bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronic inflammatory arthritis drives systemic changes in circadian energy metabolism
Authors: Downton Polly , Sanna Fabio , Maidstone Robert , Poolman Toryn M. , Hayter Edward A. , Dickson Suzanna H. , Ciccone Nick A. , Early James O. , Adamson Antony , Spiller David G. , Simpkins Devin A. , Baxter Matthew , Fischer Roman , Rattray Magnus , Loudon Andrew S. I. , Gibbs Julie E. , Bechtold David A. , Ray David W. 
Published: April 2022

Significance
Rheumatoid arthritis (RA) is a debilitating chronic inflammatory disease in which symptoms exhibit a strong time-of-day rhythmicity. RA is commonly associated with metabolic disturbance and increased incidence of diabetes and cardiovascular disease, yet the mechanisms underlying this metabolic dysregulation remain unclear. Here, we demonstrate that rhythmic inflammation drives reorganization of metabolic programs in distal liver and muscle tissues. Chronic inflammation leads to mitochondrial dysfunction and dysregulation of fatty acid metabolism, including accumulation of inflammation-associated ceramide species in a time-of-day–dependent manner. These findings reveal multiple points for therapeutic intervention centered on the circadian clock, metabolic dysregulation, and inflammatory signaling.
Matching protein surface structural patches for high-resolution blind peptide docking
Authors: Khramushin Alisa , Ben-Aharon Ziv , Tsaban Tomer , Varga Julia K. , Avraham Orly , Schueler-Furman Ora 
Published: April 2022

Significance
Modeling interactions between short peptides and their receptors is a challenging docking problem due to the peptide flexibility, resulting in a formidable sampling problem of peptide conformation in addition to its orientation. Alternatively, the peptide can be viewed as a piece that complements the receptor monomer structure. Here, we show that the peptide conformation can be determined based on the receptor backbone only and sampled using local structural motifs found in solved protein monomers and interfaces, independent of sequence similarity. This approach outperforms current peptide docking protocols and promotes new directions for peptide interface design.
Mitochondrial mutations alter endurance exercise response and determinants in mice
Authors: Schaefer Patrick M. , Rathi Komal , Butic Arrienne , Tan Wendy , Mitchell Katherine , Wallace Douglas C. 
Published: April 2022

SignificancePrimary mitochondrial diseases (PMDs) are the most prevalent inborn metabolic disorders, affecting an estimated 1 in 4,200 individuals. Endurance exercise is generally known to improve mitochondrial function, but its indication in the heterogeneous group of PMDs is unclear. We determined the relationship between mitochondrial mutations, endurance exercise response, and the underlying molecular pathways in mice with distinct mitochondrial mutations. This revealed that mitochondria are crucial regulators of exercise capacity and exercise response. Endurance exercise proved to be mostly beneficial across the different mitochondrial mutant mice with the exception of a worsened dilated cardiomyopathy in ANT1-deficient mice. Thus, therapeutic exercises, especially in patients with PMDs, should take into account the physical and mitochondrial genetic status of the patient.
Antibody-mediated blockade of the IL23 receptor destabilizes intratumoral regulatory T cells and enhances immunotherapy
Authors: Wight Andrew E. , Sido Jessica M. , Degryse Sandrine , Ao Lin , Nakagawa Hidetoshi , Qiu(Vivian) Yiguo , Shen Xianli , Oseghali Oba , Kim Hye-Jung , Cantor Harvey 
Published: April 2022

SignificanceRegulatory T cells rely on active processes to maintain a suppressive phenotype inside a tumor, leading to increased tumor burden and worse cancer outcomes. Here, we report a pathway to interfere with regulatory T cell (Treg) stability by disrupting the expression of the interleukin 23 receptor. This approach increases Treg responsiveness to interleukin 12, leading to increased production of gamma-interferon and more efficient antitumor immune responses. The combined engagement of independent pathways to destabilize Treg through the interleukin 23 receptor and the glucocorticoid-induced TNFR-related protein receptor has a synergistic impact on the Treg phenotype and promotes antitumor immune responses. These findings expand our understanding of regulatory T-cell biology and offer tools for cancer immunotherapy.
The ‘general fact’ copula in Yolmo and the influence of Tamang
Authors: Gawne Lauren , Owen-Smith Thomas 
Published: April 2022

AbstractThis paper examines the similarity of the Yolmo ‘general fact’ evidential and the ‘generic fact’ evidential in the Tamang dialect spoken in the valley of the Indrawati Khola. Yolmoòŋgeis unlike any evidential attested in other Tibetic languages, but shares features with1kha-pain the local dialect of Tamang. Semantically, they both are used for situations that are generally known facts. Structurally, both are copulas with evidential functions that are formed using the lexical verb ‘come’. We argue that language contact between Tamang speakers of the Indrawati Khola area and Yolmo speakers in the Melamchi Valley led to the Yolmo language calquing the Tamang form. We illustrate these copulas and their relationship because grammaticalisation of copulas from a lexical verb ‘come’ is cross-linguistically uncommon.
Meso scale component manufacturing: a comparative analysis of non-lithography and lithography-based processes
Authors: Khalid Azfar , Wei Yang , Saleem Muhammad Rizwan , Lughmani Waqas Akbar 
Published: April 2022

Abstract
The paper identifies the meso scale (10 µm to few millimeters) component size that can be manufactured by using both lithography and non-lithography based approaches. Non-lithography based meso/micro manufacturing is gaining popularity to make micro 3D artifacts with various engineering materials. Being in the nascent stage, this technology looks promising for future micro manufacturing trends. Currently, lithography based micro manufacturing techniques are mature, and used for mass production of 2D, 2.5D features and products extending to 3D micro parts in some cases. In this paper, both the techniques at state-of-the-art level for meso/micro scale are explained first. The comparison is arranged based on examples and a criterion is set in terms of achievable accuracy, production rate, cost, size and form of artifacts and materials used. The analysis revealed a third combined approach where a mix of both techniques can work together for meso scale products. Critical issues affecting both the manufacturing approaches, to advance in terms of accuracy, process physics, materials, machines and product design are discussed. Process effectiveness guideline with respect to the component scale, materials, achievable tolerances, production rates and application is emerged, as a result of this exercise.
Shot-by-shot 250 kHz 3D ion and MHz photoelectron imaging using Timepix3
Authors: Bromberger Hubertus , Passow Christopher , Pennicard David , Boll Rebecca , Correa Jonathan , He Lanhai , Johny Melby , Papadopoulou Christina C , Tul-Noor Atia , Wiese Joss , Trippel Sebastian , Erk Benjamin , Küpper Jochen 
Published: April 2022

Abstract
We demonstrate the application of event-driven Timepix3-based detectors in combination with a double-sided velocity-map-imaging spectrometer to record the full 3D momentum of charged particles at the free-electron-laser facility FLASH. We measured the extreme ultraviolet induced fragmentation of N2 using 250 kHz FLASH bursts with sub-pixel spatial resolution and up to 1.7 ns temporal resolution for photoelectrons. To further demonstrate the capabilities of this camera at even higher repetition rates we measured single-shot images of He(1s) photoelectrons for bursts with a repetition rate of 1 MHz. Overall, with the Timepix3 camera we overcome limitations of standard-camera technology for advanced-imaging experiments with requirements on high event-rates and high spatio-temporal resolution.
Effect of the flow rate of the shielding gas on the species fluxes in the coaxial double-tube helium atmospheric pressure plasma jet
Authors: Chen Zhongqi , Zhong An , Dai Dong , Ning Wenjun 
Published: April 2022

Abstract
The effect of ambient air as an unavoidable problem for atmospheric pressure plasma jet (APPJ) applications has attracted a lot of interest, especially when the specific scenarios are highly sensitive to ambient species such as the biomedical process. The coaxial double-tube device is a promising method for controlling the ambient species into the jet effluent and thus the chemical properties of the jet effluent. In this work, the discharge characteristics and plasma chemistry of the coaxial double-tube helium APPJ at different shielding gas (SG) flow rates are studied numerically. An experiment on optical images of the discharge is conducted to illustratively validate the variation of the (main) discharge channel widths in the model as the SG flow rate varies. The results illustrate that the discharge is enhanced at the high flow rate, while it shows the weaker discharge behavior at the low flow rate as well as that without SG. The analysis of the dielectric plate surface indicates that the species fluxes to the dielectric plate significantly increase with the increases in the flow rate, which can be attributed to the wider (main) discharge channel. Moreover, to further explore the impact of the SG on the effluent chemistry, the ions fluxes on the surfaces of the main discharge channel and the discharge channel are distinguished and discussed. The analysis shows the great difference in the ions fluxes affected by the flow rate between the two discharge channels. In summary, advancing the knowledge that the flow rate of the SG has an impact on the discharge behavior, this study further reveals that different discharge positions greatly influence the production of nitrogen/oxygen species. This work enables the previously elusive account of the effect of SG and may open new opportunities for the further application of coaxial double-tube APPJ.
Orientational disorder in sulfur hexafluoride: a neutron total scattering and reverse Monte Carlo study
Authors: Zhang Shidong , Qin Yinze , Zhang Sijie , Gao Min , Tucker Matthew G , Keen David A , Cai Guanqun , Phillips Anthony E , Dove Martin T 
Published: April 2022

Abstract
The orientational disorder in crystalline sulfur hexafluoride, SF6, has been studied using a combination of neutron total scattering and the reverse Monte Carlo method. Analysis of the atomic configurations has shown the extent of the disorder through the evaluation of the S–F bond orientational distribution function, consistent with, but improving upon, the results of earlier neutron powder diffraction data. The correlations between orientations of neighbouring molecules have been studied through analysis of the distributions of F–F distances, showing that nearest-neighbour F–F close contacts are avoided, consistent with previous molecular dynamics simulation results. The results present a new case study of the application of neutron total scattering and the reverse Monte Carlo methods for the study of orientational disorder, where in this instance the disorder arises from orientational frustration rather than from a mismatch of molecular and site symmetries.
Organic self-assembled monolayers on superconducting NbSe2: interfacial electronic structure and energetics*
Authors: Ni Xiaojuan , Li Hong , Brédas Jean-Luc 
Published: April 2022

Abstract
While organic self-assembled monolayers (SAMs) have been widely used to modify the work function of metal and metal-oxide surfaces, their application to tune the critical temperature of a superconductor has only been considered recently when SAMs were deposited on NbSe2 monolayers (Calavalle et al 2021 Nano Lett.
21 136–143). Here, we describe the results of density functional theory calculations performed on the experimentally reported organic/NbSe2 systems. Our objectives are: (i) to determine how the organic layers impact the NbSe2 work function and electronic density of states; (ii) to understand the possible correlation with the experimental variations in superconducting behavior upon SAM deposition. We find that, upon adsorption of the organic monolayers, the work-function modulation induced by the SAM and interface dipoles is consistent with the experimental results. However, there occurs no significant difference in the electronic density of states near the Fermi level, a consequence of the absence of any charge transfer across the organic/NbSe2 interfaces. Therefore, our results indicate that it is not a SAM-induced tuning of the NbSe2 density of states near the Fermi level that leads to the tuning of the superconducting critical temperature. This calls for further explorations, both experimentally and theoretically, of the mechanism underlying the superconducting critical temperature variation upon formation of SAM/NbSe2 interfaces.
Pre- and post-accident environmental transfer of radionuclides in Japan: lessons learned in the IAEA MODARIA II programme
Authors: Tagami Keiko , Hashimoto Shoji , Kusakabe Masashi , Onda Yuichi , Howard Brenda , Fesenko Sergey , Pröhl Gerhard , Harbottle Andra-Rada , Ulanowski Alexander 
Published: April 2022

Abstract
An international review of radioecological data derived after the accident at the Fukushima Daiichi nuclear power plant was an important component of activities in working group 4 of the IAEA Models and data for radiological impact assessment, phase II (MODARIA II) programme. Japanese and international scientists reviewed radioecological data in the terrestrial and aquatic environments in Japan reported both before and after the accident. The environmental transfer processes considered included: (a) interception and retention radionuclides by plants, (b) loss of radionuclides from plant and systemic transport of radionuclides in plants (translocation), (c) behaviour of radiocaesium in soil, (d) uptake of radionuclides from soil by agricultural crops and wild plants, (e) transfer of radionuclides from feedstuffs to domestic and wild animals, (f) behaviour of radiocaesium in forest trees and forest systems, (g) behaviour of radiocaesium in freshwater systems, coastal areas and in the ocean, (h) transport of radiocaesium from catchments through rivers, streams and lakes to the ocean, (i) uptake of radiocaesium by aquatic organisms, and (j) modification of radionuclide concentrations in food products during food processing and culinary preparation. These data were compared with relevant global data within IAEA TECDOC-1927 ‘Environmental transfer of radionuclides in Japan following the accident at the Fukushima Daiichi Nuclear Power Plant’. This paper summarises the outcomes of the data collation and analysis within MODARIA II work group 4 and compares the Japan-specific data with existing radioecological knowledge acquired from past and contemporary radioecological studies. The key radioecological lessons learned are outlined and discussed.
Implementing a non-local lattice particle method in the open-source large-scale atomic/molecular massively parallel simulator
Authors: Sun Hao , Ferasat Keyvan , Nowak Philip , Gravelle Liam , Gaffran Noah , Anderson Chris , Sirola Tim , Pintar Owen , Lievers W Brent , Kim Il Yong , Pilkey Keith , Béland Laurent Karim 
Published: April 2022

Abstract
Using conventional continuum-based simulation frameworks to model crack initiation and extension can be computationally challenging. As an alternative to continuum-based approaches, particle-based simulation methods are well-suited to handle the discontinuities present during fracture propagation. A well-known particle-based method is the lattice particle method (LPM), which discretizes the system into a set of interconnected particles ollowing a periodic arrangement. Discontinuities can be handled simply by removing bonds between particles. For this reason, LPM-based simulations have been employed to simulate fracture propagation in heterogeneous media, notably in civil engineering and biomaterials applications. However, a practical limitation of this method is the absence of implementation within a commonly-used software platform. This work describes such an implementation of a non-local LPM within the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). Specifically, we implemented a new LAMMPS bond style with a many-body term to tune Poisson’s ratios. In order to validate the nonlocal formalism and our implementation of this method within LAMMPS, simulated elastic properties are compared to analytical solutions reported in the literature. Good agreement between simulated and analytical values is found for systems with positive Poisson’s ratios. The computational and parallel efficiency of the LPM-LAMMPS implementation is also benchmarked. Finally, we compare the elastic response of a 3D porous structure and an aircraft wing as calculated using the LPM and finite-element analysis.
Hyperplane families creating envelopes
Authors: Nishimura Takashi 
Published: April 2022

Abstract
A simple geometric mechanism: ‘the locus of intersections of perpendicular bisectors and normal lines’, often arises in many guises in nonlinear sciences. In this paper, a new application of this simple geometric mechanism is given. Namely, we show that this mechanism gives answers to all four basic problems on envelopes created by hyperplane families (existence problem, representation problem, equivalence problem of definitions, uniqueness problem) at once.
External beam irradiation angle measurement using a hybrid Cerenkov-scintillation detector
Authors: Jean Emilie , Lambert-Girard Simon , Therriault-Proulx François , Beaulieu Luc 
Published: April 2022

Abstract

Objective. In this study, we propose a novel approach designed to take advantage of the Cerenkov light angular dependency to perform a direct measurement of an external beam irradiation angle. Approach. A Cerenkov probe composed of a 10 mm long filtered sensitive volume of clear PMMA optical fibre was built. Both filtered and raw Cerenkov signals from the transport fibre were collected through a single 1 mm diameter transport fibre. An independent plastic scintillation detector composed of 10 mm BCF12 scintillating fibre was also used for simultaneous dose measurements. A first series of measurements aimed at validating the ability to account for the Cerenkov electron energy spectrum dependency by simultaneously measuring the deposited dose, thus isolating signal variations resulting from the angular dependency. Angular calibration curve for fixed dose irradiations and incident angle measurements using electron and photon beams where also achieved. Main results. The beam nominal energy was found to have a significant impact on the shapes of the angular calibration curves. This can be linked to the electron energy spectrum dependency of the Cerenkov emission cone. Irradiation angle measurements exhibit an absolute mean error of 1.86° and 1.02° at 6 and 18 MV, respectively. Similar results were obtained with electron beams and the absolute mean error reaches 1.97°, 1.66°, 1.45° and 0.95° at 9, 12, 16 and 20 MeV, respectively. Reducing the numerical aperture of the Cerenkov probe leads to an increased angular dependency for the lowest energy while no major changes were observed at higher energy. This allowed irradiation angle measurements at 6 MeV with a mean absolute error of 4.82°. Significance. The detector offers promising perspectives as a potential tool for future quality assurance applications in radiotherapy, especially for stereotactic radiosurgery (SRS), magnetic resonance image-guided radiotherapy (MRgRT) and brachytherapy applications.
Coherent and incoherent superposition of transition matrix elements of the squeezing operator
Authors: Varró Sándor 
Published: April 2022

Abstract
We discuss the general matrix elements of the squeezing operator between number eigenstates of a harmonic oscillator (which may also represent a quantized mode of the electromagnetic radiation). These matrix elements have first been used by Popov and Perelomov (1969 Zh. Eksp. Teor. Fiz.
56 1375–90) long ago, in their thorough analysis of the parametric excitation of harmonic oscillators. They expressed the matrix elements in terms of transcendental functions, the associated Legendre functions. In the present paper we will show that these matrix elements can also be derived in a different form, expressed by the classical Gegenbauer polynomials. This new expression makes it possible to determine coherent and incoherent superpositions of these matrix elements in closed analytic forms. As an application, we describe multiphoton transitions in the system ‘charged particle + electromagnetic radiation’, induced by a (strong) coherent field or by a black-body radiation component (with a Planck–Bose photon number distribution). The exact results are compared with the semi-classical ones. We will show that in case of interaction with a thermal field, the semi-classical result (with a Gaussian stochastic field amplitude) yields an acceptable approximation only in the Rayleigh–Jeans limit, however, in the Wien limit it completely fails.
Unification of random dynamical decoupling and the quantum Zeno effect
Authors: Hahn Alexander , Burgarth Daniel , Yuasa Kazuya 
Published: April 2022

Abstract
Periodic deterministic bang–bang dynamical decoupling and the quantum Zeno effect are known to emerge from the same physical mechanism. Both concepts are based on cycles of strong and frequent kicks provoking a subdivision of the Hilbert space into independent subspaces. However, previous unification results do not capture the case of random bang–bang dynamical decoupling, which can be advantageous to the deterministic case but has an inherently acyclic structure. Here, we establish a correspondence between random dynamical decoupling and the quantum Zeno effect by investigating the average over random decoupling evolutions. This protocol is a manifestation of the quantum Zeno dynamics and leads to a unitary bath evolution. By providing a framework that we call equitability of system and bath, we show that the system dynamics under random dynamical decoupling converges to a unitary with a decoupling error that characteristically depends on the convergence speed of the Zeno limit. This reveals a unification of the random dynamical decoupling and the quantum Zeno effect.
The local PNG bias of neutral Hydrogen, HI
Authors: Barreira Alexandre 
Published: April 2022

Abstract
We use separate universe simulations with the IllustrisTNG galaxy formation model to predict the local PNG bias parameters bΦ
and bΦδ
of atomic neutral hydrogen, HI. These parameters and their relation to the linear density bias parameter b
1 play a key role in observational constraints of the local PNG parameter f
NL using the HI power spectrum and bispectrum. Our results show that the popular calculation based on the universality of the halo mass function overpredicts the bΦ
(b
1) and bΦδ
(b
1) relations measured in the simulations. In particular, our results show that at z ≲ 1 the HI power spectrum is more sensitive to f
NL compared to previously thought (bΦ
is more negative), but is less sensitive at other epochs (bΦ
is less positive). We discuss how this can be explained by the competition of physical effects such as that large-scale gravitational potentials with local PNG (i) accelerate the conversion of hydrogen to heavy elements by star formation, (ii) enhance the effects of baryonic feedback that eject the gas to regions more exposed to ionizing radiation, and (iii) promote the formation of denser structures that shield the HI more efficiently. Our numerical results can be used to revise existing forecast studies on f
NL using 21 cm line-intensity mapping data. Despite this first step towards predictions for the local PNG bias parameters of HI, we emphasize that more work is needed to assess their sensitivity on the assumed galaxy formation physics and HI modeling strategy.