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 $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has $|A|+|B|$ leaves and can be constructed in $O(|A|+|B|)$ 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 $A$ and $B$. 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 $A$ and $B$ has $|A| + l_d + l_1$ leaves where $l_d$ is the sum of the lengths of all parts of $B$ different from $A$ and $l_1$ is the sum of the lengths of some common parts of $A$ and $B$. We did not compromise the pattern search to reduce the space. Our suffix tree can be searched for a pattern $P$ in $O(|P|+occ)$ time where $occ$ is the number of occurrences of $P$ in $A$ and $B$. We also present an efficient algorithm to construct the suffix tree of alignment. When the suffix tree is constructed from scratch, the algorithm requires $O(|A| + l_d + l_1 + l_2)$ time where $l_2$ is the sum of the lengths of other common substrings of $A$ and $B$. When the suffix tree of $A$ is already given, it requires $O(l_d + l_1 + l_2)$ 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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