Fast Arc-Annotated Subsequence Matching in Linear Space

An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings $P$ and $Q$ the arc-preserving subsequence problem is to determine if $P$ can be obtained from $Q$ by deleting bases from $Q$. Whenever a base is deleted any arc with an endpoint in that base is also deleted. Arc-annotated strings where the arcs are ``nested'' are a natural model of RNA molecules that captures both the primary and secondary structure of these. The arc-preserving subsequence problem for nested arc-annotated strings is basic primitive for investigating the function of RNA molecules. Gramm et al. [ACM Trans. Algorithms 2006] gave an algorithm for this problem using $O(nm)$ time and space, where $m$ and $n$ are the lengths of $P$ and $Q$, respectively. In this paper we present a new algorithm using $O(nm)$ time and $O(n + m)$ space, thereby matching the previous time bound while significantly reducing the space from a quadratic term to linear. This is essential to process large RNA molecules where the space is likely to be a bottleneck. To obtain our result we introduce several novel ideas which may be of independent interest for related problems on arc-annotated strings.Comment: To appear in Algoritmic

Full-Course Oral Levofloxacin for Treatment of Hospitalized Patients with Community-Acquired Pneumonia

Most guidelines for the management of hospitalized patients with community-acquired pneumonia (CAP) recommend commencing therapy with intravenous antibiotics, primarily because of concern about absorption of oral antibiotics in acutely ill patients. However, patients who respond are rapidly switched to oral therapy, which has been shown to reduce costs and to shorten the length of stay. The aim of the present study was to determine whether a full course of oral antibiotics is as efficacious and as safe as intravenous-to-oral sequential antibiotic therapy for the treatment of hospitalized, non-ICU patients with CAP. In an open-labelled, controlled study, 129 hospitalized patients with CAP were randomly assigned in a 2:1 ratio to receive either a full course of oral levofloxacin (500mg q12h) or an intravenous-to-oral sequential therapy consisting of intravenous ceftriaxone (2g q24h) with or without clarithromycin (500mg q12h) followed by an oral antibiotic (a beta-lactam agent in the majority of patients). The primary study endpoint was the resolution of CAP; secondary endpoints included length of stay and overall mortality. CAP resolved in 72 of 79 (91.1%) patients in the levofloxacin group and in 34 of 37 (91.9%) patients in the intravenous-to-oral sequential therapy group (difference, −0.8%, 95%CI, −11.6-10.0). Median length of stay was 8 days (range, 2-74 days) in the levofloxacin group and 10 days (range, 3-29 days) in the intravenous-to-oral sequential therapy group (P=0.28). Day 30 mortality rates were 1.3% (1 of 79) and 8.1% (3 of 37), respectively (difference, −6.8%, 95%CI, −16.0-2.3). Full-course oral levofloxacin is as efficacious and as safe as standard intravenous-to-oral sequential antibiotic therapy for the treatment of hospitalized patients with CA

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

Comment on "c-axis Josephson tunneling in Dx2−y2D_{x^2-y^2}-wave superconductors''

This comment points out that the recent paper by Maki and Haas [Phys. Rev. B {\bf 67}, 020510 (2003)] is completely wrong.Comment: 1 page, submittted to Phys. Rev.

Theory of Bi2_2Sr2_2CaCu2_2O8+δ_{8+\delta} Cross-Whisker Josephson Junctions

Takano {\it et al.} [Phys. Rev. B {\bf 65}, 140513 (2002) and unpublished] made Josephson junctions from single crystal whiskers of Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ crossed an angle $\phi_0$ about the $c$ axis. From the mesa structures that formed at the cross-whisker interface, they inferred a critical current density $J_c(\phi_0)$. Like the single crystal results of Li {\it et al.} [Phys. Rev. Lett. {\bf 83}, 4160 (1999)], we show that the whisker data are unlikely to result from a predominantly d-wave order parameter. However, unlike the single crystals, these results, if correct, require the whisker c-axis transport to be coherent.Comment: 5 pages, 4 figures, accepted for publication in Physical Review

Towards a Definitive Measure of Repetitiveness

Unlike in statistical compression, where Shannon’s entropy is a definitive lower bound, no such clear measure exists for the compressibility of repetitive sequences. Since statistical entropy does not capture repetitiveness, ad-hoc measures like the size z of the Lempel–Ziv parse are frequently used to estimate repetitiveness. Recently, a more principled measure, the size γ of the smallest string attractor, was introduced. The measure γ lower bounds all the previous relevant ones (including z), yet length-n strings can be represented and efficiently indexed within space O(γlognγ), which also upper bounds most measures (including z). While γ is certainly a better measure of repetitiveness than z, it is NP-complete to compute, and no o(γlog n) -space representation of strings is known. In this paper, we study a smaller measure, δ≤ γ, which can be computed in linear time. We show that δ better captures the compressibility of repetitive strings. For every length n and every value δ≥ 2, we construct a string such that γ=Ω(δlognδ). Still, we show a representation of any string S in O(δlognδ) space that supports direct access to any character S[i] in time O(lognδ) and finds the occ occurrences of any pattern P[1.m] in time O(mlog n+ occlogεn) for any constant ε> 0. Further, we prove that no o(δlog n) -space representation exists: for every length n and every value 2 ≤ δ≤ n1-ε, we exhibit a string family whose elements can only be encoded in Ω(δlognδ) space. We complete our characterization of δ by showing that, although γ, z, and other repetitiveness measures are always O(δlognδ), for strings of any length n, the smallest context-free grammar can be of size Ω(δlog2n/ log log n). No such separation is known for γ

Full-course oral levofloxacin for treatment of hospitalized patients with community-acquired pneumonia.

Most guidelines for the management of hospitalized patients with community-acquired pneumonia (CAP) recommend commencing therapy with intravenous antibiotics, primarily because of concern about absorption of oral antibiotics in acutely ill patients. However, patients who respond are rapidly switched to oral therapy, which has been shown to reduce costs and to shorten the length of stay. The aim of the present study was to determine whether a full course of oral antibiotics is as efficacious and as safe as intravenous-to-oral sequential antibiotic therapy for the treatment of hospitalized, non-ICU patients with CAP. In an open-labelled, controlled study, 129 hospitalized patients with CAP were randomly assigned in a 2:1 ratio to receive either a full course of oral levofloxacin (500 mg q12 h) or an intravenous-to-oral sequential therapy consisting of intravenous ceftriaxone (2 g q24 h) with or without clarithromycin (500 mg q12 h) followed by an oral antibiotic (a beta-lactam agent in the majority of patients). The primary study endpoint was the resolution of CAP; secondary endpoints included length of stay and overall mortality. CAP resolved in 72 of 79 (91.1%) patients in the levofloxacin group and in 34 of 37 (91.9%) patients in the intravenous-to-oral sequential therapy group (difference, -0.8%, 95%CI, -11.6-10.0). Median length of stay was 8 days (range, 2-74 days) in the levofloxacin group and 10 days (range, 3-29 days) in the intravenous-to-oral sequential therapy group ( P=0.28). Day 30 mortality rates were 1.3% (1 of 79) and 8.1% (3 of 37), respectively (difference, -6.8%, 95%CI, -16.0-2.3). Full-course oral levofloxacin is as efficacious and as safe as standard intravenous-to-oral sequential antibiotic therapy for the treatment of hospitalized patients with CAP

Reconstructing past terrace fields in the Pyrenees: Insights into land management and settlement from the Bronze Age to the Early Modern era at Vilalta (1650 masl, Cerdagne, France)

© Trustees of Boston University 2015. The building of a solar power station at Thémis, at 1650 masl on the south-facing slope of the Carlit massif in the eastern Pyrenees, led to an archaeological evaluation from April-June 2009. This evaluation covered a surface of 10 ha that included a medieval village as well as the surrounding agricultural land in terraces. Non-destructive archaeological methods were used for the village. A detailed study of the 6 ha of terraces began with a fieldwalking survey, mapping every visible feature, followed by systematic trial trenches. Fifty-five trenches, 11 in the village and 44 in the fields, were opened. The stratigraphies were then compared with a series of 22 radiocarbon dates and eight relative dates provided by ceramic typologies. This combination of surface and buried evidence supported our preliminary hypothesis about the dynamics of the slope. The results suggest the existence of agrarian features beginning in the Bronze Age and reveal that the field patterns were frequently transformed, both in the Medieval and Early Modern periods. The transformations in the terrace fields after the village was abandoned are as interesting as those during occupation because, contrary to the idea of a fixed, unchanging landscape after the end of the Middle Ages, they challenge the idea that mountain zones are marginal spaces by nature, or were marginalized later.Peer Reviewe

Gaussian Tunneling Model of c-Axis Twist Josephson Junctions

We calculate the critical current density $J^J_c$ for c-axis Josephson tunneling between identical high temperature superconductors twisted an angle $\phi_0$ about the c-axis. We model the tunneling matrix element squared as a Gaussian in the change of wavevector q parallel to the junction, $<|t({\bf q})|^2>\propto\exp(-{\bf q}^2a^2/2\pi^2\sigma^2)$. The $J^J_c(\phi_0)/J^J_c(0)$ obtained for the s- and extended-s-wave order parameters (OP's) are consistent with the Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ data of Li {\it et al.}, but only for strongly incoherent tunneling, $\sigma^2\ge0.25$. A $d_{x^2-y^2}$-wave OP is always inconsistent with the data. In addition, we show that the apparent conventional sum rule violation observed by Basov et al. might be understandable in terms of incoherent c-axis tunneling, provided that the OP is not $d_{x^2-y^2}$-wave.Comment: 6 pages, 6 figure