An experimental evaluation of a loop versus a reference design for two-channel microarrays

Motivation: Despite theoretical arguments that socalled "loop designs" of two-channel DNA microarray experiments are more efficient, biologists keep on using "reference designs". We describe two sets of microarray experiments with RNA from two different biological systems (TPA-stimulated mammalian cells and Streptomyces coelicor). In each case, both a loop and a reference design were performed using the same RNA preparations with the aim to study their relative efficiency. Results: The results of these experiments show that (1) the loop design attains a much higher precision than the reference design, (2) multiplicative spot effects are a large source of variability, and if they are not accounted for in the mathematical model, for example by taking log-ratios or including spot-effects, then the model will perform poorly. The first result is reinforced by a simulation study. Practical recommendations are given on how simple loop designs can be extended to more realistic experimental designs and how standard statistical methods allow the experimentalist to use and interpret the results from loop designs in practice

Evidence for a singularity in ideal magnetohydrodynamics: implications for fast reconnection

Numerical evidence for a finite-time singularity in ideal 3D magnetohydrodynamics (MHD) is presented. The simulations start from two interlocking magnetic flux rings with no initial velocity. The magnetic curvature force causes the flux rings to shrink until they come into contact. This produces a current sheet between them. In the ideal compressible calculations, the evidence for a singularity in a finite time $t_c$ is that the peak current density behaves like $|J|_\infty \sim 1/(t_c-t)$ for a range of sound speeds (or plasma betas). For the incompressible calculations consistency with the compressible calculations is noted and evidence is presented that there is convergence to a self-similar state. In the resistive reconnection calculations the magnetic helicity is nearly conserved and energy is dissipated.Comment: 4 pages, 4 figure

Charged Rotating Black Holes on a 3-Brane

We study exact stationary and axisymmetric solutions describing charged rotating black holes localized on a 3-brane in the Randall-Sundrum braneworld. The charges of the black holes are considered to be of two types, the first being an induced tidal charge that appears as an imprint of nonlocal gravitational effects from the bulk space and the second is a usual electric charge arising due to a Maxwell field trapped on the brane. We assume a special ansatz for the metric on the brane taking it to be of the Kerr-Schild form and show that the Kerr-Newman solution of ordinary general relativity in which the electric charge is superceded by a tidal charge satisfies a closed system of the effective gravitational field equations on the brane. It turns out that the negative tidal charge may provide a mechanism for spinning up the black hole so that its rotation parameter exceeds its mass. This is not allowed in the framework of general relativity. We also find a new solution that represents a rotating black hole on the brane carrying both charges. We show that for a rapid enough rotation the combined influence of the rotational dynamics and the local bulk effects of the "squared" energy momentum tensor on the brane distort the horizon structure of the black hole in such a way that it can be thought of as composed of non-uniformly rotating null circles with growing radii from the equatorial plane to the poles. We finally study the geodesic motion of test particles in the equatorial plane of a rotating black hole with tidal charge. We show that the effects of negative tidal charge tend to increase the horizon radius, as well as the radii of the limiting photon orbit, the innermost bound and the innermost stable circular orbits for both direct and retrograde motions of the particles.Comment: RevTeX 4, 33 pages, 4 figures, new references adde

Rotating Black Holes in Higher Dimensions with a Cosmological Constant

We present the metric for a rotating black hole with a cosmological constant and with arbitrary angular momenta in all higher dimensions. The metric is given in both Kerr-Schild and Boyer-Lindquist form. In the Euclidean-signature case, we also obtain smooth compact Einstein spaces on associated S^{D-2} bundles over S^2, infinitely many for each odd D\ge 5. Applications to string theory and M-theory are indicated.Comment: 8 pages, Latex. Short version, with more compact notation, of hep-th/0404008. To appear in Phys. Rev. Let

G92-1097 Root and Crown Rot: Winterkill Complex of Winter Wheat

Root and crown rot--winterkill complex is discussed, including nature of the complex, symptoms, control, and management rationale. Root and crown rot of winter wheat is an interrelated disease complex caused by the interaction of infection of roots and crowns by Bipolaris sorokiniana and/or Fusarium graminearum and harsh winter conditions. It is an insidious, persistent and inconspicuous disease complex that reduces wheat yields each year. In extreme cases, entire fields or large areas within fields are killed. The ultimate effect is loss of stands, poor plant vigor, reduced yield and lower grain quality

Two Large HI Shells in the Outer Galaxy near l=279 degrees

As part of a survey of HI 21-cm emission in the Southern Milky Way, we have detected two large shells in the interstellar neutral hydrogen near l=279 deg. The center velocities are +36 and +59 km/s, which puts the shells at kinematic distances of 7 and 10 kpc. The larger shell is about 610 pc in diameter and very empty, with density contrast of at least 15 between the middle and the shell walls. It has expansion velocity of about 20 km/s and swept up mass of several million solar masses. The energy indicated by the expansion may be as high as 2.4 X 10^53 ergs. We estimate its age to be 15 to 20 million years. The smaller shell has diameter of about 400 pc, expansion velocity about 10 km/s and swept up mass of about 10^6 solar masses. Morphologically both regions appear to be shells, with high density regions mostly surrounding the voids, although the first appears to have channels of low density which connect with the halo above and below the HI layer. They lie on the edge of the Carina arm, which suggests that they may be expanding horizontally into the interarm region as well as vertically out of the disk. If this interpretation is correct, this is the first detection of an HI chimney which has blown out of both sides of the disk.Comment: 21 pages, 14 jpeg figures, accepted for publication in A

The 69 ms Radio Pulsar Near the Supernova Remnant RCW 103

We report the detection of the radio pulsar counterpart to the 69 ms X-ray pulsar discovered near the supernova remnant RCW 103 (G332.4-0.4). Our detection confirms that the pulsations arise from a rotation-powered neutron star, which we name PSR J1617-5055. The observed barycentric period derivative confirms that the pulsar has a characteristic age of only 8 kyr, the sixth smallest of all known pulsars. The unusual apparent youth of the pulsar and its proximity to a young remnant requires that an association be considered. Although the respective ages and distances are consistent within substantial uncertainties, the large inferred pulsar transverse velocity is difficult to explain given the observed pulsar velocity distribution, the absence of evidence for a pulsar wind nebula, and the symmetry of the remnant. Rather, we argue that the objects are likely superposed on the sky; this is reasonable given the complex area. Without an association, the question of where is the supernova remnant left behind following the birth of PSR J1617-5055 remains open. We also discuss a possible association between PSR J1617-5055 and the gamma-ray source 2CG 333+01. Though an association is energetically plausible, it is unlikely given that EGRET did not detect 2CG 333+01.Comment: 18 pages, 2 encapsulated Postscript figures, uses AAS LaTeX style files. Accepted for publication in The Astrophysical Journal Letter

Optical and Infrared Spectroscopy of the type IIn SN 1998S : Days 3-127

We present contemporary infrared and optical spectroscopic observations of the type IIn SN 1998S for the period between 3 and 127 days after discovery. In the first week the spectra are characterised by prominent broad emission lines with narrow peaks superimposed on a very blue continuum(T~24000K). In the following two weeks broad, blueshifted absorption components appeared in the spectra and the temperature dropped. By day 44, broad emission components in H and He reappeared in the spectra. These persisted to 100-130d, becoming increasingly asymmetric. We agree with Leonard et al. (2000) that the broad emission lines indicate interaction between the ejecta and circumstellar material (CSM) and deduce that progenitor of SN 1998S appears to have gone through at least two phases of mass loss, giving rise to two CSM zones. Examination of the spectra indicates that the inner zone extended to <90AU, while the outer CSM extended from 185AU to over 1800AU. Analysis of high resolution spectra shows that the outer CSM had a velocity of 40-50 km/s. Assuming a constant velocity, we can infer that the outer CSM wind commenced more than 170 years ago, and ceased about 20 years ago, while the inner CSM wind may have commenced less than 9 years ago. During the era of the outer CSM wind the outflow was high, >2x10^{-5}M_{\odot}/yr corresponding to a mass loss of at least 0.003M_{\odot} and suggesting a massive progenitor. We also model the CO emission observed in SN 1998S. We deduce a CO mass of ~10^{-3} M_{\odot} moving at ~2200km/s, and infer a mixed metal/He core of ~4M_{\odot}, again indicating a massive progenitor.Comment: 22 pages, 14 figures, accepted in MNRA