64,449 research outputs found

    Reconstruction Codes for DNA Sequences with Uniform Tandem-Duplication Errors

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    DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction problem, which is applicable whenever multiple reads of noisy data are available. This strategy is uniquely suited to the medium, which inherently replicates stored data in multiple distinct ways, caused by mutations. We consider noise introduced solely by uniform tandem-duplication, and utilize the relation to constant-weight integer codes in the Manhattan metric. By bounding the intersection of the cross-polytope with hyperplanes, we prove the existence of reconstruction codes with greater capacity than known error-correcting codes, which we can determine analytically for any set of parameters.Comment: 11 pages, 2 figures, Latex; version accepted for publicatio

    Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region

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    Mycobacterium tuberculosis, the causative agent of most human tuberculosis, infects one third of the world's population and kills an estimated 1.7 million people a year. With the world-wide emergence of drug resistance, and the finding of more functional genetic diversity than previously expected, there is a renewed interest in understanding the forces driving genome evolution of this important pathogen. Genetic diversity in M. tuberculosis is dominated by single nucleotide polymorphisms and small scale gene deletion, with little or no evidence for large scale genome rearrangements seen in other bacteria. Recently, a single report described a large scale genome duplication that was suggested to be specific to the Beijing lineage. We report here multiple independent large-scale duplications of the same genomic region of M. tuberculosis detected through whole-genome sequencing. The duplications occur in strains belonging to both M. tuberculosis lineage 2 and 4, and are thus not limited to Beijing strains. The duplications occur in both drug-resistant and drug susceptible strains. The duplicated regions also have substantially different boundaries in different strains, indicating different originating duplication events. We further identify a smaller segmental duplication of a different genomic region of a lab strain of H37Rv. The presence of multiple independent duplications of the same genomic region suggests either instability in this region, a selective advantage conferred by the duplication, or both. The identified duplications suggest that large-scale gene duplication may be more common in M. tuberculosis than previously considere

    Sample-path large deviations for tandem and priority queues with Gaussian inputs

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    This paper considers Gaussian flows multiplexed in a queueing network. A single node being a useful but often incomplete setting, we examine more advanced models. We focus on a (two-node) tandem queue, fed by a large number of Gaussian inputs. With service rates and buffer sizes at both nodes scaled appropriately, Schilder's sample-path large-deviations theorem can be applied to calculate the asymptotics of the overflow probability of the second queue. More specifically, we derive a lower bound on the exponential decay rate of this overflow probability and present an explicit condition for the lower bound to match the exact decay rate. Examples show that this condition holds for a broad range of frequently used Gaussian inputs. The last part of the paper concentrates on a model for a single node, equipped with a priority scheduling policy. We show that the analysis of the tandem queue directly carries over to this priority queueing system.Comment: Published at http://dx.doi.org/10.1214/105051605000000133 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

    Design of the first Italian roundabout with jointed plain concrete pavement

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    This work presents the results of the overall design of the first Italian roundabout with jointed plain concrete pavement. The examined case study complies with current international standards and practices for geometry of roundabouts and road pavements. The construction of a concrete pavement in an urban roundabout will better manage and slow down fast vehicular flows, and increase traffic fluidity in an important junction, trafficked by heavy vehicles, where maintenance works should be reduced to avoid queues. The design of the roundabout involved several competences for: defining the geometry of the four-arm junction, designing the thickness of the jointed plain concrete pavement both on the circular crown and the arms, studying the mix design of a high resistance concrete. As regard to the pavement, the result of the study was an un-dowelled concrete pavement composed of square slabs laid on a cement concrete subbase and a granular layer. The shape of the slabs has been designed to optimize the structural performance of their material, which is a high strength concrete mix derived from an extensive laboratory test work. In general, the results summarized approaches typical of different design conditions: urban ones for traffic flow and safety needs; high-traffic ones for the chosen pavement type; airport ones for the absence of dowel and tie bars at the joints. Indeed, the article has highlighted that the design process of a concrete roundabout requires multiple analyses to consider various features and correctly re-design anexistingurbanjunction. Its geometrical design,the structural design of the concrete pavement and the theoretical and experimental design of the concrete mix were the main phases of this process and they needed different competences to conduct comprehensive and appropriate analyses

    Deep Learning Solutions for TanDEM-X-based Forest Classification

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    In the last few years, deep learning (DL) has been successfully and massively employed in computer vision for discriminative tasks, such as image classification or object detection. This kind of problems are core to many remote sensing (RS) applications as well, though with domain-specific peculiarities. Therefore, there is a growing interest on the use of DL methods for RS tasks. Here, we consider the forest/non-forest classification problem with TanDEM-X data, and test two state-of-the-art DL models, suitably adapting them to the specific task. Our experiments confirm the great potential of DL methods for RS applications

    Towards Automatic SAR-Optical Stereogrammetry over Urban Areas using Very High Resolution Imagery

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    In this paper we discuss the potential and challenges regarding SAR-optical stereogrammetry for urban areas, using very-high-resolution (VHR) remote sensing imagery. Since we do this mainly from a geometrical point of view, we first analyze the height reconstruction accuracy to be expected for different stereogrammetric configurations. Then, we propose a strategy for simultaneous tie point matching and 3D reconstruction, which exploits an epipolar-like search window constraint. To drive the matching and ensure some robustness, we combine different established handcrafted similarity measures. For the experiments, we use real test data acquired by the Worldview-2, TerraSAR-X and MEMPHIS sensors. Our results show that SAR-optical stereogrammetry using VHR imagery is generally feasible with 3D positioning accuracies in the meter-domain, although the matching of these strongly hetereogeneous multi-sensor data remains very challenging. Keywords: Synthetic Aperture Radar (SAR), optical images, remote sensing, data fusion, stereogrammetr
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