776 research outputs found
DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing
<p>Abstract</p> <p>Background</p> <p>DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number.</p> <p>Results</p> <p>We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual.</p> <p>Conclusion</p> <p>The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads.</p
Commissioning of the CMS High Level Trigger
The CMS experiment will collect data from the proton-proton collisions
delivered by the Large Hadron Collider (LHC) at a centre-of-mass energy up to
14 TeV. The CMS trigger system is designed to cope with unprecedented
luminosities and LHC bunch-crossing rates up to 40 MHz. The unique CMS trigger
architecture only employs two trigger levels. The Level-1 trigger is
implemented using custom electronics, while the High Level Trigger (HLT) is
based on software algorithms running on a large cluster of commercial
processors, the Event Filter Farm. We present the major functionalities of the
CMS High Level Trigger system as of the starting of LHC beams operations in
September 2008. The validation of the HLT system in the online environment with
Monte Carlo simulated data and its commissioning during cosmic rays data taking
campaigns are discussed in detail. We conclude with the description of the HLT
operations with the first circulating LHC beams before the incident occurred
the 19th September 2008
Results from the first use of low radioactivity argon in a dark matter search
Liquid argon is a bright scintillator with potent particle identification
properties, making it an attractive target for direct-detection dark matter
searches. The DarkSide-50 dark matter search here reports the first WIMP search
results obtained using a target of low-radioactivity argon. DarkSide-50 is a
dark matter detector, using two-phase liquid argon time projection chamber,
located at the Laboratori Nazionali del Gran Sasso. The underground argon is
shown to contain Ar-39 at a level reduced by a factor (1.4 +- 0.2) x 10^3
relative to atmospheric argon. We report a background-free null result from
(2616 +- 43) kg d of data, accumulated over 70.9 live-days. When combined with
our previous search using an atmospheric argon, the 90 % C.L. upper limit on
the WIMP-nucleon spin-independent cross section based on zero events found in
the WIMP search regions, is 2.0 x 10^-44 cm^2 (8.6 x 10^-44 cm^2, 8.0 x 10^-43
cm^2) for a WIMP mass of 100 GeV/c^2 (1 TeV/c^2 , 10 TeV/c^2).Comment: Accepted by Phys. Rev.
Observation of Hadronic W Decays in t-tbar Events with the Collider Detector at Fermilab
We observe hadronic W decays in t-tbar -> W (-> l nu) + >= 4 jet events using
a 109 pb-1 data sample of p-pbar collisions at sqrt{s} = 1.8 TeV collected with
the Collider Detector at Fermilab (CDF). A peak in the dijet invariant mass
distribution is obtained that is consistent with W decay and inconsistent with
the background prediction by 3.3 standard deviations. From this peak we measure
the W mass to be 77.2 +- 4.6 (stat+syst) GeV/c^2. This result demonstrates the
presence of two W bosons in t-tbar candidates in the W (-> l nu) + >= 4 jet
channel.Comment: 20 pages, 4 figures, submitted to PR
Measurement of the lepton charge asymmetry in W-boson decays produced in p-pbar collisions
We describe a measurement of the charge asymmetry of leptons from W boson
decays in the rapidity range 0 enu, munu events from
110+/-7 pb^{-1}of data collected by the CDF detector during 1992-95. The
asymmetry data constrain the ratio of d and u quark momentum distributions in
the proton over the x range of 0.006 to 0.34 at Q2 \approx M_W^2. The asymmetry
predictions that use parton distribution functions obtained from previously
published CDF data in the central rapidity region (0.0<|y_l|<1.1) do not agree
with the new data in the large rapidity region (|y_l|>1.1).Comment: 13 pages, 3 tables, 1 figur
Search for charged Higgs decays of the top quark using hadronic tau decays
We present the result of a search for charged Higgs decays of the top quark,
produced in collisions at 1.8 TeV. When the charged
Higgs is heavy and decays to a tau lepton, which subsequently decays
hadronically, the resulting events have a unique signature: large missing
transverse energy and the low-charged-multiplicity tau. Data collected in the
period 1992-1993 at the Collider Detector at Fermilab, corresponding to
18.70.7~pb, exclude new regions of combined top quark and charged
Higgs mass, in extensions to the standard model with two Higgs doublets.Comment: uuencoded, gzipped tar file of LaTeX and 6 Postscript figures; 11 pp;
submitted to Phys. Rev.
Inclusive jet cross section in collisions at TeV
The inclusive jet differential cross section has been measured for jet
transverse energies, , from 15 to 440 GeV, in the pseudorapidity region
0.10.7. The results are based on 19.5 pb of data
collected by the CDF collaboration at the Fermilab Tevatron collider. The data
are compared with QCD predictions for various sets of parton distribution
functions. The cross section for jets with GeV is significantly
higher than current predictions based on O() perturbative QCD
calculations. Various possible explanations for the high- excess are
discussed.Comment: 8 pages with 2 eps uu-encoded figures Submitted to Physical Review
Letter
Measurement of the Associated Production Cross Section in Collisions at TeV
We present the first measurement of associated direct photon + muon
production in hadronic collisions, from a sample of 1.8 TeV
collisions recorded with the Collider Detector at Fermilab. Quantum
chromodynamics (QCD) predicts that these events are primarily from the Compton
scattering process , with the final state charm quark producing
a muon. Hence this measurement is sensitive to the charm quark content of the
proton. The measured cross section of is compared to a
leading-order QCD parton shower model as well as a next-to-leading-order QCD
calculation.Comment: 12 pages, 4 figures Added more detailed description of muon
background estimat
Search for a Technicolor omega_T Particle in Events with a Photon and a b-quark Jet at CDF
If the Technicolor omega_T particle exists, a likely decay mode is omega_T ->
gamma pi_T, followed by pi_T -> bb-bar, yielding the signature gamma bb-bar. We
have searched 85 pb^-1 of data collected by the CDF experiment at the Fermilab
Tevatron for events with a photon and two jets, where one of the jets must
contain a secondary vertex implying the presence of a b quark. We find no
excess of events above standard model expectations. We express the result of an
exclusion region in the M_omega_T - M_pi_T mass plane.Comment: 14 pages, 2 figures. Available from the CDF server (PS with figs):
http://www-cdf.fnal.gov/physics/pub98/cdf4674_omega_t_prl_4.ps
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