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Sample records for function cpg clustering

  1. Interferon-α/β receptor-mediated selective induction of a gene cluster by CpG oligodeoxynucleotide 2006

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    Wakiguchi Hiroshi

    2003-07-01

    Full Text Available Abstract Background Oligodeoxynucleotides containing unmethylated CpG motifs (CpG ODN are known to exert a strong adjuvant effect on Th1 immune responses. Although several genes have been reported, no comprehensive study of the gene expression profiles in human cells after stimulation with CpG ODN has been reported. Results This study was designed to identify a CpG-inducible gene cluster that potentially predicts for the molecular mechanisms of clinical efficacy of CpG ODN, by determining mRNA expression in human PBMC after stimulation with CpG ODN. PBMCs were obtained from the peripheral blood of healthy volunteers and cultured in the presence or absence of CpG ODN 2006 for up to 24 hours. The mRNA expression profile was evaluated using a high-density oligonucleotide probe array, GeneChip®. Using hierarchical clustering-analysis, out of a total of 10,000 genes we identified a cluster containing 77 genes as having been up-regulated by CpG ODN. This cluster was further divided into two sub-clusters by means of time-kinetics. (1 Inflammatory cytokines such as IL-6 and GM-CSF were up-regulated predominantly 3 to 6 hours after stimulation with CpG ODN, presumably through activation of a transcription factor, NF-κB. (2 Interferon (IFN-inducible anti-viral proteins, including IFIT1, OAS1 and Mx1, and Th1 chemoattractant IP-10, were up-regulated predominantly 6 to 24 hours after stimulation. Blocking with mAb against IFN-α/β receptor strongly inhibited the induction of these IFN-inducible genes by CpG ODN. Conclusion This study provides new information regarding the possible immunomodulatory effects of CpG ODN in vivo via an IFN-α/β receptor-mediated paracrine pathway.

  2. Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression

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    Sakaki Yoshiyuki

    2004-02-01

    Full Text Available Abstract Background Gene expression is regulated mainly by transcription factors (TFs that interact with regulatory cis-elements on DNA sequences. To identify functional regulatory elements, computer searching can predict TF binding sites (TFBS using position weight matrices (PWMs that represent positional base frequencies of collected experimentally determined TFBS. A disadvantage of this approach is the large output of results for genomic DNA. One strategy to identify genuine TFBS is to utilize local concentrations of predicted TFBS. It is unclear whether there is a general tendency for TFBS to cluster at promoter regions, although this is the case for certain TFBS. Also unclear is the identification of TFs that have TFBS concentrated in promoters and to what level this occurs. This study hopes to answer some of these questions. Results We developed the cluster score measure to evaluate the correlation between predicted TFBS clusters and promoter sequences for each PWM. Non-promoter sequences were used as a control. Using the cluster score, we identified a PWM group called PWM-PCP, in which TFBS clusters positively correlate with promoters, and another PWM group called PWM-NCP, in which TFBS clusters negatively correlate with promoters. The PWM-PCP group comprises 47% of the 199 vertebrate PWMs, while the PWM-NCP group occupied 11 percent. After reducing the effect of CpG islands (CGI against the clusters using partial correlation coefficients among three properties (promoter, CGI and predicted TFBS cluster, we identified two PWM groups including those strongly correlated with CGI and those not correlated with CGI. Conclusion Not all PWMs predict TFBS correlated with human promoter sequences. Two main PWM groups were identified: (1 those that show TFBS clustered in promoters associated with CGI, and (2 those that show TFBS clustered in promoters independent of CGI. Assessment of PWM matches will allow more positive interpretation of TFBS in

  3. The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes.

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    Gushchanskaya, Ekaterina S; Artemov, Artem V; Ulyanov, Sergey V; Logacheva, Maria D; Penin, Aleksey A; Kotova, Elena S; Akopov, Sergey B; Nikolaev, Lev G; Iarovaia, Olga V; Sverdlov, Eugene D; Gavrilov, Alexey A; Razin, Sergey V

    2014-07-01

    We used the 4C-Seq technique to characterize the genome-wide patterns of spatial contacts of several CpG islands located on chromosome 14 in cultured chicken lymphoid and erythroid cells. We observed a clear tendency for the spatial clustering of CpG islands present on the same and different chromosomes, regardless of the presence or absence of promoters within these CpG islands. Accordingly, we observed preferential spatial contacts between Sp1 binding motifs and other GC-rich genomic elements, including the DNA sequence motifs capable of forming G-quadruplexes. However, an anchor placed in a gene/CpG island-poor area formed spatial contacts with other gene/CpG island-poor areas on chromosome 14 and other chromosomes. These results corroborate the two-compartment model of the spatial organization of interphase chromosomes and suggest that the clustering of CpG islands constitutes an important determinant of the 3D organization of the eukaryotic genome in the cell nucleus. Using the ChIP-Seq technique, we mapped the genome-wide CTCF deposition sites in the chicken lymphoid and erythroid cells that were used for the 4C analysis. We observed a good correlation between the density of CTCF deposition sites and the level of 4C signals for the anchors located in CpG islands but not for an anchor located in a gene desert. It is thus possible that CTCF contributes to the clustering of CpG islands observed in our experiments.

  4. Polyethyleneimine-functionalized boron nitride nanospheres as efficient carriers for enhancing the immunostimulatory effect of CpG oligodeoxynucleotides

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    Zhang HJ

    2015-08-01

    Full Text Available Huijie Zhang,1 Shini Feng,1 Ting Yan,1 Chunyi Zhi,2 Xiao-Dong Gao,1 Nobutaka Hanagata3,41The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People’s Republic of China; 2Department of Physics and Materials Science, City University of Hong Kong, Kowlong, Hong Kong SAR, People’s Republic of China; 3Biomaterials Unit, International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Ibaraki, Japan; 4Nanotechnology Innovation Station, National Institute for Materials Science, Ibaraki, JapanAbstract: CpG oligodeoxynucleotides (ODNs stimulate innate and adaptive immune responses. Thus, these molecules are promising therapeutic agents and vaccine adjuvants against various diseases. In this study, we developed a novel CpG ODNs delivery system based on polyethyleneimine (PEI-functionalized boron nitride nanospheres (BNNS. PEI was coated on the surface of BNNS via electrostatic interactions. The prepared BNNS–PEI complexes had positive zeta potential and exhibited enhanced dispersity and stability in aqueous solution. In vitro cytotoxicity assays revealed that the BNNS–PEI complexes with concentrations up to 100 µg/mL exhibited no obvious cytotoxicity. Furthermore, the positively charged surface of the BNNS–PEI complexes greatly improved the loading capacity and cellular uptake efficiency of CpG ODNs. Class B CpG ODNs loaded on the BNNS–PEI complexes enhanced the production of interleukin-6 and tumor necrosis factor-α from peripheral blood mononuclear cells compared with CpG ODNs directly loaded on BNNS. Contrary to the free CpG ODNs or CpG ODNs directly loaded on BNNS, class B CpG ODNs loaded on the BNNS–PEI complexes induced interferon-α simultaneously. PEI coating may have changed the physical form of class B CpG ODNs on BNNS, which further affected their interaction with Toll-like receptor 9 and induced interferon

  5. Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin.

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    Bina, Minou; Wyss, Phillip; Novorolsky, Elise; Zulkelfi, Noorfatin; Xue, Jing; Price, Randi; Fay, Matthew; Gutmann, Zach; Fogler, Brian; Wang, Daidong

    2013-12-28

    Mixed Lineage Leukemia 1 (MLL1) is a mammalian ortholog of the Drosophila Trithorax. In Drosophila, Trithorax complexes transmit the memory of active genes to daughter cells through interactions with Trithorax Response Elements (TREs). However, despite their functional importance, nothing is known about sequence features that may act as TREs in mammalian genomic DNA. By analyzing results of reported DNA binding assays, we identified several CpG rich motifs as potential MLL1 binding units (defined as morphemes). We find that these morphemes are dispersed within a relatively large collection of human promoter sequences and appear densely packed near transcription start sites of protein-coding genes. Genome wide analyses localized frequent morpheme occurrences to CpG islands. In the human HOX loci, the morphemes are spread across CpG islands and in some cases tail into the surrounding shores and shelves of the islands. By analyzing results of chromatin immunoprecipitation assays, we found a connection between morpheme occurrences, CpG islands, and chromatin segments reported to be associated with MLL1. Furthermore, we found a correspondence of reported MLL1-driven "bookmarked" regions in chromatin to frequent occurrences of MLL1 morphemes in CpG islands. Our results implicate the MLL1 morphemes in sequence-features that define the mammalian TREs and provide a novel function for CpG islands. Apparently, our findings offer the first evidence for existence of potential TREs in mammalian genomic DNA and the first evidence for a connection between CpG islands and gene-bookmarking by MLL1 to transmit the memory of highly active genes during mitosis. Our results further suggest a role for overlapping morphemes in producing closely packed and multiple MLL1 binding events in genomic DNA so that MLL1 molecules could interact and reside simultaneously on extended potential transcriptional maintenance elements in human chromosomes to transmit the memory of highly active genes

  6. Transitions at CpG dinucleotides, geographic clustering of TP53 mutations and food availability patterns in colorectal cancer.

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    Fabio Verginelli

    Full Text Available BACKGROUND: Colorectal cancer is mainly attributed to diet, but the role exerted by foods remains unclear because involved factors are extremely complex. Geography substantially impacts on foods. Correlations between international variation in colorectal cancer-associated mutation patterns and food availabilities could highlight the influence of foods on colorectal mutagenesis. METHODOLOGY: To test such hypothesis, we applied techniques based on hierarchical clustering, feature extraction and selection, and statistical pattern recognition to the analysis of 2,572 colorectal cancer-associated TP53 mutations from 12 countries/geographic areas. For food availabilities, we relied on data extracted from the Food Balance Sheets of the Food and Agriculture Organization of the United Nations. Dendrograms for mutation sites, mutation types and food patterns were constructed through Ward's hierarchical clustering algorithm and their stability was assessed evaluating silhouette values. Feature selection used entropy-based measures for similarity between clusterings, combined with principal component analysis by exhaustive and heuristic approaches. CONCLUSION/SIGNIFICANCE: Mutations clustered in two major geographic groups, one including only Western countries, the other Asia and parts of Europe. This was determined by variation in the frequency of transitions at CpGs, the most common mutation type. Higher frequencies of transitions at CpGs in the cluster that included only Western countries mainly reflected higher frequencies of mutations at CpG codons 175, 248 and 273, the three major TP53 hotspots. Pearson's correlation scores, computed between the principal components of the datamatrices for mutation types, food availability and mutation sites, demonstrated statistically significant correlations between transitions at CpGs and both mutation sites and availabilities of meat, milk, sweeteners and animal fats, the energy-dense foods at the basis of

  7. Cluster functional renormalization group

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    Reuther, Johannes; Thomale, Ronny

    2014-01-01

    Functional renormalization group (FRG) has become a diverse and powerful tool to derive effective low-energy scattering vertices of interacting many-body systems. Starting from a free expansion point of the action, the flow of the RG parameter Λ allows us to trace the evolution of the effective one- and two-particle vertices towards low energies by taking into account the vertex corrections between all parquet channels in an unbiased fashion. In this work, we generalize the expansion point at which the diagrammatic resummation procedure is initiated from a free UV limit to a cluster product state. We formulate a cluster FRG scheme where the noninteracting building blocks (i.e., decoupled spin clusters) are treated exactly, and the intercluster couplings are addressed via RG. As a benchmark study, we apply our cluster FRG scheme to the spin-1/2 bilayer Heisenberg model (BHM) on a square lattice where the neighboring sites in the two layers form the individual two-site clusters. Comparing with existing numerical evidence for the BHM, we obtain reasonable findings for the spin susceptibility, the spin-triplet excitation energy, and quasiparticle weight even in coupling regimes close to antiferromagnetic order. The concept of cluster FRG promises applications to a large class of interacting electron systems.

  8. Enhancement of functional antibody responses to AMA1-C1/Alhydrogel, a Plasmodium falciparum malaria vaccine, with CpG oligodeoxynucleotide.

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    Mullen, Gregory E D; Giersing, Birgitte K; Ajose-Popoola, Olubunmi; Davis, Heather L; Kothe, Cheryl; Zhou, Hong; Aebig, Joan; Dobrescu, Gelu; Saul, Allan; Long, Carole A

    2006-03-24

    Apical membrane antigen 1 (AMA1) has been shown to be a promising malaria vaccine candidate. The multiallelic AMA1-C1 vaccine currently in Phase 1 trials in the US and Mali contains an equal mixture of the ectodomain portion of recombinant AMA1 from the FVO and 3D7 clones of Plasmodium falciparum, formulated on Alhydrogel. It is hoped that inclusion of a human-optimized CpG oligodeoxynucleotide (ODN) (CPG 7909) with our existing AMA1-C1/Alhydrogel vaccine will lead to a higher concentration of functional AMA1-C1 antibodies. Preclinical studies were performed in mice, rats and guinea pigs to assess the safety, immunogenicity and functionality of the immune response to AMA1-C1 with Alhydrogel + CPG 7909 compared to antigen with Alhydrogel alone. Day 42 mean anti-AMA1 ELISA titer values derived from individual animals were compared between Alhydrogel and Alhydrogel + CPG 7909 groups at each antigen dose for each species. Sera from Alhydrogel + CPG 7909 groups displayed significantly higher antibody titers (P CPG 7909 gave a mixed Th1/Th2 type response. When tested for functional activity by in vitro inhibition of parasite invasion, IgG isolated from serum pools of AMA1-C1/Alhydrogel + CPG 7909 animals was more effective against both FVO and 3D7 parasites than an equal concentration of IgG from animals receiving vaccines adjuvanted with Alhydrogel alone. These promising preclinical results have recently led to the start of a Phase 1 trial in the US.

  9. Analysis of CpG methylation sites and CGI among human papillomavirus DNA genomes

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    Galván Silvia C

    2011-11-01

    Full Text Available Abstract Background The Human Papillomavirus (HPV genome is divided into early and late coding sequences, including 8 open reading frames (ORFs and a regulatory region (LCR. Viral gene expression may be regulated through epigenetic mechanisms, including cytosine methylation at CpG dinucleotides. We have analyzed the distribution of CpG sites and CpG islands/clusters (CGI among 92 different HPV genomes grouped in function of their preferential tropism: cutaneous or mucosal. We calculated the proportion of CpG sites (PCS for each ORF and calculated the expected CpG values for each viral type. Results CpGs are underrepresented in viral genomes. We found a positive correlation between CpG observed and expected values, with mucosal high-risk (HR virus types showing the smallest O/E ratios. The ranges of the PCS were similar for most genomic regions except E4, where the majority of CpGs are found within islands/clusters. At least one CGI belongs to each E2/E4 region. We found positive correlations between PCS for each viral ORF when compared with the others, except for the LCR against four ORFs and E6 against three other ORFs. The distribution of CpG islands/clusters among HPV groups is heterogeneous and mucosal HR-HPV types exhibit both lower number and shorter island sizes compared to cutaneous and mucosal Low-risk (LR HPVs (all of them significantly different. Conclusions There is a difference between viral and cellular CpG underrepresentation. There are significant correlations between complete genome PCS and a lack of correlations between several genomic region pairs, especially those involving LCR and E6. L2 and L1 ORF behavior is opposite to that of oncogenes E6 and E7. The first pair possesses relatively low numbers of CpG sites clustered in CGIs while the oncogenes possess a relatively high number of CpG sites not associated to CGIs. In all HPVs, E2/E4 is the only region with at least one CGI and shows a higher content of CpG sites in every

  10. B-cell activation with CD40L or CpG measures the function of B-cell subsets and identifies specific defects in immunodeficient patients.

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    Marasco, Emiliano; Farroni, Chiara; Cascioli, Simona; Marcellini, Valentina; Scarsella, Marco; Giorda, Ezio; Piano Mortari, Eva; Leonardi, Lucia; Scarselli, Alessia; Valentini, Diletta; Cancrini, Caterina; Duse, Marzia; Grimsholm, Ola; Carsetti, Rita

    2017-01-01

    Around 65% of primary immunodeficiencies are antibody deficiencies. Functional tests are useful tools to study B-cell functions in vitro. However, no accepted guidelines for performing and evaluating functional tests have been issued yet. Here, we report our experience on the study of B-cell functions in infancy and throughout childhood. We show that T-independent stimulation with CpG measures proliferation and differentiation potential of memory B cells. Switched memory B cells respond better than IgM memory B cells. On the other hand, CD40L, a T-dependent stimulus, does not induce plasma cell differentiation, but causes proliferation of naïve and memory B cells. During childhood, the production of plasmablasts in response to CpG increases with age mirroring the development of memory B cells. The response to CD40L does not change with age. In patients with selective IgA deficiency (SIgAD), we observed that switched memory B cells are reduced due to the absence of IgA memory B cells. In agreement, IgA plasma cells are not generated in response to CpG. Unexpectedly, B cells from SIgAD patients show a reduced proliferative response to CD40L. Our results demonstrate that functional tests are an important tool to assess the functions of the humoral immune system.

  11. Functional Characterization and Drug Response of Freshly Established Patient-Derived Tumor Models with CpG Island Methylator Phenotype.

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    Claudia Maletzki

    Full Text Available Patient-individual tumor models constitute a powerful platform for basic and translational analyses both in vitro and in vivo. However, due to the labor-intensive and highly time-consuming process, only few well-characterized patient-derived cell lines and/or corresponding xenografts exist. In this study, we describe successful generation and functional analysis of novel tumor models from patients with sporadic primary colorectal carcinomas (CRC showing CpG island methylator phenotype (CIMP. Initial DNA fingerprint analysis confirmed identity with the patient in all four cases. These freshly established cells showed characteristic features associated with the CIMP-phenotype (HROC40: APCwt, TP53 mut, KRAS mut; 3/8 marker methylated; HROC43: APC mut, TP53 mut, KRAS mut; 4/8 marker methylated; HROC60: APCwt, TP53 mut, KRASwt; 4/8 marker methylated; HROC183: APC mut, TP53 mut, KRAS mut; 6/8 marker methylated. Cell lines were of epithelial origin (EpCAM+ with distinct morphology and growth kinetics. Response to chemotherapeutics was quite individual between cells, with stage I-derived cell line HROC60 being most susceptible towards standard clinically approved chemotherapeutics (e.g. 5-FU, Irinotecan. Of note, most cell lines were sensitive towards "non-classical" CRC standard drugs (sensitivity: Gemcitabin > Rapamycin > Nilotinib. This comprehensive analysis of tumor biology, genetic alterations and assessment of chemosensitivity towards a broad range of (chemo- therapeutics helps bringing forward the concept of personalized tumor therapy.

  12. Uncertainties in the cluster-cluster correlation function

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    Ling, E.N.; Barrow, J.D.; Frenk, C.S.

    1986-12-01

    The bootstrap resampling technique is applied to estimate sampling errors and significance levels of the two-point correlation functions determined for a subset of the CfA redshift survey of galaxies and a redshift sample of 104 Abell clusters. The angular correlation functions is also calculated for a sample of 1664 Abell clusters. The standard errors for the Abell data are found to be considerably larger than quoted 'Poisson errors'. The enhancement of cluster clustering over galaxy clustering is statistically significant in the presence of resampling errors.

  13. Lead exposure induces changes in 5-hydroxymethylcytosine clusters in CpG islands in human embryonic stem cells and umbilical cord blood.

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    Sen, Arko; Cingolani, Pablo; Senut, Marie-Claude; Land, Susan; Mercado-Garcia, Adriana; Tellez-Rojo, Martha M; Baccarelli, Andrea A; Wright, Robert O; Ruden, Douglas M

    2015-01-01

    Prenatal exposure to neurotoxicants such as lead (Pb) may cause stable changes in the DNA methylation (5mC) profile of the fetal genome. However, few studies have examined its effect on the DNA de-methylation pathway, specifically the dynamic changes of the 5-hydroxymethylcytosine (5hmC) profile. Therefore, in this study, we investigate the relationship between Pb exposure and 5mC and 5hmC modifications during early development. To study the changes in the 5hmC profile, we use a novel modification of the Infinium™ HumanMethylation450 assay (Illumina, Inc.), which we named HMeDIP-450K assay, in an in vitro human embryonic stem cell model of Pb exposure. We model Pb exposure-associated 5hmC changes as clusters of correlated, adjacent CpG sites, which are co-responding to Pb. We further extend our study to look at Pb-dependent changes in high density 5hmC regions in umbilical cord blood DNA from 48 mother-infant pairs from the Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) cohort. For our study, we randomly selected umbilical cord blood from 24 male and 24 female children from the 1st and 4th quartiles of Pb levels. Our data show that Pb-associated changes in the 5hmC and 5mC profiles can be divided into sex-dependent and sex-independent categories. Interestingly, differential 5mC sites are better markers of Pb-associated sex-dependent changes compared to differential 5hmC sites. In this study we identified several 5hmC and 5mC genomic loci, which we believe might have some potential as early biomarkers of prenatal Pb exposure.

  14. Distance function selection in several clustering algorithrms

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    LU Yu

    2004-01-01

    Most clustering algorithms need to describe the similarity of objects by a predefined distance function. Three distance functions which are widely used in two traditional clustering algorithms k-means and hierarchical clustering were investigated.Both theoretical analysis and detailed experimental results were given. It is shown that a distance function greatly affects clustering results and can be used to detect the outlier of a cluster by the comparison of such different results and give the shape information of clusters. In practice situation, it is suggested to use different distance function separately, compare the clustering results and pick out the "swing points". And such points may leak out more information for data analysts.

  15. Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands.

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    Bay, Daniyah H; Busch, Annika; Lisdat, Fred; Iida, Keisuke; Ikebukuro, Kazunori; Nagasawa, Kazuo; Karube, Isao; Yoshida, Wataru

    2017-06-27

    G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD spectroscopy and DMS footprinting analysis. In this study, the biological function of the 10 G-quadruplex-forming sequences in the transcriptional regulation has been analyzed using a reporter assay. When G-quadruplex-forming sequences from the Dele and Cdc6 genes have been cloned in reporter vectors carrying a minimal promoter and the luciferase gene, luciferase expression is activated. This has also been detected in experiments applying a promoterless reporter vector. Mutational analysis reveals that guanine bases, which form the G-tetrads, are important in the activation. In addition, the activation has been found to decrease by the telomestatin derivative L1H1-7OTD which can bind to the G-quadruplex DNA. When Dele and Cdc6 CpG islands, containing the G-quadruplex-forming sequence, have been cloned in the promoterless reporter vector, the luciferase expression is activated. Mutational analysis reveals that the expression level is decreased by mutation on Dele G-quadruplex; however, increased by mutation on Cdc6 G-quadruplex. Dele and Cdc6 G-quadruplex formation is significant in the transcriptional regulation. Dele and Cdc6 G-quadruplex DNA alone possess enhancer and promotor function. When studied in more complex CpG islands Dele G-quadruplex also demonstrates promotor activity, whereas Cdc6 G-quadruplex may possess a dual function of transcriptional regulation.

  16. Clustering aspects in nuclear structure functions

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    Hirai, M; Saito, K; Watanabe, T

    2010-01-01

    For understanding an anomalous nuclear effect experimentally observed for the beryllium-9 nucleus at the Thomas Jefferson National Accelerator Facility (JLab), 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 the AMD, the Be-9 nucleus consists of two alpha-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 Be-9 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 Be-9. It indicates that the anomalous Be-9 result should be explain...

  17. Clustered Protocadherins Are Required for Building Functional Neural Circuits

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    Takeshi Yagi

    2017-04-01

    Full Text Available Neuronal identity is generated by the cell-surface expression of clustered protocadherin (Pcdh isoforms. In mice, 58 isoforms from three gene clusters, Pcdhα, Pcdhβ, and Pcdhγ, are differentially expressed in neurons. Since cis-heteromeric Pcdh oligomers on the cell surface interact homophilically with that in other neurons in trans, it has been thought that the Pcdh isoform repertoire determines the binding specificity of synapses. We previously described the cooperative functions of isoforms from all three Pcdh gene clusters in neuronal survival and synapse formation in the spinal cord. However, the neuronal loss and the following neonatal lethality prevented an analysis of the postnatal development and characteristics of the clustered-Pcdh-null (Δαβγ neural circuits. Here, we used two methods, one to generate the chimeric mice that have transplanted Δαβγ neurons into mouse embryos, and the other to generate double mutant mice harboring null alleles of both the Pcdh gene and the proapoptotic gene Bax to prevent neuronal loss. First, our results showed that the surviving chimeric mice that had a high contribution of Δαβγ cells exhibited paralysis and died in the postnatal period. An analysis of neuronal survival in postnatally developing brain regions of chimeric mice clarified that many Δαβγ neurons in the forebrain were spared from apoptosis, unlike those in the reticular formation of the brainstem. Second, in Δαβγ/Bax null double mutants, the central pattern generator (CPG for locomotion failed to create a left-right alternating pattern even in the absence of neurodegeneraton. Third, calcium imaging of cultured hippocampal neurons showed that the network activity of Δαβγ neurons tended to be more synchronized and lost the variability in the number of simultaneously active neurons observed in the control network. Lastly, a comparative analysis for trans-homophilic interactions of the exogenously introduced single

  18. The IR Luminosity Functions of Rich Clusters

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    Bai, Lei; Rieke, Marcia J; Christlein, Daniel; Zabludoff, Ann I

    2008-01-01

    We present MIPS observations of the cluster A3266. About 100 spectroscopic cluster members have been detected at 24 micron. The IR luminosity function in A3266 is very similar to that in the Coma cluster down to the detection limit L_IR~10^43 ergs/s, suggesting a universal form of the bright end IR LF for local rich clusters with M~10^15 M_sun. The shape of the bright end of the A3266-Coma composite IR LF is not significantly different from that of nearby field galaxies, but the fraction of IR-bright galaxies (SFR > 0.2M_sun/yr) in both clusters increases with cluster-centric radius. The decrease of the blue galaxy fraction toward the high density cores only accounts for part of the trend; the fraction of red galaxies with moderate SFRs (0.2 < SFR < 1 M_sun/yr) also decreases with increasing galaxy density. These results suggest that for the IR bright galaxies, nearby rich clusters are distinguished from the field by a lower star-forming galaxy fraction, but not by a change in L*_IR. The composite IR LF...

  19. Cardiac mitochondria exhibit dynamic functional clustering

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    Felix Tobias Kurz

    2014-09-01

    Full Text Available Multi-oscillatory behavior of mitochondrial inner membrane potential ΔΨm in self-organized cardiac mitochondrial networks can be triggered by metabolic or oxidative stress. Spatio-temporal analyses of cardiac mitochondrial networks have shown that mitochondria are heterogeneously organized in synchronously oscillating clusters in which the mean cluster frequency and size are inversely correlated, thus suggesting a modulation of cluster frequency through local inter-mitochondrial coupling. In this study, we propose a method to examine the mitochondrial network's topology through quantification of its dynamic local clustering coefficients. Individual mitochondrial ΔΨm oscillation signals were identified for each cardiac myocyte and cross-correlated with all network mitochondria using previously described methods (Kurz et al., 2010. Time-varying inter-mitochondrial connectivity, defined for mitochondria in the whole network whose signals are at least 90% correlated at any given time point, allowed considering functional local clustering coefficients. It is shown that mitochondrial clustering in isolated cardiac myocytes changes dynamically and is significantly higher than for random mitochondrial networks that are constructed using the Erdös-Rényi model based on the same sets of vertices. The network's time-averaged clustering coefficient for cardiac myocytes was found to be 0.500 ± 0.051 (N=9 versus 0.061 ± 0.020 for random networks, respectively. Our results demonstrate that cardiac mitochondria constitute a network with dynamically connected constituents whose topological organization is prone to clustering. Cluster partitioning in networks of coupled oscillators has been observed in scale-free and chaotic systems and is therefore in good agreement with previous models of cardiac mitochondrial networks (Aon et al., 2008.

  20. Organosilane and Polyethylene Glycol Functionalized Magnetic Mesoporous Silica Nanoparticles as Carriers for CpG Immunotherapy In Vitro and In Vivo.

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    Hengrui Zheng

    Full Text Available Cytosine-guanine (CpG containing oligodeoxynucleotides (ODN have significant clinical potential as immunotherapeutics. However, limitations exist due to their transient biological stability in vivo, lack of specificity for target cells, and poor cellular uptake. To address these issues, we prepared amine magnetic mesoporous silica nanoparticles (M-MSN-A then further modified with polyethylene glycol (PEG for use as CpG delivery vectors. The PEG modified M-MSN-A (M-MSN-P had notable CpG ODN loading capacity, negligible cytotoxicity, and were easily internalized into cells where they released the loaded CpG into the cytoplasm. As a result, such complexes were effective in activating macrophages and inhibiting tumor cells when combined with chemotherapeutics in vitro. Furthermore, these complexes had excellent immuno-stimulating activity in vivo, compared to the free CpG therapeutics. We report here a highly effective MSNs-based delivery system with great potential as a therapeutic CpG formulation in cancer immunotherapy.

  1. Infrared Luminosity Function of the Coma Cluster

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    Bai, L; Rieke, M J; Hinz, J L; Kelly, D M; Blaylock, M; Bai, Lei; Rieke, George H.; Rieke, Marcia J.; Hinz, Joannah L.; Kelly, Douglas M.; Blaylock, Myra

    2006-01-01

    Using mid-IR and optical data, we deduce the total infrared (IR) luminosities of galaxies in the Coma cluster and present their infrared luminosity function (LF). The shape of the overall Coma IR LF does not show significant differences from the IR LFs of the general field, which indicates the general independence of global galaxy star formation on environment up to densities $\\sim$ 40 times greater than in the field (we cannot test such independence above $L_{ir} \\approx 10^{44} {\\rm ergs s}^{-1}$). However, a shallower faint end slope and a smaller $L_{ir}^{*}$ are found in the core region (where the densities are still higher) compared to the outskirt region of the cluster, and most of the brightest IR galaxies are found outside of the core region. The IR LF in the NGC 4839 group region does not show any unique characteristics. By integrating the IR LF, we find a total star formation rate in the cluster of about 97.0 $M_{\\sun}{\\rm yr}^{-1}$. We also studied the contributions of early- and late-type galaxie...

  2. CPG OLIGONUCLEOTIDES REGULATE OSTEOCLAST DIFFERENTIATION

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    Zhao Weigong; Han Xuezhe; Li Xinyou; Guo Xong; Liu Miao

    2005-01-01

    Objective Bacterial DNA is a pathogen-derived molecule which can regulate the innate immune system by stimulating NF-κB activation. The activity of bacterial DNA relies on its content of unmethylated CpG dinucleotides in particular base contexts("CpG motif"). In light of the pivotal role played by NF-κB in osteoclast differentiation, the ability of CpG oligodeoxynucleotides (CpG ODN) coming from bacterial DNA to modulate osteoclastogenesis was studied. Methods Bone marrow mononuclear cells (BMM) were purified from Balb/c mice, cultured in α-MEM media containing 10% FCS in the presence of mouse M-CSF, with either RANKL or ODNs for 5 days. Osteoclast formation was evaluated on day 5 according to TRAP and May-Grunwald-Giemsa staining. Results CpG ODN alone could induce osteoclast formation in the low degree in BMM culture. The relationship between CpG ODN and RANKL was that CpG ODN could inhibit RANKL-induced osteoclastogenesis when present from the beginning of BMM culture, but strongly increased RANKL-induced osteoclastogenesis in RANKL-pretreated BMMs. Conclusion The mechanism of CpG ODN regulating osteoclast differentiation was bidirectional, which might be a potential therapy for treating metabolic bone disease.

  3. Coordinating Clusters: A Cross Sectoral Study of Cluster Organization Functions in The Netherlands

    Directory of Open Access Journals (Sweden)

    Philipp J.P. Garbade

    2013-02-01

    Full Text Available The present paper aims at answering the question how cluster organization functions are implemented in a high‐tech, a medium to high‐tech and a low to medium‐tech cluster. Data were collected by semi‐structured interviews from three clusters in the Netherlands, an agri‐food cluster (as an example of a low to medium‐tech cluster, a green biotech cluster (medium to high‐tech and a high‐tech cluster. Concerning the cluster organization functions a number of similarities were found. For all three clusters it can be concluded that the network support function is considered to be very important. Sector independence can further be found concerning the innovation process support function, specifically regarding the promotion of the region as an attractive living and working area for highly qualified employees. The results also show anumber of clear differences among the investigated clusters. Only in the low‐to‐medium tech agri‐food cluster there was a clear need for internationalization support for SMEs to reach foreign markets. Only in the green biotech cluster the demand articulation was focused on the region where the cluster is based, which stands in contrast to the highly international orientation of the member companies. Only in the high‐tech innovation cluster technology road mapping was extensively used. This powerful tool, developed to align the innovation process at the company and sector level, impacted further on the execution of the demand articulation/ network formation support functions, and could also be helpful for the green biotech and the agri‐food clusters. Throughout the paper different cluster categorization schemes are besides the tech level are applied and give insights on their limitations and how to possibly deal with them in inter sectorial cluster comparison research.

  4. HOXB13, a Target of DNMT3B, Is Methylated at an Upstream CpG Island, and Functions as a Tumor Suppressor in Primary Colorectal Tumors

    OpenAIRE

    Kalpana Ghoshal; Tasneem Motiwala; Rainer Claus; Pearlly Yan; Huban Kutay; Jharna Datta; Sarmila Majumder; Shoumei Bai; Arnab Majumder; Tim Huang; Christoph Plass; Jacob, Samson T.

    2010-01-01

    BACKGROUND: A hallmark of cancer cells is hypermethylation of CpG islands (CGIs), which probably arises from upregulation of one or more DNA methyltransferases. The purpose of this study was to identify the targets of DNMT3B, an essential DNA methyltransferase in mammals, in colon cancer. METHODOLOGY/PRINCIPAL FINDINGS: Chromatin immunoprecipitation with DNMT3B specific antibody followed by CGI microarray identified genes with or without CGIs, repeat elements and genomic contigs in RKO cells....

  5. Demethylation of Cancer/Testis Antigens and CpG ODN Stimulation Enhance Dendritic Cell and Cytotoxic T Lymphocyte Function in a Mouse Mammary Model

    Directory of Open Access Journals (Sweden)

    Jun-Zhong Sun

    2013-01-01

    Full Text Available Background. Cancer/testis antigens (CTAs are ideal targets for cancer immunotherapy in virtue of their restricted expression profile in normal tissues. However, CTA-targeted immunotherapy has been rather disappointing clinical setting for CTAs are downregulated by cytosine-phosphate-guanosine (CpG methylation in their promoter regions, so that tumor cells have low immunogenicity. Methods. We reinduced mouse CTA P1A through demethylation process and generated P1A-specific cytotoxic lymphocytes (CTLs by immunizing BALB/c (H-2d mice with dendritic cells pulsed with a P1A-specific peptide and CpG oligodeoxynucleotide (ODN immune adjuvant. Results. We found that demethylation and CpG ODN immune adjuvant stimulation facilitated DC maturation and enhanced the allogenic capacity of P1A-specific CTLs against target cells both in vitro and in vivo. Conclusions. Our results suggested that CTA induction and immune adjuvant stimulation is a feasible strategy in cancer immunotherapy.

  6. Clustered functional MRI of overt speech production.

    Science.gov (United States)

    Sörös, Peter; Sokoloff, Lisa Guttman; Bose, Arpita; McIntosh, Anthony R; Graham, Simon J; Stuss, Donald T

    2006-08-01

    To investigate the neural network of overt speech production, event-related fMRI was performed in 9 young healthy adult volunteers. A clustered image acquisition technique was chosen to minimize speech-related movement artifacts. Functional images were acquired during the production of oral movements and of speech of increasing complexity (isolated vowel as well as monosyllabic and trisyllabic utterances). This imaging technique and behavioral task enabled depiction of the articulo-phonologic network of speech production from the supplementary motor area at the cranial end to the red nucleus at the caudal end. Speaking a single vowel and performing simple oral movements involved very similar activation of the cortical and subcortical motor systems. More complex, polysyllabic utterances were associated with additional activation in the bilateral cerebellum, reflecting increased demand on speech motor control, and additional activation in the bilateral temporal cortex, reflecting the stronger involvement of phonologic processing.

  7. The Mass Function of Nearby Galaxy Clusters

    CERN Document Server

    Biviano, A; Giuricin, G; Mardirossian, F; Mezzetti, M

    1993-01-01

    We present the distribution of virial masses for nearby galaxy clusters, as obtained from a data-set of 75 clusters, each having at least 20 galaxy members with measured redshifts within 1 Abell radius. After having accounted for problems of incompleteness of the data-set, we fitted a power-law to the cluster mass distribution.

  8. CONTROLLING THE FORMATION AND FUNCTIONING OF THE CLUSTER

    Directory of Open Access Journals (Sweden)

    A. S. Barzenkova

    2013-01-01

    Full Text Available The article presents the author's concept of the technique of controlling the formation and functioning of the cluster, which allows to objectively estimate the process of the formation of cluster, trace the dynamics of its life and assess the main areas and indi-cators cluster operation.

  9. CpG islands influence chromatin structure via the CpG-binding protein Cfp1.

    Science.gov (United States)

    Thomson, John P; Skene, Peter J; Selfridge, Jim; Clouaire, Thomas; Guy, Jacky; Webb, Shaun; Kerr, Alastair R W; Deaton, Aimée; Andrews, Rob; James, Keith D; Turner, Daniel J; Illingworth, Robert; Bird, Adrian

    2010-04-15

    CpG islands (CGIs) are prominent in the mammalian genome owing to their GC-rich base composition and high density of CpG dinucleotides. Most human gene promoters are embedded within CGIs that lack DNA methylation and coincide with sites of histone H3 lysine 4 trimethylation (H3K4me3), irrespective of transcriptional activity. In spite of these intriguing correlations, the functional significance of non-methylated CGI sequences with respect to chromatin structure and transcription is unknown. By performing a search for proteins that are common to all CGIs, here we show high enrichment for Cfp1, which selectively binds to non-methylated CpGs in vitro. Chromatin immunoprecipitation of a mono-allelically methylated CGI confirmed that Cfp1 specifically associates with non-methylated CpG sites in vivo. High throughput sequencing of Cfp1-bound chromatin identified a notable concordance with non-methylated CGIs and sites of H3K4me3 in the mouse brain. Levels of H3K4me3 at CGIs were markedly reduced in Cfp1-depleted cells, consistent with the finding that Cfp1 associates with the H3K4 methyltransferase Setd1 (refs 7, 8). To test whether non-methylated CpG-dense sequences are sufficient to establish domains of H3K4me3, we analysed artificial CpG clusters that were integrated into the mouse genome. Despite the absence of promoters, the insertions recruited Cfp1 and created new peaks of H3K4me3. The data indicate that a primary function of non-methylated CGIs is to genetically influence the local chromatin modification state by interaction with Cfp1 and perhaps other CpG-binding proteins.

  10. The Cluster Mass Function from Early SDSS Data: Cosmological Implications

    OpenAIRE

    Bahcall, Neta A.; Dong, Feng; Bode, Paul; Kim, Rita; Annis, James; Mckay, Timothy A.; Hansen, Sarah; Gunn, James; Ostriker, Jeremiah P.; Postman, Marc; Nichol, Robert C.; Goto, Tomotsugu; Brinkmann, Jon; Knapp, Gillian R.; Lamb, Don O.

    2002-01-01

    The mass function of clusters of galaxies is determined from 400 deg^2 of early commissioning imaging data of the Sloan Digital Sky Survey; ~300 clusters in the redshift range z = 0.1 - 0.2 are used. Clusters are selected using two independent selection methods: a Matched Filter and a red-sequence color magnitude technique. The two methods yield consistent results. The cluster mass function is compared with large-scale cosmological simulations. We find a best-fit cluster normalization relatio...

  11. Clustering and the Three-Point Function

    CERN Document Server

    Jiang, Yunfeng; Kostov, Ivan; Serban, Didina

    2016-01-01

    We develop analytical methods for computing the structure constant for three heavy operators, starting from the recently proposed hexagon approach. Such a structure constant is a semiclassical object, with the scale set by the inverse length of the operators playing the role of the Planck constant. We reformulate the hexagon expansion in terms of multiple contour integrals and recast it as a sum over clusters generated by the residues of the measure of integration. We test the method on two examples. First, we compute the asymptotic three-point function of heavy fields at any coupling and show the result in the semiclassical limit matches both the string theory computation at strong coupling and the tree-level results obtained before. Second, in the case of one non-BPS and two BPS operators at strong coupling we sum up all wrapping corrections associated with the opposite bridge to the non-trivial operator, or the "bottom" mirror channel. We also give an alternative interpretation of the results in terms of a...

  12. Nucleosome dynamics and maintenance of epigenetic states of CpG islands

    Science.gov (United States)

    Sneppen, Kim; Dodd, Ian B.

    2016-06-01

    Methylation of mammalian DNA occurs primarily at CG dinucleotides. These CpG sites are located nonrandomly in the genome, tending to occur within high density clusters of CpGs (islands) or within large regions of low CpG density. Cluster methylation tends to be bimodal, being dominantly unmethylated or mostly methylated. For CpG clusters near promoters, low methylation is associated with transcriptional activity, while high methylation is associated with gene silencing. Alternative CpG methylation states are thought to be stable and heritable, conferring localized epigenetic memory that allows transient signals to create long-lived gene expression states. Positive feedback where methylated CpG sites recruit enzymes that methylate nearby CpGs, can produce heritable bistability but does not easily explain that as clusters increase in size or density they change from being primarily methylated to primarily unmethylated. Here, we show that an interaction between the methylation state of a cluster and its occupancy by nucleosomes provides a mechanism to generate these features and explain genome wide systematics of CpG islands.

  13. The luminosity function of young star clusters: implications for the maximum mass and luminosity of clusters

    CERN Document Server

    Gieles, M; Bastian, N; Stein, I; Gieles, Mark; Larsen, Soeren; Bastian, Nate; Stein, Ilaan

    2005-01-01

    We introduce a method to relate a possible truncation of the star cluster mass function at the high mass end to the shape of the cluster luminosity function (LF). We compare the observed LFs of five galaxies containing young star clusters with synthetic cluster population models with varying initial conditions. The LF of the SMC, the LMC and NGC 5236 are characterized by a power-law behavior NdL~L^-a dL, with a mean exponent of = 2.0 +/- 0.2. This can be explained by a cluster population formeda with a constant cluster formation rate, in which the maximum cluster mass per logarithmic age bin is determined by the size-of-sample effect and therefore increases with log(age/yr). The LFs of NGC 6946 and M51 are better described by a double power-law distribution or a Schechter function. When a cluster population has a mass function that is truncated below the limit given by the size-of-sample effect, the total LF shows a bend at the magnitude of the maximum mass, with the age of the oldest cluster in the populati...

  14. Functional Clustering Algorithm for High-Dimensional Proteomics Data

    Directory of Open Access Journals (Sweden)

    Halima Bensmail

    2005-01-01

    Full Text Available Clustering proteomics data is a challenging problem for any traditional clustering algorithm. Usually, the number of samples is largely smaller than the number of protein peaks. The use of a clustering algorithm which does not take into consideration the number of features of variables (here the number of peaks is needed. An innovative hierarchical clustering algorithm may be a good approach. We propose here a new dissimilarity measure for the hierarchical clustering combined with a functional data analysis. We present a specific application of functional data analysis (FDA to a high-throughput proteomics study. The high performance of the proposed algorithm is compared to two popular dissimilarity measures in the clustering of normal and human T-cell leukemia virus type 1 (HTLV-1-infected patients samples.

  15. Technology evaluation: CpG-7909, Coley.

    Science.gov (United States)

    Paul, Stéphane

    2003-10-01

    Coley Pharmaceutical (formerly CpG ImmunoPharmaceuticals) is developing CpG-7909 (ProMune) for use in the potential treatment of cancer and as a vaccine adjuvant. By April 2000, CpG-7909 had entered phase I/II trials for cancer and in March 2002, Coley initiated a phase I trial in non-Hodgkin's lymphoma in combination with rituximab (Rituxan). By October 2002, CpG-7909 was in phase II trials as a vaccine adjuvant. Cpg-7909 is currently also undergoing phase II trials for melanoma.

  16. Modeling the mammalian locomotor CPG: insights from mistakes and perturbations.

    Science.gov (United States)

    McCrea, David A; Rybak, Ilya A

    2007-01-01

    A computational model of the mammalian spinal cord circuitry incorporating a two-level central pattern generator (CPG) with separate half-center rhythm generator (RG) and pattern formation (PF) networks is reviewed. The model consists of interacting populations of interneurons and motoneurons described in the Hodgkin-Huxley style. Locomotor rhythm generation is based on a combination of intrinsic (persistent sodium current dependent) properties of excitatory RG neurons and reciprocal inhibition between the two half-centers comprising the RG. The two-level architecture of the CPG was suggested from an analysis of deletions (spontaneous omissions of activity) and the effects of afferent stimulation on the locomotor pattern and rhythm observed during fictive locomotion in the cat. The RG controls the activity of the PF network that in turn defines the rhythmic pattern of motoneuron activity. The model produces realistic firing patterns of two antagonist motoneuron populations and generates locomotor oscillations encompassing the range of cycle periods and phase durations observed during cat locomotion. A number of features of the real CPG operation can be reproduced with separate RG and PF networks, which would be difficult if not impossible to demonstrate with a classical single-level CPG. The two-level architecture allows the CPG to maintain the phase of locomotor oscillations and cycle timing during deletions and during sensory stimulation. The model provides a basis for functional identification of spinal interneurons involved in generation and control of the locomotor pattern.

  17. A functional clustering algorithm for the analysis of neural relationships

    CERN Document Server

    Feldt, S; Hetrick, V L; Berke, J D; Zochowski, M

    2008-01-01

    We formulate a novel technique for the detection of functional clusters in neural data. In contrast to prior network clustering algorithms, our procedure progressively combines spike trains and derives the optimal clustering cutoff in a simple and intuitive manner. To demonstrate the power of this algorithm to detect changes in network dynamics and connectivity, we apply it to both simulated data and real neural data obtained from the mouse hippocampus during exploration and slow-wave sleep. We observe state-dependent clustering patterns consistent with known neurophysiological processes involved in memory consolidation.

  18. Nuclear clustering in the energy density functional approach

    Energy Technology Data Exchange (ETDEWEB)

    Ebran, J.-P., E-mail: jean-paul.ebran@cea.fr [CEA,DAM,DIF, F-91297 Arpajon (France); Khan, E. [Institut de Physique Nucléaire, Université Paris-Sud CEA, IN2P3 CNRS, F-91406 Orsay Cedex (France); Nikšić, T.; Vretenar, D. [Physics Department, Faculty of Science, University of Zagreb, 10000 Zagreb (Croatia)

    2015-10-15

    Nuclear Energy Density Functionals (EDFs) are a microscopic tool of choice extensively used over the whole chart to successfully describe the properties of atomic nuclei ensuing from their quantum liquid nature. In the last decade, they also have proved their ability to deal with the cluster phenomenon, shedding a new light on its fundamental understanding by treating on an equal footing both quantum liquid and cluster aspects of nuclei. Such a unified microscopic description based on nucleonic degrees of freedom enables to tackle the question pertaining to the origin of the cluster phenomenon and emphasizes intrinsic mechanisms leading to the emergence of clusters in nuclei.

  19. Star Cluster Luminosity Functions and Cluster Formation Efficiencies in LEGUS Dwarf Galaxies

    Science.gov (United States)

    Cook, David O.; Lee, Janice C.; Adamo, Angela; Kim, Hwiyun; Ryon, Jenna E.; LEGUS Team

    2017-01-01

    We present preliminary results of star cluster luminosity functions (LFs) and cluster formation efficiencies (Γ) in the LEGUS dwarf galaxy sub-sample. We have used a combination of automated and visual identification techniques to allow us to construct a more complete sample of clusters in these low-mass, low-SFR environments compared to previous studies of dwarf galaxies. Cluster properties are derived from fitting UV and optical (NUV-I) HST photometry to both deterministic and stochastic single-aged stellar populations models. We compare the cluster formation efficiencies and LF slopes to those of previous studies in both dwarf and massive spiral galaxy environments. Recent studies have found that both the LF slope and Γ form trends with galaxy environment. Our LF slope and Γ measurements in the LEGUS dwarfs will allow us to test these trends in the extreme, low-SFR regime and provide a better understanding of the star formation process.

  20. Gravitational Focusing and the Star Cluster Initial Mass Function

    Science.gov (United States)

    Kuznetsova, Aleksandra; Hartmann, Lee; Burkert, Andreas

    2017-02-01

    We discuss the possibility that gravitational focusing is responsible for the power-law mass function of star clusters N({log}M)\\propto {M}-1. This power law can be produced asymptotically when the mass accretion rate of an object depends upon the mass of the accreting body, as \\dot{M}\\propto {M}2. Although Bondi–Hoyle–Lyttleton accretion formally produces this dependence on mass in a uniform medium, realistic environments are much more complicated. However, numerical simulations in SPH that allow for sink formation yield such an asymptotic power-law mass function. We perform pure N-body simulations to isolate the effects of gravity from those of gas physics and to show that clusters naturally result with the power-law mass distribution. We also consider the physical conditions necessary to produce clusters on appropriate timescales. Our results help support the idea that gravitationally dominated accretion is the most likely mechanism for producing the cluster mass function.

  1. 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...... and a maximum likelihood analysis of the observed luminosity-redshift distribution fit with a model luminosity function. The negative evolution signal is more than 3 sigma regardless of the adopted local luminosity function or cosmological framework. Our results and those from several other surveys...

  2. High Frequency Cluster Radio Galaxies: Luminosity Functions and Implications for SZE Selected Cluster Samples

    Science.gov (United States)

    Gupta, N.; Saro, A.; Mohr, J. J.; Benson, B. A.; Bocquet, S.; Capasso, R.; Carlstrom, J. E.; Chiu, I.; Crawford, T. M.; de Haan, T.; Dietrich, J. P.; Gangkofner, C.; Holzapfel, W. L.; McDonald, M.; Rapetti, D.; Reichardt, C. L.

    2017-01-01

    We study the overdensity of point sources in the direction of X-ray-selected galaxy clusters from the Meta-Catalog of X-ray detected Clusters of galaxies (MCXC; = 0.14) at South Pole Telescope (SPT) and Sydney University Molonglo Sky Survey (SUMSS) frequencies. Flux densities at 95, 150 and 220 GHz are extracted from the 2500 deg2 SPT-SZ survey maps at the locations of SUMSS sources, producing a multi-frequency catalog of radio galaxies. In the direction of massive galaxy clusters, the radio galaxy flux densities at 95 and 150 GHz are biased low by the cluster Sunyaev-Zel'dovich Effect (SZE) signal, which is negative at these frequencies. We employ a cluster SZE model to remove the expected flux bias and then study these corrected source catalogs. We find that the high frequency radio galaxies are centrally concentrated within the clusters and that their luminosity functions (LFs) exhibit amplitudes that are characteristically an order of magnitude lower than the cluster LF at 843 MHz. We use the 150 GHz LF to estimate the impact of cluster radio galaxies on an SPT-SZ like survey. The radio galaxy flux typically produces a small bias on the SZE signal and has negligible impact on the observed scatter in the SZE mass-observable relation. If we assume there is no redshift evolution in the radio galaxy LF then 1.8 ± 0.7 percent of the clusters with detection significance ξ ≥ 4.5 would be lost from the sample. Allowing for redshift evolution of the form (1 + z)2.5 increases the incompleteness to 5.6 ± 1.0 percent. Improved constraints on the evolution of the cluster radio galaxy LF require a larger cluster sample extending to higher redshift.

  3. On the accuracy of the high redshift cluster luminosity function

    CERN Document Server

    Muñoz, Roberto P; Barrientos, Luis F

    2008-01-01

    We study the reliability of the statistical background subtraction method for computing the Ks-band luminosity function of cluster galaxies at z~1 using mock Red-sequence Cluster Survey cluster catalogues constructed from GALFORM semi-analytic galaxies. The underlying cluster luminosity function in the mocks are compatible with recent estimates at z~1 by several authors. We simulate different samples where the number of clusters with Ks-band photometry goes from 5 to a maximum of 50, in order to find the most suitable observational sample to carry out this study; the current observational status in the nIR wavelength range has been reached using 5 real clusters at z~1. We compute the composite luminosity function for several samples of galaxy clusters with masses 1.5x10^14 M_sun assuming a flux limited, complete sample of galaxies down to Ks=21.0 magnitudes. We find that the Schechter fit parameters Ks* and alpha for a sample of galaxies with no redshift information are rather poorly constrained if both param...

  4. Energetics of H$_2$ clusters from density functional and coupled cluster theories

    CERN Document Server

    Trail, J R; Needs, R J

    2016-01-01

    We use coupled-cluster quantum chemical methods to calculate the energetics of molecular clusters cut out of periodic molecular hydrogen structures that model observed phases of solid hydrogen. The hydrogen structures are obtained from Kohn-Sham density functional theory (DFT) calculations at pressures of 150, 250 and 350 GPa, which are within the pressure range in which phases II, III and IV are found to be stable. The calculated deviations in the DFT energies from the coupled-cluster data are reported for different functionals, and optimized functionals are generated which provide reduced errors. We give recommendations for semi-local and hybrid density functionals that are expected to accurately describe hydrogen at high pressures.

  5. Energetics of H2 clusters from density functional and coupled cluster theories

    Science.gov (United States)

    Trail, J. R.; López Ríos, P.; Needs, R. J.

    2017-03-01

    We use coupled-cluster quantum chemical methods to calculate the energetics of molecular clusters cut out of periodic molecular hydrogen structures that model observed phases of solid hydrogen. The hydrogen structures are obtained from Kohn-Sham density functional theory (DFT) calculations at pressures of 150, 250, and 350 GPa, which are within the pressure range in which phases II, III, and IV are found to be stable. The calculated deviations in the DFT energies from the coupled-cluster data are reported for different functionals, and optimized functionals are generated which provide reduced errors. We give recommendations for semilocal and hybrid density functionals that are expected to provide an accurate description of hydrogen at high pressures.

  6. The K-band luminosity functions of cluster galaxies

    CERN Document Server

    De Propris, R

    2016-01-01

    We derive the galaxy luminosity function in the $K_s$ band for galaxies in 24 clusters to provide a local reference for higher redshift studies and to analyse how and if the luminosity function varies according to environment and cluster properties. We use new, deep $K$ band imaging and match the photometry to available redshift information and to optical photometry from the SDSS or the UKST/POSS: $>80\\%$ of the galaxies to $K \\sim 14.5$ have measured redshifts. We derive composite luminosity functions, for the entire sample and for cluster subsamples . We consider the luminosity functions for red sequence and blue cloud galaxies. The full composite luminosity function has $K^*=12.79 \\pm 0.14$ ($M_K=-24.81$) and $\\alpha=-1.41 \\pm 0.10$. We find that $K^*$ is largely unaffected by the environment but that the slope $\\alpha$ increases towards lower mass clusters and clusters with Bautz-Morgan type $<$ II. The red sequence luminosity function seems to be approximately universal (within errors) in all environm...

  7. Toward the creation of stable, functionalized metal clusters.

    Science.gov (United States)

    Negishi, Yuichi; Kurashige, Wataru; Niihori, Yoshiki; Nobusada, Katsuyuki

    2013-11-21

    Nanomaterials which exhibit both stability and functionality are currently considered to hold the most promise as components of nanotechnology devices. Thiolate (RS)-protected gold nanoclusters (Aun(SR)m) have attracted significant attention in this regard and, among these, the magic clusters are believed to be the best candidates since they are the most stable. We have investigated the effects of heteroatom doping, protection by selenolate ligands and protection by photoresponsive thiolates on the stability and physical/chemical properties of these clusters. Through such studies, we have attempted to establish methods of modifying magic Aun(SR)m clusters as a means of creating metal clusters that are both robust and functional. This paper summarizes our studies towards this goal and the obtained results.

  8. Time dependent density functional calculation of plasmon response in clusters

    Institute of Scientific and Technical Information of China (English)

    Wang Feng(王锋); Zhang Feng-Shou(张丰收); Eric Suraud

    2003-01-01

    We have introduced a theoretical scheme for the efficient description of the optical response of a cluster based on the time-dependent density functional theory. The practical implementation is done by means of the fully fledged timedependent local density approximation scheme, which is solved directly in the time domain without any linearization.As an example we consider the simple Na2 cluster and compute its surface plasmon photoabsorption cross section, which is in good agreement with the experiments.

  9. The ACS Virgo Cluster Survey. XII. The Luminosity Function of Globular Clusters in Early Type Galaxies

    CERN Document Server

    Jordan, A; Côté, P; Ferrarese, L; Peng, E W; Mei, S; Villegas, D; Merritt, D; Tonry, J L; West, M J; Jordan, Andres; Laughlin, Dean E. Mc; Cote, Patrick; Ferrarese, Laura; Peng, Eric W.; Mei, Simona; Villegas, Daniela; Merritt, David; Tonry, John L.; West, Michael J.

    2007-01-01

    We analyze the luminosity function of the globular clusters (GCs) belonging to the early-type galaxies observed in the ACS Virgo Cluster Survey. We have obtained estimates for a Gaussian representation of the GC luminosity function (GCLF) for 89 galaxies. We have also fit the GCLFs with an "evolved Schechter function", which is meant to reflect the preferential depletion of low-mass GCs, primarily by evaporation due to two-body relaxation, from an initial Schechter mass function similar to that of young massive clusters. We find a significant trend of the GCLF dispersion with galaxy luminosity, in the sense that smaller galaxies have narrower GCLFs. We show that this narrowing of the GCLF in a Gaussian description is driven by a steepening of the GC mass function above the turnover mass, as one moves to smaller host galaxies. We argue that this behavior at the high-mass end of the GC mass function is most likely a consequence of systematic variations of the initial cluster mass function. The GCLF turnover mas...

  10. High Frequency Cluster Radio Galaxies: Luminosity Functions and Implications for SZE Selected Cluster Samples

    CERN Document Server

    Gupta, N; Mohr, J J; Benson, B A; Bocquet, S; Carlstrom, J E; Capasso, R; Chiu, I; Crawford, T M; de Haan, T; Dietrich, J P; Gangkofner, C; Holzapfel, W L; McDonald, M; Rapetti, D; Reichardt, C L

    2016-01-01

    We study the overdensity of point sources in the direction of X-ray-selected galaxy clusters from the Meta-Catalog of X-ray detected Clusters of galaxies (MCXC; $\\langle z \\rangle = 0.14$) at South Pole Telescope (SPT) and Sydney University Molonglo Sky Survey (SUMSS) frequencies. Flux densities at 95, 150 and 220 GHz are extracted from the 2500 deg$^2$ SPT-SZ survey maps at the locations of SUMSS sources, producing a multi-frequency catalog of radio galaxies. In the direction of massive galaxy clusters, the radio galaxy flux densities at 95 and 150 GHz are biased low by the cluster Sunyaev-Zel'dovich Effect (SZE) signal, which is negative at these frequencies. We employ a cluster SZE model to remove the expected flux bias and then study these corrected source catalogs. We find that the high frequency radio galaxies are centrally concentrated within the clusters and that their luminosity functions (LFs) exhibit amplitudes that are characteristically an order of magnitude lower than the cluster LF at 843 MHz. ...

  11. Cerebellar Functional Parcellation Using Sparse Dictionary Learning Clustering

    Directory of Open Access Journals (Sweden)

    Changqing eWang

    2016-05-01

    Full Text Available The human cerebellum has recently been discovered to contribute to cognition and emotion beyond the planning and execution of movement, suggesting its functional heterogeneity. We aimed to identify the functional parcellation of the cerebellum using information from resting-state functional magnetic resonance imaging (rs-fMRI. For this, we introduced a new data-driven decomposition-based functional parcellation algorithm, called Sparse Dictionary Learning Clustering (SDLC. SDLC integrates dictionary learning, sparse representation of rs-fMRI, and k-means clustering into one optimization problem. The dictionary is comprised of an over-complete set of time course signals, with which a sparse representation of rs-fMRI signals can be constructed. Cerebellar functional regions were then identified using k-means clustering based on the sparse representation of rs-fMRI signals. We solved SDLC using a multi-block hybrid proximal alternating method that guarantees strong convergence. We evaluated the reliability of SDLC and benchmarked its classification accuracy against other clustering techniques using simulated data. We then demonstrated that SDLC can identify biologically reasonable functional regions of the cerebellum as estimated by their cerebello-cortical functional connectivity. We further provided new insights into the cerebello-cortical functional organisation in children.

  12. Cerebellar Functional Parcellation Using Sparse Dictionary Learning Clustering.

    Science.gov (United States)

    Wang, Changqing; Kipping, Judy; Bao, Chenglong; Ji, Hui; Qiu, Anqi

    2016-01-01

    The human cerebellum has recently been discovered to contribute to cognition and emotion beyond the planning and execution of movement, suggesting its functional heterogeneity. We aimed to identify the functional parcellation of the cerebellum using information from resting-state functional magnetic resonance imaging (rs-fMRI). For this, we introduced a new data-driven decomposition-based functional parcellation algorithm, called Sparse Dictionary Learning Clustering (SDLC). SDLC integrates dictionary learning, sparse representation of rs-fMRI, and k-means clustering into one optimization problem. The dictionary is comprised of an over-complete set of time course signals, with which a sparse representation of rs-fMRI signals can be constructed. Cerebellar functional regions were then identified using k-means clustering based on the sparse representation of rs-fMRI signals. We solved SDLC using a multi-block hybrid proximal alternating method that guarantees strong convergence. We evaluated the reliability of SDLC and benchmarked its classification accuracy against other clustering techniques using simulated data. We then demonstrated that SDLC can identify biologically reasonable functional regions of the cerebellum as estimated by their cerebello-cortical functional connectivity. We further provided new insights into the cerebello-cortical functional organization in children.

  13. HOXB13, a target of DNMT3B, is methylated at an upstream CpG island, and functions as a tumor suppressor in primary colorectal tumors.

    Directory of Open Access Journals (Sweden)

    Kalpana Ghoshal

    Full Text Available BACKGROUND: A hallmark of cancer cells is hypermethylation of CpG islands (CGIs, which probably arises from upregulation of one or more DNA methyltransferases. The purpose of this study was to identify the targets of DNMT3B, an essential DNA methyltransferase in mammals, in colon cancer. METHODOLOGY/PRINCIPAL FINDINGS: Chromatin immunoprecipitation with DNMT3B specific antibody followed by CGI microarray identified genes with or without CGIs, repeat elements and genomic contigs in RKO cells. ChIP-Chop analysis showed that the majority of the target genes including P16, DCC, DISC1, SLIT1, CAVEOLIN1, GNA11, TBX5, TBX18, HOXB13 and some histone variants, that harbor CGI in their promoters, were methylated in multiple colon cancer cell lines but not in normal colon epithelial cells. Further, these genes were reactivated in RKO cells after treatment with 5-aza-2'-deoxycytidine, a DNA hypomethylating agent. COBRA showed that the CGIs encompassing the promoter and/or coding region of DCC, TBX5, TBX18, SLIT1 were methylated in primary colorectal tumors but not in matching normal colon tissues whereas GNA11 was methylated in both. MassARRAY analysis demonstrated that the CGI located approximately 4.5 kb upstream of HOXB13 +1 site was tumor-specifically hypermethylated in primary colorectal cancers and cancer cell lines. HOXB13 upstream CGI was partially hypomethylated in DNMT1(-/- HCT cells but was almost methylation free in cells lacking both DNMT1 and DNMT3B. Analysis of tumor suppressor properties of two aberrantly methylated transcription factors, HOXB13 and TBX18, revealed that both inhibited growth and clonogenic survival of colon cancer cells in vitro, but only HOXB13 abolished tumor growth in nude mice. CONCLUSIONS/SIGNIFICANCE: This is the first report that identifies several important tumor suppressors and transcription factors as direct DNMT3B targets in colon cancer and as potential biomarkers for this cancer. Further, this study shows that

  14. The K-band luminosity functions of cluster galaxies

    Science.gov (United States)

    De Propris, Roberto

    2017-03-01

    We derive the galaxy luminosity function in the Ks band for galaxies in 24 clusters to provide a local reference for higher redshift studies and to analyse how and if the luminosity function varies according to environment and cluster properties. We use new, deep K-band imaging and match the photometry to available redshift information and to optical photometry from the SDSS or the UKST/POSS: More than 80 per cent of the galaxies to K ∼ 14.5 have measured redshifts. We derive composite luminosity functions, for the entire sample and for cluster subsamples. We consider the luminosity functions for red-sequence and blue cloud galaxies. The full composite luminosity function has K* = 12.79 ± 0.14 (MK = -24.81) and α = -1.41 ± 0.10. We find that K* is largely unaffected by the environment, but that the slope α increases towards lower mass clusters and clusters with Bautz-Morgan type function seems to be approximately universal (within errors) in all environments: It has parameters K* = 13.16 ± 0.15 (MK = -24.44) and α = -1.00 ± 0.12 (for all galaxies). Blue galaxies do not show a good fit to a Schechter function, but the best values for its parameters are K* = 13.51 ± 0.41 (MK = -24.09) and α = -1.60 ± 0.29: We do not have enough statistics to consider environmental variations for these galaxies. We find some evidence that K* in clusters is brighter than in the field and α is steeper, but note that this comparison is based (for the field) on 2MASS photometry, while our data are considerably deeper.

  15. Density functional theory study of BnC clusters.

    Science.gov (United States)

    Liu, Chunhui; Han, Peilin; Tang, Mingsheng

    2011-05-15

    B(n)C clusters (n = 3-10) were studied at the density functional theory (DFT) (B3LYP)/6-311G** level of theory. The calculations predicted that the most stable configurations of the B(n) C clusters are the (n + 1)-membered cyclic structures. For boron-carbon clusters, the configurations containing greater numbers of three-membered boron rings are more favorable, except for the B(7)C and B(9)C clusters. Through molecular orbital analysis of these B(n)C clusters, we have concluded that π-electron delocalization plays a crucial role in the stability of n + 1-membered cyclic structures. In this paper, the relative stability of each cluster is discussed based on their single atomic-binding energies. The capability of clusters to obtain or lose an electron was also discussed, based on their vertical electron detachment energies (VDEs), adiabatic electron detachment energies (ADEs), vertical electron affinities (VEAs) and adiabatic electron affinities (AEAs). Copyright © 2011 John Wiley & Sons, Ltd.

  16. The Relation Between the Globular Cluster Mass and Luminosity Functions

    CERN Document Server

    Kruijssen, J M Diederik

    2009-01-01

    The relation between the globular cluster luminosity function (GCLF, dN/dlogL) and globular cluster mass function (GCMF, dN/dlogM) is considered. Due to low-mass star depletion, dissolving GCs have mass-to-light (M/L) ratios that are lower than expected from their metallicities. This has been shown to lead to an M/L ratio that increases with GC mass and luminosity. We model the GCLF and GCMF and show that the power law slopes inherently differ (1.0 versus 0.7, respectively) when accounting for the variability of M/L. The observed GCLF is found to be consistent with a Schechter-type initial cluster mass function and a mass-dependent mass-loss rate.

  17. Correlation Functions of the APM Clusters of Galaxies

    CERN Document Server

    Park, C; Park, Changbom; Lee, Sungho

    1998-01-01

    We have found that the two-point correlation function of the APM clusters of galaxies has an amplitude much higher than that claimed by the APM group. As the richness limit increases from R = 53 to 80, the correlation length increases from 17.5 to 28.9 h^{-1}Mpc. This indicates that the richness dependence of the APM cluster correlation function is also much stronger than what the APM group has reported. The richness dependence can be represented by a fitting formula r_0 = 0.53 d_c + 0.01, which is consistent with the Bahcall's formula r_0 = 0.4 d_c. We have tried to find the possible reason for discrepancies. However, our estimates for the APM cluster correlation function are found to be robust against variation of the method of calculation and of sample definition.

  18. Identification of a boron nitride nanosphere-binding peptide for the intracellular delivery of CpG oligodeoxynucleotides

    Science.gov (United States)

    Zhang, Huijie; Yamazaki, Tomohiko; Zhi, Chunyi; Hanagata, Nobutaka

    2012-09-01

    CpG oligonucleotides (CpG ODNs) interact with Toll-like receptor 9 (TLR9), which results in the induction of immunostimulatory cytokines. We delivered CpG ODNs intracellularly using boron nitride nanospheres (BNNS). To enhance the loading capacity of CpG ODNs on BNNS, we used a phage display technique to identify a 12-amino acid peptide designated as BP7, with specific affinity for BNNS, and used it as a linker to load CpG ODNs on BNNS. The tyrosine residue (Y) at the eighth position from the N-terminus played a crucial role in the affinity of BP7 to BNNS. BNNS that bound BP7 (BNNS-BP7) were taken up by cells and showed no cytotoxicity, and CpG ODNs were successfully crosslinked with BP7 to create BP7-CpG ODN conjugates. Using BP7 as a linker, the loading efficiency of CpG ODNs on BNNS increased 5-fold compared to the direct binding of CpG ODNs to BNNS. Furthermore, the BP7-CpG ODN conjugate-loaded BNNS had a greater capacity to induce interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) production from peripheral blood mononuclear cells (PBMCs) than that of CpG ODNs directly loaded on BNNS. The higher amount of cytokine induction by BP7-CpG ODN conjugate-loaded BNNS may be attributed to a higher loading capacity and stronger binding to BNNS of the linker BP7. The greater functionality of BP7-conjugated CpG ODNs on BNNS expands the potential of BNNS for drug delivery applications.CpG oligonucleotides (CpG ODNs) interact with Toll-like receptor 9 (TLR9), which results in the induction of immunostimulatory cytokines. We delivered CpG ODNs intracellularly using boron nitride nanospheres (BNNS). To enhance the loading capacity of CpG ODNs on BNNS, we used a phage display technique to identify a 12-amino acid peptide designated as BP7, with specific affinity for BNNS, and used it as a linker to load CpG ODNs on BNNS. The tyrosine residue (Y) at the eighth position from the N-terminus played a crucial role in the affinity of BP7 to BNNS. BNNS that bound BP7

  19. Functional clustering algorithm for the analysis of dynamic network data

    Science.gov (United States)

    Feldt, S.; Waddell, J.; Hetrick, V. L.; Berke, J. D.; Żochowski, M.

    2009-05-01

    We formulate a technique for the detection of functional clusters in discrete event data. The advantage of this algorithm is that no prior knowledge of the number of functional groups is needed, as our procedure progressively combines data traces and derives the optimal clustering cutoff in a simple and intuitive manner through the use of surrogate data sets. In order to demonstrate the power of this algorithm to detect changes in network dynamics and connectivity, we apply it to both simulated neural spike train data and real neural data obtained from the mouse hippocampus during exploration and slow-wave sleep. Using the simulated data, we show that our algorithm performs better than existing methods. In the experimental data, we observe state-dependent clustering patterns consistent with known neurophysiological processes involved in memory consolidation.

  20. Clustering and pasta phases in nuclear density functional theory

    CERN Document Server

    Schuetrumpf, Bastian; Nazarewicz, Witold

    2016-01-01

    Nuclear density functional theory (DFT) is the tool of choice in describing properties of complex nuclei and intricate phases of bulk nucleonic matter. It is a microscopic approach based on an energy density functional representing the nuclear interaction. An attractive feature of nuclear DFT is that it can be applied to both finite nuclei and pasta phases appearing in the inner crust of neutron stars. While nuclear pasta clusters in a neutron star can be easily characterized through their density distributions, the level of clustering of nucleons in a nucleus can often be difficult to assess. To this end, we use the concept of nucleonic localization. We demonstrate that the localization measure provides us with fingerprints of clusters in light and heavy nuclei, including fissioning systems. Furthermore we investigate the rod-like pasta phase using twist-averaged boundary conditions, which enable calculations in finite volumes accessible by state of the art DFT solvers.

  1. 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 gr

  2. Collaborations between CpG sites in DNA methylation

    Science.gov (United States)

    Song, You; Ren, Honglei; Lei, Jinzhi

    2017-08-01

    DNA methylation patterns have profound impacts on genome stability, gene expression and development. The molecular base of DNA methylation patterns has long been focused at single CpG sites level. Here, we construct a kinetic model of DNA methylation with collaborations between CpG sites, from which a correlation function was established based on experimental data. The function consists of three parts that suggest three possible sources of the correlation: movement of enzymes along DNA, collaboration between DNA methylation and nucleosome modification, and global enzyme concentrations within a cell. Moreover, the collaboration strength between DNA methylation and nucleosome modification is universal for mouse early embryo cells. The obtained correlation function provides insightful understanding for the mechanisms of inheritance of DNA methylation patterns.

  3. Select and Cluster: A Method for Finding Functional Networks of Clustered Voxels in fMRI

    Science.gov (United States)

    DonGiovanni, Danilo

    2016-01-01

    Extracting functional connectivity patterns among cortical regions in fMRI datasets is a challenge stimulating the development of effective data-driven or model based techniques. Here, we present a novel data-driven method for the extraction of significantly connected functional ROIs directly from the preprocessed fMRI data without relying on a priori knowledge of the expected activations. This method finds spatially compact groups of voxels which show a homogeneous pattern of significant connectivity with other regions in the brain. The method, called Select and Cluster (S&C), consists of two steps: first, a dimensionality reduction step based on a blind multiresolution pairwise correlation by which the subset of all cortical voxels with significant mutual correlation is selected and the second step in which the selected voxels are grouped into spatially compact and functionally homogeneous ROIs by means of a Support Vector Clustering (SVC) algorithm. The S&C method is described in detail. Its performance assessed on simulated and experimental fMRI data is compared to other methods commonly used in functional connectivity analyses, such as Independent Component Analysis (ICA) or clustering. S&C method simplifies the extraction of functional networks in fMRI by identifying automatically spatially compact groups of voxels (ROIs) involved in whole brain scale activation networks. PMID:27656202

  4. Cluster functions and scattering amplitudes for six and seven points

    Science.gov (United States)

    Harrington, Thomas; Spradlin, Marcus

    2017-07-01

    Scattering amplitudes in planar super-Yang-Mills theory satisfy several basic physical and mathematical constraints, including physical constraints on their branch cut structure and various empirically discovered connections to the mathematics of cluster algebras. The power of the bootstrap program for amplitudes is inversely proportional to the size of the intersection between these physical and mathematical constraints: ideally we would like a list of constraints which determine scattering amplitudes uniquely. We explore this intersection quantitatively for two-loop six- and seven-point amplitudes by providing a complete taxonomy of the Gr(4, 6) and Gr(4, 7) cluster polylogarithm functions of [15] at weight 4.

  5. On the Globular Cluster Initial Mass Function below 1 Msolar

    Science.gov (United States)

    Paresce, Francesco; De Marchi, Guido

    2000-05-01

    Accurate luminosity functions (LFs) for a dozen globular clusters have now been measured at or just beyond their half-light radius using HST. They span almost the entire cluster main sequence (MS) below 0.75 Msolar. All these clusters exhibit LFs that rise continuously from an absolute I magnitude MI~=6 to a peak at MI~=8.5-9 and then drop with increasing MI. Transformation of the LFs into mass functions (MFs) by means of mass-luminosity (ML) relations that are consistent with all presently available data on the physical properties of low-mass, low-metallicity stars shows that all the LFs observed so far can be obtained from MFs having the shape of a lognormal distribution with characteristic mass mc=0.33+/-0.03 Msolar and standard deviation σ=0.34+/-0.04. In particular, the LFs of the four clusters in the sample that extend well beyond the peak luminosity down to close to the hydrogen-burning limit (NGC 6341, NGC 6397, NGC 6752, and NGC 6809) can only be reproduced by such distributions and not by a single power law in the 0.1-0.6 Msolar range. After correction for the effects of mass segregation, the variation of the ratio of the number of higher to lower mass stars with cluster mass or any simple orbital parameter or the expected time to disruption recently computed for these clusters shows no statistically significant trend over a range of this last parameter of more than a factor of ~100. We conclude that the global MFs of these clusters have not been measurably modified by evaporation and tidal interactions with the Galaxy and, thus, should reflect the initial distribution of stellar masses. Since the lognormal function that we find is also very similar to the one obtained independently for much younger clusters and to the form expected theoretically, the implication seems to be unavoidable that it represents the true stellar initial mass function for this type of star in this mass range. Based on observations with the NASA/ESA Hubble Space Telescope

  6. The Observational Mass Function of Nearby Galaxy Clusters

    CERN Document Server

    Girardi, M; Giuricin, G; Mardirossian, F; Mezzetti, M

    1998-01-01

    We present a new determination of the mass function of galaxy clusters, based on optical virial mass estimates for a large sample of 152 nearby (z M_lim)=(6.3\\pm 1.2) 10^{-6} (h^{-1} Mpc)^{-3} for cluster masses estimated within a 1.5 h^{-1} Mpc radius. Our mass function is intermediate between the two previous estimates by Bahcall & Cen (1993) and by Biviano et al. (1993). Based on the Press--Schechter approach, we use this mass function to constrain the amplitude of the fluctuation power spectrum at the cluster scale. After suitably convolving the PS predictions with observational errors on cluster masses and COBE--normalizing the fluctuation power spectrum, we find sigma_8=(0.60\\pm 0.04) Omega_0^{-0.46+0.09Omega_0} for flat low--density models and \\sigma_8=(0.60\\pm 0.04) Omega_0^{-0.48+0.17Omega_0} for open models (at the 90% c.l.).

  7. The Luminosity Function of Low-Redshift Abell Galaxy Clusters

    CERN Document Server

    Barkhouse, Wayne A; López-Cruz, Omar

    2007-01-01

    We present the results from a survey of 57 low-redshift Abell galaxy clusters to study the radial dependence of the luminosity function (LF). The dynamical radius of each cluster, r200, was estimated from the photometric measurement of cluster richness, Bgc. The shape of the LFs are found to correlate with radius such that the faint-end slope, alpha, is generally steeper on the cluster outskirts. The sum of two Schechter functions provides a more adequate fit to the composite LFs than a single Schechter function. LFs based on the selection of red and blue galaxies are bimodal in appearance. The red LFs are generally flat for -22 -18. The blue LFs contain a larger contribution from faint galaxies than the red LFs. The blue LFs have a rising faint-end component (alpha ~ -1.7) for M_Rc > -21, with a weaker dependence on radius than the red LFs. The dispersion of M* was determined to be 0.31 mag, which is comparable to the median measurement uncertainty of 0.38 mag. This suggests that the bright-end of the LF is...

  8. Galaxy Luminosity Function of Dynamically Young Abell 119 Cluster: Probing the Cluster Assembly

    CERN Document Server

    Lee, Youngdae; Hilker, Michael; Sheen, Yun-Kyeong; Yi, Sukyoung K

    2016-01-01

    We present the galaxy luminosity function (LF) of the Abell 119 cluster down to $M_r\\sim-14$ mag based on deep images in the $u$-, $g$-, and $r$-bands taken by using MOSAIC II CCD mounted on the Blanco 4m telescope at the CTIO. The cluster membership was accurately determined based on the radial velocity information as well as on the color-magnitude relation for bright galaxies and the scaling relation for faint galaxies. The overall LF exhibits a bimodal behavior with a distinct dip at $r\\sim18.5$ mag ($M_r\\sim-17.8$ mag), which is more appropriately described by a two-component function. The shape of the LF strongly depends on the cluster-centric distance and on the local galaxy density. The LF of galaxies in the outer, low-density region exhibits a steeper slope and more prominent dip compared with that of counterparts in the inner, high-density region. We found evidence for a substructure in the projected galaxy distribution in which several overdense regions in the Abell 119 cluster appear to be closely ...

  9. Study of Magnesium Diboride Clusters Using Hybrid Density Functional Theory

    Directory of Open Access Journals (Sweden)

    D. Rodríguez

    2007-12-01

    Full Text Available Using hybrid density functional theory and a relatively large basis set, the lowest energy equilibrium structure, vibrational spectrum, and natural orbital analysis were obtained for magnesium diboride clusters [(MgB2x for x=1,2, and 3]. For comparison, boron clusters [Bx for x=2,4, and 6] were also considered. The MgB2 and (MgB22 showed equilibrium structures with the boron atoms in arrangements similar to what was obtained for pure boron atoms, whereas, for (MgB23 a different arrangement of boron was obtained. From the population analysis, large electron density in the boron atoms forming the clusters was observed.

  10. A Density Functional Study of Bare and Hydrogenated Platinum Clusters

    CERN Document Server

    Sebetci, A

    2006-01-01

    We perform density functional theory calculations using Gaussian atomic-orbital methods within the generalized gradient approximation for the exchange and correlation to study the interactions in the bare and hydrogenated platinum clusters. The minimum-energy structures, binding energies, relative stabilities, vibrational frequencies and the highest occupied and lowest unoccupied molecular-orbital gaps of Pt_nH_m (n=1-5, m=0-2) clusters are calculated and compared with previously studied pure platinum and hydrogenated platinum clusters. We investigate any magic behavior in hydrogenated platinum clusters and find that Pt_4H_2 is more stable than its neighboring sizes. Our results do not agree with a previous conclusion that 3D geometries of Pt tetramer and pentamer are unfavored. On the contrary, the lowest energy structure of Pt_4 is found to be a distorted tetrahedron and that of Pt_5 is found to be a bridge site capped tetrahedron which is a new global minimum for Pt_5 cluster. The successive addition of H ...

  11. Clustering of protein domains for functional and evolutionary studies

    Directory of Open Access Journals (Sweden)

    Long Paul F

    2009-10-01

    Full Text Available Abstract Background The number of protein family members defined by DNA sequencing is usually much larger than those characterised experimentally. This paper describes a method to divide protein families into subtypes purely on sequence criteria. Comparison with experimental data allows an independent test of the quality of the clustering. Results An evolutionary split statistic is calculated for each column in a protein multiple sequence alignment; the statistic has a larger value when a column is better described by an evolutionary model that assumes clustering around two or more amino acids rather than a single amino acid. The user selects columns (typically the top ranked columns to construct a motif. The motif is used to divide the family into subtypes using a stochastic optimization procedure related to the deterministic annealing EM algorithm (DAEM, which yields a specificity score showing how well each family member is assigned to a subtype. The clustering obtained is not strongly dependent on the number of amino acids chosen for the motif. The robustness of this method was demonstrated using six well characterized protein families: nucleotidyl cyclase, protein kinase, dehydrogenase, two polyketide synthase domains and small heat shock proteins. Phylogenetic trees did not allow accurate clustering for three of the six families. Conclusion The method clustered the families into functional subtypes with an accuracy of 90 to 100%. False assignments usually had a low specificity score.

  12. Dose-effect relationship of CpG oligodeoxyribonucleotide 1826 in murine Lewis lung cancer treated with irradiation

    Directory of Open Access Journals (Sweden)

    Zhuang XB

    2013-05-01

    Full Text Available Xibing Zhuang,1 Tiankui Qiao,1 Sujuan Yuan,1 Wei Chen,1 Lin Zha,2 Li Yan11Department of Oncology, Jinshan Hospital, Medical Center of Fudan University, Shanghai, People's Republic of China; 2Department of Oncology, Tongling People's Hospital, Tongling, Anhui, People's Republic of ChinaBackground: Cytosine-phosphate-guanine (CpG oligodeoxyribonucleotides (ODNs, which induce signaling via Toll-like receptor 9, have recently been suggested to enhance sensitivity to traditional therapies, including chemotherapy, in certain cancer cell lines. This study aimed to define the dose-effect relationship for CpG ODN 1826 in increasing radiosensitivity and its impact on immune function in a mouse model of Lewis lung cancer.Methods: The tumor-bearing mouse model was induced by injecting Lewis lung cancer cells into the right anterior leg subcutaneously. Sixty-four C57BL/6 J mice were evenly randomized into eight groups, comprising: a control group; an irradiation group; a CpG ODN 0.15 group; a CpG ODN 0.3 group; a CpG ODN 0.45 group; a CpG 0.15 + irradiation group; a CpG 0.3 + irradiation group; and a CpG 0.45 + irradiation group. Tumor growth, serum tumor necrosis factor-alpha and interleukin-12 concentrations, spleen and thymus exponents, and effect of CpG on the secondary immune response were measured, and apoptosis of tumor cells was investigated using TdT-mediated dUTP nick end labeling (TUNEL after treatment.Results: Tumor volumes in the treated groups were smaller than in the control group, with those of the CpG 0.45 + irradiation group being the smallest. TUNEL showed that the apoptosis rate in all the active treatment groups was higher than in the control group. CpG ODN apoptosis rate, serum tumor necrosis factor-alpha and interleukin-12 levels, and the spleen and thymus exponent showed greater improvement in the groups receiving combination therapy of CpG ODN and irradiation than the control group or the group receiving irradiation alone. With the

  13. Distinguishing Functional DNA Words; A Method for Measuring Clustering Levels

    Science.gov (United States)

    Moghaddasi, Hanieh; Khalifeh, Khosrow; Darooneh, Amir Hossein

    2017-01-01

    Functional DNA sub-sequences and genome elements are spatially clustered through the genome just as keywords in literary texts. Therefore, some of the methods for ranking words in texts can also be used to compare different DNA sub-sequences. In analogy with the literary texts, here we claim that the distribution of distances between the successive sub-sequences (words) is q-exponential which is the distribution function in non-extensive statistical mechanics. Thus the q-parameter can be used as a measure of words clustering levels. Here, we analyzed the distribution of distances between consecutive occurrences of 16 possible dinucleotides in human chromosomes to obtain their corresponding q-parameters. We found that CG as a biologically important two-letter word concerning its methylation, has the highest clustering level. This finding shows the predicting ability of the method in biology. We also proposed that chromosome 18 with the largest value of q-parameter for promoters of genes is more sensitive to dietary and lifestyle. We extended our study to compare the genome of some selected organisms and concluded that the clustering level of CGs increases in higher evolutionary organisms compared to lower ones. PMID:28128320

  14. Distinguishing Functional DNA Words; A Method for Measuring Clustering Levels

    Science.gov (United States)

    Moghaddasi, Hanieh; Khalifeh, Khosrow; Darooneh, Amir Hossein

    2017-01-01

    Functional DNA sub-sequences and genome elements are spatially clustered through the genome just as keywords in literary texts. Therefore, some of the methods for ranking words in texts can also be used to compare different DNA sub-sequences. In analogy with the literary texts, here we claim that the distribution of distances between the successive sub-sequences (words) is q-exponential which is the distribution function in non-extensive statistical mechanics. Thus the q-parameter can be used as a measure of words clustering levels. Here, we analyzed the distribution of distances between consecutive occurrences of 16 possible dinucleotides in human chromosomes to obtain their corresponding q-parameters. We found that CG as a biologically important two-letter word concerning its methylation, has the highest clustering level. This finding shows the predicting ability of the method in biology. We also proposed that chromosome 18 with the largest value of q-parameter for promoters of genes is more sensitive to dietary and lifestyle. We extended our study to compare the genome of some selected organisms and concluded that the clustering level of CGs increases in higher evolutionary organisms compared to lower ones.

  15. The evolution of the stellar mass function in star clusters

    CERN Document Server

    Kruijssen, J M Diederik

    2009-01-01

    (Abridged) The dynamical ejection of stars from star clusters affects the shape of the stellar mass function (MF) in these clusters, because the escape probability of a star depends on its mass. The objective of this paper is to provide and to apply a simple physical model for the evolution of the MF in star clusters for a large range of the parameter space. The model is derived from the basic principles of two-body encounters and energy considerations. It is independent of the adopted mass loss rate or initial mass function (IMF), and contains stellar evolution, stellar remnant retention, dynamical dissolution in a tidal field, and mass segregation. It is found that the MF evolution in star clusters depends on the disruption time, remnant retention fraction, initial-final stellar mass relation, and IMF. Low-mass stars are preferentially ejected after t~400 Myr. Before that time, masses around 15-20% of the maximum stellar mass are lost. The degree of low-mass star depletion grows for increasing disruption ti...

  16. Luminosity Function of the Cluster of Galaxies Abell 566

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    We investigate the Luminosity Function (LF) of the cluster of galaxies Abell 566. The photometric data of 15 intermediate-bands are obtained from the Beijing- Arizona-Taiwan-Connecticut (BATC) photometric sky survey. For each of the 15 wavebands, the LF of cluster galaxies is well modelled by the Schechter function, with characteristic luminosities from -18.0 to -21.9 magnitude, from the a- to the p-band. Morphological dependence of the LF is investigated by separating the cluster members into 'red' and 'blue' subsamples. It is clear that late type galaxies have a steeper shape of LF than the early type galaxies. We also divided the sample galaxies by their local environment. It was found that galaxies in the sparser region have steeper shape of LF than galaxies in the denser region. Combining the results of morphological and environmental dependence of LFs, we show that Abell 566 is a well relaxed cluster with positive evidence of galaxy interaction and merger, and excess number of bright early type galaxies located in its denser region.

  17. Globular Cluster Systems in Brightest Cluster Galaxies: A Near-Universal Luminosity Function?

    CERN Document Server

    Harris, William E; Gnedin, Oleg Y; O'Halloran, Heather; Blakeslee, John P; Whitmore, Bradley C; Cote, Patrick; Geisler, Douglas; Peng, Eric W; Bailin, Jeremy; Rothberg, Barry; Cockcroft, Robert; DeGraaff, Regina Barber

    2014-01-01

    We present the first results from our HST Brightest Cluster Galaxy (BCG) survey of seven central supergiant cluster galaxies and their globular cluster (GC) systems. We measure a total of 48000 GCs in all seven galaxies, representing the largest single GC database. We find that a log-normal shape accurately matches the observed luminosity function (LF) of the GCs down to the GCLF turnover point, which is near our photometric limit. In addition, the LF has a virtually identical shape in all seven galaxies. Our data underscore the similarity in the formation mechanism of massive star clusters in diverse galactic environments. At the highest luminosities (log L > 10^7 L_Sun) we find small numbers of "superluminous" objects in five of the galaxies; their luminosity and color ranges are at least partly consistent with those of UCDs (Ultra-Compact Dwarfs). Lastly, we find preliminary evidence that in the outer halo (R > 20 kpc), the LF turnover point shows a weak dependence on projected distance, scaling as L_0 ~ R...

  18. Formulation of vaccines containing CpG oligonucleotides and alum

    OpenAIRE

    Aebig, Joan A.; Mullen, Gregory E. D.; Dobrescu, Gelu; Rausch, Kelly; Lambert, Lynn; Ajose-Popoola, Olubunmi; Long, Carole A.; Saul, Allan; Miles, Aaron P.

    2007-01-01

    CpG oligodeoxynucleotides are potent immunostimulants. For parenterally delivered alum based vaccines, the immunostimulatory effect of CpG depends on the association of the CpG and antigen to the alum. We describe effects of buffer components on the binding of CPG 7909 to aluminum hydroxide (Alhydrogel), assays for measuring binding of CPG 7909 to alum and CPG 7909 induced dissociation of antigen from the alum. Free CPG 7909 is a potent inducer of IP-10 in mice. However the lack of IP-10 prod...

  19. Formulation of vaccines containing CpG oligonucleotides and alum.

    Science.gov (United States)

    Aebig, Joan A; Mullen, Gregory E D; Dobrescu, Gelu; Rausch, Kelly; Lambert, Lynn; Ajose-Popoola, Olubunmi; Long, Carole A; Saul, Allan; Miles, Aaron P

    2007-06-30

    CpG oligodeoxynucleotides are potent immunostimulants. For parenterally delivered alum-based vaccines, the immunostimulatory effect of CpG depends on the association of the CpG and antigen to the alum. We describe effects of buffer components on the binding of CPG 7909 to aluminum hydroxide (Alhydrogel), assays for measuring binding of CPG 7909 to alum and CPG 7909 induced dissociation of antigen from the alum. Free CPG 7909 is a potent inducer of IP-10 in mice. However the lack of IP-10 production from formulations containing bound CPG 7909 suggested that CPG 7909 does not rapidly dissociate from the alum after injection. It also suggests that IP-10 assays are not a good basis for potency assays for alum-based vaccines containing CPG 7909.

  20. CpG demethylation enhances alpha-synuclein expression and affects the pathogenesis of Parkinson's disease.

    Directory of Open Access Journals (Sweden)

    Lumine Matsumoto

    Full Text Available BACKGROUND: Alpha-synuclein (SNCA gene expression is an important factor in the pathogenesis of Parkinson's disease (PD. Gene multiplication can cause inherited PD, and promoter polymorphisms that increase SNCA expression are associated with sporadic PD. CpG methylation in the promoter region may also influence SNCA expression. METHODOLOGY/PRINCIPAL FINDINGS: By using cultured cells, we identified a region of the SNCA CpG island in which the methylation status altered along with increased SNCA expression. Postmortem brain analysis revealed regional non-specific methylation differences in this CpG region in the anterior cingulate and putamen among controls and PD; however, in the substantia nigra of PD, methylation was significantly decreased. CONCLUSIONS/SIGNIFICANCE: This CpG region may function as an intronic regulatory element for SNCA gene. Our findings suggest that a novel epigenetic regulatory mechanism controlling SNCA expression influences PD pathogenesis.

  1. Density Functional Studies of Methanol Decomposition on Subnanometer Pd Clusters

    Energy Technology Data Exchange (ETDEWEB)

    Mehmood, Faisal; Greeley, Jeffrey P.; Curtiss, Larry A.

    2009-12-31

    A density functional theory study of the decomposition of methanol on subnanometer palladium clusters (primarily Pd4) is presented. Methanol dehydrogenation through C-H bond breaking to form hydroxymethyl (CH2OH) as the initial step, followed by steps involving formation of hydroxymethylene (CHOH), formyl (CHO), and carbon monoxide (CO), is found to be the most favorable reaction pathway. A competing dehydrogenation pathway with O-H bond breaking as the first step, followed by formation of methoxy (CH3O) and formaldehyde (CH2O), is slightly less favorable. In contrast, pathways involving C-O bond cleavage are much less energetically favorable, and no feasible pathways involving C-O bond formation to yield dimethyl ether (CH3OCH3) are found. Comparisons of the results are made with methanol decomposition products adsorbed on more extended Pd surfaces; all reaction intermediates are found to bind slightly more strongly to the clusters than to the surfaces.

  2. Cluster Functions and Scattering Amplitudes for Six and Seven Points

    CERN Document Server

    Harrington, Thomas

    2015-01-01

    Scattering amplitudes in planar super-Yang-Mills theory satisfy several basic physical and mathematical constraints, including physical constraints on their branch cut structure and various empirically discovered connections to the mathematics of cluster algebras. The power of the bootstrap program for amplitudes is inversely proportional to the size of the intersection between these physical and mathematical constraints: ideally we would like a list of constraints which determine scattering amplitudes uniquely. We explore this intersection quantitatively for two-loop six- and seven-point amplitudes by providing a complete taxonomy of the Gr(4,6) and Gr(4,7) cluster polylogarithm functions of arXiv:1401.6446 at weight 4.

  3. Abnormal brain functional connectivity of the hypothalamus in cluster headaches.

    Directory of Open Access Journals (Sweden)

    Enchao Qiu

    Full Text Available The aim of this study was to detect the abnormality of the brain functional connectivity of the hypothalamus during acute spontaneous cluster headache (CH attacks ('in attack' and headache-free intervals ('out of attack' using resting-state functional magnetic resonance imaging (RS-fMRI technique. The RS-fMRI data from twelve male CH patients during 'in attack' and 'out of attack' periods and twelve age- and sex-matched normal controls were analyzed by the region-of-interest -based functional connectivity method using SPM5 software. Abnormal brain functional connectivity of the hypothalamus is present in CH, which is located mainly in the pain system during the spontaneous CH attacks. It extends beyond the pain system during CH attack intervals.

  4. Environmental effects on the Coma cluster luminosity function

    CERN Document Server

    Lobo, C; Durret, F; Gerbal, D; Lefèvre, O; Mazure, A; Slezak, E

    1996-01-01

    Using our catalogue of V_{26.5} isophotal magnitudes for 6756 galaxies in a region covering 60~\\times~25~arcmin^2 in the center of the Coma cluster, plus 267 galaxies in a region of 9.7~\\times~9.4~arcmin^2 around NGC~4839, we derive the luminosity function in the magnitude range 13.5\\leq V_{26.5} < 21.0 (corresponding to the absolute magnitude range -22.24 < M_{V26.5} \\leq -14.74). The luminosity function for this region is well fitted by the combination of a gaussian in its bright part and of a steep Schechter function (of index \\alpha =-1.8) in its faint part. Luminosity functions derived for individual regions surrounding the brightest galaxies show less steep slopes, strongly suggesting the existence of environmental effects. The implications of such effects and galaxy formation scenarios are discussed.

  5. Structure-function clustering in multiplex brain networks

    Science.gov (United States)

    Crofts, J. J.; Forrester, M.; O'Dea, R. D.

    2016-10-01

    A key question in neuroscience is to understand how a rich functional repertoire of brain activity arises within relatively static networks of structurally connected neural populations: elucidating the subtle interactions between evoked “functional connectivity” and the underlying “structural connectivity” has the potential to address this. These structural-functional networks (and neural networks more generally) are more naturally described using a multilayer or multiplex network approach, in favour of standard single-layer network analyses that are more typically applied to such systems. In this letter, we address such issues by exploring important structure-function relations in the Macaque cortical network by modelling it as a duplex network that comprises an anatomical layer, describing the known (macro-scale) network topology of the Macaque monkey, and a functional layer derived from simulated neural activity. We investigate and characterize correlations between structural and functional layers, as system parameters controlling simulated neural activity are varied, by employing recently described multiplex network measures. Moreover, we propose a novel measure of multiplex structure-function clustering which allows us to investigate the emergence of functional connections that are distinct from the underlying cortical structure, and to highlight the dependence of multiplex structure on the neural dynamical regime.

  6. Regulation of DNA transposition by CpG methylation and chromatin structure in human cells.

    Science.gov (United States)

    Jursch, Tobias; Miskey, Csaba; Izsvák, Zsuzsanna; Ivics, Zoltán

    2013-05-15

    The activity of transposable elements can be regulated by different means. DNA CpG methylation is known to decrease or inhibit transpositional activity of diverse transposons. However, very surprisingly, it was previously shown that CpG methylation of the Sleeping Beauty (SB) transposon significantly enhanced transposition in mouse embryonic stem cells. In order to investigate the unexpected response of SB transposition to CpG methylation, related transposons from the Tc1/mariner superfamily, that is, Tc1, Himar1, Hsmar1, Frog Prince (FP) and Minos were tested to see how transposition was affected by CpG methylation. A significant increase of >20-fold in transposition of SB, FP and Minos was seen, whereas Tc1, Himar1 and Hsmar1 showed no difference in transposition upon CpG-methylation. The terminal inverted repeats (TIRs) of the SB, FP and Minos elements share a common structure, in which each TIR contains two functionally important binding sites for the transposase (termed the IR/DR structure). The group of IR/DR elements showed increased excision after CpG methylation compared to untreated transposon donor plasmids. We found that de novo CpG methylation is not required for transposition. A mutated FP donor plasmid with depleted CpG sites in both TIRs was as efficient in transposition as the wild-type transposon, indicating that CpG sites inside the TIRs are not responsible for altered binding of factors potentially modulating transposition. By using an in vivo one-hybrid DNA-binding assay in cultured human cells we found that CpG methylation had no appreciable effect on the affinity of SB transposase to its binding sites. However, chromatin immunoprecipitation indicated that CpG-methylated transposon donor plasmids are associated with a condensed chromatin structure characterized by trimethylated histone H3K9. Finally, DNA compaction by protamine was found to enhance SB transposition. We have shown that DNA CpG methylation upregulates transposition of IR

  7. 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

  8. Tissue specific DNA methylation of CpG islands in normal human adult somatic tissues distinguishes neural from non-neural tissues.

    Science.gov (United States)

    Ghosh, Srimoyee; Yates, Allan J; Frühwald, Michael C; Miecznikowski, Jeffrey C; Plass, Christoph; Smiraglia, Dominic

    2010-08-16

    Although most CpG islands are generally thought to remain unmethylated in all adult somatic tissues, recent genome-wide approaches have found that some CpG islands have distinct methylation patterns in various tissues, with most differences being seen between germ cells and somatic tissues. Few studies have addressed this among human somatic tissues and fewer still have studied the same sets of tissues from multiple individuals. In the current study, we used Restriction Landmark Genomic Scanning to study tissue specific methylation patterns in a set of twelve human tissues collected from multiple individuals. We identified 34 differentially methylated CpG islands among these tissues, many of which showed consistent patterns in multiple individuals. Of particular interest were striking differences in CpG island methylation, not only among brain regions, but also between white and grey matter of the same region. These findings were confirmed for selected loci by quantitative bisulfite sequencing. Cluster analysis of the RLGS data indicated that several tissues clustered together, but the strongest clustering was in brain. Tissues from different brain regions clustered together, and, as a group, brain tissues were distinct from either mesoderm or endoderm derived tissues which demonstrated limited clustering. These data demonstrate consistent tissue specific methylation for certain CpG islands, with clear differences between white and grey matter of the brain. Furthermore, there was an overall pattern of tissue specifically methylated CpG islands that distinguished neural tissues from non-neural.

  9. Density functional studies of methanol decomposition on subnanometer Pd clusters.

    Energy Technology Data Exchange (ETDEWEB)

    Mehmood, F.; Greeley, J.; Curtiss, L. A.

    2009-12-31

    A density functional theory study of the decomposition of methanol on subnanometer palladium clusters (primarily Pd{sub 4}) is presented. Methanol dehydrogenation through C-H bond breaking to form hydroxymethyl (CH{sub 2}OH) as the initial step, followed by steps involving formation of hydroxymethylene (CHOH), formyl (CHO), and carbon monoxide (CO), is found to be the most favorable reaction pathway. A competing dehydrogenation pathway with O-H bond breaking as the first step, followed by formation of methoxy (CH{sub 3}O) and formaldehyde (CH{sub 2}O), is slightly less favorable. In contrast, pathways involving C-O bond cleavage are much less energetically favorable, and no feasible pathways involving C-O bond formation to yield dimethyl ether (CH{sub 3}OCH{sub 3}) are found. Comparisons of the results are made with methanol decomposition products adsorbed on more extended Pd surfaces; all reaction intermediates are found to bind slightly more strongly to the clusters than to the surfaces.

  10. Cluster density functional theory for lattice models based on the theory of Möbius functions

    Science.gov (United States)

    Lafuente, Luis; Cuesta, José A.

    2005-08-01

    Rosenfeld's fundamental-measure theory for lattice models is given a rigorous formulation in terms of the theory of Möbius functions of partially ordered sets. The free-energy density functional is expressed as an expansion in a finite set of lattice clusters. This set is endowed with a partial order, so that the coefficients of the cluster expansion are connected to its Möbius function. Because of this, it is rigorously proven that a unique such expansion exists for any lattice model. The low-density analysis of the free-energy functional motivates a redefinition of the basic clusters (zero-dimensional cavities) which guarantees a correct zero-density limit of the pair and triplet direct correlation functions. This new definition extends Rosenfeld's theory to lattice models with any kind of short-range interaction (repulsive or attractive, hard or soft, one or multicomponent ...). Finally, a proof is given that these functionals have a consistent dimensional reduction, i.e. the functional for dimension d' can be obtained from that for dimension d (d' < d) if the latter is evaluated at a density profile confined to a d'-dimensional subset.

  11. Cluster density functional theory for lattice models based on the theory of Moebius functions

    Energy Technology Data Exchange (ETDEWEB)

    Lafuente, Luis; Cuesta, Jose A [Grupo Interdisciplinar de Sistemas Complejos (GISC), Departamento de Matematicas, Universidad Carlos III de Madrid, 28911 Leganes, Madrid (Spain)

    2005-08-26

    Rosenfeld's fundamental-measure theory for lattice models is given a rigorous formulation in terms of the theory of Moebius functions of partially ordered sets. The free-energy density functional is expressed as an expansion in a finite set of lattice clusters. This set is endowed with a partial order, so that the coefficients of the cluster expansion are connected to its Moebius function. Because of this, it is rigorously proven that a unique such expansion exists for any lattice model. The low-density analysis of the free-energy functional motivates a redefinition of the basic clusters (zero-dimensional cavities) which guarantees a correct zero-density limit of the pair and triplet direct correlation functions. This new definition extends Rosenfeld's theory to lattice models with any kind of short-range interaction (repulsive or attractive, hard or soft, one or multicomponent ...). Finally, a proof is given that these functionals have a consistent dimensional reduction, i.e. the functional for dimension d' can be obtained from that for dimension d (d' < d) if the latter is evaluated at a density profile confined to a d'-dimensional subset.

  12. Deep VLT search for globular clusters in NGC 5128 color-magnitude diagrams and globular cluster luminosity function

    CERN Document Server

    Rejkuba, M

    2001-01-01

    At the distance of NGC 5128 (3.6 \\pm 0.2 Mpc) it is possible to resolve globular clusters with high resolution imaging from the ground, thus allowing the globular cluster candidate selection primarily through their morphological properties. I report the discovery of 71 globular clusters in NGC 5128 on VLT UT1+FORS1 images, including the faintest members (Mv ~ -5) known to date in this galaxy as well as 5 previously known clusters. U- and V-band photometry has been measured for all the candidates and the luminosity function, spanning -10.1cluster luminosity functions in an elliptical galaxy determined so far. The Kolmogorov-Smirnov statistics show that the difference between the globular cluster luminosity functions of NGC 5128 and the MW is not larger than the difference between the ones of M31 and the MW. The (U-V)o color histogram shows a bimodal distribution. For 23 globular clusters I obtained K-band images with SOFI at the...

  13. Structures and energetics of neutral and ionic silicon-germanium clusters: density functional theory and coupled cluster studies.

    Science.gov (United States)

    Wang, Yi-Siang; Chao, Sheng D

    2011-03-10

    We have calculated the structural and energetic properties of neutral and ionic (singly charged anionic and cationic) semiconductor binary silicon-germanium clusters Si(m)Ge(n) for s = m + n ≤ 12 using the density functional theory (DFT-B3LYP) and coupled cluster [CCSD(T)] methods with Pople's 6-311++G(3df, 3pd) basis set. Neutral and anionic clusters share similar ground state structures for s = 3-7, independent of the stoichiometry and atom locations, but start to deviate at s = 8. The relative energetic stability of the calculated ground state structures among possible isomers has been analyzed through a bond strength propensity model where the pair interactions of Si-Si, Si-Ge, and Ge-Ge are competing. Electron affinities, ionization potentials, energy gaps between the highest and lowest occupied molecular orbitals (HOMO-LUMO gaps), and cluster mixing energies were calculated and analyzed. Overall, for a fixed s, the vertical ionization potential increases as the number of silicon atoms m increases, while the vertical electron affinity shows a dip at m = 2. As s increases, the ionization potentials increase from s = 2 to s = 3 and then decrease slowly to s = 8. The mixing energies for neutral and ionic clusters are all negative, indicating that the binary clusters are more stable than pure elemental clusters. Except for s = 4 and 8, cationic clusters are more stable than anionic ones and, thus, are more likely to be observed in experiments.

  14. CpG ODN 免疫佐剂效应研究进展%Progress on Immunoadjuvant Effect of CpG ODN

    Institute of Scientific and Technical Information of China (English)

    董鹏; 程世鹏; 李真光; 杨洺扬; 胡桂学; 冷雪

    2015-01-01

    Synthetic oligodeoxynucleotides containing CpG motifs (CpG ODN)could combine with Toll-like receptor 9 (TLR-9)on endoplasmic reticulum from dendritic cells,B cells,monocytes and macrophages to mount an immune response characterized by the production of Th1 and proinflammatory cytokines,as an immune enhancer to resistance to pathogen invasion and antitumor in the hosts.In recent years,CpG ODN as a new immune adjuvant has received more attention.This article mainly introduced the research progress on the kinds of CpG ODN and its structure and function characteristics,mechanisms of action,immune en-hancement livestock and poultry in to strengthen and safety for CpG ODN as vaccine adjuvants to offer ref-erence to further research and its veterinary usage in clinic.%人工合成的含非甲基化 CpG 基序的寡聚脱氧核苷酸(CpG ODN)能够与树突状细胞、B 细胞、单核细胞及巨噬细胞等免疫细胞内质网膜上的 Toll 样受体9(TLR-9)结合,通过产生 Th1型免疫反应和分泌促炎因子来增强免疫应答的强度,在机体抵抗病原入侵和抗肿瘤等方面起到免疫增强剂的作用。近年来, CpG ODN 作为一种新型免疫佐剂受到了人们越来越多的关注。论文主要介绍了 CpG ODN 的种类及其结构和功能特征、作用机制、对畜禽的免疫增强作用、安全性等方面的研究进展,为 CpG ODN 作为疫苗佐剂的进一步研究和在兽医临床上的应用提供参考。

  15. Cluster-cluster clustering

    Science.gov (United States)

    Barnes, J.; Dekel, A.; Efstathiou, G.; Frenk, C. S.

    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.

  16. Cluster-cluster clustering

    Energy Technology Data Exchange (ETDEWEB)

    Barnes, J.; Dekel, A.; Efstathiou, G.; Frenk, C.S.

    1985-08-01

    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.

  17. 17beta-estradiol enhances the response of plasmacytoid dendritic cell to CpG.

    Directory of Open Access Journals (Sweden)

    Xiaoxi Li

    Full Text Available Gender differences in immune capabilities suggest that sex hormones such as estrogens were involved in the regulation of the immunocompetence. Numerous studies also suggest that plasmacytoid dendritic cells (PDCs play a pathogenic role in SLE. However, it is unclear whether estrogen can modulate the function of PDCs to influence the development of SLE. In the present study, PDCs from murine spleens were treated with 17beta-estradiol (E2 and CpG respectively or both in vitro, then cell viability, costimulatory molecule expression, cytokine secretion of PDCs, as well as stimulatory capacity of PDCs to B cells were analyzed. Results showed that E2 and CpG increased the cell viability and costimulatory molecule expression on PDCs synergistically. Moreover, the intracellular and extracellular secretion of IFN-alpha was increased by E2 or E2 plus CpG. In addition, E2 and CpG also increased the stimulatory capacity of PDCs to B cells, and the viability of B cells was decreased after neutralizing IFN-alpha significantly. In the experiments in vivo, mice received daily s.c. injections of E2 and CpG respectively or both, then we found that the plasma concentration of IgM were elevated by E2 and CpG synergistically and the expression of IFN-alpha/beta in spleens were noticeably increased by CpG plus E2 compared with the treatment of E2 or CpG only. This study indicates that E2 could exacerbate PDCs' activation with CpG, which further activates B cells to upregulate susceptibility to autoantigens. IFN-alpha plays an important role in the stimulatory effect of PDCs on B cells. E2 stimulation of IFN-alpha production may result in female prevalence in autoimmune diseases such as SLE through activation of PDCs. This study provides novel evidence of relationship between estrogen and SLE and also sheds light on gender biases among SLE patients.

  18. Association of the CpG methylation pattern of the proximal insulin gene promoter with type 1 diabetes.

    Science.gov (United States)

    Fradin, Delphine; Le Fur, Sophie; Mille, Clémence; Naoui, Nadia; Groves, Chris; Zelenika, Diana; McCarthy, Mark I; Lathrop, Mark; Bougnères, Pierre

    2012-01-01

    The insulin (INS) region is the second most important locus associated with Type 1 Diabetes (T1D). The study of the DNA methylation pattern of the 7 CpGs proximal to the TSS in the INS gene promoter revealed that T1D patients have a lower level of methylation of CpG -19, -135 and -234 (p = 2.10(-16)) and a higher methylation of CpG -180 than controls, while methylation was comparable for CpG -69, -102, -206. The magnitude of the hypomethylation relative to a control population was 8-15% of the corresponding levels in controls and was correlated in CpGs -19 and -135 (r = 0.77) and CpG -135 and -234 (r = 0.65). 70/485 (14%) of T1D patients had a simultaneous decrease in methylation of CpG -19, -135, -234 versus none in 317 controls. CpG methylation did not correlate with glycated hemoglobin or with T1D duration. The methylation of CpG -69, -102, -180, -206, but not CpG -19, -135, -234 was strongly influenced by the cis-genotype at rs689, a SNP known to show a strong association with T1D. We hypothesize that part of this genetic association could in fact be mediated at the statistical and functional level by the underlying changes in neighboring CpG methylation. Our observation of a CpG-specific, locus-specific methylation pattern, although it can provide an epigenetic biomarker of a multifactorial disease, does not indicate whether the reported epigenetic pattern preexists or follows the establishment of T1D. To explore the effect of chronic hyperglycemia on CpG methylation, we studied non obese patients with type 2 diabetes (T2D) who were found to have decreased CpG-19 methylation versus age-matched controls, similar to T1D (p = 2.10(-6)) but increased CpG-234 methylation (p = 5.10(-8)), the opposite of T1D. The causality and natural history of the different epigenetic changes associated with T1D or T2D remain to be determined.

  19. Association of the CpG methylation pattern of the proximal insulin gene promoter with type 1 diabetes.

    Directory of Open Access Journals (Sweden)

    Delphine Fradin

    Full Text Available The insulin (INS region is the second most important locus associated with Type 1 Diabetes (T1D. The study of the DNA methylation pattern of the 7 CpGs proximal to the TSS in the INS gene promoter revealed that T1D patients have a lower level of methylation of CpG -19, -135 and -234 (p = 2.10(-16 and a higher methylation of CpG -180 than controls, while methylation was comparable for CpG -69, -102, -206. The magnitude of the hypomethylation relative to a control population was 8-15% of the corresponding levels in controls and was correlated in CpGs -19 and -135 (r = 0.77 and CpG -135 and -234 (r = 0.65. 70/485 (14% of T1D patients had a simultaneous decrease in methylation of CpG -19, -135, -234 versus none in 317 controls. CpG methylation did not correlate with glycated hemoglobin or with T1D duration. The methylation of CpG -69, -102, -180, -206, but not CpG -19, -135, -234 was strongly influenced by the cis-genotype at rs689, a SNP known to show a strong association with T1D. We hypothesize that part of this genetic association could in fact be mediated at the statistical and functional level by the underlying changes in neighboring CpG methylation. Our observation of a CpG-specific, locus-specific methylation pattern, although it can provide an epigenetic biomarker of a multifactorial disease, does not indicate whether the reported epigenetic pattern preexists or follows the establishment of T1D. To explore the effect of chronic hyperglycemia on CpG methylation, we studied non obese patients with type 2 diabetes (T2D who were found to have decreased CpG-19 methylation versus age-matched controls, similar to T1D (p = 2.10(-6 but increased CpG-234 methylation (p = 5.10(-8, the opposite of T1D. The causality and natural history of the different epigenetic changes associated with T1D or T2D remain to be determined.

  20. Back to the Future: Estimating Initial Globular Cluster Masses from their Present Day Stellar Mass Functions

    CERN Document Server

    Webb, Jeremy J

    2015-01-01

    We use N-body simulations to model the 12 Gyr evolution of a suite of star clusters with identical initial stellar mass functions over a range of initial cluster masses, sizes, and orbits. Our models reproduce the distribution of present-day global stellar mass functions that is observed in the Milky Way globular cluster population. We find that the slope of a star cluster's stellar mass function is strongly correlated with the fraction of mass that the cluster has lost, independent of the cluster's initial mass, and nearly independent of its orbit and initial size. Thus, the mass function - initial mass relation can be used to determine a Galactic cluster's initial total stellar mass, if the initial stellar mass function is known. We apply the mass function - initial mass relation presented here to determine the initial stellar masses of 33 Galactic globular clusters, assuming an universal Kroupa initial mass function. Our study suggests that globular clusters had initial masses that were on average a factor...

  1. The Extended Zel'dovich Mass Functions of Clusters and Isolated Clusters in the Presence of Primordial Non-Gaussianity

    Science.gov (United States)

    Lim, Seunghwan; Lee, Jounghun

    2014-09-01

    We present new formulae for the mass functions of the clusters and the isolated clusters with non-Gaussian initial conditions. For this study, we adopt the extended Zel'dovich (EZL) model as a basic framework, focusing on the case of primordial non-Gaussianity of the local type whose degree is quantified by a single parameter, f nl. By making a quantitative comparison with the N-body results, we first demonstrate that the EZL formula with the constant values of three fitting parameters still works remarkably well for the local f nl case. We also modify the EZL formula to find an analytic expression for the mass function of isolated clusters, which turns out to have only one fitting parameter other than the overall normalization factor and showed that the modified EZL formula with a constant value of the fitting parameter matches excellently the N-body results with various values of f nl at various redshifts. Given the simplicity of the generalized EZL formulae and their good agreements with the numerical results, we finally conclude that the EZL mass functions of the massive clusters and isolated clusters should be useful as an analytic guideline to constrain the scale dependence of the primordial non-Gaussianity of the local type.

  2. Detection of Functional Change Using Cluster Trend Analysis in Glaucoma.

    Science.gov (United States)

    Gardiner, Stuart K; Mansberger, Steven L; Demirel, Shaban

    2017-05-01

    Global analyses using mean deviation (MD) assess visual field progression, but can miss localized changes. Pointwise analyses are more sensitive to localized progression, but more variable so require confirmation. This study assessed whether cluster trend analysis, averaging information across subsets of locations, could improve progression detection. A total of 133 test-retest eyes were tested 7 to 10 times. Rates of change and P values were calculated for possible re-orderings of these series to generate global analysis ("MD worsening faster than x dB/y with P cluster analyses ("n locations [or clusters] worsening faster than x dB/y with P cluster analysis criterion, and 4.1 years (95% CI, 4.0-4.5) for the best pointwise criterion. However, for pointwise analysis, only 38% of these changes were confirmed, compared with 61% for clusters and 76% for MD. The time until 25% of eyes showed subsequently confirmed deterioration was 6.3 years (95% CI, 6.0-7.2) for global, 6.3 years (95% CI, 6.0-7.0) for pointwise, and 6.0 years (95% CI, 5.3-6.6) for cluster analyses. Although the specificity is still suboptimal, cluster trend analysis detects subsequently confirmed deterioration sooner than either global or pointwise analyses.

  3. Structural and electronic properties of small silver-sulfur clusters: A density functional study

    Science.gov (United States)

    Li, Yan-Fang; Li, Yang; Li, Ying; Tan, Jia-Jin; Li, Hui-Li

    2016-10-01

    Density functional theory calculations have been performed to systematically investigate the structural and electronic properties of neutral and anionic AgnSm (2≤n+m≤6) clusters. The results show that the ground-state structures of neutral clusters are different from those of anionic clusters. Theoretical electron detachment energies (both vertical and adiabatic) are compared with the experimental measurements to verify the ground states of silver-sulfur clusters obtained in the present study. For both neutral and anionic systems, the highest occupied-lowest unoccupied molecular orbital energy gaps exhibit an odd-even oscillation as a function of the cluster size. In addition, the natural population analysis reveals that the charges transfer from Ag atoms to S atoms in AgnSm clusters, and the extra electron of AgnSm- clusters is mainly localized on the 3p subshells of S atoms.

  4. Functional impairments as symptoms in the symptom cluster analysis of patients newly diagnosed with advanced cancer.

    Science.gov (United States)

    Fodeh, Samah J; Lazenby, Mark; Bai, Mei; Ercolano, Elizabeth; Murphy, Terrence; McCorkle, Ruth

    2013-10-01

    Symptoms and subsequent functional impairment have been associated with the biological processes of disease, including the interaction between disease and treatment in a measurement model of symptoms. However, hitherto cluster analysis has primarily focused on symptoms. This study among patients within 100 days of diagnosis with advanced cancer explored whether self-reported physical symptoms and functional impairments formed clusters at the time of diagnosis. We applied cluster analysis to self-reported symptoms and activities of daily living of 111 patients newly diagnosed with advanced gastrointestinal (GI), gynecological, head and neck, and lung cancers. Based on content expert evaluations, the best techniques and variables were identified, yielding the best solution. The best cluster solution used a K-means algorithm and cosine similarity and yielded five clusters of physical as well as emotional symptoms and functional impairments. Cancer site formed the predominant organizing principle of composition for each cluster. The top five symptoms and functional impairments in each cluster were Cluster 1 (GI): outlook, insomnia, appearance, concentration, and eating/feeding; Cluster 2 (GI): appetite, bowel, insomnia, eating/feeding, and appearance; Cluster 3 (gynecological): nausea, insomnia, eating/feeding, concentration, and pain; Cluster 4 (head and neck): dressing, eating/feeding, bathing, toileting, and walking; and Cluster 5 (lung): cough, walking, eating/feeding, breathing, and insomnia. Functional impairments in patients newly diagnosed with late-stage cancers behave as symptoms during the diagnostic phase. Health care providers need to expand their assessments to include both symptoms and functional impairments. Early recognition of functional changes may accelerate diagnosis at an earlier cancer stage. Copyright © 2013 U.S. Cancer Pain Relief Committee. Published by Elsevier Inc. All rights reserved.

  5. Synaptic clusters function as odor operators in the olfactory bulb

    OpenAIRE

    Migliore, Michele; Cavarretta, Francesco; Marasco, Addolorata; Tulumello, Eleonora; Michael L Hines; Shepherd, Gordon M.

    2015-01-01

    How the olfactory bulb organizes and processes odor inputs through fundamental operations of its microcircuits is still controversial. To reveal these operations we hypothesize that one of the key mechanisms underlying odor coding is the interaction among spatially restricted and well-defined clusters of potentiated mitral–granule cell synapses. These experimentally observed clusters selectively gate the propagation of neuronal activity within the olfactory bulb and extensively contribute to ...

  6. Homogeneous clusters over India using probability density function of daily rainfall

    Science.gov (United States)

    Kulkarni, Ashwini

    2017-07-01

    The Indian landmass has been divided into homogeneous clusters by applying the cluster analysis to the probability density function of a century-long time series of daily summer monsoon (June through September) rainfall at 357 grids over India, each of approximately 100 km × 100 km. The analysis gives five clusters over Indian landmass; only cluster 5 happened to be the contiguous region and all other clusters are dispersed away which confirms the erratic behavior of daily rainfall over India. The area averaged seasonal rainfall over cluster 5 has a very strong relationship with Indian summer monsoon rainfall; also, the rainfall variability over this region is modulated by the most important mode of climate system, i.e., El Nino Southern Oscillation (ENSO). This cluster could be considered as the representative of the entire Indian landmass to examine monsoon variability. The two-sample Kolmogorov-Smirnov test supports that the cumulative distribution functions of daily rainfall over cluster 5 and India as a whole do not differ significantly. The clustering algorithm is also applied to two time epochs 1901-1975 and 1976-2010 to examine the possible changes in clusters in a recent warming period. The clusters are drastically different in two time periods. They are more dispersed in recent period implying the more erroneous distribution of daily rainfall in recent period.

  7. The Extended Zel'dovich Mass Functions of Clusters and Isolated Clusters in the Presence of Primordial Non-Gaussianity

    OpenAIRE

    Lim, Seunghwan; Lee, Jounghun

    2014-01-01

    We present new formulae for the mass functions of the clusters and the isolated clusters with non Gaussian initial conditions. For this study, we adopt the Extended Zel'dovich (EZL) model as a basic framework, focusing on the case of primordial non-Gaussianity of the local type whose degree is quantified by a single parameter $f_{nl}$. By making a quantitative comparison with the N-body results, we first demonstrate that the EZL formula with the constant values of three fitting parameters sti...

  8. Functional differences between Streptococcus pyogenes cluster 1 and cluster 2b streptokinases are determined by their β-domains.

    Science.gov (United States)

    Zhang, Yueling; Liang, Zhong; Glinton, Kristofor; Ploplis, Victoria A; Castellino, Francis J

    2013-05-02

    Cluster 1 streptokinases (SK1) from Streptococcus pyogenes (GAS) show substantially higher human plasminogen (hPg) activation activities and tighter hPg binding affinities than cluster 2b streptokinases (SK2b) in solution. The extent to which the different domains of SK are responsible for these differences is unknown. We exchanged each of the three known SK domains (α, β, and γ) between SK1 and SK2b and assessed the function of the resulting variants. Our results show that primary structural differences in the β-domains dictate these functional differences. This first report on the primary structure-functional relationship between naturally occurring SK1 and SK2b sheds new light on the mechanism of hPg activation by SK, a critical virulence determinant in this species of human pathogenic bacteria.

  9. Pseudopotential Density-Functional Calculations for Structures of Small Carbon Clusters CN (N = 2~8)

    Institute of Scientific and Technical Information of China (English)

    BAI Yu-Lin; CHEN Xiang-Rong; YANG Xiang-Dong; LU Peng-Fei

    2004-01-01

    We introduce a first-principles density-functional theory, i.e. the finite-difference pseudopotential densityfunctional theory in real space and the Langevin molecular dynamics annealing technique, to the descriptions of structures and some properties of small carbon clusters (CN, N = 2 ~ 8). It is shown that the odd-numbered clusters have linear structures and most of the even-numbered clusters prefer cyclic structures.

  10. Aberrant development and plasticity of excitatory visual cortical networks in the absence of cpg15.

    Science.gov (United States)

    Picard, Nathalie; Leslie, Jennifer H; Trowbridge, Sara K; Subramanian, Jaichandar; Nedivi, Elly; Fagiolini, Michela

    2014-03-05

    During development, experience plays a crucial role in sculpting neuronal connections. Patterned neural activity guides formation of functional neural circuits through the selective stabilization of some synapses and the pruning of others. Activity-regulated factors are fundamental to this process, but their roles in synapse stabilization and maturation is still poorly understood. CPG15, encoded by the activity-regulated gene candidate plasticity gene 15, is a small, glycosylphosphatidylinositol (GPI)-linked, extracellular protein that promotes synapse stabilization. Here we show that global knock-out of cpg15 results in abnormal postnatal development of the excitatory network in visual cortex and an associated disruption in development of visual receptive field properties. In addition, whereas repeated stimulation induced potentiation and depression in wild-type mice, the depression was slower in cpg15 knock-out mice, suggesting impairment in short-term depression-like mechanisms. These findings establish the requirement for cpg15 in activity-dependent development of the visual system and demonstrate the importance of timely excitatory network development for normal visual function.

  11. A computational investigation of boron-doped chromium and chromium clusters by density functional theory

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The geometries,stabilities and electronic properties of Crn and CrnB(n=2-9) clusters have been systematically investigated by density functional theory.The results suggest that the lowest energy structures for CrnB clusters can be obtained by substituting one Cr atom in Crn+1 clusters with B atom.The geometries of CrnB clusters are similar to that of Crn+1 clusters except for local structural distortion.The second-order difference and fragmentation energy show Cr4,Cr6,Cr8,Cr3B,Cr5B and Cr8B cluster are the most stable among these studied clusters.The impurity B increases the stabilities of chromium cluster.When B is doped on the Crn clusters,cluster geometry does dominate positive role in enhancing their stability.The doped B atom does not change the coupling way of the Cr site in Crn clusters,but breaks the symmetry and the Cr atoms are no longer equivalent.The doped B atom increases the total magnetic moments of Crn in most cases.

  12. 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. PMID:24906136

  13. 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.

  14. Optimized Architecture-centric Function Points’ Clustering and Aggregating About Service Flow

    Directory of Open Access Journals (Sweden)

    Xiaona Xia

    2013-05-01

    Full Text Available This study puts forward the “Cluster” concept about service function points. For the uniform of timely information’s capturing, logical optimization and requirement implementation, service topology’s relationship is adaptively formed. Tracking architecture goal and building distributed clustering logic timely, “Cluster head” and “Cluster node” are serialized and optimal architecture-centric “Cluster group” is formed, it is to achieve the balance service adjustment of service topology network driven by goal.

  15. Functional Analysis of the Fusarielin Biosynthetic Gene Cluster

    Directory of Open Access Journals (Sweden)

    Aida Droce

    2016-12-01

    Full Text Available Fusarielins are polyketides with a decalin core produced by various species of Aspergillus and Fusarium. Although the responsible gene cluster has been identified, the biosynthetic pathway remains to be elucidated. In the present study, members of the gene cluster were deleted individually in a Fusarium graminearum strain overexpressing the local transcription factor. The results suggest that a trans-acting enoyl reductase (FSL5 assists the polyketide synthase FSL1 in biosynthesis of a polyketide product, which is released by hydrolysis by a trans-acting thioesterase (FSL2. Deletion of the epimerase (FSL3 resulted in accumulation of an unstable compound, which could be the released product. A novel compound, named prefusarielin, accumulated in the deletion mutant of the cytochrome P450 monooxygenase FSL4. Unlike the known fusarielins from Fusarium, this compound does not contain oxygenized decalin rings, suggesting that FSL4 is responsible for the oxygenation.

  16. Spectroscopic Constraints on the Form of the Stellar Cluster Mass Function

    CERN Document Server

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

    2012-01-01

    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 (<10 Myr) clusters, however this has proven difficult due to low-number statistics. In this contribution we use an alternative method based on the luminosities of the brightest clusters, combined with their ages. 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 exp...

  17. The Density Functional Theory Study of Structural and Electronical Properties of ZnO Clusters

    Directory of Open Access Journals (Sweden)

    O.V. Bovgyra

    2013-03-01

    Full Text Available Density functional theory studies of structural and electronic properties of small clusters were performed. For each cluster an optimization of structure and the basic properties of the band structure were conducted. It was determined that with increasing (n energetically more efficient in the small clusters is stabilization from the ring to fulleren-like structures containing tetragonal and hexagonal faces and all atoms have coordination number equal three. Among the clusters (ZnO12 with doped atoms most stable are clusters where Zn was replaced by Mn, Cu and Co atoms. Band gap in the electronic spectrum of doped clusters decreases due to p-d hybridization orbitals of the impurity atom with the orbitals of the oxygen atom.

  18. The massive star Initial Mass Function of the Arches cluster

    CERN Document Server

    Espinoza, Pablo; Melnick, Jorge

    2009-01-01

    The massive Arches cluster near the Galactic Center is in principle an ideal laboratory to investigate massive star formation under extreme conditions. But it comes at a high price: the cluster is hidden behind several tens of magnitudes of visual extinction. Severe crowding requires space or AO-assisted instruments to resolve the stellar populations, and even with the best instruments the interpretation of the data is far from direct. Several investigations using NICMOS and the most advanced AO imagers on the gro und revealed an overall top-heavy IMF for the cluster, with a very flat IMF near the center. There are a number of effects, however, that could potentially bias these results, in particular the strong differential extinction and the problem of transforming the observations to a standard photometric system in the presence of strong reddening. We present new observations obtained with the NAOS-Conica (NACO) AO-imager on the VLT. The problem of photometric transformation is avoided by working in the na...

  19. HST luminosity functions of the globular clusters M10, M22, and M55. A comparison with other clusters

    Science.gov (United States)

    Piotto, G.; Zoccali, M.

    1999-05-01

    From a combination of deep Hubble Space Telescope V and I images with groundbased images in the same bands, we have obtained color-magnitude diagrams of M10, M22, and M55, extending from just above the hydrogen burning limit to the tip of the red giant branch, down to the white dwarf cooling sequence. We have used the color-magnitude arrays to extract main sequence luminosity functions (LFs) from the turnoff to m ~ 0.13m_sun. The LFs of M10 is significantly steeper than that for the other two clusters. The difference cannot be due to a difference in metallicity. A comparison with the LFs from Piotto et al. (1997), shows a large spread in the LF slopes. This spread is also present in the local mass functions (MFs) obtained from the observed LFs using different theoretical mass-luminosity relations. The dispersion in the MF slopes remains also after removing the mass segregation effects by using multimass King-Michie models. The globular cluster MF slopes are also flatter than the MF slope of the field stars and of the Galactic clusters in the same mass interval. We interpret the MF slope dispersion and the MF flatness as an evidence of dynamical evolution which makes the present day globular cluster stellar MFs different from the initial MFs. The slopes of the present day MFs exclude that the low mass star can be dynamically relevant for the Galactic globular clusters. Based on HST observations retrieved from the ESO ST-ECF Archive, and on observations made at the European Southern Observatory, La Silla, Chile, and at the JKT telescope at La Palma, Islas Canarias.

  20. On the origin of the Schechter-like mass function of young star clusters in disk galaxies

    CERN Document Server

    Lieberz, Patrick

    2016-01-01

    The mass function of freshly formed star clusters is empirically often described as a power law. However the cluster mass function of populations of young clusters over the scale of a galaxy has been found to be described by a Schechter-function. Here we address this apparent discrepancy. We assume that in an annulus of an isolated self- regulated radially-exponential axially-symmetric disk galaxy, the local mass function of very young (embedded) clusters is a power law with an upper mass limit which depends on the local star formation rate density. Radial integration of this mass function yields a galaxy-wide embedded cluster mass function. This integrated embedded cluster mass function has a Schechter-type form, which results from the addition of many low mass clusters forming at all galactocentric distances and rarer massive clusters only forming close to the center of the galaxy.

  1. On the origin of the Schechter-like mass function of young star clusters in disc galaxies

    Science.gov (United States)

    Lieberz, P.; Kroupa, P.

    2017-03-01

    The mass function of freshly formed star clusters is empirically often described as a power law. However, the cluster mass function of populations of young clusters over the scale of a galaxy has been found to be described by a Schechter-function. Here we address this apparent discrepancy. We assume that in an annulus of an isolated self-regulated radially exponential axially symmetric disc galaxy, the local mass function of very young (embedded) clusters is a power law with an upper mass limit which depends on the local star formation rate density. Radial integration of this mass function yields a galaxy-wide embedded cluster mass function. This integrated embedded cluster mass function has a Schechter-type form, which results from the addition of many low-mass clusters forming at all galactocentric distances and rarer massive clusters only forming close to the centre of the galaxy.

  2. Modeling the Near-Infrared Luminosity Function of Young Stellar Clusters

    Science.gov (United States)

    Muench, A. A.; Lada, E. A.; Lada, C. J.

    1999-12-01

    We present the results of numerical experiments designed to evaluate the usefulness of near-infrared luminosity functions for constraining the Initial Mass Function (IMF) of young (0-10 Myr) stellar populations. Using Monte Carlo techniques, we create a suite of model luminosity functions systematically varying each of these basic underlying relations: the underlying IMF, cluster star forming history, and theoretical pre-main sequence mass-to-luminosity relations. Our modeling techniques also allow us to explore the effects of unresolved binaries, infrared excess emission from circumstellar disks, and interstellar extinction on the cluster luminosity function. From this numerical modeling, we find that the luminosity function of a young stellar population is considerably more sensitive to variations in the underlying initial mass function than to either variations in the star forming history or assumed pre-main-sequence (PMS) mass-to-luminosity relation. To illustrate the potential effectiveness of using the KLF of a young cluster to constrain its IMF, we model the observed K band luminosity function of the nearby Trapezium cluster. Our derived mass function for the Trapezium spans two orders of magnitude in stellar mass (5>Msun>0.02) and has a peak near the hydrogen burning limit. Below the hydrogen burning limit, the mass function steadily decreases with decreasing mass throughout the brown dwarf regime. We also test the hypothesis of a space varying IMF by performing model fits to the K band luminosity functions of several other young clusters.

  3. 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

  4. The luminosity function of cluster galaxies relations among M$_{1}$, M* and the morphological type

    CERN Document Server

    Trevese, D; Appodia, B

    1996-01-01

    A study of the luminosity function of 36 Abell clusters of galaxies has been carried out using photographic plates obtained with the Palomar 1.2 m Schmidt telescope. The relation between the magnitude M_1 of the brightest cluster member and the Schechter function parameter M* has been analyzed. A positive correlation between M* and M_1 is found. However clusters appear segregated in the M_1-M* plane according to their Rood & Sastry class in such a way that on average M_1 becomes brighter while M* becomes fainter going from late to early Rood & Sastry and also Bautz & Morgan classes. Also a partial correlation analysis involving the magnitude M_10 of the 10th brightest galaxy, shows a negative intrinsic correlation between M_1 and M*. These results agree with the cannibalism model for the formation of brightest cluster members, and provide new constraints for theories of cluster formation and evolution.

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

    Directory of Open Access Journals (Sweden)

    Fujita André

    2012-10-01

    Full Text Available Abstract 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.

  6. Semi-automatic time-series transfer functions via temporal clustering and sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Woodring, Jonathan L [Los Alamos National Laboratory; Shen, H W [OHIO STATE UNIV.

    2009-01-01

    When creating transfer functions for time-varying data, it is not clear what range of values to use for classification, as data value ranges and distributions change over time. In order to generate time-varying transfer functions, they search the data for classes that have similar behavior over time, assuming that data points that behave similarly belong to the same feature. They utilize a method they call temporal clustering and sequencing to find dynamic features in value space and create a corresponding transfer function. First, clustering finds groups of data points that have the same value space activity over time. Then, sequencing derives a progression of clusters over time, creating chains that follow value distribution changes. Finally, the cluster sequences are used to create transfer functions, as sequences describe the value range distributions over time in a data set.

  7. 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.

  8. Detection of Functional Change Using Cluster Trend Analysis in Glaucoma

    Science.gov (United States)

    Gardiner, Stuart K.; Mansberger, Steven L.; Demirel, Shaban

    2017-01-01

    Purpose Global analyses using mean deviation (MD) assess visual field progression, but can miss localized changes. Pointwise analyses are more sensitive to localized progression, but more variable so require confirmation. This study assessed whether cluster trend analysis, averaging information across subsets of locations, could improve progression detection. Methods A total of 133 test–retest eyes were tested 7 to 10 times. Rates of change and P values were calculated for possible re-orderings of these series to generate global analysis (“MD worsening faster than x dB/y with P trend analysis detects subsequently confirmed deterioration sooner than either global or pointwise analyses. PMID:28715580

  9. Electronic properties and STM images of vacancy clusters and chains in functionalized silicene and germanene

    Science.gov (United States)

    Jamdagni, Pooja; Kumar, Ashok; Sharma, Munish; Thakur, Anil; Ahluwalia, P. K.

    2017-01-01

    Electronic properties and STM topographical images of X (=F, H, O) functionalized silicene and germanene have been investigated by introducing various kind of vacancy clusters and chain patterns in monolayers within density functional theory (DFT) framework. The relative ease of formation of vacancy clusters and chain patterns is found to be energetically most favorable in hydrogenated silicene and germanene. F- and H-functionalized silicene and germanene are direct bandgap semiconducting with bandgap ranging between 0.1-1.9 eV, while O-functionalized monolayers are metallic in nature. By introducing various vacancy clusters and chain patterns in both silicene and germanene, the electronic and magnetic properties get modified in significant manner e.g. F- and H-functionalized silicene and germanene with hexagonal and rectangle vacancy clusters are non-magnetic semiconductors with modified bandgap values while pentagonal and triangle vacancy clusters induce metallicity and magnetic character in monolayers; hexagonal vacancy chain patterns induce direct-to-indirect gap transition while zigzag vacancy chain patterns retain direct bandgap nature of monolayers. Calculated STM topographical images show distinctly different characteristics for various type of vacancy clusters and chain patterns which may be used as electronic fingerprints to identify various vacancy patterns in silicene and germanene created during the process of functionalization.

  10. The Extended Zel'dovich Mass Functions of Clusters and Isolated Clusters in the Presence of Primordial Non-Gaussianity

    CERN Document Server

    Lim, Seunghwan

    2014-01-01

    We present new formulae for the mass functions of the clusters and the isolated clusters with non Gaussian initial conditions. For this study, we adopt the Extended Zel'dovich (EZL) model as a basic framework, focusing on the case of primordial non-Gaussianity of the local type whose degree is quantified by a single parameter $f_{nl}$. By making a quantitative comparison with the N-body results, we first demonstrate that the EZL formula with the constant values of three fitting parameters still works remarkably well for the local $f_{nl}$ case. We also modify the EZL formula to find an analytic expression for the mass function of isolated clusters which turns out to have only one fitting parameter other than the overall normalization factor and showed that the modified EZL formula with a constant value of the fitting parameter matches excellently the N-body results with various values of $f_{nl}$ at various redshifts. Given the simplicity of the generalized EZL formulae and their good agreements with the nume...

  11. A novel CpG island set identifies tissue-specific methylation at developmental gene loci.

    Directory of Open Access Journals (Sweden)

    Robert Illingworth

    2008-01-01

    Full Text Available CpG islands (CGIs are dense clusters of CpG sequences that punctuate the CpG-deficient human genome and associate with many gene promoters. As CGIs also differ from bulk chromosomal DNA by their frequent lack of cytosine methylation, we devised a CGI enrichment method based on nonmethylated CpG affinity chromatography. The resulting library was sequenced to define a novel human blood CGI set that includes many that are not detected by current algorithms. Approximately half of CGIs were associated with annotated gene transcription start sites, the remainder being intra- or intergenic. Using an array representing over 17,000 CGIs, we established that 6%-8% of CGIs are methylated in genomic DNA of human blood, brain, muscle, and spleen. Inter- and intragenic CGIs are preferentially susceptible to methylation. CGIs showing tissue-specific methylation were overrepresented at numerous genetic loci that are essential for development, including HOX and PAX family members. The findings enable a comprehensive analysis of the roles played by CGI methylation in normal and diseased human tissues.

  12. SIZES, HALF-MASS DENSITIES, AND MASS FUNCTIONS OF STAR CLUSTERS IN THE MERGER REMNANT NGC 1316: CLUES TO THE FATE OF SECOND-GENERATION GLOBULAR CLUSTERS

    Energy Technology Data Exchange (ETDEWEB)

    Goudfrooij, Paul, E-mail: goudfroo@stsci.edu [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States)

    2012-05-10

    We study mass functions of globular clusters derived from Hubble Space Telescope/Advanced Camera for Surveys images of the early-type merger remnant galaxy NGC 1316, which hosts a significant population of metal-rich globular clusters of intermediate age ({approx}3 Gyr). For the old, metal-poor ({sup b}lue{sup )} clusters, the peak mass of the mass function M{sub p} increases with internal half-mass density {rho}{sub h} as M{sub p}{proportional_to}{rho}{sub h}{sup 0.44}, whereas it stays approximately constant with galactocentric distance R{sub gal}. The mass functions of these clusters are consistent with a simple scenario in which they formed with a Schechter initial mass function and evolved subsequently by internal two-body relaxation. For the intermediate-age population of metal-rich ({sup r}ed{sup )} clusters, the faint end of the previously reported power-law luminosity function of the clusters with R{sub gal} > 9 kpc is due to many of those clusters having radii larger than the theoretical maximum value imposed by the tidal field of NGC 1316 at their R{sub gal}. This renders disruption by two-body relaxation ineffective. Only a few such diffuse clusters are found in the inner regions of NGC 1316. Completeness tests indicate that this is a physical effect. Using comparisons with star clusters in other galaxies and cluster disruption calculations using published models, we hypothesize that most red clusters in the low-{rho}{sub h} tail of the initial distribution have already been destroyed in the inner regions of NGC 1316 by tidal shocking, and that several remaining low-{rho}{sub h} clusters will evolve dynamically to become similar to 'faint fuzzies' that exist in several lenticular galaxies. Finally, we discuss the nature of diffuse red clusters in early-type galaxies.

  13. Ferrocene-Functionalized Cu(I)/Ag(I) Dithiocarbamate Clusters.

    Science.gov (United States)

    Kishore, Pilli V V N; Liao, Jian-Hong; Hou, Hsing-Nan; Lin, Yan-Ru; Liu, C W

    2016-04-04

    A series of compounds, namely, [Cu8(μ4-H){S2CNMeCH2Fc}6](PF6) (1), [Cu7(μ4-H) {S2CN(i)PrCH2Fc}6] (2), [Cu3{S2CN(Bz) (CH2Fc)}2(dppf)2](PF6) (3), and [Ag2{S2CNMe(CH2Fc)}2(PPh3)2] (4) (dppf = 1,1'-bis(diphenylphosphino)ferrocene), supported by multiferrocene assemblies, were synthesized. All the compounds were characterized by (1)H NMR, Fourier transform infrared, elemental analysis, and electrospray ionization mass spectrometry techniques. Single-crystal X-ray structural analysis revealed that 1 is a monocationic octanuclear Cu(I) cluster and that 2 is a neutral heptanuclear Cu(I) cluster with tetracapped tetrahedral (1) and tricapped tetrahedral (2) geometries entrapped with an interstitial hydride, anchored by six ferrocene units at the periphery of the core. Compounds 3 and 4 comprise trimetallic Cu(I) and dimetallic Ag(I) cores enfolded by four and two ferrocene moieties. Interestingly both chelating and bridging modes of binding are observed for dppf ligand in 3. Further the formation and isolation of polyhydrido copper clusters [Cu28H15{S2CN(i)PrCH2Fc}12](PF6) (5) and [Cu28H15{S2CN(n)Bu2}12](PF6) (7), stabilized by bulky ferrocenyl and n-butyl dithiocarbamate ligands, was demonstrated. They are readily identified by (2)H NMR studies on their deuterium analogues, [Cu28D15{S2CN(i)PrCH2Fc}12](PF6) (6) and [Cu28D15{S2CN(n)Bu2}12](PF6) (8). Though the structure details as well as spectroscopic characterizations of 5 are yet to be investigated, the compound 7 is fully characterized by variety of spectroscopy including single-crystal X-ray diffraction. The cyclic voltammetry studies for compounds 1, 2, and 4 display irreversible redox peaks for Fe(2+)/Fe(3+) couple wherein the reduction peaks are not well-resolved due to some adsorption of the complex onto the electrode surface.

  14. All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues

    Directory of Open Access Journals (Sweden)

    Myakishev Maxim V

    2008-02-01

    Full Text Available Abstract Background The promoters of housekeeping genes are well-bound by RNA polymerase II (RNAP in different tissues. Although the promoters of these genes are known to contain CpG islands, the specific DNA sequences that are associated with high RNAP binding to housekeeping promoters has not been described. Results ChIP-chip experiments from three mouse tissues, liver, heart ventricles, and primary keratinocytes, indicate that 94% of promoters have similar RNAP binding, ranging from well-bound to poorly-bound in all tissues. Using all 8-base pair long sequences as a test set, we have identified the DNA sequences that are enriched in promoters of housekeeping genes, focusing on those DNA sequences which are preferentially localized in the proximal promoter. We observe a bimodal distribution. Virtually all sequences enriched in promoters with high RNAP binding values contain a CpG dinucleotide. These results suggest that only transcription factor binding sites (TFBS that contain the CpG dinucleotide are involved in RNAP binding to housekeeping promoters while TFBS that do not contain a CpG are involved in regulated promoter activity. Abundant 8-mers that are preferentially localized in the proximal promoters and exhibit the best enrichment in RNAP bound promoters are all variants of six known CpG-containing TFBS: ETS, NRF-1, BoxA, SP1, CRE, and E-Box. The frequency of these six DNA motifs can predict housekeeping promoters as accurately as the presence of a CpG island, suggesting that they are the structural elements critical for CpG island function. Experimental EMSA results demonstrate that methylation of the CpG in the ETS, NRF-1, and SP1 motifs prevent DNA binding in nuclear extracts in both keratinocytes and liver. Conclusion In general, TFBS that do not contain a CpG are involved in regulated gene expression while TFBS that contain a CpG are involved in constitutive gene expression with some CpG containing sequences also involved in

  15. The initial mass function of young open clusters in the Galaxy: A preliminary result

    CERN Document Server

    Lim, Beomdu; Hur, Hyeonoh; Park, Byeong-Gon

    2015-01-01

    The initial mass function (IMF) is an essential tool with which to study star formation processes. We have initiated the photometric survey of young open clusters in the Galaxy, from which the stellar IMFs are obtained in a homogeneous way. A total of 16 famous young open clusters have preferentially been studied up to now. These clusters have a wide range of surface densities (log sigma = -1 to 3 [stars pc^2] for stars with mass larger than 5M_sun) and cluster masses (M_cl = 165 to 50,000M_sun), and also are distributed in five different spiral arms in the Galaxy. It is possible to test the dependence of star formation processes on the global properties of individual clusters or environmental conditions. We present a preliminary result on the variation of the IMF in this paper.

  16. Structural and electronic properties of stable Lin (n=2-10) clusters: A density functional study

    Science.gov (United States)

    Chetri, Pawan; Deka, Ramesh Ch.; Choudhury, Amarjyoti

    2013-12-01

    Structure and relative stability of Lin clusters for n=1-10 were investigated using density functional methods based DMol3 program. The structures of Li clusters were determined in terms of Li-Li bond length and the results are in very good agreement with experimental values. Stability of the clusters was determined from their relative energy values binding energies and second difference energy. We also determined fragmentation energy of each size of cluster. We arrived at some interesting result like the transition of Lin from 2-dimension to 3-dimension for a particular value of n and also the variation of HOMO-LUMO gap with cluster size. Many structures are characterized for the first time in this work.

  17. Polarizabilities of Intermediate Sized Lithium Clusters From Density-Functional Theory

    CERN Document Server

    Zope, Rajendra R; Pederson, Mark R

    2007-01-01

    We present a detailed investigation of static dipole polarizability of lithium clusters containing up to 22 atoms. We first build a database of lithium clusters by optimizing several candidate structures for the ground state geometry for each size. Full polarizability tensor is determined for about 5-6 isomers of each cluster size using the finite-field method. All calculations are performed using large Gaussian basis sets, and within the generalized gradient approximation to the density functional theory, as implemented in the NRLMOL suite of codes. The average polarizability per atom varies from 11 to 9 Angstrom^3, within the 8-22 size range, in general agreement with experimental results. While the average polarizability exhibits a relatively weak dependence on cluster conformation, significant changes in the degree of anisotropy of the polarizability tensor are observed. Interestingly, in addition to the expected even odd (0 and 1 $\\mu_B$) magnetic states, our results show several cases where clusters wit...

  18. Geometries, stabilities, and electronic properties of Be-doped gold clusters: a density functional theory study

    Institute of Scientific and Technical Information of China (English)

    Chen Dong-Dong; Kuang Xiao-Yu; Zhao Ya-Ru; Shao Peng; Li Yan-Fang

    2011-01-01

    We have systematically investigated the geometrical structures, relative stabilities and electronic properties of small bimetallic AunBe (n = 1, 2, ..., 8) clusters using a density functional method at BP86 level. The optimized geometries reveal that the impurity beryllium atom dramatically affects the structures of the Aun clusters. The averaged binding energies, fragmentation energies, second-order difference of energies, the highest occupied-lowest unoccupied molecular orbital energy gaps and chemical hardness are investigated. All of them exhibit a pronounced odd-even alternation,manifesting that the clusters with even number of gold atoms possess relatively higher stabilities. Especially, the linear Au2Be cluster is magic cluster with the most stable chemical stability. According to the natural population analysis, it is found that charge-transferring direction between Au atom and Be atom changes at the size of n = 4.

  19. 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.

  20. Comparative Density Functional Study of Methanol Decomposition on Cu4 and Co4 Clusters

    Energy Technology Data Exchange (ETDEWEB)

    Mehmood, Faisal; Greeley, Jeffrey P.; Zapol, Peter; Curtiss, Larry A.

    2010-11-18

    A density functional theory study of the decomposition of methanol on Cu4 and Co4 clusters is presented. The reaction intermediates and activation barriers have been determined for reaction steps to form H2 and CO. For both clusters, methanol decomposition initiated by C-H and O-H bond breaking was investigated. In the case of a Cu4 cluster, methanol dehydrogenation through hydroxymethyl (CH2OH), hydroxymethylene (CHOH), formyl (CHO), and carbon monoxide (CO) is found to be slightly more favorable. For a Co4 cluster, the dehydrogenation pathway through methoxy (CH3O) and formaldehyde (CH2O) is slightly more favorable. Each of these pathways results in formation of CO and H2. The Co cluster pathway is very favorable thermodynamically and kinetically for dehydrogenation. However, since CO binds strongly, it is likely to poison methanol decomposition to H2 and CO at low temperatures. In contrast, for the Cu cluster, CO poisoning is not likely to be a problem since it does not bind strongly, but the dehydrogenation steps are not energetically favorable. Pathways involving C-O bond cleavage are even less energetically favorable. The results are compared to our previous study of methanol decomposition on Pd4 and Pd8 clusters. Finally, all reaction energy changes and transition state energies, including those for the Pd clusters, are related in a linear, Broensted-Evans-Polanyi plot.

  1. Probing the structural evolution of ruthenium doped germanium clusters: Photoelectron spectroscopy and density functional theory calculations

    Science.gov (United States)

    Jin, Yuanyuan; Lu, Shengjie; Hermann, Andreas; Kuang, Xiaoyu; Zhang, Chuanzhao; Lu, Cheng; Xu, Hongguang; Zheng, Weijun

    2016-07-01

    We present a combined experimental and theoretical study of ruthenium doped germanium clusters, RuGen- (n = 3-12), and their corresponding neutral species. Photoelectron spectra of RuGen- clusters are measured at 266 nm. The vertical detachment energies (VDEs) and adiabatic detachment energies (ADEs) are obtained. Unbiased CALYPSO structure searches confirm the low-lying structures of anionic and neutral ruthenium doped germanium clusters in the size range of 3 ≤ n ≤ 12. Subsequent geometry optimizations using density functional theory (DFT) at PW91/LANL2DZ level are carried out to determine the relative stability and electronic properties of ruthenium doped germanium clusters. It is found that most of the anionic and neutral clusters have very similar global features. Although the global minimum structures of the anionic and neutral clusters are different, their respective geometries are observed as the low-lying isomers in either case. In addition, for n > 8, the Ru atom in RuGen-/0 clusters is absorbed endohedrally in the Ge cage. The theoretically predicted vertical and adiabatic detachment energies are in good agreement with the experimental measurements. The excellent agreement between DFT calculations and experiment enables a comprehensive evaluation of the geometrical and electronic structures of ruthenium doped germanium clusters.

  2. EVIDENCE FOR TWO DISTINCT STELLAR INITIAL MASS FUNCTIONS: REVISITING THE EFFECTS OF CLUSTER DYNAMICAL EVOLUTION

    Energy Technology Data Exchange (ETDEWEB)

    Zaritsky, Dennis [Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Colucci, Janet E.; Bernstein, Rebecca A. [Department of Astronomy and Astrophysics, 1156 High Street, UCO/Lick Observatory, University of California, Santa Cruz, CA 95064 (United States); Pessev, Peter M. [Gemini South Observatory, c/o AURA Inc., Casilla 603, La Serena (Chile); Chandar, Rupali, E-mail: dzaritsky@as.arizona.edu [Department of Physics and Astronomy, The University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606 (United States)

    2013-06-20

    We measure the velocity dispersions of six galactic globular clusters using spatially integrated spectra, to test for the effects of internal dynamical evolution in the stellar mass-to-light ratios, Y{sub *}, of star clusters. In particular, we revisit whether the low values of Y{sub *} that we found in our previous study, from which we concluded that there are at least two population of stellar clusters with distinct stellar initial mass functions, are artificially depressed by relaxation driven mass loss. The combination of our previous sample of five old clusters and these six now provide an order of magnitude range in cluster mass with which to explore this issue. We find no relationship between cluster mass, or relaxation time, and Y{sub *}. Because relaxation is mass dependent, we conclude that the values of Y{sub *} for these clusters are not strongly affected by dynamical effects, and so confirm the presence of the population of clusters with low Y{sub *}.

  3. 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.

  4. Geometries, stabilities and electronic properties of copper and selenium doped copper clusters: Density functional theory study

    Science.gov (United States)

    Li, Cheng-Gang; Zhang, Jie; Yuan, Yu-Quan; Tang, Ya-Nan; Ren, Bao-Zeng; Chen, Wei-Guang

    2017-02-01

    The structures properties of Cun+1 and CunSe clusters have been investigated using an unbiased CALYPSO structure searching method. Firstly, an unbiased search relying on several structurally different initial clusters have been undertaken. Subsequently, geometry optimization by means of density functional theory is carried out to determine the relative stability of various candidates for low lying clusters obtained from the unconstrained search. The results shown that the ground state Cu9 cluster is found to prefer a unique and previously unrecognized structure, with the total energies much lower than all structures proposed in the literature so far. The Cu2Se cluster is the most stable geometries for CunSe clusters. Additionally, the calculated HOMO-LUMO gaps ranges from 1.27 to 2.85 eV, which make CunSe clusters suitable candidates in photocatalyst materials. Lastly, the molecular orbital energy and density of states; the adaptive natural density partitioning; the electron localization function, localized orbital locator and Mayer Bond order are also studied for the ground state to develop a deeper understanding on the electronic properties.

  5. 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

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

    Directory of Open Access Journals (Sweden)

    Nan Lin

    Full Text Available 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.

  7. Clusters of bound particles in the derivative δ-function Bose gas

    Energy Technology Data Exchange (ETDEWEB)

    Basu-Mallick, B., E-mail: bireswar.basumallick@saha.ac.in [Theory Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700 064 (India); Bhattacharyya, Tanaya, E-mail: tanaya.bhattacharyya@googlemail.com [Department of Physics, St. Xavier' s College, 30 Park Street, Kolkata 700 016 (India); Sen, Diptiman, E-mail: diptiman@cts.iisc.ernet.in [Centre for High Energy Physics, Indian Institute of Science, Bangalore 560 012 (India)

    2013-06-11

    In this paper we discuss a novel procedure for constructing clusters of bound particles in the case of a quantum integrable derivative δ-function Bose gas in one dimension. It is shown that clusters of bound particles can be constructed for this Bose gas for some special values of the coupling constant, by taking the quasi-momenta associated with the corresponding Bethe state to be equidistant points on a single circle in the complex momentum plane. We also establish a connection between these special values of the coupling constant and some fractions belonging to the Farey sequences in number theory. This connection leads to a classification of the clusters of bound particles associated with the derivative δ-function Bose gas and allows us to study various properties of these clusters like their size and their stability under the variation of the coupling constant.

  8. Stability and structure of rare-gas ionic clusters using density functional methods: A study of helium clusters

    Energy Technology Data Exchange (ETDEWEB)

    Gianturco, F.A.; De Lara-Castells, M.P. [Univ. of Rome (Italy)

    1996-10-05

    Several modelings of exchange and correlation forces which can be carried out using density functional theory (DFT) methods have been analyzed to study their efficiency and reliability when evaluating possible competing structures of helium ionic clusters of increasing size. This study examines He{sub n}{sup +} systems with n from 1 to 7 and compares the present calculations with earlier evaluations that used more conventional, and more computationally intensive, methods with configuration interaction (CI) approaches. The present results indicate that it is indeed possible to strike a fruitful balance between reduction of computational times and quality of the ensuing structural information. 62 refs., 1 fig., 8 tabs.

  9. Minkowski Functionals and Cluster Analysis for CMB Maps

    CERN Document Server

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

    1999-01-01

    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, it allows 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.

  10. Functional protein clusters and regulatory motifs in Hypsibius dujardini und Milnesium tardigradum

    OpenAIRE

    Förster, Frank; Liang, Chunguang; Beisser, Daniela; Frohme, Marcus; Schill, Ralph O.; Dandekar, Thomas

    2009-01-01

    Functional protein clusters and regulatory motifs do not only mediate the unique adaptation of tardigrades against extreme temperature and other harsh environmental conditions, but are important markers to distinguish species and taxonomic units. We show here in detail results of our current comparison between Hypsibius dujardini and Milnesium tardigradum. We found 50 different clusters of sequence similar proteins between both tardigrades of which 10 are tardigrade specific. Proteins of othe...

  11. A clustering technique for digital communications channel equalization using radial basis function networks.

    Science.gov (United States)

    Chen, S; Mulgrew, B; Grant, P M

    1993-01-01

    The application of a radial basis function network to digital communications channel equalization is examined. It is shown that the radial basis function network has an identical structure to the optimal Bayesian symbol-decision equalizer solution and, therefore, can be employed to implement the Bayesian equalizer. The training of a radial basis function network to realize the Bayesian equalization solution can be achieved efficiently using a simple and robust supervised clustering algorithm. During data transmission a decision-directed version of the clustering algorithm enables the radial basis function network to track a slowly time-varying environment. Moreover, the clustering scheme provides an automatic compensation for nonlinear channel and equipment distortion. Computer simulations are included to illustrate the analytical results.

  12. Basic Tools for Studies on the Formation and Disruption of Star Clusters: the Luminosity Function

    CERN Document Server

    Gieles, M

    2009-01-01

    The luminosity function (LF) of young star clusters is often approximated by a power law function. For clusters in a wide range of galactic environments this has resulted in fit indices near -2, but on average slightly steeper. A fundamental property of the -2 power law function is that the luminosity of the brightest object (L_max) scales linearly with the total number of clusters, which is close to what is observed. This suggests that the formation of Young Massive Clusters (YMCs) is a result of the size of the sample, i.e. when the SFR is high it is statistically more likely to form YMCs, but no particular physical conditions are required. In this contribution we provide evidence that the LF of young clusters is not a -2 power law, but instead is curved, showing a systematic decrease of the (logarithmic) slope from roughly -1.8 at low luminosities to roughly -2.8 at high luminosities. The empirical LFs can be reproduced by model LFs using an underlying cluster IMF with a Schechter type truncation around M*...

  13. 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.

  14. Familial clustering of executive functioning in affected sibling pair families with ADHD.

    NARCIS (Netherlands)

    Slaats-Willemse, D.I.; Swaab-Barneveld, H.J.; Sonneville, L.

    2005-01-01

    OBJECTIVE: To investigate familial clustering of executive functioning (i.e., response inhibition, fine visuomotor functioning, and attentional control) in attention-deficit/hyperactivity disorder (ADHD)-affected sibling pairs. METHOD: Fifty-two affected sibling pairs aged 6 to 18 years and diagnose

  15. Superclusters : a search for novel structures and functions of biological iron-sulfur clusters

    NARCIS (Netherlands)

    Arendsen, A.F.

    1996-01-01


    Iron sulfur (Fe-S) proteins are found in a variety of organisms. They usually function in electron transport, but they may also be involved in other functions like gene regulation and Lewis acid catalysis. The structure and spectroscopic properties of Fe-S clusters holding one, two,

  16. The clustering of functionally related genes contributes to CNV-mediated disease

    NARCIS (Netherlands)

    Andrews, T.; Honti, F.; Pfundt, R.P.; Leeuw, N. de; Hehir, J.Y.; Vulto-van Silfhout, A.T.; Vries, B. de; Webber, C.

    2015-01-01

    Clusters of functionally related genes can be disrupted by a single copy number variant (CNV). We demonstrate that the simultaneous disruption of multiple functionally related genes is a frequent and significant characteristic of de novo CNVs in patients with developmental disorders (P = 1 x 10(-3))

  17. Modeling the Near-Infrared Luminosity Functions of Young Stellar Clusters

    Science.gov (United States)

    Muench, August A.; Lada, Elizabeth A.; Lada, Charles J.

    2000-04-01

    We present the results of numerical experiments designed to evaluate the usefulness of near-infrared (NIR) luminosity functions for constraining the initial mass function (IMF) of young stellar populations. We test the sensitivity of the NIR K-band luminosity function (KLF) of a young stellar cluster to variations in the underlying IMF, star-forming history, and pre-main-sequence mass-to-luminosity relations. Using Monte Carlo techniques, we create a suite of model luminosity functions systematically varying each of these basic underlying relations. From this numerical modeling, we find that the luminosity function of a young stellar population is considerably more sensitive to variations in the underlying initial mass function than to either variations in the star-forming history or assumed pre-main-sequence (PMS) mass-to-luminosity relation. Variations in a cluster's star-forming history are also found to produce significant changes in the KLF. In particular, we find that the KLFs of young clusters evolve in a systematic manner with increasing mean age. Our experiments indicate that variations in the PMS mass-to-luminosity relation, resulting from differences in adopted PMS tracks, produce only small effects on the form of the model luminosity functions and that these effects are mostly likely not detectable observationally. To illustrate the potential effectiveness of using the KLF of a young cluster to constrain its IMF, we model the observed KLF of the nearby Trapezium cluster. With knowledge of the star-forming history of this cluster obtained from optical spectroscopic studies, we derive the simplest underlying IMF whose model luminosity function matches the observations. Our derived mass function for the Trapezium spans 2 orders of magnitude in stellar mass (5>Msolar>0.02) and has a peak near the hydrogen-burning limit. Below the hydrogen-burning limit, the mass function steadily decreases with decreasing mass throughout the brown dwarf regime. Comparison

  18. Liposomal SLA co-incorporated with PO CpG ODNs or PS CpG ODNs induce the same protection against the murine model of leishmaniasis.

    Science.gov (United States)

    Shargh, Vahid Heravi; Jaafari, Mahmoud Reza; Khamesipour, Ali; Jaafari, Iman; Jalali, Seyed Amir; Abbasi, Azam; Badiee, Ali

    2012-06-06

    First generation Leishmania vaccines consisting of whole killed parasites with or without adjuvants have reached phase 3 trial and failed to show enough efficacy mainly due to the lack of an appropriate adjuvant. In this study, the nuclease-resistant phosphorothioate CpG oligodeoxynucleotides (PS CpG) or nuclease-sensitive phosphodiester CpG ODNs (PO CpG) were used as adjuvants to enhance immunogenicity and rate of protection against leishmaniasis. Due to the susceptibility of PO CpG to nuclease degradation, an efficient liposomal delivery system was developed to protect them from degradation. 1, 2-dioleoyl-3-trimethylammonium-propane (DOTAP) as a cationic lipid was used because of its unique adjuvanticity and electrostatic interaction with negatively charged CpG ODNs. To evaluate the role of liposomal formulation in protection rate and enhanced immune response, BALB/c mice were immunized subcutaneously with liposomal soluble Leishmania antigens (SLA) co-incorporated with PO CpG (Lip-SLA-PO CpG), Lip-SLA-PS CpG, SLA+PO CpG, SLA+PS CpG, SLA or buffer. As criteria for protection, footpad swelling at the site of challenge, parasite loads, the levels of IFN-γ and IL-4, and the IgG subtypes were evaluated. The groups of mice receiving Lip-SLA-PO CpG or Lip-SLA-PS CpG showed a high protection rate compared with the control groups. In addition, there was no significant difference in immune response generation between mice immunized with PS CpG and the group receiving PO CpG when incorporated into the liposomes. The results suggested that liposomal form of PO CpG might be used instead of PS CpG in future vaccine formulations as an efficient adjuvant. Copyright © 2012 Elsevier Ltd. All rights reserved.

  19. Near-Infrared Properties of Moderate-Redshift Galaxy Clusters: Luminosity Functions and Density Profiles

    Energy Technology Data Exchange (ETDEWEB)

    Muzzin, Adam; Yee, H.K.C.; /Toronto U., Astron. Dept.; Hall, Patrick B.; /York U., Canada; Ellingson, E.; /Colorado U., CASA; Lin, Huan; /Fermilab

    2006-12-01

    We present K-band imaging for 15 of the Canadian Network for Observational Cosmology (CNOC1) clusters. The extensive spectroscopic dataset available for these clusters allows us to determine the cluster K-band luminosity function and density profile without the need for statistical background subtraction. The luminosity density and number density profiles can be described by NFW models with concentration parameters of c{sub l} = 4.28 {+-} 0.70 and c{sub g} = 4.13 {+-} 0.57 respectively. Comparing these to the dynamical mass analysis of the same clusters shows that the galaxy luminosity and number density profiles are similar to the dark matter profile, and are not less concentrated like in local clusters. The luminosity functions show that the evolution of K. over the redshift range 0.2 < z < 0.5 is consistent with a scenario where the majority of stars in cluster galaxies form at high-redshift (z{sub f} > 1.5) and evolve passively thereafter. The best-fit for the faint-end slope of the luminosity function is {alpha} = -0.84 {+-} 0.08, which indicates that it does not evolve between z = 0 and z = 0.3. Using Principal Component Analysis of the spectra we classify cluster galaxies as either star-forming/recently-star-forming (EM+BAL) or non-star forming (ELL) and compute their respective luminosity functions. The faint-end slope of the ELL luminosity function is much shallower than for the EM+BAL galaxies at z = 0.3, and suggests the number of faint ELL galaxies in clusters decreases by a factor of {approx} 3 from z = 0 to z = 0.3. The redshift evolution of K* for both EM+BAL and ELL types is consistent with a passively evolving stellar population formed at high-redshift. Passive evolution in both classes, as well as the total cluster luminosity function, demonstrates that the bulk of the stellar population in all bright cluster galaxies is formed at high-redshift and subsequent transformations in morphology/color/spectral-type have little effect on the total stellar

  20. 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.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...

  2. HST Luminosity Functions of the Globular Clusters M10, M22, and M55. A comparison with other clusters

    CERN Document Server

    Piotto, G

    1999-01-01

    From a combination of deep Hubble Space Telescope V and I images with groundbased images in the same bands, we have obtained color-magnitude diagrams of M10, M22, and M55, extending from just above the hydrogen burning limit to the tip of the red giant branch, down to the white dwarf cooling sequence. We have used the color-magnitude arrays to extract main sequence luminosity functions (LFs) from the turnoff to about 0.13 solar masses. The LFs of M10 is significantly steeper than that for the other two clusters. The difference cannot be due to a difference in metallicity. A comparison with the LFs from Piotto, Cool, and King (1997), shows a large spread in the LF slopes. This spread is also present in the local mass functions (MFs) obtained from the observed LFs using different theoretical mass--luminosity relations. The dispersion in the MF slopes remains also after removing the mass segregation effects by using multimass King-Michie models. The globular cluster MF slopes are also flatter than the MF slope o...

  3. CpG distribution and methylation pattern in porcine parvovirus.

    Directory of Open Access Journals (Sweden)

    Renáta Tóth

    Full Text Available Based on GC content and the observed/expected CpG ratio (oCpGr, we found three major groups among the members of subfamily Parvovirinae: Group I parvoviruses with low GC content and low oCpGr values, Group II with low GC content and high oCpGr values and Group III with high GC content and high oCpGr values. Porcine parvovirus belongs to Group I and it features an ascendant CpG distribution by position in its coding regions similarly to the majority of the parvoviruses. The entire PPV genome remains hypomethylated during the viral lifecycle independently from the tissue of origin. In vitro CpG methylation of the genome has a modest inhibitory effect on PPV replication. The in vitro hypermethylation disappears from the replicating PPV genome suggesting that beside the maintenance DNMT1 the de novo DNMT3a and DNMT3b DNA methyltransferases can't methylate replicating PPV DNA effectively either, despite that the PPV infection does not seem to influence the expression, translation or localization of the DNA methylases. SNP analysis revealed high mutability of the CpG sites in the PPV genome, while introduction of 29 extra CpG sites into the genome has no significant biological effects on PPV replication in vitro. These experiments raise the possibility that beyond natural selection mutational pressure may also significantly contribute to the low level of the CpG sites in the PPV genome.

  4. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin

    DEFF Research Database (Denmark)

    Tariq, M.; Saze, H.; Probst, A.;

    2003-01-01

    DNA methylation to histone methylation, however, is less understood. Its recent examination in Arabidopsis with a partial loss of function in DNA methyltransferase 1 (responsible for maintenance of CpG methylation) yielded conflicting results. Here we report that complete removal of CpG methylation...... in an Arabidopsis mutant null for DNA maintenance methyltransferase results in a clear loss of histone H3 methylation at lysine 9 in heterochromatin and also at heterochromatic loci that remain transcriptionally silent. Surprisingly, these dramatic alterations are not reflected in heterochromatin relaxation....

  5. Density functional calculations for structural, electronic, and magnetic properties of gadolinium-oxide clusters

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-04-21

    Gadolinium-oxide clusters in various sizes and stoichiometries have been systematically studied by employing the density functional theory with the generalized gradient approximation. The clusters in bulk stoichiometry are relatively more stable and their binding energies increase with the increasing size. Stoichiometric (Gd{sub 2}O{sub 3}){sub n} clusters of n = 1–3 prefer cage-like structures, whereas the clusters of n = 4–30 prefer compact structures layered by wedge-like units and exhibit a rough feature toward the bulk-like arrangement with small disorders of atomic positions. The polyhedral-cages analogous to carbon-fullerenes are stable isomers yet not the minimum energy configurations. Their stabilities can be improved by embedding one oxygen atom or a suitable cage to form core-shell configurations. The mostly favored antiferromagnetic couplings between adjacent Gd atoms are nearly degenerated in energy with their ferromagnetic couplings, resulting in super-paramagnetic characters of gadolinium-oxide clusters. The Ruderman-Kittel-Kasuya-Yosida (RKKY)-type mechanism together with the superexchange-type mechanism plays cooperation role for the magnetic interactions in clusters. We present, as a function of n, calculated binding energies, ionization potential, electron affinity, and electronic dipole moment.

  6. 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.

  7. The mass function and dynamical mass of young star clusters: Why their initial crossing-time matters crucially

    CERN Document Server

    Parmentier, Genevieve

    2012-01-01

    We highlight the impact of cluster-mass-dependent evolutionary rates upon the evolution of the cluster mass function during violent relaxation, that is, while clusters dynamically respond to the expulsion of their residual star-forming gas. Mass-dependent evolutionary rates arise when the mean volume density of cluster-forming regions is mass-dependent. In that case, even if the initial conditions are such that the cluster mass function at the end of violent relaxation has the same shape as the embedded-cluster mass function (i.e. infant weight-loss is mass-independent), the shape of the cluster mass function does change transiently {\\it during} violent relaxation. In contrast, for cluster-forming regions of constant mean volume density, the cluster mass function shape is preserved all through violent relaxation since all clusters then evolve at the same mass-independent rate. On the scale of individual clusters, we model the evolution of the ratio between the dynamical mass and luminous mass of a cluster aft...

  8. A Theoretical Study of Lithium-Doped Gallium Clusters by Density Functional Theory

    Science.gov (United States)

    Şentürk, Şükrü; Ekincioğlu, Yavuz

    2012-05-01

    The geometrical structures, stabilities, and electronic properties of GanLi (n = 1 - 13) clusters were investigated within the density functional theory (DFT). The impurity lithium atom enhances the stability of GanLi (n = 1 - 13) clusters, especially GanLi (n = 9 - 13) compared to Gan(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 Ga7Li, Ga9Li, and Ga11Li 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.

  9. Infrared and density functional theory studies of formic acid hydrate clusters in noble gas matrices

    Science.gov (United States)

    Ito, Fumiyuki

    2016-08-01

    Infrared absorption spectra of formic acid hydrate clusters (HCOOH)m(H2O)n have been measured in noble gas matrices (Ar and Kr). The concentration dependence of the spectra and the comparison with a previous experimental study on HCOOH(H2O) and HCOOH(H2O)2 [Geoge et al., Spectrochim. Acta, Part A 60 (2004) 3225] led to the identification of large clusters. Density functional theory calculations at the B3LYP-DCP/6-31+G(2d,2p) level were carried out to determine the anharmonic vibrational properties of the clusters, enabling a consistent assignment of the observed vibrational peaks to specific clusters.

  10. Vanadium-doped small silicon clusters: Photoelectron spectroscopy and density-functional calculations

    Science.gov (United States)

    Xu, Hong-Guang; Zhang, Zeng-Guang; Feng, Yuan; Yuan, Jinyun; Zhao, Yuchao; Zheng, Weijun

    2010-03-01

    Vanadium-doped small silicon clusters, VSin- and VSin- ( n = 3-6), have been studied by anion photoelectron spectroscopy. The vertical detachment energies (VDEs) and adiabatic detachment energies (ADEs) of these clusters were obtained from their photoelectron spectra. We have also conducted density-functional calculations of VSin- and VSin- clusters and determined their structures by comparison of theoretical calculations with experimental results. Our results show that two V atoms in VSin- clusters tend to form a strong V-V bond. VSi6- has D3d symmetry with the six Si atoms forming a chair like six-membered ring similar to the ring in cyclohexane and the two vanadium atoms are joined with a δ bond.

  11. Deprojection technique for galaxy cluster considering the point spread function

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    We present a new method for the analysis of Abell 1835 observed by XMM-Newton.The method is a combination of the Direct Demodulation technique and deprojection.We eliminate the effects of the point spread function(PSF) with the Direct Demodulation technique.We then use a traditional deprojection technique to study the properties of Abell 1835.Compared to only using a deprojection method,the central electron density derived from this method increases by 30%,while the temperature profile is similar.

  12. Modeling the Near-Infrared Luminosity Functions of Young Stellar Clusters

    CERN Document Server

    Münch, A; Lada, C J; Muench, August A.; Lada, Elizabeth A.; Lada, Charles J.

    1999-01-01

    We present the results of numerical experiments designed to evaluate the usefulness of near-infrared luminosity functions for constraining the Initial Mass Function (IMF) of young stellar populations. From this numerical modeling, we find that the luminosity function of a young stellar population is considerably more sensitive to variations in the underlying initial mass function than to either variations in the star forming history or assumed pre-main-sequence (PMS) mass-to-luminosity relation. To illustrate the potential effectiveness of using the KLF of a young cluster to constrain its IMF, we model the observed K band luminosity function of the nearby Trapezium cluster. Our derived mass function for the Trapezium spans two orders of magnitude in stellar mass (5 Msun to 0.02 Msun), has a peak near the hydrogen burning limit, and has an IMF for Brown Dwarfs which steadily decreases with decreasing mass.

  13. Interrogating the function of metazoan histones using engineered gene clusters.

    Science.gov (United States)

    McKay, Daniel J; Klusza, Stephen; Penke, Taylor J R; Meers, Michael P; Curry, Kaitlin P; McDaniel, Stephen L; Malek, Pamela Y; Cooper, Stephen W; Tatomer, Deirdre C; Lieb, Jason D; Strahl, Brian D; Duronio, Robert J; Matera, A Gregory

    2015-02-09

    Histones and their posttranslational modifications influence the regulation of many DNA-dependent processes. Although an essential role for histone-modifying enzymes in these processes is well established, defining the specific contribution of individual histone residues remains a challenge because many histone-modifying enzymes have nonhistone targets. This challenge is exacerbated by the paucity of suitable approaches to genetically engineer histone genes in metazoans. Here, we describe a platform in Drosophila for generating and analyzing any desired histone genotype, and we use it to test the in vivo function of three histone residues. We demonstrate that H4K20 is neither essential for DNA replication nor for completion of development, unlike inferences drawn from analyses of H4K20 methyltransferases. We also show that H3K36 is required for viability and H3K27 is essential for maintenance of cellular identity but not for gene activation. These findings highlight the power of engineering histones to interrogate genome structure and function in animals. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Superclusters. A search for novel structures and functions of biological iron-sulfur clusters.

    OpenAIRE

    Arendsen, A.F.

    1996-01-01

    Iron sulfur (Fe-S) proteins are found in a variety of organisms. They usually function in electron transport, but they may also be involved in other functions like gene regulation and Lewis acid catalysis. The structure and spectroscopic properties of Fe-S clusters holding one, two, three, or four iron atoms is known to a great extent. These 'common' clusters share some basic properties. Firstly, they contain not more than four iron atoms. Secondly, despite the fact that they may contain more...

  15. The role of cluster mergers and travelling shocks in shaping the Hα luminosity function at z ˜ 0.2: `sausage' and `toothbrush' clusters

    Science.gov (United States)

    Stroe, Andra; Sobral, David; Röttgering, Huub J. A.; van Weeren, Reinout J.

    2014-02-01

    The most extreme cluster mergers can lead to massive cluster-wide travelling shock waves. The CIZA J2242.8+5301 (`sausage') and 1RXS J0603.3+4213 (`toothbrush') clusters (z ˜ 0.2) host enormous radio-emitting shocks with simple geometry. We investigate the role of mergers and shocks in shaping the Hα luminosity function, using custom-made narrow-band filters matching the cluster redshifts mounted on the Isaac Newton Telescope. We surveyed ˜0.28 deg2 for each cluster and found 181 line emitters in the `sausage' (volume of 3.371 × 103 Mpc3 for Hα at z = 0.1945) and 141 in the `toothbrush' (4.546 × 103 Mpc3 for Hα at z = 0.225), out of which 49 (`sausage') and 30 (`toothbrush') are expected to be Hα. We build luminosity functions for the field-of-view down to an average limiting star formation rate of 0.14 M⊙ yr-1, find good agreement with field luminosity functions at z = 0.2, but significant differences between the shapes of the luminosity functions for the two clusters. We discover extended, tens-of-kpc-wide Hα haloes in galaxies neighbouring relics, which were possibly disrupted by the passage of the shock wave. By comparing the `sausage' cluster with blank fields and other clusters, we also uncover an order of magnitude boost (at 9σ level) in the normalization φ* of the luminosity function in the relic areas. Our results suggest that cluster mergers may play an important role in the evolution of cluster galaxies through shock-induced star formation.

  16. Mass segregation in rich clusters in the Large Magellanic Cloud - III. Implications for the initial mass function

    CERN Document Server

    De Grijs, R; MacKey, A D; Wilkinson, M I; Beaulieu, S F; Johnson, R A; Santiago, B X

    2002-01-01

    The distribution of core radii of rich clusters in the Large Magellanic Cloud (LMC) systematically increases in both upper limit and spread with increasing cluster age. Cluster-to-cluster variations in the stellar initial mass function (IMF) have been suggested as an explanation. We discuss the implications of the observed degree of mass segregation in our sample clusters for the shape of the initial mass function. Our results are based on Hubble Space Telescope/WFPC2 observations of six rich star clusters in the LMC, selected to include three pairs of clusters of similar age, metallicity, and distance from the LMC centre, and exhibiting a large spread in core radii between the clusters in each pair. All clusters show clear evidence of mass segregation: (i) their luminosity function slopes steepen with increasing cluster radius, and (ii) the brighter stars are characterized by smaller core radii. For all sample clusters, both the slope of the luminosity function in the cluster centres and the degree of mass s...

  17. IL-4 and IL-13 alter plasmacytoid dendritic cell responsiveness to CpG DNA and herpes simplex virus-1

    NARCIS (Netherlands)

    Tel, J.; Torensma, R.; Figdor, C.G.; Vries, I.J.M. de

    2011-01-01

    Human plasmacytoid dendritic cells (pDCs) are found in skin lesions in a wide variety of diseases. The role of the microenvironment in these lesions on the function of human pDCs remains elusive. We sought to determine the effect of T(h)2 cytokines on the ability of human pDCs to respond to CpG

  18. The XXL Survey. II. The bright cluster sample: catalogue and luminosity function

    Science.gov (United States)

    Pacaud, F.; Clerc, N.; Giles, P. A.; Adami, C.; Sadibekova, T.; Pierre, M.; Maughan, B. J.; Lieu, M.; Le Fèvre, J. P.; Alis, S.; Altieri, B.; Ardila, F.; Baldry, I.; Benoist, C.; Birkinshaw, M.; Chiappetti, L.; Démoclès, J.; Eckert, D.; Evrard, A. E.; Faccioli, L.; Gastaldello, F.; Guennou, L.; Horellou, C.; Iovino, A.; Koulouridis, E.; Le Brun, V.; Lidman, C.; Liske, J.; Maurogordato, S.; Menanteau, F.; Owers, M.; Poggianti, B.; Pomarède, D.; Pompei, E.; Ponman, T. J.; Rapetti, D.; Reiprich, T. H.; Smith, G. P.; Tuffs, R.; Valageas, P.; Valtchanov, I.; Willis, J. P.; Ziparo, F.

    2016-06-01

    Context. The XXL Survey is the largest survey carried out by the XMM-Newton satellite and covers a total area of 50 square degrees distributed over two fields. It primarily aims at investigating the large-scale structures of the Universe using the distribution of galaxy clusters and active galactic nuclei as tracers of the matter distribution. The survey will ultimately uncover several hundreds of galaxy clusters out to a redshift of ~2 at a sensitivity of ~10-14 erg s-1 cm-2 in the [0.5-2] keV band. Aims: This article presents the XXL bright cluster sample, a subsample of 100 galaxy clusters selected from the full XXL catalogue by setting a lower limit of 3 × 10-14 erg s-1 cm-2 on the source flux within a 1' aperture. Methods: The selection function was estimated using a mixture of Monte Carlo simulations and analytical recipes that closely reproduce the source selection process. An extensive spectroscopic follow-up provided redshifts for 97 of the 100 clusters. We derived accurate X-ray parameters for all the sources. Scaling relations were self-consistently derived from the same sample in other publications of the series. On this basis, we study the number density, luminosity function, and spatial distribution of the sample. Results: The bright cluster sample consists of systems with masses between M500 = 7 × 1013 and 3 × 1014 M⊙, mostly located between z = 0.1 and 0.5. The observed sky density of clusters is slightly below the predictions from the WMAP9 model, and significantly below the prediction from the Planck 2015 cosmology. In general, within the current uncertainties of the cluster mass calibration, models with higher values of σ8 and/or ΩM appear more difficult to accommodate. We provide tight constraints on the cluster differential luminosity function and find no hint of evolution out to z ~ 1. We also find strong evidence for the presence of large-scale structures in the XXL bright cluster sample and identify five new superclusters. Based on

  19. Cluster-span threshold: An unbiased threshold for binarising weighted complete networks in functional connectivity analysis.

    Science.gov (United States)

    Smith, Keith; Azami, Hamed; Parra, Mario A; Starr, John M; Escudero, Javier

    2015-08-01

    We propose a new unbiased threshold for network analysis named the Cluster-Span Threshold (CST). This is based on the clustering coefficient, C, following logic that a balance of `clustering' to `spanning' triples results in a useful topology for network analysis and that the product of complementing properties has a unique value only when perfectly balanced. We threshold networks by fixing C at this balanced value, rather than fixing connection density at an arbitrary value, as has been the trend. We compare results from an electroencephalogram data set of volunteers performing visual short term memory tasks of the CST alongside other thresholds, including maximum spanning trees. We find that the CST holds as a sensitive threshold for distinguishing differences in the functional connectivity between tasks. This provides a sensitive and objective method for setting a threshold on weighted complete networks which may prove influential on the future of functional connectivity research.

  20. Scattering cluster wave functions on the lattice using the adiabatic projection method

    CERN Document Server

    Rokash, Alexander; Elhatisari, Serdar; Lee, Dean; Epelbaum, Evgeny; Krebs, Hermann

    2015-01-01

    The adiabatic projection method is a general framework for studying scattering and reactions on the lattice. It provides a low-energy effective theory for clusters which becomes exact in the limit of large Euclidean projection time. Previous studies have used the adiabatic projection method to extract scattering phase shifts from finite periodic-box energy levels using L\\"uschers method. In this paper we demonstrate that scattering observables can be computed directly from asymptotic cluster wave functions. For a variety of examples in one and three spatial dimensions, we extract elastic phase shifts from asymptotic cluster standing waves corresponding to spherical wall boundary conditions. We find that this approach of extracting scattering wave functions from the adiabatic Hamiltonian to be less sensitive to small stochastic and systematic errors as compared with using periodic-box energy levels.

  1. The effect of cluster size imbalance and covariates on the estimation performance of quadratic inference functions.

    Science.gov (United States)

    Westgate, Philip M; Braun, Thomas M

    2012-09-10

    Generalized estimating equations (GEE) are commonly used for the analysis of correlated data. However, use of quadratic inference functions (QIFs) is becoming popular because it increases efficiency relative to GEE when the working covariance structure is misspecified. Although shown to be advantageous in the literature, the impacts of covariates and imbalanced cluster sizes on the estimation performance of the QIF method in finite samples have not been studied. This cluster size variation causes QIF's estimating equations and GEE to be in separate classes when an exchangeable correlation structure is implemented, causing QIF and GEE to be incomparable in terms of efficiency. When utilizing this structure and the number of clusters is not large, we discuss how covariates and cluster size imbalance can cause QIF, rather than GEE, to produce estimates with the larger variability. This occurrence is mainly due to the empirical nature of weighting QIF employs, rather than differences in estimating equations classes. We demonstrate QIF's lost estimation precision through simulation studies covering a variety of general cluster randomized trial scenarios and compare QIF and GEE in the analysis of data from a cluster randomized trial. Copyright © 2012 John Wiley & Sons, Ltd.

  2. 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/.

  3. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.

    Science.gov (United States)

    Knutson, Stacy T; Westwood, Brian M; Leuthaeuser, Janelle B; Turner, Brandon E; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D; Harper, Angela F; Brown, Shoshana D; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C; Fetrow, Jacquelyn S

    2017-01-05

    Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results.

  4. Biases on Initial Mass Function Determinations. III. Cluster Masses Derived from Unresolved Photometry

    Science.gov (United States)

    Maíz Apellániz, J.

    2009-07-01

    It is currently common to use spatially unresolved multifilter broadband photometry to determine the masses of individual stellar clusters (and hence the cluster mass function, CMF). I analyze the stochastic effects introduced by the sampling of the stellar initial mass function (SIMF) in the derivation of the individual masses and the CMF, and I establish that such effects are the largest contributor to the observational uncertainties. An analytical solution, valid in the limit where uncertainties are small, is provided to establish the range of cluster masses over which the CMF slope can be obtained with a given accuracy. The validity of the analytical solution is extended to higher mass uncertainties using Monte Carlo simulations and the Gamma approximation. The value of the Poisson mass is calculated for a large range of ages and a variety of filters for solar-metallicity clusters measured with single-filter photometry. A method that uses the code CHORIZOS is presented to simultaneously derive masses, ages, and extinctions. The classical method of using unweighted UBV photometry to simultaneously establish ages and extinctions of stellar clusters is found to be unreliable for clusters older than ≈30 Ma, even for relatively large cluster masses. On the other hand, augmenting the filter set to include longer-wavelength filters and using weights for each filter increases the range of masses and ages that can be accurately measured with unresolved photometry. Nevertheless, a relatively large range of masses and ages is found to be dominated by SIMF sampling effects that render the observed masses useless, even when using UBVRIJHK photometry. A revision of some literature results affected by these effects is presented and possible solutions for future observations and analyses are suggested.

  5. Gaits-transferable CPG controller for a snake-like robot

    Institute of Scientific and Technical Information of China (English)

    LU Zhen Li; MA ShuGen; LI Bin; WANG YueChao

    2008-01-01

    With slim and legless body, particular ball articulation, and rhythmic locomotion, a nature snake adapted itself to many terrains under the control of a neuron system. Based on analyzing the locomotion mechanism, the main functional features of the motor system in snakes are specified in detail. Furthermore, a bidirectional cyclic inhibitory (BCI) CPG model is applied for the first time to imitate the pattern gen- eration for the locomotion control of the snake-like robot, and its characteristics are discussed, particularly for the generation of three kinds of rhythmic locomotion. Moreover, we introduce the neuron network organized by the BCI-CPGs connected in line with unilateral excitation to switch automatically locomotion pattern of a snake-like robot under different commands from the higher level control neuron and present a necessary condition for the CPG neuron network to sustain a rhythmic output. The validity for the generation of different kinds of rhythmic lo- comotion modes by the CPG network are verified by the dynamic simulations and experiments. This research provided a new method to model the generation mechanism of the rhythmic pattern of the snake.

  6. Dynamic Modelling of a CPG-Controlled Amphibious Biomimetic Swimming Robot

    Directory of Open Access Journals (Sweden)

    Rui Ding

    2013-04-01

    Full Text Available This paper focuses on the modelling and control problems of a self‐propelled, multimodal amphibious robot. Inspired by the undulatory body motions of fish and dolphins, the amphibious robot propels itself underwater by oscillations of several modular fish‐like propelling units coupled with a pair of pectoral fins capable of non‐continuous 360 degree rotation. In order to mimic fish‐like undulating propulsion, a control architecture based on Central Pattern Generator (CPG is applied to the amphibious robot for robust swimming gaits, including forward and backward swimming and turning, etc. With the simplification of the robot as a multi‐link serial mechanism, a Lagrangian function is employed to establish the hydrodynamic model for steady swimming. The CPG motion control law is then imported into the Lagrangian‐based dynamic model, where an associated system of kinematics and dynamics is formed to solve real‐time movements and, further, to guide the exploration of the CPG parameters and steady locomotion gaits. Finally, comparative results between the simulations and experiments are provided to show the effectiveness of the built control models.

  7. Dynamic Modelling of a CPG-Controlled Amphibious Biomimetic Swimming Robot

    Directory of Open Access Journals (Sweden)

    Rui Ding

    2013-04-01

    Full Text Available This paper focuses on the modelling and control problems of a self-propelled, multimodal amphibious robot. Inspired by the undulatory body motions of fish and dolphins, the amphibious robot propels itself underwater by oscillations of several modular fish-like propelling units coupled with a pair of pectoral fins capable of non-continuous 360 degree rotation. In order to mimic fish-like undulating propulsion, a control architecture based on Central Pattern Generator (CPG is applied to the amphibious robot for robust swimming gaits, including forward and backward swimming and turning, etc. With the simplification of the robot as a multi-link serial mechanism, a Lagrangian function is employed to establish the hydrodynamic model for steady swimming. The CPG motion control law is then imported into the Lagrangian-based dynamic model, where an associated system of kinematics and dynamics is formed to solve real-time movements and, further, to guide the exploration of the CPG parameters and steady locomotion gaits. Finally, comparative results between the simulations and experiments are provided to show the effectiveness of the built control models.

  8. Humanoids Learning to Walk: a Natural CPG-Actor-Critic Architecture

    Directory of Open Access Journals (Sweden)

    CAI eLI

    2013-04-01

    Full Text Available The identification of learning mechanisms for locomotion has been the subject of much researchfor some time but many challenges remain. Dynamic systems theory (DST offers a novel approach to humanoid learning through environmental interaction. Reinforcement learning (RL has offered a promising method to adaptively link the dynamic system to the environment it interacts with via a reward-based value system.In this paper, we propose a model that integrates the above perspectives and applies it to the case of a humanoid (NAO robot learning to walk the ability of which emerges from its value-based interaction with the environment. In the model,a simplified central pattern generator (CPG architecture inspired by neuroscientific research and DST is integrated with an actor-critic approach to RL (cpg-actor-critic. In the cpg-actor-critic architecture, least-square-temporal-difference (LSTD based learning converges to the optimal solution quickly by using natural gradient and balancing exploration and exploitation. Futhermore, rather than using a traditional (designer-specified reward it uses a dynamic value function as a stability indicator (SI that adapts to the environment.The results obtained are analyzed and explained by using a novel DST embodied cognition approach. Learning to walk, from this perspective, is a process of integrating sensorimotor levels and value.

  9. Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting

    CERN Document Server

    Veatch, Sarah; Shelby, Sarah; Chiang, Ethan; Holowka, David; Baird, Barbara

    2011-01-01

    We present an analytical method to quantify clustering in super-resolution localization images of static surfaces in two dimensions. The method also describes how over-counting of labeled molecules contributes to apparent self-clustering and how the effective lateral resolution of an image can be determined. This treatment applies to clustering of proteins and lipids in membranes, where there is significant interest in using super-resolution localization techniques to probe membrane heterogeneity. When images are quantified using pair correlation functions, the magnitude of apparent clustering due to over-counting will vary inversely with the surface density of labeled molecules and does not depend on the number of times an average molecule is counted. Over-counting does not yield apparent co-clustering in double label experiments when pair cross-correlation functions are measured. We apply our analytical method to quantify the distribution of the IgE receptor (Fc{\\epsilon}RI) on the plasma membranes of chemi...

  10. The functional vanGCd cluster of Clostridium difficile does not confer vancomycin resistance.

    Science.gov (United States)

    Ammam, Fariza; Meziane-Cherif, Djalal; Mengin-Lecreulx, Dominique; Blanot, Didier; Patin, Delphine; Boneca, Ivo G; Courvalin, Patrice; Lambert, Thierry; Candela, Thomas

    2013-08-01

    vanGCd, a cryptic gene cluster highly homologous to the vanG gene cluster of Enterococcus faecalis is largely spread in Clostridium difficile. Since emergence of vancomycin resistance would have dramatic clinical consequences, we have evaluated the capacity of the vanGCd cluster to confer resistance. We showed that expression of vanGCd is inducible by vancomycin and that VanGCd , VanXYCd and VanTCd are functional, exhibiting D-Ala : D-Ser ligase, D,D-dipeptidase and D-Ser racemase activities respectively. In other bacteria, these enzymes are sufficient to promote vancomycin resistance. Trans-complementation of C. difficile with the vanC resistance operon of Enterococcus gallinarum faintly impacted the MIC of vancomycin, but did not promote vancomycin resistance in C. difficile. Sublethal concentration of vancomycin led to production of UDP-MurNAc-pentapeptide[D-Ser], suggesting that the vanGCd gene cluster is able to modify the peptidoglycan precursors. Our results indicated amidation of UDP-MurNAc-tetrapeptide, UDP-MurNAc-pentapeptide[D-Ala] and UDP-MurNAc-pentapeptide[D-Ser]. This modification is passed on the mature peptidoglycan where a muropeptide Tetra-Tetra is amidated on the meso-diaminopimelic acid. Taken together, our results suggest that the vanGCd gene cluster is functional and is prevented from promoting vancomycin resistance in C. difficile. © 2013 John Wiley & Sons Ltd.

  11. 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 transpl...

  12. The K Band Luminosity Functions of Galaxies in High Redshift Clusters

    CERN Document Server

    Ellis, S C

    2004-01-01

    K band luminosity functions (LFs) of three, massive, high redshift clusters of galaxies are presented. The evolution of K*, the characteristic magnitude of the LF, is consistent with purely passive evolution, and a redshift of forma tion z = 1.5-2.

  13. H2 adsorption on 3d transition metal clusters: a combined infrared and density functional study

    NARCIS (Netherlands)

    Swart, I.; de Groot, F.M.F.; Weckhuysen, B.M.; Gruene, P.; Meijer, G.; Fielicke, A.

    2008-01-01

    The adsorption of H2 on a series of gas-phase transition metal (scandium, vanadium, iron, cobalt, and nickel) clusters containing up to 20 metal atoms is studied using IR-multiple photon dissociation spectroscopy complemented with density functional theory based calculations. Comparison of the exper

  14. Enhanced antibody production in mice to the malaria antigen AMA1 by CPG 7909 requires physical association of CpG and antigen

    OpenAIRE

    Mullen, Gregory E. D.; Aebig, Joan A.; Dobrescu, Gelu; Rausch, Kelly; Lambert, Lynn; Long, Carole A.; Miles, Aaron P.; Saul, Allan

    2007-01-01

    CpG oligodeoxynucleotides are potent immunostimulants. In this study, CPG 7909 was formulated with the recombinant Plasmodium falciparum protein AMA1-C1 adsorbed to Alhydrogel (aluminum hydroxide) and used to immunize mice. Mice receiving free CPG 7909 in a separate same site injection to the AMA1-C1/Alhydrogel had the same antibody responses as mice receiving AMA1-C1/Alhydrogel alone. For mice immunized with CPG 7909 bound to the AMA1-C1/Alhydrogel formulation, there was a bell shaped CPG 79...

  15. The Radio Luminosity Function and Galaxy Evolution in the Coma Cluster

    Science.gov (United States)

    Miller, Neal A.; Hornschemeier, Ann E.; Mabasher, Bahram; Brudgesm Terrry J.; Hudson, Michael J.; Marzke, Ronald O.; Smith, Russell J.

    2008-01-01

    We investigate the radio luminosity function and radio source population for two fields within the Coma cluster of galaxies, with the fields centered on the cluster core and southwest infall region and each covering about half a square degree. Using VLA data with a typical rms sensitivity of 28 (mu)Jy per 4.4" beam, we identify 249 radio sources with optical counterparts brighter than r = 22 (equivalent to M(sub r) = -13 for cluster member galaxies). Comprehensive optical spectroscopy identifies 38 of these as members of the Coma cluster, evenly split between sources powered by an active nucleus and sources powered by active star formation. The radio-detected star-forming galaxies are restricted to radio luminosities between about 10(exp 21) and 10(exp 22) W/Hz, an interesting result given that star formation dominates field radio luminosity functions below about 10(exp 23) W/Hz. The majority of the radio-detected star-forming galaxies have characteristics of starbursts, including high specific star formation rates and optical spectra with strong emission lines. In conjunction with prior studies on post-starburst galaxies within the Coma cluster, this is consistent with a picture in which late-type galaxies entering Coma undergo a starburst prior to a rapid cessation of star formation. Optically bright elliptical galaxies (Mr less than or equals -20.5) make the largest contribution to the radio luminosity function at both the high (> approx. 3x10(exp 22) W/Hz) and low (< approx. 10(exp 21) W/Hz) ends. Through a stacking analysis of these optically-bright ellipticals we find that they continue to harbor radio sources down to luminosities as faint as 3x10(exp 19) W/Hz. However, contrary to published results for the Virgo cluster we find no evidence for the existence of a population of optically faint (M(sub r) approx. equals -14) dwarf ellipticals hosting strong radio AGN.

  16. Determination of the globular cluster and halo stellar mass functions and stellar and brown dwarf densities

    CERN Document Server

    Chabrier, G; Chabrier, Gilles; Méra, Dominique

    1997-01-01

    We use recent low-mass star models, which reproduce accurately the observed sequences of various globular clusters, to convert the observed luminosity functions into bolometric luminosity functions and mass functions down to the bottom of the main sequence. These mass functions are well describedby a slowly rising power-law $dN/dm\\propto m^{-\\alpha}$, with $0.5\\wig < \\alpha \\wig < 1.5$, down to $\\sim 0.1 \\msol$, independently of the metallicity, suggesting a rather universal behaviour of the cluster initial mass functions. We predict luminosity functions in the NICMOS filters in the stellar and in the brown dwarf domains for different mass functions and metallicities. We apply these calculations to the determination, slope and normalization, of the mass function of the Galactic halo (spheroid and dark halo). The spheroid mass function is well described by the afore-mentioned power-law function with function below $\\sim 0.15 \\msol$ can not be excluded with the data presently available. Comparison with th...

  17. Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting.

    Directory of Open Access Journals (Sweden)

    Sarah L Veatch

    Full Text Available We present an analytical method using correlation functions to quantify clustering in super-resolution fluorescence localization images and electron microscopy images of static surfaces in two dimensions. We use this method to quantify how over-counting of labeled molecules contributes to apparent self-clustering and to calculate the effective lateral resolution of an image. This treatment applies to distributions of proteins and lipids in cell membranes, where there is significant interest in using electron microscopy and super-resolution fluorescence localization techniques to probe membrane heterogeneity. When images are quantified using pair auto-correlation functions, the magnitude of apparent clustering arising from over-counting varies inversely with the surface density of labeled molecules and does not depend on the number of times an average molecule is counted. In contrast, we demonstrate that over-counting does not give rise to apparent co-clustering in double label experiments when pair cross-correlation functions are measured. We apply our analytical method to quantify the distribution of the IgE receptor (FcεRI on the plasma membranes of chemically fixed RBL-2H3 mast cells from images acquired using stochastic optical reconstruction microscopy (STORM/dSTORM and scanning electron microscopy (SEM. We find that apparent clustering of FcεRI-bound IgE is dominated by over-counting labels on individual complexes when IgE is directly conjugated to organic fluorophores. We verify this observation by measuring pair cross-correlation functions between two distinguishably labeled pools of IgE-FcεRI on the cell surface using both imaging methods. After correcting for over-counting, we observe weak but significant self-clustering of IgE-FcεRI in fluorescence localization measurements, and no residual self-clustering as detected with SEM. We also apply this method to quantify IgE-FcεRI redistribution after deliberate clustering by

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

    Science.gov (United States)

    2017-05-05

    frequencies within the IR and UV - visible ranges. The absorption spectrum corresponding to excitation states of SixOy-nH2O molecular clusters consisting of...Energies and IR Spectra……………………….......................….4 DFT Calculation of UV -Vis Spectra………………………………………………………….……5 Conclusion...calculation of approximate UV -Vis absorption spectra for SixOy molecular clusters, which uses time-dependent density functional theory (TD-DFT) as

  19. Increased incidence of rare codon clusters at 5' and 3' gene termini:implications for function

    Directory of Open Access Journals (Sweden)

    Clark Patricia L

    2010-02-01

    Full Text Available Abstract Background The process of translation can be affected by the use of rare versus common codons within the mRNA transcript. Results Here, we show that rare codons are enriched at the 5' and 3' termini of genes from E. coli and other prokaryotes. Genes predicted to be secreted show significant enrichment in 5' rare codon clusters, but not 3' rare codon clusters. Surprisingly, no correlation between 5' mRNA structure and rare codon usage was observed. Conclusions Potential functional roles for the enrichment of rare codons at terminal positions are explored.

  20. Combining multiobjective optimization and cluster analysis to study vocal fold functional morphology.

    Science.gov (United States)

    Palaparthi, Anil; Riede, Tobias; Titze, Ingo R

    2014-07-01

    Morphological design and the relationship between form and function have great influence on the functionality of a biological organ. However, the simultaneous investigation of morphological diversity and function is difficult in complex natural systems. We have developed a multiobjective optimization (MOO) approach in association with cluster analysis to study the form-function relation in vocal folds. An evolutionary algorithm (NSGA-II) was used to integrate MOO with an existing finite element model of the laryngeal sound source. Vocal fold morphology parameters served as decision variables and acoustic requirements (fundamental frequency, sound pressure level) as objective functions. A two-layer and a three-layer vocal fold configuration were explored to produce the targeted acoustic requirements. The mutation and crossover parameters of the NSGA-II algorithm were chosen to maximize a hypervolume indicator. The results were expressed using cluster analysis and were validated against a brute force method. Results from the MOO and the brute force approaches were comparable. The MOO approach demonstrated greater resolution in the exploration of the morphological space. In association with cluster analysis, MOO can efficiently explore vocal fold functional morphology.

  1. CpG 7909: PF 3512676, PF-3512676.

    Science.gov (United States)

    2006-01-01

    CpG 7909 [PF-3512676] is an immunomodulating synthetic oligonucleotide designed to specifically agonise the Toll-like receptor 9 (TLR9). It is being developed for the treatment of cancer [ProMune] as a monotherapy and in combination with chemotherapeutic agents, and it is also under development as an adjuvant [VaxImmune] for vaccines against cancer and infectious diseases. CpG 7909, acting through the TLR9 receptor present in B cells and plasmacytoid dendritic cells, stimulates human B-cell proliferation, enhances antigen-specific antibody production and induces interferon-alpha production, interleukin-10 secretion and natural killer cell activity. Coley Pharmaceutical Group originally developed CpG 7909 using its CpG DNA technology. In March 2005, Coley granted Pfizer an exclusive global license to develop and commercialise CPG 7909 [ProMune] for the treatment, control and prevention of multiple cancer indications. Coley licensed CpG 7909 [VaxImmune] to Chiron Corporation for adjuvant use with Chiron's prophylactic vaccine candidates against infectious diseases in December 2003. Chiron was acquired by and merged into Novartis in April 2006. In 2002, GlaxoSmithKline (GSK) was granted a worldwide, non-exclusive licence to Coley's CpG immunostimulatory oligonucleotides, including CpG 7909 [VaxImmune], for their use as adjuvants for cancer vaccines. In 2000, Coley entered into a co-exclusive licensing agreement with GSK for the development of therapeutic and prophylactic vaccines against infectious diseases. This licensing agreement included CpG 7909 [VaxImmune] and other CpG-based immunostimulatory oligonucleotides. In September 2004, Coley Pharmaceuticals was awarded a 16.9 million US dollars, 5-year contract from the National Institute of Allergy and Infectious Diseases (NIAID), one of the National Institutes of Health (NIH), to support the development of novel immune-activating drugs for defense against bioterror agents. This contract will be used to expand Coley

  2. The initial luminosity and mass functions of the Galactic open clusters

    CERN Document Server

    Piskunov, A E; Schilbach, E; Röser, S; Scholz, R -D; Zinnecker, H

    2008-01-01

    (... abridged) The observed luminosity function can be constructed in a range of absolute integrated magnitudes $I_{M_V}= [-10, -0.5]$ mag, i.e. about 5 magnitudes deeper than in the most nearby galaxies. It increases linearly from the brightest limit to a turnover at about $I_{M_V}\\approx-2.5$. The slope of this linear portion is $a=0.41\\pm0.01$, which agrees perfectly with the slope deduced for star cluster observations in nearby galaxies. (...) We find that the initial mass function of open clusters (CIMF) has a two-segment structure with the slopes $\\alpha=1.66\\pm0.14$ in the range $\\log M_c/M_\\odot=3.37...4.93$ and $\\alpha=0.82\\pm0.14$ in the range $\\log M_c/M_\\odot=1.7...3.37$. The average mass of open clusters at birth is $4.5\\cdot 10^3 M_\\odot$, which should be compared to the average observed mass of about $700 M_\\odot$. The average cluster formation rate derived from the comparison of initial and observed mass functions is $\\bar{\\upsilon}=0.4 \\mathrm{kpc}^{-2}\\mathrm{Myr}^{-1}$. Multiplying by the a...

  3. Enhanced antibody production in mice to the malaria antigen AMA1 by CPG 7909 requires physical association of CpG and antigen.

    Science.gov (United States)

    Mullen, Gregory E D; Aebig, Joan A; Dobrescu, Gelu; Rausch, Kelly; Lambert, Lynn; Long, Carole A; Miles, Aaron P; Saul, Allan

    2007-07-20

    CpG oligodeoxynucleotides are potent immunostimulants. In this study, CPG 7909 was formulated with the recombinant Plasmodium falciparum protein AMA1-C1 adsorbed to Alhydrogel (aluminum hydroxide) and used to immunize mice. Mice receiving free CPG 7909 in a separate same site injection to the AMA1-C1/Alhydrogel had the same antibody responses as mice receiving AMA1-C1/Alhydrogel alone. For mice immunized with CPG 7909 bound to the AMA1-C1/Alhydrogel formulation, there was a bell shaped CPG 7909 dose-response curve with the highest antibody response co-incident with the concentration of CPG 7909 that saturated binding to the Alhydrogel. At a higher CPG 7909 dose where 74% was unbound, there was no enhancement of response over AMA1-C1/Alhydrogel alone. Our results suggest that the adjuvant effects of CpGs are optimal when adsorbed to Alhydrogel and highlight the need for careful characterization of the vaccine formulation.

  4. Coupled-cluster Green's function: Analysis of properties originating in the exponential parametrization of the ground-state wave function

    Science.gov (United States)

    Peng, Bo; Kowalski, Karol

    2016-12-01

    In this paper we derive basic properties of the Green's-function matrix elements stemming from the exponential coupled-cluster (CC) parametrization of the ground-state wave function. We demonstrate that all intermediates used to express the retarded (or, equivalently, ionized) part of the Green's function in the ω representation can be expressed only through connected diagrams. Similar properties are also shared by the first-order ω derivative of the retarded part of the CC Green's function. Moreover, the first-order ω derivative of the CC Green's function can be evaluated analytically. This result can be generalized to any order of ω derivatives. Through the Dyson equation, derivatives of the corresponding CC self-energy operator can be evaluated analytically. In analogy to the CC Green's function, the corresponding CC self-energy operator can be represented by connected terms. Our analysis can easily be generalized to the advanced part of the CC Green's function.

  5. 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.

  6. General transformation of α cluster model wave function to jj-coupling shell model in various 4N nuclei

    Science.gov (United States)

    Itagaki, N.; Matsuno, H.; Suhara, T.

    2016-09-01

    The antisymmetrized quasi-cluster model (AQCM) is a method to describe transitions from the α cluster wave functions to jj-coupling shell model wave functions. In this model, the cluster-shell transition is characterized by only two parameters: R representing the distance between α clusters and Λ describing the breaking of α clusters. The contribution of the spin-orbit interaction, very important in the jj-coupling shell model, can be taken into account starting with the α cluster model wave function. In this article we show the generality of AQCM by extending the application to heavier regions: various 4N nuclei from 4He to 100Sn. The characteristic magic numbers of the jj-coupling shell model, 28 and 50, are described starting with the α cluster model. The competition of two different configurations is discussed in 20Ne (16O + one quasi-cluster and 12C + two quasi-clusters) and 28Si (pentagon shape of five quasi-clusters and 12C + 16O). Also, we compare the energy curves for the α + 40Ca cluster configuration calculated with and without the α breaking effect in 44Ti.

  7. Apples to apples A2 - II. Cluster selection functions for next-generation surveys

    Science.gov (United States)

    Ascaso, B.; Mei, S.; Bartlett, J. G.; Benítez, N.

    2017-01-01

    We present the cluster selection function for three of the largest next-generation stage-IV surveys in the optical and infrared: Euclid-Optimistic, Euclid-Pessimistic and the Large Synoptic Survey Telescope (LSST). To simulate these surveys, we use the realistic mock catalogues introduced in the first paper of this series. We detected galaxy clusters using the Bayesian Cluster Finder in the mock catalogues. We then modelled and calibrated the total cluster stellar mass observable-theoretical mass (M^{*}_CL-M_h) relation using a power-law model, including a possible redshift evolution term. We find a moderate scatter of σ _{M^{*}_CL | M_h} of 0.124, 0.135 and 0.136 dex for Euclid-Optimistic, Euclid-Pessimistic and LSST, respectively, comparable to other work over more limited ranges of redshift. Moreover, the three data sets are consistent with negligible evolution with redshift, in agreement with observational and simulation results in the literature. We find that Euclid-Optimistic will be able to detect clusters with >80 per cent completeness and purity down to 8 × 1013 h-1 M⊙ up to z < 1. At higher redshifts, the same completeness and purity are obtained with the larger mass threshold of 2 × 1014 h-1 M⊙ up to z = 2. The Euclid-Pessimistic selection function has a similar shape with ˜10 per cent higher mass limit. LSST shows ˜5 per cent higher mass limit than Euclid-Optimistic up to z < 0.7 and increases afterwards, reaching a value of 2 × 1014 h-1 M⊙ at z = 1.4. Similar selection functions with only 80 per cent completeness threshold have also been computed. The complementarity of these results with selection functions for surveys in other bands is discussed.

  8. The Velocity Distribution Function of Galaxy Clusters as a Cosmological Probe

    Science.gov (United States)

    Ntampaka, M.; Trac, H.; Cisewski, J.; Price, L. C.

    2017-01-01

    We present a new approach for quantifying the abundance of galaxy clusters and constraining cosmological parameters using dynamical measurements. In the standard method, galaxy line-of-sight velocities, v, or velocity dispersions are used to infer cluster masses, M, to quantify the halo mass function (HMF), {dn}(M)/d{log}(M), which is strongly affected by mass measurement errors. In our new method, the probability distributions of velocities for each cluster in the sample are summed to create a new statistic called the velocity distribution function (VDF), {dn}(v)/{dv}. The VDF can be measured more directly and precisely than the HMF and can be robustly predicted with cosmological simulations that capture the dynamics of subhalos or galaxies. We apply these two methods to realistic (ideal) mock cluster catalogs with (without) interlopers and forecast the bias and constraints on the matter density parameter Ωm and the amplitude of matter fluctuations σ8 in flat ΛCDM cosmologies. For an example observation of 200 massive clusters, the VDF with (without) interloping galaxies constrains the parameter combination {σ }8 {{{Ω }}}m0.29(0.29)=0.589+/- 0.014 (0.584+/- 0.011) and shows only minor bias. However, the HMF with interlopers is biased to low Ωm and high σ8 and the fiducial model lies well outside of the forecast constraints, prior to accounting for Eddington bias. When the VDF is combined with constraints from the cosmic microwave background, the degeneracy between cosmological parameters can be significantly reduced. Upcoming spectroscopic surveys that probe larger volumes and fainter magnitudes will provide clusters for applying the VDF as a cosmological probe.

  9. The Gaia-ESO Survey: membership and Initial Mass Function of the Gamma Velorum cluster

    CERN Document Server

    Prisinzano, L; Micela, G; Jeffries, R D; Franciosini, E; Sacco, G G; Frasca, A; Klutsch, A; Lanzafame, A; Alfaro, E J; Biazzo, K; Bonito, R; Bragaglia, A; Caramazza, M; Vallenari, A; Carraro, G; Costado, M T; Flaccomio, E; Jofre', P; Lardo, C; Monaco, L; Morbidelli, L; Mowlavi, N; Pancino, E; Randich, S; Zaggia, S

    2016-01-01

    Understanding the properties of young open clusters, such as the Initial Mass Function (IMF), star formation history and dynamic evolution, is crucial to obtain reliable theoretical predictions of the mechanisms involved in the star formation process. We want to obtain a list, as complete as possible, of confirmed members of the young open cluster Gamma Velorum, with the aim of deriving general cluster properties such as the IMF. We used all available spectroscopic membership indicators within the Gaia-ESO public archive together with literature photometry and X-ray data and, for each method, we derived the most complete list of candidate cluster members. Then, we considered photometry, gravity and radial velocities as necessary conditions to select a subsample of candidates whose membership was confirmed by using the lithium and H$\\alpha$ lines and X-rays as youth indicators. We found 242 confirmed and 4 possible cluster members for which we derived masses using very recent stellar evolutionary models. The c...

  10. The WARPS Survey. VIII. Evolution of the Galaxy Cluster X-ray Luminosity Function

    CERN Document Server

    Koens, L A; Jones, L R; Ebeling, H; Horner, D J; Perlman, E S; Phillipps, S; Scharf, C A

    2012-01-01

    We present measurements of the galaxy cluster X-ray Luminosity Function (XLF) from the Wide Angle ROSAT Pointed Survey (WARPS) and quantify its evolution. WARPS is a serendipitous survey of the central region of ROSAT pointed observations and was carried out in two phases (WARPS-I and WARPS-II). The results here are based on a final sample of 124 clusters, complete above a flux limit of 6.5 10E-15 erg/s/cm2, with members out to redshift z ~ 1.05, and a sky coverage of 70.9 deg2. We find significant evidence for negative evolution of the XLF, which complements the majority of X-ray cluster surveys. To quantify the suggested evolution, we perform a maximum likelihood analysis and conclude that the evolution is driven by a decreasing number density of high luminosity clusters with redshift, while the bulk of the cluster population remains nearly unchanged out to redshift z ~ 1.1, as expected in a low density Universe. The results are found to be insensitive to a variety of sources of systematic uncertainty that ...

  11. Evolution of the Mass and Luminosity Functions of Globular Star Clusters

    Science.gov (United States)

    Goudfrooij, Paul; Fall, S. Michael

    2016-12-01

    We reexamine the dynamical evolution of the mass and luminosity functions of globular star clusters (GCMF and GCLF). Fall & Zhang (2001, FZ01) showed that a power-law MF, as commonly seen among young cluster systems, would evolve by dynamical processes over a Hubble time into a peaked MF with a shape very similar to the observed GCMF in the Milky Way and other galaxies. To simplify the calculations, the semi-analytical FZ01 model adopted the “classical” theory of stellar escape from clusters, and neglected variations in the M/L ratios of clusters. Kruijssen & Portegies Zwart (2009, KPZ09) modified the FZ01 model to include “retarded” and mass-dependent stellar escape, the latter causing significant M/L variations. KPZ09 asserted that their model was compatible with observations, whereas the FZ01 model was not. We show here that this claim is not correct; the FZ01 and KPZ09 models fit the observed Galactic GCLF equally well. We also show that there is no detectable correlation between M/L and L for GCs in the Milky Way and Andromeda galaxies, in contradiction with the KPZ09 model. Our comparisons of the FZ01 and KPZ09 models with observations can be explained most simply if stars escape at rates approaching the classical limit for high-mass clusters, as expected on theoretical grounds.

  12. The Starburst Cluster Westerlund 1: The Initial Mass Function and Mass Segregation

    CERN Document Server

    Lim, Beomdu; Sung, Hwankyung; Park, Byeong-Gon; Lee, Jae-Joon; Sohn, Sangmo T; Hur, Hyeonoh; Bessell, Michael S

    2012-01-01

    Westerlund 1 is the most important starburst cluster in the Galaxy due to its massive star content. We have performed BVIc and JKs photometry to investigate the initial mass function (IMF). By comparing the observed color with the spectral type - intrinsic color relation, we obtain the mean interstellar reddening of =4.19+/-0.23 and =1.70+/-0.21. Due to the heavy extinction toward the cluster, the zero-age main sequence fitting method based on optical photometry proved to be inappropriate for the distance determination, while the near-infrared photometry gave a reliable distance to the cluster -- 3.8 kpc from the empirical relation. Using the recent theoretical stellar evolution models with rotation, the age of the cluster is estimated to be 5.0+/-1.0 Myr. We derived the IMF in the massive part and obtained a fairly shallow slope of {\\Gamma} = -0.8 +/- 0.1. The integration of the IMF gave a total mass for the cluster in excess of 5.0 x 10^4 solar mass. The IMF shows a clear radial variation indicating the pre...

  13. The galaxy luminosity function in the cluster of galaxies Abell 496

    CERN Document Server

    Durret, F; Lobo, C; Durret, Florence; Adami, Christophe; Lobo, Catarina

    2002-01-01

    We have derived the galaxy luminosity function (GLF) in the cluster of galaxies Abell 496 from a wide field image in the I band. A single Schechter function reproduces quite well the GLF in the 17$\\leq {\\rm I_{AB}} \\leq$22 ($-19.5\\leq {\\rm M_I} \\leq -14.5$) magnitude interval, and the power law index of this function is found to be somewhat steeper in the outer regions than in the inner regions. This result agrees with the idea that faint galaxies are more abundant in the outer regions of clusters, while in the denser inner regions they have partly been accreted by larger galaxies or have been dimmed or even disrupted by tidal interactions.

  14. Velocity autocorrelation functions of particles and clusters in liquids. A possible criterion for correlation length of incipient glass formation

    Science.gov (United States)

    Variyar, Jayasankar E.; Kivelson, Daniel; Lynden-Bell, R. M.

    1992-12-01

    We have carried out molecular-dynamics simulations over a range of densities in two and three dimensions for particles that interact through soft repulsive potentials. We have also carried out calculations of the corresponding systems in which all particles except a tagged particle and its neighbors within a certain distance are frozen. Velocity autocorrelation functions for a single particle, for clusters containing the particle, and for the velocity of the particle relative to an embedding cluster were obtained. The single-particle velocity autocorrelation function can be resolved into correlation functions describing the local rattling in a cage or a cluster, the motion of the cluster itself, and a small cross-correlation term; the function for the single particle is sensitive to the structure of the fluid over a much shorter time scale than are those of clusters, and the shape of the single-particle velocity autocorrelation function comes primarily from rattling motion within a cage. We show that the velocity autocorrelation functions of clusters are probably better probes than that for the single particle for investigating incipient glass formation since they can be used to establish a correlation length which increases when a liquid is cooled. The dynamics of clusters at a given state point depend upon their sizes, and the nature of their motions changes qualitatively from ``rattling'' for small to ``diffusional'' for large clusters, the ``critical'' size at which the change occurs increasing with decreasing temperature. A simple model for this cluster behavior is presented.

  15. The Galaxy Cluster Mid-Infrared Luminosity Function at 1.3

    CERN Document Server

    Wylezalek, Dominika; 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 {\\mu}m luminosity functions for galaxies identified in 178 candidate galaxy clusters at 1.3 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 {\\alpha} = -1 describes the luminosity function very well in all redshifts 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 towards 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. Modelling shows that a contribu...

  16. 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.

  17. 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.

  18. The Luminosity Function of the NoSOCS Galaxy Cluster Sample

    CERN Document Server

    De Filippis, E; Longo, G; La Barbera, F; de Carvalho, R R; Gal, R

    2011-01-01

    We present the analysis of the luminosity function of a large sample of galaxy clusters from the Northern Sky Optical Cluster Survey, using latest data from the Sloan Digital Sky Survey. Our global luminosity function (down to M_r<= -16) does not show the presence of an upturn at faint magnitudes, while we do observe a strong dependence of its shape on both richness and cluster-centric radius, with a brightening of M^* and an increase of the dwarf to giant ratio with richness, indicating that more massive systems are more efficient in creating/retaining a population of dwarf satellites. This is observed both within physical (0.5 R_200) and fixed (0.5 Mpc) apertures, suggesting that the trend is either due to a global effect, operating at all scales, or to a local one but operating on even smaller scales. We further observe a decrease of the relative number of dwarf galaxies towards the cluster center; this is most probably due to tidal collisions or collisional disruption of the dwarfs since merging proces...

  19. Biases on initial mass function determinations. III. Cluster masses derived from unresolved photometry

    CERN Document Server

    Apellániz, J Maíz

    2009-01-01

    It is currently common to use spatially unresolved multi-filter broad-band photometry to determine the masses of individual stellar clusters (and hence the cluster mass function, CMF). I analyze the stochastic effects introduced by the sampling of the stellar initial mass function (SIMF) in the derivation of the individual masses and the CMF and I establish that such effects are the largest contributor to the observational uncertainties. An analytical solution, valid in the limit where uncertainties are small, is provided to establish the range of cluster masses over which the CMF slope can be obtained with a given accuracy. The validity of the analytical solution is extended to higher mass uncertainties using Monte Carlo simulations and the Gamma approximation. The value of the Poisson mass is calculated for a large range of ages and a variety of filters for solar-metallicity clusters measured with single-filter photometry. A method that uses the code CHORIZOS is presented to simultaneously derive masses, ag...

  20. The Velocity Distribution Function of Galaxy Clusters as a Cosmological Probe

    CERN Document Server

    Ntampaka, M; Cisewski, J; Price, L C

    2016-01-01

    We present a new approach for quantifying the abundance of galaxy clusters and constraining cosmological parameters using dynamical measurements. In the standard method, galaxy line-of-sight (LOS) velocities, $v$, or velocity dispersions are used to infer cluster masses, $M$, in order to quantify the halo mass function (HMF), $dn(M)/d\\log(M)$, which is strongly affected by mass measurement errors. In our new method, the probability distribution of velocities for each cluster in the sample are summed to create a new statistic called the velocity distribution function (VDF), $dn(v)/dv$. The VDF can be measured more directly and precisely than the HMF and it can also be robustly predicted with cosmological simulations which capture the dynamics of subhalos or galaxies. We apply these two methods to mock cluster catalogs and forecast the bias and constraints on the matter density parameter $\\Omega_m$ and the amplitude of matter fluctuations $\\sigma_8$ in flat $\\Lambda$CDM cosmologies. For an example observation o...

  1. Trends in the Globular Cluster Luminosity Function of Early-Type Galaxies

    CERN Document Server

    Jordan, A; Côté, P; Ferrarese, L; Peng, E W; Blakeslee, J P; Mei, S; Villegas, D; Merritt, D; Tonry, J L; West, M J; Jordan, Andres; Laughlin, Dean E. Mc; Cote, Patrick; Ferrarese, Laura; Peng, Eric W.; Blakeslee, John P.; Mei, Simona; Villegas, Daniela; Merritt, David; Tonry, John L.; West, Michael J.

    2006-01-01

    We present results from a study of the globular cluster luminosity function (GCLF) in a sample of 89 early-type galaxies observed as part of the ACS Virgo Cluster Survey. Using a Gaussian parametrization of the GCLF, we find a highly significant correlation between the GCLF dispersion, sigma, and the galaxy luminosity, M_B, in the sense that the GC systems in fainter galaxies have narrower luminosity functions. The GCLF dispersions in the Milky Way and M31 are fully consistent with this trend, implying that the correlation between sigma and galaxy luminosity is more fundamental than older suggestions that GCLF shape is a function of galaxy Hubble type. We show that the sigma - M_B relation results from a bonafide narrowing of the distribution of (logarithmic) cluster masses in fainter galaxies. We further show that this behavior is mirrored by a steepening of the GC mass function for relatively high masses, M >~ 3 x 10^5 M_sun, a mass regime in which the shape of the GCLF is not strongly affected by dynamical...

  2. Spatial dependence of 2MASS luminosity and mass functions in the old open cluster NGC 188

    CERN Document Server

    Bonatto, C; Santos, J F C

    2005-01-01

    Luminosity and mass functions in the old open cluster NGC 188 are analysed by means of J and H 2MASS photometry. Within the uncertainties, the observed projected radial density profile of NGC 188 departs from the two-parameter King model in two inner regions, which reflects the non-virialized dynamical state and possibly, some degree of non-sphericity in the spatial shape of this old open cluster. Fits with two and three-parameter King models to the radial distribution of stars resulted in a core radius of 1.3 pc and a tidal radius of 21 pc. The present 2MASS analysis resulted in significant slope variations with distance in the mass function $\\phi(m)\\propto m^{-(1+\\chi)}$, being flat in the central parts ($\\chi=0.6\\pm0.7$) and steep in the cluster outskirts ($\\chi=7.2\\pm0.6$). The overall mass function has a slope $\\chi=1.9\\pm0.7$, slightly steeper than a standard Salpeter mass function. Solar metallicity Padova isochrone fits to the near-infrared colour-magnitude diagram of NGC 188 resulted in an age of $7....

  3. Identification of functional modules in a PPI network by clique percolation clustering.

    Science.gov (United States)

    Zhang, Shihua; Ning, Xuemei; Zhang, Xiang-Sun

    2006-12-01

    Large-scale experiments and data integration have provided the opportunity to systematically analyze and comprehensively understand the topology of biological networks and biochemical processes in cells. Modular architecture which encompasses groups of genes/proteins involved in elementary biological functional units is a basic form of the organization of interacting proteins. Here we apply a graph clustering algorithm based on clique percolation clustering to detect overlapping network modules of a protein-protein interaction (PPI) network. Our analysis of the yeast Sacchromyces cerevisiae suggests that most of the detected modules correspond to one or more experimentally functional modules and half of these annotated modules match well with experimentally determined protein complexes. Our method of analysis can of course be applied to protein-protein interaction data for any species and even other biological networks.

  4. Photoelectron spectroscopy and density functional study of Co(n)C2(-) (n = 1-5) clusters.

    Science.gov (United States)

    Yuan, Jin-Yun; Xu, Hong-Guang; Zheng, Wei-Jun

    2014-03-21

    ConC2(-) (n = 1-5) cluster anions were investigated using anion photoelectron spectroscopy. The adiabatic detachment energies (ADEs) and the vertical detachment energies (VDEs) of the ConC2(-) (n = 1-5) cluster anions were determined from their photoelectron spectra. Density functional calculations were performed for the ConC2 (n = 1-5) cluster anions and neutrals. Our studies show that the structures of ConC2(-) (n = 1-5) can be described as attaching C2 to the top sites, bridge sites, or hollow sites of the Con clusters. The C2 retains an integral structure unit in the ConC2 (n = 1-5) cluster anions and neutrals, rather than being separated by the Con clusters. The C2 unit in the ConC2 (n = 1-5) cluster anions and neutrals has the characteristics of a double-bond.

  5. CpG oligodeoxyribonucleotides protect mice from Burholderia pseudomallei but not Francisella tularensis Schu 54 aersols

    Science.gov (United States)

    2010-01-01

    CpG ODN 10103 performs comparably in mice to CpG ODN 7909 (5’-TCGTCGTTTTGTCGTTTTGTCGTT-3’), which was previously reported to protect the BALB/c mice...SHORT REPORT Open Access CpG oligodeoxyribonucleotides protect mice from Burkholderia pseudomallei but not Francisella tularensis Schu S4 aerosols...that CpG oligodeoxyribonucleotides (ODN) protect mice from various bacterial pathogens, including Burkholderia pseudomallei and Francisella tularensis

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

    OpenAIRE

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

    2015-01-01

    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 M...

  7. [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.

  8. The role of cluster mergers and travelling shocks in shaping the H$\\alpha$ luminosity function at $\\bf z\\sim0.2$: `sausage' and `toothbrush' clusters

    CERN Document Server

    Stroe, Andra; Röttgering, Huub J A; van Weeren, Reinout J

    2013-01-01

    The most extreme cluster mergers can lead to massive cluster-wide travelling shock waves. The CIZA J2242.8+5301 ('sausage') and 1RXS J0603.3+4213 (`toothbrush') clusters ($z\\sim0.2$) host enormous radio-emitting shocks with simple geometry. We investigate the role of mergers and shocks in shaping the H$\\alpha$ luminosity function, using custom-made narrow-band filters matching the cluster redshifts mounted on the INT. We surveyed $\\sim0.28$ deg$^2$ for each cluster and found $181$ line emitters in the `sausage' (volume of $3.371\\times10^3$ Mpc$^3$ for H$\\alpha$ at $z=0.1945$) and $141$ in the `toothbrush' ($4.546\\times10^3$ Mpc$^3$ for H$\\alpha$ at $z=0.225$), out of which $49$ (`sausage') and $30$ (`toothbrush') are expected to be H$\\alpha$. We build luminosity functions for the field-of-view down to an average limiting star formation rate of $0.14$ M$_{\\odot}$ yr$^{-1}$, find good agreement with field luminosity functions at $z=0.2$, but significant differences between the shapes of the luminosity functions...

  9. Optical Luminosity Functions of the Abell Galaxy Cluster ABCG 209 at z=0.21

    CERN Document Server

    Mercurio, A; Merluzzi, P; Girardi, M; La Barbera, F; Busarello, G

    2003-01-01

    We derive the luminosity functions in three bands (BVR) for the rich galaxy cluster ABCG 209 at z=0.21. The data cover an area of ~78 arcmin^2 in the B and R band, while a mosaic of three pointings was obtained in the V band, covering an area of approximately 160 arcmin^2. The galaxy sample is complete to B = 22.8 (N_gal = 339), V = 22.5 (N_gal = 1078) and R = 22.0 (N_gal = 679). The luminosity functions present dips in the range V = 20.5-21.5 and R = 20.0-21.0 and therefore are better described by a sum of two Schechter functions for bright and for faint galaxies respectively. We find a marked luminosity segregation in the sense that the number ratio of bright-to-faint galaxies decreases by a factor ~4 from the center to outer regions. Our analysis supports the idea that ABCG 209 is an evolved cluster, resulting from the merger of two or more sub-clusters.

  10. Deep Advanced Camera for Surveys Imaging in the Globular Cluster NGC 6397: the Cluster Color-Magnitude Diagram and Luminosity Function

    Science.gov (United States)

    Richer, Harvey B.; Dotter, Aaron; Hurley, Jarrod; Anderson, Jay; King, Ivan; Davis, Saul; Fahlman, Gregory G.; Hansen, Brad M. S.; Kalirai, Jason; Paust, Nathaniel; Rich, R. Michael; Shara, Michael M.

    2008-06-01

    We present the color-magnitude diagram (CMD) from deep Hubble Space Telescope imaging in the globular cluster NGC 6397. The Advanced Camera for Surveys (ACS) was used for 126 orbits to image a single field in two colors (F814W, F606W) 5' SE of the cluster center. The field observed overlaps that of archival WFPC2 data from 1994 and 1997 which were used to proper motion (PM) clean the data. Applying the PM corrections produces a remarkably clean CMD which reveals a number of features never seen before in a globular cluster CMD. In our field, the main-sequence stars appeared to terminate close to the location in the CMD of the hydrogen-burning limit predicted by two independent sets of stellar evolution models. The faintest observed main-sequence stars are about a magnitude fainter than the least luminous metal-poor field halo stars known, suggesting that the lowest-luminosity halo stars still await discovery. At the bright end the data extend beyond the main-sequence turnoff to well up the giant branch. A populous white dwarf cooling sequence is also seen in the cluster CMD. The most dramatic features of the cooling sequence are its turn to the blue at faint magnitudes as well as an apparent truncation near F814W = 28. The cluster luminosity and mass functions were derived, stretching from the turnoff down to the hydrogen-burning limit. It was well modeled with either a very flat power-law or a lognormal function. In order to interpret these fits more fully we compared them with similar functions in the cluster core and with a full N-body model of NGC 6397 finding satisfactory agreement between the model predictions and the data. This exercise demonstrates the important role and the effect that dynamics has played in altering the cluster initial mass function.

  11. 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.

  12. Density functional theory study on the structural and electronic properties of Ag-adsorbed (MgO)n clusters

    Institute of Scientific and Technical Information of China (English)

    GE GuiXian; JING Qun; LUO YouHua

    2009-01-01

    Equilibrium geometries, charge distributions, stabilities and electronic properties of the Ag-adsorbed (MgO)n(n=1-8) clusters have been investigated by density functional theory (DFT)with generalized gradient approximation (GGA) for exchange-correlation functional. The results show that hollow site is energetically preferred for n≥4, and the incoming Ag atoms tend to cluster on the existing Ag cluster.The Mulliken populations indicate that the interaction between the Ag atom and Magnesia clusters is mainly induced by a weak atomic polarization. The adsorbed Ag atom only causes charge redistributions of the atoms near itself. The effect of the adsorbed Ag atom on the bonding natures and structural features of Magnesia clusters is minor. Furthermore, the investigations on the first energy difference,fragmentation energies and electron affinities show that the Ag(MgO)4 and Ag(MgO)6 are the most stable among studied clusters.

  13. Density functional theory study on the structural and electronic properties of Ag-adsorbed (MgO)_n clusters

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Equilibrium geometries, charge distributions, stabilities and electronic properties of the Ag-adsorbed (MgO)n (n = 1-8) clusters have been investigated by density functional theory (DFT) with generalized gradient approximation (GGA) for exchange-correlation functional. The results show that hollow site is energetically preferred for n≥4, and the incoming Ag atoms tend to cluster on the existing Ag cluster. The Mulliken populations indicate that the interaction between the Ag atom and Magnesia clusters is mainly induced by a weak atomic polarization. The adsorbed Ag atom only causes charge redistributions of the atoms near itself. The effect of the adsorbed Ag atom on the bonding natures and structural features of Magnesia clusters is minor. Furthermore, the investigations on the first energy difference, fragmentation energies and electron affinities show that the Ag(MgO)4 and Ag(MgO)6 are the most stable among studied clusters.

  14. The low-mass Initial Mass Function in the 30 Doradus starburst cluster

    CERN Document Server

    Andersen, M; Moneti, A; McCaughrean, M J; Brandl, B; Brandner, W; Meylan, G; Hunter, D

    2009-01-01

    We present deep Hubble Space Telescope (HST) NICMOS 2 F160W band observations of the central 56*57" (14pc*14.25pc) region around R136 in the starburst cluster 30 Dor (NGC 2070) located in the Large Magellanic Cloud. Our aim is to derive the stellar Initial Mass Function (IMF) down to ~1 Msun in order to test whether the IMF in a massive metal-poor cluster is similar to that observed in nearby young clusters and the field in our Galaxy. We estimate the mean age of the cluster to be 3 Myr by combining our F160W photometry with previously obtained HST WFPC2 optical F555W and F814W band photometry and comparing the stellar locus in the color-magnitude diagram with main sequence and pre-main sequence isochrones. The color-magnitude diagrams show the presence of differential extinction and possibly an age spread of a few megayears. We convert the magnitudes into masses adopting both a single mean age of 3 Myr isochrone and a constant star formation history from 2 to 4 Myr. We derive the IMF after correcting for inc...

  15. The XXL Survey. II. The bright cluster sample: catalogue and luminosity function

    CERN Document Server

    Pacaud, F; Giles, P A; Adami, C; Sadibekova, T; Pierre, M; Maughan, B J; Lieu, M; Fèvre, J -P Le; Alis, S; Altieri, B; Ardila, F; Baldry, I; Benoist, C; Birkinshaw, M; Chiappetti, L; Démoclès, J; Eckert, D; Evrard, A E; Faccioli, L; Gastaldello, F; Guennou, L; Horellou, C; Iovino, A; Koulouridis, E; Brun, V Le; Lidman, C; Liske, J; Maurogordato, S; Menanteau, F; Owers, M; Poggianti, B; Pomarède, D; Pompei, E; Ponman, T J; Rapetti, D; Reiprich, T H; Smith, G P; Tuffs, R; Valageas, P; Valtchanov, I; Willis, J P; Ziparo, F

    2015-01-01

    Context. The XXL Survey is the largest survey carried out by the XMM-Newton satellite and covers a total area of 50 square degrees distributed over two fields. It primarily aims at investigating the large-scale structures of the Universe using the distribution of galaxy clusters and active galactic nuclei as tracers of the matter distribution. Aims. This article presents the XXL bright cluster sample, a subsample of 100 galaxy clusters selected from the full XXL catalogue by setting a lower limit of $3\\times 10^{-14}\\,\\mathrm{erg \\,s^{-1}cm^{-2}}$ on the source flux within a 1$^{\\prime}$ aperture. Methods. The selection function was estimated using a mixture of Monte Carlo simulations and analytical recipes that closely reproduce the source selection process. An extensive spectroscopic follow-up provided redshifts for 97 of the 100 clusters. We derived accurate X-ray parameters for all the sources. Scaling relations were self-consistently derived from the same sample in other publications of the series. On th...

  16. A density functional study on the adsorption of hydrogen molecule onto small copper clusters

    Indian Academy of Sciences (India)

    Xiang-Jun Kuang; Xin-Qiang Wang; Gao-Bin Liu

    2011-09-01

    An all-electron scalar relativistic calculation on the adsorption of hydrogen molecule onto small copper clusters has been performed by using density functional theory with the generalized gradient approximation (GGA) at PW91 level. Our results reveal that after adsorption of H2 molecule, the Cu-Cu interaction is strengthened and the H-H interaction is weakened, the reactivity enhancement of H2 molecule is obvious. The VIPs, HLGs and VEAs of CuH2 clusters show an obvious odd-even oscillation. It is suggested that the H2 molecule is more favourable to be adsorbed by the even-numbered small copper clusters. Meanwhile, the odd-even alteration of magnetic moments is also observed and may be served as the material with tunable code capacity of `0’ and `1' by adsorbing hydrogen molecule onto odd or even-numbered small copper clusters. Some discrepancies of dissociative adsorption between our work and previous works are found and may be understood in terms of the electron pairing effect and the scalar relativistic effect.

  17. 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.

  18. 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.

  19. Evolution of the Mass and Luminosity Functions of Globular Star Clusters

    CERN Document Server

    Goudfrooij, Paul

    2016-01-01

    We reexamine the dynamical evolution of the mass and luminosity functions of globular star clusters (GCMF and GCLF). Fall & Zhang (2001, hereafter FZ01) showed that a power-law MF, as commonly seen among young cluster systems, would evolve by dynamical processes over a Hubble time into a peaked MF with a shape very similar to the observed GCMF in the Milky Way and other galaxies. To simplify the calculations, the semi-analytical FZ01 model adopted the "classical" theory of stellar escape from clusters, and neglected variations in the $M/L$ ratios of clusters. Kruijssen & Portegies Zwart (2009, hereafter KPZ09) modified the FZ01 model to include "retarded" and mass-dependent stellar escape, the latter causing significant $M/L$ variations. KPZ09 asserted that their model was compatible with observations whereas the FZ01 model was not. We show here that this claim is not correct; the FZ01 and KPZ09 models fit the observed Galactic GCLF equally well. We also show that there is no detectable correlation be...

  20. 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

    We present a new method for deriving cosmological constraints based on the evolution of the baryon mass function of galaxy clusters and implement it using 17 distant clusters from our 160 deg(2) ROSAT survey. The method uses the cluster baryon mass as a proxy for the total mass, thereby avoiding...... the cosmic microwave background and Type Ia supernovae near Omega(m) = 0.3 and Lambda = 0.7....

  1. A Method of Clustering Components into Modules Based on Products' Functional and Structural Analysis

    Institute of Scientific and Technical Information of China (English)

    MENG Xiang-hui; JIANG Zu-hua; ZHENG Ying-fei

    2006-01-01

    Modularity is the key to improving the cost-variety trade-off in product development. To achieve the functional independency and structural independency of modules, a method of clustering components to identify modules based on functional and structural analysis was presented. Two stages were included in the method. In the first stage the products' function was analyzed to determine the primary level of modules. Then the objective function for modules identifying was formulated to achieve functional independency of modules. Finally the genetic algorithm was used to solve the combinatorial optimization problem in modules identifying to form the primary modules of products. In the second stage the cohesion degree of modules and the coupling degree between modules were analyzed. Based on this structural analysis the modular scheme was refined according to the thinking of structural independency. A case study on the gear reducer was conducted to illustrate the validity of the presented method.

  2. Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing.

    Directory of Open Access Journals (Sweden)

    Zhifu Sun

    Full Text Available We used deep sequencing technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+ and negative breast cancer. Total mRNA sequence, gene copy number, and genomic CpG island methylation were carried out using the Illumina Genome Analyzer. Sequences were mapped to the human genome to obtain digitized gene expression data, DNA copy number in reference to the non-tumor cell line (MCF10A, and methylation status of 21,570 CpG islands to identify differentially expressed genes that were correlated with methylation or copy number changes. These were evaluated in a dataset from 129 primary breast tumors. Gene expression in cell lines was dominated by ER-associated genes. ER+ and ER- cell lines formed two distinct, stable clusters, and 1,873 genes were differentially expressed in the two groups. Part of chromosome 8 was deleted in all ER- cells and part of chromosome 17 amplified in all ER+ cells. These loci encoded 30 genes that were overexpressed in ER+ cells; 9 of these genes were overexpressed in ER+ tumors. We identified 149 differentially expressed genes that exhibited differential methylation of one or more CpG islands within 5 kb of the 5' end of the gene and for which mRNA abundance was inversely correlated with CpG island methylation status. In primary tumors we identified 84 genes that appear to be robust components of the methylation signature that we identified in ER+ cell lines. Our analyses reveal a global pattern of differential CpG island methylation that contributes to the transcriptome landscape of ER+ and ER- breast cancer cells and tumors. The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations.

  3. The extended Zel'dovich mass functions of clusters and isolated clusters in the presence of primordial non-gaussianity

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Seunghwan [Department of Astronomy, University of Massachusetts, LGRT-B 619E, 710 North Pleasant Street, Amherst, MA 01003-9305 (United States); Lee, Jounghun, E-mail: slim@astro.umass.edu, E-mail: jounghun@astro.snu.ac.kr [Astronomy Program, Department of Physics and Astronomy, FPRD, Seoul National University, Seoul 151-747 (Korea, Republic of)

    2014-09-10

    We present new formulae for the mass functions of the clusters and the isolated clusters with non-Gaussian initial conditions. For this study, we adopt the extended Zel'dovich (EZL) model as a basic framework, focusing on the case of primordial non-Gaussianity of the local type whose degree is quantified by a single parameter, f {sub nl}. By making a quantitative comparison with the N-body results, we first demonstrate that the EZL formula with the constant values of three fitting parameters still works remarkably well for the local f {sub nl} case. We also modify the EZL formula to find an analytic expression for the mass function of isolated clusters, which turns out to have only one fitting parameter other than the overall normalization factor and showed that the modified EZL formula with a constant value of the fitting parameter matches excellently the N-body results with various values of f {sub nl} at various redshifts. Given the simplicity of the generalized EZL formulae and their good agreements with the numerical results, we finally conclude that the EZL mass functions of the massive clusters and isolated clusters should be useful as an analytic guideline to constrain the scale dependence of the primordial non-Gaussianity of the local type.

  4. 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.

  5. 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.

  6. From light to mass: accessing the initial and present-day Galactic globular cluster mass functions

    CERN Document Server

    Bonatto, Charles

    2012-01-01

    The initial and present-day mass functions (ICMF and PDMF, respectively) of the Galactic globular clusters (GCs) are constructed based on their observed luminosities, the stellar evolution and dynamical mass-loss processes, and the mass-to-light ratio (MLR). Under these conditions, a Schechter-like ICMF is evolved for approximately a Hubble time and converted into the luminosity function (LF), which requires finding the values of 5 free parameters: the mean GC age (\\tA), the dissolution timescale of a $10^5 \\ms$ cluster ($\\tau_5$), the exponential truncation mass (\\mc) and 2 MLR parametrising constants. This is achieved by minimising the residuals between the evolved and observed LFs, with the minimum residuals and realistic parameters obtained with MLRs that increase with luminosity (or mass). The optimum PMDFs indicate a total stellar mass of $\\sim4\\times10^7$ \\ms\\ still bound to GCs, representing $\\sim15%$ of the mass in clusters at the beginning of the gas-free evolution. The corresponding ICMFs resemble ...

  7. The Norma cluster (ACO3627): II. The near infrared K_s-band luminosity function

    CERN Document Server

    Skelton, R E; Kraan-Korteweg, R C

    2009-01-01

    A deep K_s-band photometric catalogue of galaxies at the core of the rich, nearby Norma cluster (ACO3627) is presented. The survey covers about 45 by 45 square arcmin (slightly less than 1/3 Abell radius), which corresponds to approx. 0.8 Mpc^2 at the adopted distance (v_cmb/H0) of 70 Mpc of this cluster. The survey is estimated to be complete to a magnitude of M_Ks <~ -19.5 mag. This extends into the dwarf regime, 6 magnitudes below M_Ks*. The catalogue contains 390 objects, 235 of which are classified as likely or definite galaxies and 155 as candidate galaxies. The Ks-band luminosity function (LF) is constructed from the photometric sample, using a spectroscopic subsample to correct for fore- and background contamination. We fit a Schechter function with a characteristic magnitude of M_Ks* = -25.39 \\pm 0.80 mag and faint-end slope of alpha = -1.26 \\pm 0.10 to the data. The shape of the LF is similar to those found in previous determinations of the cluster LF, in both optical and near infrared. The Schec...

  8. A distinct group of CpG islands shows differential DNA methylation between replicas of the same cell line in vitro.

    Science.gov (United States)

    Cocozza, Sergio; Scala, Giovanni; Miele, Gennaro; Castaldo, Imma; Monticelli, Antonella

    2013-10-10

    CpG dinucleotide-rich genomic DNA regions, known as CpG islands (CGIs), can be methylated at their cytosine residues as an epigenetic mark that is stably inherited during cell mitosis. Differentially methylated regions (DMRs) are genomic regions showing different degrees of DNA methylation in multiple samples. In this study, we focused our attention on CGIs showing different DNA methylation between two culture replicas of the same cell line. We used methylation data of 35 cell lines from the Encyclopedia of DNA Elements (ENCODE) consortium to identify CpG islands that were differentially methylated between replicas of the same cell line and denoted them Inter Replicas Differentially Methylated CpG islands (IRDM-CGIs). We identified a group of IRDM-CGIs that was consistently shared by different cell lines, and denoted it common IRDM-CGIs. X chromosome CGIs were overrepresented among common IRDM-CGIs. Autosomal IRDM-CGIs were preferentially located in gene bodies and intergenic regions had a lower G + C content, a smaller mean length, and a reduced CpG percentage. Functional analysis of the genes associated with autosomal IRDM-CGIs showed that many of them are involved in DNA binding and development. Our results show that several specific functional and structural features characterize common IRDM-CGIs. They may represent a specific subset of CGIs that are more prone to being differentially methylated for their intrinsic characteristics.

  9. 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 organ

  10. DoD Planewave: A General Scalable Density Functional Code For Solids And Clusters

    Science.gov (United States)

    Kim, Seong-Gon; Singh, D. J.; Kajihara, S. A.; Woodward, C.

    2000-03-01

    We will present our latest version of the DoD Planewave code, a general purpose scalable planewave basis density functional code. DoD Planewave is written in highly portable Fortran 90 and runs on many high-performance parallel machines including IBM SP2, SGI Orgin 2000 clusters and Pentium machines running Linux. The package including the complete source code and example runs is freely available. The code is capable of treating clusters or bulk structures of insulators, semiconductors, metals and magnetic materials, with general symmetry. The present version performs self-consistent electronic structure, total energy and force calculations within the Local Density Approximation (LDA) and Generalized Gradient Approximation (GGA). It also does automatic structure optimization and ab initio molecular dynamics. Calculations demonstrating the capabilities of the code are presented. Further information may be found on our web-site (http://cst- www.nrl.navy.mil/people/singh/planewave/).

  11. Density functional theory study of neutral AlSn(n = 2-9) clusters

    Institute of Scientific and Technical Information of China (English)

    Li Ting-Xin; Wang Lin; Wang Fei; Chen Jun; Jiang Zhen-Yi; Li Li-Sha

    2011-01-01

    This paper investigates the geometrical structures and relative stabilities of neutral AlSn(n = 2-9) using the density functional theory. Structural optimisation and frequency analysis are performed at the B3LYP/6-311G(d) level. The ground state structures of the AlSn show that the sulfur atoms prefer not only to evenly distribute on both sides of the aluminum atom but also to form stable structures in AlSn clusters. The structures of pure Sn are fundamentally changed due to the doping of the Al atom. The fragmentation energies and the second-order energy differences are calculated and discussed. Among neutral AlSn(n = 2-9) clusters, AlS4 and AlS6 are the most stable.

  12. Characterizing the Properties of Clusters of Galaxies As a Function of Luminosity and Redshift

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; /MIT /Stockholm U. /SLAC; Peterson, J.R.; /Purdue U.; Madejski, G.; /SLAC /KIPAC, Menlo Park; Goobar, A.; /Stockholm U. /Stockholm U., OKC

    2009-02-24

    We report the application of the new Monte Carlo method, Smoothed Particle Inference (SPI, described in a pair of companion papers), towards analysis and interpretation of X-ray observations of clusters of galaxies with the XMM-Newton satellite. Our sample consists of publicly available well-exposed observations of clusters at redshifts z > 0.069, totaling 101 objects. We determine the luminosity and temperature structure of the X-ray emitting gas, with the goal to quantify the scatter and the evolution of the L{sub X} - T relation, as well as to investigate the dependence on cluster substructure with redshift. This work is important for the establishment of the potential robustness of mass estimates from X-ray data which in turn is essential towards the use of clusters for measurements of cosmological parameters. We use the luminosity and temperature maps derived via the SPI technique to determine the presence of cooling cores, via measurements of luminosity and temperature contrast. The L{sub X}-T relation is investigated, and we confirm that L{sub X} {proportional_to} T{sup 3}. We find a weak redshift dependence ({proportional_to} (1 + z){sup {beta}{sub LT}}, {beta}{sub LT} = 0.50 {+-} 0.34), in contrast to some Chandra results. The level of dynamical activity is established using the 'power ratios' method, and we compare our results to previous application of this method to Chandra data for clusters. We find signs of evolution in the P{sub 3}/P{sub 0} power ratio. A new method, the 'temperature two-point correlation function', is proposed. This method is used to determine the 'power spectrum' of temperature fluctuations in the X-ray emitting gas as a function of spatial scale. We show how this method can be fruitfully used to identify cooling core clusters as well as those with disturbed structures, presumably due to on-going or recent merger activity.

  13. The Rest-Frame Optical Luminosity Function of Cluster Galaxies at z<0.8 and the Assembly of the Cluster Red Sequence

    CERN Document Server

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

    2009-01-01

    We present the rest-frame optical luminosity function (LF) of red sequence galaxies in 16 clusters at 0.4Cluster 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 build-up of the faint end of the red sequence towards 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 co-eval red sequence galaxies in the field and find that the bright end of the LFs agree. However, relative to the number of br...

  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. DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Silvis Remko

    2008-12-01

    Full Text Available Abstract Background A typical step in the analysis of gene expression data is the determination of clusters of genes that exhibit similar expression patterns. Researchers are confronted with the seemingly arbitrary choice between numerous algorithms to perform cluster analysis. Results We developed an exploratory application that benchmarks the results of clustering methods using functional annotations. In addition, a de novo DNA motif discovery algorithm is integrated in our program which identifies overrepresented DNA binding sites in the upstream DNA sequences of genes from the clusters that are indicative of sites of transcriptional control. The performance of our program was evaluated by comparing the original results of a time course experiment with the findings of our application. Conclusion DISCLOSE assists researchers in the prokaryotic research community in systematically evaluating results of the application of a range of clustering algorithms to transcriptome data. Different performance measures allow to quickly and comprehensively determine the best suited clustering approach for a given dataset.

  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. Doping-enhanced hyperpolarizabilities of silicon clusters: a global ab initio and density functional theory study of Si10 (Li, Na, K)n (n=1, 2) clusters.

    Science.gov (United States)

    Karamanis, Panaghiotis; Marchal, Remi; Carbonniére, Philippe; Pouchan, Claude

    2011-07-28

    A global theoretical study of the (hyper)polarizabilities of alkali doped Si(10) is presented and discussed. First, a detailed picture about the low lying isomers of Si(10)Li, Si(10)Na, Si(10)K, Si(10)Li(2), Si(10)Na(2), and Si(10)K(2) has been obtained in a global manner. Then, the microscopic first (hyper)polarizabilities of the most stable configurations have been determined by means of ab initio methods of high predictive capability such as those based on the Møller-Plesset perturbation and coupled cluster theory, paying extra attention to the (hyper)polarizabilities of the open shell mono-doped systems Si(10)Li, Si(10)Na, Si(10)K, and the influence of spin contamination. These results were used to assess the performance of methods of low computational cost based on density functional theory (DFT) in the reliable computation of these properties in order to proceed with an in-depth study of their evolution as a function of the alkali metal, the cluster composition, and the cluster structure. The most interesting outcomes of the performed (hyper)polarizability study indicate that while alkali doping leaves the per atom polarizability practically unaffected, influences dramatically the hyperpolarizabilities of Si(10). The lowest energy structures of the mono-doped clusters are characterized by significantly enhanced hyperpolarizabilities as compared to the analogue neutral or charged bare silicon clusters Si(10) and Si(11), while, certain patterns governed by the type and the number of the doping agents are followed. The observed hyperpolarizability increase is found to be in close connection with specific cluster to alkali metal charge transfer excited states and to the cluster structures. Moreover, an interesting correlation between the anisotropy of the electron density, and the hyperpolarizabilities of these systems has been observed. Finally, it is important to note that the presented method assessment points out that among the various DFT functionals used

  18. Effect of amino groups of mesoporous silica nanoparticles on CpG oligodexynucleotide delivery

    Science.gov (United States)

    Xu, Yi; Claiden, Peter; Zhu, Yufang; Morita, Hiromi; Hanagata, Nobutaka

    2015-08-01

    In this study, we proposed to modify mesoporous silica nanoparticles (MSNs) with 3-aminopropyltriethoxysilane (NH2-TES), aminoethylaminopropyltriethoxysilane (2NH2-TES) and 3-[2-(2-aminoethylamino)ethylamino] propyl-trimethoxysilane (3NH2-TES) for binding of cytosine-phosphate-guanosine oligodexynucleotides (CpG ODN), and investigated the effect of different amino groups of MSNs on the CpG ODN delivery. Serum stability, in vitro cytotoxicity, and cytokine interleukin-6 (IL-6) induction by MSN-NH2/CpG, MSN-2NH2/CpG and MSN-3NH2/CpG complexes were investigated in detail. The results showed that three kinds of aminated-MSN-based CpG ODN delivery systems had no cytotoxicity to RAW264.7 cells, and binding of CpG ODN to MSN-NH2, MSN-2NH2 and MSN-3NH2 nanoparticles enhanced the serum stability of CpG ODN due to protection by the nanoparticles. However, three aminated MSN-based CpG ODN delivery systems exhibited different CpG ODN delivery efficiency, and MSN-NH2/CpG complexes had the highest ability to induce IL-6 secretion.

  19. CpG traffic lights are markers of regulatory regions in humans

    KAUST Repository

    Khamis, Abdullah M.

    2016-12-29

    DNA methylation is involved in regulation of gene expression. Although modern methods profile DNA methylation at single CpG sites, methylation levels are usually averaged over genomic regions in the downstream analyses. In this study we demonstrate that single CpG methylation can serve as a more accurate predictor of gene expression compared to average promoter / gene body methylation. CpG positions with significant correlation between methylation and expression of a gene nearby (named CpG traffic lights) are evolutionary conserved and enriched for exact TSS positions and active enhancers. Among all promoter types, CpG traffic lights are especially enriched in poised promoters. Genes that harbor CpG traffic lights are associated with development and signal transduction. Methylation levels of individual CpG traffic lights vary between cell types dramatically with the increased frequency of intermediate methylation levels, indicating cell population heterogeneity in CpG methylation levels. Being in line with the concept of the inherited stochastic epigenetic variation, methylation of such CpG positions might contribute to transcriptional regulation. Alternatively, one can hypothesize that traffic lights are markers of absent gene expression resulting from inactivation of their regulatory elements. The CpG traffic lights provide a promising insight into mechanisms of enhancer activity and gene regulation linking methylation of single CpG to expression.

  20. Phase 1 trial of the Plasmodium falciparum blood stage vaccine MSP1(42-C1/Alhydrogel with and without CPG 7909 in malaria naive adults.

    Directory of Open Access Journals (Sweden)

    Ruth D Ellis

    Full Text Available BACKGROUND: Merozoite surface protein 1(42 (MSP1(42 is a leading blood stage malaria vaccine candidate. In order to induce immune responses that cover the major antigenic polymorphisms, FVO and 3D7 recombinant proteins of MSP1(42 were mixed (MSP1(42-C1. To improve the level of antibody response, MSP1(42-C1 was formulated with Alhydrogel plus the novel adjuvant CPG 7909. METHODS: A Phase 1 clinical trial was conducted in healthy malaria-naïve adults at the Center for Immunization Research in Washington, D.C., to evaluate the safety and immunogenicity of MSP1(42-C1/Alhydrogel +/- CPG 7909. Sixty volunteers were enrolled in dose escalating cohorts and randomized to receive three vaccinations of either 40 or 160 microg protein adsorbed to Alhydrogel +/- 560 microg CPG 7909 at 0, 1 and 2 months. RESULTS: Vaccinations were well tolerated, with only one related adverse event graded as severe (Grade 3 injection site erythema and all other vaccine related adverse events graded as either mild or moderate. Local adverse events were more frequent and severe in the groups receiving CPG. The addition of CPG enhanced anti-MSP1(42 antibody responses following vaccination by up to 49-fold two weeks after second immunization and 8-fold two weeks after the third immunization when compared to MSP1(42-C1/Alhydrogel alone (p<0.0001. After the third immunization, functionality of the antibody was tested by an in vitro growth inhibition assay. Inhibition was a function of antibody titer, with an average of 3% (range -2 to 10% in the non CPG groups versus 14% (3 to 32% in the CPG groups. CONCLUSION/SIGNIFICANCE: The favorable safety profile and high antibody responses induced with MSP1(42-C1/Alhydrogel + CPG 7909 are encouraging. MSP1(42-C1/Alhydrogel is being combined with other blood stage antigens and will be taken forward in a formulation adjuvanted with CPG 7909. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT00320658.

  1. 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

    2017-09-14

    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. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  2. The shape of the initial cluster mass function: what it tells us about the local star formation efficiency

    CERN Document Server

    Parmentier, G; Kroupa, P; Baumgardt, H

    2008-01-01

    We explore how the expulsion of gas from star-cluster forming cloud-cores due to supernova explosions affects the shape of the initial cluster mass function, that is, the mass function of star clusters when effects of gas expulsion are over. We demonstrate that if the radii of cluster-forming gas cores are roughly constant over the core mass range, as supported by observations, then more massive cores undergo slower gas expulsion. Therefore, for a given star formation efficiency, more massive cores retain a larger fraction of stars after gas expulsion. The initial cluster mass function may thus differ from the core mass function substantially, with the final shape depending on the star formation efficiency. A mass-independent star formation efficiency of about 20 per cent turns a power-law core mass function into a bell-shaped initial cluster mass function, while mass-independent efficiencies of order 40 per cent preserve the shape of the core mass function.

  3. A turn-over in the galaxy luminosity function of the coma cluster core?

    CERN Document Server

    Adami, C; Durret, F; Nichol, R C; Mazure, A; Holden, B P; Romer, A K; Savine, C

    2000-01-01

    Our previous study of the faint end (R$\\leq$21.5) of the galaxy luminosity function (GLF) was based on spectroscopic data in a small region near the Coma cluster center. In this previous study Adami et al. (1998) suggested, with moderate statistical significance, that the number of galaxies actually belonging to the cluster was much smaller than expected. This led us to increase our spectroscopic sample. Here, we have improved the statistical significance of the results of the Coma GLF faint end study (R$\\leq$22.5) by using a sample of 85 redshifts. This includes both new spectroscopic data and a literature compilation. The relatively small number of faint galaxies belonging to Coma that was suggested by Adami et al. (1998) and Secker et al. (1998) has been confirmed with these new observations. We also confirm that the color-magnitude relation is not well suited for finding the galaxies inside the Coma cluster core, close to the center at magnitudes fainter than R$\\sim$19. We show that there is an enhancemen...

  4. The High-Mass Stellar Initial Mass Function in M31 Clusters

    CERN Document Server

    Weisz, Daniel R; Foreman-Mackey, Daniel; Dolphin, Andrew E; Beerman, Lori C; Williams, Benjamin F; Dalcanton, Julianne J; Rix, Hans-Walter; Hogg, David W; Fouesneau, Morgan; Johnson, Benjamin D; Bell, Eric F; Boyer, Martha L; Gouliermis, Dimitrios; Guhathakurta, Puragra; Kalirai, Jason S; Lewis, Alexia R; Seth, Anil C; Skillman, Evan D

    2015-01-01

    We have undertaken the largest systematic study of the high-mass stellar initial mass function (IMF) to date using the optical color-magnitude diagrams (CMDs) of 85 resolved, young (4 Myr 2 Msun. For the ensemble of clusters, the distribution of stellar MF slopes is best described by $\\Gamma=+1.45^{+0.03}_{-0.06}$ with a very small intrinsic scatter. The data also imply no significant dependencies of the MF slope on cluster age, mass, and size, providing direct observational evidence that the measured MF represents the IMF. This analysis implies that the high-mass IMF slope in M31 clusters is universal with a slope ($\\Gamma=+1.45^{+0.03}_{-0.06}$) that is steeper than the canonical Kroupa (+1.30) and Salpeter (+1.35) values. Using our inference model on select Milky Way (MW) and LMC high-mass IMF studies from the literature, we find $\\Gamma_{\\rm MW} \\sim+1.15\\pm0.1$ and $\\Gamma_{\\rm LMC} \\sim+1.3\\pm0.1$, both with intrinsic scatter of ~0.3-0.4 dex. Thus, while the high-mass IMF in the Local Group may be unive...

  5. 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.

  6. Young and embedded clusters in Cygnus-X: evidence for building up the initial mass function?

    Science.gov (United States)

    Maia, F. F. S.; Moraux, E.; Joncour, I.

    2016-05-01

    We provide a new view on the Cygnus-X north complex by accessing for the first time the low mass content of young stellar populations in the region. Canada-France-Hawaii Telescope/Wide-Field Infrared Camera was used to perform a deep near-infrared survey of this complex, sampling stellar masses down to ˜0.1 M⊙. Several analysis tools, including a extinction treatment developed in this work, were employed to identify and uniformly characterize a dozen unstudied young star clusters in the area. Investigation of their mass distributions in low-mass domain revealed a relatively uniform log-normal initial mass function (IMF) with a characteristic mass of 0.32 ± 0.08 M⊙ and mass dispersion of 0.40 ± 0.06. In the high-mass regime, their derived slopes showed that while the youngest clusters (age build up' their IMF by accreting low-mass stars formed in their vicinity during their first ˜3 Myr, before the gas expulsion phase, emerging at the age of ˜4 Myr with a fully fledged IMF. Finally, the derived distances to these clusters confirmed the existence of at least three different star-forming regions throughout Cygnus-X north complex, at distances of 500-900 pc, 1.4-1.7 and 3.0 kpc, and revealed evidence of a possible interaction between some of these stellar populations and the Cygnus OB2 association.

  7. Shaping the Globular Cluster Mass Function by Stellar-Dynamical Evaporation

    CERN Document Server

    McLaughlin, Dean E

    2007-01-01

    Dynamical-evolution models of old globular cluster mass functions (GCMFs), in which the depletion of an initial power-law distribution at low masses is caused predominantly by evaporation driven by internal two-body relaxation, can explain the turnover mass scale M_{TO} and the generic shape of the GCMF at M < M_{TO}. We point out that such models inherently predict that the GCMF should depend on the cluster half-mass density, rho_h, and we show that the Galactic GCMF exhibits precisely the expected variations: M_{TO} increases systematically with rho_h, while the width of the distribution decreases. The quantitative details are consistent with a cluster mass-loss rate, -dM/dt = mu_{ev} ~ rho_h^{1/2} with rho_h approximately constant in time, which we adopt as the simplest description of evaporation. The normalization of mu_{ev} is within a factor of two of standard theoretical expectations. We show that the known, weak dependence of the Milky Way GCMF on Galactocentric position r_{gc} results from its bas...

  8. Functional clustering drives encoding improvement in a developing brain network during awake visual learning.

    Directory of Open Access Journals (Sweden)

    Kaspar Podgorski

    2012-01-01

    Full Text Available Sensory experience drives dramatic structural and functional plasticity in developing neurons. However, for single-neuron plasticity to optimally improve whole-network encoding of sensory information, changes must be coordinated between neurons to ensure a full range of stimuli is efficiently represented. Using two-photon calcium imaging to monitor evoked activity in over 100 neurons simultaneously, we investigate network-level changes in the developing Xenopus laevis tectum during visual training with motion stimuli. Training causes stimulus-specific changes in neuronal responses and interactions, resulting in improved population encoding. This plasticity is spatially structured, increasing tuning curve similarity and interactions among nearby neurons, and decreasing interactions among distant neurons. Training does not improve encoding by single clusters of similarly responding neurons, but improves encoding across clusters, indicating coordinated plasticity across the network. NMDA receptor blockade prevents coordinated plasticity, reduces clustering, and abolishes whole-network encoding improvement. We conclude that NMDA receptors support experience-dependent network self-organization, allowing efficient population coding of a diverse range of stimuli.

  9. Structure-dependent immunostimulatory effect of CpG oligodeoxynucleotides and their delivery system

    Directory of Open Access Journals (Sweden)

    Hanagata N

    2012-04-01

    Full Text Available Nobutaka HanagataNanotechnology Innovation Station, National Institute for Materials Science, Tsukuba, Ibaraki, and Graduate School of Life Science, Hokkaido University, Kita-ku, Sapporo, JapanAbstract: Unmethylated cytosine-phosphate-guanosine (CpG oligodeoxynucleotides (ODNs are recognized by Toll-like receptor 9 (TLR9 found in antigen-presenting cells and B cells and can activate the immune system. Using CpG ODNs as an adjuvant has been found to be effective for treating infectious diseases, cancers, and allergies. Because natural ODNs with only a phosphodiester backbone are easily degraded by nuclease (deoxyribonuclease [DNase] in serum, CpG ODNs with a phosphorothioate backbone have been studied for clinical application. CpG ODNs with a phosphorothioate backbone have raised concern regarding undesirable side effects; however, several CpG ODNs with only a phosphodiester backbone have been reported to be stable in serum and to show an immunostimulatory effect. In recent years, research has been conducted on delivery systems for CpG ODNs using nanoparticles (NPs. The advantages of NP-based delivery of CpG ODN include (1 it can protect CpG ODN from DNase, (2 it can retain CpG ODN inside the body for a long period of time, (3 it can improve the cellular uptake efficiency of CpG ODN, and (4 it can deliver CpG ODN to the target tissues. Because the target cells of CpG ODN are cells of the immune system and TLR9, the receptor of CpG ODN is localized in endolysosomes, CpG ODN delivery systems are required to have qualities different from other nucleic acid drugs such as antisense DNA and small interfering RNA. Studies until now have reported various NPs as carriers for CpG ODN delivery. This review presents DNase-resistant CpG ODNs with various structures and their immunostimulatory effects and also focuses on delivery systems of CpG ODNs that utilize NPs. Because CpG ODNs interact with TLR9 and activate both the innate and the adaptive immune

  10. CpG DNA assists the whole inactivated H9N2 influenza virus in crossing the intestinal epithelial barriers via transepithelial uptake of dendritic cell dendrites.

    Science.gov (United States)

    Yin, Y; Qin, T; Wang, X; Lin, J; Yu, Q; Yang, Q

    2015-07-01

    Intestinal mucosa remains a pivotal barrier for the oral vaccine absorption of H9N2 whole inactivated influenza virus (WIV). However, CpG DNA, as an adjuvant, can effectively improve relevant mucosal and systemic immunity. The downstream mechanism is well confirmed, yet the evidence of CpG DNA assisting H9N2 WIV in transepithelial delivery is lacking. Here, we reported both in vitro and in vivo that CpG DNA combined with H9N2 WIV was capable of recruiting additional dendritic cells (DCs) to the intestinal epithelial cells (ECs) to form transepithelial dendrites (TEDs) for luminal viral uptake. Both CD103(+) and CD103(-) DCs participated in this process. The engagement of the chemokine CCL20 from the apical ECs and the DCs drove DC recruitment and TED formation. Virus-loaded CD103(+) but not CD103(-) DCs also quickly migrated into mesenteric lymph nodes within 2 h. Moreover, the mechanism of CpG DNA was independent of epithelial transcytosis and disruption of the epithelial barriers. Finally, the subsequent phenotypic and functional maturation of DCs was also enhanced. Our findings indicated that CpG DNA improved the delivery of H9N2 WIV via TEDs of intestinal DCs, and this may be an important mechanism for downstream effective antigen-specific immune responses.

  11. Equilibrium Structures and Absorption Spectra for SixOy-nH2O Molecular Clusters using Density Functional Theory

    Science.gov (United States)

    2017-05-04

    College, City University of New York, New York, NY 10065 ONR Absorption spectra Density Functional Theory Molecular clusters Contents Introduction ...Clusters using Density Functional Theory May 4, 2017 Approved for public release; distribution is unlimited. L. Huang S.g. LambrakoS Center for...reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching

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

    OpenAIRE

    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 organization theory, the networking formation function is the most important one, next demand articulation and innovation process management. However, our findings indicate that also visionary leadershi...

  13. Determination of the Linear Mass Power Spectrum From the Mass Function of Galaxy Clusters

    CERN Document Server

    Sánchez, A G; Lambas, D G

    2002-01-01

    We develop a new method to determine the linear mass power spectrum using the mass function of galaxy clusters. We obtain the rms mass fluctuation sigma (M) using the expression for the mass function in the Press & Schechter (1974), Sheth, Mo & Tormen (2001) and Jenkins et al. (2001) formalisms. We apply different techniques to recover the adimensional power spectrum Delta ^{2}(k) from sigma (M) namely the k_{eff} approximation, the singular value decomposition and the linear regularization method. The application of these techniques to the tCDM and LCDM GIF simulations shows a high efficiency in recovering the theoretical power spectrum over a wide range of scales. We compare our results with those derived from the power spectrum of the spatial distribution of the same sample of clusters in the simulations obtained by application of the classical Feldman, Kaiser & Peacock (1994), FKP, method. We find that the mass function based method presented here can provide a very accurate estimate of the li...

  14. Deep ACS Imaging in the Globular Cluster NGC 6397: The Cluster Color Magnitude Diagram and Luminosity Function

    CERN Document Server

    Richer, Harvey B; Hurley, Jarrod; Anderson, Jay; King, Ivan; Davis, Saul; Fahlman, Gregory G; Hansen, Brad M S; Kalirai, Jason; Paust, Nathaniel; Rich, R Michael; Shara, Michael M

    2007-01-01

    We present the CMD from deep HST imaging in the globular cluster NGC 6397. The ACS was used for 126 orbits to image a single field in two colors (F814W, F606W) 5 arcmin SE of the cluster center. The field observed overlaps that of archival WFPC2 data from 1994 and 1997 which were used to proper motion (PM) clean the data. Applying the PM corrections produces a remarkably clean CMD which reveals a number of features never seen before in a globular cluster CMD. In our field, the main sequence stars appeared to terminate close to the location in the CMD of the hydrogen-burning limit predicted by two independent sets of stellar evolution models. The faintest observed main sequence stars are about a magnitude fainter than the least luminous metal-poor field halo stars known, suggesting that the lowest luminosity halo stars still await discovery. At the bright end the data extend beyond the main sequence turnoff to well up the giant branch. A populous white dwarf cooling sequence is also seen in the cluster CMD. Th...

  15. SUBSTELLAR OBJECTS IN NEARBY YOUNG CLUSTERS. VII. THE SUBSTELLAR MASS FUNCTION REVISITED

    Energy Technology Data Exchange (ETDEWEB)

    Scholz, Alexander; Geers, Vincent [School of Cosmic Physics, Dublin Institute for Advanced Studies, 31 Fitzwilliam Place, Dublin 2 (Ireland); Clark, Paul [Zentrum für Astronomie der Universität Heidelberg, Institut für Theoretische Astrophysik, Albert-Ueberle-Str. 2, D-69120 Heidelberg (Germany); Jayawardhana, Ray [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George Street, Toronto, ON M5S 3H4 (Canada); Muzic, Koraljka, E-mail: as110@st-andrews.ac.uk [European Southern Observatory, Alonso de Córdova 3107, Casilla 19, 19001 Santiago (Chile)

    2013-10-01

    The abundance of brown dwarfs (BDs) in young clusters is a diagnostic of star formation theory. Here we revisit the issue of determining the substellar initial mass function (IMF) based on a comparison between NGC 1333 and IC348, two clusters in the Perseus star-forming region. We derive their mass distributions for a range of model isochrones, varying distances, extinction laws, and ages with comprehensive assessments of the uncertainties. We find that the choice of isochrone and other parameters have significant effects on the results, thus we caution against comparing IMFs obtained using different approaches. For NGC 1333, we find that the star/BD ratio R is between 1.9 and 2.4 for all plausible scenarios, consistent with our previous work. For IC348, R is found to be between 2.9 and 4.0, suggesting that previous studies have overestimated this value. Thus the star-forming process generates about 2.5-5 substellar objects per 10 stars. The derived star/BD ratios correspond to a slope of the power-law mass function of α = 0.7-1.0 for the 0.03-1.0 M{sub ☉} mass range. The median mass in these clusters—the typical stellar mass—is between 0.13 and 0.30 M{sub ☉}. Assuming that NGC 1333 is at a shorter distance than IC348, we find a significant difference in the cumulative distribution of masses between the two clusters, resulting from an overabundance of very low mass objects in NGC 1333. Gaia astrometry will constrain the cluster distances better and will lead to a more definitive conclusion. Furthermore, the star/BD ratio is somewhat larger in IC348 compared with NGC 1333, although this difference is still within the margins of error. Our results indicate that environments with higher object density may produce a larger fraction of very low mass objects, in line with predictions for BD formation through gravitational fragmentation of filaments falling into a cluster potential.

  16. Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

    Energy Technology Data Exchange (ETDEWEB)

    Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

    2017-08-01

    The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

  17. Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

    Energy Technology Data Exchange (ETDEWEB)

    Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

    2017-01-24

    The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

  18. Detecting multiple outliers in linear functional relationship model for circular variables using clustering technique

    Science.gov (United States)

    Mokhtar, Nurkhairany Amyra; Zubairi, Yong Zulina; Hussin, Abdul Ghapor

    2017-05-01

    Outlier detection has been used extensively in data analysis to detect anomalous observation in data and has important application in fraud detection and robust analysis. In this paper, we propose a method in detecting multiple outliers for circular variables in linear functional relationship model. Using the residual values of the Caires and Wyatt model, we applied the hierarchical clustering procedure. With the use of tree diagram, we illustrate the graphical approach of the detection of outlier. A simulation study is done to verify the accuracy of the proposed method. Also, an illustration to a real data set is given to show its practical applicability.

  19. CPG Control for Biped Hopping Robot in Unpredictable Environment

    Institute of Scientific and Technical Information of China (English)

    Tingting Wang; Wei Guo; Mantian Li; Fusheng Zha; Lining Sun

    2012-01-01

    A CPG control mechanism is proposed for hopping motion control of biped robot in unpredictable environment.Based on analysis of robot motion and biological observation of animal's control mechanism,the motion control task is divided into two simple parts:motion sequence control and output force control.Inspired by a two-level CPG model,a two-level CPG control mechanism is constructed to coordinate the drivers of robot joint,while various feedback information are introduced into the control mechanism.Interneurons within the control mechanism are modeled to generate motion rhythm and pattern promptly for motion sequence control; motoneurons are modeled to control output forces of joint drivers in real time according to feedbacks.The control system can perceive changes caused by unknown perturbations and environment changes according to feedback information,and adapt to unpredictable environment by adjusting outputs of neurons.The control mechanism is applied to a biped hopping robot in unpredictable environment on simulation platform,and stable adaptive motions are obtained.

  20. Electrophysiological Representation of Scratching CPG Activity in the Cerebellum

    Science.gov (United States)

    Martínez-Silva, Lourdes; Manjarrez, Elias; Gutiérrez-Ospina, Gabriel; Quevedo, Jorge N.

    2014-01-01

    We analyzed the electrical activity of neuronal populations in the cerebellum and the lumbar spinal cord during fictive scratching in adult decerebrate cats before and after selective sections of the Spino-Reticulo Cerebellar Pathway (SRCP) and the Ventral-Spino Cerebellar Tract (VSCT). During fictive scratching, we found a conspicuous sinusoidal electrical activity, called Sinusoidal Cerebellar Potentials (SCPs), in the cerebellar vermis, which exhibited smaller amplitude in the paravermal and hemisphere cortices. There was also a significant spino-cerebellar coherence between these SCPs and the lumbar sinusoidal cord dorsum potentials (SCDPs). However, during spontaneous activity such spino-cerebellar coherence between spontaneous potentials recorded in the same regions decreased. We found that the section of the SRCP and the VSCT did not abolish the amplitude of the SCPs, suggesting that there are additional pathways conveying information from the spinal CPG to the cerebellum. This is the first evidence that the sinusoidal activity associated to the spinal CPG circuitry for scratching has a broad representation in the cerebellum beyond the sensory representation from hindlimbs previously described. Furthermore, the SCPs represent the global electrical activity of the spinal CPG for scratching in the cerebellar cortex. PMID:25350378

  1. The substellar mass function in the central region of the open cluster Praesepe from deep LBT observations

    CERN Document Server

    Wang, W; Goldman, B; Henning, Th; Caballero, J A; Bailer-Jones, C A L

    2010-01-01

    Studies of the mass function (MF) of open clusters of different ages allow us to probe the efficiency with which brown dwarfs (BDs) are evaporated from clusters to populate the field. Surveys in old clusters (age > 100 Myr) do not suffer so severely from several problems encountered in young clusters, such as intra-cluster extinction and large uncertainties in BD models. Here we present the results of a deep photometric survey to study the MF of the old open cluster Praesepe (age 590 Myr and distance 190 pc), down to a 5 sigma detection limit at i~25.6 mag (~40M_Jup). We identify 62 cluster member candidates, of which 40 are substellar, from comparison with predictions from a dusty atmosphere model. The MF rises from the substellar boundary until ~60M_Jup and then declines. This is quite different from the form inferred for other open clusters older than 50 Myr, but seems to be similar to those found in very young open cluster, whose MFs peak at ~10M_Jup. Either Praesepe really does have a different MF from o...

  2. 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.

  3. Properties of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions through photoelectron spectroscopy and density functional theory calculations.

    Science.gov (United States)

    Yin, Shi; Bernstein, Elliot R

    2016-10-21

    A new magnetic-bottle time-of-flight photoelectron spectroscopy (PES) apparatus is constructed in our laboratory. The PES spectra of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide [FeSm(SH)n(-); m, n = 0-3, 0 density functional theory. The most probable structures and ground state spin multiplicity for these cluster anions are tentatively assigned by comparing their theoretical first vertical detachment energies (VDEs) with their respective experiment values. The behavior of S and (SH) as ligands in these iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions is investigated and compared. The experimental first VDEs for Fe(SH)1-3(-) cluster anions are lower than those found for their respective FeS1-3(-) cluster anions. The experimental first VDEs for FeS1-3(-) clusters are observed to increase for the first two S atoms bound to Fe(-); however, due to the formation of an S-S bond for the FeS3(-) cluster, its first VDE is found to be ∼0.41 eV lower than the first VDE for the FeS2(-) cluster. The first VDEs of Fe(SH)1-3(-) cluster anions are observed to increase with the increasing numbers of SH groups. The calculated partial charges of the Fe atom for ground state FeS1-3(-) and Fe(SH)1-3(-) clusters are apparently related to and correlated with their determined first VDEs. The higher first VDE is correlated with a higher, more positive partial charge for the Fe atom of these cluster anions. Iron sulfide/hydrosulfide mixed cluster anions are also explored in this work: the first VDE for FeS(SH)(-) is lower than that for FeS2(-), but higher than that for Fe(SH)2(-); the first VDEs for FeS2(SH)(-) and FeS(SH)2(-) are close to that for FeS3(-), but higher than that for Fe(SH)3(-). The first VDEs of general iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide clusters [FeSm(SH)n(-); m, n = 0-3, 0 number of hydrosulfide ligands in the cluster. The higher the partial charge on the Fe atom of these clusters, the larger the first VDE

  4. Accurate dipole polarizabilities for water clusters n=2-12 at the coupled-cluster level of theory and benchmarking of various density functionals

    Energy Technology Data Exchange (ETDEWEB)

    Hammond, Jeffrey R.; Govind, Niranjan; Kowalski, Karol; Autschbach, Jochen; Xantheas, Sotiris S.

    2009-12-07

    The static dipole polarizabilities of water clusters are determined at the Coupled-Cluster level of theory (CCSD). For the dipole polarizability of the water monomer it was determined that the role of the basis set is even more important than that of electron correlation and that the basis set augmentation converges with two sets of diffuse functions. The CCSD results are used to benchmark a variety of density functionals while the performance of several families of basis sets (Dunning, Pople and Sadlej) in producing accurate values for the polarizabilities was also examined. The Sadlej family of basis sets was found to produce accurate results when compared to the ones obtained with the much larger Dunning basis sets. It was furthermore determined that the PBE0 density functional with the aug-cc-pVDZ basis set produces overall remarkably accurate polarizabilities at a moderate computational cost.

  5. 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...

  6. A non-parametric statistical test to compare clusters with applications in functional magnetic resonance imaging data.

    Science.gov (United States)

    Fujita, André; Takahashi, Daniel Y; Patriota, Alexandre G; Sato, João R

    2014-12-10

    Statistical inference of functional magnetic resonance imaging (fMRI) data is an important tool in neuroscience investigation. One major hypothesis in neuroscience is that the presence or not of a psychiatric disorder can be explained by the differences in how neurons cluster in the brain. Therefore, it is of interest to verify whether the properties of the clusters change between groups of patients and controls. The usual method to show group differences in brain imaging is to carry out a voxel-wise univariate analysis for a difference between the mean group responses using an appropriate test and to assemble the resulting 'significantly different voxels' into clusters, testing again at cluster level. In this approach, of course, the primary voxel-level test is blind to any cluster structure. Direct assessments of differences between groups at the cluster level seem to be missing in brain imaging. For this reason, we introduce a novel non-parametric statistical test called analysis of cluster structure variability (ANOCVA), which statistically tests whether two or more populations are equally clustered. The proposed method allows us to compare the clustering structure of multiple groups simultaneously and also to identify features that contribute to the differential clustering. We illustrate the performance of ANOCVA through simulations and an application to an fMRI dataset composed of children with attention deficit hyperactivity disorder (ADHD) and controls. Results show that there are several differences in the clustering structure of the brain between them. Furthermore, we identify some brain regions previously not described to be involved in the ADHD pathophysiology, generating new hypotheses to be tested. The proposed method is general enough to be applied to other types of datasets, not limited to fMRI, where comparison of clustering structures is of interest. Copyright © 2014 John Wiley & Sons, Ltd.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hochkeppel, Stephan

    2008-07-25

    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

  8. 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.

  9. 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.

  10. Substellar Objects in Nearby Young Clusters VII: The substellar mass function revisited

    CERN Document Server

    Scholz, Aleks; Clark, Paul; Jayawardhana, Ray; Muzic, Koraljka

    2013-01-01

    The abundance of brown dwarfs (BDs) in young clusters is a diagnostic of star formation theory. Here we revisit the issue of determining the substellar initial mass function (IMF), based on a comparison between NGC1333 and IC348, two clusters in the Perseus star-forming region. We derive their mass distributions for a range of model isochrones, varying distances, extinction laws and ages, with comprehensive assessments of the uncertainties. We find that the choice of isochrone and other parameters have significant effects on the results, thus we caution against comparing IMFs obtained using different approaches. For NGC1333, we find that the star/BD ratio R is between 1.9 and 2.4, for all plausible scenarios, consistent with our previous work. For IC348, R is between 2.9 and 4.0, suggesting that previous studies have overestimated this value. Thus, the star forming process generates about 2.5-5 substellar objects per 10 stars. The derived star/BD ratios correspond to a slope of the power-law mass function of ...

  11. Method of Moments of Coupled-Cluster Equations: Externally Corrected Approaches Employing Configuration Interaction Wave Functions

    Directory of Open Access Journals (Sweden)

    Ian S.O. Pimienta

    2002-05-01

    Full Text Available Abstract: A new approach to the many-electron correlation problem, termed the method of moments of coupled-cluster equations (MMCC, is further developed and tested. The main idea of the MMCC theory is that of the noniterative energy corrections which, when added to the energies obtained in the standard coupled-cluster calculations, recover the exact (full configuration interaction energy. The MMCC approximations require that a guess is provided for the electronic wave function of interest. The idea of using simple estimates of the wave function, provided by the inexpensive configuration interaction (CI methods employing small sets of active orbitals to define higher–than–double excitations, is tested in this work. The CI-corrected MMCC methods are used to study the single bond breaking in HF and the simultaneous breaking of both O–H bonds in H2O.

  12. Post-Nonlinear Sparse Component Analysis Using Single-Source Zones and Functional Data Clustering

    CERN Document Server

    Puigt, Matthieu; Mouchtaris, Athanasios

    2012-01-01

    In this paper, we introduce a general extension of linear sparse component analysis (SCA) approaches to postnonlinear (PNL) mixtures. In particular, and contrary to the state-of-art methods, our approaches use a weak sparsity source assumption: we look for tiny temporal zones where only one source is active. We investigate two nonlinear single-source confidence measures, using the mutual information and a local linear tangent space approximation (LTSA). For this latter measure, we derive two extensions of linear single-source measures, respectively based on correlation (LTSA-correlation) and eigenvalues (LTSA-PCA). A second novelty of our approach consists of applying functional data clustering techniques to the scattered observations in the above single-source zones, thus allowing us to accurately estimate them.We first study a classical approach using a B-spline approximation, and then two approaches which locally approximate the nonlinear functions as lines. Finally, we extend our PNL methods to more gener...

  13. Clustered Natural Frequencies in Multi-Span Beams with Constrained Characteristic Functions

    Directory of Open Access Journals (Sweden)

    Khodabakhsh Saeedi

    2011-01-01

    Full Text Available A study of the natural frequencies and mode shapes of a multi-span beam is carried out by introducing constrained beam characteristic functions. The conventional method used for the dynamic analysis of such a beam is to consider span-wise characteristic function solution and then to solve it by using compatibility conditions such as the continuity in the a slope and bending moment at the intermediate supports and boundary conditions at the ends. In the method proposed here, the matrix size is reduced and, if the support conditions are symmetric about the midpoint, the symmetry and anti-symmetry conditions at the midpoint can be conveniently exploited for computational economy. The natural frequencies occur in clusters, each one containing the number of natural frequencies equal to the number of spans. The results are presented and discussed.

  14. Spin and charge distribution in iron porphyrin models: a coupled cluster and density-functional study.

    Science.gov (United States)

    Johansson, Mikael P; Sundholm, Dage

    2004-02-15

    We recently performed detailed analyses of the electronic structure of low-spin iron porphyrins using density-functional theory (DFT). Both the spin-density distributions of the oxidized, ferric forms, as well as the changes in total charge density upon reduction to the ferrous forms have been explored. Here, we compare the DFT results with wave-function theory, more specifically, with the approximate singles and doubles coupled-cluster method (CC2). Different spin states are considered by studying representative models of low spin, intermediate spin, and high spin species. The CC2 calculations corroborate the DFT results; the spin density exhibits the same amount of molecular spin polarization, and the charge delocalization is of comparable magnitude. Slight differences in the descriptions are noted and discussed.

  15. Expansion schemes for gravitational clustering: computing two-point and three-point functions

    CERN Document Server

    Valageas, P

    2007-01-01

    We describe various expansion schemes that can be used to study gravitational clustering. Obtained from the equations of motion or their path-integral formulation, they provide several perturbative expansions that are organized in different fashion or involve different partial resummations. We focus on the two-point and three-point correlation functions, but these methods also apply to all higher-order correlation and response functions. We present the general formalism, which holds for the gravitational dynamics as well as for similar models, such as the Zeldovich dynamics, that obey similar hydrodynamical equations of motion with a quadratic nonlinearity. We give our explicit analytical results up to one-loop order for the simpler Zeldovich dynamics. For the gravitational dynamics, we compare our one-loop numerical results with numerical simulations. We check that the standard perturbation theory is recovered from the path integral by expanding over Feynman's diagrams. However, the latter expansion is organ...

  16. Structural and electronic properties of stable Li{sub n} (n=2–10) clusters: A density functional study

    Energy Technology Data Exchange (ETDEWEB)

    Chetri, Pawan [Department of Physics, Tezpur University, Napaam, Tezpur 784028, Assam (India); Deka, Ramesh Ch., E-mail: ramesh@tezu.ernet.in [Department of Chemical Sciences, Tezpur University, Napaam, Tezpur 784028, Assam (India); Choudhury, Amarjyoti [Department of Physics, Tezpur University, Napaam, Tezpur 784028, Assam (India)

    2013-12-01

    Structure and relative stability of Li{sub n} clusters for n=1–10 were investigated using density functional methods based DMol{sup 3} program. The structures of Li clusters were determined in terms of Li–Li bond length and the results are in very good agreement with experimental values. Stability of the clusters was determined from their relative energy values binding energies and second difference energy. We also determined fragmentation energy of each size of cluster. We arrived at some interesting result like the transition of Li{sub n} from 2-dimension to 3-dimension for a particular value of n and also the variation of HOMO–LUMO gap with cluster size. Many structures are characterized for the first time in this work.

  17. An algorithm for the direct reconstruction of the dark matter correlation function from weak lensing and galaxy clustering

    CERN Document Server

    Baldauf, Tobias; Seljak, Uros; Mandelbaum, Rachel

    2009-01-01

    The clustering of matter on cosmological scales is an essential probe for studying the physical origin and composition of our Universe. To date, most of the direct studies have focused on shear-shear weak lensing correlations, but it is also possible to extract the dark matter clustering by combining galaxy-clustering and galaxy-galaxy-lensing measurements. In this study we develop a method that can constrain the dark matter correlation function from galaxy clustering and galaxy-galaxy-lensing measurements, by focusing on the correlation coefficient between the galaxy and matter overdensity fields. To generate a mock galaxy catalogue for testing purposes, we use the Halo Occupation Distribution approach applied to a large ensemble of N-body simulations to model pre-existing SDSS Luminous Red Galaxy sample observations. Using this mock catalogue, we show that a direct comparison between the excess surface mass density measured by lensing and its corresponding galaxy clustering quantity is not optimal. We devel...

  18. Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains.

    Science.gov (United States)

    Singer, Meromit; Engström, Alexander; Schönhuth, Alexander; Pachter, Lior

    2011-09-23

    Recent experimental and computational work confirms that CpGs can be unmethylated inside coding exons, thereby showing that codons may be subjected to both genomic and epigenomic constraint. It is therefore of interest to identify coding CpG islands (CCGIs) that are regions inside exons enriched for CpGs. The difficulty in identifying such islands is that coding exons exhibit sequence biases determined by codon usage and constraints that must be taken into account. We present a method for finding CCGIs that showcases a novel approach we have developed for identifying regions of interest that are significant (with respect to a Markov chain) for the counts of any pattern. Our method begins with the exact computation of tail probabilities for the number of CpGs in all regions contained in coding exons, and then applies a greedy algorithm for selecting islands from among the regions. We show that the greedy algorithm provably optimizes a biologically motivated criterion for selecting islands while controlling the false discovery rate. We applied this approach to the human genome (hg18) and annotated CpG islands in coding exons. The statistical criterion we apply to evaluating islands reduces the number of false positives in existing annotations, while our approach to defining islands reveals significant numbers of undiscovered CCGIs in coding exons. Many of these appear to be examples of functional epigenetic specialization in coding exons.

  19. The Initial Mass Function of Low-Mass Stars and Brown Dwarfs in Young Clusters

    Science.gov (United States)

    Luhman, K. L.; Rieke, G. H.; Young, Erick T.; Cotera, Angela S.; Chen, H.; Rieke, Marcia J.; Schneider, Glenn; Thompson, Rodger I.

    2000-09-01

    We have obtained images of the Trapezium Cluster (140''×140'' 0.3 pc×0.3 pc) with the Hubble Space Telescope Near-Infrared Camera and Multi-Object Spectrometer (NICMOS). Combining these data with new ground-based K-band spectra (R=800) and existing spectral types and photometry, we have constructed an H-R diagram and used it and other arguments to infer masses and ages. To allow comparison with the results of our previous studies of IC 348 and ρ Oph, we first use the models of D'Antona & Mazzitelli. With these models, the distributions of ages of comparable samples of stars in the Trapezium, ρ Oph, and IC 348 indicate median ages of ~0.4 Myr for the first two regions and ~1-2 Myr for the latter. The low-mass initial mass functions (IMFs) in these sites of clustered star formation are similar over a wide range of stellar densities (ρ Oph, n=0.2-1×103 pc-3 IC 348, n=1×103 pc-3 Trapezium, n=1-5×104 pc-3) and other environmental conditions (e.g., presence or absence of OB stars). With current data, we cannot rule out modest variations in the substellar mass functions among these clusters. We then make the best estimate of the true form of the IMF in the Trapezium by using the evolutionary models of Baraffe et al. and an empirically adjusted temperature scale and compare this mass function to recent results for the Pleiades and the field. All of these data are consistent with an IMF that is flat or rises slowly from the substellar regime to about 0.6 Msolar and then rolls over into a power law that continues from about 1 Msolar to higher masses with a slope similar to or somewhat larger than the Salpeter value of 1.35. For the Trapezium, this behavior holds from our completeness limit of ~0.02 Msolar and probably, after a modest completeness correction, even from 0.01-0.02 Msolar. These data include ~50 likely brown dwarfs. We test the predictions of theories of the IMF against (1) the shape of the IMF, which is not log-normal, in clusters and the field, (2) the

  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. Multimodal function optimization using minimal representation size clustering and its application to planning multipaths.

    Science.gov (United States)

    Hocaoğlu, C; Sanderson, A C

    1997-01-01

    A novel genetic algorithm (GA) using minimal representation size cluster (MRSC) analysis is designed and implemented for solving multimodal function optimization problems. The problem of multimodal function optimization is framed within a hypothesize-and-test paradigm using minimal representation size (minimal complexity) for species formation and a GA. A multiple-population GA is developed to identify different species. The number of populations, thus the number of different species, is determined by the minimal representation size criterion. Therefore, the proposed algorithm reveals the unknown structure of the multimodal function when a priori knowledge about the function is unknown. The effectiveness of the algorithm is demonstrated on a number of multimodal test functions. The proposed scheme results in a highly parallel algorithm for finding multiple local minima. In this paper, a path-planning algorithm is also developed based on the MRSC_GA algorithm. The algorithm utilizes MRSC_GA for planning paths for mobile robots, piano-mover problems, and N-link manipulators. The MRSC_GA is used for generating multipaths to provide alternative solutions to the path-planning problem. The generation of alternative solutions is especially important for planning paths in dynamic environments. A novel iterative multiresolution path representation is used as a basis for the GA coding. The effectiveness of the algorithm is demonstrated on a number of two-dimensional path-planning problems.

  2. The substellar mass function in the central region of the open cluster Praesepe from deep LBT observations

    CERN Document Server

    Wang, Wei; Goldman, Bertrand; Henning, Thomas; Caballero, Jose A; Bailer-Jones, Coryn A L

    2011-01-01

    Studies of the mass function (MF) of open clusters of different ages allow us to probe the efficiency with which brown dwarfs evaporate from clusters to populate the field. Surveys of older clusters (age >100 Myr) are not affected so severely by several problems encountered in young clusters, such as intra-cluster extinction and large uncertainties in brown dwarf models. We present the results of a deep photometric survey to study the MF of the central region of the old open cluster Praesepe (age~590$^{+150}_{-120}$ Myr, distance ~190$^{+6.0}_{-5.8}$ pc), down to the substellar regime. We performed an optical ($riz$ and $Y$-band) photometric survey of Praesepe using the Large Binocular Telescope Camera covering an area of ~0.59 deg$^2$ in the cluster centre from $i$~19.0 mag (~100 M_Jup) down to a 5$\\sigma$ detection limit at $i$~25.6mag (~40 M_Jup). The survey is approximately 95% complete at $i=23.8$ mag and $z=22.0$ mag (~55 M_Jup). We identify 59 cluster member candidates, of which 37 are substellar, by c...

  3. Photoelectron spectroscopy and density functional calculations of C(n)S(m)(-) (n = 2-7; m = 1, 2) clusters.

    Science.gov (United States)

    Xu, Xi-Ling; Deng, Xiao-Jiao; Xu, Hong-Guang; Zheng, Wei-Jun

    2015-12-14

    CnSm(-) (n = 2-7; m = 1, 2) clusters were investigated by using photoelectron spectroscopy combined with density functional theory calculations. We found that the vertical detachment energies of both CnS(-) and CnS2(-) (n = 2-7) clusters exhibit a strong odd-even alternation with an increasing number of carbon atoms: the VDEs of even-n clusters are higher than those of adjacent odd-n clusters. The most stable structures of the anionic and neutral CnS (n = 2-7) clusters are linear with the S atom locating at one end of the carbon chain except that the structure of C3S(-) is slightly bent. The ground state isomers of the anionic and neutral CnS2 (n = 2-7) clusters are all linear structures with two S atoms locating at two ends of the carbon chain. The electron affinities of the neutral CnS (n = 2, 4-7) and CnS2 (n = 2-7) clusters are determined based on the experimental adiabatic detachment energies of the corresponding anion species, because the most stable structures of the neutral clusters are similar to those of the corresponding anions.

  4. 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.

  5. 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), 10.1063/1.4858458] 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.

  6. The lower mass function of the young open cluster Blanco 1: from 30 Mjup to 3 Mo

    CERN Document Server

    Moraux, Estelle; Stauffer, John; Navascues, David Barrado Y; Cuillandre, Jean-Charles

    2007-01-01

    We performed a deep wide field optical survey of the young (~100-150 Myr) open cluster Blanco1 to study its low mass population well down into the brown dwarf regime and estimate its mass function over the whole cluster mass range.The survey covers 2.3 square degrees in the I and z-bands down to I ~ z ~ 24 with the CFH12K camera. Considering two different cluster ages (100 and 150 Myr), we selected cluster member candidates on the basis of their location in the (I,I-z) CMD relative to the isochrones, and estimated the contamination by foreground late-type field dwarfs using statistical arguments, infrared photometry and low-resolution optical spectroscopy. We find that our survey should contain about 57% of the cluster members in the 0.03-0.6 Mo mass range, including 30-40 brown dwarfs. The candidate's radial distribution presents evidence that mass segregation has already occured in the cluster. We took it into account to estimate the cluster mass function across the stellar/substellar boundary. We find that...

  7. Prioritization, clustering and functional annotation of MicroRNAs using latent semantic indexing of MEDLINE abstracts.

    Science.gov (United States)

    Roy, Sujoy; Curry, Brandon C; Madahian, Behrouz; Homayouni, Ramin

    2016-10-06

    The amount of scientific information about MicroRNAs (miRNAs) is growing exponentially, making it difficult for researchers to interpret experimental results. In this study, we present an automated text mining approach using Latent Semantic Indexing (LSI) for prioritization, clustering and functional annotation of miRNAs. For approximately 900 human miRNAs indexed in miRBase, text documents were created by concatenating titles and abstracts of MEDLINE citations which refer to the miRNAs. The documents were parsed and a weighted term-by-miRNA frequency matrix was created, which was subsequently factorized via singular value decomposition to extract pair-wise cosine values between the term (keyword) and miRNA vectors in reduced rank semantic space. LSI enables derivation of both explicit and implicit associations between entities based on word usage patterns. Using miR2Disease as a gold standard, we found that LSI identified keyword-to-miRNA relationships with high accuracy. In addition, we demonstrate that pair-wise associations between miRNAs can be used to group them into categories which are functionally aligned. Finally, term ranking by querying the LSI space with a group of miRNAs enabled annotation of the clusters with functionally related terms. LSI modeling of MEDLINE abstracts provides a robust and automated method for miRNA related knowledge discovery. The latest collection of miRNA abstracts and LSI model can be accessed through the web tool miRNA Literature Network (miRLiN) at http://bioinfo.memphis.edu/mirlin .

  8. Methylation of the estrogen receptor CpG island distinguishes spontaneous and plutonium-induced tumors from nitrosamine-induced lung tumors

    Energy Technology Data Exchange (ETDEWEB)

    Belinsky, S.A.; Baylin, S.B.; Issa, J.J. [Johns Hopkins Univ., Baltimore, MD (United States)

    1995-12-01

    CpG islands located in the promoter region of genes constitute one mechanism for regulating transcription. These islands are normally free of methylation, regardless of the expression state of the gene. Hypermethylation of CpG islands, the addition of a methyl group to the internal cytosine within CpG dinucleotides, can cause silencing of a gene. Hypermethylation has been detected as an early event at specific chromosome loci during the development of colon cancer and represents one mechanism used by neoplatic cells to inactivate tumor suppressor genes. Recent studies have demonstrated this mechanism in inactivation of the VHL tumor suppressor gene in 19% of sporadic renal tumors and the p16 {sup INK4a} tumor suppressor gene in 30% of non-small cell lung cancers. A recent report indicates that the estrogen receptor gene could also be inactivated through methylation. In addition, estrogen receptor CpG island methylation arises as a direct function of age in normal colonic mucosa and is present in virtually all colonic tumors. In cultured colon cancer cells, methylation-associated loss of expression of the estrogen receptor gene results in deregulated growth, suggesting a role for the estrogen receptor in colon cancer development. These results provide further evidence that gene silencing through methylation could be a predominant epigenetic mechanism underlying the development of many different types of cancer. The purpose of the current investigation was to determine whether estrogen receptor CpG island methylation is involved in the development of lung cancer. The frequency for methylation of the estrogen receptor CpG island in rodent lung tumors is summarized.

  9. Radial gradients in initial mass function sensitive absorption features in the Coma brightest cluster galaxies

    CERN Document Server

    Zieleniewski, Simon; Thatte, Niranjan; Davies, Roger L; Vaughan, Sam P

    2016-01-01

    Using the Oxford Short Wavelength Integral Field specTrograph (SWIFT), we trace radial variations of initial mass function (IMF) sensitive absorption features of three galaxies in the Coma cluster. We obtain resolved spectroscopy of the central 5kpc for the two central brightest-cluster galaxies (BCGs) NGC4889, NGC4874, and the BCG in the south-west group NGC4839, as well as unresolved data for NGC4873 as a low-$\\sigma_*$ control. We present radial measurements of the IMF-sensitive features sodium NaI$_{\\rm{SDSS}}$, calcium triplet CaT and iron-hydride FeH0.99, along with the magnesium MgI0.88 and titanium oxide TiO0.89 features. We employ two separate methods for both telluric correction and sky-subtraction around the faint FeH feature to verify our analysis. Within NGC4889 we find strong gradients of NaI$_{\\rm{SDSS}}$ and CaT but a flat FeH profile, which from comparing to stellar population synthesis models, suggests an old, $\\alpha$-enhanced population with a Chabrier, or even bottom-light IMF. The age an...

  10. Study on Cluster Formation of Poly 2-HYDROXYETHYL Methacrylate Functionalized Single-Walled Carbon Nanotubes

    Science.gov (United States)

    Ashok Kumar, Nanjundan; Kim, Sung Hun; Kim, Jong Tae; Lim, Kwon Taek; Jeong, Yeon Tae

    Cluster-like network structures of single-walled carbon nanotubes (SWNTs) were synthesized by chemical grafting poly 2-hydroxyethyl methacrylate (polyHEMA) to the sidewalls of SWNTs. Acid chloride-functionalized tubes were coupled with commercially available HEMA monomer, which was in turn polymerized using a radical initiator. Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy were used to identify the surface changes on the nanocomposites. Microscopic observations of the nanotube complexes by field emission scanning electron microscopy (FE-SEM) show that the tubes were dispersed and formed cluster-like network, branched structures with less bundling, thus, strongly suggesting a firm coating of the polymer on nanotube walls. The coating was further confirmed by transmission electron microscopy. The thermal properties of the nanotube complex as studied by thermal gravimetric analysis (TGA) revealed that coating enhanced stability of the complex, when compared to that of bulk polyHEMA and pristine SWNTs. The nanotube complexes showed excellent suspension stability when dispersed in organic solvent.

  11. 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.

  12. The ACS Fornax Cluster Survey. VIII. The Luminosity Function of Globular Clusters in Virgo and Fornax Early-Type Galaxies and its Use as a Distance Indicator

    CERN Document Server

    Villegas, Daniela; Peng, Eric W; Blakeslee, John P; Cote, Patrick; Ferrarese, Laura; Kissler-Patig, Markus; Mei, Simona; Infante, Leopoldo; Tonry, John L; West, Michael J

    2010-01-01

    We use a highly homogeneous set of data from 132 early-type galaxies in the Virgo and Fornax clusters in order to study the properties of the globular cluster luminosity function (GCLF). The globular cluster system of each galaxy was studied using a maximum likelihood approach to model the intrinsic GCLF after accounting for contamination and completeness effects. The results presented here update our Virgo measurements and confirm our previous results showing a tight correlation between the dispersion of the GCLF and the absolute magnitude of the parent galaxy. Regarding the use of the GCLF as a standard candle, we have found that the relative distance modulus between the Virgo and Fornax clusters is systematically lower than the one derived by other distance estimators, and in particular it is 0.22mag lower than the value derived from surface brightness fluctuation measurements performed on the same data. From numerical simulations aimed at reproducing the observed dispersion of the value of the turnover ma...

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

    Science.gov (United States)

    Mörchen, Fabian

    2004-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Fouque, A.L.; Ciuciu, Ph.; Risser, L. [NeuroSpin/CEA, F-91191 Gif-sur-Yvette (France); Fouque, A.L.; Ciuciu, Ph.; Risser, L. [IFR 49, Institut d' Imagerie Neurofonctionnelle, Paris (France)

    2009-07-01

    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)

  15. Depletion of CpG Dinucleotides in Papillomaviruses and Polyomaviruses: A Role for Divergent Evolutionary Pressures.

    Directory of Open Access Journals (Sweden)

    Mohita Upadhyay

    Full Text Available Papillomaviruses and polyomaviruses are small ds-DNA viruses infecting a wide-range of vertebrate hosts. Evidence supporting co-evolution of the virus with the host does not fully explain the evolutionary path of papillomaviruses and polyomaviruses. Studies analyzing CpG dinucleotide frequencies in virus genomes have provided interesting insights on virus evolution. CpG dinucleotide depletion has not been extensively studied among papillomaviruses and polyomaviruses. We sought to analyze the relative abundance of dinucleotides and the relative roles of evolutionary pressures in papillomaviruses and polyomaviruses.We studied 127 full-length sequences from papillomaviruses and 56 full-length sequences from polyomaviruses. We analyzed the relative abundance of dinucleotides, effective codon number (ENC, differences in synonymous codon usage. We examined the association, if any, between the extent of CpG dinucleotide depletion and the evolutionary lineage of the infected host. We also investigated the contribution of mutational pressure and translational selection to the evolution of papillomaviruses and polyomaviruses.All papillomaviruses and polyomaviruses are CpG depleted. Interestingly, the evolutionary lineage of the infected host determines the extent of CpG depletion among papillomaviruses and polyomaviruses. CpG dinucleotide depletion was more pronounced among papillomaviruses and polyomaviruses infecting human and other mammals as compared to those infecting birds. Our findings demonstrate that CpG depletion among papillomaviruses is linked to mutational pressure; while CpG depletion among polyomaviruses is linked to translational selection. We also present evidence that suggests methylation of CpG dinucleotides may explain, at least in part, the depletion of CpG dinucleotides among papillomaviruses but not polyomaviruses.The extent of CpG depletion among papillomaviruses and polyomaviruses is linked to the evolutionary lineage of the

  16. Enhancement of the Anthrax AVA Vaccine with CpG ODN’s

    Science.gov (United States)

    2005-08-28

    NUMBER OF PAGES 20. LIMITATION OF ABSTRACT UL - 28-Aug-2005 Final Report on ACCELERATE ANTHRAX: CpG 7909 Vaccine Adjuvant Program Report Title...Vaccine Adsorbed (BioThrax?) Combined with CPG 7909 in Normal Volunteers” was completed and presented at the 2005 Interscience Conference on Antimicrobial...Agents and Chemotherapy in a poster entitled “Marked Enhancement Of Antibody Response To Anthrax Vaccine Adsorbed With CPG 7909 In Healthy

  17. Assessment of Density Functional Theory in Predicting Structures and Free Energies of Reaction of Atmospheric Prenucleation Clusters.

    Science.gov (United States)

    Elm, Jonas; Bilde, Merete; Mikkelsen, Kurt V

    2012-06-12

    This work assesses different computational strategies for predicting structures and Gibb's free energies of reaction of atmospheric prenucleation clusters. The performance of 22 Density Functional Theory functionals in predicting equilibrium structures of molecules and water prenucleation clusters of atmospheric relevance is evaluated against experimental data using a test set of eight molecules and prenucleation clusters: SO2, H2SO4, CO2·H2O, CS2·H2O, OCS·H2O, SO2·H2O, SO3·H2O, and H2SO4·H2O. Furthermore, the functionals are tested and compared for their ability to predict the free energy of reaction for the formation of five benchmark atmospheric prenucleation clusters: H2SO4·H2O, H2SO4·(H2O)2, H2SO4·NH3, HSO4(-)·H2O, and HSO4(-)·(H2O)2. The performance is evaluated against experimental data, coupled cluster, and complete basis set extrapolation procedure methods. Our investigation shows that the utilization of the M06-2X functional with the 6-311++G(3df,3pd) basis set represents an improved approach compared to the conventionally used PW91 functional, yielding mean absolute errors of 0.48 kcal/mol and maximum errors of 0.67 kcal/mol compared to experimental results.

  18. Prognostic significance of CpG island methylator phenotype in surgically resected small cell lung carcinoma.

    Science.gov (United States)

    Saito, Yuichi; Nagae, Genta; Motoi, Noriko; Miyauchi, Eisaku; Ninomiya, Hironori; Uehara, Hirofumi; Mun, Mingyon; Okumura, Sakae; Ohyanagi, Fumiyoshi; Nishio, Makoto; Satoh, Yukitoshi; Aburatani, Hiroyuki; Ishikawa, Yuichi

    2016-03-01

    Methylation is closely involved in the development of various carcinomas. However, few datasets are available for small cell lung cancer (SCLC) due to the scarcity of fresh tumor samples. The aim of the present study is to clarify relationships between clinicopathological features and results of the comprehensive genome-wide methylation profile of SCLC. We investigated the genome-wide DNA methylation status of 28 tumor and 13 normal lung tissues, and gene expression profiling of 25 SCLC tissues. Following unsupervised hierarchical clustering and non-negative matrix factorization, gene ontology analysis was performed. Clustering of SCLC led to the important identification of a CpG island methylator phenotype (CIMP) of the tumor, with a significantly poorer prognosis (P = 0.002). Multivariate analyses revealed that postoperative chemotherapy and non-CIMP were significantly good prognostic factors. Ontology analyses suggested that the extrinsic apoptosis pathway was suppressed, including TNFRSF1A, TNFRSF10A and TRADD in CIMP tumors. Here we revealed that CIMP was an important prognostic factor for resected SCLC. Delineation of this phenotype may also be useful for the development of novel apoptosis-related chemotherapeutic agents for treatment of the aggressive tumor.

  19. Magnetic behavior in Cr2@Gen (1≤n≤12) clusters: A density functional investigation

    Science.gov (United States)

    Dhaka, Kapil; Trivedi, Ravi; Bandyopadhyay, Debashis

    2014-04-01

    With a goal to produce magnetic moment in Cr2 Doped Gen clusters which will be useful for practical applications, we have considered the structure and magnetic properties of Pure Germanium clusters and substitutionally doped it with Cr dimer to produce Cr2@Gen clusters. As the first step of calculation, geometrical optimizations of the nanoclusters have been done. These optimized geometries have been used in calculate the average binding energy per atom (BE), HOMO-LUMO gap and hence the relative stability of the clusters. These parameters have been demonstrated as structural and electronic properties of the clusters. Gap between highest occupied molecular orbital and lowest unoccupied molecular orbital indicate cluster to be a potential motif for generating magnetic cluster assembled materials. Based on these values a comparative study on different sized clusters has been done in order to understand the origin of structures, electronic and magnetic properties of Cr2@Gen nanoclusters.

  20. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases.

    Directory of Open Access Journals (Sweden)

    Julia Arand

    2012-06-01

    Full Text Available The enzymatic control of the setting and maintenance of symmetric and non-symmetric DNA methylation patterns in a particular genome context is not well understood. Here, we describe a comprehensive analysis of DNA methylation patterns generated by high resolution sequencing of hairpin-bisulfite amplicons of selected single copy genes and repetitive elements (LINE1, B1, IAP-LTR-retrotransposons, and major satellites. The analysis unambiguously identifies a substantial amount of regional incomplete methylation maintenance, i.e. hemimethylated CpG positions, with variant degrees among cell types. Moreover, non-CpG cytosine methylation is confined to ESCs and exclusively catalysed by Dnmt3a and Dnmt3b. This sequence position-, cell type-, and region-dependent non-CpG methylation is strongly linked to neighboring CpG methylation and requires the presence of Dnmt3L. The generation of a comprehensive data set of 146,000 CpG dyads was used to apply and develop parameter estimated hidden Markov models (HMM to calculate the relative contribution of DNA methyltransferases (Dnmts for de novo and maintenance DNA methylation. The comparative modelling included wild-type ESCs and mutant ESCs deficient for Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3a/3b, respectively. The HMM analysis identifies a considerable de novo methylation activity for Dnmt1 at certain repetitive elements and single copy sequences. Dnmt3a and Dnmt3b contribute de novo function. However, both enzymes are also essential to maintain symmetrical CpG methylation at distinct repetitive and single copy sequences in ESCs.

  1. CpG oligodeoxynucleotides induce strong up-regulation of interleukin 33 via Toll-like receptor 9.

    Science.gov (United States)

    Shimosato, Takeshi; Fujimoto, Megumi; Tohno, Masanori; Sato, Takashi; Tateo, Mariko; Otani, Hajime; Kitazawa, Haruki

    2010-03-26

    We previously reported the strong immunostimulatory effects of a CpG oligodeoxynucleotide (ODN), designated MsST, from the lacZ gene of Streptococcus (S.) thermophilus ATCC19258. Here we show that 24h of stimulation with MsST in mouse splenocytes and peritoneal macrophages strongly induces expression of interleukin (IL)-33, a cytokine in the IL-1 superfamily. Other IL-1 superfamily members, including IL-1alpha, IL-1beta and IL-18, are down-regulated after 24h of stimulation of MsST. We also found that MsST-induced IL-33 mRNA expression is inhibited by the suppressive ODN A151, which can inhibit Toll-like receptor 9 (TLR9)-mediated responses. This is the first report to show that IL-33 can be induced by CpG ODNs. The strong induction of IL-33 by MsST suggests that it may be a potential therapeutic ODN for the treatment of inflammatory disease. The presence of a strong CpG ODN in S. thermophilus also suggests that the bacterium may be a good candidate as a starter culture for the development of new physiologically functional foods.

  2. CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato

    DEFF Research Database (Denmark)

    Hobolth, Asger; Nielsen, Rasmus; Wang, Ying

    2006-01-01

    We develop codon-based models for simultaneously inferring the mutational effects of CpG and CpNpG methylation in coding regions. In a data set of 369 tomato genes, we show that there is very little effect of CpNpG methylation but a strong effect of CpG methylation affecting almost all genes. We...... further show that the CpNpG and CpG effects are largely uncorrelated. Our results suggest different roles of CpG and CpNpG methylation, with CpNpG methylation possibly playing a specialized role in defense against transposons and RNA viruses....

  3. Consolidated Recovered Materials Advisory Notice (RMAN) for the Comprehensive Procurement Guideline (CPG)

    Data.gov (United States)

    U.S. Environmental Protection Agency — EPA's Comprehensive Procurement Guideline (CPG) designates recycled content products that government agencies should buy. EPA publishes purchasing guidance and...

  4. Definition of a family of tissue-protective cytokines using functional cluster analysis: a proof-of-concept study

    Directory of Open Access Journals (Sweden)

    Manuela eMengozzi

    2014-03-01

    Full Text Available The discovery of the tissue-protective activities of erythropoietin (EPO has underlined the importance of some cytokines in tissue protection, repair and remodeling. As such activities have been reported for other cytokines, we asked whether we could define a class of tissue-protective cytokines. We therefore explored a novel approach based on functional clustering. In this pilot study, we started by analyzing a small number of cytokines (30. We functionally classified the 30 cytokines according to their interactions by using the bioinformatics tool STRING (Search Tool for the Retrieval of Interacting Genes, followed by hierarchical cluster analysis. The results of this functional clustering were different from those obtained by clustering cytokines simply according to their sequence. We previously reported that the protective activity of EPO in a model of cerebral ischemia was paralleled by an upregulation of synaptic plasticity genes, particularly early growth response 2 (EGR2. To assess the predictivity of functional clustering, we tested some of the cytokines clustering close to EPO (interleukin-11, IL-11; kit ligand, KITLG; leukemia inhibitory factor, LIF; thrombopoietin, THPO in an in vitro model of human neuronal cells for their ability to induce EGR2. Two of these, LIF and IL-11, induced EGR2 expression. Although these data would need to be extended to a larger number of cytokines and the biological validation should be done using more robust in vivo models, rather then just one cell line, this study shows the feasibility of this approach. This type of functional cluster analysis could be extended to other fields of cytokine research and help design biological experiments.

  5. Definition of a Family of Tissue-Protective Cytokines Using Functional Cluster Analysis: A Proof-of-Concept Study.

    Science.gov (United States)

    Mengozzi, Manuela; Ermilov, Peter; Annenkov, Alexander; Ghezzi, Pietro; Pearl, Frances

    2014-01-01

    The discovery of the tissue-protective activities of erythropoietin (EPO) has underlined the importance of some cytokines in tissue-protection, repair, and remodeling. As such activities have been reported for other cytokines, we asked whether we could define a class of tissue-protective cytokines. We therefore explored a novel approach based on functional clustering. In this pilot study, we started by analyzing a small number of cytokines (30). We functionally classified the 30 cytokines according to their interactions by using the bioinformatics tool STRING (Search Tool for the Retrieval of Interacting Genes), followed by hierarchical cluster analysis. The results of this functional clustering were different from those obtained by clustering cytokines simply according to their sequence. We previously reported that the protective activity of EPO in a model of cerebral ischemia was paralleled by an upregulation of synaptic plasticity genes, particularly early growth response 2 (EGR2). To assess the predictivity of functional clustering, we tested some of the cytokines clustering close to EPO (interleukin-11, IL-11; kit ligand, KITLG; leukemia inhibitory factor, LIF; thrombopoietin, THPO) in an in vitro model of human neuronal cells for their ability to induce EGR2. Two of these, LIF and IL-11, induced EGR2 expression. Although these data would need to be extended to a larger number of cytokines and the biological validation should be done using more robust in vivo models, rather then just one cell line, this study shows the feasibility of this approach. This type of functional cluster analysis could be extended to other fields of cytokine research and help design biological experiments.

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

    CERN Document Server

    Garza, Alejandro J; Scuseria, Gustavo E

    2015-01-01

    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 $f^0$ actinyl series (UO$_2^{2+}$, NpO$_2^{2+}$, PuO$_2^{2+}$), the isoelectronic NUN, and Thorium (ThO, ThO$^{2+}$) and Nobelium (NoO, NoO$_2$) oxides are studied.

  7. Dynamic clustering of hazard functions: an application to disease progression in chronic heart failure.

    Science.gov (United States)

    Ieva, Francesca; Paganoni, Anna Maria; Pietrabissa, Teresa

    2016-02-04

    We analyse data collected from the administrative datawarehouse of an Italian regional district (Lombardia) concerning patients affected by Chronic Heart Failure. The longitudinal data gathering for each patient hospital readmissions in time, as well as patient-specific covariates, is studied as a realization of non homogeneous Poisson process. Since the aim behind this study is to identify groups of patients behaving similarly in terms of disease progression and then healthcare consumption, we conjectured the time segments between two consecutive hospitalizations to be Weibull distributed in each hidden cluster. Adding a frailty term to take into account the within subjects unknown variability, the corresponding patient-specific hazard functions are reconstructed. Therefore, the comprehensive distribution for each time to event variable is modelled as a Weibull Mixture. We are then able to easily interpret the related hidden groups as healthy, sick, and terminally ill subjects.

  8. Teaching a functional leisure skill cluster to rehabilitation clients: the art of macrame.

    Science.gov (United States)

    Halasz-Dees, M; Cuvo, A J

    1986-01-01

    Disabled people often do not use leisure time productively. Past research has focused on teaching specific recreational activities isolated from related skills that would provide subjects a functional independent living repertoire. In the present study disabled subjects were taught the art of macrame. Additionally, they role-played related shopping skills such as buying materials, engaging in appropriate social-interpersonal skills, making monetary transactions, and securing their own transportation to and from the store. Subjects were taught six basic macrame knots using an instructional manual, series of error-correction procedures, and social reinforcement. After mastering those basic knots they independently used the instructional materials to make three complete macrame projects without direct instruction on the projects themselves. Subjects also demonstrated skill maintenance and generalization by making a novel project after independently engaging in all relevant shopping behavior. Two varieties of the multiple baseline design were employed. The importance of teaching a leisure skill cluster and adapting instructional materials were emphasized.

  9. 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...... and non-links in the graphs as missing. We find that the model is performing well above chance for all subjects....... networks. We visualize the solution found by performing evidence accumulation clustering on the maximum a posterior solutions found in 100 runs of the sampling scheme. The striatal groupings found are symmetric between hemispheres indicating that the model is able to group voxels across hemispheres, which...

  10. Density Functional Theory Study of Water Diffusion and Clustering on Pd(111)

    Institute of Scientific and Technical Information of China (English)

    CHEN Jin-Wen; TU Xue-Yan; TIAN Kai; DAI Shu-Shan

    2006-01-01

    The internal structures as well as adsorption and hopping energies of monomers,dimers, trimers, tetramers, pentamers and hexamers of water on Pd(111) have been studied by density functional theory (DFT) plane-wave pseudopotential method which performs the firstprinciples quantum-mechanical calculations to explore the properties of crystals and surfaces in materials. Based on the calculations, we suppose that their absorption is via one water molecule for monomers, dimmers and trimers, but three water molecules for pentamers and hexamers. Moreover,there is one water molecule bonding with Pd atom by O atom in pentamers and hexamers, which explains why pentamers and hexamers are stable. The binding energies of polymers may be used to explain why the trimer comes close to two nearby monomers to form a stable pentamer instead of tetramer. And the difference of mobility of small water clusters is due to their different hopping energies.

  11. 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...... increase in insulin section indicating some sensitivity towards glucose. Hormone content as well as the number of hormone-containing cells increased for the first 14 days of culture. When NICCs were stained for hormones, proliferation (Ki67), and duct cells (CK7), some insulin- and glucagon-positive cells...... 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...

  12. Potential Functions of Al2 by the Relativistic Fock-Space Coupled Cluster Method

    Directory of Open Access Journals (Sweden)

    Uzi Kaldor

    2002-05-01

    Full Text Available Abstract: Potential functions of the ground and low excited states of Al2 are calculated by the relativistic Fock-space coupled cluster method in the framework of the projected Dirac-Coulomb Hamiltonian. A moderate-size basis [16s11p3d3f/6s6p3d2f] is used. 3Πu is confirmed as the ground state of the system. Its spin orbit splittings are reproduced well, with the Λ = 1, 2 states lying 32.5 and 66.1 cm−1, respectively, above the Λ = 0 minimum (experimental values are 30.4 and 63.4 cm−1. The bond is somewhat too weak, with De 0.14 eV below experiment, Re too high by 0.08 ˚A, and ωe 21 cm−1 too low. It is speculated that the better agreement obtained in earlier calculations may be due to neglect of basis set superposition errors. The description of bonding in the molecule may be improved by the use of a better basis and the inclusion of more correlation by the intermediate Hamiltonian coupled cluster method, which makes it possible to handle larger P spaces and extend the potential functions to the whole range of internuclear separations.

  13. Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians.

    Directory of Open Access Journals (Sweden)

    Adam G Marsh

    Full Text Available Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus. We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera and an anemone (Nematostella vectensis. Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to

  14. The Next Generation Virgo Cluster Survey (NGVS). XIII. The Luminosity and Mass Function of Galaxies in the Core of the Virgo Cluster and the Contribution from Disrupted Satellites

    CERN Document Server

    Ferrarese, Laura; Sanchez-Janssen, Ruben; Roediger, Joel; McConnachie, Alan W; Durrell, Patrick R; MacArthur, Lauren A; Blakeslee, John P; Duc, Pierre-Alain; Boissier, S; Boselli, Alessandro; Courteau, Stephane; Cuillandre, Jean-Charles; Emsellem, Eric; Gwyn, S D J; Guhathakurta, Puragra; Jordan, Andres; Lancon, Ariane; Liu, Chengze; Mei, Simona; Mihos, J Christopher; Puzia, Thomas H; Taylor, James E; Zhang, Hongxin

    2016-01-01

    We present measurements of the galaxy luminosity and stellar mass function in a 3.71 deg$^2$ (0.3 Mpc$^2$) area in the core of the Virgo cluster, based on $ugriz$ data from the Next Generation Virgo Cluster Survey (NGVS). The galaxy sample consists of 352 objects brighter than $M_g=-9.13$ mag, the 50% completeness limit of the survey. Using a Bayesian analysis, we find a best-fit faint end slope of $\\alpha=-1.33 \\pm 0.02$ for the g-band luminosity function; consistent results are found for the stellar mass function as well as the luminosity function in the other four NGVS bandpasses. We discuss the implications for the faint-end slope of adding 92 ultra compact dwarfs galaxies (UCDs) -- previously compiled by the NGVS in this region -- to the galaxy sample, assuming that UCDs are the stripped remnants of nucleated dwarf galaxies. Under this assumption, the slope of the luminosity function (down to the UCD faint magnitude limit, $M_g = -9.6$ mag) increases dramatically, up to $\\alpha = -1.60 \\pm 0.06$ when cor...

  15. A review of the role of CpG oligodeoxynucleotides as toll-like receptor 9 agonists in prophylactic and therapeutic vaccine development in infectious diseases.

    Science.gov (United States)

    Gupta, Kaveri; Cooper, Curtis

    2008-01-01

    This article reviews the biology of Toll-like receptors, the current understanding of the mechanism by which CpG oligodeoxynucleotides (ODNs) perturb immune function and the published literature describing their evaluation in the development of vaccines in humans. The role of these molecules as immune modulators in HCV treatment is also considered. There has been considerable research evaluating the role of CpG ODNs as an adjuvant and immune modulator in hepatitis B, hepatitis C and influenza. The safety and immunogenicity of the 1018 ISS compound in combination with Engerix-B was assessed in 99 healthy, adult seronegative volunteers. One month following the first immunization dose, 78.7% in the rHBsAg plus 1018 ISS group versus 11.8% in the Engerix-B group achieved protective titres. One hundred percent of rHBsAg plus 1018 ISS and 18.0% of hepatitis B vaccine-alone recipients were seroprotected 1 week following the second dose of study vaccine. After all doses of vaccine had been administered, seroprotection rates were 100% and 64%, respectively (p CPG 7909 was co-administered with Engerix-B in 56 healthy adults. After the second injection (week 6 time point), seroprotection was achieved in 100% of CPG 7909 recipients (0.5 mg 13/13; 1.0 mg 12/12; 0.125 mg 12/12) compared with 55% (6/11) of control participants (p = 0.0003). Twelve months post prime, all subjects who had received the full course of vaccination maintained seroprotective anti-HBs titres. The safety and immunogenicity of Engerix B plus CPG 7909 was assessed in HIV seropositive patients. All CPG 7909 recipients (n = 19) and 17/19 (89%) control subjects achieved seroprotection by 2 weeks after the third and final injection (10 weeks). Seroprotective titres remained in all CPG 7909 recipients at 48 weeks (100%) versus 12/19 (63%) for controls (p = 0.008). This cohort of HIV-infected patients was followed at 6-month intervals for up to 60 months after enrolment. The difference in seroprotection (> or =10

  16. Stellar mass function of cluster galaxies at z $\\sim$ 1.5: evidence for reduced quenching efficiency at high redshift

    CERN Document Server

    Nantais, Julie B; Lidman, Chris; Demarco, Ricardo; Noble, Allison; Wilson, Gillian; Muzzin, Adam; Foltz, Ryan; DeGroot, Andrew; Cooper, Mike

    2016-01-01

    We present the stellar mass functions (SMFs) of passive and star-forming galaxies with a limiting mass of 10$^{10.1}$ M$_{\\odot}$ in four spectroscopically confirmed Spitzer Adaptation of the Red-sequence Cluster Survey (SpARCS) galaxy clusters at 1.37 $<$ z $<$ 1.63. The clusters have 113 spectroscopically confirmed members combined, with 8-45 confirmed members each. We construct $Ks$-band-selected photometric catalogs for each cluster with an average of 11 photometric bands ranging from $u$ to 8 $\\mu$m. We compare our cluster galaxies to a field sample derived from a similar $Ks$-band-selected catalog in the UltraVISTA/COSMOS field. The SMFs resemble those of the field, but with signs of environmental quenching. We find that 30 $\\pm$ 20\\% of galaxies that would normally be forming stars in the field are quenched in the clusters. The environmental quenching efficiency shows little dependence on projected cluster-centric distance out to $\\sim$ 4 Mpc, providing tentative evidence of pre-processing and/or...

  17. Optical Rotation from Coupled Cluster and Density Functional Theory: The Role of Basis Set Convergence.

    Science.gov (United States)

    Haghdani, Shokouh; Åstrand, Per-Olof; Koch, Henrik

    2016-02-01

    We have calculated the electronic optical rotation of seven molecules using coupled cluster singles-doubles (CCSD) and the second-order approximation (CC2) employing the aug-cc-pVXZ (X = D, T, or Q) basis sets. We have also compared to time-dependent density functional theory (TDDFT) by utilizing two functionals B3LYP and CAM-B3LYP and the same basis sets. Using relative and absolute error schemes, our calculations demonstrate that the CAM-B3LYP functional predicts optical rotation with the minimum deviations compared to CCSD at λ = 355 and 589.3 nm. Furthermore, our results illustrate that the aug-cc-pVDZ basis set provides the optical rotation in good agreement with the larger basis sets for molecules not possessing small-angle optical rotation at λ = 589.3 nm. We have also performed several two-point inverse power extrapolations for the basis set convergence, i.e., OR(∞) + AX(-n), using the CC2 model at λ = 355 and 589.3 nm. Our results reveal that a two-point inverse power extrapolation with the aug-cc-pVTZ and aug-cc-pVQZ basis sets at n = 5 provides optical rotation deviations similar to those of aug-cc-pV5Z with respect to the basis limit.

  18. Different equation-of-motion coupled cluster methods with different reference functions: The formyl radical

    Science.gov (United States)

    Kuś, Tomasz; Bartlett, Rodney J.

    2008-09-01

    The doublet and quartet excited states of the formyl radical have been studied by the equation-of-motion (EOM) coupled cluster (CC) method. The Sz spin-conserving singles and doubles (EOM-EE-CCSD) and singles, doubles, and triples (EOM-EE-CCSDT) approaches, as well as the spin-flipped singles and doubles (EOM-SF-CCSD) method have been applied, subject to unrestricted Hartree-Fock (HF), restricted open-shell HF, and quasirestricted HF references. The structural parameters, vertical and adiabatic excitation energies, and harmonic vibrational frequencies have been calculated. The issue of the reference function choice for the spin-flipped (SF) method and its impact on the results has been discussed using the experimental data and theoretical results available. The results show that if the appropriate reference function is chosen so that target states differ from the reference by only single excitations, then EOM-EE-CCSD and EOM-SF-CCSD methods give a very good description of the excited states. For the states that have a non-negligible contribution of the doubly excited configurations one is able to use the SF method with such a reference function, that in most cases the performance of the EOM-SF-CCSD method is better than that of the EOM-EE-CCSD approach.

  19. Levels of DNA Methylation Vary at CpG Sites across the BRCA1 Promoter, and Differ According to Triple Negative and "BRCA-Like" Status, in Both Blood and Tumour DNA.

    Directory of Open Access Journals (Sweden)

    Sarah L Daniels

    Full Text Available Triple negative breast cancer is typically an aggressive and difficult to treat subtype. It is often associated with loss of function of the BRCA1 gene, either through mutation, loss of heterozygosity or methylation. This study aimed to measure methylation of the BRCA1 gene promoter at individual CpG sites in blood, tumour and normal breast tissue, to assess whether levels were correlated between different tissues, and with triple negative receptor status, histopathological scoring for BRCA-like features and BRCA1 protein expression. Blood DNA methylation levels were significantly correlated with tumour methylation at 9 of 11 CpG sites examined (p<0.0007. The levels of tumour DNA methylation were significantly higher in triple negative tumours, and in tumours with high BRCA-like histopathological scores (10 of 11 CpG sites; p<0.01 and p<0.007 respectively. Similar results were observed in blood DNA (6 of 11 CpG sites; p<0.03 and 7 of 11 CpG sites; p<0.02 respectively. This study provides insight into the pattern of CpG methylation across the BRCA1 promoter, and supports previous studies suggesting that tumours with BRCA1 promoter methylation have similar features to those with BRCA1 mutations, and therefore may be suitable for the same targeted therapies.

  20. The Origin of Dwarf Galaxies in Clusters: The Faint-End Slope of Abell 85 Galaxy Luminosity Function

    Science.gov (United States)

    Agulli, I.; Aguerri, J. A. L.; Barrena, R.; Diaferio, A.; Sánchez-Janssen, R.

    2016-10-01

    Dwarf galaxies (Mb>-18) are important because of their cosmological interest as tests of hierarchical theories. The formation of these galaxies is still an open question but red dwarf galaxies are preferentially located in high density environments, indicating that they are end-products of galaxy transformations in clusters. Deep spectroscopic studies of galaxy clusters are needed to put some constraints on dwarf galaxy formation and evolution. We have observed and analyzed Abell 85, a nearby (z = 0.055) and massive cluster down to M*+6, using the MOS instruments VIMOS@VLT and AF2@WHT. The first and powerful tool to study the characteristics of galaxies and compare with different density environments is the galaxy luminosity function. The comparison of the results for Abell 85 with literature outcomes for clusters and field, allows us to conclude that, at least for this cluster, the environment plays a major role in the nature of the faint-end galaxies, transforming blue dwarfs in the field into red ones in the cluster, but not in the formation of the luminosity function slope.

  1. Hypersensitive dual-function luminescence switching of a silver-chalcogenolate cluster-based metal-organic framework

    Science.gov (United States)

    Huang, Ren-Wu; Wei, Yong-Sheng; Dong, Xi-Yan; Wu, Xiao-Hui; Du, Chen-Xia; Zang, Shuang-Quan; Mak, Thomas C. W.

    2017-07-01

    Silver(I) chalcogenide/chalcogenolate clusters are promising photofunctional materials for sensing, optoelectronics and solar energy harvesting applications. However, their instability and poor room-temperature luminescent quantum yields have hampered more extensive study. Here, we graft such clusters to adaptable bridging ligands, enabling their interconnection and the formation of rigid metal-organic frameworks. By controlling the spatial separation and orientation of the clusters, they then exhibit enhanced stability (over one year) and quantum yield (12.1%). Ultrafast dual-function fluorescence switching (volatile organic compounds. Single-crystal X-ray diffraction of the inclusion materials, obtained by single-crystal-to-single-crystal transformation, enables precise determination of the position of the small molecules within the framework, elucidating the switching mechanism. The work enriches the cluster-based metal-organic framework portfolio, bridges the gap between silver chalcogenide/chalcogenolate clusters and metal-organic frameworks, and provides a foundation for further development of functional silver-cluster-based materials.

  2. Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice.

    Science.gov (United States)

    Wang, Jun; Linnenbrink, Miriam; Künzel, Sven; Fernandes, Ricardo; Nadeau, Marie-Josée; Rosenstiel, Philip; Baines, John F

    2014-07-01

    Understanding the origins of gut microbial community structure is critical for the identification and interpretation of potential fitness-related 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 evaluation criteria. We identify support for two clusters that are compositionally similar to clusters identified in humans, chimpanzees, and laboratory mice, characterized by differences in Bacteroides, Robinsoniella, and unclassified genera belonging to the family Lachnospiraceae. To further evaluate these clusters, we (i) monitored community changes associated with moving mice from the natural to a laboratory environment, (ii) performed functional metagenomic sequencing, and (iii) subjected wild-caught samples to stable isotope analysis to reconstruct dietary patterns. This process reveals differences in the proportions of genes involved in carbohydrate versus protein metabolism in the functional metagenome, as well as differences in plant- versus meat-derived food sources between clusters. In conjunction with wild-caught mice quickly changing their enterotype classification upon transfer to a standard laboratory chow diet, these results provide strong evidence that dietary history contributes to the presence of enterotype-like clustering in wild mice.

  3. The Stellar Mass Functions of the CLASH-VLT Clusters MACS J1206-0847 and Abell 209

    Science.gov (United States)

    Annunziatella, M.; Biviano, A.; Mercurio, A.; Nonino, M.; Rosati, P.; Balestra, I.; Girardi, M.; Grillo, C.

    The study of the galaxy stellar mass function, and in particular its dependence from the environment, represents a key observable to discriminate between different models of galaxy evolution. We determined the stellar mass function (SMF) of passive and star-forming (SF) galaxies in different regions of two clusters in the CLASH-VLT sample, MACS J1206.2-0847 and Abell 209. Since these two clusters are at different redshifts, the comparison between the results obtained in the two cases can inform us about the evolution of the SMF with cosmic time.

  4. Structural and functional characterization of an iron-sulfur cluster assembly scaffold protein-SufA from Plasmodium vivax.

    Science.gov (United States)

    Pala, Zarna Rajeshkumar; Saxena, Vishal; Saggu, Gagandeep Singh; Yadav, Sushil Kumar; Pareek, R P; Kochar, Sanjay Kumar; Kochar, Dhanpat Kumar; Garg, Shilpi

    2016-07-01

    Iron-sulfur (Fe-S) clusters are utilized as prosthetic groups in all living organisms for diverse range of cellular processes including electron transport in respiration and photosynthesis, sensing of ambient conditions, regulation of gene expression and catalysis. In Plasmodium, two Fe-S cluster biogenesis pathways are reported, of which the Suf pathway in the apicoplast has been shown essential for the erythrocytic stages of the parasite. While the initial components of this pathway detailing the sulfur mobilization have been elucidated, the components required for the assembly and transfer of Fe-S clusters are not reported from the parasite. In Escherichia coli, SufB acts as a scaffold protein and SufA traffics the assembled Fe-S cluster from SufB to target apo-proteins. However, in Plasmodium, the homologs of these proteins are yet to be characterized for their function. Here, we report a putative SufA protein from Plasmodium vivax with signature motifs of A-type scaffold proteins, which is evolutionarily conserved. The presence of the [Fe4S4](3+) cluster under reduced conditions was confirmed by UV-visible and EPR spectroscopy and the interaction of these clusters with the conserved cysteine residues of chains A and B of PvSufA, validates its existence as a dimer, similar to that in E. coli. The H-bond interactions at the PvSufA-SufB interface demonstrate SufA as a scaffold protein in conjunction with SufB for the pre-assembly of Fe-S clusters and their transfer to the target proteins. Co-localization of the protein to the apicoplast further provides an experimental evidence of a functional scaffold protein SufA for the biogenesis of Fe-S clusters in apicoplast of Plasmodium.

  5. On the Link Between Energy Equipartition and Radial Variation in the Stellar Mass Function of Star Clusters

    Science.gov (United States)

    Webb, Jeremy J.; Vesperini, Enrico

    2016-10-01

    We make use of N-body simulations to determine the relationship between two observable parameters that are used to quantify mass segregation and energy equipartition in star clusters. Mass segregation can be quantified by measuring how the slope of a cluster's stellar mass function α changes with clustercentric distance r, and then calculating δ _α = d α (r)/d ln(r/r_m) where rm is the cluster's half-mass radius. The degree of energy equipartition in a cluster is quantified by η, which is a measure of how stellar velocity dispersion σ depends on stellar mass m via σ(m)∝m-η. Through a suite of N-body star cluster simulations with a range of initial sizes, binary fractions, orbits, black hole retention fractions, and initial mass functions, we present the co-evolution of δα and η. We find that measurements of the global η are strongly affected by the radial dependence of σ and mean stellar mass and the relationship between η and δα depends mainly on the cluster's initial conditions and the tidal field. Within rm, where these effects are minimized, we find that η and δα initially share a linear relationship. However, once the degree of mass segregation increases such that the radial dependence of σ and mean stellar mass become a factor within rm, or the cluster undergoes core collapse, the relationship breaks down. We propose a method for determining η within rm from an observational measurement of δα. In cases where η and δα can be measured independently, this new method offers a way of measuring the cluster's dynamical state.

  6. On the link between energy equipartition and radial variation in the stellar mass function of star clusters

    Science.gov (United States)

    Webb, Jeremy J.; Vesperini, Enrico

    2017-01-01

    We make use of N-body simulations to determine the relationship between two observable parameters that are used to quantify mass segregation and energy equipartition in star clusters. Mass segregation can be quantified by measuring how the slope of a cluster's stellar mass function α changes with clustercentric distance r, and then calculating δ _α = d α (r)/d ln(r/r_m), where rm is the cluster's half-mass radius. The degree of energy equipartition in a cluster is quantified by η, which is a measure of how stellar velocity dispersion σ depends on stellar mass m via σ(m) ∝ m-η. Through a suite of N-body star cluster simulations with a range of initial sizes, binary fractions, orbits, black hole retention fractions, and initial mass functions, we present the co-evolution of δα and η. We find that measurements of the global η are strongly affected by the radial dependence of σ and mean stellar mass and the relationship between η and δα depends mainly on the cluster's initial conditions and the tidal field. Within rm, where these effects are minimized, we find that η and δα initially share a linear relationship. However, once the degree of mass segregation increases such that the radial dependence of σ and mean stellar mass become a factor within rm, or the cluster undergoes core collapse, the relationship breaks down. We propose a method for determining η within rm from an observational measurement of δα. In cases where η and δα can be measured independently, this new method offers a way of measuring the cluster's dynamical state.

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

    Science.gov (United States)

    Babbitt, Patricia C.; Ferrin, Thomas E.

    2017-01-01

    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 demonstrated

  8. 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.

  9. Radial gradients in initial mass function sensitive absorption features in the Coma brightest cluster galaxies

    Science.gov (United States)

    Zieleniewski, Simon; Houghton, Ryan C. W.; Thatte, Niranjan; Davies, Roger L.; Vaughan, Sam P.

    2017-02-01

    Using the Oxford Short Wavelength Integral Field specTrograph, we trace radial variations of initial mass function (IMF)-sensitive absorption features of three galaxies in the Coma cluster. We obtain resolved spectroscopy of the central 5 kpc for the two central brightest cluster galaxies (BCGs) NGC4889, NGC4874, and the BCG in the south-west group NGC4839, as well as unresolved data for NGC4873 as a low-σ* control. We present radial measurements of the IMF-sensitive features: sodium Na ISDSS, calcium triplet CaT, and iron-hydride FeH0.99, along with the magnesium Mg I0.88 and titanium oxide TiO0.89 features. We employ two separate methods for both telluric correction and sky subtraction around the faint FeH feature to verify our analysis. Within NGC4889 we find strong gradients of Na ISDSS and CaT but a flat FeH profile, which, from comparing to stellar population synthesis models, suggests an old, α-enhanced population with a Chabrier, or even bottom-light IMF. The age and abundance are in line with previous studies but the normal IMF is in contrast to recent results suggesting an increased IMF slope with increased velocity dispersion. We measure flat Na ISDSS and FeH profiles within NGC4874, and determine an old, possibly slightly α-enhanced and Chabrier IMF population. We find an α-enhanced, Chabrier IMF population in NGC4873. Within NGC4839 we measure both strong Na ISDSS and strong FeH, although with a large systematic uncertainty, suggesting a possible heavier IMF. The IMFs we infer for these galaxies are supported by published dynamical modelling. We stress that IMF constraints should be corroborated by further spectral coverage and independent methods on a galaxy-by-galaxy basis.

  10. Psychophysiological responses to visceral and somatic pain in functional chest pain identify clinically relevant pain clusters.

    Science.gov (United States)

    Farmer, A D; Coen, S J; Kano, M; Naqvi, H; Paine, P A; Scott, S M; Furlong, P L; Lightman, S L; Knowles, C H; Aziz, Q

    2014-01-01

    Despite chronic pain being a feature of functional chest pain (FCP) its experience is variable. The factors responsible for this variability remain unresolved. We aimed to address these knowledge gaps, hypothesizing that the psychophysiological profiles of FCP patients will be distinct from healthy subjects. 20 Rome III defined FCP patients (nine males, mean age 38.7 years, range 28-59 years) and 20 healthy age-, sex-, and ethnicity-matched controls (nine males, mean 38.2 years, range 24-49) had anxiety, depression, and personality traits measured. Subjects had sympathetic and parasympathetic nervous system parameters measured at baseline and continuously thereafter. Subjects received standardized somatic (nail bed pressure) and visceral (esophageal balloon distension) stimuli to pain tolerance. Venous blood was sampled for cortisol at baseline, post somatic pain and post visceral pain. Patients had higher neuroticism, state and trait anxiety, and depression scores but lower extroversion scores vs controls (all p visceral stimulus (p = 0.009) and had a higher cortisol at baseline, and following pain (all p pain they increased their parasympathetic tone (p ≤ 0.008). The amalgamating the data, we identified two psychophysiologically distinct 'pain clusters'. Patients were overrepresented in the cluster characterized by high neuroticism, trait anxiety, baseline cortisol, pain hypersensitivity, and parasympathetic response to pain (all p < 0.03). In future, such delineations in FCP populations may facilitate individualization of treatment based on psychophysiological profiling. © 2013 John Wiley & Sons Ltd.

  11. Clustering, Cosmology and a New Era of Black Hole Demographics: The Conditional Luminosity Function of AGNs

    Science.gov (United States)

    Ballantyne, David R.

    2017-01-01

    Deep X-ray surveys have provided a comprehensive and largely unbiased view of active galactic nuclei (AGN) evolution stretching back to z~5. However, it has been challenging to use the survey results to connect this evolution to the cosmological environment that AGNs inhabit. Exploring this connection will be crucial to understanding the triggering mechanisms of AGNs and how these processes manifest in observations at all wavelengths. In anticipation of upcoming wide-field X-ray surveys that will allow quantitative analysis of AGN environments, we present a method to observationally constrain the Conditional Luminosity Function (CLF) of AGNs at a specific z. Once measured, the CLF allows the calculation of the AGN bias, mean dark matter halo mass, AGN lifetime, halo occupation number, and AGN correlation function -- all as a function of luminosity. The CLF can be constrained using a measurement of the X-ray luminosity function and the correlation length at different luminosities. The method is illustrated at z≈0 and 0.9 using the limited data that is currently available, and a clear luminosity dependence in the AGN bias and mean halo mass is predicted at both, supporting the idea that there are at least two different modes of AGN triggering. In addition, the CLF predicts that z≈0.9 quasars may be commonly hosted by haloes with Mh ~ 1014 M⊙. These `young cluster' environments may provide the necessary interactions between gas-rich galaxies to fuel luminous accretion. The results derived from this method will be useful to populate AGNs of different luminosities in cosmological simulations.

  12. Water cluster anions studied by the long-range corrected density functional theory.

    Science.gov (United States)

    Yagi, Kiyoshi; Okano, Yuko; Sato, Takeshi; Kawashima, Yukio; Tsuneda, Takao; Hirao, Kimihiko

    2008-10-09

    Long-range corrected density functional theory (LC-DFT) is applied to a series of small water cluster anions(n= 2-6) to compute their vertical detachment energies (VDEs). The LC scheme is shown to eliminate an unphysical overestimation of the electron-water attraction in the hybrid functional by properly accounting for the long-range exchange repulsions. It is shown that a correct correlation energy behavior for a rapidly varying density is also important for describing a spatially extent, excess electron. The one-parameter progressive (OP) correlation functional, which satisfies this condition, leads to a remarkable improvement in the calculated VDE over the conventional one. The LC-BOP method produces highly accurate VDEs with a mean absolute deviation of 13.8 meV from the reference CCSD(T) results, reducing the error of B3LYP by more than 15 times. LC-BOP is found to be more accurate than MP2 which yields an excess electron underbound by 43.6 meV. The effect of basis sets on the calculated VDE is also examined. The aug-cc-pVDZ basis set with an extra diffuse function is found to be more accurate and reliable than the extended Pople-type basis sets used in the previous works. The extrapolation of the calculated VDE of different electron binding motifs is compared with the VDEs of experimentally observed three isomers (Verlet, J. R. R.; Bragg,A. E.; Kammrath, A.; Cheshnovsky, O.; Neumark, D. M. Science 2005, 307, 93).

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

    Science.gov (United States)

    Cataneo, Matteo; Rapetti, David; Lombriser, Lucas; Li, Baojiu

    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 lesssim 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.

  14. Identification and Functional Analysis of the Mycophenolic Acid Gene Cluster of Penicillium roqueforti.

    Directory of Open Access Journals (Sweden)

    Abdiel Del-Cid

    Full Text Available The filamentous fungus Penicillium roqueforti is widely known as the ripening agent of blue-veined cheeses. Additionally, this fungus is able to produce several secondary metabolites, including the meroterpenoid compound mycophenolic acid (MPA. Cheeses ripened with P. roqueforti are usually contaminated with MPA. On the other hand, MPA is a commercially valuable immunosuppressant. However, to date the molecular basis of the production of MPA by P. roqueforti is still unknown. Using a bioinformatic approach, we have identified a genomic region of approximately 24.4 kbp containing a seven-gene cluster that may be involved in the MPA biosynthesis in P. roqueforti. Gene silencing of each of these seven genes (named mpaA, mpaB, mpaC, mpaDE, mpaF, mpaG and mpaH resulted in dramatic reductions in MPA production, confirming that all of these genes are involved in the biosynthesis of the compound. Interestingly, the mpaF gene, originally described in P. brevicompactum as a MPA self-resistance gene, also exerts the same function in P. roqueforti, suggesting that this gene has a dual function in MPA metabolism. The knowledge of the biosynthetic pathway of MPA in P. roqueforti will be important for the future control of MPA contamination in cheeses and the improvement of MPA production for commercial purposes.

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

    CERN Document Server

    Cataneo, Matteo; Lombriser, Lucas; Li, Baojiu

    2016-01-01

    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 fractional enhancement of the $f(R)$ halo abundance with respect to that of General Relativity (GR) within a precision of $\\lesssim 5\\%$ 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 flexi...

  16. Density functional study of Agn-1Y (n =2-10) clusters

    Institute of Scientific and Technical Information of China (English)

    Liu Xiao-Yong; Zhu Zheng-He; Sheng Yong

    2011-01-01

    properties of Agn-1Y (n =2-10) clusters in this paper.The structural optimization and the frequency analysis are performed at the B3LYP/LANL2DZ level.Meanwhile,the differences in geometry,stability and electronic properties between Agn and Agn-1Y (n =2-10) clusters are also studied.The results show that for the doping of the yttrium atoms,the structures and the average binding lengths of the Agn clusters are greatly changed. In addition,the thermodynamic stabilities of the Agn clusters are enhanced generally with the doping of the Y atoms.In addition,the chemical stabilities of the Agn- 1 Y clusters are still improved compared with that of the three-dimensional Agn clusters.

  17. Suppression of HIV replication in vitro by CpG and CpG conjugated to the non toxic B subunit of cholera toxin.

    Science.gov (United States)

    Nowroozalizadeh, Salma; Jansson, Marianne; Adamsson, Jenni; Lindblad, Marianne; Fenyö, Eva-Maria; Holmgren, Jan; Harandi, Ali M

    2008-05-01

    Administration of oligodeoxynucleotides (ODNs) containing CpG motifs generates a rapid and potent response of CC-chemokines, known as ligands of the HIV-1 co-receptor CCR5, in the murine female genital tract. The present study explored the potential HIV inhibitory activities of different human CpG prototypes either alone or conjugated to the non-toxic subunit of cholera toxin (CTB). Results showed that in vitro replication of both HIV-1 and HIV-2 can be suppressed by different human CpG prototypes. Importantly, the conjugation of CpG ODN to CTB (CTB-CpG) enhanced the antiviral activity of CpG against primary HIV-1 isolates of both R5 and X4 phenotypes in peripheral blood mononuclear cells (PBMC) as well as U87.CD4 co-receptor indicator cells. CTB-CpGs triggered higher amounts of MIP-1alpha, and MIP-1beta in PBMC than the corresponding CpG ODNs, which may explain the superior antiviral effect of CTB-CpG against R5 virus in PBMC. Incubation of PBMC with CpG ODN and CTB-CpG did not alter surface expression of HIV-1 receptors indicating that the observed anti-HIV-1 effect is not mediated through down regulation of HIV-1 receptors on target cells. Further, the enhanced antiviral effect of CTB-CpG was dependent on the presence of phosphorothioate backbone in the ODN, whereas the presence of CpG motif in ODNs was dispensable. These results have implications for the development of novel intervention strategies to prevent HIV infection.

  18. CpG dinucleotide frequencies reveal the role of host methylation capabilities in parvovirus evolution.

    Science.gov (United States)

    Upadhyay, Mohita; Samal, Jasmine; Kandpal, Manish; Vasaikar, Suhas; Biswas, Banhi; Gomes, James; Vivekanandan, Perumal

    2013-12-01

    Parvoviruses are rapidly evolving viruses that infect a wide range of hosts, including vertebrates and invertebrates. Extensive methylation of the parvovirus genome has been recently demonstrated. A global pattern of methylation of CpG dinucleotides is seen in vertebrate genomes, compared to "fractional" methylation patterns in invertebrate genomes. It remains unknown if the loss of CpG dinucleotides occurs in all viruses of a given DNA virus family that infect host species spanning across vertebrates and invertebrates. We investigated the link between the extent of CpG dinucleotide depletion among autonomous parvoviruses and the evolutionary lineage of the infected host. We demonstrate major differences in the relative abundance of CpG dinucleotides among autonomous parvoviruses which share similar genome organization and common ancestry, depending on the infected host species. Parvoviruses infecting vertebrate hosts had significantly lower relative abundance of CpG dinucleotides than parvoviruses infecting invertebrate hosts. The strong correlation of CpG dinucleotide depletion with the gain in TpG/CpA dinucleotides and the loss of TpA dinucleotides among parvoviruses suggests a major role for CpG methylation in the evolution of parvoviruses. Our data present evidence that links the relative abundance of CpG dinucleotides in parvoviruses to the methylation capabilities of the infected host. In sum, our findings support a novel perspective of host-driven evolution among autonomous parvoviruses.

  19. Effects of systemic pretreatment with CpG oligodeoxynucleotides on skin wound healing in mice.

    Science.gov (United States)

    Hergert, Bettina; Grambow, Eberhard; Butschkau, Antje; Vollmar, Brigitte

    2013-01-01

    Unmethylated CpG oligodeoxynucleotides (ODN) bind to the Toll-like receptor 9, thus stimulating the immune system. To study the effects of systemic pretreatment with CpG ODN on dermal regeneration, C57BL6/J Tyr mice were treated with CpG or control ODN 6 days prior to implantation of a dorsal skinfold chamber and skin wounding. Wound epithelialization was analyzed by planimetric microscopy. On day 18, wound tissues were taken for (immuno)histochemical staining. CpG ODN increased epithelialization compared with control ODN treatment. Histological analysis revealed reduced capillary density, reduced wound cellularity, and reduced numbers of infiltrating leukocytes, as well as reduced F4/80-positive macrophages, but increased numbers of RELM-α-positive M2 macrophages after CpG ODN treatment, reflecting a better quality of wound healing on day 18 compared with control ODN treatment. Reverse transcription-polymerase chain reaction analysis of Toll-like receptor 9 showed the receptor expression on both fibroblasts and keratinocytes. Fibroblasts showed an increase of migration upon increasing dosages of CpG and not control ODN, reaching ∼50% of the response of basic fibroblast growth factor-exposed cells. Keratinocytes dose-dependently responded to both CpG and control ODN up to values found in keratinocyte growth factor-exposed cells. In summary, CpG ODN support late tissue-remodeling processes that contribute to resolution of inflammation and solid wounds during skin regeneration.

  20. Modulation of CpG oligodeoxynucleotide-mediated immune stimulation by locked nucleic acid (LNA)

    DEFF Research Database (Denmark)

    Vollmer, Jörg; Jepsen, Jan Stenvang; Uhlmann, Eugen

    2004-01-01

    Locked nucleic acid (LNA) is an RNA derivative that when introduced into oligodeoxynucleotides (ODN), mediates high efficacy and stability. CpG ODNs are potent immune stimulators and are recognized by toll-like receptor-9 (TLR9). Some phosphorothioate antisense ODNs bearing CpG dinucleotides have...

  1. Application of functional data analysis in classification and clustering of functional near-infrared spectroscopy signal in response to noxious stimuli

    Science.gov (United States)

    Pourshoghi, Ahmad; Zakeri, Issa; Pourrezaei, Kambiz

    2016-10-01

    We introduce the application of functional data analysis (fDA) on functional near-infrared spectroscopy (fNIRS) signals for the development of an accurate and clinically practical assessment method of pain perception. We used the cold pressor test to induce different levels of pain in healthy subjects while the fNIRS signal was recorded from the frontal regions of the brain. We applied fDA on the collected fNIRS data to convert discrete samples into continuous curves. This method enabled us to represent the curves as a linear combination of basis functions. We utilized bases coefficients as features that represent the shape of the signals (as opposed to extracting defined features from signal) and used them to train a support vector machine to classify the signals based on the level of induced pain. We achieved 94% of accuracy to classify low-pain and high-pain signals. Moreover applying hierarchical clustering on the coefficients, we found three clusters in the data which represented low-pain (one cluster) and high-pain groups (two clusters) with an accuracy of 91.2%. The center of these clusters can represent the prototype fNIRS response of that pain level.

  2. A comparative density functional study of methanol decomposition on Cu{sub 4} and Co{sub 4} clusters.

    Energy Technology Data Exchange (ETDEWEB)

    Mehmood, F.; Greeley, J.; Zapol, P.; Curtiss, L. A.

    2010-08-12

    A density functional theory study of the decomposition of methanol on Cu{sub 4} and Co{sub 4} clusters is presented. The reaction intermediates and activation barriers have been determined for reaction steps to form H{sub 2} and CO. For both clusters, methanol decomposition initiated by C-H and O-H bond breaking was investigated. In the case of a Cu{sub 4} cluster, methanol dehydrogenation through hydroxymethyl (CH{sub 2}OH), hydroxymethylene (CHOH), formyl (CHO), and carbon monoxide (CO) is found to be slightly more favorable. For a Co{sub 4} cluster, the dehydrogenation pathway through methoxy (CH{sub 3}O) and formaldehyde (CH{sub 2}O) is slightly more favorable. Each of these pathways results in formation of CO and H{sub 2}. The Co cluster pathway is very favorable thermodynamically and kinetically for dehydrogenation. However, since CO binds strongly, it is likely to poison methanol decomposition to H{sub 2} and CO at low temperatures. In contrast, for the Cu cluster, CO poisoning is not likely to be a problem since it does not bind strongly, but the dehydrogenation steps are not energetically favorable. Pathways involving C-O bond cleavage are even less energetically favorable. The results are compared to our previous study of methanol decomposition on Pd{sub 4} and Pd{sub 8} clusters. Finally, all reaction energy changes and transition state energies, including those for the Pd clusters, are related in a linear, Broensted?Evans?Polanyi plot.

  3. CpG sites with continuously increasing or decreasing methylation from early to late human fetal brain development.

    Science.gov (United States)

    Schneider, Eberhard; Dittrich, Marcus; Böck, Julia; Nanda, Indrajit; Müller, Tobias; Seidmann, Larissa; Tralau, Tim; Galetzka, Danuta; El Hajj, Nady; Haaf, Thomas

    2016-10-30

    Normal human brain development is dependent on highly dynamic epigenetic processes for spatial and temporal gene regulation. Recent work identified wide-spread changes in DNA methylation during fetal brain development. We profiled CpG methylation in frontal cortex of 27 fetuses from gestational weeks 12-42, using Illumina 450K methylation arrays. Sites showing genome-wide significant correlation with gestational age were compared to a publicly available data set from gestational weeks 3-26. Altogether, we identified 2016 matching developmentally regulated differentially methylated positions (m-dDMPs): 1767m-dDMPs were hypermethylated and 1149 hypomethylated during fetal development. M-dDMPs are underrepresented in CpG islands and gene promoters, and enriched in gene bodies. They appear to cluster in certain chromosome regions. M-dDMPs are significantly enriched in autism-associated genes and CpGs. Our results promote the idea that reduced methylation dynamics during fetal brain development may predispose to autism. In addition, m-dDMPs are enriched in genes with human-specific brain expression patterns and/or histone modifications. Collectively, we defined a subset of dDMPs exhibiting constant methylation changes from early to late pregnancy. The same epigenetic mechanisms involving methylation changes in cis-regulatory regions may have been adopted for human brain evolution and ontogeny. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  4. A codon substitution model that incorporates the effect of the GC contents, the gene density and the density of CpG islands of human chromosomes

    Directory of Open Access Journals (Sweden)

    Misawa Kazuharu

    2011-08-01

    Full Text Available Abstract Background Developing a model for codon substitutions is essential for the analyses of protein sequences. Recent studies on the mutation rates in the non-coding regions have shown that CpG mutation rates in the human genome are negatively correlated to the local GC content and to the densities of functional elements. This study aimed at understanding the effect of genomic features, namely, GC content, gene density, and frequency of CpG islands, on the rates of codon substitution in human chromosomes. Results Codon substitution rates of CpG to TpG mutations, TpG to CpG mutations, and non-CpG transitions and transversions in humans were estimated by comparing the coding regions of thousands of human and chimpanzee genes and inferring their ancestral sequences by using macaque genes as the outgroup. Since the genomic features are depending on each other, partial regression coefficients of these features were obtained. Conclusion The substitution rates of codons depend on gene densities of the chromosomes. Transcription-associated mutation is one such pressure. On the basis of these results, a model of codon substitutions that incorporates the effect of genomic features on codon substitution in human chromosomes was developed.

  5. On the Link Between Energy Equipartition and Radial Variation in the Stellar Mass Function of Star Clusters

    CERN Document Server

    Webb, Jeremy J

    2016-01-01

    We make use of $N$-body simulations to determine the relationship between two observable parameters that are used to quantify mass segregation and energy equipartition in star clusters. Mass segregation can be quantified by measuring how the slope of a cluster's stellar mass function $\\alpha$ changes with clustercentric distance r, and then calculating $\\delta_\\alpha = \\frac{d \\alpha(r)}{d ln(r/r_m)}$ where $r_m$ is the cluster's half-mass radius. The degree of energy equipartition in a cluster is quantified by $\\eta$, which is a measure of how stellar velocity dispersion $\\sigma$ depends on stellar mass m via $\\sigma(m) \\propto m^{-\\eta}$. Through a suite of $N$-body star cluster simulations with a range of initial sizes, binary fractions, orbits, black hole retention fractions, and initial mass functions, we present the co-evolution of $\\delta_\\alpha$ and $\\eta$. We find that measurements of the global $\\eta$ are strongly affected by the radial dependence of $\\sigma$ and mean stellar mass and the relationsh...

  6. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

    Okabe, Nobuhiro [Kavli Institute for the Physics and Mathematics of the Universe (WPI), Todai Institutes for Advanced Study, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8583 (Japan); Futamase, Toshifumi; Kuroshima, Risa [Astronomical Institute, Tohoku University, Sendai 980-8578 (Japan); Kajisawa, Masaru, E-mail: nobuhiro.okabe@ipmu.jp [Research Center for Space and Cosmic Evolution, Ehime University, Bunkyo-cho 2-5, Matsuyama 790-8577 (Japan)

    2014-04-01

    We present a 4 deg{sup 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{sup –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 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{sub −0.32}{sup +0.42} for the former model and 0.99{sub −0.23}{sup +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 {sup –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.

  9. Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations.

    Science.gov (United States)

    Hume, David A; Summers, Kim M; Raza, Sobia; Baillie, J Kenneth; Freeman, Thomas C

    2010-06-01

    Very large microarray datasets showing gene expression across multiple tissues and cell populations provide a window on the transcriptional networks that underpin the differences in functional activity between biological systems. Clusters of co-expressed genes provide lineage markers, candidate regulators of cell function and, by applying the principle of guilt by association, candidate functions for genes of currently unknown function. We have analysed a dataset comprising pure cell populations from hemopoietic and non-hemopoietic cell types (http://biogps.gnf.org). Using a novel network visualisation and clustering approach, we demonstrate that it is possible to identify very tight expression signatures associated specifically with embryonic stem cells, mesenchymal cells and hematopoietic lineages. Selected examples validate the prediction that gene function can be inferred by co-expression. One expression cluster was enriched in phagocytes, which, alongside endosome-lysosome constituents, contains genes that may make up a 'pathway' for phagocyte differentiation. Promoters of these genes are enriched for binding sites for the ETS/PU.1 and MITF families. Another cluster was associated with the production of a specific extracellular matrix, with high levels of gene expression shared by cells of mesenchymal origin (fibroblasts, adipocytes, osteoblasts and myoblasts). We discuss the limitations placed upon such data by the presence of alternative promoters with distinct tissue specificity within many protein-coding genes.

  10. Addition of CpG ODN to recombinant Pseudomonas aeruginosa ExoProtein A conjugates of AMA1 and Pfs25 greatly increases the number of responders.

    Science.gov (United States)

    Qian, Feng; Rausch, Kelly M; Muratova, Olga; Zhou, Hong; Song, Guanhong; Diouf, Ababacar; Lambert, Lynn; Narum, David L; Wu, Yimin; Saul, Allan; Miller, Louis H; Long, Carole A; Mullen, Gregory E D

    2008-05-12

    Both the blood-stage protein apical membrane antigen 1 (AMA1) and the 25-kDa sexual-stage protein (Pfs25) of Plasmodium falciparum are two leading candidates in malarial vaccine development. We have previously demonstrated that conjugation of these malarial antigens to recombinant Pseudomonas aeruginosa ExoProtein A (rEPA) significantly increased the mean-specific functional antibody responses in mice; however, some mice responded poorly and were unable to demonstrate a functional response. We hypothesized that the immunogenicities of these two malarial antigens could be further enhanced by the inclusion of a CpG oligodeoxynucleotide in the formulation. Mice were immunized with either rEPA-conjugated or unconjugated AMA1 and Pfs25 formulated on Alhydrogel with or without the addition of CPG 7909. Mice received the formulations on days 0 and 28, and mouse sera were collected on day 42. ELISA analyses on these sera showed that the addition of CPG 7909 to AMA1-rEPA and Pfs25-rEPA formulated on Alhydrogel induced significantly higher mean antibody titers than the formulations without CPG 7909, and led to a mixed Th1/Th2 response as demonstrated by the production of mouse IgG1 and IgG2a subclasses. The presence of CPG 7909 in the formulations of both conjugated antigens greatly increased the proportion of responders with antibody titers sufficient to inhibit blood-stage parasite growth in vitro or block transmission of sexual-stage parasites to mosquitoes. The results obtained in this study indicate the potential use of a combination strategy to increase the number of responders to malarial antigens in humans.

  11. Cluster-Expanded Solids: A Strategy for Assembling Functional Porous Materials

    Energy Technology Data Exchange (ETDEWEB)

    Long, Jeffrey R.

    2008-10-31

    This grant provided (partial) support for the research efforts of three graduate students and two undergraduate students. The intention of the program was to explore the use of molecular precursors in generating functional porous materials with precisely tailored structures and properties. Prior work in our laboratory had demonstrated the feasibility of employing face-capped octahedral clusters of the type [Re{sub 6}Q{sub 8}(CN){sub 6}]{sup 3-/4-} (Q = S, Se, Te) in the expansion of known metal-cyanide frameworks. For example, the use of [Re{sub 6}Se{sub 8}(CN){sub 6}]{sup 4-} as a reactant in place of [Fe(CN){sub 6}]{sup 4-} resulted in formation of Fe{sub 4}[Re{sub 6}Se{sub 8}(CN){sub 6}]{sub 3}·36H{sub 2}O, featuring an expanded form of the porous three-dimensional framework of Prussian blue (Fe{sub 4}[Fe(CN){sub 6}]{sub 3}·14H{sub 2}O). This compound could be dehydrated without loss of integrity, and the increase in void volume significantly enhances its capacity as a molecular sieve, enabling absorption of larger molecules. For this project, we continued with our efforts to devise new routes to microporous coordination solids that function as molecular sieves, sensors, or catalysts. In particular, our focus was on: (i) the synthesis of new molecular precursors of specific utility for such purposes, and (ii) attempts to incorporate these and existing molecular precursors into new coordination solids. Investigations of the terminal ligand substitution chemistry of the carbon-centered, trigonal prismatic cluster [W{sub 6}CCl{sub 18}]{sup 2-} generated the solvated species [W{sub 6}CCl{sub 12}(DMF){sub 6}]{sup 2+} and [W{sub 6}CCl{sub 12}(py){sub 6}]{sup 2+}, as well as the potential framework building units [W{sub 6}C(CN){sub 18}]{sup 3-}, [W6CCl{sub 12}(pyrazine){sub 6}]{sup 2+}, [W6CCl{sub 12}(4-cyanopyridine){sub 6}]{sup 2+}, and [W{sub 6}CCl{sub12}(4,4-bipyridine){sub 6}]{sup 2+}. Efforts to produce microporous magnets capable of performing magnetic

  12. Functional Analytic Psychotherapy (FAP) for Cluster B Personality Disorders: Creating Meaning, Mattering, and Skills

    Science.gov (United States)

    Pankey, Julieann

    2012-01-01

    There are ten identified personality disorders, broken into three clusters: A, B, and C. Individuals with a cluster B diagnosis may demonstrate marked displays of emotional instability, erratic and disruptive patterns around interpersonal relationships, a myopic and restricted range of affect, a pronounced lack of empathy and insight, barriers…

  13. U-, B- and r-band luminosity functions of galaxies in the Coma cluster

    NARCIS (Netherlands)

    Beijersbergen, M; Hoekstra, H; van Dokkum, PG; van der Hulst, T

    2002-01-01

    We present a deep multicolour CCD mosaic of the Coma cluster (Abell 1656), covering 5.2 deg(2) in the B and r bands, and 1.3 deg(2) in the U band. This large, homogeneous data set provides a valuable low-redshift comparison sample for studies of galaxies in distant clusters. In this paper we present

  14. A functional foot type classification with cluster analysis based on plantar pressure distribution during jogging.

    Science.gov (United States)

    De Cock, A; Willems, T; Witvrouw, E; Vanrenterghem, J; De Clercq, D

    2006-04-01

    The purpose of this study was to establish a reference dataset for peak pressures and pressure-time integrals during jogging, to compare this reference dataset with existing walking data and to develop a foot type classification, all based on plantar pressure data obtained from 215 healthy young adults. The subjects ran at 3.3 m s(-1) over a 16.5 m long running track, with a built-in pressure platform mounted on top of a force platform. Peak pressures, regional impulses and relative regional impulses were measured. These variables were found to be reliable (all intra class correlation coefficients above 0.75) and, except for the heel areas, gender and asymmetry effects could be neglected. Highest peak pressures were found under the heel due to large impact forces during initial contact phase (ICP). In the forefoot, the highest peak pressure was found under the second metatarsal (64.2 +/- 21.1 N cm(-2)). Compared to walking data, overall higher peak pressures and impulses and difference in hallux loading were found during barefoot jogging. Four pressure loading patterns were identified using a K-means cluster analysis, based on the relative regional impulses underneath the forefoot: medial M1 pattern, medial M2 pattern, central pattern and central-lateral pattern. These four pressure loading patterns could help in the functional interpretation of the foot behaviour during the stance phase in slow running.

  15. On the local radio luminosity function of galaxies; 1, the Virgo cluster

    CERN Document Server

    Gavazzi, G

    1999-01-01

    We cross-correlate the galaxies brighter than mB=18 in the Virgo cluster with the radio sources in the NVSS survey (1.4 GHz), resulting in 180 radio-optical identifications. We determine the radio luminosity function of the Virgo galaxies, separately for the early- and late-types. Late-type galaxies develop radio sources with a probability proportional to their optical luminosity. In fact their radio/optical (RB) distribution is gaussian, centered at log RB=-0.5, i.e. the radio luminosity is 0.3 of the optical one. The probability of late-type galaxies to develop radio sources is almost independent of their detailed Hubble type, except for Sa (and S0+S0a) which are a factor of 5 less frequent than later types at any RB. Giant elliptical galaxies feed "monster" radio sources with a probability strongly increasing with mass. However the frequency of fainter radio sources is progressively less sensitive on the system mass. The faintest giant E galaxies (MB=-17) have a probability of feeding low power radio sourc...

  16. 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.

  17. Improving the galaxy clustering Fisher matrix: window function, bin cross-correlation, and bin redshift uncertainty

    CERN Document Server

    Bailoni, Alberto; Amendola, Luca

    2016-01-01

    The Fisher matrix is a widely used tool to forecast the performance of future experiments and approximate the likelihood of large data sets. Most of the forecasts for cosmological parameters in galaxy clustering studies rely on the Fisher matrix approach for large-scale experiments like DES, Euclid, or SKA. Here we improve upon the standard method by taking into account three effects: the finite window function, the correlation between redshift bins, and the uncertainty on the bin redshift. The first two effects are negligible only in the limit of infinite surveys. The third effect, on the contrary, is negligible for infinitely small bins. Here we show how to take into account these effects and what the impact on forecasts of a Euclid-type experiment will be. The main result of this article is that the windowing and the bin cross-correlation induce a considerable change in the forecasted errors, of the order of 10-30% for most cosmological parameters, while the redshift bin uncertainty can be neglected for bi...

  18. Joint likelihood function of cluster number counts and weak lensing power spectrum

    CERN Document Server

    Takada, Masahiro

    2013-01-01

    A coherent over- or under-density contrast across a finite survey volume causes an upward- or downward- fluctuation in the number of halos. This fluctuation in halo number adds a significant co-variant scatter in the observed amplitudes of weak lensing power spectrum at nonlinear, small scales. Because of this covariance, the amount of information that can be extracted from a measurement of the weak lensing power spectrum is significantly smaller than naive estimates. In this paper, we show that by measuring both the number counts of clusters and the power spectrum in the same survey region, we can mitigate this loss of information and significantly enhance the scientific return from the upcoming surveys. First, using the halo model approach, we derive the joint likelihood function of the halo number counts and the weak lensing power spectrum, taking into account the super-sample co-variance effect on the two observables. We show that the analytical model matches the distributions measured from 1000 realizati...

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

    Science.gov (United States)

    Ehlers, Claudia; Veit, Katharina; Gottschalk, Gerhard; Schmitz, Ruth A

    2002-09-01

    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.

  20. The Redshift-Space Cluster-Galaxy Cross-Correlation Function: I. Modeling Galaxy Infall onto Millennium Simulation Clusters and SDSS Groups

    CERN Document Server

    Zu, Ying

    2012-01-01

    The large scale infall of galaxies around massive clusters provides a potentially powerful diagnostic of structure growth, dark energy, and cosmological deviations from General Relativity. We develop and test a method to recover galaxy infall kinematics (GIK) from measurements of the redshift-space cluster-galaxy cross-correlation function \\xi_{cg}(r_p,r_\\pi). Using galaxy and halo samples from the Millennium simulation, we calibrate an analytic model of the galaxy kinematic profiles comprised of a virialized component with an isotropic Gaussian velocity distribution and an infall component described by a skewed 2D t-distribution with a characteristic infall velocity v_r and separate radial and tangential dispersions. We show that convolving the real-space cross-correlation function with this velocity distribution accurately predicts the redshift-space \\xi_{cg}, and we show that measurements of \\xi_{cg} can be inverted to recover the four distinct elements of the GIK profiles. These in turn provide diagnostic...

  1. The Luminosity Functions of the Galaxy Cluster MS1054-0321 at z=0.83 based on ACS Photometry

    OpenAIRE

    Goto, Tomotsugu; Postman, Marc; Cross, Nicholas J. G.; Illingworth, G. D.; Tran, K.; Magee, D.; Franx, M.; Benitez, N.; Bouwens, R J; Demarco, R.; Ford, H.C.; Homeier, N. L.; Martel, A. R.; Menanteau, F.; Clampin, M.

    2004-01-01

    We present new measurements of the galaxy luminosity function (LF) and its dependence on local galaxy density, color, morphology, and clustocentric radius for the massive z=0.83 cluster MS1054-0321. Our analyses are based on imaging performed with the ACS onboard the HST in the F606W, F775W and F850LP passbands and extensive spectroscopic data obtained with the Keck LRIS. Our main results are based on a spectroscopically selected sample of 143 cluster members with morphological classification...

  2. Cluster analysis reveals a binary effect of storage on boar sperm motility function.

    Science.gov (United States)

    Henning, Heiko; Petrunkina, Anna M; Harrison, Robin A P; Waberski, Dagmar

    2014-06-01

    Storage of liquid-preserved boar spermatozoa is associated with a loss of fertilising ability of the preserved spermatozoa, which standard semen parameters barely reflect. Monitoring responses to molecular effectors of sperm function (e.g. bicarbonate) has proven to be a more sensitive approach to investigating storage effects. Bicarbonate not only initiates capacitation in spermatozoa, but also induces motility activation. This occurs at ejaculation, but also happens throughout passage through the oviduct. In the present study we tested whether the specific response of boar sperm subpopulations to bicarbonate, as assessed by motility activation, is altered with the duration of storage in vitro. Three ejaculates from each of seven boars were diluted in Beltsville thawing solution and stored at 17°C. Only minor changes in the parameters of diluted semen were revealed over a period of 72h storage. For assessment of bicarbonate responses, subsamples of diluted spermatozoa were centrifuged through a discontinuous Percoll gradient after 12, 24 and 72h storage. Subsequently, spermatozoa were incubated in two Ca2+-free variants of Tyrode's medium either without (TyrControl) or with (TyrBic) 15mM bicarbonate, and computer-aided sperm analysis motility measurements were made. Cluster analysis of imaging data from motile spermatozoa revealed the presence of five major sperm subpopulations with distinct motility characteristics, differing between TyrBic and TyrControl at any given time (Psperm motility function descriptors to storage: although the quantitative descriptor (percentage of motile spermatozoa) declines in washed semen samples, the qualitative descriptor (percentage of spermatozoa stimulated into fast linear motion by bicarbonate) is sustained independent of the duration of storage.

  3. Vibrational absorption spectra from vibrational coupled cluster damped linear response functions calculated using an asymmetric Lanczos algorithm

    DEFF Research Database (Denmark)

    Thomsen, Bo; Hansen, Mikkel Bo; Seidler, Peter

    2012-01-01

    We report the theory and implementation of vibrational coupled cluster (VCC) damped response functions. From the imaginary part of the damped VCC response function the absorption as function of frequency can be obtained, requiring formally the solution of the now complex VCC response equations...... with results from the recently reported [P. Seidler, M. B. Hansen, W. Györffy, D. Toffoli, and O. Christiansen, J. Chem. Phys. 132, 164105 (2010)] vibrational configuration interaction damped response function calculated using a symmetric Lanczos algorithm. Calculations of IR spectra of oxazole, cyclopropene...

  4. 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.

  5. Iron-sulphur clusters, their biosynthesis, and biological functions in protozoan parasites.

    Science.gov (United States)

    Ali, Vahab; Nozaki, Tomoyoshi

    2013-01-01

    Fe-S clusters are ensembles of sulphide-linked di-, tri-, and tetra-iron centres of a variety of metalloproteins that play important roles in reduction and oxidation of mitochondrial electron transport, energy metabolism, regulation of gene expression, cell survival, nitrogen fixation, and numerous other metabolic pathways. The Fe-S clusters are assembled by one of four distinct systems: NIF, SUF, ISC, and CIA machineries. The ISC machinery is a house-keeping system conserved widely from prokaryotes to higher eukaryotes, while the other systems are present in a limited range of organisms and play supplementary roles under certain conditions such as stress. Fe-S cluster-containing proteins and the components required for Fe-S cluster biosynthesis are modulated under stress conditions, drug resistance, and developmental stages. It is also known that a defect in Fe-S proteins and Fe-S cluster biogenesis leads to many genetic disorders in humans, which indicates the importance of the systems. In this review, we describe the biological and physiological significance of Fe-S cluster-containing proteins and their biosynthesis in parasitic protozoa including Plasmodium, Trypanosoma, Leishmania, Giardia, Trichomonas, Entamoeba, Cryptosporidium, Blastocystis, and microsporidia. We also discuss the roles of Fe-S cluster biosynthesis in proliferation, differentiation, and stress response in protozoan parasites. The heterogeneity of the systems and the compartmentalization of Fe-S cluster biogenesis in the protozoan parasites likely reflect divergent evolution under highly diverse environmental niches, and influence their parasitic lifestyle and pathogenesis. Finally, both Fe-S cluster-containing proteins and their biosynthetic machinery in protozoan parasites are remarkably different from those in their mammalian hosts. Thus, they represent a rational target for the development of novel chemotherapeutic and prophylactic agents against protozoan infections.

  6. A Functional Bikaverin Biosynthesis Gene Cluster in Rare Strains of Botrytis cinerea Is Positively Controlled by VELVET

    Science.gov (United States)

    Schumacher, Julia; Gautier, Angélique; Morgant, Guillaume; Studt, Lena; Ducrot, Paul-Henri; Le Pêcheur, Pascal; Azeddine, Saad; Fillinger, Sabine; Leroux, Pierre; Tudzynski, Bettina; Viaud, Muriel

    2013-01-01

    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. PMID:23308280

  7. 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.

  8. Anion-radical oxygen centers in small (AgO)n clusters: density functional theory predictions

    CERN Document Server

    Trushin, Egor V

    2012-01-01

    Anion-radical form of the oxygen centers O(-) is predicted at the DFT level for small silver oxide particles having the AgO stoichiometry. Model clusters (AgO)n appear to be ferromagnetic with appreciable spin density at the oxygen centers. In contrast to these clusters, the Ag2O model cluster have no unpaired electrons in the ground state. The increased O/Ag ratio in the oxide particles is proved to be responsible for the spin density at oxygen centers.

  9. Hydrogen storage on metal oxide model clusters using density-functional methods and reliable van der Waals corrections.

    Science.gov (United States)

    Gebhardt, Julian; Viñes, Francesc; Bleiziffer, Patrick; Hieringer, Wolfgang; Görling, Andreas

    2014-03-21

    We investigate the capability of low-coordinated sites on small model clusters to act as active centers for hydrogen storage. A set of small magic clusters with the formula (XY)6 (X = Mg, Ba, Be, Zn, Cd, Na, Li, B and Y = O, Se, S, F, I, N) and a "drumlike" hexagonal shape showing a low coordination number of three was screened. Oxide clusters turned out to be the most promising candidates for hydrogen storage. For these ionic compounds we explored the suitability of different van der Waals (vdW) corrections to density-functional calculations by comparing the respective H2 physisorption profile to highly accurate CCSD(T) (Coupled Cluster Singles Doubles with perturbative Triples) calculations. The Grimme D3 vdW correction in combination with the Perdew-Burke-Ernzerhof exchange-correlation functional was found to be the best approach compared to CCSD(T) hydrogen physisorption profiles and is, therefore, suited to study these and other light metal oxide systems. H2 adsorption on sites of oxide model clusters is found to meet the adsorption energy criteria for H2 storage, with bond strengths ranging from 0.15 to 0.21 eV. Energy profiles and estimates of kinetic constants for the H2 splitting reaction reveal that H2 is likely to be adsorbed molecularly on sites of (MgO)6, (BaO)6, and (BeO)6 clusters, suggesting a rapid H2 uptake/release at operating temperatures and moderate pressures. The small mass of beryllium and magnesium makes such systems appealing for meeting the gravimetric criterion for H2 storage.

  10. The Luminosity Functions of the Galaxy Cluster MS1054-0321 at z=0.83 based on ACS Photometry

    CERN Document Server

    Goto, T; Cross, N J G; Illingworth, G D; Tran, K; Magee, D; Franx, M; Benítez, N; Bouwens, R J; Demarco, R; Ford, H C; Homeier, N L; Martel, A R; Menanteau, F; Clampin, M; Hartig, G F; Ardila, D R; Bartko, F; Blakeslee, J P; Bradley, L D; Broadhurst, T J; Brown, R A; Burrows, C J; Cheng, E S; Feldman, P D; Golimowski, D A; Gronwall, C; Holden, B; Infante, L; Jee, M J; Krist, J E; Lesser, M P; Mei, S; Meurer, G R; Miley, G K; Motta, V; Overzier, R; Rosati, P; Sirianni, M; Sparks, W B; Tran, H D; Tsvetanov, Z I; White, R L; Zheng, W; Zirm, A W; Goto, Tomotsugu; Postman, Marc; Cross, Nicholas J.G.

    2004-01-01

    We present new measurements of the galaxy luminosity function (LF) and its dependence on local galaxy density, color, morphology, and clustocentric radius for the massive $z=0.83$ cluster MS1054-0321. Our analyses are based on imaging performed with the ACS onboard the HST in the F606W, F775W and F850LP passbands and extensive spectroscopic data obtained with the Keck LRIS. Our main results are based on a spectroscopically selected sample of 143 cluster members with morphological classifications derived from the ACS observations. Our three primary findings are (1) the faint-end slope of the LF is steepest in the bluest filter, (2) the LF in the inner part of the cluster (or highest density regions) has a flatter faint-end slope, and (3) the fraction of early-type galaxies is higher at the bright end of the LF, and gradually decreases toward fainter magnitudes. These characteristics are consistent with those in local galaxy clusters, indicating that, at least in massive clusters, the common characteristics of ...

  11. Characterization and functional study of a cluster of four highly conserved orphan adhesion-GPCR in mouse.

    Science.gov (United States)

    Prömel, Simone; Waller-Evans, Helen; Dixon, John; Zahn, Dirk; Colledge, William H; Doran, Joanne; Carlton, Mark B L; Grosse, Johannes; Schöneberg, Torsten; Russ, Andreas P; Langenhan, Tobias

    2012-10-01

    Adhesion G protein-coupled receptors (aGPCR) constitute a structurally and functionally diverse class of seven-transmembrane receptor proteins. Although for some of the members important roles in immunology, neurology, as well as developmental biology have been suggested, most receptors have been poorly characterized. We have studied evolution, expression, and function of an entire receptor group containing four uncharacterized aGPCR: Gpr110, Gpr111, Gpr115, and Gpr116. We show that the genomic loci of these four receptors are clustered tightly together in mouse and human genomes and that this cluster likely derives from a single common ancestor gene. Using transcriptional profiling on wild-type and knockout/LacZ reporter knockin mice strains, we have obtained detailed expression maps that show ubiquitous expression of Gpr116, co-expression of Gpr111 and Gpr115 in developing skin, and expression of Gpr110 in adult kidney. Loss of Gpr110, Gpr111, or Gpr115 function did not result in detectable defects, indicating that genes of this aGPCR group might function redundantly. The aGPCR cluster Gpr110, Gpr111, Gpr115, and Gpr116 developed from one common ancestor in vertebrates. Expression suggests a role in epithelia, and one can speculate about a possible redundant function of GPR111 and GPR115. Copyright © 2012 Wiley Periodicals, Inc.

  12. Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades

    OpenAIRE

    Frohme Marcus; Schnölzer Martina; Engelmann Julia C; Beisser Daniela; Shkumatov Alexander; Liang Chuanguang; Förster Frank; Müller Tobias; Schill Ralph O; Dandekar Thomas

    2009-01-01

    Abstract Background Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. Results To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade ...

  13. Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades

    OpenAIRE

    Frohme Marcus; Schnölzer Martina; Engelmann Julia C; Beisser Daniela; Shkumatov Alexander; Liang Chuanguang; Förster Frank; Müller Tobias; Schill Ralph O; Dandekar Thomas

    2009-01-01

    Abstract Background Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. Results To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade ...

  14. CpG oligodeoxynucleotide nanomedicines for the prophylaxis or treatment of cancers, infectious diseases, and allergies

    Science.gov (United States)

    Hanagata, Nobutaka

    2017-01-01

    Unmethylated cytosine-guanine dinucleotide-containing oligodeoxynucleotides (CpG ODNs), which are synthetic agonists of Toll-like receptor 9 (TLR9), activate humoral and cellular immunity and are being developed as vaccine adjuvants to prevent or treat cancers, infectious diseases, and allergies. Free CpG ODNs have been used in many clinical trials implemented to verify their effects. However, recent research has reported that self-assembled CpG ODNs, protein/peptide–CpG ODN conjugates, and nanomaterial–CpG ODN complexes demonstrate higher adjuvant effects than free CpG ODNs, owing to their improved uptake efficiency into cells expressing TLR9. Moreover, protein/peptide–CpG ODN conjugates and nanomaterial–CpG ODN complexes are able to deliver CpG ODNs and antigens (or allergens) to the same types of cells, which enables a higher degree of prophylaxis or therapeutic effect. In this review, the author describes recent trends in the research and development of CpG ODN nanomedicines containing self-assembled CpG ODNs, protein/peptide–CpG ODN conjugates, and nanomaterial–CpG ODN complexes, focusing mainly on the results of preclinical and clinical studies. PMID:28144136

  15. Epigenetic analysis of HIV-1 proviral genomes from infected individuals: predominance of unmethylated CpG's.

    Science.gov (United States)

    Weber, Stefanie; Weiser, Barbara; Kemal, Kimdar S; Burger, Harold; Ramirez, Christina M; Korn, Klaus; Anastos, Kathryn; Kaul, Rupert; Kovacs, Colin; Doerfler, Walter

    2014-01-20

    Efforts to cure HIV-1 infections aim at eliminating proviral DNA. Integrated DNA from various viruses often becomes methylated de novo and transcriptionally inactivated. We therefore investigated CpG methylation profiles of 55 of 94 CpG's (58.5%) in HIV-1 proviral genomes including ten CpG's in each LTR and additional CpG's in portions of gag, env, nef, rev, and tat genes. We analyzed 33 DNA samples from PBMC's of 23 subjects representing a broad spectrum of HIV-1 disease. In 22 of 23 HIV-1-infected individuals, there were only unmethylated CpG's regardless of infection status. In one long term nonprogressor, however, methylation of proviral DNA varied between 0 and 75% over an 11-year period although the CD4+ counts remained stable. Hence levels of proviral DNA methylation can fluctuate. The preponderance of unmethylated CpG's suggests that proviral methylation is not a major factor in regulating HIV-1 proviral activity in PBMC's. Unmethylated CpG's may play a role in HIV-1 immunopathogenesis. © 2013 Elsevier Inc. All rights reserved.

  16. CpG islands undermethylation in human genomic regions under selective pressure.

    Directory of Open Access Journals (Sweden)

    Sergio Cocozza

    Full Text Available DNA methylation at CpG islands (CGIs is one of the most intensively studied epigenetic mechanisms. It is fundamental for cellular differentiation and control of transcriptional potential. DNA methylation is involved also in several processes that are central to evolutionary biology, including phenotypic plasticity and evolvability. In this study, we explored the relationship between CpG islands methylation and signatures of selective pressure in Homo Sapiens, using a computational biology approach. By analyzing methylation data of 25 cell lines from the Encyclopedia of DNA Elements (ENCODE Consortium, we compared the DNA methylation of CpG islands in genomic regions under selective pressure with the methylation of CpG islands in the remaining part of the genome. To define genomic regions under selective pressure, we used three different methods, each oriented to provide distinct information about selective events. Independently of the method and of the cell type used, we found evidences of undermethylation of CGIs in human genomic regions under selective pressure. Additionally, by analyzing SNP frequency in CpG islands, we demonstrated that CpG islands in regions under selective pressure show lower genetic variation. Our findings suggest that the CpG islands in regions under selective pressure seem to be somehow more "protected" from methylation when compared with other regions of the genome.

  17. Multi-layered multi-pattern CPG for adaptive locomotion of humanoid robots.

    Science.gov (United States)

    Nassour, John; Hénaff, Patrick; Benouezdou, Fethi; Cheng, Gordon

    2014-06-01

    In this paper, we present an extended mathematical model of the central pattern generator (CPG) in the spinal cord. The proposed CPG model is used as the underlying low-level controller of a humanoid robot to generate various walking patterns. Such biological mechanisms have been demonstrated to be robust in locomotion of animal. Our model is supported by two neurophysiological studies. The first study identified a neural circuitry consisting of a two-layered CPG, in which pattern formation and rhythm generation are produced at different levels. The second study focused on a specific neural model that can generate different patterns, including oscillation. This neural model was employed in the pattern generation layer of our CPG, which enables it to produce different motion patterns-rhythmic as well as non-rhythmic motions. Due to the pattern-formation layer, the CPG is able to produce behaviors related to the dominating rhythm (extension/flexion) and rhythm deletion without rhythm resetting. The proposed multi-layered multi-pattern CPG model (MLMP-CPG) has been deployed in a 3D humanoid robot (NAO) while it performs locomotion tasks. The effectiveness of our model is demonstrated in simulations and through experimental results.

  18. All three classes of CpG ODNs up-regulate IP-10 gene in pigs.

    Science.gov (United States)

    Dar, Arshud; Nichani, Anil; Lai, Ken; Potter, Andy; Gerdts, Volker; Babiuk, Lorne A; Mutwiri, George

    2010-04-01

    The analysis of CpG ODN induced innate immune responses in different animal species has shown substantial similarities and differences in levels and types of induced cytokines profile. The objectives of these studies were to identify innate immune biomarkers activated by three classes of CpG ODNs in pigs. For this purpose, we investigated the kinetics of innate immune responses in immune cells from pigs following in vitro and in vivo stimulation with CpG ODNs. The mRNA expression of cytokine and chemokine genes were assayed by SYBR green based quantitative real time PCR. A-class CpG ODN induced significant but transient levels of IFN-gamma, IL-12 (P40), IL-6, IL-4 and TNF-alpha mRNA, C-class CpG ODN induced significant level of IFN-gamma, IFN-alpha and IL-12 mRNA and the lowest level of IL-4 (Th-2 type) mRNA. A very low level of some cytokines stimulation was observed by GC ODNs. It is noteworthy, that IL-12 (P35) mRNA was significantly stimulated by B-class GpC ODN 7909. Interestingly, all classes of CpG ODNs induced significant level of IP-10 at 12h post stimulation. These in vitro and in vivo observations suggest that interferon-gamma inducible protein 10 (IP-10) may be a reliable biomarker for immune activity induced by CpG ODNs in pigs.

  19. CpG stimulation of precursor B-lineage acute lymphoblastic leukemia induces a distinct change in costimulatory molecule expression and shifts allogeneic T cells toward a Th1 response.

    Science.gov (United States)

    Reid, Gregor S D; She, Kevin; Terrett, Luke; Food, Michael R; Trudeau, Jacqueline D; Schultz, Kirk R

    2005-05-01

    Immunostimulatory DNA containing unmethylated cytosine-phosphate-guanosine (CpG) induces the development of T helper 1 (Th1) immune responses. The response of B cells to CpG stimulation involves increased proliferation, cytokine production, and costimulatory molecule expression. Similar effects have been observed following CpG stimulation of a variety of malignant B cells. Pediatric precursor B acute lymphoblastic leukemia (B-ALL) cells express low levels of costimulatory molecules and are generally poor stimulators of T-cell responses. In this study, we evaluated the impact of CpG stimulation on precursor B-ALL cell lines and pediatric patient-derived samples. The ability to respond to CpG oligodeoxynucleotides was determined by the level of Toll-like receptor 9 (TLR9) expression. In contrast to both nonleukemic B-cell precursors and mature B cells, the response of precursor B-ALL cells was characterized by increased CD40 expression but only small changes in CD86 levels and no induction of CD80 expression. CpG stimulation of ALL blasts produced increased levels of interleukin-6 (IL-6), IL-8, and IL-10 but no detectable IL-12p70 and led to a skewing of allogeneic T cells, with enhanced interferon gamma (IFN-gamma) production and reduced secretion of IL-5. These results demonstrate the functional relevance of CpG stimulation of precursor B-ALL cells and provide a rational basis for study of these agents for use in treatment of this disease.

  20. 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.

  1. 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.

  2. 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.

  3. Universal scaling functions for bond percolation on planar random and square lattices with multiple percolating clusters

    OpenAIRE

    Hsu, Hsiao-Ping; Lin, Simon C.; Hu, Chin-Kun

    2001-01-01

    Percolation models with multiple percolating clusters have attracted much attention in recent years. Here we use Monte Carlo simulations to study bond percolation on $L_{1}\\times L_{2}$ planar random lattices, duals of random lattices, and square lattices with free and periodic boundary conditions, in vertical and horizontal directions, respectively, and with various aspect ratio $L_{1}/L_{2}$. We calculate the probability for the appearance of $n$ percolating clusters, $W_{n},$ the percolati...

  4. Advantages of cluster analysis for multifunctional and intercrossing brain area distribution Evaluation by functional magnetic resonance imaging

    Institute of Scientific and Technical Information of China (English)

    Hongchang Zhai; Xudong Xu; Shengyong Xiao

    2008-01-01

    BACKGROUND: Multiple linear regression, general linear test and calculation of correlation values are commonly used in studies of brain function using functional magnetic resonance imaging (fMRI). However, there are some limitations in their applications. In non-signal data statistics, cluster analysis functions as a very mature method, but it is not reliable in signal data statistics. OBJECTIVE: To investigate the spatial distribution of complex function in brain areas during motor tasks by cluster analysis, and to compare this with multiple linear regression. DESIGN, TIME AND SETTING: Block design, performed at the MR laboratory of Guangzhou University of Chinese Medicine. PARTICIPANTS: Fifteen right-handed, healthy university students (10 males and 5 females, aged 19-21 years).METHODS: fMRI was performed while the subjects performed a finger movement task with the right hand. The screen showed a gray hand, with red spots presented in a random order on one of the index, middle, ring and little fingers. The subjects were required to remember the sequence of the red spots on the display. After a delay of 14 seconds, the subjects tapped their fingers according to the order of the red spots, as soon as the red spots turned green. After an interval of 14 seconds, another sequence appeared. Every sequence lasted for 28 seconds, including preparation and execution phases. A total of nine sequences per subject were performed. The data were analyzed using deconvolution and cluster methods, and program "cluster" was used to statistically analyze the coordinate positions of deconvolution and cluster data. MAIN OUTCOME MEASURES: Brain activation maps by deconvolution and brain function maps by clustering of the maximum peak values; blood oxygenation level dependent curves by deconvolution; coordinates of peak values and activation volumes by the two methods. RESULTS: The deconvolution method could not integrate the brain activation maps during different tasks into one

  5. Comprehensive analysis of CpG islands in human chromosomes 21 and 22

    Science.gov (United States)

    Takai, Daiya; Jones, Peter A.

    2002-03-01

    CpG islands are useful markers for genes in organisms containing 5-methylcytosine in their genomes. In addition, CpG islands located in the promoter regions of genes can play important roles in gene silencing during processes such as X-chromosome inactivation, imprinting, and silencing of intragenomic parasites. The generally accepted definition of what constitutes a CpG island was proposed in 1987 by Gardiner-Garden and Frommer [Gardiner-Garden, M. & Frommer, M. (1987) J. Mol. Biol. 196, 261-282] as being a 200-bp stretch of DNA with a C+G content of 50% and an observed CpG/expected CpG in excess of 0.6. Any definition of a CpG island is somewhat arbitrary, and this one, which was derived before the sequencing of mammalian genomes, will include many sequences that are not necessarily associated with controlling regions of genes but rather are associated with intragenomic parasites. We have therefore used the complete genomic sequences of human chromosomes 21 and 22 to examine the properties of CpG islands in different sequence classes by using a search algorithm that we have developed. Regions of DNA of greater than 500 bp with a G+C equal to or greater than 55% and observed CpG/expected CpG of 0.65 were more likely to be associated with the 5' regions of genes and this definition excluded most Alu-repetitive elements. We also used genome sequences to show strong CpG suppression in the human genome and slight suppression in Drosophila melanogaster and Saccharomyces cerevisiae. This finding is compatible with the recent detection of 5-methylcytosine in Drosophila, and might suggest that S. cerevisiae has, or once had, CpG methylation.

  6. Roles of Cell Division and Gene Transcription in the Methylation of CpG Islands

    Science.gov (United States)

    Bender, Christina M.; Gonzalgo, Mark L.; Gonzales, Felicidad A.; Nguyen, Carvell T.; Robertson, Keith D.; Jones, Peter A.

    1999-01-01

    De novo methylation of CpG islands within the promoters of eukaryotic genes is often associated with their transcriptional repression, yet the methylation of CpG islands located downstream of promoters does not block transcription. We investigated the kinetics of mRNA induction, demethylation, and remethylation of the p16 promoter and second-exon CpG islands in T24 cells after 5-aza-2′-deoxycytidine (5-Aza-CdR) treatment to explore the relationship between CpG island methylation and gene transcription. The rates of remethylation of both CpG islands were associated with time but not with the rate of cell division, and remethylation of the p16 exon 2 CpG island occurred at a higher rate than that of the p16 promoter. We also examined the relationship between the remethylation of coding sequence CpG islands and gene transcription. The kinetics of remethylation of the p16 exon 2, PAX-6 exon 5, c-ABL exon 11, and MYF-3 exon 3 loci were examined following 5-Aza-CdR treatment because these genes contain exonic CpG islands which are hypermethylated in T24 cells. Remethylation occurred most rapidly in the p16, PAX-6, and c-ABL genes, shown to be transcribed prior to drug treatment. These regions also exhibited higher levels of remethylation in single-cell clones and subclones derived from 5-Aza-CdR-treated T24 cells. Our data suggest that de novo methylation is not restricted to the S phase of the cell cycle and that transcription through CpG islands does not inhibit their remethylation. PMID:10490608

  7. Probing Electronic Wave Functions of Sodium-Doped Clusters: Dyson Orbitals, Anisotropy Parameters, and Ionization Cross-Sections.

    Science.gov (United States)

    Gunina, Anastasia O; Krylov, Anna I

    2016-12-15

    We apply high-level ab initio methods to describe the electronic structure of small clusters of ammonia and dimethyl ether (DME) doped with sodium, which provide a model for solvated electrons. We investigate the effect of the solvent and cluster size on the electronic states. We consider both energies and properties, with a focus on the shape of the electronic wave function and the related experimental observables such as photoelectron angular distributions. The central quantity in modeling photoionization experiments is the Dyson orbital, which describes the difference between the initial N-electron and final (N-1)-electron states of a system. Dyson orbitals enter the expression of the photoelectron matrix element, which determines total and partial photoionization cross-sections. We compute Dyson orbitals for the Na(NH3)n and Na(DME)m clusters using correlated wave functions (obtained with equation-of-motion coupled-cluster model for electron attachment with single and double substitutions) and compare them with more approximate Hartree-Fock and Kohn-Sham orbitals. We also analyze the effect of correlation and basis sets on the shapes of Dyson orbitals and the experimental observables.

  8. A latent pro-survival function for the mir-290-295 cluster in mouse embryonic stem cells.

    Directory of Open Access Journals (Sweden)

    Grace X Y Zheng

    2011-05-01

    Full Text Available MicroRNAs (miRNAs post-transcriptionally regulate the expression of thousands of distinct mRNAs. While some regulatory interactions help to maintain basal cellular functions, others are likely relevant in more specific settings, such as response to stress. Here we describe such a role for the mir-290-295 cluster, the dominant miRNA cluster in mouse embryonic stem cells (mESCs. Examination of a target list generated from bioinformatic prediction, as well as expression data following miRNA loss, revealed strong enrichment for apoptotic regulators, two of which we validated directly: Caspase 2, the most highly conserved mammalian caspase, and Ei24, a p53 transcriptional target. Consistent with these predictions, mESCs lacking miRNAs were more likely to initiate apoptosis following genotoxic exposure to gamma irradiation or doxorubicin. Knockdown of either candidate partially rescued this pro-apoptotic phenotype, as did transfection of members of the mir-290-295 cluster. These findings were recapitulated in a specific mir-290-295 deletion line, confirming that they reflect miRNA functions at physiological levels. In contrast to the basal regulatory roles previously identified, the pro-survival phenotype shown here may be most relevant to stressful gestations, where pro-oxidant metabolic states induce DNA damage. Similarly, this cluster may mediate chemotherapeutic resistance in a neoplastic context, making it a useful clinical target.

  9. Numbers of presynaptic Ca(2+) channel clusters match those of functionally defined vesicular docking sites in single central synapses.

    Science.gov (United States)

    Miki, Takafumi; Kaufmann, Walter A; Malagon, Gerardo; Gomez, Laura; Tabuchi, Katsuhiko; Watanabe, Masahiko; Shigemoto, Ryuichi; Marty, Alain

    2017-06-27

    Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such "simple synapses" indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1-10) and 2.03 at 4 wk (range: 1-4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1-8) and 2.37 at 4 wk (range: 1-5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm(2) to 0.0234 μm(2)), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels.

  10. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses

    Science.gov (United States)

    Miki, Takafumi; Kaufmann, Walter A.; Malagon, Gerardo; Gomez, Laura; Tabuchi, Katsuhiko; Watanabe, Masahiko; Shigemoto, Ryuichi; Marty, Alain

    2017-01-01

    Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. PMID:28607047

  11. Evolution of the real-space correlation function from next generation cluster surveys. Recovering the real-space correlation function from photometric redshifts

    Science.gov (United States)

    Sridhar, Srivatsan; Maurogordato, Sophie; Benoist, Christophe; Cappi, Alberto; Marulli, Federico

    2017-04-01

    Context. The next generation of galaxy surveys will provide cluster catalogues probing an unprecedented range of scales, redshifts, and masses with large statistics. Their analysis should therefore enable us to probe the spatial distribution of clusters with high accuracy and derive tighter constraints on the cosmological parameters and the dark energy equation of state. However, for the majority of these surveys, redshifts of individual galaxies will be mostly estimated by multiband photometry which implies non-negligible errors in redshift resulting in potential difficulties in recovering the real-space clustering. Aims: We investigate to which accuracy it is possible to recover the real-space two-point correlation function of galaxy clusters from cluster catalogues based on photometric redshifts, and test our ability to detect and measure the redshift and mass evolution of the correlation length r0 and of the bias parameter b(M,z) as a function of the uncertainty on the cluster redshift estimate. Methods: We calculate the correlation function for cluster sub-samples covering various mass and redshift bins selected from a 500 deg2 light-cone limited to H z=0)=\\frac{σz{1+z_c} = 0.005,0.010,0.030} and 0.050, in order to cover the typical values expected in forthcoming surveys. The correlation function in real-space is then computed through estimation and deprojection of wp(rp). Four mass ranges (from Mhalo > 2 × 1013h-1M⊙ to Mhalo > 2 × 1014h-1M⊙) and six redshift slices covering the redshift range [0, 2] are investigated, first using cosmological redshifts and then for the four photometric redshift configurations. Results: From the analysis of the light-cone in cosmological redshifts we find a clear increase of the correlation amplitude as a function of redshift and mass. The evolution of the derived bias parameter b(M,z) is in fair agreement with theoretical expectations. We calculate the r0-d relation up to our highest mass, highest redshift sample

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

    Science.gov (United States)

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

    2009-10-01

    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.

  13. Brown dwarfs and very low mass stars in the Praesepe open cluster: a dynamically unevolved mass function?

    CERN Document Server

    Boudreault, S; Goldman, B; Henning, T; Caballero, J A

    2009-01-01

    [Abridged] In this paper, we present the results of a photometric survey to identify low mass and brown dwarf members of the old open cluster Praesepe (age of 590[+150][-120]Myr and distance of 190[+6.0][-5.8]pc) and use this to infer its mass function which we compare with that of other clusters. We have performed an optical (Ic-band) and near-infrared (J and Ks-band) photometric survey of Praesepe with a spatial coverage of 3.1deg^2. With 5sigma detection limits of Ic=23.4 and J=20.0, our survey is sensitive to objects with masses from about 0.6 to 0.05Msol. The mass function of Praesepe rises from 0.6Msol down to 0.1Msol and then turns-over at ~0.1Msol. The rise observed is in agreement with the mass function derived by previous studies, including a survey based on proper motion and photometry. Comparing our mass function with that for another open cluster with a similar age, the Hyades (age ~ 600Myr), we see a significant difference. Possible reasons are that dynamical evaporation has not influenced the H...

  14. Is It Possible To Obtain Coupled Cluster Quality Energies at near Density Functional Theory Cost? Domain-Based Local Pair Natural Orbital Coupled Cluster vs Modern Density Functional Theory.

    Science.gov (United States)

    Liakos, Dimitrios G; Neese, Frank

    2015-09-08

    The recently developed domain-based local pair natural orbital coupled cluster theory with single, double, and perturbative triple excitations (DLPNO-CCSD(T)) delivers results that are closely approaching those of the parent canonical coupled cluster method at a small fraction of the computational cost. A recent extended benchmark study established that, depending on the three main truncation thresholds, it is possible to approach the canonical CCSD(T) results within 1 kJ (default setting, TightPNO), 1 kcal/mol (default setting, NormalPNO), and 2-3 kcal (default setting, LoosePNO). Although thresholds for calculations with TightPNO are 2-4 times slower than those based on NormalPNO thresholds, they are still many orders of magnitude faster than canonical CCSD(T) calculations, even for small and medium sized molecules where there is little locality. The computational effort for the coupled cluster step scales nearly linearly with system size. Since, in many instances, the coupled cluster step in DLPNO-CCSD(T) is cheaper or at least not much more expensive than the preceding Hartree-Fock calculation, it is useful to compare the method against modern density functional theory (DFT), which requires an effort comparable to that of Hartree-Fock theory (at least if Hartree-Fock exchange is part of the functional definition). Double hybrid density functionals (DHDF's) even require a MP2-like step. The purpose of this article is to evaluate the cost vs accuracy ratio of DLPNO-CCSD(T) against modern DFT (including the PBE, B3LYP, M06-2X, B2PLYP, and B2GP-PLYP functionals and, where applicable, their van der Waals corrected counterparts). To eliminate any possible bias in favor of DLPNO-CCSD(T), we have chosen established benchmark sets that were specifically proposed for evaluating DFT functionals. It is demonstrated that DLPNO-CCSD(T) with any of the three default thresholds is more accurate than any of the DFT functionals. Furthermore, using the aug-cc-pVTZ basis set and

  15. Efficient floating diffuse functions for accurate characterization of the surface-bound excess electrons in water cluster anions.

    Science.gov (United States)

    Zhang, Changzhe; Bu, Yuxiang

    2017-01-25

    In this work, the effect of diffuse function types (atom-centered diffuse functions versus floating functions and s-type versus p-type diffuse functions) on the structures and properties of three representative water cluster anions featuring a surface-bound excess electron is studied and we find that an effective combination of such two kinds of diffuse functions can not only reduce the computational cost but also, most importantly, considerably improve the accuracy of results and even avoid incorrect predictions of spectra and the EE shape. Our results indicate that (a) simple augmentation of atom-centered diffuse functions is beneficial for the vertical detachment energy convergence, but it leads to very poor descriptions for the singly occupied molecular orbital (SOMO) and lowest unoccupied molecular orbital (LUMO) distributions of the water cluster anions featuring a surface-bound excess electron and thus a significant ultraviolet spectrum redshift; (b) the ghost-atom-based floating diffuse functions can not only contribute to accurate electronic calculations of the ground state but also avoid poor and even incorrect descriptions of the SOMO and the LUMO induced by excessive augmentation of atom-centered diffuse functions; (c) the floating functions can be realized by ghost atoms and their positions could be determined through an optimization routine along the dipole moment vector direction. In addition, both the s- and p-type floating functions are necessary to supplement in the basis set which are responsible for the ground (s-type character) and excited (p-type character) states of the surface-bound excess electron, respectively. The exponents of the diffuse functions should also be determined to make the diffuse functions cover the main region of the excess electron distribution. Note that excessive augmentation of such diffuse functions is redundant and even can lead to unreasonable LUMO characteristics.

  16. Immunogenicity and safety of liposome-vaccine encapsulating hepatitis B surface antigen and phosphodiester CpG oligodeoxynucleotides

    Institute of Scientific and Technical Information of China (English)

    CHUN YAN HE; QING LIANG LIU

    2006-01-01

    CpG oligodeoxynucleotides (CpG ODN) as adjuvant have been extensively studied in recent years. Phosphodiester CpG ODN (PO CpG ODN) can perfectly mimic bacterial DNA in enhancing immune response but are vulnerable to nucleases in vivo. This study aimed to evaluate the immunostimu latory potential and safety of phosphodiester CpG ODN encapsulated in nonphospholipid liposomes.BALB/c mice were immunized intramuscularly with different formulations of liposomes, CpG ODN and hepatitis B surface antigen (HBsAg). The results demonstrated that the encapsulated PO CpG ODN were protected against rapid degradation in vivo and retained their adjuvant activity. PO CpG ODN encapsulated with HBsAg in liposomes induced strong Th1-biased or Th1/Th2 mixed humoral immune response in mice with the magnitude similar to their phosphothioate equivalent in the same formulation.High IFN-gamma production induced by this formulation confirmed the generation of strong cellular immune response. Additionally, co-delivery of HBsAg and PO CpG ODN improved the immune response over that obtained with separate delivery. Safety experiment showed that liposome-encapsulaed PO CpG ODN and HBsAg caused mild systemic and moderate local adverse reaction. In conclusion, our data shows that PO CpG ODN encapsulated in liposomes fully exhibit their Th1-type adjuvant activity and act as a potential adjuvant for vaccines.

  17. 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)

  18. 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.

  19. The Red-Sequence Luminosity Function in Galaxy Clusters since z~1

    CERN Document Server

    Gilbank, David G; Ellingson, E; Gladders, M D; Loh, Y -S; Barrientos, L F; Barkhouse, W A

    2007-01-01

    We use a statistical sample of ~500 rich clusters taken from 72 square degrees of the Red-Sequence Cluster Survey (RCS-1) to study the evolution of ~30,000 red-sequence galaxies in clusters over the redshift range 0.35 -19.7) with their numbers increasing towards the present epoch. This is consistent with the `down-sizing` picture in which star-formation ended at earlier times for the most massive (luminous) galaxies and more recently for less massive (fainter) galaxies. We observe a richness dependence to the down-sizing effect in the sense that, at a given redshift, the drop-off of faint red galaxies is greater for poorer (less massive) clusters, suggesting that star-formation ended earlier for galaxies in more massive clusters. The decrease in faint red-sequence galaxies is accompanied by an increase in faint blue galaxies, implying that the process responsible for this evolution of faint galaxies is the termination of star-formation, possibly with little or no need for merging. At the bright end, we also ...

  20. Identification of hyperhalogens in Ag(n)(BO2)(m) (n = 1-3, m = 1-2) clusters: anion photoelectron spectroscopy and density functional calculations.

    Science.gov (United States)

    Kong, Xiang-Yu; Xu, Hong-Guang; Koirala, Pratik; Zheng, Wei-Jun; Kandalam, Anil K; Jena, Puru

    2014-12-21

    The electronic and structural properties of neutral and anionic Agn(BO2)m (n = 1-3, m = 1-2) clusters are investigated by using mass-selected anion photoelectron spectroscopy and density functional theory calculations. Agreement between the measured and calculated vertical detachment energies (VDEs) allows us to validate the equilibrium geometries of [Agn(BO2)m](-) clusters obtained from theory. The ground state structures of anionic Ag2(BO2) and Agn(BO2)2 (n = 1-3) clusters are found to be very different from those of their neutral counterparts. The structures of anionic clusters are chain-like while those of the neutral clusters are closed-rings. The presence of multiple isomers for [Ag2(BO2)2](-) and [Ag3(BO2)2](-) in the cluster beam has also been confirmed. Several of these clusters are found to be hyperhalogens.

  1. Cryotherapy with concurrent CpG oligonucleotide treatment controls local tumor recurrence and modulates Her2/neu immunity

    Science.gov (United States)

    Veenstra, Jesse J.; Gibson, Heather M.; Littrup, Peter J.; Reyes, Joyce D.; Cher, Michael L.; Takashima, Akira; Wei, Wei-Zen

    2014-01-01

    Percutaneous cryoablation is a minimally invasive procedure for tumor destruction, which can potentially initiate or amplify antitumor immunity through the release of tumor-associated antigens. However, clinically efficacious immunity is lacking and regional recurrences are a limiting factor relative to surgical excision. To understand the mechanism of immune activation by cryoablation, comprehensive analyses of innate immunity and Her2/neu humoral and cellular immunity following cryoablation with or without peritumoral CpG injection was conducted using two Her2/neu+ tumor systems in wild type, neu-tolerant, and SCID mice. Cryoablation of neu+ TUBO tumor in BALB/c mice resulted in systemic immune priming, but not in neu-tolerant BALB NeuT mice. Cryoablation of human Her2+ D2F2/E2 tumor enabled the functionality of tumor-induced immunity but secondary tumors were refractory to anti-tumor immunity if rechallenge occurred during the resolution phase of the cryoablated tumor. A step-wise increase in local recurrence was observed in wild type, neu-tolerant, and SCID mice indicating a role of adaptive immunity in controlling residual tumor foci. Importantly, local recurrences were eliminated or greatly reduced in wild type, neu tolerant and SCID mice when CpG was incorporated in the cryoablation regimen, showing significant local control by innate immunity. For long-term protection, however, adaptive immunity was required because most SCID mice eventually succumbed to local tumor recurrence even with combined cryoablation and CpG treatment. This improved understanding of the mechanisms by which cryoablation affects innate and adaptive immunity will help guide appropriate combination of therapeutic interventions to improve treatment outcomes. PMID:25092895

  2. The lower mass function of the young open cluster Blanco 1: from 30 MJup to 3 M⊙

    Science.gov (United States)

    Moraux, E.; Bouvier, J.; Stauffer, J. R.; Barrado y Navascués, D.; Cuillandre, J.-C.

    2007-08-01

    Aims:We performed a deep wide field optical survey of the young (~ 100-150 Myr) open cluster Blanco 1 to study its low mass population well down into the brown dwarf regime and estimate its mass function over the whole cluster mass range. Methods: The survey covers 2.3 square degrees in the I and z-bands down to I≃ z≃ 24 with the CFH12K camera. Considering two different cluster ages (100 and 150 Myr), we selected cluster member candidates on the basis of their location in the (I,I-z) CMD relative to the isochrones, and estimated the contamination by foreground late-type field dwarfs using statistical arguments, infrared photometry and low-resolution optical spectroscopy. Results: We find that our survey should contain about 57% of the cluster members in the 0.03-0.6~M⊙ mass range, including 30-40 brown dwarfs. The candidate's radial distribution presents evidence that mass segregation has already occured in the cluster. We took it into account to estimate the cluster mass function across the stellar/substellar boundary. We find that, between 0.03~M⊙ and 0.6~M⊙, the cluster mass distribution does not depend much on its exact age, and is well represented by a single power-law, with an index α=0.69± 0.15. Over the whole mass domain, from 0.03 M⊙ to 3 M⊙, the mass function is better fitted by a log-normal function with m0=0.36± 0.07~M⊙ and σ=0.58±0.06. Conclusions: Comparison between the Blanco 1 mass function, other young open clusters' MF, and the galactic disc MF suggests that the IMF, from the substellar domain to the higher mass part, does not depend much on initial conditions. We discuss the implications of this result on theories developed to date to explain the origin of the mass distribution. Based on observations obtained at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council of Canada, the Institut National des Sciences de l'Univers of the Centre National de la Recherche Scientifique of France

  3. Synthesis of DPA dendron encapsulated gold clusters with metal-assembling function

    Directory of Open Access Journals (Sweden)

    Yi Men, Masayoshi Higuchi and Kimihisa Yamamoto

    2006-01-01

    Full Text Available Gold clusters modified with first, second and third generation dendritic polyphenylazomethines (DPA were synthesized by an exchanged reaction of corresponding DPA dendron thiols. Measurements by high performance perfect sizer (HPPS and TEM reveal that their diameters increase with a change in the chain length of the modifying molecules from the first to third generation. These gold clusters with DPA dendrons exhibit coordination quantitatively to metal ions such as Fe3+, Sn2+, etc., because of their imine groups; this then resulted in self-aggregation to form a large sphere.

  4. Galaxy sizes as a function of environment at intermediate redshift from the ESO Distant Cluster Survey

    CERN Document Server

    Kelkar, Kshitija; Gray, Meghan E; Maltby, David; Vulcani, Benedetta; De Lucia, Gabriella; Poggianti, Bianca M; Zaritsky, Dennis

    2015-01-01

    In order to assess whether the environment has a significant effect on galaxy sizes, we compare the mass--size relations of cluster and field galaxies in the $0.4 1$), with early-type/passive galaxies in higher density environments growing earlier. Such dependence disappears at lower redshifts. Therefore, if the reported difference at higher-$z$ is real, the growth of field galaxies has caught up with that of cluster galaxies by $z\\sim1$. Any putative mechanism responsible for galaxy growth has to account for the existence of environmental differences at high redshift and their absence (or weakening) at lower redshifts.

  5. Ionic dissociations of chlorosulfonic acid in microsolvated clusters: A density functional theory and ab initio MO study

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Ionic dissociation of chlorosulfonic acid (HSO3Cl) in the molecular clusters HSO3Cl-(H2O)n (n = 1-4) and HSO3Cl-NH3-(H2O)n (n = 0-3) was investigated by density functional theory and ab initio molecular orbital theory. The equilibrium structures, binding energies, and thermodynamic properties, such as relative enthalpy and relative Gibbs free energy, and were calculated using the hybrid density func- tional (B3LYP) method and the second order M?ller-Plesset approximation (MP2) method with the 6-311++G** basis set. Chlorosulfonic acid was found to require a minimum of three water molecules for ionization to occur and at least one water molecule to protonate ammonia. The corresponding clusters with fewer water molecules were found to be strongly hydrogen-bonded. The related properties and acid strength of chlorosulfonic acid were discussed and compared to the acid strengths of perchloric acid and sulfuric acid in the context of clusters with ammonia and water. The relative stabilities of these clusters were also investigated.

  6. Virus-like attachment sites and plastic CpG islands:landmarks of diversity in plant Del retrotransposons.

    Directory of Open Access Journals (Sweden)

    Guilherme M Q Cruz

    Full Text Available Full-length Del elements from ten angiosperm genomes, 5 monocot and 5 dicot, were retrieved and putative attachment (att sites were identified. In the 2432 Del elements, two types of U5 att sites and a single conserved type of U3 att site were identified. Retroviral att sites confer specificity to the integration process, different att sites types therefore implies lineage specificity. While some features are common to all Del elements, CpG island patterns within the LTRs were particular to lineage specific clusters. All eudicot copies grouped into one single clade while the monocots harbour a more diverse collection of elements. Furthermore, full-length Del elements and truncated copies were unevenly distributed amongst chromosomes. Elements of Del lineage are organized in plants into three clusters and each cluster is composed of elements with distinct LTR features. Our results suggest that the Del lineage efficiently amplified in the monocots and that one branch is probably a newly emerging sub-lineage. Finally, sequences in all groups are under purifying selection. These results show the LTR region is dynamic and important in the evolution of LTR-retrotransposons, we speculate that it is a trigger for retrotransposon diversification.

  7. 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 clusters by retaining the I-NSD and splitting the I-SSD cluster into two: I-SSD A (n = 29): defined by high WASO and I-SSD B (n = 14): a second I-SSD cluster with high SOL and medium WASO. The I-SSD B cluster performed worse than I-SSD A and I-NSD for sustained attention (P ≤ 0.05). In an exploratory analysis, q-EEG revealed reduced spectral power also in I-SSD B before (Delta, Alpha, Beta-1) and after sleep-onset (Beta-2) compared to I-SSD A and I-NSD (P ≤ 0.05). Two 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.

  8. 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.)

  9. Vibrational absorption spectra from vibrational coupled cluster damped linear response functions calculated using an asymmetric Lanczos algorithm

    DEFF Research Database (Denmark)

    Thomsen, Bo; Hansen, Mikkel Bo; Seidler, Peter

    2012-01-01

    We report the theory and implementation of vibrational coupled cluster (VCC) damped response functions. From the imaginary part of the damped VCC response function the absorption as function of frequency can be obtained, requiring formally the solution of the now complex VCC response equations....... The absorption spectrum can in this formulation be seen as a matrix function of the characteristic VCC Jacobian response matrix. The asymmetric matrix version of the Lanczos method is used to generate a tridiagonal representation of the VCC response Jacobian. Solving the complex response equations...... in the relevant Lanczos space provides a method for calculating the VCC damped response functions and thereby subsequently the absorption spectra. The convergence behaviour of the algorithm is discussed theoretically and tested for different levels of completeness of the VCC expansion. Comparison is made...

  10. Real-time Walking Pattern Generation for a Biped Robot with Hybrid CPG-ZMP Algorithm

    Directory of Open Access Journals (Sweden)

    Bin He

    2014-10-01

    Full Text Available Biped robots have better mobility than conventional wheeled robots. The bio-inspired method based on a central pattern generator (CPG can be used to control biped robot walking in a manner like human beings. However, to achieve stable locomotion, it is difficult to modulate the parameters for the neural networks to coordinate every degree of freedom of the walking robot. The zero moment point (ZMP method is very popular for the stability control of biped robot walking. However, the reference trajectories have low energy efficiency, lack naturalness and need significant offline calculation. This paper presents a new method for biped real-time walking generation using a hybrid CPG-ZMP control algorithm. The method can realize a stable walking pattern by combining the ZMP criterion with rhythmic motion control. The CPG component is designed to generate the desired motion for each robot joint, which is modulated by phase resetting according to foot contact information. By introducing the ZMP location, the activity of the CPG output signal is adjusted to coordinate the limbs’ motion and allow the robot to maintain balance during the process of locomotion. The numerical simulation results show that, compared with the CPG method, the new hybrid CPG-ZMP algorithm can enhance the robustness of the CPG parameters and improve the stability of the robot. In addition, the proposed algorithm is more energy efficient than the ZMP method. The results also demonstrate that the control system can generate an adaptive walking pattern through interactions between the robot, the CPG and the environment.

  11. Activity-dependent regulation of the K/Cl transporter KCC2 membrane diffusion, clustering, and function in hippocampal neurons.

    Science.gov (United States)

    Chamma, Ingrid; Heubl, Martin; Chevy, Quentin; Renner, Marianne; Moutkine, Imane; Eugène, Emmanuel; Poncer, Jean Christophe; Lévi, Sabine

    2013-09-25

    The neuronal K/Cl transporter KCC2 exports chloride ions and thereby influences the efficacy and polarity of GABA signaling in the brain. KCC2 is also critical for dendritic spine morphogenesis and the maintenance of glutamatergic transmission in cortical neurons. Because KCC2 plays a pivotal role in the function of central synapses, it is of particular importance to understand the cellular and molecular mechanisms underlying its regulation. Here, we studied the impact of membrane diffusion and clustering on KCC2 function. KCC2 forms clusters in the vicinity of both excitatory and inhibitory synapses. Using quantum-dot-based single-particle tracking on rat primary hippocampal neurons, we show that KCC2 is slowed down and confined at excitatory and inhibitory synapses compared with extrasynaptic regions. However, KCC2 escapes inhibitory synapses faster than excitatory synapses, reflecting stronger molecular constraints at the latter. Interfering with KCC2-actin interactions or inhibiting F-actin polymerization releases diffusion constraints on KCC2 at excitatory but not inhibitory synapses. Thus, F-actin constrains KCC2 diffusion at excitatory synapses, whereas KCC2 is confined at inhibitory synapses by a distinct mechanism. Finally, increased neuronal activity rapidly increases the diffusion coefficient and decreases the dwell time of KCC2 at excitatory synapses. This effect involves NMDAR activation, Ca(2+) influx, KCC2 S940 dephosphorylation and calpain protease cleavage of KCC2 and is accompanied by reduced KCC2 clustering and ion transport function. Thus, activity-dependent regulation of KCC2 lateral diffusion and clustering allows for a rapid regulation of chloride homeostasis in neurons.

  12. Functional Analysis of Promoters in the Nisin Gene Cluster of Lactococcus lactis

    NARCIS (Netherlands)

    Ruyter, Pascalle G.G.A. de; Kuipers, Oscar P.; Beerthuyzen, Marke M.; Alen-Boerrigter, Ingrid van; Vos, Willem M. de

    1996-01-01

    The promoters in the nisin gene cluster nisABTCIPRKFEG of Lactococcus lactis were characterized by primer extension and transcriptional fusions to the Escherichia coli promoterless β-glucuronidase gene (gusA). Three promoters preceding the nisA, nisR, and nisF genes, which all give rise to gusA expr

  13. On the physics of radio haloes in galaxy clusters: scaling relations and luminosity functions

    NARCIS (Netherlands)

    Zandanel, F.; Pfrommer, C.; Prada, F.

    2014-01-01

    The underlying physics of giant and mini radio haloes in galaxy clusters is still an open question. We find that mini haloes (such as in Perseus and Ophiuchus) can be explained by radio-emitting electrons that are generated in hadronic cosmic ray (CR) interactions with protons of the intracluster me

  14. Subspace clustering through attribute clustering

    Institute of Scientific and Technical Information of China (English)

    Kun NIU; Shubo ZHANG; Junliang CHEN

    2008-01-01

    Many recently proposed subspace clustering methods suffer from two severe problems. First, the algorithms typically scale exponentially with the data dimensionality or the subspace dimensionality of clusters. Second, the clustering results are often sensitive to input parameters. In this paper, a fast algorithm of subspace clustering using attribute clustering is proposed to over-come these limitations. This algorithm first filters out redundant attributes by computing the Gini coefficient. To evaluate the correlation of every two non-redundant attributes, the relation matrix of non-redundant attributes is constructed based on the relation function of two dimensional united Gini coefficients. After applying an overlapping clustering algorithm on the relation matrix, the candidate of all interesting subspaces is achieved. Finally, all subspace clusters can be derived by clustering on interesting subspaces. Experiments on both synthesis and real datasets show that the new algorithm not only achieves a significant gain of runtime and quality to find subspace clusters, but also is insensitive to input parameters.

  15. Boron Clusters as a Platform for New Materials: Synthesis of Functionalized o-Carborane (C2 B10 H12 ) Derivatives Incorporating DNA Fragments.

    Science.gov (United States)

    Janczak, Slawomir; Olejniczak, Agnieszka; Balabańska, Sandra; Chmielewski, Marcin K; Lupu, Marius; Viñas, Clara; Lesnikowski, Zbigniew J

    2015-10-19

    A synthetic strategy for functionalization of the three vertices of o-carborane and the attachment of the obtained triped to the solid support was developed. Further functionalization of the triped with short DNA sequences by automated DNA synthesis was achieved. The proposed methodology is a first example of boron cluster chemistry on a solid support opening new perspectives in boron cluster functionalization. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Design of a cyclic inhibitory CPG controller for the locomotion of a snakelike robot

    Institute of Scientific and Technical Information of China (English)

    LU Zhen-li; MA Shu-gen; LI Bin; WANG Yue-chao

    2006-01-01

    The rhythmic locomotion of a creature is a serf-excitation behavior of the CPG (central pattern generator),which makes it supremely adapted for environment.Based on this fact,firstly,a snake-like robot controller with cyclic inhibitory CPG model was designed,and then the stability of a single neuron,CPG model and the NON(neuron oscillator network) was analyzed.By implementing this control architecture to a simulator based on the mechanical dynamics of a real snake-like robot named Perambulator-I,we presented preliminary rules for parameter setting of the CPG controller to modulate the number of S shapes,the curve of the body shape,locomotion velocity,and the curve of the locomotion trajectory for serpentine locomotion.Moreover,we demonstrated that Perambulator-I can successfully exhibit serpentine locomotion by using the output of the proposed CPG controller.The results of this paper provide a realistic approach for designing an artificial CPG controller.

  17. CpG oligodeoxynucleotides with crude parasite antigens reduce worm recovery in Opisthorchis viverrini infected hamsters.

    Science.gov (United States)

    Kaewraemruaen, Chamraj; Sermswan, Rasana W; Wongratanacheewin, Surasakdi

    2016-12-01

    Opisthorchis viverrini, a human liver fluke, is still an endemic parasitic infection in Thailand and nearly all countries in Southeast Asia. O. viverrini induces a chronic stage of infection in hamsters. During the first 2 weeks of infection, Th1 inducing cytokine, IL-12, increased but was down regulated in chronic infection. In this study it was found that unmethylated-CpG ODN (oligodeoxynucleotides) 1826 increased hamster mononuclear cell proliferation and stimulated IFN-γ production in vitro. The IFN-γ levels in hamster sera were significantly increased in hamsters injected with CpG ODN 1826 alone or plus crude somatic antigens (CSAg). Further investigation using the flow cytometer found that CD4(+)T cells and IFN-γ(+) CD4(+)T cells (Th1-like cells) in the hamster blood were significantly increased. The role of these cells in the protective responses in hamsters was evaluated by challenging with 25 metacercaria and observation for 3 months. The number of worms recovered was significantly reduced in the hamsters injected with CpG ODN 1826 with CSAg, but not in CpG ODN 1826 alone groups when compared to PBS control. The percent of reduction in hamsters against this parasite were 32.95% and 21.49% in the CpG ODN 1826 with CSAg and CpG ODN 1826 alone. This study indicates that CpG ODN 1826 plus parasite antigens elicit a Th1-like response that leads to the enhancement of worm reduction.

  18. CpG ODN Enhances Immunization Effects of Hepatitis B Vaccine in Aged Mice

    Institute of Scientific and Technical Information of China (English)

    Weibing Qin; Jianwei Jiang; Qiaoer Chen; Ning Yang; Yifeng Wang; Xiangcai Wei; Ruqiang Ou

    2004-01-01

    Oligodeoxynucleotides (ODN) containing unmethylated CpG dinucleotides in contexts of unique sequence (CpG motifs) is active as adjuvant in induction of cellular and humoral immune responses in young mice. To date, there are only limited reports about effect of CpG ODN on immune responses against hepatitis B (HB) infection in aged mice. Our studies demonstrated there were significant increases in secreting of total anti-HB IgG, IgG1 and IgG2a, as well as of IL-12 and IFN-γ, when CpG ODNs were injected together with hepatitis B antigen in aged mice. Moreover, CpG ODN could stimulate proliferation of spleen lymphocytes in a dose-dependent manner. Taken together, the results we obtained indicate that the adding of CpG ODN into the vaccine antigen might be useful in development of more effective vaccination for inducing anti-HB virus responses in the elderly.

  19. CpG ODN Enhances Immunization Effects of Hepatitis B Vaccine in Aged Mice

    Institute of Scientific and Technical Information of China (English)

    WeibingQin; JianweiJiang; QiaoerChen; NingYang; YifengWang; XiangcaiWei; RuqiangOu

    2004-01-01

    Oligodeoxynucleotides (ODN) containing unmethylated CpG dinucleotides in contexts of unique sequence (CpG motifs) is active as adjuvant in induction of cellular and humoral immune responses in young mice. To date, there are only limited reports about effect of CpG ODN on immune responses against hepatitis B (HB) infection in aged mice. Our studies demonstrated there were significant increases in secreting of total anti-HB IgG, IgG1 and IgG2a, as well as of IL-12 and IFN-γ, when CpG ODNs were injected together with hepatitis B antigen in aged mice. Moreover, CpG ODN could stimulate proliferation of spleen lymphocytes in a dose-dependent manner. Taken together, the results we obtained indicate that the adding of CpG ODN into the vaccine antigen might be useful in development of more effective vaccination for inducing anti-HB virus responses in the elderly. Cellular & Molecular Immunology. 2004;1(2):148-152.

  20. Effects of CpG ODN on dendritic cells and its mechanisms%含CpG基序的寡核苷酸对树突状细胞的作用及其机制

    Institute of Scientific and Technical Information of China (English)

    李岩; 邢飞跃

    2005-01-01

    Oligodeoxynucleotide containing unmethylated cytosine phosphate- guanosine motif(CpG ODN) may induce high expression of CD80, CD86, CD83, HLA Ⅰ and HLA Ⅱ molecules on dendritic cells(DC) and stimulate DC to produce highlevel of IL-6, IL-12, TNF-α and IFN-α. CpG ODN is demonstrated in vivo to be a very potent adjuvant for Thl cells, regulating Th0 cells to develop toward Thl cells. Its role for DC is characteristics of CpG ODN sequence specificity and species specificity. CpG ODN is, at present, considered as a pathogen associated molecular pattern which binds its specific receptor,Toll-like receptor 9, then functions through TLR/IL-1R signaling pathway. It may represent a new therapeutic drug for broad applications in infectious disease, autoimmune disease, allergy and cancer therapy.

  1. 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

  2. The gp63 Gene Cluster Is Highly Polymorphic in Natural Leishmania (Viannia) braziliensis Populations, but Functional Sites Are Conserved

    Science.gov (United States)

    Medina, Lilian S.; Souza, Bruno Araújo; Queiroz, Adriano; Guimarães, Luiz Henrique; Lima Machado, Paulo Roberto; M Carvalho, Edgar; Wilson, Mary Edythe; Schriefer, Albert

    2016-01-01

    GP63 or leishmanolysin is the major surface protease of Leishmania spp. involved in parasite virulence and host cell interaction. As such, GP63 is a potential target of eventual vaccines against these protozoa. In the current study we evaluate the polymorphism of gp63 in Leishmania (Viannia) braziliensis isolated from two sets of American tegumentary leishmaniasis (ATL) cases from Corte de Pedra, Brazil, including 35 cases diagnosed between 1994 and 2001 and 6 cases diagnosed between 2008 and 2011. Parasites were obtained from lesions by needle aspiration and cultivation. Genomic DNA was extracted, and 405 bp fragments, including sequences encoding the putative macrophage interacting sites, were amplified from gp63 genes of all isolates. DNA amplicons were cloned into plasmid vectors and ten clones per L. (V.) braziliensis isolate were sequenced. Alignment of cloned sequences showed extensive polymorphism among gp63 genes within, and between parasite isolates. Overall, 45 different polymorphic alleles were detected in all samples, which could be segregated into two clusters. Cluster one included 25, and cluster two included 20 such genotypes. The predicted peptides showed overall conservation below 50%. In marked contrast, the conservation at segments with putative functional domains approached 90% (Fisher’s exact test p<0.0001). These findings show that gp63 is very polymorphic even among parasites from a same endemic focus, but the functional domains interacting with the mammalian host environment are conserved. PMID:27648939

  3. Function Clustering Self-Organization Maps (FCSOMs) for mining differentially expressed genes in Drosophila and its correlation with the growth medium.

    Science.gov (United States)

    Liu, L L; Liu, M J; Ma, M

    2015-09-28

    The central task of this study was to mine the gene-to-medium relationship. Adequate knowledge of this relationship could potentially improve the accuracy of differentially expressed gene mining. One of the approaches to differentially expressed gene mining uses conventional clustering algorithms to identify the gene-to-medium relationship. Compared to conventional clustering algorithms, self-organization maps (SOMs) identify the nonlinear aspects of the gene-to-medium relationships by mapping the input space into another higher dimensional feature space. However, SOMs are not suitable for huge datasets consisting of millions of samples. Therefore, a new computational model, the Function Clustering Self-Organization Maps (FCSOMs), was developed. FCSOMs take advantage of the theory of granular computing as well as advanced statistical learning methodologies, and are built specifically for each information granule (a function cluster of genes), which are intelligently partitioned by the clustering algorithm provided by the DAVID_6.7 software platform. However, only the gene functions, and not their expression values, are considered in the fuzzy clustering algorithm of DAVID. Compared to the clustering algorithm of DAVID, these experimental results show a marked improvement in the accuracy of classification with the application of FCSOMs. FCSOMs can handle huge datasets and their complex classification problems, as each FCSOM (modeled for each function cluster) can be easily parallelized.

  4. Adsorption of NO on the Rh-13, Pd-13, Ir-13, and Pt-13 Clusters: A Density Functional Theory Investigation

    DEFF Research Database (Denmark)

    Piotrowski, Mauricio J.; Piquini, Paulo; Zeng, Zhenhua

    2012-01-01

    of real catalyst devices. In this study, we report a density functional theory study of the adsorption properties of NO on the TM13 (TM = Rh, Pd, Ir, Pt) clusters employing the projected augmented wave method. We found that the interaction of NO with TM13 is much more complex than that for NO/TM(111...... of the binding energy of NO to the TM13 clusters compared with the TM(111) surfaces, as the antibonding NO states are not occupied for NO/TM13, and the general relationship based on the d-band model between adsorption energy and the center of gravity of the occupied d-states does not hold for the studied TM13...

  5. Immunization of aged pigs with attenuated pseudorabies virus vaccine combined with CpG oligodeoxynucleotide restores defective Th1 immune responses.

    Directory of Open Access Journals (Sweden)

    Feiping Ming

    Full Text Available BACKGROUND AND AIMS: Attempts to immunize aged subjects often result in the failure to elicit a protective immune response. Murine model studies have shown that oligonucleotides containing CpG motifs (CpG ODN can stimulate immune system in aged mice as effectively as in young mice. Since many physiological and pathophysiological data of pigs can be transferred to humans, research in pigs is important to confirm murine data. Here we investigated whether immunization of aged pig model with attenuated pseudorabies virus vaccine (PRV vaccine formulated with CpG ODN could promote a successful development of immune responses that were comparable to those induced in young pigs in a similar manner. METHODOLOGY: Young and aged pigs were immunized IM with PRV vaccine alone, or in combination with CpG ODN respectively. At days 3, 7, 14 post immunization sera were assayed by ELISA for IgG titres, at day 7 for IgG1 and IgG2 subtypes titres. All blood samples collected in evacuated test tubes with K-EDTA at day 7 were analyzed for flow cytometer assay. Blood samples at day 7 collected in evacuated test tubes with heparin were analysed for antigen-specific cytokines production and peripheral blood mononuclear cells (PBMCs proliferative responses. RESULTS: CpG ODN could enhance Th1 responses (PRV-specific IgG2/IgG1 ratio, proliferative responses, Th1 cytokines production when used as an adjuvant for the vaccination of aged pigs, which were correlated with enhanced CD4+ T cells percentage, decreased CD4+CD8+CD45RO+ T cells percentage and improved PRV-specific CD4+ T cells activation. CONCLUSIONS: Our results demonstrate a utility for CpG ODN, as a safe vaccine adjuvant for promoting effective systemic immune responses in aged pig model. This agent could have important clinical uses in overcoming some of age-associated depressions in immune function that occur in response to vaccination.

  6. Safety and immunogenicity of CPG 7909 injection as an adjuvant to Fluarix influenza vaccine.

    Science.gov (United States)

    Cooper, C L; Davis, H L; Morris, M L; Efler, S M; Krieg, A M; Li, Y; Laframboise, C; Al Adhami, M J; Khaliq, Y; Seguin, I; Cameron, D W

    2004-08-13

    CPG 7909, a 24-mer B-Class CpG oligodeoxynucleotide (ODN), was tested for safety, tolerability and its ability to augment the immunogenicity of a commercial trivalent killed split influenza vaccine (Fluarix containing A/Beijing/262/95, A/Sydney/5/97 and B/Harbin/7/94; SmithKline Beecham) in a phase Ib blinded, randomized, controlled clinical trial. Sixty healthy volunteers were recruited in two consecutive cohorts of 30 subjects, who were randomly assigned to receive Fluarix plus 1mg CPG 7909 or Fluarix plus saline control (15 subjects each). Vaccines were administered by intramuscular injection on a single occasion with subjects in the first cohort receiving a 1/10th dose of Fluarix and those in the second cohort receiving the full-dose. All safety measures including physical evaluation, laboratory blood assays, and assays for DNA autoimmunity were within normal values except for transient and clinically inconsequential decreases in total white blood cell counts in groups receiving CPG 7909. All vaccines were found to be generally well tolerated with similar frequency and intensity for most adverse reactions for groups receiving CPG 7909 as controls. Exceptions were injection site pain and headache, which were reduced in frequency in subjects receiving the 1/10th Fluarix dose without CpG, compared to the frequency in all other groups. There was a lack of pre-existing immunity, defined as hemagglutinin inhibition (HI) activity CPG 7909, except in individuals with pre-existing immunity to A/Sydney/5/97 strain (baseline HI activity titre >20), where there was a trend to higher HI activity with CPG 7909 (P = 0.06). The addition of CPG 7909 to the 1/10th dose of Fluarix did however result in significantly higher levels of IFN-gamma secretion from peripheral blood mononuclear cells recovered at 4 weeks and restimulated ex vivo with A/Beijing/262/95 (P = 0.048) and B/Harbin/7/94 (P = 0.0057), restoring these to the level seen with full-dose vaccine. These results suggest

  7. VizieR Online Data Catalog: 72 WINGS nearby clusters luminosity functions (Moretti+, 2015)

    Science.gov (United States)

    Moretti, A.; Bettoni, D.; Poggianti, B. M.; Fasano, G.; Varela, J.; D'Onofrio, M.; Vulcani, B.; Cava, A.; Fritz, J.; Couch, W. J.; Moles, M.; Kjaergaard, P.

    2015-11-01

    We used the Sextractor photometric catalogue of WINGS galaxies described in Varela et al. (2009A&A...497..667V, Cat. J/A+A/497/667), which refers to optical (B,V) photometry of 76 cluster of galaxies, either observed with the INT telescope at La Palma, or with the 2.2m ESO telescope at La Silla. (1 data file).

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

    OpenAIRE

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

    2012-01-01

    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....

  9. Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis

    Directory of Open Access Journals (Sweden)

    Gong Zhiyuan

    2011-01-01

    Full Text Available Abstract Background DNA methylation is an epigenetic mechanism associated with regulation of gene expression and it is modulated during chemical carcinogenesis. The zebrafish is increasingly employed as a human disease model; however there is a lack of information on DNA methylation in zebrafish and during fish tumorigenesis. Results A novel CpG island tiling array containing 44,000 probes, in combination with immunoprecipitation of methylated DNA, was used to achieve the first comprehensive methylation profiling of normal adult zebrafish liver. DNA methylation alterations were detected in zebrafish liver tumors induced by the environmental carcinogen 7, 12-dimethylbenz(aanthracene. Genes significantly hypomethylated in tumors were associated particularly with proliferation, glycolysis, transcription, cell cycle, apoptosis, growth and metastasis. Hypermethylated genes included those associated with anti-angiogenesis and cellular adhesion. Of 49 genes that were altered in expression within tumors, and which also had appropriate CpG islands and were co-represented on the tiling array, approximately 45% showed significant changes in both gene expression and methylation. Conclusion The functional pathways containing differentially methylated genes in zebrafish hepatocellular carcinoma have also been reported to be aberrantly methylated during tumorigenesis in humans. These findings increase the confidence in the use of zebrafish as a model for human cancer in addition to providing the first comprehensive mapping of DNA methylation in the normal adult zebrafish liver.

  10. HST/ACS imaging of M82: A comparison of mass and size distribution functions of the younger nuclear and older disk clusters

    CERN Document Server

    Mayya, Y D; Rodríguez-Merino, L H; Luna, A; Carrasco, L; Rosa-Gonzalez, D

    2008-01-01

    We present the results obtained from an objective search for stellar clusters, both in the currently active nuclear starburst region, and in the post-starburst disk of M82. Images obtained with the HST/ACS in F435W(B), F555W(V), and F814W(I) filters were used in the search for the clusters. We detected 653 clusters of which 393 are located outside the central 450 pc in the post-starburst disk of M82. The luminosity function of the detected clusters show an apparent turnover at B=22 mag (M_B=-5.8), which we interpret from Monte Carlo simulations as due to incompleteness in the detection of faint clusters, rather than an intrinsic log-normal distribution. We derived a photometric mass of every detected cluster from models of simple stellar populations assuming a mean age of either an 8 (nuclear clusters) or 100 (disk clusters) million years old. The mass functions of the disk (older) and the nuclear (younger) clusters follow power-laws, the former being marginally flatter (alpha=1.5+/-0.1) than the latter (alph...

  11. Co-administration of a CpG adjuvant (VaxImmune, CPG 7909) with CETP vaccines increased immunogenicity in rabbits and mice.

    Science.gov (United States)

    Thomas, Lawrence J; Hammond, Russell A; Forsberg, Eric M; Geoghegan-Barek, Kathleen M; Karalius, Brad H; Marsh, Henry C; Rittershaus, Charles W

    2009-02-01

    Cholesteryl ester transfer protein (CETP) is a plasma glycoprotein that facilitates the transfer of neutral lipids and phospholipids between lipoproteins and contributes to the regulation of the plasma concentration of high density lipoprotein cholesterol (HDL-C). Vaccines have been developed that elicit antibodies that bind to and reduce the lipid transfer function of CETP as a way to increase the plasma concentration of HDL-C and prevent or treat atherosclerosis. This study assessed the immunogenicity of two vaccine peptides. The first, CETi-1, is a dimerized synthetic peptide, including residues 461-476 of human CETP and residues 830-843 of tetanus toxoid, TT(830-843). The second, PADRE-CETP, is a monomeric peptide, in which a PADRE T cell epitope (aK-Cha-VAAWTLKAa) replaces the TT(830-843) T cell epitope of CETi-1. Both peptides were formulated with aluminum-containing adjuvants (Alhydrogel), and tested in mice and rabbits with or without the co-administration of the investigational TLR9 agonist VaxImmune (CPG 7909). In both mice and rabbits, the vaccine peptide utilizing the PADRE T cell epitope elicited stronger anti-CETP antibody responses than the CETi-1 vaccine. Also, co-administration of VaxImmune enhanced the anti-CETP antibody responses to both vaccines. Isotype analysis of the murine anti-CETP antibody response to both vaccines demonstrated a switch from IgG1 to IgG2a upon co-administration of VaxImmune. We conclude that (1) the PADRE T cell epitope is more potent than the TT(830-843) epitope in providing help for the anti-CETP antibody response; and (2) co-administration of VaxImmune with either vaccine increased immunogenicity as measured by antibody response.

  12. Functional identification of gene cluster for the aniline metabolic pathway mediated by transposable element

    Institute of Scientific and Technical Information of China (English)

    LIANG Quanfeng; Takeo Masahiro; LIN Min; CHEN Ming; XU Yuquan; ZHANG Wei; PING Shuzhen; LU Wei; SONG Xianlong; WANG Weiwei; GENG Lizhao

    2005-01-01

    A convenient and widely applicable method has been developed to clone aniline metabolic gene cluster in this study. Three positive recombinant plasmids pDA1, pDB2 and pDB11 were cloned from genomic library of aniline degradation strain AD9. The result of aniline dioxygenase (AD) activity and catechol 2,3-oxygenase (C23O) activity assay showed that pDA1 and pDB11 contain aniline dioxygenase genes and catechol 2,3-dioxygenase genes, respectively. The sequence analysis of the total 24.7-kb region revealed that this region contains 25 ORFs, of which 17 genes involve metabolism of aniline. In the gene cluster, the first five genes (tadQTA1A2B) and the subsequent gene (tadR1) were predicted to encode a multi-component aniline dioxygenase and a LysR-type regulator, respectively, while the others (tadD1C1D2C2EFGIJKL) were expected to encode meta- cleavage pathway enzymes for catechol degradation. The gene cluster was surrounded by two IS1071 sequences.

  13. Graphene-supported small transition-metal clusters: A density functional theory investigation within van der Waals corrections

    Science.gov (United States)

    Rêgo, Celso R. C.; Tereshchuk, Polina; Oliveira, Luiz N.; Da Silva, Juarez L. F.

    2017-06-01

    Transition-metal nanoparticles adsorbed on graphene are of great interest due to the unique catalytic and magnetic properties resulting from nanoparticles-graphene interactions. Comparison between the physical properties of such systems and those of the same nanoparticles in the gas phase is especially important. Here we report a systematic density functional investigation of the structural, energetic, and magnetic properties of small Nin, Pdn, and Ptn clusters, comprising from n =1 to 6 atoms, in the gas phase and adsorbed on a graphene monolayer. Our results show that the Ni adatom binds to the graphene hollow site, with -1.47 -meV adsorption energy, while Pd and Pt prefer the bridge sites, with -1.14 - and -1.62 -meV adsorption energies, respectively. This difference is determined by a competition between quantum and classical forces. Ni2 and Pt2 dimers bind perpendicularly on hollow and bridge sites, respectively, while Pd2 lies parallel to the graphene sheet, with each adatom on a bridge site. For larger TMn (TM = Ni , Pd , Pt ; n =3 -6 ) clusters, either two or three atoms bind to bridge graphene sites. In almost all cases the adsorbed clusters retain their gas-phase structures. The exceptions are Ni5 and Pt4, which acquire more compact structures with effective coordination number 12 and 19 % larger than in the gas phase, respectively. As the number of atoms grows, the cluster binds more weakly to the graphene, while its binding energy mounts up. Van der Waals corrections to the plain density functional theory (DFT) total energy raise the adsorption energy, but leave the cluster structure unchanged, in the gas phase or upon adsorption. Bader charge analysis shows that adsorption causes minor charge redistribution: the TM atoms bound to C atoms become positively charged, while the remaining metal atoms acquire negative charge. We have derived an approximate analytical expression for the local densities of states for the d orbitals of Ni , Pd , and Pt adatoms

  14. Assessment of density functional theory optimized basis sets for gradient corrected functionals to transition metal systems: the case of small Nin (nclusters.

    Science.gov (United States)

    López Arvizu, Gregorio; Calaminici, Patrizia

    2007-05-21

    Density functional calculations have been performed for small nickel clusters, Ni(n), Ni(n) (+), and Ni(n)(-) (ntheory approach. Newly developed nickel all-electron basis sets optimized for generalized gradient approximation (GGA) as well as an all-electron basis set optimized for the local density approximation were employed. For both neutral and charged systems, several isomers and different multiplicities were studied in order to determine the lowest energy structures. A vibrational analysis was performed in order to characterize these isomers. Structural parameters, harmonic frequencies, binding energies, ionization potentials, and electron affinities are reported. This work shows that the employed GGA basis sets for the nickel atom are important for the correct prediction of the ground state structures of small nickel clusters and that the structural assignment of these systems can be performed, with a good resolution, over the ionization potential.

  15. CPG-based Locomotion Controller Design for a Boxfish-like Robot

    Directory of Open Access Journals (Sweden)

    Wei Wang

    2014-06-01

    Full Text Available This paper focuses on a Central Pattern Generator (CPG-based locomotion controller design for a boxfish-like robot. The bio-inspired controller is aimed at flexible switching in multiple 3D swimming patterns and exact attitude control of yaw and roll such that the robot will swim more like a real boxfish. The CPG network comprises two layers, the lower layer is the network of coupled linear oscillators and the upper is the transition layer where the lower-dimensional locomotion stimuli are transformed into the higher-dimensional control parameters serving for all the oscillators. Based on such a two-layer framework, flexible switching between multiple three-dimensional swimming patterns, such as swimming forwards/backwards, turning left/right, swimming upwards/downwards and rolling clockwise/counter-clockwise, can be simply realized by inputting different stimuli. Moreover, the stability of the CPG network is strictly proved to guarantee the intrinsic stability of the swimming patterns. As to exact attitude control, based on this open-loop CPG network and the sensory feedback from the Inertial Measurement Unit (IMU, a closed-loop CPG controller is advanced for yaw and roll control of the robotic fish for the first time. This CPG-based online attitude control for a robotic fish will greatly facilitate high-level practical underwater applications. A series of relevant experiments with the robotic fish are conducted systematically to validate the effectiveness and stability of the open-loop and closed-loop CPG controllers.

  16. Structures of Mn clusters

    Indian Academy of Sciences (India)

    Tina M Briere; Marcel H F Sluiter; Vijay Kumar; Yoshiyuki Kawazoe

    2003-01-01

    The geometries of several Mn clusters in the size range Mn13–Mn23 are studied via the generalized gradient approximation to density functional theory. For the 13- and 19-atom clusters, the icosahedral structures are found to be most stable, while for the 15-atom cluster, the bcc structure is more favoured. The clusters show ferrimagnetic spin configurations.

  17. Dissolution of Globular Clusters

    OpenAIRE

    Baumgardt, Holger

    2006-01-01

    Globular clusters are among the oldest objects in galaxies, and understanding the details of their formation and evolution can bring valuable insight into the early history of galaxies. This review summarises the current knowledge about the dissolution of star clusters and discusses the implications of star cluster dissolution for the evolution of the mass function of star cluster systems in galaxies.

  18. Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences.

    Science.gov (United States)

    Lemesle-Varloot, L; Henrissat, B; Gaboriaud, C; Bissery, V; Morgat, A; Mornon, J P

    1990-08-01

    Hydrophobic cluster analysis (HCA) [15] is a very efficient method to analyse and compare protein sequences. Despite its effectiveness, this method is not widely used because it relies in part on the experience and training of the user. In this article, detailed guidelines as to the use of HCA are presented and include discussions on: the definition of the hydrophobic clusters and their relationships with secondary and tertiary structures; the length of the clusters; the amino acid classification used for HCA; the HCA plot programs; and the working strategies. Various procedures for the analysis of a single sequence are presented: structural segmentation, structural domains and secondary structure evaluation. Like most sequence analysis methods, HCA is more efficient when several homologous sequences are compared. Procedures for the detection and alignment of distantly related proteins by HCA are described through several published examples along with 2 previously unreported cases: the beta-glucosidase from Ruminococcus albus is clearly related to the beta-glucosidases from Clostridum thermocellum and Hansenula anomala although they display a reverse organization of their constitutive domains; the alignment of the sequence of human GTPase activating protein with that of the Crk oncogene is presented. Finally, the pertinence of HCA in the identification of important residues for structure/function as well as in the preparation of homology modelling is discussed.

  19. Automatic determination of the arterial input function in dynamic susceptibility contrast MRI: comparison of different reproducible clustering algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Jiandong; Yang, Jiawen; Guo, Qiyong [Shengjing Hospital of China Medical University, Department of Radiology, Shenyang (China)

    2015-05-01

    Arterial input function (AIF) plays an important role in the quantification of cerebral hemodynamics. The purpose of this study was to select the best reproducible clustering method for AIF detection by comparing three algorithms reported previously in terms of detection accuracy and computational complexity. First, three reproducible clustering methods, normalized cut (Ncut), hierarchy (HIER), and fast affine propagation (FastAP), were applied independently to simulated data which contained the true AIF. Next, a clinical verification was performed where 42 subjects participated in dynamic susceptibility contrast MRI (DSC-MRI) scanning. The manual AIF and AIFs based on the different algorithms were obtained. The performance of each algorithm was evaluated based on shape parameters of the estimated AIFs and the true or manual AIF. Moreover, the execution time of each algorithm was recorded to determine the algorithm that operated more rapidly in clinical practice. In terms of the detection accuracy, Ncut and HIER method produced similar AIF detection results, which were closer to the expected AIF and more accurate than those obtained using FastAP method; in terms of the computational efficiency, the Ncut method required the shortest execution time. Ncut clustering appears promising because it facilitates the automatic and robust determination of AIF with high accuracy and efficiency. (orig.)

  20. Diffuse light in z~0.25 galaxy clusters: constraining tidal damage and the faint end of the Luminosity Function

    CERN Document Server

    Zibetti, S; Zibetti, Stefano; White, Simon D.M.

    2005-01-01

    The starlight coming from the intergalactic space in galaxy clusters and groups witnesses the violent tidal interactions that galaxies experience in these dense environments. Such interactions may be (at least partly) responsible for the transformation of normal star-forming galaxies into passive dwarf ellipticals (dEs). In this contribution we present the first systematic study of the IntraCluster Light (ICL) for a statistically representative sample (Zibetti et al. 2005), which comprises 683 clusters selected between z=0.2 and 0.3 from ~1500 deg^2 in the SDSS. Their ICL is studied by stacking the images in the g-, r-, and i-band after masking out all galaxies and polluting sources. In this way a very uniform background illumination is obtained, that allows us to measure surface brightnesses as faint as 31 mag/arcsec^2 and to trace the ICL out to 700 kpc from the central galaxy. We find that the local fraction of light contributed by intracluster stars rapidly decreases as a function of the clustercentric di...

  1. Determination of structures, stabilities, and electronic properties for bimetallic cesium-doped gold clusters: a density functional theory study.

    Science.gov (United States)

    Cheng, Lu; Xiao-Yu, Kuang; Zhi-Wen, Lu; Ai-Jie, Mao; Yan-Ming, Ma

    2011-08-25

    The equilibrium geometric structures, stabilities, and electronic properties of bimetallic Au(n)Cs (n = 1-10) and pure gold Au(n) (n ≤ 11) clusters have been systematically investigated by using density functional theory with meta-generalized gradient approximation. The optimized geometries show that one Au atom capped on Au(n-1)Cs structures and Cs atom capped Au(n) structures for different sized Au(n)Cs (n = 1-10) clusters are two dominant growth patterns. Theoretical calculated results indicate that the most stable isomers have three-dimensional structures at n = 4 and 6-10. Averaged atomic binding energies, fragmentation energies, and second-order difference of energies exhibit a pronounced even-odd alternations phenomenon. The same even-odd alternations are found in the highest occupied-lowest unoccupied molecular orbital gaps, vertical ionization potential, vertical electron affinity, and hardnesses. In addition, it is found that the charge in corresponding Au(n)Cs clusters transfers from the Cs atom to the Au(n) host in the range of 0.851-1.036 electrons.

  2. 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.

  3. 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

  4. Luminosity functions in the CLASH-VLT cluster MACS J1206.2-0847: the importance of tidal interactions

    CERN Document Server

    Mercurio, A; Biviano, A; Nonino, M; Rosati, P; Balestra, I; Brescia, M; Girardi, M; Gobat, R; Grillo, C; Lombardi, M; Sartoris, B

    2015-01-01

    We present the optical luminosity functions (LFs) of galaxies for the CLASH-VLT cluster MACS J1206.2-0847 at z=0.439, based on HST and SUBARU data, including ~600 spectroscopically confirmed member galaxies. The LFs on the wide SUBARU FoV are well described by a single Schechter function down to M~M*+3, whereas this fit is poor for HST data, due to a faint-end upturn visible down M~M*+7, suggesting a bimodal behaviour. We also investigate the effect of local environment by deriving the LFs in four different regions, according to the distance from the centre, finding an increase in the faint-end slope going from the core to the outer rings. Our results confirm and extend our previous findings on the analysis of mass functions, which showed that the galaxies with stellar mass below 10^10.5, M_sun have been significantly affected by tidal interaction effects, thus contributing to the intra cluster light.

  5. A CpG oligonucleotide can protect mice from a low aerosol challenge dose of Burkholderia mallei.

    Science.gov (United States)

    Waag, David M; McCluskie, Michael J; Zhang, Ningli; Krieg, Arthur M

    2006-03-01

    Treatment with an oligodeoxynucleotide (ODN) containing CPG motifs (CpG ODN 7909) was found to protect BALB/c mice from lung infection or death after aerosol challenge with Burkholderia mallei. Protection was associated with enhanced levels of gamma interferon (IFN-gamma)-inducible protein 10, interleukin-12 (IL-12), IFN-gamma, and IL-6. Preexposure therapy with CpG ODNs may protect victims of a biological attack from glanders.

  6. A CpG Oligonucleotide Can Protect Mice from a Low Aerosol Challenge Dose of Burkholderia mallei

    OpenAIRE

    Waag, David M.; Michael J. McCluskie; Zhang, Ningli; Krieg, Arthur M.

    2006-01-01

    Treatment with an oligodeoxynucleotide (ODN) containing CPG motifs (CpG ODN 7909) was found to protect BALB/c mice from lung infection or death after aerosol challenge with Burkholderia mallei. Protection was associated with enhanced levels of gamma interferon (IFN-γ)-inducible protein 10, interleukin-12 (IL-12), IFN-γ, and IL-6. Preexposure therapy with CpG ODNs may protect victims of a biological attack from glanders.

  7. CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure

    OpenAIRE

    Christoph Bock; Martina Paulsen; Sascha Tierling; Thomas Mikeska; Thomas Lengauer; Jörn Walter

    2006-01-01

    CpG island methylation plays an important role in epigenetic gene control during mammalian development and is frequently altered in disease situations such as cancer. The majority of CpG islands is normally unmethylated, but a sizeable fraction is prone to become methylated in various cell types and pathological situations. The goal of this study is to show that a computational epigenetics approach can discriminate between CpG islands that are prone to methylation from...

  8. Methylation of specific CpG sites in the P2 promoter of parathyroid hormone-related protein determines the invasive potential of breast cancer cell lines.

    Science.gov (United States)

    Tost, Jörg; Hamzaoui, Hinda; Busato, Florence; Neyret, Aymeric; Mourah, Samia; Dupont, Jean-Michel; Bouizar, Zhor

    2011-08-01

    Parathyroid hormone-related protein (PTHrP) is upregulated in primary breast cancers and a major candidate for osteoclastic bone resorption present at sites of breast cancer to bone metastases. Using a human model of mammary epithelial cell lines differing in tumorigenicity and PTHrP expression, we investigated the role of epigenetic modifications for PTHrP expression. Quantitative analysis of the DNA methylation patterns at a total of 104 CpGs in the promoter region of PTHrP by pyrosequencing showed the absence of methylation in all analyzed cell lines in the large CpG island upstream of exon 1C. In the second intron of promoter 2 (P2) a region was identified containing 4 CpG nucleotides for which differential methylation correlated with the PTHrP expression level. The functional importance of this control mechanism was confirmed by the ability of the demethylating agent 5'-azacytidine to induce PTHrP mRNA and iPTHrP protein expression in previously non-expressing cell lines and increase their production by metastatic NS2T2A1 cells. In particular, transcription from P2 was activated non-tumoral S1T3 cells upon treatment with 5'-azacytidine. Our findings support the hypothesis that the methylation status of specific CpG dinucleotides is the dominant mechanism involved in silencing of PTHrP expression rather than the overall methylation of the CpG island. Methylation of the PTHrP P2 is a potential marker of breast cancer progression and might be used to evaluate the metastatic potential of breast tumors.

  9. Plasmacytoid Dendritic Cell Response to CpG ODN Correlates with CXCL16 Expression and Is Inhibited by ox-LDL

    Directory of Open Access Journals (Sweden)

    Mayda Gursel

    2013-01-01

    Full Text Available Structurally distinct classes of synthetic CpG oligonucleotides (ODN differentially activate human immune cells. K-type ODN trigger plasmacytoid dendritic cells (pDCs to differentiate and produce TNFα. In contrast, D-type ODN stimulate large amounts of IFNα secretion from pDCs. The cell-surface receptor CXCL16 was previously shown to influence the nature and specificity of CpG ODN-induced immune activation. Here, we evaluated the expression and function of CXCL16 on pDC from healthy volunteers. We report that increased CXCL16 expression correlated with enhanced in vitro response exclusively to D-type CpG ODN. Conversely, enzymatic digestion of the receptor resulted in a decrease in IFNα production. Moreover, ox-LDL presence significantly inhibited D-ODN mediated IFNα production by pDCs. Coculture of enriched pDCs with the CXCR6 expressing Jurkat T cells decreased the activation threshold of these cells responding to D-ODN, suggesting that CXCL16/CXCR6 interaction may play an important role in modifying the response of pDCs to environmental danger signals.

  10. The immune responses triggered by CpG ODNs in shrimp Litopenaeus vannamei are associated with LvTolls.

    Science.gov (United States)

    Sun, Rui; Wang, Mengqiang; Wang, Lingling; Yue, Feng; Yi, Qilin; Huang, Mengmeng; Liu, Rui; Qiu, Limei; Song, Linsheng

    2014-03-01

    CpG oligodeoxynucleotides (ODNs) represent a kind of pathogen-associated molecular patterns (PAMPs) as well as a novel adjuvant that activate the innate immune system through interaction with Toll-like receptor 9 (TLR9) in mammals. In the present study, the synthetic oligodeoxynucleotides, CpG ODN 2395, was employed to investigate the interactive mode of CpG ODNs with three known Tolls (LvToll1-3) from shrimp Litopenaeus vannamei. The mature peptides of extracellular domains of LvTolls (LvToll-ECDs) were recombinant expressed and their binding activities to CpG ODN 2395 were further examined by ELISA. rLvToll1-ECD and rLvToll3-ECD exhibited affinity to CpG ODN 2395 in a dose-dependent manner when their concentrations ranged from 0.25 to 2.00 μmol/L, while rLvToll2-ECD did not show any binding activities to CpG ODN 2395 in tested concentrations. Additionally, after the stimulation of CpG ODN 2395, the luciferase activities of HEK293T cells transfected with LvToll1-mosaic or LvToll3-mosaic were significantly increased to 2.38-fold (pvannamei were indispensable for the triggering of immune responses by CpG ODNs, and the results provided a foundation for the application of CpG ODNs as the novel immunostimulants in aquaculture.

  11. CpG Oligodeoxynucleotides Induce Differential Cytokine and Chemokine Gene Expression Profiles in Dapulian and Landrace Pigs

    OpenAIRE

    Jiaqing Hu; Yongqing Zeng; Wei Chen; Hui Wang; Dandan Yang; Chuanhao Li

    2016-01-01

    Oligodeoxynucleotides containing unmethylated CpG motifs (CpG ODN) mimic the immunostimulatory activity of microbial DNA by interacting with Toll-like receptor 9 (TLR9) to activate both the innate and adaptive immune responses in different species. However, few studies have been published to compare the effects of CpG ODN on different pig breeds. Therefore, in this study, whole blood gene expression profiles of DPL and Landrace pigs treated with CpG ODN were studied using RNA-seq technology. ...

  12. On the Physics of Radio Halos in Galaxy Clusters: Scaling Relations and Luminosity Functions

    CERN Document Server

    Zandanel, Fabio

    2014-01-01

    The underlying physics of giant and mini radio halos in galaxy clusters is still an open question. We find that mini halos (such as in Perseus and Ophiuchus) can be explained by radio-emitting electrons that are generated in hadronic cosmic ray (CR) interactions with protons of the intracluster medium. By contrast, the hadronic model either fails to explain the extended emission of giant radio halos (as in Coma at low frequencies) or would require a flat CR profile, which can be realized through outward streaming and diffusion of CRs (in Coma and A2163 at 1.4 GHz). We suggest that a second, leptonic component could be responsible for the missing flux in the outer parts of giant halos within a new hybrid scenario and we describe its possible observational consequences. To study the hadronic emission component of the radio halo population statistically, we use a cosmological mock galaxy cluster catalog built from the MultiDark simulation. Because of the properties of CR streaming and the different scalings of t...

  13. Nonribosomal peptide synthase gene clusters for lipopeptide biosynthesis in Bacillus subtilis 916 and their phenotypic functions.

    Science.gov (United States)

    Luo, Chuping; Liu, Xuehui; Zhou, Huafei; Wang, Xiaoyu; Chen, Zhiyi

    2015-01-01

    Bacillus cyclic lipopeptides (LPs) have been well studied for their phytopathogen-antagonistic activities. Recently, research has shown that these LPs also contribute to the phenotypic features of Bacillus strains, such as hemolytic activity, swarming motility, biofilm formation, and colony morphology. Bacillus subtilis 916 not only coproduces the three families of well-known LPs, i.e., surfactins, bacillomycin Ls (iturin family), and fengycins, but also produces a new family of LP called locillomycins. The genome of B. subtilis 916 contains four nonribosomal peptide synthase (NRPS) gene clusters, srf, bmy, fen, and loc, which are responsible for the biosynthesis of surfactins, bacillomycin Ls, fengycins, and locillomycins, respectively. By studying B. subtilis 916 mutants lacking production of one, two, or three LPs, we attempted to unveil the connections between LPs and phenotypic features. We demonstrated that bacillomycin Ls and fengycins contribute mainly to antifungal activity. Although surfactins have weak antifungal activity in vitro, the strain mutated in srfAA had significantly decreased antifungal activity. This may be due to the impaired productions of fengycins and bacillomycin Ls. We also found that the disruption of any LP gene cluster other than fen resulted in a change in colony morphology. While surfactins and bacillomycin Ls play very important roles in hemolytic activity, swarming motility, and biofilm formation, the fengycins and locillomycins had little influence on these phenotypic features. In conclusion, B. subtilis 916 coproduces four families of LPs which contribute to the phenotypic features of B. subtilis 916 in an intricate way.

  14. Expanding our understanding of sequence-function relationships of type II polyketide biosynthetic gene clusters: bioinformatics-guided identification of Frankiamicin A from Frankia sp. EAN1pec.

    Directory of Open Access Journals (Sweden)

    Yasushi Ogasawara

    Full Text Available A large and rapidly increasing number of unstudied "orphan" natural product biosynthetic gene clusters are being uncovered in sequenced microbial genomes. An important goal of modern natural products research is to be able to accurately predict natural product structures and biosynthetic pathways from these gene cluster sequences. This requires both development of bioinformatic methods for global analysis of these gene clusters and experimental characterization of select products produced by gene clusters with divergent sequence characteristics. Here, we conduct global bioinformatic analysis of all available type II polyketide gene cluster sequences and identify a conserved set of gene clusters with unique ketosynthase α/β sequence characteristics in the genomes of Frankia species, a group of Actinobacteria with underexploited natural product biosynthetic potential. Through LC-MS profiling of extracts from several Frankia species grown under various conditions, we identified Frankia sp. EAN1pec as producing a compound with spectral characteristics consistent with the type II polyketide produced by this gene cluster. We isolated the compound, a pentangular polyketide which we named frankiamicin A, and elucidated its structure by NMR and labeled precursor feeding. We also propose biosynthetic and regulatory pathways for frankiamicin A based on comparative genomic analysis and literature precedent, and conduct bioactivity assays of the compound. Our findings provide new information linking this set of Frankia gene clusters with the compound they produce, and our approach has implications for accurate functional prediction of the many other type II polyketide clusters present in bacterial genomes.

  15. 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.

  16. 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.

  17. Hypermethylation of the CPG Island of p16 Gene Correlates with Gene Inactivation in Brain Glioma

    Institute of Scientific and Technical Information of China (English)

    JIAOBaohua; GENGShaomei; 等

    2002-01-01

    Objective:To study the correlation between hypermethylation of the CPG island of p16 gene and its inactivation in gliomas.Mehtods:In 50 cases of brain glioma,immunohistochemical method was applied to detect the expression of p16 protein; PCR a-nalysis was performed to identify the deletion of exons 1,2 of p16 gene and hypermethylation of CPG island of exon 1 of p16 gene in brain glioma.Results:Immunohistochemical analysis showed that p16 protein expression was negative in 27 cases(54%) and positive in 23 cases(46%) of 50 cases of brain gliomas.In the group with negative p16 protein expression(n=27 cases),RT-PCR analysis showed that there were 9 cases(33%) with homozygous deletions ofp16 gene and 7 cases(26%) with hypermethylation of CPG island of p16 gene.Conclusion:The transcriptional inhibition of p16 gene may be induced by aberrant hypermethylation of p16 gene 5'-CPG island in some of the cases without the homozygous deletions of p16 gene.Hypermethylation of 5'-CPG island is one of the important mechanisms for p16 gene inactivation.

  18. CpG methylation increases the DNA binding of 9-aminoacridine carboxamide Pt analogues.

    Science.gov (United States)

    Kava, Hieronimus W; Murray, Vincent

    2016-10-01

    This study investigated the effect of CpG methylation on the DNA binding of cisplatin analogues with an attached aminoacridine intercalator. DNA-targeted 9-aminoacridine carboxamide Pt complexes are known to bind at 5'-CpG sequences. Their binding to methylated and non-methylated 5'-CpG sequences was determined and compared with cisplatin. The damage profiles of each platinum compound were quantified via a polymerase stop assay with fluorescently labelled primers and capillary electrophoresis. Methylation at 5'-CpG was shown to significantly increase the binding intensity for the 9-aminoacridine carboxamide compounds, whereas no significant increase was found for cisplatin. 5'-CpG methylation had the largest effect on the 9-ethanolamine-acridine carboxamide Pt complex, followed by the 9-aminoacridine carboxamide Pt complex and the 7-fluoro complex. The methylation state of a cell's genome is important in maintaining normal gene expression, and is often aberrantly altered in cancer cells. An analogue of cisplatin which differentially targets methylated DNA may be able to improve its therapeutic activity, or alter its range of targets and evade the chemoresistance which hampers cisplatin efficacy in clinical use.

  19. Nucleosome Positions and Differential Methylation Status of Various Regions within MLH1 CpG Island

    Institute of Scientific and Technical Information of China (English)

    BAI Hua; ZHOU Jing; DENG Da-jun

    2008-01-01

    Objective:To determine the relationship between nucleosome positions and formation of differential methylation of the reported region A,B,C,and D within the MLH1 CpG island. Methods:Methylation of the MLH1 promoter was analyzed by combined of bisulfite restriction assay.Chromatin of RKO and MGC803 cells were extracted and digested by Mnase.Mononucleosomal DNA fragment was isolated and used as templates for detection of nucleosomal distribution by a battery of quantitative PCRs covering the full MLH1 promoter region. Results:The MLH1 was methylated in RKO and unmethylated in MGC803.At the region B,where methylation of CpG sites did not correlated with transcription of this gene well,qPCR product of the M-3(-599nt~-475nt)fragment was amplified in both RKO and MGC803 cells.However,at the region C and D within the core promoter,where methylation of CpG sites correlated with loss of MLH1 transcription well,the M-7(-257nt~-153nt)and M-8(-189nt~-71nt)fragments were amplified remarkably only in RKO cells. Conclusion:Nucleosome may be the basic unit for both CpG methylation and methylation-related regulation of gene transcription.Methylation status of CpG sites within the same nucleosome may be homogeneous;between different nucleosomes,homogeneous or heterogeneous.

  20. Probing the Structures and Electronic Properties of Dual-Phosphorus-Doped Gold Cluster Anions (AunP-2, n = 1–8): A Density functional Theory Investigation

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Kang-Ming; Huang, Teng; Liu, Yi-Rong; Jiang, Shuai; Zhang, Yang; Lv, Yu-Zhou; Gai, Yan-Bo; Huang, Wei

    2015-07-29

    The geometries of gold clusters doped with two phosphorus atoms, (AunP-2, n = 1–8) were investigated using density functional theory (DFT) methods. Various two-dimensional (2D) and three-dimensional (3D) structures of the doped clusters were studied. The results indicate that the structures of dual-phosphorus-doped gold clusters exhibit large differences from those of pure gold clusters with small cluster sizes. In our study, as for Au6P-2, two cis–trans isomers were found. The global minimum of Au8P-2 presents a similar configuration to that of Au-20, a pyramid-shaped unit, and the potential novel optical and catalytic properties of this structure warrant further attention. The higher stability of AunP-2 clusters relative to Au-n+2 (n = 1–8) clusters was verified based on various energy parameters, and the results indicate that the phosphorus atom can improve the stabilities of the gold clusters. We then explored the evolutionary path of (n = 1–8) clusters. We found that AunP-2 clusters exhibit the 2D–3D structural transition at n = 6, which is much clearer and faster than that of pure gold clusters and single-phosphorus-doped clusters. The electronic properties of AunP-2 (n = 1–8) were then investigated. The photoelectron spectra provide additional fundamental information on the structures and molecular orbitals shed light on the evolution of AunP-2 (n = 1–8). Natural bond orbital (NBO) described the charge distribution in stabilizing structures and revealed the strong relativistic effects of the gold atoms.

  1. Coupled-cluster Green's function: Analysis of properties originating in the exponential parametrization of the ground-state wave function

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Bo; Kowalski, Karol

    2016-12-23

    In this paper we derive basic properties of the Green’s function matrix elements stemming from the exponential coupled cluster (CC) parametrization of the ground-state wave function. We demon- strate that all intermediates used to express retarded (or equivalently, ionized) part of the Green’s function in the ω-representation can be expressed through connected diagrams only. Similar proper- ties are also shared by the first order ω-derivatives of the retarded part of the CC Green’s function. This property can be extended to any order ω-derivatives of the Green’s function. Through the Dyson equation of CC Green’s function, the derivatives of corresponding CC self-energy can be evaluated analytically. In analogy to the CC Green’s function, the corresponding CC self-energy is expressed in terms of connected diagrams only. Moreover, the ionized part of the CC Green’s func- tion satisfies the non-homogeneous linear system of ordinary differential equations, whose solution may be represented in the exponential form. Our analysis can be easily generalized to the advanced part of the CC Green’s function.

  2. Serial changes in expression of functionally clustered genes in progression of liver fibrosis in hepatitis C patients

    Institute of Scientific and Technical Information of China (English)

    Yoshiyuki Takahara; Mitsuo Takahashi; Qing-Wei Zhang; Hirotaka Wagatsuma; Maiko Mori; Akihiro Tamori; Susumu Shiomi; Shuhei Nishiguchi

    2008-01-01

    AIM: To investigate the relationship of changes in expression of marker genes in functional categories or molecular networks comprising one functional category or multiple categories in progression of hepatic fibrosis in hepatitis C (HCV) patients.METHODS: Marker genes were initially identified using DNA microarray data from a rat liver fibrosis model. The expression level of each fibrosis associated marker gene was analyzed using reverse transcription-polymerase chain reaction (RT-PCR) in clinical biopsy specimens from HCV-positive patients (n = 61). Analysis of changes in expression patterns and interactions of marker genes in functional categories was used to assess the biological mechanism of fibrosis.RESULTS: The profile data showed several biological changes associated with progression of hepatic fibrosis. Clustered genes in functional categories showed sequential changes in expression. Several sets of clustered genes, including those related to the extracellular matrix (ECM), inflammation, lipid metabolism, steroid metabolism, and some transcription factors important for hepatic biology showed expression changes in the immediate early phase (F1/F2) of fibrosis. Genes associated with aromatic amino acid (AA) metabolism, sulfur-containing AA metabolism and insulin/ Wnt signaling showed expression changes in the middle phase (F2/F3), and some genes related to glucose metabolism showed altered expression in the late phase of fibrosis (F3/F4). Therefore, molecular networks showing serial changes in gene expression are present in liver fibrosis progression in hepatitis C patients.CONCLUSION: Analysis of gene expression profiles from a perspective of functional categories or molecular networks provides an understanding of disease and suggests new diagnostic methods. Selected marker genes have potential utility for biological identification of advanced fibrosis.

  3. Density functional theory assessment of molecular structures and energies of neutral and anionic Al(n) (n = 2-10) clusters.

    Science.gov (United States)

    Paranthaman, Selvarengan; Hong, Kiryong; Kim, Joonghan; Kim, Dong Eon; Kim, Tae Kyu

    2013-09-26

    We report the results of a benchmarking study on hybrid, hybrid-meta, long-range-corrected, meta-generalized gradient approximation (meta-GGA), and GGA density functional theory (DFT) methods for aluminum (Al) clusters. A range of DFT functionals, such as B3LYP, B1B95, PBE0, mPW1PW91, M06, M06-2X, ωB97X, ωB97XD, TPSSh, BLYP, PBE, mPWPW91, M06-L, and TPSS, have been used to optimize the molecular structures and calculate the vibrational frequencies and four energetic parameters for neutral and anionic Al(n) (n = 2-10) clusters. The performances of these functionals are assessed systematically by calculating the vertical ionization energy for neutral Al clusters and the vertical electron detachment energy for anionic Al clusters, along with the cohesive energy and dissociation energy. The results are compared with the available experimental and high-level ab initio calculated results. The calculated results showed that the PBE0 and mPW1PW91 functionals generally provide better results than the other functionals studied. TPSS can be a good choice for the calculations of very large Al clusters. On the other hand, the B3LYP, BLYP, and M06-L functionals are in poor agreement with the available experimental and theoretical results. The calculated results suggest that the hybrid DFT functionals like B3LYP do not always provide better performance than GGA functionals.

  4. Non-DSB clustered DNA lesions induced by ionizing radiation are largely