Weighted ancestors in suffix trees

The classical, ubiquitous, predecessor problem is to construct a data structure for a set of integers that supports fast predecessor queries. Its generalization to weighted trees, a.k.a. the weighted ancestor problem, has been extensively explored and successfully reduced to the predecessor problem. It is known that any solution for both problems with an input set from a polynomially bounded universe that preprocesses a weighted tree in O(n polylog(n)) space requires \Omega(loglogn) query time. Perhaps the most important and frequent application of the weighted ancestors problem is for suffix trees. It has been a long-standing open question whether the weighted ancestors problem has better bounds for suffix trees. We answer this question positively: we show that a suffix tree built for a text w[1..n] can be preprocessed using O(n) extra space, so that queries can be answered in O(1) time. Thus we improve the running times of several applications. Our improvement is based on a number of data structure tools and a periodicity-based insight into the combinatorial structure of a suffix tree.Comment: 27 pages, LNCS format. A condensed version will appear in ESA 201

Protection Against Chronic Pyelonephritis in Rats by Suppression of Acute Suppuration: Effect of Colchicine and Neutropenia

Previous experiments in rats have suggested that renal scarring after acute, obstructive pyelonephritis due to Escherichia coli results from parenchymal damage due to acute inflammation and suppuration. To assess the role of acute infiltration by polymorphonuclear leukocytes (PMNLs) in the pathogenesis of chronic pyelonephritis (CPN), rats were either treated with colchicine to depress leukcoyte motility or rendered neutropenic with a single dose of cyclophosphamide. Colchicine given during acute pyelonephritis reduced kidney inflammation and protected against CPN two months later. Similarly, neutropenia reduced acute inflammation and protected against chronic parenchymal destruction and scarring. Protection against renal scarring in both colchicine-treated and neutropenic rats occurred despite higher renal bacterial counts during acute pyelonephritis. These experiments provide further evidence that CPN (renal scarring) results from kidney damage that occurs during early acute obstructive pyelonephritis. This damage appears to result from infiltration of the kidney by PMNLs rather than direct damage from bacterial infectio

Prophylaxis of pyelonephritis by aminoglycosides accumulated in the kidney

When given prophylactically, gentamicin accumulates and persists in the rat kidney and affords protection against obstructive acute Escherichia coli pyelonephritis. Similar protection is observed after administration of amikacin, netilmicin and tobramycin, which accumulate to various degrees in the renal parenchyma. In those animals developing pyelonephritis despite aminoglycoside prophylaxis, renal infection and inflammation are reduced during the acute phase of the disease. This results in almost complete protection against renal scarring later on. Administrée à titre prophylactique, la Gentamicine s'accurnule dans le rein du rat et le protège contre l'apparition de pyélonéphrite aiguë à E. coli. Un effet protecteur identique est observé aprés administration d'Amikacine, de Nétilmicine, et de Tobramycine, qui s'accumulent à des degrés divers dans le parenchyme rénal. Chez l'animal, lorsqu'apparait une pyélonéphrite, malgré le traitement prophylactique par les aminoglycosides, l'infection et l'inflammation rénales sont diminuées durant la phase aiguë de la maladie. Ceci réduit le risque de lésion et de formation ultérieure de tissu cicatricie

In-vitro activity of temafloxacin for Gram-positive pathogens

The antimicrobial activity of tcmafioxacin against aerobic Gram-positive cocci was compared to that of ciprofloxacin, ofloxacin, fleroxacin and pefloxacin using the broth microdilution technique. Temafloxacin was mom active than the other four fluoroquinolones, particularly for viridans streptococci and Streptococcus pneumoniaeniae. The MIC90 of temafloxacin was at least four-fold lower than that of ciprofloxacin and ofloxacin for viridans strtptococci and penicillin-susceptible pneumococci. The MIC50s and MIC90s of temafloxacin were equal to or lower than those of the other fluoroquinolones for rnethicillin-susceptible Staphylococnu aureus (MSSA), methicillin-resistant S.aureus (MRSA), and methicillin-susceptible and methicillin-resistant coagulasc-negative staphylococci Temafloxadn was more active against all the other Gram-positive aerobes (except Enterococcus faecalis) tested than the other fluorquinolone

String Indexing for Patterns with Wildcards

We consider the problem of indexing a string $t$ of length $n$ to report the occurrences of a query pattern $p$ containing $m$ characters and $j$ wildcards. Let $occ$ be the number of occurrences of $p$ in $t$, and $\sigma$ the size of the alphabet. We obtain the following results. - A linear space index with query time $O(m+\sigma^j \log \log n + occ)$. This significantly improves the previously best known linear space index by Lam et al. [ISAAC 2007], which requires query time $\Theta(jn)$ in the worst case. - An index with query time $O(m+j+occ)$ using space $O(\sigma^{k^2} n \log^k \log n)$, where $k$ is the maximum number of wildcards allowed in the pattern. This is the first non-trivial bound with this query time. - A time-space trade-off, generalizing the index by Cole et al. [STOC 2004]. We also show that these indexes can be generalized to allow variable length gaps in the pattern. Our results are obtained using a novel combination of well-known and new techniques, which could be of independent interest

Single-Dose Rifampin Prophylaxis for Experimental Endocarditis Induced by High Bacterial Inocula of Viridans Streptococci

In rats challenged with viridans streptococci poorly susceptible to antibiotic killing, single doses of antibiotics only prevent endocarditis induced by bacterial inoculum sizes that produce disease in 90% of control animals (ID90) : additional doses are required to protect against inocula exceeding the ID90. We investigated whether single-dose rifampin would extend the efficacy of single-dose prophylaxis to inocula exceeding the ID90. We used two strains of viridans streptococci highly susceptible to killing by rifampin and two resistant strains. All rats wereinjected with 10-1,000 times the ID90 of the four strains. Single-dose rifampin successfully prevented endocarditis due to all four strains. A few prophylaxis failures were observed after challenge with the two poorly susceptible strains, but in vivo emergence of resistant variants did not account for these failures. Thus, rifampin was the first antibiotic given as a single dose that successfully prevented experimental streptococcus endocarditis after challenge with high bacterial inocul

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

An Epidemic of Food-Borne Listeriosis in Western Switzerland: Description of 57 Cases Involving Adults

This article describes 57 cases of listeriosis that occurred in adults in western Switzerland during an outbreak associated with the consumption of a soft cheese. Twenty-one percent of the cases were of bacteremia, 40% were of meningitis, and 39% were of meningoencephalitis. Overall, 42% of the patients had an underlying disease and 54% were >65 years of age. Patients with bacteremia were significantly older than those with meningitis or meningoencephalitis (median ages, 75, 69, and 55 years, respectively). The epidemic strain, defined by phage typing, was isolated in three-quarters of the listerial cases observed during the epidemic period and did not appear to differ significantly from the nonepidemic strains in terms of virulence. The overall mortality associated with the 57 cases was 32%. Among the patients' characteristics, age and type of clinical presentation were independent predictors of death in a multivariate logistic regression model (pseudo-r2 [coefficient of determination], .26; both P values <.05), and a presentation of meningoencephalitis was associated with an increased death risk (odds ratio, 6.5; 95% confidence interval, 1.1-39.5; P < .05). Neurological sequelae developed in 30% of the survivors of CNS listeriosi

Fast Indexes for Gapped Pattern Matching

We describe indexes for searching large data sets for variable-length-gapped (VLG) patterns. VLG patterns are composed of two or more subpatterns, between each adjacent pair of which is a gap-constraint specifying upper and lower bounds on the distance allowed between subpatterns. VLG patterns have numerous applications in computational biology (motif search), information retrieval (e.g., for language models, snippet generation, machine translation) and capture a useful subclass of the regular expressions commonly used in practice for searching source code. Our best approach provides search speeds several times faster than prior art across a broad range of patterns and texts.Comment: This research is supported by Academy of Finland through grant 319454 and has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 69094