The convergence of a column generation algorithm can be improved in practice by using stabilization techniques. Smoothing and proximal methods based on penalizing the deviation from the incumbent ...dual solution have become standards of the domain. Interpreting column generation as cutting plane strategies in the dual problem, we analyze the mechanisms on which stabilization relies. In particular, the link is established between smoothing and in-out separation strategies to derive generic convergence properties. For penalty function methods as well as for smoothing, we describe proposals for parameter self-adjusting schemes. Such schemes make initial parameter tuning less of an issue as corrections are made dynamically. Such adjustments also allow us to adapt the parameters to the phase of the algorithm. We provide extensive test reports that validate our self-adjusting parameter scheme and highlight their performances. Our results also show that using smoothing in combination with a penalty function yields a cumulative effect on convergence speed-ups.
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DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Theoretical predictions for Bhabha scattering observables are presented including complete one-loop electroweak radiative corrections. Longitudinal polarization of the initial beams is taken into ...account. Numerical results for the asymmetry ALR and the relative correction δ are given for the set of future e+e− collider energies Ecm=250, 500, 1000 GeV with various polarization degrees.
The ratio of the elastic e(+)p to e(-)p scattering cross sections has been measured precisely, allowing the determination of the two-photon exchange contribution to these processes. This neglected ...contribution is believed to be the cause of the discrepancy between the Rosenbluth and polarization transfer methods of measuring the proton electromagnetic form factors. The experiment was performed at the VEPP-3 storage ring at beam energies of 1.6 and 1.0 GeV and at lepton scattering angles between 15° and 105°. The data obtained show evidence of a significant two-photon exchange effect. The results are compared with several theoretical predictions.
This paper presents high-precision theoretical predictions for s-channel e+e− → l−l+ scattering. The calculations are performed using the sanc system. They take into account complete one-loop ...electroweak radiative corrections as well as the longitudinal polarization of the initial beams. The reaction observables are obtained using the helicity amplitude method with taking into account the initial- and final-state fermion masses. Numerical results are given for the center-of-mass energy range √s = 250 – 1000 GeV with various degrees of polarization.
We propose a new experimental method to probe the photon parton distribution function inside the proton (photon PDF) at LHC energies. The method is based on the measurement of dilepton production ...from the γp→ℓ+ℓ−+X reaction in proton-lead collisions. These experimental conditions guarantee a clean environment, both in terms of reconstruction of the final state and in terms of possible background. We first calculate the cross sections for this process with collinear photon PDFs, where we identify the optimal choice of the scale, in analogy to deep inelastic scattering kinematics. We then perform calculations including the transverse-momentum dependence of the probed photon. Finally, we estimate rates of the process for the existing LHC data samples.
The global regulator CodY links nutrient availability to the regulation of virulence factor gene expression in
, including many genes whose products affect biofilm formation. Antithetical phenotypes ...of both biofilm deficiency and accumulation have been reported for
-null mutants; thus, the role of CodY in biofilm development remains unclear.
mutant cells of a strain producing a robust biofilm elaborate proaggregation surface-associated features not present on
mutant cells that do not produce a robust biofilm. Biochemical analysis of the clinical isolate SA564, which aggregates when deficient for CodY, revealed that these features are sensitive to nuclease treatment and are resistant to protease exposure. Genetic analyses revealed that disrupting
(the diacylglycerol transferase gene) in
mutant cells severely weakened aggregation, indicating a role for lipoproteins in the attachment of the biofilm matrix to the cell surface. An additional and critical role of IcaB in producing functional poly-
-acetylglucosamine (PIA) polysaccharide in extracellular DNA (eDNA)-dependent biofilm formation was shown. Moreover, overproducing PIA is sufficient to promote aggregation in a DNA-dependent manner regardless of source of nucleic acids. Taken together, our results point to PIA synthesis as the primary determinant of biofilm formation when CodY activity is reduced and suggest a modified electrostatic net model for matrix attachment whereby PIA associates with eDNA, which interacts with the cell surface via covalently attached membrane lipoproteins. This work counters the prevailing view that polysaccharide- and eDNA/protein-based biofilms are mutually exclusive. Rather, we demonstrate that eDNA and PIA can work synergistically to form a biofilm.
remains a global health concern and exemplifies the ability of an opportunistic pathogen to adapt and persist within multiple environments, including host tissue. Not only does biofilm contribute to persistence and immune evasion in the host environment, it also may aid in the transition to invasive disease. Thus, understanding how biofilms form is critical for developing strategies for dispersing biofilms and improving biofilm disease-related outcomes. Using biochemical, genetic, and cell biology approaches, we reveal a synergistic interaction between PIA and eDNA that promotes cell aggregation and biofilm formation in a CodY-dependent manner in
We also reveal that envelope-associated lipoproteins mediate attachment of the biofilm matrix to the cell surface.
subverts innate defenses during infection in part by killing host immune cells to exacerbate disease. This human pathogen intercepts host cues and activates a transcriptional response via the
...exoprotein expression (SaeR/SaeS SaeR/S) two-component system to secrete virulence factors critical for pathogenesis. We recently showed that the transcriptional repressor CodY adjusts nuclease (
) gene expression via SaeR/S, but the mechanism remained unknown. Here, we identified two CodY binding motifs upstream of the
P1 promoter, which suggested direct regulation by this global regulator. We show that CodY shares a binding site with the positive activator SaeR and that alleviating direct CodY repression at this site is sufficient to abrogate stochastic expression, suggesting that CodY represses
expression by blocking SaeR binding. Epistasis experiments support a model that CodY also controls
indirectly through Agr and Rot-mediated repression of the
P1 promoter. We also demonstrate that CodY repression of
restrains production of secreted cytotoxins that kill human neutrophils. We conclude that CodY plays a previously unrecognized role in controlling virulence gene expression via SaeR/S and suggest a mechanism by which CodY acts as a master regulator of pathogenesis by tying nutrient availability to virulence gene expression.
Bacterial mechanisms that mediate the switch from a commensal to pathogenic lifestyle are among the biggest unanswered questions in infectious disease research. Since the expression of most virulence genes is often correlated with nutrient depletion, this implies that virulence is a response to the lack of nourishment in host tissues and that pathogens like
produce virulence factors in order to gain access to nutrients in the host. Here, we show that specific nutrient depletion signals appear to be funneled to the SaeR/S system through the global regulator CodY. Our findings reveal a strategy by which
delays the production of immune evasion and immune-cell-killing proteins until key nutrients are depleted.
Staphylococcus aureus is a leading cause of community-associated and nosocomial infections. Imperative to the success of S. aureus is the ability to adapt and utilize nutrients that are readily ...available. Genomic sequencing suggests that S. aureus has the genes required for synthesis of all twenty amino acids. However, in vitro experimentation demonstrates that staphylococci have multiple amino acid auxotrophies, including arginine. Although S. aureus possesses the highly conserved anabolic pathway that synthesizes arginine via glutamate, we demonstrate here that inactivation of ccpA facilitates the synthesis of arginine via the urea cycle utilizing proline as a substrate. Mutations within putA, rocD, arcB1, argG and argH abolished the ability of S. aureus JE2 ccpA::tetL to grow in the absence of arginine, whereas an interruption in argJBCF, arcB2, or proC had no effect. Furthermore, nuclear magnetic resonance demonstrated that JE2 ccpA::ermB produced (13)C(5) labeled arginine when grown with (13)C(5) proline. Taken together, these data support the conclusion that S. aureus synthesizes arginine from proline during growth on secondary carbon sources. Furthermore, although highly conserved in all sequenced S. aureus genomes, the arginine anabolic pathway (ArgJBCDFGH) is not functional under in vitro growth conditions. Finally, a mutation in argH attenuated virulence in a mouse kidney abscess model in comparison to wild type JE2 demonstrating the importance of arginine biosynthesis in vivo via the urea cycle. However, mutations in argB, argF, and putA did not attenuate virulence suggesting both the glutamate and proline pathways are active and they, or their pathway intermediates, can complement each other in vivo.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
HERAFitter Alekhin, S.; Behnke, O.; Belov, P. ...
The European physical journal. C, Particles and fields,
07/2015, Letnik:
75, Številka:
7
Journal Article
Recenzirano
Odprti dostop
HERAFitter is an open-source package that provides a framework for the determination of the parton distribution functions (PDFs) of the proton and for many different kinds of analyses in Quantum ...Chromodynamics (QCD). It encodes results from a wide range of experimental measurements in lepton–proton deep inelastic scattering and proton–proton (proton–antiproton) collisions at hadron colliders. These are complemented with a variety of theoretical options for calculating PDF-dependent cross section predictions corresponding to the measurements. The framework covers a large number of the existing methods and schemes used for PDF determination. The data and theoretical predictions are brought together through numerous methodological options for carrying out PDF fits and plotting tools to help to visualise the results. While primarily based on the approach of collinear factorisation, HERAFitter also provides facilities for fits of dipole models and transverse-momentum dependent PDFs. The package can be used to study the impact of new precise measurements from hadron colliders. This paper describes the general structure of HERAFitter and its wide choice of options.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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