Analysis of Gene Sets Based on the Underlying Regulatory Network

Networks are often used to represent the interactions among genes and proteins. These interactions are known to play an important role in vital cell functions and should be included in the analysis of genes that are differentially expressed. Methods of gene set analysis take advantage of external biological information and analyze a priori defined sets of genes. These methods can potentially preserve the correlation among genes; however, they do not directly incorporate the information about the gene network. In this paper, we propose a latent variable model that directly incorporates the network information. We then use the theory of mixed linear models to present a general inference framework for the problem of testing the significance of subnetworks. Several possible test procedures are introduced and a network based method for testing the changes in expression levels of genes as well as the structure of the network is presented. The performance of the proposed method is compared with methods of gene set analysis using both simulation studies, as well as real data on genes related to the galactose utilization pathway in yeast.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78147/1/cmb.2008.0081.pd

Correlation effects in ionic crystals: I. The cohesive energy of MgO

High-level quantum-chemical calculations, using the coupled-cluster approach and extended one-particle basis sets, have been performed for (Mg2+)n (O2-)m clusters embedded in a Madelung potential. The results of these calculations are used for setting up an incremental expansion for the correlation energy of bulk MgO. This way, 96% of the experimental cohesive energy of the MgO crystal is recovered. It is shown that only 60% of the correlation contribution to the cohesive energy is of intra-ionic origin, the remaining part being caused by van der Waals-like inter-ionic excitations.Comment: LaTeX, 20 pages, no figure

Study of the B^0 Semileptonic Decay Spectrum at the Upsilon(4S) Resonance

We have made a first measurement of the lepton momentum spectrum in a sample of events enriched in neutral B's through a partial reconstruction of B0 --> D*- l+ nu. This spectrum, measured with 2.38 fb**-1 of data collected at the Upsilon(4S) resonance by the CLEO II detector, is compared directly to the inclusive lepton spectrum from all Upsilon(4S) events in the same data set. These two spectra are consistent with having the same shape above 1.5 GeV/c. From the two spectra and two other CLEO measurements, we obtain the B0 and B+ semileptonic branching fractions, b0 and b+, their ratio, and the production ratio f+-/f00 of B+ and B0 pairs at the Upsilon(4S). We report b+/b0=0.950 (+0.117-0.080) +- 0.091, b0 = (10.78 +- 0.60 +- 0.69)%, and b+ = (10.25 +- 0.57 +- 0.65)%. b+/b0 is equivalent to the ratio of charged to neutral B lifetimes, tau+/tau0.Comment: 14 page, postscript file also available at http://w4.lns.cornell.edu/public/CLN

Technical summary

Human interference with the climate system is occurring. Climate change poses risks for human and natural systems. The assessment of impacts, adaptation, and vulnerability in the Working Group II contribution to the IPCC's Fifth Assessment Report (WGII AR5) evaluates how patterns of risks and potential benefits are shifting due to climate change and how risks can be reduced through mitigation and adaptation. It recognizes that risks of climate change will vary across regions and populations, through space and time, dependent on myriad factors including the extent of mitigation and adaptation

Measurement of the Mass Splittings between the bbˉχb,J(1P)b\bar{b}\chi_{b,J}(1P) States

We present new measurements of photon energies and branching fractions for the radiative transitions: Upsilon(2S)->gamma+chi_b(J=0,1,2). The masses of the chi_b states are determined from the measured radiative photon energies. The ratio of mass splittings between the chi_b substates, r==(M[J=2]-M[J=1])/(M[J=1]-M[J=0]) with M the chi_b mass, provides information on the nature of the bbbar confining potential. We find r(1P)=0.54+/-0.02+/-0.02. This value is in conflict with the previous world average, but more consistent with the theoretical expectation that r(1P)<r(2P); i.e., that this mass splittings ratio is smaller for the chi_b(1P) triplet than for the chi_b(2P) triplet.Comment: 11 page postscript file, postscript file also available through http://w4.lns.cornell.edu/public/CLN

Radiative Decay Modes of the D0D^{0} Meson

Using data recorded by the CLEO-II detector at CESR we have searched for four radiative decay modes of the $D^0$ meson: $D^0\to\phi\gamma$, $D^0\to\omega\gamma$, $D^0\to\bar{K}^{*}\gamma$, and $D^0\to\rho^0\gamma$. We obtain 90% CL upper limits on the branching ratios of these modes of $1.9\times 10^{-4}$, $2.4\times 10^{-4}$, $7.6\times 10^{-4}$ and $2.4\times 10^{-4}$ respectively.Comment: 15 page postscript file, postscript file also available through http://w4.lns.cornell.edu/public/CLN

Integral potential method for a transmission problem with Lipschitz interface in R^3 for the Stokes and Darcy–Forchheimer–Brinkman PDE systems

The purpose of this paper is to obtain existence and uniqueness results in weighted Sobolev spaces for transmission problems for the non-linear Darcy-Forchheimer-Brinkman system and the linear Stokes system in two complementary Lipschitz domains in R3, one of them is a bounded Lipschitz domain with connected boundary, and the other one is the exterior Lipschitz domain R3 n. We exploit a layer potential method for the Stokes and Brinkman systems combined with a fixed point theorem in order to show the desired existence and uniqueness results, whenever the given data are suitably small in some weighted Sobolev spaces and boundary Sobolev spaces

The roles of the formal and informal sectors in the provision of effective science education

For many years, formal school science education has been criticised by students, teachers, parents and employers throughout the world. This article presents an argument that a greater collaboration between the formal and the informal sector could address some of these criticisms. The causes for concern about formal science education are summarised and the major approaches being taken to address them are outlined. The contributions that the informal sector currently makes to science education are identified. It is suggested that the provision of an effective science education entails an enhanced complementarity between the two sectors. Finally, there is a brief discussion of the collaboration and communication still needed if this is to be effective