Mycobacterium leprae: genes, pseudogenes and genetic diversity

Science.gov (United States)

Singh, Pushpendra; Cole, Stewart T

2011-01-01

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

Pseudogenes regulate parental gene expression via ceRNA network.

Science.gov (United States)

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

2017-01-01

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

U1 snDNA clusters in grasshoppers: chromosomal dynamics and genomic organization

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

2015-01-01

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

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

DEFF Research Database (Denmark)

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

2008-01-01

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

H2A/K pseudogene mutation may promote cell proliferation

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

2016-05-15

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

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

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

2011-09-01

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

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

Science.gov (United States)

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

2010-01-01

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

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

International Nuclear Information System (INIS)

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

1994-01-01

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

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

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

2010-05-01

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

Human Nanog pseudogene8 promotes the proliferation of gastrointestinal cancer cells

International Nuclear Information System (INIS)

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

2012-01-01

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

Pseudogene accumulation might promote the adaptive microevolution of Yersinia pestis

DEFF Research Database (Denmark)

Tong, Zongzhong; Zhou, Dongsheng; Song, Yajun

2005-01-01

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

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

Directory of Open Access Journals (Sweden)

Susely F.S. Tada

2006-01-01

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

Human Nanog pseudogene8 promotes the proliferation of gastrointestinal cancer cells

Energy Technology Data Exchange (ETDEWEB)

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

2012-09-10

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

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

Science.gov (United States)

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

2014-06-01

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

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

Directory of Open Access Journals (Sweden)

Lahey Cora

2006-08-01

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

Structure of gene and pseudogenes of human apoferritin H

Energy Technology Data Exchange (ETDEWEB)

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

1986-01-24

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

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

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Graham David E

2009-07-01

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

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

DEFF Research Database (Denmark)

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

1999-01-01

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

The correlation functions for the clustering of galaxies and Abell clusters

International Nuclear Information System (INIS)

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

1985-01-01

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

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

Science.gov (United States)

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

2017-05-01

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

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

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Marco De Martino

2017-11-01

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

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

Science.gov (United States)

Zhu, Tao; Niu, Deng-Ke

2013-03-05

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

Clustering aspects in nuclear structure functions

International Nuclear Information System (INIS)

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

2011-01-01

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

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

Czech Academy of Sciences Publication Activity Database

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

2014-01-01

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

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

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Marcio Roberto Silva

2011-02-01

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

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

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

2010-05-01

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

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

International Nuclear Information System (INIS)

Shiga, Kiyoto; Yamamoto, Hiroshi; Okamoto, Hiroshi

1990-01-01

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

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

Science.gov (United States)

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

2017-02-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1997-02-01

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

Mass functions for eight galactic clusters in the solar neighborhood

International Nuclear Information System (INIS)

Francic, S.P.

1989-01-01

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

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

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Watanabe Haruo

2005-10-01

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

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

Science.gov (United States)

Collery, Mark M; Smyth, Cyril J

2007-02-01

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

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

DEFF Research Database (Denmark)

Mandrup, S; Hummel, R; Ravn, S

1992-01-01

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

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

Science.gov (United States)

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

2018-01-01

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

Improved Density Functional Tight Binding Potentials for Metalloid Aluminum Clusters

Science.gov (United States)

2016-06-01

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

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

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van der Loo Wessel

2012-08-01

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

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

International Nuclear Information System (INIS)

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

1989-01-01

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

Clustering of near clusters versus cluster compactness

International Nuclear Information System (INIS)

Yu Gao; Yipeng Jing

1989-01-01

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

Lithuanian medical tourism cluster: conditions and background for functioning

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Korol A. N.

2017-10-01

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

Cranked cluster wave function for molecular states

International Nuclear Information System (INIS)

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

1986-01-01

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

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

Science.gov (United States)

Schuster, W; Brennicke, A

1991-01-01

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

Inelastic electron scattering as an indicator of clustering in wave functions

International Nuclear Information System (INIS)

1998-01-01

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

Evolution of the cluster X-ray luminosity function

DEFF Research Database (Denmark)

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

2004-01-01

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

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

Science.gov (United States)

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

2017-04-25

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

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.

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

DEFF Research Database (Denmark)

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

1992-01-01

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

Evolution of the cluster x-ray luminosity function slope

International Nuclear Information System (INIS)

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

1982-01-01

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

Estimation of cluster stability using the theory of electron density functional

International Nuclear Information System (INIS)

Borisov, Yu.A.

1985-01-01

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

Photoluminescence quenching of chemically functionalized porous silicon by a ruthenium cluster

Energy Technology Data Exchange (ETDEWEB)

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

2003-05-01

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

Photoluminescence quenching of chemically functionalized porous silicon by a ruthenium cluster

Science.gov (United States)

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

2003-05-01

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

A Clustering-Based Automatic Transfer Function Design for Volume Visualization

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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.

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

Science.gov (United States)

Angelov, Kiril; Kaynakchieva, Vesela

2017-12-01

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

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

Directory of Open Access Journals (Sweden)

Carla Maria Meireles

1999-09-01

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

Pseudogene of dihydrolipoyl succinyltransferase (E2k) found by PCR amplification and direct sequencing of rodent-human cell hybrid DNAs

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Cai, X.; Ali, G.; Blass, J.P. [Cornell Univ. Medical College, White Plains, NY (United States); Szabo, P. [Cornell Univ. Medical College, New York, NY (United States); Tanzi, R.E. [Massachusetts General Hospital, Boston, MA (United States)

1994-07-01

Previous studies have indicated that the cDNA for the E2k component of the human {alpha}-ketoglutarate dehydrogenase complex (KGDHC) hybridized not only to a major locus on chromosome 14q24.3 in a region associated with familial Alzheimer`s disease and with Joseph-Machado disease, but also to another locus on chromosome 1p31. The authors now report that PCR of genomic DNA and direct sequencing indicated that the chromosome 1 locus is an intronless pseudogene. PCR of genomic DNA amplified E2k fragments from mouse-human cell hybrids containing human chromosome 1 DNA but not from hybrids containing human chromosome 14 DNA. The resulting amplicons were of comparable sizes to those when the cDNA was used to template. The direct sequencing of these amplicons confirmed the lack of introns and indicated a frame shift, which led to the presence of four termination codons early in the coding region. PCR followed by direct sequencing of the amplicons appears to be a convenient method for identifying intronless pseudogenes.

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

Directory of Open Access Journals (Sweden)

Maddalena Di Sanzo

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

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

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

Science.gov (United States)

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

2018-01-01

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

Cluster-cluster clustering

International Nuclear Information System (INIS)

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

1985-01-01

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

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

Science.gov (United States)

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

2017-01-01

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

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

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Zhang; Fall

1999-12-20

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

Diffusion Geometry Unravels the Emergence of Functional Clusters in Collective Phenomena

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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.

Evolution of the paralogous hap and iga genes in Haemophilus influenzae: evidence for a conserved hap pseudogene associated with microcolony formation in the recently diverged Haemophilus aegyptius and H. influenzae biogroup aegyptius

DEFF Research Database (Denmark)

Kilian, Mogens; Poulsen, Knud; Lomholt, Hans Bredsted

2002-01-01

genetic polymorphism and pronounced mosaic-like patterns in both genes, but no evidence of intrastrain recombination between the two genes. A conserved hap pseudogene was present in all strains of H. aegyptius and H. influenzae biogroup aegyptius, each of which constituted distinct subpopulations...... on conjunctival cells, previously termed microcolony formation. The fact that individual hap pseudogenes differed from the ancestral sequence by zero to two positions within a 1.5 kb stretch suggests that the silencing event happened approximately 2000-11,000 years ago. Divergence of H. aegyptius and H...

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

International Nuclear Information System (INIS)

Sasakawa, T.

1979-01-01

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

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

International Nuclear Information System (INIS)

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

2010-01-01

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

Immunoglobulin Genomics in the Guinea Pig (Cavia porcellus)

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Guo, Yongchen; Bao, Yonghua; Meng, Qingwen; Hu, Xiaoxiang; Meng, Qingyong; Ren, Liming; Li, Ning; Zhao, Yaofeng

2012-01-01

In science, the guinea pig is known as one of the gold standards for modeling human disease. It is especially important as a molecular and cellular biology model for studying the human immune system, as its immunological genes are more similar to human genes than are those of mice. The utility of the guinea pig as a model organism can be further enhanced by further characterization of the genes encoding components of the immune system. Here, we report the genomic organization of the guinea pig immunoglobulin (Ig) heavy and light chain genes. The guinea pig IgH locus is located in genomic scaffolds 54 and 75, and spans approximately 6,480 kb. 507 VH segments (94 potentially functional genes and 413 pseudogenes), 41 DH segments, six JH segments, four constant region genes (μ, γ, ε, and α), and one reverse δ remnant fragment were identified within the two scaffolds. Many VH pseudogenes were found within the guinea pig, and likely constituted a potential donor pool for gene conversion during evolution. The Igκ locus mapped to a 4,029 kb region of scaffold 37 and 24 is composed of 349 Vκ (111 potentially functional genes and 238 pseudogenes), three Jκ and one Cκ genes. The Igλ locus spans 1,642 kb in scaffold 4 and consists of 142 Vλ (58 potentially functional genes and 84 pseudogenes) and 11 Jλ -Cλ clusters. Phylogenetic analysis suggested the guinea pig’s large germline VH gene segments appear to form limited gene families. Therefore, this species may generate antibody diversity via a gene conversion-like mechanism associated with its pseudogene reserves. PMID:22761756

Spectroscopic constraints on the form of the stellar cluster mass function

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

2012-05-01

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

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

Science.gov (United States)

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

2004-01-01

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

The luminosity function for globular clusters, 4: M3

International Nuclear Information System (INIS)

Simoda, Mahiro; Fukuoka, Takashi

1976-01-01

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

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.

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

International Nuclear Information System (INIS)

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

2014-01-01

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

A-dependence of structure functions and multiquark clusters in nuclei

International Nuclear Information System (INIS)

Kondratyuk, L.; Shmatikov, M.

1984-01-01

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

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

Science.gov (United States)

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

2015-04-01

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

Topological defect clustering and plastic deformation mechanisms in functionalized graphene

Science.gov (United States)

Nunes, Ricardo; Araujo, Joice; Chacham, Helio

2011-03-01

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

Density functional study of the bonding in small silicon clusters

International Nuclear Information System (INIS)

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

1992-01-01

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

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

Science.gov (United States)

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

2018-04-01

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

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

Science.gov (United States)

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

2011-01-17

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

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

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Xia Li

2005-07-01

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

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

Directory of Open Access Journals (Sweden)

2005-07-01

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

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.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

Theoretical stellar luminosity functions and globular cluster ages and compositions

International Nuclear Information System (INIS)

Ratcliff, S.J.

1985-01-01

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

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

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

2002-08-01

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

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

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

Science.gov (United States)

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

2008-02-01

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

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

Science.gov (United States)

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

2006-03-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1989-11-11

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

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

Science.gov (United States)

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

2015-12-01

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

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

Science.gov (United States)

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

2018-06-01

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

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

Science.gov (United States)

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

2018-01-01

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

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.

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.

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

Directory of Open Access Journals (Sweden)

Jorge Pimenta

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

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

Directory of Open Access Journals (Sweden)

Simone Pascucci

2018-04-01

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

Isomers of Cu6 cluster: a density function theory study

International Nuclear Information System (INIS)

Jia Yanhui; Wang Shanshan; Li Gongping

2008-01-01

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

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

Directory of Open Access Journals (Sweden)

Crnovčić I

2017-04-01

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

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

International Nuclear Information System (INIS)

Priyanka,; Dharamvir, Keya; Sharma, Hitesh

2011-01-01

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

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

Science.gov (United States)

de Marchi, G.; Paresce, F.

1995-12-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1990-08-28

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

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

Science.gov (United States)

Xu, Enhua; Li, Shuhua

2015-03-07

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

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

Science.gov (United States)

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

2012-11-28

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

Identification of four genomic loci highly related to casein-kinase-2-alpha cDNA and characterization of a casein kinase-2-alpha pseudogene within the mouse genome

DEFF Research Database (Denmark)

Boldyreff, B; Wehr, K; Hecht, R

1992-01-01

positive clone was further analyzed by sequencing a 3.1 kb XbaI fragment. This clone displays the characteristics of a pseudogene, i.e. lack of introns and several nucleotide insertions and deletions. In its 3' region it contains a 91 bp large CT-rich stretch which consists of (CCTT) and (CT) repeats...

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

International Nuclear Information System (INIS)

Sinnott, S.B.

1993-01-01

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

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

OpenAIRE

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

2002-01-01

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

Symmetrized partial-wave method for density-functional cluster calculations

International Nuclear Information System (INIS)

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

1994-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1996-06-01

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

Anchoring selenido-carbonyl ruthenium clusters to functionalized silica xerogels

International Nuclear Information System (INIS)

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

2003-01-01

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

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

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

International Nuclear Information System (INIS)

Dunlap, B.I.

1996-01-01

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

Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms.

Directory of Open Access Journals (Sweden)

Chao Shi

Full Text Available Plant chloroplast genes are usually co-transcribed while its posttranscriptional splicing is fairly complex and remains largely unsolved. On basis of sequencing the three complete Camellia (Theaceae chloroplast genomes for the first time, we comprehensively analyzed the evolutionary patterns of ycf15, a plastid gene quite paradoxical in terms of its function and evolution, along the inferred angiosperm phylogeny. Although many species in separate lineages including the three species reported here contained an intact ycf15 gene in their chloroplast genomes, the phylogenetic mixture of both intact and obviously disabled ycf15 genes imply that they are all non-functional. Both intracellular gene transfer (IGT and horizontal gene transfer (HGT failed to explain such distributional anomalies. While, transcriptome analyses revealed that ycf15 was transcribed as precursor polycistronic transcript which contained ycf2, ycf15 and antisense trnL-CAA. The transcriptome assembly was surprisingly found to cover near the complete Camellia chloroplast genome. Many non-coding regions including pseudogenes were mapped by multiple transcripts, indicating the generality of pseudogene transcriptions. Our results suggest that plastid DNA posttranscriptional splicing may involve complex cleavage of non-functional genes.

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

International Nuclear Information System (INIS)

Gardet, G.

1995-01-01

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

Diametrical clustering for identifying anti-correlated gene clusters.

Science.gov (United States)

Dhillon, Inderjit S; Marcotte, Edward M; Roshan, Usman

2003-09-01

Clustering genes based upon their expression patterns allows us to predict gene function. Most existing clustering algorithms cluster genes together when their expression patterns show high positive correlation. However, it has been observed that genes whose expression patterns are strongly anti-correlated can also be functionally similar. Biologically, this is not unintuitive-genes responding to the same stimuli, regardless of the nature of the response, are more likely to operate in the same pathways. We present a new diametrical clustering algorithm that explicitly identifies anti-correlated clusters of genes. Our algorithm proceeds by iteratively (i). re-partitioning the genes and (ii). computing the dominant singular vector of each gene cluster; each singular vector serving as the prototype of a 'diametric' cluster. We empirically show the effectiveness of the algorithm in identifying diametrical or anti-correlated clusters. Testing the algorithm on yeast cell cycle data, fibroblast gene expression data, and DNA microarray data from yeast mutants reveals that opposed cellular pathways can be discovered with this method. We present systems whose mRNA expression patterns, and likely their functions, oppose the yeast ribosome and proteosome, along with evidence for the inverse transcriptional regulation of a number of cellular systems.

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

Science.gov (United States)

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

2017-12-30

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

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

Science.gov (United States)

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

1991-11-01

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

Genital and extra-genital screening for gonorrhoea using the BD Probetec ET system with an in-house PCR method targeting the porA pseudogene as confirmatory test

DEFF Research Database (Denmark)

Skovgaard, Sissel; Larsen, Helle Kiellberg; Sand, Carsten

2012-01-01

for Chlamydia trachomatis testing were also examined for GC on the BD Viper™ platform using the BD Probetec ET system. In order to avoid false-positive results all GC BD reactive samples were re-tested using a PCR method with the porA pseudogene as target. Using this method we screened 170% more samples for GC...

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

NARCIS (Netherlands)

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

2013-01-01

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

Dyadic Green's function of a cluster of spheres.

Science.gov (United States)

Moneda, Angela P; Chrissoulidis, Dimitrios P

2007-11-01

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

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

Science.gov (United States)

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

2018-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2012-05-15

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

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

International Nuclear Information System (INIS)

Balzer, Matthias

2008-01-01

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

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

Directory of Open Access Journals (Sweden)

Kollmar Martin

2008-02-01

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

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

Science.gov (United States)

Li, Chiang-Shan R.

2014-01-01

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

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

International Nuclear Information System (INIS)

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

2012-01-01

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

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.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

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

Directory of Open Access Journals (Sweden)

Irene Keller

2007-02-01

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

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

Science.gov (United States)

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

2018-05-01

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

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

Science.gov (United States)

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

2018-05-01

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

CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks.

Science.gov (United States)

Li, Min; Li, Dongyan; Tang, Yu; Wu, Fangxiang; Wang, Jianxin

2017-08-31

Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect protein complexes or functional modules. In addition, BinGO is used to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. CytoCluster can be easily expanded, so that more clustering algorithms and functions can be added to this plugin. Since it was created in July 2013, CytoCluster has been downloaded more than 9700 times in the Cytoscape App store and has already been applied to the analysis of different biological networks. CytoCluster is available from http://apps.cytoscape.org/apps/cytocluster.

Interplay between experiments and calculations for organometallic clusters and caged clusters

International Nuclear Information System (INIS)

Nakajima, Atsushi

2015-01-01

Clusters consisting of 10-1000 atoms exhibit size-dependent electronic and geometric properties. In particular, composite clusters consisting of several elements and/or components provide a promising way for a bottom-up approach for designing functional advanced materials, because the functionality of the composite clusters can be optimized not only by the cluster size but also by their compositions. In the formation of composite clusters, their geometric symmetry and dimensionality are emphasized to control the physical and chemical properties, because selective and anisotropic enhancements for optical, chemical, and magnetic properties can be expected. Organometallic clusters and caged clusters are demonstrated as a representative example of designing the functionality of the composite clusters. Organometallic vanadium-benzene forms a one dimensional sandwich structure showing ferromagnetic behaviors and anomalously large HOMO-LUMO gap differences of two spin orbitals, which can be regarded as spin-filter components for cluster-based spintronic devices. Caged clusters of aluminum (Al) are well stabilized both geometrically and electronically at Al 12 X, behaving as a “superatom”

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

International Nuclear Information System (INIS)

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

2009-01-01

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

Cluster evolution

International Nuclear Information System (INIS)

Schaeffer, R.

1987-01-01

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

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

Science.gov (United States)

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

2015-05-01

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

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.

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

DEFF Research Database (Denmark)

Durkin, M E; Jäger, A C; Khurana, T S

1999-01-01

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

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

Science.gov (United States)

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

2017-04-27

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

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

Science.gov (United States)

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

2016-01-01

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

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

Science.gov (United States)

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

2016-06-01

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

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

International Nuclear Information System (INIS)

Hochkeppel, Stephan

2008-01-01

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

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.

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

Science.gov (United States)

2017-05-05

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

Identification of Flood Reactivity Regions via the Functional Clustering of Hydrographs

Science.gov (United States)

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

2018-03-01

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

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.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

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

Science.gov (United States)

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

2018-05-01

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

A density functional study of structures and stability of SinCN clusters

International Nuclear Information System (INIS)

Gai Zhigang; Yang Li; Zhao Jie; Chu Shibo

2011-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-04-01

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

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

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Fabio Stella

2013-09-01

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

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

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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/.

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

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

2009-10-14

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

Comprehensive cluster analysis with Transitivity Clustering.

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Wittkop, Tobias; Emig, Dorothea; Truss, Anke; Albrecht, Mario; Böcker, Sebastian; Baumbach, Jan

2011-03-01

Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers three user-friendly interfaces: a powerful stand-alone version, a web interface, and a collection of Cytoscape plug-ins. In this paper, we describe three major workflows: (i) protein (super)family detection with Cytoscape, (ii) protein homology detection with incomplete gold standards and (iii) clustering of gene expression data. This protocol guides the user through the most important features of Transitivity Clustering and takes ∼1 h to complete.

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

Science.gov (United States)

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

2002-08-01

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

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

Science.gov (United States)

Emerling, Christopher A

2018-01-01

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

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

Science.gov (United States)

Santra, Biswajit; Michaelides, Angelos; Scheffler, Matthias

2007-11-01

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

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

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Christian, Pierre; Mocz, Philip; Loeb, Abraham

2018-05-01

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

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

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Angela F Harper

2017-02-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2017-02-10

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

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

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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.

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

Science.gov (United States)

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

1998-01-01

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

A recently transferred cluster of bacterial genes in Trichomonas vaginalis - lateral gene transfer and the fate of acquired genes

Science.gov (United States)

2014-01-01

Background Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes. PMID:24898731

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

International Nuclear Information System (INIS)

Jiang Yuanqi; Duan Haiming

2011-01-01

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

Relativistic form factors for clusters with nonrelativistic wave functions

International Nuclear Information System (INIS)

Mitra, A.N.; Kumari, I.

1977-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Balzer, Matthias

2008-07-01

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

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

Science.gov (United States)

Shamasundar, K. R.

2018-06-01

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

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

Science.gov (United States)

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

2017-10-01

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

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

Functional evolution of the trace amine associated receptors in mammals and the loss of TAAR1 in dogs

Directory of Open Access Journals (Sweden)

Westmoreland Susan V

2010-02-01

Full Text Available Abstract Background The trace amine associated receptor family is a diverse array of GPCRs that arose before the first vertebrates walked on land. Trace amine associated receptor 1 (TAAR1 is a wide spectrum aminergic receptor that acts as a modulator in brain monoaminergic systems. Other trace amine associated receptors appear to relate to environmental perception and show a birth-and-death pattern in mammals similar to olfactory receptors. Results Across mammals, avians, and amphibians, the TAAR1 gene is intact and appears to be under strong purifying selection based on rates of amino acid fixation compared to neutral mutations. We have found that in dogs it has become a pseudogene. Our analyses using a comparative genetics approach revealed that the pseudogenization event predated the emergence of the Canini tribe rather than being coincident with canine domestication. By assessing the effects of the TAAR1 agonist β-phenylethylamine on [3H]dopamine uptake in canine striatal synaptosomes and comparing the degree and pattern of uptake inhibition to that seen in other mammals, including TAAR1 knockout mice, wild type mice and rhesus monkey, we found that the TAAR1 pseudogenization event resulted in an uncompensated loss of function. Conclusion The gene family has seen expansions among certain mammals, notably rodents, and reductions in others, including primates. By placing the trace amine associated receptors in an evolutionary context we can better understand their function and their potential associations with behavior and neurological disease.

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

Science.gov (United States)

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

2009-06-01

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

An original SERPINA3 gene cluster: Elucidation of genomic organization and gene expression in the Bos taurus 21q24 region

Directory of Open Access Journals (Sweden)

Ouali Ahmed

2008-04-01

Full Text Available Abstract Background The superfamily of serine proteinase inhibitors (serpins is involved in numerous fundamental biological processes as inflammation, blood coagulation and apoptosis. Our interest is focused on the SERPINA3 sub-family. The major human plasma protease inhibitor, α1-antichymotrypsin, encoded by the SERPINA3 gene, is homologous to genes organized in clusters in several mammalian species. However, although there is a similar genic organization with a high degree of sequence conservation, the reactive-centre-loop domains, which are responsible for the protease specificity, show significant divergences. Results We provide additional information by analyzing the situation of SERPINA3 in the bovine genome. A cluster of eight genes and one pseudogene sharing a high degree of identity and the same structural organization was characterized. Bovine SERPINA3 genes were localized by radiation hybrid mapping on 21q24 and only spanned over 235 Kilobases. For all these genes, we propose a new nomenclature from SERPINA3-1 to SERPINA3-8. They share approximately 70% of identity with the human SERPINA3 homologue. In the cluster, we described an original sub-group of six members with an unexpected high degree of conservation for the reactive-centre-loop domain, suggesting a similar peptidase inhibitory pattern. Preliminary expression analyses of these bovSERPINA3s showed different tissue-specific patterns and diverse states of glycosylation and phosphorylation. Finally, in the context of phylogenetic analyses, we improved our knowledge on mammalian SERPINAs evolution. Conclusion Our experimental results update data of the bovine genome sequencing, substantially increase the bovSERPINA3 sub-family and enrich the phylogenetic tree of serpins. We provide new opportunities for future investigations to approach the biological functions of this unusual subset of serine proteinase inhibitors.

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

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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.

Choosing the Number of Clusters in K-Means Clustering

Science.gov (United States)

Steinley, Douglas; Brusco, Michael J.

2011-01-01

Steinley (2007) provided a lower bound for the sum-of-squares error criterion function used in K-means clustering. In this article, on the basis of the lower bound, the authors propose a method to distinguish between 1 cluster (i.e., a single distribution) versus more than 1 cluster. Additionally, conditional on indicating there are multiple…

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

Science.gov (United States)

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

2018-01-01

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

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.

Cluster polylogarithms for scattering amplitudes

International Nuclear Information System (INIS)

Golden, John; Paulos, Miguel F; Spradlin, Marcus; Volovich, Anastasia

2014-01-01

Motivated by the cluster structure of two-loop scattering amplitudes in N=4 Yang-Mills theory we define cluster polylogarithm functions. We find that all such functions of weight four are made up of a single simple building block associated with the A 2 cluster algebra. Adding the requirement of locality on generalized Stasheff polytopes, we find that these A 2 building blocks arrange themselves to form a unique function associated with the A 3 cluster algebra. This A 3 function manifests all of the cluster algebraic structure of the two-loop n-particle MHV amplitudes for all n, and we use it to provide an explicit representation for the most complicated part of the n = 7 amplitude as an example. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Cluster algebras in mathematical physics’. (paper)

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

Science.gov (United States)

Guo, Ling

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

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

Institute of Scientific and Technical Information of China (English)

朱保华; 胡斌; 张伟强; 边治国; 赵全义; 殷元骐; 孙杰

2003-01-01

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

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

Science.gov (United States)

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

2017-11-01

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

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

International Nuclear Information System (INIS)

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

2011-01-01

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

Clustering on Membranes

DEFF Research Database (Denmark)

Johannes, Ludger; Pezeshkian, Weria; Ipsen, John H

2018-01-01

Clustering of extracellular ligands and proteins on the plasma membrane is required to perform specific cellular functions, such as signaling and endocytosis. Attractive forces that originate in perturbations of the membrane's physical properties contribute to this clustering, in addition to direct...... protein-protein interactions. However, these membrane-mediated forces have not all been equally considered, despite their importance. In this review, we describe how line tension, lipid depletion, and membrane curvature contribute to membrane-mediated clustering. Additional attractive forces that arise...... from protein-induced perturbation of a membrane's fluctuations are also described. This review aims to provide a survey of the current understanding of membrane-mediated clustering and how this supports precise biological functions....

Derivation of the density functional theory from the cluster expansion.

Science.gov (United States)

Hsu, J Y

2003-09-26

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

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.

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

International Nuclear Information System (INIS)

Liu Xuan; Ito, Haruhiko; Torikai, Eiko

2012-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2012-08-15

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

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

Science.gov (United States)

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

2007-06-14

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

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

International Nuclear Information System (INIS)

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

2015-01-01

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

Globular clusters and galaxy halos

International Nuclear Information System (INIS)

Van Den Bergh, S.

1984-01-01

Using semipartial correlation coefficients and bootstrap techniques, a study is made of the important features of globular clusters with respect to the total number of galaxy clusters and dependence of specific galaxy cluster on parent galaxy type, cluster radii, luminosity functions and cluster ellipticity. It is shown that the ellipticity of LMC clusters correlates significantly with cluster luminosity functions, but not with cluster age. The cluter luminosity value above which globulars are noticeably flattened may differ by a factor of about 100 from galaxy to galaxy. Both in the Galaxy and in M31 globulars with small core radii have a Gaussian distribution over luminosity, whereas clusters with large core radii do not. In the cluster systems surrounding the Galaxy, M31 and NGC 5128 the mean radii of globular clusters was found to increase with the distance from the nucleus. Central galaxies in rich clusters have much higher values for specific globular cluster frequency than do other cluster ellipticals, suggesting that such central galaxies must already have been different from normal ellipticals at the time they were formed

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

Science.gov (United States)

Yang, Zhi; Xiong, Shi-Jie

2008-09-28

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

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.

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

Science.gov (United States)

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

2017-11-01

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

Modified genetic algorithms to model cluster structures in medium-size silicon clusters

International Nuclear Information System (INIS)

Bazterra, Victor E.; Ona, Ofelia; Caputo, Maria C.; Ferraro, Marta B.; Fuentealba, Patricio; Facelli, Julio C.

2004-01-01

This paper presents the results obtained using a genetic algorithm (GA) to search for stable structures of medium size silicon clusters. In this work the GA uses a semiempirical energy function to find the best cluster structures, which are further optimized using density-functional theory. For small clusters our results agree well with previously reported structures, but for larger ones different structures appear. This is the case of Si 36 where we report a different structure, with significant lower energy than those previously found using limited search approaches on common structural motifs. This demonstrates the need for global optimization schemes when searching for stable structures of medium-size silicon clusters

Mouse Nkrp1-Clr gene cluster sequence and expression analyses reveal conservation of tissue-specific MHC-independent immunosurveillance.

Directory of Open Access Journals (Sweden)

Qiang Zhang

Full Text Available The Nkrp1 (Klrb1-Clr (Clec2 genes encode a receptor-ligand system utilized by NK cells as an MHC-independent immunosurveillance strategy for innate immune responses. The related Ly49 family of MHC-I receptors displays extreme allelic polymorphism and haplotype plasticity. In contrast, previous BAC-mapping and aCGH studies in the mouse suggest the neighboring and related Nkrp1-Clr cluster is evolutionarily stable. To definitively compare the relative evolutionary rate of Nkrp1-Clr vs. Ly49 gene clusters, the Nkrp1-Clr gene clusters from two Ly49 haplotype-disparate inbred mouse strains, BALB/c and 129S6, were sequenced. Both Nkrp1-Clr gene cluster sequences are highly similar to the C57BL/6 reference sequence, displaying the same gene numbers and order, complete pseudogenes, and gene fragments. The Nkrp1-Clr clusters contain a strikingly dissimilar proportion of repetitive elements compared to the Ly49 clusters, suggesting that certain elements may be partly responsible for the highly disparate Ly49 vs. Nkrp1 evolutionary rate. Focused allelic polymorphisms were found within the Nkrp1b/d (Klrb1b, Nkrp1c (Klrb1c, and Clr-c (Clec2f genes, suggestive of possible immune selection. Cell-type specific transcription of Nkrp1-Clr genes in a large panel of tissues/organs was determined. Clr-b (Clec2d and Clr-g (Clec2i showed wide expression, while other Clr genes showed more tissue-specific expression patterns. In situ hybridization revealed specific expression of various members of the Clr family in leukocytes/hematopoietic cells of immune organs, various tissue-restricted epithelial cells (including intestinal, kidney tubular, lung, and corneal progenitor epithelial cells, as well as myocytes. In summary, the Nkrp1-Clr gene cluster appears to evolve more slowly relative to the related Ly49 cluster, and likely regulates innate immunosurveillance in a tissue-specific manner.

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.

Dynamical aspects of galaxy clustering

International Nuclear Information System (INIS)

Fall, S.M.

1980-01-01

Some recent work on the origin and evolution of galaxy clustering is reviewed, particularly within the context of the gravitational instability theory and the hot big-bang cosmological model. Statistical measures of clustering, including correlation functions and multiplicity functions, are explained and discussed. The close connection between galaxy formation and clustering is emphasized. Additional topics include the dependence of galaxy clustering on the spectrum of primordial density fluctuations and the mean mass density of the Universe. (author)

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

Science.gov (United States)

Mushotzky, Richard (Technical Monitor); Markevitch, Maxim

2004-01-01

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

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

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.

Range-clustering queries

NARCIS (Netherlands)

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

2017-01-01

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

Cluster-cluster correlations in the two-dimensional stationary Ising-model

International Nuclear Information System (INIS)

Klassmann, A.

1997-01-01

In numerical integration of the Cahn-Hillard equation, which describes Oswald rising in a two-phase matrix, N. Masbaum showed that spatial correlations between clusters scale with respect to the mean cluster size (itself a function of time). T. B. Liverpool showed by Monte Carlo simulations for the Ising model that the analogous correlations have a similar form. Both demonstrated that immediately around each cluster there is some depletion area followed by something like a ring of clusters of the same size as the original one. More precisely, it has been shown that the distribution of clusters around a given cluster looks like a sinus-curve decaying exponentially with respect to the distance to a constant value

The Argonaute protein TbAGO1 contributes to large and mini-chromosome segregation and is required for control of RIME retroposons and RHS pseudogene-associated transcripts.

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Durand-Dubief, Mickaël; Absalon, Sabrina; Menzer, Linda; Ngwabyt, Sandra; Ersfeld, Klaus; Bastin, Philippe

2007-12-01

The protist Trypanosoma brucei possesses a single Argonaute gene called TbAGO1 that is necessary for RNAi silencing. We previously showed that in strain 427, TbAGO1 knock-out leads to a slow growth phenotype and to chromosome segregation defects. Here we report that the slow growth phenotype is linked to defects in segregation of both large and mini-chromosome populations, with large chromosomes being the most affected. These phenotypes are completely reversed upon inducible re-expression of TbAGO1 fused to GFP, demonstrating their link with TbAGO1. Trypanosomes that do not express TbAGO1 show a general increase in the abundance of transcripts derived from the short retroposon RIME (Ribosomal Interspersed Mobile Element). Supplementary large RIME transcripts emerge in the absence of RNAi, a phenomenon coupled to the disappearance of short transcripts. These fluctuations are reversed by inducible expression of GFP::TbAGO1. Furthermore, we use a combination of Northern blots, RT-PCR and sequencing to reveal that RNAi controls expression of transcripts derived from RHS (Retrotransposon Hot Spot) pseudogenes (RHS genes with retro-element(s) integrated within their coding sequence). Absence of RNAi also leads to an increase of steady-state transcripts from regular RHS genes (those without retro-element), indicating a role for pseudogene in control of gene expression. However, analysis of retroposon abundance and arrangement in the genome of multiple clonal cell lines of TbAGO1-/- failed to reveal movement of mobile elements despite the increased amounts of retroposon transcripts.

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

Energy Technology Data Exchange (ETDEWEB)

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

2017-09-12

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

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

Science.gov (United States)

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

2018-01-01

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

Statistical Issues in Galaxy Cluster Cosmology

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Mantz, Adam

2013-01-01

The number and growth of massive galaxy clusters are sensitive probes of cosmological structure formation. Surveys at various wavelengths can detect clusters to high redshift, but the fact that cluster mass is not directly observable complicates matters, requiring us to simultaneously constrain scaling relations of observable signals with mass. The problem can be cast as one of regression, in which the data set is truncated, the (cosmology-dependent) underlying population must be modeled, and strong, complex correlations between measurements often exist. Simulations of cosmological structure formation provide a robust prediction for the number of clusters in the Universe as a function of mass and redshift (the mass function), but they cannot reliably predict the observables used to detect clusters in sky surveys (e.g. X-ray luminosity). Consequently, observers must constrain observable-mass scaling relations using additional data, and use the scaling relation model in conjunction with the mass function to predict the number of clusters as a function of redshift and luminosity.

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

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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.

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

International Nuclear Information System (INIS)

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

2012-01-01

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

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

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

2017-08-31

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

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Electronic structure and properties of designer clusters and cluster-assemblies

International Nuclear Information System (INIS)

Khanna, S.N.; Jena, P.

1995-01-01

Using self-consistent calculations based on density functional theory, we demonstrate that electronic shell filling and close atomic packing criteria can be used to design ultra-stable clusters. Interaction of these clusters with each other and with gas atoms is found to be weak confirming their chemical inertness. A crystal composed of these inert clusters is expected to have electronic properties that are markedly different from crystals where atoms are the building blocks. The recent observation of ferromagnetism in potassium clusters assembled in zeolite cages is discussed. (orig.)

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

Directory of Open Access Journals (Sweden)

Morris John H

2011-11-01

Full Text Available Abstract Background In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present clusterMaker, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. clusterMaker is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view, k-means, k-medoid, SCPS, AutoSOME, and native (Java MCL. Results Results are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast Saccharomyces cerevisiae; and the cluster analysis of the vicinal oxygen chelate (VOC enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section. Conclusions The Cytoscape plugin cluster

Clustering and visualizing similarity networks of membrane proteins.

Science.gov (United States)

Hu, Geng-Ming; Mai, Te-Lun; Chen, Chi-Ming

2015-08-01

We proposed a fast and unsupervised clustering method, minimum span clustering (MSC), for analyzing the sequence-structure-function relationship of biological networks, and demonstrated its validity in clustering the sequence/structure similarity networks (SSN) of 682 membrane protein (MP) chains. The MSC clustering of MPs based on their sequence information was found to be consistent with their tertiary structures and functions. For the largest seven clusters predicted by MSC, the consistency in chain function within the same cluster is found to be 100%. From analyzing the edge distribution of SSN for MPs, we found a characteristic threshold distance for the boundary between clusters, over which SSN of MPs could be properly clustered by an unsupervised sparsification of the network distance matrix. The clustering results of MPs from both MSC and the unsupervised sparsification methods are consistent with each other, and have high intracluster similarity and low intercluster similarity in sequence, structure, and function. Our study showed a strong sequence-structure-function relationship of MPs. We discussed evidence of convergent evolution of MPs and suggested applications in finding structural similarities and predicting biological functions of MP chains based on their sequence information. © 2015 Wiley Periodicals, Inc.

Cluster management.

Science.gov (United States)

Katz, R

1992-11-01

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

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

Science.gov (United States)

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

2016-03-01

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

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Science.gov (United States)

Chen, Gary K.; Chi, Eric C.; Ranola, John Michael O.; Lange, Kenneth

2015-01-01

The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics.ucla.edu/software/ PMID:25965340

Alpha condensates and nonlocalized cluster structures

International Nuclear Information System (INIS)

Funaki, Yasuro

2014-01-01

We discuss a container structure for non-gaslike cluster states, in which single Tohsaki-Horiuchi-Schuck-ROpke (THSR) wave functions are shown to be almost 100% equivalent to the full solutions of the corresponding RGM/GCM equations, for the inversion doublet band states in 20 Ne, α-linear-chain states, and α + α + A cluster states in 9 Λ Be. The recognition of the fact that the THSR wave function describes well not only gaslike cluster states but also non-gaslike cluster states is a recent remarkable development of nuclear cluster physics. This fact tells us that the cluster structure is composed of cluster-mean-field motion under the constraint of inter-cluster Pauli repulsion, in which we call the cluster-mean-field potential the container. We demonstrate that the evolution of the cluster structure of a nucleus is governed by the size parameter of the cluster-mean-field potential (container), for 16 O nucleus

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

Science.gov (United States)

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

2015-05-17

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

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

International Nuclear Information System (INIS)

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

2011-01-01

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

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

Science.gov (United States)

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

2018-06-01

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

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.

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

Science.gov (United States)

Damianos, Konstantina; Ferrando, Riccardo

2012-02-21

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

Global survey of star clusters in the Milky Way. VI. Age distribution and cluster formation history

Science.gov (United States)

Piskunov, A. E.; Just, A.; Kharchenko, N. V.; Berczik, P.; Scholz, R.-D.; Reffert, S.; Yen, S. X.

2018-06-01

Context. The all-sky Milky Way Star Clusters (MWSC) survey provides uniform and precise ages, along with other relevant parameters, for a wide variety of clusters in the extended solar neighbourhood. Aims: In this study we aim to construct the cluster age distribution, investigate its spatial variations, and discuss constraints on cluster formation scenarios of the Galactic disk during the last 5 Gyrs. Methods: Due to the spatial extent of the MWSC, we have considered spatial variations of the age distribution along galactocentric radius RG, and along Z-axis. For the analysis of the age distribution we used 2242 clusters, which all lie within roughly 2.5 kpc of the Sun. To connect the observed age distribution to the cluster formation history we built an analytical model based on simple assumptions on the cluster initial mass function and on the cluster mass-lifetime relation, fit it to the observations, and determined the parameters of the cluster formation law. Results: Comparison with the literature shows that earlier results strongly underestimated the number of evolved clusters with ages t ≳ 100 Myr. Recent studies based on all-sky catalogues agree better with our data, but still lack the oldest clusters with ages t ≳ 1 Gyr. We do not observe a strong variation in the age distribution along RG, though we find an enhanced fraction of older clusters (t > 1 Gyr) in the inner disk. In contrast, the distribution strongly varies along Z. The high altitude distribution practically does not contain clusters with t < 1 Gyr. With simple assumptions on the cluster formation history, the cluster initial mass function and the cluster lifetime we can reproduce the observations. The cluster formation rate and the cluster lifetime are strongly degenerate, which does not allow us to disentangle different formation scenarios. In all cases the cluster formation rate is strongly declining with time, and the cluster initial mass function is very shallow at the high mass end.

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.

LMC clusters: young

International Nuclear Information System (INIS)

Freeman, K.C.

1980-01-01

The young globular clusters of the LMC have ages of 10 7 -10 8 y. Their masses and structure are similar to those of the smaller galactic globular clusters. Their stellar mass functions (in the mass range 6 solar masses to 1.2 solar masses) vary greatly from cluster to cluster, although the clusters are similar in total mass, age, structure and chemical composition. It would be very interesting to know why these clusters are forming now in the LMC and not in the Galaxy. The author considers the 'young globular' or 'blue populous' clusters of the LMC. The ages of these objects are 10 7 to 10 8 y, and their masses are 10 4 to 10 5 solar masses, so they are populous enough to be really useful for studying the evolution of massive stars. The author concentrates on the structure and stellar content of these young clusters. (Auth.)

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

OpenAIRE

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

2004-01-01

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

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

OpenAIRE

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

2014-01-01

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

Cluster synchronization induced by one-node clusters in networks with asymmetric negative couplings

International Nuclear Information System (INIS)

Zhang, Jianbao; Ma, Zhongjun; Zhang, Gang

2013-01-01

This paper deals with the problem of cluster synchronization in networks with asymmetric negative couplings. By decomposing the coupling matrix into three matrices, and employing Lyapunov function method, sufficient conditions are derived for cluster synchronization. The conditions show that the couplings of multi-node clusters from one-node clusters have beneficial effects on cluster synchronization. Based on the effects of the one-node clusters, an effective and universal control scheme is put forward for the first time. The obtained results may help us better understand the relation between cluster synchronization and cluster structures of the networks. The validity of the control scheme is confirmed through two numerical simulations, in a network with no cluster structure and in a scale-free network

Cluster synchronization induced by one-node clusters in networks with asymmetric negative couplings

Science.gov (United States)

Zhang, Jianbao; Ma, Zhongjun; Zhang, Gang

2013-12-01

This paper deals with the problem of cluster synchronization in networks with asymmetric negative couplings. By decomposing the coupling matrix into three matrices, and employing Lyapunov function method, sufficient conditions are derived for cluster synchronization. The conditions show that the couplings of multi-node clusters from one-node clusters have beneficial effects on cluster synchronization. Based on the effects of the one-node clusters, an effective and universal control scheme is put forward for the first time. The obtained results may help us better understand the relation between cluster synchronization and cluster structures of the networks. The validity of the control scheme is confirmed through two numerical simulations, in a network with no cluster structure and in a scale-free network.

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

Science.gov (United States)

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

2011-01-01

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

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

Science.gov (United States)

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

2014-04-01

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

[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.

Species specificity in major urinary proteins by parallel evolution.

Directory of Open Access Journals (Sweden)

Darren W Logan

Full Text Available Species-specific chemosignals, pheromones, regulate social behaviors such as aggression, mating, pup-suckling, territory establishment, and dominance. The identity of these cues remains mostly undetermined and few mammalian pheromones have been identified. Genetically-encoded pheromones are expected to exhibit several different mechanisms for coding 1 diversity, to enable the signaling of multiple behaviors, 2 dynamic regulation, to indicate age and dominance, and 3 species-specificity. Recently, the major urinary proteins (Mups have been shown to function themselves as genetically-encoded pheromones to regulate species-specific behavior. Mups are multiple highly related proteins expressed in combinatorial patterns that differ between individuals, gender, and age; which are sufficient to fulfill the first two criteria. We have now characterized and fully annotated the mouse Mup gene content in detail. This has enabled us to further analyze the extent of Mup coding diversity and determine their potential to encode species-specific cues.Our results show that the mouse Mup gene cluster is composed of two subgroups: an older, more divergent class of genes and pseudogenes, and a second class with high sequence identity formed by recent sequential duplications of a single gene/pseudogene pair. Previous work suggests that truncated Mup pseudogenes may encode a family of functional hexapeptides with the potential for pheromone activity. Sequence comparison, however, reveals that they have limited coding potential. Similar analyses of nine other completed genomes find Mup gene expansions in divergent lineages, including those of rat, horse and grey mouse lemur, occurring independently from a single ancestral Mup present in other placental mammals. Our findings illustrate that increasing genomic complexity of the Mup gene family is not evolutionarily isolated, but is instead a recurring mechanism of generating coding diversity consistent with a species

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

Science.gov (United States)

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

2017-10-12

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

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)

Structure and physical properties of silicon clusters and of vacancy clusters in bulk silicon

International Nuclear Information System (INIS)

Sieck, A.

2000-01-01

In this thesis the growth-pattern of free silicon clusters and vacancy clusters in bulk silicon is investigated. The aim is to describe and to better understand the cluster to bulk transition. Silicon structures in between clusters and solids feature new interesting physical properties. The structure and physical properties of silicon clusters can be revealed by a combination of theory and experiment, only. Low-energy clusters are determined with different optimization techniques and a density-functional based tight-binding method. Additionally, infrared and Raman spectra, and polarizabilities calculated within self-consistent field density-functional theory are provided for the smaller clusters. For clusters with 25 to 35 atoms an analysis of the shape of the clusters and the related mobilities in a buffer gas is given. Finally, the clusters observed in low-temperature experiments are identified via the best match between calculated properties and experimental data. Silicon clusters with 10 to 15 atoms have a tricapped trigonal prism as a common subunit. Clusters with up to about 25 atoms follow a prolate growth-path. In the range from 24 to 30 atoms the geometry of the clusters undergoes a transition towards compact spherical structures. Low-energy clusters with up to 240 atoms feature a bonding pattern strikingly different from the tetrahedral bonding in the solid. It follows that structures with dimensions of several Angstroem have electrical and optical properties different from the solid. The calculated stabilities and positron-lifetimes of vacancy clusters in bulk silicon indicate the positron-lifetimes of about 435 ps detected in irradiated silicon to be related to clusters of 9 or 10 vacancies. The vacancies in these clusters form neighboring hexa-rings and, therefore, minimize the number of dangling bonds. (orig.)

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

Science.gov (United States)

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

2016-01-01

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

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

DEFF Research Database (Denmark)

Mikosch, Thomas Valentin; Wintenberger, Olivier

2014-01-01

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

Synergy between pair coupled cluster doubles and pair density functional theory

Energy Technology Data Exchange (ETDEWEB)

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

2015-01-28

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

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...

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

Science.gov (United States)

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

2014-01-01

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

Functional clustering in hippocampal cultures: relating network structure and dynamics

International Nuclear Information System (INIS)

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

2010-01-01

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

Simulating star clusters with the AMUSE software framework. I. Dependence of cluster lifetimes on model assumptions and cluster dissolution modes

International Nuclear Information System (INIS)

Whitehead, Alfred J.; McMillan, Stephen L. W.; Vesperini, Enrico; Portegies Zwart, Simon

2013-01-01

We perform a series of simulations of evolving star clusters using the Astrophysical Multipurpose Software Environment (AMUSE), a new community-based multi-physics simulation package, and compare our results to existing work. These simulations model a star cluster beginning with a King model distribution and a selection of power-law initial mass functions and contain a tidal cutoff. They are evolved using collisional stellar dynamics and include mass loss due to stellar evolution. After studying and understanding that the differences between AMUSE results and results from previous studies are understood, we explored the variation in cluster lifetimes due to the random realization noise introduced by transforming a King model to specific initial conditions. This random realization noise can affect the lifetime of a simulated star cluster by up to 30%. Two modes of star cluster dissolution were identified: a mass evolution curve that contains a runaway cluster dissolution with a sudden loss of mass, and a dissolution mode that does not contain this feature. We refer to these dissolution modes as 'dynamical' and 'relaxation' dominated, respectively. For Salpeter-like initial mass functions, we determined the boundary between these two modes in terms of the dynamical and relaxation timescales.

Cluster structure of 20Ne and 40Ca

International Nuclear Information System (INIS)

Taniguchi, Yasutaka

2004-01-01

A d-constraint for calculating the wave functions of various kinds of configurations of cluster structure and optimizing the inside wave functions of the cluster was developed. The wave functions of various kinds of cluster structures were calculated by constraining and energy variation of the antisymmetrized molecular dynamics wave functions. The cluster structure of nucleus was reproduced by linear combination of the above wave functions by the generator coordinate method. By superposition of both wave functions calculated using d-constraint and β-constraint, K π =O 3 + rotation band of 20 Ne was reproduced. The excitation energies of 20 Ne were calculated. The result of calculation energies of α- 36 Ar structure of 40 Ca are higher values than expected them. Framework, AMD wave function, constraint, calculation results and discussions are stated. (S.Y.)

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

Directory of Open Access Journals (Sweden)

Zuopeng Wu

2016-05-01

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

Color Gradients Within Globular Clusters: Restricted Numerical Simulation

Directory of Open Access Journals (Sweden)

Young-Jong Sohn

1997-06-01

Full Text Available The results of a restricted numerical simulation for the color gradients within globular clusters have been presented. The standard luminosity function of M3 and Salpeter's initial mass functions were used to generate model clusters as a fundamental population. Color gradients with the sample clusters for both King and power law cusp models of surface brightness distributions are discussed in the case of using the standard luminosity function. The dependence of color gradients on several parameters for the simulations with Salpeter's initial mass functions, such as slope of initial mass functions, cluster ages, metallicities, concentration parameters of King model, and slopes of power law, are also discussed. No significant radial color gradients are shown to the sample clusters which are regenerated by a random number generation technique with various parameters in both of King and power law cusp models of surface brightness distributions. Dynamical mass segregation and stellar evolution of horizontal branch stars and blue stragglers should be included for the general case of model simulations to show the observed radial color gradients within globular clusters.

Cluster growth kinetics

International Nuclear Information System (INIS)

Dubovik, V.M.; Gal'perin, A.G.; Rikhvitskij, V.S.; Lushnikov, A.A.

2000-01-01

Processes of some traffic blocking coming into existence are considered as probabilistic ones. We study analytic solutions for models for the dynamics of both cluster growth and cluster growth with fragmentation in the systems of finite number of objects. Assuming rates constancy of both coalescence and fragmentation, the models under consideration are linear on the probability functions

Monoxides of small terbium clusters: A density functional theory investigation

Energy Technology Data Exchange (ETDEWEB)

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

2014-12-28

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

COSMOLOGICAL CONSTRAINTS FROM GALAXY CLUSTERING AND THE MASS-TO-NUMBER RATIO OF GALAXY CLUSTERS

International Nuclear Information System (INIS)

Tinker, Jeremy L.; Blanton, Michael R.; Sheldon, Erin S.; Wechsler, Risa H.; Becker, Matthew R.; Rozo, Eduardo; Zu, Ying; Weinberg, David H.; Zehavi, Idit; Busha, Michael T.; Koester, Benjamin P.

2012-01-01

We place constraints on the average density (Ω m ) and clustering amplitude (σ 8 ) of matter using a combination of two measurements from the Sloan Digital Sky Survey: the galaxy two-point correlation function, w p (r p ), and the mass-to-galaxy-number ratio within galaxy clusters, M/N, analogous to cluster M/L ratios. Our w p (r p ) measurements are obtained from DR7 while the sample of clusters is the maxBCG sample, with cluster masses derived from weak gravitational lensing. We construct nonlinear galaxy bias models using the Halo Occupation Distribution (HOD) to fit both w p (r p ) and M/N for different cosmological parameters. HOD models that match the same two-point clustering predict different numbers of galaxies in massive halos when Ω m or σ 8 is varied, thereby breaking the degeneracy between cosmology and bias. We demonstrate that this technique yields constraints that are consistent and competitive with current results from cluster abundance studies, without the use of abundance information. Using w p (r p ) and M/N alone, we find Ω 0.5 m σ 8 = 0.465 ± 0.026, with individual constraints of Ω m = 0.29 ± 0.03 and σ 8 = 0.85 ± 0.06. Combined with current cosmic microwave background data, these constraints are Ω m = 0.290 ± 0.016 and σ 8 = 0.826 ± 0.020. All errors are 1σ. The systematic uncertainties that the M/N technique are most sensitive to are the amplitude of the bias function of dark matter halos and the possibility of redshift evolution between the SDSS Main sample and the maxBCG cluster sample. Our derived constraints are insensitive to the current level of uncertainties in the halo mass function and in the mass-richness relation of clusters and its scatter, making the M/N technique complementary to cluster abundances as a method for constraining cosmology with future galaxy surveys.

COSMOLOGICAL CONSTRAINTS FROM GALAXY CLUSTERING AND THE MASS-TO-NUMBER RATIO OF GALAXY CLUSTERS

Energy Technology Data Exchange (ETDEWEB)

Tinker, Jeremy L.; Blanton, Michael R. [Center for Cosmology and Particle Physics, Department of Physics, New York University, New York, NY 10013 (United States); Sheldon, Erin S. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Wechsler, Risa H. [Kavli Institute for Particle Astrophysics and Cosmology, Physics Department, and SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305 (United States); Becker, Matthew R.; Rozo, Eduardo [Kavli Institute for Cosmological Physics, University of Chicago, Chicago, IL 60637 (United States); Zu, Ying; Weinberg, David H. [Department of Astronomy, Ohio State University, Columbus, OH 43210 (United States); Zehavi, Idit [Department of Astronomy and CERCA, Case Western Reserve University, Cleveland, OH 44106 (United States); Busha, Michael T. [Institute for Theoretical Physics, Department of Physics, University of Zurich, CH-8057 Zurich (Switzerland); Koester, Benjamin P. [Department of Astronomy and Astrophysics, University of Chicago, Chicago, IL 6037 (United States)

2012-01-20

We place constraints on the average density ({Omega}{sub m}) and clustering amplitude ({sigma}{sub 8}) of matter using a combination of two measurements from the Sloan Digital Sky Survey: the galaxy two-point correlation function, w{sub p} (r{sub p} ), and the mass-to-galaxy-number ratio within galaxy clusters, M/N, analogous to cluster M/L ratios. Our w{sub p} (r{sub p} ) measurements are obtained from DR7 while the sample of clusters is the maxBCG sample, with cluster masses derived from weak gravitational lensing. We construct nonlinear galaxy bias models using the Halo Occupation Distribution (HOD) to fit both w{sub p} (r{sub p} ) and M/N for different cosmological parameters. HOD models that match the same two-point clustering predict different numbers of galaxies in massive halos when {Omega}{sub m} or {sigma}{sub 8} is varied, thereby breaking the degeneracy between cosmology and bias. We demonstrate that this technique yields constraints that are consistent and competitive with current results from cluster abundance studies, without the use of abundance information. Using w{sub p} (r{sub p} ) and M/N alone, we find {Omega}{sup 0.5}{sub m}{sigma}{sub 8} = 0.465 {+-} 0.026, with individual constraints of {Omega}{sub m} = 0.29 {+-} 0.03 and {sigma}{sub 8} = 0.85 {+-} 0.06. Combined with current cosmic microwave background data, these constraints are {Omega}{sub m} = 0.290 {+-} 0.016 and {sigma}{sub 8} = 0.826 {+-} 0.020. All errors are 1{sigma}. The systematic uncertainties that the M/N technique are most sensitive to are the amplitude of the bias function of dark matter halos and the possibility of redshift evolution between the SDSS Main sample and the maxBCG cluster sample. Our derived constraints are insensitive to the current level of uncertainties in the halo mass function and in the mass-richness relation of clusters and its scatter, making the M/N technique complementary to cluster abundances as a method for constraining cosmology with future galaxy

Clustering Coefficients for Correlation Networks

Directory of Open Access Journals (Sweden)

Naoki Masuda

2018-03-01

Full Text Available Graph theory is a useful tool for deciphering structural and functional networks of the brain on various spatial and temporal scales. The clustering coefficient quantifies the abundance of connected triangles in a network and is a major descriptive statistics of networks. For example, it finds an application in the assessment of small-worldness of brain networks, which is affected by attentional and cognitive conditions, age, psychiatric disorders and so forth. However, it remains unclear how the clustering coefficient should be measured in a correlation-based network, which is among major representations of brain networks. In the present article, we propose clustering coefficients tailored to correlation matrices. The key idea is to use three-way partial correlation or partial mutual information to measure the strength of the association between the two neighboring nodes of a focal node relative to the amount of pseudo-correlation expected from indirect paths between the nodes. Our method avoids the difficulties of previous applications of clustering coefficient (and other measures in defining correlational networks, i.e., thresholding on the correlation value, discarding of negative correlation values, the pseudo-correlation problem and full partial correlation matrices whose estimation is computationally difficult. For proof of concept, we apply the proposed clustering coefficient measures to functional magnetic resonance imaging data obtained from healthy participants of various ages and compare them with conventional clustering coefficients. We show that the clustering coefficients decline with the age. The proposed clustering coefficients are more strongly correlated with age than the conventional ones are. We also show that the local variants of the proposed clustering coefficients (i.e., abundance of triangles around a focal node are useful in characterizing individual nodes. In contrast, the conventional local clustering coefficients

Clustering Coefficients for Correlation Networks.

Science.gov (United States)

Masuda, Naoki; Sakaki, Michiko; Ezaki, Takahiro; Watanabe, Takamitsu

2018-01-01

Graph theory is a useful tool for deciphering structural and functional networks of the brain on various spatial and temporal scales. The clustering coefficient quantifies the abundance of connected triangles in a network and is a major descriptive statistics of networks. For example, it finds an application in the assessment of small-worldness of brain networks, which is affected by attentional and cognitive conditions, age, psychiatric disorders and so forth. However, it remains unclear how the clustering coefficient should be measured in a correlation-based network, which is among major representations of brain networks. In the present article, we propose clustering coefficients tailored to correlation matrices. The key idea is to use three-way partial correlation or partial mutual information to measure the strength of the association between the two neighboring nodes of a focal node relative to the amount of pseudo-correlation expected from indirect paths between the nodes. Our method avoids the difficulties of previous applications of clustering coefficient (and other) measures in defining correlational networks, i.e., thresholding on the correlation value, discarding of negative correlation values, the pseudo-correlation problem and full partial correlation matrices whose estimation is computationally difficult. For proof of concept, we apply the proposed clustering coefficient measures to functional magnetic resonance imaging data obtained from healthy participants of various ages and compare them with conventional clustering coefficients. We show that the clustering coefficients decline with the age. The proposed clustering coefficients are more strongly correlated with age than the conventional ones are. We also show that the local variants of the proposed clustering coefficients (i.e., abundance of triangles around a focal node) are useful in characterizing individual nodes. In contrast, the conventional local clustering coefficients were strongly

Clustering Coefficients for Correlation Networks

Science.gov (United States)

Masuda, Naoki; Sakaki, Michiko; Ezaki, Takahiro; Watanabe, Takamitsu

2018-01-01

Graph theory is a useful tool for deciphering structural and functional networks of the brain on various spatial and temporal scales. The clustering coefficient quantifies the abundance of connected triangles in a network and is a major descriptive statistics of networks. For example, it finds an application in the assessment of small-worldness of brain networks, which is affected by attentional and cognitive conditions, age, psychiatric disorders and so forth. However, it remains unclear how the clustering coefficient should be measured in a correlation-based network, which is among major representations of brain networks. In the present article, we propose clustering coefficients tailored to correlation matrices. The key idea is to use three-way partial correlation or partial mutual information to measure the strength of the association between the two neighboring nodes of a focal node relative to the amount of pseudo-correlation expected from indirect paths between the nodes. Our method avoids the difficulties of previous applications of clustering coefficient (and other) measures in defining correlational networks, i.e., thresholding on the correlation value, discarding of negative correlation values, the pseudo-correlation problem and full partial correlation matrices whose estimation is computationally difficult. For proof of concept, we apply the proposed clustering coefficient measures to functional magnetic resonance imaging data obtained from healthy participants of various ages and compare them with conventional clustering coefficients. We show that the clustering coefficients decline with the age. The proposed clustering coefficients are more strongly correlated with age than the conventional ones are. We also show that the local variants of the proposed clustering coefficients (i.e., abundance of triangles around a focal node) are useful in characterizing individual nodes. In contrast, the conventional local clustering coefficients were strongly

Cluster algebras in mathematical physics

International Nuclear Information System (INIS)

Francesco, Philippe Di; Gekhtman, Michael; Kuniba, Atsuo; Yamazaki, Masahito

2014-01-01

This special issue of Journal of Physics A: Mathematical and Theoretical contains reviews and original research articles on cluster algebras and their applications to mathematical physics. Cluster algebras were introduced by S Fomin and A Zelevinsky around 2000 as a tool for studying total positivity and dual canonical bases in Lie theory. Since then the theory has found diverse applications in mathematics and mathematical physics. Cluster algebras are axiomatically defined commutative rings equipped with a distinguished set of generators (cluster variables) subdivided into overlapping subsets (clusters) of the same cardinality subject to certain polynomial relations. A cluster algebra of rank n can be viewed as a subring of the field of rational functions in n variables. Rather than being presented, at the outset, by a complete set of generators and relations, it is constructed from the initial seed via an iterative procedure called mutation producing new seeds successively to generate the whole algebra. A seed consists of an n-tuple of rational functions called cluster variables and an exchange matrix controlling the mutation. Relations of cluster algebra type can be observed in many areas of mathematics (Plücker and Ptolemy relations, Stokes curves and wall-crossing phenomena, Feynman integrals, Somos sequences and Hirota equations to name just a few examples). The cluster variables enjoy a remarkable combinatorial pattern; in particular, they exhibit the Laurent phenomenon: they are expressed as Laurent polynomials rather than more general rational functions in terms of the cluster variables in any seed. These characteristic features are often referred to as the cluster algebra structure. In the last decade, it became apparent that cluster structures are ubiquitous in mathematical physics. Examples include supersymmetric gauge theories, Poisson geometry, integrable systems, statistical mechanics, fusion products in infinite dimensional algebras, dilogarithm

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

Science.gov (United States)

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

2018-06-01

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

Reproducibility of Cognitive Profiles in Psychosis Using Cluster Analysis.

Science.gov (United States)

Lewandowski, Kathryn E; Baker, Justin T; McCarthy, Julie M; Norris, Lesley A; Öngür, Dost

2018-04-01

Cognitive dysfunction is a core symptom dimension that cuts across the psychoses. Recent findings support classification of patients along the cognitive dimension using cluster analysis; however, data-derived groupings may be highly determined by sampling characteristics and the measures used to derive the clusters, and so their interpretability must be established. We examined cognitive clusters in a cross-diagnostic sample of patients with psychosis and associations with clinical and functional outcomes. We then compared our findings to a previous report of cognitive clusters in a separate sample using a different cognitive battery. Participants with affective or non-affective psychosis (n=120) and healthy controls (n=31) were administered the MATRICS Consensus Cognitive Battery, and clinical and community functioning assessments. Cluster analyses were performed on cognitive variables, and clusters were compared on demographic, cognitive, and clinical measures. Results were compared to findings from our previous report. A four-cluster solution provided a good fit to the data; profiles included a neuropsychologically normal cluster, a globally impaired cluster, and two clusters of mixed profiles. Cognitive burden was associated with symptom severity and poorer community functioning. The patterns of cognitive performance by cluster were highly consistent with our previous findings. We found evidence of four cognitive subgroups of patients with psychosis, with cognitive profiles that map closely to those produced in our previous work. Clusters were associated with clinical and community variables and a measure of premorbid functioning, suggesting that they reflect meaningful groupings: replicable, and related to clinical presentation and functional outcomes. (JINS, 2018, 24, 382-390).

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

Science.gov (United States)

Hu, Zhongwei; Autschbach, Jochen; Jensen, Lasse

2014-09-28

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

Description of an α-cluster tail in 8Be and 20Ne: Delocalization of the α cluster by quantum penetration

Science.gov (United States)

Kanada-En'yo, Yoshiko

2014-10-01

We analyze the α-cluster wave functions in cluster states of ^8Be and ^{20}Ne by comparing the exact relative wave function obtained by the generator coordinate method (GCM) with various types of trial functions. For the trial functions, we adopt the fixed range shifted Gaussian of the Brink-Bloch (BB) wave function, the spherical Gaussian with the adjustable range parameter of the spherical Tohsaki-Horiuchi-Schuck-Röpke (sTHSR), the deformed Gaussian of the deformed THSR (dTHSR), and a function with the Yukawa tail (YT). The quality of the description of the exact wave function with a trial function is judged by the squared overlap between the trial function and the GCM wave function. A better result is obtained with the sTHSR wave function than the BB wave function, and further improvement can be made with the dTHSR wave function because these wave functions can describe the outer tail better. The YT wave function gives almost an equal quality to or even better quality than the dTHSR wave function, indicating that the outer tail of α-cluster states is characterized by the Yukawa-like tail rather than the Gaussian tail. In weakly bound α-cluster states with small α separation energy and the low centrifugal and Coulomb barriers, the outer tail part is the slowly damping function described well by the quantum penetration through the effective barrier. This outer tail characterizes the almost zero-energy free α gas behavior, i.e., the delocalization of the cluster.

Quantum annealing for combinatorial clustering

Science.gov (United States)

Kumar, Vaibhaw; Bass, Gideon; Tomlin, Casey; Dulny, Joseph

2018-02-01

Clustering is a powerful machine learning technique that groups "similar" data points based on their characteristics. Many clustering algorithms work by approximating the minimization of an objective function, namely the sum of within-the-cluster distances between points. The straightforward approach involves examining all the possible assignments of points to each of the clusters. This approach guarantees the solution will be a global minimum; however, the number of possible assignments scales quickly with the number of data points and becomes computationally intractable even for very small datasets. In order to circumvent this issue, cost function minima are found using popular local search-based heuristic approaches such as k-means and hierarchical clustering. Due to their greedy nature, such techniques do not guarantee that a global minimum will be found and can lead to sub-optimal clustering assignments. Other classes of global search-based techniques, such as simulated annealing, tabu search, and genetic algorithms, may offer better quality results but can be too time-consuming to implement. In this work, we describe how quantum annealing can be used to carry out clustering. We map the clustering objective to a quadratic binary optimization problem and discuss two clustering algorithms which are then implemented on commercially available quantum annealing hardware, as well as on a purely classical solver "qbsolv." The first algorithm assigns N data points to K clusters, and the second one can be used to perform binary clustering in a hierarchical manner. We present our results in the form of benchmarks against well-known k-means clustering and discuss the advantages and disadvantages of the proposed techniques.

Functional Annotation, Genome Organization and Phylogeny of the Grapevine (Vitis vinifera Terpene Synthase Gene Family Based on Genome Assembly, FLcDNA Cloning, and Enzyme Assays

Directory of Open Access Journals (Sweden)

Toub Omid

2010-10-01

Full Text Available Abstract Background Terpenoids are among the most important constituents of grape flavour and wine bouquet, and serve as useful metabolite markers in viticulture and enology. Based on the initial 8-fold sequencing of a nearly homozygous Pinot noir inbred line, 89 putative terpenoid synthase genes (VvTPS were predicted by in silico analysis of the grapevine (Vitis vinifera genome assembly 1. The finding of this very large VvTPS family, combined with the importance of terpenoid metabolism for the organoleptic properties of grapevine berries and finished wines, prompted a detailed examination of this gene family at the genomic level as well as an investigation into VvTPS biochemical functions. Results We present findings from the analysis of the up-dated 12-fold sequencing and assembly of the grapevine genome that place the number of predicted VvTPS genes at 69 putatively functional VvTPS, 20 partial VvTPS, and 63 VvTPS probable pseudogenes. Gene discovery and annotation included information about gene architecture and chromosomal location. A dense cluster of 45 VvTPS is localized on chromosome 18. Extensive FLcDNA cloning, gene synthesis, and protein expression enabled functional characterization of 39 VvTPS; this is the largest number of functionally characterized TPS for any species reported to date. Of these enzymes, 23 have unique functions and/or phylogenetic locations within the plant TPS gene family. Phylogenetic analyses of the TPS gene family showed that while most VvTPS form species-specific gene clusters, there are several examples of gene orthology with TPS of other plant species, representing perhaps more ancient VvTPS, which have maintained functions independent of speciation. Conclusions The highly expanded VvTPS gene family underpins the prominence of terpenoid metabolism in grapevine. We provide a detailed experimental functional annotation of 39 members of this important gene family in grapevine and comprehensive information

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

CERN Document Server

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

2014-01-01

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

MD simulation of cluster formation during sputtering

International Nuclear Information System (INIS)

Muramoto, T.; Okai, M.; Yamashita, Y.; Yorizane, K.; Yamamura, Y.

2001-01-01

The cluster ejection due to cluster impact on a solid surface is studied through molecular dynamics (MD) simulations. Simulations are performed for Cu cluster impacts on the Cu(1 1 1) surface for cluster energy 100 eV/atom, and for clusters of 6, 13, 28 and 55 atoms. Interatomic interactions are described by the AMLJ-EAM potential. The vibration energy spectrum is independent of the incident cluster size and energy. This comes from the fact that sputtered clusters become stable through the successive fragmentation of nascent large sputtered clusters. The vibration energy spectra for large sputtered clusters have a peak, whose energy corresponds to the melting temperature of Cu. The exponent of the power-law fit of the abundance distribution and the total sputtering yield for the cluster impacts are higher than that for the monatomic ion impacts with the same total energy, where the exponent δ is given by Y n ∝n δ and Y n is the yield of sputtered n-atom cluster. The exponent δ follows a unified function of the total sputtering yield, which is a monotonic increase function, and it is nearly equal to δ ∼ -3 for larger yield

clusters

Indian Academy of Sciences (India)

2017-09-27

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

The cylindrical K-function and Poisson line cluster point processes

DEFF Research Database (Denmark)

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

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

Quantification of the clustering properties of nuclear states

International Nuclear Information System (INIS)

Beck, R.; Dickmann, F.

1985-05-01

The amount of particular type of clustering in a nuclear state is defined in this paper as the norm square of the projection of the wave function onto the particular cluster model subspace. It is pointed out that, although the clusters can not be localized in space by measurement, the amount of clustering characterizes the cluster formation in close analogy with a quantum mechanical probability. The cluster model component of the wave function is proved to have a variational property. This facilitates the computation of the amount of clustering. The model dependence of the amounts of various clusterings and their relationship to the corresponding spectroscopic factors are studied via numerical examples for two models of sup(6)Li. It is concluded that, in a relative sense, the spectroscopic factor, which is more directly related to experiment, is also characteristic of the clustering contents of different states of the same nucleus, but it can not be used for comparisons between different nuclei or clusterings. (author)

Structure and bonding in clusters

International Nuclear Information System (INIS)

Kumar, V.

1991-10-01

We review here the recent progress made in the understanding of the electronic and atomic structure of small clusters of s-p bonded materials using the density functional molecular dynamics technique within the local density approximation. Starting with a brief description of the method, results are presented for alkali metal clusters, clusters of divalent metals such as Mg and Be which show a transition from van der Waals or weak chemical bonding to metallic behaviour as the cluster size grows and clusters of Al, Sn and Sb. In the case of semiconductors, we discuss results for Si, Ge and GaAs clusters. Clusters of other materials such as P, C, S, and Se are also briefly discussed. From these and other available results we suggest the possibility of unique structures for the magic clusters. (author). 69 refs, 7 figs, 1 tab

Are pelvic adhesions associated with pain, physical, emotional and functional characteristics of women presenting with chronic pelvic pain? A cluster analysis.

Science.gov (United States)

Cheong, Ying; Saran, Mili; Hounslow, James William; Reading, Isabel Claire

2018-01-08

Chronic pelvic pain is a debilitating condition. It is unknown if there is a clinical phenotype for adhesive disorders. This study aimed to determine if the presence or absence, nature, severity and extent of adhesions correlated with demographic and patient reported clinical characteristics of women presenting with CPP. Women undergoing a laparoscopy for the investigation of chronic pelvic pain were recruited prospectively; their pain and phenotypic characteristics were entered into a hierarchical cluster analysis. The groups with differing baseline clinical and operative characteristics in terms of adhesions involvement were analyzed. Sixty two women were recruited where 37 had adhesions. A low correlation was found between women's reported current pain scores and that of most severe (r = 0.34) or average pain experienced (r = 0.44) in the last 6 months. Three main groups of women with CPP were identified: Cluster 1 (n = 35) had moderate severity of pain, with poor average and present pain intensity; Cluster 2 (n = 14) had a long duration of symptoms/diagnosis, the worst current pain and worst physical, emotional and social functions; Cluster 3 (n = 11) had the shortest duration of pain and showed the best evidence of coping with low (good) physical, social and emotional scores. This cluster also had the highest proportion of women with adhesions (82%) compared to 51% in Cluster 1 and 71% in Cluster 2. In this study, we found that there is little or no correlation between patient-reported pain, physical, emotional and functional characteristics scores with the presence or absence of intra-abdominal/pelvic adhesions found during investigative laparoscopy. Most women who had adhesions had the lowest reported current pain scores.

Thermodynamically accessible titanium clusters TiN, N = 2-32.

Science.gov (United States)

Lazauskas, Tomas; Sokol, Alexey A; Buckeridge, John; Catlow, C Richard A; Escher, Susanne G E T; Farrow, Matthew R; Mora-Fonz, David; Blum, Volker W; Phaahla, Tshegofatso M; Chauke, Hasani R; Ngoepe, Phuti E; Woodley, Scott M

2018-05-10

We have performed a genetic algorithm search on the tight-binding interatomic potential energy surface (PES) for small TiN (N = 2-32) clusters. The low energy candidate clusters were further refined using density functional theory (DFT) calculations with the PBEsol exchange-correlation functional and evaluated with the PBEsol0 hybrid functional. The resulting clusters were analysed in terms of their structural features, growth mechanism and surface area. The results suggest a growth mechanism that is based on forming coordination centres by interpenetrating icosahedra, icositetrahedra and Frank-Kasper polyhedra. We identify centres of coordination, which act as centres of bulk nucleation in medium sized clusters and determine the morphological features of the cluster.

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

Science.gov (United States)

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

2016-01-04

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

Cosmology with EMSS Clusters of Galaxies

Science.gov (United States)

Donahue, Megan; Voit, G. Mark

1999-01-01

We use ASCA observations of the Extended Medium Sensitivity Survey sample of clusters of galaxies to construct the first z = 0.5 - 0.8 cluster temperature function. This distant cluster temperature function, when compared to local z approximately 0 and to a similar moderate redshift (z = 0.3 - 0.4) temperature function strongly constrains the matter density of the universe. Best fits to the distributions of temperatures and redshifts of these cluster samples results in Omega(sub M) = 0.45 +/- 0.1 if Lambda = 0 and Omega = 0.27 +/- 0.1 if Lambda + Omega(sub M) = 1. The uncertainties are 1sigma statistical. We examine the systematics of our approach and find that systematics, stemming mainly from model assumptions and not measurement errors, are about the same size as the statistical uncertainty +/- 0.1. In this poster proceedings, we clarify the issue of a8 as reported in our paper Donahue & Voit (1999), since this was a matter of discussion at the meeting.

Ages of young star clusters, massive blue stragglers, and the upper mass limit of stars: Analyzing age-dependent stellar mass functions

Energy Technology Data Exchange (ETDEWEB)

Schneider, F. R. N.; Izzard, R. G.; Langer, N.; Stolte, A.; Hußmann, B. [Argelander-Institut für Astronomie der Universität Bonn, Auf dem Hügel 71, D-53121 Bonn (Germany); De Mink, S. E. [Observatories of the Carnegie Institution for Science, 813 Santa Barbara St, Pasadena, CA 91101 (United States); De Koter, A.; Sana, H. [Astronomical Institute " Anton Pannekoek" , Amsterdam University, Science Park 904, 1098 XH, Amsterdam (Netherlands); Gvaramadze, V. V. [Sternberg Astronomical Institute, Lomonosov Moscow State University, Universitetskij Pr. 13, Moscow 119992 (Russian Federation); Liermann, A., E-mail: fschneid@astro.uni-bonn.de [Max Planck Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany)

2014-01-10

Massive stars rapidly change their masses through strong stellar winds and mass transfer in binary systems. The latter aspect is important for populations of massive stars as more than 70% of all O stars are expected to interact with a binary companion during their lifetime. We show that such mass changes leave characteristic signatures in stellar mass functions of young star clusters that can be used to infer their ages and to identify products of binary evolution. We model the observed present-day mass functions of the young Galactic Arches and Quintuplet star clusters using our rapid binary evolution code. We find that the shaping of the mass function by stellar wind mass loss allows us to determine the cluster ages as 3.5 ± 0.7 Myr and 4.8 ± 1.1 Myr, respectively. Exploiting the effects of binary mass exchange on the cluster mass function, we find that the most massive stars in both clusters are rejuvenated products of binary mass transfer, i.e., the massive counterpart of classical blue straggler stars. This resolves the problem of an apparent age spread among the most luminous stars exceeding the expected duration of star formation in these clusters. We perform Monte Carlo simulations to probe stochastic sampling, which support the idea of the most massive stars being rejuvenated binary products. We find that the most massive star is expected to be a binary product after 1.0 ± 0.7 Myr in Arches and after 1.7 ± 1.0 Myr in Quintuplet. Today, the most massive 9 ± 3 stars in Arches and 8 ± 3 in Quintuplet are expected to be such objects. Our findings have strong implications for the stellar upper mass limit and solve the discrepancy between the claimed 150 M {sub ☉} limit and observations of four stars with initial masses of 165-320 M {sub ☉} in R136 and of supernova 2007bi, which is thought to be a pair-instability supernova from an initial 250 M {sub ☉} star. Using the stellar population of R136, we revise the upper mass limit to values in the range

Ages of young star clusters, massive blue stragglers, and the upper mass limit of stars: Analyzing age-dependent stellar mass functions

International Nuclear Information System (INIS)

Schneider, F. R. N.; Izzard, R. G.; Langer, N.; Stolte, A.; Hußmann, B.; De Mink, S. E.; Anton Pannekoek, Amsterdam University, Science Park 904, 1098 XH, Amsterdam (Netherlands))" data-affiliation=" (Astronomical Institute Anton Pannekoek, Amsterdam University, Science Park 904, 1098 XH, Amsterdam (Netherlands))" >De Koter, A.; Anton Pannekoek, Amsterdam University, Science Park 904, 1098 XH, Amsterdam (Netherlands))" data-affiliation=" (Astronomical Institute Anton Pannekoek, Amsterdam University, Science Park 904, 1098 XH, Amsterdam (Netherlands))" >Sana, H.; Gvaramadze, V. V.; Liermann, A.

2014-01-01

Massive stars rapidly change their masses through strong stellar winds and mass transfer in binary systems. The latter aspect is important for populations of massive stars as more than 70% of all O stars are expected to interact with a binary companion during their lifetime. We show that such mass changes leave characteristic signatures in stellar mass functions of young star clusters that can be used to infer their ages and to identify products of binary evolution. We model the observed present-day mass functions of the young Galactic Arches and Quintuplet star clusters using our rapid binary evolution code. We find that the shaping of the mass function by stellar wind mass loss allows us to determine the cluster ages as 3.5 ± 0.7 Myr and 4.8 ± 1.1 Myr, respectively. Exploiting the effects of binary mass exchange on the cluster mass function, we find that the most massive stars in both clusters are rejuvenated products of binary mass transfer, i.e., the massive counterpart of classical blue straggler stars. This resolves the problem of an apparent age spread among the most luminous stars exceeding the expected duration of star formation in these clusters. We perform Monte Carlo simulations to probe stochastic sampling, which support the idea of the most massive stars being rejuvenated binary products. We find that the most massive star is expected to be a binary product after 1.0 ± 0.7 Myr in Arches and after 1.7 ± 1.0 Myr in Quintuplet. Today, the most massive 9 ± 3 stars in Arches and 8 ± 3 in Quintuplet are expected to be such objects. Our findings have strong implications for the stellar upper mass limit and solve the discrepancy between the claimed 150 M ☉ limit and observations of four stars with initial masses of 165-320 M ☉ in R136 and of supernova 2007bi, which is thought to be a pair-instability supernova from an initial 250 M ☉ star. Using the stellar population of R136, we revise the upper mass limit to values in the range 200-500 M ☉ .

Ages of Young Star Clusters, Massive Blue Stragglers, and the Upper Mass Limit of Stars: Analyzing Age-dependent Stellar Mass Functions

Science.gov (United States)

Schneider, F. R. N.; Izzard, R. G.; de Mink, S. E.; Langer, N.; Stolte, A.; de Koter, A.; Gvaramadze, V. V.; Hußmann, B.; Liermann, A.; Sana, H.

2014-01-01

Massive stars rapidly change their masses through strong stellar winds and mass transfer in binary systems. The latter aspect is important for populations of massive stars as more than 70% of all O stars are expected to interact with a binary companion during their lifetime. We show that such mass changes leave characteristic signatures in stellar mass functions of young star clusters that can be used to infer their ages and to identify products of binary evolution. We model the observed present-day mass functions of the young Galactic Arches and Quintuplet star clusters using our rapid binary evolution code. We find that the shaping of the mass function by stellar wind mass loss allows us to determine the cluster ages as 3.5 ± 0.7 Myr and 4.8 ± 1.1 Myr, respectively. Exploiting the effects of binary mass exchange on the cluster mass function, we find that the most massive stars in both clusters are rejuvenated products of binary mass transfer, i.e., the massive counterpart of classical blue straggler stars. This resolves the problem of an apparent age spread among the most luminous stars exceeding the expected duration of star formation in these clusters. We perform Monte Carlo simulations to probe stochastic sampling, which support the idea of the most massive stars being rejuvenated binary products. We find that the most massive star is expected to be a binary product after 1.0 ± 0.7 Myr in Arches and after 1.7 ± 1.0 Myr in Quintuplet. Today, the most massive 9 ± 3 stars in Arches and 8 ± 3 in Quintuplet are expected to be such objects. Our findings have strong implications for the stellar upper mass limit and solve the discrepancy between the claimed 150 M ⊙ limit and observations of four stars with initial masses of 165-320 M ⊙ in R136 and of supernova 2007bi, which is thought to be a pair-instability supernova from an initial 250 M ⊙ star. Using the stellar population of R136, we revise the upper mass limit to values in the range 200-500 M ⊙.

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

Science.gov (United States)

Boldogköi, Zsolt

2012-01-01

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

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

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

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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.

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

International Nuclear Information System (INIS)

Li, Zhi; Zhao, Zhen

2017-01-01

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

Genome-Wide Identification and Comparative Analysis of the 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR Gene Family in Gossypium

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Wei Liu

2018-01-01

Full Text Available Terpenes are the largest and most diverse class of secondary metabolites in plants and play a very important role in plant adaptation to environment. 3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR is a rate-limiting enzyme in the process of terpene biosynthesis in the cytosol. Previous study found the HMGR genes underwent gene expansion in Gossypium raimondii, but the characteristics and evolution of the HMGR gene family in Gossypium genus are unclear. In this study, genome-wide identification and comparative study of HMGR gene family were carried out in three Gossypium species with genome sequences, i.e., G. raimondii, Gossypium arboreum, and Gossypium hirsutum. In total, nine, nine and 18 HMGR genes were identified in G. raimondii, G. arboreum, and G. hirsutum, respectively. The results indicated that the HMGR genes underwent gene expansion and a unique gene cluster containing four HMGR genes was found in all the three Gossypium species. The phylogenetic analysis suggested that the expansion of HMGR genes had occurred in their common ancestor. There was a pseudogene that had a 10-bp deletion resulting in a frameshift mutation and could not be translated into functional proteins in G. arboreum and the A-subgenome of G. hirsutum. The expression profiles of the two pseudogenes showed that they had tissue-specific expression. Additionally, the expression pattern of the pseudogene in the A-subgenome of G. hirsutum was similar to its paralogous gene in the D-subgenome of G. hirsutum. Our results provide useful information for understanding cytosolic terpene biosynthesis in Gossypium species.

Duplication and relocation of the functional DPY19L2 gene within low copy repeats

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Cheung Joseph

2006-03-01

Full Text Available Abstract Background Low copy repeats (LCRs are thought to play an important role in recent gene evolution, especially when they facilitate gene duplications. Duplicate genes are fundamental to adaptive evolution, providing substrates for the development of new or shared gene functions. Moreover, silencing of duplicate genes can have an indirect effect on adaptive evolution by causing genomic relocation of functional genes. These changes are theorized to have been a major factor in speciation. Results Here we present a novel example showing functional gene relocation within a LCR. We characterize the genomic structure and gene content of eight related LCRs on human Chromosomes 7 and 12. Two members of a novel transmembrane gene family, DPY19L, were identified in these regions, along with six transcribed pseudogenes. One of these genes, DPY19L2, is found on Chromosome 12 and is not syntenic with its mouse orthologue. Instead, the human locus syntenic to mouse Dpy19l2 contains a pseudogene, DPY19L2P1. This indicates that the ancestral copy of this gene has been silenced, while the descendant copy has remained active. Thus, the functional copy of this gene has been relocated to a new genomic locus. We then describe the expansion and evolution of the DPY19L gene family from a single gene found in invertebrate animals. Ancient duplications have led to multiple homologues in different lineages, with three in fish, frogs and birds and four in mammals. Conclusion Our results show that the DPY19L family has expanded throughout the vertebrate lineage and has undergone recent primate-specific evolution within LCRs.

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

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Klaudius eKalcher

2015-12-01

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

Clustering of noise-induced oscillations

DEFF Research Database (Denmark)

Sosnovtseva, Olga; Fomin, A I; Postnov, D E

2001-01-01

The subject of our study is clustering in a population of excitable systems driven by Gaussian white noise and with randomly distributed coupling strength. The cluster state is frequency-locked state in which all functional units run at the same noise-induced frequency. Cooperative dynamics...

Globular clusters - Fads and fallacies

International Nuclear Information System (INIS)

White, R.E.

1991-01-01

The types of globular clusters observed in the Milky Way Galaxy are described together with their known characteristics, with special attention given to correcting the erroneous statements made earlier about globular clusters. Among these are the following statements: the Galaxy is surrounded by many hundreds of globular clusters; all globular clusters are located toward the Galactic center, all globular clusters are metal poor and move about the Galaxy in highly elliptical paths; all globular clusters contain RR Lyrae-type variable stars, and the RR Lyrae stars found outside of globulars have come from cluster dissolution or ejection; all of the stars in a given cluster were born at the same time and have the same chemical composition; X-ray globulars are powered by central black holes; and the luminosity functions for globular clusters are well defined and well determined. Consideration is given to the fact that globular clusters in the Magellanic Clouds differ from those in the Milky Way by their age distribution and that the globulars of the SMC differ from those of the LMC

Persistence drives gene clustering in bacterial genomes

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Rocha Eduardo PC

2008-01-01

Full Text Available Abstract Background Gene clustering plays an important role in the organization of the bacterial chromosome and several mechanisms have been proposed to explain its extent. However, the controversies raised about the validity of each of these mechanisms remind us that the cause of this gene organization remains an open question. Models proposed to explain clustering did not take into account the function of the gene products nor the likely presence or absence of a given gene in a genome. However, genomes harbor two very different categories of genes: those genes present in a majority of organisms – persistent genes – and those present in very few organisms – rare genes. Results We show that two classes of genes are significantly clustered in bacterial genomes: the highly persistent and the rare genes. The clustering of rare genes is readily explained by the selfish operon theory. Yet, genes persistently present in bacterial genomes are also clustered and we try to understand why. We propose a model accounting specifically for such clustering, and show that indispensability in a genome with frequent gene deletion and insertion leads to the transient clustering of these genes. The model describes how clusters are created via the gene flux that continuously introduces new genes while deleting others. We then test if known selective processes, such as co-transcription, physical interaction or functional neighborhood, account for the stabilization of these clusters. Conclusion We show that the strong selective pressure acting on the function of persistent genes, in a permanent state of flux of genes in bacterial genomes, maintaining their size fairly constant, that drives persistent genes clustering. A further selective stabilization process might contribute to maintaining the clustering.

Functional connectivity analysis of the neural bases of emotion regulation: A comparison of independent component method with density-based k-means clustering method.

Science.gov (United States)

Zou, Ling; Guo, Qian; Xu, Yi; Yang, Biao; Jiao, Zhuqing; Xiang, Jianbo

2016-04-29

Functional magnetic resonance imaging (fMRI) is an important tool in neuroscience for assessing connectivity and interactions between distant areas of the brain. To find and characterize the coherent patterns of brain activity as a means of identifying brain systems for the cognitive reappraisal of the emotion task, both density-based k-means clustering and independent component analysis (ICA) methods can be applied to characterize the interactions between brain regions involved in cognitive reappraisal of emotion. Our results reveal that compared with the ICA method, the density-based k-means clustering method provides a higher sensitivity of polymerization. In addition, it is more sensitive to those relatively weak functional connection regions. Thus, the study concludes that in the process of receiving emotional stimuli, the relatively obvious activation areas are mainly distributed in the frontal lobe, cingulum and near the hypothalamus. Furthermore, density-based k-means clustering method creates a more reliable method for follow-up studies of brain functional connectivity.

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

International Nuclear Information System (INIS)

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

2006-01-01

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

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

Science.gov (United States)

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

2006-09-01

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

Maximum-entropy clustering algorithm and its global convergence analysis

Institute of Scientific and Technical Information of China (English)

无

2001-01-01

Constructing a batch of differentiable entropy functions touniformly approximate an objective function by means of the maximum-entropy principle, a new clustering algorithm, called maximum-entropy clustering algorithm, is proposed based on optimization theory. This algorithm is a soft generalization of the hard C-means algorithm and possesses global convergence. Its relations with other clustering algorithms are discussed.

A Novel Cluster Head Selection Algorithm Based on Fuzzy Clustering and Particle Swarm Optimization.

Science.gov (United States)

Ni, Qingjian; Pan, Qianqian; Du, Huimin; Cao, Cen; Zhai, Yuqing

2017-01-01

An important objective of wireless sensor network is to prolong the network life cycle, and topology control is of great significance for extending the network life cycle. Based on previous work, for cluster head selection in hierarchical topology control, we propose a solution based on fuzzy clustering preprocessing and particle swarm optimization. More specifically, first, fuzzy clustering algorithm is used to initial clustering for sensor nodes according to geographical locations, where a sensor node belongs to a cluster with a determined probability, and the number of initial clusters is analyzed and discussed. Furthermore, the fitness function is designed considering both the energy consumption and distance factors of wireless sensor network. Finally, the cluster head nodes in hierarchical topology are determined based on the improved particle swarm optimization. Experimental results show that, compared with traditional methods, the proposed method achieved the purpose of reducing the mortality rate of nodes and extending the network life cycle.

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

International Nuclear Information System (INIS)

Payami, M.

2004-01-01

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

Cluster processing business level monitor

International Nuclear Information System (INIS)

Muniz, Francisco J.

2017-01-01

This article describes a Cluster Processing Monitor. Several applications with this functionality can be freely found doing a search in the Google machine. However, those applications may offer more features that are needed on the Processing Monitor being proposed. Therefore, making the monitor output evaluation difficult to be understood by the user, at-a-glance. In addition, such monitors may add unnecessary processing cost to the Cluster. For these reasons, a completely new Cluster Processing Monitor module was designed and implemented. In the CDTN, Clusters are broadly used, mainly, in deterministic methods (CFD) and non-deterministic methods (Monte Carlo). (author)

Cluster processing business level monitor

Energy Technology Data Exchange (ETDEWEB)

Muniz, Francisco J., E-mail: muniz@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)

2017-07-01

This article describes a Cluster Processing Monitor. Several applications with this functionality can be freely found doing a search in the Google machine. However, those applications may offer more features that are needed on the Processing Monitor being proposed. Therefore, making the monitor output evaluation difficult to be understood by the user, at-a-glance. In addition, such monitors may add unnecessary processing cost to the Cluster. For these reasons, a completely new Cluster Processing Monitor module was designed and implemented. In the CDTN, Clusters are broadly used, mainly, in deterministic methods (CFD) and non-deterministic methods (Monte Carlo). (author)

ABOUT THE TYPES OF REGIONAL INNOVATION CLUSTERS

Directory of Open Access Journals (Sweden)

Aleksandr S. Voronov

2016-01-01

Full Text Available This article describes the main characteristics of innovation clusters, analyzed the develop-ment plans of the cluster areas of growth on the basis of innovation in the various subjects of the federation, it proposed the principle of clustering of the «nuclear» type, dened by problems in the functioning of specialized distributed clusters on the basis of the organi-zational and marketing innovations, proposed scheme for sustainable innovation develop-ment of specialized distributed cluster.

CHANDRA CLUSTER COSMOLOGY PROJECT III: COSMOLOGICAL PARAMETER CONSTRAINTS

International Nuclear Information System (INIS)

Vikhlinin, A.; Forman, W. R.; Jones, C.; Murray, S. S.; Kravtsov, A. V.; Burenin, R. A.; Voevodkin, A.; Ebeling, H.; Hornstrup, A.; Nagai, D.; Quintana, H.

2009-01-01

Chandra observations of large samples of galaxy clusters detected in X-rays by ROSAT provide a new, robust determination of the cluster mass functions at low and high redshifts. Statistical and systematic errors are now sufficiently small, and the redshift leverage sufficiently large for the mass function evolution to be used as a useful growth of a structure-based dark energy probe. In this paper, we present cosmological parameter constraints obtained from Chandra observations of 37 clusters with (z) = 0.55 derived from 400 deg 2 ROSAT serendipitous survey and 49 brightest z ∼ 0.05 clusters detected in the All-Sky Survey. Evolution of the mass function between these redshifts requires Ω Λ > 0 with a ∼5σ significance, and constrains the dark energy equation-of-state parameter to w 0 = -1.14 ± 0.21, assuming a constant w and a flat universe. Cluster information also significantly improves constraints when combined with other methods. Fitting our cluster data jointly with the latest supernovae, Wilkinson Microwave Anisotropy Probe, and baryonic acoustic oscillation measurements, we obtain w 0 = -0.991 ± 0.045 (stat) ±0.039 (sys), a factor of 1.5 reduction in statistical uncertainties, and nearly a factor of 2 improvement in systematics compared with constraints that can be obtained without clusters. The joint analysis of these four data sets puts a conservative upper limit on the masses of light neutrinos Σm ν M h and σ 8 from the low-redshift cluster mass function.

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

Directory of Open Access Journals (Sweden)

Ifeoluwapo Matthew Joshua

2017-04-01

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

Clustering of galaxies with f(R) gravity

Science.gov (United States)

Capozziello, Salvatore; Faizal, Mir; Hameeda, Mir; Pourhassan, Behnam; Salzano, Vincenzo; Upadhyay, Sudhaker

2018-02-01

Based on thermodynamics, we discuss the galactic clustering of expanding Universe by assuming the gravitational interaction through the modified Newton's potential given by f(R) gravity. We compute the corrected N-particle partition function analytically. The corrected partition function leads to more exact equations of state of the system. By assuming that the system follows quasi-equilibrium, we derive the exact distribution function that exhibits the f(R) correction. Moreover, we evaluate the critical temperature and discuss the stability of the system. We observe the effects of correction of f(R) gravity on the power-law behaviour of particle-particle correlation function also. In order to check the feasibility of an f(R) gravity approach to the clustering of galaxies, we compare our results with an observational galaxy cluster catalogue.

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

Science.gov (United States)

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

2017-02-01

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

Clinical Characteristics of Exacerbation-Prone Adult Asthmatics Identified by Cluster Analysis.

Science.gov (United States)

Kim, Mi Ae; Shin, Seung Woo; Park, Jong Sook; Uh, Soo Taek; Chang, Hun Soo; Bae, Da Jeong; Cho, You Sook; Park, Hae Sim; Yoon, Ho Joo; Choi, Byoung Whui; Kim, Yong Hoon; Park, Choon Sik

2017-11-01

Asthma is a heterogeneous disease characterized by various types of airway inflammation and obstruction. Therefore, it is classified into several subphenotypes, such as early-onset atopic, obese non-eosinophilic, benign, and eosinophilic asthma, using cluster analysis. A number of asthmatics frequently experience exacerbation over a long-term follow-up period, but the exacerbation-prone subphenotype has rarely been evaluated by cluster analysis. This prompted us to identify clusters reflecting asthma exacerbation. A uniform cluster analysis method was applied to 259 adult asthmatics who were regularly followed-up for over 1 year using 12 variables, selected on the basis of their contribution to asthma phenotypes. After clustering, clinical profiles and exacerbation rates during follow-up were compared among the clusters. Four subphenotypes were identified: cluster 1 was comprised of patients with early-onset atopic asthma with preserved lung function, cluster 2 late-onset non-atopic asthma with impaired lung function, cluster 3 early-onset atopic asthma with severely impaired lung function, and cluster 4 late-onset non-atopic asthma with well-preserved lung function. The patients in clusters 2 and 3 were identified as exacerbation-prone asthmatics, showing a higher risk of asthma exacerbation. Two different phenotypes of exacerbation-prone asthma were identified among Korean asthmatics using cluster analysis; both were characterized by impaired lung function, but the age at asthma onset and atopic status were different between the two. Copyright © 2017 The Korean Academy of Asthma, Allergy and Clinical Immunology · The Korean Academy of Pediatric Allergy and Respiratory Disease

Orbit Clustering Based on Transfer Cost

Science.gov (United States)

Gustafson, Eric D.; Arrieta-Camacho, Juan J.; Petropoulos, Anastassios E.

2013-01-01

We propose using cluster analysis to perform quick screening for combinatorial global optimization problems. The key missing component currently preventing cluster analysis from use in this context is the lack of a useable metric function that defines the cost to transfer between two orbits. We study several proposed metrics and clustering algorithms, including k-means and the expectation maximization algorithm. We also show that proven heuristic methods such as the Q-law can be modified to work with cluster analysis.

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.

METHOD OF CONSTRUCTION OF GENETIC DATA CLUSTERS

Directory of Open Access Journals (Sweden)

N. A. Novoselova

2016-01-01

Full Text Available The paper presents a method of construction of genetic data clusters (functional modules using the randomized matrices. To build the functional modules the selection and analysis of the eigenvalues of the gene profiles correlation matrix is performed. The principal components, corresponding to the eigenvalues, which are significantly different from those obtained for the randomly generated correlation matrix, are used for the analysis. Each selected principal component forms gene cluster. In a comparative experiment with the analogs the proposed method shows the advantage in allocating statistically significant different-sized clusters, the ability to filter non- informative genes and to extract the biologically interpretable functional modules matching the real data structure.

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-09-07

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-09-07

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

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Fatigue Feature Extraction Analysis based on a K-Means Clustering Approach

Directory of Open Access Journals (Sweden)

M.F.M. Yunoh

2015-06-01

Full Text Available This paper focuses on clustering analysis using a K-means approach for fatigue feature dataset extraction. The aim of this study is to group the dataset as closely as possible (homogeneity for the scattered dataset. Kurtosis, the wavelet-based energy coefficient and fatigue damage are calculated for all segments after the extraction process using wavelet transform. Kurtosis, the wavelet-based energy coefficient and fatigue damage are used as input data for the K-means clustering approach. K-means clustering calculates the average distance of each group from the centroid and gives the objective function values. Based on the results, maximum values of the objective function can be seen in the two centroid clusters, with a value of 11.58. The minimum objective function value is found at 8.06 for five centroid clusters. It can be seen that the objective function with the lowest value for the number of clusters is equal to five; which is therefore the best cluster for the dataset.

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

Science.gov (United States)

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

2016-11-01

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

The Voronoi Tessellation cluster finder in 2+1 dimensions

Energy Technology Data Exchange (ETDEWEB)

Soares-Santos, Marcelle; /Fermilab /Sao Paulo U.; de Carvalho, Reinaldo R.; /Sao Jose, INPE; Annis, James; /Fermilab; Gal, Roy R.; /Hawaii U.; La Barbera, Francesco; /Capodimonte Observ.; Lopes, Paulo A.A.; /Valongo Observ.; Wechsler, Risa H.; Busha, Michael T.; Gerke, Brian F.; /SLAC /KIPAC, Menlo Park

2010-11-01

We present a detailed description of the Voronoi Tessellation (VT) cluster finder algorithm in 2+1 dimensions, which improves on past implementations of this technique. The need for cluster finder algorithms able to produce reliable cluster catalogs up to redshift 1 or beyond and down to 10{sup 13.5} solar masses is paramount especially in light of upcoming surveys aiming at cosmological constraints from galaxy cluster number counts. We build the VT in photometric redshift shells and use the two-point correlation function of the galaxies in the field to both determine the density threshold for detection of cluster candidates and to establish their significance. This allows us to detect clusters in a self-consistent way without any assumptions about their astrophysical properties. We apply the VT to mock catalogs which extend to redshift 1.4 reproducing the {Lambda}CDM cosmology and the clustering properties observed in the Sloan Digital Sky Survey data. An objective estimate of the cluster selection function in terms of the completeness and purity as a function of mass and redshift is as important as having a reliable cluster finder. We measure these quantities by matching the VT cluster catalog with the mock truth table. We show that the VT can produce a cluster catalog with completeness and purity >80% for the redshift range up to {approx}1 and mass range down to {approx}10{sup 13.5} solar masses.

The Voronoi Tessellation Cluster Finder in 2 1 Dimensions

Energy Technology Data Exchange (ETDEWEB)

Soares-Santos, Marcelle; /Fermilab /Sao Paulo U.; de Carvalho, Reinaldo R.; /Sao Jose, INPE; Annis, James; /Fermilab; Gal, Roy R.; /Hawaii U.; La Barbera, Francesco; /Capodimonte Observ.; Lopes, Paulo A.A.; /Valongo Observ.; Wechsler, Risa H.; Busha, Michael T.; Gerke, Brian F.; /SLAC /KIPAC, Menlo Park

2011-06-23

We present a detailed description of the Voronoi Tessellation (VT) cluster finder algorithm in 2+1 dimensions, which improves on past implementations of this technique. The need for cluster finder algorithms able to produce reliable cluster catalogs up to redshift 1 or beyond and down to 10{sup 13.5} solar masses is paramount especially in light of upcoming surveys aiming at cosmological constraints from galaxy cluster number counts. We build the VT in photometric redshift shells and use the two-point correlation function of the galaxies in the field to both determine the density threshold for detection of cluster candidates and to establish their significance. This allows us to detect clusters in a self-consistent way without any assumptions about their astrophysical properties. We apply the VT to mock catalogs which extend to redshift 1.4 reproducing the ?CDM cosmology and the clustering properties observed in the Sloan Digital Sky Survey data. An objective estimate of the cluster selection function in terms of the completeness and purity as a function of mass and redshift is as important as having a reliable cluster finder. We measure these quantities by matching the VT cluster catalog with the mock truth table. We show that the VT can produce a cluster catalog with completeness and purity >80% for the redshift range up to {approx}1 and mass range down to {approx}10{sup 13.5} solar masses.

THE VORONOI TESSELLATION CLUSTER FINDER IN 2+1 DIMENSIONS

International Nuclear Information System (INIS)

Soares-Santos, Marcelle; Annis, James; De Carvalho, Reinaldo R.; Gal, Roy R.; La Barbera, Francesco; Lopes, Paulo A. A.; Wechsler, Risa H.; Busha, Michael T.; Gerke, Brian F.

2011-01-01

We present a detailed description of the Voronoi Tessellation (VT) cluster finder algorithm in 2+1 dimensions, which improves on past implementations of this technique. The need for cluster finder algorithms able to produce reliable cluster catalogs up to redshift 1 or beyond and down to 10 13.5 solar masses is paramount especially in light of upcoming surveys aiming at cosmological constraints from galaxy cluster number counts. We build the VT in photometric redshift shells and use the two-point correlation function of the galaxies in the field to both determine the density threshold for detection of cluster candidates and to establish their significance. This allows us to detect clusters in a self-consistent way without any assumptions about their astrophysical properties. We apply the VT to mock catalogs which extend to redshift 1.4 reproducing the ΛCDM cosmology and the clustering properties observed in the Sloan Digital Sky Survey data. An objective estimate of the cluster selection function in terms of the completeness and purity as a function of mass and redshift is as important as having a reliable cluster finder. We measure these quantities by matching the VT cluster catalog with the mock truth table. We show that the VT can produce a cluster catalog with completeness and purity >80% for the redshift range up to ∼1 and mass range down to ∼10 13.5 solar masses.

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.

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

Science.gov (United States)

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

2008-05-01

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

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...

Small gold clusters on graphene, their mobility and clustering: a DFT study

International Nuclear Information System (INIS)

Amft, Martin; Sanyal, Biplab; Eriksson, Olle; Skorodumova, Natalia V

2011-01-01

Motivated by the experimentally observed high mobility of gold atoms on graphene and their tendency to form nanometer-sized clusters, we present a density functional theory study of the ground state structures of small gold clusters on graphene, their mobility and clustering. Our detailed analysis of the electronic structures identifies the opportunity to form strong gold-gold bonds and the graphene-mediated interaction of the pre-adsorbed fragments as the driving forces behind gold's tendency to aggregate on graphene. While clusters containing up to three gold atoms have one unambiguous ground state structure, both gas phase isomers of a cluster with four gold atoms can be found on graphene. In the gas phase the diamond-shaped Au 4 D cluster is the ground state structure, whereas the Y-shaped Au 4 Y becomes the actual ground state when adsorbed on graphene. As we show, both clusters can be produced on graphene by two distinct clustering processes. We also studied in detail the stepwise formation of a gold dimer out of two pre-adsorbed adatoms, as well as the formation of Au 3 . All reactions are exothermic and no further activation barriers, apart from the diffusion barriers, were found. The diffusion barriers of all studied clusters range from 4 to 36 meV only, and are substantially exceeded by the adsorption energies of - 0.1 to - 0.59 eV. This explains the high mobility of Au 1-4 on graphene along the C-C bonds.

X-ray cluster Abell 744

International Nuclear Information System (INIS)

Kurtz, M.J.; Huchra, J.P.; Beers, T.C.; Geller, M.J.; Gioia, I.M.

1985-01-01

X-ray and optical observations of the cluster of galaxies Abell 744 are presented. The X-ray flux (assuming H(0) = 100 km/s per Mpc) is about 9 x 10 to the 42nd erg/s. The X-ray source is extended, but shows no other structure. Photographic photometry (in Kron-Cousins R), calibrated by deep CCD frames, is presented for all galaxies brighter than 19th magnitude within 0.75 Mpc of the cluster center. The luminosity function is normal, and the isopleths show little evidence of substructure near the cluster center. The cluster has a dominant central galaxy, which is classified as a normal brightest-cluster elliptical on the basis of its luminosity profile. New redshifts were obtained for 26 galaxies in the vicinity of the cluster center; 20 appear to be cluster members. The spatial distribution of redshifts is peculiar; the dispersion within the 150 kpc core radius is much greater than outside. Abell 744 is similar to the nearby cluster Abell 1060. 31 references

Extensive polycistronism and antisense transcription in the mammalian Hox clusters.

Directory of Open Access Journals (Sweden)

Gaëll Mainguy

Full Text Available The Hox clusters play a crucial role in body patterning during animal development. They encode both Hox transcription factor and micro-RNA genes that are activated in a precise temporal and spatial sequence that follows their chromosomal order. These remarkable collinear properties confer functional unit status for Hox clusters. We developed the TranscriptView platform to establish high resolution transcriptional profiling and report here that transcription in the Hox clusters is far more complex than previously described in both human and mouse. Unannotated transcripts can represent up to 60% of the total transcriptional output of a cluster. In particular, we identified 14 non-coding Transcriptional Units antisense to Hox genes, 10 of which (70% have a detectable mouse homolog. Most of these Transcriptional Units in both human and mouse present conserved sizeable sequences (>40 bp overlapping Hox transcripts, suggesting that these Hox antisense transcripts are functional. Hox clusters also display at least seven polycistronic clusters, i.e., different genes being co-transcribed on long isoforms (up to 30 kb. This work provides a reevaluated framework for understanding Hox gene function and dys-function. Such extensive transcriptions may provide a structural explanation for Hox clustering.

Electronic and magnetic properties of small rhodium clusters

Energy Technology Data Exchange (ETDEWEB)

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

2015-04-24

We report a theoretical study of the electronic and magnetic properties of rhodium-atomic clusters. The lowest energy structures at the semi-empirical level of rhodium clusters are first obtained from a novel global-minimum search algorithm, known as PTMBHGA, where Gupta potential is used to describe the atomic interaction among the rhodium atoms. The structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof generalized gradient approximation. For the purpose of calculating the magnetic moment of a given cluster, we calculate the optimized structure as a function of the spin multiplicity within the DFT framework. The resultant magnetic moments with the lowest energies so obtained allow us to work out the magnetic moment as a function of cluster size. Rhodium atomic clusters are found to display a unique variation in the magnetic moment as the cluster size varies. However, Rh{sub 4} and Rh{sub 6} are found to be nonmagnetic. Electronic structures of the magnetic ground-state structures are also investigated within the DFT framework. The results are compared against those based on different theoretical approaches available in the literature.

Time-series clustering of gene expression in irradiated and bystander fibroblasts: an application of FBPA clustering

Directory of Open Access Journals (Sweden)

Markatou Marianthi

2011-01-01

Full Text Available Abstract Background The radiation bystander effect is an important component of the overall biological response of tissues and organisms to ionizing radiation, but the signaling mechanisms between irradiated and non-irradiated bystander cells are not fully understood. In this study, we measured a time-series of gene expression after α-particle irradiation and applied the Feature Based Partitioning around medoids Algorithm (FBPA, a new clustering method suitable for sparse time series, to identify signaling modules that act in concert in the response to direct irradiation and bystander signaling. We compared our results with those of an alternate clustering method, Short Time series Expression Miner (STEM. Results While computational evaluations of both clustering results were similar, FBPA provided more biological insight. After irradiation, gene clusters were enriched for signal transduction, cell cycle/cell death and inflammation/immunity processes; but only FBPA separated clusters by function. In bystanders, gene clusters were enriched for cell communication/motility, signal transduction and inflammation processes; but biological functions did not separate as clearly with either clustering method as they did in irradiated samples. Network analysis confirmed p53 and NF-κB transcription factor-regulated gene clusters in irradiated and bystander cells and suggested novel regulators, such as KDM5B/JARID1B (lysine (K-specific demethylase 5B and HDACs (histone deacetylases, which could epigenetically coordinate gene expression after irradiation. Conclusions In this study, we have shown that a new time series clustering method, FBPA, can provide new leads to the mechanisms regulating the dynamic cellular response to radiation. The findings implicate epigenetic control of gene expression in addition to transcription factor networks.

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

International Nuclear Information System (INIS)

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

2009-01-01

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

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

Science.gov (United States)

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

2017-02-28

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

Clustering environments of BL Lac objects

Science.gov (United States)

Wurtz, Ronald; Ellingson, Erica; Stocke, John T.; Yee, H. K. C.

1993-01-01

We report measurements of the amplitude of the BL Lac galaxy spatial covariance function, B(gb), for the fields of five BL Lacertae objects. We present evidence for rich clusters around MS 1207+39 and MS 1407+59, and confirm high richness for the cluster containing H0414+009. We discuss the ease of 3C 66 A and find evidence for a poor cluster based on an uncertain redshift of z = 0.444. These data suggest that at least some BL Lac objects are consistent with being FR 1 radio galaxies in rich clusters.

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

Science.gov (United States)

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

2016-01-01

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

Magnetism of iron, cobalt and nickel clusters studied in molecular beams

International Nuclear Information System (INIS)

Billas, I.

1995-01-01

The magnetic properties of iron, cobalt and nickel clusters in a molecular beam have been studied in a magnetic Stern-Gerlach deflection experiment. The molecular beam apparatus consists of a laser vaporization cluster source with high intensity and stability and a high-resolution time-of-flight mass spectrometer for the deflection measurements. Several novel experimental features have been developed in this work, like a nozzle which can be heated up to 1000 K and a chopper to measure the dwell times of the clusters in the source and their corresponding velocities. These new developments have allowed the measurement and the control of the temperature of the free clusters. The Stern-Gerlach deflection experiments have been performed on Fe, Co and Ni clusters in the mass range from 20 to 700 atoms. All clusters show single-sided deflection toward increasing field. This observation indicates that a spin relaxation process occurs within the isolated clusters. The participation of both the cluster rotational and vibrational degrees of freedom to the spin relaxation has been experimentally demonstrated. The cluster magnetization has been determined as a function of applied magnetic field B and as a function of dwell times of the clusters in the source before the supersonic expansion into vacuum. Superparamagnetic behavior has been observed when the cluster rotational speed is much larger than the Larmor frequency of the cluster magnetic moment μ in the field B. In particular, for μB<< kT, the cluster magnetization depends on B/T. For lower rotational speeds, reduced values of the magnetization have been observed. The magnetic moments of the superparamagnetic Fe, Co and Ni clusters have been measured as a) a function of cluster size N at low temperature and b) as a function of cluster temperature T for various size ranges. (author) figs., tabs., refs

Atomic and electronic structure of clusters from car-Parrinello method

International Nuclear Information System (INIS)

Kumar, V.

1994-06-01

With the development of ab-initio molecular dynamics method, it has now become possible to study the static and dynamical properties of clusters containing up to a few tens of atoms. Here I present a review of the method within the framework of the density functional theory and pseudopotential approach to represent the electron-ion interaction and discuss some of its applications to clusters. Particular attention is focussed on the structure and bonding properties of clusters as a function of their size. Applications to clusters of alkali metals and Al, non-metal - metal transition in divalent metal clusters, molecular clusters of carbon and Sb are discussed in detail. Some results are also presented on mixed clusters. (author). 121 refs, 24 ifigs

Deciphering the Origin, Evolution, and Physiological Function of the Subtelomeric Aryl-Alcohol Dehydrogenase Gene Family in the Yeast Saccharomyces cerevisiae.

Science.gov (United States)

Yang, Dong-Dong; de Billerbeck, Gustavo M; Zhang, Jin-Jing; Rosenzweig, Frank; Francois, Jean-Marie

2018-01-01

Homology searches indicate that Saccharomyces cerevisiae strain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). Yeast AAD genes are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes, AAD4 and AAD14 , encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with the oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns. Other yeast AAD genes are undergoing pseudogenization. The 5' sequence of AAD15 has been deleted from the genome. Repair of an AAD3 missense mutation at the catalytically essential Tyr 73 residue did not result in a functional enzyme. However, ancestral-state reconstruction by fusing Aad6 with Aad16 and by N-terminal repair of Aad10 restores NADPH-dependent aryl-alcohol dehydrogenase activities. Phylogenetic analysis indicates that AAD genes are narrowly distributed in wood-saprophyte fungi and in yeast that occupy lignocellulosic niches. Because yeast AAD genes exhibit activity on veratraldehyde, cinnamaldehyde, and vanillin, they could serve to detoxify aryl-aldehydes released during lignin degradation. However, none of these compounds induce yeast AAD gene expression, and Aad activities do not relieve aryl-aldehyde growth inhibition. Our data suggest an ancestral role for AAD genes in lignin degradation that is degenerating as a result of yeast's domestication and use in brewing, baking, and other industrial applications. IMPORTANCE Functional characterization of hypothetical genes remains one of the chief tasks of the postgenomic era. Although the first Saccharomyces cerevisiae genome sequence was published over 20 years ago, 22% of its estimated 6,603 open reading frames (ORFs) remain unverified. One outstanding example of this category of genes is the enigmatic seven-member AAD family. Here, we demonstrate that proteins encoded by two

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

Science.gov (United States)

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

2010-09-20

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

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

International Nuclear Information System (INIS)

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

2014-01-01

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

TRANSPORT AND LOGISTICS CLUSTER IN AN ECONOMIC SYSTEM OF A REGION

Directory of Open Access Journals (Sweden)

I.G. Menshenina

2008-09-01

Full Text Available The main types of clusters are described in the article. The function of a transport and logistics model is also described using the theory of graphs. The relationship of clusters is shown in the economic system of a region, and the main role of transport and logistics cluster is emphasized as a good condition for the effective functioning of other clusters in the region.

Deep CCD photometry in globular clusters. VII. M30

International Nuclear Information System (INIS)

Richer, H.B.; Fahlman, G.G.; Vandenberg, D.A.

1988-01-01

New UBV CCD photometry in a single field of the globular cluster M30 was obtained, and the data were used to obtain the color magnitude diagram (CMD) of the cluster, its luminosity function, and to derive fundamental cluster parameters. No blue stragglers were found, nor any evidence of a binary sequence in the data even though the field under study is only 21 core radii from the cluster center. The cluster reddening is observed to be 0.068 + or - 0.035, significantly higher than that adopted in most current papers on M30. An intercomparison of the CMDs of three very metal-poor clusters clearly shows that there is no evidence for any age difference between them. The age of M30 itself is found to be about 14 Gyr. The luminosity function of M30 is determined to be M(V) = 8. Comparison of this function with one found by Bolte (1987) at 65 core radii shows clear evidence of mass segregation in the low-mass stars. 44 references

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods

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Olszewski Kellen L

2007-07-01

Full Text Available Abstract Background The availability of microarrays measuring thousands of genes simultaneously across hundreds of biological conditions represents an opportunity to understand both individual biological pathways and the integrated workings of the cell. However, translating this amount of data into biological insight remains a daunting task. An important initial step in the analysis of microarray data is clustering of genes with similar behavior. A number of classical techniques are commonly used to perform this task, particularly hierarchical and K-means clustering, and many novel approaches have been suggested recently. While these approaches are useful, they are not without drawbacks; these methods can find clusters in purely random data, and even clusters enriched for biological functions can be skewed towards a small number of processes (e.g. ribosomes. Results We developed Nearest Neighbor Networks (NNN, a graph-based algorithm to generate clusters of genes with similar expression profiles. This method produces clusters based on overlapping cliques within an interaction network generated from mutual nearest neighborhoods. This focus on nearest neighbors rather than on absolute distance measures allows us to capture clusters with high connectivity even when they are spatially separated, and requiring mutual nearest neighbors allows genes with no sufficiently similar partners to remain unclustered. We compared the clusters generated by NNN with those generated by eight other clustering methods. NNN was particularly successful at generating functionally coherent clusters with high precision, and these clusters generally represented a much broader selection of biological processes than those recovered by other methods. Conclusion The Nearest Neighbor Networks algorithm is a valuable clustering method that effectively groups genes that are likely to be functionally related. It is particularly attractive due to its simplicity, its success in the

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

DEFF Research Database (Denmark)

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

2003-01-01

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

Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog

Czech Academy of Sciences Publication Activity Database

Ma, W.; Gabriel, T.S.; Martis, M.M.; Gursinsky, T.; Schubert, V.; Vrána, Jan; Doležel, Jaroslav; Grundlach, H.; Altschmied, L.; Scholz, U.; Himmelbach, A.; Behrens, S.E.; Banaei-Moghaddam, A.M.; Houben, A.

2017-01-01

Roč. 213, č. 2 (2017), s. 916-928 ISSN 0028-646X R&D Projects: GA MŠk(CZ) LO1204; GA ČR GBP501/12/G090 Institutional support: RVO:61389030 Keywords : rna-polymerase-ii * ribosomal-rna * accessory chromosomes * plant argonautes * gene-expression * evolution * transcription * pseudogenes * sequences * identification * Argonaute * B chromosomes * B-located genes * gene erosion. gene expression * pseudogenization * Secale cereale Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 7.330, year: 2016

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.

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

Energy Technology Data Exchange (ETDEWEB)

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

2017-02-01

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

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

Science.gov (United States)

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

2018-06-07

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

X-ray clusters of galaxies

International Nuclear Information System (INIS)

McKee, J.D.

1980-01-01

This work is in three chapters, of which the first is an introduction to clusters of galaxies. The second chapter describes the HEAO A-2 Survey of Abell Clusters. The 225 clusters of galaxies listed in Abell's (1958) catalog which are of distance class four or less, were surveyed for 2 to 10 keV x-ray emission. Thirty-two identifications of x-ray sources with the clusters were made, fluxes and error boxes were determined for these sources; twelve of the identifications are new. The x-ray luminosity function has been derived and analytical fits have been made, the best fit is f(L) = 26.9 x 10 -8 exp( - L 44 /1.7) per Mpc per 10 44 erg s -1 per 2 to 10 keV band pass. The relationship between x-ray luminosity, Bautz-Morgan type, Rood-Sastry type, and richness has also been examined. The contribution of clusters to the x-ray background has been calculated from the luminosity function and has been found to be 3.5%, and with 90% certainty, less than 8% in the 2 to 10 keV band pass, assuming that clusters were not brighter in the past than they are at present. If they were bright enough in the past to account for the x-ray background, the evolution must have scaled more rapidly than (1 + z) 7 if clusters formed at z = 3, or (1 + z) 5 if clusters formed at z = 10. Chapter Three examines x-ray emission from poor clusters of galaxies. Burns and Owens' (1979) sample of 25 4C radio sources which coincide with Zwicky clusters of galaxies has been searched for x-ray emission in the HEAO A-2 data base. X-ray emission was detected from five sources at the 3sigma level, two exceeded 5 sigma. The search for x-ray emission was prompted by the knowledge of the existence of distorted radio sources in the clusters. The distortion implies the presence of a relatively dense intracluster medium which is expected to produce thermal bremsstrahlung x-ray emission

Fitting Latent Cluster Models for Networks with latentnet

Directory of Open Access Journals (Sweden)

Pavel N. Krivitsky

2007-12-01

Full Text Available latentnet is a package to fit and evaluate statistical latent position and cluster models for networks. Hoff, Raftery, and Handcock (2002 suggested an approach to modeling networks based on positing the existence of an latent space of characteristics of the actors. Relationships form as a function of distances between these characteristics as well as functions of observed dyadic level covariates. In latentnet social distances are represented in a Euclidean space. It also includes a variant of the extension of the latent position model to allow for clustering of the positions developed in Handcock, Raftery, and Tantrum (2007.The package implements Bayesian inference for the models based on an Markov chain Monte Carlo algorithm. It can also compute maximum likelihood estimates for the latent position model and a two-stage maximum likelihood method for the latent position cluster model. For latent position cluster models, the package provides a Bayesian way of assessing how many groups there are, and thus whether or not there is any clustering (since if the preferred number of groups is 1, there is little evidence for clustering. It also estimates which cluster each actor belongs to. These estimates are probabilistic, and provide the probability of each actor belonging to each cluster. It computes four types of point estimates for the coefficients and positions: maximum likelihood estimate, posterior mean, posterior mode and the estimator which minimizes Kullback-Leibler divergence from the posterior. You can assess the goodness-of-fit of the model via posterior predictive checks. It has a function to simulate networks from a latent position or latent position cluster model.

Optical response of small magnesium clusters

DEFF Research Database (Denmark)

Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

2004-01-01

We predict strong enhancement in the photoabsorption of small Mg clusters in the region of 4–5 eV due to the resonant excitation of the plasmon oscillations of cluster electrons. Photoabsorption spectra for neutral Mg clusters consisting of up to N = 11 atoms have been calculated using an ab initio...... framework based on the time-dependent density functional theory (TDDFT). The nature of predicted resonances has been elucidated by comparison of the results of the an ab initio calculations with the results of the classical Mie theory. The splitting of the plasmon resonances caused by the cluster...

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

International Nuclear Information System (INIS)

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

1983-01-01

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

Uncovering the molecular organization of unusual highly scattered 5S rDNA: The case of Chariesterus armatus (Heteroptera).

Science.gov (United States)

Bardella, Vanessa Bellini; Cabral-de-Mello, Diogo Cavalcanti

2018-03-10

One cluster of 5S rDNA per haploid genome is the most common pattern among Heteroptera. However, in Chariesterus armatus, highly scattered signals were noticed. We isolated and characterized the entire 5S rDNA unit of C. armatus aiming to a deeper knowledge of molecular organization of the 5S rDNA among Heteroptera and to understand possible causes and consequences of 5S rDNA chromosomal spreading. For a comparative analysis, we performed the same approach in Holymenia histrio with 5S rDNA restricted to one bivalent. Multiple 5S rDNA variants were observed in both species, though they were more variable in C. armatus, with some of variants corresponding to pseudogenes. These pseudogenes suggest birth-and-death mechanism, though homogenization was also observed (concerted evolution), indicating evolution through mixed model. Association between transposable elements and 5S rDNA was not observed, suggesting spreading of 5S rDNA through other mechanisms, like ectopic recombination. Scattered organization is a rare example for 5S rDNA, and such organization in C. armatus genome could have led to the high diversification of sequences favoring their pseudogenization. Copyright © 2017. Published by Elsevier B.V.

Self-similar gravitational clustering

International Nuclear Information System (INIS)

Efstathiou, G.; Fall, S.M.; Hogan, C.

1979-01-01

The evolution of gravitational clustering is considered and several new scaling relations are derived for the multiplicity function. These include generalizations of the Press-Schechter theory to different densities and cosmological parameters. The theory is then tested against multiplicity function and correlation function estimates for a series of 1000-body experiments. The results are consistent with the theory and show some dependence on initial conditions and cosmological density parameter. The statistical significance of the results, however, is fairly low because of several small number effects in the experiments. There is no evidence for a non-linear bootstrap effect or a dependence of the multiplicity function on the internal dynamics of condensed groups. Empirical estimates of the multiplicity function by Gott and Turner have a feature near the characteristic luminosity predicted by the theory. The scaling relations allow the inference from estimates of the galaxy luminosity function that galaxies must have suffered considerable dissipation if they originally formed from a self-similar hierarchy. A method is also developed for relating the multiplicity function to similar measures of clustering, such as those of Bhavsar, for the distribution of galaxies on the sky. These are shown to depend on the luminosity function in a complicated way. (author)

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

Science.gov (United States)

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

2014-01-01

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

Study of Cluster-size Effect on Damage Formation

International Nuclear Information System (INIS)

Aoki, Takaaki; Seki, Toshio; Nakai, Atsuko; Matsuo, Jiro; Takaoka, Gikan

2003-01-01

Computer simulation and experiments were performed in order to understand the effect of cluster size on damage formation. Results of molecular dynamics simulations of cluster impact on solid targets derived the model function, which explains the relationship among cluster size, incident energy and number of displacements. On the other hand, time of flight mass measurement system was installed a cluster irradiation system, so that cluster ion beam which cluster size distribution is well known can be irradiated on the target. The damage properties under various cluster irradiation conditions were examined using RBS. The results from computer simulations and experiments showed good agreements with each other, which suggests that irradiation damage by cluster ion beam can be controlled by selecting cluster size distribution and incident energy

Supersonic copper clusters

International Nuclear Information System (INIS)

Powers, D.E.; Hansen, S.G.; Geusic, M.E.; Michalopoulos, D.L.; Smalley, R.E.

1983-01-01

Copper clusters ranging in size from 1 to 29 atoms have been prepared in a supersonic beam by laser vaporization of a rotating copper target rod within the throat of a pulsed supersonic nozzle using helium for the carrier gas. The clusters were cooled extensively in the supersonic expansion [T(translational) 1 to 4 K, T(rotational) = 4 K, T(vibrational) = 20 to 70 K]. These clusters were detected in the supersonic beam by laser photoionization with time-of-flight mass analysis. Using a number of fixed frequency outputs of an exciplex laser, the threshold behavior of the photoionization cross section was monitored as a function of cluster size.nce two-photon ionization (R2PI) with mass selective detection allowed the detection of five new electronic band systems in the region between 2690 and 3200 A, for each of the three naturally occurring isotopic forms of Cu 2 . In the process of scanning the R2PI spectrum of these new electronic states, the ionization potential of the copper dimer was determined to be 7.894 +- 0.015 eV

Electromagnetic properties of 6Li in a cluster model with breathing clusters

International Nuclear Information System (INIS)

Kruppa, A.T.; Beck, R.; Dickmann, F.

1987-01-01

Electromagnetic properties of 6 Li are studied using a microscopic (α+δ) cluster model. In addition to the ground state of the clusters, their breathing excited states are included in the wave function in order to take into account the distortion of the clusters. The elastic charge form factor is in good agreement with experiment up to a momentum transfer of 8 fm -2 . The ground state magnetic form factor and the inelastic charge form factor are also well described. The effect of the breathing states of α on the form factors proves to be negligible except at high momentum transfer. The ground-state charge density, rms charge radius, the magnetic dipole moment and a reduced transition strength are also obtained in fair agreement with experiment. (author)

Infrared Multiple Photon Dissociation Spectroscopy Of Metal Cluster-Adducts

Science.gov (United States)

Cox, D. M.; Kaldor, A.; Zakin, M. R.

1987-01-01

Recent development of the laser vaporization technique combined with mass-selective detection has made possible new studies of the fundamental chemical and physical properties of unsupported transition metal clusters as a function of the number of constituent atoms. A variety of experimental techniques have been developed in our laboratory to measure ionization threshold energies, magnetic moments, and gas phase reactivity of clusters. However, studies have so far been unable to determine the cluster structure or the chemical state of chemisorbed species on gas phase clusters. The application of infrared multiple photon dissociation IRMPD to obtain the IR absorption properties of metal cluster-adsorbate species in a molecular beam is described here. Specifically using a high power, pulsed CO2 laser as the infrared source, the IRMPD spectrum for methanol chemisorbed on small iron clusters is measured as a function of the number of both iron atoms and methanols in the complex for different methanol isotopes. Both the feasibility and potential utility of IRMPD for characterizing metal cluster-adsorbate interactions are demonstrated. The method is generally applicable to any cluster or cluster-adsorbate system dependent only upon the availability of appropriate high power infrared sources.

The young star cluster population of M51 with LEGUS - I. A comprehensive study of cluster formation and evolution

Science.gov (United States)

Messa, M.; Adamo, A.; Östlin, G.; Calzetti, D.; Grasha, K.; Grebel, E. K.; Shabani, F.; Chandar, R.; Dale, D. A.; Dobbs, C. L.; Elmegreen, B. G.; Fumagalli, M.; Gouliermis, D. A.; Kim, H.; Smith, L. J.; Thilker, D. A.; Tosi, M.; Ubeda, L.; Walterbos, R.; Whitmore, B. C.; Fedorenko, K.; Mahadevan, S.; Andrews, J. E.; Bright, S. N.; Cook, D. O.; Kahre, L.; Nair, P.; Pellerin, A.; Ryon, J. E.; Ahmad, S. D.; Beale, L. P.; Brown, K.; Clarkson, D. A.; Guidarelli, G. C.; Parziale, R.; Turner, J.; Weber, M.

2018-01-01

Recently acquired WFC3 UV (F275W and F336W) imaging mosaics under the Legacy Extragalactic UV Survey (LEGUS), combined with archival ACS data of M51, are used to study the young star cluster (YSC) population of this interacting system. Our newly extracted source catalogue contains 2834 cluster candidates, morphologically classified to be compact and uniform in colour, for which ages, masses and extinction are derived. In this first work we study the main properties of the YSC population of the whole galaxy, considering a mass-limited sample. Both luminosity and mass functions follow a power-law shape with slope -2, but at high luminosities and masses a dearth of sources is observed. The analysis of the mass function suggests that it is best fitted by a Schechter function with slope -2 and a truncation mass at 1.00 ± 0.12 × 105 M⊙. Through Monte Carlo simulations, we confirm this result and link the shape of the luminosity function to the presence of a truncation in the mass function. A mass limited age function analysis, between 10 and 200 Myr, suggests that the cluster population is undergoing only moderate disruption. We observe little variation in the shape of the mass function at masses above 1 × 104 M⊙ over this age range. The fraction of star formation happening in the form of bound clusters in M51 is ∼ 20 per cent in the age range 10-100 Myr and little variation is observed over the whole range from 1 to 200 Myr.

Cluster analysis of obesity and asthma phenotypes.

Directory of Open Access Journals (Sweden)

E Rand Sutherland

Full Text Available Asthma is a heterogeneous disease with variability among patients in characteristics such as lung function, symptoms and control, body weight, markers of inflammation, and responsiveness to glucocorticoids (GC. Cluster analysis of well-characterized cohorts can advance understanding of disease subgroups in asthma and point to unsuspected disease mechanisms. We utilized an hypothesis-free cluster analytical approach to define the contribution of obesity and related variables to asthma phenotype.In a cohort of clinical trial participants (n = 250, minimum-variance hierarchical clustering was used to identify clinical and inflammatory biomarkers important in determining disease cluster membership in mild and moderate persistent asthmatics. In a subset of participants, GC sensitivity was assessed via expression of GC receptor alpha (GCRα and induction of MAP kinase phosphatase-1 (MKP-1 expression by dexamethasone. Four asthma clusters were identified, with body mass index (BMI, kg/m(2 and severity of asthma symptoms (AEQ score the most significant determinants of cluster membership (F = 57.1, p<0.0001 and F = 44.8, p<0.0001, respectively. Two clusters were composed of predominantly obese individuals; these two obese asthma clusters differed from one another with regard to age of asthma onset, measures of asthma symptoms (AEQ and control (ACQ, exhaled nitric oxide concentration (F(ENO and airway hyperresponsiveness (methacholine PC(20 but were similar with regard to measures of lung function (FEV(1 (% and FEV(1/FVC, airway eosinophilia, IgE, leptin, adiponectin and C-reactive protein (hsCRP. Members of obese clusters demonstrated evidence of reduced expression of GCRα, a finding which was correlated with a reduced induction of MKP-1 expression by dexamethasoneObesity is an important determinant of asthma phenotype in adults. There is heterogeneity in expression of clinical and inflammatory biomarkers of asthma across obese individuals

Computation cluster for Monte Carlo calculations

Energy Technology Data Exchange (ETDEWEB)

Petriska, M.; Vitazek, K.; Farkas, G.; Stacho, M.; Michalek, S. [Dep. Of Nuclear Physics and Technology, Faculty of Electrical Engineering and Information, Technology, Slovak Technical University, Ilkovicova 3, 81219 Bratislava (Slovakia)

2010-07-01

Two computation clusters based on Rocks Clusters 5.1 Linux distribution with Intel Core Duo and Intel Core Quad based computers were made at the Department of the Nuclear Physics and Technology. Clusters were used for Monte Carlo calculations, specifically for MCNP calculations applied in Nuclear reactor core simulations. Optimization for computation speed was made on hardware and software basis. Hardware cluster parameters, such as size of the memory, network speed, CPU speed, number of processors per computation, number of processors in one computer were tested for shortening the calculation time. For software optimization, different Fortran compilers, MPI implementations and CPU multi-core libraries were tested. Finally computer cluster was used in finding the weighting functions of neutron ex-core detectors of VVER-440. (authors)

Clustering high dimensional data using RIA

Energy Technology Data Exchange (ETDEWEB)

Aziz, Nazrina [School of Quantitative Sciences, College of Arts and Sciences, Universiti Utara Malaysia, 06010 Sintok, Kedah (Malaysia)

2015-05-15

Clustering may simply represent a convenient method for organizing a large data set so that it can easily be understood and information can efficiently be retrieved. However, identifying cluster in high dimensionality data sets is a difficult task because of the curse of dimensionality. Another challenge in clustering is some traditional functions cannot capture the pattern dissimilarity among objects. In this article, we used an alternative dissimilarity measurement called Robust Influence Angle (RIA) in the partitioning method. RIA is developed using eigenstructure of the covariance matrix and robust principal component score. We notice that, it can obtain cluster easily and hence avoid the curse of dimensionality. It is also manage to cluster large data sets with mixed numeric and categorical value.

Computation cluster for Monte Carlo calculations

International Nuclear Information System (INIS)

Petriska, M.; Vitazek, K.; Farkas, G.; Stacho, M.; Michalek, S.

2010-01-01

Two computation clusters based on Rocks Clusters 5.1 Linux distribution with Intel Core Duo and Intel Core Quad based computers were made at the Department of the Nuclear Physics and Technology. Clusters were used for Monte Carlo calculations, specifically for MCNP calculations applied in Nuclear reactor core simulations. Optimization for computation speed was made on hardware and software basis. Hardware cluster parameters, such as size of the memory, network speed, CPU speed, number of processors per computation, number of processors in one computer were tested for shortening the calculation time. For software optimization, different Fortran compilers, MPI implementations and CPU multi-core libraries were tested. Finally computer cluster was used in finding the weighting functions of neutron ex-core detectors of VVER-440. (authors)

Lattice dynamics of impurity clusters : application to pairs

International Nuclear Information System (INIS)

Chandralekha Devi, N.; Behera, S.N.

1979-01-01

A general solution is obtained for the lattice dynamics of a cluster of n-impurity atoms using the double-time Green's function formalism. The cluster is characterized by n-mass defect and m-force constant change parameters. It is shown that this general solution for the Green's function for the n-impurity cluster can also be expressed in terms of the Green's function for the (n-1)-impurity cluster. As an application, the cluster impurity modes for a pair are calculated using the Debye model for the host lattice dynamics. The splitting of the high frequency local modes and nearly zero frequency resonant modes due to pairs show an oscillatory behaviour on varying the distance of separation between the two impurity atoms. These oscillations are most prominent for two similar impurities and get damped for two dissimilar impurities or if one of the impurities produces a force constant change. The predictions of the calculation provide qualitative explanation of the data obtained from the infrared measurements of the resonant modes in mixed crystal system of KBrsub(1-c)Clsub(c):Lisup(+) and KBrsub(1-c)Isub(c):Lisup(+). (author)

Perspective: Size selected clusters for catalysis and electrochemistry

Science.gov (United States)

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro; Vajda, Stefan

2018-03-01

Size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization, and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition, cluster-support interactions, and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modeling based on density functional theory sampling of local minima and energy barriers or ab initio molecular dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Finally, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.

Symptom Clusters in People Living with HIV Attending Five Palliative Care Facilities in Two Sub-Saharan African Countries: A Hierarchical Cluster Analysis.

Science.gov (United States)

Moens, Katrien; Siegert, Richard J; Taylor, Steve; Namisango, Eve; Harding, Richard

2015-01-01

Symptom research across conditions has historically focused on single symptoms, and the burden of multiple symptoms and their interactions has been relatively neglected especially in people living with HIV. Symptom cluster studies are required to set priorities in treatment planning, and to lessen the total symptom burden. This study aimed to identify and compare symptom clusters among people living with HIV attending five palliative care facilities in two sub-Saharan African countries. Data from cross-sectional self-report of seven-day symptom prevalence on the 32-item Memorial Symptom Assessment Scale-Short Form were used. A hierarchical cluster analysis was conducted using Ward's method applying squared Euclidean Distance as the similarity measure to determine the clusters. Contingency tables, X2 tests and ANOVA were used to compare the clusters by patient specific characteristics and distress scores. Among the sample (N=217) the mean age was 36.5 (SD 9.0), 73.2% were female, and 49.1% were on antiretroviral therapy (ART). The cluster analysis produced five symptom clusters identified as: 1) dermatological; 2) generalised anxiety and elimination; 3) social and image; 4) persistently present; and 5) a gastrointestinal-related symptom cluster. The patients in the first three symptom clusters reported the highest physical and psychological distress scores. Patient characteristics varied significantly across the five clusters by functional status (worst functional physical status in cluster one, ppeople living with HIV with longitudinally collected symptom data to test cluster stability and identify common symptom trajectories is recommended.

Evaluation of the energetics of copper-vacancy clusters in Fe

Energy Technology Data Exchange (ETDEWEB)

Morishita, Kazunori, E-mail: morishita@iae.kyoto-u.ac.jp; Nakasuji, Toshiki; Ruan, Xiaoyong

2017-02-15

Highlights: • Thermodynamics evaluation of the nucleation process of copper-vacancy clusters in Fe is performed. • Nucleation free energy of copper-vacancy clusters in Fe is formulated. • With this energetics, two different nucleation paths of clusters are found as a function of the damage rate. - Abstract: A theoretical study is conducted to evaluate the nucleation free energy of copper-vacancy clusters in Fe as a function of the numbers of copper atoms and of vacancies in a cluster. Using this free energy value, cluster nucleation processes during irradiation are investigated. The results clearly show that there are two different types of cluster nucleation paths on the free energy surface; one is the formation of empty voids by jumping over the ridge of the free energy surface, and the other corresponds to a path for the formation of copper clusters by going around the ridge. The dependence of easy nucleation paths on the damage rate is discussed.

A self-consistent model of rich clusters of galaxies. I. The galactic component of a cluster

International Nuclear Information System (INIS)

Konyukov, M.V.

1985-01-01

It is shown that to obtain the distribution function for the galactic component of a cluster reduces in the last analysis to solving the boundary-value problem for the gravitational potential of a self-consistent field. The distribution function is determined by two main parameters. An algorithm is constructed for the solution of the problem, and a program is set up to solve it. It is used to establish the region of values of the parameters in the problem for which solutions exist. The scheme proposed is extended to the case where there exists in the cluster a separate central body with a known density distribution (for example, a cD galaxy). A method is indicated for the estimation of the parameters of the model from the results of observations of clusters of galaxies in the optical range

I Cluster geografici

Directory of Open Access Journals (Sweden)

Maurizio Rosina

2010-03-01

Full Text Available Geographic ClustersOver the past decade, public alphanumeric database have been growing at exceptional rate. Most of data can be georeferenced, so that is possible gaining new knowledge from such databases. The contribution of this paper is two-fold. We first present a model of geographic clusters, which uses only geographic and functionally data properties. The model is useful to process huge amount of public/government data, even daily upgrading. After that, we merge the model into the framework GEOPOI (GEOcoding Points Of Interest, and show some graphic map results.

I Cluster geografici

Directory of Open Access Journals (Sweden)

Maurizio Rosina

2010-03-01

Full Text Available Geographic Clusters Over the past decade, public alphanumeric database have been growing at exceptional rate. Most of data can be georeferenced, so that is possible gaining new knowledge from such databases. The contribution of this paper is two-fold. We first present a model of geographic clusters, which uses only geographic and functionally data properties. The model is useful to process huge amount of public/government data, even daily upgrading. After that, we merge the model into the framework GEOPOI (GEOcoding Points Of Interest, and show some graphic map results.

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

Science.gov (United States)

Yin, Shi; Bernstein, Elliot R

2017-10-05

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

Clustering and segregation of small vacancy clusters near tungsten (0 0 1) surface

Science.gov (United States)

Duan, Guohua; Li, Xiangyan; Xu, Yichun; Zhang, Yange; Jiang, Yan; Hao, Congyu; Liu, C. S.; Fang, Q. F.; Chen, Jun-Ling; Luo, G.-N.; Wang, Zhiguang

2018-01-01

Nanoporous metals have been shown to exhibit radiation-tolerance due to the trapping of the defects by the surface. However, the behavior of vacancy clusters near the surface is not clear which involves the competition between the self-trapping and segregation of small vacancy clusters (Vn) nearby the surface. In this study, we investigated the energetic and kinetic properties of small vacancy clusters near tungsten (0 0 1) surface by combining molecular statics (MS) calculations and object Kinetic Monte Carlo (OKMC) simulations. Results show that vacancies could be clustered with the reduced formation energy and migration energy of the single vacancy around a cluster as the respective energetic and kinetic driving forces. The small cluster has a migration energy barrier comparable to that for the single vacancy; the migration energy barriers for V1-5 and V7 are 1.80, 1.94, 2.17, 2.78, 3.12 and 3.11 eV, respectively. Clusters and become unstable near surface (0 0 1) and tend to dissociate into the surface. At the operation temperature of 1000 K, the single vacancy, V2, 2 V 3 V3 and V4 were observed to segregate to the surface within a time of one hour. Meanwhile, larger clusters survived near the surface, which could serve as nucleating center for voids near the surface. Our results suggest that under a low radiation dose, surface (0 0 1) could act as a sink for small vacancy clusters, alleviating defect accumulation in the material under a low radiation dose. We also obtained several empirical expressions for the vacancy cluster formation energy, binding energy, and trapping radius as a function of the number of vacancies in the cluster.

Hydrodynamic clustering of droplets in turbulence

Science.gov (United States)

Kunnen, Rudie; Yavuz, Altug; van Heijst, Gertjan; Clercx, Herman

2017-11-01

Small, inertial particles are known to cluster in turbulent flows: particles are centrifuged out of eddies and gather in the strain-dominated regions. This so-called preferential concentration is reflected in the radial distribution function (RDF; a quantitative measure of clustering). We study clustering of water droplets in a loudspeaker-driven turbulence chamber. We track the motion of droplets in 3D and calculate the RDF. At moderate scales (a few Kolmogorov lengths) we find the typical power-law scaling of preferential concentration in the RDF. However, at even smaller scales (a few droplet diameters), we encounter a hitherto unobserved additional clustering. We postulate that the additional clustering is due to hydrodynamic interactions, an effect which is typically disregarded in modeling. Using a perturbative expansion of inertial effects in a Stokes-flow description of two interacting spheres, we obtain an expression for the RDF which indeed includes the additional clustering. The additional clustering enhances the collision probability of droplets, which enhances their growth rate due to coalescence. The additional clustering is thus an essential effect in precipitation modeling.

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

Science.gov (United States)

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

2015-12-01

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

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

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

Science.gov (United States)

Zentner, Andrew R.

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

The evolution of the cluster optical galaxy luminosity function between z = 0.4 and 0.9 in the DAFT/FADA survey

Science.gov (United States)

Martinet, Nicolas; Durret, Florence; Guennou, Loïc; Adami, Christophe; Biviano, Andrea; Ulmer, Melville P.; Clowe, Douglas; Halliday, Claire; Ilbert, Olivier; Márquez, Isabel; Schirmer, Mischa

2015-03-01

Context. There is some disagreement about the abundance of faint galaxies in high-redshift clusters, with contradictory results in the literature arising from studies of the optical galaxy luminosity function (GLF) for small cluster samples. Aims: We compute GLFs for one of the largest medium-to-high-redshift (0.4 ≤ z DAFT/FADA survey in the B,V,R, and I rest-frame bands. We used photometric redshifts computed from BVRIZJ images to constrain galaxy cluster membership. We carried out a detailed estimate of the completeness of our data. We distinguished the red-sequence and blue galaxies using a V - I versus I colour-magnitude diagram. We studied the evolution of these two populations with redshift. We fitted Schechter functions to our stacked GLFs to determine average cluster characteristics. Results: We find that the shapes of our GLFs are similar for the B,V,R, and I bands with a drop at the red GLF faint ends that is more pronounced at high redshift: αred ~ -0.5 at 0.40 ≤ z 0.1 at 0.65 ≤ z < 0.90. The blue GLFs have a steeper faint end (αblue ~ -1.6) than the red GLFs, which appears to be independent of redshift. For the full cluster sample, blue and red GLFs meet at MV = -20, MR = -20.5, and MI = -20.3. A study of how galaxy types evolve with redshift shows that late-type galaxies appear to become early types between z ~ 0.9 and today. Finally, the faint ends of the red GLFs of more massive clusters appear to be richer than less massive clusters, which is more typical of the lower redshift behaviour. Conclusions: Our results indicate that these clusters form at redshifts higher than z = 0.9 from galaxy structures that already have an established red sequence. Late-type galaxies then appear to evolve into early types, enriching the red sequence between this redshift and today. This effect is consistent with the evolution of the faint-end slope of the red sequence and the galaxy type evolution that we find. Finally, faint galaxies accreted from the field

What is the best density functional to describe water clusters: evaluation of widely used density functionals with various basis sets for (H2O)n (n = 1-10)

Czech Academy of Sciences Publication Activity Database

Li, F.; Wang, L.; Zhao, J.; Xie, J. R. H.; Riley, Kevin Eugene; Chen, Z.

2011-01-01

Roč. 130, 2/3 (2011), s. 341-352 ISSN 1432-881X Institutional research plan: CEZ:AV0Z40550506 Keywords : water cluster * density functional theory * MP2 . CCSD(T) * basis set * relative energies Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.162, year: 2011

TURBULENT CLUSTERING OF PROTOPLANETARY DUST AND PLANETESIMAL FORMATION

International Nuclear Information System (INIS)

Pan Liubin; Padoan, Paolo; Scalo, John; Kritsuk, Alexei G.; Norman, Michael L.

2011-01-01

We study the clustering of inertial particles in turbulent flows and discuss its applications to dust particles in protoplanetary disks. Using numerical simulations, we compute the radial distribution function (RDF), which measures the probability of finding particle pairs at given distances, and the probability density function of the particle concentration. The clustering statistics depend on the Stokes number, St, defined as the ratio of the particle friction timescale, τ p , to the Kolmogorov timescale in the flow. In agreement with previous studies, we find that, in the dissipation range, the clustering intensity strongly peaks at St ≅ 1, and the RDF for St ∼ 1 shows a fast power-law increase toward small scales, suggesting that turbulent clustering may considerably enhance the particle collision rate. Clustering at inertial-range scales is of particular interest to the problem of planetesimal formation. At these large scales, the strongest clustering is from particles with τ p in the inertial range. Clustering of these particles occurs primarily around a scale where the eddy turnover time is ∼τ p . We find that particles of different sizes tend to cluster at different locations, leading to flat RDFs between different particles at small scales. In the presence of multiple particle sizes, the overall clustering strength decreases as the particle size distribution broadens. We discuss particle clustering in two recent models for planetesimal formation. We argue that, in the model based on turbulent clustering of chondrule-size particles, the probability of finding strong clusters that can seed planetesimals may have been significantly overestimated. We discuss various clustering mechanisms in simulations of planetesimal formation by gravitational collapse of dense clumps of meter-size particles, in particular the contribution from turbulent clustering due to the limited numerical resolution.

Percolation approach for atomic and molecular cluster formation

International Nuclear Information System (INIS)

Knospe, O.; Seifert, G.

1987-12-01

We apply a percolation approach for the theoretical analysis of mass spectra of molecular microclusters obtained by adiabatic expansion technique. The evolution of the shape of the experimental size distributions as function of stagnation pressure and stagnation temperature are theoretically reproduced by varying the percolation parameter. Remaining discrepancies between theory and experiment are discussed. In addition, the even-odd alternation as well as the 'magic' shell structure within metallic, secondary ion mass spectra are investigated by introducing statistical weights for the cluster formation probabilities. Shell correction energies of atomic clusters as function of cluster-size are deduced from the experimental data. (orig.)

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

Science.gov (United States)

Bailyn, Charles D.; Pinsonneault, Marc H.

1995-01-01

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

Fine structure of cluster decays

International Nuclear Information System (INIS)

Dumitrescu, O.

1993-07-01

Within the one level R-matrix approach the hindrance factors of the radioactive decays in which are emitted α and 14 C - nuclei are calculated. The generalization to radioactive decays in which are emitted heavier clusters such as e.g. 20 O, 24 Ne, 25 Ne, 28 Mg. 30 Mg, 32 Si and 34 Si is straightforward. The interior wave functions are supposed to be given by the shell model with effective residual interactions (e.g. the large scale shell model code-OXBASH - in the Michigan State University version for nearly spherical nuclei or by the enlarged superfluid model - ESM - recently proposed for deformed nuclei). The exterior wave functions are calculated from a cluster - nucleus double - folding model potential obtained with the M3Y interaction. As examples of the cluster decay fine structure we analyzed the particular cases of α - decay of 241 Am and 14 C -decay of 233 Ra. Good agreement with the experimental data is obtained. (author). 78 refs, 2 figs, 6 tabs

Coexistence of Cluster Structure and Mean-field-type Structure in Medium-weight Nuclei

International Nuclear Information System (INIS)

Taniguchi, Yasutaka; Horiuchi, Hisashi; Kimura, Masaaki

2006-01-01

We have studied the coexistence of cluster structure and mean-field-type structure in 20Ne and 40Ca using Antisymmetrized Molecular Dynamics (AMD) + Generator Coordinate Method (GCM). By energy variation with new constraint for clustering, we calculate cluster structure wave function. Superposing cluster structure wave functions and mean-field-type structure wave function, we found that 8Be-12C, α-36Ar and 12C-28Si cluster structure are important components of K π = 0 3 + band of 20Ne, that of normal deformed band of 40Ca and that of super deformed band of 40Ca, respectively

Measuring the Scatter of the Mass–Richness Relation in Galaxy Clusters in Photometric Imaging Surveys by Means of Their Correlation Function

Energy Technology Data Exchange (ETDEWEB)

Campa, Julia; Estrada, Juan; Flaugher, Brenna

2017-02-03

The knowledge of the scatter in the mass-observable relation is a key ingredient for a cosmological analysis based on galaxy clusters in a photometric survey. We demonstrate here how the linear bias measured in the correlation function for clusters can be used to determine the value of the scatter. The new method is tested in simulations of a 5.000 square degrees optical survey up to z~1, similar to the ongoing Dark Energy Survey. The results indicate that the scatter can be measured with a precision of 5% using this technique.

The smart cluster method. Adaptive earthquake cluster identification and analysis in strong seismic regions

Science.gov (United States)

Schaefer, Andreas M.; Daniell, James E.; Wenzel, Friedemann

2017-07-01

Earthquake clustering is an essential part of almost any statistical analysis of spatial and temporal properties of seismic activity. The nature of earthquake clusters and subsequent declustering of earthquake catalogues plays a crucial role in determining the magnitude-dependent earthquake return period and its respective spatial variation for probabilistic seismic hazard assessment. This study introduces the Smart Cluster Method (SCM), a new methodology to identify earthquake clusters, which uses an adaptive point process for spatio-temporal cluster identification. It utilises the magnitude-dependent spatio-temporal earthquake density to adjust the search properties, subsequently analyses the identified clusters to determine directional variation and adjusts its search space with respect to directional properties. In the case of rapid subsequent ruptures like the 1992 Landers sequence or the 2010-2011 Darfield-Christchurch sequence, a reclassification procedure is applied to disassemble subsequent ruptures using near-field searches, nearest neighbour classification and temporal splitting. The method is capable of identifying and classifying earthquake clusters in space and time. It has been tested and validated using earthquake data from California and New Zealand. A total of more than 1500 clusters have been found in both regions since 1980 with M m i n = 2.0. Utilising the knowledge of cluster classification, the method has been adjusted to provide an earthquake declustering algorithm, which has been compared to existing methods. Its performance is comparable to established methodologies. The analysis of earthquake clustering statistics lead to various new and updated correlation functions, e.g. for ratios between mainshock and strongest aftershock and general aftershock activity metrics.

Chromosomal evolution of the PKD1 gene family in primates

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Krawczak Michael

2008-09-01

Full Text Available Abstract Background The autosomal dominant polycystic kidney disease (ADPKD is mostly caused by mutations in the PKD1 (polycystic kidney disease 1 gene located in 16p13.3. Moreover, there are six pseudogenes of PKD1 that are located proximal to the master gene in 16p13.1. In contrast, no pseudogene could be detected in the mouse genome, only a single copy gene on chromosome 17. The question arises how the human situation originated phylogenetically. To address this question we applied comparative FISH-mapping of a human PKD1-containing genomic BAC clone and a PKD1-cDNA clone to chromosomes of a variety of primate species and the dog as a non-primate outgroup species. Results Comparative FISH with the PKD1-cDNA clone clearly shows that in all primate species studied distinct single signals map in subtelomeric chromosomal positions orthologous to the short arm of human chromosome 16 harbouring the master PKD1 gene. Only in human and African great apes, but not in orangutan, FISH with both BAC and cDNA clones reveals additional signal clusters located proximal of and clearly separated from the PKD1 master genes indicating the chromosomal position of PKD1 pseudogenes in 16p of these species, respectively. Indeed, this is in accordance with sequencing data in human, chimpanzee and orangutan. Apart from the master PKD1 gene, six pseudogenes are identified in both, human and chimpanzee, while only a single-copy gene is present in the whole-genome sequence of orangutan. The phylogenetic reconstruction of the PKD1-tree reveals that all human pseudogenes are closely related to the human PKD1 gene, and all chimpanzee pseudogenes are closely related to the chimpanzee PKD1 gene. However, our statistical analyses provide strong indication that gene conversion events may have occurred within the PKD1 family members of human and chimpanzee, respectively. Conclusion PKD1 must have undergone amplification very recently in hominid evolution. Duplicative

Theory of boundary-free two-dimensional dust clusters

International Nuclear Information System (INIS)

Tsytovich, V.N.; Gousein-zade, N.G.; Morfill, G.E.

2006-01-01

It is shown theoretically that a stable two-dimensional (2D) grain cluster can exist in plasmas without external confinement if the shadow attraction of grains is taken into account. These are considered as boundary-free clusters. The equilibrium radius of the clusters is investigated numerically. It is found that it is rapidly decreasing with an increase of the attraction coefficient and with an increase of the number of grains N in the cluster. Comparison of energies of one shell cluster containing N grains with the energies of a cluster with N-1 grains in the shell and an additional one grain in the center as functions of the attraction coefficient is used to find the magic numbers for new shell creation. It is demonstrated that a dissociation of the cluster in several smaller clusters requires less energy than a removal of one of the grains from the cluster. The computations were performed for the Debye screening and for the nonlinear screening models and show that the structure of the clusters is sensitive to the type of screening. Frequencies of all collective modes of the 2D boundary-free clusters are calculated up to N=7 grains in the cluster for the case where all grains form one shell cluster and for the case where N=6 grains form one shell cluster and one of the grains is located at the center of the cluster. The frequencies of the modes increase with a decrease of the cluster radius. Stable and unstable modes are investigated as a function of the attraction coefficient. The presence of instability indicates that this type of equilibrium cluster does not correspond to the minimum energy in all directions and will be converted into another stable configuration. The universal magic number N m of grains in one shell cluster, such that for N=N m +1 the modes of the shell start to be unstable and the cluster converts to the cluster with N m grains in the shell and one grain in the center, is found for both the Yukawa screening and for the nonlinear screening

Confirmation of translatability and functionality certifies the dual endothelin1/VEGFsp receptor (DEspR) protein.

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Herrera, Victoria L M; Steffen, Martin; Moran, Ann Marie; Tan, Glaiza A; Pasion, Khristine A; Rivera, Keith; Pappin, Darryl J; Ruiz-Opazo, Nelson

2016-06-14

In contrast to rat and mouse databases, the NCBI gene database lists the human dual-endothelin1/VEGFsp receptor (DEspR, formerly Dear) as a unitary transcribed pseudogene due to a stop [TGA]-codon at codon#14 in automated DNA and RNA sequences. However, re-analysis is needed given prior single gene studies detected a tryptophan [TGG]-codon#14 by manual Sanger sequencing, demonstrated DEspR translatability and functionality, and since the demonstration of actual non-translatability through expression studies, the standard-of-excellence for pseudogene designation, has not been performed. Re-analysis must meet UNIPROT criteria for demonstration of a protein's existence at the highest (protein) level, which a priori, would override DNA- or RNA-based deductions. To dissect the nucleotide sequence discrepancy, we performed Maxam-Gilbert sequencing and reviewed 727 RNA-seq entries. To comply with the highest level multiple UNIPROT criteria for determining DEspR's existence, we performed various experiments using multiple anti-DEspR monoclonal antibodies (mAbs) targeting distinct DEspR epitopes with one spanning the contested tryptophan [TGG]-codon#14, assessing: (a) DEspR protein expression, (b) predicted full-length protein size, (c) sequence-predicted protein-specific properties beyond codon#14: receptor glycosylation and internalization, (d) protein-partner interactions, and (e) DEspR functionality via DEspR-inhibition effects. Maxam-Gilbert sequencing and some RNA-seq entries demonstrate two guanines, hence a tryptophan [TGG]-codon#14 within a compression site spanning an error-prone compression sequence motif. Western blot analysis using anti-DEspR mAbs targeting distinct DEspR epitopes detect the identical glycosylated 17.5 kDa pull-down protein. Decrease in DEspR-protein size after PNGase-F digest demonstrates post-translational glycosylation, concordant with the consensus-glycosylation site beyond codon#14. Like other small single-transmembrane proteins, mass

Exotic cluster structures on

CERN Document Server

Gekhtman, M; Vainshtein, A

2017-01-01

This is the second paper in the series of papers dedicated to the study of natural cluster structures in the rings of regular functions on simple complex Lie groups and Poisson-Lie structures compatible with these cluster structures. According to our main conjecture, each class in the Belavin-Drinfeld classification of Poisson-Lie structures on \\mathcal{G} corresponds to a cluster structure in \\mathcal{O}(\\mathcal{G}). The authors have shown before that this conjecture holds for any \\mathcal{G} in the case of the standard Poisson-Lie structure and for all Belavin-Drinfeld classes in SL_n, n<5. In this paper the authors establish it for the Cremmer-Gervais Poisson-Lie structure on SL_n, which is the least similar to the standard one.

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

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

2018-05-01

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

Structure and Mobility of Metal Clusters in MOFs: Au, Pd, and AuPd Clusters in MOF-74

DEFF Research Database (Denmark)

Vilhelmsen, Lasse; Walton, Krista S.; Sholl, David S.

2012-01-01

is just as important for nanocluster adsorption as open Zn or Mg metal sites. Using the large number of clusters generated by the GA, we developed a systematic method for predicting the mobility of adsorbed clusters. Through the investigation of diffusion paths a relationship between the cluster......Understanding the adsorption and mobility of metal–organic framework (MOF)-supported metal nanoclusters is critical to the development of these catalytic materials. We present the first theoretical investigation of Au-, Pd-, and AuPd-supported clusters in a MOF, namely MOF-74. We combine density...... functional theory (DFT) calculations with a genetic algorithm (GA) to reliably predict the structure of the adsorbed clusters. This approach allows comparison of hundreds of adsorbed configurations for each cluster. From the investigation of Au8, Pd8, and Au4Pd4 we find that the organic part of the MOF...

A robust approach based on Weibull distribution for clustering gene expression data

Directory of Open Access Journals (Sweden)

Gong Binsheng

2011-05-01

Full Text Available Abstract Background Clustering is a widely used technique for analysis of gene expression data. Most clustering methods group genes based on the distances, while few methods group genes according to the similarities of the distributions of the gene expression levels. Furthermore, as the biological annotation resources accumulated, an increasing number of genes have been annotated into functional categories. As a result, evaluating the performance of clustering methods in terms of the functional consistency of the resulting clusters is of great interest. Results In this paper, we proposed the WDCM (Weibull Distribution-based Clustering Method, a robust approach for clustering gene expression data, in which the gene expressions of individual genes are considered as the random variables following unique Weibull distributions. Our WDCM is based on the concept that the genes with similar expression profiles have similar distribution parameters, and thus the genes are clustered via the Weibull distribution parameters. We used the WDCM to cluster three cancer gene expression data sets from the lung cancer, B-cell follicular lymphoma and bladder carcinoma and obtained well-clustered results. We compared the performance of WDCM with k-means and Self Organizing Map (SOM using functional annotation information given by the Gene Ontology (GO. The results showed that the functional annotation ratios of WDCM are higher than those of the other methods. We also utilized the external measure Adjusted Rand Index to validate the performance of the WDCM. The comparative results demonstrate that the WDCM provides the better clustering performance compared to k-means and SOM algorithms. The merit of the proposed WDCM is that it can be applied to cluster incomplete gene expression data without imputing the missing values. Moreover, the robustness of WDCM is also evaluated on the incomplete data sets. Conclusions The results demonstrate that our WDCM produces clusters

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

Science.gov (United States)

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

2014-05-01

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

Testing the Large-scale Environments of Cool-core and Non-cool-core Clusters with Clustering Bias

Energy Technology Data Exchange (ETDEWEB)

Medezinski, Elinor; Battaglia, Nicholas; Cen, Renyue; Gaspari, Massimo; Strauss, Michael A.; Spergel, David N. [Department of Astrophysical Sciences, 4 Ivy Lane, Princeton, NJ 08544 (United States); Coupon, Jean, E-mail: elinorm@astro.princeton.edu [Department of Astronomy, University of Geneva, ch. dEcogia 16, CH-1290 Versoix (Switzerland)

2017-02-10

There are well-observed differences between cool-core (CC) and non-cool-core (NCC) clusters, but the origin of this distinction is still largely unknown. Competing theories can be divided into internal (inside-out), in which internal physical processes transform or maintain the NCC phase, and external (outside-in), in which the cluster type is determined by its initial conditions, which in turn leads to different formation histories (i.e., assembly bias). We propose a new method that uses the relative assembly bias of CC to NCC clusters, as determined via the two-point cluster-galaxy cross-correlation function (CCF), to test whether formation history plays a role in determining their nature. We apply our method to 48 ACCEPT clusters, which have well resolved central entropies, and cross-correlate with the SDSS-III/BOSS LOWZ galaxy catalog. We find that the relative bias of NCC over CC clusters is b = 1.42 ± 0.35 (1.6 σ different from unity). Our measurement is limited by the small number of clusters with core entropy information within the BOSS footprint, 14 CC and 34 NCC clusters. Future compilations of X-ray cluster samples, combined with deep all-sky redshift surveys, will be able to better constrain the relative assembly bias of CC and NCC clusters and determine the origin of the bimodality.

Testing the Large-scale Environments of Cool-core and Non-cool-core Clusters with Clustering Bias

International Nuclear Information System (INIS)

Medezinski, Elinor; Battaglia, Nicholas; Cen, Renyue; Gaspari, Massimo; Strauss, Michael A.; Spergel, David N.; Coupon, Jean

2017-01-01

There are well-observed differences between cool-core (CC) and non-cool-core (NCC) clusters, but the origin of this distinction is still largely unknown. Competing theories can be divided into internal (inside-out), in which internal physical processes transform or maintain the NCC phase, and external (outside-in), in which the cluster type is determined by its initial conditions, which in turn leads to different formation histories (i.e., assembly bias). We propose a new method that uses the relative assembly bias of CC to NCC clusters, as determined via the two-point cluster-galaxy cross-correlation function (CCF), to test whether formation history plays a role in determining their nature. We apply our method to 48 ACCEPT clusters, which have well resolved central entropies, and cross-correlate with the SDSS-III/BOSS LOWZ galaxy catalog. We find that the relative bias of NCC over CC clusters is b = 1.42 ± 0.35 (1.6 σ different from unity). Our measurement is limited by the small number of clusters with core entropy information within the BOSS footprint, 14 CC and 34 NCC clusters. Future compilations of X-ray cluster samples, combined with deep all-sky redshift surveys, will be able to better constrain the relative assembly bias of CC and NCC clusters and determine the origin of the bimodality.

Predictive coupled-cluster isomer orderings for some SinCm (m, n ≤ 12) clusters: A pragmatic comparison between DFT and complete basis limit coupled-cluster benchmarks

International Nuclear Information System (INIS)

Byrd, Jason N.; Lutz, Jesse J.; Jin, Yifan; Ranasinghe, Duminda S.; Perera, Ajith; Bartlett, Rodney J.; Montgomery, John A.; Duan, Xiaofeng F.; Burggraf, Larry W.; Sanders, Beverly A.

2016-01-01

The accurate determination of the preferred Si 12 C 12 isomer is important to guide experimental efforts directed towards synthesizing SiC nano-wires and related polymer structures which are anticipated to be highly efficient exciton materials for the opto-electronic devices. In order to definitively identify preferred isomeric structures for silicon carbon nano-clusters, highly accurate geometries, energies, and harmonic zero point energies have been computed using coupled-cluster theory with systematic extrapolation to the complete basis limit for set of silicon carbon clusters ranging in size from SiC 3 to Si 12 C 12 . It is found that post-MBPT(2) correlation energy plays a significant role in obtaining converged relative isomer energies, suggesting that predictions using low rung density functional methods will not have adequate accuracy. Utilizing the best composite coupled-cluster energy that is still computationally feasible, entailing a 3-4 SCF and coupled-cluster theory with singles and doubles extrapolation with triple-ζ (T) correlation, the closo Si 12 C 12 isomer is identified to be the preferred isomer in the support of previous calculations [X. F. Duan and L. W. Burggraf, J. Chem. Phys. 142, 034303 (2015)]. Additionally we have investigated more pragmatic approaches to obtaining accurate silicon carbide isomer energies, including the use of frozen natural orbital coupled-cluster theory and several rungs of standard and double-hybrid density functional theory. Frozen natural orbitals as a way to compute post-MBPT(2) correlation energy are found to be an excellent balance between efficiency and accuracy.

Radio emission of Abell galaxy clusters with red shifts from 0.02 to 0.075 at 102.5 MHz. Observations of clusters southward from the galactic plane

International Nuclear Information System (INIS)

Gubanov, A.G.

1983-01-01

The sample of 121 Abell clusters of galaxies with measured red shifts from 0.02 to 0.075, delta= 10 deg - +80 deg and within the completeness galactic-latitude region is presented. The completeness. with respect to the Abell's catalog is 80%. The completeness of the sample in function of distance (the completeness function) was constructed and the mean cluster density of 1.5x10 -6 Mpc -3 was derived. Observations at 102.5 MHz of 39 clusters southward from the galactic plane were carried out with BSA radio telescope. Flux density measurements for radio sources in the directions of the clusters have been made, integrated fluxes of clusters and luminosity estimations for their radio halos are presented. Radio emission of 11 clusters was detected , and for two of these and for other clust rs radio sources detected in the directions to the outskirts of clusters. Radio halos having the luminosity comparable to that of the A1656 (Coma) cluster are not typical for clusters

Calibrating the Planck cluster mass scale with CLASH

Science.gov (United States)

Penna-Lima, M.; Bartlett, J. G.; Rozo, E.; Melin, J.-B.; Merten, J.; Evrard, A. E.; Postman, M.; Rykoff, E.

2017-08-01

We determine the mass scale of Planck galaxy clusters using gravitational lensing mass measurements from the Cluster Lensing And Supernova survey with Hubble (CLASH). We have compared the lensing masses to the Planck Sunyaev-Zeldovich (SZ) mass proxy for 21 clusters in common, employing a Bayesian analysis to simultaneously fit an idealized CLASH selection function and the distribution between the measured observables and true cluster mass. We used a tiered analysis strategy to explicitly demonstrate the importance of priors on weak lensing mass accuracy. In the case of an assumed constant bias, bSZ, between true cluster mass, M500, and the Planck mass proxy, MPL, our analysis constrains 1-bSZ = 0.73 ± 0.10 when moderate priors on weak lensing accuracy are used, including a zero-mean Gaussian with standard deviation of 8% to account for possible bias in lensing mass estimations. Our analysis explicitly accounts for possible selection bias effects in this calibration sourced by the CLASH selection function. Our constraint on the cluster mass scale is consistent with recent results from the Weighing the Giants program and the Canadian Cluster Comparison Project. It is also consistent, at 1.34σ, with the value needed to reconcile the Planck SZ cluster counts with Planck's base ΛCDM model fit to the primary cosmic microwave background anisotropies.