Open string derivation of winding states in thermal noncommutative field theories

The `winding state' behavior appears in the two-loop nonplanar contribution to the partition function in thermal noncommutative field theories. We derive this feature directly from the purely open string theory analysis in the presence of the constant background $B$-field; we compute the two-loop partition function for worldsheets with a handle and a boundary when the time direction of the Euclideanized target space is compactified. In contrast to the closed-string-inspired approach, it is not necessary to add infinite number of extra degrees of freedom. Furthermore, we find a piece of supporting evidence toward the conjecture that, in the UV limit, the noncommutativity parameter plays the role of the effective string scale in noncommutative field theories.Comment: 12 pages, late

Role of filaggrin in skin barrier function and atopic dermatitis

Loss-­of-­function mutations in the filaggrin gene(FLG) have recently been shown to be strongly associated with atopic dermatitis (AD). The overall aim of this study was to explore the role of filaggrin in skin barrier function and AD. There were two main focuses in this study. The first was a functional study whose primary objective was to determine if FLG mutations correlated with skin barrier dysfunction in AD. Fifty-­five mild to moderate AD individuals were recruited, genotyped and had their skin barrier assessed using three different measures -­ transepidermal water loss 9TEWL), skin capacitance and the number of tape strips required to abrogate skin barrier. A secondary aim of this functional study was to test the hypothesis that corneocytes were less adherent to one another in filaggrin-­related AD compared to wild-­type AD skin. The second main focus of this thesis was a structural study aimed at interrogating the structure-­function relationship of filaggrin. Filaggrin protein was extracted and purified from a total of 21 AD and non-­AD subjects and analysed using mass spectrometric techniques. Specifically, matrix assisted laser desorption/ionisation time-­of-­flight(MALDI-­‐TOF)mass spectrometry(MS)and nano liquid chromatography tandem MS(LC-­MS/MS) were utilised. Part of this structural study also involved developing and optimising the extraction and purification of filaggrin protein, including a novel way of extracting filaggrin from skin using tape stripping. In addition, novel filaggrin-­specific enzyme-­linked immunosorbant assay (ELISA) was also developed, which could serve as a useful screening test for the protein. In this study, FLG mutations were found to correlate with higher TEWL and fewer number of tape strips required to abrogate skin barrier, but not with skin capacitance. FLG mutations were also not shown to correlate with AD severity. The mean amount of protein extracted from filaggrin-­related AD skin was also significantly higher compared to wild-­type AD skin, supporting the hypothesis that corneocytes were less adherent to one another(and therefore, densely packed) in filaggrin-­related AD skin. MS analysis of filaggrin confirmed the heterogeneic nature of filaggrin protein, even within a single individual. Interestingly, this structural study also showed that filaggrin was only minimally expressed in the skin of all the AD individuals studied, whether or not they possessed any FLG mutation. Due to the limited amount of filaggrin extracted from AD skin, it was not possible to conduct comparative structural analysis between filaggrin from AD and non-­AD skin

Database integration with the Web for biologists to share data and information

The Internet has fundamentally changed the way we conduct our business. Even 10 years ago or so, it was not possible to order a book or access a sequence database in another continent using the computer in our office. All these become possible due to the progress in information technology. It is especially important for biologists to realise that information technology has brought us enormous opportunities in sharing our data. In this paper, authors review and introduce the technologies relating to biological data, database, dynamic integration of databases with the World Wide Web (Web hereafter), and data standardisation

Database integration with the Web for biologists to share data and information

The Internet has fundamentally changed the way we conduct our business. Even 10 years ago or so, it was not possible to order a book or access a sequence database in another continent using the computer in our office. All these become possible due to the progress in information technology. It is especially important for biologists to realise that information technology has brought us enormous opportunities in sharing our data. In this paper, authors review and introduce the technologies relating to biological data, database, dynamic integration of databases with the World Wide Web (Web hereafter), and data standardisation

Time Dependent Floquet Theory and Absence of an Adiabatic Limit

Quantum systems subject to time periodic fields of finite amplitude, lambda, have conventionally been handled either by low order perturbation theory, for lambda not too large, or by exact diagonalization within a finite basis of N states. An adiabatic limit, as lambda is switched on arbitrarily slowly, has been assumed. But the validity of these procedures seems questionable in view of the fact that, as N goes to infinity, the quasienergy spectrum becomes dense, and numerical calculations show an increasing number of weakly avoided crossings (related in perturbation theory to high order resonances). This paper deals with the highly non-trivial behavior of the solutions in this limit. The Floquet states, and the associated quasienergies, become highly irregular functions of the amplitude, lambda. The mathematical radii of convergence of perturbation theory in lambda approach zero. There is no adiabatic limit of the wave functions when lambda is turned on arbitrarily slowly. However, the quasienergy becomes independent of time in this limit. We introduce a modification of the adiabatic theorem. We explain why, in spite of the pervasive pathologies of the Floquet states in the limit N goes to infinity, the conventional approaches are appropriate in almost all physically interesting situations.Comment: 13 pages, Latex, plus 2 Postscript figure

A comprehensive functional map of the hepatitis C virus genome provides a resource for probing viral proteins.

UnlabelledPairing high-throughput sequencing technologies with high-throughput mutagenesis enables genome-wide investigations of pathogenic organisms. Knowledge of the specific functions of protein domains encoded by the genome of the hepatitis C virus (HCV), a major human pathogen that contributes to liver disease worldwide, remains limited to insight from small-scale studies. To enhance the capabilities of HCV researchers, we have obtained a high-resolution functional map of the entire viral genome by combining transposon-based insertional mutagenesis with next-generation sequencing. We generated a library of 8,398 mutagenized HCV clones, each containing one 15-nucleotide sequence inserted at a unique genomic position. We passaged this library in hepatic cells, recovered virus pools, and simultaneously assayed the abundance of mutant viruses in each pool by next-generation sequencing. To illustrate the validity of the functional profile, we compared the genetic footprints of viral proteins with previously solved protein structures. Moreover, we show the utility of these genetic footprints in the identification of candidate regions for epitope tag insertion. In a second application, we screened the genetic footprints for phenotypes that reflected defects in later steps of the viral life cycle. We confirmed that viruses with insertions in a region of the nonstructural protein NS4B had a defect in infectivity while maintaining genome replication. Overall, our genome-wide HCV mutant library and the genetic footprints obtained by high-resolution profiling represent valuable new resources for the research community that can direct the attention of investigators toward unidentified roles of individual protein domains.ImportanceOur insertional mutagenesis library provides a resource that illustrates the effects of relatively small insertions on local protein structure and HCV viability. We have also generated complementary resources, including a website (http://hangfei.bol.ucla.edu) and a panel of epitope-tagged mutant viruses that should enhance the research capabilities of investigators studying HCV. Researchers can now detect epitope-tagged viral proteins by established antibodies, which will allow biochemical studies of HCV proteins for which antibodies are not readily available. Furthermore, researchers can now quickly look up genotype-phenotype relationships and base further mechanistic studies on the residue-by-residue information from the functional profile. More broadly, this approach offers a general strategy for the systematic functional characterization of viruses on the genome scale

Noncommutative Field Theory from String Theory: Two-loop Analysis

Noncommutative \phi^3 field theory in six dimensions exhibits the logarithmic UV/IR mixing at the two-loop order. We show that open string theory in the presence of constant background NS-NS two-form field yields the same amplitude upon taking a decoupling limit. The stretched string picture proposed on the basis of one-loop analysis naturally generalizes to the two-loop amplitudes in consideration. Our string theory formulation can incorporate the closed string insertions as well as open string insertions. Furthermore, the analysis of the world-sheet partition function and propagators can be straightforwardly generalized to Riemann surfaces with genus zero but with an arbitrary number of boundaries.Comment: 25 pages, 3 figures; v2. a reference added and typos corrected. Version to appear in Nuclear Physics

Speckle from phase ordering systems

The statistical properties of coherent radiation scattered from phase-ordering materials are studied in detail using large-scale computer simulations and analytic arguments. Specifically, we consider a two-dimensional model with a nonconserved, scalar order parameter (Model A), quenched through an order-disorder transition into the two-phase regime. For such systems it is well established that the standard scaling hypothesis applies, consequently the average scattering intensity at wavevector _k and time t' is proportional to a scaling function which depends only on a rescaled time, t ~ |_k|^2 t'. We find that the simulated intensities are exponentially distributed, with the time-dependent average well approximated using a scaling function due to Ohta, Jasnow, and Kawasaki. Considering fluctuations around the average behavior, we find that the covariance of the scattering intensity for a single wavevector at two different times is proportional to a scaling function with natural variables mt = |t_1 - t_2| and pt = (t_1 + t_2)/2. In the asymptotic large-pt limit this scaling function depends only on z = mt / pt^(1/2). For small values of z, the scaling function is quadratic, corresponding to highly persistent behavior of the intensity fluctuations. We empirically establish a connection between the intensity covariance and the two-time, two-point correlation function of the order parameter. This connection allows sensitive testing, either experimental or numerical, of existing theories for two-time correlations in systems undergoing order-disorder phase transitions. Comparison between theory and our numerical results requires no adjustable parameters.Comment: 18 pgs RevTeX, to appear in PR

Convalescent COVID-19 Patients Without Comorbidities Display Similar Immunophenotypes Over Time Despite Divergent Disease Severities

COVID-19, the disease caused by SARS-CoV-2 infection, can assume a highly variable disease course, ranging from asymptomatic infection, which constitutes the majority of cases, to severe respiratory failure. This implies a diverse host immune response to SARS-CoV-2. However, the immunological underpinnings underlying these divergent disease courses remain elusive. We therefore set out to longitudinally characterize immune signatures of convalescent COVID-19 patients stratified according to their disease severity. Our unique convalescent COVID-19 cohort consists of 74 patients not confounded by comorbidities. This is the first study of which we are aware that excludes immune abrogations associated with non-SARS-CoV-2 related risk factors of disease severity. Patients were followed up and analyzed longitudinally (2, 4 and 6 weeks after infection) by high-dimensional flow cytometric profiling of peripheral blood mononuclear cells (PSPRINGER NATUREs), in-depth serum analytics, and transcriptomics. Immune phenotypes were correlated to disease severity. Convalescence was overall associated with uniform immune signatures, but distinct immune signatures for mildly versus severely affected patients were detectable within a 2-week time window after infection

Error-analysis and comparison to analytical models of numerical waveforms produced by the NRAR Collaboration

The Numerical–Relativity–Analytical–Relativity (NRAR) collaboration is a joint effort between members of the numerical relativity, analytical relativity and gravitational-wave data analysis communities. The goal of the NRAR collaboration is to produce numerical-relativity simulations of compact binaries and use them to develop accurate analytical templates for the LIGO/Virgo Collaboration to use in detecting gravitational-wave signals and extracting astrophysical information from them. We describe the results of the first stage of the NRAR project, which focused on producing an initial set of numerical waveforms from binary black holes with moderate mass ratios and spins, as well as one non-spinning binary configuration which has a mass ratio of 10. All of the numerical waveforms are analysed in a uniform and consistent manner, with numerical errors evaluated using an analysis code created by members of the NRAR collaboration. We compare previously-calibrated, non-precessing analytical waveforms, notably the effective-one-body (EOB) and phenomenological template families, to the newly-produced numerical waveforms. We find that when the binary's total mass is ~100–200M_⊙, current EOB and phenomenological models of spinning, non-precessing binary waveforms have overlaps above 99% (for advanced LIGO) with all of the non-precessing-binary numerical waveforms with mass ratios ≤4, when maximizing over binary parameters. This implies that the loss of event rate due to modelling error is below 3%. Moreover, the non-spinning EOB waveforms previously calibrated to five non-spinning waveforms with mass ratio smaller than 6 have overlaps above 99.7% with the numerical waveform with a mass ratio of 10, without even maximizing on the binary parameters