The Chern-Simons diffusion rate in strongly coupled N=4 SYM plasma in an external magnetic field

We calculate the Chern-Simons diffusion rate in a strongly coupled N=4 SUSY Yang-Mills plasma in the presence of a constant external $U(1)_R$ magnetic flux via the holographic correspondence. Due to the strong interactions between the charged fields and non-Abelian gauge fields, the external Abelian magnetic field affects the thermal Yang-Mills dynamics and increases the diffusion rate, regardless of its strength. We obtain the analytic results for the Chern-Simons diffusion rate both in the weak and strong magnetic field limits. In the latter limit, we show that the diffusion rate scales as $B\times T^2$ and this can be understood as a result of a dynamical dimensional reduction.Comment: 10 pages, 1 figure, typos corrected, comments adde

Dynamics of the Chiral Magnetic Effect in a weak magnetic field

We investigate the real-time dynamics of the chiral magnetic effect in quantum electrodynamics (QED) and quantum chromodynamics (QCD). We consider a field configuration of parallel (chromo)electric and (chromo)magnetic fields with a weak perpendicular electromagnetic magnetic field. The chiral magnetic effect induces an electromagnetic current along this perpendicular magnetic field, which we will compute using linear response theory. We discuss specific results for a homogeneous sudden switch-on and a pulsed (chromo)electric field in a static and homogeneous (chromo)magnetic field. Our methodology can be easily extended to more general situations. The results are useful for investigating the chiral magnetic effect with heavy ion collisions and with lasers that create strong electromagnetic fields. As a side result we obtain the rate of chirality production for massive fermions in parallel electric and magnetic fields that are static and homogeneous.Comment: 13 pages, 7 figures, revte

Chiral Magnetic Effect on the Lattice

We review recent progress on the lattice simulations of the chiral magnetic effect. There are two different approaches to analyze the chiral magnetic effect on the lattice. In one approach, the charge density distribution or the current fluctuation is measured under a topological background of the gluon field. In the other approach, the topological effect is mimicked by the chiral chemical potential, and the induced current is directly measured. Both approaches are now developing toward the exact analysis of the chiral magnetic effect.Comment: to appear in Lect. Notes Phys. "Strongly interacting matter in magnetic fields" (Springer), edited by D. Kharzeev, K. Landsteiner, A. Schmitt, H.-U. Ye

Murine factor H co-produced in yeast with protein disulfide isomerase ameliorated C3 dysregulation in factor H-Deficient mice

Recombinant human factor H (hFH) has potential for treating diseases linked to aberrant complement regulation including C3 glomerulopathy (C3G) and dry age-related macular degeneration. Murine FH (mFH), produced in the same host, is useful for pre-clinical investigations in mouse models of disease. An abundance of FH in plasma suggests high doses, and hence microbial production, will be needed. Previously, Pichia pastoris produced useful but modest quantities of hFH. Herein, a similar strategy yielded miniscule quantities of mFH. Since FH has 40 disulfide bonds, we created a P. pastoris strain containing a methanol-inducible codon-modified gene for protein-disulfide isomerase (PDI) and transformed this with codon-modified DNA encoding mFH under the same promoter. What had been barely detectable yields of mFH became multiple 10s of mg/L. Our PDI-overexpressing strain also boosted hFH overproduction, by about tenfold. These enhancements exceeded PDI-related production gains reported for other proteins, all of which contain fewer disulfide-stabilized domains. We optimized fermentation conditions, purified recombinant mFH, enzymatically trimmed down its (non-human) N-glycans, characterised its functions in vitro and administered it to mice. In FH-knockout mice, our de-glycosylated recombinant mFH had a shorter half-life and induced more anti-mFH antibodies than mouse serum-derived, natively glycosylated, mFH. Even sequential daily injections of recombinant mFH failed to restore wild-type levels of FH and C3 in mouse plasma beyond 24 hours after the first injection. Nevertheless, mFH functionality appeared to persist in the glomerular basement membrane because C3-fragment deposition here, a hallmark of C3G, remained significantly reduced throughout and beyond the ten-day dosing regimen

A three-dimensional discriminant analysis approach for hyperspectral images

Raman hyperspectral imaging is a powerful technique that provides both chemical and spatial information of a sample matrix being studied. The generated data are composed of three-dimensional (3D) arrays containing the spatial information across the x- and y-axis, and the spectral information in the z-axis. Unfolding procedures are commonly employed to analyze this type of data in a multivariate fashion, where the spatial dimension is reshaped and the spectral data fits into a two-dimensional (2D) structure and, thereafter, common first-order chemometric algorithms are applied to process the data. There are only a few algorithms capable of working with the full 3D array. Herein, we propose new algorithms for 3D discriminant analysis of hyperspectral images based on a three-dimensional principal component analysis linear discriminant analysis (3D-PCA-LDA) and a three-dimensional discriminant analysis quadratic discriminant analysis (3D-PCA-QDA) approach. The analysis was performed in order to discriminate simulated and real-world data, comprising benign controls and ovarian cancer samples based on Raman hyperspectral imaging, in which 3D-PCA-LDA and 3D-PCA-QDA achieved far superior performance than classical algorithms using unfolding procedures (PCA-LDA, PCA-QDA, partial lest squares discriminant analysis [PLS-DA], and support vector machines [SVM]), where the classification accuracies improved from 66% to 83% (simulated data) and from 50% to 100% (real-world dataset) after employing the 3D techniques. 3D-PCA-LDA and 3D-PCA-QDA are new approaches for discriminant analysis of hyperspectral images multisets to provide faster and superior classification performance than traditional techniques

Lattice QCD Simulations in External Background Fields

We discuss recent results and future prospects regarding the investigation, by lattice simulations, of the non-perturbative properties of QCD and of its phase diagram in presence of magnetic or chromomagnetic background fields. After a brief introduction to the formulation of lattice QCD in presence of external fields, we focus on studies regarding the effects of external fields on chiral symmetry breaking, on its restoration at finite temperature and on deconfinement. We conclude with a few comments regarding the effects of electromagnetic background fields on gluodynamics.Comment: 31 pages, 10 figures, minor changes and references added. To appear in Lect. Notes Phys. "Strongly interacting matter in magnetic fields" (Springer), edited by D. Kharzeev, K. Landsteiner, A. Schmitt, H.-U. Ye

Myosin-5, kinesin-1 and myosin-17 cooperate in secretion of fungal chitin synthase

The interactions between cytoskeletal motors are here explored in the context of polarized secretion in fungi, revealing unexpected complexity in the regulation of vesicle transport to and docking at the hyphal tip

Ammoniated electron as a solvent stabilized multimer radical anion

The excess electron in liquid ammonia ("ammoniated electron") is commonly viewed as a cavity electron in which the s-type wave function fills the interstitial void between 6-9 ammonia molecules. Here we examine an alternative model in which the ammoniated electron is regarded as a solvent stabilized multimer radical anion, as was originally suggested by Symons [Chem. Soc. Rev. 1976, 5, 337]. In this model, most of the excess electron density resides in the frontier orbitals of N atoms in the ammonia molecules forming the solvation cavity; a fraction of this spin density is transferred to the molecules in the second solvation shell. The cavity is formed due to the repulsion between negatively charged solvent molecules. Using density functional theory calculations for small ammonia cluster anions in the gas phase, it is demonstrated that such core anions would semi-quantitatively account for the observed pattern of Knight shifts for 1-H and 14-N nuclei observed by NMR spectroscopy and the downshifted stretching and bending modes observed by infrared spectroscopy. It is speculated that the excess electrons in other aprotic solvents (but not in water and alcohols) might be, in this respect, analogous to the ammoniated electron, with substantial transfer of the spin density into the frontier N and C orbitals of methyl, amino, and amide groups forming the solvation cavity.Comment: 34 pages, 12 figures; to be submitted to J Phys Chem

MetWAMer: eukaryotic translation initiation site prediction

<p>Abstract</p> <p>Background</p> <p>Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations.</p> <p>Results</p> <p>MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the <it>k</it>-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage.</p> <p>Conclusion</p> <p>We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.</p

The Chiral MagnetoHydroDynamics of QCD fluid at RHIC and LHC

The experimental results on heavy ion collisions at RHIC and LHC indicate that QCD plasma behaves as a nearly perfect fluid described by relativistic hydrodynamics. Hydrodynamics is an effective low-energy Theory Of Everything stating that the response of a system to external perturbations is dictated by conservation laws that are a consequence of the symmetries of the underlying theory. In the case of QCD fluid produced in heavy ion collisions, this theory possesses anomalies, so some of the apparent classical symmetries are broken by quantum effects. Even though the anomalies appear as a result of UV regularization and so look like a short distance phenomenon, it has been realized recently that they also affect the large distance, macroscopic behavior in hydrodynamics. One of the manifestations of anomalies in relativistic hydrodynamics is the Chiral Magnetic Effect (CME). At this conference, a number of evidences for CME have been presented, including i) the disappearance of charge asymmetry fluctuations in the low-energy RHIC data where the energy density is thought to be below the critical one for deconfinement; ii) the observation of charge asymmetry fluctuations in Pb-Pb collisions at the LHC. Here I give a three-page summary of some of the recent theoretical and experimental developments and of the future tests that may allow to establish (or to refute) the CME as the origin of the observed charge asymmetry fluctuations.Comment: 4 pages, talk at Quark Matter 2011 Conference, Annecy, France, 23-28 May 201