bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small-scale effects on the radial vibration of an elastic nanosphere based on nonlocal strain gradient theory
Authors: Ducottet S , El Baroudi A 
Published: December 2022

Abstract
Nonlocal strain gradient theory is widely used when dealing with micro- and nano-structures. In such framework, small-scale effects cannot be ignored. In this paper a model of radial vibration of an isotropic elastic nanosphere is theoretically investigated. The frequency equation is obtained from a nonlocal elastic constitutive law, based on a mix between local and nonlocal strain. This model is composed of both the classical gradient model and the Eringen’s nonlocal elasticity model. To check the validity and accuracy of this theoretical approach, a comparison is made with the literature in certain specific cases, which shows a good agreement. Numerical examples are finally conducted to show the impact of small-scale effects in the radial vibration, which need to be included in the nonlocal strain gradient theory of nanospheres. It reveals that the vibration behavior greatly depends on the nanosphere size and nonlocal and strain gradient parameters. Particularly, when the nanospheres radius is smaller than a critical radius, the small-scale effects play a key role. Thus, the obtained frequency equation for radial vibration is very useful to interpret the experimental measurements of vibrational characteristics of nanospheres.
Smooth generalized interval exchange transformations with wandering intervals, from explicit derived from pseudo-Anosov maps
Authors: Carrand Jérôme 
Published: December 2022

Abstract
Starting from any pseudo-Anosov map ϕ on a surface of genus

g
⩾
2

, we construct explicitly a family of Derived from pseudo-Anosov maps f by adapting the construction of Smale’s derived from Anosov maps on the two-torus. This is done by perturbing ϕ at some fixed points. We first consider perturbations at every conical fixed point and then at regular fixed points. We establish the existence of a measure µ, supported by the non-trivial unique minimal component of the stable foliation of f, with respect to which f is mixing. In the process, we construct a uniquely ergodic generalized interval exchange transformation (GIET) with a wandering interval that is semi-conjugated to a self-similar interval exchange transformation. This GIET is obtained as the Poincaré map of a flow renormalized by f which parametrizes stable foliation. When f is

, the flow and the GIET are

.
Overview of tokamak turbulence stabilization by fast ions
Authors: Citrin J , Mantica P 
Published: December 2022

Abstract
In recent years tokamak experiments and modelling have increasingly indicated that the interaction between suprathermal (fast) ions and thermal plasma can lead to a reduction of turbulence and an improvement of confinement. The regimes in which this stabilization occurs are relevant to burning plasmas, and their understanding will inform reactor scenario optimization. This review summarizes observations, simulations, theoretical understanding, and open questions on this emerging topic.
In situ infrared absorption probing of plasma catalysis: vibrationally-excited species induced Mars–van Krevelen type mechanism
Authors: Kim Dae-Yeong , Saito Atsushi , Sasaki Koichi , Nozaki Tomohiro 
Published: December 2022

Abstract
Nonthermal plasma (NTP) assisted catalysis has recently received attention as an attractive technology that can overcome the energy barriers involved in conventional thermal catalysis. It is important to obtain fundamental insight into the synergistic effects arising from interactions between NTP-activated species and catalysis. However, it remains a challenge due to difficulties associated with the in situ characterization of NTP-activated species. In this study, CO was explored in dielectric barrier discharge by applying in situ transmission infrared (TIR) absorption spectroscopy; TIR enables the measurement of the vibrational temperature of CO while observing the surface reaction of excited CO to form intermediates species over wurtzite ZnO. The reaction behavior of activated CO correlates with the vibrational temperature of CO, showing vibrationally-excited CO reacts with lattice oxygen via the Mars–van Krevelen type mechanism; thus leading to higher activity compared with conventional thermal catalysis. This work helps to understand the fundamental chemistry and provides new insight into NTP-activated CO and its catalysis.
Vortex-ring quantum droplets in a radially-periodic potential
Authors: Liu Bin , Chen Yi Xi , Yang Ao Wei , Cai Xiao Yan , Liu Yan , Luo Zhi Huan , Qin Xi Zhou , Jiang Xun Da , Li Yong Yao , Malomed Boris A 
Published: December 2022

Abstract
We establish stability and characteristics of two-dimensional (2D) vortex ring-shaped quantum droplets (QDs) formed by binary Bose–Einstein condensates. The system is modeled by the Gross–Pitaevskii (GP) equation with the cubic term multiplied by a logarithmic factor (as produced by the Lee-Huang-Yang correction to the mean-field theory) and a potential which is a periodic function of the radial coordinate. Narrow vortex rings with high values of the topological charge, trapped in particular circular troughs of the radial potential, are produced. These results suggest an experimentally relevant method for the creation of vortical QDs (thus far, only zero-vorticity ones have been reported). The 2D GP equation for the narrow rings is approximately reduced to the one-dimensional form, which makes it possible to study the modulational stability of the rings against azimuthal perturbations. Full stability areas are delineated for these modes. The trapping capacity of the circular troughs is identified for the vortex rings with different winding numbers (WNs). Stable compound states in the form of mutually nested concentric multiple rings are constructed too, including ones with opposite signs of the WNs. Other robust compound states combine a modulationally stable narrow ring in one circular potential trough and an azimuthal soliton performing orbital motion in an adjacent one. The results may be used to design a device employing coexisting ring-shaped modes with different WNs for data storage.
Zonal flow excitation in electron-scale tokamak turbulence
Authors: Tirkas Stefan , Chen Haotian , Merlo Gabriele , Jenko Frank , Parker Scott 
Published: December 2022

Abstract
The derivation of an intermediate-scale gyrokinetic-electron theory in nonuniform tokamak plasmas (Chen et al 2021 Nucl. Fusion
61
066017) has shown that a Navier–Stokes type nonlinearity couples electron-temperature-gradient (ETG) modes and zonal flow (ZF) modes with wavelengths much shorter than the ion gyroradius but much longer than the electron gyroradius. This intermediate-scale ETG-ZF coupling is typically stronger than the Hasegawa–Mima type nonlinearity characteristic of the fluid approximation and is predicted to lead to relevant ZF generation and ETG mode regulation. Electron-scale, continuum, gyrokinetic simulation results are presented here which include both single-mode ETG and full-spectrum ETG turbulence. The ZF generation due to single ETG modes is investigated and the single-mode intermediate-scale results are found to be in agreement with theory. The full-spectrum results are then presented and explained qualitatively in terms of the single-mode results. It is found that the ETG-driven ZFs regulate intermediate-scale electron heat flux transport to levels in the predicted range.
Tools for numerical modelling of nonlinear propagation in hollow capillary fibres and their application
Authors: Crego Aurora , San Roman Julio , Conejero Jarque Enrique 
Published: December 2022

Abstract
The development of new coherent and ultrashort light sources is of great relevance for exploring fundamental processes and different applications in science. The most successful technique for generating ultrashort laser pulses, in terms of energy and pulse duration, is using hollow capillary fibre (HCF) compressors. The different strategies to further increase the pulse energy and to achieve shorter pulses at non-conventional wavelengths, lead to continuous improvement of this technique. In this work, we present the theoretical framework of the nonlinear propagation in HCFs through the propagation equation and the spatio-temporal effects that appear in the nonlinear dynamics. To numerically study the nonlinear propagation of the pulse in the HCF, we present different numerical models considering only the spatial effects, (1 + 1)D model, the full spatio-temporal dynamics and ionization, (2 + 1)D model, or the case with lack of cylindrical symmetry, (3 + 1)D model. To show the performance of some of these models in a particular case, we study the generation of ultrashort and energetic dispersive waves (DWs) inside the HCF. We show that the emission of a DW at a fixed wavelength for different pump wavelengths is possible by parameter scaling.
Size of an interspecific competitor may be a source of information in reproductive decisions
Authors: Hämäläinen Reetta , Välimäki Panu , Forsman Jukka T 
Published: December 2022

Abstract
Animals use inter-specific cues as a source of information in decisions-making, but the full costs and benefits of inter-specific information use are unknown. We tested whether pied flycatchers use the body size and clutch size of great tits as cues in their reproductive decisions and what are the possible fitness consequences as a function of great tit size. The size of great tit females associated positively with flycatcher’s probability to settle near a tit nest over a territory further away. Flycatcher egg mass was positively correlated with great tit female size regardless of flycatcher territory choice. However, in flycatchers that had chosen to nest near great tits, the size of nestlings decreased in relation to increasing great tit female size. Our results demonstrate the use of size of inter-specifics as a cue in reproductive decisions and the trade-off between the value of information and costs of competition information users face when using inter-specific information in decision-making.
Cloud-native distributed genomic pileup operations
Authors: Wiewiórka Marek , Szmurło Agnieszka , Stankiewicz Paweł , Gambin Tomasz 
Published: December 2022

Abstract

Motivation
Pileup analysis is a building block of many bioinformatics pipelines, including variant calling and genotyping. This step tends to become a bottleneck of the entire assay since the straightforward pileup implementations involve processing of all base calls from all alignments sequentially. On the other hand, a distributed version of the algorithm faces the intrinsic challenge of splitting reads-oriented file formats into self-contained partitions to avoid costly data exchange between computational nodes.

Results
Here, we present a scalable, distributed and efficient implementation of a pileup algorithm that is suitable for deploying in cloud computing environments. In particular, we implemented: (i) our custom data-partitioning algorithm optimized to work with the alignment reads, (ii) a novel and unique approach to process alignment events from sequencing reads using the MD tags, (iii) the source code micro-optimizations for recurrent operations, and (iv) a modular structure of the algorithm. We have proven that our novel approach consistently and significantly outperforms other state-of-the-art distributed tools in terms of execution time (up to 6.5× faster) and memory usage (up to 2× less), resulting in a substantial cloud cost reduction. SeQuiLa is a cloud-native solution that can be easily deployed using any managed Kubernetes and Hadoop services available in public clouds, like Microsoft Azure Cloud, Google Cloud Platform, or Amazon Web Services. Together with the already implemented distributed range join and coverage calculations, our package provides end-users with a unified SQL interface for convenient analyses of population-scale genomic data in an interactive way.

Availability and implementation
https://biodatageeks.github.io/sequila/
The stress granule protein G3BP1 alleviates spinocerebellar ataxia-associated deficits
Authors: Koppenol Rebekah , Conceição André , Afonso Inês T , Afonso-Reis Ricardo , Costa Rafael G , Tomé Sandra , Teixeira Diogo , da Silva Joana Pinto , Côdesso José Miguel , Brito David V C , Mendonça Liliana , Marcelo Adriana , Pereira de Almeida Luís , Matos Carlos A , Nóbrega Clévio 
Published: December 2022

Abstract
Polyglutamine diseases are a group of neurodegenerative disorders caused by an abnormal expansion of CAG repeat tracts in the codifying regions of nine, otherwise unrelated, genes. While the protein products of these genes are suggested to play diverse cellular roles, the pathogenic mutant proteins bearing an expanded polyglutamine sequence share a tendency to self-assemble, aggregate and engage in abnormal molecular interactions. Understanding the shared paths that link polyglutamine protein expansion to the nervous system dysfunction and the degeneration that takes place in these disorders is instrumental to the identification of targets for therapeutic intervention. Among polyglutamine diseases, spinocerebellar ataxias (SCAs) share many common aspects, including the fact that they involve dysfunction of the cerebellum, resulting in ataxia. Our work aimed at exploring a putative new therapeutic target for the two forms of SCA with higher worldwide prevalence, SCA type 2 (SCA2) and type 3 (SCA3), which are caused by expanded forms of ataxin-2 (ATXN2) and ataxin-3 (ATXN3), respectively. The pathophysiology of polyglutamine diseases has been described to involve an inability to properly respond to cell stress. We evaluated the ability of GTPase-activating protein-binding protein 1 (G3BP1), an RNA-binding protein involved in RNA metabolism regulation and stress responses, to counteract SCA2 and SCA3 pathology, using both in vitro and in vivo disease models. Our results indicate that G3BP1 overexpression in cell models leads to a reduction of ATXN2 and ATXN3 aggregation, associated with a decrease in protein expression. This protective effect of G3BP1 against polyglutamine protein aggregation was reinforced by the fact that silencing G3bp1 in the mouse brain increases human expanded ATXN2 and ATXN3 aggregation. Moreover, a decrease of G3BP1 levels was detected in cells derived from patients with SCA2 and SCA3, suggesting that G3BP1 function is compromised in the context of these diseases. In lentiviral mouse models of SCA2 and SCA3, G3BP1 overexpression not only decreased protein aggregation but also contributed to the preservation of neuronal cells. Finally, in an SCA3 transgenic mouse model with a severe ataxic phenotype, G3BP1 lentiviral delivery to the cerebellum led to amelioration of several motor behavioural deficits. Overall, our results indicate that a decrease in G3BP1 levels may be a contributing factor to SCA2 and SCA3 pathophysiology, and that administration of this protein through viral vector-mediated delivery may constitute a putative approach to therapy for these diseases, and possibly other polyglutamine disorders.
A novel frameshift variant ofLMX1Athat leads to autosomal dominant non-syndromic sensorineural hearing loss: functional characterization of the C-terminal domain in LMX1A
Authors: Xiao Min , Zheng Yan , Huang Kuo-Hsiang , Yu Shanhe , Zhang Wenbi , Xi Yanping , Dou Yan , Sun Xiaoxi , Lei Caixia , Yu Huiqian 
Published: December 2022

AbstractNon-syndromic sensorineural hearing loss (NSHL) is a group of genetically heterogeneous conditions with broad phenotypic heterogeneity. There is, at present, no curative treatment for genetic hearing loss (HL). Early molecular diagnosis of progressive disorders and elucidation of the causes and pathomechanisms are essential for developing therapeutic strategies. Here, we identified a novel rare frameshift variant of LMX1A (c.915dup), which resulted in the C-terminal-altered and -truncated LMX1A (p.Val306Cysfs*32). This C-terminal frameshift mutation co-segregated with autosomal dominant (AD) NSHL in a four-generation Chinese family, suggesting that the LMX1A non-missense mutation is also contributed to ADNSHL. In this family, the affected individuals exhibited the variable auditory phenotypes ranging from profound congenital deafness at birth or to mild/moderate HL in adulthood. We also found that the embryonic cells carrying with the heterozygous variant significantly expressed several upregulated HL-associated genes at transcriptional level. In vitro splicing assay suggested that the LMX1A mRNA with c.915dup did not cause nonsense-mediated decay and was translated into a truncated LMX1A. In addition, electrophoresis mobility shift assay and luciferase assays have shown that the highly conserved C-terminal domain (amino acid 306–382) of the LMX1A was required for regulating the protein–DNA interaction and transactivation in vitro. Furthermore, apoptosis assays suggested that the C-terminal domain of the LMX1A was important for mediating apoptosis in the cochlear hair cells. Our work provided the multiline of the evidence to support that non-missense mutation of LMX1A leads to ADNSHL and the C-terminal domain of LMX1A is important for mediating transcriptional activity and associated with promoting apoptosis in the cells.
A review of the importance of various areas for northern contingent West-Atlantic mackerel spawning
Authors: Van Beveren Elisabeth , Plourde Stéphane , Pepin Pierre , Cogliati Karen , Castonguay Martin 
Published: December 2022

Abstract
The southern Gulf of St. Lawrence (sGSL) is considered to be the dominant spawning area of northern contingent West-Atlantic mackerel (Scomber scombrus). This premise underlies our basic understanding of the stock and its assessment. Because there are however indications of spawning outside the sGSL, we aimed to review the potential importance of various external regions for spawning, based on a weight of evidence approach. Fundamentally, important spawning areas can only exist where there is evidence of a considerable spawning stock biomass being present when environmental conditions are suitable for spawning. This should lead to direct observations of significant egg and larval densities. Based on an ensemble of evidence (migration patterns, environmental conditions, and ichthyoplankton observations), we investigated the dominance of the sGSL for northern contingent mackerel spawning. Elsewhere, such as on the Scotian Shelf, where mackerel starts its spring migration, there is evidence of minor but relatively consistent egg production. Spawning off Newfoundland, where mackerel can migrate to later in the year, appears sporadic and highly variable in intensity. This review should alleviate some of the uncertainty associated with the mackerel stock assessments and be a baseline to further our knowledge on mackerel spatial spawning dynamics.
Emergence of vortices at the edges of planet-driven gaps in protoplanetary discs
Authors: Cimerman Nicolas P , Rafikov Roman R 
Published: December 2022

ABSTRACT
Young planets embedded in protoplanetary discs (PPDs) excite spiral density waves, which propagate shock and deposit angular momentum in the disc. This results in gap opening around the planetary orbit, even for low (sub-thermal) mass planets, provided that the effective viscosity in the disc is low. The edges of these planet-induced gaps are known to be prone to emergence of observable vortices via the Rossby wave instability (RWI). We study time-scales for the development of vortices driven by low-mass planets in inviscid discs. We employ a recently developed semi-analytical theory of vortensity production by the planet-driven shock to predict vortensity evolution near the planet, from which we derive the radial profile of the planet-induced gap as a function of time (this procedure can have multiple other uses, e.g. to study dust trapping, suppression of pebble accretion, etc.). We then analyse the linear stability of the gap edges against the RWI, obtaining the time-scales for the first appearance of unstable modes and (later) fully developed vortices at gap edges. We present useful formulae for these time-scales as functions of planetary and disc parameters and provide their physical justification. We also thoroughly test our semi-analytical framework against high-resolution 2D hydrodynamic simulations, confirming the accuracy of our theoretical predictions. We discuss ways in which our semi-analytical framework can be extended to incorporate additional physics, e.g. planetary accretion, migration, and non-zero disc viscosity. Our results can be used to interpret observations of PPDs and to predict emergence of vortices in simulations.
Transmission strings: a technique for spatially mapping exoplanet atmospheres around their terminators
Authors: Grant David , Wakeford Hannah R 
Published: December 2022

ABSTRACT
Exoplanet transmission spectra, which measure the absorption of light passing through a planet’s atmosphere during transit, are most often assessed globally, resulting in a single spectrum per planetary atmosphere. However, the inherent 3D nature of planetary atmospheres, via thermal, chemical, and dynamical processes, can imprint inhomogeneous structure and properties in the observables. In this work, we devise a technique for spatially mapping the atmospheres of exoplanets in transmission. Our approach relaxes the assumption that transit light curves are created from circular stars occulted by circular planets, and instead we allow for flexibility in the planet’s sky-projected shape. We define the planet’s radius to be a single-valued function of angle around its limb, and we refer to this mathematical object as a transmission string. These transmission strings are parametrized in terms of Fourier series, a choice motivated by these series having adjustable complexity, generating physically practical shapes, while being reducible to the classical circular case. The utility of our technique is primarily intended for high-precision multiwavelength light curves, from which inferences of transmission spectra can be made as a function of angle around a planet’s terminator, enabling analysis of the multidimensional physics at play in exoplanet atmospheres. More generally, the technique can be applied to any transit light curve to derive the shape of the transiting body. The algorithm we develop is available as an open-source package, called harmonica1.