Search results for "string"

Linear-time sequence comparison using minimal absent words & applications

2016

Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free techniques, which are based on measures referring to the composition of sequences in terms of their constituent patterns. These measures, such as q-gram distance, are usually computed in time linear with respect to the length of the sequences. In this article, we focus on the complementary idea: how two sequences can be efficiently compared based on information that does not occur in the sequences. A word is an absent word of some sequence if it does not occur in…

Entropic Interactions between Two Knots on a Semiflexible Polymer.

2017

Two knots on a string can either be separated or intertwined, and may even pass through each other. At the microscopic scale, such transitions may occur spontaneously, driven by thermal fluctuations, and can be associated with a topological free energy barrier. In this manuscript, we study the respective location of a trefoil ( 3 1 ) and a figure-eight ( 4 1 ) knot on a semiflexible polymer, which is parameterized to model dsDNA in physiological conditions. Two cases are considered: first, end monomers are grafted to two confining walls of varying distance. Free energy profiles and transition barriers are then compared to a subset of free chains, which contain exactly one 3 1 and one 4 1 kn…

Mechanisms of astringency: Structural alteration of the oral mucosal pellicle by dietary tannins and protective effect of bPRPs

2018

International audience; The interaction of tannins with salivary proteins is involved in astringency. This paper focussed on saliva liningoral mucosae, the mucosal pellicle. Using a cell-based model, the impact of two dietary tannins (EgC and EgCG)on the mucosal pellicle structure and properties was investigated by microscopic techniques. The role of basicProline-Rich-Proteins (bPRPs) in protecting the mucosal pellicle was also evaluated.At low (0.05 mM) tannin concentration, below the sensory detection threshold, the distribution of salivarymucins MUC5B on cells remained unaffected. At 0.5 and 1 mM, MUC5B-tannin aggregates were observed andtheir size increased with tannin concentration and…

ParDRe: faster parallel duplicated reads removal tool for sequencing studies

2016

This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record [insert complete citation information here] is available online at: https://doi.org/10.1093/bioinformatics/btw038 [Abstract] Summary: Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but can increase memory requirements and computational time of downstream analysis. In this work we present ParDRe , a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of S…

Discovering unbounded unions of regular pattern languages from positive examples

1996

The problem of learning unions of certain pattern languages from positive examples is considered. We restrict to the regular patterns, i.e., patterns where each variable symbol can appear only once, and to the substring patterns, which is a subclass of regular patterns of the type xαy, where x and y are variables and α is a string of constant symbols. We present an algorithm that, given a set of strings, finds a good collection of patterns covering this set. The notion of a ‘good covering’ is defined as the most probable collection of patterns likely to be present in the examples, assuming a simple probabilistic model, or equivalently using the Minimum Description Length (MDL) principle. Ou…

Influence of Centerline Intermetallic Stringers on Pitting Corrosion Resistance of Superduplex Stainless Steel

2021

Superduplex stainless steel UNS S32750 / EN 1.4410 is commonly used in marine environment, petrochemical, oil and gas, chemical and desalination industries, requiring materials with superior corrosion and mechanical properties. Very few residual intermetallic particles may be present under the form of centerline stringers whose effects on corrosion properties are not well documented. A previous study demonstrated the negligible influence of the intermetallic phases in centerline stringers (typically < 0.1% over thickness) on the hydrogen embrittlement susceptibility of superduplex stainless steel [1]. The present study aims at highlighting the impact of centerline intermetallic stringers on…

Computing the Original eBWT Faster, Simpler, and with Less Memory

2021

Mantaci et al. [TCS 2007] defined the \(\mathrm {eBWT}\) to extend the definition of the \(\mathrm {BWT}\) to a collection of strings. However, since this introduction, it has been used more generally to describe any \(\mathrm {BWT}\) of a collection of strings, and the fundamental property of the original definition (i.e., the independence from the input order) is frequently disregarded. In this paper, we propose a simple linear-time algorithm for the construction of the original \(\mathrm {eBWT}\), which does not require the preprocessing of Bannai et al. [CPM 2021]. As a byproduct, we obtain the first linear-time algorithm for computing the \(\mathrm {BWT}\) of a single string that uses …

Caratterizzazione microstrutturale e meccanica di giunti friction skin-stringer (2024/t4-7075/t6) saldati a basso e alto apporto termico

2011

Active learning strategies for the deduplication of electronic patient data using classification trees.

2012

Graphical abstractDisplay Omitted Highlights? Active learning for medical record linkage is used on a large data set. ? We compare a simple active learning strategy with a more sophisticated variant. ? The active learning method of Sarawagi and Bhamidipaty (2002) 6] is extended. ? We deliver insights into the variations of the results due to random sampling in the active learning strategies. IntroductionSupervised record linkage methods often require a clerical review to gain informative training data. Active learning means to actively prompt the user to label data with special characteristics in order to minimise the review costs. We conducted an empirical evaluation to investigate whether…

Effect of Practice, Mapping, Stimulus and Size on String Matching

1987

The same-different discrepancy on a matching task on which the subject had to determine the number of common elements (physically identical and appearing in the same position) between two strings of size 1 to 4 was investigated. Manipulated also were the type of presentation (fixed or varied sets), amount of practice (four blocks), and type of stimulus (letters, words). Reaction times for pure positive responses (all same at each level) were faster than negative responses (all different), confirming the usual discrepancy shown in previous studies. The discrepancy was smaller for well-learned sets (fixed sets) and for words, indicating the development of a comparison process based on global…