University of Warsaw

About: University of Warsaw is a education organization based out in Warsaw, Poland. It is known for research contribution in the topics: Population & Large Hadron Collider. The organization has 20832 authors who have published 56617 publications receiving 1185084 citations. The organization is also known as: Uniwersytet Warszawski & Warsaw University.

Planck 2013 results. XXV. Searches for cosmic strings and other topological defects

Abstract: Planck data have been used to provide stringent new constraints on cosmic strings and other defects. We describe forecasts of the CMB power spectrum induced by cosmic strings, calculating these from network models and simulations using line-of-sight Boltzmann solvers. We have studied Nambu-Goto cosmic strings, as well as field theory strings for which radiative effects are important, thus spanning the range of theoretical uncertainty in strings models. We have added the angular power spectrum from strings to that for a simple adiabatic model, with the extra fraction defined as $f_{10}$ at multipole $\ell=10$. This parameter has been added to the standard six parameter fit using COSMOMC with flat priors. For the Nambu-Goto string model, we have obtained a constraint on the string tension of $G\mu/c^2 < 1.5 x 10^{-7}$ and $f_{10} < 0.015$ at 95% confidence that can be improved to $G\mu/c^2 < 1.3 x 10^{-7}$ and $f_{10} < 0.010$ on inclusion of high-$\ell$ CMB data. For the abelian-Higgs field theory model we find, $G\mu_{AH}/c^2 < 3.2 x 10^{-7}$ and $f_{10} < 0.028$. The marginalized likelihoods for $f_{10}$ and in the $f_{10}$--$\Omega_b h^2$ plane are also presented. We have also obtained constraints on $f_{10}$ for models with semi-local strings and global textures for which $G\mu/c^2 < 1.1 x 10^{-6}$. We have made complementarity searches for the specific non-Gaussian signatures of cosmic strings, calibrating with all-sky Planck resolution CMB maps generated from networks of post-recombination strings. We have obtained upper limits on the string tension at 95% confidence of $G\mu/c^2 < 8.8 x 10^{-7}$ using modal bispectrum estimation and $G\mu/c^2 < 7.8 x 10^{-7}$ for real space searches with Minkowski functionals. These are conservative upper bounds because only post-recombination string contributions have been included in the non-Gaussian analysis.

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

Abstract: Docking is one of the most commonly used techniques in drug design. It is used for both identifying correct poses of a ligand in the binding site of a protein as well as for the estimation of the strength of protein-ligand interaction. Because millions of compounds must be screened, before a suitable target for biological testing can be identified, all calculations should be done in a reasonable time frame. Thus, all programs currently in use exploit empirically based algorithms, avoiding systematic search of the conformational space. Similarly, the scoring is done using simple equations, which makes it possible to speed up the entire process. Therefore, docking results have to be verified by subsequent in vitro studies. The purpose of our work was to evaluate seven popular docking programs (Surflex, LigandFit, Glide, GOLD, FlexX, eHiTS, and AutoDock) on the extensive dataset composed of 1300 protein-ligands complexes from PDBbind 2007 database, where experimentally measured binding affinity values were also available. We compared independently the ability of proper posing [according to Root mean square deviation (or Root mean square distance) of predicted conformations versus the corresponding native one] and scoring (by calculating the correlation between docking score and ligand binding strength). To our knowledge, it is the first large-scale docking evaluation that covers both aspects of docking programs, that is, predicting ligand conformation and calculating the strength of its binding. More than 1000 protein-ligand pairs cover a wide range of different protein families and inhibitor classes. Our results clearly showed that the ligand binding conformation could be identified in most cases by using the existing software, yet we still observed the lack of universal scoring function for all types of molecules and protein families.

Search for dark matter WIMPs using upward through-going muons in Super-Kamiokande

Abstract: We present the results of indirect searches for Weakly Interacting Massive Particles (WIMPs), with 1679.6 live days of data from the Super-Kamiokande detector using neutrino-induced upward through-going muons. The search is performed by looking for an excess of high energy muon neutrinos from WIMP annihilations in the Sun, the core of the Earth, and the Galactic Center, as compared to the number expected from the atmospheric neutrino background. No statistically significant excess was seen. We calculate the flux limits in various angular cones around each of the above celestial objects. We obtain conservative model-independent upper limits on the WIMP-nucleon cross section as a function of WIMP mass, and compare these results with the corresponding results from direct dark matter detection experiments.

Novel “anti-reverse” cap analogs with superior translational properties

Abstract: Synthetic analogs of the 5'-terminal caps of eukaryotic mRNAs and snRNAs are used in elucidating such physiological processes as mRNA translation, pre-mRNA splicing, intracellular transport of mRNA and snRNAs, and mRNA turnover. Particularly useful are RNAs capped with synthetic analogs, which are produced by in vitro transcription of a DNA template using a bacteriophage RNA polymerase in the presence of ribonucleoside triphosphates and a cap dinucleotide such as m(7)Gp(3)G. Unfortunately, because of the presence of a 3'-OH on both the m(7)Guo and Guo moieties, up to half of the mRNAs contain caps incorporated in the reverse orientation. Previously we designed and synthesized two "anti-reverse" cap analogs (ARCAs), m(7)3'dGp(3)G and m(2)(7,3'-)(O)Gp(3)G, that cannot be incorporated in the reverse orientation because of modifications at the C3' position of m(7)Guo. In the present study, we have synthesized seven new cap analogs modified in the C2' and C3' positions of m(7)Guo and in the number of phosphate residues, m(2)(7,2'-)(O)Gp(3)G, m(7)2'dGp(3)G, m(7)2'dGp(4)G, m(2)(7,2'-)(O)Gp(4)G, m(2)(7,3'-)(O)Gp(4)G, m(7)Gp(5)G, and m(2)(7,3'-)(O)Gp(5)G. These were analyzed for conformation in solution, binding affinity to eIF4E, inhibition of in vitro translation, degree of reverse capping during in vitro transcription, capping efficiency, and the ability to stimulate cap-dependent translation in vitro when incorporated into mRNA. The results indicate that modifications at C2', like those at C3', prevent reverse incorporation, that tetra- and pentaphosphate cap analogs bind eIF4E and inhibit translation more strongly than their triphosphate counterparts, and that tetraphosphate ARCAs promote cap-dependent translation more effectively than previous cap analogs.