysis of electron signals covers observables such as total ionization, Photo-Electron Spectra (PES), Photoelectron Angular Distributions (PAD), and ideally combined PES/PAD. It has a long history in molecular physics and was increasingly used in cluster physics as well. Recent progress in the design of new light sources (high intensity, high frequency, ultra short pulses) opens new possibilities for measurements and thus has renewed the interest on these observables, especially for the analysis of various dynamical scenarios, well beyond a simple access to electronic density of states. This, in turn, has motivated many theoretical investigations of the dynamics of electronic emission for molecules and clusters up to such a complex and interesting system as C 60 . A theoretical tool of choice is here Time-Dependent Density Functional Theory (TDDFT) propagated in real time and on a spatial grid, and augmented by a Self-Interaction Correction (SIC). This provides a pertinent, robust, and efficient description of electronic emission including the detailed pattern of PES and PAD. A direct comparison between experiments and well founded elaborate microscopic theories is thus readily possible, at variance with more demanding observables such as for example fragmentation or dissociation cross sections. The purpose of this paper is to describe the theoretical tools developed on the basis of real-time and real-space TDDFT and to address in a realistic manner the analysis of electronic emission following irradiation of clusters and molecules by various laser pulses. After a general introduction, we shall present in a second part the available experimental results motivating such studies, starting from the simplest

  7. A relativistic density functional study of Sin (n = 7-13) clusters with rare earth ytterbium impurity

    International Nuclear Information System (INIS)

    Zhao Running; Han Juguang; Bai Jintao; Liu Fuyi; Sheng Liusi

    2010-01-01

    Graphical abstract: Geometries, relative stabilities, HOMO-LUMO gaps, and growth-pattern of YbSi n (n = 7-13) clusters have been systematically studied. The calculated results show that Yb atom always prefers capping on the surface site of the silicon frame and no cagelike geometries are found up to n = 13, and that the most stable YbSi n (n = 7-13) clusters keep basically the analogous frameworks as the low-lying Si n+1 clusters. The relative stabilities of YbSi n (n = 7-13) clusters are studied, YbSi n (n = 8, 10, and 13) clusters have stronger relative stabilities in comparison with the corresponding neighbors. Furthermore, the charges in the most stable YbSi n (n = 7-13) clusters are transferred from Yb atom to silicon frame. Interestingly, the inserted Yb raises the chemical activities, increases the metallic in character of YbSi n clusters. In addition, the most stable charged YbSi n (n = 8-10, 13) geometries are deformed their neutral geometries. - Abstract: Geometries, relative stabilities, HOMO-LUMO gaps, and growth-pattern of YbSi n (n = 7-13) clusters have been systematically studied. The calculated results show that Yb atom always prefers capping on the surface site of the silicon frame and no cagelike geometries are found up to n = 13, and that the most stable YbSi n (n = 7-13) clusters keep basically the analogous frameworks as the low-lying Si n+1 clusters. The relative stabilities of YbSi n (n = 7-13) clusters are studied, YbSi n (n = 8, 10, and 13) clusters have stronger relative stabilities in comparison with the corresponding neighbors. Furthermore, the charges in the most stable YbSi n (n = 7-13) clusters are transferred from Yb atom to silicon frame. Interestingly, the inserted Yb raises the chemical activities, increases the metallic in character of YbSi n clusters. In addition, the most stable charged YbSi n (n = 8-10, 13) geometries are deformed their neutral geometries.

  8. C-M diagram and luminosity function of the Galactic globular cluster NGC 7099. I. Photographic photometry

    International Nuclear Information System (INIS)

    Piotto, G.; Rosino, L.; Capaccioli, M.; Ortolani, S.; Alcaino, G.; Osservatorio Astronomico, Padua, Italy; Ministerio de Educacion de Chile, Instituto Isaac Newton, Santiago)

    1987-01-01

    New photographic photometry of about 4400 stars in the field of the Galactic globular cluster NGC 7099 = M30 is presented. A C-M diagram and a luminosity function are obtained from this photometry. The distance modulus is estimated at 14.5 + or - 0.5 assuming V(HB) = 15.11 + or - 0.10 and E(B-V) = 0.03 + or - 0.03. The metallicity is (Fe/H) = 1.9 + or - 0.3 based on the dereddened color index (B-V)0,g = 0.71 + or - 0.03. The theoretical isochrones of VandenBerg and Bell (1985) give a better fit to the observations assuming (Fe/H) = -1.8, (m-M)V = 14.6, and E(B-V) = 0.02. A fair fit is also obtained using isochrones of low iron content with an oxygen enhancement of 0.7. From the fit, an age of 17 + or - 4 Gyr is deduced. 41 references

  9. Functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in Sphingobium sp. PNB

    Directory of Open Access Journals (Sweden)

    Pratick Khara

    2014-01-01

    Full Text Available Sphingobium sp. PNB, like other sphingomonads, has multiple ring-hydroxylating oxygenase (RHO genes. Three different fosmid clones have been sequenced to identify the putative genes responsible for the degradation of various aromatics in this bacterial strain. Comparison of the map of the catabolic genes with that of different sphingomonads revealed a similar arrangement of gene clusters that harbors seven sets of RHO terminal components and a sole set of electron transport (ET proteins. The presence of distinctly conserved amino acid residues in ferredoxin and in silico molecular docking analyses of ferredoxin with the well characterized terminal oxygenase components indicated the structural uniqueness of the ET component in sphingomonads. The predicted substrate specificities, derived from the phylogenetic relationship of each of the RHOs, were examined based on transformation of putative substrates and their structural homologs by the recombinant strains expressing each of the oxygenases and the sole set of available ET proteins. The RHO AhdA1bA2b was functionally characterized for the first time and was found to be capable of transforming ethylbenzene, propylbenzene, cumene, p-cymene and biphenyl, in addition to a number of polycyclic aromatic hydrocarbons. Overexpression of aromatic catabolic genes in strain PNB, revealed by real-time PCR analyses, is a way forward to understand the complex regulation of degradative genes in sphingomonads.

  10. Effects of micro-encapsulation on morphology and endocrine function of cryopreserved neonatal porcine islet-like cell clusters.

    Science.gov (United States)

    Murakami, M; Satou, H; Kimura, T; Kobayashi, T; Yamaguchi, A; Nakagawara, G; Iwata, H

    2000-10-27

    For the success of clinical islets transplantation, the development of a long-term storage method is necessary. However, the structure of digested islets is scanty for culture and cryopreservation. In this study, the effect of micro-encapsulation to cryopreserved porcine islet-like cell clusters (ICCs) was investigated. The ICCs prepared from neonatal pigs by collagenase digestion and culture technique were cryopreserved and micro-encapsulated in 5% agarose membranes. After cryopreservation, ICC cultured without encapsulation (group A) and cultured with encapsulation (group B) were assessed by comparison with no cryopreserved ICC (control) both in vitro by static incubation test and in vivo in a xenotransplantation study. Micro-encapsulation was able to maintain the fine morphology and the number of ICCs of group B after 7 days of culture. There were not significant differences in insulin secretion of group B and control on day 1 and 7 of culture (1 day:11+/-0.99, 7 days: 5.30+/-1.08 microU/ICC/hr NS versus control). On day 7 of culture, the retrieval rate of group B (105.2+/-9.8%) is obviously higher compared with group A (63.0+/-6.3%). In the xenotransplatation model, the ICCs of group B showed long survival time (7.9+/-0.4 weeks) and good transplantation effect. Our study suggests that micro-encapsulation is one of the useful method for cryopreserved ICC to maintain the fine morphology and effectively recover the endocrine function.

  11. LMC clusters: young

    International Nuclear Information System (INIS)

    Freeman, K.C.

    1980-01-01

    The young globular clusters of the LMC have ages of 10 7 -10 8 y. Their masses and structure are similar to those of the smaller galactic globular clusters. Their stellar mass functions (in the mass range 6 solar masses to 1.2 solar masses) vary greatly from cluster to cluster, although the clusters are similar in total mass, age, structure and chemical composition. It would be very interesting to know why these clusters are forming now in the LMC and not in the Galaxy. The author considers the 'young globular' or 'blue populous' clusters of the LMC. The ages of these objects are 10 7 to 10 8 y, and their masses are 10 4 to 10 5 solar masses, so they are populous enough to be really useful for studying the evolution of massive stars. The author concentrates on the structure and stellar content of these young clusters. (Auth.)

  12. One-pot solvothermal synthesis of highly water-dispersible size-tunable functionalized magnetite nanocrystal clusters for lipase immobilization.

    Science.gov (United States)

    Zhu, Hao; Hou, Chen; Li, Yijing; Zhao, Guanghui; Liu, Xiao; Hou, Ke; Li, Yanfeng

    2013-07-01

    A facile one-pot synthesis of highly water-dispersible size-tunable magnetite (Fe3O4) nanocrystal clusters (MNCs) end-functionalized with amino or carboxyl groups by a modified solvothermal reduction reaction has been developed. Dopamine and 3,4-dihydroxyhydroxycinnamic acid were used for the first time as both a surfactant and interparticle linker in a polylol process for economical and environment-friendly purposes. Morphology, chemical composition, and magnetic properties of the prepared particles were investigated by several methods, including FESEM, TEM, XRD, XPS, Raman, FTIR, TGA, zeta potential, and VSM. The sizes of the particles could be easily tuned over a wide range from 175 to 500 nm by varying the surfactant concentration. Moreover, ethylene glycol/diethylene glycol (EG/DEG) solvent mixtures with different ratios could be used as reductants to obtain the particles with smaller sizes. The XRD data demonstrated that the surfactants restrained the crystal growth of the grains. The nanoparticles showed superior magnetic properties and high colloidal stability in water. The cytotoxicity results indicated the feasibility of using the synthesized nanocrystals in biology-related fields. To estimate the applicability of the obtained MNCs in biotechnology, Candida rugosa lipase was selected for the enzyme immobilization process. The immobilized lipase exhibited excellent thermal stability and reusability in comparison with the free enzyme. This novel strategy would simplify the reaction protocol and improve the efficiency of materials functionalization, thus offering new potential applications in biotechnology and organocatalysis. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. The function and properties of the iron-sulfur center in spinach ferredoxin: Thioredoxin reductase: A new biological role for iron-sulfur clusters

    Energy Technology Data Exchange (ETDEWEB)

    Staples, C.R.; Ameyibor, E.; Fu, Weiguang; Johnson, M.K. [Univ. of Georgia, Athens, GA (United States)] [and others

    1996-09-03

    Thioredoxin reduction in chloroplasts in catalyzed by a unique class of disulfide reductases which use a [2Fe-2S]{sup 2+/+} ferredoxin as the electron donor and contain an Fe-S cluster as the sole prosthetic group in addition to the active-site disulfide. The nature, properties, and function of the Fe-S cluster in spinach ferredoxin: thioredoxin reductase (FTR) have been investigated by the combination of UV/visible absorption, variable-temperature magnetic circular dichroism (MCD), EPR, and resonance Raman (RR) spectroscopies. 66 refs., 5 figs., 1 tab.

  14. Evaluation of B3LYP, X3LYP, and M06-class density functionals for predicting the binding energies of neutral, protonated, and deprotonated water clusters

    OpenAIRE

    Bryantsev, Vyacheslav S.; Diallo, Mamadou S.; van Duin, Adri C. T.; Goddard, William A., III

    2009-01-01

    In this paper we assess the accuracy of the B3LYP, X3LYP, and newly developed M06-L, M06-2X, and M06 functionals to predict the binding energies of neutral and charged water clusters including (H_2O)_n, n = 2−8, 20), H_3O+(H_2O_)n, n = 1−6, and OH−(H_2O)_n, n = 1−6. We also compare the predicted energies of two ion hydration and neutralization reactions on the basis of the calculated binding energies. In all cases, we use as benchmarks calculated binding energies of water clusters extrapolate...

  15. Measuring the Scatter of the Mass–Richness Relation in Galaxy Clusters in Photometric Imaging Surveys by Means of Their Correlation Function

    Energy Technology Data Exchange (ETDEWEB)

    Campa, Julia; Estrada, Juan; Flaugher, Brenna

    2017-02-03

    The knowledge of the scatter in the mass-observable relation is a key ingredient for a cosmological analysis based on galaxy clusters in a photometric survey. We demonstrate here how the linear bias measured in the correlation function for clusters can be used to determine the value of the scatter. The new method is tested in simulations of a 5.000 square degrees optical survey up to z~1, similar to the ongoing Dark Energy Survey. The results indicate that the scatter can be measured with a precision of 5% using this technique.

  16. Pseudogene of dihydrolipoyl succinyltransferase (E2k) found by PCR amplification and direct sequencing of rodent-human cell hybrid DNAs

    Energy Technology Data Exchange (ETDEWEB)

    Cai, X.; Ali, G.; Blass, J.P. [Cornell Univ. Medical College, White Plains, NY (United States); Szabo, P. [Cornell Univ. Medical College, New York, NY (United States); Tanzi, R.E. [Massachusetts General Hospital, Boston, MA (United States)

    1994-07-01

    Previous studies have indicated that the cDNA for the E2k component of the human {alpha}-ketoglutarate dehydrogenase complex (KGDHC) hybridized not only to a major locus on chromosome 14q24.3 in a region associated with familial Alzheimer`s disease and with Joseph-Machado disease, but also to another locus on chromosome 1p31. The authors now report that PCR of genomic DNA and direct sequencing indicated that the chromosome 1 locus is an intronless pseudogene. PCR of genomic DNA amplified E2k fragments from mouse-human cell hybrids containing human chromosome 1 DNA but not from hybrids containing human chromosome 14 DNA. The resulting amplicons were of comparable sizes to those when the cDNA was used to template. The direct sequencing of these amplicons confirmed the lack of introns and indicated a frame shift, which led to the presence of four termination codons early in the coding region. PCR followed by direct sequencing of the amplicons appears to be a convenient method for identifying intronless pseudogenes.

  17. Photoelectron spectroscopy and density functional theory studies of (FeS)mH- (m = 2-4) cluster anions: effects of the single hydrogen.

    Science.gov (United States)

    Yin, Shi; Bernstein, Elliot R

    2017-12-20

    Single hydrogen containing iron hydrosulfide cluster anions (FeS) m H - (m = 2-4) are studied by photoelectron spectroscopy (PES) at 3.492 eV (355 nm) and 4.661 eV (266 nm) photon energies, and by Density Functional Theory (DFT) calculations. The structural properties, relative energies of different spin states and isomers, and the first calculated vertical detachment energies (VDEs) of different spin states for these (FeS) m H - (m = 2-4) cluster anions are investigated at various reasonable theory levels. Two types of structural isomers are found for these (FeS) m H - (m = 2-4) clusters: (1) the single hydrogen atom bonds to a sulfur site (SH-type); and (2) the single hydrogen atom bonds to an iron site (FeH-type). Experimental and theoretical results suggest such available different SH- and FeH-type structural isomers should be considered when evaluating the properties and behavior of these single hydrogen containing iron sulfide clusters in real chemical and biological systems. Compared to their related, respective pure iron sulfur (FeS) m - clusters, the first VDE trend of the diverse type (FeS) m H 0,1 - (m = 1-4) clusters can be understood through (1) the different electron distribution properties of their highest singly occupied molecular orbital employing natural bond orbital analysis (NBO/HSOMO), and (2) the partial charge distribution on the NBO/HSOMO localized sites of each cluster anion. Generally, the properties of the NBO/HSOMOs play the principal role with regard to the physical and chemical properties of all the anions. The change of cluster VDE from low to high is associated with the change in nature of their NBO/HSOMO from a dipole bound and valence electron mixed character, to a valence p orbital on S, to a valence d orbital on Fe, and to a valence p orbital on Fe or an Fe-Fe delocalized valence bonding orbital. For clusters having the same properties for NBO/HSOMOs, the partial charge distributions at the NBO/HSOMO localized sites additionally

  18. Density-functional study of the structures and properties of holmium-doped silicon clusters HoSi n (n = 3-9) and their anions.

    Science.gov (United States)

    Hou, Liyuan; Yang, Jucai; Liu, Yuming

    2017-04-01

    The structures and properties of Ho-doped Si clusters, including their adiabatic electron affinities (AEAs), simulated photoelectron spectra (PESs), stabilities, magnetic moments, and charge-transfer characteristics, were systematically investigated using four density-functional methods. The results show that the double-hybrid functional (which includes an MP2 correlation component) can accurately predict the ground-state structure and properties of Ho-doped Si clusters. The ground-state structures of HoSi n (n = 3-9) are sextuplet electronic states. The structures of these Ho-doped Si clusters (aside from HoSi 7 ) are substitutional. The ground-state structures of HoSi n - are quintuplet electronic states. Their predicted AEAs are in excellent agreement with the experimental ones. The mean absolute error in the theoretical AEAs of HoSi n (n = 4-9) is only 0.04 eV. The simulated PESs for HoSi n - (n = 5-9) are in good agreement with the experimental PESs. Based on its simulated PES and theoretical AEA, we reassigned the experimental PES of HoSi 4 - and obtained an experimental AEA of 2.2 ± 0.1 eV. The dissociation energies of Ho from HoSi n and HoSi n - (n = 3-9) were evaluated to test the relative stabilities of the clusters. HOMO-LUMO gap analysis indicated that doping the Si clusters with the rare-earth metal atom significantly increases their photochemical reactivity. Natural population analysis showed that the magnetic moments of HoSi n (n = 3-9) and their anions derive mainly from the Ho atom. It was also found that the magnetic moments of Ho in the HoSi n clusters are larger than the magnetic moment of an isolated Ho atom.

  19. Carbon X-ray absorption spectra of fluoroethenes and acetone: a study at the coupled cluster, density functional, and static-exchange levels of theory.

    Science.gov (United States)

    Fransson, Thomas; Coriani, Sonia; Christiansen, Ove; Norman, Patrick

    2013-03-28

    Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as the state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger π-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to π∗-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate π∗-peak separations due to spectral compressions, a characteristic which is inherent to this

  20. Regulation of EphA4 kinase activity is required for a subset of axon guidance decisions suggesting a key role for receptor clustering in Eph function

    DEFF Research Database (Denmark)

    Egea, Joaquim; Nissen, Ulla Vig; Dufour, Audrey

    2005-01-01

    Signaling by receptor tyrosine kinases (RTKs) is mediated by their intrinsic kinase activity. Typically, kinase-activating mutations result in ligand-independent signaling and gain-of-function phenotypes. Like other RTKs, Ephs require kinase activity to signal, but signaling by Ephs in vitro also...... requires clustering by their membrane bound ephrin ligands. The relative importance of Eph kinase activity and clustering for in vivo functions is unknown. We find that knockin mice expressing a mutant form of EphA4 (EphA4 EE), whose kinase is constitutively activated in the absence of ephrinB ligands......, are deficient in the development of thalamocortical projections and some aspects of central pattern generator rhythmicity. Surprisingly, other functions of EphA4 were regulated normally by EphA4EE, including midline axon guidance, hindlimb locomotion, in vitro growth cone collapse, and phosphorylation...

  1. Evolution of the paralogous hap and iga genes in Haemophilus influenzae: evidence for a conserved hap pseudogene associated with microcolony formation in the recently diverged Haemophilus aegyptius and H. influenzae biogroup aegyptius

    DEFF Research Database (Denmark)

    Kilian, Mogens; Poulsen, Knud; Lomholt, Hans Bredsted

    2002-01-01

    genetic polymorphism and pronounced mosaic-like patterns in both genes, but no evidence of intrastrain recombination between the two genes. A conserved hap pseudogene was present in all strains of H. aegyptius and H. influenzae biogroup aegyptius, each of which constituted distinct subpopulations...... on conjunctival cells, previously termed microcolony formation. The fact that individual hap pseudogenes differed from the ancestral sequence by zero to two positions within a 1.5 kb stretch suggests that the silencing event happened approximately 2000-11,000 years ago. Divergence of H. aegyptius and H...

  2. From Stars to Superplanets: The Low-Mass Initial Mass Function in the Young Cluster IC 348

    National Research Council Canada - National Science Library

    Najita, Joan R; Tiede, Glenn P; Carr, John S

    2000-01-01

    We investigate the low-mass population of the young cluster IC 348 down to the deuterium-burning limit, a fiducial boundary between brown dwarf and planetary mass objects, using a new and innovative...

  3. Size-based emphysema cluster analysis on low attenuation area in 3D volumetric CT: comparison with pulmonary functional test

    Science.gov (United States)

    Lee, Minho; Kim, Namkug; Lee, Sang Min; Seo, Joon Beom; Oh, Sang Young

    2015-03-01

    To quantify low attenuation area (LAA) of emphysematous regions according to cluster size in 3D volumetric CT data of chronic obstructive pulmonary disease (COPD) patients and to compare these indices with their pulmonary functional test (PFT). Sixty patients with COPD were scanned by a more than 16-multi detector row CT scanner (Siemens Sensation 16 and 64) within 0.75mm collimation. Based on these LAA masks, a length scale analysis to estimate each emphysema LAA's size was performed as follows. At first, Gaussian low pass filter from 30mm to 1mm kernel size with 1mm interval on the mask was performed from large to small size, iteratively. Centroid voxels resistant to the each filter were selected and dilated by the size of the kernel, which was regarded as the specific size emphysema mask. The slopes of area and number of size based LAA (slope of semi-log plot) were analyzed and compared with PFT. PFT parameters including DLco, FEV1, and FEV1/FVC were significantly (all p-value< 0.002) correlated with the slopes (r-values; -0.73, 0.54, 0.69, respectively) and EI (r-values; -0.84, -0.60, -0.68, respectively). In addition, the D independently contributed regression for FEV1 and FEV1/FVC (adjust R sq. of regression study: EI only, 0.70, 0.45; EI and D, 0.71, 0.51, respectively). By the size based LAA segmentation and analysis, we evaluated the Ds of area, number, and distribution of size based LAA, which would be independent factors for predictor of PFT parameters.

  4. Generating information-rich high-throughput experimental materials genomes using functional clustering via multitree genetic programming and information theory.

    Science.gov (United States)

    Suram, Santosh K; Haber, Joel A; Jin, Jian; Gregoire, John M

    2015-04-13

    High-throughput experimental methodologies are capable of synthesizing, screening and characterizing vast arrays of combinatorial material libraries at a very rapid rate. These methodologies strategically employ tiered screening wherein the number of compositions screened decreases as the complexity, and very often the scientific information obtained from a screening experiment, increases. The algorithm used for down-selection of samples from higher throughput screening experiment to a lower throughput screening experiment is vital in achieving information-rich experimental materials genomes. The fundamental science of material discovery lies in the establishment of composition-structure-property relationships, motivating the development of advanced down-selection algorithms which consider the information value of the selected compositions, as opposed to simply selecting the best performing compositions from a high throughput experiment. Identification of property fields (composition regions with distinct composition-property relationships) in high throughput data enables down-selection algorithms to employ advanced selection strategies, such as the selection of representative compositions from each field or selection of compositions that span the composition space of the highest performing field. Such strategies would greatly enhance the generation of data-driven discoveries. We introduce an informatics-based clustering of composition-property functional relationships using a combination of information theory and multitree genetic programming concepts for identification of property fields in a composition library. We demonstrate our approach using a complex synthetic composition-property map for a 5 at. % step ternary library consisting of four distinct property fields and finally explore the application of this methodology for capturing relationships between composition and catalytic activity for the oxygen evolution reaction for 5429 catalyst compositions in a

  5. Cluster headache

    Science.gov (United States)

    Histamine headache; Headache - histamine; Migrainous neuralgia; Headache - cluster; Horton's headache; Vascular headache - cluster ... Doctors do not know exactly what causes cluster headaches. They ... (chemical in the body released during an allergic response) or ...

  6. Identification and functional analysis of gene cluster involvement in biosynthesis of the cyclic lipopeptide antibiotic pelgipeptin produced by Paenibacillus elgii

    Directory of Open Access Journals (Sweden)

    Qian Chao-Dong

    2012-09-01

    Full Text Available Abstract Background Pelgipeptin, a potent antibacterial and antifungal agent, is a non-ribosomally synthesised lipopeptide antibiotic. This compound consists of a β-hydroxy fatty acid and nine amino acids. To date, there is no information about its biosynthetic pathway. Results A potential pelgipeptin synthetase gene cluster (plp was identified from Paenibacillus elgii B69 through genome analysis. The gene cluster spans 40.8 kb with eight open reading frames. Among the genes in this cluster, three large genes, plpD, plpE, and plpF, were shown to encode non-ribosomal peptide synthetases (NRPSs, with one, seven, and one module(s, respectively. Bioinformatic analysis of the substrate specificity of all nine adenylation domains indicated that the sequence of the NRPS modules is well collinear with the order of amino acids in pelgipeptin. Additional biochemical analysis of four recombinant adenylation domains (PlpD A1, PlpE A1, PlpE A3, and PlpF A1 provided further evidence that the plp gene cluster involved in pelgipeptin biosynthesis. Conclusions In this study, a gene cluster (plp responsible for the biosynthesis of pelgipeptin was identified from the genome sequence of Paenibacillus elgii B69. The identification of the plp gene cluster provides an opportunity to develop novel lipopeptide antibiotics by genetic engineering.

  7. The evolution of the cluster optical galaxy luminosity function between z = 0.4 and 0.9 in the DAFT/FADA survey

    Science.gov (United States)

    Martinet, Nicolas; Durret, Florence; Guennou, Loïc; Adami, Christophe; Biviano, Andrea; Ulmer, Melville P.; Clowe, Douglas; Halliday, Claire; Ilbert, Olivier; Márquez, Isabel; Schirmer, Mischa

    2015-03-01

    Context. There is some disagreement about the abundance of faint galaxies in high-redshift clusters, with contradictory results in the literature arising from studies of the optical galaxy luminosity function (GLF) for small cluster samples. Aims: We compute GLFs for one of the largest medium-to-high-redshift (0.4 ≤ z DAFT/FADA survey in the B,V,R, and I rest-frame bands. We used photometric redshifts computed from BVRIZJ images to constrain galaxy cluster membership. We carried out a detailed estimate of the completeness of our data. We distinguished the red-sequence and blue galaxies using a V - I versus I colour-magnitude diagram. We studied the evolution of these two populations with redshift. We fitted Schechter functions to our stacked GLFs to determine average cluster characteristics. Results: We find that the shapes of our GLFs are similar for the B,V,R, and I bands with a drop at the red GLF faint ends that is more pronounced at high redshift: αred ~ -0.5 at 0.40 ≤ z 0.1 at 0.65 ≤ z < 0.90. The blue GLFs have a steeper faint end (αblue ~ -1.6) than the red GLFs, which appears to be independent of redshift. For the full cluster sample, blue and red GLFs meet at MV = -20, MR = -20.5, and MI = -20.3. A study of how galaxy types evolve with redshift shows that late-type galaxies appear to become early types between z ~ 0.9 and today. Finally, the faint ends of the red GLFs of more massive clusters appear to be richer than less massive clusters, which is more typical of the lower redshift behaviour. Conclusions: Our results indicate that these clusters form at redshifts higher than z = 0.9 from galaxy structures that already have an established red sequence. Late-type galaxies then appear to evolve into early types, enriching the red sequence between this redshift and today. This effect is consistent with the evolution of the faint-end slope of the red sequence and the galaxy type evolution that we find. Finally, faint galaxies accreted from the field

  8. What is the best density functional to describe water clusters: evaluation of widely used density functionals with various basis sets for (H2O)n (n = 1-10)

    Czech Academy of Sciences Publication Activity Database

    Li, F.; Wang, L.; Zhao, J.; Xie, J. R. H.; Riley, Kevin Eugene; Chen, Z.

    2011-01-01

    Roč. 130, 2/3 (2011), s. 341-352 ISSN 1432-881X Institutional research plan: CEZ:AV0Z40550506 Keywords : water cluster * density functional theory * MP2 . CCSD(T) * basis set * relative energies Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.162, year: 2011

  9. Synthesis and Characterization of Rh—Co Butterfly Clusters Capped by Functionally Substituted 1—Alkynes

    Institute of Scientific and Technical Information of China (English)

    ZHUBao-Hua; SUNJie; 等

    2003-01-01

    By the reactions of [Rh2Co2(CO2)12]1 with functionaly substituted alkyne ligands HC≡CR 2(R=FeCp2) and 3(R=2-OH-C6H4COOCH2),respectively in n-hexane at room temperature,two new cluster derivatives [Rh2Co2(CO)6(μ-CO)4(μ4,η2-HC≡CR)] 4(R=FeCp2) and 5 (R=2-OH-C6H4COOCH2) were obtained respectively,The alkyne was inserted into the Co-Co bond of cluster 1 to give two butterfly clusters.Cluster 4 has been determined by single-crystal X-ray diffraction,Crystallographic data:C22H10Co2FeO18Rh2,Mr=813.83,orthorhombic ,space group P212121,a=11.53187(7),b=12.6572(7),c=17.018(1)°↑A,V=2483.9(3)°↑A3,Z=4,Dc=2.176 g/cm3,F(000)=1568,μ=3.233mm-1,the final R=0.0366 and wR=0.0899 for 5367 observed reflections with I>2σ(I).The two clusters have also been characterized by elemental analysis ,IR and 1H-NMR spectroscopy.

  10. Evaluation of B3LYP, X3LYP, and M06-Class Density Functionals for Predicting the Binding Energies of Neutral, Protonated, and Deprotonated Water Clusters.

    Science.gov (United States)

    Bryantsev, Vyacheslav S; Diallo, Mamadou S; van Duin, Adri C T; Goddard, William A

    2009-04-14

    In this paper we assess the accuracy of the B3LYP, X3LYP, and newly developed M06-L, M06-2X, and M06 functionals to predict the binding energies of neutral and charged water clusters including (H2O)n, n = 2-8, 20), H3O(+)(H2O)n, n = 1-6, and OH(-)(H2O)n, n = 1-6. We also compare the predicted energies of two ion hydration and neutralization reactions on the basis of the calculated binding energies. In all cases, we use as benchmarks calculated binding energies of water clusters extrapolated to the complete basis set limit of the second-order Møller-Plesset perturbation theory with the effects of higher order correlation estimated at the coupled-cluster theory with single, double, and perturbative triple excitations in the aug-cc-pVDZ basis set. We rank the accuracy of the functionals on the basis of the mean unsigned error (MUE) between calculated benchmark and density functional theory energies. The corresponding MUE (kcal/mol) for each functional is listed in parentheses. We find that M06-L (0.73) and M06 (0.84) give the most accurate binding energies using very extended basis sets such as aug-cc-pV5Z. For more affordable basis sets, the best methods for predicting the binding energies of water clusters are M06-L/aug-cc-pVTZ (1.24), B3LYP/6-311++G(2d,2p) (1.29), and M06/aug-cc-PVTZ (1.33). M06-L/aug-cc-pVTZ also gives more accurate energies for the neutralization reactions (1.38), whereas B3LYP/6-311++G(2d,2p) gives more accurate energies for the ion hydration reactions (1.69).

  11. Changing ionization conditions in SDSS galaxies with active galactic nuclei as a function of environment from pairs to clusters

    International Nuclear Information System (INIS)

    Khabiboulline, Emil T.; Steinhardt, Charles L.; Silverman, John D.; Ellison, Sara L.; Mendel, J. Trevor; Patton, David R.

    2014-01-01

    We study how active galactic nucleus (AGN) activity changes across environments from galaxy pairs to clusters using 143,843 galaxies with z < 0.2 from the Sloan Digital Sky Survey. Using a refined technique, we apply a continuous measure of AGN activity, characteristic of the ionization state of the narrow-line emitting gas. Changes in key emission-line ratios ([N II] λ6548/Hα, [O III] λ5007/Hβ) between different samples allow us to disentangle different environmental effects while removing contamination. We confirm that galaxy interactions enhance AGN activity. However, conditions in the central regions of clusters are inhospitable for AGN activity even if galaxies are in pairs. These results can be explained through models of gas dynamics in which pair interactions stimulate the transfer of gas to the nucleus and clusters suppress gas availability for accretion onto the central black hole.

  12. Changing ionization conditions in SDSS galaxies with active galactic nuclei as a function of environment from pairs to clusters

    Energy Technology Data Exchange (ETDEWEB)

    Khabiboulline, Emil T.; Steinhardt, Charles L. [California Institute of Technology, 1200 East-California Boulevard, Pasadena, CA 91125 (United States); Silverman, John D. [Kavli Institute for the Physics and Mathematics of the Universe, University of Tokyo, Kashiwanoha 5-1-5, Kashiwa-Shi, Chiba 277-8583 (Japan); Ellison, Sara L. [Department of Physics and Astronomy, University of Victoria, Finnerty Road, Victoria, British Columbia, V8P 1A1 (Canada); Mendel, J. Trevor [Max Planck Institute for Extraterrestrial Physics, Giessenbachstrasse, D-85748 Garching (Germany); Patton, David R., E-mail: ekhabibo@caltech.edu [Department of Physics and Astronomy, Trent University, 1600 West Bank Drive, Peterborough, Ontario, K9J 7B8 (Canada)

    2014-11-01

    We study how active galactic nucleus (AGN) activity changes across environments from galaxy pairs to clusters using 143,843 galaxies with z < 0.2 from the Sloan Digital Sky Survey. Using a refined technique, we apply a continuous measure of AGN activity, characteristic of the ionization state of the narrow-line emitting gas. Changes in key emission-line ratios ([N II] λ6548/Hα, [O III] λ5007/Hβ) between different samples allow us to disentangle different environmental effects while removing contamination. We confirm that galaxy interactions enhance AGN activity. However, conditions in the central regions of clusters are inhospitable for AGN activity even if galaxies are in pairs. These results can be explained through models of gas dynamics in which pair interactions stimulate the transfer of gas to the nucleus and clusters suppress gas availability for accretion onto the central black hole.

  13. Ages of young star clusters, massive blue stragglers, and the upper mass limit of stars: Analyzing age-dependent stellar mass functions

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, F. R. N.; Izzard, R. G.; Langer, N.; Stolte, A.; Hußmann, B. [Argelander-Institut für Astronomie der Universität Bonn, Auf dem Hügel 71, D-53121 Bonn (Germany); De Mink, S. E. [Observatories of the Carnegie Institution for Science, 813 Santa Barbara St, Pasadena, CA 91101 (United States); De Koter, A.; Sana, H. [Astronomical Institute " Anton Pannekoek" , Amsterdam University, Science Park 904, 1098 XH, Amsterdam (Netherlands); Gvaramadze, V. V. [Sternberg Astronomical Institute, Lomonosov Moscow State University, Universitetskij Pr. 13, Moscow 119992 (Russian Federation); Liermann, A., E-mail: fschneid@astro.uni-bonn.de [Max Planck Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany)

    2014-01-10

    Massive stars rapidly change their masses through strong stellar winds and mass transfer in binary systems. The latter aspect is important for populations of massive stars as more than 70% of all O stars are expected to interact with a binary companion during their lifetime. We show that such mass changes leave characteristic signatures in stellar mass functions of young star clusters that can be used to infer their ages and to identify products of binary evolution. We model the observed present-day mass functions of the young Galactic Arches and Quintuplet star clusters using our rapid binary evolution code. We find that the shaping of the mass function by stellar wind mass loss allows us to determine the cluster ages as 3.5 ± 0.7 Myr and 4.8 ± 1.1 Myr, respectively. Exploiting the effects of binary mass exchange on the cluster mass function, we find that the most massive stars in both clusters are rejuvenated products of binary mass transfer, i.e., the massive counterpart of classical blue straggler stars. This resolves the problem of an apparent age spread among the most luminous stars exceeding the expected duration of star formation in these clusters. We perform Monte Carlo simulations to probe stochastic sampling, which support the idea of the most massive stars being rejuvenated binary products. We find that the most massive star is expected to be a binary product after 1.0 ± 0.7 Myr in Arches and after 1.7 ± 1.0 Myr in Quintuplet. Today, the most massive 9 ± 3 stars in Arches and 8 ± 3 in Quintuplet are expected to be such objects. Our findings have strong implications for the stellar upper mass limit and solve the discrepancy between the claimed 150 M {sub ☉} limit and observations of four stars with initial masses of 165-320 M {sub ☉} in R136 and of supernova 2007bi, which is thought to be a pair-instability supernova from an initial 250 M {sub ☉} star. Using the stellar population of R136, we revise the upper mass limit to values in the range

  14. Ages of young star clusters, massive blue stragglers, and the upper mass limit of stars: Analyzing age-dependent stellar mass functions

    International Nuclear Information System (INIS)

    Schneider, F. R. N.; Izzard, R. G.; Langer, N.; Stolte, A.; Hußmann, B.; De Mink, S. E.; Anton Pannekoek, Amsterdam University, Science Park 904, 1098 XH, Amsterdam (Netherlands))" data-affiliation=" (Astronomical Institute Anton Pannekoek, Amsterdam University, Science Park 904, 1098 XH, Amsterdam (Netherlands))" >De Koter, A.; Anton Pannekoek, Amsterdam University, Science Park 904, 1098 XH, Amsterdam (Netherlands))" data-affiliation=" (Astronomical Institute Anton Pannekoek, Amsterdam University, Science Park 904, 1098 XH, Amsterdam (Netherlands))" >Sana, H.; Gvaramadze, V. V.; Liermann, A.

    2014-01-01

    Massive stars rapidly change their masses through strong stellar winds and mass transfer in binary systems. The latter aspect is important for populations of massive stars as more than 70% of all O stars are expected to interact with a binary companion during their lifetime. We show that such mass changes leave characteristic signatures in stellar mass functions of young star clusters that can be used to infer their ages and to identify products of binary evolution. We model the observed present-day mass functions of the young Galactic Arches and Quintuplet star clusters using our rapid binary evolution code. We find that the shaping of the mass function by stellar wind mass loss allows us to determine the cluster ages as 3.5 ± 0.7 Myr and 4.8 ± 1.1 Myr, respectively. Exploiting the effects of binary mass exchange on the cluster mass function, we find that the most massive stars in both clusters are rejuvenated products of binary mass transfer, i.e., the massive counterpart of classical blue straggler stars. This resolves the problem of an apparent age spread among the most luminous stars exceeding the expected duration of star formation in these clusters. We perform Monte Carlo simulations to probe stochastic sampling, which support the idea of the most massive stars being rejuvenated binary products. We find that the most massive star is expected to be a binary product after 1.0 ± 0.7 Myr in Arches and after 1.7 ± 1.0 Myr in Quintuplet. Today, the most massive 9 ± 3 stars in Arches and 8 ± 3 in Quintuplet are expected to be such objects. Our findings have strong implications for the stellar upper mass limit and solve the discrepancy between the claimed 150 M ☉ limit and observations of four stars with initial masses of 165-320 M ☉ in R136 and of supernova 2007bi, which is thought to be a pair-instability supernova from an initial 250 M ☉ star. Using the stellar population of R136, we revise the upper mass limit to values in the range 200-500 M ☉ .

  15. Ages of Young Star Clusters, Massive Blue Stragglers, and the Upper Mass Limit of Stars: Analyzing Age-dependent Stellar Mass Functions

    Science.gov (United States)

    Schneider, F. R. N.; Izzard, R. G.; de Mink, S. E.; Langer, N.; Stolte, A.; de Koter, A.; Gvaramadze, V. V.; Hußmann, B.; Liermann, A.; Sana, H.

    2014-01-01

    Massive stars rapidly change their masses through strong stellar winds and mass transfer in binary systems. The latter aspect is important for populations of massive stars as more than 70% of all O stars are expected to interact with a binary companion during their lifetime. We show that such mass changes leave characteristic signatures in stellar mass functions of young star clusters that can be used to infer their ages and to identify products of binary evolution. We model the observed present-day mass functions of the young Galactic Arches and Quintuplet star clusters using our rapid binary evolution code. We find that the shaping of the mass function by stellar wind mass loss allows us to determine the cluster ages as 3.5 ± 0.7 Myr and 4.8 ± 1.1 Myr, respectively. Exploiting the effects of binary mass exchange on the cluster mass function, we find that the most massive stars in both clusters are rejuvenated products of binary mass transfer, i.e., the massive counterpart of classical blue straggler stars. This resolves the problem of an apparent age spread among the most luminous stars exceeding the expected duration of star formation in these clusters. We perform Monte Carlo simulations to probe stochastic sampling, which support the idea of the most massive stars being rejuvenated binary products. We find that the most massive star is expected to be a binary product after 1.0 ± 0.7 Myr in Arches and after 1.7 ± 1.0 Myr in Quintuplet. Today, the most massive 9 ± 3 stars in Arches and 8 ± 3 in Quintuplet are expected to be such objects. Our findings have strong implications for the stellar upper mass limit and solve the discrepancy between the claimed 150 M ⊙ limit and observations of four stars with initial masses of 165-320 M ⊙ in R136 and of supernova 2007bi, which is thought to be a pair-instability supernova from an initial 250 M ⊙ star. Using the stellar population of R136, we revise the upper mass limit to values in the range 200-500 M ⊙.

  16. Functional connectivity analysis of the neural bases of emotion regulation: A comparison of independent component method with density-based k-means clustering method.

    Science.gov (United States)

    Zou, Ling; Guo, Qian; Xu, Yi; Yang, Biao; Jiao, Zhuqing; Xiang, Jianbo

    2016-04-29

    Functional magnetic resonance imaging (fMRI) is an important tool in neuroscience for assessing connectivity and interactions between distant areas of the brain. To find and characterize the coherent patterns of brain activity as a means of identifying brain systems for the cognitive reappraisal of the emotion task, both density-based k-means clustering and independent component analysis (ICA) methods can be applied to characterize the interactions between brain regions involved in cognitive reappraisal of emotion. Our results reveal that compared with the ICA method, the density-based k-means clustering method provides a higher sensitivity of polymerization. In addition, it is more sensitive to those relatively weak functional connection regions. Thus, the study concludes that in the process of receiving emotional stimuli, the relatively obvious activation areas are mainly distributed in the frontal lobe, cingulum and near the hypothalamus. Furthermore, density-based k-means clustering method creates a more reliable method for follow-up studies of brain functional connectivity.

  17. CO Oxidation by Subnanometer AgxAu3–x Supported Clusters via Density Functional Theory Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Negreiros, Fabio R.; Sementa, Luca; Barcaro, Giovanni; Vajda, S.; Apra, Edoardo; Fortunelli, Alessandro

    2012-09-07

    The activity of AgxAu3–x/MgO(100) clusters in CO oxidation is investigated computationally via systematic sampling techniques. It is found that these subnanometer species transform after ligand adsorption into reaction complexes which catalyze CO oxidation through a variety of different mechanisms, occurring via both Langmuir–Hinshelwood and Eley–Rideal paths and in some cases directly involving the oxide support. The alloyed Ag2Au1 cluster is proposed as the best catalyst in terms of efficiency and robustness.

  18. Comprehensive cluster analysis with Transitivity Clustering.

    Science.gov (United States)

    Wittkop, Tobias; Emig, Dorothea; Truss, Anke; Albrecht, Mario; Böcker, Sebastian; Baumbach, Jan

    2011-03-01

    Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers three user-friendly interfaces: a powerful stand-alone version, a web interface, and a collection of Cytoscape plug-ins. In this paper, we describe three major workflows: (i) protein (super)family detection with Cytoscape, (ii) protein homology detection with incomplete gold standards and (iii) clustering of gene expression data. This protocol guides the user through the most important features of Transitivity Clustering and takes ∼1 h to complete.

  19. Structures, stabilities, and electronic properties of small-sized Zr{sub 2}Si{sub n} (n=1-11) clusters. A density functional study

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Jing-He; Liu, Chang-Xin [Henan Institute of Education, Zhengzhou (China). Dept. of Physics; Wang, Ping; Zhang, Shuai; Lu, Cheng [Nanyang Normal Univ (China). Dept. of Physics; Yang, Gui [Anyang Normal Univ. (China). Dept. of Physics and Electrical Engineering

    2015-07-01

    Ab initio methods based on density functional theory at B3LYP level have been applied in investigating the equilibrium geometries, growth patterns, relative stabilities, and electronic properties of Zr{sub 2}-doped Si{sub n} clusters. The optimisation results shown that the lowest-energy configurations for Zr{sub 2}Si{sub n} clusters do not keep the corresponding silicon framework unchanged, which reflects that the doped Zr atoms dramatically affect the most stable structures of the Si{sub n} clusters. By analysing the relative stabilities, it is found that the doping of zirconium atoms reduces the chemical stabilities of silicon host. The Zr{sub 2}Si{sub 4} and Zr{sub 2}Si{sub 7} clusters are the magic numbers. The natural population and natural electronic configuration analyses indicated that the Zr atoms possess positive charge for n=1-6 and negative charge for n=7-11. In addition, the chemical hardness, chemical potential, infrared, and Raman spectra are also discussed.

  20. Genital and extra-genital screening for gonorrhoea using the BD Probetec ET system with an in-house PCR method targeting the porA pseudogene as confirmatory test

    DEFF Research Database (Denmark)

    Skovgaard, Sissel; Larsen, Helle Kiellberg; Sand, Carsten

    2012-01-01

    for Chlamydia trachomatis testing were also examined for GC on the BD Viper™ platform using the BD Probetec ET system. In order to avoid false-positive results all GC BD reactive samples were re-tested using a PCR method with the porA pseudogene as target. Using this method we screened 170% more samples for GC...

  1. Identification of four genomic loci highly related to casein-kinase-2-alpha cDNA and characterization of a casein kinase-2-alpha pseudogene within the mouse genome

    DEFF Research Database (Denmark)

    Boldyreff, B; Wehr, K; Hecht, R

    1992-01-01

    positive clone was further analyzed by sequencing a 3.1 kb XbaI fragment. This clone displays the characteristics of a pseudogene, i.e. lack of introns and several nucleotide insertions and deletions. In its 3' region it contains a 91 bp large CT-rich stretch which consists of (CCTT) and (CT) repeats...

  2. Weighted Clustering

    DEFF Research Database (Denmark)

    Ackerman, Margareta; Ben-David, Shai; Branzei, Simina

    2012-01-01

    We investigate a natural generalization of the classical clustering problem, considering clustering tasks in which different instances may have different weights.We conduct the first extensive theoretical analysis on the influence of weighted data on standard clustering algorithms in both...... the partitional and hierarchical settings, characterizing the conditions under which algorithms react to weights. Extending a recent framework for clustering algorithm selection, we propose intuitive properties that would allow users to choose between clustering algorithms in the weighted setting and classify...

  3. Independent-cluster parametrizations of wave functions in model field theories. 1. Introduction to their holomorphic representations

    International Nuclear Information System (INIS)

    Arponen, J.S.; Bishop, R.F.

    1991-01-01

    The configuration-interaction method (CIM), normal coupled-cluster method (NCCM), and extended coupled-cluster method (ECCM) form a rather natural hierarchy of formulations of increasing sophistication for describing interacting systems of quantum-mechanical particles or fields. They are denoted generically as independent-cluster (IC) parameterizations in a view of the way in which they incorporate the many-body correlations via sets of amplitudes that describe the various correlated clusters within the interacting system as mutually independent entities. They differ primarily by the way in which they incorporate the exact locality and separability properties. Each method is shown to provide, in principle, an exact mapping of the original quantum-mechanical problem into a corresponding classical Hamiltonian mechanics in terms of a set of multiconfigurational canonical field amplitudes. In perturbation-theoretic terms the IC methods incorporate infinite classes of diagrams at each order of approximation. The diagrams differ in their connectivity or linkedness properties. The structure of the ECCM in particular makes it capable of describing such phenomena as phase transitions, spontaneous symmetry breaking , and topological states. The authors address such fundamentally important questions as the existence and convergence properties of the three IC parameterizations by formulating the holomorphic representation of each one for the class of single-mode bosonic field theories which include the anharmonic oscillators

  4. Dynamical aspects of galaxy clustering

    International Nuclear Information System (INIS)

    Fall, S.M.

    1980-01-01

    Some recent work on the origin and evolution of galaxy clustering is reviewed, particularly within the context of the gravitational instability theory and the hot big-bang cosmological model. Statistical measures of clustering, including correlation functions and multiplicity functions, are explained and discussed. The close connection between galaxy formation and clustering is emphasized. Additional topics include the dependence of galaxy clustering on the spectrum of primordial density fluctuations and the mean mass density of the Universe. (author)

  5. A Density Functional Theory Investigation of Nin , Pdn , and Ptn Clusters (n=1-4) Adsorbed on Buckminsterfullerene.

    Science.gov (United States)

    Pham, Nguyet N T; Le, Hung M

    2017-05-19

    In this study, we examine the adsorptions of Ni, Pd, and Pt clusters on C 60 by using a computational approach. Our calculation results show that the base structure of C 60 can host Ni n /Pd n /Pt n (n=1-4) clusters with good adsorption stability and the complexes establish either two or no unpaired electrons. The binding energy of Pd and Pt clusters increases as the number of metal atoms increases, implying that the coverage of C 60 with Pd or Pt preferentially establishes a large-size metal cluster. A single metal atom favorably occupies the C-C bridge site. For dimer clusters, the three metals of interest share a similar binding fashion, in which two metal atoms establish direct interactions with the C-C bridge sites. For trimer adsorptions, the formation of linear and triangular structures is observed. Both Pt 3 and Ni 3 preferably constitute isosceles triangles on C 60 , whilst Pd 3 favorably establishes a linear shape. Finally, for each of the Ni 4 and Pd 4 adsorption cases, we observed three stable binding configurations: rhombus, tetrahedron, and Y-form. Whereas Ni 4 establishes a tetrahedral form, Pd 4 attains the most stable form with the Y-shape geometry on C 60 . Overall, we observe that the trend of Pd binding to C 60 tends to go beyond the fashion of Ni and Pt. In terms of magnetic alignment, the Pd n -C 60 systems seem to be non-magnetic in most cases, unlike the Ni and Pt cases, the structures of which possess magnetic moments of 2 μB in their most stable forms. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Cluster growth kinetics

    International Nuclear Information System (INIS)

    Dubovik, V.M.; Gal'perin, A.G.; Rikhvitskij, V.S.; Lushnikov, A.A.

    2000-01-01

    Processes of some traffic blocking coming into existence are considered as probabilistic ones. We study analytic solutions for models for the dynamics of both cluster growth and cluster growth with fragmentation in the systems of finite number of objects. Assuming rates constancy of both coalescence and fragmentation, the models under consideration are linear on the probability functions

  7. The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease.

    Science.gov (United States)

    Karmi, Ola; Marjault, Henri-Baptiste; Pesce, Luca; Carloni, Paolo; Onuchic, Jose' N; Jennings, Patricia A; Mittler, Ron; Nechushtai, Rachel

    2018-02-12

    NEET proteins comprise a new class of [2Fe-2S] cluster proteins. In human, three genes encode for NEET proteins: cisd1 encodes mitoNEET (mNT), cisd2 encodes the Nutrient-deprivation autophagy factor-1 (NAF-1) and cisd3 encodes MiNT (Miner2). These recently discovered proteins play key roles in many processes related to normal metabolism and disease. Indeed, NEET proteins are involved in iron, Fe-S, and reactive oxygen homeostasis in cells and play an important role in regulating apoptosis and autophagy. mNT and NAF-1 are homodimeric and reside on the outer mitochondrial membrane. NAF-1 also resides in the membranes of the ER associated mitochondrial membranes (MAM) and the ER. MiNT is a monomer with distinct asymmetry in the molecular surfaces surrounding the clusters. Unlike its paralogs mNT and NAF-1, it resides within the mitochondria. NAF-1 and mNT share similar backbone folds to the plant homodimeric NEET protein (At-NEET), while MiNT's backbone fold resembles a bacterial MiNT protein. Despite the variation of amino acid composition among these proteins, all NEET proteins retained their unique CDGSH domain harboring their unique 3Cys:1His [2Fe-2S] cluster coordination through evolution. The coordinating exposed His was shown to convey the lability to the NEET proteins' [2Fe-2S] clusters. In this minireview, we discuss the NEET fold and its structural elements. Special attention is given to the unique lability of the NEETs' [2Fe-2S] cluster and the implication of the latter to the NEET proteins' cellular and systemic function in health and disease.

  8. Higher-order superclustering in the Ostriker explosion scenario I. Three-point correlation functions of clusters in the constant and power-law models

    International Nuclear Information System (INIS)

    Jing Yipeng.

    1989-08-01

    We study the three-point correlation functions ρ(r, u, v) of clusters in the two types of explosion models by numerical simulations. The clusters are identified as the ''knots'' where three shells intersect. The shells are assumed to have the constant radii (the constant models) or have the power law radius distributions (the power law models). In both kinds of models, we find that ρ can be approximately expressed by the scaling form: ρ = Q(ξ 1 ξ 2 + ξ 2 ξ 3 + ξ 3 ξ 1 ), and Q is about 1, which are consistent with the observations. More detailed studies of r-, u- and v-dependences of Q show that Q remains constant in the constant models. In the power-law models, Q is independent of the shape parameters u and v, while it has some moderate r-dependences (variations with r about a factor of 1 or 2). (author). 27 refs, 9 figs

  9. Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice

    OpenAIRE

    Wang, Jun; Linnenbrink, Miriam; Künzel, Sven; Fernandes, Ricardo; Nadeau, Marie-Josée; Rosenstiel, Philip; Baines, John F.

    2014-01-01

    Understanding the origins of gut microbial community structure is critical for the identification and interpretation of potential fitnessrelated traits for the host. The presence of community clusters characterized by differences in the abundance of signature taxa, referred to as enterotypes, is a debated concept first reported in humans and later extended to other mammalian hosts. In this study, we provide a thorough assessment of their existence in wild house mice using a panel of evaluatio...

  10. Enhancing Executive Functions Among Dutch Elementary School Children Using the Train Your Mind Program : Protocol for a Cluster Randomized Trial

    NARCIS (Netherlands)

    Bervoets, Joachim; Jonkman, Lisa M; Mulkens, Sandra; de Vries, Hein; Kok, Gerjo

    2018-01-01

    BACKGROUND: Executive functions are higher cognitive control functions, which are essential to physical and psychological well-being, academic performance, and healthy social relationships. Executive functions can be trained, albeit without broad transfer, to this date. Broad transfer entails the

  11. Understanding Hematopoietic Stem Cell Development through Functional Correlation of Their Proliferative Status with the Intra-aortic Cluster Architecture.

    Science.gov (United States)

    Batsivari, Antoniana; Rybtsov, Stanislav; Souilhol, Celine; Binagui-Casas, Anahi; Hills, David; Zhao, Suling; Travers, Paul; Medvinsky, Alexander

    2017-06-06

    During development, hematopoietic stem cells (HSCs) emerge in the aorta-gonad-mesonephros (AGM) region through a process of multi-step maturation and expansion. While proliferation of adult HSCs is implicated in the balance between self-renewal and differentiation, very little is known about the proliferation status of nascent HSCs in the AGM region. Using Fucci reporter mice that enable in vivo visualization of cell-cycle status, we detect increased proliferation during pre-HSC expansion followed by a slowing down of cycling once cells start to acquire a definitive HSC state, similar to fetal liver HSCs. We observe time-specific changes in intra-aortic hematopoietic clusters corresponding to HSC maturation stages. The proliferative architecture of the clusters is maintained in an orderly anatomical manner with slowly cycling cells at the base and more actively proliferating cells at the more apical part of the cluster, which correlates with c-KIT expression levels, thus providing an anatomical basis for the role of SCF in HSC maturation. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Understanding Hematopoietic Stem Cell Development through Functional Correlation of Their Proliferative Status with the Intra-aortic Cluster Architecture

    Directory of Open Access Journals (Sweden)

    Antoniana Batsivari

    2017-06-01

    Full Text Available During development, hematopoietic stem cells (HSCs emerge in the aorta-gonad-mesonephros (AGM region through a process of multi-step maturation and expansion. While proliferation of adult HSCs is implicated in the balance between self-renewal and differentiation, very little is known about the proliferation status of nascent HSCs in the AGM region. Using Fucci reporter mice that enable in vivo visualization of cell-cycle status, we detect increased proliferation during pre-HSC expansion followed by a slowing down of cycling once cells start to acquire a definitive HSC state, similar to fetal liver HSCs. We observe time-specific changes in intra-aortic hematopoietic clusters corresponding to HSC maturation stages. The proliferative architecture of the clusters is maintained in an orderly anatomical manner with slowly cycling cells at the base and more actively proliferating cells at the more apical part of the cluster, which correlates with c-KIT expression levels, thus providing an anatomical basis for the role of SCF in HSC maturation.

  13. Copper Sensing Function of Drosophila Metal-Responsive Transcription Factor-1 Is Mediated By a Tetranuclear Cu(I) Cluster

    Energy Technology Data Exchange (ETDEWEB)

    Chen, X.; Hua, H.; Balamurugan, K.; Kong, X.; Zhang, L.; George, G.N.; Georgiev, O.; Schaffner, W.; Giedroc, D.P.

    2009-05-12

    Drosophila melanogaster MTF-1 (dMTF-1) is a copper-responsive transcriptional activator that mediates resistance to Cu, as well as Zn and Cd. Here, we characterize a novel cysteine-rich domain which is crucial for sensing excess intracellular copper by dMTF-1. Transgenic flies expressing mutant dMTF-1 containing alanine substitutions of two, four or six cysteine residues within the sequence {sup 547}CNCTNCKCDQTKSCHGGDC{sup 565} are significantly or completely impaired in their ability to protect flies from copper toxicity and fail to up-regulate MtnA (metallothionein) expression in response to excess Cu. In contrast, these flies exhibit wild-type survival in response to copper deprivation thus revealing that the cysteine cluster domain is required only for sensing Cu load by dMTF-1. Parallel studies show that the isolated cysteine cluster domain is required to protect a copper-sensitive S. cerevisiae ace1 strain from copper toxicity. Cu(I) ligation by a Cys-rich domain peptide fragment drives the cooperative assembly of a polydentate [Cu{sub 4}-S{sub 6}] cage structure, characterized by a core of trigonally S{sub 3} coordinated Cu(I) ions bound by bridging thiolate ligands. While reminiscent of Cu{sub 4}-L{sub 6} (L = ligand) tetranuclear clusters in copper regulatory transcription factors of yeast, the absence of significant sequence homology is consistent with convergent evolution of a sensing strategy particularly well suited for Cu(I).

  14. NEW ISOLATED PLANETARY-MASS OBJECTS AND THE STELLAR AND SUBSTELLAR MASS FUNCTION OF THE σ ORIONIS CLUSTER

    International Nuclear Information System (INIS)

    Peña Ramírez, K.; Béjar, V. J. S.; Zapatero Osorio, M. R.; Martín, E. L.; Petr-Gotzens, M. G.

    2012-01-01

    We report on our analysis of the VISTA Orion ZY JHK s photometric data (completeness magnitudes of Z = 22.6 and J = 21.0 mag) focusing on a circular area of 2798.4 arcmin 2 around the young σ Orionis star cluster (∼3 Myr, ∼352 pc, and solar metallicity). The combination of the VISTA photometry with optical, WISE and Spitzer data allows us to identify a total of 210 σ Orionis member candidates with masses in the interval 0.25-0.004 M ☉ , 23 of which are new planetary-mass object findings. These discoveries double the number of cluster planetary-mass candidates known so far. One object has colors compatible with a T spectral type. The σ Orionis cluster harbors about as many brown dwarfs (69, 0.072-0.012 M ☉ ) and planetary-mass objects (37, 0.012-0.004 M ☉ ) as very low mass stars (104, 0.25-0.072 M ☉ ). Based on Spitzer data, we derive a disk frequency of ∼40% for very low mass stars, brown dwarfs, and planetary-mass objects in σ Orionis. The radial density distributions of these three mass intervals are alike: all are spatially concentrated within an effective radius of 12' (1.2 pc) around the multiple star σ Ori, and no obvious segregation between disk-bearing and diskless objects is observed. Using the VISTA data and the Mayrit catalog, we derive the cluster mass spectrum (ΔN/ΔM ∼ M –α ) from ∼19 to 0.006 M ☉ (VISTA ZJ completeness), which is reasonably described by two power-law expressions with indices of α = 1.7 ± 0.2 for M > 0.35 M ☉ , and α = 0.6 ± 0.2 for M ☉ . The σ Orionis mass spectrum smoothly extends into the planetary-mass regime down to 0.004 M ☉ . Our findings of T-type sources ( ☉ ) in the VISTA σ Orionis exploration appear to be smaller than what is predicted by the extrapolation of the cluster mass spectrum down to the survey J-band completeness.

  15. NEW ISOLATED PLANETARY-MASS OBJECTS AND THE STELLAR AND SUBSTELLAR MASS FUNCTION OF THE {sigma} ORIONIS CLUSTER

    Energy Technology Data Exchange (ETDEWEB)

    Pena Ramirez, K.; Bejar, V. J. S. [Instituto de Astrofisica de Canarias, C/. Via Lactea s/n, E-38205 La Laguna, Tenerife (Spain); Zapatero Osorio, M. R.; Martin, E. L. [Centro de Astrobiologia (CSIC-INTA), Crta. Ajalvir km 4, E-28850 Torrejon de Ardoz, Madrid (Spain); Petr-Gotzens, M. G., E-mail: karla@iac.es, E-mail: vbejar@iac.es, E-mail: mosorio@cab.inta-csic.es, E-mail: ege@cab.inta-csic.es, E-mail: mpetr@eso.org [European Southern Observatory, Karl-Schwarzschild-Str. 2, 85748 Garching bei Muenchen (Germany)

    2012-07-20

    We report on our analysis of the VISTA Orion ZY JHK{sub s} photometric data (completeness magnitudes of Z = 22.6 and J = 21.0 mag) focusing on a circular area of 2798.4 arcmin{sup 2} around the young {sigma} Orionis star cluster ({approx}3 Myr, {approx}352 pc, and solar metallicity). The combination of the VISTA photometry with optical, WISE and Spitzer data allows us to identify a total of 210 {sigma} Orionis member candidates with masses in the interval 0.25-0.004 M{sub Sun }, 23 of which are new planetary-mass object findings. These discoveries double the number of cluster planetary-mass candidates known so far. One object has colors compatible with a T spectral type. The {sigma} Orionis cluster harbors about as many brown dwarfs (69, 0.072-0.012 M{sub Sun }) and planetary-mass objects (37, 0.012-0.004 M{sub Sun }) as very low mass stars (104, 0.25-0.072 M{sub Sun }). Based on Spitzer data, we derive a disk frequency of {approx}40% for very low mass stars, brown dwarfs, and planetary-mass objects in {sigma} Orionis. The radial density distributions of these three mass intervals are alike: all are spatially concentrated within an effective radius of 12' (1.2 pc) around the multiple star {sigma} Ori, and no obvious segregation between disk-bearing and diskless objects is observed. Using the VISTA data and the Mayrit catalog, we derive the cluster mass spectrum ({Delta}N/{Delta}M {approx} M{sup -{alpha}}) from {approx}19 to 0.006 M{sub Sun} (VISTA ZJ completeness), which is reasonably described by two power-law expressions with indices of {alpha} = 1.7 {+-} 0.2 for M > 0.35 M{sub Sun }, and {alpha} = 0.6 {+-} 0.2 for M < 0.35 M{sub Sun }. The {sigma} Orionis mass spectrum smoothly extends into the planetary-mass regime down to 0.004 M{sub Sun }. Our findings of T-type sources (<0.004 M{sub Sun }) in the VISTA {sigma} Orionis exploration appear to be smaller than what is predicted by the extrapolation of the cluster mass spectrum down to the survey J

  16. Isotopic clusters

    International Nuclear Information System (INIS)

    Geraedts, J.M.P.

    1983-01-01

    Spectra of isotopically mixed clusters (dimers of SF 6 ) are calculated as well as transition frequencies. The result leads to speculations about the suitability of the laser-cluster fragmentation process for isotope separation. (Auth.)

  17. Cluster Headache

    Science.gov (United States)

    ... a role. Unlike migraine and tension headache, cluster headache generally isn't associated with triggers, such as foods, hormonal changes or stress. Once a cluster period begins, however, drinking alcohol ...

  18. Choosing the Number of Clusters in K-Means Clustering

    Science.gov (United States)

    Steinley, Douglas; Brusco, Michael J.

    2011-01-01

    Steinley (2007) provided a lower bound for the sum-of-squares error criterion function used in K-means clustering. In this article, on the basis of the lower bound, the authors propose a method to distinguish between 1 cluster (i.e., a single distribution) versus more than 1 cluster. Additionally, conditional on indicating there are multiple…

  19. Cluster Headache

    OpenAIRE

    Pearce, Iris

    1985-01-01

    Cluster headache is the most severe primary headache with recurrent pain attacks described as worse than giving birth. The aim of this paper was to make an overview of current knowledge on cluster headache with a focus on pathophysiology and treatment. This paper presents hypotheses of cluster headache pathophysiology, current treatment options and possible future therapy approaches. For years, the hypothalamus was regarded as the key structure in cluster headache, but is now thought to be pa...

  20. Categorias Cluster

    OpenAIRE

    Queiroz, Dayane Andrade

    2015-01-01

    Neste trabalho apresentamos as categorias cluster, que foram introduzidas por Aslak Bakke Buan, Robert Marsh, Markus Reineke, Idun Reiten e Gordana Todorov, com o objetivo de categoriíicar as algebras cluster criadas em 2002 por Sergey Fomin e Andrei Zelevinsky. Os autores acima, em [4], mostraram que existe uma estreita relação entre algebras cluster e categorias cluster para quivers cujo grafo subjacente é um diagrama de Dynkin. Para isto desenvolveram uma teoria tilting na estrutura triang...

  1. Globular clusters and galaxy halos

    International Nuclear Information System (INIS)

    Van Den Bergh, S.

    1984-01-01

    Using semipartial correlation coefficients and bootstrap techniques, a study is made of the important features of globular clusters with respect to the total number of galaxy clusters and dependence of specific galaxy cluster on parent galaxy type, cluster radii, luminosity functions and cluster ellipticity. It is shown that the ellipticity of LMC clusters correlates significantly with cluster luminosity functions, but not with cluster age. The cluter luminosity value above which globulars are noticeably flattened may differ by a factor of about 100 from galaxy to galaxy. Both in the Galaxy and in M31 globulars with small core radii have a Gaussian distribution over luminosity, whereas clusters with large core radii do not. In the cluster systems surrounding the Galaxy, M31 and NGC 5128 the mean radii of globular clusters was found to increase with the distance from the nucleus. Central galaxies in rich clusters have much higher values for specific globular cluster frequency than do other cluster ellipticals, suggesting that such central galaxies must already have been different from normal ellipticals at the time they were formed

  2. Meaningful Clusters

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

    2004-05-26

    We present an approach to the disambiguation of cluster labels that capitalizes on the notion of semantic similarity to assign WordNet senses to cluster labels. The approach provides interesting insights on how document clustering can provide the basis for developing a novel approach to word sense disambiguation.

  3. Horticultural cluster

    OpenAIRE

    SHERSTIUK S.V.; POSYLAYEVA K.I.

    2013-01-01

    In the article there are the theoretical and methodological approaches to the nature and existence of the cluster. The cluster differences from other kinds of cooperative and integration associations. Was develop by scientific-practical recommendations for forming a competitive horticultur cluster.

  4. High stability of the goldalloy fullerenes: A density functional theory investigation of M12@Au20 (M = Na, Al, Ag, Sc, Y, La, Lu, and Au) clusters

    International Nuclear Information System (INIS)

    Zhang Meng; Feng Xiao-Juan; Zhao Li-Xia; Zhang Hong-Yu; Luo You-Hua

    2012-01-01

    Discovering highly stable metal fullerenes such as the celebrated C 60 is interesting in cluster science as they have potential applications as building blocks in new nanostructures. We here investigated the structural and electronic properties of the fullerenes M 12 @Au 20 (M = Na, Al, Ag, Sc, Y, La, Lu, and Au), using a first-principles investigation with the density functional theory. It is found that these compound clusters possess a similar cage structure to the icosahedral Au 32 fullerene. La 12 @Au 20 is found to be particularly stable among these clusters. The binding energy of La 12 @Au 20 is 3.43 eV per atom, 1.05 eV larger than that in Au 32 . The highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap of La 12 @Au 20 is only 0.31 eV, suggesting that it should be relatively chemically reactive. (condensed matter: structural, mechanical, and thermal properties)

  5. Creation of a 3Mn/1Fe cluster in the oxygen-evolving complex of photosystem II and investigation of its functional activity.

    Science.gov (United States)

    Semin, B К; Davletshina, L N; Seibert, M; Rubin, A B

    2018-01-01

    Extraction of Mn cations from the oxygen-evolving complex (OEC) of Ca-depleted PSII membranes (PSII[-Ca,4Mn]) by reductants like hydroquinone (H 2 Q) occurs with lower efficiency at acidic pH (2Mn/reaction center [RC] are extracted at pH5.7) than at neutral pH (3Mn/RC are extracted at pH6.5) [Semin et al. Photosynth. Res. 125 (2015) 95]. Fe(II) also extracts Mn cations from PSII(-Ca,4Mn), but only 2Mn/RC at pH6.5, forming a heteronuclear 2Mn/2Fe cluster [Semin and Seibert, J. Bioenerg. Biomembr. 48 (2016) 227]. Here we investigated the efficiency of Mn extraction by Fe(II) at acidic pH and found that Fe(II) cations can extract only 1Mn/RC from PSII(-Ca,4Mn) membranes at pH 5.7, forming a 3Mn/1Fe cluster. Also we found that the presence of Fe cations in a heteronuclear cluster (2Mn/2Fe) increases the resistance of the remaining Mn cations to H 2 Q action, since H 2 Q can extract Mn cations from homonuclear Mn clusters of PSII(-Ca,4Mn) and PSII(-Ca,2Mn) membranes but not from the heteronuclear cluster in PSII(-Ca,2Mn,2Fe) membranes. H 2 Q also cannot extract Mn from PSII membranes obtained by incubation of PSII(-Ca,4Mn) membranes with Fe(II) cations at pH5.7, which suggests the formation of a heteronuclear 3Mn/1Fe cluster in the OEC. Functional activity of PSII with a 3Mn/1Fe cluster was investigated. PSII preparations with a 3Mn/1Fe cluster in the OEC are able to photoreduce the exogenous electron acceptor 2,6-dichlorophenolindophenol, possibly due to incomplete oxidation of water molecules as is the case with PSII(-Ca,2Mn,2Fe) samples. However, in the contrast to PSII(-Ca,2Mn,2Fe) samples PSII(-Ca,3Mn,1Fe) membranes can evolve O 2 at a low rate in the presence of exogenous Ca 2+ (at about 27% of the rate of O 2 evolution in native PSII membranes). The explanation for this phenomenon (either water splitting and production of molecular O 2 by the 3Mn/1Fe cluster or apparent O 2 evolution due to minor contamination of PSII(3Mn,1Fe) samples with PSII(-Ca,4Mn) membranes

  6. The clinical obesity maintenance model: an integration of psychological constructs including mood, emotional regulation, disordered overeating, habitual cluster behaviours, health literacy and cognitive function.

    Science.gov (United States)

    Raman, Jayanthi; Smith, Evelyn; Hay, Phillipa

    2013-01-01

    Psychological distress and deficits in executive functioning are likely to be important barriers to effective weight loss maintenance. The purpose of this paper is twofold. First, in the light of recent evidence in the fields of neuropsychology and obesity, particularly on the deficits in the executive function in overweight and obese individuals, a conceptual and theoretical framework of obesity maintenance is introduced by way of a clinical obesity maintenance model (COMM). It is argued that psychological variables, that of habitual cluster Behaviors, emotional dysregulation, mood, and health literacy, interact with executive functioning and impact on the overeating/binge eating behaviors of obese individuals. Second, cognizant of this model, it is argued that the focus of obesity management should be extended to include a broader range of maintaining mechanisms, including but not limited to cognitive deficits. Finally, a discussion on potential future directions in research and practice using the COMM is provided.

  7. The Clinical Obesity Maintenance Model: An Integration of Psychological Constructs including Mood, Emotional Regulation, Disordered Overeating, Habitual Cluster Behaviours, Health Literacy and Cognitive Function

    Directory of Open Access Journals (Sweden)

    Jayanthi Raman

    2013-01-01

    Full Text Available Psychological distress and deficits in executive functioning are likely to be important barriers to effective weight loss maintenance. The purpose of this paper is twofold. First, in the light of recent evidence in the fields of neuropsychology and obesity, particularly on the deficits in the executive function in overweight and obese individuals, a conceptual and theoretical framework of obesity maintenance is introduced by way of a clinical obesity maintenance model (COMM. It is argued that psychological variables, that of habitual cluster Behaviors, emotional dysregulation, mood, and health literacy, interact with executive functioning and impact on the overeating/binge eating behaviors of obese individuals. Second, cognizant of this model, it is argued that the focus of obesity management should be extended to include a broader range of maintaining mechanisms, including but not limited to cognitive deficits. Finally, a discussion on potential future directions in research and practice using the COMM is provided.

  8. Structures and reaction rates of the gaseous oxidation of SO2 by an O− 3 (H2O)0–5 cluster – a density functional theory investigation

    DEFF Research Database (Denmark)

    Bork, Nicolai Christian; Kurten, T.; Enghoff, Martin Andreas Bødker

    2011-01-01

    Based on density functional theory calculations we present a study of the gaseous oxidation of SO2 to SO3 by an anionic O3−(H2On cluster, n=0–5. The configurations of the most relevant reactants, transition states, and products are discussed and compared to previous findings. Two different classes......, the most energetically favorable class of transition states vary with the number of water molecules attached. A kinetic model is utilized, taking into account the most likely outcomes of the initial SO2O3−(H2O)n collision complexes. This model shows that the reaction takes place at collision rates...

  9. The zebrafish miR-462/miR-731 cluster is induced under hypoxic stress via hypoxia-inducible factor 1α and functions in cellular adaptations.

    Science.gov (United States)

    Huang, Chun-Xiao; Chen, Nan; Wu, Xin-Jie; Huang, Cui-Hong; He, Yan; Tang, Rong; Wang, Wei-Min; Wang, Huan-Ling

    2015-12-01

    Hypoxia, a unique and essential environmental stress, evokes highly coordinated cellular responses, and hypoxia-inducible factor (HIF) 1 in the hypoxia signaling pathway, an evolutionarily conserved cellular signaling pathway, acts as a master regulator of the transcriptional response to hypoxic stress. MicroRNAs (miRNAs), a major class of posttranscriptional gene expression regulators, also play pivotal roles in orchestrating hypoxia-mediated cellular adaptations. Here, global miRNA expression profiling and quantitative real-time PCR indicated that the up-regulation of the miR-462/miR-731 cluster in zebrafish larvae is induced by hypoxia. It was further validated that miR-462 and miR-731 are up-regulated in a Hif-1α-mediated manner under hypoxia and specifically target ddx5 and ppm1da, respectively. Overexpression of miR-462 and miR-731 represses cell proliferation through blocking cell cycle progress of DNA replication, and induces apoptosis. In situ detection revealed that the miR-462/miR-731 cluster is highly expressed in a consistent and ubiquitous manner throughout the early developmental stages. Additionally, the transcripts become restricted to the notochord, pharyngeal arch, liver, and gut regions from postfertilization d 3 to 5. These data highlight a previously unidentified role of the miR-462/miR-731 cluster as a crucial signaling mediator for hypoxia-mediated cellular adaptations and provide some insights into the potential function of the cluster during embryonic development. © FASEB.

  10. Genomic and Functional Characterization of the Unusual pLOCK 0919 Plasmid Harboring the spaCBA Pili Cluster in Lactobacillus casei LOCK 0919

    Science.gov (United States)

    Aleksandrzak-Piekarczyk, Tamara; Koryszewska-Bagińska, Anna; Grynberg, Marcin; Nowak, Adriana; Cukrowska, Bożena; Kozakova, Hana; Bardowski, Jacek

    2016-01-01

    Here, we report the extensive bioinformatic and functional analyses of the unusual pLOCK 0919, a plasmid originating from the probiotic Lactobacillus casei LOCK 0919 strain. This plasmid is atypical because it harbors the spaCBA-srtC gene cluster encoding SpaCBA pili. We show that all other spaCBA-srtC sequences of the Lactobacillus genus that have been previously described and deposited in GenBank are present in the chromosomal DNA. Another important observation for pLOCK 0919 is that the spaCBA-srtC gene cluster and its surrounding genes are highly similar to the respective DNA region that is present in the most well-known and active SpaCBA pili producer, the probiotic Lactobacillus rhamnosus GG strain. Our results demonstrate that the spaCBA-srtC clusters of pLOCK 0919 and L. rhamnosus GG are genealogically similar, located in DNA regions that are rich in transposase genes and are poorly conserved among the publicly available sequences of Lactobacillus sp. In contrast to chromosomally localized pilus gene clusters from L. casei and Lactobacillus paracasei, the plasmidic spaC of L. casei LOCK 0919 is expressed and undergoes a slight glucose-induced repression. Moreover, results of series of in vitro tests demonstrate that L. casei LOCK 0919 has an adhesion potential, which is largely determined by the presence of the pLOCK 0919 plasmid. In particular, the plasmid occurrence positively influenced the hydrophobicity and aggregation abilities of L. casei LOCK 0919. Moreover, in vivo studies indicate that among the three Lactobacillus strains used to colonize the gastrointestinal tract of germ-free mice, already after 2 days of colonization, L. casei LOCK 0919 became the dominant strain and persisted there for at least 48 days. PMID:26637469

  11. The regulatory network of cluster-root function and development in phosphate-deficient white lupin (Lupinus albus) identified by transcriptome sequencing.

    Science.gov (United States)

    Wang, Zhengrui; Straub, Daniel; Yang, Huaiyu; Kania, Angelika; Shen, Jianbo; Ludewig, Uwe; Neumann, Günter

    2014-07-01

    Lupinus albus serves as model plant for root-induced mobilization of sparingly soluble soil phosphates via the formation of cluster-roots (CRs) that mediate secretion of protons, citrate, phenolics and acid phosphatases (APases). This study employed next-generation sequencing to investigate the molecular mechanisms behind these complex adaptive responses at the transcriptome level. We compared different stages of CR development, including pre-emergent (PE), juvenile (JU) and the mature (MA) stages. The results confirmed that the primary metabolism underwent significant modifications during CR maturation, promoting the biosynthesis of organic acids, as had been deduced from physiological studies. Citrate catabolism was downregulated, associated with citrate accumulation in MA clusters. Upregulation of the phenylpropanoid pathway reflected the accumulation of phenolics. Specific transcript expression of ALMT and MATE transporter genes correlated with the exudation of citrate and flavonoids. The expression of transcripts related to nucleotide degradation and APases in MA clusters coincided with the re-mobilization and hydrolysis of organic phosphate resources. Most interestingly, hormone-related gene expression suggested a central role of ethylene during CR maturation. This was associated with the upregulation of the iron (Fe)-deficiency regulated network that mediates ethylene-induced expression of Fe-deficiency responses in other species. Finally, transcripts related to abscisic acid and jasmonic acid were upregulated in MA clusters, while auxin- and brassinosteroid-related genes and cytokinin receptors were most strongly expressed during CR initiation. Key regulations proposed by the RNA-seq data were confirmed by quantitative real-time polymerase chain reaction (RT-qPCR) and some physiological analyses. A model for the gene network regulating CR development and function is presented. © 2014 Scandinavian Plant Physiology Society.

  12. Cluster Matters

    DEFF Research Database (Denmark)

    Gulati, Mukesh; Lund-Thomsen, Peter; Suresh, Sangeetha

    2018-01-01

    sell their products successfully in international markets, but there is also an increasingly large consumer base within India. Indeed, Indian industrial clusters have contributed to a substantial part of this growth process, and there are several hundred registered clusters within the country...... of this handbook, which focuses on the role of CSR in MSMEs. Hence we contribute to the literature on CSR in industrial clusters and specifically CSR in Indian industrial clusters by investigating the drivers of CSR in India’s industrial clusters....

  13. Amines in the Earth’s Atmosphere: A Density Functional Theory Study of the Thermochemistry of Pre-Nucleation Clusters

    Directory of Open Access Journals (Sweden)

    Jason Herb

    2011-02-01

    Full Text Available The impact of organic species which are present in the Earth’s atmosphere on the burst of new particles is critically important for the understanding of the molecular nature of atmospheric nucleation phenomena. Amines have recently been proposed as possible stabilizers of binary pre-nucleation clusters. In order to advance the understanding of atmospheric nucleation phenomena, a quantum-chemical study of hydrogen-bonded complexes of binary sulfuric acid-water clusters with methyl-, dimethyl- and trimethylamines representing common atmospheric organic species, vegetation products and laboratory impurities has been carried out. The thermochemical stability of the sulfuric acid-amines-water complexes was found to be higher than that of the sulfuric acid-ammonia-water complexes, in qualitative agreement with the previous studies. However, the enhancement in stability due to amines appears to not be large enough to overcome the difference in typical atmospheric concentrations of ammonia and amines. Further research is needed in order to address the existing uncertainties and to reach a final conclusion about the importance of amines for the atmospheric nucleation.

  14. Two gene clusters co-ordinate for a functional N-acetylglucosamine catabolic pathway in Vibrio cholerae.

    Science.gov (United States)

    Ghosh, Swagata; Rao, K Hanumantha; Sengupta, Manjistha; Bhattacharya, Sujit K; Datta, Asis

    2011-06-01

    Pathogenic microorganisms like Vibrio cholerae are capable of adapting to diverse living conditions, especially when they transit from their environmental reservoirs to human host. V. cholerae attaches to N-acetylglucosamine (GlcNAc) residues in glycoproteins and lipids present in the intestinal epithelium and chitinous surface of zoo-phytoplanktons in the aquatic environment for its survival and colonization. GlcNAc utilization thus appears to be important for the pathogen to reach sufficient titres in the intestine for producing clinical symptoms of cholera. We report here the involvement of a second cluster of genes working in combination with the classical genes of GlcNAc catabolism, suggesting the occurrence of a novel variant of the process of biochemical conversion of GlcNAc to Fructose-6-phosphate as has been described in other organisms. Colonization was severely attenuated in mutants that were incapable of utilizing GlcNAc. It was also shown that N-acetylglucosamine specific repressor (NagC) performs a dual role - while the classical GlcNAc catabolic genes are under its negative control, the genes belonging to the second cluster are positively regulated by it. Further application of tandem affinity purification to NagC revealed its interaction with a novel partner. Our results provide a genetic program that probably enables V. cholerae to successfully utilize amino - sugars and also highlights a new mode of transcriptional regulation, not described in this organism. © 2011 Blackwell Publishing Ltd.

  15. A recently transferred cluster of bacterial genes in Trichomonas vaginalis - lateral gene transfer and the fate of acquired genes

    Science.gov (United States)

    2014-01-01

    Background Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes. PMID:24898731

  16. An original SERPINA3 gene cluster: Elucidation of genomic organization and gene expression in the Bos taurus 21q24 region

    Directory of Open Access Journals (Sweden)

    Ouali Ahmed

    2008-04-01

    Full Text Available Abstract Background The superfamily of serine proteinase inhibitors (serpins is involved in numerous fundamental biological processes as inflammation, blood coagulation and apoptosis. Our interest is focused on the SERPINA3 sub-family. The major human plasma protease inhibitor, α1-antichymotrypsin, encoded by the SERPINA3 gene, is homologous to genes organized in clusters in several mammalian species. However, although there is a similar genic organization with a high degree of sequence conservation, the reactive-centre-loop domains, which are responsible for the protease specificity, show significant divergences. Results We provide additional information by analyzing the situation of SERPINA3 in the bovine genome. A cluster of eight genes and one pseudogene sharing a high degree of identity and the same structural organization was characterized. Bovine SERPINA3 genes were localized by radiation hybrid mapping on 21q24 and only spanned over 235 Kilobases. For all these genes, we propose a new nomenclature from SERPINA3-1 to SERPINA3-8. They share approximately 70% of identity with the human SERPINA3 homologue. In the cluster, we described an original sub-group of six members with an unexpected high degree of conservation for the reactive-centre-loop domain, suggesting a similar peptidase inhibitory pattern. Preliminary expression analyses of these bovSERPINA3s showed different tissue-specific patterns and diverse states of glycosylation and phosphorylation. Finally, in the context of phylogenetic analyses, we improved our knowledge on mammalian SERPINAs evolution. Conclusion Our experimental results update data of the bovine genome sequencing, substantially increase the bovSERPINA3 sub-family and enrich the phylogenetic tree of serpins. We provide new opportunities for future investigations to approach the biological functions of this unusual subset of serine proteinase inhibitors.

  17. Characterization and prediction of the backscattered form function of an immersed cylindrical shell using hybrid fuzzy clustering and bio-inspired algorithms.

    Science.gov (United States)

    Agounad, Said; Aassif, El Houcein; Khandouch, Younes; Maze, Gérard; Décultot, Dominique

    2018-02-01

    The acoustic scattering of a plane wave by an elastic cylindrical shell is studied. A new approach is developed to predict the form function of an immersed cylindrical shell of the radius ratio b/a ('b' is the inner radius and 'a' is the outer radius). The prediction of the backscattered form function is investigated by a combined approach between fuzzy clustering algorithms and bio-inspired algorithms. Four famous fuzzy clustering algorithms: the fuzzy c-means (FCM), the Gustafson-Kessel algorithm (GK), the fuzzy c-regression model (FCRM) and the Gath-Geva algorithm (GG) are combined with particle swarm optimization and genetic algorithm. The symmetric and antisymmetric circumferential waves A, S 0 , A 1 , S 1 and S 2 are investigated in a reduced frequency (k 1 a) range extends over 0.1functions. This representation is used as a comparison criterion between the calculated form function by the analytical method and that predicted by the proposed approach on the one hand and is used to extract the predicted cut-off frequencies on the other hand. Moreover, the transverse velocity of the material constituting the cylindrical shell is extracted. The computational results show that the proposed approach is very efficient to predict the form function and consequently, for acoustic characterization purposes. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Examining the effectiveness of discriminant function analysis and cluster analysis in species identification of male field crickets based on their calling songs.

    Directory of Open Access Journals (Sweden)

    Ranjana Jaiswara

    Full Text Available Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6-7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species

  19. New advantages and challenges for laser-induced nanostructured cluster materials: functional capability for experimental verification of macroscopic quantum phenomena

    International Nuclear Information System (INIS)

    Abramov, D V; Antipov, A A; Arakelian, S M; Khor’kov, K S; Kucherik, A O; Kutrovskaya, S V; Prokoshev, V G

    2014-01-01

    The main goal of our work is the laser fabrication of nanostructured materials including the nano- and microclusters for control of electrical, optical and other properties of obtained structures. First, we took an opportunity to select nanoparticles in various sizes and weights and also in topology distribution for some materials (carbon, Ni, PbTe, etc). Second, for a deposited extended array of nanoparticles we used a method of laser-induced nanoparticle fabrication in colloid and deposition metal (and/or oxide) nanoparticles from colloidal systems (LDPCS) to obtain the multilayered nanostructures with controlled topology, including the fractal cluster structures (for Ni, Pb Te et al). Electrophysical properties are analyzed for such nanocluster systems as well. A brief analogy of the obtained nanocluster structures with a quantum correlated state evidence is carried out. (paper)

  20. Association of papillomavirus E6 proteins with either MAML1 or E6AP clusters E6 proteins by structure, function, and evolutionary relatedness.

    Directory of Open Access Journals (Sweden)

    Nicole Brimer

    2017-12-01

    Full Text Available Papillomavirus E6 proteins bind to LXXLL peptide motifs displayed on targeted cellular proteins. Alpha genus HPV E6 proteins associate with the cellular ubiquitin ligase E6AP (UBE3A, by binding to an LXXLL peptide (ELTLQELLGEE displayed by E6AP, thereby stimulating E6AP ubiquitin ligase activity. Beta, Gamma, and Delta genera E6 proteins bind a similar LXXLL peptide (WMSDLDDLLGS on the cellular transcriptional co-activator MAML1 and thereby repress Notch signaling. We expressed 45 different animal and human E6 proteins from diverse papillomavirus genera to ascertain the overall preference of E6 proteins for E6AP or MAML1. E6 proteins from all HPV genera except Alpha preferentially interacted with MAML1 over E6AP. Among animal papillomaviruses, E6 proteins from certain ungulate (SsPV1 from pigs and cetacean (porpoises and dolphins hosts functionally resembled Alpha genus HPV by binding and targeting the degradation of E6AP. Beta genus HPV E6 proteins functionally clustered with Delta, Pi, Tau, Gamma, Chi, Mu, Lambda, Iota, Dyokappa, Rho, and Dyolambda E6 proteins to bind and repress MAML1. None of the tested E6 proteins physically and functionally interacted with both MAML1 and E6AP, indicating an evolutionary split. Further, interaction of an E6 protein was insufficient to activate degradation of E6AP, indicating that E6 proteins that target E6AP co-evolved to separately acquire both binding and triggering of ubiquitin ligase activation. E6 proteins with similar biological function clustered together in phylogenetic trees and shared structural features. This suggests that the divergence of E6 proteins from either MAML1 or E6AP binding preference is a major event in papillomavirus evolution.

  1. Isolation of CYP3A5P cDNA from human liver: a reflection of a novel cytochrome P-450 pseudogene.

    Science.gov (United States)

    Schuetz, J D; Guzelian, P S

    1995-03-14

    We have isolated, from a human liver cDNA library, a 1627 bp CYP3A5 cDNA variant (CYP3A5P) that contains several large insertions, deletions, and in-frame termination codons. By comparison with the genomic structure of other CYP3A genes, the major insertions in CYP3A5P cDNA demarcate the inferred sites of several CYP3A5 exons. The segments inserted in CYP3A5P have no homology with splice donor acceptor sites. It is unlikely that CYP3A5P cDNA represents an artifact of the cloning procedures since Southern blot analysis of human genomic DNA disclosed that CYP3A5P cDNA hybridized with a DNA fragment distinct from fragments that hybridized with either CYP3A5, CYP3A3 or CYP3A4. Moreover, analysis of adult human liver RNA on Northern blots hybridized with a CYP3A5P cDNA fragment revealed the presence of an mRNA with the predicted size of CYP3A5P. We conclude that CYP3A5P cDNA was derived from a separate gene, CYP3A5P, most likely a pseudogene evolved from CYP3A5.

  2. Clustering on Membranes

    DEFF Research Database (Denmark)

    Johannes, Ludger; Pezeshkian, Weria; Ipsen, John H

    2018-01-01

    Clustering of extracellular ligands and proteins on the plasma membrane is required to perform specific cellular functions, such as signaling and endocytosis. Attractive forces that originate in perturbations of the membrane's physical properties contribute to this clustering, in addition to direct...... protein-protein interactions. However, these membrane-mediated forces have not all been equally considered, despite their importance. In this review, we describe how line tension, lipid depletion, and membrane curvature contribute to membrane-mediated clustering. Additional attractive forces that arise...... from protein-induced perturbation of a membrane's fluctuations are also described. This review aims to provide a survey of the current understanding of membrane-mediated clustering and how this supports precise biological functions....

  3. Cluster polylogarithms for scattering amplitudes

    International Nuclear Information System (INIS)

    Golden, John; Paulos, Miguel F; Spradlin, Marcus; Volovich, Anastasia

    2014-01-01

    Motivated by the cluster structure of two-loop scattering amplitudes in N=4 Yang-Mills theory we define cluster polylogarithm functions. We find that all such functions of weight four are made up of a single simple building block associated with the A 2 cluster algebra. Adding the requirement of locality on generalized Stasheff polytopes, we find that these A 2 building blocks arrange themselves to form a unique function associated with the A 3 cluster algebra. This A 3 function manifests all of the cluster algebraic structure of the two-loop n-particle MHV amplitudes for all n, and we use it to provide an explicit representation for the most complicated part of the n = 7 amplitude as an example. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Cluster algebras in mathematical physics’. (paper)

  4. Measuring the stellar luminosity function and spatial density profile of the inner 0.5 pc of the Milky Way nuclear star cluster

    Science.gov (United States)

    Do, Tuan; Ghez, Andrea; Lu, Jessica R.; Morris, Mark R.; Yelda, Sylvana; Martinez, Gregory D.; Peter, Annika H. G.; Wright, Shelley; Bullock, James; Kaplinghat, Manoj; Matthews, K.

    2012-07-01

    We report on measurements of the luminosity function of early (young) and late-type (old) stars in the central 0.5 pc of the Milky Way nuclear star cluster as well as the density profiles of both components. The young (~ 6 Myr) and old stars (> 1 Gyr) in this region provide different physical probes of the environment around a supermassive black hole; the luminosity function of the young stars offers us a way to measure the initial mass function from star formation in an extreme environment, while the density profile of the old stars offers us a probe of the dynamical interaction of a star cluster with a massive black hole. The two stellar populations are separated through a near-infrared spectroscopic survey using the integral-field spectrograph OSIRIS on Keck II behind the laser guide star adaptive optics system. This spectroscopic survey is able to separate early-type (young) and late-type (old) stars with a completeness of 50% at K' = 15.5. We describe our method of completeness correction using a combination of star planting simulations and Bayesian inference. The completeness corrected luminosity function of the early-type stars contains significantly more young stars at faint magnitudes compared to previous surveys with similar depth. In addition, by using proper motion and radial velocity measurements along with anisotropic spherical Jeans modeling of the cluster, it is possible to measure the spatial density profile of the old stars, which has been difficult to constrain with number counts alone. The most probable model shows that the spatial density profile, n(r) propto r-γ, to be shallow with γ = 0.4 ± 0.2, which is much flatter than the dynamically relaxed case of γ = 3/2 to 7/4, but does rule out a 'hole' in the distribution of old stars. We show, for the first time, that the spatial density profile, the black hole mass, and velocity anisotropy can be fit simultaneously to obtain a black hole mass that is consistent with that derived from

  5. Structure and bonding in clusters

    International Nuclear Information System (INIS)

    Kumar, V.

    1991-10-01

    We review here the recent progress made in the understanding of the electronic and atomic structure of small clusters of s-p bonded materials using the density functional molecular dynamics technique within the local density approximation. Starting with a brief description of the method, results are presented for alkali metal clusters, clusters of divalent metals such as Mg and Be which show a transition from van der Waals or weak chemical bonding to metallic behaviour as the cluster size grows and clusters of Al, Sn and Sb. In the case of semiconductors, we discuss results for Si, Ge and GaAs clusters. Clusters of other materials such as P, C, S, and Se are also briefly discussed. From these and other available results we suggest the possibility of unique structures for the magic clusters. (author). 69 refs, 7 figs, 1 tab

  6. Density functional theory study on the structures, electronic and magnetic properties of the MFe3n‑1O4n (n = 1–3) (M=Mn, Co and Ni) clusters

    Science.gov (United States)

    Li, Zhi; Zhao, Zhen; Wang, Qi; Yin, Xi-tao

    2018-04-01

    The structures, electronic and magnetic properties of the MFe3n‑1O4n (n = 1–3) (M=Mn, Co and Ni) clusters are obtained by using the GGA-PBE functional. The results found that the CoFe3n‑1O4n (n = 1–3) clusters are more stable than the corresponding NiFe3n‑1O4n and MnFe3n‑1O4n clusters. The NiFe2O4, MnFe5O8 and CoFe5O8 clusters have higher kinetic stability than their neighbors. The average magnetic moments of MFe3n‑1O4n (n = 1–3) (M=Mn, Co and Ni) clusters are successively: NiFe3n‑1O4n > CoFe3n‑1O4n > MnFe3n‑1O4n. For NiFe3n‑1O4n and CoFe3n‑1O4n clusters, the average magnetic moments are decreased with the cluster size increasing while for MnFe3n‑1O4n, the opposite situation is occur. The difference of 3d orbital electrons of M (M=Mn, Co and Ni) atoms influence the magnetic properties of MFe3n‑1O4n clusters.

  7. Density functional investigation of mercury and arsenic adsorption on nitrogen doped graphene decorated with palladium clusters: A promising heavy metal sensing material in farmland

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Chunjiang, E-mail: zhaocj_nercita@163.com [National Engineering Research Center for Information Technology in Agriculture, Beijing 100097 (China); Beijing Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097 (China); Key Laboratory for Information Technologies in Agriculture, Ministry of Agriculture, Beijing100097 (China); Wu, Huarui, E-mail: wuhrnercita@163.com [National Engineering Research Center for Information Technology in Agriculture, Beijing 100097 (China); Beijing Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097 (China); Key Laboratory for Information Technologies in Agriculture, Ministry of Agriculture, Beijing100097 (China)

    2017-03-31

    Highlights: • PNG can be acted as micro-sensor for monitoring heavy metal in agriculture. • The most favorable adsorption site of Pd atom or cluster on PNG is the vacancy site. • The Pd atom or cluster enhance the reactivity of PNG toward Hg and AsH{sub 3} adsorption. • The efficiency of a sorbent can be tuned by tailoring the ε{sub d} of adsorbed metals. - Abstract: Density functional theory calculations are carried out to study the adsorption of mercury and arsenic on Pd{sub n} (n = 1–6) supported on pyridine-like nitrogen doped graphene (PNG). Owing to the promising sensitivity in trace amounts of atoms or molecules, PNG can be acted as micro-sensor for sensing heavy metals in agriculture soils. Through the analyses of structural and electronic properties of pristine PNG and Pd atom decorated PNG, we find that the most favorable adsorption site for Pd atom is the vacancy site. The analyses of structural and electronic properties reveal that the Pd atom or clusters can enhance the reactivity for Hg and AsH{sub 3} adsorption on PNG. The adsorption ability of Hg on Pd{sub n} decorated PNG is found to be related to the d-band center (ε{sub d}) of the Pd{sub n}, in which the closer ε{sub d} of Pd{sub n} to the Fermi level, the higher adsorption strength for Hg on Pd{sub n} decorated PNG. Moreover, the charge transfer between Pd{sub n} and arsenic may constitute arsenic adsorption on Pd{sub n} decorated PNG. Further design of highly efficient carbon based sorbents for heavy metals removal should be focused on tailoring ε{sub d} of adsorbed metals.

  8. Density functional investigation of mercury and arsenic adsorption on nitrogen doped graphene decorated with palladium clusters: A promising heavy metal sensing material in farmland

    International Nuclear Information System (INIS)

    Zhao, Chunjiang; Wu, Huarui

    2017-01-01

    Highlights: • PNG can be acted as micro-sensor for monitoring heavy metal in agriculture. • The most favorable adsorption site of Pd atom or cluster on PNG is the vacancy site. • The Pd atom or cluster enhance the reactivity of PNG toward Hg and AsH_3 adsorption. • The efficiency of a sorbent can be tuned by tailoring the ε_d of adsorbed metals. - Abstract: Density functional theory calculations are carried out to study the adsorption of mercury and arsenic on Pd_n (n = 1–6) supported on pyridine-like nitrogen doped graphene (PNG). Owing to the promising sensitivity in trace amounts of atoms or molecules, PNG can be acted as micro-sensor for sensing heavy metals in agriculture soils. Through the analyses of structural and electronic properties of pristine PNG and Pd atom decorated PNG, we find that the most favorable adsorption site for Pd atom is the vacancy site. The analyses of structural and electronic properties reveal that the Pd atom or clusters can enhance the reactivity for Hg and AsH_3 adsorption on PNG. The adsorption ability of Hg on Pd_n decorated PNG is found to be related to the d-band center (ε_d) of the Pd_n, in which the closer ε_d of Pd_n to the Fermi level, the higher adsorption strength for Hg on Pd_n decorated PNG. Moreover, the charge transfer between Pd_n and arsenic may constitute arsenic adsorption on Pd_n decorated PNG. Further design of highly efficient carbon based sorbents for heavy metals removal should be focused on tailoring ε_d of adsorbed metals.

  9. The clustering of galaxies in the completed SDSS-III Baryon Oscillation Spectroscopic Survey: theoretical systematics and Baryon Acoustic Oscillations in the galaxy correlation function

    Science.gov (United States)

    Vargas-Magaña, Mariana; Ho, Shirley; Cuesta, Antonio J.; O'Connell, Ross; Ross, Ashley J.; Eisenstein, Daniel J.; Percival, Will J.; Grieb, Jan Niklas; Sánchez, Ariel G.; Tinker, Jeremy L.; Tojeiro, Rita; Beutler, Florian; Chuang, Chia-Hsun; Kitaura, Francisco-Shu; Prada, Francisco; Rodríguez-Torres, Sergio A.; Rossi, Graziano; Seo, Hee-Jong; Brownstein, Joel R.; Olmstead, Matthew; Thomas, Daniel

    2018-06-01

    We investigate the potential sources of theoretical systematics in the anisotropic Baryon Acoustic Oscillation (BAO) distance scale measurements from the clustering of galaxies in configuration space using the final Data Release (DR12) of the Baryon Oscillation Spectroscopic Survey (BOSS). We perform a detailed study of the impact on BAO measurements from choices in the methodology such as fiducial cosmology, clustering estimators, random catalogues, fitting templates, and covariance matrices. The theoretical systematic uncertainties in BAO parameters are found to be 0.002 in the isotropic dilation α and 0.003 in the quadrupolar dilation ɛ. The leading source of systematic uncertainty is related to the reconstruction techniques. Theoretical uncertainties are sub-dominant compared with the statistical uncertainties for BOSS survey, accounting 0.2σstat for α and 0.25σstat for ɛ (σα, stat ˜ 0.010 and σɛ, stat ˜ 0.012, respectively). We also present BAO-only distance scale constraints from the anisotropic analysis of the correlation function. Our constraints on the angular diameter distance DA(z) and the Hubble parameter H(z), including both statistical and theoretical systematic uncertainties, are 1.5 per cent and 2.8 per cent at zeff = 0.38, 1.4 per cent and 2.4 per cent at zeff = 0.51, and 1.7 per cent and 2.6 per cent at zeff = 0.61. This paper is part of a set that analyses the final galaxy clustering data set from BOSS. The measurements and likelihoods presented here are cross-checked with other BAO analysis in Alam et al. The systematic error budget concerning the methodology on post-reconstruction BAO analysis presented here is used in Alam et al. to produce the final cosmological constraints from BOSS.

  10. Implementing structured functional assessments in general practice for persons with long-term sick leave: a cluster randomised controlled trial

    Directory of Open Access Journals (Sweden)

    Benth Jūratė

    2009-05-01

    Full Text Available Abstract Background The increasing attention on functional assessments in medical and vocational rehabilitation requires a focus change for the general practitioners (GP into paying attention to patient resources, possibilities and coping instead of symptoms, problems and limitations. The GPs report difficulties in performing the requested explicit functional assessments. The purpose of this study was to implement a structured method in general practice for assessing functional ability in persons with long-term sick leave. The study aim was to evaluate intervention effects on important GP parameters; knowledge, attitudes, self-efficacy towards functional assessments and knowledge about patient work factors. Methods Fifty-seven GPs were randomly assigned to an intervention or a control group. The intervention group GPs attended an introductory one-day work-shop and implemented structured functional assessments during an eight months intervention period. GP knowledge, GP attitudes, and GP self-efficacy towards functional assessments, as well as GP knowledge of patient work factors, were collected before, after and six months after the intervention period started. Evaluation score-sheets were filled in by both the intervention GPs and their patients immediately after the consultation to evaluate the GPs' knowledge of patient work factors. Results The intervention GPs reported increased knowledge (B: 0.56, 95% CI (0.19, 0.91 and self-efficacy (B: 0.90, 95% CI (0.53, 1.26 towards functional assessments, and increased knowledge about their patients' workplace (B: 0.75, 95% CI (0.35, 1.15 and perceived stressors (B: 0.55, 95% CI (0.23, 0.88 with lasting effects at the second follow-up. No intervention effect was seen in relation to GP attitudes. Both before and after the intervention, the GPs were most informed about physical stressors, and less about mental and work organisational stressors (Guttman's reproducibility coefficient: 0.95 and 1.00. After

  11. Implementing structured functional assessments in general practice for persons with long-term sick leave: a cluster randomised controlled trial.

    Science.gov (United States)

    Østerås, Nina; Gulbrandsen, Pål; Benth, Jūrate Saltyte; Hofoss, Dag; Brage, Søren

    2009-05-06

    The increasing attention on functional assessments in medical and vocational rehabilitation requires a focus change for the general practitioners (GP) into paying attention to patient resources, possibilities and coping instead of symptoms, problems and limitations. The GPs report difficulties in performing the requested explicit functional assessments. The purpose of this study was to implement a structured method in general practice for assessing functional ability in persons with long-term sick leave. The study aim was to evaluate intervention effects on important GP parameters; knowledge, attitudes, self-efficacy towards functional assessments and knowledge about patient work factors. Fifty-seven GPs were randomly assigned to an intervention or a control group. The intervention group GPs attended an introductory one-day work-shop and implemented structured functional assessments during an eight months intervention period. GP knowledge, GP attitudes, and GP self-efficacy towards functional assessments, as well as GP knowledge of patient work factors, were collected before, after and six months after the intervention period started. Evaluation score-sheets were filled in by both the intervention GPs and their patients immediately after the consultation to evaluate the GPs' knowledge of patient work factors. The intervention GPs reported increased knowledge (B: 0.56, 95% CI (0.19, 0.91)) and self-efficacy (B: 0.90, 95% CI (0.53, 1.26)) towards functional assessments, and increased knowledge about their patients' workplace (B: 0.75, 95% CI (0.35, 1.15)) and perceived stressors (B: 0.55, 95% CI (0.23, 0.88)) with lasting effects at the second follow-up. No intervention effect was seen in relation to GP attitudes. Both before and after the intervention, the GPs were most informed about physical stressors, and less about mental and work organisational stressors (Guttman's reproducibility coefficient: 0.95 and 1.00). After the consultation, both the intervention GPs

  12. Cluster headache

    Directory of Open Access Journals (Sweden)

    Ducros Anne

    2008-07-01

    Full Text Available Abstract Cluster headache (CH is a primary headache disease characterized by recurrent short-lasting attacks (15 to 180 minutes of excruciating unilateral periorbital pain accompanied by ipsilateral autonomic signs (lacrimation, nasal congestion, ptosis, miosis, lid edema, redness of the eye. It affects young adults, predominantly males. Prevalence is estimated at 0.5–1.0/1,000. CH has a circannual and circadian periodicity, attacks being clustered (hence the name in bouts that can occur during specific months of the year. Alcohol is the only dietary trigger of CH, strong odors (mainly solvents and cigarette smoke and napping may also trigger CH attacks. During bouts, attacks may happen at precise hours, especially during the night. During the attacks, patients tend to be restless. CH may be episodic or chronic, depending on the presence of remission periods. CH is associated with trigeminovascular activation and neuroendocrine and vegetative disturbances, however, the precise cautive mechanisms remain unknown. Involvement of the hypothalamus (a structure regulating endocrine function and sleep-wake rhythms has been confirmed, explaining, at least in part, the cyclic aspects of CH. The disease is familial in about 10% of cases. Genetic factors play a role in CH susceptibility, and a causative role has been suggested for the hypocretin receptor gene. Diagnosis is clinical. Differential diagnoses include other primary headache diseases such as migraine, paroxysmal hemicrania and SUNCT syndrome. At present, there is no curative treatment. There are efficient treatments to shorten the painful attacks (acute treatments and to reduce the number of daily attacks (prophylactic treatments. Acute treatment is based on subcutaneous administration of sumatriptan and high-flow oxygen. Verapamil, lithium, methysergide, prednisone, greater occipital nerve blocks and topiramate may be used for prophylaxis. In refractory cases, deep-brain stimulation of the

  13. Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)

    DEFF Research Database (Denmark)

    Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K

    2011-01-01

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA....... The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5......a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2...

  14. Investigation on the neutral and anionic BxAlyH2 (x + y = 7, 8, 9) clusters using density functional theory combined with photoelectron spectroscopy.

    Science.gov (United States)

    Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Ding, Lei; Yuan, Tao Li

    2016-08-17

    The structure and bonding nature of neutral and negatively charged BxAlyH2 (x + y = 7, 8, 9) clusters are investigated with the aid of previously published experimental photoelectron spectra combined with the present density functional theory calculations. The comparison between the experimental photoelectron spectra and theoretical simulated spectra helps to identify the ground state structures. The accuracy of the obtained ground state structures is further verified by calculating their adiabatic electron affinities and vertical detachment energies and comparing them against available experimental data. The results show that the structures of BxAlyH2 transform from three-dimensional to planar structures as the number of boron atoms increases. Moreover, boron atoms tend to bind together forming Bn units. The hydrogen atoms prefer to bind with boron atoms rather than aluminum atoms. The analyses of the molecular orbital on the ground state structures further support the abovementioned results.

  15. An efficient formulation and implementation of the analytic energy gradient method to the single and double excitation coupled-cluster wave function - Application to Cl2O2

    Science.gov (United States)

    Rendell, Alistair P.; Lee, Timothy J.

    1991-01-01

    The analytic energy gradient for the single and double excitation coupled-cluster (CCSD) wave function has been reformulated and implemented in a new set of programs. The reformulated set of gradient equations have a smaller computational cost than any previously published. The iterative solution of the linear equations and the construction of the effective density matrices are fully vectorized, being based on matrix multiplications. The new method has been used to investigate the Cl2O2 molecule, which has recently been postulated as an important intermediate in the destruction of ozone in the stratosphere. In addition to reporting computational timings, the CCSD equilibrium geometries, harmonic vibrational frequencies, infrared intensities, and relative energetics of three isomers of Cl2O2 are presented.

  16. Comprehensive geriatric assessment, multifactorial interventions and nurse-led care coordination to prevent functional decline in community-dwelling older persons: protocol of a cluster randomized trial

    Directory of Open Access Journals (Sweden)

    Suijker Jacqueline J

    2012-04-01

    Full Text Available Abstract Background Functional decline in community-dwelling older persons is associated with the loss of independence, the need for hospital and nursing-home care and premature death. The effectiveness of multifactorial interventions in preventing functional decline remains controversial. The aim of this study is to investigate whether functional decline in community-dwelling older persons can be delayed or prevented by a comprehensive geriatric assessment, multifactorial interventions and nurse-led care coordination. Methods/Design In a cluster randomized controlled trial, with the general practice as the unit of randomization, 1281 participants from 25 general practices will be enrolled in each condition to compare the intervention with usual care. The intervention will focus on older persons who are at increased risk for functional decline, identified by an Identification of Seniors at Risk Primary Care (ISAR-PC score (≥ 2. These older persons will receive a comprehensive geriatric assessment, an individually tailored care and treatment plan, consisting of multifactorial, evidence-based interventions and subsequent nurse-led care coordination. The control group will receive 'care as usual' by the general practitioner (GP. The main outcome after 12 months is the level of physical functioning on the modified Katz-15 index score. The secondary outcomes are health-related quality of life, psychological and social functioning, healthcare utilization and institutionalization. Furthermore, a process evaluation and cost-effectiveness analysis will be performed. Discussion This study will provide new knowledge regarding the effectiveness and feasibility of a comprehensive geriatric assessment, multifactorial interventions and nurse-led elderly care in general practice. Trial registration NTR2653 Grant Unrestricted grant 'The Netherlands Organisation for Health Research and development' no 313020201

  17. Ultra-faint ultraviolet galaxies at z ∼ 2 behind the lensing cluster A1689: The luminosity function, dust extinction, and star formation rate density

    Energy Technology Data Exchange (ETDEWEB)

    Alavi, Anahita; Siana, Brian; Freeman, William R.; Dominguez, Alberto [Department of Physics and Astronomy, University of California, Riverside, CA 92521 (United States); Richard, Johan [Centre de Recherche Astrophysique de Lyon, Université Lyon 1, 9 Avenue Charles André, F-69561 Saint Genis Laval Cedex (France); Stark, Daniel P.; Robertson, Brant [Department of Astronomy, Steward Observatory, University of Arizona, 933 North Cherry Avenue, Rm N204, Tucson, AZ 85721 (United States); Scarlata, Claudia [Minnesota Institute for Astrophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Teplitz, Harry I.; Rafelski, Marc [Infrared Processing and Analysis Center, Caltech, Pasadena, CA 91125 (United States); Kewley, Lisa, E-mail: anahita.alavi@email.ucr.edu [Research School of Astronomy and Astrophysics, The Australian National University, Cotter Road, Weston Creek, ACT 2611 (Australia)

    2014-01-10

    We have obtained deep ultraviolet imaging of the lensing cluster A1689 with the WFC3/UVIS camera onboard the Hubble Space Telescope in the F275W (30 orbits) and F336W (4 orbits) filters. These images are used to identify z ∼ 2 star-forming galaxies via their Lyman break, in the same manner that galaxies are typically selected at z ≥ 3. Because of the unprecedented depth of the images and the large magnification provided by the lensing cluster, we detect galaxies 100× fainter than previous surveys at this redshift. After removing all multiple images, we have 58 galaxies in our sample in the range –19.5 < M {sub 1500} < –13 AB mag. Because the mass distribution of A1689 is well constrained, we are able to calculate the intrinsic sensitivity of the observations as a function of source plane position, allowing for accurate determinations of effective volume as a function of luminosity. We fit the faint-end slope of the luminosity function to be α = –1.74 ± 0.08, which is consistent with the values obtained for 2.5 < z < 6. Notably, there is no turnover in the luminosity function down to M {sub 1500} = –13 AB mag. We fit the UV spectral slopes with photometry from existing Hubble optical imaging. The observed trend of increasingly redder slopes with luminosity at higher redshifts is observed in our sample, but with redder slopes at all luminosities and average reddening of (E(B – V)) = 0.15 mag. We assume the stars in these galaxies are metal poor (0.2 Z {sub ☉}) compared to their brighter counterparts (Z {sub ☉}), resulting in bluer assumed intrinsic UV slopes and larger derived values for dust extinction. The total UV luminosity density at z ∼ 2 is 4.31{sub −0.60}{sup +0.68}×10{sup 26} erg s{sup –1} Hz{sup –1} Mpc{sup –3}, more than 70% of which is emitted by galaxies in the luminosity range of our sample. Finally, we determine the global star formation rate density from UV-selected galaxies at z ∼ 2 (assuming a constant dust

  18. Scattering of a proton with the Li{sub 4} cluster: Non-adiabatic molecular dynamics description based on time-dependent density-functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Castro, A., E-mail: acastro@bifi.es [Institute for Biocomputation and Physics of Complex Systems (BIFI) and Zaragoza Scientific Center for Advanced Modelling (ZCAM), University of Zaragoza, 50018 Zaragoza (Spain); Isla, M. [Departamento de Fisica Teorica, Atomica y Optica, Universidad de Valladolid, 47005 Valladolid (Spain); Martinez, Jose I. [Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, ES-28049 Madrid (Spain); Alonso, J.A. [Departamento de Fisica Teorica, Atomica y Optica, Universidad de Valladolid, 47005 Valladolid (Spain)

    2012-05-03

    Graphical abstract: Two trajectories for the collision of a proton with the Lithium tetramer. On the left, the proton is scattered away, and a Li{sub 2} molecule plus two isolated Lithium atoms result. On the right, the proton is captured and a LiH molecule is created. Highlights: Black-Right-Pointing-Pointer Scattering of a proton with Lithium clusters described from first principles. Black-Right-Pointing-Pointer Description based on non-adiabatic molecular dynamics. Black-Right-Pointing-Pointer The electronic structure is described with time-dependent density-functional theory. Black-Right-Pointing-Pointer The method allows to discern reaction channels depending on initial parameters. - Abstract: We have employed non-adiabatic molecular dynamics based on time-dependent density-functional theory to characterize the scattering behavior of a proton with the Li{sub 4} cluster. This technique assumes a classical approximation for the nuclei, effectively coupled to the quantum electronic system. This time-dependent theoretical framework accounts, by construction, for possible charge transfer and ionization processes, as well as electronic excitations, which may play a role in the non-adiabatic regime. We have varied the incidence angles in order to analyze the possible reaction patterns. The initial proton kinetic energy of 10 eV is sufficiently high to induce non-adiabatic effects. For all the incidence angles considered the proton is scattered away, except in one interesting case in which one of the Lithium atoms captures it, forming a LiH molecule. This theoretical formalism proves to be a powerful, effective and predictive tool for the analysis of non-adiabatic processes at the nanoscale.

  19. Clustering Dycom

    KAUST Repository

    Minku, Leandro L.

    2017-10-06

    Background: Software Effort Estimation (SEE) can be formulated as an online learning problem, where new projects are completed over time and may become available for training. In this scenario, a Cross-Company (CC) SEE approach called Dycom can drastically reduce the number of Within-Company (WC) projects needed for training, saving the high cost of collecting such training projects. However, Dycom relies on splitting CC projects into different subsets in order to create its CC models. Such splitting can have a significant impact on Dycom\\'s predictive performance. Aims: This paper investigates whether clustering methods can be used to help finding good CC splits for Dycom. Method: Dycom is extended to use clustering methods for creating the CC subsets. Three different clustering methods are investigated, namely Hierarchical Clustering, K-Means, and Expectation-Maximisation. Clustering Dycom is compared against the original Dycom with CC subsets of different sizes, based on four SEE databases. A baseline WC model is also included in the analysis. Results: Clustering Dycom with K-Means can potentially help to split the CC projects, managing to achieve similar or better predictive performance than Dycom. However, K-Means still requires the number of CC subsets to be pre-defined, and a poor choice can negatively affect predictive performance. EM enables Dycom to automatically set the number of CC subsets while still maintaining or improving predictive performance with respect to the baseline WC model. Clustering Dycom with Hierarchical Clustering did not offer significant advantage in terms of predictive performance. Conclusion: Clustering methods can be an effective way to automatically generate Dycom\\'s CC subsets.

  20. Clustering analysis

    International Nuclear Information System (INIS)

    Romli

    1997-01-01

    Cluster analysis is the name of group of multivariate techniques whose principal purpose is to distinguish similar entities from the characteristics they process.To study this analysis, there are several algorithms that can be used. Therefore, this topic focuses to discuss the algorithms, such as, similarity measures, and hierarchical clustering which includes single linkage, complete linkage and average linkage method. also, non-hierarchical clustering method, which is popular name K -mean method ' will be discussed. Finally, this paper will be described the advantages and disadvantages of every methods

  1. Cluster analysis

    CERN Document Server

    Everitt, Brian S; Leese, Morven; Stahl, Daniel

    2011-01-01

    Cluster analysis comprises a range of methods for classifying multivariate data into subgroups. By organizing multivariate data into such subgroups, clustering can help reveal the characteristics of any structure or patterns present. These techniques have proven useful in a wide range of areas such as medicine, psychology, market research and bioinformatics.This fifth edition of the highly successful Cluster Analysis includes coverage of the latest developments in the field and a new chapter dealing with finite mixture models for structured data.Real life examples are used throughout to demons

  2. Cluster editing

    DEFF Research Database (Denmark)

    Böcker, S.; Baumbach, Jan

    2013-01-01

    . The problem has been the inspiration for numerous algorithms in bioinformatics, aiming at clustering entities such as genes, proteins, phenotypes, or patients. In this paper, we review exact and heuristic methods that have been proposed for the Cluster Editing problem, and also applications......The Cluster Editing problem asks to transform a graph into a disjoint union of cliques using a minimum number of edge modifications. Although the problem has been proven NP-complete several times, it has nevertheless attracted much research both from the theoretical and the applied side...

  3. [Gene deletion and functional analysis of the heptyl glycosyltransferase (waaF) gene in Vibrio parahemolyticus O-antigen cluster].

    Science.gov (United States)

    Zhao, Feng; Meng, Songsong; Zhou, Deqing

    2016-02-04

    To construct heptyl glycosyltransferase gene II (waaF) gene deletion mutant of Vibrio parahaemolyticus, and explore the function of the waaF gene in Vibrio parahaemolyticus. The waaF gene deletion mutant was constructed by chitin-based transformation technology using clinical isolates, and then the growth rate, morphology and serotypes were identified. The different sources (O3, O5 and O10) waaF gene complementations were constructed through E. coli S17λpir strains conjugative transferring with Vibrio parahaemolyticus, and the function of the waaF gene was further verified by serotypes. The waaF gene deletion mutant strain was successfully constructed and it grew normally. The growth rate and morphology of mutant were similar with the wild type strains (WT), but the mutant could not occurred agglutination reaction with O antisera. The O3 and O5 sources waaF gene complementations occurred agglutination reaction with O antisera, but the O10 sources waaF gene complementations was not. The waaF gene was related with O-antigen synthesis and it was the key gene of O-antigen synthesis pathway in Vibrio parahaemolyticus. The function of different sources waaF gene were not the same.

  4. Dark Energy Survey Year 1 Results: Methodology and Projections for Joint Analysis of Galaxy Clustering, Galaxy Lensing, and CMB Lensing Two-point Functions

    Energy Technology Data Exchange (ETDEWEB)

    Giannantonio, T.; et al.

    2018-02-14

    Optical imaging surveys measure both the galaxy density and the gravitational lensing-induced shear fields across the sky. Recently, the Dark Energy Survey (DES) collaboration used a joint fit to two-point correlations between these observables to place tight constraints on cosmology (DES Collaboration et al. 2017). In this work, we develop the methodology to extend the DES Collaboration et al. (2017) analysis to include cross-correlations of the optical survey observables with gravitational lensing of the cosmic microwave background (CMB) as measured by the South Pole Telescope (SPT) and Planck. Using simulated analyses, we show how the resulting set of five two-point functions increases the robustness of the cosmological constraints to systematic errors in galaxy lensing shear calibration. Additionally, we show that contamination of the SPT+Planck CMB lensing map by the thermal Sunyaev-Zel'dovich effect is a potentially large source of systematic error for two-point function analyses, but show that it can be reduced to acceptable levels in our analysis by masking clusters of galaxies and imposing angular scale cuts on the two-point functions. The methodology developed here will be applied to the analysis of data from the DES, the SPT, and Planck in a companion work.

  5. Coupled cluster and density functional theory calculations of atomic hydrogen chemisorption on pyrene and coronene as model systems for graphene hydrogenation.

    Science.gov (United States)

    Wang, Ying; Qian, Hu-Jun; Morokuma, Keiji; Irle, Stephan

    2012-07-05

    Ab initio coupled cluster and density functional theory studies of atomic hydrogen addition to the central region of pyrene and coronene as molecular models for graphene hydrogenation were performed. Fully relaxed potential energy curves (PECs) were computed at the spin-unrestricted B3LYP/cc-pVDZ level of theory for the atomic hydrogen attack of a center carbon atom (site A), the midpoint of a neighboring carbon bond (site B), and the center of a central hexagon (site C). Using the B3LYP/cc-pVDZ PEC geometries, we evaluated energies at the PBE density functional, as well as ab initio restricted open-shell ROMP2, ROCCSD, and ROCCSD(T) levels of theory, employing cc-pVDZ and cc-pVTZ basis sets, and performed a G2MS extrapolation to the ROCCSD(T)/cc-pVTZ level of theory. In agreement with earlier studies, we find that only site A attack leads to chemisorption. The G2MS entrance channel barrier heights, binding energies, and PEC profiles are found to agree well with a recent ab initio multireference wave function theory study (Bonfanti et al. J. Chem. Phys.2011, 135, 164701), indicating that single-reference open-shell methods including B3LYP are sufficient for the theoretical treatment of the interaction of graphene with a single hydrogen atom.

  6. Mitochondrial DNA as a non-invasive biomarker: Accurate quantification using real time quantitative PCR without co-amplification of pseudogenes and dilution bias

    International Nuclear Information System (INIS)

    Malik, Afshan N.; Shahni, Rojeen; Rodriguez-de-Ledesma, Ana; Laftah, Abas; Cunningham, Phil

    2011-01-01

    Highlights: → Mitochondrial dysfunction is central to many diseases of oxidative stress. → 95% of the mitochondrial genome is duplicated in the nuclear genome. → Dilution of untreated genomic DNA leads to dilution bias. → Unique primers and template pretreatment are needed to accurately measure mitochondrial DNA content. -- Abstract: Circulating mitochondrial DNA (MtDNA) is a potential non-invasive biomarker of cellular mitochondrial dysfunction, the latter known to be central to a wide range of human diseases. Changes in MtDNA are usually determined by quantification of MtDNA relative to nuclear DNA (Mt/N) using real time quantitative PCR. We propose that the methodology for measuring Mt/N needs to be improved and we have identified that current methods have at least one of the following three problems: (1) As much of the mitochondrial genome is duplicated in the nuclear genome, many commonly used MtDNA primers co-amplify homologous pseudogenes found in the nuclear genome; (2) use of regions from genes such as β-actin and 18S rRNA which are repetitive and/or highly variable for qPCR of the nuclear genome leads to errors; and (3) the size difference of mitochondrial and nuclear genomes cause a 'dilution bias' when template DNA is diluted. We describe a PCR-based method using unique regions in the human mitochondrial genome not duplicated in the nuclear genome; unique single copy region in the nuclear genome and template treatment to remove dilution bias, to accurately quantify MtDNA from human samples.

  7. Noise reduction and functional maps image quality improvement in dynamic CT perfusion using a new k-means clustering guided bilateral filter (KMGB).

    Science.gov (United States)

    Pisana, Francesco; Henzler, Thomas; Schönberg, Stefan; Klotz, Ernst; Schmidt, Bernhard; Kachelrieß, Marc

    2017-07-01

    Dynamic CT perfusion (CTP) consists in repeated acquisitions of the same volume in different time steps, slightly before, during and slightly afterwards the injection of contrast media. Important functional information can be derived for each voxel, which reflect the local hemodynamic properties and hence the metabolism of the tissue. Different approaches are being investigated to exploit data redundancy and prior knowledge for noise reduction of such datasets, ranging from iterative reconstruction schemes to high dimensional filters. We propose a new spatial bilateral filter which makes use of the k-means clustering algorithm and of an optimal calculated guiding image. We named the proposed filter as k-means clustering guided bilateral filter (KMGB). In this study, the KMGB filter is compared with the partial temporal non-local means filter (PATEN), with the time-intensity profile similarity (TIPS) filter, and with a new version derived from it, by introducing the guiding image (GB-TIPS). All the filters were tested on a digital in-house developed brain CTP phantom, were noise was added to simulate 80 kV and 200 mAs (default scanning parameters), 100 mAs and 30 mAs. Moreover, the filters performances were tested on 7 noisy clinical datasets with different pathologies in different body regions. The original contribution of our work is two-fold: first we propose an efficient algorithm to calculate a guiding image to improve the results of the TIPS filter, secondly we propose the introduction of the k-means clustering step and demonstrate how this can potentially replace the TIPS part of the filter obtaining better results at lower computational efforts. As expected, in the GB-TIPS, the introduction of the guiding image limits the over-smoothing of the TIPS filter, improving spatial resolution by more than 50%. Furthermore, replacing the time-intensity profile similarity calculation with a fuzzy k-means clustering strategy (KMGB) allows to control the edge preserving

  8. Occupational Clusters.

    Science.gov (United States)

    Pottawattamie County School System, Council Bluffs, IA.

    The 15 occupational clusters (transportation, fine arts and humanities, communications and media, personal service occupations, construction, hospitality and recreation, health occupations, marine science occupations, consumer and homemaking-related occupations, agribusiness and natural resources, environment, public service, business and office…

  9. Fuzzy Clustering

    DEFF Research Database (Denmark)

    Berks, G.; Keyserlingk, Diedrich Graf von; Jantzen, Jan

    2000-01-01

    A symptom is a condition indicating the presence of a disease, especially, when regarded as an aid in diagnosis.Symptoms are the smallest units indicating the existence of a disease. A syndrome on the other hand is an aggregate, set or cluster of concurrent symptoms which together indicate...... and clustering are the basic concerns in medicine. Classification depends on definitions of the classes and their required degree of participant of the elements in the cases' symptoms. In medicine imprecise conditions are the rule and therefore fuzzy methods are much more suitable than crisp ones. Fuzzy c......-mean clustering is an easy and well improved tool, which has been applied in many medical fields. We used c-mean fuzzy clustering after feature extraction from an aphasia database. Factor analysis was applied on a correlation matrix of 26 symptoms of language disorders and led to five factors. The factors...

  10. Cluster generator

    Science.gov (United States)

    Donchev, Todor I [Urbana, IL; Petrov, Ivan G [Champaign, IL

    2011-05-31

    Described herein is an apparatus and a method for producing atom clusters based on a gas discharge within a hollow cathode. The hollow cathode includes one or more walls. The one or more walls define a sputtering chamber within the hollow cathode and include a material to be sputtered. A hollow anode is positioned at an end of the sputtering chamber, and atom clusters are formed when a gas discharge is generated between the hollow anode and the hollow cathode.

  11. Cluster Bulleticity

    OpenAIRE

    Massey, Richard; Kitching, Thomas; Nagai, Daisuke

    2010-01-01

    The unique properties of dark matter are revealed during collisions between clusters of galaxies, such as the bullet cluster (1E 0657−56) and baby bullet (MACS J0025−12). These systems provide evidence for an additional, invisible mass in the separation between the distributions of their total mass, measured via gravitational lensing, and their ordinary ‘baryonic’ matter, measured via its X-ray emission. Unfortunately, the information available from these systems is limited by their rarity. C...

  12. Cluster headache

    OpenAIRE

    Leroux, Elizabeth; Ducros, Anne

    2008-01-01

    Abstract Cluster headache (CH) is a primary headache disease characterized by recurrent short-lasting attacks (15 to 180 minutes) of excruciating unilateral periorbital pain accompanied by ipsilateral autonomic signs (lacrimation, nasal congestion, ptosis, miosis, lid edema, redness of the eye). It affects young adults, predominantly males. Prevalence is estimated at 0.5–1.0/1,000. CH has a circannual and circadian periodicity, attacks being clustered (hence the name) in bouts that can occur ...

  13. Cluster analysis of indicators of liver functional and preoperative low branched-chain amino acid tyrosine ration indicate a high risk of early recurrence in analysis of 165 hepatocellular carcinoma patients after initial hepatectomy.

    Science.gov (United States)

    Nakamura, Yukio; Mizuguchi, Toru; Kawamoto, Masaki; Meguro, Makoto; Harada, Kohei; Ota, Shigenori; Hirata, Koichi

    2011-08-01

    Cluster analysis is used for dividing many prognostic indicators, including liver function, tumor progression, and operative variables, into specific clusters. The albumin (ALB), hepatocyte growth factor (HGF), and branched chain amino-acid to tyrosine ratio (BTR) may represent the severity of liver disease and function of the hepatic reserve. We developed the ALB-BTR and HGF-BTR classifications depending on each level to find specific unique subgroups. Our aim was to identify specific subgroups destined for favorable and poor prognoses after initial hepatectomy. Between 2002 and 2008, 165 patients were analyzed retrospectively. Liver function indicators, including BTR, tumor-related factors, and operative variables, were evaluated by cluster analysis with Ward's criterion. The ALB-BTR classification was divided into 4 groups depending on ALB (cutoff value, 4.0 g/dL) and BTR (cutoff value, 6.0). The HGF-BTR classification was also divided into 4 groups depending on HGF (cutoff value, 0.35 ng/mL) and BTR (cutoff value, 6.0). The prognoses of the subgroups were compared by the log-rank test. Cluster analysis divided multiple indicators into 5 different clusters. In each cluster, we further analyzed subgroups using the ALB-BTR and HGF-BTR classification. Mean recurrence-free survival times in ALB-GI (19.1 ± 2.4 months) and HGF-GIII (29.4 ± 3.8 months) were less than their mean overall survival times. Cluster analysis is useful to find similar and different indicators. Even though liver function was well preserved, low BTR could identify early recurrence in hepatocellular carcinoma patients after resection. Copyright © 2011 Mosby, Inc. All rights reserved.

  14. Density functional study of the stability and magnetic behaviour of Au{sub n}TM{sup +} clusters (TM=Au,Sc,Ti,V,Cr,Mn,Fe; 1{<=}n{<=}9)

    Energy Technology Data Exchange (ETDEWEB)

    Torres, M.B. [Dpto. de Matematicas y Computacion, Univ. de Burgos, Avda. de Cantabria s/n, 09006-Burgos (Spain); Fernandez, E.M.; Balbas, L.C. [Dpto. de Fisica Teorica, Univ. de Valladolid, Prado de la Magdalena s/n, 47011-Valladolid (Spain)

    2005-03-01

    We study the element- and size-dependent electron stability of Au{sub n}TM{sup +} clusters (TM=Sc,Ti,V,Cr,Mn,Fe,Au; 1{<=}n{<=}9) by means of first-principles density functional calculations. The interplay between the cluster atomic arrangements and their electronic and magnetic structure is investigated for the few lower energy isomeric-states in dependence of the TM-atom and its environment in the cluster. We explain the experimental magic-numbers, observed recently, as well as the trend of the impurity local magnetic moment in dependence with the size of the cluster and the position of the impurity in the host. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  15. Mutational analysis of the myxovirescin biosynthetic gene cluster reveals novel insights into the functional elaboration of polyketide backbones.

    Science.gov (United States)

    Simunovic, Vesna; Müller, Rolf

    2007-07-23

    It has been proposed that two acyl carrier proteins (ACPs)-TaB and TaE--and two 3-hydroxy-3-methylglutaryl synthases (HMGSs)--TaC and TaF--could constitute two functional ACP-HMGS pairs (TaB/TaC and TaE/TaF) responsible for the incorporation of acetate and propionate units into the myxovirescin A scaffold, leading to the formation of beta-methyl and beta-ethyl groups, respectively. It has been suggested that three more proteins--TaX and TaY, which are members of the superfamily of enoyl-CoA hydratases (ECHs), and a variant ketosynthase (KS) TaK--are shared between two ACP-HMGS pairs, to give the complete set of enzymes required to perform the beta-alkylations. The beta-methyl branch is presumably further hydroxylated (by TaH) and methylated to produce the methoxymethyl group observed in myxovirescin A. To substantiate this hypothesis, a series of gene-deletion mutants were created, and the effects of these mutations on myxovirescin production were examined. As predicted, DeltataB and DeltataE ACP mutants revealed similar phenotypes to their associated HMGS mutants DeltataC and DeltataF, respectively, thus providing direct evidence for the role of TaE/TaF in the formation of the beta-ethyl branch and implying a role for TaB/TaC in the formation of the beta-methyl group. Production of myxovirescin A was dramatically reduced in a DeltataK mutant and abolished in both the DeltataX and the DeltataY mutant backgrounds. Analysis of a DeltataH mutant confirmed the role of the cytochrome P450 TaH in hydroxylation of the beta-methyl group. Taken together, these experiments support a model in which the discrete ACPs TaB and TaE are compatible only with their associated HMGSs TaC and TaF, respectively, and function in a substrate-specific manner. Both TaB and TaC are essential for myxovirescin production, and the TaB/TaC pair can rescue antibiotic production in the absence of either TaE or TaF. Finally, the reduced level of myxovirescin production in the DeltataE mutant

  16. Associations of interleukin-1 gene cluster polymorphisms with C-reactive protein concentration and lung function decline in smoking-induced chronic obstructive pulmonary disease

    Science.gov (United States)

    Wang, Yu; Shumansky, Karey; Sin, Don D; Man, SF Paul; Akhabir, Loubna; Connett, John E; Anthonisen, Nicholas R; Paré, Peter D; Sandford, Andrew J; He, Jian-Qing

    2015-01-01

    Objective: We reported association of haplotypes formed by IL-1b (IL1B)-511C/T (rs16944) and a variable number of tandem repeats (rs2234663) in intron 3 of IL-1 receptor antagonist (IL1RN) with rate of lung function decline in smoking-induced COPD. The aim of current study was to further investigate this association. Methods: We genotyped an additional 19 polymorphisms in IL1 cluster (including IL1A, IL1B and IL1RN) in non-Hispanic whites who had the fastest (n = 268) and the slowest (n = 292) decline of FEV1% predicted in the same study. We also analyzed the association of all 21 polymorphisms with serum CRP levels. Results: None of 21 polymorphisms showed significant association with rate of decline of lung function or CRP levels after adjusting for multiple comparisons. Before adjusting for multiple comparisons, only IL1RN_19327 (rs315949) showed significant association with lung function decline (P = 0.03, additive model). The frequencies of genotypes containing the IL1RN_19327A allele were 71.9% and 62.2%, respectively in the fast and slow decline groups (P = 0.02, odds ratio = 1.6, 95% confidence interval = 1.1-2.3); the IL1B_5200 (rs1143633) and rs2234663 in IL1RN were associated with serum CRP levels (P=0.04 and 0.03, respectively). Conclusions: No single marker was significantly associated with either rate of lung function decline or serum CRP levels. PMID:26722511

  17. Combinations of coupled cluster, density functionals, and the random phase approximation for describing static and dynamic correlation, and van der Waals interactions

    Science.gov (United States)

    Garza, Alejandro J.; Bulik, Ireneusz W.; Alencar, Ana G. Sousa; Sun, Jianwei; Perdew, John P.; Scuseria, Gustavo E.

    2016-04-01

    Contrary to standard coupled cluster doubles (CCD) and Brueckner doubles (BD), singlet-paired analogues of CCD and BD (denoted here as CCD0 and BD0) do not break down when static correlation is present, but neglect substantial amounts of dynamic correlation. In fact, CCD0 and BD0 do not account for any contributions from multielectron excitations involving only same-spin electrons at all. We exploit this feature to add - without introducing double counting, self-interaction, or increase in cost - the missing correlation to these methods via meta-GGA (generalised gradient approximation) density functionals (Tao-Perdew-Staroverov-Scuseria and strongly constrained and appropriately normed). Furthermore, we improve upon these CCD0+DFT blends by invoking range separation: the short- and long-range correlations absent in CCD0/BD0 are evaluated with density functional theory and the direct random phase approximation, respectively. This corrects the description of long-range van der Waals forces. Comprehensive benchmarking shows that the combinations presented here are very accurate for weakly correlated systems, while also providing a reasonable description of strongly correlated problems without resorting to symmetry breaking.

  18. Expression and function of the miR-143/145 cluster in vitro and in vivo in human breast cancer.

    Directory of Open Access Journals (Sweden)

    Charles Johannessen

    Full Text Available MicroRNAs (miRNAs are small non-coding RNAs that function as post-transcriptional regulators of gene expression and are dysregulated in cancer. Studies of miRNAs to explore their potential as diagnostic and prognostic markers are of great scientific interest. Here, we investigate the functional properties and expression of the miR-143/145 cluster in breast cancer (BC in vitro and in vivo. The ER positive MCF7, the HER2 positive SK-BR-3, and the triple negative cell line MDA-MB-231 were used to assess cell proliferation and cell invasion. Expression of miRNA in 108 breast cancers in the Norwegian Women and Cancer Study and 44 benign tissue controls were analyzed by microarray and validated by RT-PCR. Further, in situ hybridization (ISH was used to study the cellular and subcellular distribution of the miRNAs. In vitro, miR-143 promoted proliferation of MCF7 and MDA-MB-231 cells, whereas miR-145 and the cotransfection of both miRNAs inhibited proliferation in all three cell lines. The cells' invasive capacity was reduced after transfection and cotransfection of the miRNAs. In line with the tumor suppressive functions in vitro, the expression of miR-143 and miR-145 was lower in malignant compared to benign breast tissue, and lower in the more aggressive tumors with higher tumor grade, loss of ER and the basal-like phenotype. ISH revealed miR-143 to be cytoplasmatic and predominantly expressed in luminal cells in benign tissue, whilst miR-145 was nuclear and with strong staining in myoepithelial cells. Both miRNAs were present in malignant epithelial cells and stromal fibroblasts in BC. This study demonstrates that miR-143 and -145 have functional properties and expression patterns typical for tumor suppressors, but the function is influenced by cellular factors such as cell type and miRNA cotransfection. Further, the nuclear functions of miR-145 should be explored for a more complete understanding of the complexity of miRNA regulation and function

  19. Cluster processing business level monitor

    International Nuclear Information System (INIS)

    Muniz, Francisco J.

    2017-01-01

    This article describes a Cluster Processing Monitor. Several applications with this functionality can be freely found doing a search in the Google machine. However, those applications may offer more features that are needed on the Processing Monitor being proposed. Therefore, making the monitor output evaluation difficult to be understood by the user, at-a-glance. In addition, such monitors may add unnecessary processing cost to the Cluster. For these reasons, a completely new Cluster Processing Monitor module was designed and implemented. In the CDTN, Clusters are broadly used, mainly, in deterministic methods (CFD) and non-deterministic methods (Monte Carlo). (author)

  20. Cluster processing business level monitor

    Energy Technology Data Exchange (ETDEWEB)

    Muniz, Francisco J., E-mail: muniz@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)

    2017-07-01

    This article describes a Cluster Processing Monitor. Several applications with this functionality can be freely found doing a search in the Google machine. However, those applications may offer more features that are needed on the Processing Monitor being proposed. Therefore, making the monitor output evaluation difficult to be understood by the user, at-a-glance. In addition, such monitors may add unnecessary processing cost to the Cluster. For these reasons, a completely new Cluster Processing Monitor module was designed and implemented. In the CDTN, Clusters are broadly used, mainly, in deterministic methods (CFD) and non-deterministic methods (Monte Carlo). (author)

  1. Diametrical clustering for identifying anti-correlated gene clusters.

    Science.gov (United States)

    Dhillon, Inderjit S; Marcotte, Edward M; Roshan, Usman

    2003-09-01

    Clustering genes based upon their expression patterns allows us to predict gene function. Most existing clustering algorithms cluster genes together when their expression patterns show high positive correlation. However, it has been observed that genes whose expression patterns are strongly anti-correlated can also be functionally similar. Biologically, this is not unintuitive-genes responding to the same stimuli, regardless of the nature of the response, are more likely to operate in the same pathways. We present a new diametrical clustering algorithm that explicitly identifies anti-correlated clusters of genes. Our algorithm proceeds by iteratively (i). re-partitioning the genes and (ii). computing the dominant singular vector of each gene cluster; each singular vector serving as the prototype of a 'diametric' cluster. We empirically show the effectiveness of the algorithm in identifying diametrical or anti-correlated clusters. Testing the algorithm on yeast cell cycle data, fibroblast gene expression data, and DNA microarray data from yeast mutants reveals that opposed cellular pathways can be discovered with this method. We present systems whose mRNA expression patterns, and likely their functions, oppose the yeast ribosome and proteosome, along with evidence for the inverse transcriptional regulation of a number of cellular systems.

  2. I Cluster geografici

    Directory of Open Access Journals (Sweden)

    Maurizio Rosina

    2010-03-01

    Full Text Available Geographic ClustersOver the past decade, public alphanumeric database have been growing at exceptional rate. Most of data can be georeferenced, so that is possible gaining new knowledge from such databases. The contribution of this paper is two-fold. We first present a model of geographic clusters, which uses only geographic and functionally data properties. The model is useful to process huge amount of public/government data, even daily upgrading. After that, we merge the model into the framework GEOPOI (GEOcoding Points Of Interest, and show some graphic map results.

  3. I Cluster geografici

    Directory of Open Access Journals (Sweden)

    Maurizio Rosina

    2010-03-01

    Full Text Available Geographic Clusters Over the past decade, public alphanumeric database have been growing at exceptional rate. Most of data can be georeferenced, so that is possible gaining new knowledge from such databases. The contribution of this paper is two-fold. We first present a model of geographic clusters, which uses only geographic and functionally data properties. The model is useful to process huge amount of public/government data, even daily upgrading. After that, we merge the model into the framework GEOPOI (GEOcoding Points Of Interest, and show some graphic map results.

  4. Comparative cost-effectiveness of two interventions to promote work functioning by targeting mental health complaints among nurses: pragmatic cluster randomised trial.

    Science.gov (United States)

    Noben, Cindy; Smit, Filip; Nieuwenhuijsen, Karen; Ketelaar, Sarah; Gärtner, Fania; Boon, Brigitte; Sluiter, Judith; Evers, Silvia

    2014-10-01

    The specific job demands of working in a hospital may place nurses at elevated risk for developing distress, anxiety and depression. Screening followed by referral to early interventions may reduce the incidence of these health problems and promote work functioning. To evaluate the comparative cost-effectiveness of two strategies to promote work functioning among nurses by reducing symptoms of mental health complaints. Three conditions were compared: the control condition consisted of online screening for mental health problems without feedback about the screening results. The occupational physician condition consisted of screening, feedback and referral to the occupational physician for screen-positive nurses. The third condition included screening, feedback, and referral to e-mental health. The study was designed as an economic evaluation alongside a pragmatic cluster randomised controlled trial with randomisation at hospital-ward level. The study included 617 nurses in one academic medical centre in the Netherlands. Treatment response was defined as an improvement on the Nurses Work Functioning Questionnaire of at least 40% between baseline and follow-up. Total per-participant costs encompassed intervention costs, direct medical and non-medical costs, and indirect costs stemming from lost productivity due to absenteeism and presenteeism. All costs were indexed for the year 2011. At 6 months follow-up, significant improvement in work functioning occurred in 20%, 24% and 16% of the participating nurses in the control condition, the occupational physician condition and the e-mental health condition, respectively. In these conditions the total average annualised costs were €1752, €1266 and €1375 per nurse. The median incremental cost-effectiveness ratio for the occupational physician condition versus the control condition was dominant, suggesting cost savings of €5049 per treatment responder. The incremental cost-effectiveness ratio for the e-mental health

  5. Effectiveness of Balancing Everyday Life (BEL) versus standard occupational therapy for activity engagement and functioning among people with mental illness - a cluster RCT study.

    Science.gov (United States)

    Eklund, Mona; Tjörnstrand, Carina; Sandlund, Mikael; Argentzell, Elisabeth

    2017-11-09

    Many with a mental illness have an impoverished everyday life with few meaningful activities and a sedentary lifestyle. The study aim was to evaluate the effectiveness of the 16-week Balancing Everyday Life (BEL) program, compared to care as usual (CAU), for people with mental illness in specialized and community-based psychiatric services. The main outcomes concerned different aspects of subjectively evaluated everyday activities, in terms of the engagement and satisfaction they bring, balance among activities, and activity level. Secondary outcomes pertained to various facets of well-being and functioning. It was hypothesized that those who received the BEL intervention would improve more than the comparison group regarding activity, well-being and functioning outcomes. BEL is a group and activity-based lifestyle intervention. CAU entailed active support, mainly standard occupational therapy. The BEL group included 133 participants and the CAU group 93. They completed self-report questionnaires targeting activity and well-being on three occasions - at baseline, after completed intervention (at 16 weeks) and at a six-month follow-up. A research assistant rated the participants' level of functioning and symptom severity on the same occasions. Non-parametric statistics were used since these instruments produced ordinal data. The BEL group improved more than the CAU group from baseline to 16 weeks on primary outcomes in terms of activity engagement (p life) more than the CAU group from baseline to the follow-up (p = 0.049). No differences were found at that time for activity balance, level of functioning and symptom severity. The BEL program was effective compared to CAU in terms of activity engagement. Their improvements were not, however, greater concerning other subjective perceptions, such as satisfaction with daily activities and self-rated health, and clustering effects lowered the dependability regarding findings of improvements on symptoms and

  6. Clustering Dycom

    KAUST Repository

    Minku, Leandro L.; Hou, Siqing

    2017-01-01

    baseline WC model is also included in the analysis. Results: Clustering Dycom with K-Means can potentially help to split the CC projects, managing to achieve similar or better predictive performance than Dycom. However, K-Means still requires the number

  7. Convex Clustering: An Attractive Alternative to Hierarchical Clustering

    Science.gov (United States)

    Chen, Gary K.; Chi, Eric C.; Ranola, John Michael O.; Lange, Kenneth

    2015-01-01

    The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics.ucla.edu/software/ PMID:25965340

  8. Globular clusters - Fads and fallacies

    International Nuclear Information System (INIS)

    White, R.E.

    1991-01-01

    The types of globular clusters observed in the Milky Way Galaxy are described together with their known characteristics, with special attention given to correcting the erroneous statements made earlier about globular clusters. Among these are the following statements: the Galaxy is surrounded by many hundreds of globular clusters; all globular clusters are located toward the Galactic center, all globular clusters are metal poor and move about the Galaxy in highly elliptical paths; all globular clusters contain RR Lyrae-type variable stars, and the RR Lyrae stars found outside of globulars have come from cluster dissolution or ejection; all of the stars in a given cluster were born at the same time and have the same chemical composition; X-ray globulars are powered by central black holes; and the luminosity functions for globular clusters are well defined and well determined. Consideration is given to the fact that globular clusters in the Magellanic Clouds differ from those in the Milky Way by their age distribution and that the globulars of the SMC differ from those of the LMC

  9. Present structure of the Finnish environmental cluster and improvement of its functioning particularly from the business perspective; SYKLI - Suomen ympaeristoeklusterin nykyrakenne ja sen toimivuuden parantaminen erityisesti liiketoimintaosan naekoekulmasta

    Energy Technology Data Exchange (ETDEWEB)

    Silvennoinen, A.; Apilo, S.; Vaara, M.

    2002-07-01

    There is an emerging environmental cluster in Finland, but its definition has proved problematic and given rise to lively discussion. It is characteristic of this environmental cluster that it overlaps with other cluster structures. The objective of the SYKLI project was to map out the existing environmental clusters and networks. This identification process was carried out in terns of both the overall activity of the Finnish environmental cluster and the regional parts. In practice, the study was conducted on regional level as business-based corporate interviews. The term cluster here refers, in application of M. Porter, to an operationally well-organised branch, which has been formed inside a nation and which succeeds in international competition. The study was based on a review Finland's Natural Resources and the Environment published by Statistics Finland. According to this review, the total turnover of the core regions in the environmental sector in 1998 was estimated at c. FIM 20.7 billion and the employment effect at 24 000 person/years. It was discovered about the environmental business in Finland that it is an entity related to neighbouring regions and assisted areas, which is divided into several branches. The products of enterprises are usually based on know-how and technology. The enterprise size is rather small on average and the enterprises are young. On the regional scale, environmental business is dispersed, although the public actors have mainly concentrated in Helsinki. The low standard of marketing know-how is felt to be a national deficiency, and there is a distinct need for knowledge and know-how regarding internationalisation at all levels. Weak cluster structures and operational networks developing especially with sub-contractors can be discerned in the activities of enterprises. Networking takes place between the environmental sector and the neighbouring regions and assisted areas, and not so much inside the environmental sector itself

  10. Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE).

    Science.gov (United States)

    Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K; Graham, Shirley; Liu, Huanting; Naismith, James H; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J; White, Malcolm F; Lawrence, C Martin

    2011-06-17

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.

  11. FORMATION OF A INNOVATION REGIONAL CLUSTER MODEL

    Directory of Open Access Journals (Sweden)

    G. S. Merzlikina

    2015-01-01

    Full Text Available Summary. As a result of investigation of science and methodical approaches related problems of building and development of innovation clusters there were some issues in functional assignments of innovation and production clusters. Because of those issues, article’s authors differ conceptions of innovation cluster and production cluster, as they explain notion of innovation-production cluster. The main goal of this article is to reveal existing organizational issues in cluster building and its successful development. Based on regional clusters building analysis carried out there was typical practical structure of cluster members interaction revealed. This structure also have its cons, as following: absence cluster orientation to marketing environment, lack of members’ prolonged relations’ building and development system, along with ineffective management of information, financial and material streams within cluster, narrow competence difference and responsibility zones between cluster members, lack of transparence of cluster’s action, low environment changes adaptivity, hard to use cluster members’ intellectual property, and commercialization of hi-tech products. When all those issues listed above come together, it reduces life activity of existing models of innovative cluster-building along with practical opportunity of cluster realization. Because of that, authors offer an upgraded innovative-productive cluster building model with more efficient business processes management system, which includes advanced innovative cluster structure, competence matrix and subcluster responsibility zone. Suggested model differs from other ones by using unified innovative product development control center, which also controls production and marketing realization.

  12. Quantum annealing for combinatorial clustering

    Science.gov (United States)

    Kumar, Vaibhaw; Bass, Gideon; Tomlin, Casey; Dulny, Joseph

    2018-02-01

    Clustering is a powerful machine learning technique that groups "similar" data points based on their characteristics. Many clustering algorithms work by approximating the minimization of an objective function, namely the sum of within-the-cluster distances between points. The straightforward approach involves examining all the possible assignments of points to each of the clusters. This approach guarantees the solution will be a global minimum; however, the number of possible assignments scales quickly with the number of data points and becomes computationally intractable even for very small datasets. In order to circumvent this issue, cost function minima are found using popular local search-based heuristic approaches such as k-means and hierarchical clustering. Due to their greedy nature, such techniques do not guarantee that a global minimum will be found and can lead to sub-optimal clustering assignments. Other classes of global search-based techniques, such as simulated annealing, tabu search, and genetic algorithms, may offer better quality results but can be too time-consuming to implement. In this work, we describe how quantum annealing can be used to carry out clustering. We map the clustering objective to a quadratic binary optimization problem and discuss two clustering algorithms which are then implemented on commercially available quantum annealing hardware, as well as on a purely classical solver "qbsolv." The first algorithm assigns N data points to K clusters, and the second one can be used to perform binary clustering in a hierarchical manner. We present our results in the form of benchmarks against well-known k-means clustering and discuss the advantages and disadvantages of the proposed techniques.

  13. Effects of a free school breakfast programme on school attendance, achievement, psychosocial function, and nutrition: a stepped wedge cluster randomised trial

    Directory of Open Access Journals (Sweden)

    Maddison Ralph

    2010-11-01

    Full Text Available Abstract Background Approximately 55,000 children in New Zealand do not eat breakfast on any given day. Regular breakfast skipping has been associated with poor diets, higher body mass index, and adverse effects on children's behaviour and academic performance. Research suggests that regular breakfast consumption can improve academic performance, nutrition and behaviour. This paper describes the protocol for a stepped wedge cluster randomised trial of a free school breakfast programme. The aim of the trial is to determine the effects of the breakfast intervention on school attendance, achievement, psychosocial function, dietary habits and food security. Methods/Design Sixteen primary schools in the North Island of New Zealand will be randomised in a sequential stepped wedge design to a free before-school breakfast programme consisting of non-sugar coated breakfast cereal, milk products, and/or toast and spreads. Four hundred children aged 5-13 years (approximately 25 per school will be recruited. Data collection will be undertaken once each school term over the 2010 school year (February to December. The primary trial outcome is school attendance, defined as the proportion of students achieving an attendance rate of 95% or higher. Secondary outcomes are academic achievement (literacy, numeracy, self-reported grades, sense of belonging at school, psychosocial function, dietary habits, and food security. A concurrent process evaluation seeks information on parents', schools' and providers' perspectives of the breakfast programme. Discussion This randomised controlled trial will provide robust evidence of the effects of a school breakfast programme on students' attendance, achievement and nutrition. Furthermore the study provides an excellent example of the feasibility and value of the stepped wedge trial design in evaluating pragmatic public health intervention programmes. Trial Registration Number Australian New Zealand Clinical Trials Registry

  14. Effects of a free school breakfast programme on school attendance, achievement, psychosocial function, and nutrition: a stepped wedge cluster randomised trial.

    Science.gov (United States)

    Ni Mhurchu, Cliona; Turley, Maria; Gorton, Delvina; Jiang, Yannan; Michie, Jo; Maddison, Ralph; Hattie, John

    2010-11-29

    Approximately 55,000 children in New Zealand do not eat breakfast on any given day. Regular breakfast skipping has been associated with poor diets, higher body mass index, and adverse effects on children's behaviour and academic performance. Research suggests that regular breakfast consumption can improve academic performance, nutrition and behaviour. This paper describes the protocol for a stepped wedge cluster randomised trial of a free school breakfast programme. The aim of the trial is to determine the effects of the breakfast intervention on school attendance, achievement, psychosocial function, dietary habits and food security. Sixteen primary schools in the North Island of New Zealand will be randomised in a sequential stepped wedge design to a free before-school breakfast programme consisting of non-sugar coated breakfast cereal, milk products, and/or toast and spreads. Four hundred children aged 5-13 years (approximately 25 per school) will be recruited. Data collection will be undertaken once each school term over the 2010 school year (February to December). The primary trial outcome is school attendance, defined as the proportion of students achieving an attendance rate of 95% or higher. Secondary outcomes are academic achievement (literacy, numeracy, self-reported grades), sense of belonging at school, psychosocial function, dietary habits, and food security. A concurrent process evaluation seeks information on parents', schools' and providers' perspectives of the breakfast programme. This randomised controlled trial will provide robust evidence of the effects of a school breakfast programme on students' attendance, achievement and nutrition. Furthermore the study provides an excellent example of the feasibility and value of the stepped wedge trial design in evaluating pragmatic public health intervention programmes. Australian New Zealand Clinical Trials Registry (ANZCTR) - ACTRN12609000854235.

  15. Exotic cluster structures on

    CERN Document Server

    Gekhtman, M; Vainshtein, A

    2017-01-01

    This is the second paper in the series of papers dedicated to the study of natural cluster structures in the rings of regular functions on simple complex Lie groups and Poisson-Lie structures compatible with these cluster structures. According to our main conjecture, each class in the Belavin-Drinfeld classification of Poisson-Lie structures on \\mathcal{G} corresponds to a cluster structure in \\mathcal{O}(\\mathcal{G}). The authors have shown before that this conjecture holds for any \\mathcal{G} in the case of the standard Poisson-Lie structure and for all Belavin-Drinfeld classes in SL_n, n<5. In this paper the authors establish it for the Cremmer-Gervais Poisson-Lie structure on SL_n, which is the least similar to the standard one.

  16. Projected coupled cluster theory.

    Science.gov (United States)

    Qiu, Yiheng; Henderson, Thomas M; Zhao, Jinmo; Scuseria, Gustavo E

    2017-08-14

    Coupled cluster theory is the method of choice for weakly correlated systems. But in the strongly correlated regime, it faces a symmetry dilemma, where it either completely fails to describe the system or has to artificially break certain symmetries. On the other hand, projected Hartree-Fock theory captures the essential physics of many kinds of strong correlations via symmetry breaking and restoration. In this work, we combine and try to retain the merits of these two methods by applying symmetry projection to broken symmetry coupled cluster wave functions. The non-orthogonal nature of states resulting from the application of symmetry projection operators furnishes particle-hole excitations to all orders, thus creating an obstacle for the exact evaluation of overlaps. Here we provide a solution via a disentanglement framework theory that can be approximated rigorously and systematically. Results of projected coupled cluster theory are presented for molecules and the Hubbard model, showing that spin projection significantly improves unrestricted coupled cluster theory while restoring good quantum numbers. The energy of projected coupled cluster theory reduces to the unprojected one in the thermodynamic limit, albeit at a much slower rate than projected Hartree-Fock.

  17. Cluster forcing

    DEFF Research Database (Denmark)

    Christensen, Thomas Budde

    The cluster theory attributed to Michael Porter has significantly influenced industrial policies in countries across Europe and North America since the beginning of the 1990s. Institutions such as the EU, OECD and the World Bank and governments in countries such as the UK, France, The Netherlands...... or management. Both the Accelerate Wales and the Accelerate Cluster programmes target this issue by trying to establish networks between companies that can be used to supply knowledge from research institutions to manufacturing companies. The paper concludes that public sector interventions can make...... businesses. The universities were not considered by the participating companies to be important parts of the local business environment and inputs from universities did not appear to be an important source to access knowledge about new product development or new techniques in production, distribution...

  18. Regional Innovation Clusters

    Data.gov (United States)

    Small Business Administration — The Regional Innovation Clusters serve a diverse group of sectors and geographies. Three of the initial pilot clusters, termed Advanced Defense Technology clusters,...

  19. Cluster analysis

    OpenAIRE

    Mucha, Hans-Joachim; Sofyan, Hizir

    2000-01-01

    As an explorative technique, duster analysis provides a description or a reduction in the dimension of the data. It classifies a set of observations into two or more mutually exclusive unknown groups based on combinations of many variables. Its aim is to construct groups in such a way that the profiles of objects in the same groups are relatively homogenous whereas the profiles of objects in different groups are relatively heterogeneous. Clustering is distinct from classification techniques, ...

  20. Density functional theory study of small X-doped Mg(n) (X = Fe, Co, Ni, n = 1-9) bimetallic clusters: equilibrium structures, stabilities, electronic and magnetic properties.

    Science.gov (United States)

    Kong, Fanjie; Hu, Yanfei

    2014-03-01

    The geometries, stabilities, and electronic and magnetic properties of Mg(n) X (X = Fe, Co, Ni, n = 1-9) clusters were investigated systematically within the framework of the gradient-corrected density functional theory. The results show that the Mg(n)Fe, Mg(n)Co, and Mg(n)Ni clusters have similar geometric structures and that the X atom in Mg(n)X clusters prefers to be endohedrally doped. The average atomic binding energies, fragmentation energies, second-order differences in energy, and HOMO-LUMO gaps show that Mg₄X (X = Fe, Co, Ni) clusters possess relatively high stability. Natural population analysis was performed and the results showed that the 3s and 4s electrons always transfer to the 3d and 4p orbitals in the bonding atoms, and that electrons also transfer from the Mg atoms to the doped atoms (Fe, Co, Ni). In addition, the spin magnetic moments were analyzed and compared. Several clusters, such as Mg₁,₂,₃,₄,₅,₆,₈,₉Fe, Mg₁,₂,₄,₅,₆,₈,₉Co, and Mg₁,₂,₅,₆,₇,₉Ni, present high magnetic moments (4 μ(B), 3 μ(B), and 2 μ(B), respectively).

  1. Cluster algebras in mathematical physics

    International Nuclear Information System (INIS)

    Francesco, Philippe Di; Gekhtman, Michael; Kuniba, Atsuo; Yamazaki, Masahito

    2014-01-01

    This special issue of Journal of Physics A: Mathematical and Theoretical contains reviews and original research articles on cluster algebras and their applications to mathematical physics. Cluster algebras were introduced by S Fomin and A Zelevinsky around 2000 as a tool for studying total positivity and dual canonical bases in Lie theory. Since then the theory has found diverse applications in mathematics and mathematical physics. Cluster algebras are axiomatically defined commutative rings equipped with a distinguished set of generators (cluster variables) subdivided into overlapping subsets (clusters) of the same cardinality subject to certain polynomial relations. A cluster algebra of rank n can be viewed as a subring of the field of rational functions in n variables. Rather than being presented, at the outset, by a complete set of generators and relations, it is constructed from the initial seed via an iterative procedure called mutation producing new seeds successively to generate the whole algebra. A seed consists of an n-tuple of rational functions called cluster variables and an exchange matrix controlling the mutation. Relations of cluster algebra type can be observed in many areas of mathematics (Plücker and Ptolemy relations, Stokes curves and wall-crossing phenomena, Feynman integrals, Somos sequences and Hirota equations to name just a few examples). The cluster variables enjoy a remarkable combinatorial pattern; in particular, they exhibit the Laurent phenomenon: they are expressed as Laurent polynomials rather than more general rational functions in terms of the cluster variables in any seed. These characteristic features are often referred to as the cluster algebra structure. In the last decade, it became apparent that cluster structures are ubiquitous in mathematical physics. Examples include supersymmetric gauge theories, Poisson geometry, integrable systems, statistical mechanics, fusion products in infinite dimensional algebras, dilogarithm

  2. Genomic and Functional Characterization of the Unusual pLOCK 0919 Plasmid Harboring the spaCBA Pili Cluster in Lactobacillus casei LOCK 0919

    Czech Academy of Sciences Publication Activity Database

    Aleksandrzak-Piekarczyk, T.; Koryszewska-Baginska, A.; Grynberg, M.; Nowak, A.; Cukrowska, B.; Kozáková, Hana; Bardowski, J.

    2016-01-01

    Roč. 8, č. 1 (2016), s. 202-217 ISSN 1759-6653 Institutional support: RVO:61388971 Keywords : adhesion * spaCBA pilus cluster * lactobacillus Subject RIV: EC - Immunology Impact factor: 3.979, year: 2016

  3. Shape of Multireference, Equation-of-Motion Coupled-Cluster, and Density Functional Theory Potential Energy Surfaces at a Conical Intersection.

    Science.gov (United States)

    Gozem, Samer; Melaccio, Federico; Valentini, Alessio; Filatov, Michael; Huix-Rotllant, Miquel; Ferré, Nicolas; Frutos, Luis Manuel; Angeli, Celestino; Krylov, Anna I; Granovsky, Alexander A; Lindh, Roland; Olivucci, Massimo

    2014-08-12

    We report and characterize ground-state and excited-state potential energy profiles using a variety of electronic structure methods along a loop lying on the branching plane associated with a conical intersection (CI) of a reduced retinal model, the penta-2,4-dieniminium cation (PSB3). Whereas the performance of the equation-of-motion coupled-cluster, density functional theory, and multireference methods had been tested along the excited- and ground-state paths of PSB3 in our earlier work, the ability of these methods to correctly describe the potential energy surface shape along a CI branching plane has not yet been investigated. This is the focus of the present contribution. We find, in agreement with earlier studies by others, that standard time-dependent DFT (TDDFT) does not yield the correct two-dimensional (i.e., conical) crossing along the branching plane but rather a one-dimensional (i.e., linear) crossing along the same plane. The same type of behavior is found for SS-CASPT2(IPEA=0), SS-CASPT2(IPEA=0.25), spin-projected SF-TDDFT, EOM-SF-CCSD, and, finally, for the reference MRCISD+Q method. In contrast, we found that MRCISD, CASSCF, MS-CASPT2(IPEA=0), MS-CASPT2(IPEA=0.25), XMCQDPT2, QD-NEVPT2, non-spin-projected SF-TDDFT, and SI-SA-REKS yield the expected conical crossing. To assess the effect of the different crossing topologies (i.e., linear or conical) on the PSB3 photoisomerization efficiency, we discuss the results of 100 semiclassical trajectories computed by CASSCF and SS-CASPT2(IPEA=0.25) for a PSB3 derivative. We show that for the same initial conditions, the two methods yield similar dynamics leading to isomerization quantum yields that differ by only a few percent.

  4. HUBBLE FRONTIER FIELDS FIRST COMPLETE CLUSTER DATA: FAINT GALAXIES AT z ∼ 5-10 FOR UV LUMINOSITY FUNCTIONS AND COSMIC REIONIZATION

    International Nuclear Information System (INIS)

    Ishigaki, Masafumi; Ouchi, Masami; Ono, Yoshiaki; Kawamata, Ryota; Shimasaku, Kazuhiro; Oguri, Masamune

    2015-01-01

    We present comprehensive analyses of faint dropout galaxies up to z ∼ 10 with the first full-depth data set of the A2744 lensing cluster and parallel fields observed by the Hubble Frontier Fields (HFF) program. We identify 54 dropouts at z ∼ 5-10 in the HFF fields and enlarge the size of the z ∼ 9 galaxy sample obtained to date. Although the number of highly magnified (μ ∼ 10) galaxies is small because of the tiny survey volume of strong lensing, our study reaches the galaxies' intrinsic luminosities comparable to the deepest-field HUDF studies. We derive UV luminosity functions with these faint dropouts, carefully evaluating by intensive simulations the combination of observational incompleteness and lensing effects in the image plane, including magnification, distortion, and multiplication of images, with the evaluation of mass model dependencies. Our results confirm that the faint-end slope, α, is as steep as –2 at z ∼ 6-8 and strengthen the evidence for the rapid decrease of UV luminosity densities, ρ UV , at z > 8 from the large z ∼ 9 sample. We examine whether the rapid ρ UV decrease trend can be reconciled with the large Thomson scattering optical depth, τ e , measured by cosmic microwave background experiments, allowing a large space of free parameters, such as an average ionizing photon escape fraction and a stellar-population-dependent conversion factor. No parameter set can reproduce both the rapid ρ UV decrease and the large τ e . It is possible that the ρ UV decrease moderates at z ≳ 11, that the free parameters significantly evolve toward high z, or that there exist additional sources of reionization such as X-ray binaries and faint active galactic nuclei

  5. HUBBLE FRONTIER FIELDS FIRST COMPLETE CLUSTER DATA: FAINT GALAXIES AT z ∼ 5-10 FOR UV LUMINOSITY FUNCTIONS AND COSMIC REIONIZATION

    Energy Technology Data Exchange (ETDEWEB)

    Ishigaki, Masafumi; Ouchi, Masami; Ono, Yoshiaki [Institute for Cosmic Ray Research, The University of Tokyo, Kashiwa, Chiba 277-8582 (Japan); Kawamata, Ryota; Shimasaku, Kazuhiro [Department of Astronomy, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Oguri, Masamune, E-mail: ishigaki@icrr.u-tokyo.ac.jp [Department of Physics, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)

    2015-01-20

    We present comprehensive analyses of faint dropout galaxies up to z ∼ 10 with the first full-depth data set of the A2744 lensing cluster and parallel fields observed by the Hubble Frontier Fields (HFF) program. We identify 54 dropouts at z ∼ 5-10 in the HFF fields and enlarge the size of the z ∼ 9 galaxy sample obtained to date. Although the number of highly magnified (μ ∼ 10) galaxies is small because of the tiny survey volume of strong lensing, our study reaches the galaxies' intrinsic luminosities comparable to the deepest-field HUDF studies. We derive UV luminosity functions with these faint dropouts, carefully evaluating by intensive simulations the combination of observational incompleteness and lensing effects in the image plane, including magnification, distortion, and multiplication of images, with the evaluation of mass model dependencies. Our results confirm that the faint-end slope, α, is as steep as –2 at z ∼ 6-8 and strengthen the evidence for the rapid decrease of UV luminosity densities, ρ{sub UV}, at z > 8 from the large z ∼ 9 sample. We examine whether the rapid ρ{sub UV} decrease trend can be reconciled with the large Thomson scattering optical depth, τ{sub e}, measured by cosmic microwave background experiments, allowing a large space of free parameters, such as an average ionizing photon escape fraction and a stellar-population-dependent conversion factor. No parameter set can reproduce both the rapid ρ{sub UV} decrease and the large τ {sub e}. It is possible that the ρ{sub UV} decrease moderates at z ≳ 11, that the free parameters significantly evolve toward high z, or that there exist additional sources of reionization such as X-ray binaries and faint active galactic nuclei.

  6. Global survey of star clusters in the Milky Way. VI. Age distribution and cluster formation history

    Science.gov (United States)

    Piskunov, A. E.; Just, A.; Kharchenko, N. V.; Berczik, P.; Scholz, R.-D.; Reffert, S.; Yen, S. X.

    2018-06-01

    Context. The all-sky Milky Way Star Clusters (MWSC) survey provides uniform and precise ages, along with other relevant parameters, for a wide variety of clusters in the extended solar neighbourhood. Aims: In this study we aim to construct the cluster age distribution, investigate its spatial variations, and discuss constraints on cluster formation scenarios of the Galactic disk during the last 5 Gyrs. Methods: Due to the spatial extent of the MWSC, we have considered spatial variations of the age distribution along galactocentric radius RG, and along Z-axis. For the analysis of the age distribution we used 2242 clusters, which all lie within roughly 2.5 kpc of the Sun. To connect the observed age distribution to the cluster formation history we built an analytical model based on simple assumptions on the cluster initial mass function and on the cluster mass-lifetime relation, fit it to the observations, and determined the parameters of the cluster formation law. Results: Comparison with the literature shows that earlier results strongly underestimated the number of evolved clusters with ages t ≳ 100 Myr. Recent studies based on all-sky catalogues agree better with our data, but still lack the oldest clusters with ages t ≳ 1 Gyr. We do not observe a strong variation in the age distribution along RG, though we find an enhanced fraction of older clusters (t > 1 Gyr) in the inner disk. In contrast, the distribution strongly varies along Z. The high altitude distribution practically does not contain clusters with t < 1 Gyr. With simple assumptions on the cluster formation history, the cluster initial mass function and the cluster lifetime we can reproduce the observations. The cluster formation rate and the cluster lifetime are strongly degenerate, which does not allow us to disentangle different formation scenarios. In all cases the cluster formation rate is strongly declining with time, and the cluster initial mass function is very shallow at the high mass end.

  7. Structure-function relationship between the octopus perimeter cluster mean sensitivity and sector retinal nerve fiber layer thickness measured with the RTVue optical coherence tomography and scanning laser polarimetry.

    Science.gov (United States)

    Naghizadeh, Farzaneh; Garas, Anita; Vargha, Péter; Holló, Gábor

    2014-01-01

    To determine structure-function relationship between each of 16 Octopus perimeter G2 program clusters and the corresponding 16 peripapillary sector retinal nerve fiber layer thickness (RNFLT) values measured with the RTVue-100 Fourier-domain optical coherence tomography (RTVue OCT) and scanning laser polarimetry with variable corneal compensation (GDx-VCC) and enhanced corneal compensation (GDx-ECC) corneal compensation. One eye of 110 white patients (15 healthy, 20 ocular hypertensive, and 75 glaucoma eyes) were investigated. The Akaike information criterion and the F test were used to identify the best fitting model. Parabolic relationship with logarithmic cluster mean sensitivity and linear sector RNFLT values provided the best fit. For RTVue OCT, significant (P0.05) was found for the control eyes. Mean sensitivity of the Octopus visual field clusters showed significant parabolic relationship with the corresponding peripapillary RNFLT sectors. The relationship was more general with the RTVue OCT than GDx-VCC or GDx-ECC. The results show that visual field clusters of the Octopus G program can be applied for detailed structure-function research.

  8. CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks.

    Science.gov (United States)

    Li, Min; Li, Dongyan; Tang, Yu; Wu, Fangxiang; Wang, Jianxin

    2017-08-31

    Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect protein complexes or functional modules. In addition, BinGO is used to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. CytoCluster can be easily expanded, so that more clustering algorithms and functions can be added to this plugin. Since it was created in July 2013, CytoCluster has been downloaded more than 9700 times in the Cytoscape App store and has already been applied to the analysis of different biological networks. CytoCluster is available from http://apps.cytoscape.org/apps/cytocluster.

  9. Orbit Clustering Based on Transfer Cost

    Science.gov (United States)

    Gustafson, Eric D.; Arrieta-Camacho, Juan J.; Petropoulos, Anastassios E.

    2013-01-01

    We propose using cluster analysis to perform quick screening for combinatorial global optimization problems. The key missing component currently preventing cluster analysis from use in this context is the lack of a useable metric function that defines the cost to transfer between two orbits. We study several proposed metrics and clustering algorithms, including k-means and the expectation maximization algorithm. We also show that proven heuristic methods such as the Q-law can be modified to work with cluster analysis.

  10. The Epstein-Barr Virus BART miRNA Cluster of the M81 Strain Modulates Multiple Functions in Primary B Cells

    Science.gov (United States)

    Lin, Xiaochen; Tsai, Ming-Han; Shumilov, Anatoliy; Poirey, Remy; Bannert, Helmut; Middeldorp, Jaap M.; Feederle, Regina; Delecluse, Henri-Jacques

    2015-01-01

    The Epstein-Barr virus (EBV) is a B lymphotropic virus that infects the majority of the human population. All EBV strains transform B lymphocytes, but some strains, such as M81, also induce spontaneous virus replication. EBV encodes 22 microRNAs (miRNAs) that form a cluster within the BART region of the virus and have been previously been found to stimulate tumor cell growth. Here we describe their functions in B cells infected by M81. We found that the BART miRNAs are downregulated in replicating cells, and that exposure of B cells in vitro or in vivo in humanized mice to a BART miRNA knockout virus resulted in an increased proportion of spontaneously replicating cells, relative to wild type virus. The BART miRNAs subcluster 1, and to a lesser extent subcluster 2, prevented expression of BZLF1, the key protein for initiation of lytic replication. Thus, multiple BART miRNAs cooperate to repress lytic replication. The BART miRNAs also downregulated pro- and anti-apoptotic mediators such as caspase 3 and LMP1, and their deletion did not sensitize B-cells to apoptosis. To the contrary, the majority of humanized mice infected with the BART miRNA knockout mutant developed tumors more rapidly, probably due to enhanced LMP1 expression, although deletion of the BART miRNAs did not modify the virus transforming abilities in vitro. This ability to slow cell growth could be confirmed in non-humanized immunocompromized mice. Injection of resting B cells exposed to a virus that lacks the BART