Confined Phase In The Real Time Formalism And The Fate Of The World Behind The Horizon

In the real time formulation of finite temperature field theories, one introduces an additional set of fields (type-2 fields) associated to each field in the original theory (type-1 field). In hep-th/0106112, in the context of the AdS-CFT correspondence, Maldacena interpreted type-2 fields as living on a boundary behind the black hole horizon. However, below the Hawking-Page transition temperature, the thermodynamically preferred configuration is the thermal AdS without a black hole, and hence there are no horizon and boundary behind it. This means that when the dual gauge theory is in confined phase, the type-2 fields cannot be associated with the degrees of freedom behind the black hole horizon. I argue that in this case the role of the type-2 fields is to make up bulk type-2 fields of classical closed string field theory on AdS at finite temperature in the real time formalism.Comment: v2: cases divided into sections with more detailed explanations. considerably enlarged with examples and a lot of figures. sec 4.1.2 for general closed cut-out circuits and appendix A for a sample calculation newly added. many minor corrections and clarifying comments. refs added. v3: refs and related discussion added. 1+46 pages, 26 figures. published versio

Finite size spectrum, magnon interactions and magnetization of S=1 Heisenberg spin chains

We report our density matrix renormalization-group and analytical work on S=1 antiferromagnetic Heisenberg spin chains. We study the finite size behavior within the framework of the non-linear sigma model. We study the effect of magnon-magnon interactions on the finite size spectrum and on the magnetization curve close to the critical magnetic field, determine the magnon scattering length and compare it to the prediction from the non-linear $\sigma$ model.Comment: 28 pages, 8 figures, made substantial improvement

The Degenerate Parametric Oscillator and Ince's Equation

We construct Green's function for the quantum degenerate parametric oscillator in terms of standard solutions of Ince's equation in a framework of a general approach to harmonic oscillators. Exact time-dependent wave functions and their connections with dynamical invariants and SU(1,1) group are also discussed.Comment: 10 pages, no figure

An initial event in insect innate immune response: structural and biological studies of interactions between β-1,3-glucan and the N-terminal domain of β-1,3-glucan recognition protein

In response to invading microorganisms, insect β-1,3-glucan recognition protein (βGRP), a soluble receptor in the hemolymph, binds to the surfaces of bacteria and fungi and activates serine protease cascades that promote destruction of pathogens by means of melanization or expression of antimicrobial peptides. Here we report on the NMR solution structure of the N-terminal domain of βGRP (N-βGRP) from Indian meal moth (Plodia interpunctella), which is sufficient to activate the prophenoloxidase (proPO) pathway resulting in melanin formation. NMR and isothermal calorimetric titrations of N-βGRP with laminarihexaose, a glucose hexamer containing β-1,3 links, suggest a weak binding of the ligand. However, addition of laminarin, a glucose polysaccharide (~ 6 kDa) containing β-1,3 and β-1,6 links that activates the proPO pathway, to N-βGRP results in the loss of NMR cross-peaks from the backbone 15N-1H groups of the protein, suggesting the formation of a large complex. Analytical ultra centrifugation (AUC) studies of formation of N-βGRP:laminarin complex show that ligand-binding induces sel-fassociation of the protein:carbohydrate complex into a macro structure, likely containing six protein and three laminarin molecules (~ 102 kDa). The macro complex is quite stable, as it does not undergo dissociation upon dilution to sub-micromolar concentrations. The structural model thus derived from the present studies for N-βGRP:laminarin complex in solution differs from the one in which a single N-βGRP molecule has been proposed to bind to a triple helical form of laminarin on the basis of an X-ray crystallographic structure of N-βGRP:laminarihexaose complex [Kanagawa, M., Satoh, T., Ikeda, A., Adachi, Y., Ohno, N., and Yamaguchi, Y. (2011) J. Biol. Chem. 286, 29158-29165]. AUC studies and phenoloxidase activation measurements carried out with the designed mutants of N-βGRP indicate that electrostatic interactions involving Asp45, Arg54, and Asp68 between the ligand-bound protein molecules contribute in part to the stability of N-βGRP:laminarin macro complex and that a decreased stability is accompanied by a reduced activation of the proPO pathway. Increased β-1,6 branching in laminarin also results in destabilization of the macro complex. These novel findings suggest that ligand-induced self-association of βGRP:β-1,3-glucan complex may form a platform on a microbial surface for recruitment of downstream proteases, as a means of amplification of the initial signal of pathogen recognition for the activation of the proPO pathway

Advances in perturbative thermal field theory

The progress of the last decade in perturbative quantum field theory at high temperature and density made possible by the use of effective field theories and hard-thermal/dense-loop resummations in ultrarelativistic gauge theories is reviewed. The relevant methods are discussed in field theoretical models from simple scalar theories to non-Abelian gauge theories including gravity. In the simpler models, the aim is to give a pedagogical account of some of the relevant problems and their resolution, while in the more complicated but also more interesting models such as quantum chromodynamics, a summary of the results obtained so far are given together with references to a few most recent developments and open problems.Comment: 84 pages, 18 figues, review article submitted to Reports on Progress in Physics; v2, v3: minor additions and corrections, more reference

Innate Immune Suppression Enables Frequent Transfection with RNA Encoding Reprogramming Proteins

BACKGROUND: Generating autologous pluripotent stem cells for therapeutic applications will require the development of efficient DNA-free reprogramming techniques. Transfecting cells with in vitro-transcribed, protein-encoding RNA is a straightforward method of directly expressing high levels of reprogramming proteins without genetic modification. However, long-RNA transfection triggers a potent innate immune response characterized by growth inhibition and the production of inflammatory cytokines. As a result, repeated transfection with protein-encoding RNA causes cell death. METHODOLOGY/PRINCIPAL FINDINGS: RNA viruses have evolved methods of disrupting innate immune signaling by destroying or inhibiting specific proteins to enable persistent infection. Starting from a list of known viral targets, we performed a combinatorial screen to identify siRNA cocktails that could desensitize cells to exogenous RNA. We show that combined knockdown of interferon-beta (Ifnb1), Eif2ak2, and Stat2 rescues cells from the innate immune response triggered by frequent long-RNA transfection. Using this technique, we were able to transfect primary human fibroblasts every 24 hours with RNA encoding the reprogramming proteins Oct4, Sox2, Klf4, and Utf1. We provide evidence that the encoded protein is active, and we show that expression can be maintained for many days, through multiple rounds of cell division. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that suppressing innate immunity enables frequent transfection with protein-encoding RNA. This technique represents a versatile tool for investigating expression dynamics and protein interactions by enabling precise control over levels and timing of protein expression. Our finding also opens the door for the development of reprogramming and directed-differentiation methods based on long-RNA transfection

Thermally Responsive Amphiphilic Conetworks and Gels Based on Poly(N‑isopropylacrylamide) and Polyisobutylene

Novel amphiphilic conetworks (APCN) consisting of thermoresponsive poly(N-isoproplyacrylamide) (PNiPAAm) cross-linked by hydrophobic methacrylate-telechelic polyisobutylene (MA-PIB-MA) were successfully synthesized in a broad composition range. The resulting PNiPAAm-l-PIB conetworks (“l” stands for “linked by”) were obtained by radical copolymerization of NiPAAm with MA-PIB-MA in tetrahydrofuran, a cosolvent for all the components. Low amounts of extractables substantiated efficient network formation. The composition dependent two glass transition temperatures (Tg) by DSC analysis indicate microphase separation of the cross-linked components without mixed phases. It was found that the PNiPAAm-l-PIB conetworks are uniformly swellable in both water and n-hexane; i.e., these new materials behave either as hydrogels or as hydrophobic gels in aqueous or nonpolar media, respectively. The uniform swelling in both polar and nonpolar solutes indicates cocontinuous (bicontinuous) phase morphology. The equilibrium swelling degrees (R) depend on composition, that is, the higher the PIB content, the lower the R in water and the higher in n-hexane. The PNiPAAm phase keeps its thermoresponsive behavior in the conetworks as shown by significant decrease of the swelling degree in water between 20 and 35 °C. The lower critical solubility temperature (LCST) values determined by DSC are found to decrease from 34.1 °C (for the pure PNiPAAm homopolymer) to the range of 25–28 °C in the conetworks, and the extent of the LCST decrease is proportional with the PIB content. Deswelling-swelling, i.e., heating–cooling, cycle indicates insignificant hysteresis in these new thermoresponsive materials. This indicates that PNiPAAm-l-PIB conetworks with predetermined and thermoresponsive swelling behavior can be designed and utilized in several advanced applications on the basis of results obtained in the course of this study

Brain type carnosinase in dementia: a pilot study

Research articl

Correlated Evolution of Nearby Residues in Drosophilid Proteins

Here we investigate the correlations between coding sequence substitutions as a function of their separation along the protein sequence. We consider both substitutions between the reference genomes of several Drosophilids as well as polymorphisms in a population sample of Zimbabwean Drosophila melanogaster. We find that amino acid substitutions are “clustered” along the protein sequence, that is, the frequency of additional substitutions is strongly enhanced within ≈10 residues of a first such substitution. No such clustering is observed for synonymous substitutions, supporting a “correlation length” associated with selection on proteins as the causative mechanism. Clustering is stronger between substitutions that arose in the same lineage than it is between substitutions that arose in different lineages. We consider several possible origins of clustering, concluding that epistasis (interactions between amino acids within a protein that affect function) and positional heterogeneity in the strength of purifying selection are primarily responsible. The role of epistasis is directly supported by the tendency of nearby substitutions that arose on the same lineage to preserve the total charge of the residues within the correlation length and by the preferential cosegregation of neighboring derived alleles in our population sample. We interpret the observed length scale of clustering as a statistical reflection of the functional locality (or modularity) of proteins: amino acids that are near each other on the protein backbone are more likely to contribute to, and collaborate toward, a common subfunction