bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamical ergodicity DDA reveals causal structure in time series
Authors: Lainscsek Claudia , Cash Sydney S. , Sejnowski Terrence J. , Kurths Jürgen
Published: October 2021

Determining synchronization, causality, and dynamical similarity in highly complex nonlinear systems like brains is challenging. Although distinct, these measures are related by the unknown deterministic structure of the underlying dynamical system. For two systems that are not independent on each other, either because they result from a common process or they are already synchronized, causality measures typically fail. Here, we introduce dynamical ergodicity to assess dynamical similarity between time series and then combine this new measure with cross-dynamical delay differential analysis to estimate causal interactions between time series. We first tested this approach on simulated data from coupled Rössler systems where ground truth was known. We then applied it to intracranial electroencephalographic data from patients with epilepsy and found distinct dynamical states that were highly predictive of epileptic seizures.
Natural convection over vertical and horizontal heated flat surfaces: A review of recent progress focusing on underpinnings and implications for heat transfer and environmental applications
Authors: Fan Yifan , Zhao Yongling , Torres Juan F. , Xu Feng , Lei Chengwang , Li Yuguo , Carmeliet Jan
Published: October 2021

Natural convection arising over vertical and horizontal heated flat surfaces is one of the most ubiquitous flows at a range of spatiotemporal scales. Despite significant developments over more than a century contributing to our fundamental understanding of heat transfer in natural convection boundary layers, certain “hidden” characteristics of these flows have received far less attention. Here, we review scattered progress on less visited fundamental topics that have strong implications to heat and mass transfer control. These topics include the instability characteristics, laminar-to-turbulent transition, and spatial flow structures of vertical natural convection boundary layers and large-scale plumes, dome, and circulating flows over discretely and entirely heated horizontal surfaces. Based on the summarized advancements in fundamental research, we elaborate on the selection of perturbations and provide an outlook on the development of perturbation generators and methods of altering large-scale flow structures as a potential means for heat and mass transfer control where natural convection is dominant.
Scaling relations of exciton diffusion in linear aggregates with static and dynamic disorder
Authors: Kunsel T. , Jansen T. L. C. , Knoester J.
Published: October 2021

Exciton diffusion plays an important role in many opto-electronic processes and phenomena. Understanding the interplay of intermolecular coupling, static energetic disorder, and dephasing caused by environmental fluctuations (dynamic disorder) is crucial to optimize exciton diffusion under various physical conditions. We report on a systematic analysis of the exciton diffusion constant in linear aggregates using the Haken–Strobl–Reineker model to describe this interplay. We numerically investigate the static-disorder scaling of (i) the diffusion constant in the limit of small dephasing rate, (ii) the dephasing rate at which the diffusion is optimized, and (iii) the value of the diffusion constant at the optimal dephasing rate. Three scaling regimes are found, associated with, respectively, fully delocalized exciton states (finite-size effects), weakly localized states, and strongly localized states. The scaling powers agree well with analytically estimated ones. In particular, in the weakly localized regime, the numerical results corroborate the so-called quantum Goldilocks principle to find the optimal dephasing rate and maximum diffusion constant as a function of static disorder, while in the strong-localization regime, these quantities can be derived fully analytically.
Concepts and the Physical Realms
Authors: Singh Anirudh
Published: October 2021

Humans live in many different worlds, each of which has its own representation in mind space. The world of the scientist will be called the physical realms. The laws of physics are an integral part of the real world, and humans acquire a natural understanding of these laws without regard to any mathematical formulation.

While the experimental physicist studies the behavior of the real world, the theoretical physicist develops and studies its representation in the mathematical world (i.e., mind space). It is not necessary to know the mathematical equations to be able to carry out a physical investigation. This can be performed through observation and recording of the data numerically, and using the processes of interpolation and extrapolation.

Practicing physicists usually find that they must adopt the roles of both the theoretical as well as the experimental physicist to achieve the aims of an experiment.

Observers play a vital role in physics. They become important when their state of motion changes, or when their presence affects the results of the experiment. The observer can be either animate or inanimate. Unlike inanimate observers, animate observers have access to mind space, which allows them to make decisions from collected information.
Anapole States and Toroidal Multipole Excitations in Photonic Metastructures
Authors: Zografopoulos Dimitrios C. , Ferraro Antonio
Published: October 2021

A growing research field has recently emerged on the investigation of toroidal multipole resonances and the closely related nonradiating anapole state in both dielectric and metallic metastructures working in the visible, near-infrared, and terahertz spectrum. Here we provide an overview on the anapole state and toroidal multipole excitations in photonic metastructures. We cover the key points of the underlying electromagnetic theory and discuss the practical realization of both dielectric and plasmonic metastructures, which exhibit a strong toroidal response. Then, we present examples of toroidal-enabled applications in various photonic platforms, which span from nanolasing, higher-harmonic generation, and cloaking to photodetection, filtering, and sensing.
Hybrid Modes and Hybrid Metastructures for Color Reproduction
Authors: Es-saidi Soukaina , Blaize Sylvain , Macías Demetrio
Published: October 2021

We explore the possibilities of hybrid metal-dielectric metastructures for color generation. In a first stage, we briefly discuss the main physical phenomena underlying the chromatic response of a hybrid structure. This should settle the basis for the solution of a special kind of inverse problem: To tailor the geometrical parameters of a hybrid diffractive structure to reproduce a specific color. To this end, we outline an inversion scheme recently proposed, based on multi-objective meta-heuristic optimization and Artificial Intelligence techniques, that has been successfully used on the solution of the inverse problem just cited.
Hybrid Photonic–Plasmonic Metastructures
Authors: Lio Giuseppe Emanuele , Caputo Roberto
Published: October 2021

This chapter considers hybrid metastructures operating in waveguide configuration. This configuration can unlock unprecedented functionalities when the interplay between quantum emitters and plasmonic nanostructures is efficiently exploited. The chapter begins with an introduction of the Purcell effect responsible for the emission enhancement of fluorescent subentities when located in nanocavities. Introductory paragraphs also explain the basic mechanisms of the plasmon–exciton exchange. The design of a hybrid system follows including plasmonic nanotapers (NTs) with quantum dots (QDs) positioned in proximity to their apices. The various phases of the fabrication procedure of the designed metastructure, involving a mixed top-down and bottom-up nanofabrication approach, are accurately illustrated. A fluorescent spectroscopy characterization of the prototype evidences a sensitive Purcell enhancement of the emission of the quantum dots located in proximity of the NTs. Finally, a numerical study of this hybrid system is reported that demonstrates how the light enhancement can be controlled to efficiently route and modulate high-frequency optical signals in a photonic–plasmonic transistor effect.
Photothermal Metastructure Platforms toward Precision Biomedical Applications
Authors: Caputo Roberto , Lio Giuseppe Emanuele , Ferraro Antonio
Published: October 2021

Plasmonic nanostructures show outstanding promise in allowing sensitive temperature control, due to their natural ability to strongly confine a nanoscale electric field and release heat. In this chapter, the evolution of thermoresponsive metastructures is described from their introduction as amorphous arrangements of homogeneously distributed gold nanoparticles (AuNPs) to their fine improvement through the design and experimental characterization of specific distributions of thermal hot spots. Thermoplasmonic metastructures actuated by optical and mechanical stimuli have been numerically designed and experimentally realized. Quite significant is the experimental realization and characterization of arrays of functionalized nanoheaters with optimized “flower” geometry showing a significant thermal response upon laser excitation.
Formation of negative-ion resonance and dissociative attachment in collisions of NO2 with electrons
Authors: Liu Hainan , Jiang Xianwu , Yuen Chi-Hong , Kokoouline Viatcheslav , Ayouz Mehdi
Published: October 2021

The process of electron attachment to the NO2 molecule is investigated theoretically using an approach based on a study by O’Malley (1966 Phys. Rev.
150 14). The approach combines the normal mode approximation for representation of vibrational dynamics of NO2 and one-dimensional treatment, along each normal mode, of the attachment process as in O’Malley’s theory, such that only a modest computational effort is required to compute the attachment cross section. Taking into account the survival probability of the formed resonant state of

N
O

2

−

, the cross section for dissociative electron attachment to NO2 is also estimated. To compare with available experimental data, the theoretical cross section is convoluted with energy distribution of NO2–e− collisions with uncertainties reported in experimental studies. Peak values of the convoluted theoretical cross section are found to be about a factor of 2–10 larger than the experimental results.
Effect of helium flux on near-surface helium accumulation in plasma-exposed tungsten
Authors: Nandipati Giridhar , Hammond Karl D , Maroudas Dimitrios , Roche Kenneth J , Kurtz Richard J , Wirth Brian D , Setyawan Wahyu
Published: October 2021

We report results of object kinetic Monte Carlo (OKMC) simulations to understand the effect of helium flux on the near-surface helium accumulation in plasma-facing tungsten, which is initially pristine, defect-free, and has a (100) surface orientation. These OKMC simulations are performed at 933 K for fluxes ranging from 1022 to 4 × 1025 He/m2 s with 100 eV helium atoms impinging on a (100) surface up to a maximum fluence of 4 × 1019 He/m2. In the near-surface region, helium clusters interact elastically with the free surface. The interaction is attractive and results in the drift of mobile helium clusters towards the surface as well as increased trap mutation rates. The associated kinetics and energetics of the above-mentioned processes obtained from molecular dynamics simulations are also considered. The OKMC simulations indicate that in pristine tungsten, as the flux decreases, the retention of implanted helium decreases, and its depth distribution shifts to deeper below the surface. Furthermore, the fraction of retained helium diffusing into the bulk increases as well, so much so that for the flux of 1022 He/m2 s, almost all of the retained helium diffused into the bulk with minimal/negligible near-surface helium accumulation. At a given flux, with increasing fluence, the fraction of retained helium initially decreases and then starts to increase after reaching a minimum. The occurrence of the retention minimum shifts to higher fluences as the flux decreases. Although the near-surface helium accumulation spreads deeper into the material with decreasing flux and increasing fluence, the spread appears to saturate at depths between 80 and 100 nm. We present a detailed analysis of the influence of helium flux on the size and depth distribution of total helium and helium bubbles.
High temperature W-band complex permittivity measurements of thermally cycled ceramic-metal composites: AlN:Mo with 0.25 to 4.0 vol% Mo from 25 °C to 1000 °C in air
Authors: Cohick Zane W , Schaub Samuel C , Hoff Brad W , Dynys Frederick W , Baros Anthony E , Telmer Maxwell , Orozco Haylie , Grudt Rachael O , Hayden Steven C , Rittersdorf Ian M , Savrun Ender
Published: October 2021

An apparatus for measuring the W-band (75–110 GHz) complex permittivity of dielectrics at 1000 °C was developed. This apparatus allows for measurements at approximately twice the temperature of previously published high temperature free-space measurement systems while maintaining similar precision. Challenges were addressed related to high temperature measurements, including temperature uniformity, the accuracy of temperature measurements, and preventing temperature related changes to mm-wave measurement systems. The details of complex permittivity extraction from the measured S-parameters are discussed. Sources of error related to permittivity measurement and mathematical models were identified and are discussed in detail herein. Thermally-cycled, mm-wave absorbing, aluminum nitride ceramic composites containing varying levels of molybdenum additives were measured over the range of 25 °C–1000 °C. These measurements were compared to the same composites before thermal cycling. It was found that ceramic composites are largely stable after thermal cycling in terms of dielectric properties despite the presence of visible surface modifications.
Plasma flux and energy enhancement in BP-HiPIMS discharge via auxiliary anode and solenoidal coil
Authors: Han Mingyue , Luo Yang , Tang Ling , Gu Jiabin , Li Hua , Xu Ye , Luo Sida , Li LiuHe
Published: October 2021

As an emerging and extraordinary plasma source, the bipolar-pulse high power impulse magnetron sputtering (BP-HiPIMS) has promising prospects and wide industrial applications. In this paper, an effort to optimize the plasma flux and energy in BP-HiPIMS via auxiliary anode and solenoidal coil was made. This novel plasma source contains two types of auxiliary anode voltage (direct current and pulse) and one type of solenoidal coil current (direct current) to synergistically enhance the plasma generation and diffusion by electric field and magnetic field together. Systematic evaluations of discharge characteristics demonstrate that applying auxiliary anode voltage and coil magnetic field effectively contribute to a reduction in delay time of target current onset and increase in peak amplitude of target current, which are beneficial for improving plasma generation and target sputtering. The complex plasma dynamics are diagnosed by Langmuir probe and optical emission spectroscopy, and simulated by particle-in-cell/Monte Carlo collision approach. These comprehensive investigations on plasma parameters demonstrate that the plasma density, emission intensity of the metal ions, substrate current density, and ionization fraction of sputtered target particles have been improved with the increase of coil current. The observations of the increase in excitation temperature T
exc of Ar atoms, and more extended high-energy tails in electron energy distribution function curves imply that the plasma can be significantly heated by the auxiliary anode. Combining the simulation results and theoretical model proposed in the last sub-content, the diffusion and transport mechanism of charged-particles in complex electric and magnetic fields are discussed. From the theoretical analysis, the qualitative relation between the plasma density and coil current is well consistent with the measurements of electron density obtained by Langmuir probe. These evidences all support the idea that the plasma flux and energy can be enhanced in BP-HiPIMS discharge via auxiliary anode and solenoidal coil together.
Analyses on the nonequilibrium transport processes in a free-burning argon arc plasma under different operating conditions
Authors: Fang Chuan , Chen Jian , Li Jing , Zhang Zi-Ming , Guo Heng , Li Zhi-Hui , Zeng Shi , Li He-Ping
Published: October 2021

During discharges of an arc plasma, complex mass, momentum and energy exchanges exist between the arc column and the surrounding cold gas, forming a nonequilibrium region deviating from both the local thermodynamic equilibrium and local chemical equilibrium states. The nonequilibrium synergistic transport plays a crucial role not only in controlling the characteristics of the arc plasmas theoretically, but also in optimizing the plasma material processing qualities in actual applications. In this paper, the nonequilibrium transport processes in free-burning argon arc plasmas under different operating pressures and arc currents are studied based on a complete nonequilibrium fluid model, and are also validated by comparing with measured data. The energy transfer processes under various operating conditions, especially Joule heating, elastic and inelastic collisions, conductive and convective heat transfer, and energy transfer related to the temperature ratio spatial gradient, are analyzed based on the concept of the ‘energy tree.’ The revealed major energy transfer channels in the high-pressure argon arc plasmas also provide some possibilities to control the characteristics of thermal plasmas in the future.
Local, expressive, quantum-number-preserving VQE ansätze for fermionic systems
Authors: Anselmetti Gian-Luca R , Wierichs David , Gogolin Christian , Parrish Robert M
Published: October 2021

We propose VQE circuit fabrics with advantageous properties for the simulation of strongly correlated ground and excited states of molecules and materials under the Jordan–Wigner mapping that can be implemented linearly locally and preserve all relevant quantum numbers: the number of spin up (α) and down (β) electrons and the total spin squared. We demonstrate that our entangler circuits are expressive already at low depth and parameter count, appear to become universal, and may be trainable without having to cross regions of vanishing gradient, when the number of parameters becomes sufficiently large and when these parameters are suitably initialized. One particularly appealing construction achieves this with just orbital rotations and pair exchange gates. We derive optimal four-term parameter shift rules for and provide explicit decompositions of our quantum number preserving gates and perform numerical demonstrations on highly correlated molecules on up to 20 qubits.
Light Dirac neutrino portal dark matter with observable ΔN
eff
Authors: Biswas Anirban , Borah Debasish , Nanda Dibyendu
Published: October 2021

We propose a Dirac neutrino portal dark matter scenario
by minimally extending the particle content of the Standard Model
(SM) with three right-handed neutrinos (ν
R
), a Dirac fermion
dark matter candidate (ψ) and a complex scalar (ϕ), all
of which are singlets under the SM gauge group. An additional ℤ4
symmetry has been introduced for the stability of dark matter
candidate ψ and also ensuring the Dirac nature of light
neutrinos at the same time. Both the right handed neutrinos and
the dark matter thermalise with the SM plasma due to a new Yukawa
interaction involving ν
R
, ψ and ϕ while the latter
maintains thermal contact via the Higgs portal interaction.
The decoupling of ν
R
occurs when ϕ
loses its kinetic equilibrium with the SM plasma and thereafter
all three ℤ4 charged particles form an equilibrium
among themselves with a temperature TνR

.
The dark matter candidate ψ finally freezes out within the dark
sector and preserves its relic abundance. We have found that in the
present scenario, some portion of low mass dark matter (M
ψ ≲ 10 GeV)
is already excluded by the Planck 2018 data for keeping ν
R
s
in the thermal bath below a temperature of 600 MeV and thereby
producing an excess contribution to N
eff. The next
generation experiments like CMB-S4, SPT-3G etc. will have the required sensitivities to probe the entire
model parameter space of this minimal scenario,
especially the low mass range of ψ where direct detection
experiments are still not capable enough for detection.
Testing no-hair theorem
by quasi-periodic oscillations:
the
quadrupole of GRO J1655–40
Authors: Allahyari Alireza , Shao Lijing
Published: October 2021

We perform an observational test of no-hair theorem using
quasi-periodic oscillations within the relativistic precession model. Two
well motivated metrics we apply are Kerr-Q and Hartle-Thorne metrics in
which the quadrupole is the parameter that possibly encodes deviations from
the Kerr black hole. The expressions for the quasi-periodic frequencies are
derived before comparing the models with the observation. We encounter a
degeneracy in constraining spin and quadrupole parameters that makes it
difficult to measure their values. In particular, we here propose a novel
test of no-hair theorem by adapting the Hartle-Thorne metric. We complement our study by doing a model comparison. We find
that there is strong evidence that Kerr black hole is the source of the central object in GRO
J1655–40 given the present observational precisions.
Dolbeault cohomology of complex manifolds with torus action
Authors: Krutowski Roman , Panov Taras
Published: October 2021

We describe the basic Dolbeault cohomology algebra of the canonical foliation on a class of complex manifolds with a torus symmetry group. This class includes complex moment-angle manifolds, LVM- and LVMB-manifolds and, in most generality, complex manifolds with a maximal holomorphic torus action. We also provide a DGA model for the ordinary Dolbeault cohomology algebra. The Hodge decomposition for the basic Dolbeault cohomology is proved by reducing to the transversely Kähler (equivalently, polytopal) case using a foliated analogue of toric blow-up.
Poincaré polynomials of generic torus orbit closures in Schubert varieties
Authors: Lee Eunjeong , Masuda Mikiya , Park Seonjeong , Song Jongbaek
Published: October 2021

The closure of a generic torus orbit in the flag variety

G

/

B

G/B

of type 

A
A

is known to be a permutohedral variety, and its Poincaré polynomial agrees with the Eulerian polynomial. In this paper, we study the Poincaré polynomial of a generic torus orbit closure in a Schubert variety in 

G

/

B

G/B

. When the generic torus orbit closure in a Schubert variety is smooth, its Poincaré polynomial is known to agree with a certain generalization of the Eulerian polynomial. We extend this result to an arbitrary generic torus orbit closure which is not necessarily smooth.
Higher order Massey products and applications
Authors: Limonchenko Ivan , Millionshchikov Dmitry
Published: October 2021

In this survey, we discuss two research areas related to Massey’s higher operations. The first direction is connected with the cohomology of Lie algebras and the theory of representations. The second main theme is at the intersection of toric topology, homotopy theory of polyhedral products, and the homology theory of local rings, Stanley–Reisner rings of simplicial complexes.
Group actions: Entropy, mixing, spectra, and generic properties
Authors: Stepin Anatoly , Tikhonov Sergey
Published: October 2021

We talk about several directions of V. Rokhlin’s heritage in ergodic theory: ideas that influenced the further development of investigations (genericity, approximations), problems put forward by V. Rokhlin in his papers, problems that V. Rokhlin put forward verbally (in particular, the question about homogeneous spectrum of finite multiplicity). We touch upon the directions close to the authors of this text and their school. Many of the questions raised by Rokhlin have analogs for different classes of transformations, for group actions, and versions about the genericity of properties appearing in these formulations. We will consider the corresponding topics in such a generalized sense.
Maximally inflected real trigonal curves on Hirzebruch surfaces
Authors: Zvonilov V.
Published: October 2021

In 2014 A. Degtyarev, I. Itenberg, and the author gave a description, up to fiberwise equivariant deformations, of maximally inflected real trigonal curves of type I (over a base

B
B

of an arbitrary genus) in terms of the combinatorics of sufficiently simple graphs and for

B
=

P

1

B=\mathbb {P}^1

obtained a complete classification of such curves. In this paper, the mentioned results are extended to maximally inflected real trigonal curves of type II over

B
=

P

1

B=\mathbb {P}^1

.
Genetic divergence ofDeschampsia antarctica(Poaceae) population groups in the maritime Antarctic
Authors: Andreev Igor O , Parnikoza Ivan Yu , Konvalyuk Iryna I , Metcheva Roumiana , Kozeretska Iryna A , Kunakh Viktor A
Published: October 2021

We used inter-simple sequence repeats and inter-retrotransposon amplified polymorphism markers to assess genetic variation in Deschampsia antarctica populations in the context of its uneven distribution in the northern and central maritime Antarctic. Genetic diversity and population structure and differentiation were assessed in nine populations from geographically isolated population groups of D. antarctica, including the South Shetland Islands, Anvers Island and the Argentine Islands regions. In total, 265 amplified DNA fragments were scored, of which 220 (83.0%) were polymorphic. The total sample showed low genetic diversity (unbiased expected heterozygosity = 0.081 and Shannon diversity index = 0.115) and high population differentiation (molecular variance among populations = 0.659). We also found a trend toward a decrease in genetic diversity and an increase in population differentiation toward the southern edge of the species range. Principal coordinates analysis of polymerase chain reaction data and Bayesian population structure analysis showed three main clusters, which included plants originating from three spatially isolated population groups. The unweighted pair group method with arithmetic mean clustering of populations based on Nei’s genetic distances was mainly in agreement with this pattern. Testing of isolation by distance using the Mantel test demonstrated a significant correlation between genetic and ln-transformed geographical distance (r = 0.703). The data obtained indicate that the geographically isolated D. antarctica populations in the maritime Antarctic might form genetic clusters within the total range.
Multitargeted interventions to reduce dialysis-induced systemic stress
Authors: Canaud Bernard , Stephens Melanie P , Nikam Milind , Etter Michael , Collins Allan
Published: October 2021

Hemodialysis (HD) is a life-sustaining therapy as well as an intermittent and repetitive stress condition for the patient. In ridding the blood of unwanted substances and excess fluid from the blood, the extracorporeal procedure simultaneously induces persistent physiological changes that adversely affect several organs. Dialysis patients experience this systemic stress condition usually thrice weekly and sometimes more frequently depending on the treatment schedule. Dialysis-induced systemic stress results from multifactorial components that include treatment schedule (i.e. modality, treatment time), hemodynamic management (i.e. ultrafiltration, weight loss), intensity of solute fluxes, osmotic and electrolytic shifts and interaction of blood with components of the extracorporeal circuit. Intradialytic morbidity (i.e. hypovolemia, intradialytic hypotension, hypoxia) is the clinical expression of this systemic stress that may act as a disease modifier, resulting in multiorgan injury and long-term morbidity. Thus, while lifesaving, HD exposes the patient to several systemic stressors, both hemodynamic and non-hemodynamic in origin. In addition, a combination of cardiocirculatory stress, greatly conditioned by the switch from hypervolemia to hypovolemia, hypoxemia and electrolyte changes may create pro-arrhythmogenic conditions. Moreover, contact of blood with components of the extracorporeal circuit directly activate circulating cells (i.e. macrophages–monocytes or platelets) and protein systems (i.e. coagulation, complement, contact phase kallikrein–kinin system), leading to induction of pro-inflammatory cytokines and resulting in chronic low-grade inflammation, further contributing to poor outcomes. The multifactorial, repetitive HD-induced stress that globally reduces tissue perfusion and oxygenation could have deleterious long-term consequences on the functionality of vital organs such as heart, brain, liver and kidney. In this article, we summarize the multisystemic pathophysiological consequences of the main circulatory stress factors. Strategies to mitigate their effects to provide more cardioprotective and personalized dialytic therapies are proposed to reduce the systemic burden of HD.
Legislation and the Stress of Environmental Problems
Authors: Scotford Eloise
Published: October 2021

For lawyers and legal scholars, legislation seems a known quantity—a relatively permanent, public expression of democratic processes in parliamentary democracies and of the rule of law. This ‘knowable’ character can however be misleading, particularly in the field of environmental law. This article examines why research into environmental legislation is challenging but critically important. A short history of UK environmental law provides salient examples of political stress and highly complex, unsettled, even unknowable, environmental legislation. Collective environmental problems demand legislative responses in shaping individual behaviours and guiding social policies—but knowing how to craft these responses and how to evaluate the resulting legislation is often uncharted legal territory. Navigating that legislative terrain is a vital task for legal scholars and practitioners, particularly to investigate the serious legal problems that can arise from its construction, including poor legibility, legal fragmentation, and concerns about compatibility with the rule of law.
TORC1 signaling modulates Cdk8-dependent GAL gene expression in Saccharomyces cerevisiae
Authors: Horvath Riley , Hawe Nicole , Lam Cindy , Mestnikov Konstantin , Eji-Lasisi Mariam , Rohde John , Sadowski Ivan
Published: October 2021

Cdk8 of the RNA polymerase II mediator kinase complex regulates gene expression by phosphorylating sequence-specific transcription factors. This function is conserved amongst eukaryotes, but the signals and mechanisms regulating Cdk8 activity and phosphorylation of its substrates are unknown. Full induction of the GAL genes in yeast requires phosphorylation of the transcriptional activator Gal4 by Cdk8. We used a screen to identify regulators of the Cdk8-dependent phosphorylation on Gal4, from which we identified multiple mutants with defects in TORC1 signaling. One mutant, designated gal four throttle 1 (gft1) was identified as a recessive allele of hom3, encoding aspartokinase, and mutations in hom3 caused effects typical of inhibition of TORC1, including rapamycin sensitivity and enhanced nuclear localization of the TORC1-responsive transcription factor Gat1. Mutations in hom3 also inhibit phosphorylation of Gal4 in vivo at the Cdk8-dependent site on Gal4, as did mutations of tor1, but these mutations did not affect activity of Cdk8 assayed in vitro. Disruption of cdc55, encoding a regulatory subunit of the TORC1-regulated protein phosphatase PP2A, suppressed the effect of hom3 and tor1 mutations on GAL expression, and also restored phosphorylation of Gal4 at the Cdk8-dependent site in vivo. These observations demonstrate that TORC1 signaling regulates GAL induction through the activity of PP2A/Cdc55 and suggest that Cdk8-dependent phosphorylation of Gal4 is opposed by PP2A/Cdc55 dephosphorylation. These results provide insight into how induction of transcription by a specific inducer can be modulated by global nutritional signals through regulation of Cdk8-dependent phosphorylation.
Constructing a regional human rights legal order: The Inter-American Court, national courts, and judicial dialogue, 1988–2014
Authors: Gonzalez-Ocantos Ezequiel , Sandholtz Wayne
Published: October 2021

Why do courts rely on specific bodies of jurisprudence to justify decisions? We analyze judicial dialogue in the Inter-American System, where the Inter-American Court of Human Rights (IACtHR) has defined its mission as the construction of a regional legal order. This order needs courts at all levels to engage with each other. Original databases of citations by the IACtHR to the judgments of national courts, and in the opposite direction, allow us to establish whether such practices are emerging. Furthermore, the article asks why the IACtHR cites some courts but not others, and to what end. Statistical models reveal that the IACtHR is more likely to cite case law from countries that exhibit characteristics that are more conducive to the creation of a regional human rights legal order, and jurisprudence from countries with which it has had more extensive experience and interaction. Qualitative content analysis suggests that the IACtHR uses citations as a source of persuasive authority, but also to showcase domestic acceptance of its doctrines and decisions. This leads us to characterize citations as an effort to educate courts in the use of Inter-American jurisprudence and thus foster greater integration. At the national level, we find considerable temporal/cross-country variation in openness to the dialogue. We rely on original quantitative indicators and case studies to show this is as a function of the IACtHR’s growing visibility and networking efforts, as well as country-level changes in legal cultures and judicial personnel that push courts away from formalism.
Econazole as adjuvant to conventional antibiotics is able to eradicate starvation-induced tolerant bacteria by causing proton motive force dissipation
Authors: Wang Miaomiao , Chan Edward Wai Chi , Xu Chen , Chen Kaichao , Yang Chen , Chen Sheng
Published: October 2021

Objectives

Bacterial antibiotic tolerance is responsible for the recalcitrance of chronic infections. This study aims to investigate a potential drug that can effectively kill antibiotic-tolerant bacteria and evaluate the ability of this drug on the eradication of tolerant cells both in vitro and in vivo.

Methods

The in vitro effect of econazole on eradicating starvation-induced tolerant bacterial populations was studied by testing the amount of survival bacteria in the presence of econazole combining conventional antibiotics. Proton motive force (PMF) was determined after econazole treatment by DiOC2(3). Finally, mouse infection models were used to detect the ability of econazole on killing the tolerant populations in vivo.

Results

Econazole eradicated starvation-induced tolerant cells of various bacterial species within 24 or 96 h when used in combination with conventional antibiotics. Moreover, mouse survival rate drastically increased along with the decrease of in vivo bacterial count after treatment of infected mice with the econazole and ceftazidime combination for 72 h. PMF was found to have dissipated almost completely in econazole-treated cells.

Conclusions

Econazole could act in combination with conventional antibiotics to effectively eradicate bacterial tolerant cells. The combined use of econazole and ceftazidime was shown to be effective for eradicating tolerant cells in a mouse infection model. The ability of econazole to eradicate tolerant cells was due to its ability to cause dissipation of bacterial transmembrane PMF. Econazole-mediated PMF disruption is a feasible strategy for the treatment of chronic and recurrent bacterial infections.
Caspofungin-resistance in Candida auris is cell wall-dependent phenotype and potential prevention by zinc oxide nanoparticles
Authors: Fayed Bahgat , Jayakumar Manju Nidagodu , Soliman Sameh S M
Published: October 2021

Candida auris is an emergent nosocomial multi-drug-resistant yeast that represents a global health threat. Recently, C. auris clinical isolates with caspofungin resistance were identified. Mutation in FKS1 gene was determined as a mechanism of resistance. However, the ability of C. auris to develop acquired and cross-resistance has never been investigated. Herein, this resistance ability due to caspofungin and associate mechanisms were investigated. C. auris clinical isolate was successively cultured for ten generations in the presence of caspofungin compared to fluconazole-treatment and untreated controls. This was followed by the analysis of target gene expression and phenotypic changes. The obtained results showed that caspofungin-treated C. auris exhibited elevated MIC50(caspofungin), slower growth, elevated chitin content, overexpression of caspofungin target genes, and cross-resistance to fluconazole. Interestingly, caspofungin exposure induced cell-cell adhesion and biofilm formation. C. auris gradually lost caspofungin resistance after removal of antifungal pressure, while keeping the overexpression of fungal cell wall-related genes including ALS5. We propose that C. auris ageing in the presence of caspofungin caused the development of persistent phenotypic changes in the fungal cell wall, leading to acquired and physical cross-resistance mechanisms. Surprisingly, formulation of caspofungin in zinc oxide nanoparticles prevented the aforementioned behavioral changes regardless of the pathogen generations.

Lay summary

Candida auris developed resistance against caspofungin. Our data indicated that this resistance mechanism is unique because of changes in the genes related to cell wall adhesions. Formulation of caspofungin in ZnO nanoparticles was able to overcome these phenotypic changes.
A new framework for understanding systematic errors in cluster lens modelling – II. Constraint selection
Authors: Zimmerman Dhruv T , Keeton Charles R , Raney Catie A
Published: October 2021

Cluster lens models are affected by a variety of choices in the lens modelling process. We have begun a programme to develop a systematic error budget for cluster lens modelling. Here, we examine the selection of image constraints as a potential systematic effect. For constraining the mass model, we find that it is more important to have images be spatially distributed around the cluster than to have them distributed in redshift. We also find that some image sets appear to be more important than others in terms of how well they constrain the models; the ‘important’ image sets typically include an image that lies close to a lensing critical curve as well as an image that is relatively isolated from other images (providing constraints in a region that would otherwise lack lensing information). These conclusions can help guide observing programmes that seek follow-up data for candidate lensed images.
Tightly Constrained Genome Reduction and Relaxation of Purifying Selection during Secondary Plastid Endosymbiosis
Authors: Uthanumallian Kavitha , Iha Cintia , Repetti Sonja I , Chan Cheong Xin , Bhattacharya Debashish , Duchene Sebastian , Verbruggen Heroen
Published: October 2021

Endosymbiosis, the establishment of a former free-living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids or chloroplasts, the light-harvesting organelle of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin has occurred multiple times in evolution. Here, we investigate the genomic signature of molecular processes acting through secondary plastid endosymbiosis—the origination of a new plastid from a free-living eukaryotic alga. We used phylogenetic comparative methods to study gene loss and changes in selective regimes on plastid genomes, focusing on green algae that have given rise to three independent lineages with secondary plastids (euglenophytes, chlorarachniophytes, and Lepidodinium). Our results show an overall increase in gene loss associated with secondary endosymbiosis, but this loss is tightly constrained by the retention of genes essential for plastid function. The data show that secondary plastids have experienced temporary relaxation of purifying selection during secondary endosymbiosis. However, this process is tightly constrained, with selection relaxed only relative to the background in primary plastids. Purifying selection remains strong in absolute terms even during the endosymbiosis events. Selection intensity rebounds to pre-endosymbiosis levels following endosymbiosis events, demonstrating the changes in selection efficiency during different origin phases of secondary plastids. Independent endosymbiosis events in the euglenophytes, chlorarachniophytes, and Lepidodinium differ in their degree of relaxation of selection, highlighting the different evolutionary contexts of these events. This study reveals the selection–drift interplay during secondary endosymbiosis and evolutionary parallels during organellogenesis.
Assessing Sex, Gender Identity, Sexual Orientation, Race, Ethnicity, Socioeconomic Status, and Mental Health Concerns in Tobacco Use Disorder Treatment Research: Measurement Challenges and Recommendations From a Society for Research on Nicotine and Tobacco Pre-conference Workshop
Authors: Weinberger Andrea H , Steinberg Marc L , Mills Sarah D , Dermody Sarah S , Heffner Jaimee L , Kong Amanda Y , Pang Raina D , Rosen Rachel L
Published: October 2021

This paper reports on topics discussed at a Society for Research on Nicotine and Tobacco pre-conference workshop at the 2019 annual Society for Research on Nicotine and Tobacco meeting. The goal of the pre-conference workshop was to help develop a shared understanding of the importance of several tobacco-related priority groups in tobacco use disorder (TUD) treatment research and to highlight challenges in measurement related to these groups. The workshop focused on persons with minoritized sex, gender identity, and sexual orientation identities; persons with minoritized racial and ethnic backgrounds; persons with lower socioeconomic status (SES); and persons with mental health concerns. In addition to experiencing commercial tobacco-related health disparities, these groups are also underrepresented in tobacco research, including TUD treatment studies. Importantly, there is wide variation in how and whether researchers are identifying variation within these priority groups. Best practices for measuring and reporting sex, gender identity, sexual orientation, race, ethnicity, SES, and mental health concerns in TUD treatment research are needed. This paper provides information about measurement challenges when including these groups in TUD treatment research and specific recommendations about how to measure these groups and assess potential disparities in outcomes. The goal of this paper is to encourage TUD treatment researchers to use measurement best practices in these priority groups in an effort to conduct meaningful and equity-promoting research. Increasing the inclusion and visibility of these groups in TUD treatment research will help to move the field forward in decreasing tobacco-related health disparities.

Implications: Tobacco-related disparities exist for a number of priority groups including, among others, women, individuals with minoritized sexual and gender identities, individuals with minoritized racial and ethnic backgrounds, individuals with lower SES, and individuals with mental health concerns. Research on TUD treatments for many of these subgroups is lacking. Accurate assessment and consideration of these subgroups will provide needed information about efficacious and effective TUD treatments, about potential mediators and moderators, and for accurately describing study samples, all critical elements for reducing tobacco-related disparities, and improving diversity, equity, and inclusion in TUD treatment research.
Scaling Up the Discovery of Hesitancy Profiles by Identifying the Framing of Beliefs towards Vaccine Confidence in Twitter Discourse
Authors: Weinzierl Maxwell A. , Hopfer Suellen , Harabagiu Sanda M.
Published: October 2021

Our study focused on the inference of the framing of confidence in the HPV vaccine throughout a collection of 422,078 tweets as well as the framing of confidence in the COVID-19 vaccines through a collection of 5,865,046 tweets. The vaccine confidence framings were inferred by using a novel Question/Answering framework enabling the derivation of a misinformation taxonomy as well as trust taxonomies for these two vaccines. These taxonomies, along with the analysis of vaccine literacy, the implied moral foundations and the tension between vaccine mandates and civil rights allowed us to discover several profiles of hesitancy for each vaccine across 138,779 Twitter users referring to confidence in HPV vaccine and 665,798 users referring to confidence in COVID-19 vaccines. These hesitancy profiles inform public health messaging approaches to effectively reach Twitter users with promise to shift or bolster vaccine attitudes.
Characterization and Structural Prediction of ORF10, ORF7b, ORF7a, ORF6, Membrane Glycoprotein, and Envelope Protein in SARS-CoV-2 Bangladeshi Variant through Bioinformatics Approach
Authors: Debnath Pinky , Khan Umama , Khan Md. Salauddin
Published: October 2021

The acute respiratory disease induced by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has become a global epidemic in just less than a year by the first half of 2020. The subsequent efficient human-to-human transmission of this virus eventually affected millions of people worldwide. The most devastating thing is that the infection rate is continuously uprising and resulting in significant mortality especially among the older age population and those with health co-morbidities. This enveloped, positive-sense RNA virus is chiefly responsible for the infection of the upper respiratory system. The virulence of the SARS-CoV-2 is mostly regulated by its proteins like entry to the host cell through fusion mechanism, fusion of infected cells with neighboring uninfected cells to spread the virus, inhibition of host gene expression, cellular differentiation, apoptosis, mitochondrial biogenesis, etc. But very little is known about the protein structures and functionalities. Therefore, the main purpose of this study is to learn more about these proteins through bioinformatics approaches. In this study, ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein have been selected from a Bangladeshi Corona-virus strain G039392 and a number of bioinformatics tools (MEGA-X-V10.1.7, PONDR®, ProtScale, ProtParam, SCRIBER, NetSurfP v2.0, IntFOLD, UCSF Chimera, and PyMol) and strategies were implemented for multiple sequence alignment and phylogeny analysis with 9 different variants, predicting hydropathicity, amino acid compositions, protein-binding propensity, protein disorders, 2D and 3D protein modeling. Selected proteins were characterized as highly flexible, structurally and electrostatically extremely stable, ordered, biologically active, hydrophobic, and closely related to the proteins of different variants. This detailed information regarding the characterization and structure of proteins of SARS-CoV-2 Bangladeshi variant was performed for the first time ever to unveil the deep mechanism behind the virulence features and also, this robust appraisal paves the future way for molecular docking, vaccine development targeting these characterized proteins.