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

On the state of low luminous accreting neutron stars

Observational appearance of a neutron star in the subsonic propeller state which is a companion of a wind-fed mass-exchange close binary system is discussed. During the subsonic propeller state the neutron star magnetosphere is surrounded by a spherical quasi-static plasma envelope, which is extended from the magnetospheric boundary up to the star accretion radius. The energy input to the envelope due to the propeller action by the neutron star exceeds the radiative losses and the plasma temperature in the envelope is of the order of the free-fall temperature. Under this condition the magnetospheric boundary is interchange stable. Nevertheless, I find that the rate of plasma penetration from the envelope into the magnetic field of the neutron star due to diffusion and magnetic field line reconnection processes is large enough for the accretion power to dominate the spindown power. I show that the accretion luminosity of the neutron star in the subsonic propeller state is 5*10**{30} - 10**{33} (dM/dt)_{15} erg/s, where dM/dt is the strength of the normal companion stellar wind which is parametrized in terms of the maximum possible mass accretion rate onto the neutron star magnetosphere. On this basis I suggest that neutron stars in the subsonic propeller state are expected to be observed as low luminous accretion-powered pulsars. The magnetospheric radius of the neutron star in this state is determined by the strength of the stellar wind, (dM/dt)_c, while the accretion luminosity is determined by the rate of plasma penetration into the star magnetosphere, (dM/dt)_a, which is (dM/dt)_a << (dM/dt)_c. That is why the classification of the neutron star state in these objects using the steady accretion model (i.e. setting (dM/dt)_a = (dM/dt)_c) can lead to a mistaken conclusion.Comment: 6 pages, accepted for publication in A&

Liquid phase immunoassay utilizing magnetic marker and high Tc superconducting quantum interference device

We have developed a liquid phase immunoassay system utilizing a magnetic marker and a superconducting quantum interference device (SQUID). In this system, the magnetic marker was used to detect the biological material called antigen. The magnetic marker was designed so as to generate a remanence, and the remanence field of the markers that bound to the antigens was measured with the SQUID. The measurement was performed in a solution that contained both the bound and free (or unbound) markers, i.e., without using the so-called bound/free (BF) separation process. The Brownian rotation of the free markers in the solution was used to distinguish the bound markers from the free ones. Using the system, we conducted the detection of biological material called IgE without BF separation. At present, we could detect the IgE down to 7 pg (or 39 amol

Electric polarization induced by Neel order without magnetic superlattice: experimental study of Cu3Mo2O9 and numerical study of a small spin cluster

We clarify that the antiferromagnetic order in the distorted tetrahedral quasi-one dimensional spin system induces electric polarizations. In this system, the effects of the low dimensionality and the magnetic frustration are expected to appear simultaneously. We obtain the magnetic-field-temperature phase diagram in Cu3Mo2O9 by studying the dielectric constant and the spontaneous electric polarization. Around the tricritical point at 10 T and 8 K, the change of the direction in the electric polarization causes a colossal magnetocapacitance. We calculate the charge redistribution in the small spin cluster consisting of two magnetic tetrahedra to demonstrate the electric polarization induced by the antiferromagnetism.Comment: 10 pages 6 figures, in press in J. Phys. Soc. Jp

Mass-Enhanced Fermi Liquid Ground State in Na1.5_{1.5}Co2_2O4_4

Magnetic, transport, and specific heat measurements have been performed on layered metallic oxide Na$_{1.5}$Co$_2$O$_4$ as a function of temperature $T$. Below a characteristic temperature $T^*$=30$-$40 K, electrical resistivity shows a metallic conductivity with a $T^2$ behavior and magnetic susceptibility deviates from the Curie-Weiss behavior showing a broad peak at $\sim$14 K. The electronic specific heat coefficient $\gamma$ is $\sim$60 mJ/molK$^2$ at 2 K. No evidence for magnetic ordering is found. These behaviors suggest the formation of mass-enhanced Fermi liquid ground state analogous to that in $d$-electron heavy fermion compound LiV$_2$O$_4$.Comment: 4 pages, 4 figures, to be published in Phys. Rev. B 69 (2004

Theoretical studies of EBT

A one-dimensional time dependent model of plasma particle and energy transport was used to predict the performance of an EBT experiment large enough to test confinement scaling in a parameter range (n, T, tau, etc.) close to reactor conditions. Such a device is referred to as EBT-P. The model is based on a computer code which uses the magnetic field lines as the basis for the coordinate system, and so includes some EBT geometrical effects, with neoclassical transport perpendicular to the surfaces of constant pressure. The geometry is self-consistent, i.e., the plasma pressure reacts on the magnetic field

Search for Charmless Two-body Baryonic Decays of B Mesons

We report the results of a search for the rare baryonic decays $B^0 \to p\bar{p}$, $\Lambda\bar{\Lambda}$, and $B^+ \to p\bar{\Lambda}$. The analysis is based on a data set of $31.7\times 10^6 B\bar{B}$ events collected by the Belle detector at the KEKB $e^+e^-$ collider. No statistically significant signals are found, and we set branching fraction upper limits ${\mathcal B}(B^0 \to p\bar{p}) < 1.2 \times 10^{-6}$, ${\mathcal B}(B^0 \to \Lambda\bar{\Lambda}) < 1.0 \times 10^{-6}$, and ${\mathcal B}(B^+ \to p\bar{\Lambda}) < 2.2 \times 10^{-6}$ at the 90% confidence level.Comment: 6 pages, 4 figures and 1 table. Submitted to Phys. Rev. D Rapid Communication

Observation of chi_c2 Production in B-meson Decay

We report the first observation of chi_c2 production in B-meson decays. We find an inclusive B -> chi_c2 X branching fraction of (1.80^{+0.23}_{-0.28}+/- 0.26) 10^-3. The data set, collected with the Belle detector at the KEKB e^+e^- collider, consists of 31.9 million B\bar B events. We also present branching fractions and momentum spectra for both chi_c1 and chi_c2 production.Comment: 5 pages with 2 figure