400 research outputs found
Duel and sweep algorithm for order-preserving pattern matching
Given a text and a pattern over alphabet , the classic exact
matching problem searches for all occurrences of pattern in text .
Unlike exact matching problem, order-preserving pattern matching (OPPM)
considers the relative order of elements, rather than their real values. In
this paper, we propose an efficient algorithm for OPPM problem using the
"duel-and-sweep" paradigm. Our algorithm runs in time in
general and time under an assumption that the characters in a string
can be sorted in linear time with respect to the string size. We also perform
experiments and show that our algorithm is faster that KMP-based algorithm.
Last, we introduce the two-dimensional order preserved pattern matching and
give a duel and sweep algorithm that runs in time for duel stage and
time for sweeping time with preprocessing time.Comment: 13 pages, 5 figure
Log-Poisson Cascade Description of Turbulent Velocity Gradient Statistics
The Log-Poisson phenomenological description of the turbulent energy cascade
is evoked to discuss high-order statistics of velocity derivatives and the
mapping between their probability distribution functions at different Reynolds
numbers. The striking confirmation of theoretical predictions suggests that
numerical solutions of the flow, obtained at low/moderate Reynolds numbers can
play an important quantitative role in the analysis of experimental high
Reynolds number phenomena, where small scales fluctuations are in general
inaccessible from direct numerical simulations
The effect of protein mutations on drug binding suggests ensuing personalised drug selection
The advent of personalised medicine promises a deeper understanding of mechanisms and therefore therapies. However, the connection between genomic sequences and clinical treatments is often unclear. We studied 50 breast cancer patients belonging to a population-cohort in the state of Qatar. From Sanger sequencing, we identified several new deleterious mutations in the estrogen receptor 1 gene (ESR1). The effect of these mutations on drug treatment in the protein target encoded by ESR1, namely the estrogen receptor, was achieved via rapid and accurate protein-ligand binding affinity interaction studies which were performed for the selected drugs and the natural ligand estrogen. Four nonsynonymous mutations in the ligand-binding domain were subjected to molecular dynamics simulation using absolute and relative binding free energy methods, leading to the ranking of the efficacy of six selected drugs for patients with the mutations. Our study shows that a personalised clinical decision system can be created by integrating an individual patient's genomic data at the molecular level within a computational pipeline which ranks the efficacy of binding of particular drugs to variant proteins
Hodgkin's lymphoma in remission after first-line therapy: which patients need FDG-PET/CT for follow-up?
Background: The purpose of the study was to evaluate the impact of 2-[fluorine-18]fluoro-2-deoxy-D-glucose-positron emission tomography (FDG-PET)/computed tomography (CT) during follow-up of patients with Hodgkin's lymphoma. Patients and methods: Patients in complete remission or an unconfirmed complete remission after first-line therapy who received FDG-PET/CT during their follow-up were analyzed retrospectively. Confirmatory biopsy was mandatory in case of recurrence. Results: Overall, 134 patients were analyzed. Forty-two (31.3%) patients had a recurrence. The positive predictive value of FDG-PET/CT was 0.98. Single-factor analysis identified morphological residual mass [P = 0.0005, hazard ratio (HR) 3.4, 95% confidence interval (CI) 1.7-6.6] and symptoms (P 24 months). Conclusions: Asymptomatic patients without morphological residues and an early stage of disease do not need a routine FDG-PET/CT for follow-up. Asymptomatic patients with morphological residues should receive routine follow-up FDG-PET/CT for the first 24 months. Only patients with advanced initial stage do need a routine follow-up FDG-PET/CT beyond 24 month
Risk-adapted FDG-PET/CT-based follow-up in patients with diffuse large B-cell lymphoma after first-line therapy
Background: The purpose of this study was to evaluate the impact of 2-[fluorine-18]fluoro-2-deoxy-D-glucose-positron emission tomography/computed tomography (FDG-PET/CT) during follow-up of patients with diffuse large B-cell lymphoma (DLBCL) being in complete remission or unconfirmed complete remission after first-line therapy. Patients and methods: DLBCL patients receiving FDG-PET/CT during follow-up were analyzed retrospectively. Confirmatory biopsy was mandatory in cases of suspected disease recurrence. Results: Seventy-five patients were analyzed and 23 (30%) had disease recurrence. The positive predictive value (PPV) of FDG-PET/CT was 0.85. Patients >60 years [P = 0.036, hazard ratio (HR) = 3.82, 95% confidence interval (CI) 1.02-7.77] and patients with symptoms indicative of a relapse (P = 0.015; HR = 4.1; 95% CI 1.20-14.03) had a significantly higher risk for relapse. A risk score on the basis of signs of relapse, age >60 years, or a combination of these factors identified patients at high risk for recurrence (P = 0.041). Conclusions: FDG-PET/CT detects recurrent DLBCL after first-line therapy with high PPV. However, it should not be used routinely and if only in selected high-risk patients to reduce radiation burden and costs. On the basis of our retrospective data, FDG-PET/CT during follow-up is indicated for patients 60 years with and without clinical signs of relaps
Physical tests for Random Numbers in Simulations
We propose three physical tests to measure correlations in random numbers
used in Monte Carlo simulations. The first test uses autocorrelation times of
certain physical quantities when the Ising model is simulated with the Wolff
algorithm. The second test is based on random walks, and the third on blocks of
n successive numbers. We apply the tests to show that recent errors in high
precision simulations using generalized feedback shift register algorithms are
due to short range correlations in random number sequences. We also determine
the length of these correlations.Comment: 16 pages, Post Script file, HU-TFT-94-
Approximate Quantum Fourier Transform and Decoherence
We discuss the advantages of using the approximate quantum Fourier transform
(AQFT) in algorithms which involve periodicity estimations. We analyse quantum
networks performing AQFT in the presence of decoherence and show that extensive
approximations can be made before the accuracy of AQFT (as compared with
regular quantum Fourier transform) is compromised. We show that for some
computations an approximation may imply a better performance.Comment: 14 pages, 10 fig. (8 *.eps files). More information on
http://eve.physics.ox.ac.uk/QChome.html
http://www.physics.helsinki.fi/~kasuomin
http://www.physics.helsinki.fi/~kira/group.htm
Rank Statistics in Biological Evolution
We present a statistical analysis of biological evolution processes.
Specifically, we study the stochastic replication-mutation-death model where
the population of a species may grow or shrink by birth or death, respectively,
and additionally, mutations lead to the creation of new species. We rank the
various species by the chronological order by which they originate. The average
population N_k of the kth species decays algebraically with rank, N_k ~ M^{mu}
k^{-mu}, where M is the average total population. The characteristic exponent
mu=(alpha-gamma)/(alpha+beta-gamma)$ depends on alpha, beta, and gamma, the
replication, mutation, and death rates. Furthermore, the average population P_k
of all descendants of the kth species has a universal algebraic behavior, P_k ~
M/k.Comment: 4 pages, 3 figure
Anomalous scaling in random shell models for passive scalars
A shell-model version of Kraichnan's (1994 {\it Phys. Rev. Lett. \bf 72},
1016) passive scalar problem is introduced which is inspired from the model of
Jensen, Paladin and Vulpiani (1992 {\it Phys. Rev. A\bf 45}, 7214). As in the
original problem, the prescribed random velocity field is Gaussian,
delta-correlated in time and has a power-law spectrum ,
where is the wavenumber. Deterministic differential equations for second
and fourth-order moments are obtained and then solved numerically. The
second-order structure function of the passive scalar has normal scaling, while
the fourth-order structure function has anomalous scaling. For the
anomalous scaling exponents are determined for structure functions up
to by Monte Carlo simulations of the random shell model, using a
stochastic differential equation scheme, validated by comparison with the
results obtained for the second and fourth-order structure functions.Comment: Plain LaTex, 15 pages, 4 figure available upon request to
[email protected]
Random Numbers Certified by Bell's Theorem
Randomness is a fundamental feature in nature and a valuable resource for
applications ranging from cryptography and gambling to numerical simulation of
physical and biological systems. Random numbers, however, are difficult to
characterize mathematically, and their generation must rely on an unpredictable
physical process. Inaccuracies in the theoretical modelling of such processes
or failures of the devices, possibly due to adversarial attacks, limit the
reliability of random number generators in ways that are difficult to control
and detect. Here, inspired by earlier work on nonlocality based and device
independent quantum information processing, we show that the nonlocal
correlations of entangled quantum particles can be used to certify the presence
of genuine randomness. It is thereby possible to design of a new type of
cryptographically secure random number generator which does not require any
assumption on the internal working of the devices. This strong form of
randomness generation is impossible classically and possible in quantum systems
only if certified by a Bell inequality violation. We carry out a
proof-of-concept demonstration of this proposal in a system of two entangled
atoms separated by approximately 1 meter. The observed Bell inequality
violation, featuring near-perfect detection efficiency, guarantees that 42 new
random numbers are generated with 99% confidence. Our results lay the
groundwork for future device-independent quantum information experiments and
for addressing fundamental issues raised by the intrinsic randomness of quantum
theory.Comment: 10 pages, 3 figures, 16 page appendix. Version as close as possible
to the published version following the terms of the journa
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