bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stem–loop formation drives RNA folding in mechanical unzipping experiments
Authors: Rissone Paolo , Bizarro Cristiano V. , Ritort Felix 
Published: January 2022

Significance
Understanding how complementary RNA single strands anneal to form the native structure requires accurate knowledge of the energetics of hybridization and the kinetics driving the hairpin fold. The annealing dynamics are highly complex for RNA, where multiple long-lived intermediate states occur along the folding pathway. In this framework, single-molecule experiments allow us to derive the thermodynamics and kinetics of RNA folding and the characterization of the intermediates along the folding pathway. We mechanically unzip a 2-kbp RNA hairpin with optical tweezers in sodium and magnesium, deriving the 10 RNA nearest-neighbor free energies and modeling the hybridization kinetics in a barrier energy landscape of stem–loop secondary structures. Our study contributes to a better understanding of the RNA folding problem.
Microscopic mechanisms of cooperative communications within single nanocatalysts
Authors: Punia Bhawakshi , Chaudhury Srabanti , Kolomeisky Anatoly B. 
Published: January 2022

Significance
Catalysis is an experimental approach to accelerate chemical reactions. It plays a critical role in modern industries. Recent experimental studies uncovered striking observations of cooperative communications for reactions on nanocatalysts. In these experiments, it was shown that the chemical reactions observed at specific active sites might effectively stimulate the same reactions at the neighboring sites. We developed a theoretical model to investigate the microscopic mechanisms of these phenomena. Our idea is that the catalytic communication is the result of the complex dynamics of charged holes. Explicit calculations are able to quantitatively explain all experimental observations, clarifying the molecular origin of cooperative communications. The presented theoretical framework might be utilized for developing efficient catalytic systems with better control over chemical reactions.
Expanding quasiperiodicity in soft matter: Supramolecular decagonal quasicrystals by binary giant molecule blends
Authors: Liu Yuchu , Liu Tong , Yan Xiao-Yun , Guo Qing-Yun , Lei Huanyu , Huang Zongwu , Zhang Rui , Wang Yu , Wang Jing , Liu Feng , Bian Feng-Gang , Meijer E.W. , Aida Takuzo , Huang Mingjun , Cheng Stephen Z.D. 
Published: January 2022

SignificanceAs the formation of quasicrystalline ordering in both metal alloys and soft matters reinforces the scale-invariance principle, however, it remains unknown that why metallic quasicrystals prefer decagonal quasicrystalline (DQC, 10-fold) ordering, and the condensed soft maters only exhibit dodecagonal quasicrystalline (DDQC, 12-fold) ordering. By tuning the self-sorting ability in a pair of giant molecules, the well-mixed binary blends generate a metastable DQC phase and corresponding unprecedent phase sequence (DQC → DDQC → Frank–Kasper σ) during thermal annealing. These peculiar assembling behaviors result from interplays of submesoatomic and mesoatomic packings. Reducing the self-sorting strength has induced an extra complexity in the sub-mesoatomic packings of giant molecules, which further influences the clustering on the mesoatomic level.
SNX27 suppresses SARS-CoV-2 infection by inhibiting viral lysosome/late endosome entry
Authors: Yang Bo , Jia Yuanyuan , Meng Yumin , Xue Ying , Liu Kefang , Li Yan , Liu Shichao , Li Xiaoxiong , Cui Kaige , Shang Lina , Cheng Tianyou , Zhang Zhichao , Hou Yingxiang , Yang Xiaozhu , Yan Hong , Duan Liqiang , Tong Zhou , Wu Changxin , Liu Zhida , Gao Shan , Zhuo Shu , Huang Weijin , Gao George Fu , Qi Jianxun , Shang Guijun 
Published: January 2022

SignificanceWe here established the interaction between PDZ binding motif (PBM) at the C terminal of ACE2 and PDZ domain of sorting nexin 27 (SNX27) and solved the crystal structure of ACE2-PBM/SNX27-PDZ complex. Together with retromer complex, SNX27 was found to regulate the homeostasis of cell surface ACE2 under physiological conditions. When endocytic pathway was used during SARS-CoV-2 infection, SNX27-retromer sorts ACE2/SARS-CoV-2 complex at early endosome and prevents it from entering lysosome/late endosome, inhibiting the cell entry of the virus. These findings add substantially to the current understanding of the important role of cytosolic tail of ACE2 during the invasion of SARS-CoV-2, and it could be used as a new therapeutic target for drug development.
Grammar and variation in the classroom
Authors: Dovalil Vít , Hanulíková Adriana 
Published: January 2022

AbstractGrammar is the structural foundation of successful communication, language use, and literacy development. Grammar is therefore sometimes viewed as the heart of language with an important place in language teaching. In a classroom setting, regulation of grammar knowledge through teachers is strongly influenced by teachers’ linguistic competence and beliefs. In this paper, we will first show the diversity in this knowledge by means of teacher interviews and speeded grammatical-acceptability data from pupils and students. We will then sketch a socio- and psycholinguistic perspective on several selected morphosyntactic variables in German. These will be discussed with reference to social forces that determine what is standard in a language (language norm authorities, language experts, model texts, and codifiers). Finally, we will draw a roadmap for teachers, language practitioners and editors looking for a qualified solution to grammatical cases of doubt in contemporary German and provide practical examples by drawing upon the German reference corpus.
Trametes versicolor
. [Descriptions of Fungi and Bacteria].
Authors: Minter D. W. , Soliman G. S. 
Published: January 2022

Abstract

A description is provided for
Trametes versicolor
. Some information on morphological characteristics, its associated organisms and substrata, habitats, economic impacts, dispersal and transmission, conservation status is given, along with details of its geographical distribution (Africa (Benin, Burundi, Cameroon, Democratic Republic of the Congo, Ethiopia, Kenya, Libya, Malawi, Morocco, Nigeria, Rwanda, Sierra Leone, South Africa, Tanzania, Uganda, Zimbabwe.), Antarctica, Asia (Armenia, Azerbaijan, China, Anhui, Gansu, Guangdong, Guanxi, Guizhou, Hainan, Hebei, Heilongjang, Henan, Hong Kong, Hubei, Hunan, Jiangsu, Jiangxi, Jilin, Liaoning, Nei Mongol Autonomous Region, Qinghai, Shandong, Shanxi, Sichuan, Xinjiang, Yunnan, Zhejiang, Cyprus, Georgia, India, Assam, Goa, Himachal Pradesh, Jammu and Kashmir, Karnataka, Kerala, Madhya Pradesh, Maharashtra, Meghalaya, Punjab, Rajasthan, Sikkim, Tamil Nadu, Uttarakhand, West Bengal, Indonesia, Iran, Iraq, Japan, Kazakhstan (Almaty), Kyrgyzstan, Laos, Malaysia, Mongolia, Myanmar, Nepal, Pakistan, Philippines, Russia, Singapore, South Korea, Sri Lanka, Taiwan, Tajikistan, Thailand, Turkey, Turkmenistan, Uzbekistan, Vietnam, Atlantic Ocean (Bermuda), Australasia (Australia, Australian Capital Territory, New South Wales, Queensland, South Australia, Tasmania, Victoria, Western Australia, New Zealand), Caribbean (Cuba, Dominican Republic, Haiti, Jamaica, Puerto Rico), Central America (Belize, Costa Rica, El Salvador, Guatemala, Nicaragua, Panama), Europe (Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Isle of Man, Italy, Kosovo, Latvia, Lithuania, Luxembourg, Moldova, Netherlands, Norway, Poland, Portugal, Romania, Russia, Serbia, Slovakia, Slovenia, Spain, Sweden, Switzerland, Ukraine, UK), Indian Ocean (Réunion), North America (Canada, Alberta, British Columbia, Manitoba, New Brunswick, Newfoundland and Labrador, Northwest Territories, Nova Scotia, Ontario, Prince Edward Island, Quebec, Saskatchewan, Yukon, Mexico, USA, Alabama, Alaska, Arizona, Arkansas, California, Colorado, Connecticut, Delaware, District of Columbia, Florida, Georgia, Idaho, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Maine, Maryland, Massachusetts, Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska, Nevada, New Hampshire, New Jersey, New Mexico, New York, North Carolina, North Dakota, Ohio, Oklahoma, Oregon, Pennsylvania, Rhode Island, South Carolina, South Dakota, Tennessee, Texas, Utah, Vermont, Virginia, Washington, West Virginia, Wisconsin, Wyoming), Pacific Ocean (USA, Hawaii), South America (Argentina, Bolivia, Brazil, Acre, Amazonas, Bahia, Distrito Federal, Espírito Santo, Mato Grosso do Sul, Minas Gerais, Pará, Paraná, Pernambuco, Rio Grande do Sul, Rio de Janeiro, Rondônia, Roraima, Santa Catarina São Paulo, Chile, Colombia, Ecuador, Paraguay, Peru, Suriname, Uruguay, Venezuela))).
Ultrafast manipulation of magnetic anisotropy in a uniaxial intermetallic heterostructure TbCo2/FeCo
Authors: Ovcharenko Sergei , Gaponov Mikhail , Klimov Alexey , Tiercelin Nicolas , Pernod Philippe , Mishina Elena , Sigov Alexander , Preobrazhensky Vladimir 
Published: January 2022

Abstract
We study experimentally and theoretically the dynamics of spin relaxation motion excited by a femtosecond pulse in the TbCo2/FeCo multilayer structures with different ratios of TbCo2 to FeCo thicknesses

r
d

=

d

T
b
C

o
2

/

d

F
e
C
o

. The main attribute of the structure is in-plane magnetic anisotropy that is artificially induced during sputtering under a DC magnetic field. The optical pump-probe method revealed strongly damped high-frequency oscillations of the dynamical Kerr rotation angle, followed by its slow relaxation to the initial state. Modeling experimental results using the Landau–Lifshitz-Gilbert (LLG) equation showed that the observed entire dynamics is due to destruction and restoration of magnetic anisotropy rather than to demagnetization. For the pumping fluence of 7 mJ cm−2, the maximal photo-induced disruption of the anisotropy field is about 14% for the sample with

r
d

=
1

and decreases when r

d
increases. The anisotropy relaxation is a three-stage process: the ultrafast one occurs within several picoseconds, and the slow one occurs on a nanosecond time scale. The Gilbert damping in the multilayers is found to be one order of magnitude higher than that in the constituent monolayers.
Cross-free in both lateral and axial directions for Fourier-domain full-field optical coherence tomography
Authors: Li Jinxi , Zhang Jason , Zhang Luozhi , Bai Xing , Yu Zhan , Yang Zhongzhuo , Wang Yujie , Chen Xingyu , Zhou Xin 
Published: January 2022

Abstract
Fourier-domain full-field optical coherence tomography has the advantages of high resolution and parallel detection. However, using parallel detection can result in optical crosstalk. Toward minimizing crosstalk, we implemented a very fast deformable membrane (DM) that introduces random phase illumination, which can effectively reduce the crosstalk by washing out fringes originating from multiply scattered light. However, although the application of DM has reduced the crosstalk problem in parallel detection to a certain extent, there will still be a lot of background noise, which may come from the circadian rhythm of the sample and multiple scattered photons. The problem could be solved by employing adaptive singular value decomposition (SVD) filtering. We also combined SVD with the cumulative sum method, which can significanlty improve image resolution. Also, the random phase introduced by DM in the spectral domain will cause axial crosstalk after an inverse Fourier transform. As far as we know, we are the first team to notice axial crosstalk and propose that this problem can be solved by controlling the deformation range of DM. We have carried out a theoretical analysis of the above methods and verified its feasibility by simulation.
A dual-ended 400 km OFDR for vibration detection
Authors: Qin Zujun , Hu Yiwei , Yue Yaoli , Tan Chao 
Published: January 2022

Abstract
Optical frequency-domain reflectometer (OFDR) has been widely used in vibration detection because of its unique advantages of simple configuration and high spatial resolution. Based on remote fiber amplification, an unrepeated OFDR is experimentally investigated for vibration detection. To locate the vibration, we present an algorithm by calculating segmental cross-correlation between the beating signals with and without disturbances over the sensing fiber. It is shown that the OFDR demonstrates the ability of detecting the vibration over 222 km testing distance (112 km + 110 km). After sensing the first spool fiber of 112 km, the remnant laser is amplified by a remote-pumped erbium-doped fiber amplifier before proceeding to probe the vibration in the second spool one of 110 km. To be specific, the piezoelectric ceramic transducer-induced vibrations positioned at z = 110.9 km and z = 220.9 km are detected, respectively. More importantly, the OFDR system can be extended to operate in bi-directional sensing mode for the purpose of doubling the detection range, i.e. 400 km.
Robust phase unwrapping algorithm based on Zernike polynomial fitting and Swin-Transformer network
Authors: Zhao Zixin , Zhou Menghang , Du Yijun , Li Junxiang , Fan Chen , Zhang Xuchao , Wei Xiang , Zhao Hong 
Published: January 2022

AbstractPhase unwrapping plays an important role in optical phase measurements. In particular, phase unwrapping under heavy noise conditions remains an open issue. In this paper, a deep learning-based method is proposed to conduct the phase unwrapping task by combining Zernike polynomial fitting and a Swin-Transformer network. In this proposed method, phase unwrapping is regarded as a regression problem, and the Swin-Transformer network is used to map the relationship between the wrapped phase data and the Zernike polynomial coefficients. Because of the self-attention mechanism of the transformer network, the fitting coefficients can be estimated accurately even under extremely harsh noise conditions. Simulation and experimental results are presented to demonstrate the outperformance of the proposed method over the other two polynomial fitting-based methods. This is a promising phase unwrapping method in optical metrology, especially in electronic speckle pattern interferometry.
Controlled release of metal phenolic network protected phage for treating bacterial infection
Authors: Sun Weilun , Xu Jingjing , Liu Bo , Zhao Yuan-Di , Yu Ling , Chen Wei 
Published: January 2022

Abstract
Phage is a promising therapeutic agent for treating antibiotic resistant bacteria. However, in the process of treatment, phage may be cleared by the immune system and cleaved by protease, which could affect the efficacy of phage. In order to solve the above problems, phage encapsulation is usually adopted. In this study, we employed metal phenolic network (MPN) for efficient phage encapsulation which could protect phage from the cleavage of protease, and keep cytotoxicity weak. In the model of skin wound infection, the encapsulated phage could be released in response to pH change to achieve good antibacterial effect. Furthermore, the MPN encapsulation could prolong the T4 phage residence time at the wound. Our findings suggest that MPN can be a promising material for phage encapsulation.
Electrical impedance tomography: a potential tool for intraoperative imaging of the tongue base
Authors: Brazey B , Haddab Y , Koebel L , Zemiti N 
Published: January 2022

Abstract

Background. The presence of a tumor in the tongue is a pathology that requires surgical intervention from a certain stage. This type of surgery is difficult to perform because of the limited space available around the base of the tongue for the insertion of surgical tools. During the procedure, the surgeon has to stretch and then fix the tongue firmly in order to optimize the available space and prevent tissue movement. As a result, the preoperative images of the inside of the tongue no longer give a reliable indication of the position and shape of the cancerous tissue due to the deformation of the overall tissue in the area. Thus, new images are needed during the operation, but are very difficult to obtain using conventional techniques due to the presence of surgical tools. Objective. Electrical Impedance Tomography (EIT) is an imaging technique that maps the resistivity or difference of resistivity of biological tissues from electrical signals. The small size of the electrodes makes it a potentially interesting tool to obtain intraoperative images of the inside of the tongue. In this paper, the objective is to study the possibility of using EIT for this purpose is investigated. Main results. A detection method is proposed, including an original configuration of the electrodes, consistent with the anatomical specificities of the tongue. The proposed method is studied in simulation and then a proof of concept is obtained experimentally on a 3D printed test tank filled with saline solution and plant tissue.
Beta-induced Alfvén eigenmodes and geodesic acoustic modes in the presence of strong tearing activity during the current ramp-down on JET
Authors: Pucella G , Alessi E , Auriemma F , Buratti P , Falessi M V , Giovannozzi E , Zonca F , Baruzzo M , Challis C D , Dumont R , Frigione D , Garzotti L , Hobirk J , Kappatou A , Keeling D L , King D , Kiptily V G , Lerche E , Lomas P J , Maslov M , Nunes I , Rimini F , Sirén P , Sozzi C , Stamp M F , Stancar Z , Sun H , Van Eester D , Zerbini M 
Published: January 2022

Abstract
The analysis of the current ramp-down phase of JET plasmas has revealed the occurrence of additional magnetic oscillations in pulses characterized by large magnetic islands. The frequencies of these oscillations range from 5 to

20

kHz

, being well below the toroidal gap in the Alfvén continuum and of the same order as the low-frequency gap opened by plasma compressibility. The additional oscillations only appear when the magnetic island width exceeds a critical threshold, suggesting that the oscillations could tap their energy from the tearing mode (TM) by a non-linear coupling mechanism. A possible role of fast ions in the excitation process can be excluded, being the pulse phase considered in the observations characterized by very low additional heating. The calculation of the coupled Alfvén–acoustic continuum in toroidal geometry suggests the possibility of beta-induced Alfvén eigenmodes (BAEs) rather than beta-induced Alfvén–acoustic eigenmodes. As a main novelty compared to previous work, the analysis of the electron temperature profiles from electron cyclotron emission has shown the simultaneous presence of magnetic islands on different rational surfaces in pulses with multiple magnetic oscillations in the low-frequency gap of the Alfvén continuum. This observation supports the hypothesis of different BAE with toroidal mode number n = 1 associated with different magnetic islands. As another novelty, the observation of magnetic oscillations with n = 2 in the BAE range is reported for the first time in this work. Some pulses, characterized by slowly rotating magnetic islands, exhibit additional oscillations with n = 0, likely associated with geodesic acoustic modes (GAMs), and a cross-spectral bicoherence analysis has confirmed a non-linear interaction between TM, BAE and GAM, with the novelty of the observation of multiple triplets (twin BAEs plus GAM), due to the simultaneous presence of several magnetic islands in the plasma.
Characterization of ultra-intense laser in radiation damping regime using ponderomotive scattering
Authors: Holkundkar Amol R , Mackenroth Felix 
Published: January 2022

Abstract
We present a novel approach to analyzing phase-space distributions of electrons ponderomotively scattered off an ultra-intense laser pulse and comment on the implications for the thus conceivable in-situ laser-characterization schemes. To this end, we present fully relativistic test particle simulations of electrons scattered from an ultra-intense, counter-propagating laser pulse. The simulations unveil non-trivial scalings of the scattered electron distribution with the laser intensity, pulse duration, beam waist, and energy of the electron bunch. We quantify the found scalings by means of an analytical expression for the scattering angle of an electron bunch ponderomotively scattered from a counter-propagating, ultra-intense laser pulse, also accounting for radiation reaction (RR) through the Landau–Lifshitz (LL) model. For various laser and bunch parameters, the derived formula is in excellent quantitative agreement with the simulations. We also demonstrate how, in the radiation-dominated regime, a simple re-scaling of our model’s input parameter yields quantitative agreement with numerical simulations based on the LL model.
A nonlinear piezoelectric shunt absorber with 2:1 internal resonance: experimental proof of concept
Authors: Shami Zein Alabidin , Giraud-Audine Christophe , Thomas Olivier 
Published: January 2022

Abstract
An experimental proof of concept of a new semi-passive nonlinear piezoelectric shunt absorber, introduced theoretically in a companion article, is presented in this work. This absorber is obtained by connecting, through a piezoelectric transducer, an elastic structure to a resonant circuit that includes a quadratic nonlinearity. This nonlinearity is obtained by including in the circuit a voltage source proportional to the square of the voltage across the piezoelectric transducer, thanks to an analog multiplier circuit. Then, by tuning the electric resonance of the circuit to half the value of one of the resonances of the elastic structure, a two-to-one internal resonance is at hand. As a result, a strong energy transfer occurs from the mechanical mode to be attenuated to the electrical mode of the shunt, leading to two essential features: a nonlinear antiresonance in place of the mechanical resonance and an amplitude saturation. Namely, the amplitude of the elastic structure oscillations at the antiresonance becomes, above a given threshold, independent of the forcing level, contrary to a classical linear resonant shunt. This paper presents the experimental setup, the designed nonlinear shunt circuit and the main experimental results.
Measurement and data-assisted simulation of bit error rate in RQL circuits
Authors: Herr Quentin , Braun Alex , Brownfield Andrew , Rudman Ed , Dosch Dan , Josephsen Trent , Herr Anna 
Published: January 2022

Abstract
A circuit-simulation-based method is used to determine the thermally-induced bit error rate of superconducting Single Flux Quantum logic circuits. Simulations are used to evaluate the multidimensional Gaussian integral across noise current sources attached to the active devices. The method is data-assisted and has predictive power. Measurement determines the value of a single parameter, effective noise bandwidth, for each error mechanism. The errors in the distributed networks of comparator-free Reciprocal Quantum Logic nucleate across multiple Josephson junctions, so the effective critical current is about three times that of the individual devices. The effective noise bandwidth is only 6%–23% of the junction plasma frequency at a modest clock rate of 3.4 GHz, which is 1% of the plasma frequency. This analysis shows the ways measured bit error rate comes out so much lower than simplistic estimates based on isolated devices.