Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes

Many types of tumors exhibit chromosomal losses or gains, as well as local amplifications and deletions. Within any given tumor type, sample specific amplifications and deletionsare also observed. Typically, a region that is aberrant in more tumors,or whose copy number change is stronger, would be considered as a more promising candidate to be biologically relevant to cancer. We sought for an intuitive method to define such aberrations and prioritize them. We define V, the volume associated with an aberration, as the product of three factors: a. fraction of patients with the aberration, b. the aberrations length and c. its amplitude. Our algorithm compares the values of V derived from real data to a null distribution obtained by permutations, and yields the statistical significance, p value, of the measured value of V. We detected genetic locations that were significantly aberrant and combined them with chromosomal arm status to create a succint fingerprint of the tumor genome. This genomic fingerprint is used to visualize the tumors, highlighting events that are co ocurring or mutually exclusive. We allpy the method on three different public array CGH datasets of Medulloblastoma and Neuroblastoma, and demonstrate its ability to detect chromosomal regions that were known to be altered in the tested cancer types, as well as to suggest new genomic locations to be tested. We identified a potential new subtype of Medulloblastoma, which is analogous to Neuroblastoma type 1.Comment: 34 pages, 3 figures; to appear in Cancer Informatic

Calculation of Scattering by the Distorted Wave Born Approximation

An approximate scattering theory that utilizes the exact solutions for spherical defects is being developed. A defect of arbitrary shape can be represented by a sphere S and a remainder volume δv. By treating δv as a perturbation, one obtains an approximate solution that contains non-trivial frequency dependence and phase information. The approach is expected to be useful for studying defects with small but significant deviations (such as sharp edges) from spherical shape

Crack Identification and Characterization in the Rayleigh Limit

We discuss apparent characteristic features of Rayleigh scattering of elastic waves from cracks. Interpreting these features, we propose a procedure that in some experimental situations may be useful to distinguish generally-shaped cracks from volume defects. For elliptically-shaped cracks, we propose additional procedures that in principle allow the unique specification of crack size, shape and orientation; however, we suggest that in practice only the crack plane orientation and a lower bound on the crack length is measurable. We also comment upon the inversion procedure of Kahn and Rice

Elastic Wave Scattering by General Shaped Defects: the Distorted Wave Born Approximation

An approximate theory for scattering of elastic wave by general shaped defects has been developed. A defect of arbitrary shape can be represented by a sphere S and a remainder volume R. Using the exact solution for a sphere and treating R as a perturbation, the solution corresponding to the Distorted Wave Born Approximation is obtained. This solution contains non-trivial frequency dependence and phase information. Preliminary comparisons with experiments will be presented

Predicted signatures of p-wave superfluid phases and Majorana zero modes of fermionic atoms in RF absorption

We study the superfluid phases of quasi-2D atomic Fermi gases interacting via a p-wave Feshbach resonance. We calculate the absorption spectra of these phases under a hyperfine transition, for both non-rotating and rotating superfluids. We show that one can identify the different phases of the p-wave superfluid from the absorption spectrum. The absorption spectrum shows clear signatures of the existence of Majorana zero modes at the cores of vortices of the weakly-pairing $p_x+ip_y$ phase

Dynamic stability of crack fronts: Out-of-plane corrugations

The dynamics and stability of brittle cracks are not yet fully understood. Here we use the Willis-Movchan 3D linear perturbation formalism [J. Mech. Phys. Solids {\bf 45}, 591 (1997)] to study the out-of-plane stability of planar crack fronts in the framework of linear elastic fracture mechanics. We discuss a minimal scenario in which linearly unstable crack front corrugations might emerge above a critical front propagation speed. We calculate this speed as a function of Poisson's ratio and show that corrugations propagate along the crack front at nearly the Rayleigh wave-speed. Finally, we hypothesize about a possible relation between such corrugations and the long-standing problem of crack branching.Comment: 5 pages, 2 figures + supplementary informatio

Distributed CSMA with pairwise coding

We consider distributed strategies for joint routing, scheduling, and network coding to maximize throughput in wireless networks. Network coding allows for an increase in network throughput under certain routing conditions. We previously developed a centralized control policy to jointly optimize for routing and scheduling combined with a simple network coding strategy using max-weight scheduling (MWS) [9]. In this work we focus on pairwise network coding and develop a distributed carrier sense multiple access (CSMA) policy that supports all arrival rates allowed by the network subject to the pairwise coding constraint. We extend our scheme to optimize for packet overhearing to increase the number of beneficial coding opportunities. Simulation results show that the CSMA strategy yields the same throughput as the optimal centralized policy of [9], but at the cost of increased delay. Moreover, overhearing provides up to an additional 25% increase in throughput on random topologies.United States. Dept. of Defense. Assistant Secretary of Defense for Research & EngineeringUnited States. Air Force (Air Force Contract FA8721-05-C-0002

Optimal routing and scheduling for a simple network coding scheme

We consider jointly optimal routing, scheduling, and network coding strategies to maximize throughput in wireless networks. While routing and scheduling techniques for wireless networks have been studied for decades, network coding is a relatively new technique that allows for an increase in throughput under certain topological and routing conditions. In this work we introduce k-tuple coding, a generalization of pairwise coding with next-hop decodability, and fully characterize the region of arrival rates for which the network queues can be stabilized under this coding strategy. We propose a dynamic control policy for routing, scheduling, and k-tuple coding, and prove that our policy is throughput optimal subject to the k-tuple coding constraint. We provide analytical bounds on the coding gain of our policy, and present numerical results to support our analytical findings. We show that most of the gains are achieved with pairwise coding, and that the coding gain is greater under 2-hop than 1-hop interference. Simulations show that under 2-hop interference our policy yields median throughput gains of 31% beyond optimal scheduling and routing on random topologies with 16 nodes.National Science Foundation (U.S.) (grant CNS-0915988)United States. Office of Naval Research (grant N00014-12-1-0064)United States. Office of Naval Research. Multidisciplinary University Research Initiative (grant number W911NF-08-1-0238)United States. Air ForceUnited States. Dept. of Defense (Contract No. FA8721-05-C-0002

Topology control for wireless networks with highly-directional antennas

In order to steer antenna beams towards one another for communication, wireless nodes with highly-directional antennas must track the channel state of their neighbors. To keep this overhead manageable, each node must limit the number of neighbors that it tracks. The subset of neighbors that each node chooses to track constitutes a network topology over which traffic can be routed. We consider this topology design problem, taking into account channel modeling, transmission scheduling, and traffic demand. We formulate the optimal topology design problem, with the objective of maximizing the scaling of traffic demand, and propose a distributed method, where each node rapidly builds a segment of the topology around itself by forming connections with its nearest neighbors in discretized angular regions. The method has low complexity and message passing overhead. The resulting topologies are shown to have desirable structural properties and approach the optimal solution in high path loss environments.National Science Foundation (U.S.) (Grant CNS-1524317)National Science Foundation (U.S.) (Grant CNS-1116209)National Science Foundation (U.S.) (Grant AST-1547331)United States. Air Force (Contract FA8721-05-C-0002