Evaluation of the susceptibility of pathogenic Candida species to fluconazole

A fluconazole 25 ug disk diffusion test was used to test 2230 consecutively isolatedCandida strains from 42 different hospital laboratories in 23 countries. Ninety seven percent of 1634Candida albicans isolates and 83.4% of 596 non-Candida albicans isolates were susceptible to fluconazole, applying the proposed breakpoints (≥26 mm for susceptible strains and 18-25 mm for dosedependent susceptible strains). This is the first hospital laboratory study to evaluate a large number and wide range of sequentialCandida isolates from patients with all types of hospital infections. The fluconazole disk diffusion test appears to be a low-cost, reproducible, and accurate means of assessing the in vitro susceptibility ofCandida isolate

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

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

Random Access to Grammar Compressed Strings

Grammar based compression, where one replaces a long string by a small context-free grammar that generates the string, is a simple and powerful paradigm that captures many popular compression schemes. In this paper, we present a novel grammar representation that allows efficient random access to any character or substring without decompressing the string. Let $S$ be a string of length $N$ compressed into a context-free grammar $\mathcal{S}$ of size $n$. We present two representations of $\mathcal{S}$ achieving $O(\log N)$ random access time, and either $O(n\cdot \alpha_k(n))$ construction time and space on the pointer machine model, or $O(n)$ construction time and space on the RAM. Here, $\alpha_k(n)$ is the inverse of the $k^{th}$ row of Ackermann's function. Our representations also efficiently support decompression of any substring in $S$: we can decompress any substring of length $m$ in the same complexity as a single random access query and additional $O(m)$ time. Combining these results with fast algorithms for uncompressed approximate string matching leads to several efficient algorithms for approximate string matching on grammar-compressed strings without decompression. For instance, we can find all approximate occurrences of a pattern $P$ with at most $k$ errors in time $O(n(\min\{|P|k, k^4 + |P|\} + \log N) + occ)$, where $occ$ is the number of occurrences of $P$ in $S$. Finally, we generalize our results to navigation and other operations on grammar-compressed ordered trees. All of the above bounds significantly improve the currently best known results. To achieve these bounds, we introduce several new techniques and data structures of independent interest, including a predecessor data structure, two "biased" weighted ancestor data structures, and a compact representation of heavy paths in grammars.Comment: Preliminary version in SODA 201

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

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

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

Top Tree Compression of Tries

We present a compressed representation of tries based on top tree compression [ICALP 2013] that works on a standard, comparison-based, pointer machine model of computation and supports efficient prefix search queries. Namely, we show how to preprocess a set of strings of total length n over an alphabet of size sigma into a compressed data structure of worst-case optimal size O(n/log_sigma n) that given a pattern string P of length m determines if P is a prefix of one of the strings in time O(min(m log sigma,m + log n)). We show that this query time is in fact optimal regardless of the size of the data structure. Existing solutions either use Omega(n) space or rely on word RAM techniques, such as tabulation, hashing, address arithmetic, or word-level parallelism, and hence do not work on a pointer machine. Our result is the first solution on a pointer machine that achieves worst-case o(n) space. Along the way, we develop several interesting data structures that work on a pointer machine and are of independent interest. These include an optimal data structures for random access to a grammar-compressed string and an optimal data structure for a variant of the level ancestor problem