bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copy number-dependent DNA methylation of the Pyricularia oryzae MAGGY retrotransposon is triggered by DNA damage
Authors: Van Vu Ba , Nguyen Quyet , Kondo-Takeoka Yuki , Murata Toshiki , Kadotani Naoki , Thi Nguyen Giang , Arazoe Takayuki , Ohsato Shuichi , Nakayashiki Hitoshi 
Published: March 2021

AbstractTransposable elements are common targets for transcriptional and post-transcriptional gene silencing in eukaryotic genomes. However, the molecular mechanisms responsible for sensing such repeated sequences in the genome remain largely unknown. Here, we show that machinery of homologous recombination (HR) and RNA silencing play cooperative roles in copy number-dependent de novo DNA methylation of the retrotransposon MAGGY in the fungus Pyricularia oryzae. Genetic and physical interaction studies revealed that RecA domain-containing proteins, including P. oryzae homologs of Rad51, Rad55, and Rad57, together with an uncharacterized protein, Ddnm1, form complex(es) and mediate either the overall level or the copy number-dependence of de novo MAGGY DNA methylation, likely in conjunction with DNA repair. Interestingly, P. oryzae mutants of specific RNA silencing components (MoDCL1 and MoAGO2) were impaired in copy number-dependence of MAGGY methylation. Co-immunoprecipitation of MoAGO2 and HR components suggested a physical interaction between the HR and RNA silencing machinery in the process.
A combinatorial action of GmMYB176 and GmbZIP5 controls isoflavonoid biosynthesis in soybean (Glycine max)
Authors: Anguraj Vadivel Arun Kumaran , McDowell Tim , Renaud Justin B. , Dhaubhadel Sangeeta 
Published: March 2021

AbstractGmMYB176 is an R1 MYB transcription factor that regulates multiple genes in the isoflavonoid biosynthetic pathway, thereby affecting their levels in soybean roots. While GmMYB176 is important for isoflavonoid synthesis, it is not sufficient for the function and requires additional cofactor(s). The aim of this study was to identify the GmMYB176 interactome for the regulation of isoflavonoid biosynthesis in soybean. Here, we demonstrate that a bZIP transcription factor GmbZIP5 co-immunoprecipitates with GmMYB176 and shows protein–protein interaction in planta. RNAi silencing of GmbZIP5 reduced the isoflavonoid level in soybean hairy roots. Furthermore, co-overexpression of GmMYB176 and GmbZIP5 enhanced the level of multiple isoflavonoid phytoallexins including glyceollin, isowighteone and a unique O-methylhydroxy isoflavone in soybean hairy roots. These findings could be utilized to develop biotechnological strategies to manipulate the metabolite levels either to enhance plant defense mechanisms or for human health benefits in soybean or other economically important crops.
GmBTB/POZ promotes the ubiquitination and degradation of LHP1 to regulate the response of soybean to Phytophthora sojae
Authors: Zhang Chuanzhong , Cheng Qun , Wang Huiyu , Gao Hong , Fang Xin , Chen Xi , Zhao Ming , Wei Wanling , Song Bo , Liu Shanshan , Wu Junjiang , Zhang Shuzhen , Xu Pengfei 
Published: March 2021

AbstractPhytophthora sojaeis a pathogen that causes stem and root rot in soybean (Glycine max[L.] Merr.). We previously demonstrated that GmBTB/POZ, a BTB/POZ domain-containing nuclear protein, enhances resistance toP. sojaein soybean, via a process that depends on salicylic acid (SA). Here, we demonstrate that GmBTB/POZ associates directly with soybean LIKE HETEROCHROMATIN PROTEIN1 (GmLHP1) in vitro and in vivo and promotes its ubiquitination and degradation. Both overexpression and RNA interference analysis of transgenic lines demonstrate that GmLHP1 negatively regulates the response of soybean toP. sojaeby reducing SA levels and repressingGmPR1expression. The WRKY transcription factor gene,GmWRKY40, a SA-induced gene in the SA signaling pathway, is targeted by GmLHP1, which represses its expression via at least two mechanisms (directly binding to its promoter and impairing SA accumulation). Furthermore, the nuclear localization of GmLHP1 is required for the GmLHP1-mediated negative regulation of immunity, SA levels and the suppression ofGmWRKY40expression. Finally, GmBTB/POZ releases GmLHP1-regulatedGmWRKY40suppression and increases resistance toP. sojaeinGmLHP1-OEhairy roots. These findings uncover a regulatory mechanism by which GmBTB/POZ-GmLHP1 modulates resistance toP. sojaein soybean, likely by regulating the expression of downstream target geneGmWRKY40.
Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale
Authors: Jeffet Jonathan , Margalit Sapir , Michaeli Yael , Ebenstein Yuval 
Published: March 2021

Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method’s basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method’s resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
Effects of flux derating methods on torque production of fault‐tolerant polyphase inductiondrives
Authors: Tousizadeh Mahdi , Che Hang Seng , Abdel‐Khalik Ayman Samy , Munim W.N.W.A , Selvaraj Jeyraj , Abd. Rahim Nasrudin 
Published: March 2021

AbstractFault‐tolerant drives have been gaining increasing attention due to the need to enhance the reliability and robustness of electric drive systems, particularly for safety critical applications. However, in postfault control, it is often necessary to derate the machine, that is to reduce the torque and/or flux currents, to satisfy the current constraints of the power electronic devices. For induction motors, there are different approaches to quantify the current components in postfault operation while maintaining a stable operation within the current constraints. The efficiency enhancement of a faulted drive through flux current reduction is one of the methods reported in literature, however, the details of power components, that is, achievable torque and speed, are not addressed. This study broadly investigates the effect of flux and/or torque current partitioning on postfault capability of polyphase (three and more phases) induction machines in terms of achievable torque and speed. It is demonstrated that the magnetising inductance characteristics, which depend on the machine design and its power rating, have a profound effect on the choice of postfault current partitioning, and hence the machine performance. Theoretical discussion is supported with experimental verification using three‐phase and symmetrical six‐phase induction motors.
AMBCR: Low‐light image enhancement via attention guided multi‐branch construction and Retinex theory
Authors: Li Miao , Zhou Dongming , Nie Rencan , Xie Shidong , Liu Yanyu 
Published: March 2021

AbstractDue to different lighting environments and equipment limitations, low‐light images have high noise, low contrast and unobvious colours. The main purpose of low‐light image enhancement is to preserve the details and suppress noise as much as possible while improving the contrast of the image. Here, different networks are first combined to construct a multi‐branch module for features extraction, and use the module and Retinex theory to extract the reflection map of the image. Then an attention mechanism is introduced into the multi‐branch construction to balance the feature weight of each branch, and get the final result by the reconstruction module. The Retinex theory is used to calculate the L1 loss and the gradient loss for the intermediate feature map of the entire model to train our framework. The entire process is completed in an end‐to‐end‐way, which avoids the hand‐crafted reconstruction rules and reduces the workload. What's more, a large number of experiments demonstrate that the proposed framework performs better results than state‐of‐the‐art algorithms in both quantitative and qualitative evaluations of image enhancement.
A robust sperm cell tracking algorithm using uneven lighting image fixing and improved branch and bound algorithm
Authors: Alhaj Alabdulla Ahmad , Haşıloğlu Abdulsamet , Hicazi Aksu Emrah 
Published: March 2021

AbstractAn accurate and robust sperm cells tracking algorithm that is able to detect and track sperm cells in videos with high accuracy and efficiency is presented. It is fast enough to process approximately 30 frames per second. It can find the correct path and measure motility parameters for each sperm. It can also adapt with different types of images coming from different cameras and bad recording conditions. Specifically, a new way is offered to optimize uneven lighting images to improve sperm cells detection which gives us the ability to get more accurate tracking results. The shape of each detected object is used to specify collided sperms and utilized dynamic gates which become bigger and smaller according to the sperm cell's speed. For assigning tracks to the detected sperm cells positions an improved version of branch and bound algorithm which is faster than the normal one is offered. This sperm cells tracking algorithm outperforms many of the previous algorithms as it has lower error rate in both sperm detection and tracking. It is compared with six other algorithms, and it gives lower tracking error rates. This method will allow doctors and researchers to obtain sperm motility data instantly and accurately.
Distributed adaptive robust H∞ control of intelligent‐connected electric vehicles platooning subject to communication delay
Authors: Wang Jingyao , Zheng Huaqing , Guo Jinghua , Fan Jingjing , Li Keqiang 
Published: March 2021

AbstractWith an aim to improve the performances of intelligent‐connected electric vehicle platoon with communication delay, we present a distributed adaptive robust control scheme in this paper. First, the longitudinal non‐linear dynamic model of vehicle i is established, and in order to reduce the difficulty of analysing such a non‐linear system, a simplified uncertain dynamic model of vehicle i is obtained via a feedback linearisation method. Second, a novel distributed state‐feedback robust platoon controller is designed by using the relative information between neighbouring electric vehicles. Third, we derive the sufficient condition that the presented distributed robust platoon controller exists under the influence of communication delay. This condition is given in the form of a linear matrix inequality, which is low dimensional and whose dimension is independent of the length of the intelligent electric vehicle platoon. Furthermore, the closed‐loop platoon system controlled by the presented controller is proved stable subject to communication delay by using the Lyapunov stability theory. In addition, an adaptive control term is added to the robust platoon controller. We present the sufficient condition that such a modified controller exists and prove the platoon string stability. Finally, the effectiveness of the presented adaptive robust platoon control scheme is verified by conducting numerical simulation tests.
Magnetic signatures on mixed-mode frequencies
Authors: Bugnet L. , Prat V. , Mathis S. , Astoul A. , Augustson K. , García R. A. , Mathur S. , Amard L. , Neiner C. 
Published: March 2021

Context. The discovery of moderate differential rotation between the core and the envelope of evolved solar-like stars could be the signature of a strong magnetic field trapped inside the radiative interior. The population of intermediate-mass red giants presenting surprisingly low-amplitude mixed modes (i.e. oscillation modes that behave as acoustic modes in their external envelope and as gravity modes in their core) could also arise from the effect of an internal magnetic field. Indeed, stars more massive than about 1.1 solar masses are known to develop a convective core during their main sequence. The field generated by the dynamo triggered by this convection could be the progenitor of a strong fossil magnetic field trapped inside the core of the star for the remainder of its evolution.
Aims. Observations of mixed modes can constitute an excellent probe of the deepest layers of evolved solar-like stars, and magnetic fields in those regions can impact their propagation. The magnetic perturbation on mixed modes may therefore be visible in asteroseismic data. To unravel which constraints can be obtained from observations, we theoretically investigate the effects of a plausible mixed axisymmetric magnetic field with various amplitudes on the mixed-mode frequencies of evolved solar-like stars.
Methods. First-order frequency perturbations due to an axisymmetric magnetic field were computed for dipolar and quadrupolar mixed modes. These computations were carried out for a range of stellar ages, masses, and metallicities.
Conclusions. We show that typical fossil-field strengths of 0.1 − 1 MG, consistent with the presence of a dynamo in the convective core during the main sequence, provoke significant asymmetries on mixed-mode frequency multiplets during the red giant branch. We provide constraints and methods for the detectability of such magnetic signatures. We show that these signatures may be detectable in asteroseismic data for field amplitudes small enough for the amplitude of the modes not to be affected by the conversion of gravity into Alfvén waves inside the magnetised interior. Finally, we infer an upper limit for the strength of the field and the associated lower limit for the timescale of its action in order to redistribute angular momentum in stellar interiors.
Enlightening Diagnosis and Differential Diagnosis of Dental Fluorosis—A Hidden Entity in a Crowd
Authors: Patidar Deepika , Sogi Suma , Patidar Dinesh Chand , Sharma Atul , Jain Mansi , Prasad Priyanka 
Published: March 2021

Abstract
Aim To provide diagnosis as well as differential diagnosis of dental fluorosis.
Background Dental fluorosis is a developmental defect of enamel, due to consecutive exposures of tooth during the formative stage of development to the higher concentration of fluoride, resulting in enamel with lesser mineral content and enhanced porosity. Several epidemiological indices have been utilized for diagnosis and assessment of dental fluorosis on the basis of clinical appearance. Fluorosis of the deciduous teeth occurs less commonly and is milder than that of permanent teeth.
Highlights The diagnostic difficulties are usually associated between fluorotic and nonfluoride opacities. A complete history of the clinical condition, teeth affected with specific areas, pattern of lesion, color and its method of detection are the few important diagnostic criteria for differentiating dental fluorosis from nonfluoride discolorations of the teeth.
Conclusion This review article has enlightened the diagnosis and differential diagnosis of dental fluorosis among various nonfluoride tooth discolorations. A correct diagnosis results in an appropriate and early management of dental fluorosis and plays an important role in oral epidemiology and public health.
Cryogenic suspension design for a kilometer-scale gravitational-wave detector
Authors: Ushiba Takafumi , Akutsu Tomotada , Araki Sakae , Bajpai Rishabh , Chen Dan , Craig Kieran , Enomoto Yutaro , Hagiwara Ayako , Haino Sadakazu , Inoue Yuki , Izumi Kiwamu , Kimura Nobuhiro , Kumar Rahul , Michimura Yuta , Miyoki Shinji , Murakami Iwao , Namai Yoshikazu , Nakano Masayuki , Ohashi Masatake , Okutomi Koki , Shishido Takaharu , Shoda Ayaka , Somiya Kentaro , Suzuki Toshikazu , Takada Suguru , Takahashi Masahiro , Takahashi Ryutaro , Terashima Shinichi , Tomaru Takayuki , Travasso Flavio , Ueda Ayako , Vocca Helios , Yamada Tomohiro , Yamamoto Kazuhiro , Zeidler Simon 
Published: March 2021

Abstract
We report the mirror suspension design for large-scale cryogenic gravitational wave telescope, KAGRA, during bKAGRA phase 1. Mirror thermal noise is one of the fundamental noises for room-temperature gravitational-wave detectors such as Advanced LIGO and Advanced Virgo. Thus, reduction of thermal noise is required for further improvement of their sensitivity. One effective approach for reducing thermal noise is to cool the mirrors. There are many technical challenges that must be overcome to cool the mirrors, such as cryocooler induced vibrations, thermal drift in suspensions, and reduction in duty cycling due to the increased number of potential failure mechanisms. Our mirror suspension has a black coating that makes radiative cooling more efficient. For conduction cooling, we developed ultra high purity aluminum heat links, which yield high thermal conductivity while keeping the spring constant sufficiently small. A unique inclination adjustment system, called moving mass, is used for aligning the mirror orientation in pitch. Photo-reflective displacement sensors, which have a large range, are installed for damping control on marionette recoil mass and intermediate recoil mass. Samarium cobalt magnets are used for coil-magnet actuators to prevent significant change of magnetism between room temperature and cryogenic temperature. In this paper, the design of our first cryogenic payload and its performance during bKAGRA phase 1 are discussed.
Lattice elasticity, waves and temperature from an interaction potential
Authors: Ocaya R O 
Published: March 2021

Abstract
Kinetic theory is taught to first-year students of physics as a plausible account of thermal equilibrium on the microscopic scale. However, it does not adequately clarify important properties like elasticity, lattice waves, phonons, optical oscillations, bandgap and so on, that are postulated through atomic vibrations. In this article, we apply simple computational tools in four computational experiments to study the effects of the vibrations of 373 atoms of a face-centered cubic crystal such as copper. We also discuss the perturbation modelling approach, the Sutton–Chen potential, and discrete integration. The experiments have different aims e.g. determining the steady-state atom arrangement starting from an arbitrarily specified cluster, the elasticity, the ensuing wave motion, lattice resonance, acoustic properties, and temperature rise. The calculated results agree well with their literature values.
Extrapolating from neural network models: a cautionary tale
Authors: Pastore A , Carnini M 
Published: March 2021

Abstract
We present three different methods to estimate error bars on the predictions made using a neural network (NN). All of them represent lower bounds for the extrapolation errors. At first, we illustrate the methods through a simple toy model, then, we apply them to some realistic case related to nuclear masses. By using theoretical data simulated either with a liquid-drop model or a Skyrme energy density functional, we benchmark the extrapolation performance of the NN in regions of the Segrè chart far away from the ones used for the training and validation. Finally, we discuss how error bars can help identifying when the extrapolation becomes too uncertain and thus not reliable.
First-principles study of the liquid and amorphous phases of Sb2Te phase change memory material
Authors: Kang Lei , Chen Leng 
Published: March 2021

Abstract
We have investigated the local structure of liquid and amorphous phases of Sb2Te phase change memory material by the means of density functional theory-molecular dynamics simulations. The models of liquid and amorphous states were generated by quenching from the melt. The results show that the local environment of liquid Sb2Te is a mixed bonding geometry, where the average coordination numbers (CNs) of Sb and Te atoms are 4.93 and 4.23, respectively. Compared with crystalline state, there are more Sb–Sb bonds (∼53%) and less Sb–Te bonds (∼42%) with the presence of Te–Te bonds (∼5%) in liquid Sb2Te. Therefore, the formation of homopolar bonds and the breaking of heteropolar bonds are important structural transformations in melt process. For amorphous Sb2Te, the average CNs of Sb and Te atoms are 4.54 and 3.57, respectively. They are mostly in an octahedral environment, similar to the case in crystalline phase. The fractions of Sb–Sb, Te–Te, and Sb–Te bonds are ∼52%, ∼2%, and ∼46%, respectively. Thus, the increase in the fraction of octahedron accompanied with the decrease in average CN is the major structural changes in quenching process. Furthermore, the octahedral geometry in both the crystalline and amorphous Sb2Te increases the local structural similarity, facilitating the rapid low-energy crystallization.
Improved synaptic functionalities of Li-based nano-ionic synaptic transistor with ultralow conductance enabled by Al2O3 barrier layer
Authors: Lee Kyumin , Kwak Myounghoon , Choi Wooseok , Lee Chuljun , Lee Jongwon , Noh Sujung , Lee Jisung , Lee Hansaem , Hwang Hyunsang 
Published: March 2021

Abstract
In this study, we investigated the effect of an Al2O3 barrier layer in an all-solid-state inorganic Li-based nano-ionic synaptic transistor (LST) with Li3PO4 electrolyte/WO
x
channel structure. Near-ideal synaptic behavior in the ultralow conductance range (∼50 nS) was obtained by controlling the abrupt ion migration through the introduction of a sputter-deposited thin (∼3 nm) Al2O3 interfacial layer. A trade-off relationship between the weight update linearity and on/off ratio with varying Al2O3 layer thickness was also observed. To determine the origin of the Al2O3 barrier layer effects, cyclic voltammetry analysis was conducted, and the optimal ionic diffusivity and mobility were found to be key parameters in achieving ideal synaptic behavior. Owing to the controlled ion migration, the retention characteristics were considerably improved by the Al2O3 barrier. Finally, a highly improved pattern recognition accuracy (83.13%) was achieved using the LST with an Al2O3 barrier of optimal thickness.