cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Isolation and Characterization of Nonchemotactic CheZ Mutants of Escherichia coli
Creators: name: Bourret, R. B.
name: Silversmith, R. E.
name: Boesch, K. C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2000

description: The Escherichia coli CheZ protein stimulates dephosphorylation of CheY, a response regulator in the chemotaxis signal transduction pathway, by an unknown mechanism. Genetic analysis of CheZ has lagged behind biochemical and biophysical characterization. To identify putative regions of functional importance in CheZ, we subjected cheZ to random mutagenesis and isolated 107 nonchemotactic CheZ mutants. Missense mutations clustered in six regions of cheZ, whereas nonsense and frameshift mutations were scattered reasonably uniformly across the gene. Intragenic complementation experiments showed restoration of swarming activity when compatible plasmids containing genes for the truncated CheZ1–189 peptide and either CheZA65V, CheZL90S, or CheZD143G were both present, implying the existence of at least two independent functional domains in each chain of the CheZ dimer. Six mutant CheZ proteins, one from each cluster of loss-of-function missense mutations, were purified and characterized biochemically. All of the tested mutant proteins were defective in their ability to dephosphorylate CheY-P, with activities ranging from 0.45 to 16% of that of wild-type CheZ. There was good correlation between the phosphatase activity of CheZ and the ability to form large chemically cross-linked complexes with CheY in the presence of the CheY phosphodonor acetyl phosphate. In consideration of both the genetic and biochemical data, the most severe functional impairments in this set of CheZ mutants seemed to be concentrated in regions which are located in a proposed large N-terminal domain of the CheZ protein.
Joint moments of proper delay times
Creators: name: Martínez-Argüello, Angel M.
name: Martínez-Mares, Moisés
name: García, Julio C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We calculate negative moments of the $N$-dimensional Laguerre distribution for the orthogonal, unitary, and symplectic symmetries. These moments correspond to those of the proper delay times, which are needed to determine the statistical fluctuations of several transport properties through classically chaotic cavities, like quantum dots and microwave cavities with ideal coupling.
Two Nonredundant SecA Homologues Function in Mycobacteria
Creators: name: Braunstein, M.
name: Kurtz, S.
name: Brown, A. M.
name: Jacobs, W. R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2001

description: The proper extracytoplasmic localization of proteins is an important aspect of mycobacterial physiology and the pathogenesis of Mycobacterium tuberculosis. The protein export systems of mycobacteria have remained unexplored. The Sec-dependent protein export pathway has been well characterized in Escherichia coli and is responsible for transport across the cytoplasmic membrane of proteins containing signal sequences at their amino termini. SecA is a central component of this pathway, and it is highly conserved throughout bacteria. Here we report on an unusual property of mycobacterial protein export—the presence of two homologues of SecA (SecA1 and SecA2). Using an allelic-exchange strategy in Mycobacterium smegmatis, we demonstrate that secA1 is an essential gene. In contrast, secA2 can be deleted and is the first example of a nonessential secA homologue. The essential nature of secA1, which is consistent with the conserved Sec pathway, leads us to believe that secA1 represents the equivalent of E. coli secA. The results of a phenotypic analysis of a ΔsecA2 mutant of M. smegmatis are presented here and also indicate a role for SecA2 in protein export. Based on our study, it appears that SecA2 can assist SecA1 in the export of some proteins via the Sec pathway. However, SecA2 is not the functional equivalent of SecA1. This finding, in combination with the fact that SecA2 is highly conserved throughout mycobacteria, suggests a second role for SecA2. The possibility exists that another role for SecA2 is to export a specific subset of proteins.
Hamilton-Jacobi Quantization of Landau-Ginzburg Theory
Creators: name: Eshraim, Walaa. I.
Publisher: name: arXiv
Year: 2013
Subjects: subject: General Physics (physics.gen-ph)
subject: FOS: Physical sciences

description: We discuss the Hamilton-Jacobi approach for a constrained system. We obtain the equation of motion for a singular system as total differential equations in many variables. We investigate the integrability conditions without using any gauge fixing condition. The path integral quantization for systems with finite degrees of freedom is applied to the field theories with constraints. So, we apply the Hamilton-Jacobi quantization to obtain the path integral of the Landau-Ginzburg theory.
description: 9 pages
THE ROLE OF NOTCH PATHWAY IN MULTIPLE MYELOMA PROGRESSION: CONTROL OF IL-6 EXPRESSION IN MALIGNANT PLASMA CELLS AND BONE MARROW NICHE
Creators: name: GALLETTI, SERENA
Publisher: name: Universit� degli Studi di Milano
Year: 2017

description: Multiple myeloma (MM) is an incurable hematological tumor characterized by the accumulation of malignant plasma cells (PCs) within the bone marrow (BM). MM cells create a very strictly interaction with the surrounding BM niche that directly supports tumor growth through adhesion molecules and soluble factors, the most important of which is interleukin-6 (IL-6). IL-6 is probably the most important factor for MM cells growth and survival in vivo and it mainly produced by non-neoplastic cells of the BM microenvironment, and at less extent by malignant plasma cells. Recent studies suggest the involvement of NOTCH pathway in the pathogenesis of multiple myeloma. The NOTCH pathway is composed by four isoforms of receptors (NOTCH1-4) and two family of ligands, the Serrate-like ligands (JAGGED1 and 2) and the Delta-like ligands (DLL1/3/4). NOTCH pathway plays an important role in several cellular processes such as proliferation, survival, differentiation and stemness in various tissues and tumors. Regarding MM, the up-regulation of NOTCH signaling is due to the over-expression of both receptors (NOTCH1 and NOTCH2) and ligands (JAGGED1 and JAGGED2): these alterations promote tumor growth, pharmacological resistance, and bone disease. Furthermore, NOTCH pathway plays an important role in the pathological interaction between malignant PCs and the BM niche. This study indicates that there is a correlation between levels of NOTCH signaling members (JAGGED1, NOTCH2, HES5 and HES6) and the malignant progression of the disease. Indeed, NOTCH pathway is involved in multiple myeloma progression since it is able to increase the release of IL-6 produced by BM stromal cells (BMSCs). Our in vitro studies show that NOTCH pathway induces IL-6 gene expression in MM cells as well as in the surrounding BMSCs through the over-expression of JAGGED ligands. The activation of NOTCH pathway in the BMSCs renders these cells able to support tumor cells growth through the production of IL-6. These data are confirmed also by correlation analysis on gene expression profiles of MM patients and immunohistochemical studies. The ability of NOTCH pathway to positively regulate IL-6 in the non-neoplastic cells of BM microenvironment renders this pathway an important mediator of tumor-directed reprogramming of bone marrow niche. These results support the rationale for a NOTCH-direct therapeutic approach that can specifically target JAGGED ligands in order to reduce side effects associated with common NOTCH signaling inhibitor.
Emergent Synchronization and Flocking in Purely Repulsive Self-Navigating Particles
Creators: name: Casiulis, Mathias
name: Levine, Dov
Publisher: name: arXiv
Year: 2022
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Physical sciences

description: Inspired by groups of animals and robots, we study the collective dynamics of large numbers of active particles, each one trying to get to its own randomly placed target, while avoiding collisions with each other. The particles we study are repulsive homing active Brownian particles (HABPs) - self-propelled particles whose orientation relaxes at a finite rate towards an absorbing target in $2d$ continuous space. For a wide range of parameters, these particles form synchronised system-wide chiral flocks, in spite of the absence of explicit alignment interactions. We show that this dramatic behavior obtains for different system sizes and density, that it is robust against the addition of noise, polydispersity, and bounding walls, and that it can exhibit dynamical topological defects. We develop an analogy to an off-lattice, ferromagnetic XY model, which allows us to interpret the different phases, as well as the topological defects.
description: 17 pages, 10 figures. Ancillary videos available
Support Vector Machine Classification on a Biased Training Set: Multi-Jet Background Rejection at Hadron Colliders
Creators: name: Sforza, Federico
name: Lippi, Vittorio
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: This paper describes an innovative way to optimize a multivariate classifier, in particular a Support Vector Machine algorithm, on a problem characterized by a biased training sample. This is possible thanks to the feedback of a signal-background template fit performed on a validation sample and included both in the optimization process and in the input variable selection. The procedure is applied to a real case of interest at hadron collider experiments: the reduction and the estimate of the multi-jet background in the $W\to e ν$ plus jets data sample collected by the CDF experiment. The training samples, partially derived from data and partially from simulation, are described in detail together with the input variables exploited for the classification. At present, the reached performance is superior to any other prescription applied to the same final state at hadron collider experiments.
description: 24 pages, 8 figures, preprint of NIM paper
Slowly Decaying Waves on Spherically Symmetric Spacetimes and an Instability of Ultracompact Neutron Stars
Creators: name: Keir, Joseph
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Analysis of PDEs (math.AP)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We prove that, in a class of spherically symmetric spacetimes exhibiting stable trapping of null geodesics, linear waves cannot (uniformly) decay faster than logarithmically. When these linear waves are treated as a model for nonlinear perturbations, this slow decay is highly suggestive of nonlinear instability. We also prove that, in a large class of asymptotically flat, spherically symmetric spacetimes, logarithmic decay actually holds as a uniform upper bound. In the presence of stable trapping, this result is therefore the best one can obtain. In addition, we provide an application of these results to ultracompact neutron stars, suggesting that all stars with r < 3M might be unstable.
description: 43 pages, 3 figure. Updated version to match journal
Converting the NiFeS Carbon Monoxide Dehydrogenase to a Hydrogenase and a Hydroxylamine Reductase
Creators: name: Wolfe, M. T.
name: Staples, C. R.
name: Heo, J.
name: Ludden, P. W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Substitution of one amino acid for another at the active site of an enzyme usually diminishes or eliminates the activity of the enzyme. In some cases, however, the specificity of the enzyme is changed. In this study, we report that the changing of a metal ligand at the active site of the NiFeS-containing carbon monoxide dehydrogenase (CODH) converts the enzyme to a hydrogenase or a hydroxylamine reductase. CODH with alanine substituted for Cys531 exhibits substantial uptake hydrogenase activity, and this activity is enhanced by treatment with CO. CODH with valine substituted for His265 exhibits hydroxylamine reductase activity. Both Cys531 and His265 are ligands to the active-site cluster of CODH. Further, CODH with Fe substituted for Ni at the active site acquires hydroxylamine reductase activity.
Lowest weight modules of Sp_4(R) and nearly holomorphic Siegel modular forms
Creators: name: Pitale, Ameya
name: Saha, Abhishek
name: Schmidt, Ralf
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: We undertake a detailed study of the lowest weight modules for the Hermitian symmetric pair (G,K), where G=Sp_4(R) and K is its maximal compact subgroup. In particular, we determine K-types and composition series, and write down explicit differential operators that navigate all the highest weight vectors of such a module starting from the unique lowest-weight vector. By rewriting these operators in classical language, we show that the automorphic forms on G that correspond to the highest weight vectors are exactly those that arise from nearly holomorphic vector-valued Siegel modular forms of degree 2. Further, by explicating the algebraic structure of the relevant space of n-finite automorphic forms, we are able to prove a structure theorem for the space of nearly holomorphic vector-valued Siegel modular forms of (arbitrary) weight $det^\ell$ sym^m with respect to an arbitrary congruence subgroup of Sp_4(Q). We show that the cuspidal part of this space is the direct sum of subspaces obtained by applying explicit differential operators to holomorphic vector-valued cusp forms of weight $det^{\ell'} sym^{m'}$ with $(\ell', m')$ varying over a certain set. The structure theorem for the space of all modular forms is similar, except that we may now have an additional component coming from certain nearly holomorphic forms of weight $det^{3}sym^{m'}$ that cannot be obtained from holomorphic forms. As an application of our structure theorem, we prove several arithmetic results concerning nearly holomorphic modular forms that improve previously known results in that direction.
description: 51 pages. Accepted version, to appear in Kyoto J. Math
Hydroxylamine Reductase Activity of the Hybrid Cluster Protein from Escherichia coli
Creators: name: Garavelli, J. S.
name: Ludden, P. W.
name: Wolfe, M. T.
name: Heo, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: The hybrid cluster protein (HCP; formerly termed the prismane protein) has been extensively studied due to its unique spectroscopic properties. Although the structural and spectroscopic characteristics are well defined, its enzymatic function, up to this point, has remained unidentified. While it was proposed that HCP acts in some step of nitrogen metabolism, a specific role for this enzyme remained unknown. Recent studies of HCP purified from Escherichia coli have identified a novel hydroxylamine reductase activity. These data reveal the ability of HCP to reduce hydroxylamine in vitro to form NH3 and H2O. Further biochemical analyses were completed in order to determine the effects of various electron donors, different pH levels, and the presence of CN− on in vitro hydroxylamine reduction.
Analysis of photoinjector transverse phase space in action and phase coordinates
Creators: name: Qian, Houjun
name: Krasilnikov, Mikhail
name: Aboulbanine, Zakaria
name: Adhikari, Gowri
name: Aftab, Namra
name: Boonpornpras, Prach
name: Georgiev, Georgi
name: Good, James
name: Gross, Matthias
name: Koschitzki, Christian
name: Li, Xiangkun
name: Lishilin, Osip
name: Lueangaramwong, Anusorn
name: Niemczyk, Raffael
name: Oppelt, Anne
name: Shu, Guan
name: Stephan, Frank
name: Vashchenko, Grygorii
name: Weilbach, Tobias
Publisher: name: arXiv
Year: 2022
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: Photoinjectors are the main high brightness electron sources for X-ray free electron lasers (XFEL). Photoinjector emittance reduction is one of the key knobs for improving XFEL lasing, so precise emittance measurement is critical. It's well known that rms emittance is very sensitive to low intensity tails of particle distributions in the phase space, whose measurement depend on the signal to noise ratio (SNR) and image processing procedures. Such sensitivities make the interpretations of beam transverse brightness challenging, leading to different emittance definitions to reduce the impact of tail particles. In this paper, transverse phase space is analyzed in action and phase coordinates for both analytical models and experiments, which give a more intuitive way to calculate the beam core brightness.
Pervasive variation of transcription factor orthologs contributes to regulatory network evolution
Creators: name: Nadimpalli, Shilpa
name: Persikov, Anton V.
name: Singh, Mona
Publisher: name: arXiv
Year: 2014
Subjects: subject: Genomics (q-bio.GN)
subject: Populations and Evolution (q-bio.PE)
subject: FOS: Biological sciences

description: Differences in transcriptional regulatory networks underlie much of the phenotypic variation observed across organisms. Changes to cis-regulatory elements are widely believed to be the predominant means by which regulatory networks evolve, yet examples of regulatory network divergence due to transcription factor (TF) variation have also been observed. To systematically ascertain the extent to which TFs contribute to regulatory divergence, we analyzed the evolution of the largest class of metazoan TFs, Cys2-His2 zinc finger (C2H2-ZF) TFs, across 12 Drosophila species spanning ~45 million years of evolution. Remarkably, we uncovered that a significant fraction of all C2H2-ZF 1-to-1 orthologs in flies exhibit variations that can affect their DNA-binding specificities. In addition to loss and recruitment of C2H2-ZF domains, we found diverging DNA-contacting residues in ~47% of domains shared between D. melanogaster and the other fly species. These diverging DNA-contacting residues, found in ~66% of the D. melanogaster C2H2-ZF genes in our analysis and corresponding to ~24% of all annotated D. melanogaster TFs, show evidence of functional constraint: they tend to be conserved across phylogenetic clades and evolve slower than other diverging residues. These same variations were rarely found as polymorphisms within a population of D. melanogaster flies, indicating their rapid fixation. The predicted specificities of these dynamic domains gradually change across phylogenetic distances, suggesting stepwise evolutionary trajectories for TF divergence. Further, whereas proteins with conserved C2H2-ZF domains are enriched in developmental functions, those with varying domains exhibit no functional enrichments. Our work suggests that a subset of highly dynamic and largely unstudied TFs are a likely source of regulatory variation in Drosophila and other metazoans.
description: 29 pages, 5 figures, 5 supplemental figures, 3 supplemental tables
Quasinormal modes of a black hole with a cloud of strings in Einstein-Gauss-Bonnet gravity
Creators: name: Graça, J. P. Morais
name: Salako, Godonou I.
name: Bezerra, V. B.
Publisher: name: arXiv
Year: 2016
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The quasinormal modes for a scalar field in the background spacetime corresponding to a black hole, with a cloud of strings, in Einstein-Gauss-Bonnet gravity, and the tensor quasinormal modes corresponding to perturbations in such spacetime, were both calculated using the WKB approximation. In the obtained results we emphasize the role played by the parameter associated with the string cloud, comparing them with the results already obtained for the Boulware-Deser metric. We also study how the Gauss-Bonnet correction to general relativity affects the results for the quasinormal modes, comparing them with the same background in general relativity.
description: 15 pages, 7 figures; To appear in IJMPD
Overexpression of the MtrC-MtrD-MtrE Efflux Pump Due to an mtrR Mutation Is Required for Chromosomally Mediated Penicillin Resistance in Neisseria gonorrhoeae
Creators: name: Nicholas, R. A.
name: Shafer, W. M.
name: Veal, W. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: The importance of the mtrCDE-encoded efflux pump in conferring chromosomally mediated penicillin resistance on certain strains of Neisseria gonorrhoeae was determined by using genetic derivatives of penicillin-sensitive strain FA19 bearing defined mutations (mtrR, penA, and penB) donated by a clinical isolate (FA6140) expressing high-level resistance to penicillin and antimicrobial hydrophobic agents (HAs). When introduced into strain FA19 by transformation, a single base pair deletion in the mtrR promoter sequence from strain FA6140 was sufficient to provide high-level resistance to HAs (e.g., erythromycin and Triton X-100) but only a twofold increase in resistance to penicillin. When subsequent mutations in penA and porIB were introduced from strain FA6140 into strain WV30 (FA19 mtrR) by transformation, resistance to penicillin increased incrementally up to a MIC of 1.0 μg/ml. Insertional inactivation of the gene (mtrD) encoding the membrane transporter component of the Mtr efflux pump in these transformant strains and in strain FA6140 decreased the MIC of penicillin by 16-fold. Genetic analyses revealed that mtrR mutations, such as the single base pair deletion in its promoter, are needed for phenotypic expression of penicillin and tetracycline resistance afforded by the penB mutation. As penB represents amino acid substitutions within the third loop of the outer membrane PorIB protein that modulate entry of penicillin and tetracycline, the results presented herein suggest that PorIB and the MtrC-MtrD-MtrE efflux pump act synergistically to confer resistance to these antibiotics.
Fast 3C 279 gamma flares by a merging medium size black hole jet aligned to the AGN one by tidal torque?
Creators: name: Fargion, Daniele
name: Oliva, Pietro
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The shorter-than-Schwarzschild 3C 279 variability flare on June 2015 is very puzzling. Its nature cannot be due to any NS merging nor to a medium sized (hundred million solar mass) BH collapse. Our preliminary model is based on the long-life (a third of a year) merging of a medium size BH (hundred of solar mass) jet spiralling toward the largest AGN one, (billion solar mass), that is dragging by tidal torques the medium small size BH jet along the main AGN 3C 279 one. The tidal torque is aligning both jets toward Earth. The twin overlapping blazars may offer at once a long and a short scale variability consistent with the surprising Fermi discovers.
description: 7 pages, 1 figure, PoS
A Bayesian Deep Learning Approach to Near-Term Climate Prediction
Creators: name: Luo, Xihaier
name: Nadiga, Balasubramanya T.
name: Ren, Yihui
name: Park, Ji Hwan
name: Xu, Wei
name: Yoo, Shinjae
Publisher: name: arXiv
Year: 2022
Subjects: subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: Machine Learning (cs.LG)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Since model bias and associated initialization shock are serious shortcomings that reduce prediction skills in state-of-the-art decadal climate prediction efforts, we pursue a complementary machine-learning-based approach to climate prediction. The example problem setting we consider consists of predicting natural variability of the North Atlantic sea surface temperature on the interannual timescale in the pre-industrial control simulation of the Community Earth System Model (CESM2). While previous works have considered the use of recurrent networks such as convolutional LSTMs and reservoir computing networks in this and other similar problem settings, we currently focus on the use of feedforward convolutional networks. In particular, we find that a feedforward convolutional network with a Densenet architecture is able to outperform a convolutional LSTM in terms of predictive skill. Next, we go on to consider a probabilistic formulation of the same network based on Stein variational gradient descent and find that in addition to providing useful measures of predictive uncertainty, the probabilistic (Bayesian) version improves on its deterministic counterpart in terms of predictive skill. Finally, we characterize the reliability of the ensemble of ML models obtained in the probabilistic setting by using analysis tools developed in the context of ensemble numerical weather prediction.
description: 32 pages, 12 figures
Point Mutations in HpuB Enable Gonococcal HpuA Deletion Mutants To Grow on Hemoglobin
Creators: name: Thomas, C. E.
name: Chen, C.-J.
name: Anderson, J. E.
name: Sparling, P. F.
name: Mclean, D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Neisseria gonorrhoeae ordinarily requires both HpuA and HpuB to use hemoglobin (Hb) as a source of iron for growth. Deletion of HpuA resulted in reduced Hb binding and failure of growth on Hb. We identified rare Hb-utilizing colonies (Hb+) from an hpuA deletion mutant of FA1090, which fell into two phenotypic classes. One class of the Hb+ revertants required expression of both TonB and HpuB for growth on Hb, while the other class required neither TonB nor HpuB. All TonB/HpuB-dependent mutants had single amino acid alterations in HpuB, which occurred in clusters, particularly near the C terminus. The point mutations in HpuB did not restore normal Hb binding. Human serum albumin inhibited Hb-dependent growth of HpuB point mutants lacking HpuA but did not inhibit growth when expression of HpuA was restored. Thus, HpuB point mutants internalized heme in the absence of HpuA despite reduced binding of Hb. HpuA facilitated Hb binding and was important in allowing use of heme from Hb for growth.
Ideal-adic completion of quasi-excellent rings (after Gabber)
Creators: name: Kurano, Kazuhiko
name: Shimomoto, Kazuma
Publisher: name: arXiv
Year: 2016
Subjects: subject: Commutative Algebra (math.AC)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: In this paper, we give a detailed proof to a result of Gabber (unpublished) on the lifting problem of quasi-excellent rings, extending the previous work on Nishimura-Nishimura. As a corollary, we establish that an ideal-adic completion of an excellent (resp. quasi-excellent) ring is excellent (resp. quasi-excellent).
description: The final version, accepted by Kyoto J. Math
Analyticity constraints bound the decay of the spectral form factor
Creators: name: Martinez-Azcona, Pablo
name: Chenu, Aurélia
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Quantum chaos cannot develop faster than $λ\leq 2 π/(\hbar β)$ for systems in thermal equilibrium [Maldacena, Shenker & Stanford, JHEP (2016)]. This `MSS bound' on the Lyapunov exponent $λ$ is set by the width of the strip on which the regularized out-of-time-order correlator is analytic. We show that similar constraints also bound the decay of the spectral form factor (SFF), that measures spectral correlation and is defined from the Fourier transform of the two-level correlation function. Specifically, the inflection exponent $η$, that we introduce to characterize the early-time decay of the SFF, is bounded as $η\leq π/(2\hbarβ)$. This bound is universal and exists outside of the chaotic regime. The results are illustrated in systems with regular, chaotic, and tunable dynamics, namely the single-particle harmonic oscillator, the many-particle Calogero-Sutherland model, an ensemble from random matrix theory, and the quantum kicked top. The relation of the derived bound with other known bounds, including quantum speed limits, is discussed.
description: 9+3 pages, 6+3 figures. Accepted for publication in Quantum
Synchronization in arrays of vacuum microdiodes
Creators: name: Ilkov, Marjan
name: Torfason, Kristinn
name: Manolescu, Andrei
name: Valfells, Ágúst
Publisher: name: arXiv
Year: 2014
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Simulations have shown that space-charge effects can lead to regular modulation of photoemitted beams in vacuum diodes with gap sizes on the order of 1 micron and accelerating voltage on the order of 1V. These modulations are in the THz regime and can be tuned by simply changing the emitter area or accelerating vacuum field. The average current in the diode corresponds to the Child-Langmuir current, but the amplitude of the oscillations is affected by various factors. Given the small size and voltage of the system, the maximum radiated AC power is expected to be small. In this work we show that an array of small emitters produces higher frequency signals than a single large emitter of same area, and how these emitters may be synchronized to produce higher power signals.
description: 6 pages, 7 figures
CheZ-Mediated Dephosphorylation of the Escherichia coli Chemotaxis Response Regulator CheY: Role for CheY Glutamate 89
Creators: name: Zhao, R.
name: Silversmith, R. E.
name: Guanga, G. P.
name: Chu, C.
name: Bourret, R. B.
name: Betts, L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: The swimming behavior of Escherichia coli at any moment is dictated by the intracellular concentration of the phosphorylated form of the chemotaxis response regulator CheY, which binds to the base of the flagellar motor. CheY is phosphorylated on Asp57 by the sensor kinase CheA and dephosphorylated by CheZ. Previous work (Silversmith et al., J. Biol. Chem. 276:18478, 2001) demonstrated that replacement of CheY Asn59 with arginine resulted in extreme resistance to dephosphorylation by CheZ despite proficient binding to CheZ. Here we present the X-ray crystal structure of CheYN59R in a complex with Mn2+ and the stable phosphoryl analogue BeF3−. The overall folding and active site architecture are nearly identical to those of the analogous complex containing wild-type CheY. The notable exception is the introduction of a salt bridge between Arg59 (on the β3α3 loop) and Glu89 (on the β4α4 loop). Modeling this structure into the (CheY-BeF3−-Mg2+)2CheZ2 structure demonstrated that the conformation of Arg59 should not obstruct entry of the CheZ catalytic residue Gln147 into the active site of CheY, eliminating steric interference as a mechanism for CheZ resistance. However, both CheYE89A and CheYE89Q, like CheYN59R, conferred clockwise flagellar rotation phenotypes in strains which lacked wild-type CheY and displayed considerable (≈40-fold) resistance to dephosphorylation by CheZ. CheYE89A and CheYE89Q had autophosphorylation and autodephosphorylation properties similar to those of wild-type CheY and could bind to CheZ with wild-type affinity. Therefore, removal of Glu89 resulted specifically in CheZ resistance, suggesting that CheY Glu89 plays a role in CheZ-mediated dephosphorylation. The CheZ resistance of CheYN59R can thus be largely explained by the formation of the salt bridge between Arg59 and Glu89, which prevents Glu89 from executing its role in catalysis.
On uniform flag bundles on Fano manifolds
Creators: name: Muñoz, Roberto
name: Occhetta, Gianluca
name: Conde, Luis E. Solá
Publisher: name: arXiv
Year: 2016
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14J45 (Primary), 14E30, 14M15, 14M17 (Secondary)

description: As a natural extension of the theory of uniform vector bundles on Fano manifolds, we consider uniform principal bundles, and study them by means of the associated flag bundles, as their natural projective geometric realizations. In this paper we develop the necessary background, and prove some theorems that are flag bundle counterparts of some of the central results in the theory of uniform vector bundles.
Gravitation radiation observations
Creators: name: Glass, E. N.
Publisher: name: arXiv
Year: 2017
Subjects: subject: General Physics (physics.gen-ph)
subject: FOS: Physical sciences

description: The notion of gravitational radiation begins with electromagnetic radiation. In 1887 Heinrich Hertz, working in one room, generated and received electromagnetic radiation. Maxwell's equations describe the electromagnetic field. The quanta of electromagnetic radiation are spin 1 photons. They are fundamental to atomic physics and quantum electrodynamics.
STRAIN-RATE DEPENDENT CHARACTERIZATION OF ARMOX 500T FOR  GISSMO PARAMETERIZATION USING 3D DIGITAL IMAGE CORRELATION
Creators: Mateos, Diego
Boakye-Yiadom, Solomon
Publisher: name: University of Alberta Library
Year: 2022

Conference abstract. Part of the Proceedings of the Canadian Society for Mechanical Engineering International Congress 2022.
Genetic Variation at the vlsE Locus of Borrelia burgdorferi within Ticks and Mice over the Course of a Single Transmission Cycle
Creators: name: Ohnishi, J.
name: de Silva, A. M.
name: Messer, W. B.
name: Schneider, B.
name: Piesman, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: The Lyme disease spirochete, Borrelia burgdorferi, causes a persistent infection in the vertebrate host even though infected animals mount an active immune response against the spirochete. One strategy used by the spirochete to evade vertebrate host immunity is to vary the structure and expression of outer membrane antigens. The vlsE locus represents the best-studied example of antigenic variation in B. burgdorferi. During vertebrate host infection, recombination between the active vlsE locus and silent, partial vlsE copies leads to gene conversion events and the generation of novel alleles at the expression site. In the present study, we followed a population of B. burgdorferi organisms moving through vertebrate host and tick stages to complete one transmission cycle. The major goal of the study was to determine if the vlsE locus was subject to different selective pressure and/or recombination frequency at different stages of the spirochete's life cycle. We report here that the vlsE genetic diversity generated within the rodent host was maintained through the larval and nymphal tick stages. Therefore, naturally infected ticks are likely to transmit spirochete populations with multiple vlsE alleles into naive vertebrate hosts. Although vlsE genetic diversity in mice was maintained through tick stages, the dominant vlsE alleles were different between tick stages as well as between individual ticks. We propose that population-level bottlenecks experienced by spirochetes, especially during the larval-to-nymphal molt, are responsible for individual infected ticks harboring different dominant vlsE alleles. Although vlsE genetic diversity is maintained through tick stages, the VlsE protein is unlikely to be of functional importance in the vector, because the protein was expressed by very few (
Investigation of the Role of Electrostatic Charge in Activation of the Escherichia coli Response Regulator CheY
Creators: name: Smith, J. G.
name: Latiolais, J. A.
name: Guanga, G. P.
name: Silversmith, R. E.
name: Bourret, R. B.
name: Citineni, S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: In a two-component regulatory system, an important means of signal transduction in microorganisms, a sensor kinase phosphorylates a response regulator protein on an aspartyl residue, resulting in activation. The active site of the response regulator is highly charged (containing a lysine, the phosphorylatable aspartate, two additional aspartates involved in metal binding, and an Mg2+ ion), and introduction of the dianionic phosphoryl group results in the repositioning of charged moieties. Furthermore, substitution of one of the Mg2+-coordinating aspartates with lysine or arginine in the Escherichia coli chemotaxis response regulator CheY results in phosphorylation-independent activation. In order to examine the consequences of altered charge distribution for response regulator activity and to identify possible additional amino acid substitutions that result in phosphorylation-independent activation, we made 61 CheY mutants in which residues close to the site of phosphorylation (Asp57) were replaced by various charged amino acids. Most substitutions (47 of 61) resulted in the complete loss of CheY activity, as measured by the inability to support clockwise flagellar rotation. However, 10 substitutions, all introducing a new positive charge, resulted in the loss of chemotaxis but in the retention of some clockwise flagellar rotation. Of the mutants in this set, only the previously identified CheY13DK and CheY13DR mutants displayed clockwise activity in the absence of the CheA sensor kinase. The absence of negatively charged substitution mutants with residual activity suggests that the introduction of additional negative charges into the active site is particularly deleterious for CheY function. Finally, the spatial distribution of positions at which amino acid substitutions are functionally tolerated or not tolerated is consistent with the presently accepted mechanism of response regulator activation and further suggests a possible role for Met17 in signal transduction by CheY.
Cybersecurity Challenges in the Offshore Oil and Gas Industry: An Industrial Cyber-Physical Systems (ICPS) Perspective
Creators: name: Mohammed, Abubakar Sadiq
name: Reinecke, Philipp
name: Burnap, Pete
name: Rana, Omer
name: Anthi, Eirini
Publisher: name: arXiv
Year: 2022
Subjects: subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: The offshore oil and gas industry has recently been going through a digitalisation drive, with use of `smart' equipment using technologies like the Industrial Internet of Things (IIoT) and Industrial Cyber-Physical Systems (ICPS). There has also been a corresponding increase in cyber attacks targeted at oil and gas companies. Oil production offshore is usually in remote locations, requiring remote access and control. This is achieved by integrating ICPS, Supervisory, Control and Data Acquisition (SCADA) systems, and IIoT technologies. A successful cyber attack against an oil and gas offshore asset could have a devastating impact on the environment, marine ecosystem and safety of personnel. Any disruption to the world's supply of oil and gas (O\&G) can also have an effect on oil prices and in turn, the global economy. This makes it important to secure the industry against cyber threats. We describe the potential cyberattack surface within the oil and gas industry, discussing emerging trends in the offshore sub-sector, and provide a timeline of known cyberattacks. We also present a case study of a subsea control system architecture typically used in offshore oil and gas operations and highlight potential vulnerabilities affecting the components of the system. This study is the first to provide a detailed analysis on the attack vectors in a subsea control system and is crucial to understanding key vulnerabilities, primarily to implement efficient mitigation methods that safeguard the safety of personnel and the environment when using such systems.
description: 19 pages, 8 figures
Adelic Cartier divisors with base conditions and the continuity of volumes
Creators: name: Ikoma, Hideaki
Publisher: name: arXiv
Year: 2017
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14G40 (Primary), 11G50 (Secondary)

description: In the previous paper [7], we introduced a notion of pairs of adelic R-Cartier divisors and R-base conditions. The purpose of this paper is to propose an extended notion of adelic R-Cartier divisors that we call an l1-adelic R-Cartier divisors, and to show that the arithmetic volume function defined on the space of pairs of l1-adelic R-Cartier divisors and R-base conditions is continuous along the directions of l1-adelic R-Cartier divisors.
description: 36 pages
Slow ground state molecules from matrix isolation sublimation
Creators: name: Oliveira, Alvaro N.
name: Sacramento, Rodrigo L.
name: Alves, Bruno X.
name: Silva, Bruno A.
name: Wolff, Wania
name: Cesar, Claudio L.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We describe the generation and properties of a cryogenic beam of $^7$Li$_2$ dimers from sublimation of a neon matrix where lithium atoms have been implanted via laser ablation of solid precursors of metallic lithium or lithium hydride (LiH). Different sublimation regimes lead to pulsed molecular beams with different temperatures, densities and forward velocities. With laser absorption spectroscopy these parameters were measured using the molecular $^7$Li$_2$ (R) transitions A$^1Σ_u^+(v'=4,J'=J''+1)\leftarrow $X$^1Σ_g^+ (v''=0,J''=0,1,3)$. In a typical regime, sublimating a matrix at 16 K, translational temperatures of 6--8 K with a drift velocity of 130 m$\,$s$^{-1}$ in a free expanding pulsed beam with molecular density of 10$^9$ cm$^{-3}$, averaged along the laser axis, were observed. Rotational temperatures around 5--7 K were obtained. In recent experiments we were able to monitor the atomic Li signal -- in the D2 line -- concomitantly with the molecular signal in order to compare them as a function of the number of ablation pulses. Based on the data and a simple model, we discuss the possibility that a fraction of these molecules are being formed in the matrix, by mating atoms from different ablation pulses, which would open up the way to formation of other more interesting and difficult molecules to be studied at low temperatures. Such a source of cryogenic molecules have possible applications encompassing fundamental physics tests, quantum information studies, cold collisions, chemistry, and trapping.
description: 8 pages, 6 figures
A Mutant Form of the Neisseria gonorrhoeae Pilus Secretin Protein PilQ Allows Increased Entry of Heme and Antimicrobial Compounds
Creators: name: Seifert, H. S.
name: Thomas, C. E.
name: Tobiason, D. M.
name: Shafer, W. M.
name: Sparling, P. F.
name: Chen, C.-j.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: A spontaneous point mutation in pilQ (pilQ1) resulted in phenotypic suppression of a hemoglobin (Hb) receptor mutant (hpuAB mutant), allowing gonococci to grow on Hb as the sole source of iron. PilQ, formerly designated OMP-MC, is a member of the secretin family of proteins located in the outer membrane and is required for pilus biogenesis. The pilQ1 mutant also showed decreased piliation and transformation efficiency. Insertional inactivation of pilQ1 resulted in the loss of the Hb utilization phenotype and decreased entry of free heme. Despite the ability of the pilQ1 mutant to use Hb for iron acquisition and porphyrin, there was no demonstrable binding of Hb to the cell surface. The pilQ1 mutant was more sensitive to the toxic effect of free heme in growth medium and hypersensitive to the detergent Triton X-100 and multiple antibiotics. Double mutation in pilQ1 and tonB had no effect on these phenotypes, but a double pilQ1 pilT mutant showed a reduction in Hb-dependent growth and decreased sensitivity to heme and various antimicrobial agents. Insertional inactivation of wild-type pilQ also resulted in reduced entry of heme, Triton X-100, and some antibiotics. These results show that PilQ forms a channel that allows entry of heme and certain antimicrobial compounds and that a gain-of function point mutation in pilQ results in TonB-independent, PilT-dependent increase of entry.
PT-/non-PT-Symmetric and non-Hermitian Hellmann Potential: Approximate Bound and Scattering States with Any $\ell$-Values
Creators: name: Arda, Altug
name: Sever, Ramazan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We investigate the approximate bound state solutions of the Schrödinger equation for the PT-/non-PT-symmetric and non Hermitian Hellmann potential. Exact energy eigenvalues and corresponding normalized wave functions are obtained. Numerical values of energy eigenvalues for the bound states are compared with the ones obtained before. Scattering state solutions are also studied. Phase shifts of the potential are written in terms of the angular momentum quantum number $\ell$.
description: 14 pages, 1 figure
title: O poglądach naukowych Profesora Tadeusza Bigi
Creators: name: Kiczka, Karol
Publisher: name: E-Wydawnictwo. Prawnicza i Ekonomiczna Biblioteka Cyfrowa. Wydział Prawa, Administracji i Ekonomii Uniwersytetu Wrocławskiego
Year: 2020

description: Ustalenia naukowe profesora Tadeusza Bigi mają ważne znaczenie także na gruncie współczesnego prawodawstwa i praktyki prawa administracyjnego. Dotyczy to zarówno organizacji administracji publicznej, jak i jej działalności w demokratycznym państwie prawnym w warunkach Unii Europejskiej. Jego prace naukowe są źródłem inspiracji dla dzisiejszych badawczy prawa publicznego, wyróżnia je swoiste podejście poznawcze oraz to, że analizują wartości nieprzemijające dla zagwarantowania przyrodzonej i niezbywalnej godności człowieka oraz właściwego funkcjonowania instytucji publicznych.
title: EFFICACY OF THE KETOGENIC DIET IN PEDIATRIC PATIENTS WITH REFRACTORY EPILEPSY ON THE CONTROL OF SEIZURES. OVERVIEW
Creators: name: Sánchez, Lucía Méndez
name: Klünder, Miguel Klünder
name: Flores-Resendiz, Constantino
name: López-Contreras, Iris Nallely
Publisher: name: OSF Registries
Year: 2023
Subjects: subject: Dietetics and Clinical Nutrition
subject: Medicine and Health Sciences

description: It is a review of systematic reviews of the literature on the effect of the ketogenic diet in pediatric patients with refractory epilepsy.
Identification of Campylobacter jejuni ATCC 43431-Specific Genes by Whole Microbial Genome Comparisons
Creators: name: Poly, F.
name: Stintzi, A.
name: Threadgill, D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: This study describes a novel approach to identify unique genomic DNA sequences from the unsequenced strain C. jejuni ATCC 43431 by comparison with the sequenced strain C. jejuni NCTC 11168. A shotgun DNA microarray was constructed by arraying 9,600 individual DNA fragments from a C. jejuni ATCC 43431 genomic library onto a glass slide. DNA fragments unique to C. jejuni ATCC 43431 were identified by competitive hybridization to the array with genomic DNA of C. jejuni NCTC 11168. The plasmids containing unique DNA fragments were sequenced, allowing the identification of up to 130 complete and incomplete genes. Potential biological roles were assigned to 66% of the unique open reading frames. The mean G+C content of these unique genes (26%) differs significantly from the G+C content of the entire C. jejuni genome (30.6%). This suggests that they may have been acquired through horizontal gene transfer from an organism with a G+C content lower than that of C. jejuni. Because the two C. jejuni strains differ by Penner serotype, a large proportion of the unique ATCC 43431 genes encode proteins involved in lipooligosaccharide and capsular biosynthesis, as expected. Several unique open reading frames encode enzymes which may contribute to genetic variability, i.e., restriction-modification systems and integrases. Interestingly, many of the unique C. jejuni ATCC 43431 genes show identity with a possible pathogenicity island from Helicobacter hepaticus and components of a potential type IV secretion system. In conclusion, this study provides a valuable resource to further investigate Campylobacter diversity and pathogenesis.