Showing papers by "Hungarian Academy of Sciences published in 2012"

Review of AdS/CFT Integrability: An Overview

Abstract: This is the introductory chapter of a review collection on integrability in the context of the AdS/CFT correspondence. In the collection we present an overview of the achievements and the status of this subject as of the year 2010.

Cutoff Finder: A Comprehensive and Straightforward Web Application Enabling Rapid Biomarker Cutoff Optimization

Abstract: Gene or protein expression data are usually represented by metric or at least ordinal variables. In order to translate a continuous variable into a clinical decision, it is necessary to determine a cutoff point and to stratify patients into two groups each requiring a different kind of treatment. Currently, there is no standard method or standard software for biomarker cutoff determination. Therefore, we developed Cutoff Finder, a bundle of optimization and visualization methods for cutoff determination that is accessible online. While one of the methods for cutoff optimization is based solely on the distribution of the marker under investigation, other methods optimize the correlation of the dichotomization with respect to an outcome or survival variable. We illustrate the functionality of Cutoff Finder by the analysis of the gene expression of estrogen receptor (ER) and progesterone receptor (PgR) in breast cancer tissues. This distribution of these important markers is analyzed and correlated with immunohistologically determined ER status and distant metastasis free survival. Cutoff Finder is expected to fill a relevant gap in the available biometric software repertoire and will enable faster optimization of new diagnostic biomarkers. The tool can be accessed at http://molpath.charite.de/cutoff.

Implementing an online tool for genome-wide validation of survival-associated biomarkers in ovarian-cancer using microarray data from 1287 patients.

Abstract: The validation of prognostic biomarkers in large independent patient cohorts is a major bottleneck in ovarian cancer research. We implemented an online tool to assess the prognostic value of the expression levels of all microarray-quantified genes in ovarian cancer patients. First, a database was set up using gene expression data and survival information of 1287 ovarian cancer patients downloaded from Gene Expression Omnibus and The Cancer Genome Atlas (Affymetrix HG-U133A, HG-U133A 2.0, and HG-U133 Plus 2.0 microarrays). After quality control and normalization, only probes present on all three Affymetrix platforms were retained (n=22,277). To analyze the prognostic value of the selected gene, we divided the patients into two groups according to various quantile expressions of the gene. These groups were then compared using progression-free survival (n=1090) or overall survival (n=1287). A Kaplan-Meier survival plot was generated and significance was computed. The tool can be accessed online at www.kmplot.com/ovar. We used this integrative data analysis tool to validate the prognostic power of 37 biomarkers identified in the literature. Of these, CA125 (MUC16; P=3.7×10(-5), hazard ratio (HR)=1.4), CDKN1B (P=5.4×10(-5), HR=1.4), KLK6 (P=0.002, HR=0.79), IFNG (P=0.004, HR=0.81), P16 (P=0.02, HR=0.66), and BIRC5 (P=0.00017, HR=0.75) were associated with survival. The combination of several probe sets can further increase prediction efficiency. In summary, we developed a global online biomarker validation platform that mines all available microarray data to assess the prognostic power of 22,277 genes in 1287 ovarian cancer patients. We specifically used this tool to evaluate the effect of 37 previously published biomarkers on ovarian cancer prognosis.

Decreased expression of synapse-related genes and loss of synapses in major depressive disorder

Abstract: Previous imaging and postmortem studies have reported a lower brain volume and a smaller size and density of neurons in the dorsolateral prefrontal cortex (dlPFC) of subjects with major depressive disorder (MDD). These findings suggest that synapse number and function are decreased in the dlPFC of patients with MDD. However, there has been no direct evidence reported for synapse loss in MDD, and the gene expression alterations underlying these effects have not been identified. Here we use microarray gene profiling and electron microscopic stereology to reveal lower expression of synaptic-function–related genes (CALM2, SYN1, RAB3A, RAB4B and TUBB4) in the dlPFC of subjects with MDD and a corresponding lower number of synapses. We also identify a transcriptional repressor, GATA1, expression of which is higher in MDD and that, when expressed in PFC neurons, is sufficient to decrease the expression of synapse-related genes, cause loss of dendritic spines and dendrites, and produce depressive behavior in rat models of depression.

Definition and synergies of cognitive infocommunications

Abstract: In this paper, we provide the finalized definition of Cognitive Infocommunications (CogInfoCom). Following the definition, we briefly describe the scope and goals of CogInfoCom, and discuss the common interests between CogInfoCom and the various research disciplines which contribute to this new field in a synergistic way.

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

Abstract: The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta)<2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.

D2P2: database of disordered protein predictions

Abstract: We present the Database of Disordered Protein Prediction (D2P2), available at http://d2p2.pro (including website source code). A battery of disorder predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz and IUPred, were run on all protein sequences from 1765 complete proteomes (to be updated as more genomes are completed). Integrated with these results are all of the predicted (mostly structured) SCOP domains using the SUPERFAMILY predictor. These disorder/structure annotations together enable comparison of the disorder predictors with each other and examination of the overlap between disordered predictions and SCOP domains on a large scale. D2P2 will increase our understanding of the interplay between disorder and structure, the genomic distribution of disorder, and its evolutionary history. The parsed data are made available in a unified format for download as flat files or SQL tables either by genome, by predictor, or for the complete set. An interactive website provides a graphical view of each protein annotated with the SCOP domains and disordered regions from all predictors overlaid (or shown as a consensus). There are statistics and tools for browsing and comparing genomes and their disorder within the context of their position on the tree of life. © The Author(s) 2012. Published by Oxford University Press.

Multiple Functions of Endocannabinoid Signaling in the Brain

Abstract: Despite being regarded as a hippie science for decades, cannabinoid research has finally found its well-deserved position in mainstream neuroscience. A series of groundbreaking discoveries revealed that endocannabinoid molecules are as widespread and important as conventional neurotransmitters such as glutamate or GABA, yet they act in profoundly unconventional ways. We aim to illustrate how uncovering the molecular, anatomical, and physiological characteristics of endocannabinoid signaling has revealed new mechanistic insights into several fundamental phenomena in synaptic physiology. First, we summarize unexpected advances in the molecular complexity of biogenesis and inactivation of the two endocannabinoids, anandamide and 2-arachidonoylglycerol. Then, we show how these new metabolic routes are integrated into well-known intracellular signaling pathways. These endocannabinoid-producing signalosomes operate in phasic and tonic modes, thereby differentially governing homeostatic, short-term, and long-ter...

Study of high-p(T) charged particle suppression in PbPb compared to pp collisions at root s(NN)=2.76 TeV

Abstract: The transverse momentum spectra of charged particles have been measured in pp and PbPb collisions at sqrt(sNN) = 2.76 TeV by the CMS experiment at the LHC. In the transverse momentum range pt = 5-10 GeV/c, the charged particle yield in the most central PbPb collisions is suppressed by up to a factor of 5 compared to the pp yield scaled by the number of incoherent nucleon-nucleon collisions. At higher pt, this suppression is significantly reduced, approaching roughly a factor of 2 for particles with pt in the range pt=40-100 GeV/c.

Controlling edge dynamics in complex networks

Abstract: Surprisingly little is known about how network dynamics might be controlled, despite extensive research into how they behave. A study of the controllability of network edge dynamics reveals that it differs from that of nodal dynamics, and that real-world networks are easier to control than their random counterparts.

A 2D Quantum Walk Simulation of Two-Particle Dynamics

Abstract: Multidimensional quantum walks can exhibit highly nontrivial topological structure, providing a powerful tool for simulating quantum information and transport systems. We present a flexible implementation of a two-dimensional (2D) optical quantum walk on a lattice, demonstrating a scalable quantum walk on a nontrivial graph structure. We realized a coherent quantum walk over 12 steps and 169 positions by using an optical fiber network. With our broad spectrum of quantum coins, we were able to simulate the creation of entanglement in bipartite systems with conditioned interactions. Introducing dynamic control allowed for the investigation of effects such as strong nonlinearities or two-particle scattering. Our results illustrate the potential of quantum walks as a route for simulating and understanding complex quantum systems.

On the forest cover–water yield debate: from demand‐ to supply‐side thinking

Abstract: Several major articles from the past decade and beyond conclude the impact of reforestation or afforestation on water yield is negative: additional forest cover will reduce and removing forests will raise downstream water availability. A second group of authors argue the opposite: planting additional forests should raise downstream water availability and intensify the hydrologic cycle. Obtaining supporting evidence for this second group of authors has been more difficult due to the larger scales at which the positive effects of forests on the water cycle may be seen. We argue that forest cover is inextricably linked to precipitation. Forest-driven evapotranspiration removed from a particular catchment contributes to the availability of atmospheric moisture vapor and its cross-continental transport, raising the likelihood of precipitation events and increasing water yield, in particular in continental interiors more distant from oceans. Seasonal relationships heighten the importance of this phenomenon. We review the arguments from different scales and perspectives. This clarifies the generally beneficial relationship between forest cover and the intensity of the hydrologic cycle. While evidence supports both sides of the argument – trees can reduce runoff at the small catchment scale – at larger scales, trees are more clearly linked to increased precipitation and water availability. Progressive deforestation, land conversion from forest to agriculture and urbanization have potentially negative consequences for global precipitation, prompting us to think of forest ecosystems as global public goods. Policy-making attempts to measure product water footprints, estimate the value of ecosystem services, promote afforestation, develop drought mitigation strategies and otherwise manage land use must consider the linkage of forests to the supply of precipitation.

Release probability of hippocampal glutamatergic terminals scales with the size of the active zone

Abstract: Using functional and morphological analysis, this study demonstrates that in CA3 pyramidal cell recurrent axon terminals, the release probability and the number of voltage-gated calcium channels are linearly correlated with the size of the active zone.

Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing

Abstract: Background: Renewable energy production is currently a major issue worldwide. Biogas is a promising renewable energy carrier as the technology of its production combines the elimination of organic waste with the formation of a versatile energy carrier, methane. In consequence of the complexity of the microbial communities and metabolic pathways involved the biotechnology of the microbiological process leading to biogas production is poorly understood. Metagenomic approaches are suitable means of addressing related questions. In the present work a novel high-throughput technique was tested for its benefits in resolving the functional and taxonomical complexity of such microbial consortia. Results: It was demonstrated that the extremely parallel SOLiD™ short-read DNA sequencing platform is capable of providing sufficient useful information to decipher the systematic and functional contexts within a biogasproducing community. Although this technology has not been employed to address such problems previously, the data obtained compare well with those from similar high-throughput approaches such as 454-pyrosequencing GS FLX or Titanium. The predominant microbes contributing to the decomposition of organic matter include members of the Eubacteria, class Clostridia, order Clostridiales, family Clostridiaceae. Bacteria belonging in other systematic groups contribute to the diversity of the microbial consortium. Archaea comprise a remarkably small minority in this community, given their crucial role in biogas production. Among the Archaea, the predominant order is the Methanomicrobiales and the most abundant species is Methanoculleus marisnigri. The Methanomicrobiales are hydrogenotrophic methanogens. Besides corroborating earlier findings on the significance of the contribution of the Clostridia to organic substrate decomposition, the results demonstrate the importance of the metabolism of hydrogen within the biogas producing microbial community. Conclusions: Both microbiological diversity and the regulatory role of the hydrogen metabolism appear to be the driving forces optimizing biogas-producing microbial communities. The findings may allow a rational design of these communities to promote greater efficacy in large-scale practical systems. The composition of an optimal biogas-producing consortium can be determined through the use of this approach, and this systematic methodology allows the design of the optimal microbial community structure for any biogas plant. In this way, metagenomic studies can contribute to significant progress in the efficacy and economic improvement of biogas production.

Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes

Abstract: The understanding of brain computations requires methods that read out neural activity on different spatial and temporal scales. Following signal propagation and integration across a neuron and recording the concerted activity of hundreds of neurons pose distinct challenges, and the design of imaging systems has been mostly focused on tackling one of the two operations. We developed a high-resolution, acousto-optic two-photon microscope with continuous three-dimensional (3D) trajectory and random-access scanning modes that reaches near-cubic-millimeter scan range and can be adapted to imaging different spatial scales. We performed 3D calcium imaging of action potential backpropagation and dendritic spike forward propagation at sub-millisecond temporal resolution in mouse brain slices. We also performed volumetric random-access scanning calcium imaging of spontaneous and visual stimulation-evoked activity in hundreds of neurons of the mouse visual cortex in vivo. These experiments demonstrate the subcellular and network-scale imaging capabilities of our system.

Asteroseismology of old open clusters with Kepler: direct estimate of the integrated red giant branch mass-loss in NGC 6791 and 6819

Abstract: Mass-loss of red giant branch (RGB) stars is still poorly determined, despite its crucial role in the chemical enrichment of galaxies. Thanks to the recent detection of solar-like oscillations in G–K giants in open clusters with Kepler, we can now directly determine stellar masses for a statistically significant sample of stars in the old open clusters NGC 6791 and 6819. The aim of this work is to constrain the integrated RGB mass-loss by comparing the average mass of stars in the red clump (RC) with that of stars in the low-luminosity portion of the RGB [i.e. stars with L L(RC)]. Stellar masses were determined by combining the available seismic parameters νmax and �ν with additional photometric constraints and with independent distance estimates. We measured the masses of 40 stars on the RGB and 19 in the RC of the old metal-rich cluster NGC 6791. We find that the difference between the average mass of RGB and RC stars is small, but significant [� M = 0.09 ± 0.03 (random) ±0.04 (systematic)

Electrically driven single-photon source at room temperature in diamond

Abstract: Researchers demonstrate single-photon generation by electrical excitation from a single neutral nitrogen–vacancy centre in a p–i–n diamond diode. The photon generation rate at room temperature was 4 × 104 photons s−1 for an injection current of 14 mA. The researchers also investigated the carrier recombination dynamics of the device.

Al13Fe4 as a low-cost alternative for palladium in heterogeneous hydrogenation

Abstract: Replacing noble metals in heterogeneous catalysts by low-cost and ubiquitous substitutes such as iron is highly desirable especially because it does not bear potential health risks. A low cost and environmentally benign intermetallic compound Al13Fe4 is now identified as an active and selective semi-hydrogenation catalyst, which could prove to be applicable to a wide range of heterogeneously catalysed reactions.

Observation of sequential Υ suppression in PbPb collisions

Abstract: The suppression of the individual Υ(nS) states in PbPb collisions with respect to their yields in pp data has been measured. The PbPb and pp data sets used in the analysis correspond to integrated luminosities of 150 μb^(-1) and 230 nb^(-1), respectively, collected in 2011 by the CMS experiment at the LHC, at a center-of-mass energy per nucleon pair of 2.76 TeV. The Υ(nS) yields are measured from the dimuon invariant mass spectra. The suppression of the Υ(nS) yields in PbPb relative to the yields in pp, scaled by the number of nucleon-nucleon collisions, R_(AA), is measured as a function of the collision centrality. Integrated over centrality, the R_(AA) values are 0.56±0.08(stat)±0.07(syst), 0.12±0.04(stat)±0.02(syst), and lower than 0.10 (at 95% confidence level), for the Υ(1S), Υ(2S), and Υ(3S) states, respectively. The results demonstrate the sequential suppression of the Υ(nS) states in PbPb collisions at LHC energies.

Jet momentum dependence of jet quenching in PbPb collisions at sNN=2.76 TeV

Abstract: Dijet production in PbPb collisions at a nucleon–nucleon center-of-mass energy of 276 TeV is studied with the CMS detector at the LHC A data sample corresponding to an integrated luminosity of 150 μb−1 is analyzed Jets are reconstructed using combined information from tracking and calorimetry, using the anti-kT algorithm with R=03 The dijet momentum balance and angular correlations are studied as a function of collision centrality and leading jet transverse momentum For the most peripheral PbPb collisions, good agreement of the dijet momentum balance distributions with pp data and reference calculations at the same collision energy is found, while more central collisions show a strong imbalance of leading and subleading jet transverse momenta attributed to the jet-quenching effect The dijets in central collisions are found to be more unbalanced than the reference, for leading jet transverse momenta up to the highest values studied

Synaptic amplification by dendritic spines enhances input cooperativity

Abstract: Dendritic spines are the nearly ubiquitous site of excitatory synaptic input onto neurons and as such are critically positioned to influence diverse aspects of neuronal signalling. Decades of theoretical studies have proposed that spines may function as highly effective and modifiable chemical and electrical compartments that regulate synaptic efficacy, integration and plasticity. Experimental studies have confirmed activity-dependent structural dynamics and biochemical compartmentalization by spines. However, there is a longstanding debate over the influence of spines on the electrical aspects of synaptic transmission and dendritic operation. Here we measure the amplitude ratio of spine head to parent dendrite voltage across a range of dendritic compartments and calculate the associated spine neck resistance (R(neck)) for spines at apical trunk dendrites in rat hippocampal CA1 pyramidal neurons. We find that R(neck) is large enough (~500 MΩ) to amplify substantially the spine head depolarization associated with a unitary synaptic input by ~1.5- to ~45-fold, depending on parent dendritic impedance. A morphologically realistic compartmental model capable of reproducing the observed spatial profile of the amplitude ratio indicates that spines provide a consistently high-impedance input structure throughout the dendritic arborization. Finally, we demonstrate that the amplification produced by spines encourages electrical interaction among coactive inputs through an R(neck)-dependent increase in spine head voltage-gated conductance activation. We conclude that the electrical properties of spines promote nonlinear dendritic processing and associated forms of plasticity and storage, thus fundamentally enhancing the computational capabilities of neurons.

Measurement of the inclusive W± and Z/γ∗ cross sections in the e and μ decay channels in pp collisions at √s=7TeV with the ATLAS detector

Abstract: The production cross sections of the inclusive Drell-Yan processes W-+/- -> l nu and Z/gamma* -> ll (l = e, mu) are measured in proton-proton collisions at root s = 7 TeV with the ATLAS detector. The cross sections are reported integrated over a fiducial kinematic range, extrapolated to the full range, and also evaluated differentially as a function of the W decay lepton pseudorapidity and the Z boson rapidity, respectively. Based on an integrated luminosity of about 35 pb(-1) collected in 2010, the precision of these measurements reaches a few percent. The integrated and the differential W-+/- and Z/gamma* cross sections in the e and mu channels are combined, and compared with perturbative QCD calculations, based on a number of different parton distribution sets available at next-to-next-to-leading order.

Geochemistry of Ocean Floor and Fore-arc Serpentinites: Constraints on the Ultramafic Input to Subduction Zones

Abstract: Free to read at publisher's site. We provide new insights into the geochemistry of serpentinites from mid-ocean ridges (Mid-Atlantic Ridge and Hess Deep), passive margins (Iberia Abyssal Plain and Newfoundland) and fore-arcs (Mariana and Guatemala) based on bulk-rock and in situ mineral major and trace element compositional data collected on drill cores from the Deep Sea Drilling Project and Ocean Drilling Program. These data are important for constraining the serpentinite-hosted trace element inventory of subduction zones. Bulk serpentinites show up to several orders of magnitude enrichments in Cl, B, Sr, U, Sb, Pb, Rb, Cs and Li relative to elements of similar compatibility during mantle melting, which correspond to the highest primitive mantle-normalized B/Nb, B/Th, U/Th, Sb/Ce, Sr/Nd and Li/Y among subducted lithologies of the oceanic lithosphere (serpentinites, sediments and altered igneous oceanic crust). Among the elements showing relative enrichment, Cl and B are by far the most abundant with bulk concentrations mostly above 1000 mu g g(-1) and 30 mu g g(-1), respectively. All other trace elements showing relative enrichments are generally present in low concentrations (mu g g(-1) level), except Sr in carbonate-bearing serpentinites (thousands of mu g g(-1)). In situ data indicate that concentrations of Cl, B, Sr, U, Sb, Rb and Cs are, and that of Li can be, increased by serpentinization. These elements are largely hosted in serpentine (lizardite and chrysotile, but not antigorite). Aragonite precipitation leads to significant enrichments in Sr, U and B, whereas calcite is important only as an Sr host. Commonly observed brucite is trace element-poor. The overall enrichment patterns are comparable among serpentinites from mid-ocean ridges, passive margins and fore-arcs, whereas the extents of enrichments are often specific to the geodynamic setting. Variability in relative trace element enrichments within a specific setting (and locality) can be several orders of magnitude. Mid-ocean ridge serpentinites often show pronounced bulk-rock U enrichment in addition to ubiquitous Cl, B and Sr enrichment. They also exhibit positive Eu anomalies on chondrite-normalized rare earth element plots. Passive margin serpentinites tend to have higher overall incompatible trace element contents than mid-ocean ridge and fore-arc serpentinites and show the highest B enrichment among all the studied serpentinites. Fore-arc serpentinites are characterized by low overall trace element contents and show the lowest Cl, but the highest Rb, Cs and Sr enrichments. Based on our data, subducted dehydrating serpentinites are likely to release fluids with high B/Nb, B/Th, U/Th, Sb/Ce and Sr/Nd, rendering them one of the potential sources of some of the characteristic trace element fingerprints of arc magmas (e.g. high B/Nb, high Sr/Nd, high Sb/Ce). However, although serpentinites are a substantial part of global subduction zone chemical cycling, owing to their low overall trace element contents (except for B and Cl) their geochemical imprint on arc magma sources (apart from addition of H2O, B and Cl) can be masked considerably by the trace element signal from subducted crustal components.

Dynamics of conflicts in Wikipedia.

Abstract: In this work we study the dynamical features of editorial wars in Wikipedia (WP). Based on our previously established algorithm, we build up samples of controversial and peaceful articles and analyze the temporal characteristics of the activity in these samples. On short time scales, we show that there is a clear correspondence between conflict and burstiness of activity patterns, and that memory effects play an important role in controversies. On long time scales, we identify three distinct developmental patterns for the overall behavior of the articles. We are able to distinguish cases eventually leading to consensus from those cases where a compromise is far from achievable. Finally, we analyze discussion networks and conclude that edit wars are mainly fought by few editors only.

Suppression of non-prompt J/ψ, prompt J/ψ, and Y(1S) in PbPb collisions at √s NN = 2.76 TeV

Abstract: Yields of prompt and non-prompt J/psi, as well as Y(1S) mesons, are measured by the CMS experiment via their dimuon decays in PbPb and pp collisions at sqrt(sNN) = 2.76 TeV for quarkonium rapidity |y|<2.4. Differential cross sections and nuclear modification factors are reported as functions of y and transverse momentum pt, as well as collision centrality. For prompt J/psi with relatively high pt (6.5