bluuebunny/crossref_metadata_2025 huggingface dataset:
Disease-associated polyalanine expansion mutations impair UBA6-dependent ubiquitination
Authors: Amer-Sarsour Fatima , Falik Daniel , Berdichevsky Yevgeny , Kordonsky Alina , Eid Sharbel , Rabinski Tatiana , Ishtayeh Hasan , Cohen-Adiv Stav , Braverman Itzhak , Blumen Sergiu C , Laviv Tal , Prag Gali , Vatine Gad D , Ashkenazi Avraham
Published: January 2024

Expansion mutations in polyalanine stretches are associated with a growing number of diseases sharing a high degree of genotypic and phenotypic commonality. These similarities prompted us to query the normal function of physiological polyalanine stretches and to investigate whether a common molecular mechanism is involved in these diseases. Here, we show that UBA6, an E1 ubiquitin-activating enzyme, recognizes a polyalanine stretch within its cognate E2 ubiquitin-conjugating enzyme USE1. Aberrations in this polyalanine stretch reduce ubiquitin transfer to USE1 and, subsequently, polyubiquitination and degradation of its target, the ubiquitin ligase E6AP. Furthermore, we identify competition for the UBA6-USE1 interaction by various proteins with polyalanine expansion mutations in the disease state. The deleterious interactions of expanded polyalanine tract proteins with UBA6 in mouse primary neurons alter the levels and ubiquitination-dependent degradation of E6AP, which in turn affects the levels of the synaptic protein Arc. These effects are also observed in induced pluripotent stem cell-derived autonomic neurons from patients with polyalanine expansion mutations, where UBA6 overexpression increases neuronal resilience to cell death. Our results suggest a shared mechanism for such mutations that may contribute to the congenital malformations seen in polyalanine tract diseases.
The NSP3 protein of SARS-CoV-2 binds fragile X mental retardation proteins to disrupt UBAP2L interactions
Authors: Garvanska Dimitriya H , Alvarado R Elias , Mundt Filip Oskar , Lindqvist Richard , Duel Josephine Kerzel , Coscia Fabian , Nilsson Emma , Lokugamage Kumari , Johnson Bryan A , Plante Jessica A , Morris Dorothea R , Vu Michelle N , Estes Leah K , McLeland Alyssa M , Walker Jordyn , Crocquet-Valdes Patricia A , Mendez Blanca Lopez , Plante Kenneth S , Walker David H , Weisser Melanie Bianca , Överby Anna K , Mann Matthias , Menachery Vineet D , Nilsson Jakob
Published: January 2024

Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1, FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have attenuated replication in vitro and reduced levels of viral antigen in lungs during the early stages of infection. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins and provides molecular insight into the possible underlying molecular defects in fragile X syndrome.
Regulation of the structure and density of KN5 frameworks with CH3COOK and CF3COOK
Authors: Jiang Shuaijie , Zhou Jianxin , Xu Yuangang , Lin Qiuhan , Wang Pengcheng , Lu Ming
Published: January 2024

Two novel KN5 frameworks were achieved with CH3COOK and CF3COOK. The unique nanocages and channels were constructed by KN5 with CH3COOK and CF3COOK, respectively.
Graphyne and graphdiyne nanoribbons: from their structures and properties to potential applications
Authors: Liu Qiaohan , Wang Xiaorong , Yu Jing , Wang Jingang
Published: January 2024

Graphyne (GY) and graphdiyne (GDY) have properties including unique sp- and sp2-hybrid carbon atomic structures, natural non-zero band gaps, and highly conjugated π electrons.
First-principles calculations on the intrinsic resistivity of realistic metals: a case study of monolayer V2N
Authors: Zhang Binyuan , Gong Weijiang
Published: January 2024

The intrinsic resistivity of the V2N monolayer arising from electron–phonon interactions is studied using first-principles calculations. The validity of the Ziman resistivity formula is revealed and a modified Ziman resistivity formula suggested.
What is behind a gas stream scrubbing liquid? Monoethanolamine/water mixtures as seen by dielectric relaxation spectroscopy
Authors: Agieienko Vira , Buchner Richard
Published: January 2024

Dielectric spectra of monoethanolamine (MEA)/water mixtures constitute a sum of relaxations arising from MEA in a composition of its aggregates, MEA hydrates and more-or-less unperturbed water.
Exploring potooxidative degradation pathways of harmol and harmalol alkaloids in water: effects of pH, excitation sources and atmospheric conditions
Authors: Villarruel Fernando D. , Denofrio M. Paula , de León Tobías Schmidt , Erra-Balsells Rosa , Wolcan Ezequiel , García Einschlag Fernando S. , Cabrerizo Franco M.
Published: January 2024

This work explores the photochemical degradation of cationic species of harmol (1C) and the corresponding partially hydrogenated derivative harmalol (2C) in aqueous solution.
Crystalline porous organic salts
Authors: Xing Guolong , Peng Daoling , Ben Teng
Published: January 2024

CPOSs, formed through self-assembly of organic acids and organic bases, are gradually evolving into a field full of opportunities and challenges.
Oxygen reduction reaction (ORR) in alkaline solution catalysed by an atomically precise catalyst based on a Pd(ii) complex supported on multi-walled carbon nanotubes (MWCNTs). Electrochemical and structural considerations
Authors: Monini Valeria , Bonechi Marco , Bazzicalupi Carla , Bianchi Antonio , Gentilesca Pietro , Giurlani Walter , Innocenti Massimo , Meoli Arianna , Romano Giammarco Maria , Savastano Matteo
Published: January 2024

Apical interaction of O2 with a square planar macrocyclic Pd(ii) complex anchored on MWCNTs gives rise to a significant electrocatalytic activity towards the oxygen reduction reaction (ORR). This finding confirms previous computational data.
Tailoring the electronic structure of the NaTi2(PO4)3 anode for high-performing sodium-ion batteries via defect engineering
Authors: Wang Qinchao , He Sha , Chen Hao , Peng Zhaoquan , Xu Zhixin , Zeng Zhiyong , Wang Chao , Xue Pan , Ni Lubin , Li Xiaoge , Han Jie
Published: January 2024

Defect engineering was used to address the poor electronic conductivity of NaTi2(PO4)3. Sufficient VO promotes the localization of Ti1, Ti2, and P1 cations, while delocalizes O atoms, which boosts Na storage efficiency and rapid diffusion kinetics.
Microfluidics in environmental analysis: advancements, challenges, and future prospects for rapid and efficient monitoring
Authors: Aryal Prakash , Hefner Claire , Martinez Brandaise , Henry Charles S.
Published: January 2024

This review highlights the latest advancements in microfluidic devices in environmental monitoring during the last 5 years. We also emphasize the current limitations in the devices and propose effective strategies to improve environmental monitoring.
Antibodies, repertoires and microdevices in antibody discovery and characterization
Authors: Schlotheuber Luca Johannes , Lüchtefeld Ines , Eyer Klaus
Published: January 2024

Essential in treating numerous diseases, novel therapeutic antibody candidates are needed. This critical review examines recent advances in microdevices and the challenges associated with candidate discovery and characterization.
Ligand-modified eggshells for rapid naked-eye detection and removal of trace level Ni2+ ions
Authors: Rosaiah P. , Vadivel S. , Dayanidhi Kalaivani , Karim Mohammad Rezaul , Alnaser Ibrahim A. , Sangaraju Sambasivam , Dhananjaya M. , Joo Sang Woo
Published: January 2024

Waste to wealth-eggshell wastes as colorimetric sensors.
One-pot, efficient synthesis of fused quinoline analogues via room temperature C(sp3)–N cleavage/aromatization reaction
Authors: Prasanna Kumari Subramaniyan , Thamotharan Subbiah , Selva Ganesan Subramaniapillai
Published: January 2024

One-pot transformation of N,N-dimethylaniline to fused quinoline derivatives was achieved through sequential oxidative cyclization followed by a concomitant C(sp3)–N cleavage/aromatization reaction.
Aquatic photolysis of strobilurin fungicide kresoxim-methyl: kinetics, pathways, and effects of adjuvants
Authors: Zhang Xuewei , Ye Jing , Ni Zhigang , Yang Xuerui , Ji Yuefei , Chovelon Jean-Marc , Xiu Guangli , Zhou Lei
Published: January 2024

Investigations of fungicide kresoxim-methyl's phototransformation elucidated the kinetics, intermediates, pathways, and toxicological impacts, also emphasizing the modulation of adjuvants.
Highly flexible PEG-LifeAct constructs act as tunable biomimetic actin crosslinkers
Authors: Jorgenson Tyler D. , Baboolall Kashmeera D. , Suarez Cristian , Kovar David R. , Gardel Margaret L. , Rowan Stuart J.
Published: January 2024

Bio-synthetic telechelics consisting of polyethylene glycol chains end-capped with the actin-binding peptide, LifeAct, are effective F-actin crosslinkers with contour length dependent control over network mechanics and structure.
Effect of local active fluctuations on structure and dynamics of flexible biopolymers
Authors: Dutta Sayantan , Ghosh Ashesh , Spakowitz Andrew J.
Published: January 2024

Active fluctuations play a significant role in the structure and dynamics of biopolymers (e.g. chromatin and cytoskeletal proteins) that are instrumental in the functioning of living cells.
Corporate management, green finance, and sustainability
Authors: Zhao Zhihua , Xing Zhenjiang
Published: January 2024

This study aimed to assess the impact of green finance and corporate management on China’s sustainable development index from 1990 to 2020 using time series analysis. The findings reveal that a 1% increase in the green financial market corresponds to a 0.31% and 0.69% enhancement in China’s sustainable development index in the short and long-term, respectively. Similarly, a 1% improvement in the corporate governance index is associated with a 0.16% and 0.29% increase in the short- and long-term. Interestingly, the green tax policy, acting as a proxy for green fiscal policy, negatively influences the sustainable development index. Additionally, the poverty rate emerges as a concerning factor hindering sustainable development in China. The policy implications include advocating for the digitalization of green finance, expanding poverty alleviation efforts, reforming the green taxation system, and implementing corporate sustainable management education programs.
Acoustic vortex filter based on tunable metasurfaces
Authors: Li Liulin , Liu Bingyi , Li Zhixiang , Guo Kai , Guo Zhongyi
Published: January 2024

In this paper, we present an acoustic vortex filter (AVF) based on tunable metasurfaces, which can selectively filter the incident multiplexed vortices that carry different orbital angular momentum (OAM). Our metasurface-based AVF is composed of an upper acoustic metasurface (UAM) and a lower acoustic metasurface, of which the intrinsic topological charge (ITC) can be tuned by mechanically rotating the UAM along its central axis. Due to the critical order of the propagating vortex modes in waveguide, controlling the ITC of the AVF allows for the selective filtering of incoming multiplexed acoustic vortex beams based on the sound vortex diffraction in phase-gradient metasurface, which endows the vortex filter the capability that let the incident vortex of specific OAM pass through it. In the following demonstration, both in theory and experiment, we design the AVF and effectively filter the acoustic vortices with two opposite topological charges by simply altering the orientation angle of the UAM. Based on this, we further demonstrate its application in asymmetric acoustic wave transmission. Our work offers an approach to selectively filter the incident acoustic vortex, which improves the capability to control the acoustic OAM via metasurfaces.
Ultrastrong-coupled magnon–polariton in a dynamical inductor based on magnetic-insulator/topological-insulator bilayers
Authors: Chiba Takahiro , Komine Takashi , Aono Tomosuke
Published: January 2024

We theoretically study a magnon–polariton in a dynamical inductor consisting of a coil and a bilayer of ferromagnetic insulator (FI) with perpendicular magnetization and a three-dimensional topological insulator (TI). Taking into account the coherent magnetic-dipole (Zeeman) interaction as well as the dissipative spin pumping effect on the FI/TI interface, we formulate a dynamical permeability of the FI/TI bilayer and calculate a corresponding electric admittance of an RLC-circuit. As a result, the spin pumping gives rise to a competitive effect on the modes hybridization, whereas a huge level repulsion due to the coherent coupling, which reaches the ultrastrong coupling regime, is found at room temperature for realistic parameter sets. Our work may open a new avenue for designing on-chip microwave devices based on a magnon–polariton in the RLC-circuit.
Estimation of negative membrane tension in lipid bilayers and its effect on antimicrobial peptide magainin 2-induced pore formation
Authors: Ahmed Marzuk , Billah Md. Masum , Tamba Yukihiro , Yamazaki Masahito
Published: January 2024

Positive membrane tension in the stretched plasma membrane of cells and in the stretched lipid bilayer of vesicles has been well analyzed quantitatively, whereas there is limited quantitative information on negative membrane tension in compressed plasma membranes and lipid bilayers. Here, we examined negative membrane tension quantitatively. First, we developed a theory to describe negative membrane tension by analyzing the free energy of lipid bilayers to obtain a theoretical equation for negative membrane tension. This allowed us to obtain an equation describing the negative membrane tension (σosm) for giant unilamellar vesicles (GUVs) in hypertonic solutions due to negative osmotic pressure (Π). Then, we experimentally estimated the negative membrane tension for GUVs in hypertonic solutions by measuring the rate constant (kr) of rupture of the GUVs induced by the constant tension (σex) due to an external force as a function of σex. We found that larger σex values were required to induce the rupture of GUVs under negative Π compared with GUVs in isotonic solution and quantitatively determined the negative membrane tension induced by Π (σosm) by the difference between these σex values. At small negative Π, the experimental values of negative σosm agree with their theoretical values within experimental error, but as negative Π increases, the deviation increases. Negative tension increased the stability of GUVs because higher tensions were required for GUV rupture, and the rate constant of antimicrobial peptide magainin 2-induced pore formation decreased.
Swirling flow of two immiscible fluids in a cylindrical container: Lattice Boltzmann and volume-of-fluid study
Authors: Salnikov Mikhail V. , Vozhakov Ivan S. , Naumov Igor V. , Mullyadzhanov Rustam I.
Published: January 2024

An experimental and numerical study of a multicomponent swirl flow of a liquid in a closed cylinder is carried out for various values of the relative cylinder elongation and the Reynolds number. The experimental technique for flow characteristics measurement is based on the PIV (particle image velocimetry) technique. To study the flow characteristics in detail, we simulated the problem numerically using the Palabos and Basilisk software open-source packages. The current implementation of the Palabos package uses the LBM (lattice Boltzmann method) approach, in which the collision integral is determined by the MRT (multiple-relaxation-time) approximation, and the intercomponent interaction is established according to the Shan–Chen pseudopotential approximation. The Basilisk package uses VOF (volume-of-fluid) approach to approximate the fluid interface. In this paper, for the first time, the data considering the emergence conditions for the zone of axial isolated recirculation in a multicomponent vortex flow were obtained at different viscosity ratios of two fluids. It is shown that with a decrease in the viscosities ratio, the recirculation zone existence curve shifts closer to that corresponding to the case of a one-component flow. In the course of numerical analysis, we found that both numerical implementations of this problem describe flow characteristics with high accuracy. Both methods recreate the recirculation zone on the cylinder axis observed experimentally. However, the velocity shift on the interface is observed only in the LBM approach.
Convection velocities in droplets before and after their collisions
Authors: Volkov Roman , Tkachenko Pavel , Podgornaya Elizaveta , Strizhak Pavel
Published: January 2024

High-speed video recording was used together with particle image velocimetry with tracer particles of titanium dioxide to study the characteristics of shifting and mixing of liquid layers in the coalescence, disruption, and separation of droplets. Convection velocities (Uc) were determined in droplets before and after their collisions. Vortex contours of different sizes and in different cross sections of droplets were derived. The average values of Uc were calculated. The effect of a group of factors on Uc was investigated. These factors include the relative velocity before the collision Urel, the ratio of droplet sizes Δ, the Weber number, the impact angle, and the rheological properties of liquid. Uc changed most significantly (more than threefold) from variations in Δ, Urel, and We. When varying the dimensionless linear interaction parameter B, Uc changed by 20%–40%. In disruption, Uc increased more than eightfold. In separation and coalescence, they increased by a factor of 10 and 11, respectively. The convection velocity was maximum after the collision. Then, 0.29–0.37 s after the collision, it fell to the values corresponding to a free-falling droplet. An increase in the convection velocity was compared for different droplet sizes and velocities before and after their interaction. Mathematical equations were obtained to predict the convection velocities affected by several investigated factors, taken separately or in combination. For the first time, the ranges of Uc were found, and the effect of a wide group of parameters (geometric sizes and velocities of droplets, rheological characteristics) on the velocities of convective flows was identified.
A novel Lagrangian–Eulerian weighted-least squares scheme coupled with other stable techniques for multi-physical fluid flow around complex obstacle
Authors: Shi Qiushuang , Zhao Jingjun , Jiang Tao
Published: January 2024

In this paper, a stable novel meshless coupled method is proposed to simulate the non-isothermal magnetohydrodynamics (MHD) flow problems (multi-physics quantities) inside a lid-driven cavity around complex obstacle. The proposed method is mainly motivated by a Lagrangian–Eulerian (L–E) weighted-least squares (WLS) scheme combined with a stream function-vorticity (SFV) and other stable techniques, and it is further to investigate the non-isothermal MHD flow around an airfoil obstacle at large Hartmann (Ha) or Reynolds (Re) number, for the first time. In the present meshless coupled approach (named L–E WLS–SFV), the traditional MHD equations are derived as another form with an SFV method under divergence-free constraint, which can avoid the tedious treatment of pressure on complex irregular obstacle. Then, a stable L–E WLS coupled algorithm is proposed to approximate the space derivatives of multi-physical quantities (velocity, magnetic, temperature, etc.), in which a corrected particle shifting technique is employed to improve the tensile instability among Lagrangian particles moving inside the domain and a second-order upwind scheme is adopted to stabilize large Re number problem in Eulerian fixed nodes near the boundary. Several benchmarks are simulated to show the numerical accuracy and convergence rates of the proposed WLS scheme for MHD flow at different parameters. Subsequently, the case of the non-isothermal MHD flow around a square obstacle under large parameters is simulated by the proposed L–E WLS–SFV method and compared with other numerical results to demonstrate the validity and capacity of the proposed method for multi-physical flow and the necessity of imposing the above two stable techniques. Finally, the case of non-isothermal MHD flow around the circular or airfoil obstacle is numerically investigated, and the important effects of the Hartmann, Rayleigh, and Reynolds numbers on the multi-physical quantities (stream function, vorticity, temperature, and magnetic field) are discussed. The advantages of the proposed method for the muti-physical flow around irregular obstacles are also exemplified. All the numerical results show that the proposed L–E WLS–SVF method is robust and accurate to simulate the multi-physical fluid flow around complex obstacles.
The motion of three-dimensional fractal aggregates in homogeneous shear flow
Authors: Yu Zhengdong , Niu Xiaojing
Published: January 2024

A model for the motion of aggregates in low Reynolds number flow has been established by utilizing the Stokesian dynamics and applying the quaternion as global attitude parameter. The model has been validated by the theorical solution of sphere doublet in shear flow, the simple helical aggregates, and the experiment on the settling of some specific objects in still water. The motion of fractal aggregates has been further studied, aiming to get better understanding of the dynamic behavior of fine-grained sediment flocs in shear flow. The fractal aggregates have been generated using the diffusion-limited aggregation model, which has similar fractal dimension as natural flocs. The results illustrate that fractal aggregates undergo a complex rotation in shear flow, which exhibit a bi-periodic characteristic. The motion of a particle within the fractal aggregate shows three-dimensional trajectory in a simple shear flow, affected by its initial orientation. The major rotation period is approximately 4π/γ̇, which corresponds to the rotation period of a sphere with shear strength γ̇. The deviation decreases with the increase in the size of the fractal aggregate.
Polygon model for solution of non-linear velocity gradient of interface and asymmetric break-up of droplet
Authors: Heydarpoor Saleh , Famili Navid M.
Published: January 2024

In this study, a novel model is proposed to accurately depict the changes in the droplet-matrix interface as a function of the velocity gradient at different times. Using the iteration method and drawing the droplet shape, the interface velocity gradient-matrix shear rate non-linear equation is simultaneously solved. The initial droplet shape is assumed to be a polygon, with each side independently undergoing modifications under stress. By sequentially adjusting each side at different time points, the overall shape of the droplet is reconstructed. The experimental section examines droplets consisting of alcohols (polyvinyl alcohol and polyethylene glycol) in water-soluble form with different concentrations and glycerol. The matrix material used is poly dimethyl siloxane. The viscosity ratio between the droplet and matrix falls within the range of 0.18–3.08. The experimental findings show two types of droplet breakup: a single-end bulb and two non-uniform end bulbs of different sizes. The simulation results from the model align well with the experimental observations, accurately capturing the dimensions and volume of the droplets and the aspect ratio of the bulbs. The model also predicts the aspect ratio, lateral area, and rotation of the droplets before breakup with minimal deviation from the experimental data.
Plasma screening effect in warm solid-density iron plasma
Authors: Faussurier Gérald
Published: January 2024

We study a plasma screening effect in a warm solid-density iron plasma. All the calculations are done using the average atom model in the muffin-tin approximation using the density functional theory in local density approximation at finite temperature in local thermodynamic equilibrium. Between temperatures equal to 15 and 20 eV, the system undergoes a huge change due to the 3d orbital becoming bound. In clear, four electrons become bound. Various average ionizations are defined to see this effect. At temperature equal to 20 eV, all the average ionizations agree to predict a Fermi energy and a plasma frequency that are close to the temperature of the medium. The density of states show a prominent resonance due to d orbital just below temperature equal to 15 eV. We show that the spectral opacity is drastically modified near the L shell threshold due to the appearance of a 2p→3d absorption line.
Numerical simulation and analysis of droplet formation within an amphiphilic particle
Authors: Song Xinpei , Destgeer Ghulam
Published: January 2024

An instrument-free particle-templated droplet formation can be achieved upon simple mixing of amphiphilic particles with aqueous and oil phases in a well plate by using a common lab pipette. Here, a two-dimensional, two-phase flow model was established using a finite element method to mimic the droplet formation within a concentric amphiphilic particle, which consisted of an outer hydrophobic layer and an inner hydrophilic layer. Immiscible water and oil phases selectively interacted with the hydrophilic and hydrophobic layers of the particle, respectively, to form an isolated aqueous compartment within a cavity. Three extreme models were also simulated, including completely hydrophilic, completely hydrophobic, and oppositely amphiphilic particle, which indicated that a right order of the particle layers was necessary to capture the droplet inside the cavity. Moreover, we performed a systematic study of particle-templated droplet formation by varying the individual layer thicknesses of particle, particle height, interfacial tension between water and oil, contact angle of interface with different surfaces, velocity of incoming oil media, and distance between neighboring particles. The volume fraction of water droplet trapped within the target cavity region was calculated to characterize the droplet formation. Our work will help to optimize the particle fabrication process, predict the experiment droplet formation, and explain the physical mechanism underlying compartmentalization phenomena.
Regulating droplet impact dynamics of nanoparticle suspension: Phenomena, mechanisms, and implications
Authors: A Hubao , Cao Hao , Hu Ran , Chen Yi-Feng , Gui Chengqun , Yang Zhibing
Published: January 2024

Droplet impact on solid substrates is a ubiquitous phenomenon in nature, agriculture, and industrial processes, playing a crucial role in numerous applications including self-cleaning, pesticide utilization, and inkjet printing. As a promising technique, adding nanoparticles into simple fluids to form nanofluids can effectively manipulate droplet impact behaviors. However, a comprehensive understanding of how nanoparticles modify the droplet impact dynamics, especially on the nanoscale, is still far from being fully explored. Hence, in this work, through the combined effort of molecular dynamics simulations and theoretical analysis, we elaborate on the influences of nanoparticles on droplet impact process. Using simple droplets as a control, we summarize four typical droplet impact modes and reveal how nanoparticles alter the impact behaviors of droplets, taking into account the key parameters including substrate wettability, impact velocity, volume fraction, and mass fraction of nanoparticles. We also demonstrate that with appropriate modifications, the theoretical/empirical models to predict the maximum contact diameter and the occurrence of breakup for simple droplets still hold to predict those of nanofluid droplets. Our findings and results enhance the understanding of the impact of nanoparticles on the droplet impact dynamics, with promising possibilities for various applications where regulating droplet impact behaviors is desired.
Internal friction as a factor in the anomalous chain length dependence of DNA transcriptional dynamics
Authors: Cherayil Binny J.
Published: January 2024

Recent experiments by Brückner et al. [Science 380, 1357 (2023)] have observed an anomalous chain length dependence of the time of near approach of widely separated pairs of genomic elements on transcriptionally active chromosomal DNA. In this paper, I suggest that the anomaly may have its roots in internal friction between neighboring segments on the DNA backbone. The basis for this proposal is a model of chain dynamics formulated in terms of a continuum scaled Brownian walk (sBw) of polymerization index N. The sBw is an extension of the simple Brownian walk model widely used in path integral calculations of polymer properties, differing from it in containing an additional parameter H (the Hurst index) that can be tuned to produce varying degrees of correlation between adjacent monomers. A calculation using the sBw of the mean time τc for chain closure predicts—under the Wilemski–Fixman approximation for diffusion-controlled reactions—that at early times, τc varies as the 2/3 power of N, in close agreement with the findings of the Brückner et al. study. Other scaling relations of that study, including those related to the probability of loop formation and the mean square displacements of terminal monomers, are also satisfactorily accounted for by the model.
Experimental study on Q-learning control of airfoil trailing-edge flow separation using plasma synthetic jets
Authors: Zong Haohua , Wu Yun , Liang Hua , Su Zhi , Li Jinping
Published: January 2024

In this paper, a continuous Q-learning algorithm is deployed to optimize the control strategy of a trailing-edge airfoil flow separation at a chord-based Reynolds number of 2×105. With plasma synthetic jets issued at the middle chord and a hot wire placed in the separated shear layer acting as the actuator and sensor, respectively, a high-speed reinforcement learning control at an interaction frequency of 500 Hz is realized by a field-programmable gate array. The results show that in the Q-learning control, the controller only needs several seconds to elevate the instantaneous reward to a level close to the final mean reward, and convergence of the control law typically takes less than 100 s. Although the relative drag reduction achieved by Q-learning control (10.2%) is only slightly higher than the best open-loop periodical control at F∗=4 (9.6%), the maximum power saving ratio is improved noticeably by 62.5%. Physically, Q-learning control creates more turbulent fluctuations, earning more rewards by increasing the transition possibilities toward high-value states. With increasing penalty strength of plasma actuation, the final control laws obtained from Q-learning exhibit a decreasing number of active states. Detailed comparisons between the open-loop and Q-learning control strategies show that the statistics of the controlled velocity fields remain similar, yet the turbulent fluctuations contributed by the vortex shedding mode are reduced by constant-frequency plasma actuation.
Coordination environment-induced ionic–electronic transport transition in LiVO3
Authors: Zhao Xingxing , Xing Zhenfang , Ma Liang , Peng Di , Cai Jinqun , Han Yonghao , Zhao Lin
Published: January 2024

Lithium metavanadate (LiVO3) is a typical ionic conductor with a monoclinic pyroxene-type structure at ambient conditions. Here, we investigated the structural and electrical transport properties of LiVO3 under high pressures by combining in situ Raman scattering, x-ray diffraction, impedance spectroscopy measurements, and first-principles calculations. All experimental and theoretical results demonstrated that LiVO3 undergoes a structural transition from monoclinic to triclinic phase at around 5 GPa, during which partial VO4 tetrahedrons are transformed into a VO6 octahedron. The ion migration of LiVO3 was significantly suppressed above 5 GPa and an ionic–electronic transition was discovered at 10.7 GPa. The structural evolution involving coordination environment change results in an electron density rearrangement around Li and O atoms, which are responsible for the transformation of electrical transport mechanism in LiVO3 under high pressures. These results expand our understanding of the electrical and structural properties of LiVO3 under high pressures and provide insights into the pressure effects on ion migration in solid electrolytes.
Germantown revisited
Authors: McMullen Gabrielle L.
Published: January 2024

Germans were among the earliest settlers in the Geelong region — their presence was visibly identifiable in the early township of Germantown, now Grovedale. This paper makes a contribution to recognising the legacy of the pioneering Germans in the region and the Humboldtian visualisation of Geelong captured by German artist Eugene von Guérard. The stimulus for the paper was the contemporary German event in Geelong when Deakin University generously hosted the 2022 conference of the Australian and New Zealand Associations of von Humboldt Fellows at its Waterfront Campus.
Eugene von Guérard and the Ethnological Museum in Berlin: Correspondence 1878–1880
Authors: Darragh Thomas A. , Pullin V. Ruth
Published: January 2024

This paper details the correspondence between nineteenth-century landscape painter Eugene von Guérard and the Ethnological Museum, Berlin. It includes complete translations of the relevant correspondence from Old German script. The letters contain information on the provenance of the collection of Australian Aboriginal cultural possessions that von Guérard sold to Berlin, as well as documentation of the items purchased by him on behalf of the museum. They record unexpected cross-cultural exchanges, document the building of individual and institutional collections of First Nations’ cultural belongings in colonial Victoria and they trace the people and processes involved in the transfer of this collection to a major German museum. The information recorded in the letters has the potential to inform the process of reconnecting specific objects with source communities.
The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids
Authors: Yuan Jiaqing , Kitchener Andrew C. , Lackey Laurie Bingaman , Sun Ting , Jiangzuo Qigao , Tuohetahong Yilamujiang , Zhao Le , Yang Peng , Wang Guiqiang , Huang Chen , Wang Jinhong , Hou Wenhui , Liu Yang , Chen Wu , Mi Da , Murphy William J. , Li Gang
Published: January 2024

Habitat degradation and loss of genetic diversity are common threats faced by almost all of today’s wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat,
Felis nigripes
, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions.
StratoLAMP: Label-free, multiplex digital loop-mediated isothermal amplification based on visual stratification of precipitate
Authors: Jin Meichi , Ding Jingyi , Zhou Yu , Chen Jiazhao , Wang Yi , Li Zida
Published: January 2024

Multiplex, digital nucleic acid detections have important biomedical applications, but the multiplexity of existing methods is predominantly achieved using fluorescent dyes or probes, making the detection complicated and costly. Here, we present the StratoLAMP for label-free, multiplex digital loop-mediated isothermal amplification based on visual stratification of the precipitate byproduct. The StratoLAMP designates two sets of primers with different concentrations to achieve different precipitate yields when amplifying different nucleic acid targets. In the detection, deep learning image analysis is used to stratify the precipitate within each droplet and determine the encapsulated targets for nucleic acid quantification. We investigated the effect of the amplification reagents and process on the precipitate generation and optimized the assay conditions. We then implemented a deep-learning image analysis pipeline for droplet detection, achieving an overall accuracy of 94.3%. In the application, the StratoLAMP successfully achieved the simultaneous quantification of two nucleic acid targets with high accuracy. By eliminating the need for fluorescence, StratoLAMP represents a unique concept toward label-free, multiplex nucleic acid assays and an analytical tool with great cost-effectiveness.
Essential parameters needed for a U-Net-based segmentation of individual bones on planning CT images in the head and neck region using limited datasets for radiotherapy application
Authors: Yawson Ama Katseena , Walter Alexandra , Wolf Nora , Klüter Sebastian , Hoegen Philip , Adeberg Sebastian , Debus Jürgen , Frank Martin , Jäkel Oliver , Giske Kristina
Published: January 2024

Objective. The field of radiotherapy is highly marked by the lack of datasets even with the availability of public datasets. Our study uses a very limited dataset to provide insights on essential parameters needed to automatically and accurately segment individual bones on planning CT images of head and neck cancer patients. Approach. The study was conducted using 30 planning CT images of real patients acquired from 5 different cohorts. 15 cases from 4 cohorts were randomly selected as training and validation datasets while the remaining were used as test datasets. Four experimental sets were formulated to explore parameters such as background patch reduction, class-dependent augmentation and incorporation of a weight map on the loss function. Main results. Our best experimental scenario resulted in a mean Dice score of 0.93 ± 0.06 for other bones (skull, mandible, scapulae, clavicles, humeri and hyoid), 0.93 ± 0.02 for ribs and 0.88 ± 0.03 for vertebrae on 7 test cases from the same cohorts as the training datasets. We compared our proposed solution approach to a retrained nnU-Net and obtained comparable results for vertebral bones while outperforming in the correct identification of the left and right instances of ribs, scapulae, humeri and clavicles. Furthermore, we evaluated the generalization capability of our proposed model on a new cohort and the mean Dice score yielded 0.96 ± 0.10 for other bones, 0.95 ± 0.07 for ribs and 0.81 ± 0.19 for vertebrae on 8 test cases. Significance. With these insights, we are challenging the utilization of an automatic and accurate bone segmentation tool into the clinical routine of radiotherapy despite the limited training datasets.
A levitated atom-nanosphere hybrid quantum system
Authors: Hopper A , Barker P F
Published: January 2024

Near-field, radially symmetric optical potentials supported by a levitated nanosphere can be used for sympathetic cooling and for creating a bound nanosphere-atom system analogous to a large molecule. We demonstrate that the long range, Coulomb-like potential produced by a single blue detuned field increases the collisional cross-section by eight orders of magnitude, allowing fast sympathetic cooling of a trapped nanosphere to microKelvin temperatures using cold atoms. By using two optical fields to create a combination of repulsive and attractive potentials, we demonstrate that a cold atom can be bound to a nanosphere creating a new levitated hybrid quantum system suitable for exploring quantum mechanics with massive particles.
Fractional electrical impurity
Authors: Molina Mario I
Published: January 2024

We examine the localized mode and the transmission of plane waves across a capacitive impurity of strength Δ, in a 1D bi-inductive electrical transmission line where the usual discrete Laplacian is replaced by a fractional one characterized by a fractional exponent s. In the absence of the impurity, the plane wave dispersion is computed in closed form in terms of hypergeometric functions. It is observed that the bandwidth decreases steadily, as s decreases towards zero, reaching a minimum width at s = 0. The localized mode energy and spatial profiles are computed in closed form vía lattice Green functions. The profiles show a remnant of the staggered-unstaggered symmetry that is common in non-fractional chains. The width of the localized mode decreases with decreasing s, becoming completely localized at the impurity site at s = 0. The transmission coefficient of plane waves across the impurity is qualitatively similar to its non-fractional counterpart (s = 1), except at low s values (

s
≪
1

). For a fixed exponent s, the transmission decreases with increasing Δ.
Laser-free trapped ion entangling gates with AESE: adiabatic elimination of spin-motion entanglement
Authors: Tyler Sutherland R , Foss-Feig Michael
Published: January 2024

We discuss a laser-free, two-qubit geometric phase gate technique for generating high-fidelity entanglement between two trapped ions. The scheme works by ramping the spin-dependent force on and off slowly relative to the gate detunings, which adiabatically eliminates the spin-motion entanglement (AESE). We show how gates performed with AESE can eliminate spin-motion entanglement with multiple modes simultaneously, without having to specifically tune the control field detunings. This is because the spin-motion entanglement is suppressed by operating the control fields in a certain parametric limit, rather than by engineering an optimized control sequence. We also discuss physical implementations that use either electronic or ferromagnetic magnetic field gradients. In the latter, we show how to ‘AESE’ the system by smoothly turning on the effective spin-dependent force by shelving from a magnetic field insensitive state to a magnetic field sensitive state slowly relative to the gate mode frequencies. We show how to do this with a Rabi or adiabatic rapid passage transition. Finally, we show how gating with AESE significantly decreases the gate’s sensitivity to common sources of motional decoherence, making it easier to perform high-fidelity gates at Doppler temperatures.
Improving precision and accuracy in cosmology with model-independent spectrum and bispectrum
Authors: Amendola Luca , Marinucci Marco , Pietroni Massimo , Quartin Miguel
Published: January 2024

A new and promising avenue was recently developed for analyzing large-scale structure data with a model-independent approach, in which the linear power spectrum shape is parametrized with a large number of freely varying wavebands rather than by assuming specific cosmological models. We call this method FreePower.
Here we show, using a Fisher matrix approach, that precision of this method for the case of the one-loop power spectrum is greatly improved with the inclusion of the tree-level bispectrum. We also show that accuracy can be similarly improved by employing perturbation theory kernels whose structure is entirely determined by symmetries instead of evolution equations valid in particular models (like in the usual Einstein-de Sitter approximation). The main result is that with the Euclid survey one can precisely measure the Hubble function, distance and (k-independent) growth rate f(z) in seven redshift bins in the range z ∈ [0.6, 2.0]. The typical errors for the lower zbins are around 1% (for H), 0.7–1% (for D), and 2–3% (for f). The use of general perturbation theory allows us, for the first time, to study constraints on the nonlinear kernels of cosmological perturbations, that is, beyond the linear growth factor, showing that they can be probed at the 10–20% level. We find that the combination of spectrum and bispectrum is particularly effective in constraining the perturbation parameters, both at linear and quadratic order.
Revisiting the Transtheoretical Model for Physical Activity: A Large-Scale Cross-Sectional Study on Japanese-Speaking Adults
Authors: Oba Takeyuki , Takano Keisuke , Katahira Kentaro , Kimura Kenta
Published: January 2024

Background

The Transtheoretical Model (TTM) has been the basis of health promotion programs, which are, for example, used to tailor behavioral interventions according to the stages of change. Empirical studies have shown that the TTM effectively describes the processes of behavioral adaptation to acquire healthier lifestyles; however, it has been argued that TTM-based interventions are not superior to non-TTM-based interventions for promoting physical activity (PA). Evidence has also highlighted some inconsistencies with theoretical assumptions, especially regarding how each process-of-change strategy emerges across the stages.

Purpose

Therefore, we investigated (a) how well the TTM describes the distributional characteristics of PA levels as well as other relevant variables (e.g., process of change, self-efficacy) across stages, and (b) how predictive the TTM variables are of PA levels within each stage.

Methods

We analyzed data from 20,573 Japanese-speaking adults who completed online questionnaires on PA and TTM variables.

Results

The results replicated previous findings that stage membership is associated with PA, the process of change, decisional balance, and self-efficacy, albeit with inconclusive evidence of temptations. Regression analyses revealed that some processes of change (self-reevaluation, reinforcement management, and self-liberation) were more predictive of PA in pre-active stages than in post-action stages; self-efficacy was predictive of PA only in the maintenance stage but not in the other stages.

Conclusions

Overall, the data support the theoretical assumptions of the TTM, but the stage specificity of the active processes may not always be consistent with the theory.