cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Identification of Two Mycobacterium smegmatis Lipoproteins Exported by a SecA2-Dependent Pathway
Creators: name: Braunstein, M.
name: Wolschendorf, F.
name: Abshire, M.
name: Niederweis, M.
name: Gibbons, H. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: The SecA2 protein is part of a specialized protein export system of mycobacteria. We set out to identify proteins exported to the bacterial cell envelope by the mycobacterial SecA2 system. By comparing the protein profiles of cell wall and membrane fractions from wild-type and ΔsecA2 mutant Mycobacterium smegmatis, we identified the Msmeg1712 and Msmeg1704 proteins as SecA2-dependent cell envelope proteins. These are the first endogenous M. smegmatis proteins identified as dependent on SecA2 for export. Both proteins are homologous to periplasmic sugar-binding proteins of other bacteria, and both contain functional amino-terminal signal sequences with lipobox motifs. These two proteins appeared to be genuine lipoproteins as shown by Triton X-114 fractionation and sensitivity to globomycin, an inhibitor of lipoprotein signal peptidase. The role of SecA2 in the export of these proteins was specific; not all mycobacterial lipoproteins required SecA2 for efficient localization or processing. Finally, Msmeg1704 was recognized by the SecA2 pathway of Mycobacterium tuberculosis, as indicated by the appearance of an export intermediate when the protein was expressed in a ΔsecA2 mutant of M. tuberculosis. Taken together, these results indicate that a select subset of envelope proteins containing amino-terminal signal sequences can be substrates of the mycobacterial SecA2 pathway and that some determinants for SecA2-dependent export are conserved between M. smegmatis and M. tuberculosis.
Nanomechanical spectroscopy of 2D materials
Creators: name: Kirchhof, Jan N.
name: Yu, Yuefeng
name: Antheaume, Gabriel
name: Gordeev, Georgy
name: Yagodkin, Denis
name: Elliott, Peter
name: de Araújo, Daniel B.
name: Sharma, Sangeeta
name: Reich, Stephanie
name: Bolotin, Kirill I.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Applied Physics (physics.app-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We introduce a nanomechanical platform for fast and sensitive measurements of the spectrally-resolved optical dielectric function of 2D materials. At the heart of our approach is a suspended 2D material integrated into a nanomechanical resonator illuminated by a wavelength-tunable laser source. From the heating-related frequency shift of the resonator as well as its optical reflection measured as a function of photon energy, we obtain the real and imaginary parts of the dielectric function. Our measurements are unaffected by substrate-related screening and do not require any assumptions on the underling optical constants. This fast ($τ_{rise}$ $\sim$ 135 ns), sensitive (noise-equivalent power = 90 $\frac{pW}{\sqrt{Hz}}$ ), and broadband (1.2 $-$ 3.1 eV, extendable to UV-THz) method provides an attractive alternative to spectroscopic or ellipsometric characterisation techniques.
Superposition principle for nonlinear Josephson plasma waves in layered superconductors
Creators: name: Rokhmanova, T. N.
name: Apostolov, S. S.
name: Maizelis, Z. A.
name: Yampol'skii, V. A.
name: Nori, Franco
Publisher: name: arXiv
Year: 2014
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We show that a specific superposition principle is valid for \emph{nonlinear} Josephson plasma waves in layered superconductors. We study theoretically the reflection and transmission of terahertz waves through a finite-size superconducting slab placed inside a rectangular waveguide with ideal-metal walls. We assume that the superconducting layers are parallel to the waveguide axis. We show that there exist two specific mutually-orthogonal polarizations for waves which, in spite of the nonlinearity, reflect and transmit through the superconductor \emph{independently}. The wave of the first polarization causes a strong shielding current along the crystallographic \textbf{ab}-plane of the superconductor. Therefore, this wave reflects nearly completely from the superconductor and excites only an evanescent mode inside it. The wave of the other polarization does not contain the electric field component parallel to both the sample surface and the crystallographic \textbf{ab}-plane, and excites much weaker shielding currents. Therefore, it partially reflects and partially transmits through the sample. Moreover, this wave excites the nonlinear mode in the layered superconductor, and the transmission coefficient of the superconductor depends on the amplitude of the incident wave of this polarization.On the basis of the discussed superposition principle, we suggest a new method for solving nonlinear problems of waves interaction in layered superconductors. Namely, it is reasonably to represent incident, reflected, and transmitted waves of any polarizations as superpositions of the modes with the two specific polarizations considered here, and then solve the problem separately for these modes. We apply this method to the case of nonlinear interaction and mutual transformation of the transverse electric and transverse magnetic modes in layered superconductors.
description: 6 figures. Submitted to PRB
Height distribution of equipotential lines in a region confined by a rough conducting boundary
Creators: name: de Castro, C. P.
name: de Assis, T. A.
name: de Castilho, C. M. C.
name: Andrade, R. F. S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: This work considers the behavior of the height distributions of the equipotential lines in a region confined by two interfaces: a cathode with an irregular interface and a distant flat anode. Both boundaries, which are maintained at distinct and constant potential values, are assumed to be conductors. The morphology of the cathode interface results from the deposit of $2 \times 10^{4}$ monolayers that are produced using a single competitive growth model based on the rules of the Restricted Solid on Solid and Ballistic Deposition models, both of which belong to the Kadar-Parisi-Zhang (KPZ) universality class. At each time step, these rules are selected with probability $p$ and $q = 1 - p$. For several irregular profiles that depend on $p$, a family of equipotential lines is evaluated. The lines are characterized by the skewness and kurtosis of the height distribution. The results indicate that the skewness of the equipotential line increases when they approach the flat anode, and this increase has a non-trivial convergence to a delta distribution that characterizes the equipotential line in a uniform electric field. The morphology of the equipotential lines is discussed; the discussion emphasizes their features for different ranges of $p$ that correspond to positive, null and negative values of the coefficient of the non-linear term in the KPZ equation.
description: 16 pages, 6 figures
Pseudomonas aeruginosa Type IV Pilus Expression in Neisseria gonorrhoeae: Effects of Pilin Subunit Composition on Function and Organelle Dynamics
Creators: name: Aas, F. E.
name: Egge-Jacobsen, W. M.
name: Koomey, M.
name: Wolfgang, M. C.
name: Maier, B.
name: van Putten, J. P. M.
name: Roos, N.
name: Winther-Larsen, H. C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Type IV pili (TFP) play central roles in the expression of many phenotypes including motility, multicellular behavior, sensitivity to bacteriophages, natural genetic transformation, and adherence. In Neisseria gonorrhoeae, these properties require ancillary proteins that act in conjunction with TFP expression and influence organelle dynamics. Here, the intrinsic contributions of the pilin protein itself to TFP dynamics and associated phenotypes were examined by expressing the Pseudomonas aeruginosa PilAPAK pilin subunit in N. gonorrhoeae. We show here that, although PilAPAK pilin can be readily assembled into TFP in this background, steady-state levels of purifiable fibers are dramatically reduced relative those of endogenous pili. This defect is due to aberrant TFP dynamics as it is suppressed in the absence of the PilT pilus retraction ATPase. Functionally, PilAPAK pilin complements gonococcal adherence for human epithelial cells but only in a pilT background, and this property remains dependent on the coexpression of both the PilC adhesin and the PilV pilin-like protein. Since P. aeruginosa pilin only moderately supports neisserial sequence-specific transformation despite its assembly proficiency, these results together suggest that PilAPAK pilin functions suboptimally in this environment. This appears to be due to diminished compatibility with resident proteins essential for TFP function and dynamics. Despite this, PilAPAK pili support retractile force generation in this background equivalent to that reported for endogenous pili. Furthermore, PilAPAK pili are both necessary and sufficient for bacteriophage PO4 binding, although the strain remains phage resistant. Together, these findings have significant implications for TFP biology in both N. gonorrhoeae and P. aeruginosa.
Correlations and entanglement in flat band models with variable Chern numbers
Creators: name: Udagawa, Masafumi
name: Bergholtz, Emil J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We discuss a number of illuminating results for tight binding models supporting a band with variable Chern number, and illustrate them explicitly for a simple class of two-banded models. First, for models with a fixed number of bands, we show that the minimal hopping range needed to achieve a given Chern number $C$ is increasing with $C$, and that the band flattening requires an exponential tail of long-range processes. We further verify that the entanglement spectrum corresponding to a real-space partitioning contains $C$ chiral modes and thereby complies with the archetypal correspondence between the bulk entanglement and the edge energetics. Finally, we address the issue of interactions and study the problem of two interacting particles projected to the flattened band as a function of the Chern number. Our results provide valuable insights for the full interacting problem of a partially filled Chern band at variable filling fractions and Chern numbers.
description: 17 pages, 6 figures, submitted to Journal of Statistical Mechanics as a proceedings of ESICQW12
ATPase Activity of Mycobacterium tuberculosis SecA1 and SecA2 Proteins and Its Importance for SecA2 Function in Macrophages
Creators: name: Hou, J. M.
name: Rigel, N. W.
name: Teschke, C. M.
name: Gibbons, H. S.
name: Braunstein, M.
name: McCann, J. R.
name: D'Lima, N. G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: The Sec-dependent translocation pathway that involves the essential SecA protein and the membrane-bound SecYEG translocon is used to export many proteins across the cytoplasmic membrane. Recently, several pathogenic bacteria, including Mycobacterium tuberculosis, were shown to possess two SecA homologs, SecA1 and SecA2. SecA1 is essential for general protein export. SecA2 is specific for a subset of exported proteins and is important for M. tuberculosis virulence. The enzymatic activities of two SecA proteins from the same microorganism have not been defined for any bacteria. Here, M. tuberculosis SecA1 and SecA2 are shown to bind ATP with high affinity, though the affinity of SecA1 for ATP is weaker than that of SecA2 or Escherichia coli SecA. Amino acid substitution of arginine or alanine for the conserved lysine in the Walker A motif of SecA2 eliminated ATP binding. We used the SecA2(K115R) variant to show that ATP binding was necessary for the SecA2 function of promoting intracellular growth of M. tuberculosis in macrophages. These results are the first to show the importance of ATPase activity in the function of accessory SecA2 proteins.
Genetic and Functional Analyses of PptA, a Phospho-Form Transferase Targeting Type IV Pili in Neisseria gonorrhoeae
Creators: name: Koomey, M.
name: Naessan, C. L.
name: Winther-Larsen, H. C.
name: Heiniger, R. W.
name: Aas, F. E.
name: Egge-Jacobsen, W.
name: Rohr, A.
name: Wolfgang, M. C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: The PilE pilin subunit protein of Neisseria gonorrhoeae undergoes unique covalent modifications with phosphoethanolamine (PE) and phosphocholine (PC). The pilin phospho-form transferase A (PptA) protein, required for these modifications, shows sequence relatedness with and architectural similarities to lipopolysaccharide PE transferases. Here, we used regulated expression and mutagenesis as means to better define the relationships between PptA structure and function, as well as to probe the mechanisms by which other factors impact the system. We show here that pptA expression is coupled at the level of transcription to its distal gene, murF, in a division/cell wall gene operon and that PptA can act in a dose-dependent fashion in PilE phospho-form modification. Molecular modeling and site-directed mutagenesis provided the first direct evidence that PptA is a member of the alkaline phosphatase superfamily of metalloenzymes with similar metal-binding sites and conserved structural folds. Through phylogenetic analyses and sequence alignments, these conclusions were extended to include the lipopolysaccharide PE transferases, including members of the disparate Lpt6 subfamily, and the MdoB family of phosphoglycerol transferases. Each of these enzymes thus likely acts as a phospholipid head group transferase whose catalytic mechanism involves a trans-esterification step generating a protein-phospho-form ester intermediate. Coexpression of PptA with PilE in Pseudomonas aeruginosa resulted in high levels of PE modification but was not sufficient for PC modification. This and other findings show that PptA-associated PC modification is governed by as-yet-undefined ancillary factors unique to N. gonorrhoeae.
Equivariant minimax dominators of the MLE in the array normal model
Creators: name: Gerard, David
name: Hoff, Peter
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: 62H12, 62C20, 62F10, 62F15

description: Inference about dependencies in a multiway data array can be made using the array normal model, which corresponds to the class of multivariate normal distributions with separable covariance matrices. Maximum likelihood and Bayesian methods for inference in the array normal model have appeared in the literature, but there have not been any results concerning the optimality properties of such estimators. In this article, we obtain results for the array normal model that are analogous to some classical results concerning covariance estimation for the multivariate normal model. We show that under a lower triangular product group, a uniformly minimum risk equivariant estimator (UMREE) can be obtained via a generalized Bayes procedure. Although this UMREE is minimax and dominates the MLE, it can be improved upon via an orthogonally equivariant modification. Numerical comparisons of the risks of these estimators show that the equivariant estimators can have substantially lower risks than the MLE.
Reciprocal Expression of ospA and ospC in Single Cells of Borrelia burgdorferi
Creators: name: de Silva, A. M.
name: Srivastava, S. Y.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Outer surface proteins (Osp) A and C of the Lyme disease spirochete (Borrelia burgdorferi) are selectively produced and of functional significance in the tick vector and mammalian host, respectively. Some studies indicate a simple, reciprocal relationship where the signals and pathways that turn on ospC also turn off ospA. Other studies indicate a more complex regulation where many spirochetes produce both proteins and others produce one of the proteins or neither protein. Here, we have used flow cytometry to characterize ospA and ospC transcript and protein levels in individual bacterial cells grown in culture. The results support a simple, reciprocal model where, at the level of single cells, the transcription of ospC is linked to the repression of ospA. We also demonstrate that under conditions conducive for OspC production, spirochetes display an “all or none” response, with some cells displaying high levels of ospC transcription and others demonstrating little or no transcription. Despite the reciprocal regulation of ospA and ospC at the single-cell level, we propose that spirochetes display an array of phenotypes due to stochasticity in the pathways that regulate osp expression and the slow turnover of outer surface proteins.
Codimension one foliations with numerically trivial canonical class on singular spaces
Creators: name: Druel, Stéphane
Publisher: name: arXiv
Year: 2018
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 37F75

description: In this article, we describe the structure of codimension one foliations with canonical singularities and numerically trivial canonical class on varieties with terminal singularities, extending a result of Loray, Pereira and Touzet to this context.
Dynamic Component Composition
Creators: name: Grinkrug, Efim
Publisher: name: arXiv
Year: 2014
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: This paper presents an approach to dynamic component composition that facilitates creating new composed components using existing ones at runtime and without any code generation. The dynamic abilities are supported by extended type notion and implementation based on additional superstructure provided with its Java API and corresponding JavaBeans components. The new component composition is performed by building the composed prototype object that can be dynamically transformed into the new instantiable type (component). That approach demonstrates interrelations between prototype-based and class-based component-oriented programming. The component model proposed can be used when implementing user-defined types in declarative languages for event-driven applications programming.
description: 19 pages
Mutations in ampG and Lytic Transglycosylase Genes Affect the Net Release of Peptidoglycan Monomers from Vibrio fischeri
Creators: name: Adin, D. M.
name: Goldman, W. E.
name: Stabb, E. V.
name: Engle, J. T.
name: McFall-Ngai, M. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The light-organ symbiont Vibrio fischeri releases N-acetylglucosaminyl-1,6-anhydro-N-acetylmuramylalanyl-γ-glutamyldiaminopimelylalanine, a disaccharide-tetrapeptide component of peptidoglycan that is referred to here as “PG monomer.” In contrast, most gram-negative bacteria recycle PG monomer efficiently, and it does not accumulate extracellularly. PG monomer can stimulate normal light-organ morphogenesis in the host squid Euprymna scolopes, resulting in regression of ciliated appendages similar to that triggered by infection with V. fischeri. We examined whether the net release of PG monomers by V. fischeri resulted from lytic transglycosylase activity or from defects in AmpG, the permease through which PG monomers enter the cytoplasm for recycling. An ampG mutant displayed a 100-fold increase in net PG monomer release, indicating that AmpG is functional. The ampG mutation also conferred the uncharacteristic ability to induce light-organ morphogenesis even when placed in a nonmotile flaJ mutant that cannot infect the light-organ crypts. We targeted five potential lytic transglycosylase genes singly and in specific combinations to assess their role in PG monomer release. Combinations of mutations in ltgA, ltgD, and ltgY decreased net PG monomer release, and a triple mutant lacking all three of these genes had little to no accumulation of PG monomers in culture supernatants. This mutant colonized the host as well as the wild type did; however, the mutant-infected squid were more prone to later superinfection by a second V. fischeri strain. We propose that the lack of PG monomer release by this mutant results in less regression of the infection-promoting ciliated appendages, leading to this propensity for superinfection.
Inverse moving point source problem for the wave equation
Creators: name: Jebawy, Hanin Al
name: Badia, Abdellatif El
name: Triki, Faouzi
Publisher: name: arXiv
Year: 2022
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: In this paper, we consider the problem of identifying a single moving point source for a three-dimensional wave equation from boundary measurements. Precisely, we show that the knowledge of the field generated by the source at six different points of the boundary over a finite time interval is sufficient to determine uniquely its trajectory. We also derive a Lipschitz stability estimate for the inversion.
Pseudomonas aeruginosa AlgR Controls Cyanide Production in an AlgZ-Dependent Manner
Creators: name: Frisk, A.
name: Wolfgang, M. C.
name: Jackson, D.
name: Carterson, A. J.
name: Pritchett, C. L.
name: Cody, W. L.
name: Schurr, M. J.
name: Jones, A. K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Pseudomonas aeruginosa is an opportunistic pathogen that causes chronic infections in individuals suffering from the genetic disorder cystic fibrosis. In P. aeruginosa, the transcriptional regulator AlgR controls a variety of virulence factors, including alginate production, twitching motility, biofilm formation, quorum sensing, and hydrogen cyanide (HCN) production. In this study, the regulation of HCN production was examined. Strains lacking AlgR or the putative AlgR sensor AlgZ produced significantly less HCN than did a nonmucoid isogenic parent. In contrast, algR and algZ mutants showed increased HCN production in an alginate-producing (mucoid) background. HCN production was optimal in a 5% O2 environment. In addition, cyanide production was elevated in bacteria grown on an agar surface compared to bacteria grown in planktonic culture. A conserved AlgR phosphorylation site (aspartate at amino acid position 54), which is required for surface-dependent twitching motility but not alginate production, was found to be critical for cyanide production. Nuclease protection mapping of the hcnA promoter identified a new transcriptional start site required for HCN production. A subset of clinical isolates that lack this start site produced small amounts of cyanide. Taken together, these data show that the P. aeruginosa hcnA promoter contains three transcriptional start sites and that HCN production is regulated by AlgZ and AlgR and is maximal under microaerobic conditions when the organism is surface attached.
Nearly Fuchsian surface subgroups of finite covolume Kleinian groups
Creators: name: Kahn, Jeremy
name: Wright, Alex
Publisher: name: arXiv
Year: 2018
Subjects: subject: Geometric Topology (math.GT)
subject: Differential Geometry (math.DG)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics

description: Let Gamma < PSL_2(C) be discrete, cofinite volume, and noncocompact. We prove that for all K > 1, there is a subgroup H < Gamma that is K-quasiconformally conjugate to a discrete cocompact subgroup of PSL_2(R). Along with previous work of Kahn and Markovic, this proves that every finite covolume Kleinian group has a nearly Fuchsian surface subgroup.
description: v2: Final prepublication version
The Complete Genome Sequence of Helicobacter pylori Strain G27
Creators: name: Baltrus, D. A.
name: Salama, N. R.
name: Guillemin, K.
name: Stein, M.
name: Ottemann, K. M.
name: Lowe, T. M.
name: Merrell, D. S.
name: Amieva, M. R.
name: Covacci, A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Helicobacter pylori is a gram-negative pathogen that colonizes the stomachs of over half the world's population and causes a spectrum of gastric diseases including gastritis, ulcers, and gastric carcinoma. The H. pylori species exhibits unusually high levels of genetic variation between strains. Here we announce the complete genome sequence of H. pylori strain G27, which has been used extensively in H. pylori research.
Principals’ transformational leadership in strengthening character education at senior high school level (SMA) in Indonesia
Creators: name: Rustan Effendi, Yulius
name: Sahertian, Pieter
Publisher: name: figshare
Year: 2022
Subjects: subject: Education
subject: 130103 Higher Education
subject: FOS: Educational sciences

description: Character education reinforcement in secondary schools is one of the educational programmes aimed at anticipating the tendency of moral perversion as a result of moral decadence. Various forms of moral deviations that occur among high school students result in them being alienated from life because they conflict with cultural norms, school discipline, and life ethics in society. In this article we aim to discuss the relation of character value reinforcement and the principal’s transformational leadership strategy to shape students’ characters in a descriptive-critical manner. The objective of this study
 was investigating school strategies for optimising the implementation of character education reinforcement. In this research we used a qualitative method with a case study design. The data validity measurement was based on the levels of credibility, transferability, dependability, and confirmability. The results emphasise the importance of shaping student character as an anticipatory step to minimise moral distortions among high school students, and the effectiveness of the principal’s transformational leadership role in optimising the implementation of education programmes for the strengthening of students’ characters in schools.
Conservation of Structure and Protein-Protein Interactions Mediated by the Secreted Mycobacterial Proteins EsxA, EsxB, and EspA
Creators: name: Nguyen, K.
name: Eisele, L.
name: Valdes, K.
name: Crossman, D. K.
name: Callahan, B.
name: Derbyshire, K. M.
name: Caplow, M.
name: Steyn, A. J. C.
name: Collins, A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Mycobacterium tuberculosis EsxA and EsxB proteins are founding members of the WXG100 (WXG) protein family, characterized by their small size (∼100 amino acids) and conserved WXG amino acid motif. M. tuberculosis contains 11 tandem pairs of WXG genes; each gene pair is thought to be coexpressed to form a heterodimer. The precise role of these proteins in the biology of M. tuberculosis is unknown, but several of the heterodimers are secreted, which is important for virulence. However, WXG proteins are not simply virulence factors, since nonpathogenic mycobacteria also express and secrete these proteins. Here we show that three WXG heterodimers have structures and properties similar to those of the M. tuberculosis EsxBA (MtbEsxBA) heterodimer, regardless of their host species and apparent biological function. Biophysical studies indicate that the WXG proteins from M. tuberculosis (EsxG and EsxH), Mycobacterium smegmatis (EsxA and EsxB), and Corynebacterium diphtheriae (EsxA and EsxB) are heterodimers and fold into a predominately α-helical structure. An in vivo protein-protein interaction assay was modified to identify proteins that interact specifically with the native WXG100 heterodimer. MtbEsxA and MtbEsxB were fused into a single polypeptide, MtbEsxBA, to create a biomimetic bait for the native heterodimer. The MtbEsxBA bait showed specific association with several esx-1-encoded proteins and EspA, a virulence protein secreted by ESX-1. The MtbEsxBA fusion peptide was also utilized to identify residues in both EsxA and EsxB that are important for establishing protein interactions with Rv3871 and EspA. Together, the results are consistent with a model in which WXG proteins perform similar biological roles in virulent and nonvirulent species.
Coupled dynamical phase transitions in driven disk packings
Creators: name: Ghosh, Akash
name: Radhakrishnan, Jaikumar
name: Chaikin, Paul M.
name: Levine, Dov
name: Ghosh, Shankar
Publisher: name: arXiv
Year: 2022
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Under the influence of oscillatory shear, a mono-layer of frictional granular disks exhibits two dynamical phase transitions: a transition from an initially disordered state to an ordered crystalline state, and a dynamic active-absorbing phase transition. Although there is no reason, {\it a-priori}, for these to be at the same critical point, they are. The transitions may also be characterized by the disk trajectories, which are non-trivial loops breaking time-reversal invariance.
Probing the bulk plasmon continuum of layered materials through electron energy loss spectroscopy in a reflection geometry
Creators: name: Boyd, Christian
name: Yeo, Luke
name: Phillips, Philip W.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: A periodic arrangement of 2D conducting planes is known to host a (bulk) plasmon dispersion that interpolates between the typical, gapped behavior of 3D metals and a gapless, acoustic regime as a function of the out-of-plane wavevector. The semi-infinite system -- the configuration relevant to Electron Energy Loss Spectroscopy (EELS) in a reflection geometry, as in High Resolution EELS (HREELS) -- is known to host a surface plasmon that ceases to propagate below a cutoff wavevector. As the f-sum rule requires a finite response whether or not there exist sharp excitations, we demonstrate that what remains in the surface loss function -- the material response probed by HREELS -- is the contribution from the (bulk) plasmon of the infinite system. In particular, we provide a one-to-one mapping between the plasmon continuum and the spectral weight in the surface loss function. In light of this result, we suggest that HREELS be considered a long wavelength probe of the plasmon continuum in layered materials.
description: 10 pages, 9 figures. Corrected erroneous Bi-2212 parameters and f-sum rule formula (no change to figures)
Slip of submerged two-dimensional liquid-infused surfaces in the presence of surfactants
Creators: name: Sundin, Johan
name: Bagheri, Shervin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Using numerical simulations, we investigate the effects of Marangoni stresses induced by surfactants on the effective slip length of liquid-infused surfaces (LIS) with transverse grooves. The surfactants are assumed soluble in the external liquid shearing the surface and can adsorb onto the interfaces. Two different adsorption models are used: a classical Frumkin model and a more advanced model that better describes the decrease of surface tension for minuscule concentrations. The simulations show that LIS may face even more severe effects of surfactants than previously investigated superhydrophobic surfaces. Constructing an analytical model for the effective slip length, we can predict the critical surfactant concentration for which the slip length decreases significantly. This analytical model describes both adsorption models of LIS on a unified framework if properly adjusted. We also advance the understanding of when surfactant advection gives rise to highly skewed interfacial concentrations - the so-called partial stagnant cap regime. To a good approximation, this regime can only exist below a specific surfactant concentration given by the Marangoni number and the strength of the surfactants.
description: 34 pages, 13 figures
Sub-40nm Nanogratings Self-Organized in PVP-based Polymer Composite Film by Photoexcitation and Two Sequent Splitting under Femtosecond Laser Irradiation
Creators: name: Chen, Li-Yun
name: Guo, Cheng-Cheng
name: Pan, Ming-Ming
name: Lai, Chen
name: Wang, Yun-Xia
name: Liao, Guo-Cai
name: Ma, Zi-Wei
name: Zhang, Fan-Wei
name: Suriyaprakash, Jagadeesh
name: Guo, Lijing
name: Akinoglu, Eser
name: Li, Qiang
name: Wu, Li-Jun
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optics (physics.optics)
subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: Laser-induced periodic surface structures (LIPSSs) on various materials have been extensively investigated because of their wide applications. The combination of different materials allows for greater freedom in tailoring their functions and achieving responses not possible in a homogeneous material. By utilizing a femtosecond (fs) laser to irradiate the Fe-doped Polyvinyl Pyrrolidone (PVP) composite film, highly regular ultrafine nanogratings (U-nanogratings) with a period as small as 35.0 ($\pm$ 2.0) nm can be self-organized on the surface with extremely high efficiency. The period of the U-nanogratings can be controlled by varying the scanning speed of the laser beam (deposited energy) and the thickness of the composite film. Based on the experimental, theoretical, and simulation results, we propose a two-step formation mechanism: composite film excitation and two sequent grating-splitting. The high photosensitivity and low glass transition temperature of the composite film facilitate the fabrication of the ultrafine nanostructures. The proposed design method for the composite material and fabrication process could not only provide a strategy for obtaining highly regular U-nanogratings, but also offer a platform to explore the interaction physics between ultra-short pulses and matter under extreme conditions.
A relation between higher-rank PT stable objects and quotients of coherent sheaves
Creators: name: Lo, Jason
Publisher: name: arXiv
Year: 2018
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14J30 (Primary) 14D23 (Secondary)

description: On a smooth projective threefold, we construct an essentially surjective functor $\mathcal{F}$ from a category of two-term complexes to a category of quotients of coherent sheaves, and describe the fibers of this functor. Under a coprime assumption on rank and degree, the domain of $\mathcal{F}$ coincides with the category of higher-rank PT stable objects, which appear on one side of Toda's higher-rank DT/PT correspondence formula. The codomain of $\mathcal{F}$ is the category of objects that appear on one side of another correspondence formula by Gholampour-Kool, between the generating series of topological Euler characteristics of two types of quot schemes.
description: 19 pages
Identification of YsrT and Evidence that YsrRST Constitute a Unique Phosphorelay System in Yersinia enterocolitica
Creators: name: Miller, V. L.
name: Walker, K. A.
name: Mildiner-Earley, S.
name: Obrist, M. W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Two-component systems (TCS) and phosphorelay systems are mechanisms used by bacteria and fungi to quickly adapt to environmental changes to produce proteins necessary for survival in new environments. Bacterial pathogens use TCS and phosphorelay systems to regulate genes necessary to establish infection within their hosts, including type III secretion systems (T3SS). The Yersinia enterocolitica ysa T3SS is activated in response to NaCl by YsrS and YsrR, a putative hybrid sensor kinase and a response regulator, respectively. Hybrid TCS consist of a sensor kinase that typically has three well-conserved sites of phosphorylation: autophosphorylation site H1, D1 within a receiver domain, and H2 in the histidine phosphotransferase (HPt) domain. From H2, the phosphoryl group is transferred to D2 on the response regulator. A curious feature of YsrS is that it lacks the terminal HPt domain. We report here the identification of the HPt-containing protein (YsrT) that provides this activity for the Ysr system. YsrT is an 82-residue protein predicted to be cytosolic and α-helical in nature and is encoded by a gene adjacent to ysrS. To demonstrate predicted functions of YsrRST as a phosphorelay system, we introduced alanine substitutions at H1, D1, H2, and D2 and tested the mutant proteins for the ability to activate a ysaE-lacZ reporter. As expected, substitutions at H1, H2, and D2 resulted in a loss of activation of ysaE expression. This indicates an interruption of normal protein function, most likely from loss of phosphorylation. A similar result was expected for D1; however, an intriguing “constitutive on” phenotype was observed. In addition, the unusual feature of a separate HPt domain led us to compare the sequences surrounding the ysrS-ysrT junction in several Yersinia strains. In every strain examined, ysrT is a separate gene, leading to speculation that there is a functional advantage to YsrT being an independent protein.
Effect of Curvature and Confinement on the Casimir-Polder Interaction
Creators: name: Rodriguez-Lopez, Pablo
name: Emig, Thorsten
name: Noruzifar, Ehsan
name: Zandi, Roya
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Modifications of Casimir-Polder interactions due to confinement inside a cylindrical cavity and due to curvature in- and outside the cavity are studied. We consider a perfectly conducting cylindrical shell with a single particle (atom or macroscopic sphere) located next to its interior or exterior surface, or two atoms placed inside the shell. By employing the scattering approach, we obtain the particle-cavity interaction and the modification of the two-particle interaction due to the cavity. We consider both retardation and thermal effects. While for the atoms a dipole description is sufficient, for the macroscopic sphere we sum (numerically) over many multipole fluctuations to compute the interaction at short separations. In the latter limit we compare to the proximity approximation and a gradient expansion and find agreement. Our results indicate an confinement induced suppression of the force between atoms. General criteria for suppression and enhancement of Casimir interactions due to confinement are discussed.
description: 13 pages, 11 figures
In Vitro and In Vivo Characterization of the Pseudomonas aeruginosa Cyclic AMP (cAMP) Phosphodiesterase CpdA, Required for cAMP Homeostasis and Virulence Factor Regulation
Creators: name: Fehr, A. R.
name: Klem, E. R.
name: Wolfgang, M. C.
name: Brutinel, E. D.
name: Yahr, T. L.
name: Fuchs, E. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Cyclic AMP (cAMP) is an important second messenger signaling molecule that controls a wide variety of eukaryotic and prokaryotic responses to extracellular cues. For cAMP-dependent signaling pathways to be effective, the intracellular cAMP concentration is tightly controlled at the level of synthesis and degradation. In the opportunistic human pathogen Pseudomonas aeruginosa, cAMP is a key regulator of virulence gene expression. To better understand the role of cAMP homeostasis in this organism, we identified and characterized the enzyme CpdA, a putative cAMP phosphodiesterase. We demonstrate that CpdA possesses 3′,5′-cAMP phosphodiesterase activity in vitro and that it utilizes an iron-dependent catalytic mechanism. Deletion of cpdA results in the accumulation of intracellular cAMP and altered regulation of P. aeruginosa virulence traits. Further, we demonstrate that the cAMP-dependent transcription factor Vfr directly regulates cpdA expression in response to intracellular cAMP accumulation, thus providing a feedback mechanism for controlling cAMP levels and fine-tuning virulence factor expression.
The Pseudomonas aeruginosa Vfr Regulator Controls Global Virulence Factor Expression through Cyclic AMP-Dependent and -Independent Mechanisms
Creators: name: Yahr, T. L.
name: Fulcher, N. B.
name: Brutinel, E. D.
name: Urbanowski, M. L.
name: Jones, A. K.
name: Fuchs, E. L.
name: Wolfgang, M. C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Vfr is a global regulator of virulence factor expression in the human pathogen Pseudomonas aeruginosa. Although indirect evidence suggests that Vfr activity is controlled by cyclic AMP (cAMP), it has been hypothesized that the putative cAMP binding pocket of Vfr may accommodate additional cyclic nucleotides. In this study, we used two different approaches to generate apo-Vfr and examined its ability to bind a representative set of virulence gene promoters in the absence and presence of different allosteric effectors. Of the cyclic nucleotides tested, only cAMP was able to restore DNA binding activity to apo-Vfr. In contrast, cGMP was capable of inhibiting cAMP-Vfr DNA binding. Further, we demonstrate that vfr expression is autoregulated and cAMP dependent and involves Vfr binding to a previously unidentified site within the vfr promoter region. Using a combination of in vitro and in vivo approaches, we show that cAMP is required for Vfr-dependent regulation of a specific subset of virulence genes. In contrast, we discovered that Vfr controls expression of the lasR promoter in a cAMP-independent manner. In summary, our data support a model in which Vfr controls virulence gene expression by distinct (cAMP-dependent and -independent) mechanisms, which may allow P. aeruginosa to fine-tune its virulence program in response to specific host cues or environments.
Explicit inner product formulas and Bessel period formulas for HST lifts
Creators: name: Namikawa, Kenichi
Publisher: name: arXiv
Year: 2018
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 11F27, 11F67

description: We explicitly give an inner product formula and a Bessel period formula for theta series on GSp(4), which was studied by Harris, Soudry and Taylor. As a consequence, we prove a non-vanishing of the theta series of small weights and we give a criterion for the non-vanishing of the theta series modulo a prime.
Solitonic Boson Stars: Numerical solutions beyond the thin-wall approximation
Creators: name: Collodel, Lucas G.
name: Doneva, Daniela D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: In this paper we present several set of solutions of static and spherically symmetric solitonic boson stars. Each set is characterized by the value of σ that defines the solitonic potential in the complex scalar field theory. The main features peculiar to this potential occur for small values of σ, but for which the equations become so stiff as to pose numerical challenges. Without making approximations we build the sets for decreasing σ values and show how they change their behavior in the parameter space, giving special attention to the region where thin-wall configurations dwell. The validity of the thin-wall approximation is explored as well as the possibility of the solution sets being discontinuous. We investigate five different possible definitions of a radius for boson stars and employ them to calculate the compactness of each solution in order to assess how different the outcomes might be.
Ext Data File 2 CEACAM6_Lit Profiles_Entities_Step3c_2022 Sept14
Creators: name: Chaussabel, Damien
Publisher: name: figshare
Year: 2022
Subjects: Biomarkers

description: Extended Data File 2: a spreadsheet in the MS Excel format listing cell type and disease entities and their prevalence in the literature associated with CEACAM6
Single-valued integration and double copy
Creators: name: Brown, Francis
name: Dupont, Clément
Publisher: name: arXiv
Year: 2018
Subjects: subject: Number Theory (math.NT)
subject: High Energy Physics - Theory (hep-th)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We study a single-valued integration pairing between differential forms and dual differential forms which subsumes some classical constructions in mathematics and physics. It can be interpreted as a $p$-adic period pairing at the infinite prime. The single-valued integration pairing is defined by transporting the action of complex conjugation from singular to de Rham cohomology via the comparison isomorphism. We show how quite general families of period integrals admit canonical single-valued versions and prove some general formulas for them. This implies an elementary 'double copy' formula expressing certain singular volume integrals over the complex points of a smooth projective variety as a quadratic expression in ordinary period integrals of half the dimension. We provide several examples, including non-holomorphic modular forms, archimedean Néron-Tate heights on curves, single-valued multiple zeta values and polylogarithms. In a sequel to this paper we apply this formalism to the moduli space of curves of genus zero with marked points, to deduce a recent conjecture due to Stieberger in string perturbation theory, which states that closed string amplitudes are the single-valued projections of open string amplitudes.
description: The results are unchanged. We made some minor corrections and added several remarks and clarifications
Bishop-Phelps-Bollobás property for bilinear forms on spaces of continuous functions
Creators: name: Kim, Sun Kwang
name: Lee, Han Ju
name: Martin, Miguel
Publisher: name: arXiv
Year: 2014
Subjects: subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: Primary 46B20, Secondary 46B04, 46B22

description: It is shown that the Bishop-Phelps-Bollobás theorem holds for bilinear forms on the complex $C_0(L_1)\times C_0(L_2)$ for arbitrary locally compact topological Hausdorff spaces $L_1$ and $L_2$.