476 research outputs found
Composite repetition-aware data structures
In highly repetitive strings, like collections of genomes from the same
species, distinct measures of repetition all grow sublinearly in the length of
the text, and indexes targeted to such strings typically depend only on one of
these measures. We describe two data structures whose size depends on multiple
measures of repetition at once, and that provide competitive tradeoffs between
the time for counting and reporting all the exact occurrences of a pattern, and
the space taken by the structure. The key component of our constructions is the
run-length encoded BWT (RLBWT), which takes space proportional to the number of
BWT runs: rather than augmenting RLBWT with suffix array samples, we combine it
with data structures from LZ77 indexes, which take space proportional to the
number of LZ77 factors, and with the compact directed acyclic word graph
(CDAWG), which takes space proportional to the number of extensions of maximal
repeats. The combination of CDAWG and RLBWT enables also a new representation
of the suffix tree, whose size depends again on the number of extensions of
maximal repeats, and that is powerful enough to support matching statistics and
constant-space traversal.Comment: (the name of the third co-author was inadvertently omitted from
previous version
Suffix Tree of Alignment: An Efficient Index for Similar Data
We consider an index data structure for similar strings. The generalized
suffix tree can be a solution for this. The generalized suffix tree of two
strings and is a compacted trie representing all suffixes in and
. It has leaves and can be constructed in time.
However, if the two strings are similar, the generalized suffix tree is not
efficient because it does not exploit the similarity which is usually
represented as an alignment of and .
In this paper we propose a space/time-efficient suffix tree of alignment
which wisely exploits the similarity in an alignment. Our suffix tree for an
alignment of and has leaves where is the sum of
the lengths of all parts of different from and is the sum of the
lengths of some common parts of and . We did not compromise the pattern
search to reduce the space. Our suffix tree can be searched for a pattern
in time where is the number of occurrences of in and
. We also present an efficient algorithm to construct the suffix tree of
alignment. When the suffix tree is constructed from scratch, the algorithm
requires time where is the sum of the lengths
of other common substrings of and . When the suffix tree of is
already given, it requires time.Comment: 12 page
Vortex-mediated relaxation of magnon BEC into light Higgs quasiparticles
A magnon Bose-Einstein condensate (BEC) in superfluid 3He is a fine instrument for studying the surrounding macroscopic quantum system. At zero temperature, the BEC is subject to a few distinct forms of decay into other collective excitations, owing to momentum and energy conservation in a quantum vacuum. We study the vortex-Higgs mechanism: The vortices relax the requirement for momentum conservation, allowing the optical magnons of the BEC to transform into light Higgs quasiparticles. This facilitates a direct measurement of the dimensions of the B-phase double-core vortex, providing experimental access to elusive phenomena, such as the Kelvin wave cascade and core-bound Majorana fermions. Our paper expands the spectrum of possible interactions between magnetic quasiparticles in 3He-B and lays the groundwork for building magnon-based quantum devices
Nonlinear two-level dynamics of quantum time crystals
A time crystal is a macroscopic quantum system in periodic motion in its ground state. In our experiments, two coupled time crystals consisting of spin-wave quasiparticles (magnons) form a macroscopic two-level system. The two levels evolve in time as determined intrinsically by a nonlinear feedback, allowing us to construct spontaneous two-level dynamics. In the course of a level crossing, magnons move from the ground level to the excited level driven by the Landau-Zener effect, combined with Rabi population oscillations. We demonstrate that magnon time crystals allow access to every aspect and detail of quantum-coherent interactions in a single run of the experiment. Our work opens an outlook for the detection of surface-bound Majorana fermions in the underlying superfluid system, and invites technological exploitation of coherent magnon phenomena – potentially even at room temperature
Rotating quantum wave turbulence
Turbulence under strong influence of rotation is described as an ensemble of interacting inertial waves across a wide range of length scales. In macroscopic quantum condensates, the quasiclassical turbulent dynamics at large scales is altered at small scales, where the quantization of vorticity is essential. The nature of this transition remains an unanswered question. Here we expand the concept of wave-driven turbulence to rotating quantum fluids where the spectrum of waves extends to microscopic scales as Kelvin waves on quantized vortices. We excite inertial waves at the largest scale by periodic modulation of the angular velocity and observe dissipation-independent transfer of energy to smaller scales and the eventual onset of the elusive Kelvin wave cascade at the lowest temperatures. We further find that energy is pumped to the system through a boundary layer distinct from the classical Ekman layer and support our observations with numerical simulations. Our experiments demonstrate a regime of turbulent motion in quantum fluids where the role of vortex reconnections can be neglected, thus stripping the transition between the classical and the quantum regimes of turbulence down to its constituent components
Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts
We study the approximate string matching and regular expression matching
problem for the case when the text to be searched is compressed with the
Ziv-Lempel adaptive dictionary compression schemes. We present a time-space
trade-off that leads to algorithms improving the previously known complexities
for both problems. In particular, we significantly improve the space bounds,
which in practical applications are likely to be a bottleneck
Wave Energy: a Pacific Perspective
This is the author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by The Royal Society and can be found at: http://rsta.royalsocietypublishing.org/.This paper illustrates the status of wave energy development in Pacific Rim countries by characterizing the available resource and introducing the region‟s current and potential future leaders in wave energy converter development. It also describes the existing licensing and permitting process as well as potential environmental concerns. Capabilities of Pacific Ocean testing facilities are described in addition to the region‟s vision of the future of wave energy
Range Quantile Queries: Another Virtue of Wavelet Trees
We show how to use a balanced wavelet tree as a data structure that stores a
list of numbers and supports efficient {\em range quantile queries}. A range
quantile query takes a rank and the endpoints of a sublist and returns the
number with that rank in that sublist. For example, if the rank is half the
sublist's length, then the query returns the sublist's median. We also show how
these queries can be used to support space-efficient {\em coloured range
reporting} and {\em document listing}.Comment: Added note about generalization to any constant number of dimensions
Linear response of mutans streptococci to increasing frequency of xylitol chewing gum use: a randomized controlled trial [ISRCTN43479664]
BACKGROUND: Xylitol is a naturally occurring sugar substitute that has been shown to reduce the level of mutans streptococci in plaque and saliva and to reduce tooth decay. It has been suggested that the degree of reduction is dependent on both the amount and the frequency of xylitol consumption. For xylitol to be successfully and cost-effectively used in public health prevention strategies dosing and frequency guidelines should be established. This study determined the reduction in mutans streptococci levels in plaque and unstimulated saliva to increasing frequency of xylitol gum use at a fixed total daily dose of 10.32 g over five weeks. METHODS: Participants (n = 132) were randomized to either active groups (10.32 g xylitol/day) or a placebo control (9.828 g sorbitol and 0.7 g maltitol/day). All groups chewed 12 pieces of gum per day. The control group chewed 4 times/day and active groups chewed xylitol gum at a frequency of 2 times/day, 3 times/day, or 4 times/day. The 12 gum pieces were evenly divided into the frequency assigned to each group. Plaque and unstimulated saliva samples were taken at baseline and five-weeks and were cultured on modified Mitis Salivarius agar for mutans streptococci enumeration. RESULTS: There were no significant differences in mutans streptococci level among the groups at baseline. At five-weeks, mutans streptococci levels in plaque and unstimulated saliva showed a linear reduction with increasing frequency of xylitol chewing gum use at the constant daily dose. Although the difference observed for the group that chewed xylitol 2 times/day was consistent with the linear model, the difference was not significant. CONCLUSION: There was a linear reduction in mutans streptococci levels in plaque and saliva with increasing frequency of xylitol gum use at a constant daily dose. Reduction at a consumption frequency of 2 times per day was small and consistent with the linear-response line but was not statistically significant
Validation of [18F]fluorodeoxyglucose and positron emission tomography (PET) for the measurement of intestinal metabolism in pigs, and evidence of intestinal insulin resistance in patients with morbid obesity
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