Modelling the multi-wavelength emissions from PSR B1259-63/LS 2883: the effects of the stellar disc on shock radiations

PSR B1259-63/LS 2883 is an elliptical pulsar/Be star binary and emits broadband emissions from radio to TeV $\gamma$-rays. The massive star possesses an equatorial disc, which is inclined with the orbital plane of the pulsar. The non-thermal emission from the system is believed to be produced by the pulsar wind shock and the double-peak profiles in the X-ray and TeV $\gamma$-ray light curves are related to the phases of the pulsar passing through the disc region of the star. In this paper, we investigate the interactions between the pulsar wind and stellar outflows, especially with the presence of the disc, and present a multi-wavelength modelling of the emission from this system. We show that the double-peak profiles of X-ray and TeV $\gamma$-ray light curves are caused by the enhancements of the magnetic field and the soft photons at the shock during the disc passages. As the pulsar is passing through the equatorial disc, the additional pressure of the disc pushes the shock surface closer to the pulsar, which causes the enhancement of magnetic field in the shock, and thus increases the synchrotron luminosity. The TeV $\gamma$-rays due to the inverse-Compton (IC) scattering of shocked electrons with seed photons from the star is expected to peak around periastron which is inconsistent with observations. However, the shock heating of the stellar disc could provide additional seed photons for IC scattering during the disc passages, and thus produces the double-peak profiles as observed in the TeV $\gamma$-ray light curve. Our model can possibly be examined and applied to other similar gamma-ray binaries, such as PSR J2032+4127/MT91 213, HESS J0632+057, and LS I+61$^{\circ}$303.Comment: 14 pages, 6 figure

GPER-induced signaling is essential for the survival of breast cancer stem cells.

G protein-coupled estrogen receptor-1 (GPER), a member of the G protein-coupled receptor (GPCR) superfamily, mediates estrogen-induced proliferation of normal and malignant breast epithelial cells. However, its role in breast cancer stem cells (BCSCs) remains unclear. Here we showed greater expression of GPER in BCSCs than non-BCSCs of three patient-derived xenografts of ER- /PR+ breast cancers. GPER silencing reduced stemness features of BCSCs as reflected by reduced mammosphere forming capacity in vitro, and tumor growth in vivo with decreased BCSC populations. Comparative phosphoproteomics revealed greater GPER-mediated PKA/BAD signaling in BCSCs. Activation of GPER by its ligands, including tamoxifen (TMX), induced phosphorylation of PKA and BAD-Ser118 to sustain BCSC characteristics. Transfection with a dominant-negative mutant BAD (Ser118Ala) led to reduced cell survival. Taken together, GPER and its downstream signaling play a key role in maintaining the stemness of BCSCs, suggesting that GPER is a potential therapeutic target for eradicating BCSCs

Fermions in gravity and gauge backgrounds on a brane world

We solve the fermionic zero modes in gravity and gauge backgrounds on a brane involving a warped geometry, and study the localization of spin 1/2 fermionic field on the brane world. The result is that there exist massless spin 1/2 fermions which can be localized on the bulk with the exponentially decreasing warp factor if including U(1) gauge background. Two special cases of gauge backgrounds on the extra dimensional manifold are discussed.Comment: 11 pages, no figures, final versio

Information Flow in Interaction Networks

Interaction networks, consisting of agents linked by their interactions, are ubiquitous across many disciplines of modern science. Many methods of analysis of interaction networks have been proposed, mainly concentrating on node degree distribution or aiming to discover clusters of agents that are very strongly connected between themselves. These methods are principally based on graph-theory or machine learning. We present a mathematically simple formalism for modelling context-specific information propagation in interaction networks based on random walks. The context is provided by selection of sources and destinations of information and by use of potential functions that direct the flow towards the destinations. We also use the concept of dissipation to model the aging of information as it diffuses from its source. Using examples from yeast protein-protein interaction networks and some of the histone acetyltransferases involved in control of transcription, we demonstrate the utility of the concepts and the mathematical constructs introduced in this paper.Comment: 30 pages, 5 figures. This paper was published in 2007 in Journal of Computational Biology. The version posted here does not include post peer-review change

RAId_DbS: Peptide Identification using Database Searches with Realistic Statistics

<p>Abstract</p> <p>Background</p> <p>The key to mass-spectrometry-based proteomics is peptide identification. A major challenge in peptide identification is to obtain realistic <it>E</it>-values when assigning statistical significance to candidate peptides.</p> <p>Results</p> <p>Using a simple scoring scheme, we propose a database search method with theoretically characterized statistics. Taking into account possible skewness in the random variable distribution and the effect of finite sampling, we provide a theoretical derivation for the tail of the score distribution. For every experimental spectrum examined, we collect the scores of peptides in the database, and find good agreement between the collected score statistics and our theoretical distribution. Using Student's <it>t</it>-tests, we quantify the degree of agreement between the theoretical distribution and the score statistics collected. The T-tests may be used to measure the reliability of reported statistics. When combined with reported <it>P</it>-value for a peptide hit using a score distribution model, this new measure prevents exaggerated statistics. Another feature of RAId_DbS is its capability of detecting multiple co-eluted peptides. The peptide identification performance and statistical accuracy of RAId_DbS are assessed and compared with several other search tools. The executables and data related to RAId_DbS are freely available upon request.</p

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

<p>Abstract</p> <p>Background</p> <p>Existing scientific literature is a rich source of biological information such as disease markers. Integration of this information with data analysis may help researchers to identify possible controversies and to form useful hypotheses for further validations. In the context of proteomics studies, individualized proteomics era may be approached through consideration of amino acid substitutions/modifications as well as information from disease studies. Integration of such information with peptide searches facilitates speedy, dynamic information retrieval that may significantly benefit clinical laboratory studies.</p> <p>Description</p> <p>We have integrated from various sources annotated single amino acid polymorphisms, post-translational modifications, and their documented disease associations (if they exist) into one enhanced database per organism. We have also augmented our peptide identification software RAId_DbS to take into account this information while analyzing a tandem mass spectrum. In principle, one may choose to respect or ignore the <it>correlation </it>of amino acid polymorphisms/modifications within each protein. The former leads to targeted searches and avoids scoring of unnecessary polymorphism/modification combinations; the latter explores possible polymorphisms in a controlled fashion. To facilitate new discoveries, RAId_DbS also allows users to conduct searches permitting <it>novel </it>polymorphisms as well as to search a knowledge database created by the users.</p> <p>Conclusion</p> <p>We have finished constructing enhanced databases for 17 organisms. The web link to RAId_DbS and the enhanced databases is <url>http://www.ncbi.nlm.nih.gov/CBBResearch/qmbp/RAId_DbS/index.html</url>. The relevant databases and binaries of RAId_DbS for Linux, Windows, and Mac OS X are available for download from the same web page.</p