WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.

MotivationCopy number variations (CNVs) are a major source of genomic variability and are especially significant in cancer. Until recently microarray technologies have been used to characterize CNVs in genomes. However, advances in next-generation sequencing technology offer significant opportunities to deduce copy number directly from genome sequencing data. Unfortunately cancer genomes differ from normal genomes in several aspects that make them far less amenable to copy number detection. For example, cancer genomes are often aneuploid and an admixture of diploid/non-tumor cell fractions. Also patient-derived xenograft models can be laden with mouse contamination that strongly affects accurate assignment of copy number. Hence, there is a need to develop analytical tools that can take into account cancer-specific parameters for detecting CNVs directly from genome sequencing data.ResultsWe have developed WaveCNV, a software package to identify copy number alterations by detecting breakpoints of CNVs using translation-invariant discrete wavelet transforms and assign digitized copy numbers to each event using next-generation sequencing data. We also assign alleles specifying the chromosomal ratio following duplication/loss. We verified copy number calls using both microarray (correlation coefficient 0.97) and quantitative polymerase chain reaction (correlation coefficient 0.94) and found them to be highly concordant. We demonstrate its utility in pancreatic primary and xenograft sequencing data.Availability and implementationSource code and executables are available at https://github.com/WaveCNV. The segmentation algorithm is implemented in MATLAB, and copy number assignment is implemented [email protected] informationSupplementary data are available at Bioinformatics online

Multi-Scale 3D Scene Flow from Binocular Stereo Sequences

Scene flow methods estimate the three-dimensional motion field for points in the world, using multi-camera video data. Such methods combine multi-view reconstruction with motion estimation. This paper describes an alternative formulation for dense scene flow estimation that provides reliable results using only two cameras by fusing stereo and optical flow estimation into a single coherent framework. Internally, the proposed algorithm generates probability distributions for optical flow and disparity. Taking into account the uncertainty in the intermediate stages allows for more reliable estimation of the 3D scene flow than previous methods allow. To handle the aperture problems inherent in the estimation of optical flow and disparity, a multi-scale method along with a novel region-based technique is used within a regularized solution. This combined approach both preserves discontinuities and prevents over-regularization – two problems commonly associated with the basic multi-scale approaches. Experiments with synthetic and real test data demonstrate the strength of the proposed approach.National Science Foundation (CNS-0202067, IIS-0208876); Office of Naval Research (N00014-03-1-0108

Wireless magnetic sensor network for road traffic monitoring and vehicle classification

Efficiency of transportation of people and goods is playing a vital role in economic growth. A key component for enabling effective planning of transportation networks is the deployment and operation of autonomous monitoring and traffic analysis tools. For that reason, such systems have been developed to register and classify road traffic usage. In this paper, we propose a novel system for road traffic monitoring and classification based on highly energy efficient wireless magnetic sensor networks. We develop novel algorithms for vehicle speed and length estimation and vehicle classification that use multiple magnetic sensors. We also demonstrate that, using such a low-cost system with simplified installation and maintenance compared to current solutions, it is possible to achieve highly accurate estimation and a high rate of positive vehicle classification

Jump-preserving monitoring of dependent time series using pilot estimators

An important problem of the statistical analysis of time series is to detect change-points in the mean structure. Since this problem is a one-dimensional version of the higher dimensional problem of detecting edges in images, we study detection rules which benefit from results obtained in image processing. For the sigma-filter studied there to detect edges, asymptotic bounds for the normed delay have been established for independent data. These results are considerably extended in two directions. First, we allow for dependent processes satisfying a certain conditional mixing property. Second, we allow for more general pilot estimators, e.g., the median, resulting in better detection properties. A simulation study indicates that our new procedure indeed performs much more better. --Image processing,Nonparametric regression,Quality Control,Structural Change

Digital design of medical replicas via desktop systems: shape evaluation of colon parts

In this paper, we aim at providing results concerning the application of desktop systems for rapid prototyping of medical replicas that involve complex shapes, as, for example, folds of a colon. Medical replicas may assist preoperative planning or tutoring in surgery to better understand the interaction among pathology and organs. Major goals of the paper concern with guiding the digital design workflow of the replicas and understanding their final performance, according to the requirements asked by the medics (shape accuracy, capability of seeing both inner and outer details, and support and possible interfacing with other organs). In particular, after the analysis of these requirements, we apply digital design for colon replicas, adopting two desktop systems. ,e experimental results confirm that the proposed preprocessing strategy is able to conduct to the manufacturing of colon replicas divided in self-supporting segments, minimizing the supports during printing. ,is allows also to reach an acceptable level of final quality, according to the request of having a 3D presurgery overview of the problems. ,ese replicas are compared through reverse engineering acquisitions made by a structured-light system, to assess the achieved shape and dimensional accuracy. Final results demonstrate that low-cost desktop systems, coupled with proper strategy of preprocessing, may have shape deviation in the range of ±1 mm, good for physical manipulations during medical diagnosis and explanation

Recursive Motion and Structure Estimation with Complete Error Characterization

We present an algorithm that perfom recursive estimation of ego-motion andambient structure from a stream of monocular Perspective images of a number of feature points. The algorithm is based on an Extended Kalman Filter (EKF) that integrates over time the instantaneous motion and structure measurements computed by a 2-perspective-views step. Key features of our filter are (I) global observability of the model, (2) complete on-line characterization of the uncertainty of the measurements provided by the two-views step. The filter is thus guaranteed to be well-behaved regardless of the particular motion undergone by the observel: Regions of motion space that do not allow recovery of structure (e.g. pure rotation) may be crossed while maintaining good estimates of structure and motion; whenever reliable measurements are available they are exploited. The algorithm works well for arbitrary motions with minimal smoothness assumptions and no ad hoc tuning. Simulations are presented that illustrate these characteristics