Showing papers by "University of Warsaw published in 2011"
TL;DR: A review of several hundred empirical and theoretical papers and chapters reveals that despite mobility and globalization processes, place continues to be an object of strong attachments as discussed by the authors, and the main message of the three components of the tripartite model of place attachment (Scannell & Gifford, 2010a ), the Person component has attracted disproportionately more attention than the Place and Process components.
1,676 citations
TL;DR: In this paper, a novel definition for the hydrogen bond is proposed, which takes into account the theoretical and experimental knowledge acquired over the past century, and six criteria are listed that could be used as evidence for the presence of a hydrogen bond.
Abstract: A novel definition for the hydrogen bond is recommended here. It takes into account the theoretical and experimental knowledge acquired over the past century. This def- inition insists on some evidence. Six criteria are listed that could be used as evidence for the presence of a hydrogen bond.
1,367 citations
TL;DR: The T2K experiment observes indications of ν (μ) → ν(e) appearance in data accumulated with 1.43×10(20) protons on target, and under this hypothesis, the probability to observe six or more candidate events is 7×10(-3), equivalent to 2.5σ significance.
Abstract: The T2K experiment observes indications of nu(mu) -> nu(mu) e appearance in data accumulated with 1.43 x 10(20) protons on target. Six events pass all selection criteria at the far detector. In a three-flavor neutrino oscillation scenario with |Delta m(23)(2)| = 2.4 x 10(-3) eV(2), sin(2)2 theta(23) = 1 and sin(2)2 theta(13) = 0, the expected number of such events is 1.5 +/- 0.3(syst). Under this hypothesis, the probability to observe six or more candidate events is 7 x 10(-3), equivalent to 2.5 sigma significance. At 90% C.L., the data are consistent with 0.03(0.04) < sin(2)2 theta(13) < 0.28(0.34) for delta(CP) = 0 and a normal (inverted) hierarchy.
1,361 citations
Marcos Daniel Actis1, G. Agnetta2, Felix Aharonian3, A. G. Akhperjanian +682 more•Institutions (109)
TL;DR: The ground-based gamma-ray astronomy has had a major breakthrough with the impressive results obtained using systems of imaging atmospheric Cherenkov telescopes as mentioned in this paper, which is an international initiative to build the next generation instrument, with a factor of 5-10 improvement in sensitivity in the 100 GeV-10 TeV range and the extension to energies well below 100GeV and above 100 TeV.
Abstract: Ground-based gamma-ray astronomy has had a major breakthrough with the impressive results obtained using systems of imaging atmospheric Cherenkov telescopes. Ground-based gamma-ray astronomy has a huge potential in astrophysics, particle physics and cosmology. CTA is an international initiative to build the next generation instrument, with a factor of 5-10 improvement in sensitivity in the 100 GeV-10 TeV range and the extension to energies well below 100 GeV and above 100 TeV. CTA will consist of two arrays (one in the north, one in the south) for full sky coverage and will be operated as open observatory. The design of CTA is based on currently available technology. This document reports on the status and presents the major design concepts of CTA.
1,006 citations
TL;DR: In this paper, a new definition of the hydrogen bond is proposed, which emphasizes the need for evidence, and a list of criteria has been provided, and these can be used as evidence for hydrogen bond formation.
Abstract: The term "hydrogen bond" has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material sci- entists, there has been a continual debate about what this term means. This debate has inten- sified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X-HY hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some char- acteristics that are observed in typical hydrogen-bonding environments.
809 citations
TL;DR: In this article, the transverse momentum balance in dijet and γ/Z+jets events is used to measure the jet energy response in the CMS detector, as well as the transversal momentum resolution.
Abstract: Measurements of the jet energy calibration and transverse momentum resolution in CMS are presented, performed with a data sample collected in proton-proton collisions at a centre-of-mass energy of 7TeV, corresponding to an integrated luminosity of 36pb−1. The transverse momentum balance in dijet and γ/Z+jets events is used to measure the jet energy response in the CMS detector, as well as the transverse momentum resolution. The results are presented for three different methods to reconstruct jets: a calorimeter-based approach, the ``Jet-Plus-Track'' approach, which improves the measurement of calorimeter jets by exploiting the associated tracks, and the ``Particle Flow'' approach, which attempts to reconstruct individually each particle in the event, prior to the jet clustering, based on information from all relevant subdetectors
750 citations
Fermilab1, University of Sussex2, Argonne National Laboratory3, University of Oxford4, University of Minnesota5, Brookhaven National Laboratory6, University of Cambridge7, University of Texas at Austin8, Harvard University9, Tufts University10, State University of Campinas11, Indiana University12, University of Pittsburgh13, University College London14, College of the Holy Cross15, Universidade Federal de Goiás16, University of São Paulo17, Illinois Institute of Technology18, University of Warsaw19, California Institute of Technology20, Stanford University21
TL;DR: The results of a search for ν(e) appearance in a ν (μ) beam in the MINOS long-baseline neutrino experiment find that 2 sin(2) (θ(23))sin(2)(2θ (13))<0.12 at 90% confidence level for δ = 0 and the normal (inverted) neutrinos mass hierarchy.
Abstract: We report the results of a search for ν(e) appearance in a ν(μ) beam in the MINOS long-baseline neutrino experiment. With an improved analysis and an increased exposure of 8.2 × 10(20) protons on the NuMI target at Fermilab, we find that 2 sin(2) (θ(23))sin(2)(2θ(13))<0.12(0.20) at 90% confidence level for δ = 0 and the normal (inverted) neutrino mass hierarchy, with a best-fit of 2sin(2) (θ(23))sin(2)(2θ(13)) = 0.041(-0.031)(+0.047) (0.079(-0.053) (+0.071)). The θ(13) = 0 hypothesis is disfavored by the MINOS data at the 89% confidence level.
730 citations
[...]
11 Dec 2011-Nuclear Instruments & Methods in Physics Research Section A-accelerators Spectrometers Detectors and Associated Equipment
TL;DR: The T2K experiment as discussed by the authors is a long-baseline neutrino oscillation experiment whose main goal is to measure the last unknown lepton sector mixing angle by observing its appearance in a particle beam generated by the J-PARC accelerator.
Abstract: The T2K experiment is a long-baseline neutrino oscillation experiment Its main goal is to measure the last unknown lepton sector mixing angle {\theta}_{13} by observing {
u}_e appearance in a {
u}_{\mu} beam It also aims to make a precision measurement of the known oscillation parameters, {\Delta}m^{2}_{23} and sin^{2} 2{\theta}_{23}, via {
u}_{\mu} disappearance studies Other goals of the experiment include various neutrino cross section measurements and sterile neutrino searches The experiment uses an intense proton beam generated by the J-PARC accelerator in Tokai, Japan, and is composed of a neutrino beamline, a near detector complex (ND280), and a far detector (Super-Kamiokande) located 295 km away from J-PARC This paper provides a comprehensive review of the instrumentation aspect of the T2K experiment and a summary of the vital information for each subsystem
714 citations
Swedish University of Agricultural Sciences1, Commonwealth Scientific and Industrial Research Organisation2, University of Exeter3, University of Bath4, George Washington University5, Ghent University6, Centre for DNA Fingerprinting and Diagnostics7, University of Copenhagen8, Kansas State University9, University of Montpellier10, Max Planck Society11, University of Warsaw12, University of Georgia13, National Autonomous University of Mexico14, Australian National University15, University of Valencia16, Wageningen University and Research Centre17, Agriculture and Agri-Food Canada18, University of Saskatchewan19, Stockholm University20, Eötvös Loránd University21, University of Tokyo22, National Institute of Advanced Industrial Science and Technology23, Plant & Food Research24, Oregon State University25, Agricultural Research Service26, Leiden University27, University of Manitoba28
TL;DR: Despite a large variation in the data, trends that are found are that RNAi is particularly successful in the family Saturniidae and in genes involved in immunity and that gene expression in epidermal tissues seems to be most difficult to silence.
698 citations
University of Glasgow1, University of Salerno2, Max Planck Society3, University of Southampton4, University of Paris-Sud5, University of Nice Sophia Antipolis6, Washington State University7, Istituto Nazionale di Fisica Nucleare8, University of Warsaw9, University of Naples Federico II10, University of Birmingham11, Cardiff University12, University of Rome Tor Vergata13, Moscow State University14, California Institute of Technology15, VU University Amsterdam16, fondazione bruno kessler17, Leibniz University of Hanover18, University of Cambridge19, University of Tübingen20, University of Urbino21, University of Jena22, University of the Balearic Islands23, Northwestern University24, University of Minnesota25, University of Savoy26, Pennsylvania State University27, University of Pisa28, Roma Tre University29, Sapienza University of Rome30, University of Mississippi31
TL;DR: In this article, a special focus is set on evaluating the frequency band below 10 Hz where a complex mixture of seismic, gravity gradient, suspension thermal and radiation pressure noise dominates, including the most relevant fundamental noise contributions.
Abstract: Advanced gravitational wave detectors, currently under construction, are expected to directly observe gravitational wave signals of astrophysical origin. The Einstein Telescope (ET), a third-generation gravitational wave detector, has been proposed in order to fully open up the emerging field of gravitational wave astronomy. In this paper we describe sensitivity models for ET and investigate potential limits imposed by fundamental noise sources. A special focus is set on evaluating the frequency band below 10 Hz where a complex mixture of seismic, gravity gradient, suspension thermal and radiation pressure noise dominates. We develop the most accurate sensitivity model, referred to as ET-D, for a third-generation detector so far, including the most relevant fundamental noise contributions.
682 citations
TL;DR: In this article, the authors studied the effect of collision centrality on the transverse momentum of PbPb collisions at the LHC with a data sample of 6.7 inverse microbarns.
Abstract: Jet production in PbPb collisions at a nucleon-nucleon center-of-mass energy of 2.76 TeV was studied with the CMS detector at the LHC, using a data sample corresponding to an integrated luminosity of 6.7 inverse microbarns. Jets are reconstructed using the energy deposited in the CMS calorimeters and studied as a function of collision centrality. With increasing collision centrality, a striking imbalance in dijet transverse momentum is observed, consistent with jet quenching. The observed effect extends from the lower cut-off used in this study (jet transverse momentum = 120 GeV/c) up to the statistical limit of the available data sample (jet transverse momentum approximately 210 GeV/c). Correlations of charged particle tracks with jets indicate that the momentum imbalance is accompanied by a softening of the fragmentation pattern of the second most energetic, away-side jet. The dijet momentum balance is recovered when integrating low transverse momentum particles distributed over a wide angular range relative to the direction of the away-side jet.
TL;DR: The European Space Agency's Planck satellite was launched on 14 May 2009, and has been surveying the sky stably and continuously since 13 August 2009 as mentioned in this paper, and it will continue to gather scientific data until the end of its cryogenic lifetime.
Abstract: The European Space Agency's Planck satellite was launched on 14 May 2009, and has been surveying the sky stably and continuously since 13 August 2009. Its performance is well in line with expectations, and it will continue to gather scientific data until the end of its cryogenic lifetime. We give an overview of the history of Planck in its first year of operations, and describe some of the key performance aspects of the satellite. This paper is part of a package submitted in conjunction with Planck's Early Release Compact Source Catalogue, the first data product based on Planck to be released publicly. The package describes the scientific performance of the Planck payload, and presents results on a variety of astrophysical topics related to the sources included in the Catalogue, as well as selected topics on diffuse emission.
TL;DR: In this article, the authors derived mass distributions of stellar compact remnants and provided analytical prescriptions for compact object masses for major population synthesis codes, and demonstrated that these qualitatively new results for compact objects can explain the observed gap in the remnant mass distribution between ~2-5 solar masses and place strong constraints on the nature of the supernova engine.
Abstract: The mass distribution of neutron stars and stellar-mass black holes provides vital clues into the nature of stellar core collapse and the physical engine responsible for supernova explosions. Using recent advances in our understanding of supernova engines, we derive mass distributions of stellar compact remnants. We provide analytical prescriptions for compact object masses for major population synthesis codes. In an accompanying paper, Belczynski et al., we demonstrate that these qualitatively new results for compact objects can explain the observed gap in the remnant mass distribution between ~2-5 solar masses and that they place strong constraints on the nature of the supernova engine. Here, we show that advanced gravitational radiation detectors (like LIGO/VIRGO or the Einstein Telescope) will be able to further test the supernova explosion engine models once double black hole inspirals are detected.
TL;DR: In this paper, an all sky map of the apparent temperature and optical depth of thermal dust emission is constructed using the Planck-HFI (350μm to 2 mm) and IRAS(100μm) data.
Abstract: An all sky map of the apparent temperature and optical depth of thermal dust emission is constructed using the Planck-HFI (350μm to 2 mm) andIRAS(100μm) data. The optical depth maps are correlated with tracers of the atomic (Hi) and molecular gas traced by CO. The correlation with the column density of observed gas is linear in the lowest column density regions at high Galactic latitudes. At high N(H), the correlation is consistent with that of the lowest NH, for a given choice of the CO-to-H(2) conversion factor. In the intermediate NH range, a departure from linearity is observed, with the dust optical depth in excess of the correlation. This excess emission is attributed to thermal emission by dust associated with a dark gas phase, undetected in the available Hi and CO surveys. The 2D spatial distribution of the dark gas in the solar neighbourhood (|b(II)| > 10°) is shown to extend around known molecular regions traced by CO. The average dust emissivity in the Hi phase in the solar neighbourhood is found to be τ(D)/N(H)(tot) = 5.2×10(-26) cm(2) at 857 GHz. It follows roughly a power law distribution with a spectral index β = 1.8 all the way down to 3 mm, although the SED flattens slightly in the millimetre. Taking into account the spectral shape of the dust optical depth, the emissivity is consistent with previous values derived fromFIRAS measurements at high latitudes within 10%. The threshold for the existence of the dark gas is found at N(H)(tot) = (8.0±0.58)×10(20) H cm(−2) (A(V )= 0.4mag). Assuming the same high frequency emissivity for the dust in the atomic and the molecular phases leads to an average X(CO) = (2.54 ± 0.13) × 10(20) H(2) cm(-2)/(K km s(-1)). The mass of dark gas is found to be 28% of the atomic gas and 118% of the CO emitting gas in the solar neighbourhood. The Galactic latitude distribution shows that its mass fraction is relatively constant down to a few degrees from the Galactic plane. A possible explanation for the dark gas lies in a dark molecular phase, where H2 survives photodissociation but CO does not. The observed transition for the onsetof this phase in the solar neighbourhood (AV = 0.4mag) appears consistent with recent theoretical predictions. It is also possible that up to half of the dark gas could be in atomic form, due to optical depth effects in the Hi measurements.
TL;DR: The first all-sky sample of galaxy clusters detected blindly by the Planck satellite through the Sunyaev-Zeldovich (SZ) effect from its six highest frequencies was presented in this paper.
Abstract: We present the first all-sky sample of galaxy clusters detected blindly by the Planck satellite through the Sunyaev-Zeldovich (SZ) effect from its six highest frequencies. This early SZ (ESZ) sample is comprised of 189 candidates, which have a high signal-to-noise ratio ranging from 6 to 29. Its high reliability (purity above 95%) is further ensured by an extensive validation process based on Planck internal quality assessments and by external cross-identification and follow-up observations. Planck provides the first measured SZ signal for about 80% of the 169 previouslyknown ESZ clusters. Planck furthermore releases 30 new cluster candidates, amongst which 20 meet the ESZ signal-to-noise selection criterion. At the submission date, twelve of the 20 ESZ candidates were confirmed as new clusters, with eleven confirmed using XMM-Newton snapshot observations, most of them with disturbed morphologies and low luminosities. The ESZ clusters are mostly at moderate redshifts (86% with z below 0.3) and span more than a decade in mass, up to the rarest and most massive clusters with masses above 1 × 10 15 M� .
German Cancer Research Center1, University of Toronto2, University Hospital Heidelberg3, Uniformed Services University of the Health Sciences4, The Catholic University of America5, Virginia Commonwealth University6, University of California, San Francisco7, University of Warsaw8, McMaster University9, Harvard University10, Heidelberg University11
TL;DR: Identification and optimization of immunohistochemical (IHC) markers for PF ependymoma subgroups allowed validation of the findings on a third independent cohort, using a human ependyoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependedymoma patients.
University of Tokyo1, Kyoto University2, University of California, Irvine3, Autonomous University of Madrid4, Boston University5, University of Wisconsin-Madison6, Brookhaven National Laboratory7, California State University, Dominguez Hills8, Chonnam National University9, Duke University10, Fukuoka Institute of Technology11, Gifu University12, Kanagawa University13, Kobe University14, Miyagi University of Education15, Nagoya University16, Stony Brook University17, Niigata University18, Okayama University19, Osaka University20, Seoul National University21, Shizuoka University22, Sungkyunkwan University23, Tokai University24, Tsinghua University25, University of Warsaw26, University of Washington27, University of Minnesota28
TL;DR: The results of the third phase of the Super-Kamiokande solar neutrino measurement are presented and compared to the first and second phase results in this article, where improved detector calibrations, a full detector simulation, and improved analysis methods are estimated to be approximately 2.1%, which is about two thirds of the systematic uncertainty for the first phase.
Abstract: The results of the third phase of the Super-Kamiokande solar neutrino measurement are presented and compared to the first and second phase results. With improved detector calibrations, a full detector simulation, and improved analysis methods, the systematic uncertainty on the total neutrino flux is estimated to be $\ifmmode\pm\else\textpm\fi{}2.1%$, which is about two thirds of the systematic uncertainty for the first phase of Super-Kamiokande. The observed $^{8}\mathrm{B}$ solar flux in the 5.0 to 20 MeV total electron energy region is $2.32\ifmmode\pm\else\textpm\fi{}0.04(\mathrm{stat})\ifmmode\pm\else\textpm\fi{}0.05(\mathrm{sys})\ifmmode\times\else\texttimes\fi{}{10}^{6}\text{ }\text{ }{\mathrm{cm}}^{\ensuremath{-}2}\text{ }{\mathrm{sec}}^{\ensuremath{-}1}$ under the assumption of pure electron-flavor content, in agreement with previous measurements. A combined oscillation analysis is carried out using SK-I, II, and III data, and the results are also combined with the results of other solar neutrino experiments. The best-fit oscillation parameters are obtained to be ${sin }^{2}{\ensuremath{\theta}}_{12}={0.30}_{\ensuremath{-}0.01}^{+0.02}({tan }^{2}{\ensuremath{\theta}}_{12}={0.42}_{\ensuremath{-}0.02}^{+0.04})$ and $\ensuremath{\Delta}{m}_{21}^{2}={6.2}_{\ensuremath{-}1.9}^{+1.1}\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}5}\text{ }\text{ }{\mathrm{eV}}^{2}$. Combined with KamLAND results, the best-fit oscillation parameters are found to be ${sin }^{2}{\ensuremath{\theta}}_{12}=0.31\ifmmode\pm\else\textpm\fi{}0.01({tan }^{2}{\ensuremath{\theta}}_{12}=0.44\ifmmode\pm\else\textpm\fi{}0.03)$ and $\ensuremath{\Delta}{m}_{21}^{2}=7.6\ifmmode\pm\else\textpm\fi{}0.2\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}5}\text{ }\text{ }{\mathrm{eV}}^{2}$. The $^{8}\mathrm{B}$ neutrino flux obtained from global solar neutrino experiments is $5.3\ifmmode\pm\else\textpm\fi{}0.2(\mathrm{stat}+\mathrm{sys})\ifmmode\times\else\texttimes\fi{}{10}^{6}\text{ }\text{ }{\mathrm{cm}}^{\ensuremath{-}2}\text{ }{\mathrm{s}}^{\ensuremath{-}1}$, while the $^{8}\mathrm{B}$ flux becomes $5.1\ifmmode\pm\else\textpm\fi{}0.1(\mathrm{stat}+\mathrm{sys})\ifmmode\times\else\texttimes\fi{}{10}^{6}\text{ }\text{ }{\mathrm{cm}}^{\ensuremath{-}2}\text{ }{\mathrm{s}}^{\ensuremath{-}1}$ by adding KamLAND results. In a three-flavor analysis combining all solar neutrino experiments, the upper limit of ${sin }^{2}{\ensuremath{\theta}}_{13}$ is 0.060 at 95% C.L.. After combination with KamLAND results, the upper limit of ${sin }^{2}{\ensuremath{\theta}}_{13}$ is found to be 0.059 at 95% C.L.
TL;DR: In this paper, the authors investigated the nature of the observed short-term variability of the progenitor of V1309-Sco and found that the binary was a contact binary with an orbital period of 1.4 days.
Abstract: Context. Stellar mergers are expected to take place in numerous circumstences in the evolution of stellar systems. In particular, they are considered as a plausible origin of stellar eruptions of the V838 Mon type. V1309 Sco is the most recent eruption of this type in our Galaxy. The object was discovered in September 2008.Aims. Our aim is to investigate the nature of V1309 Sco.Methods. V1309 Sco has been photometrically observed in course of the OGLE project since August 2001. We analyse these observations in different ways. In particular, periodogram analyses were done to investigate the nature of the observed short-term variability of the progenitor.Results. We find that the progenitor of V1309 Sco was a contact binary with an orbital period of ~1.4 day. This period was decreasing with time. The light curve of the binary was also evolving, indicating that the system evolved towards its merger. The violent phase of the merger, marked by the systematic brightenning of the object, began in March 2008, i.e. half a year before the outburst discovery. We also investigate the observations of V1309 Sco during the outburst and the decline and show that they can be fully accounted for within the merger hypothesis. Conclusions. For the first time in the literature we show from direct observations that contact binaries indeed end up by merging into a single object, as was suggested in numerous theoretical studies of these systems. Our study also shows that stellar mergers indeed result in eruptions of the V838 Mon type.
TL;DR: The results suggest that human nuclear exosome degradation pathways comprise modules of spatially organized cofactors that diverge from the yeast model.
TL;DR: It is shown here that human GW182 independently interacts with the PAN2–PAN3 and CCR4–NOT deadenylase complexes, and serves as both a platform that recruitsdeadenylases and as a deadenyase coactivator that facilitates the removal of the poly(A) tail by CCR 4–NOT.
Abstract: miRNAs recruit the miRNA-induced silencing complex (miRISC), which includes Argonaute and GW182 as core proteins. GW182 proteins effect translational repression and deadenylation of target mRNAs. However, the molecular mechanisms of GW182-mediated repression remain obscure. We show here that human GW182 independently interacts with the PAN2-PAN3 and CCR4-NOT deadenylase complexes. Interaction of GW182 with CCR4-NOT is mediated by two newly discovered phylogenetically conserved motifs. Although either motif is sufficient to bind CCR4-NOT, only one of them can promote processive deadenylation of target mRNAs. Thus, GW182 serves as both a platform that recruits deadenylases and as a deadenylase coactivator that facilitates the removal of the poly(A) tail by CCR4-NOT.
TL;DR: This work 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, and observed the lack of universal scoring function for all types of molecules and protein families.
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.
Royal Netherlands Meteorological Institute1, Max Planck Society2, University of California, Los Angeles3, Delft University of Technology4, Centre national de la recherche scientifique5, Langley Research Center6, Colorado State University7, Stony Brook University8, Cooperative Institute for Mesoscale Meteorological Studies9, West Virginia University10, University of Kansas11, Japan Agency for Marine-Earth Science and Technology12, Met Office13, University of Warsaw14, United States Naval Research Laboratory15, National Center for Atmospheric Research16
TL;DR: In this paper, the authors compared 12 large-eddy simulations, with a wide range of microphysical representations, to each other and to independent measurements and the initial and forcing data for the simulations are taken from the undisturbed period of the Rain in Cumulus over the Ocean (RICO) field study.
Abstract: Twelve large-eddy simulations, with a wide range of microphysical representations, are compared to each other and to independent measurements. The measurements and the initial and forcing data for the simulations are taken from the undisturbed period of the Rain in Cumulus over the Ocean (RICO) field study. A regional downscaling of meteorological analyses is performed so as to provide forcing data consistent with the measurements. The ensemble average of the simulations plausibly reproduces many features of the observed clouds, including the vertical structure of cloud fraction, profiles of cloud and rain water, and to a lesser degree the population density of rain drops. The simulations do show considerable departures from one another in the representation of the cloud microphysical structure and the ensuant surface precipitation rates, increasingly so for the more simplified microphysical models. There is a robust tendency for simulations that develop rain to produce a shallower, somewhat more stable cloud layer. Relations between cloud cover and precipitation are ambiguous.
TL;DR: Measurements indicate that CVD grown graphene is under less compressive strain than its epitaxial counterpart and confirms the existence of an electronic energy band gap, which are essential for future applications of graphene electronics based on wafer scale graphene growth.
Abstract: We demonstrate the growth of high quality graphene layers by chemical vapor deposition (CVD) on insulating and conductive SiC substrates. This method provides key advantages over the well-developed...
25 Jun 2011
TL;DR: 14th International Conference, RSFDGrC 2013, Halifax, NS, Canada, October 11-14, 2013.
TL;DR: In this paper, the binding energy of the Pt 4f signal for platinum nanoparticles on an oxide support was significantly lower in comparison to samples where Pt was solely supported onto carbon.
Abstract: Platinum nanoparticles have been selectively deposited on composites of titanium oxide-carbon and tungsten oxide-carbon. Selectivity of the deposition made it possible to investigate changes in electronic properties of both platinum and oxide support, induced by the so-called strong metal–support interactions (SMSI). X-ray photoelectron spectroscopy (XPS) was used, and changes in binding energy of Pt 4f, Ti 2p, and W 4f core-levels and Pt 4f peak asymmetry were determined. These parameters allowed us to state the changes in local electron density, when Pt is deposited on oxide support. In all cases the binding energy of the Pt 4f signal for platinum deposited on an oxide support was significantly lower in comparison to samples where Pt was solely supported onto carbon. The increase in Pt 4f XPS signal asymmetry was observed. This suggests an increased electron density on Pt. No electron donor could be identified from the analysis of the oxide supports. To explain the observed data, at least two effects mu...
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TL;DR: It is shown that the aforementioned gap cannot be breached for some problems that aim to maximize the number of connected components like Cycle Packing, and in several cases it is able to show that improving those constants would cause the Strong Exponential Time Hypothesis to fail.
Abstract: For the vast majority of local graph problems standard dynamic programming techniques give c^tw V^O(1) algorithms, where tw is the treewidth of the input graph. On the other hand, for problems with a global requirement (usually connectivity) the best-known algorithms were naive dynamic programming schemes running in tw^O(tw) V^O(1) time.
We breach this gap by introducing a technique we dubbed Cut&Count that allows to produce c^tw V^O(1) Monte Carlo algorithms for most connectivity-type problems, including Hamiltonian Path, Feedback Vertex Set and Connected Dominating Set, consequently answering the question raised by Lokshtanov, Marx and Saurabh [SODA'11] in a surprising way. We also show that (under reasonable complexity assumptions) the gap cannot be breached for some problems for which Cut&Count does not work, like CYCLE PACKING.
The constant c we obtain is in all cases small (at most 4 for undirected problems and at most 6 for directed ones), and in several cases we are able to show that improving those constants would cause the Strong Exponential Time Hypothesis to fail.
Our results have numerous consequences in various fields, like FPT algorithms, exact and approximate algorithms on planar and H-minor-free graphs and algorithms on graphs of bounded degree. In all these fields we are able to improve the best-known results for some problems.
TL;DR: In this paper, a search for events with jets and missing transverse energy is performed in a data sample of pp collisions collected at 7 TeV by the CMS experiment at the LHC.
Abstract: A search for events with jets and missing transverse energy is performed in a data sample of pp collisions collected at sqrt(s) = 7 TeV by the CMS experiment at the LHC. The analyzed data sample corresponds to an integrated luminosity of 1.14 inverse femtobarns. In this search, a kinematic variable, alphaT, is used as the main discriminator between events with genuine and misreconstructed missing transverse energy. No excess of events over the standard model expectation is found. Exclusion limits in the parameter space of the constrained minimal supersymmetric extension of the standard model are set. In this model, squark masses below 1.1 TeV are excluded at 95% CL. Gluino masses below 1.1 TeV are also ruled out at 95% CL for values of the universal scalar mass parameter below 500 GeV.
TL;DR: The Planck Early Release Compact Source Catalogue (ERCSC) as mentioned in this paper is an early version of the ERCSC, which consists of data that consists of mapping the entire sky once and 60% of the sky a second time by Planck.
Abstract: A brief description of the methodology of construction, contents and usage of the Planck Early Release Compact Source Catalogue (ERCSC), including the Early Cold Cores (ECC) and the Early Sunyaev-Zeldovich (ESZ) cluster catalogue is provided. The catalogue is based on data that consist of mapping the entire sky once and 60% of the sky a second time by Planck, thereby comprising the first high sensitivity radio/submillimetre observations of the entire sky. Four source detection algorithms were run as part of the ERCSC pipeline. A Monte-Carlo algorithm based on the injection and extraction of artificial sources into the Planck maps was implemented to select reliable sources among all extracted candidates such that the cumulative reliability of the catalogue is ≥90%. There is no requirement on completeness for the ERCSC. As a result of the Monte-Carlo assessment of reliability of sources from the different techniques, an implementation of the PowellSnakes source extraction technique was used at the five frequencies between 30 and 143GHz while the SExtractor technique was used between 217 and 857GHz. The 10σ photometric flux density limit of the catalogue at |b| > 30° is 0.49, 1.0, 0.67, 0.5, 0.33, 0.28, 0.25, 0.47 and 0.82 Jy at each of the nine frequencies between 30 and 857GHz. Sources which are up to a factor of ~2 fainter than this limit, and which are present in “clean” regions of the Galaxy where the sky background due to emission from the interstellar medium is low, are included in the ERCSC if they meet the high reliability criterion. The Planck ERCSC sources have known associations to stars with dust shells, stellar cores, radio galaxies, blazars, infrared luminous galaxies and Galactic interstellar medium features. A significant fraction of unclassified sources are also present in the catalogs. In addition, two early release catalogs that contain 915 cold molecular cloud core candidates and 189 SZ cluster candidates that have been generated using multifrequency algorithms are presented. The entire source list, with more than 15000 unique sources, is ripe for follow-up characterisation with Herschel, ATCA, VLA, SOFIA, ALMA and other ground-based observing facilities.
22 Oct 2011
TL;DR: Cut&Count as mentioned in this paper is a Monte Carlo algorithm that runs in O(1) time for most connectivity-type problems, including Hamiltonian Path, Steiner Tree, Feedback Vertex Set and Connected Dominating Set.
Abstract: For the vast majority of local problems on graphs of small tree width (where by local we mean that a solution can be verified by checking separately the neighbourhood of each vertex), standard dynamic programming techniques give c^tw |V|^O(1) time algorithms, where tw is the tree width of the input graph G = (V, E) and c is a constant. On the other hand, for problems with a global requirement (usually connectivity) the best -- known algorithms were naive dynamic programming schemes running in at least tw^tw time. We breach this gap by introducing a technique we named Cut&Count that allows to produce c^tw |V|^O(1) time Monte Carlo algorithms for most connectivity-type problems, including Hamiltonian Path, Steiner Tree, Feedback Vertex Set and Connected Dominating Set. These results have numerous consequences in various fields, like parameterized complexity, exact and approximate algorithms on planar and H-minor-free graphs and exact algorithms on graphs of bounded degree. The constant c in our algorithms is in all cases small, and in several cases we are able to show that improving those constants would cause the Strong Exponential Time Hypothesis to fail. In contrast to the problems aiming to minimize the number of connected components that we solve using Cut&Count as mentioned above, we show that, assuming the Exponential Time Hypothesis, the aforementioned gap cannot be breached for some problems that aim to maximize the number of connected components like Cycle Packing.
TL;DR: Despite evident inducibility of saponin production in plant cell cultures, the possible role of these compounds as phytoalexins synthesized in intact plants after pathogen infection is still not well documented.
Abstract: Saponins are a large group of secondary metabolites occurring in significant amounts in many plant species. However, the saponin content of plants is variable and it can be influenced by the surrounding environment. The local geoclimate, seasonal changes, external conditions such as light, temperature, humidity and soil fertility, as well as cultivation techniques, affect both the quantitative amount and qualitative composition of saponins. Such variation substantially impacts on the quality and properties of wild and cultivated plants exploited for pharmaceutical, nutritional and industrial applications. This review summarizes the available data on the effects of abiotic environmental factors on saponin level in plants, especially those of considerable economic importance, highlighting current problems such as the reduction in natural plant resources, over-exploitation and destruction of wild habitats, climate shifts as well as the consequences of the growing demand for plant-derived medicinal and industrial products. The need for a theoretical basis for a reasonable harvest, attempts at the domestication of wild plant species and the development of new agricultural technologies allowing high production under optimized conditions are also discussed.