Identification of functional modules in human protein interaction networks.

The novel method proposed in this thesis is able to identify functional modules making use of large-scale interaction and expression data. While theveri tion of these subnetworks remains di ult, they identify sets of proteins, which may play a key role in the development of malignancies. The modules provide an attractive basis for further research and may provide new targets for drug development

ConsensusPathDB: toward a more complete picture of cell biology

ConsensusPathDB is a meta-database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With 155,432 human, 194,480 yeast and 13,648 mouse complex functional interactions (originating from 18 databases on human and eight databases on yeast and mouse interactions each), ConsensusPathDB currently constitutes the most comprehensive publicly available interaction repository for these species. The Web interface at http://cpdb.molgen.mpg.de offers different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways

Precise Extraction of the Induced Polarization in the He-4(e,e(l)(p)over-right-arrow)H-3 Reaction

We measured with unprecedented precision the induced polarization P-y in He-4(e, e(l)(p) over right arrow)H-3 at Q(2) = 0.8 and 1.3 (GeV/c)(2). The induced polarization is indicative of reaction-mechanism effects beyond the impulse approximation. Our results are in agreement with a relativistic distorted-wave impulse approximation calculation but are overestimated by a calculation with strong charge-exchange effects. Our data are used to constrain the strength of the spin-independent charge-exchange term in the latter calculation

Polarization Components in pi(0) Photoproduction at Photon Energies up to 5.6 GeV

We present new data for the polarization observables of the final state proton in the H-1((gamma) over right arrow, (p) over right arrow)pi(0) reaction. These data can be used to test predictions based on hadron helicity conservation and perturbative QCD. These data have both small statistical and systematic uncertainties and were obtained with beam energies between 1.8 and 5.6 GeV and for pi(0) scattering angles larger than 75 degrees in the center-of-mass frame. The data extend the polarization measurements database for neutral pion photoproduction up to E-gamma = 5.6 GeV. The results show a nonzero induced polarization above the resonance region. The polarization transfer components vary rapidly with the photon energy and pi(0) scattering angle in the center-of-mass frame. This indicates that hadron helicity conservation does not hold and that the perturbative QCD limit is still not reached in the energy regime of this experiment

Polarization Transfer in Wide-Angle Compton Scattering and Single-Pion Photoproduction from the Proton

Wide-angle exclusive Compton scattering and single-pion photoproduction from the proton have been investigated via measurement of the polarization transfer from a circularly polarized photon beam to the recoil proton. The wide-angle Compton scattering polarization transfer was analyzed at an incident photon energy of 3.7 GeV at a proton scattering angle of theta(p)(cm) cm = 70 degrees. The longitudinal transfer K-LL, measured to be 0.645 +/- 0.059 +/- 0.048, where the first error is statistical and the second is systematic, has the same sign as predicted for the reaction mechanism in which the photon interacts with a single quark carrying the spin of the proton. However, the observed value is similar to 3 times larger than predicted by the generalized-parton-distribution-based calculations, which indicates a significant unknown contribution to the scattering amplitude

Is the LHCb Pc(4312)+P_c(4312)^+ plausible in the GlueX γp→J/ψp\gamma p\to J/\psi p total cross sections ?

New high-statistics total cross section data for $\gamma p\to J/\psi p$ from the GLUonic EXcitation (GlueX) experiment are fitted in a search for the exotic $P_c(4312)^+$ state observed by the Large Hadron Collider beauty (LHCb) collaboration. The integrated luminosity of this GlueX experiment was about $320~\mathrm{pb^{-1}}$. The fits show that destructive interference involving an $S$-wave resonance and associated non-resonance background produces a sharp dip structure about $75~\mathrm{MeV}$ below the LHCb mass, in the same location as a similar structure is seen in the data. Limitations of the employed model and the need for improved statistics are discussed.Comment: 4 pages, 3 figures, 2 table

Separated Response Function Ratios in Exclusive, Forward pi(+/-) Electroproduction

The study of exclusive pi(+/-) electroproduction on the nucleon, including separation of the various structure functions, is of interest for a number of reasons. The ratio R-L=sigma(pi-)(L) / sigma(pi+)(L) is sensitive to isoscalar contamination to the dominant isovector pion exchange amplitude, which is the basis for the determination of the charged pion form factor from electroproduction data. A change in the value of R-T=sigma(pi-)(L) / sigma(pi+)(L) from unity at small -t, to 1/4 at large -t, would suggest a transition from coupling to a (virtual) pion to coupling to individual quarks. Furthermore, the mentioned ratios may show an earlier approach to perturbative QCD than the individual cross sections. We have performed the first complete separation of the four unpolarized electromagnetic structure functions above the dominant resonances in forward, exclusive p pi(+/-) electroproduction on the deuteron at central Q(2) values of 0.6, 1.0, 1.6 GeV2 at W=1.95 GeV, and Q(2)=2.45 GeV2 at W=2.22 GeV. Here, we present the L and T cross sections, with emphasis on R-L and R-T, and compare them with theoretical calculations. Results for the separated ratio R-L indicate dominance of the pion-pole diagram at low -t, while results for R-T are consistent with a transition between pion knockout and quark knockout mechanisms

Separated response functions in exclusive, forward pi(+/-) electroproduction on deuterium

Background: Measurements of forward exclusive meson production at different squared four-momenta of the exchanged virtual photon, Q(2), and at different four-momentum transfer, t, can be used to probe QCD\u27s transition from meson-nucleon degrees of freedom at long distances to quark-gluon degrees of freedom at short scales. Ratios of separated response functions in pi(-) and pi(+) electroproduction are particularly informative. The ratio for transverse photons may allow this transition to be more easily observed, while the ratio for longitudinal photons provides a crucial verification of the assumed pole dominance, needed for reliable extraction of the pion form factor from electroproduction data. Purpose: We perform the first complete separation of the four unpolarized electromagnetic structure functions L/T/LT/TT in forward, exclusive pi(+/-) electroproduction on deuterium above the dominant resonances. Method: Data were acquired with 2.6-5.2-GeV electron beams and the HMS + SOS spectrometers in Jefferson Lab Hall C at central Q(2) values of 0.6, 1.0, and 1.6 GeV2 at W = 1.95 GeV, and Q(2) = 2.45 GeV2 at W = 2.22 GeV. There was significant coverage in phi and is an element of, which allowed separation of sigma(L), T, LT, TT. Results: sigma(L) shows a clear signature of the pion pole, with a sharp rise at small -t. In contrast, sigma(T) is much flatter versus t. The longitudinal/transverse ratios evolve with Q(2) and t and at the highest Q(2) = 2.45 GeV2 show a slight enhancement for pi(-) production compared to pi(+). The pi(-)/pi(+) ratio for transverse photons exhibits only a small Q(2) dependence, following a nearly universal curve with t, with a steep transition to a value of about 0.25, consistent with s-channel quark knockout. The sigma(TT)/sigma(T) ratio also drops rapidly with Q(2), qualitatively consistent with s-channel helicity conservation. The pi(-)/pi(+) ratio for longitudinal photons indicates a small isoscalar contamination at W = 1.95 GeV, consistent with what was observed in our earlier determination of the pion form factor at these kinematics. Conclusions: The separated cross sections are compared to a variety of theoretical models, which generally describe sigma(L) but have varying success with sigma(T). Further theoretical input is required to provide a more profound insight into the relevant reaction mechanisms for longitudinal and transverse photons, such as whether the observed transverse ratio is indeed attributable to a transition from pion to quark knockout mechanisms and provide useful information regarding the twist-3 transversity generalized parton distribution, H-