cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Precise Q value measurements of $^{112,113}$Ag and $^{115}$Cd with the Canadian Penning trap for evaluation of potential ultra-low Q value $β$-decays
Creators: name: Gamage, Nadeesha D.
name: Sandler, Rachel
name: Buchinger, Fritz
name: Clark, Jason A.
name: Ray, Dwaipayan
name: Orford, Rodney
name: Porter, William S.
name: Redshaw, Matthew
name: Savard, Guy
name: Sharma, Kumar S.
name: Valverde, Adrian A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: An ultra-low Q value $β$-decay can occur from a parent nuclide to an excited state in the daughter with $Q_{UL}$ <1 keV. These decays are of interest for nuclear $β$-decay theory and as potential candidates in neutrino mass determination experiments. To date, only one ultra-low Q value $β$-decay has been observed -- that of $^{115}$In with $Q_β$ = 147(10) eV. A number of other potential candidates exist, but improved mass measurements are necessary to determine if the decays are energetically allowed and, in fact, ultra-low. We performed precise $β$-decay Q value measurements of $^{112,113}$Ag and $^{115}$Cd and combined them with nuclear energy level data for the daughter isotopes to determine if the potential UL Q value $β$-decay branches of $^{112,113}$Ag and $^{115}$Cd are energetically allowed and <1 keV. The Canadian Penning Trap at ANL was used to measure the cyclotron frequency ratios of singly-charged $^{112,113}$Ag and $^{115}$Cd ions with respect to their daughters. From these measurements, the ground-state $β$-decay Q values were obtained. The $^{112}$Ag, $^{113}$Ag, and $^{115}$Cd $β$-decay Q values were measured to be 3990.16(22) keV, 2085.7(4.6) keV, and 1451.36(34) keV, respectively. These results were compared to energies of excited states in $^{112}$Cd at 3997.75(14) keV, $^{113}$Cd at 2015.6(2.5) and 2080(10) keV, and $^{115}$In at 1448.787(9) keV, resulting in $Q_{\textrm{UL}}$ values of --7.59(26) keV, 6(11) keV, and 2.57(34) keV, respectively. The potential UL Q value decays of $^{112}$Ag and $^{115}$Cd have been ruled out. $^{113}$Ag is still a possible candidate until a more precise measurement of the 2080(10) keV, 1/2$^{+}$ state of $^{113}$Cd is available. In the course of this work we have found the ground state mass of $^{113}$Ag reported in the 2020AME to be lower than our measurement by 69(17) keV (a 4$σ$ discrepancy).
Tunable Dirac Semimetals with Higher-order Fermi Arcs in Kagome Lattices Pd$_3$Pb$_2$X$_2$ (X = S, Se)
Creators: name: Nie, Simin
name: Chen, Jia
name: Yue, Changming
name: Le, Congcong
name: Yuan, Danwen
name: Zhang, Wei
name: Weng, Hongming
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Bulk-boundary correspondence has achieved a great success in the identification of topological states. However, this elegant strategy doesn't apply to the Dirac semimetals (DSMs). Here, we propose that kagome lattices Pd$_3$Pb$_2$X$_2$ (X = S, Se) are unique type-I DSMs without surface Fermi arc states, which are different from the previous well-known DSMs, such as Na$_3$Bi and Cd$_3$As$_2$. Pd$_3$Pb$_2$X$_2$ are characterized by nontrivial topological invariant Z$_3$, guaranteeing a higher-order bulk-hinge correspondence and the existence of higher-order Fermi arcs, as well as fractional corner charges on the hinges. The type-I DSMs are located at the phase boundaries of several topological phases, including type-II DSMs and three-dimensional weak topological insulators. The phase transitions can be easily manipulated by external strain. Our results provide feasible platforms for the study of these unique DSMs and the related phase transitions.
description: 15 pages, 10 figures and 4 tables
Review of gravitational wave solutions in quadratic metric-affine gravity
Creators: name: Jiménez-Cano, Alejandro
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: In this review we consider the quadratic Metric-Affine Gauge gravity Lagrangian, which contains all the algebraic invariants up to quadratic order in torsion, nonmetricity and curvature. The goal will be to collect the known exact solutions for this theory that describe the propagation of a gravitational wave and some useful properties. We concentrate on solutions whose connections are different from the Levi-Civita one and provide also the extension of already known axial torsion solutions to more general Lagrangians. At the end, we will briefly discuss colliding waves and Riemannian solutions.
description: 31 pages, 1 figure, contribution to the Special Issue of the International Journal of Geometric Methods in Modern Physics dedicated to the conference Geometric Foundations of Gravity in Tartu 2021
Generating functionals for computational intelligence: the Fisher information as an objective function for self-limiting Hebbian learning rules
Creators: name: Echeveste, Rodrigo
name: Gros, Claudius
Publisher: name: arXiv
Year: 2014
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Neural and Evolutionary Computing (cs.NE)
subject: FOS: Biological sciences
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Generating functionals may guide the evolution of a dynamical system and constitute a possible route for handling the complexity of neural networks as relevant for computational intelligence. We propose and explore a new objective function, which allows to obtain plasticity rules for the afferent synaptic weights. The adaption rules are Hebbian, self-limiting, and result from the minimization of the Fisher information with respect to the synaptic flux. We perform a series of simulations examining the behavior of the new learning rules in various circumstances. The vector of synaptic weights aligns with the principal direction of input activities, whenever one is present. A linear discrimination is performed when there are two or more principal directions; directions having bimodal firing-rate distributions, being characterized by a negative excess kurtosis, are preferred. We find robust performance and full homeostatic adaption of the synaptic weights results as a by-product of the synaptic flux minimization. This self-limiting behavior allows for stable online learning for arbitrary durations. The neuron acquires new information when the statistics of input activities is changed at a certain point of the simulation, showing however, a distinct resilience to unlearn previously acquired knowledge. Learning is fast when starting with randomly drawn synaptic weights and substantially slower when the synaptic weights are already fully adapted.
Biased and Unreliable Media Sources
Creators: name: Strydhorst, Natasha
name: Landrum, Asheley R.
Publisher: name: OSF
Year: 2021

description: This exploratory analysis investigates news-seeking behaviors and adherence to inaccurate beliefs about COVID-19 preventatives/treatments, COVID-19 severity, and vaccines in the context of the ongoing COVID-19 pandemic and via the lens of selective exposure theory. We surveyed 3,276 American adults about their sources of COVID-19 news and perceptions of false statements regarding treatments/preventatives, vaccines, and the seriousness of the virus. The study makes use of a novel means of investigating the variables of media bias and reliability, by operationalizing these measures based on the Ad Fontes Media ratings (Ad Fontes Media, 2021) of each dimension for 129 news sources participants could select. We found that media bias and reliability are significant predictors of individuals’ perceptions of false claims regarding COVID-19 preventatives and treatments, COVID-19 severity, and vaccines. False beliefs were, in many cases, significantly correlated with additional false beliefs.
Iron Acquisition and Regulation in Campylobacter jejuni
Creators: name: Stintzi, A.
name: Palyada, K.
name: Threadgill, D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Iron affects the physiology of bacteria in two different ways: as a micronutrient for bacterial growth and as a catalyst for the formation of hydroxyl radicals. In this study, we used DNA microarrays to identify the C. jejuni genes that have their transcript abundance affected by iron availability. The transcript levels of 647 genes were affected after the addition of iron to iron-limited C. jejuni cells. Several classes of affected genes were revealed within 15 min, including immediate-early response genes as well as those specific to iron acquisition and metabolism. In contrast, only 208 genes were differentially expressed during steady-state experiments comparing iron-rich and iron-limited growth conditions. As expected, genes annotated as being involved in either iron acquisition or oxidative stress defense were downregulated during both time course and steady-state experiments, while genes encoding proteins involved in energy metabolism were upregulated. Because the level of protein glycosylation increased with iron limitation, iron may modulate the level of C. jejuni virulence by affecting the degree of protein glycosylation. Since iron homeostasis has been shown to be Fur regulated in C. jejuni, an isogenic fur mutant was used to define the Fur regulon by transcriptome profiling. A total of 53 genes were Fur regulated, including many genes not previously associated with Fur regulation. A putative Fur binding consensus sequence was identified in the promoter region of most iron-repressed and Fur-regulated genes. Interestingly, a fur mutant was found to be significantly affected in its ability to colonize the gastrointestinal tract of chicks, highlighting the importance of iron homeostasis in vivo. Directed mutagenesis of other genes identified by the microarray analyses allowed the characterization of the ferric enterobactin receptor, previously named CfrA. Chick colonization assays indicated that mutants defective in enterobactin-mediated iron acquisition were unable to colonize the gastrointestinal tract. In addition, a mutation in a receptor (Cj0178) for an uncharacterized iron source also resulted in reduced colonization potential. Overall, this work documents the complex response of C. jejuni to iron availability, describes the genetic network between the Fur and iron regulons, and provides insight regarding the role of iron in C. jejuni colonization in vivo.
Combinatorial identities associated with new families of the numbers and polynomials and their approximation values
Creators: name: Kucukoglu, Irem
name: Simsek, Yilmaz
Publisher: name: arXiv
Year: 2017
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 05A10, 05A15, 11B37, 11B68, 11B83, 11J68, 26C05

description: Recently, the numbers $Y_{n}(λ)$ and the polynomials $Y_{n}(x,λ)$ have been introduced by the second author [22]. The purpose of this paper is to construct higher-order of these numbers and polynomials with their generating functions. By using these generating functions with their functional equations and derivative equations, we derive various identities and relations including two recurrence relations, Vandermonde type convolution formula, combinatorial sums, the Bernstein basis functions, and also some well known families of special numbers and their interpolation functions such as the Apostol--Bernoulli numbers, the Apostol--Euler numbers, the Stirling numbers of the first kind, and the zeta type function. Finally, by using Stirling's approximation for factorials, we investigate some approximation values of the special case of the numbers $Y_{n}\left( λ\right) $.
description: 17 pages
CheX Is a Phosphorylated CheY Phosphatase Essential for Borrelia burgdorferi Chemotaxis
Creators: name: Bourret, R. B.
name: Bakker, R. G.
name: Charon, N. W.
name: Miller, M. R.
name: Li, C.
name: Silversmith, R. E.
name: Goldstein, S. F.
name: Motaleb, M. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Motility and chemotaxis are believed to be important in the pathogenesis of Lyme disease caused by the spirochete Borrelia burgdorferi. Controlling the phosphorylation state of CheY, a response regulator protein, is essential for regulating bacterial chemotaxis and motility. Rapid dephosphorylation of phosphorylated CheY (CheY-P) is crucial for cells to respond to environmental changes. CheY-P dephosphorylation is accomplished by one or more phosphatases in different species, including CheZ, CheC, CheX, FliY, and/or FliY/N. Only a cheX phosphatase homolog has been identified in the B. burgdorferi genome. However, a role for cheX in chemotaxis has not been established in any bacterial species. Inactivating B. burgdorferi cheX by inserting a flgB-kan cassette resulted in cells (cheX mutant cells) with a distinct motility phenotype. While wild-type cells ran, paused (stopped or flexed), and reversed, the cheX mutant cells continuously flexed and were not able to run or reverse. Furthermore, swarm plate and capillary tube chemotaxis assays demonstrated that cheX mutant cells were deficient in chemotaxis. Wild-type chemotaxis and motility were restored when cheX mutant cells were complemented with a shuttle vector expressing CheX. Furthermore, CheX dephosphorylated CheY3-P in vitro and eluted as a homodimer in gel filtration chromatography. These findings demonstrated that B. burgdorferi CheX is a CheY-P phosphatase that is essential for chemotaxis and motility, which is consistent with CheX being the only CheY-P phosphatase in the B. burgdorferi chemotaxis signal transduction pathway.
Magnetic Effects in Hot Jupiter Atmospheres
Creators: name: Rogers, Tamara M.
name: Komacek, Thaddeus D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We present magnetohydrodynamic (MHD) simulations of the atmospheres of hot Jupiters ranging in temperature from 1100-1800K. Magnetic effects are negligible in atmospheres with temperatures $\lesssim$ 1400K. At higher temperatures winds are variable and in many cases, mean equatorial flows can become westward, opposite to their hydrodynamic counterparts. Ohmic dissipation peaks at temperatures $\sim$1500-1600K, depending on field strength, with maximum values $\sim 10^{18}$W at 10bar, substantially lower than previous estimates. Based on the limited parameter study done, this value can not be increased substantially with increasing winds, higher temperatures, higher field strengths, different boundary conditions or lower diffusivities. Although not resolved in these simulations there is modest evidence that a magnetic buoyancy instability may proceed in hot atmospheres.
description: 13 pages, 13 figures, Accepted to ApJ
Higher-genus wall-crossing in the gauged linear sigma model
Creators: name: Clader, Emily
name: Janda, Felix
name: Ruan, Yongbin
Publisher: name: arXiv
Year: 2017
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14N35, 14D23

description: We introduce a technique for proving all-genus wall-crossing formulas in the gauged linear sigma model as the stability parameter varies, without assuming factorization properties of the virtual class. We implement this technique explicitly for the hybrid model, which generalizes our previous work to the Landau--Ginzburg phase.
description: 42 pages, 2 figures. v2: Added an appendix (by Yang Zhou) proving the n=0 case of the main theorem; additional substantial changes to Sections 2.5 (broad vanishing) and 4.3 (localization contributions)
Role of Borrelia burgdorferi Linear Plasmid 25 in Infection of Ixodes scapularis Ticks
Creators: name: de Silva, A.
name: Strother, K. O.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The tick-borne bacterium Borrelia burgdorferi has over 20 different circular and linear plasmids. Some B. burgdorferi plasmids are readily lost during in vitro culture or genetic manipulation. Linear plasmid 25, which is often lost in laboratory strains, is required for the infection of mice. Strains missing linear plasmid 25 (lp25−) are able to infect mice if the BBE22 gene on lp25 is provided on a shuttle vector. In this study, we examined the role of lp25 and BBE22 in tick infections. We tested the hypothesis that complementation with BBE22 in spirochetes lacking lp25 would restore the ability of spirochetes to infect ticks. A natural tick infection cycle was performed by feeding larvae on mice injected with the parental, lp25−, or lp25− BBE22-complemented spirochete strains. In addition, larvae and nymphs were artificially infected with different strains to study tick infections independent of mouse infections. B. burgdorferi missing lp25 was significantly impaired in its ability to infect larval and nymphal ticks. When an lp25− strain was complemented with BBE22, the ability to infect ticks was partially restored. Complementation with BBE22 allowed spirochetes lacking lp25 to establish short-term infections in ticks, but in most cases the infection prevalence was lower than that of the wild-type strain. In addition, the number of infected ticks decreased over time, suggesting that another gene(s) on lp25 is required for long-term persistence in ticks and completion of a natural infection cycle.
Duality for $κ$-additive complete atomic modal algebras
Creators: name: Tanaka, Yoshihito
Publisher: name: arXiv
Year: 2018
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 06E25, 03G25, 03B45

description: In this paper, we give a duality theorem between the category of $κ$-additive complete atomic modal algebras and the category of $κ$-downward directed multi-relational Kripke frames, for any cardinal number $κ$. Multi-relational Kripke frames are not Kripke frames for multi-modal logic, but frames for monomodal logics in which the modal operator $\Diamond$ does not distribute over (possibly infinite) disjunction, in general. We first define homomorphisms of multi-relational Kripke frames, and then show the equivalence between the category of $κ$-downward directed multi-relational Kripke frames and the category $κ$-complete neighborhood frames, from which the duality theorem follows. We also present another direct proof of this duality based on the technique given by Minari.
A magnetic cloud prediction model for forecasting space weather relevant properties of Earth-directed coronal mass ejections
Creators: name: Pal, Sanchita
name: Nandy, Dibyendu
name: Kilpua, Emilia K J
Publisher: name: arXiv
Year: 2022
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: Coronal Mass Ejections (CMEs) are energetic storms in the Sun that result in the ejection of large-scale magnetic clouds (MCs) in interplanetary space that contain enhanced magnetic fields with coherently changing field direction. The severity of geomagnetic perturbations depends on the direction and strength of the interplanetary magnetic field (IMF), as well as the speed and duration of passage of the storm. The coupling between the heliospheric environment and Earth's magnetosphere is the strongest when the IMF direction is persistently southward for a prolonged period. Predicting the magnetic profile of such Earth-directed CMEs is crucial for estimating their geomagnetic impact. We aim to build upon and integrate diverse techniques towards development of a comprehensive magnetic cloud prediction (MCP) model that can forecast the magnetic field vectors, Earth-impact time, speed and duration of passage of solar storms. A novelty of our scheme is the ability to predict the passage duration of the storm without recourse to computationally intensive, time-dependent dynamical equations. Our methodology is validated by comparing the MCP model output with observations of ten MCs at 1 AU. In our sample, we find that eight MCs show a root mean square deviation of less than 0.1 between predicted and observed magnetic profiles and the passage duration of seven MCs fall within the predicted range. Based on the success of this approach, we conclude that predicting the near-Earth properties of MCs based on analysis and modelling of near-Sun CME observations is a viable endeavor with potential benefits for space weather assessment.
description: 16 pages, 6 figures
Black hole horizons and quantum charged particles
Creators: name: Jaramillo, José Luis
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We point out a structural similarity between the characterization of black hole apparent horizons as stable marginally outer trapped surfaces (MOTS) and the quantum description of a non-relativistic charged particle moving in given magnetic and electric fields on a closed surface. Specifically, the spectral problem of the MOTS-stability operator corresponds to a stationary quantum particle with a formal fine-structure constant $α$ of negative sign. We discuss how such analogy enriches both problems, illustrating this with the insights into the MOTS-spectral problem gained from the analysis of the spectrum of the quantum charged particle Hamiltonian.
description: 5 pages, no figures
General off-resonance error robust symmetric composite pulses with three elementary operations
Creators: name: Kukita, Shingo
name: Kiya, Haruki
name: Kondo, Yasushi
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Accurate quantum control is a key technology for realizing quantum information processing, such as quantum communication and quantum computation. In reality, a quantum state under control suffers from undesirable effects caused by systematic errors. A composite pulse (CP) is used to eliminate the effects of systematic errors during control. One qubit control, which is the most fundamental in quantum control, is typically affected by two errors: pulse length error (PLE) and off-resonance error (ORE). In this study, we focus on ORE-robust CPs and systematically construct ORE-robust symmetric CPs with three elementary operations. We find an infinitely large number of ORE-robust CPs and evaluate their performance according to gate infidelity and operation time, both of which are important for the realization of accurate quantum control.
description: 18 pages, 5 figures
Gromov-Witten Invariants of Local P^2 and Modular Forms
Creators: name: Coates, Tom
name: Iritani, Hiroshi
Publisher: name: arXiv
Year: 2018
Subjects: subject: Algebraic Geometry (math.AG)
subject: Mathematical Physics (math-ph)
subject: Symplectic Geometry (math.SG)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We construct a sheaf of Fock spaces over the moduli space of elliptic curves E_y with Gamma_1(3)-level structure, arising from geometric quantization of H^1(E_y), and a global section of this Fock sheaf. The global section coincides, near appropriate limit points, with the Gromov-Witten potentials of local P^2 and of the orbifold C^3/mu_3. This proves that the Gromov-Witten potentials of local P^2 are quasi-modular functions for the group Gamma_1(3), as predicted by Aganagic-Bouchard-Klemm, and proves the Crepant Resolution Conjecture for [C^3/mu_3] in all genera.
description: 131 pages, 9 figures; fully commented source code included as ancillary file; for video of talk, see: https://www.youtube.com/watch?v=raqkmHxCJYI and https://www.youtube.com/watch?v=sRMESF1TSOA v2: final version, to appear in Kyoto Journal of Mathematics
Investigation of radiation-enhanced diffusion using first-passage time
Creators: name: Ryazanov, V. V.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences
subject: G.3
subject: 60-XX

description: The approach the first-passage time (FPT) of a random process to a certain level is applied to the description of radiation-enhanced diffusion. This is an integral approach to describing the problem of radiation-enhanced diffusion, which does not specify the details of the process but takes into account the overall change in entropy during the process. Relationships are obtained to take into account the influence of radiation effects on the diffusion coefficient. The theoretical results obtained are compared with the experimental ones.
description: 15 pages
The Alternative Sigma Factor AlgT Represses Pseudomonas aeruginosa Flagellum Biosynthesis by Inhibiting Expression of fleQ
Creators: name: Tart, A. H.
name: Wozniak, D. J.
name: Wolfgang, M. C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Pseudomonas aeruginosa poses a serious risk in individuals suffering from cystic fibrosis (CF). Strains colonizing the CF lung are generally motile but frequently convert to a nonmotile phenotype as the disease progresses. In many cases, this is coordinately regulated with the overproduction of the exopolysaccharide alginate. Both the expression of alginate (mucoidy) and the loss of flagellum synthesis may provide the bacterium with a selective advantage in the CF lung. Previously published data showed that the regulation of alginate production and flagellum biosynthesis in the CF isolate FRD1 is inversely controlled by the alternative sigma factor AlgT. In this study, we observed that in CF isolates, the mucoid and the nonmotile phenotypes occur predominantly together. Using microarrays, we compared the transcriptomes of isogenic AlgT+ and AlgT−P. aeruginosa and discovered that AlgT significantly downregulated the majority of flagellar genes. A pronounced inhibitory effect was observed in several genes essential for proper flagellum expression, including fleQ, which encodes an essential flagellar regulator. The microarray data were confirmed by reverse transcriptase PCR analysis and promoter fusion assays in isogenic AlgT+ and AlgT− strains. Transmission electron microscopy, motility assays, and Western blots showed that ectopic expression of FleQ in mucoid, nonmotile CF isolates restored flagellum biosynthesis and motility. Together, these data show that AlgT mediates the negative control of flagellum expression by inhibiting the expression of the flagellar regulator fleQ.
The Reality of Free Will
Creators: name: Janew, Claus
Publisher: name: figshare
Year: 2023
Subjects: Philosophy not elsewhere classified
Philosophy of cognition
Philosophy of mind (excl. cognition)
Philosophical psychology (incl. moral psychology and philosophy of action)

description: The uniqueness of each standpoint, each point of effect, can only be "overcome" by the standpoint changing to other standpoints and returning. In such alternation, which can also appear as constant change, lies the unity of the world. The wholeness of an alternation, however, is a structure of consciousness due to the special relationship between the circumscribing periphery and the infinitesimal center. This process structure unites determinacy and indeterminacy also totally in every place. Therefore, everywhere we are dealing with forms of consciousness with more or less freedom of choice and an increasingly unknown depth. We live in a world of choosing consciousness, or rather awareness. In this respect, our environment expresses a deep truth about ourselves.
 Published in: Journal of Consciousness Exploration & Research (2020), 11(1), p.1-16.
Durfee-type inequality for complete intersection surface singularities
Creators: name: Enokizono, Makoto
Publisher: name: arXiv
Year: 2018
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14B05

description: We prove that the signature of the Milnor fiber of smoothings of a $2$-dimensional isolated complete intersection singularity does not exceed the negative number determined by the geometric genus, the embedding dimension and the number of irreducible components of the exceptional set of the minimal resolution, which implies Durfee's weak conjecture and a partial answer to Kerner--Némethi's conjecture.
description: 15 pages
Generalised global supersolutions with mass control for systems with taxis
Creators: name: Zhigun, Anna
Publisher: name: arXiv
Year: 2018
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 35B45, 92C17, 35D30, 35D99, 35K55

description: The existence of generalised global supersolutions with a control upon the total mass is established for a wide family of parabolic-parabolic chemotaxis systems and general integrable initial data in any space dimension. It is verified that as long as a supersolution of this sort remains smooth, it coincides with the classical solution. At the same time, the proposed construction provides solvability beyond a blow-up time. The considered class of systems includes the basic form of the Keller-Segel model as well as the case of a chemorepellent.
description: arXiv admin note: text overlap with arXiv:1804.05333 Changes: $v>0$ a.e. in Definition 3.1 and corrections in the convergence arguments in Section 5.2
Splitting of logarithmic Gromov-Witten invariants under degeneration
Creators: name: Wu, Yixian
name: 0000-0002-2856-986X
Publisher: name: The University of Texas at Austin
Year: 2022
Subjects: Logarithmic geometry
Gromov-Witten invariants

description: In this dissertation, I study the theory of punctured Gromov-Witten invariants built by Abramovich, Chen, Gross and Siebert. I prove a splitting formula that reconstructs the logarithmic Gromov-Witten invariants of simple normal crossing varieties from the punctured Gromov-Witten invariants of their irreducible components, under the assumption of the gluing strata being toric varieties.
Terminal toric Fano three-folds with certain numerical conditions
Creators: name: Sato, Hiroshi
name: Sumiyoshi, Ryota
Publisher: name: arXiv
Year: 2018
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: Primary 14M25, Secondary 14J45

description: We completely classify the Q-factorial terminal toric Fano three-folds such that the sum of the squared torus invariant prime divisors is non-negative.
description: 12 pages, v2: minor revisions, to appear in Kyoto Journal of Mathematics
Dynamical demixing of a binary mixture under sedimentation
Creators: name: Nunes, A. S.
name: Coelho, R. C. V.
name: Braz, V. C.
name: da Gama, M. M. Telo
name: Araujo, N. A. M.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We investigate the sedimentation dynamics of a binary mixture, the species of which differ by their Stokes coefficients but are identical otherwise. We analyze the sedimentation dynamics and the morphology of the final deposits using Brownian dynamics simulations for mixtures with a range of sedimentation velocities of both species. In addition, we use the lattice Boltzmann method to study hydrodynamic effects. We found a threshold in the difference of the sedimentation velocities above which the species in the final deposit are segregated. The degree of segregation increases with the difference in the Stokes coefficients or the sedimentation velocities above the threshold. We propose a simple analytical model that captures the main features of the simulated deposits.
Angular structure of the in-medium QCD cascade
Creators: name: Blaizot, Jean-Paul
name: Mehtar-Tani, Yacine
name: Torres, Marcus A. C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We study the angular broadening of a medium-induced QCD cascade. We derive the equation that governs the evolution of the average transverse momentum squared of the gluons in the cascade as a function of the medium length, and we solve this equation analytically. Two regimes are identified. For a medium of a not too large size, and for not too soft gluons, the transverse momentum grows with the size of the medium according to standard momentum broadening. The other regime, visible for a medium of a sufficiently large size and very soft gluons, is a regime dominated by multiple branchings: there, the average transverse momentum saturates to a value that is independent of the size of the medium. This structure of the in-medium QCD cascade is, at least qualitatively, compatible with the recent data on dijet asymmetry.
description: 4 pages, 2 figures
The F-Plasmid TraI Protein Contains Three Functional Domains Required for Conjugative DNA Strand Transfer
Creators: name: Matson, S. W.
name: Ragonese, H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The F-plasmid-encoded TraI protein, also known as DNA helicase I, is a bifunctional protein required for conjugative DNA transfer. The enzyme catalyzes two distinct but functionally related reactions required for the DNA processing events associated with conjugation: the site- and strand-specific transesterification (relaxase) reaction that provides the nick required to initiate strand transfer and a processive 5′-to-3′ helicase reaction that provides the motive force for strand transfer. Previous studies have identified the relaxase domain, which encompasses the first ∼310 amino acids of the protein. The helicase-associated motifs lie between amino acids 990 and 1450. The function of the region between amino acids 310 and 990 and the region from amino acid 1450 to the C-terminal end is unknown. A protein lacking the C-terminal 252 amino acids (TraIΔ252) was constructed and shown to have essentially wild-type levels of transesterase and helicase activity. In addition, the protein was capable of a functional interaction with other components of the minimal relaxosome. However, TraIΔ252 was not able to support conjugative DNA transfer in genetic complementation experiments. We conclude that TraIΔ252 lacks an essential C-terminal domain that is required for DNA transfer. We speculate this domain may be involved in essential protein-protein interactions with other components of the DNA transfer machinery.
Explicit constructions of quilts with seam condition coming from symplectic reduction
Creators: name: Bottman, Nathaniel
Publisher: name: arXiv
Year: 2018
Subjects: subject: Symplectic Geometry (math.SG)
subject: FOS: Mathematics
subject: 53D40

description: Associated to a symplectic quotient $M/\!/G$ is a Lagrangian correspondence $Λ_G$ from $M/\!/G$ to $M$. In this note, we construct in two examples quilts with seam condition on such a correspondence, in the case of $S^1$ acting on $\mathbb{CP}^2$ with symplectic quotient $\mathbb{CP}^2/\!/ S^1 = \mathbb{CP}^1$. First, we study the quilted strips that would, if not for figure eight bubbling, identify the Floer chain groups $CF(γ,S_{\text{Cl}}^1)$ and $CF(\mathbb{RP}^2,T_{\text{Cl}}^2)$, where $γ$ is the connected double-cover of $\mathbb{RP}^1$. Second, we answer a question due to Akveld-Cannas da Silva-Wehrheim by explicitly producing a figure eight bubble which obstructs an isomorphism between two Floer chain groups. The figure eight bubbles we construct in this paper are the first concrete examples of this phenomenon.
description: 9 pages, 3 figures
The geometric Bogomolov conjecture
Creators: name: Cantat, Serge
name: Gao, Ziyang
name: Habegger, Philipp
name: Xie, Junyi
Publisher: name: arXiv
Year: 2018
Subjects: subject: Algebraic Geometry (math.AG)
subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: We prove the geometric Bogomolov conjecture over a function field of characteristic zero.
description: 18 pages
Transcriptional Analysis of the Conserved ftsZ Gene Cluster in Mycoplasma genitalium and Mycoplasma pneumoniae
Creators: name: Hutchison, C. A.
name: Powell, B. C.
name: Benders, G. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Several experimental approaches were used to construct a detailed transcriptional profile of the phylogenetically conserved ftsZ cell division gene cluster in both Mycoplasma genitalium and its closest relative, Mycoplasma pneumoniae. We determined initiation and termination points for the cluster, as well as an absolute steady-state RNA level for each gene. Transcription of this cluster in both these organisms was shown to be highly strand specific. While the four genes in this cluster are cotranscribed, their transcription unit also includes two genes of close proximity yet disparate function. A transcription initiation point immediately upstream of these two genes was detected in M. genitalium but not M. pneumoniae. In M. pneumoniae, transcription of the six genes terminates at a poly(U)-tailed hairpin. In M. genitalium, this transcription terminates at two closely spaced points by an unknown mechanism. Real-time reverse transcription-PCR analysis of this cluster in M. pneumoniae shows that mRNA levels for all six genes vary at most fivefold and form a gradient of decreasing quantity with increasing distance from the promoter at the beginning of the cluster. mRNA from coding regions was approximately 20- to 100-fold more abundant than that from intergenic regions. We estimated the most abundant mRNA we detected at 0.6 copy per cell. We conclude that groups of functionally related genes in M. genitalium and M. pneumoniae are often preceded by promoters but rarely followed by terminators. This causes functionally unrelated genes to be commonly cotranscribed in these organisms.
Porin-Mediated Antibiotic Resistance in Neisseria gonorrhoeae: Ion, Solute, and Antibiotic Permeation through PIB Proteins with penB Mutations
Creators: name: Olesky, M.
name: Rosenberg, R. L.
name: Zhao, S.
name: Nicholas, R. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Neisseria gonorrhoeae has two porins, PIA and PIB, whose genes (porA and porB, respectively) are alleles of a single por locus. We recently demonstrated that penB mutations at positions 120 and 121 in PIB, which are presumed to reside in loop 3 that forms the pore constriction zone, confer intermediate-level resistance to penicillin and tetracycline (M. Olesky, M. Hobbs, and R. A. Nicholas, Antimicrob. Agents Chemother. 46:2811-2820, 2002). In the present study, we investigated the electrophysiological properties as well as solute and antibiotic permeation rates of recombinant PIB proteins containing penB mutations (G120K, G120D/A121D, G120P/A121P, and G120R/A121H). In planar lipid bilayers, the predominant conducting state of each porin variant was 30 to 40% of the wild type, even though the anion selectivity and maximum channel conductance of each PIB variant was similar to that of the wild type. Liposome-swelling experiments revealed no significant differences in the permeation of sugars or β-lactam antibiotics through the wild type or PIB variants. Although these results are seemingly contradictory with the ability of these variants to increase antibiotic resistance, they are consistent with MIC data showing that these porin mutations confer resistance only in strains containing an mtrR mutation, which increases expression of the MtrC-MtrD-MtrE efflux pump. Moreover, both the mtrR and penB mutations were required to decrease in vivo permeation rates below those observed in the parental strain containing either mtrR or porin mutations alone. Thus, these data demonstrate a novel mechanism of porin-mediated resistance in which mutations in PIB have no affect on antibiotic permeation alone but instead act synergistically with the MtrC-MtrD-MtrE efflux pump in the development of antibiotic resistance in gonococci.
Ext Data File 1 - Information Capture Form_Generic_2022 Sept14
Creators: name: Chaussabel, Damien
Publisher: name: figshare
Year: 2022
Subjects: Biomarkers

description: Extended Data File 1: A spreadsheet in the MS Excel format that is used as a template to capture relevant information from the literature and from transcriptional profiling data analysis results.
Differential Regulation of ponA and pilMNOPQ Expression by the MtrR Transcriptional Regulatory Protein in Neisseria gonorrhoeae
Creators: name: Folster, J. P.
name: Dhulipala, V.
name: Shafer, W. M.
name: Nicholas, R. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Neisseria gonorrhoeae utilizes the mtrCDE-encoded efflux pump system to resist not only host-derived, hydrophobic antimicrobials that bathe mucosal surfaces, which likely aids in its ability to colonize and infect numerous sites within the human host, but also antibiotics that have been used clinically to treat infections. Recently, overexpression of the MtrC-MtrD-MtrE efflux pump was shown to be critically involved in the capacity of gonococci to develop chromosomally mediated resistance to penicillin G, which for over 40 years was used to treat gonococcal infections. Mutations in either the promoter or the coding sequence of the mtrR gene, which encodes a repressor of the efflux pump operon, decrease gonococcal susceptibility to penicillin. We now describe the capacity of MtrR to directly or indirectly influence the expression of two other loci that are involved in gonococcal susceptibility to penicillin: ponA, which encodes penicillin-binding protein 1 (PBP 1), and the pilMNOPQ operon, which encodes components of the type IV pilus secretion system, with PilQ acting as a channel for entry for penicillin. We determined that MtrR increases the expression of ponA directly or indirectly, resulting in increased levels of PBP 1, while repressing the expression of the divergently transcribed pilM gene, the first gene in the pilMNOPQ operon. Taken together with other studies, the results presented herein indicate that transcriptional regulation of gonococcal genes by MtrR is centrally involved in determining levels of gonococcal susceptibility to penicillin and provides a framework for understanding how resistance developed over the years.
BCOV invariants of Calabi--Yau manifolds and degenerations of Hodge structures
Creators: name: Eriksson, Dennis
name: Montplet, Gerard Freixas i
name: Mourougane, Christophe
Publisher: name: arXiv
Year: 2018
Subjects: subject: Algebraic Geometry (math.AG)
subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 14J32, 32G20, 58K55, 58J52 (Primary), 58K65 (Secondary)

description: Calabi--Yau manifolds have risen to prominence in algebraic geometry, in part because of mirror symmetry and enumerative geometry. After Bershadsky--Cecotti--Ooguri--Vafa (BCOV), it is expected that genus 1 curve counting on a Calabi--Yau manifold is related to a conjectured invariant, only depending on the complex structure of the mirror, and built from Ray--Singer holomorphic analytic torsions. To this end, extending work of Fang--Lu--Yoshikawa in dimension 3, we introduce and study the BCOV invariant of Calabi--Yau manifolds of arbitrary dimension. To determine it, knowledge of its behaviour at the boundary of moduli spaces is imperative. We address this problem by proving precise asymptotics along one-parameter degenerations, in terms of topological data and intersection theory. Central to the approach are new results on degenerations of $L^2$ metrics on Hodge bundles, combined with information on the singularities of Quillen metrics in our previous work.
description: Minor revision. Mainly restructure of the text, minor improvements and corrections. Added information about subdominant terms of $L^2$-norms
McCool groups of toral relatively hyperbolic groups
Creators: name: Guirardel, Vincent
name: Levitt, Gilbert
Publisher: name: arXiv
Year: 2014
Subjects: subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: 20F28, 20F65, 20F67, 20F34, 20E08, 57M07, 20J06

description: The outer automorphism group Out(G) of a group G acts on the set of conjugacy classes of elements of G. McCool proved that the stabilizer $Mc(c_1,...,c_n)$ of a finite set of conjugacy classes is finitely presented when G is free. More generally, we consider the group $Mc(H_1,...,H_n)$ of outer automorphisms $Φ$ of G acting trivially on a family of subgroups $H_i$, in the sense that $Φ$ has representatives $α_i$ with $α_i$ equal to the identity on $H_i$. When G is a toral relatively hyperbolic group, we show that these two definitions lead to the same subgroups of Out(G), which we call "McCool groups" of G. We prove that such McCool groups are of type VF (some finite index subgroup has a finite classifying space). Being of type VF also holds for the group of automorphisms of G preserving a splitting of G over abelian groups. We show that McCool groups satisfy a uniform chain condition: there is a bound, depending only on G, for the length of a strictly decreasing sequence of McCool groups of G. Similarly, fixed subgroups of automorphisms of G satisfy a uniform chain condition.
Effects of finite non-gaussianity on evolution of a random wind wave field
Creators: name: Annenkov, S. Y.
name: Shrira, V. I.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: FOS: Physical sciences

description: We examine long-term evolution of a random wind wave field generated by constant forcing, by comparing numerical simulations of the kinetic equation and direct numerical simulations (DNS) of the dynamical equations. While integral characteristics of spectra are in reasonably good agreement, the spectral shapes differ considerably at large times, the DNS spectral shape being in much better agreement with field observations. Varying the number of resonant and approximately resonant wave interactions in the DNS numerical scheme, we show that when the ratio of nonlinear and linear parts of the Hamiltonian tends to zero, the DNS spectral shape approaches the shape predicted by the kinetic equation. We attribute the discrepancies between the kinetic equation modelling, on one side, and the DNS and observations, on the other, to the neglect of non-gaussianity in the derivation of the kinetic equation.
description: 5 pages, 4 figures
Central Stars of Planetary Nebulae in Galactic Open Clusters: Providing additional data for the White Dwarf Initial-to-Final-Mass Relation
Creators: name: Fragkou, Vasiliki
name: Parker, Quentin A.
name: Zijlstra, Albert
name: Shaw, Richard
name: Lykou, Foteini
Publisher: name: arXiv
Year: 2018
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Accurate (<10%) distances of Galactic star clusters allow precise estimation of the physical parameters of any physically associated Planetary Nebula (PN) and also that of its central star (CSPN) and its progenitor. The progenitor's mass can be related to the PN's chemical characteristics and furthermore, provides additional data for the widely used white dwarf (WD) initial-to-final mass relation (IFMR) that is crucial for tracing the development of both carbon and nitrogen in entire galaxies. To date there is only one PN (PHR1315- 6555) confirmed to be physically associated with a Galactic open cluster (ESO 96 -SC04) that has a turn-off mass $\sim$2 M$_{\odot}$. Our deep HST photometry was used for the search of the CSPN of this currently unique PN. In this work, we present our results.
description: 2 pages, 1 figure, IAU343 Synposium