A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions

The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the reconstruction of a protein-protein subnetwork that underlies a process of interest from a genome-wide screen of associated genes. Despite intense work in this area, current algorithmic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. Here we propose a novel formulation for network reconstruction from multiple-condition data and devise an efficient integer program solution for it. We apply our algorithm to analyze the response to influenza infection in humans over time as well as to analyze a pair of ER export related screens in humans. By comparing to an extant, single-condition tool we demonstrate the power of our new approach in integrating data from multiple conditions in a compact and coherent manner, capturing the dynamics of the underlying processes.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

IP without IP addresses

D. Phoomikiattisak was funded by the Thai Government. B. Simpson was funded by Cisco Systems under a University Research Programme (URP) grant award.We discuss a key engineering challenge in implementing the Identifier- Locator Network Protocol (ILNP), as described in IRTF Experimental RFCs 6740-6748: enabling legacy applications that use the C sockets API. We have built the first two OS kernel implementations of ILNPv6 (ILNP as a superset of IPv6), in both the Linux OS kernel and the FreeBSD OS kernel. Our evaluation is in comparison with IPv6, in the context of a topical and challenging scenario: host mobility implemented as a purely end-to-end function. Our experiments show that ILNPv6 has excellent potential for deployment using existing IPv6 infrastructure, whilst offering the new properties and functionality of ILNP.Postprin

Solving the Bethe-Salpeter equation for bound states of scalar theories in Minkowski space

We apply the perturbation theory integral representation (PTIR) to solve for the bound state Bethe-Salpeter (BS) vertex for an arbitrary scattering kernel, without the need for any Wick rotation. The results derived are applicable to any scalar field theory (without derivative coupling). It is shown that solving directly for the BS vertex, rather than the BS amplitude, has several major advantages, notably its relative simplicity and superior numerical accuracy. In order to illustrate the generality of the approach we obtain numerical solutions using this formalism for a number of scattering kernels, including cases where the Wick rotation is not possible.Comment: 28 pages of LaTeX, uses psfig.sty with 5 figures. Also available via WWW at http://www.physics.adelaide.edu.au/theory/papers/ADP-97-10.T248-abs.html or via anonymous ftp at ftp://bragg.physics.adelaide.edu.au/pub/theory/ADP-97-10.T248.ps A number of (crucial) typographical errors in Appendix C corrected. To be published in Phys. Rev. D, October 199

Colloidal hydrodynamic coupling in concentric optical vortices

Optical vortex traps created from helical modes of light can drive fluid-borne colloidal particles in circular trajectories. Concentric circulating rings of particles formed by coaxial optical vortices form a microscopic Couette cell, in which the amount of hydrodynamic drag experienced by the spheres depends on the relative sense of the rings' circulation. Tracking the particles' motions makes possible measurements of the hydrodynamic coupling between the circular particle trains and addresses recently proposed hydrodynamic instabilities for collective colloidal motions on optical vortices.Comment: 7 pages, 2 figures, submitted to Europhysics Letter

The nuclear spectrum of the radio galaxy NGC 5128 (Centaurus A)

We present near-infrared spectra of the nuclear disk in the nearby radio galaxy NGC 5128 (Centaurus A). On the basis of the observed strengths of the [S III] 0.9532um and [Fe II] 1.2567um lines, we classify NGC 5128 as a LINER. Modeling of the strengths of these and additional lines suggests that the nuclear region is powered by shocks rather than photoionization.Comment: 12 pages including 2 figures, accepted by ApJ Letter

Exposure of benthic invertebrates to sediment vibration: From laboratory experiments to outdoor simulated pile-driving

Activities directly interacting with the seabed, such as pile-driving, can produce vibrations that have the potential to impact benthic invertebrates within their vicinity. This stimuli may interfere with crucial behaviors such as foraging and predator avoidance, and the sensitivity to vibration is largely unknown. Here, the responsiveness of benthic invertebrates to sediment vibration is discussed in relation to laboratory and semi-field trials with two marine species: the mussel (Mytilus edulis) and hermit crab (Pagurus bernhardus). Sensory threshold curves were produced for both species in controlled laboratory conditions, followed by small-scale pile-driving exposures in the field. The merits of behavioral indicators are discussed, in addition to using physiological measures, as a method of determining reception and measuring responses. The measurement and sensors required for sediment vibration quantification are also discussed. Response and threshold data were related to measurements taken in the vicinity of anthropogenic sources, allowing a link between responsiveness and actual operations. The impact of pile-driving on sediment-dwelling invertebrates has received relatively little research, yet the data here suggest that such activities are likely to impact key coastal species which play important roles within the marine environment

Absolute and convective instabilities of parallel propagating circularly polarized Alfven waves: Beat instability

Ruderman and Simpson [Phys. Plasmas 11, 4178 (2004)] studied the absolute and convective decay instabilities of parallel propagating circularly polarized Alfven waves in plasmas where the sound speed c(S) is smaller than the Alfven speed upsilon(A). We extend their analysis for the beat instability which occurs in plasmas with c(S)>upsilon(A). We assume that the dimensionless amplitude of the circularly polarized Alfven wave (pump wave), a, is small. Applying Briggs' method we study the problem analytically using expansions in power series with respect to a. It is shown that the pump wave is absolutely unstable in a reference frame moving with the velocity U with respect to the rest plasma if U-lU-r, the instability is convective. The signaling problem is studied in a reference frame where the pump wave is convectively unstable. It is shown that the spatially amplifying waves exist only when the signaling frequency is in two narrow symmetric frequency bands with the widths of the order of a(3). These results enable us to extend for the case when c(S)>upsilon(A) the conclusions, previously made for the case when c(S)<upsilon(A), that circularly polarized Alfven waves propagating in the solar wind are convectively unstable in a reference frame of any spacecraft moving with the velocity not exceeding a few tens of km/s in the solar reference frame. The characteristic scale of spatial amplification for these waves exceeds 1 a.u