2,535 research outputs found
Succinct Partial Sums and Fenwick Trees
We consider the well-studied partial sums problem in succint space where one
is to maintain an array of n k-bit integers subject to updates such that
partial sums queries can be efficiently answered. We present two succint
versions of the Fenwick Tree - which is known for its simplicity and
practicality. Our results hold in the encoding model where one is allowed to
reuse the space from the input data. Our main result is the first that only
requires nk + o(n) bits of space while still supporting sum/update in O(log_b
n) / O(b log_b n) time where 2 <= b <= log^O(1) n. The second result shows how
optimal time for sum/update can be achieved while only slightly increasing the
space usage to nk + o(nk) bits. Beyond Fenwick Trees, the results are primarily
based on bit-packing and sampling - making them very practical - and they also
allow for simple optimal parallelization
The effect of S-substitution at the O6-guanine site on the structure and dynamics of a DNA oligomer containing a G:T mismatch
The effect of S-substitution on the O6 guanine site of a 13-mer DNA duplex containing a G:T mismatch is studied using molecular dynamics. The structure, dynamic evolution and hydration of the S-substituted duplex are compared with those of a normal duplex, a duplex with Ssubstitution on guanine, but no mismatch and a duplex with just a G:T mismatch. The S-substituted mismatch leads to cell death rather than repair. One suggestion is that the G:T mismatch recognition protein recognises the S-substituted mismatch (GS:T) as G:T. This leads to a cycle of futile repair ending in DNA breakage and cell death. We find that some structural features of the helix are similar for the duplex with the G:T mismatch and that with the S-substituted mismatch, but differ from the normal duplex, notably the helical twist. These differences arise from the change in the hydrogen-bonding pattern of the base pair. However a marked feature of the S-substituted G:T mismatch duplex is a very large opening. This showed considerable variability. It is suggested that this enlarged opening would lend support to an alternative model of cell death in which the mismatch protein attaches to thioguanine and activates downstream damage-response pathways. Attack on the sulphur by reactive oxygen species, also leading to cell death, would also be aided by the large, variable opening
Interplay of quantum and classical fluctuations near quantum critical points
For a system near a quantum critical point (QCP), above its lower critical
dimension , there is in general a critical line of second order phase
transitions that separates the broken symmetry phase at finite temperatures
from the disordered phase. The phase transitions along this line are governed
by thermal critical exponents that are different from those associated with the
quantum critical point. We point out that, if the effective dimension of the
QCP, ( is the Euclidean dimension of the system and the
dynamic quantum critical exponent) is above its upper critical dimension ,
there is an intermingle of classical (thermal) and quantum critical
fluctuations near the QCP. This is due to the breakdown of the generalized
scaling relation between the shift exponent of the critical
line and the crossover exponent , for by a \textit{dangerous
irrelevant interaction}. This phenomenon has clear experimental consequences,
like the suppression of the amplitude of classical critical fluctuations near
the line of finite temperature phase transitions as the critical temperature is
reduced approaching the QCP.Comment: 10 pages, 6 figures, to be published in Brazilian Journal of Physic
Critical Role of the Virus-Encoded MicroRNA-155 Ortholog in the Induction of Marek's Disease Lymphomas
Notwithstanding the well-characterised roles of a number of oncogenes in neoplastic transformation, microRNAs (miRNAs) are increasingly implicated in several human cancers. Discovery of miRNAs in several oncogenic herpesviruses such as KSHV has further highlighted the potential of virus-encoded miRNAs to contribute to their oncogenic capabilities. Nevertheless, despite the identification of several possible cancer-related genes as their targets, the direct in vivo role of virus-encoded miRNAs in neoplastic diseases such as those induced by KSHV is difficult to demonstrate in the absence of suitable models. However, excellent natural disease models of rapid-onset Marek's disease (MD) lymphomas in chickens allow examination of the oncogenic potential of virus-encoded miRNAs. Using viruses modified by reverse genetics of the infectious BAC clone of the oncogenic RB-1B strain of MDV, we show that the deletion of the six-miRNA cluster 1 from the viral genome abolished the oncogenicity of the virus. This loss of oncogenicity appeared to be primarily due to the single miRNA within the cluster, miR-M4, the ortholog of cellular miR-155, since its deletion or a 2-nucleotide mutation within its seed region was sufficient to inhibit the induction of lymphomas. The definitive role of this miR-155 ortholog in oncogenicity was further confirmed by the rescue of oncogenic phenotype by revertant viruses that expressed either the miR-M4 or the cellular homolog gga-miR-155. This is the first demonstration of the direct in vivo role of a virus-encoded miRNA in inducing tumors in a natural infection model. Furthermore, the use of viruses deleted in miRNAs as effective vaccines against virulent MDV challenge, enables the prospects of generating genetically defined attenuated vaccines
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
FERMILAB-PUB-98/321-
A Study of B0 -> J/psi K(*)0 pi+ pi- Decays with the Collider Detector at Fermilab
We report a study of the decays B0 -> J/psi K(*)0 pi+ pi-, which involve the
creation of a u u-bar or d d-bar quark pair in addition to a b-bar -> c-bar(c
s-bar) decay. The data sample consists of 110 1/pb of p p-bar collisions at
sqrt{s} = 1.8 TeV collected by the CDF detector at the Fermilab Tevatron
collider during 1992-1995. We measure the branching ratios to be BR(B0 -> J/psi
K*0 pi+ pi-) = (8.0 +- 2.2 +- 1.5) * 10^{-4} and BR(B0 -> J/psi K0 pi+ pi-) =
(1.1 +- 0.4 +- 0.2) * 10^{-3}. Contributions to these decays are seen from
psi(2S) K(*)0, J/psi K0 rho0, J/psi K*+ pi-, and J/psi K1(1270)
Measurement of the B0 anti-B0 oscillation frequency using l- D*+ pairs and lepton flavor tags
The oscillation frequency Delta-md of B0 anti-B0 mixing is measured using the
partially reconstructed semileptonic decay anti-B0 -> l- nubar D*+ X. The data
sample was collected with the CDF detector at the Fermilab Tevatron collider
during 1992 - 1995 by triggering on the existence of two lepton candidates in
an event, and corresponds to about 110 pb-1 of pbar p collisions at sqrt(s) =
1.8 TeV. We estimate the proper decay time of the anti-B0 meson from the
measured decay length and reconstructed momentum of the l- D*+ system. The
charge of the lepton in the final state identifies the flavor of the anti-B0
meson at its decay. The second lepton in the event is used to infer the flavor
of the anti-B0 meson at production. We measure the oscillation frequency to be
Delta-md = 0.516 +/- 0.099 +0.029 -0.035 ps-1, where the first uncertainty is
statistical and the second is systematic.Comment: 30 pages, 7 figures. Submitted to Physical Review
Search for New Particles Decaying to top-antitop in proton-antiproton collisions at squareroot(s)=1.8 TeV
We use 106 \ipb of data collected with the Collider Detector at Fermilab to
search for narrow-width, vector particles decaying to a top and an anti-top
quark. Model independent upper limits on the cross section for narrow, vector
resonances decaying to \ttbar are presented. At the 95% confidence level, we
exclude the existence of a leptophobic \zpr boson in a model of
topcolor-assisted technicolor with mass M_{\zpr} 480 \gev for natural
width = 0.012 M_{\zpr}, and M_{\zpr} 780 \gev for =
0.04 M_{\zpr}.Comment: The CDF Collaboration, submitted to PRL 25-Feb-200
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