Analysis Of Long Sequences Research Articles

Recent advancements in multi-temporal methods applied to new generation SAR systems and applications in South America

Detection and continuous monitoring of Earth's ground surface changes, triggered by natural phenomena or induced by human activities, is nowadays possible using Earth Observation (EO) technologies. Indeed, the exploitation of remotely sensed data collected by constellations of new-generation satellite platforms, complemented with in-situ measurements and ground-based observation systems, represents a well-established practice to get valuable information on Earth's crust and subsurface dynamics. The effects of extreme natural or man-induced events (e.g., earthquakes, volcanic eruptions, flooding phenomena, sea-level rise, big fires, etc.) have severe societal and economic impacts. In particular, the technologies based on the use of Synthetic Aperture Radar (SAR) images reached significant improvements in the last decade due to the growing availability of vast amounts of data collected by multiple-satellite sensors operating at different frequency bands and with complementary viewing angles, polarization and acquisition modes. Accordingly, to process a large amount of SAR data in a timely fashion, up-to-date high-performance computing (HPC) methods and tools are required. This paper addresses the state-of-the-art of SAR technologies for the analysis of long sequences of multiple sets of SAR images and provides a perspective on the forthcoming improvements of these technologies. In particular, the emphasis is placed on novel interferometric SAR and change detection methods, giving an overview of how those processing techniques have been used for investigating sites located in South and Central America. Moreover, an overview of the new generation of SAR sensors' observational capability, especially in the field of ground deformation analysis for mitigating the risk associated with natural and human-induced hazards, is provided. COSMO-SkyMed, ALOS, Sentinel-1, and SAOCOM data are exploited to show how natural and human-induced terrain displacement phenomena can be detected and investigated in different portions (X-, L- and C-band) of the microwave spectrum using SAR technologies.

Efficient Algorithms for Sequence Analysis with Entropic Profiles.

Entropy, being closely related to repetitiveness and compressibility, is a widely used information-related measure to assess the degree of predictability of a sequence. Entropic profiles are based on information theory principles, and can be used to study the under-/over-representation of subwords, by also providing information about the scale of conserved DNA regions. Here, we focus on the algorithmic aspects related to entropic profiles. In particular, we propose linear time algorithms for their computation that rely on suffix-based data structures, more specifically on the truncated suffix tree (TST) and on the enhanced suffix array (ESA). We performed an extensive experimental campaign showing that our algorithms, beside being faster, make it possible the analysis of longer sequences, even for high degrees of resolution, than state of the art algorithms.

Full‐Field Strain Rate Measurement by White‐Light Speckle Image Correlation

Abstract: This paper explains a numerical procedure to process sequences of digital images and to return a full‐field evaluation of the strain rate. The processing procedure is based on a nonlinear least squares fitting performed globally, on the whole image, and simultaneously on several images. The use of a highly optimised code allows the analysis of long sequences in a few minutes. The results of calculations are presented as movies built by blending the colour maps of the measured strain field with the specimen pictures used in the correlation procedure. Our application is focused on studying the plastic behaviour of metals and, in particular, on highlighting any transient phenomena that might occur during yielding and strain‐hardening phases on thin sheets used in the manufacture of sheet metals. A typical example for such phenomena is the Portevin‐Le Châtelier effect, a repetitive yielding of alloys during plastic deformation.

Refined fourier-transform method of analysis of full two-dimensional digitized interferograms.

A refined Fourier-transform method of analysis of interference patterns is presented. The refinements include a method of automatic background subtraction and a way of treating the problem of heterodyning. The method proves particularly useful for analysis of long sequences of interferograms.

Strategies for phylogenetic characterization of subsurface bacteria

The purpose of this study was to evaluate approaches for phylogenetic characterization of bacteria from terrestrial subsurface environments by analysis of 16S ribosomal RNA gene (16S rDNA) nucleotide sequences. Three methods for detecting identical or very closely related strains among large groups of isolates (to reduce the number of strains that must be fully sequenced) were examined: (i) analysis of existing morphological and physiological data, (ii) restriction endonuclease analysis of genomic DNA, and (iii) analysis of short (ca. 350-base) 16S rDNA sequences. These three methods were applied to a test group of 20 subsurface bacteria and evaluated by comparing their results to those obtained by analysis of relatively long 16S rDNA sequences. Short sequence analysis yielded the most useful predictive information and, thus, appeared to be the best method for ‘prescreening’ large numbers of isolates (so that representative strains can be selected for full sequencing). The analysis of longer sequences placed 12 test-group strains in three subdivisions of the Proteobacteria (Purple Bacteria) and 8 strains in the high-G + C Gram-positive bacteria. Seven of the former were related to Pseudomonas aeruginosa or other members of the fluorescent pseudomonad group, while six of the latter were tentatively identified as Arthrobacter globiformis (based on 97–99% sequence similarity).

Automated sequencing of PCR-amplified 16S rDNA on ‘Hydrolink’ gels

A commercially available high-performance gel solution, ‘Hydrolink Long Ranger’, was used for direct automated sequencing of PCR-amplified double-stranded 16S rDNA. The 1.5 kb rDNA fragments were amplified directly from bacterial cell lysates and sequenced by using Tth DNA polymerase with the linear PCR sequencing protocol. Sequencing reactions were analyzed on an automated laser fluorescent DNA sequencer with Hydrolink gels compared to standard polyacrylamide gels. Automated Hydrolink gel electrophoresis allowed high sequencing speeds and resulted in a marked increase in readable sequences. Upon this electrophoresis, an average of 540 bases of nucleotides was resolved by automated reading in a single sequencing run, and the resolved sequence was extended up to 600 to 700 bases by manual correction of the errors and ambiguities. This sequencing strategy is useful for the analysis of long sequences of more than 500 bases and makes it possible to obtain entire 16S rDNA sequence data for several strains within 2 days, using an automated DNA sequencer with the one dye detection system.