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Lupski JR, Gonzaga-Jauregui C, Yang Y, Bainbridge MN, Jhangiani S, Buhay CJ, Kovar CL, Wang M, Hawes AC, Reid JG, Eng C, Muzny DM, Gibbs RA. Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy. Genome Med 2013; 5:57. [PMID: 23806086 PMCID: PMC3706849 DOI: 10.1186/gm461] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/20/2013] [Accepted: 06/27/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The debate regarding the relative merits of whole genome sequencing (WGS) versus exome sequencing (ES) centers around comparative cost, average depth of coverage for each interrogated base, and their relative efficiency in the identification of medically actionable variants from the myriad of variants identified by each approach. Nevertheless, few genomes have been subjected to both WGS and ES, using multiple next generation sequencing platforms. In addition, no personal genome has been so extensively analyzed using DNA derived from peripheral blood as opposed to DNA from transformed cell lines that may either accumulate mutations during propagation or clonally expand mosaic variants during cell transformation and propagation. METHODS We investigated a genome that was studied previously by SOLiD chemistry using both ES and WGS, and now perform six independent ES assays (Illumina GAII (x2), Illumina HiSeq (x2), Life Technologies' Personal Genome Machine (PGM) and Proton), and one additional WGS (Illumina HiSeq). RESULTS We compared the variants identified by the different methods and provide insights into the differences among variants identified between ES runs in the same technology platform and among different sequencing technologies. We resolved the true genotypes of medically actionable variants identified in the proband through orthogonal experimental approaches. Furthermore, ES identified an additional SH3TC2 variant (p.M1?) that likely contributes to the phenotype in the proband. CONCLUSIONS ES identified additional medically actionable variant calls and helped resolve ambiguous single nucleotide variants (SNV) documenting the power of increased depth of coverage of the captured targeted regions. Comparative analyses of WGS and ES reveal that pseudogenes and segmental duplications may explain some instances of apparent disease mutations in unaffected individuals.
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Baker S, Joecker A, Church G, Snyder M, West J, Salzberg S, Worthey E, Smith T, Wang J, Reid JG. Genome interpretation and assembly-recent progress and next steps. Nat Biotechnol 2013; 30:1081-3. [PMID: 23138307 DOI: 10.1038/nbt.2425] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Lim ET, Raychaudhuri S, Sanders SJ, Stevens C, Sabo A, MacArthur DG, Neale BM, Kirby A, Ruderfer DM, Fromer M, Lek M, Liu L, Flannick J, Ripke S, Nagaswamy U, Muzny D, Reid JG, Hawes A, Newsham I, Wu Y, Lewis L, Dinh H, Gross S, Wang LS, Lin CF, Valladares O, Gabriel SB, dePristo M, Altshuler DM, Purcell SM, State MW, Boerwinkle E, Buxbaum JD, Cook EH, Gibbs RA, Schellenberg GD, Sutcliffe JS, Devlin B, Roeder K, Daly MJ. Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders. Neuron 2013; 77:235-42. [PMID: 23352160 PMCID: PMC3613849 DOI: 10.1016/j.neuron.2012.12.029] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2012] [Indexed: 10/27/2022]
Abstract
To characterize the role of rare complete human knockouts in autism spectrum disorders (ASDs), we identify genes with homozygous or compound heterozygous loss-of-function (LoF) variants (defined as nonsense and essential splice sites) from exome sequencing of 933 cases and 869 controls. We identify a 2-fold increase in complete knockouts of autosomal genes with low rates of LoF variation (≤ 5% frequency) in cases and estimate a 3% contribution to ASD risk by these events, confirming this observation in an independent set of 563 probands and 4,605 controls. Outside the pseudoautosomal regions on the X chromosome, we similarly observe a significant 1.5-fold increase in rare hemizygous knockouts in males, contributing to another 2% of ASDs in males. Taken together, these results provide compelling evidence that rare autosomal and X chromosome complete gene knockouts are important inherited risk factors for ASD.
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English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One 2012. [PMID: 23185243 PMCID: PMC3504050 DOI: 10.1371/journal.pone.0047768] [Citation(s) in RCA: 638] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many genomes have been sequenced to high-quality draft status using Sanger capillary electrophoresis and/or newer short-read sequence data and whole genome assembly techniques. However, even the best draft genomes contain gaps and other imperfections due to limitations in the input data and the techniques used to build draft assemblies. Sequencing biases, repetitive genomic features, genomic polymorphism, and other complicating factors all come together to make some regions difficult or impossible to assemble. Traditionally, draft genomes were upgraded to “phase 3 finished” status using time-consuming and expensive Sanger-based manual finishing processes. For more facile assembly and automated finishing of draft genomes, we present here an automated approach to finishing using long-reads from the Pacific Biosciences RS (PacBio) platform. Our algorithm and associated software tool, PBJelly, (publicly available at https://sourceforge.net/projects/pb-jelly/) automates the finishing process using long sequence reads in a reference-guided assembly process. PBJelly also provides “lift-over” co-ordinate tables to easily port existing annotations to the upgraded assembly. Using PBJelly and long PacBio reads, we upgraded the draft genome sequences of a simulated Drosophila melanogaster, the version 2 draft Drosophila pseudoobscura, an assembly of the Assemblathon 2.0 budgerigar dataset, and a preliminary assembly of the Sooty mangabey. With 24× mapped coverage of PacBio long-reads, we addressed 99% of gaps and were able to close 69% and improve 12% of all gaps in D. pseudoobscura. With 4× mapped coverage of PacBio long-reads we saw reads address 63% of gaps in our budgerigar assembly, of which 32% were closed and 63% improved. With 6.8× mapped coverage of mangabey PacBio long-reads we addressed 97% of gaps and closed 66% of addressed gaps and improved 19%. The accuracy of gap closure was validated by comparison to Sanger sequencing on gaps from the original D. pseudoobscura draft assembly and shown to be dependent on initial reference quality.
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Saliba J, Trevino LR, Meng Q, Zabriskie R, Powell B, Hicks S, Kimmel M, Cheung H, Muzny DM, Reid JG, Wheeler D, Gibbs RA, Plon SE. Abstract 5113: Functional analysis of genomic variants identified through whole exome sequencing for susceptibility to lymphocytic leukemia. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-5113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The underlying genetic basis of many childhood cancers remains largely unknown, which places a significant focus on the discovery and understanding of cancer susceptibility genes. Our research is focused on the identification of novel high risk childhood cancer susceptibility genes through next generation sequencing methods and functional assays. One kindred contained four individuals diagnosed during childhood with lymphocytic leukemia or lymphoma transmitted in an autosomal dominant pattern of inheritance. Whole exome sequencing was performed on the constitutional DNA of three of the patients diagnosed with childhood cancer and one non-transmitting parent as an internal control. This analysis resulted in over 1000 unique single nucleotide variant (SNV) sites shared among the three affected family members. Of these SNVs, greater than 95% were found in control databases and excluded. Also, any variant found in the non-transmitting parent was eliminated. Systematic bioinformatics analysis resulted in a short list of seven missense SNVs predicted to be functionally important. Within this list is the missense mutation of a conserved residue (L254P) of Human Cytosolic 5′ Nucleotidase (NT5C1A). NT5C1A has a role in nucleoside metabolism as this protein primarily catalyzes the production of adenosine through the dephosphorylation of AMP. Adenosine metabolism is essential for lymphocyte maturation and viability, making NT5C1A an attractive leukemia susceptibility candidate to pursue further through functional genomic assays. Prior studies have shown that overexpression of wild type NT5C1A in HEK293 cells improves cell survival after treatment with purine and pyrimidine analogs also used in leukemia treatment. We created multiple HEK293 cell lines that stably overexpress either the NT5C1A wild type or L254P mutant protein. These cells were tested for quantitative changes in NT5C1A mediated cytotoxicity to the nucleoside analogs, Cladribine and Gemcitabine. We have replicated the prior findings in cells overexpressing wild type NT5C1A and demonstrated that resistance is dependent on the amount of exogenous NT5C1A protein expressed. Importantly, overexpression of the L254P protein is deficient in mediating resistance to these analogs, which is consistent with this novel variant interfering with NT5C1A activity. This finding has led us to hypothesize that the L254P mutation leads to a reduction in protein function, most likely through reduced substrate binding, which may increase AMP levels in early lymphocytes and predispose to tumorigenesis. Future directions include experiments to determine the L254P protein's substrate binding affinity and activity and the introduction of the mutation into murine leukemia models as well as analysis of L254P as a pharmacogenetic variant.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5113. doi:1538-7445.AM2012-5113
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Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Shafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shakir K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 2012; 485:242-5. [PMID: 22495311 PMCID: PMC3613847 DOI: 10.1038/nature11011] [Citation(s) in RCA: 1271] [Impact Index Per Article: 105.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 03/06/2012] [Indexed: 01/21/2023]
Abstract
Autism spectrum disorders (ASD) are believed to have genetic and environmental origins, yet in only a modest fraction of individuals can specific causes be identified. To identify further genetic risk factors, here we assess the role of de novo mutations in ASD by sequencing the exomes of ASD cases and their parents (n = 175 trios). Fewer than half of the cases (46.3%) carry a missense or nonsense de novo variant, and the overall rate of mutation is only modestly higher than the expected rate. In contrast, the proteins encoded by genes that harboured de novo missense or nonsense mutations showed a higher degree of connectivity among themselves and to previous ASD genes as indexed by protein-protein interaction screens. The small increase in the rate of de novo events, when taken together with the protein interaction results, are consistent with an important but limited role for de novo point mutations in ASD, similar to that documented for de novo copy number variants. Genetic models incorporating these data indicate that most of the observed de novo events are unconnected to ASD; those that do confer risk are distributed across many genes and are incompletely penetrant (that is, not necessarily sufficient for disease). Our results support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5- to 20-fold. Despite the challenge posed by such models, results from de novo events and a large parallel case-control study provide strong evidence in favour of CHD8 and KATNAL2 as genuine autism risk factors.
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Bainbridge MN, Wiszniewski W, Murdock DR, Friedman J, Gonzaga-Jauregui C, Newsham I, Reid JG, Fink JK, Morgan MB, Gingras MC, Muzny DM, Hoang LD, Yousaf S, Lupski JR, Gibbs RA. Whole-genome sequencing for optimized patient management. Sci Transl Med 2011; 3:87re3. [PMID: 21677200 DOI: 10.1126/scitranslmed.3002243] [Citation(s) in RCA: 242] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Whole-genome sequencing of patient DNA can facilitate diagnosis of a disease, but its potential for guiding treatment has been under-realized. We interrogated the complete genome sequences of a 14-year-old fraternal twin pair diagnosed with dopa (3,4-dihydroxyphenylalanine)-responsive dystonia (DRD; Mendelian Inheritance in Man #128230). DRD is a genetically heterogeneous and clinically complex movement disorder that is usually treated with l-dopa, a precursor of the neurotransmitter dopamine. Whole-genome sequencing identified compound heterozygous mutations in the SPR gene encoding sepiapterin reductase. Disruption of SPR causes a decrease in tetrahydrobiopterin, a cofactor required for the hydroxylase enzymes that synthesize the neurotransmitters dopamine and serotonin. Supplementation of l-dopa therapy with 5-hydroxytryptophan, a serotonin precursor, resulted in clinical improvements in both twins.
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Fawcett GL, Raveendran M, Deiros DR, Chen D, Yu F, Harris RA, Ren Y, Muzny DM, Reid JG, Wheeler DA, Worley KC, Shelton SE, Kalin NH, Milosavljevic A, Gibbs R, Rogers J. Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta). BMC Genomics 2011; 12:311. [PMID: 21668978 PMCID: PMC3141668 DOI: 10.1186/1471-2164-12-311] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 06/13/2011] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Rhesus macaques are the most widely utilized nonhuman primate model in biomedical research. Previous efforts have validated fewer than 900 single nucleotide polymorphisms (SNPs) in this species, which limits opportunities for genetic studies related to health and disease. Extensive information about SNPs and other genetic variation in rhesus macaques would facilitate valuable genetic analyses, as well as provide markers for genome-wide linkage analysis and the genetic management of captive breeding colonies. RESULTS We used the available rhesus macaque draft genome sequence, new sequence data from unrelated individuals and existing published sequence data to create a genome-wide SNP resource for Indian-origin rhesus monkeys. The original reference animal and two additional Indian-origin individuals were resequenced to low coverage using SOLiD™ sequencing. We then used three strategies to validate SNPs: comparison of potential SNPs found in the same individual using two different sequencing chemistries, and comparison of potential SNPs in different individuals identified with either the same or different sequencing chemistries. Our approach validated approximately 3 million SNPs distributed across the genome. Preliminary analysis of SNP annotations suggests that a substantial number of these macaque SNPs may have functional effects. More than 700 non-synonymous SNPs were scored by Polyphen-2 as either possibly or probably damaging to protein function and these variants now constitute potential models for studying functional genetic variation relevant to human physiology and disease. CONCLUSIONS Resequencing of a small number of animals identified greater than 3 million SNPs. This provides a significant new information resource for rhesus macaques, an important research animal. The data also suggests that overall genetic variation is high in this species. We identified many potentially damaging non-synonymous coding SNPs, providing new opportunities to identify rhesus models for human disease.
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Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DCY, Nazareth L, Bainbridge M, Dinh H, Jing C, Wheeler DA, McGuire AL, Zhang F, Stankiewicz P, Halperin JJ, Yang C, Gehman C, Guo D, Irikat RK, Tom W, Fantin NJ, Muzny DM, Gibbs RA. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med 2010; 362:1181-91. [PMID: 20220177 PMCID: PMC4036802 DOI: 10.1056/nejmoa0908094] [Citation(s) in RCA: 621] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Whole-genome sequencing may revolutionize medical diagnostics through rapid identification of alleles that cause disease. However, even in cases with simple patterns of inheritance and unambiguous diagnoses, the relationship between disease phenotypes and their corresponding genetic changes can be complicated. Comprehensive diagnostic assays must therefore identify all possible DNA changes in each haplotype and determine which are responsible for the underlying disorder. The high number of rare, heterogeneous mutations present in all humans and the paucity of known functional variants in more than 90% of annotated genes make this challenge particularly difficult. Thus, the identification of the molecular basis of a genetic disease by means of whole-genome sequencing has remained elusive. We therefore aimed to assess the usefulness of human whole-genome sequencing for genetic diagnosis in a patient with Charcot-Marie-Tooth disease. METHODS We identified a family with a recessive form of Charcot-Marie-Tooth disease for which the genetic basis had not been identified. We sequenced the whole genome of the proband, identified all potential functional variants in genes likely to be related to the disease, and genotyped these variants in the affected family members. RESULTS We identified and validated compound, heterozygous, causative alleles in SH3TC2 (the SH3 domain and tetratricopeptide repeats 2 gene), involving two mutations, in the proband and in family members affected by Charcot-Marie-Tooth disease. Separate subclinical phenotypes segregated independently with each of the two mutations; heterozygous mutations confer susceptibility to neuropathy, including the carpal tunnel syndrome. CONCLUSIONS As shown in this study of a family with Charcot-Marie-Tooth disease, whole-genome sequencing can identify clinically relevant variants and provide diagnostic information to inform the care of patients.
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Creighton CJ, Benham AL, Zhu H, Khan MF, Reid JG, Nagaraja AK, Fountain MD, Dziadek O, Han D, Ma L, Kim J, Hawkins SM, Anderson ML, Matzuk MM, Gunaratne PH. Discovery of novel microRNAs in female reproductive tract using next generation sequencing. PLoS One 2010; 5:e9637. [PMID: 20224791 PMCID: PMC2835764 DOI: 10.1371/journal.pone.0009637] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 02/20/2010] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that mediate post-transcriptional gene silencing. Over 700 human miRNAs have currently been identified, many of which are mutated or de-regulated in diseases. Here we report the identification of novel miRNAs through deep sequencing the small RNAome (<30 nt) of over 100 tissues or cell lines derived from human female reproductive organs in both normal and disease states. These specimens include ovarian epithelium and ovarian cancer, endometrium and endometriomas, and uterine myometrium and uterine smooth muscle tumors. Sequence reads not aligning with known miRNAs were each mapped to the genome to extract flanking sequences. These extended sequence regions were folded in silico to identify RNA hairpins. Sequences demonstrating the ability to form a stem loop structure with low minimum free energy (<-25 kcal) and predicted Drosha and Dicer cut sites yielding a mature miRNA sequence matching the actual sequence were considered putative novel miRNAs. Additional confidence was achieved when putative novel hairpins assembled a collection of sequences highly similar to the putative mature miRNA but with heterogeneous 3'-ends. A confirmed novel miRNA fulfilled these criteria and had its "star" sequence in our collection. We found 7 distinct confirmed novel miRNAs, and 51 additional novel miRNAs that represented highly confident predictions but without detectable star sequences. Our novel miRNAs were detectable in multiple samples, but expressed at low levels and not specific to any one tissue or cell type. To date, this study represents the largest set of samples analyzed together to identify novel miRNAs.
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Nagaraja AK, Creighton CJ, Yu Z, Zhu H, Gunaratne PH, Reid JG, Olokpa E, Itamochi H, Ueno NT, Hawkins SM, Anderson ML, Matzuk MM. A link between mir-100 and FRAP1/mTOR in clear cell ovarian cancer. Mol Endocrinol 2010; 24:447-63. [PMID: 20081105 PMCID: PMC2817607 DOI: 10.1210/me.2009-0295] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 11/23/2009] [Indexed: 01/26/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that direct gene regulation through translational repression and degradation of complementary mRNA. Although miRNAs have been implicated as oncogenes and tumor suppressors in a variety of human cancers, functional roles for individual miRNAs have not been described in clear cell ovarian carcinoma, an aggressive and chemoresistant subtype of ovarian cancer. We performed deep sequencing to comprehensively profile miRNA expression in 10 human clear cell ovarian cancer cell lines compared with normal ovarian surface epithelial cultures and discovered 54 miRNAs that were aberrantly expressed. Because of the critical roles of the phosphatidylinositol 3-kinase/v-akt murine thymoma viral oncogene homolog 1/mammalian target of rapamycin (mTOR) pathway in clear cell ovarian cancer, we focused on mir-100, a putative tumor suppressor that was the most down-regulated miRNA in our cancer cell lines, and its up-regulated target, FRAP1/mTOR. Overexpression of mir-100 inhibited mTOR signaling and enhanced sensitivity to the rapamycin analog RAD001 (everolimus), confirming the key relationship between mir-100 and the mTOR pathway. Furthermore, overexpression of the putative tumor suppressor mir-22 repressed the EVI1 oncogene, which is known to suppress apoptosis by stimulating phosphatidylinositol 3-kinase/v-akt murine thymoma viral oncogene homolog 1 signaling. In addition to these specific effects, reversing the expression of mir-22 and the putative oncogene mir-182 had widespread effects on target and nontarget gene populations that ultimately caused a global shift in the cancer gene signature toward a more normal state. Our experiments have revealed strong candidate miRNAs and their target genes that may contribute to the pathogenesis of clear cell ovarian cancer, thereby highlighting alternative therapeutic strategies for the treatment of this deadly cancer.
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Creighton CJ, Reid JG, Gunaratne PH. Expression profiling of microRNAs by deep sequencing. Brief Bioinform 2009; 10:490-7. [PMID: 19332473 DOI: 10.1093/bib/bbp019] [Citation(s) in RCA: 238] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MicroRNAs are short non-coding RNAs that regulate the stability and translation of mRNAs. Profiling experiments, using microarray or deep sequencing technology, have identified microRNAs that are preferentially expressed in certain tissues, specific stages of development, or disease states such as cancer. Deep sequencing utilizes massively parallel sequencing, generating millions of small RNA sequence reads from a given sample. Profiling of microRNAs by deep sequencing measures absolute abundance and allows for the discovery of novel microRNAs that have eluded previous cloning and standard sequencing efforts. Public databases provide in silico predictions of microRNA gene targets by various algorithms. To better determine which of these predictions represent true positives, microRNA expression data can be integrated with gene expression data to identify putative microRNA:mRNA functional pairs. Here we discuss tools and methodologies for the analysis of microRNA expression data from deep sequencing.
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Reid JG, Nagaraja AK, Lynn FC, Drabek RB, Muzny DM, Shaw CA, Weiss MK, Naghavi AO, Khan M, Zhu H, Tennakoon J, Gunaratne GH, Corry DB, Miller J, McManus MT, German MS, Gibbs RA, Matzuk MM, Gunaratne PH. Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. Genes Dev 2008; 18:1571-81. [PMID: 18614752 PMCID: PMC2556275 DOI: 10.1101/gr.078246.108] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 06/27/2008] [Indexed: 11/25/2022]
Abstract
Massively parallel sequencing of millions of < 30-nt RNAs expressed in mouse ovary, embryonic pancreas (E14.5), and insulin-secreting beta-cells (betaTC-3) reveals that approximately 50% of the mature miRNAs representing mostly the mmu-let-7 family display internal insertion/deletions and substitutions when compared to precursor miRNA and the mouse genome reference sequences. Approximately, 12%-20% of species associated with mmu-let-7 populations exhibit sequence discrepancies that are dramatically reduced in nucleotides 3-7 (5'-seed) and 10-15 (cleavage and anchor sites). This observation is inconsistent with sequencing error and leads us to propose that the changes arise predominantly from post-transcriptional RNA-editing activity operating on miRNA:target mRNA complexes. Internal nucleotide modifications are most enriched at the ninth nucleotide position. A common ninth base edit of U-to-G results in a significant increase in stability of down-regulated let-7a targets in inhibin-deficient mice (Inha-/-). An excess of U-insertions (14.8%) over U-deletions (1.5%) and the presence of cleaved intermediates suggest that a mammalian TUTase (terminal uridylyl transferase) mediated dUTP-dependent U-insertion/U-deletion cycle may be a possible mechanism. We speculate that mRNA target site-directed editing of mmu-let-7a duplex-bulges stabilizes "loose" miRNA:mRNA target associations and functions to expand the target repertoire and/or enhance mRNA decay over translational repression. Our results also demonstrate that the systematic study of sequence variation within specific RNA classes in a given cell type from millions of sequences generated by next-generation sequencing (NGS) technologies ("intranomics") can be used broadly to infer functional constraints on specific parts of completely uncharacterized RNAs.
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Gu P, Reid JG, Gao X, Shaw CA, Creighton C, Tran PL, Zhou X, Drabek RB, Steffen DL, Hoang DM, Weiss MK, Naghavi AO, El-daye J, Khan MF, Legge GB, Wheeler DA, Gibbs RA, Miller JN, Cooney AJ, Gunaratne PH. Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells. PLoS One 2008; 3:e2548. [PMID: 18648548 PMCID: PMC2481296 DOI: 10.1371/journal.pone.0002548] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Accepted: 05/22/2008] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND MicroRNAS (miRNAS: a class of short non-coding RNAs) are emerging as important agents of post transcriptional gene regulation and integral components of gene networks. MiRNAs have been strongly linked to stem cells, which have a remarkable dual role in development. They can either continuously replenish themselves (self-renewal), or differentiate into cells that execute a limited number of specific actions (pluripotence). METHODOLOGY/PRINCIPAL FINDINGS In order to identify novel miRNAs from narrow windows of development we carried out an in silico search for micro-conserved elements (MCE) in adult tissue progenitor transcript sequences. A plethora of previously unknown miRNA candidates were revealed including 545 small RNAs that are enriched in embryonic stem (ES) cells over adult cells. Approximately 20% of these novel candidates are down-regulated in ES (Dicer(-/-)) ES cells that are impaired in miRNA maturation. The ES-enriched miRNA candidates exhibit distinct and opposite expression trends from mmu-mirs (an abundant class in adult tissues) during retinoic acid (RA)-induced ES cell differentiation. Significant perturbation of trends is found in both miRNAs and novel candidates in ES (GCNF(-/-)) cells, which display loss of repression of pluripotence genes upon differentiation. CONCLUSION/SIGNIFICANCE Combining expression profile information with miRNA target prediction, we identified miRNA-mRNA pairs that correlate with ES cell pluripotence and differentiation. Perturbation of these pairs in the ES (GCNF(-/-)) mutant suggests a role for miRNAs in the core regulatory networks underlying ES cell self-renewal, pluripotence and differentiation.
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Nagaraja AK, Creighton CJ, Reid JG, Gunaratne PH, Ma L, Anderson ML, Matzuk MM. MicroRNAs in Human Ovarian Cancer. Biol Reprod 2008. [DOI: 10.1093/biolreprod/78.s1.200a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Weaver DB, Anzola JM, Evans JD, Reid JG, Reese JT, Childs KL, Zdobnov EM, Samanta MP, Miller J, Elsik CG. Computational and transcriptional evidence for microRNAs in the honey bee genome. Genome Biol 2008; 8:R97. [PMID: 17543122 PMCID: PMC2394756 DOI: 10.1186/gb-2007-8-6-r97] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Revised: 12/13/2006] [Accepted: 06/01/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Non-coding microRNAs (miRNAs) are key regulators of gene expression in eukaryotes. Insect miRNAs help regulate the levels of proteins involved with development, metabolism, and other life history traits. The recently sequenced honey bee genome provides an opportunity to detect novel miRNAs in both this species and others, and to begin to infer the roles of miRNAs in honey bee development. RESULTS Three independent computational surveys of the assembled honey bee genome identified a total of 65 non-redundant candidate miRNAs, several of which appear to have previously unrecognized orthologs in the Drosophila genome. A subset of these candidate miRNAs were screened for expression by quantitative RT-PCR and/or genome tiling arrays and most predicted miRNAs were confirmed as being expressed in at least one honey bee tissue. Interestingly, the transcript abundance for several known and novel miRNAs displayed caste or age-related differences in honey bees. Genes in proximity to miRNAs in the bee genome are disproportionately associated with the Gene Ontology terms 'physiological process', 'nucleus' and 'response to stress'. CONCLUSION Computational approaches successfully identified miRNAs in the honey bee and indicated previously unrecognized miRNAs in the well-studied Drosophila melanogaster genome despite the 280 million year distance between these insects. Differentially transcribed miRNAs are likely to be involved in regulating honey bee development, and arguably in the extreme developmental switch between sterile worker bees and highly fertile queens.
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Becker NS, Rodriguez JA, Gingras MC, Reid JG, Brunicardi F, Goss JA, Gibbs RA. QS445. Phosphatase and Tensin Homolog (PTEN) Mutation Detection in Hepatocellular Carcinoma Using The 454 GS and Solexa DNA Sequencing Platforms. J Surg Res 2008. [DOI: 10.1016/j.jss.2007.12.703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Adams J, Aggarwal MM, Ahammed Z, Amonett J, Anderson BD, Arkhipkin D, Averichev GS, Badyal SK, Bai Y, Balewski J, Barannikova O, Barnby LS, Baudot J, Bekele S, Belaga VV, Bellingeri-Laurikainen A, Bellwied R, Berger J, Bezverkhny BI, Bharadwaj S, Bhasin A, Bhati AK, Bhatia VS, Bichsel H, Bielcik J, Bielcikova J, Billmeier A, Bland LC, Blyth CO, Blyth SL, Bonner BE, Botje M, Boucham A, Bouchet J, Brandin AV, Bravar A, Bystersky M, Cadman RV, Cai XZ, Caines H, Sánchez MCDLB, Catu O, Cebra D, Chajecki Z, Chaloupka P, Chattopadhyay S, Chen HF, Chen JH, Chen Y, Cheng J, Cherney M, Chikanian A, Choi HA, Christie W, Coffin JP, Cormier TM, Cosentino MR, Cramer JG, Crawford HJ, Das D, Das S, Daugherity M, de Moura MM, Dedovich TG, Dephillips M, Derevschikov AA, Didenko L, Dietel T, Dogra SM, Dong WJ, Dong X, Draper JE, Du F, Dubey AK, Dunin VB, Dunlop JC, Mazumdar MRD, Eckardt V, Edwards WR, Efimov LG, Emelianov V, Engelage J, Eppley G, Erazmus B, Estienne M, Fachini P, Faivre J, Fatemi R, Fedorisin J, Filimonov K, Filip P, Finch E, Fine V, Fisyak Y, Fornazier KSF, Fox BD, Fu J, Gagliardi CA, Gaillard L, Gans J, Ganti MS, Geurts F, Ghazikhanian V, Ghosh P, Gonzalez JE, Gorbunov YG, Gos H, Grachov O, Grebenyuk O, Grosnick D, Guertin SM, Guo Y, Gupta A, Gupta N, Gutierrez TD, Hallman TJ, Hamed A, Harris JW, Heinz M, Henry TW, Hepplemann S, Hippolyte B, Hirsch A, Hjort E, Hoffmann GW, Horner MJ, Huang HZ, Huang SL, Hughes EW, Humanic TJ, Igo G, Ishihara A, Jacobs P, Jacobs WW, Jiang H, Jones PG, Judd EG, Kabana S, Kang K, Kaplan M, Keane D, Kechechyan A, Khodyrev VY, Kim BC, Kiryluk J, Kisiel A, Kislov EM, Klein SR, Koetke DD, Kollegger T, Kopytine M, Kotchenda L, Kowalik KL, Kramer M, Kravtsov P, Kravtsov VI, Krueger K, Kuhn C, Kulikov AI, Kumar A, Kutuev RK, Kuznetsov AA, Lamb R, Lamont MAC, Landgraf JM, Lange S, Laue F, Lauret J, Lebedev A, Lednicky R, Lee CH, Lehocka S, Levine MJ, Li C, Li Q, Li Y, Lin G, Lindenbaum SJ, Lisa MA, Liu F, Liu H, Liu J, Liu L, Liu QJ, Liu Z, Ljubicic T, Llope WJ, Long H, Longacre RS, Lopez-Noriega M, Love WA, Lu Y, Ludlam T, Lynn D, Ma GL, Ma JG, Ma YG, Magestro D, Mahajan S, Mahapatra DP, Majka R, Mangotra LK, Manweiler R, Margetis S, Markert C, Martin L, Marx JN, Matis HS, Matulenko YA, McClain CJ, McShane TS, Melnick Y, Meschanin A, Miller ML, Minaev NG, Mironov C, Mischke A, Mishra DK, Mitchell J, Mioduszewski S, Mohanty B, Molnar L, Moore CF, Morozov DA, Munhoz MG, Nandi BK, Nayak SK, Nayak TK, Nelson JM, Netrakanti PK, Nikitin VA, Nogach LV, Nurushev SB, Odyniec G, Ogawa A, Okorokov V, Oldenburg M, Olson D, Pal SK, Panebratsev Y, Panitkin SY, Pavlinov AI, Pawlak T, Peitzmann T, Perevoztchikov V, Perkins C, Peryt W, Petrov VA, Phatak SC, Picha R, Planinic M, Pluta J, Porile N, Porter J, Poskanzer AM, Potekhin M, Potrebenikova E, Potukuchi BVKS, Prindle D, Pruneau C, Putschke J, Rakness G, Raniwala R, Raniwala S, Ravel O, Ray RL, Razin SV, Reichhold D, Reid JG, Reinnarth J, Renault G, Retiere F, Ridiger A, Ritter HG, Roberts JB, Rogachevskiy OV, Romero JL, Rose A, Roy C, Ruan L, Russcher MJ, Sahoo R, Sakrejda I, Salur S, Sandweiss J, Sarsour M, Savin I, Sazhin PS, Schambach J, Scharenberg RP, Schmitz N, Schweda K, Seger J, Selyuzhenkov I, Seyboth P, Shabetai A, Shahaliev E, Shao M, Shao W, Sharma M, Shen WQ, Shestermanov KE, Shimanskiy SS, Sichtermann E, Simon F, Singaraju RN, Smirnov N, Snellings R, Sood G, Sorensen P, Sowinski J, Speltz J, Spinka HM, Srivastava B, Stadnik A, Stanislaus TDS, Stock R, Stolpovsky A, Strikhanov M, Stringfellow B, Suaide AAP, Sugarbaker E, Sumbera M, Surrow B, Swanger M, Symons TJM, de Toledo AS, Tai A, Takahashi J, Tang AH, Tarnowsky T, Thein D, Thomas JH, Timmins AR, Timoshenko S, Tokarev M, Trainor TA, Trentalange S, Tribble RE, Tsai OD, Ulery J, Ullrich T, Underwood DG, Buren GV, van der Kolk N, van Leeuwen M, Molen AMV, Varma R, Vasilevski IM, Vasiliev AN, Vernet R, Vigdor SE, Viyogi YP, Vokal S, Voloshin SA, Waggoner WT, Wang F, Wang G, Wang G, Wang XL, Wang Y, Wang Y, Wang ZM, Ward H, Watson JW, Webb JC, Westfall GD, Wetzler A, Whitten C, Wieman H, Wissink SW, Witt R, Wood J, Wu J, Xu N, Xu QH, Xu Z, Xu ZZ, Yepes P, Yoo IK, Yurevich VI, Zborovsky I, Zhang H, Zhang WM, Zhang Y, Zhang ZP, Zhong C, Zoulkarneev R, Zoulkarneeva Y, Zubarev AN, Zuo JX. Forward neutral pion production in p + p and d + Au collisions at square root sNN=200 GeV. PHYSICAL REVIEW LETTERS 2006; 97:152302. [PMID: 17155322 DOI: 10.1103/physrevlett.97.152302] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Indexed: 05/12/2023]
Abstract
Measurements of the production of forward pi0 mesons from p + p and d + Au collisions at square root sNN=200 GeV are reported. The p + p yield generally agrees with next-to-leading order perturbative QCD calculations. The d + Au yield per binary collision is suppressed as eta increases, decreasing to approximately 30% of the p + p yield at eta =4.00, well below shadowing expectations. Exploratory measurements of azimuthal correlations of the forward pi0 with charged hadrons at eta approximately 0 show a recoil peak in p + p that is suppressed in d + Au at low pion energy. These observations are qualitatively consistent with a saturation picture of the low-x gluon structure of heavy nuclei.
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Adams J, Adler C, Aggarwal MM, Ahammed Z, Amonett J, Anderson BD, Arkhipkin D, Averichev GS, Badyal SK, Balewski J, Barannikova O, Barnby LS, Baudot J, Bekele S, Belaga VV, Bellwied R, Berger J, Bezverkhny BI, Bhardwaj S, Bhati AK, Bichsel H, Billmeier A, Bland LC, Blyth CO, Bonner BE, Botje M, Boucham A, Brandin A, Bravar A, Cadman RV, Cai XZ, Caines H, Calderón de la Barca Sánchez M, Carroll J, Castillo J, Cebra D, Chaloupka P, Chattopadhyay S, Chen HF, Chen Y, Chernenko SP, Cherney M, Chikanian A, Christie W, Coffin JP, Cormier TM, Cramer JG, Crawford HJ, Das D, Das S, Derevschikov AA, Didenko L, Dietel T, Dong WJ, Dong X, Draper JE, Du F, Dubey AK, Dunin VB, Dunlop JC, Dutta Majumdar MR, Eckardt V, Efimov LG, Emelianov V, Engelage J, Eppley G, Erazmus B, Estienne M, Fachini P, Faine V, Faivre J, Fatemi R, Filimonov K, Filip P, Finch E, Fisyak Y, Flierl D, Foley KJ, Fu J, Gagliardi CA, Gagunashvili N, Gans J, Ganti MS, Gaudichet L, Geurts F, Ghazikhanian V, Ghosh P, Gonzalez JE, Grachov O, Grebenyuk O, Gronstal S, Grosnick D, Guertin SM, Gupta A, Gutierrez TD, Hallman TJ, Hamed A, Hardtke D, Harris JW, Heinz M, Henry TW, Heppelmann S, Herston T, Hippolyte B, Hirsch A, Hjort E, Hoffmann GW, Horsley M, Huang HZ, Huang SL, Hughes E, Humanic TJ, Igo G, Ishihara A, Jacobs P, Jacobs WW, Janik M, Jiang H, Johnson I, Jones PG, Judd EG, Kabana S, Kaplan M, Keane D, Khodyrev VY, Kiryluk J, Kisiel A, Klay J, Klein SR, Klyachko A, Koetke DD, Kollegger T, Kopytine M, Kotchenda L, Kovalenko AD, Kramer M, Kravtsov P, Kravtsov VI, Krueger K, Kuhn C, Kulikov AI, Kumar A, Kunde GJ, Kunz CL, Kutuev RK, Kuznetsov AA, Lamont MAC, Landgraf JM, Lange S, Lasiuk B, Laue F, Lauret J, Lebedev A, Lednický R, Levine MJ, Li C, Li Q, Lindenbaum SJ, Lisa MA, Liu F, Liu L, Liu Z, Liu QJ, Ljubicic T, Llope WJ, Long H, Longacre RS, Lopez-Noriega M, Love WA, Ludlam T, Lynn D, Ma J, Ma YG, Magestro D, Mahajan S, Mangotra LK, Mahapatra DP, Majka R, Manweiler R, Margetis S, Markert C, Martin L, Marx J, Matis HS, Matulenko YA, McClain CJ, McShane TS, Meissner F, Melnick Y, Meschanin A, Miller ML, Milosevich Z, Minaev NG, Mironov C, Mischke A, Mishra D, Mitchell J, Mohanty B, Molnar L, Moore CF, Mora-Corral MJ, Morozov DA, Morozov V, de Moura MM, Munhoz MG, Nandi BK, Nayak SK, Nayak TK, Nelson JM, Netrakanti PK, Nikitin VA, Nogach LV, Norman B, Nurushev SB, Odyniec G, Ogawa A, Okorokov V, Oldenburg M, Olson D, Paic G, Pal SK, Panebratsev Y, Panitkin SY, Pavlinov AI, Pawlak T, Peitzmann T, Perevoztchikov V, Perkins C, Peryt W, Petrov VA, Phatak SC, Picha R, Planinic M, Pluta J, Porile N, Porter J, Poskanzer AM, Potekhin M, Potrebenikova E, Potukuchi BVKS, Prindle D, Pruneau C, Putschke J, Rai G, Rakness G, Raniwala R, Raniwala S, Ravel O, Ray RL, Razin SV, Reichhold D, Reid JG, Renault G, Retiere F, Ridiger A, Ritter HG, Roberts JB, Rogachevski OV, Romero JL, Rose A, Roy C, Ruan LJ, Sahoo R, Sakrejda I, Salur S, Sandweiss J, Savin I, Schambach J, Scharenberg RP, Schmitz N, Schroeder LS, Schweda K, Seger J, Seyboth P, Shahaliev E, Shao M, Shao W, Sharma M, Shestermanov KE, Shimanskii SS, Singaraju RN, Simon F, Skoro G, Smirnov N, Snellings R, Sood G, Sorensen P, Sowinski J, Speltz J, Spinka HM, Srivastava B, Stanislaus TDS, Stock R, Stolpovsky A, Strikhanov M, Stringfellow B, Struck C, Suaide AAP, Sugarbaker E, Suire C, Sumbera M, Surrow B, Symons TJM, Szanto de Toledo A, Szarwas P, Tai A, Takahashi J, Tang AH, Thein D, Thomas JH, Timoshenko S, Tokarev M, Tonjes MB, Trainor TA, Trentalange S, Tribble RE, Tsai O, Ullrich T, Underwood DG, Van Buren G, Vandermolen AM, Varma R, Vasilevski I, Vasiliev AN, Vernet R, Vigdor SE, Viyogi YP, Voloshin SA, Vznuzdaev M, Waggoner W, Wang F, Wang G, Wang G, Wang XL, Wang Y, Wang ZM, Ward H, Watson JW, Webb JC, Wells R, Westfall GD, Whitten C, Wieman H, Willson R, Wissink SW, Witt R, Wood J, Wu J, Xu N, Xu Z, Xu ZZ, Yamamoto E, Yepes P, Yurevich VI, Yuting B, Zanevski YV, Zhang H, Zhang WM, Zhang ZP, Zhaomin ZP, Zizong ZP, Zołnierczuk PA, Zoulkarneev R, Zoulkarneeva J, Zubarev AN. Distributions of charged hadrons associated with high transverse momentum particles in pp and Au+Au collisions at sqrt[sNN]=200 GeV. PHYSICAL REVIEW LETTERS 2005; 95:152301. [PMID: 16241721 DOI: 10.1103/physrevlett.95.152301] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2005] [Indexed: 05/05/2023]
Abstract
Charged hadrons in [EQUATION: SEE TEXT] associated with particles of [EQUATION: SEE TEXT] are reconstructed in pp and Au+Au collisions at sqrt[sNN]=200 GeV. The associated multiplicity and p magnitude sum are found to increase from pp to central Au+Au collisions. The associated p distributions, while similar in shape on the nearside, are significantly softened on the awayside in central Au+Au relative to pp and not much harder than that of inclusive hadrons. The results, consistent with jet quenching, suggest that the awayside fragments approach equilibration with the medium traversed.
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Adams J, Aggarwal MM, Ahammed Z, Amonett J, Anderson BD, Arkhipkin D, Averichev GS, Badyal SK, Bai Y, Balewski J, Barannikova O, Barnby LS, Baudot J, Bekele S, Belaga VV, Bellingeri-Laurikainen A, Bellwied R, Berger J, Bezverkhny BI, Bharadwaj S, Bhasin A, Bhati AK, Bhatia VS, Bichsel H, Bielcik J, Bielcikova J, Billmeier A, Bland LC, Blyth CO, Blyth SL, Bonner BE, Botje M, Boucham A, Bouchet J, Brandin AV, Bravar A, Bystersky M, Cadman RV, Cai XZ, Caines H, Calderón de la Barca Sánchez M, Castillo J, Catu O, Cebra D, Chajecki Z, Chaloupka P, Chattopadhyay S, Chen HF, Chen JH, Chen Y, Cheng J, Cherney M, Chikanian A, Christie W, Coffin JP, Cormier TM, Cosentino MR, Cramer JG, Crawford HJ, Das D, Das S, Daugherity M, de Moura MM, Dedovich TG, DePhillips M, Derevschikov AA, Didenko L, Dietel T, Dogra SM, Dong WJ, Dong X, Draper JE, Du F, Dubey AK, Dunin VB, Dunlop JC, Dutta Mazumdar MR, Eckardt V, Edwards WR, Efimov LG, Emelianov V, Engelage J, Eppley G, Erazmus B, Estienne M, Fachini P, Faivre J, Fatemi R, Fedorisin J, Filimonov K, Filip P, Finch E, Fine V, Fisyak Y, Fornazier KSF, Fu J, Gagliardi CA, Gaillard L, Gans J, Ganti MS, Geurts F, Ghazikhanian V, Ghosh P, Gonzalez JE, Gos H, Grachov O, Grebenyuk O, Grosnick D, Guertin SM, Guo Y, Gupta A, Gupta N, Gutierrez TD, Hallman TJ, Hamed A, Hardtke D, Harris JW, Heinz M, Henry TW, Hepplemann S, Hippolyte B, Hirsch A, Hjort E, Hoffmann GW, Horner MJ, Huang HZ, Huang SL, Hughes EW, Humanic TJ, Igo G, Ishihara A, Jacobs P, Jacobs WW, Jedynak M, Jiang H, Jones PG, Judd EG, Kabana S, Kang K, Kaplan M, Keane D, Kechechyan A, Khodyrev VY, Kiryluk J, Kisiel A, Kislov EM, Klay J, Klein SR, Koetke DD, Kollegger T, Kopytine M, Kotchenda L, Kowalik KL, Kramer M, Kravtsov P, Kravtsov VI, Krueger K, Kuhn C, Kulikov AI, Kumar A, Kutuev RK, Kuznetsov AA, Lamont MAC, Landgraf JM, Lange S, Laue F, Lauret J, Lebedev A, Lednicky R, Lehocka S, LeVine MJ, Li C, Li Q, Li Y, Lin G, Lindenbaum SJ, Lisa MA, Liu F, Liu H, Liu J, Liu L, Liu QJ, Liu Z, Ljubicic T, Llope WJ, Long H, Longacre RS, Lopez-Noriega M, Love WA, Lu Y, Ludlam T, Lynn D, Ma GL, Ma JG, Ma YG, Magestro D, Mahajan S, Mahapatra DP, Majka R, Mangotra LK, Manweiler R, Margetis S, Markert C, Martin L, Marx JN, Matis HS, Matulenko YA, McClain CJ, McShane TS, Meissner F, Melnick Y, Meschanin A, Miller ML, Minaev NG, Mironov C, Mischke A, Mishra DK, Mitchell J, Mohanty B, Molnar L, Moore CF, Morozov DA, Munhoz MG, Nandi BK, Nayak SK, Nayak TK, Nelson JM, Netrakanti PK, Nikitin VA, Nogach LV, Nurushev SB, Odyniec G, Ogawa A, Okorokov V, Oldenburg M, Olson D, Pal SK, Panebratsev Y, Panitkin SY, Pavlinov AI, Pawlak T, Peitzmann T, Perevoztchikov V, Perkins C, Peryt W, Petrov VA, Phatak SC, Picha R, Planinic M, Pluta J, Porile N, Porter J, Poskanzer AM, Potekhin M, Potrebenikova E, Potukuchi BVKS, Prindle D, Pruneau C, Putschke J, Rakness G, Raniwala R, Raniwala S, Ravel O, Ray RL, Razin SV, Reichhold D, Reid JG, Reinnarth J, Renault G, Retiere F, Ridiger A, Ritter HG, Roberts JB, Rogachevskiy OV, Romero JL, Rose A, Roy C, Ruan L, Russcher M, Sahoo R, Sakrejda I, Salur S, Sandweiss J, Sarsour M, Savin I, Sazhin PS, Schambach J, Scharenberg RP, Schmitz N, Schweda K, Seger J, Seyboth P, Shahaliev E, Shao M, Shao W, Sharma M, Shen WQ, Shestermanov KE, Shimanskiy SS, Sichtermann E, Simon F, Singaraju RN, Smirnov N, Snellings R, Sood G, Sorensen P, Sowinski J, Speltz J, Spinka HM, Srivastava B, Stadnik A, Stanislaus TDS, Stock R, Stolpovsky A, Strikhanov M, Stringfellow B, Suaide AAP, Sugarbaker E, Suire C, Sumbera M, Surrow B, Swanger M, Symons TJM, Szanto de Toledo A, Tai A, Takahashi J, Tang AH, Tarnowsky T, Thein D, Thomas JH, Timmins AR, Timoshenko S, Tokarev M, Trentalange S, Tribble RE, Tsai OD, Ulery J, Ullrich T, Underwood DG, Van Buren G, van der Kolk N, van Leeuwen M, Vander Molen AM, Varma R, Vasilevski IM, Vasiliev AN, Vernet R, Vigdor SE, Viyogi YP, Vokal S, Voloshin SA, Waggoner WT, Wang F, Wang G, Wang G, Wang XL, Wang Y, Wang Y, Wang ZM, Ward H, Watson JW, Webb JC, Westfall GD, Wetzler A, Whitten C, Wieman H, Wissink SW, Witt R, Wood J, Wu J, Xu N, Xu Z, Xu ZZ, Yamamoto E, Yepes P, Yurevich VI, Zborovsky I, Zhang H, Zhang WM, Zhang Y, Zhang ZP, Zhong C, Zoulkarneev R, Zoulkarneeva Y, Zubarev AN, Zuo JX. Multistrange Baryon elliptic flow in Au+Au collisions at square root of sNN=200 GeV. PHYSICAL REVIEW LETTERS 2005; 95:122301. [PMID: 16197068 DOI: 10.1103/physrevlett.95.122301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Indexed: 05/04/2023]
Abstract
We report on the first measurement of elliptic flow v2(pT) of multistrange baryons Xi- +Xi+ and Omega- + Omega+ in heavy-ion collisions. In minimum-bias Au+Au collisions at square root of s(NN)=200 GeV, a significant amount of elliptic flow, comparable to other nonstrange baryons, is observed for multistrange baryons which are expected to be particularly sensitive to the dynamics of the partonic stage of heavy-ion collisions. The pT dependence of v2 of the multistrange baryons confirms the number of constituent quark scaling previously observed for lighter hadrons. These results support the idea that a substantial fraction of the observed collective motion is developed at the early partonic stage in ultrarelativistic nuclear collisions at the Relativistic Heavy Ion Collider.
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Adams J, Aggarwal MM, Ahammed Z, Amonett J, Anderson BD, Arkhipkin D, Averichev GS, Badyal SK, Bai Y, Balewski J, Barannikova O, Barnby LS, Baudot J, Bekele S, Belaga VV, Bellingeri-Laurikainen A, Bellwied R, Berger J, Bezverkhny BI, Bhardwaj S, Bhasin A, Bhati AK, Bichsel H, Bielcik J, Bielcikova J, Billmeier A, Bland LC, Blyth CO, Blyth S, Bonner BE, Botje M, Boucham A, Bouchet J, Brandin AV, Bravar A, Bystersky M, Cadman RV, Cai XZ, Caines H, de la Barca Sánchez MC, Castillo J, Catu O, Cebra D, Chajecki Z, Chaloupka P, Chattopadhyay S, Chen HF, Chen Y, Cheng J, Cherney M, Chikanian A, Christie W, Coffin JP, Cormier TM, Cosentino MR, Cramer JG, Crawford HJ, Das D, Das S, de Moura MM, Dedovich TG, Derevschikov AA, Didenko L, Dietel T, Dogra SM, Dong WJ, Dong X, Draper JE, Du F, Dubey AK, Dunin VB, Dunlop JC, Mazumdar MRD, Eckardt V, Edwards WR, Efimov LG, Emelianov V, Engelage J, Eppley G, Erazmus B, Estienne M, Fachini P, Faivre J, Fatemi R, Fedorisin J, Filimonov K, Filip P, Finch E, Fine V, Fisyak Y, Fornazier KSF, Fu J, Gagliardi CA, Gaillard L, Gans J, Ganti MS, Geurts F, Ghazikhanian V, Ghosh P, Gonzalez JE, Gos H, Grachov O, Grebenyuk O, Grosnick D, Guertin SM, Guo Y, Gupta A, Gutierrez TD, Hallman TJ, Hamed A, Hardtke D, Harris JW, Heinz M, Henry TW, Hepplemann S, Hippolyte B, Hirsch A, Hjort E, Hoffmann GW, Horner M, Huang HZ, Huang SL, Hughes EW, Humanic TJ, Igo G, Ishihara A, Jacobs P, Jacobs WW, Jedynak M, Jiang H, Jones PG, Judd EG, Kabana S, Kang K, Kaplan M, Keane D, Kechechyan A, Khodyrev VY, Kiryluk J, Kisiel A, Kislov EM, Klay J, Klein SR, Koetke DD, Kollegger T, Kopytine M, Kotchenda L, Kowalik KL, Kramer M, Kravtsov P, Kravtsov VI, Krueger K, Kuhn C, Kulikov AI, Kumar A, Kutuev RK, Kuznetsov AA, Lamont MAC, Landgraf JM, Lange S, Laue F, Lauret J, Lebedev A, Lednicky R, Lehocka S, Levine MJ, Li C, Li Q, Li Y, Lin G, Lindenbaum SJ, Lisa MA, Liu F, Liu H, Liu J, Liu L, Liu QJ, Liu Z, Ljubicic T, Llope WJ, Long H, Longacre RS, Lopez-Noriega M, Love WA, Lu Y, Ludlam T, Lynn D, Ma GL, Ma JG, Ma YG, Magestro D, Mahajan S, Mahapatra DP, Majka R, Mangotra LK, Manweiler R, Margetis S, Markert C, Martin L, Marx JN, Matis HS, Matulenko YA, McClain CJ, McShane TS, Meissner F, Melnick Y, Meschanin A, Miller ML, Minaev NG, Mironov C, Mischke A, Mishra DK, Mitchell J, Mohanty B, Molnar L, Moore CF, Morozov DA, Munhoz MG, Nandi BK, Nayak SK, Nayak TK, Nelson JM, Netrakanti PK, Nikitin VA, Nogach LV, Nurushev SB, Odyniec G, Ogawa A, Okorokov V, Oldenburg M, Olson D, Pal SK, Panebratsev Y, Panitkin SY, Pavlinov AI, Pawlak T, Peitzmann T, Perevoztchikov V, Perkins C, Peryt W, Petrov VA, Phatak SC, Picha R, Planinic M, Pluta J, Porile N, Porter J, Poskanzer AM, Potekhin M, Potrebenikova E, Potukuchi BVKS, Prindle D, Pruneau C, Putschke J, Rakness G, Raniwala R, Raniwala S, Ravel O, Ray RL, Razin SV, Reichhold D, Reid JG, Reinnarth J, Renault G, Retiere F, Ridiger A, Ritter HG, Roberts JB, Rogachevskiy OV, Romero JL, Rose A, Roy C, Ruan L, Russcher MJ, Sahoo R, Sakrejda I, Salur S, Sandweiss J, Sarsour M, Savin I, Sazhin PS, Schambach J, Scharenberg RP, Schmitz N, Schweda K, Seger J, Seyboth P, Shahaliev E, Shao M, Shao W, Sharma M, Shen WQ, Shestermanov KE, Shimanskiy SS, Sichtermann E, Simon F, Singaraju RN, Smirnov N, Snellings R, Sood G, Sorensen P, Sowinski J, Speltz J, Spinka HM, Srivastava B, Stadnik A, Stanislaus TDS, Stock R, Stolpovsky A, Strikhanov M, Stringfellow B, Suaide AAP, Sugarbaker E, Suire C, Sumbera M, Surrow B, Swanger M, Symons TJM, de Toledo AS, Tai A, Takahashi J, Tang AH, Tarnowsky T, Thein D, Thomas JH, Timoshenko S, Tokarev M, Trainor TA, Trentalange S, Tribble RE, Tsai OD, Ulery J, Ullrich T, Underwood DG, Buren GV, van Leeuwen M, Molen AMV, Varma R, Vasilevski IM, Vasiliev AN, Vernet R, Vigdor SE, Viyogi YP, Vokal S, Voloshin SA, Waggoner WT, Wang F, Wang G, Wang G, Wang XL, Wang Y, Wang Y, Wang ZM, Ward H, Watson JW, Webb JC, Westfall GD, Wetzler A, Whitten C, Wieman H, Wissink SW, Witt R, Wood J, Wu J, Xu N, Xu Z, Xu ZZ, Yamamoto E, Yepes P, Yurevich VI, Zborovsky I, Zhang H, Zhang WM, Zhang Y, Zhang ZP, Zoulkarneev R, Zoulkarneeva Y, Zubarev AN. Multiplicity and pseudorapidity distributions of photons in Au+Au collisions at square root of (S(NN)) = 62.4 GeV. PHYSICAL REVIEW LETTERS 2005; 95:062301. [PMID: 16090941 DOI: 10.1103/physrevlett.95.062301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Revised: 04/12/2005] [Indexed: 05/03/2023]
Abstract
We present the first measurement of pseudorapidity distribution of photons in the region 2.3 < or = eta < or = 3.7 for different centralities in Au+Au collisions at square root of (S(NN)) = 62.4 GeV. We find that the photon yield scales with the number of participating nucleons at all collision centralities studied. The pseudorapidity distribution of photons, dominated by pi0 decays, has been compared to those of charged pions, photons, and inclusive charged particles from heavy-ion and nucleon-nucleon collisions at various energies. The photon production has been shown to be consistent with the energy and centrality independent limiting fragmentation scenario.
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Alt C, Anticic T, Baatar B, Barna D, Bartke J, Betev L, Białkowska H, Billmeier A, Blume C, Boimska B, Botje M, Bracinik J, Bramm R, Brun R, Buncić P, Cerny V, Christakoglou P, Chvala O, Cramer JG, Csató P, Darmenov N, Dimitrov A, Dinkelaker P, Eckardt V, Farantatos G, Flierl D, Fodor Z, Foka P, Freund P, Friese V, Gál J, Gaździcki M, Georgopoulos G, Gładysz E, Grebieszkow K, Hegyi S, Höhne C, Kadija K, Karev A, Kliemant M, Kniege S, Kolesnikov VI, Kollegger T, Kornas E, Korus R, Kowalski M, Kraus I, Kreps M, van Leeuwen M, Lévai P, Litov L, Lungwitz B, Makariev M, Malakhov AI, Markert C, Mateev M, Mayes BW, Melkumov GL, Meurer C, Mischke A, Mitrovski M, Molnár J, Mrówczyński S, Pálla G, Panagiotou AD, Panayotov D, Petridis A, Pikna M, Pinsky L, Pühlhofer F, Reid JG, Renfordt R, Richard A, Roland C, Roland G, Rybczyński M, Rybicki A, Sandoval A, Sann H, Schmitz N, Seyboth P, Siklér F, Sitar B, Skrzypczak E, Stefanek G, Stock R, Ströbele H, Susa T, Szentpétery I, Sziklai J, Trainor TA, Varga D, Vassiliou M, Veres GI, Vesztergombi G, Vranić D, Wetzler A, Włodarczyk Z, Yoo IK, Zaranek J, Zimányi J. Omega- and Omega+ production in central Pb + Pb collisions at 40 and 158A GeV. PHYSICAL REVIEW LETTERS 2005; 94:192301. [PMID: 16090164 DOI: 10.1103/physrevlett.94.192301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2004] [Indexed: 05/03/2023]
Abstract
Results are presented on Omega production in central Pb+Pb collisions at 40 and 158A GeV beam energy. For the first time in heavy ion reactions, rapidity distributions and total yields were measured for the sum Omega(-) + Omega(+) at 40A GeV and for Omega(-) and Omega(+) separately at 158A GeV. The yields are strongly underpredicted by the string-hadronic UrQMD model but agree better with predictions from hadron gas models.
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73
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Adams J, Aggarwal MM, Ahammed Z, Amonett J, Anderson BD, Arkhipkin D, Averichev GS, Badyal SK, Bai Y, Balewski J, Barannikova O, Barnby LS, Baudot J, Bekele S, Belaga VV, Bellwied R, Berger J, Bezverkhny BI, Bharadwaj S, Bhasin A, Bhati AK, Bhatia VS, Bichsel H, Billmeier A, Bland LC, Blyth CO, Bonner BE, Botje M, Boucham A, Brandin AV, Bravar A, Bystersky M, Cadman RV, Cai XZ, Caines H, Calderón de la Barca Sánchez M, Castillo J, Cebra D, Chajecki Z, Chaloupka P, Chattopadhyay S, Chen HF, Chen Y, Cheng J, Cherney M, Chikanian A, Christie W, Coffin JP, Cormier TM, Cramer JG, Crawford HJ, Das D, Das S, de Moura MM, Derevschikov AA, Didenko L, Dietel T, Dogra SM, Dong WJ, Dong X, Draper JE, Du F, Dubey AK, Dunin VB, Dunlop JC, Dutta Mazumdar MR, Eckardt V, Edwards WR, Efimov LG, Emelianov V, Engelage J, Eppley G, Erazmus B, Estienne M, Fachini P, Faivre J, Fatemi R, Fedorisin J, Filimonov K, Filip P, Finch E, Fine V, Fisyak Y, Fomenko K, Fu J, Gagliardi CA, Gaillard L, Gans J, Ganti MS, Gaudichet L, Geurts F, Ghazikhanian V, Ghosh P, Gonzalez JE, Grachov O, Grebenyuk O, Grosnick D, Guertin SM, Guo Y, Gupta A, Gutierrez TD, Hallman TJ, Hamed A, Hardtke D, Harris JW, Heinz M, Henry TW, Hepplemann S, Hippolyte B, Hirsch A, Hjort E, Hoffmann GW, Huang HZ, Huang SL, Hughes EW, Humanic TJ, Igo G, Ishihara A, Jacobs P, Jacobs WW, Janik M, Jiang H, Jones PG, Judd EG, Kabana S, Kang K, Kaplan M, Keane D, Khodyrev VY, Kiryluk J, Kisiel A, Kislov EM, Klay J, Klein SR, Koetke DD, Kollegger T, Kopytine M, Kotchenda L, Kramer M, Kravtsov P, Kravtsov VI, Krueger K, Kuhn C, Kulikov AI, Kumar A, Kutuev RK, Kuznetsov AA, Lamont MAC, Landgraf JM, Lange S, Laue F, Lauret J, Lebedev A, Lednicky R, Lehocka S, LeVine MJ, Li C, Li Q, Li Y, Lin G, Lindenbaum SJ, Lisa MA, Liu F, Liu L, Liu QJ, Liu Z, Ljubicic T, Llope WJ, Long H, Longacre RS, Lopez-Noriega M, Love WA, Lu Y, Ludlam T, Lynn D, Ma GL, Ma JG, Ma YG, Magestro D, Mahajan S, Mahapatra DP, Majka R, Mangotra LK, Manweiler R, Margetis S, Markert C, Martin L, Marx JN, Matis HS, Matulenko YA, McClain CJ, McShane TS, Meissner F, Melnick Y, Meschanin A, Miller ML, Minaev NG, Mironov C, Mischke A, Mishra DK, Mitchell J, Mohanty B, Molnar L, Moore CF, Morozov DA, Munhoz MG, Nandi BK, Nayak SK, Nayak TK, Nelson JM, Netrakanti PK, Nikitin VA, Nogach LV, Nurushev SB, Odyniec G, Ogawa A, Okorokov V, Oldenburg M, Olson D, Pal SK, Panebratsev Y, Panitkin SY, Pavlinov AI, Pawlak T, Peitzmann T, Perevoztchikov V, Perkins C, Peryt W, Petrov VA, Phatak SC, Picha R, Planinic M, Pluta J, Porile N, Porter J, Poskanzer AM, Potekhin M, Potrebenikova E, Potukuchi BVKS, Prindle D, Pruneau C, Putschke J, Rakness G, Raniwala R, Raniwala S, Ravel O, Ray RL, Razin SV, Reichhold D, Reid JG, Renault G, Retiere F, Ridiger A, Ritter HG, Roberts JB, Rogachevskiy OV, Romero JL, Rose A, Roy C, Ruan L, Sahoo R, Sakrejda I, Salur S, Sandweiss J, Sarsour M, Savin I, Sazhin PS, Schambach J, Scharenberg RP, Schmitz N, Schweda K, Seger J, Seyboth P, Shahaliev E, Shao M, Shao W, Sharma M, Shen WQ, Shestermanov KE, Shimanskiy SS, Sichtermann E, Simon F, Singaraju RN, Skoro G, Smirnov N, Snellings R, Sood G, Sorensen P, Sowinski J, Speltz J, Spinka HM, Srivastava B, Stadnik A, Stanislaus TDS, Stock R, Stolpovsky A, Strikhanov M, Stringfellow B, Suaide AAP, Sugarbaker E, Suire C, Sumbera M, Surrow B, Symons TJM, Szanto de Toledo A, Szarwas P, Tai A, Takahashi J, Tang AH, Tarnowsky T, Thein D, Thomas JH, Timoshenko S, Tokarev M, Trainor TA, Trentalange S, Tribble RE, Tsai OD, Ulery J, Ullrich T, Underwood DG, Urkinbaev A, Van Buren G, van Leeuwen M, Vander Molen AM, Varma R, Vasilevski IM, Vasiliev AN, Vernet R, Vigdor SE, Viyogi YP, Vokal S, Voloshin SA, Vznuzdaev M, Waggoner WT, Wang F, Wang G, Wang G, Wang XL, Wang Y, Wang Y, Wang ZM, Ward H, Watson JW, Webb JC, Wells R, Westfall GD, Wetzler A, Whitten C, Wieman H, Wissink SW, Witt R, Wood J, Wu J, Xu N, Xu Z, Xu ZZ, Yamamoto E, Yepes P, Yurevich VI, Zanevsky YV, Zhang H, Zhang WM, Zhang ZP, Zoulkarneev R, Zoulkarneeva Y, Zubarev AN. Open charm yields in d+Au collisions at squareroot[sNN]=200 GeV. PHYSICAL REVIEW LETTERS 2005; 94:062301. [PMID: 15783724 DOI: 10.1103/physrevlett.94.062301] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Indexed: 05/24/2023]
Abstract
Midrapidity open charm spectra from direct reconstruction of D0(D0)-->K-/+pi+/- in d+Au collisions and indirect electron-positron measurements via charm semileptonic decays in p+p and d+Au collisions at squareroot[sNN]=200 GeV are reported. The D0(D0) spectrum covers a transverse momentum (pT) range of 0.1<pT<3 GeV/c, whereas the electron spectra cover a range of 1<pT<4 GeV/c. The electron spectra show approximate binary collision scaling between p+p and d+Au collisions. From these two independent analyses, the differential cross section per nucleon-nucleon binary interaction at midrapidity for open charm production from d+Au collisions at BNL RHIC is dsigma(NN)cc/dy=0.30+/-0.04(stat)+/-0.09(syst) mb. The results are compared to theoretical calculations. Implications for charmonium results in A+A collisions are discussed.
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Alt C, Anticic T, Baatar B, Barna D, Bartke J, Betev L, Białkowska H, Billmeier A, Blume C, Boimska B, Botje M, Bracinik J, Bramm R, Brun R, Buncić P, Cerny V, Christakoglou P, Chvala O, Cramer JG, Csató P, Darmenov N, Dimitrov A, Dinkelaker P, Eckardt V, Farantatos G, Flierl D, Fodor Z, Foka P, Freund P, Friese V, Gál J, Gaździcki M, Georgopoulos G, Gładysz E, Grebieszkow K, Hegyi S, Höhne C, Kadija K, Karev A, Kliemant M, Kniege S, Kolesnikov VI, Kollegger T, Kornas E, Korus R, Kowalski M, Kraus I, Kreps M, van Leeuwen M, Lévai P, Litov L, Lungwitz B, Makariev M, Malakhov AI, Markert C, Mateev M, Mayes BW, Melkumov GL, Meurer C, Mischke A, Mitrovski M, Molnár J, Mrówczyński S, Pálla G, Panagiotou AD, Panayotov D, Petridis A, Pikna M, Pinsky L, Pühlhofer F, Reid JG, Renfordt R, Richard A, Roland C, Roland G, Rybczyński M, Rybicki A, Sandoval A, Sann H, Schmitz N, Seyboth P, Siklér F, Sitar B, Skrzypczak E, Stefanek G, Stock R, Ströbele H, Susa T, Szentpétery I, Sziklai J, Trainor TA, Trubnikov V, Varga D, Vassiliou M, Veres GI, Vesztergombi G, Vranić D, Wetzler A, Włodarczyk Z, Yoo IK, Zaranek J, Zimányi J. System-size dependence of strangeness production in nucleus-nucleus collisions at squareroot[sNN]=17.3 GeV. PHYSICAL REVIEW LETTERS 2005; 94:052301. [PMID: 15783629 DOI: 10.1103/physrevlett.94.052301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2004] [Indexed: 05/24/2023]
Abstract
Emission of pi+/-, K+/-, phi, and Lambda was measured in near-central C+C and Si+Si collisions at 158 AGeV beam energy. Together with earlier data for p+p, S+S, and Pb+Pb, the system-size dependence of relative strangeness production in nucleus-nucleus collisions is obtained. Its fast rise and the saturation observed at about 60 participating nucleons can be understood as the onset of the formation of coherent systems of increasing size.
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75
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Adams J, Aggarwal MM, Ahammed Z, Amonett J, Anderson BD, Arkhipkin D, Averichev GS, Badyal SK, Bai Y, Balewski J, Barannikova O, Barnby LS, Baudot J, Bekele S, Belaga VV, Bellwied R, Berger J, Bezverkhny BI, Bharadwaj S, Bhasin A, Bhati AK, Bhatia VS, Bichsel H, Billmeier A, Bland LC, Blyth CO, Bonner BE, Botje M, Boucham A, Brandin AV, Bravar A, Bystersky M, Cadman RV, Cai XZ, Caines H, Calderón de la Barca Sánchez M, Carroll J, Castillo J, Cebra D, Chajecki Z, Chaloupka P, Chattopdhyay S, Chen HF, Chen Y, Cheng J, Cherney M, Chikanian A, Christie W, Coffin JP, Cormier TM, Cramer JG, Crawford HJ, Das D, Das S, de Moura MM, Derevschikov AA, Didenko L, Dietel T, Dogra SM, Dong WJ, Dong X, Draper JE, Du F, Dubey AK, Dunin VB, Dunlop JC, Dutta Mazumdar MR, Eckardt V, Edwards WR, Efimov LG, Emelianov V, Engelage J, Eppley G, Erazmus B, Estienne M, Fachini P, Faivre J, Fatemi R, Fedorisin J, Filimonov K, Filip P, Finch E, Fine V, Fisyak Y, Foley KJ, Fomenko K, Fu J, Gagliardi CA, Gans J, Ganti MS, Gaudichet L, Geurts F, Ghazikhanian V, Ghosh P, Gonzalez JE, Grachov O, Grebenyuk O, Grosnick D, Guertin SM, Guo Y, Gupta A, Gutierrez TD, Hallman TJ, Hamed A, Hardtke D, Harris JW, Heinz M, Henry TW, Hepplemann S, Hippolyte B, Hirsch A, Hjort E, Hoffmann GW, Huang HZ, Huang SL, Hughes EW, Humanic TJ, Igo G, Ishihara A, Jacobs P, Jacobs WW, Janik M, Jiang H, Jones PG, Judd EG, Kabana S, Kang K, Kaplan M, Keane D, Khodyrev VY, Kiryluk J, Kisiel A, Kislov EM, Klay J, Klein SR, Klyachko A, Koetke DD, Kollegger T, Kopytine M, Kotchenda L, Kramer M, Kravtsov P, Kravtsov VI, Krueger K, Kuhn C, Kulikov AI, Kumar A, Kunz CL, Kutuev RK, Kuznetsov AA, Lamont MAC, Landgraf JM, Lange S, Laue F, Lauret J, Lebedev A, Lednicky R, Lehocka S, LeVine MJ, Li C, Li Q, Li Y, Lindenbaum SJ, Lisa MA, Liu F, Liu L, Liu QJ, Liu Z, Ljubicic T, Llope WJ, Long H, Longacre RS, Lopez-Noriega M, Love WA, Lu Y, Ludlam T, Lynn D, Ma GL, Ma JG, Ma YG, Magestro D, Mahajan S, Mahapatra DP, Majka R, Mangotra LK, Manweiler R, Margetis S, Markert C, Martin L, Marx JN, Matis HS, Matulenko YA, McClain CJ, McShane TS, Meissner F, Melnick Y, Meschanin A, Miller ML, Milosevich Z, Minaev NG, Mironov C, Mischke A, Mishra DK, Mitchell J, Mohanty B, Molnar L, Moore CF, Morozov DA, Munhoz MG, Nandi BK, Nayak SK, Nayak TK, Nelson JM, Netrakanti PK, Nikitin VA, Nogach LV, Nurushev SB, Odyniec G, Ogawa A, Okorokov V, Oldenburg M, Olson D, Pal SK, Panebratsev Y, Panitkin SY, Pavlinov AI, Pawlak T, Peitzmann T, Perevoztchikov V, Perkins C, Peryt W, Petrov VA, Phatak SC, Picha R, Planinic M, Pluta J, Porile N, Porter J, Poskanzer AM, Potekhin M, Potrebenikova E, Potukuchi BVKS, Prindle D, Pruneau C, Putschke J, Rai G, Rakness G, Raniwala R, Raniwala S, Ravel O, Ray RL, Razin SV, Reichhold D, Reid JG, Renault G, Retiere F, Ridiger A, Ritter HG, Roberts JB, Rogachevskiy OV, Romero JL, Rose A, Roy C, Ruan L, Sahoo R, Sakrejda I, Salur S, Sandweiss J, Savin I, Sazhin PS, Schambach J, Scharenberg RP, Schmitz N, Schroeder LS, Schweda K, Seger J, Seyboth P, Shahaliev E, Shao M, Shao W, Sharma M, Shen WQ, Shestermanov KE, Shimanskiy SS, Sichtermann E, Simon F, Singaraju RN, Skoro G, Smirnov N, Snellings R, Sood G, Sorensen P, Sowinski J, Speltz J, Spinka HM, Srivastava B, Stadnik A, Stanislaus TDS, Stock R, Stolpovsky A, Strikhanov M, Stringfellow B, Suaide AAP, Sugarbaker E, Suire C, Sumbera M, Surrow B, Symons TJM, Szanto de Toledo A, Szarwas P, Tai A, Takahashi J, Tang AH, Tarnowsky T, Thein D, Thomas JH, Timoshenko S, Tokarev M, Trentalange S, Tribble RE, Tsai OD, Ulery J, Ullrich T, Underwood DG, Urkinbaev A, Van Buren G, van Leeuwen M, Vander Molen AM, Varma R, Vasilevski IM, Vasiliev AN, Vernet R, Vigdor SE, Viyogi YP, Vokal S, Voloshin SA, Vznuzdaev M, Waggoner WT, Wang F, Wang G, Wang G, Wang XL, Wang Y, Wang Y, Wang ZM, Ward H, Watson JW, Webb JC, Wells R, Westfall GD, Wetzler A, Whitten C, Wieman H, Wissink SW, Witt R, Wood J, Wu J, Xu N, Xu Z, Xu ZZ, Yamamoto E, Yepes P, Yurevich VI, Zanevsky YV, Zhang H, Zhang WM, Zhang ZP, Zolnierczuk PA, Zoulkarneev R, Zoulkarneeva Y, Zubarev AN. Azimuthal anisotropy and correlations at large transverse momenta in p + p and Au + Au collisions at square root sNN=200 GeV. PHYSICAL REVIEW LETTERS 2004; 93:252301. [PMID: 15697893 DOI: 10.1103/physrevlett.93.252301] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Indexed: 05/24/2023]
Abstract
Results on high transverse momentum charged particle emission with respect to the reaction plane are presented for Au + Au collisions at square root s(NN)=200 GeV. Two- and four-particle correlations results are presented as well as a comparison of azimuthal correlations in Au + Au collisions to those in p + p at the same energy. The elliptic anisotropy v(2) is found to reach its maximum at p(t) approximately 3 GeV/c, then decrease slowly and remain significant up to p(t) approximately 7-10 GeV/c. Stronger suppression is found in the back-to-back high-p(t) particle correlations for particles emitted out of plane compared to those emitted in plane. The centrality dependence of v(2) at intermediate p(t) is compared to simple models based on jet quenching.
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