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Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea (MAY, 10.1038/s41588-024-01760-4, 2024)

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NATURE GENETICS 2024年第6期56卷 1320-1320页

作者： Khan, Aamir W. Garg, Vanika Sun, Shuai Gupta, Saurabh Dudchenko, Olga Roorkiwal, Manish Chitikineni, Annapurna Bayer, Philipp E. Shi, Chengcheng Upadhyaya, Hari D. Bohra, Abhishek Bharadwaj, Chellapilla Mir, Reyazul Rouf Baruch, Kobi Yang, Bicheng Coyne, Clarice J. Bansal, Kailash C. Nguyen, Henry T. Ronen, Gil Aiden, Erez Lieberman Veneklaas, Erik Siddique, Kadambot H. M. Liu, Xin Edwards, David Varshney, Rajeev K. Center of Excellence in Genomics and Systems Biology International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru India School of Biological Sciences University of Western Australia Perth Western Australia Australia Division of Plant Science and Technology University of Missouri Columbia MO USA Centre for Crop and Food Innovation WA State Agricultural Biotechnology Centre Food Futures Institute Murdoch University Murdoch Western Australia Australia BGI Research Qingdao China Curtin Health Innovation Research Institute (CHIRI) Curtin Medical School Curtin University Perth Western Australia Australia Department of Molecular and Human Genetics Center for Genome Architecture Baylor College of Medicine Houston TX USA Khalifa Center for Genetic Engineering and Biotechnology United Arab Emirates University Al-Ain United Arab Emirates Plant Genome Mapping Laboratory The University of Georgia Athens GA USA ICAR- Indian Agricultural Research Institute (IARI) New Delhi India Division of Genetics and Plant Breeding Faculty of Agriculture (FoA) SKUAST-KashmirWadura Campus Kashmir India NRGene Ltd Park HaMada Ness Ziona Israel BGI-Australia Herston Queensland Australia USDA-ARS Plant Germplasm Introduction and Testing Washington State University Pullman WA USA National Academy of Agricultural Sciences (NAAS) NASC Complex New Delhi India UWA Institute of Agriculture and School of Agriculture and Environment University of Western Australia Perth Western Australia Australia BGI Research Shenzhen China

Chickpea (Cicer arietinum L.)—an important legume crop cultivated in arid and semiarid regions—has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.

关键词： Genome assembly algorithms Sequence annotation

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Charge-Sign Dependent Cosmic-Ray Modulation Observed with the Calorimetric Electron Telescope on the International Space Station

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Physical Review Letters 2023年第21期130卷 211001-211001页

作者： O. Adriani Y. Akaike K. Asano Y. Asaoka E. Berti G. Bigongiari W. R. Binns M. Bongi P. Brogi A. Bruno J. H. Buckley N. Cannady G. Castellini C. Checchia M. L. Cherry G. Collazuol G. A. de Nolfo K. Ebisawa A. W. Ficklin H. Fuke S. Gonzi T. G. Guzik T. Hams K. Hibino M. Ichimura K. Ioka W. Ishizaki M. H. Israel K. Kasahara J. Kataoka R. Kataoka Y. Katayose C. Kato N. Kawanaka Y. Kawakubo K. Kobayashi K. Kohri H. S. Krawczynski J. F. Krizmanic P. Maestro P. S. Marrocchesi A. M. Messineo J. W. Mitchell S. Miyake A. A. Moiseev M. Mori N. Mori H. M. Motz K. Munakata S. Nakahira J. Nishimura S. Okuno J. F. Ormes S. Ozawa L. Pacini P. Papini B. F. Rauch S. B. Ricciarini K. Sakai T. Sakamoto M. Sasaki Y. Shimizu A. Shiomi P. Spillantini F. Stolzi S. Sugita A. Sulaj M. Takita T. Tamura T. Terasawa S. Torii Y. Tsunesada Y. Uchihori E. Vannuccini J. P. Wefel K. Yamaoka S. Yanagita A. Yoshida K. Yoshida W. V. Zober Department of Physics University of Florence Via Sansone 1 - 50019 Sesto Fiorentino Italy INFN Sezione di Firenze Via Sansone 1 - 50019 Sesto Fiorentino Italy Waseda Research Institute for Science and Engineering Waseda University 17 Kikuicho Shinjuku Tokyo 162-0044 Japan JEM Utilization Center Human Spaceflight Technology Directorate Japan Aerospace Exploration Agency 2-1-1 Sengen Tsukuba Ibaraki 305-8505 Japan Institute for Cosmic Ray Research The University of Tokyo 5-1-5 Kashiwa-no-Ha Kashiwa Chiba 277-8582 Japan Institute of Applied Physics (IFAC) National Research Council (CNR) Via Madonna del Piano 10 50019 Sesto Fiorentino Italy Department of Physical Sciences Earth and Environment University of Siena via Roma 56 53100 Siena Italy INFN Sezione di Pisa Polo Fibonacci Largo B. Pontecorvo 3 - 56127 Pisa Italy Department of Physics and McDonnell Center for the Space Sciences Washington University One Brookings Drive Saint Louis Missouri 63130-4899 USA Heliospheric Physics Laboratory NASA/GSFC Greenbelt Maryland 20771 USA Center for Space Sciences and Technology University of Maryland Baltimore County 1000 Hilltop Circle Baltimore Maryland 21250 USA Astroparticle Physics Laboratory NASA/GSFC Greenbelt Maryland 20771 USA Center for Research and Exploration in Space Sciences and Technology NASA/GSFC Greenbelt Maryland 20771 USA Department of Physics and Astronomy Louisiana State University 202 Nicholson Hall Baton Rouge Louisiana 70803 USA Department of Physics and Astronomy University of Padova Via Marzolo 8 35131 Padova Italy INFN Sezione di Padova Via Marzolo 8 35131 Padova Italy Institute of Space and Astronautical Science Japan Aerospace Exploration Agency 3-1-1 Yoshinodai Chuo Sagamihara Kanagawa 252-5210 Japan Kanagawa University 3-27-1 Rokkakubashi Kanagawa Yokohama Kanagawa 221-8686 Japan Faculty of Science and Technology Graduate School of Science and Technology Hirosaki University 3 Bunkyo Hirosaki Aomori 036

We present the observation of a charge-sign dependent solar modulation of galactic cosmic rays (GCRs) with the Calorimetric Electron Telescope onboard the International Space Station over 6 yr, corresponding to the positive polarity of the solar magnetic field. The observed variation of proton count rate is consistent with the neutron monitor count rate, validating our methods for determining the proton count rate. It is observed by the Calorimetric Electron Telescope that both GCR electron and proton count rates at the same average rigidity vary in anticorrelation with the tilt angle of the heliospheric current sheet, while the amplitude of the variation is significantly larger in the electron count rate than in the proton count rate. We show that this observed charge-sign dependence is reproduced by a numerical “drift model” of the GCR transport in the heliosphere. This is a clear signature of the drift effect on the long-term solar modulation observed with a single detector.

关键词： Cosmic ray composition & spectra Cosmic ray propagation Cosmic ray sources Cosmic rays & astroparticles

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Quartz Crystal Microbalance Sensor Based on Peptide Anchored Single-Walled Carbon Nanotubes for Highly Selective TNT Explosive Detection

Quartz Crystal Microbalance Sensor Based on Peptide Anchored...

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IEEE Sensors

作者： Jin Wang Masayoshi Tanaka Mina Okochi Graduate School of Interdisciplinary Science and Engineering in Health Systems Okayama University Okayama Japan Tokyo Institute of Technology Tokyo Japan

ISBN: (数字)9781728168012

ISBN: (纸本)9781728168012;9781728168029

In this study, quartz crystal microbalance (QCM) sensor based on 2, 4, 6-trinitrotoluene (TNT) recognition peptide functionalized single-walled carbon nanotubes (SWCNTs) for TNT explosive detection was developed. The SWCNTs were immobilized on the self-assembled monolayer (SAM) cysteamine modified QCM gold-chip surface. Through π-stacking interaction, the specific TNT recognition peptide (named TNTHCDR3) was anchored on the SWCNTs surface. The results revealed that the peptide-SWCNTs hybrid modified QCM sensor offered highly selective detection of TNT explosive.

关键词： Explosives Peptides Gold Carbon nanotubes Chemical industry Quartz crystals Potassium

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Detection of Error-Related Potentials during the Robot Navigation Task by Humans

Detection of Error-Related Potentials during the Robot Navig...

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Computational Intelligence (ICCI),International Conference on

作者： Kentaro Nakamura Kiyohisa Natsume Graduate School of Life Science and Systems Engineering Kyushu Institute of Technology 2-4 Hibikino Wakamatsu-ku Kitakyushu Japan

ISBN: (数字)9781728184081

ISBN: (纸本)9781728184104

We have developed a system in which humans and autonomous robots can collaborate with each other. In the system, robots often exhibit behaviors not intended by the humans. To avoid this situation, it is necessary to convey the humans' will to the robots. To do this, we have focused on electroencephalogram (EEG) error-related Potential (ErrP), using which we can detect the ErrP when a person observes an error by a robot. In our previous study, we recorded the ErrPs from subjects in a maze task when a robot moved in directions that the subjects did not intend. However, the mean epoch number of the ErrP per subject was small. It is necessary to collect a large number of data using a deep neural network. Generally, medical data and physiological data recorded from people are small. Few Shot Learning is necessary for a small number of data. Thus, Siamese neural networks have been proposed. In this study, we combined the Siamese deep neural network with a support vector machine to discriminate between EEG data with an error (ErrP) and that without an error. Consequently, we could obtain >70% of the maximum classification accuracy among subjects and 0.60 ± 0.22 of the area under curve.

关键词： Support vector machines Frequency-domain analysis Neural networks Electroencephalography Physiology Task analysis Robots

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Synergistic phonon scattering in epitaxial silicon multilayers with germanium nanodot inclusions

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Physical Review B 2021年第5期104卷 054301-054301页

作者： Takafumi Oyake Lei Feng Makoto Kashiwagi Takuma Shiga Takuma Hori Suto Yamasaka Yoshiaki Nakamura Junichiro Shiomi Department of Mechanical Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan Department of Chemistry and Biological Science Aoyama Gakuin University 5-10-1 Fuchinobe Chuo-ku Sagamihara Kanagawa 252-5258 Japan Department of Mechanical Systems Engineering Tokyo University of Agriculture and Technology 2-24-16 Nakacho Koganei Tokyo 184-0012 Japan Graduate School of Engineering Science Osaka University 1-3 Machikaneyama Toyonaka Osaka 560-8531 Japan

Temperature-dependent thermal conductivity of epitaxial silicon (Si)/ultrathin silica multilayers film with epitaxial germanium (Ge) nanodot inclusions is measured over the range of temperature from 50 K to room temperature using time-domain thermoreflectance. The measured thermal conductivity with 5-nm Ge nanodots is much smaller than the reported values for Si/Ge superlattices, bulk SiGe, and nanostructured SiGe in the entire temperature range. The thermal conductivity of the film is analyzed with a kinetic model incorporating multiple phonon scattering processes, where intrinsic three-phonon scattering inside the Si layers is calculated by first principles, boundary scattering at the ultrathin silica layer is calculated by the atomistic Green's function, and scattering by the Ge nanodots is approximated with nanovoids. The analysis reveals that summing the multiple scattering rates by Matthiessen's rule cannot explain the extremely low thermal conductivity. The Monte Carlo ray tracing calculation that incorporates the multiple scattering effect reveals that the synergistic effect of ultrathin silica interfaces and Ge nanodots enhances phonon scattering. This suggests the merit in synergistically designing multiple nanostructures to reduce thermal conductivity, which is beneficial for developing thermoelectric materials.

关键词： Lattice dynamics Phonons Thermal conductivity Nanostructures

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A Stability Analysis of Haptic systems by Using Difference Diffrential Equation from the view point of characteristic equation 2

A Stability Analysis of Haptic Systems by Using Difference D...

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2nd World Symposium on Communication engineering, WSCE 2019

作者： Watanabe, Hitoshi Ishibashi, Yutaka Huang, Pingguo Tokyo University of Science Faculty of Engineering Tokyo Japan Nagoya Institute of Technology Graduate School of Engineering Nagoya Japan Seijoh University Faculty of Business Management Tokai Japan

ISBN: (纸本)9781728153292

In the remote robot systems using haptic communication under communication delays, there is a problem of instability of operations or behaviors. For solving the problem, we have introduced a method using 'resistance' which is proportion to the velocity and investigated the theoretical method to analyze the mechanism by using difference differential equation. However, in the former investigation, we have focused on the motion of approach to target position and mechanical howling has not been analyzed adequately. This paper shows the possibility of explanation of mechanical howling by using difference differential equation and investigates the stability condition from the view point of characteristic equation. As a result, we shew that the resistance has the effect of narrowing the stability range for approaching target position but enlarging the stability range for mechanical howling. Moreover, empirical data is examined by the method. © 2019 IEEE.

关键词： Differential equations

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Probabilistic Margins for Instance Reweighting in Adversarial Training

arXiv

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arXiv 2021年

作者： Wang, Qizhou Liu, Feng Han, Bo Liu, Tongliang Gong, Chen Niu, Gang Zhou, Mingyuan Sugiyama, Masashi Department of Computer Science Hong Kong Baptist University Hong Kong DeSI Lab Australian Artificial Intelligence Institute University of Technology Sydney Australia TML Lab School of Computer Science Faculty of Engineering The University of Sydney Australia PCA Lab Key Lab of Intelligent Perception and Systems for High-Dimensional Information of MoE Jiangsu Key Lab of Image and Video Understanding for Social Security School of Computer Science and Engineering Nanjing University of Science and Technology China McCombs School of Business The University of Texas at Austin United States Graduate School of Frontier Sciences The University of Tokyo Japan

Reweighting adversarial data during training has been recently shown to improve adversarial robustness, where data closer to the current decision boundaries are regarded as more critical and given larger weights. However, existing methods measuring the closeness are not very reliable: they are discrete and can take only a few values, and they are path-dependent, i.e., they may change given the same start and end points with different attack paths. In this paper, we propose three types of probabilistic margin (PM), which are continuous and path-independent, for measuring the aforementioned closeness and reweighting adversarial data. Specifically, a PM is defined as the difference between two estimated class-posterior probabilities, e.g., such a probability of the true label minus the probability of the most confusing label given some natural data. Though different PMs capture different geometric properties, all three PMs share a negative correlation with the vulnerability of data: data with larger/smaller PMs are safer/riskier and should have smaller/larger weights. Experiments demonstrated that PMs are reliable and PM-based reweighting methods outperformed state-of-the-art counterparts. Copyright © 2021, The Authors. All rights reserved.

关键词： Probability

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Concept Study of a Self-localization System for Snow-covered Roads Using a Four-layer Laser Scanner

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Automotive Innovation 2019年第2期2卷 110-120页

作者： Tetsushi Mimuro Naoya Taniguchi Hiroyuki Takanashi Faculty of Systems Science and Technology Akita Prefectural University84-4 EbinokuchiYurihonjoAkita 015-0055Japan Graduate School of Systems Science and Technology Akita Prefectural University84-4 EbinokuchiYurihonjoAkita 015-0055Japan College of Engineering Nihon University1 NakagawaraTokusadaTamuramachiKoriyamaFukushima 963-8642Japan

Many advanced driver assistance systems have entered the market,and automated driving technologies have been *** of them may not work in adverse weather conditions.A forward-looking camera,for example,is the most popular system used for lane detection but does not work for a snow-covered *** present paper proposes a self-localization system for snowy roads when the roadsides are covered with *** system employs a four-layer laser scanner and onboard sensors and uses only pre-existing roadside snow poles provided for drivers in a snowy region without any other road *** the landscape greatly changes in a short time during a snowstorm and snow removal works,it is necessary to restrict the landmarks used for self-localization to tall objects,like snow poles.A system incorporating this technology will support a driver’s efforts to keep to a lane even in a heavy snowstorm.

关键词： Advanced driver assistance systems Adverse weather Laser scanner Self-localization system

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Neural mechanisms of top-down divided and selective spatial attention in visual and auditory perception

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Brain science Advances 2023年第2期9卷 95-113页

作者： Zhongtian Guan Meng Lin Qiong Wu Jinglong Wu Kewei Chen Hongbin Han Dehua Chui Xu Zhang Chunlin Li School of Biomedical Engineering Capital Medical UniversityBeijing 100069China Beijing Advanced Innovation Center for Big Data-based Precision Medicine Capital Medical UniversityBeijing 100069China Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application Capital Medical UniversityBeijing 100069China Peking University First Hospital Beijing 100034China Biomedical Engineering Laboratory Graduate School of Natural Science and TechnologyOkayama University3-1-1 Tsushima-nakaOkayamaJapan Key Laboratory of Biomimetic Robots and Systems Ministry of EducationBeijing Institute of TechnologyBeijing 100081China Computational Image Analysis Banner Alzheimer’s Institute and Banner Good Samaritan Medical CentrePET CentrePhoenixAZ 85006USA Radiology Peking University Third HospitalBeijing 100191China Neuroscience Research Institute/Peking University Third Hospital Beijing 100191China

Top-down attention mechanisms require the selection of specificobjects or locations;however,the brain mechanism involved when attention is allocated across different modalities is not well *** aim of this study was to use functional magnetic resonance imaging to define the neural mechanisms underlyingdivided and selective spatial attention.A concurrent audiovisual stimulus was used,and subjects were prompted to focus on a visual,auditory and audiovisual stimulus in a Posner *** results confirmed the better performance of selectiveattention compared to devided *** found differences in the activation level of the frontoparietal network,visual/auditorycortex,the putamen and the salience network under differentattention *** further used Granger causality(GC)toexplore effective connectivity differences between *** in GC connectivity between visual and auditory selective tasksreflected the visual dominance effect under spatial *** addition,our results supported the role of the putamen inredistributing attention and the functional separation of the *** summary,we explored the audiovisual top-down allocation of attention and observed the differences in neuralmechanisms under endogenous attention modes,which revealedthe differences in cross-modal expression in visual and auditory attention under attentional modulation.

关键词： top-down mechanism divided spatial attention selective spatial attention fMRI Granger causality

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Distributing Potential Games on Graphs Part I. Game formulation

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IFAC-PapersOnLine 2020年第2期53卷 6697-6702页

作者： Mohamed I. El-Hawwary Jonas Mårtensson Division of Decision and Control Systems School of Electrical Engineering & Computer Science KTH Royal Institute of Technology SE-100 44 Stockholm Sweden Department of Electrical Power Engineering Faculty of Engineering Cairo University Giza 12613 Egypt

The paper presents the problem of distributing potential games over communication graphs. Suppose a potential game can be designed for a group of agents (players) where each has access to all others’ actions (strategies). The paper shows how to design a corresponding potential game for these agents if the full information assumption is replaced with communication over a network depicted by undirected graphs with certain properties. A state-based formulation for potential games is utilized. This provides degrees of freedom to handle the previous information limitation. Notions of Nash’s equilibria for the developed game (called here distributed potential game) are presented, and relations between these equilibria and those of the full information game are studied. In part II of the paper learning Nash equilibria for the newly developed game is studied. The development focuses on providing a way to utilize available algorithms of the full information game. The motivation for the results comes from a platoon matching problem for heavy duty vehicles. Utilizing the newly developed distributed game, recent results based on potential games can be extended, providing a basis for an on-the-go strategy where platoon matching on road networks can be solved locally.

关键词： Potential games distributed optimization multi-agents

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