Pathway databases and tools for their exploitation: benefits, current limitations and challenges

In past years, comprehensive representations of cell signalling pathways have been developed by manual curation from literature, which requires huge effort and would benefit from information stored in databases and from automatic retrieval and integration methods. Once a reconstruction of the network of interactions is achieved, analysis of its structural features and its dynamic behaviour can take place. Mathematical modelling techniques are used to simulate the complex behaviour of cell signalling networks, which ultimately sheds light on the mechanisms leading to complex diseases or helps in the identification of drug targets. A variety of databases containing information on cell signalling pathways have been developed in conjunction with methodologies to access and analyse the data. In principle, the scenario is prepared to make the most of this information for the analysis of the dynamics of signalling pathways. However, are the knowledge repositories of signalling pathways ready to realize the systems biology promise? In this article we aim to initiate this discussion and to provide some insights on this issue

Towards Prediction of Pancreatic Cancer Using SVM Study Model

published_or_final_versio

Possible improvements on the mass of the tau neutrino using leptonic Ds±D^\pm_s decays

We show how a very accurate measurement of the branching ratios of the leptonic decay modes of the $D^\pm_s$ mesons can lead to a significant improvement in the mass limit for the tau neutrino.Comment: 1 typo in Eq.2 correcte

QED Corrections to the Scattering of Solar Neutrinos and Electrons

We discuss recent calculations of the O(alpha) QED corrections to the recoil electron energy spectrum in neutrino electron scattering, and to the spectrum of the combined energy of the recoil electron and a possible accompanying photon emitted in the scattering process. We then examine the role of these corrections in the interpretation of precise measurements from solar neutrino electron scattering experiments.Comment: (16 Pages, 4 Figures) Presented at the Symposium in Honor of Professor Alberto Sirlin's 70th Birthday: ``50 Years of Precision Electroweak Physics'', New York University, October 27-28, 200

A weighted q-gram method for glycan structure classification

<p>Abstract</p> <p>Background</p> <p>Glycobiology pertains to the study of carbohydrate sugar chains, or glycans, in a particular cell or organism. Many computational approaches have been proposed for analyzing these complex glycan structures, which are chains of monosaccharides. The monosaccharides are linked to one another by glycosidic bonds, which can take on a variety of comformations, thus forming branches and resulting in complex tree structures. The <it>q</it>-gram method is one of these recent methods used to understand glycan function based on the classification of their tree structures. This <it>q</it>-gram method assumes that for a certain <it>q</it>, different <it>q</it>-grams share no similarity among themselves. That is, that if two structures have completely different components, then they are completely different. However, from a biological standpoint, this is not the case. In this paper, we propose a weighted <it>q</it>-gram method to measure the similarity among glycans by incorporating the similarity of the geometric structures, monosaccharides and glycosidic bonds among <it>q</it>-grams. In contrast to the traditional <it>q</it>-gram method, our weighted <it>q</it>-gram method admits similarity among <it>q</it>-grams for a certain <it>q</it>. Thus our new kernels for glycan structure were developed and then applied in SVMs to classify glycans.</p> <p>Results</p> <p>Two glycan datasets were used to compare the weighted <it>q</it>-gram method and the original <it>q</it>-gram method. The results show that the incorporation of <it>q</it>-gram similarity improves the classification performance for all of the important glycan classes tested.</p> <p>Conclusion</p> <p>The results in this paper indicate that similarity among <it>q</it>-grams obtained from geometric structure, monosaccharides and glycosidic linkage contributes to the glycan function classification. This is a big step towards the understanding of glycan function based on their complex structures.</p

MADNet: microarray database network web server

MADNet is a user-friendly data mining and visualization tool for rapid analysis of diverse high-throughput biological data such as microarray, phage display or even metagenome experiments. It presents biological information in the context of metabolic and signalling pathways, transcription factors and drug targets through minimal user input, consisting only of the file with the experimental data. These data are integrated with information stored in various biological databases such as NCBI nucleotide and protein databases, metabolic and signalling pathway databases (KEGG), transcription regulation (TRANSFAC©) and drug target database (DrugBank). MADNet is freely available for academic use at http://www.bioinfo.hr/madnet

QED Corrections to Neutrino Electron Scattering

We evaluate the O(alpha) QED corrections to the recoil electron energy spectrum in the process nu_l + e --> nu_l + e (+gamma), where (+gamma) indicates the possible emission of a photon and l=e, mu or tau. The soft and hard bremsstrahlung differential cross sections are computed for an arbitrary value of the photon energy threshold. We also study the O(alpha) QED corrections to the differential cross section with respect to the total combined energy of the recoil electron and a possible accompanying photon. Their difference from the corrections to the electron spectrum is investigated. We discuss the relevance and applicability of both radiative corrections, emphasizing their role in the analysis of precise solar neutrino electron scattering experiments.Comment: 14 pages + 10 figures. Minimal changes, published versio

Standard Model Contributions to the Neutrino Index of Refraction in the Early Universe

With the standard electroweak interactions, the lowest-order coherent forward scattering amplitudes of neutrinos in a CP symmetric medium (such as the early universe) are zero, and the index of refraction of a propagating neutrino can only arise from the expansion of gauge boson propagators, from radiative corrections, and from new physics interactions. Motivated by nucleosynthesis constraints on a possible sterile neutrino (suggested by the solar neutrino deficit and a possible $17\ keV$ neutrino), we calculate the standard model contributions to the neutrino index of refraction in the early universe, focusing on the period when the temperature was of the order of a few $MeV$. We find sizable radiative corrections to the tree level result obtained by the expansion of the gauge boson propagator. For $\nu_e+e(\bar{e})\to \nu_e+e(\bar{e})$ the leading log correction is about $+10\%$, while for $\nu_e+\nu_e(\bar{\nu}_e)\to \nu_e+\nu_e(\bar{\nu}_e)$ the correction is about $+20\%$. Depending on the family mixing (if any), effects from different family scattering can be dominated by radiative corrections. The result for $\nu+\gamma\to\nu+\gamma$ is zero at one-loop level, even if neutrinos are massive. The cancellation of infrared divergence in a coherent process is also discussed.Comment: 46pp, 13 figures (not included), UPR-0495