| 1. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
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| 3. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 4. |
- Abazov, V. M., et al.
(författare)
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The upgraded DO detector
- 2006
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 565:2, s. 463-537
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Tidskriftsartikel (refereegranskat)abstract
- The DO experiment enjoyed a very successful data-collection run at the Fermilab Tevatron collider between 1992 and 1996. Since then, the detector has been upgraded to take advantage of improvements to the Tevatron and to enhance its physics capabilities. We describe the new elements of the detector, including the silicon microstrip tracker, central fiber tracker, solenoidal magnet, preshower detectors, forward muon detector, and forward proton detector. The uranium/liquid -argon calorimeters and central muon detector, remaining from Run 1, are discussed briefly. We also present the associated electronics, triggering, and data acquisition systems, along with the design and implementation of software specific to DO.
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| 5. |
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- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:2
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Tidskriftsartikel (refereegranskat)
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| 6. |
- Ramdas, S., et al.
(författare)
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A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids
- 2022
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 109:8, s. 1366-1387
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Tidskriftsartikel (refereegranskat)abstract
- A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.
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| 7. |
- Abadie, J., et al.
(författare)
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Implementation and testing of the first prompt search for gravitational wave transients with electromagnetic counterparts
- 2012
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Ingår i: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 539
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Tidskriftsartikel (refereegranskat)abstract
- Aims. A transient astrophysical event observed in both gravitational wave (GW) and electromagnetic (EM) channels would yield rich scientific rewards. A first program initiating EM follow-ups to possible transient GW events has been developed and exercised by the LIGO and Virgo community in association with several partners. In this paper, we describe and evaluate the methods used to promptly identify and localize GW event candidates and to request images of targeted sky locations. Methods. During two observing periods (Dec. 17, 2009 to Jan. 8, 2010 and Sep. 2 to Oct. 20, 2010), a low-latency analysis pipeline was used to identify GW event candidates and to reconstruct maps of possible sky locations. A catalog of nearby galaxies and Milky Way globular clusters was used to select the most promising sky positions to be imaged, and this directional information was delivered to EM observatories with time lags of about thirty minutes. A Monte Carlo simulation has been used to evaluate the low-latency GW pipeline's ability to reconstruct source positions correctly. Results. For signals near the detection threshold, our low-latency algorithms often localized simulated GW burst signals to tens of square degrees, while neutron star/neutron star inspirals and neutron star/black hole inspirals were localized to a few hundred square degrees. Localization precision improves for moderately stronger signals. The correct sky location of signals well above threshold and originating from nearby galaxies may be observed with similar to 50% or better probability with a few pointings of wide-field telescopes.
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| 8. |
- Abadie, J., et al.
(författare)
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All-sky search for periodic gravitational waves in the full S5 LIGO data
- 2012
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 85:2
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Tidskriftsartikel (refereegranskat)abstract
- We report on an all-sky search for periodic gravitational waves in the frequency band 50-800 Hz and with the frequency time derivative in the range of 0 through -6 x 10(-9) Hz/s. Such a signal could be produced by a nearby spinning and slightly nonaxisymmetric isolated neutron star in our Galaxy. After recent improvements in the search program that yielded a 10x increase in computational efficiency, we have searched in two years of data collected during LIGO's fifth science run and have obtained the most sensitive all-sky upper limits on gravitational-wave strain to date. Near 150 Hz our upper limit on worst-case linearly polarized strain amplitude h(0) is 1 x 10(-24), while at the high end of our frequency range we achieve a worst-case upper limit of 3.8 x 10(-24) for all polarizations and sky locations. These results constitute a factor of 2 improvement upon previously published data. A new detection pipeline utilizing a loosely coherent algorithm was able to follow up weaker outliers, increasing the volume of space where signals can be detected by a factor of 10, but has not revealed any gravitational-wave signals. The pipeline has been tested for robustness with respect to deviations from the model of an isolated neutron star, such as caused by a low-mass or long-period binary companion.
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| 9. |
- Abadie, J., et al.
(författare)
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Search for gravitational waves from low mass compact binary coalescence in LIGO's sixth science run and Virgo's science runs 2 and 3
- 2012
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 85:8
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Tidskriftsartikel (refereegranskat)abstract
- We report on a search for gravitational waves from coalescing compact binaries using LIGO and Virgo observations between July 7, 2009, and October 20, 2010. We searched for signals from binaries with total mass between 2 and 25M(circle dot); this includes binary neutron stars, binary black holes, and binaries consisting of a black hole and neutron star. The detectors were sensitive to systems up to 40 Mpc distant for binary neutron stars, and further for higher mass systems. No gravitational-wave signals were detected. We report upper limits on the rate of compact binary coalescence as a function of total mass, including the results from previous LIGO and Virgo observations. The cumulative 90% confidence rate upper limits of the binary coalescence of binary neutron star, neutron star-black hole, and binary black hole systems are 1.3 x 10(-4), 3.1 x 10(-5), and 6.4 x 10(-6) Mpc(-3) yr(-1), respectively. These upper limits are up to a factor 1.4 lower than previously derived limits. We also report on results from a blind injection challenge.
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| 10. |
- Abazov, V. M., et al.
(författare)
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Experimental discrimination between charge 2e/3 top quark and charge 4e/3 exotic quark production scenarios
- 2007
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 98:4, s. 041801-
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Tidskriftsartikel (refereegranskat)abstract
- We present the first experimental discrimination between the 2e/3 and 4e/3 top quark electric charge scenarios, using top quark pairs (t (t) over bar) produced in p (p) over bar collisions at root s =1.96 TeV by the Fermilab Tevatron Collider. We use 370 pb(-1) of data collected by the D0 experiment and select events with at least one high transverse momentum electron or muon, high transverse energy imbalance, and four or more jets. We discriminate between b- and (b) over bar -quark jets by using the charge and momenta of tracks within the jet cones. The data are consistent with the expected electric charge, |q|=2e/3. We exclude, at the 92% C.L., that the sample is solely due to the production of exotic quark pairs Q (Q) over bar with |q|=4e/3. We place an upper limit on the fraction of Q (Q) over bar pairs rho < 0.80 at the 90% C.L.
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| 11. |
- Abazov, V. M., et al.
(författare)
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Limits on anomalous trilinear gauge couplings from WW -> e(+)e(-), WW -> e(+/-)mu(-/+), and WW ->mu(+)mu(-) events from pp collisions at root s=1.96 TeV
- 2006
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Ingår i: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 1550-7998 .- 1550-2368. ; 74:5, s. 057101-
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Tidskriftsartikel (refereegranskat)abstract
- Limits are set on anomalous WW gamma and WWZ trilinear gauge couplings using W+W--> e(+)nu(e)e(-)(nu) over bar (e), W+W--> e(+/-)nu(e)mu(-/+)nu(mu), and W+W-->mu(+)nu(mu)mu(-)(nu) over bar (mu) events. The data set was collected by the Run II D0 detector at the Fermilab Tevatron Collider and corresponds to approximately 250 pb(-1) of integrated luminosity at root s=1.96 TeV. Under the assumption that the WW gamma couplings are equal to the WWZ couplings and using a form factor scale of Lambda=2.0 TeV, the combined 95% C.L. one-dimensional coupling limits from all three channels are -0.32
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| 12. |
- Abazov, V. M., et al.
(författare)
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Measurement of B-d mixing using opposite-side flavor tagging
- 2006
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Ingår i: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 1550-7998 .- 1550-2368. ; 74:11, s. 112002-
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Tidskriftsartikel (refereegranskat)abstract
- We report on a measurement of the B-d(0) mixing frequency and the calibration of an opposite-side flavor tagger in the D0 experiment. Various properties associated with the b quark on the opposite side of the reconstructed B meson are combined using a likelihood-ratio method into a single variable with enhanced tagging power. Its performance is tested with data, using a large sample of reconstructed semileptonic B ->mu(DX)-X-0 and B ->mu(DX)-X-* decays, corresponding to an integrated luminosity of approximately 1 fb(-1). The events are divided into groups depending on the value of the combined tagging variable, and an independent analysis is performed in each group. Combining the results of these analyses, the overall effective tagging power is found to be epsilon D-2=(2.48 +/- 0.21(-0.06)(+0.08))%. The measured B-d(0) mixing frequency Delta m(d)=0.506 +/- 0.020(stat)+/- 0.016(syst) ps(-1) is in good agreement with the world average value.
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| 13. |
- Abazov, V. M., et al.
(författare)
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Measurement of the CP-violation parameter of B-0 mixing and decay with p(p)over-bar ->mu mu X data
- 2006
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Ingår i: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 1550-7998 .- 1550-2368. ; 74:9, s. 092001-
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Tidskriftsartikel (refereegranskat)abstract
- We measure the dimuon charge asymmetry A in p (p) over bar collisions at a center of mass energy root s=1960 GeV. The data was recorded with the D0 detector and corresponds to an integrated luminosity of approximately 1.0 fb(-1). Assuming that the asymmetry A is due to asymmetric B-0 <->(B) over bar (0) mixing and decay, we extract the CP-violation parameter of B-0 mixing and decay: ((epsilon B0))/(1+vertical bar epsilon B0 vertical bar 2)=(AB0)/(4)= -0.0023 +/- 0.0011(stat)+/- 0.0008(syst).A(B)(0) is the dimuon charge asymmetry from decays of B-0(B) over bar (0) pairs. The general case, with CP violation in both B-0 and B-s(0) systems, is also considered. Finally we obtain the forward-backward asymmetry that quantifies the tendency of mu(+) to go in the proton direction and mu(-) to go in the antiproton direction. The results are consistent with the standard model and constrain new physics.
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| 14. |
- Abazov, V. M., et al.
(författare)
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Measurement of the ratios of the Z/gamma*+ >= n jet production cross sections to the total inclusive Z/gamma* cross section in p(p)over-bar collisions at root s=1.96 TeV
- 2008
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 658, s. 112-
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Tidskriftsartikel (refereegranskat)abstract
- We present a study of events with Z bosons and associated jets produced at the Fermilab Tevatron collider in p p collisions at a center of mass energy of 1.96 TeV The data sample consists of nearly 14000 Z/gamma* -> e(+)e(-) candidates corresponding to an integrated luminosity of 0.4 fb(-1) collected with the D circle divide detector. Ratios of the Z/gamma*+ >= n jet cross sections to the total inclusive Z/gamma* cross section have been measured for n = 1-4 jets, and found to be in good agreement with a next-to-leading order QCD calculation and with a tree-level QCD prediction with parton shower simulation and hadronization.
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| 15. |
- Abazov, V. M., et al.
(författare)
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Measurement of the top quark mass in the lepton plus jets final state with the matrix element method
- 2006
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Ingår i: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 1550-7998 .- 1550-2368. ; 74:9, s. 092005-
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Tidskriftsartikel (refereegranskat)abstract
- We present a measurement of the top quark mass with the matrix element method in the lepton+jets final state. As the energy scale for calorimeter jets represents the dominant source of systematic uncertainty, the matrix element likelihood is extended by an additional parameter, which is defined as a global multiplicative factor applied to the standard energy scale. The top quark mass is obtained from a fit that yields the combined statistical and systematic jet energy scale uncertainty. Using a data set of 0.4 fb(-1) taken with the D0 experiment at Run II of the Fermilab Tevatron Collider, the mass of the top quark is measured using topological information to be: m(top)(center dot+jets)(topo)=169.2(-7.4)(+5.0)(stat+JES)(-1.4)(+1.5)(syst) GeV, and when information about identified b jets is included: m(top)(center dot+jets)(b-tag)=170.3(-4.5)(+4.1)(stat+ JES)(-1.8)(+1.2)(syst) GeV. The measurements yield a jet energy scale consistent with the reference scale.
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| 16. |
- Abazov, V. M., et al.
(författare)
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Search for a heavy resonance decaying into a Z plus jet final state in p(p)over-bar collisions at root s=1.96 TeV using the D0 detector
- 2006
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Ingår i: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 1550-7998 .- 1550-2368. ; 74:1, s. 011104-
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Tidskriftsartikel (refereegranskat)abstract
- We have searched for a heavy resonance decaying into a Z+jet final state in p (p) over bar collisions at a center of mass energy of 1.96 TeV at the Fermilab Tevatron collider using the D0 detector. No indication for such a resonance was found in a data sample corresponding to an integrated luminosity of 370 pb(-1). We set upper limits on the cross section times branching fraction for heavy resonance production at the 95% C.L. as a function of the resonance mass and width. The limits are interpreted within the framework of a specific model of excited quark production.
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| 17. |
- Abazov, V. M., et al.
(författare)
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Search for neutral Higgs bosons decaying to tau pairs in p(p)over-bar collisions at root s=1.96 TeV
- 2006
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 97:12, s. 121802-
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Tidskriftsartikel (refereegranskat)abstract
- A search for the production of neutral Higgs bosons Phi decaying into tau(+)tau(-) final states in p (p) over bar collisions at a center-of-mass energy of 1.96 TeV is presented. The data, corresponding to an integrated luminosity of approximately 325 pb(-1), were collected by the D0 experiment at the Fermilab Tevatron Collider. Since no excess compared to the expectation from standard model processes is found, limits on the production cross section times branching ratio are set. The results are combined with those obtained from the D0 search for Phi b((b) over bar)-> b (b) over barb((b) over bar) and are interpreted in the minimal supersymmetric standard model.
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| 18. |
- Abazov, V. M., et al.
(författare)
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Search for neutral, long-lived particles decaying into two muons in p(p)over-bar collisions at root s=1.96 TeV
- 2006
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 97:16, s. 161802-
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Tidskriftsartikel (refereegranskat)abstract
- We present a search for a neutral particle, pair produced in pp collisions at root s=1.96 TeV, which decays into two muons and lives long enough to travel at least 5 cm before decaying. The analysis uses approximate to 380 pb(-1) of data recorded with the D0 detector. The background is estimated to be about one event. No candidates are observed, and limits are set on the pair-production cross section times branching fraction into dimuons + X for such particles. For a mass of 10 GeV and lifetime of 4x10(-11) s, we exclude values greater than 0.14 pb (95% C.L.). These results are used to limit the interpretation of NuTeV's excess of dimuon events.
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| 19. |
- Abazov, V. M., et al.
(författare)
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Search for pair production of scalar bottom quarks in p(p)over-bar collisions at root s = 1.96 TeV
- 2006
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 97:17, s. 171806-
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Tidskriftsartikel (refereegranskat)abstract
- A search for direct production of scalar bottom quarks ((b) over bar) is performed with 310 pb(-1) of data collected by the D0 experiment in p (p) over bar collisions at root s = 1.96 TeV at the Fermilab Tevatron Collider. The topology analyzed consists of two b jets and an imbalance in transverse momentum due to undetected neutralinos (chi(0)(1)), with chi(0)(1) assumed to be the lightest supersymmetric particle. We find the data consistent with standard model expectations, and set a 95% C.L. exclusion domain in the (m(b), m(chi 1)(0)) mass plane, improving significantly upon the results from run I of the Tevatron.
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| 20. |
- Abazov, V. M., et al.
(författare)
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Search for particles decaying into a Z boson and a photon in p(p)over-bar collisions at root s=1.96 TeV
- 2006
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 641:6, s. 415-422
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Tidskriftsartikel (refereegranskat)abstract
- We present the results of a search for a new particle X produced in p (p) over bar collisions at root s- = 1.96 TeV and subsequently decaying to Z gamma. The search uses 0.3 fb(-1) of data collected with the DO detector at the Fermilab Tevatron Collider. We set limits on the production cross section times the branching fraction sigma(p (p) over bar -> X) x B(X -> Z gamma) that range from 0.4 to 3.5 pb at the 95% C.L. for X with invariant masses between 100 and 1000 GeV/c(2), over a wide range of X decay widths.
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| 21. |
- Abazov, V. M., et al.
(författare)
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Search for R-parity violating supersymmetry via the LL(E)over-bar couplings lambda(121), lambda(122) or lambda(133) in p(p)over-bar collisions at root s=1.96 TeV
- 2006
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 638:5-6, s. 441-449
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Tidskriftsartikel (refereegranskat)abstract
- A search for gaugino pair production with a trilepton signature in the framework of R-parity violating supersymmetry via the couplings; lambda(121), lambda(122), or lambda(133) is presented. The data, corresponding to an integrated luminosity of L approximate to 360 pb(-1), were collected from April 2002 to August 2004 with the D0 detector at the Fermilab Tevatron Collider, at a center-of-mass energy of root s = 1.96 TeV. This analysis considers final states with three charged leptons with the flavor combinations eel, mu mu l, and ee tau (l = e or mu). No evidence for supersymmetry is found and limits at the 95% confidence level are set on the gaugino pair production cross section and lower bounds on the masses of the lightest neutralino and chargino are derived in two supersymmetric models.
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| 22. |
- Abazov, V. M., et al.
(författare)
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Search for resonant second generation slepton production at the Fermilab Tevatron
- 2006
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 97:11, s. 111801-
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Tidskriftsartikel (refereegranskat)abstract
- We present a search for supersymmetry in the R-parity violating resonant production and decay of smuons and muon sneutrinos in the channels mu ->chi(0)(1)mu, mu ->chi(0)(2,3,4)mu, and nu(mu)->chi(+/-)(1,2)mu. We analyzed 0.38 fb(-1) of integrated luminosity collected between April 2002 and August 2004 with the D0 detector at the Fermilab Tevatron Collider. The observed number of events is in agreement with the standard model expectation, and we calculate 95% C.L. limits on the slepton production cross section times branching fraction to gaugino plus muon, as a function of slepton and gaugino masses. In the framework of minimal supergravity, we set limits on the coupling parameter lambda(')(211), extending significantly previous results obtained in Run I of the Tevatron and at the CERN LEP collider.
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| 23. |
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| 24. |
- Abazov, V. M., et al.
(författare)
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Search for the standard model Higgs boson in the p(p)over-bar -> ZH -> v(v)over-barb(b)over-bar channel
- 2006
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 97:16, s. 161803-
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Tidskriftsartikel (refereegranskat)abstract
- We report a search for the standard model (SM) Higgs boson based on data collected by the D0 experiment at the Fermilab Tevatron Collider, corresponding to an integrated luminosity of 260 pb(-1). We study events with missing transverse energy and two acoplanar b jets, which provide sensitivity to the ZH production cross section in the nu nu bb channel, and to WH production when the lepton from the W ->center dot nu decay is undetected. The data are consistent with the SM background expectation, and we set 95% C.L. upper limits on sigma(pp -> ZH/WH) x B(H -> bb) from 3.4/8.3 to 2.5/6.3 pb, for Higgs-boson masses between 105 and 135 GeV.
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| 25. |
- Abazov, V. M., et al.
(författare)
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Search for W ' boson production in the W ' -> t(b)over-bar decay channel
- 2006
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 641:6, s. 423-431
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Tidskriftsartikel (refereegranskat)abstract
- We present a search for the production of a new heavy gauge boson W' that decays to a top quark and a bottom quark. We have analyzed 230 pb(-1) of data collected with the DO detector at the Fermilab Tevatron collider at a center-of-mass energy of 1.96 TeV. No significant excess of events above the standard model expectation is found in any region of the final state invariant mass distribution. We set upper limits on the production cross section of W' bosons times branching ratio to top quarks at the 95% confidence level for several different W, boson masses. We exclude masses between 200 and 610 GeV for a W' boson with standard-model-like couplings, between 200 and 630 GeV for a W, boson with right-handed couplings that is allowed to decay to both leptons and quarks, and between 200 and 670 GeV for a W' boson with right-handed couplings that is only allowed to decay to quarks.
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