A suffix tree or not a suffix tree?

In this paper we study the structure of suffix trees. Given an unlabeled tree τ on n nodes and suffix links of its internal nodes, we ask the question ”Is τ a suffix tree?”, i.e., is there a string S whose suffix tree has the same topological structure as τ? We place no restrictions on S, in particular we do not require that S ends with a unique symbol. This corresponds to considering the more general definition of implicit or extended suffix trees. Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online. Deciding if τ is a suffix tree is not an easy task, because, with no restrictions on the final symbol, we cannot guess the length of a string that realizes τ from the number of leaves. And without an upper bound on the length of such a string, it is not even clear how to solve the problem by an exhaustive search. In this paper, we prove that τ is a suffix tree if and only if it is realized by a string S of length n−1, and we give a linear-time algorithm for inferring S when the first letter on each edge is known. This generalizes the work of I et al. [Discrete Appl. Math. 163, 2014]

Escherichia coli K88 adhesion: A comparison of Chinese and Large White piglets

A comparative trial was performed on 15 Large White and 12 Chinese germ-free, colostrumdeprived piglets, maintained in plastic film isolators. Shortly after successive oral inoculations of 2 E. coli strains, one K88-positive and one K88-negative, the piglets were sacrificed and bacterial numerations of the 2 strains were done on 3 different intestinal segments of each pig, using both the lumen content and the washed intestinal wall. The percentage of bacteria specifically bound to the intestinal wall was estimated, and the presence or absence of the piglet K88 intestinal receptor was thus inferred. The results tended to indicate that the 12 Chinese piglets lacked this receptor, as against 7 Large White’s. This raises the question of possible breed differences in resistance to this type of colibacillosis.Un essai comparatif a été réalisé sur 15 porcelets Large White et 12 porcelets Chinois, prélevés à la naissance de manière axénique, privés de colostrum et placés en isolateur sous film plastique. Après inoculation par voie orale de 2 souches de E. coli, l’une possédant l’antigène d’attachement K88 (K88+)l’autre dépourvue de cet antigène (K88-), les porcelets sont sacrifiés et 3 segments différents de l’intestin grêle sont prélevés sur chaque porcelet en vue de numérations des 2 souches bactériennes, à la fois dans le contenu intestinal et sur la paroi. Le pourcentage de bactéries spécifiquement attachées à la paroi est ainsi estimé et la présence ou l’absence chez le porcelet du récepteur intestinal K88 peut en être déduite. Les résultats indiquent que les 12 porcelets Chinois ne possèdent pas ce récepteur et doivent donc être résistants à l’attachement de K88, contre 7 porcelets Large White. Cela soulève la question de l’existence possible de races résistantes à cette colibacillose

Special limits and non-relativistic solutions

We study special vanishing horizon limit of `boosted' black D3-branes having a compact light-cone direction. The type IIB solution obtained by taking such a zero temperature limit is found to describe a nonrelativistic system with dynamical exponent 3. We discuss about such limits in M2-branes case also.Comment: 10 pages; V2: various changes in interpretations including title; no change in mathematical results, V3: minor font typo in eq.(7) remove

Holographic flows to IR Lifshitz spacetimes

Recently we studied `vanishing' horizon limits of `boosted' black D3-brane geometry \cite{hsnr}. The type IIB solutions obtained by taking these special double limits were found to describe nonrelativistic Lifshitz spacetimes at zero temperature. In the present work we study these limits for TsT black-hole solutions which include $B$-field. The new Galilean solutions describe a holographic RG flow from Schr\"odinger ($a=2$) spacetime in UV to a Lifshitz universe ($a=3$) in the IR.Comment: 10 pages; v2: A bad typo in eq.8 corrected; v3: Discussion and reference on Kaigorodov spaces included, correction in sec-3, to be published in JHE

Lifshitz/Schr\"odinger D-p-branes and dynamical exponents

We extend our earlier study of special double limits of `boosted' $AdS_5$ black hole solutions to include all black D$p$-branes of type II strings. We find that Lifshitz solutions can be obtained in generality, with varied dynamical exponents, by employing these limits. We then study such double limits for `boosted' D$p$-brane bubble solutions and find that the resulting non-relativistic solutions instead describe Schr\"odinger like spacetimes, having varied dynamical exponents. We get a simple map between these Lifshitz & Schr\"odinger solutions and a relationship between two types of dynamical exponents. We also discuss about the singularities of the Lifshitz solutions and an intriguing thermodynamic duality.Comment: 20 pages; 3 figures; v3: similar to JHE

The role of statins in prevention and treatment of community acquired pneumonia: a systematic review and meta-analysis.

BACKGROUND: Emerging epidemiological evidence suggests that statins may reduce the risk of community-acquired pneumonia (CAP) and its complications. PURPOSE: Performed a systematic review to address the role of statins in the prevention or treatment of CAP. DATA SOURCE: Ovid MEDLINE, Cochrane, EMBASE, ISI Web of Science, and Scopus from inception through December 2011 were searched for randomized clinical trials, cohort and case-control studies. STUDY SELECTION: Two authors independently reviewed studies that examined the role of statins in CAP. DATA EXTRACTION: Data about study characteristics, adjusted effect-estimates and quality characteristics was extracted. DATA SYNTHESIS: Eighteen studies corresponding to 21 effect-estimates (eight and 13 of which addressed the preventive and therapeutic roles of statins, respectively) were included. All studies were of good methodological quality. Random-effects meta-analyses of adjusted effect-estimates were used. Statins were associated with a lower risk of CAP, 0.84 (95% CI, 0.74-0.95), I(2) = 90.5% and a lower short-term mortality in patients with CAP, 0.68 (95% CI, 0.59-0.78), I(2) = 75.7%. Meta-regression did not identify sources of heterogeneity. A funnel plot suggested publication bias in the treatment group, which was adjusted by a novel regression method with a resultant effect-estimate of 0.85 (95% CI, 0.77-0.93). Sensitivity analyses using the rule-out approach showed that it is unlikely that the results were due to an unmeasured confounder. CONCLUSIONS: Our meta-analysis reveals a beneficial role of statins for the risk of development and mortality associated with CAP. However, the results constitute very low quality evidence as per the GRADE framework due to observational study design, heterogeneity and publication bias

Intermittent dislocation flow in viscoplastic deformation

The viscoplastic deformation (creep) of crystalline materials under constant stress involves the motion of a large number of interacting dislocations. Analytical methods and sophisticated `dislocation-dynamics' simulations have proved very effective in the study of dislocation patterning, and have led to macroscopic constitutive laws of plastic deformation. Yet, a statistical analysis of the dynamics of an assembly of interacting dislocations has not hitherto been performed. Here we report acoustic emission measurements on stressed ice single crystals, the results of which indicate that dislocations move in a scale-free intermittent fashion. This result is confirmed by numerical simulations of a model of interacting dislocations that successfully reproduces the main features of the experiment. We find that dislocations generate a slowly evolving configuration landscape which coexists with rapid collective rearrangements. These rearrangements involve a comparatively small fraction of the dislocations and lead to an intermittent behavior of the net plastic response. This basic dynamical picture appears to be a generic feature in the deformation of many other materials. Moreover, it should provide a framework for discussing fundamental aspects of plasticity, that goes beyond standard mean-field approaches that see plastic deformation as a smooth laminar flow

Holography for chiral scale-invariant models

Deformation of any d-dimensional conformal field theory by a constant null source for a vector operator of dimension (d + z -1) is exactly marginal with respect to anisotropic scale invariance, of dynamical exponent z. The holographic duals to such deformations are AdS plane waves, with z=2 being the Schrodinger geometry. In this paper we explore holography for such chiral scale-invariant models. The special case of z=0 can be realized with gravity coupled to a scalar, and is of particular interest since it is related to a Lifshitz theory with dynamical exponent two upon dimensional reduction. We show however that the corresponding reduction of the dual field theory is along a null circle, and thus the Lifshitz theory arises upon discrete light cone quantization of an anisotropic scale invariant field theory.Comment: 62 pages; v2, published version, minor improvements and references adde

Does publication bias inflate the apparent efficacy of psychological treatment for major depressive disorder? A systematic review and meta-analysis of US national institutes of health-funded trials

Background The efficacy of antidepressant medication has been shown empirically to be overestimated due to publication bias, but this has only been inferred statistically with regard to psychological treatment for depression. We assessed directly the extent of study publication bias in trials examining the efficacy of psychological treatment for depression. Methods and Findings We identified US National Institutes of Health grants awarded to fund randomized clinical trials comparing psychological treatment to control conditions or other treatments in patients diagnosed with major depressive disorder for the period 1972–2008, and we determined whether those grants led to publications. For studies that were not published, data were requested from investigators and included in the meta-analyses. Thirteen (23.6%) of the 55 funded grants that began trials did not result in publications, and two others never started. Among comparisons to control conditions, adding unpublished studies (Hedges’ g = 0.20; CI95% -0.11~0.51; k = 6) to published studies (g = 0.52; 0.37~0.68; k = 20) reduced the psychotherapy effect size point estimate (g = 0.39; 0.08~0.70) by 25%. Moreover, these findings may overestimate the "true" effect of psychological treatment for depression as outcome reporting bias could not be examined quantitatively. Conclusion The efficacy of psychological interventions for depression has been overestimated in the published literature, just as it has been for pharmacotherapy. Both are efficacious but not to the extent that the published literature would suggest. Funding agencies and journals should archive both original protocols and raw data from treatment trials to allow the detection and correction of outcome reporting bias. Clinicians, guidelines developers, and decision makers should be aware that the published literature overestimates the effects of the predominant treatments for depression

Emergent Schrodinger geometries from mass-deformed CFT

We study an M-theory solution for the holographic flow of AdS4 times Sasaki-Einstein 7-manifolds with skew-whiffing, perturbed by a mass operator. The infrared solution contains the 5 dimensional Schrodinger geometry after considering the gravity dual of the standard non-relativistic limit of relativistic field theories. The mass deformation of the field theory is discussed in detail for the case with 7 manifold being a round sphere.Comment: 20 pages, 1 figure. v2: references added, minor correction