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Search Results: 1 - 10 of 200683 matches for " P. Barta "
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Forgetting the starting distribution in finite interacting tempering
Winfried Barta
Mathematics , 2014,
Abstract: Markov chain Monte Carlo (MCMC) methods are frequently used to approximately simulate high-dimensional, multimodal probability distributions. In adaptive MCMC methods, the transition kernel is changed "on the fly" in the hope to speed up convergence. We study interacting tempering, an adaptive MCMC algorithm based on interacting Markov chains, that can be seen as a simplified version of the equi-energy sampler. Using a coupling argument, we show that under easy to verify assumptions on the target distribution (on a finite space), the interacting tempering process rapidly forgets its starting distribution. The result applies, among others, to exponential random graph models, the Ising and Potts models (in mean field or on a bounded degree graph), as well as (Edwards-Anderson) Ising spin glasses. As a cautionary note, we also exhibit an example of a target distribution for which the interacting tempering process rapidly forgets its starting distribution, but takes an exponential number of steps (in the dimension of the state space) to converge to its limiting distribution. As a consequence, we argue that convergence diagnostics that are based on demonstrating that the process has forgotten its starting distribution might be of limited use for adaptive MCMC algorithms like interacting tempering.
A probabilistic proof of cutoff in the Metropolis algorithm for the Erd?s-Rényi random graph
Winfried Barta
Mathematics , 2011,
Abstract: We study mixing of the Metropolis algorithm for a distribution on the hypercube that corresponds to the Erd\H{o}s-R\'enyi random graph with edge probability p. This Markov chain has cutoff at max{p,1-p} n log n with window size n, a result proved by Diaconis and Ram (2000) using Fourier analysis. Here we give an alternative proof that relies on coupling and a projection to a two-dimensional Markov chain. This is done in the hope that probabilistic techniques will be easier to generalize to less symmetric distributions. We also describe a close relationship between the Metropolis and Gibbs samplers for this model. Our proof extends to the case where the edge probabilities vary with n. In that case, we also show that a natural coordinate wise coupling is sharp if and only if the edge probabilities are of order 1/n.
A Link-based Approach to Entity Resolution in Social Networks
Gergo Barta
Computer Science , 2014, DOI: 10.5121/csit.2014.4409
Abstract: Social networks initially had been places for people to contact each other, find friends or new acquaintances. As such they ever proved interesting for machine aided analysis. Recent developments, however, pivoted social networks to being among the main fields of information exchange, opinion expression and debate. As a result there is growing interest in both analyzing and integrating social network services. In this environment efficient information retrieval is hindered by the vast amount and varying quality of the user-generated content. Guiding users to relevant information is a valuable service and also a difficult task, where a crucial part of the process is accurately resolving duplicate entities to real-world ones. In this paper we propose a novel approach that utilizes the principles of link mining to successfully extend the methodology of entity resolution to multitype problems. The proposed method is presented using an illustrative social network-based real-world example and validated by comprehensive evaluation of the results.
Contribution of Radiocarbon Dating to the Chronology of Eneolithic in Campania (Italy)
I. Passariello, P. Talamo, A. D'Onofrio, P. Barta, C. Lubritto, F. Terrasi
Geochronometria , 2010, DOI: 10.2478/v10003-010-0008-2
Abstract: The paper presents new and important 14C data from eight Eneolithic sites in Campania measured at the Centre for Isotopic Research of Cultural and Environmental Heritage (CIRCE) AMS laboratory in Caserta (Italy). Twenty-four 14C determinations on bone and charcoal are used here for chronological reconstruction of human habitation and dating of some volcanic eruptions affecting the settlement activity. Our research has shed new light on absolute chronology of the whole Campanian Eneolithic, a period of profound cultural transformations triggered by introduction and use of metals, in particular copper.
Haste Makes Waste: Accelerated Molt Adversely Affects the Expression of Melanin-Based and Depigmented Plumage Ornaments in House Sparrows
Csongor I. Vágási,Péter L. Pap,Zoltán Barta
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0014215
Abstract: Many animals display colorful signals in their integument which convey information about the quality of their bearer. Theoretically, these ornaments incur differential production and/or maintenance costs that enforce their honesty. However, the proximate mechanisms of production costs are poorly understood and contentious in cases of non-carotenoid-based plumage ornaments like the melanin-based badge and depigmented white wing-bar in house sparrows Passer domesticus. Costly life-history events are adaptively separated in time, thus, when reproduction is extended, the time available for molt is curtailed and, in turn, molt rate is accelerated.
Atypical Response Regulator ChxR from Chlamydia trachomatis Is Structurally Poised for DNA Binding
Michael L. Barta, John M. Hickey, Asokan Anbanandam, Kevin Dyer, Michal Hammel, P. Scott Hefty
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0091760
Abstract: ChxR is an atypical two-component signal transduction response regulator (RR) of the OmpR/PhoB subfamily encoded by the obligate intracellular bacterial pathogen Chlamydia trachomatis. Despite structural homology within both receiver and effector domains to prototypical subfamily members, ChxR does not require phosphorylation for dimer formation, DNA binding or transcriptional activation. Thus, we hypothesized that ChxR is in a conformation optimal for DNA binding with limited interdomain interactions. To address this hypothesis, the NMR solution structure of the ChxR effector domain was determined and used in combination with the previously reported ChxR receiver domain structure to generate a full-length dimer model based upon SAXS analysis. Small-angle scattering of ChxR supported a dimer with minimal interdomain interactions and effector domains in a conformation that appears to require only subtle reorientation for optimal major/minor groove DNA interactions. SAXS modeling also supported that the effector domains were in a head-to-tail conformation, consistent with ChxR recognizing tandem DNA repeats. The effector domain structure was leveraged to identify key residues that were critical for maintaining protein - nucleic acid interactions. In combination with prior analysis of the essential location of specific nucleotides for ChxR recognition of DNA, a model of the full-length ChxR dimer bound to its cognate cis-acting element was generated.
The Regionalisation of Natural Risks in the Some ul Mare Hills
Romanian Review of Regional Studies , 2006,
Abstract: The significance of studying natural risks derives from the human society’s necessity to live safely. This approach is at its best if the analysis is undertaken at a micro-scale, i.e. through regionalisation, which supposes the complex treatment of all its environmental components and the study of all the phenomena taking place in it. Most of the risk phenomena result from the interaction of many factors, each of them with different and specific laws, and evolution trends. The regionalisation of risks is necessary as it leads to highlighting the phenomena on certain risk-friendly areas. Because of the complexity of the natural and the anthropic factors, the Some ul Mare Hills are a favourable environment for the evolution of the geographic risk phenomena; hence the necessity of the regional analysis of those phenomena.
LSFEM implementation of MHD numerical solver
Jan Skala,Miroslav Barta
Physics , 2012,
Abstract: Many problems in physics are inherently of multi-scale nature. The issues of MHD turbulence or magnetic reconnection, namely in the hot and sparse, almost collision-less astrophysical plasmas, can stand as clear examples. The Finite Element Method (FEM) with adaptive gridding appears to be the appropriate numerical implementation for handling the broad range of scales contained in such high Lundquist-number MHD problems. In spite the FEM is now routinely used in engineering practice in solid-state and fluid dynamics, its usage for MHD simulations has recently only begun and only few implementations exist so far. In this paper we present our MHD solver based on the Least-Square FEM (LSFEM) formulation. We describe the transformation of the MHD equations into form required for finding the LSFEM functional and some practical issues in implementation of the method. The algorithm was tested on selected problems of ideal (non-resistive) and resistive MHD. The tests show the usability of LSFEM for solving MHD equations.
Haste Makes Waste but Condition Matters: Molt Rate–Feather Quality Trade-Off in a Sedentary Songbird
Csongor I. Vágási, Péter L. Pap, Orsolya Vincze, Zoltán Benk?, Attila Marton, Zoltán Barta
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0040651
Abstract: Background The trade-off between current and residual reproductive values is central to life history theory, although the possible mechanisms underlying this trade-off are largely unknown. The ‘molt constraint’ hypothesis suggests that molt and plumage functionality are compromised by the preceding breeding event, yet this candidate mechanism remains insufficiently explored. Methodology/Principal Findings The seasonal change in photoperiod was manipulated to accelerate the molt rate. This treatment simulates the case of naturally late-breeding birds. House sparrows Passer domesticus experiencing accelerated molt developed shorter flight feathers with more fault bars and body feathers with supposedly lower insulation capacity (i.e. shorter, smaller, with a higher barbule density and fewer plumulaceous barbs). However, the wing, tail and primary feather lengths were shorter in fast-molting birds if they had an inferior body condition, which has been largely overlooked in previous studies. The rachis width of flight feathers was not affected by the treatment, but it was still condition-dependent. Conclusions/Significance This study shows that sedentary birds might face evolutionary costs because of the molt rate–feather quality conflict. This is the first study to experimentally demonstrate that (1) molt rate affects several aspects of body feathers as well as flight feathers and (2) the costly effects of rapid molt are condition-specific. We conclude that molt rate and its association with feather quality might be a major mediator of life history trade-offs. Our findings also suggest a novel advantage of early breeding, i.e. the facilitation of slower molt and the condition-dependent regulation of feather growth.
Role of Cajal Bodies and Nucleolus in the Maturation of the U1 snRNP in Arabidopsis
Zdravko J. Lorkovi?, Andrea Barta
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003989
Abstract: Background The biogenesis of spliceosomal snRNPs takes place in both the cytoplasm where Sm core proteins are added and snRNAs are modified at the 5′ and 3′ termini and in the nucleus where snRNP-specific proteins associate. U1 snRNP consists of U1 snRNA, seven Sm proteins and three snRNP-specific proteins, U1-70K, U1A, and U1C. It has been shown previously that after import to the nucleus U2 and U4/U6 snRNP-specific proteins first appear in Cajal bodies (CB) and then in splicing speckles. In addition, in cells grown under normal conditions U2, U4, U5, and U6 snRNAs/snRNPs are abundant in CBs. Therefore, it has been proposed that the final assembly of these spliceosomal snRNPs takes place in this nuclear compartment. In contrast, U1 snRNA in both animal and plant cells has rarely been found in this nuclear compartment. Methodology/Principal Findings Here, we analysed the subnuclear distribution of Arabidopsis U1 snRNP-specific proteins fused to GFP or mRFP in transiently transformed Arabidopsis protoplasts. Irrespective of the tag used, U1-70K was exclusively found in the nucleus, whereas U1A and U1C were equally distributed between the nucleus and the cytoplasm. In the nucleus all three proteins localised to CBs and nucleoli although to different extent. Interestingly, we also found that the appearance of the three proteins in nuclear speckles differ significantly. U1-70K was mostly found in speckles whereas U1A and U1C in ~90% of cells showed diffuse nucleoplasmic in combination with CBs and nucleolar localisation. Conclusions/Significance Our data indicate that CBs and nucleolus are involved in the maturation of U1 snRNP. Differences in nuclear accumulation and distribution between U1-70K and U1A and U1C proteins may indicate that either U1-70K or U1A and U1C associate with, or is/are involved, in other nuclear processes apart from pre-mRNA splicing.
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