Search results for "Mathematic"

Measuring the clustering effect of BWT via RLE

2017

Abstract The Burrows–Wheeler Transform (BWT) is a reversible transformation on which are based several text compressors and many other tools used in Bioinformatics and Computational Biology. The BWT is not actually a compressor, but a transformation that performs a context-dependent permutation of the letters of the input text that often create runs of equal letters (clusters) longer than the ones in the original text, usually referred to as the “clustering effect” of BWT. In particular, from a combinatorial point of view, great attention has been given to the case in which the BWT produces the fewest number of clusters (cf. [5] , [16] , [21] , [23] ). In this paper we are concerned about t…

Lost Strings in Genomes: What Sense Do They Make?

2017

We studied the sets of avoided strings to be observed over a family of genomes. It was found that the length of the minimal avoided string rarely exceeds 9 nucleotides, with neither respect to a phylogeny of a genome under consideration. The lists of the avoided strings observed over the sets of (related) genomes have been analyzed. Very low correlation between the phylogeny, and the set of those strings has been found.

CLOVE: classification of genomic fusions into structural variation events

2017

Background A precise understanding of structural variants (SVs) in DNA is important in the study of cancer and population diversity. Many methods have been designed to identify SVs from DNA sequencing data. However, the problem remains challenging because existing approaches suffer from low sensitivity, precision, and positional accuracy. Furthermore, many existing tools only identify breakpoints, and so not collect related breakpoints and classify them as a particular type of SV. Due to the rapidly increasing usage of high throughput sequencing technologies in this area, there is an urgent need for algorithms that can accurately classify complex genomic rearrangements (involving more than …

Searching events in AFM force-extension curves: A wavelet approach

2016

An algorithm, based on the wavelet scalogram energy, for automatically detecting events in force-extension AFM force spectroscopy experiments is introduced. The events to be detected are characterized by a discontinuity in the signal. It is shown how the wavelet scalogram energy has different decay rates at different points depending on the degree of regularity of the signal, showing faster decay rates at regular points and slower rates at singular points (jumps). It is shown that these differences produce peaks in the scalogram energy plot at the event points. Finally, the algorithm is illustrated in a tether analysis experiment by using it for the detection of events in the AFM force-exte…

Where do we go from here? Membrane protein research beyond the structure-function horizon.

2018

Cultivation trials of hop (Humulus lupulus L.) in semi-arid environments

2020

Abstract The recent developments in the market and craft beer industry in Italy have led to an increasing demand for local raw materials, such as barley malt and hops. Few works have been addressed to evaluate suitability and productivity of hop in semi-arid Italian environments. With this purpose, two experiments were carried out in 2018 and 2019, testing the suitability to cultivation of three commonly used hop varieties (Cascade, Chinook and Nuggett) in two typical semi-arid environments in Sicily. Phenological stages were also evaluated, and GDDs accumulated in vegetative and reproductive stages were calculated according to 9 different methods, dealing with three Tbase temperatures (0 °…

Coupling News Sentiment with Web Browsing Data Improves Prediction of Intra-Day Price Dynamics

2015

The new digital revolution of big data is deeply changing our capability of understanding society and forecasting the outcome of many social and economic systems. Unfortunately, information can be very heterogeneous in the importance, relevance, and surprise it conveys, affecting severely the predictive power of semantic and statistical methods. Here we show that the aggregation of web users' behavior can be elicited to overcome this problem in a hard to predict complex system, namely the financial market. Specifically, our in-sample analysis shows that the combined use of sentiment analysis of news and browsing activity of users of Yahoo! Finance greatly helps forecasting intra-day and dai…

In vitro comparison of passive and continuous ultrasonic irrigation in curved root canals

2016

BACKGROUND The efficacy of endodontic irrigation procedures can be compromised by the complexity of the root canal system. Delivering irrigants to the apical third of curved canals presents a particular challenge to endodontists. This study compared the effects of two ultrasonic irrigation techniques on the penetration of sodium hypochlorite into the main canal and simulated lateral canals of curved roots in extracted teeth. MATERIAL AND METHODS Two sets of simulated lateral canals were created at 2, 4, and 6 mm from the working length in 60 single-rooted teeth (6 canals/tooth, n = 360 canals). The teeth were randomly divided into three experimental irrigation groups: group 1 (n = 20), posi…

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…

Association between Leptin and Complement in Hepatitis C Patients with Viral Clearance: Homeostasis of Metabolism and Immunity

2016

Background The association between leptin and complement in hepatitis C virus (HCV) infection remains unknown. Methods A prospective study was conducted including 474 (250 genotype 1, 224 genotype 2) consecutive chronic hepatitis C (CHC) patients who had completed an anti-HCV therapy course and undergone pre-therapy and 24-week post-therapy assessments of interferon λ3-rs12979860 and HCV RNA/genotypes, anthropometric measurements, metabolic and liver profiles, and complement component 3 (C3), C4, and leptin levels. Results Of the 474 patients, 395 had a sustained virological response (SVR). Pre-therapy leptin levels did not differ between patients with and without an SVR. Univariate and mul…