cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Action at a Distance: Amino Acid Substitutions That Affect Binding of the Phosphorylated CheY Response Regulator and Catalysis of Dephosphorylation Can Be Far from the CheZ Phosphatase Active Site
Creators: name: Freeman, A. M.
name: Mole, B. M.
name: Bourret, R. B.
name: Silversmith, R. E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Two-component regulatory systems, in which phosphorylation controls the activity of a response regulator protein, provide signal transduction in bacteria. For example, the phosphorylated CheY response regulator (CheYp) controls swimming behavior. In Escherichia coli, the chemotaxis phosphatase CheZ stimulates the dephosphorylation of CheYp. CheYp apparently binds first to the C terminus of CheZ and then binds to the active site where dephosphorylation occurs. The phosphatase activity of the CheZ2 dimer exhibits a positively cooperative dependence on CheYp concentration, apparently because the binding of the first CheYp to CheZ2 is inhibited compared to the binding of the second CheYp. Thus, CheZ phosphatase activity is reduced at low CheYp concentrations. The CheZ21IT gain-of-function substitution, located far from either the CheZ active site or C-terminal CheY binding site, enhances CheYp binding and abolishes cooperativity. To further explore mechanisms regulating CheZ activity, we isolated 10 intragenic suppressor mutations of cheZ21IT that restored chemotaxis. The suppressor substitutions were located along the central portion of CheZ and were not allele specific. Five suppressor mutants tested biochemically diminished the binding of CheYp and/or the catalysis of dephosphorylation, even when the suppressor substitutions were distant from the active site. One suppressor mutant also restored cooperativity to CheZ21IT. Consideration of results from this and previous studies suggests that the binding of CheYp to the CheZ active site (not to the C terminus) is rate limiting and leads to cooperative phosphatase activity. Furthermore, amino acid substitutions distant from the active site can affect CheZ catalytic activity and CheYp binding, perhaps via the propagation of structural or dynamic perturbations through a helical bundle.
Chiral Majorana Fermions in two dimensional square lattice antiferromagnet with proximity-induced superconductivity
Creators: name: Luo, Ma
Publisher: name: arXiv
Year: 2022
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Combination of proximity-induced superconductivity and ferromagnetic exchange field in a two-dimensional square-lattice antiferromagnet with spin-orbit coupling and nonsymmorphic symmetry can induce a topological superconductor phase with chiral Majorana edge states. The lattice model of the Bogoliubov-de Gennes (BdG) Hamiltonian was applied to study the phase diagram of bulks and chiral Majorana edge states in nanoribbons. By numerically studying the phase diagram, we found that the non-uniformity of either the superconducting pairing parameters or the exchange field at the two sublattices is necessary to induce a topological superconductor phase with chiral Majorana edge states. The BdG Chern number of certain topological superconductor phases is $\pm1$ or $\pm3$, such that the corresponding nanoribbons have one or three pairs of chiral Majorana edge states, respectively.
description: 4 figures
Coarse embeddings into products of trees
Creators: name: Kasprowski, Daniel
Publisher: name: arXiv
Year: 2018
Subjects: subject: Metric Geometry (math.MG)
subject: FOS: Mathematics

description: We give a short and elementary proof of the fact that every metric space of finite asymptotic dimension can be embedded into a finite product of trees.
description: 4 pages; mistake in the proof of Lemma 6 fixed and some typos corrected; to appear in Kyoto Journal of Mathematics
Expression during Host Infection and Localization of Yersinia pestis Autotransporter Proteins
Creators: name: Miller, V. L.
name: Palacios, M.
name: Lawrenz, M. B.
name: Lane, M. C.
name: Lenz, J. D.
name: Cotter, D. G.
name: Gonzalez, R. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Yersinia pestis CO92 has 12 open reading frames encoding putative conventional autotransporters (yaps), nine of which appear to produce functional proteins. Here, we demonstrate the ability of the Yap proteins to localize to the cell surface of both Escherichia coli and Yersinia pestis and show that a subset of these proteins undergoes processing by bacterial surface omptins to be released into the supernatant. Numerous autotransporters have been implicated in pathogenesis, suggesting a role for the Yaps as virulence factors in Y. pestis. Using the C57BL/6 mouse models of bubonic and pneumonic plague, we determined that all of these genes are transcribed in the lymph nodes during bubonic infection and in the lungs during pneumonic infection, suggesting a role for the Yaps during mammalian infection. In vitro transcription studies did not identify a particular environmental stimulus responsible for transcriptional induction. The primary sequences of the Yaps reveal little similarity to any characterized autotransporters; however, two of the genes are present in operons, suggesting that the proteins encoded in these operons may function together. Further work aims to elucidate the specific functions of the Yaps and clarify the contributions of these proteins to Y. pestis pathogenesis.
Homesick Lévy walk: A mobility model having Ichi-go Ichi-e and scale-free properties of human encounters
Creators: name: Fujihara, Akihiro
name: Miwa, Hiroyoshi
Publisher: name: arXiv
Year: 2014
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Social and Information Networks (cs.SI)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: In recent years, mobility models have been reconsidered based on findings by analyzing some big datasets collected by GPS sensors, cellphone call records, and Geotagging. To understand the fundamental statistical properties of the frequency of serendipitous human encounters, we conducted experiments to collect long-term data on human contact using short-range wireless communication devices which many people frequently carry in daily life. By analyzing the data we showed that the majority of human encounters occur once-in-an-experimental-period: they are Ichi-go Ichi-e. We also found that the remaining more frequent encounters obey a power-law distribution: they are scale-free. To theoretically find the origin of these properties, we introduced as a minimal human mobility model, Homesick Lévy walk, where the walker stochastically selects moving long distances as well as Lévy walk or returning back home. Using numerical simulations and a simple mean-field theory, we offer a theoretical explanation for the properties to validate the mobility model. The proposed model is helpful for evaluating long-term performance of routing protocols in delay tolerant networks and mobile opportunistic networks better since some utility-based protocols select nodes with frequent encounters for message transfer.
description: 8 pages, 10 figures
Adelic geometry on arithmetic surfaces I: idelic and adelic interpretation of the Deligne pairing
Creators: name: Dolce, Paolo
Publisher: name: arXiv
Year: 2018
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: For an arithmetic surface $X\to B=\operatorname{Spec} O_K$ the Deligne pairing $\left <\,,\,\right > \colon \operatorname{Pic}(X) \times \operatorname{Pic}(X) \to \operatorname{Pic}(B)$ gives the "schematic contribution" to the Arakelov intersection number. We present an idelic and adelic interpretation of the Deligne pairing; this is the first crucial step for a full idelic and adelic interpretation of the Arakelov intersection number. For the idelic approach we show that the Deligne pairing can be lifted to a pairing $\left<\,,\,\right>_i:\ker(d^1_\times)\times \ker(d^1_\times)\to\operatorname{Pic}(B) $, where $\ker(d^1_\times)$ is an important subspace of the two dimensional idelic group $\mathbf A_X^\times$. On the other hand, the argument for the adelic interpretation is entirely cohomological.
description: Some typos have been corrected
Genome-Wide Identification of Mycobacterium tuberculosis Exported Proteins with Roles in Intracellular Growth
Creators: name: McDonough, J. A.
name: Feltcher, M. E.
name: McCann, J. R.
name: Sullivan, J. T.
name: Braunstein, M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The exported proteins of Mycobacterium tuberculosis that are localized at the bacterial cell surface or secreted into the environment are ideally situated to interact with host factors and to function in virulence. In this study, we constructed a novel β-lactamase reporter transposon and used it directly in M. tuberculosis for genome-wide identification of exported proteins. From 177 β-lactam-resistant transposon mutants, we identified 111 different exported proteins. The majority of these proteins have no known function, and for nearly half of the proteins, our demonstration that they are exported when fused to a β-lactamase reporter is the first experimental proof of their extracytoplasmic localization. The transposon mutants in our banked library were of further value as a collection of mutants lacking individual exported proteins. By individually testing each of 111 mutants for growth in macrophages, six attenuated mutants with insertions in mce1A, mce1B, mce2F, rv0199, ctaC, and lppX were identified. Given that much of the M. tuberculosis genome encodes proteins of unknown function, our library of mapped transposon mutants is a valuable resource for efforts in functional genomics. This work also demonstrates the power of a β-lactamase reporter transposon that could be applied similarly to other bacterial pathogens.
Open-string integrals with multiple unintegrated punctures at genus one
Creators: name: Kaderli, André
name: Rodriguez, Carlos
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Number Theory (math.NT)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We study integrals appearing in intermediate steps of one-loop open-string amplitudes, with multiple unintegrated punctures on the $A$-cycle of a torus. We construct a vector of such integrals which closes after taking a total differential with respect to the $N$ unintegrated punctures and the modular parameter $τ$. These integrals are found to satisfy the elliptic Knizhnik-Zamolodchikov-Bernard (KZB) equations, and can be written as a power series in $α$' -- the string length squared -- in terms of elliptic multiple polylogarithms (eMPLs). In the $N$-puncture case, the KZB equation reveals a representation of $B_{1,N}$, the braid group of $N$ strands on a torus, acting on its solutions. We write the simplest of these braid group elements -- the braiding one puncture around another -- and obtain generating functions of analytic continuations of eMPLs. The KZB equations in the so-called universal case is written in terms of the genus-one Drinfeld-Kohno algebra $\mathfrak{t}_{1,N} \rtimes \mathfrak{d}$, a graded algebra. Our construction determines matrix representations of various dimensions for several generators of this algebra which respect its grading up to commuting terms.
description: 44+39 pages and ancillary file
Understanding the assembly of Kepler's compact planetary systems
Creators: name: Hands, T. O.
name: Alexander, R. D.
name: Dehnen, W.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: The Kepler mission has recently discovered a number of exoplanetary systems, such as Kepler-11 and Kepler-32, in which ensembles of several planets are found in very closely packed orbits (often within a few percent of an AU of one another). These compact configurations present a challenge for traditional planet formation and migration scenarios. We present a dynamical study of the assembly of these systems, using an N-body method which incorporates a parametrized model of planet migration in a turbulent protoplanetary disc. We explore a wide parameter space, and find that under suitable conditions it is possible to form compact, close-packed planetary systems via traditional disc-driven migration. We find that simultaneous migration of multiple planets is a viable mechanism for the assembly of tightly-packed planetary systems, as long as the disc provides significant eccentricity damping and the level of turbulence in the disc is modest. We discuss the implications of our preferred parameters for the protoplanetary discs in which these systems formed, and comment on the occurrence and significance of mean-motion resonances in our simulations.
description: 12 pages, 4 figures, 2 tables. Accepted for publication in Monthly Notices of the Royal Astronomical Society
Bernoulli disjointness
Creators: name: Glasner, Eli
name: Tsankov, Todor
name: Weiss, Benjamin
name: Zucker, Andy
Publisher: name: arXiv
Year: 2019
Subjects: subject: Dynamical Systems (math.DS)
subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: 37B05 (Primary) 37B10, 54H20 (Secondary)

description: Generalizing a result of Furstenberg, we show that for every infinite discrete group $G$, the Bernoulli flow $2^G$ is disjoint from every minimal $G$-flow. From this, we deduce that the algebra generated by the minimal functions $\mathfrak{A}(G)$ is a proper subalgebra of $\ell^\infty(G)$ and that the enveloping semigroup of the universal minimal flow $M(G)$ is a proper quotient of the universal enveloping semigroup $βG$. When $G$ is countable, we also prove that for any metrizable, minimal $G$-flow, there exists a free, minimal flow disjoint from it and that there exist continuum many mutually disjoint minimal, free, metrizable $G$-flows. Finally, improving a result of Frisch, Tamuz, and Vahidi Ferdowsi and answering a question of theirs, we show that if $G$ is a countable icc group, then it admits a free, minimal, proximal flow.
description: 28 pages; some details added, minor corrections
Triggered Mycobacterium tuberculosis Heparin-Binding Hemagglutinin Adhesin Folding and Dimerization
Creators: name: Tripathy, A.
name: Redinbo, M. R.
name: Lomino, J. V.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The heparin-binding hemagglutinin adhesin (HBHA) is a surface adhesin on the human pathogen Mycobacterium tuberculosis. Previously, it has been shown that HBHA exists as a dimer in solution. We investigated the detailed nature of this dimer using circular dichroism spectroscopy and analytical ultracentrifugation techniques. We demonstrate that the heparan sulfate (HS) binding region does not play a role in dimerization in solution, while the linker region between the predicted N-terminal coiled-coil and the C-terminal HS binding region does affect dimer stability. The majority of contacts responsible for dimerization, folding, and stability lie within the predicted coiled-coil region of HBHA, while the N-terminal helix preceding the coiled-coil appears to trigger the folding and dimerization of HBHA. Constructs lacking this initial helix or containing site-specific mutations produce nonhelical monomers in solution. Thus, we show that HBHA dimerization and folding are linked and that the N-terminal region of this cell surface adhesin triggers the formation of an HBHA coiled-coil dimer.
Distinguishing f(R) gravity with cosmic voids
Creators: name: Zivick, Paul
name: Sutter, P. M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We use properties of void populations identified in N-body simulations to forecast the ability of upcoming galaxy surveys to differentiate models of f(R) gravity from ΛCDM cosmology. We analyze simulations designed to mimic the densities, volumes, and clustering statistics of upcoming surveys, using the public VIDE toolkit. We examine void abundances as a basic probe at redshifts 1.0 and 0.4. We find that stronger f(R) coupling strengths produce voids up to ~20% larger in radius, leading to a significant shift in the void number function. As an initial estimate of the constraining power of voids, we use this change in the number function to forecast a constraint on the coupling strength of $Δf_{R_{0}} = 10^{-5}$.
description: To appear as proceedings of the IAU Symposium 308 "The Zeldovich Universe, Genesis and Growth of the Cosmic Web"
Cyclic Diguanylate Inversely Regulates Motility and Aggregation in Clostridium difficile
Creators: name: McBride, S. M.
name: Tamayo, R.
name: Waters, C. M.
name: Purcell, E. B.
name: McKee, R. W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Clostridium difficile-associated disease is increasing in incidence and is costly to treat. Our understanding of how this organism senses its entry into the host and adapts for growth in the large bowel is limited. The small-molecule second messenger cyclic diguanylate (c-di-GMP) has been extensively studied in Gram-negative bacteria and has been shown to modulate motility, biofilm formation, and other processes in response to environmental signals, yet little is known about the functions of this signaling molecule in Gram-positive bacteria or in C. difficile specifically. In the current study, we investigated the function of the second messenger c-di-GMP in C. difficile. To determine the role of c-di-GMP in C. difficile, we ectopically expressed genes encoding a diguanylate cyclase enzyme, which synthesizes c-di-GMP, or a phosphodiesterase enzyme, which degrades c-di-GMP. This strategy allowed us to artificially elevate or deplete intracellular c-di-GMP, respectively, and determine that c-di-GMP represses motility in C. difficile, consistent with previous studies in Gram-negative bacteria, in which c-di-GMP has a negative effect on myriad modes of bacterial motility. Elevated c-di-GMP levels also induced clumping of C. difficile cells, which may signify that C. difficile is capable of forming biofilms in the host. In addition, we directly quantified, for the first time, c-di-GMP production in a Gram-positive bacterium. This work demonstrates the effect of c-di-GMP on the motility of a Gram-positive bacterium and on aggregation of C. difficile, which may be relevant to the function of this signaling molecule during infection.
Conserved relativistic Ertel's current generating the vortical and thermodynamic aspects of spacetime
Creators: name: Sakuma, Hirofumi
name: Ojima, Izumi
name: Saigo, Hayato
name: Okamura, Kazuya
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: Motivated by Aoki et al.'s recent research on conserved charges and entropy current, we investigated the conservation of relativistic Ertel's current, which has received little attention outside the field of geophysical fluid dynamics. Ertel's charge is an important indicator of the correlation between vortex vectors and entropy gradient fields in Earth's meridional heat transport. We first show that in the generalized Hamiltonian structure of baroclinic fluids, the duality between the total energy and the Casimir as a function of Ertel's charge plays an important role in the nonrelativistic case. Then, by extending the result to relativistic cases, we show that this finding has far-reaching implications not only for spacetime issues in cosmology but also for the foundation of quantum field theory. An especially important finding is that, as an unreported dual form of the Einstein field equation, we identify a special equation satisfied not only by the vortex tensor field generated by the conserved charge but also by the Weyl tensor in interpreting the physical nature of the metric tensor $g^{μν}$, which appears in the cosmological term $Λg^{μν}$.
description: 16 pages, Submitted to Int. J. Mod. Phys. A
$K(π, 1)$-neighborhoods and comparison theorems
Creators: name: Achinger, Piotr
Publisher: name: arXiv
Year: 2014
Subjects: subject: Algebraic Geometry (math.AG)
subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 14F30

description: A technical ingredient in Faltings' original approach to p-adic comparison theorems involves the construction of $K(π, 1)$-neighborhoods for a smooth scheme X over a mixed characteristic dvr with a perfect residue field: every point of X has an open neighborhood whose general fiber is a $K(π, 1)$ scheme (a notion analogous to having a contractible universal cover). We show how to extend this result to the logarithmically smooth case, which might help to simplify some proofs in p-adic Hodge theory. The main ingredient of the proof is a variant of a trick of Nagata used in his proof of the Noether Normalization Lemma.
description: 24 pages
Kleinian Schottky groups, Patterson-Sullivan measures and Fourier decay
Creators: name: Li, Jialun
name: Naud, Frederic
name: Pan, Wenyu
Publisher: name: arXiv
Year: 2019
Subjects: subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: 37D40, 42B10, 60B15

description: Let $Γ$ be a Zariski dense Kleinian Schottky subgroup of PSL2(C). Let $Λ(Γ)$ be its limit set, endowed with a Patterson-Sullivan measure $μ$ supported on $Λ(Γ)$. We show that the Fourier transform $\widehatμ(ξ)$ enjoys polynomial decay as $\vert ξ\vert$ goes to infinity. This is a PSL2(C) version of the result of Bourgain-Dyatlov [8], and uses the decay of exponential sums based on Bourgain-Gamburd sum-product estimate on C. These bounds on exponential sums require a delicate non-concentration hypothesis which is proved using some representation theory and regularity estimates for stationary measures of certain random walks on linear groups.
description: 2 figures
The effect of spanwise heterogeneous surfaces on mixed convection in turbulent channels
Creators: name: Schäfer, K.
name: Frohnapfel, B.
name: Mellado, J. P.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Turbulent mixed convection in channel flows with heterogeneous surfaces is studied using direct numerical simulations. The relative importance between buoyancy and shear effects, characterized by the bulk Richardson number $Ri_b$, is varied in order to cover the flow regimes of forced, mixed and natural convection, which are associated with different large-scale flow organization. The heterogeneous surface consists of streamwise-aligned ridges, which are known to induce secondary motion in case of forced convection. The large-scale streamwise rolls emerging under smooth-wall mixed convection conditions are significantly affected by the heterogeneous surfaces and their appearance is considerably reduced for dense ridge spacings. It is found that the formation of these rolls requires larger buoyancy forces than over smooth walls due to the additional drag induced by the ridges. Therefore, the transition from forced convection structures to rolls is delayed towards larger $Ri_b$ for spanwise heterogeneous surfaces. The influence of the heterogeneous surface on the flow organization of mixed convection is particularly pronounced in the roll-to-cell transition range, where ridges favor the transition to convective cells at significantly lower $Ri_b$. In addition, the convective cells are observed to align perpendicular to the ridges with decreasing ridge spacing. We attribute this reorganization to the fact that flow parallel to the ridges experience less drag than flow across the ridges, which is energetically more beneficial. Furthermore, we find that streamwise rolls exhibit very slow dynamics for $Ri_b=1$ and $Ri_b=3.2$ when the ridge spacing is in the order of the rolls' width. For these cases the up- and downdrafts of the rolls move slowly across the entire channel instead of being fixed in space as observed for the smooth-wall cases.
description: 34 pages manuscript with 19 figures submitted to Journal of Fluid Mechanics
Francisella tularensis RipA Protein Topology and Identification of Functional Domains
Creators: name: Mortensen, B. L.
name: Taft-Benz, S.
name: Fuller, J. R.
name: Collins, E. J.
name: Kawula, T. H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Francisella tularensis is a Gram-negative coccobacillus and is the etiological agent of the disease tularemia. Expression of the cytoplasmic membrane protein RipA is required for Francisella replication within macrophages and other cell types; however, the function of this protein remains unknown. RipA is conserved among all sequenced Francisella species, and RipA-like proteins are present in a number of individual strains of a wide variety of species scattered throughout the prokaryotic kingdom. Cross-linking studies revealed that RipA forms homoligomers. Using a panel of RipA-green fluorescent protein and RipA-PhoA fusion constructs, we determined that RipA has a unique topology within the cytoplasmic membrane, with the N and C termini in the cytoplasm and periplasm, respectively. RipA has two significant cytoplasmic domains, one composed roughly of amino acids 1 to 50 and the second flanked by the second and third transmembrane domains and comprising amino acids 104 to 152. RipA functional domains were identified by measuring the effects of deletion mutations, amino acid substitution mutations, and spontaneously arising intragenic suppressor mutations on intracellular replication, induction of interleukin-1β (IL-1β) secretion by infected macrophages, and oligomer formation. Results from these experiments demonstrated that each of the cytoplasmic domains and specific amino acids within these domains are required for RipA function.
Experimental observation of a dissipative phase transition in a multi-mode many-body quantum system
Creators: name: Benary, Jens
name: Baals, Christian
name: Bernhart, Erik
name: Jiang, Jian
name: Röhrle, Marvin
name: Ott, Herwig
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We characterize the dissipative phase transition in a driven dissipative Bose-Einstein condensate of neutral atoms. Our results generalize the work on dissipative nonlinear Kerr resonators towards many modes and stronger interactions. We measure the effective Liouvillian gap and analyze the microscopic system dynamics, where we identify a non-equilibrium condensation process.
description: 9 pages, 7 figures
Candidate for the crystal $B(-\infty)$ for the queer Lie superalgebra
Creators: name: Salisbury, Ben
name: Scrimshaw, Travis
Publisher: name: arXiv
Year: 2019
Subjects: subject: Combinatorics (math.CO)
subject: Quantum Algebra (math.QA)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics
subject: 05E10, 17B37

description: It is shown that the direct limit of the semistandard decomposition tableau model for polynomial representations of the queer Lie superalgebra exists, which is believed to be the crystal for the upper half of the corresponding quantum group. An extension of this model to describe the direct limit combinatorially is given. Furthermore, it is shown that the polynomial representations may be recovered from the limit in most cases.
description: 25 pages, 3 figures
A Model Independent Approach to Inelastic Dark Matter Scattering
Creators: name: Barello, G.
name: Chang, Spencer
name: Newby, Christopher A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We present a model independent analysis of inelastic dark matter transitions at direct detection experiments by modifying the elastic methodology of Fitzpatrick, et al. By analyzing the kinematics of inelastic transitions, we find the relevant variables to describe these scattering processes, the primary change being a modification of the $\vec{v}^\perp$ variable. Taking this into account, we list the relevant scattering matrix elements and modify the Mathematica package of Anand, et al. to calculate the necessary form factors. As an application, we determine the matrix elements of inelastic scattering for spin transitions between a fermion to fermion, scalar to vector, and scalar to scalar. Finally, we consider fits to the DAMA/LIBRA annual modulation signal for the magnetic inelastic dark matter scenario as well as a model independent scan over relativistic operators, constraining them with limits from direct detection experiments. In the magnetic inelastic dark matter scenario or if the dark matter couples through relativistic operators involving only protons, we find that experiments with xenon and germanium targets can have consistently small rates. However, limits from iodine experiments are much more constraining, leaving small regions of allowed parameter space. We point out that existing uncertainties in the iodine quenching factor strongly affects the constraints, motivating further study to pin down the correct values.
description: 21 pages, 23 figures, revtex
2-Group Symmetries and M-Theory
Creators: name: Del Zotto, Michele
name: Etxebarria, Iñaki García
name: Schafer-Nameki, Sakura
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Quantum Field Theories engineered in M-theory can have 2-group symmetries, mixing 0-form and 1-form symmetry backgrounds in non-trivial ways. In this paper we develop methods for determining the 2-group structure from the boundary geometry of the M-theory background. We illustrate these methods in the case of 5d theories arising from M-theory on ordinary and generalised toric Calabi-Yau cones, including cases in which the resulting theory is non-Lagrangian. Our results confirm and elucidate previous results on 2-groups from geometric engineering.
description: 27 pages
Calcium Binding Properties of the Kingella kingae PilC1 and PilC2 Proteins Have Differential Effects on Type IV Pilus-Mediated Adherence and Twitching Motility
Creators: name: Johnson, M. D. L.
name: Porsch, E. A.
name: Broadnax, A. D.
name: Garrett, C. K.
name: Redinbo, M. R.
name: St. Geme, J. W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Kingella kingae is an emerging bacterial pathogen that is being recognized increasingly as an important etiology of septic arthritis, osteomyelitis, and bacteremia, especially in young children. The pathogenesis of K. kingae disease begins with bacterial adherence to respiratory epithelium, which is dependent on type IV pili and is influenced by two PilC-like proteins called PilC1 and PilC2. Production of either PilC1 or PilC2 is necessary for K. kingae piliation and bacterial adherence. In this study, we set out to further investigate the role of PilC1 and PilC2 in type IV pilus-associated phenotypes. We found that PilC1 contains a functional 9-amino-acid calcium-binding (Ca-binding) site with homology to the Pseudomonas aeruginosa PilY1 Ca-binding site and that PilC2 contains a functional 12-amino-acid Ca-binding site with homology to the human calmodulin Ca-binding site. Using targeted mutagenesis to disrupt the Ca-binding sites, we demonstrated that the PilC1 and PilC2 Ca-binding sites are dispensable for piliation. Interestingly, we showed that the PilC1 site is necessary for twitching motility and adherence to Chang epithelial cells, while the PilC2 site has only a minor influence on twitching motility and no influence on adherence. These findings establish key differences in PilC1 and PilC2 function in K. kingae and provide insights into the biology of the PilC-like family of proteins.
Asymptotic sign coherence conjecture
Creators: name: Gekhtman, Michael
name: Nakanishi, Tomoki
Publisher: name: arXiv
Year: 2019
Subjects: subject: Combinatorics (math.CO)
subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: 13F60

description: The sign coherence phenomenon is an important feature of c-vectors in cluster algebras with principal coefficients. In this note, we consider a more general version of c-vectors defined for arbitrary cluster algebras of geometric type and formulate a conjecture describing their asymptotic behavior. This conjecture, which is called the asymptotic sign coherence conjecture, states that for any infinite sequence of matrix mutations that satisfies certain natural conditions, the corresponding c-vectors eventually become sign coherent. We prove this conjecture for rank 2 cluster algebras of infinite type and for a particular sequence of mutations in a cluster algebra associated with the Markov quiver.
description: 13 pages, 2 figures
A possible solution to the Hubble constant discrepancy -- Cosmology where the local volume expansion is driven by the domain average density
Creators: name: Kasai, Masumi
name: Futamase, Toshifumi
Publisher: name: arXiv
Year: 2019
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The Hubble constant problem is the discrepancy between different measurements of the Hubble constant in different scales. We show that this problem can be resolved within the general relativistic framework of the perturbation theory in the inhomogeneous universe, with the help of spatial averaging procedure over a finite local domain in the $t=\mbox{const.}$ hypersurface. The idea presented in this paper is unique in the sense that it has all of the following properties. a) It is based on the general relativistic perturbation theory, with ordinary dust matter only. No strange matter nor energy components are required. b) The employment of the spatially invariant averaging procedure on the finite domain is essential. c) The key is the first-order effect of the inhomogeneities in the linear perturbation theory. No non-linear effects are required.
UAV Trajectory and Beamforming Optimization for Integrated Periodic Sensing and Communication
Creators: name: Meng, Kaitao
name: Wu, Qingqing
name: Ma, Shaodan
name: Chen, Wen
name: Quek, Tony Q. S.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Information Theory (cs.IT)
subject: Signal Processing (eess.SP)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Unmanned aerial vehicle (UAV) is expected to bring transformative improvement to the integrated sensing and communication (ISAC) system. However, due to shared spectrum resources, it is challenging to achieve a critical trade-off between these two integrated functionalities. To address this issue, we propose in this paper a new integrated \emph{periodic} sensing and communication mechanism for the UAV-enable ISAC system. Specifically, the user achievable rate is maximized via jointly optimizing UAV trajectory, transmit precoder, and sensing start instant, subject to the sensing frequency and beam pattern gain constraints. Despite that this problem is highly non-convex and involves an infinite number of variables, we obtain the optimal transmit precoder and derive the optimal achievable rate in closed-form for any given UAV location to facilitate the UAV trajectory design. Furthermore, we first prove the structural symmetry between optimal solutions in different ISAC frames without location constraints and then propose a high-quality UAV trajectory and sensing optimization algorithm for the general location-constrained case. Simulation results corroborate the effectiveness of the proposed design and also unveil a more flexible trade-off in ISAC systems over benchmark schemes.
description: Accepted by IEEE Wireless Communications Letters
A Herschel [CII] Galactic plane survey III: [CII] as a tracer of star formation
Creators: name: Pineda, Jorge L.
name: Langer, William D.
name: Goldsmith, Paul F.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We study the relationship between the [CII] emission and the star formation rate (SFR) in the Galactic plane and separate the relationship of different ISM phases to the SFR. We compare these relationships to those in external galaxies and local clouds, allowing examinations of these relationships over a wide range of physical scales. We compare the distribution of the [CII] emission, with its different contributing ISM phases, as a function of Galactocentric distance with the SFR derived from radio continuum observations. We also compare the SFR with the surface density distribution of atomic and molecular gas, including the CO-dark H2 component. The [CII] and SFR are well correlated at Galactic scales with a relationship that is in general agreement with that found for external galaxies. By combining [CII] and SFR data points in the Galactic plane with those in external galaxies and nearby star forming regions, we find that a single scaling relationship between the [CII] luminosity and SFR applies over six orders of magnitude. The [CII] emission from different ISM phases are each correlated with the SFR, but only the combined emission shows a slope that is consistent with extragalactic observations. These ISM components have roughly comparable contributions to the Galactic [CII] luminosity: dense PDRs (30%), cold HI (25%), CO-dark H2 (25%), and ionized gas (20%). The SFR-gas surface density relationship shows a steeper slope compared to that observed in galaxies, but one that it is consistent with those seen in nearby clouds. The different slope is a result of the use of a constant CO-to-H2 conversion factor in the extragalactic studies, which in turn is related to the assumption of constant metallicity in galaxies. We find a linear correlation between the SFR surface density and that of the dense molecular gas.
description: 14 pages, 10 figures, accepted for publication in A&A
Chebyshev polynomials in the 16th century
Creators: name: Van Assche, Walter
Publisher: name: arXiv
Year: 2022
Subjects: subject: History and Overview (math.HO)
subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: 33-03, 33C45, 01A40

description: We give a few examples of Chebyshev polynomials that appeared in mathematical problems from the 16th and 17th century. The main example is the famous equation of Adrianus Romanus (Adriaan van Roomen) containing a polynomial of degree $45$.
description: 16 pages, 4 figures
Mapping accretion and its variability in the young open cluster NGC 2264: a study based on u-band photometry
Creators: name: Venuti, Laura
name: Bouvier, Jérôme
name: Flaccomio, Ettore
name: Alencar, Silvia H. P.
name: Irwin, Jonathan
name: Stauffer, John R.
name: Cody, Ann Marie
name: Teixeira, Paula S.
name: Sousa, Alana P.
name: Micela, Giuseppina
name: Cuillandre, Jean-Charles
name: Peres, Giovanni
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We aim at characterizing the accretion properties of several hundred members of the star-forming cluster NGC 2264 (3 Myr). We performed a deep u,g,r,i mapping and a simultaneous u+r monitoring of the region with CFHT/MegaCam in order to directly probe the accretion process from UV excess measurements. Photometric properties and stellar parameters are determined homogeneously for about 750 monitored young objects, spanning the mass range 0.1-2 Mo. About 40% are classical (accreting) T Tauri stars, based on various diagnostics (H_alpha, UV and IR excesses). The remaining non-accreting members define the (photospheric+chromospheric) reference UV emission level over which flux excess is detected and measured. We revise the membership status of cluster members based on UV accretion signatures and report a new population of 50 CTTS candidates. A large range of UV excess is measured for the CTTS population, varying from a few 0.1 to 3 mag. We convert these values to accretion luminosities and obtain mass accretion rates ranging from 1e-10 to 1e-7 Mo/yr. Taking into account a mass-dependent detection threshold for weakly accreting objects, we find a >6sigma correlation between mass accretion rate and stellar mass. A power-law fit, properly accounting for upper limits, yields M_acc $\propto$ M^{1.4+/-0.3}. At any given stellar mass, we find a large spread of accretion rates, extending over about 2 orders of magnitude. The monitoring of the UV excess on a timescale of a couple of weeks indicates that its variability typically amounts to 0.5 dex, much smaller than the observed spread. We suggest that a non-negligible age spread across the cluster may effectively contribute to the observed spread in accretion rates at a given mass. In addition, different accretion mechanisms (like, e.g., short-lived accretion bursts vs. more stable funnel-flow accretion) may be associated to different M_acc regimes.
description: 24 pages, 21 figures, accepted for publication in Astronomy & Astrophysics
Stability conditions on morphisms in a category
Creators: name: Kawatani, Kotaro
Publisher: name: arXiv
Year: 2019
Subjects: subject: Algebraic Geometry (math.AG)
subject: Algebraic Topology (math.AT)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics

description: Let $\mathrm{h}\mathscr{C}$ be the homotopy category of a stable infinity category $\mathscr{C}$. Then the homotopy category $\mathrm{h}\mathscr{C}^{Δ^{1}}$ of morphisms in the stable infinity category $\mathscr{C}$ is also triangulated. Hence the space $\mathsf{Stab}\,{ \mathrm{h}\mathscr{C}^{Δ^{1}}}$ of stability conditions on $\mathrm{h}\mathscr{C}^{Δ^{1}}$ is well-defined though the non-emptiness of $\mathsf{Stab}\,{ \mathrm{h}\mathscr{C}^{Δ^{1}}}$ is not obvious. Our basic motivation is a comparison of the homotopy type of $\mathsf{Stab}{\mathrm{h}\mathscr{C}}$ and that of $\mathsf{Stab}{\mathrm{h}\mathscr{C}^{Δ^{1}}}$. Under the motivation we show that functors $d_{0}$ and $d_{1} \colon \mathscr{C}^{Δ^{1}} \rightrightarrows \mathscr{C}$ induce continuous maps from $\mathsf{Stab} {\mathrm{h}\mathscr{C}}$ to $\mathsf{Stab}{\mathrm{h}\mathscr{C}^{Δ^{1}}}$ contravariantly where $d_{0}$ (resp. $d_{1}$) takes a morphism to the target (resp. source) of the morphism. As a consequence, if $\mathsf{Stab}{\mathrm{h}\mathscr{C}}$ is nonempty then so is $\mathsf{Stab}{\mathrm{h}\mathscr{C}^{Δ^{1}}}$. Assuming $\mathscr{C}$ is the derived infinity category of the projective line over a field, we further study basic properties of $d_{0}^{*} $ and $d_{1}^{*}$. In addition, we give an example of a derived category which does not have any stability condition.
description: 26 pages, comments are welcome. For v2, added subsection 2.2 which gives a description of a Serre functor of the category of morphisms in $\mathbf D$. For v3, the proof of Proposition 3.3 has been updated. For v5, Section 6 was added. For v6, modified the proof of Proposition 6.1. For v7, minor revision for Proposition 6.1, final version
Mutational Analysis of Hemoglobin Binding and Heme Utilization by a Bacterial Hemoglobin Receptor
Creators: name: Fusco, W. G.
name: Council, S. E.
name: Collins, E. J.
name: Choudhary, N. R.
name: Leduc, I.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Iron is an essential nutrient for most living organisms. To acquire iron from their environment, Gram-negative bacteria use TonB-dependent transporters that bind host proteins at the bacterial surface and transport iron or heme to the periplasm via the Ton machinery. TonB-dependent transporters are barrel-shaped outer membrane proteins with 22 transmembrane domains, 11 surface-exposed loops, and a plug domain that occludes the pore. To identify key residues of TonB-dependent transporters involved in hemoglobin binding and heme transport and thereby locate putative protective epitopes, the hemoglobin receptor of Haemophilus ducreyi HgbA was used as a model of iron/heme acquisition from hemoglobin. Although all extracellular loops of HgbA are required by H. ducreyi to use hemoglobin as a source of iron/heme, we previously demonstrated that hemoglobin binding by HgbA only involves loops 5 and 7. Using deletion, substitution, and site-directed mutagenesis, we were able to differentiate hemoglobin binding and heme acquisition by HgbA. Deletion or substitution of the GYEAYNRQWWA region of loop 5 and alanine replacement of selected histidines affected hemoglobin binding by HgbA. Conversely, mutation of the phenylalanine in the loop 7 FRAP domain or substitution of the NRQWWA motif of loop 5 significantly abrogated utilization of heme from hemoglobin. Our findings show that hemoglobin binding and heme utilization by a bacterial hemoglobin receptor involve specific motifs of HgbA.
Systematic variations of central mass density slopes in early-type galaxies
Creators: name: Tortora, C.
name: La Barbera, F.
name: Napolitano, N. R.
name: Romanowsky, A. J.
name: Ferreras, I.
name: de Carvalho, R. R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We study the total density distribution in the central regions (~ 1 effective radius, $R_e$) of early-type galaxies (ETGs), using data from SPIDER and $\rm ATLAS^{3D}$. Our analysis extends the range of galaxy stellar mass ($M_{\star}$) probed by gravitational lensing, down to ~ $10^{10}\, \rm M_{\odot}$. We model each galaxy with two components (dark matter halo + stars), exploring different assumptions for the dark matter (DM) halo profile (i.e. NFW, NFW-contracted, and Burkert profiles), and leaving stellar mass-to-light ($M_{\star}/L$) ratios as free fitting parameters to the data. For all plausible halo models, the best-fitting $M_{\star}/L$, normalized to that for a Chabrier IMF, increases systematically with galaxy size and mass. For an NFW profile, the slope of the total mass profile is non-universal, independently of several ingredients in the modeling (e.g., halo contraction, anisotropy, and rotation velocity in ETGs). For the most massive ($M_{\star}$ ~ $10^{11.5} \, M_{\odot}$) or largest ($R_{\rm e}$ ~ $15 \, \rm kpc$) ETGs, the profile is isothermal in the central regions (~$R_{\rm e}/2$), while for the low-mass ($M_{\star}$ ~ $10^{10.2} \, M_\odot$) or smallest ($R_{\rm e}$ ~ $0.5 \, \rm kpc$) systems, the profile is steeper than isothermal, with slopes similar to those for a constant-$M/L$ profile. For a steeper concentration-mass relation than that expected from simulations, the correlation of density slope with galaxy mass tends to flatten, while correlations with $R_{\rm e}$ and velocity dispersions are more robust. Our results clearly point to a "non-homology" in the total mass distribution of ETGs, which simulations of galaxy formation suggest may be related to a varying role of dissipation with galaxy mass.
description: 15 pages, 6 figures, 3 tables, MNRAS in press