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Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq

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American Journal of Molecular Biology 2017年第4期7卷 153-168页

作者： Ak.ra S. Hirao Yoshihik. Onda Rie shimizu-Inatsugi Jun Sese k.ntaro k. shimizu Tanak. k.nta Sugadaira Research Station Mountain Science Center University of Tsukuba Ueda Japan Sugadaira Montane Research Center University of Tsukuba Ueda Japan Cellulose Production Research Team Biomass Engineering Research Division RIKEN Center for Sustainable Resource Science Yokohama Japan k.hara Institute for Biological Research Yokohama City University Yokohama Japan Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland Artificial Intelligence Research Center National Institute of Advanced Industrial Science and Technology Tokyo Japan

Population genetics studies of allopolyploid species lag behind those of diploid species because of practical difficulties in analysis of homeologs-duplicated gene copies originating from hybridized parental species. Pool-Seq, i.e. massive parallel sequencing of pooled individuals, has high potential for detecting nucleotide polymorphisms within and among multiple populations;however, its use has been limited to diploid species. We applied Pool-Seq to an allopolyploid species by developing a bioinformatic pipeline that assigns reads to each homeolog as well as to each polymorphic allele within each homeolog. We simultaneously sequenced eight genes from twenty individuals from each of 24 populations, and found over 100 polymorphic sites in each homeolog. For two sites, we estimated allele frequencies using the number of reads and then validated these estimations by mak.ng individual-based estimations. Pool-Seq using our bioinformatic pipeline allows efficient evaluation of nucleotide polymorphisms in a large number of individuals, even in allopolyploid species.

关键词： Arabidopsis k.mchatica Allele Frequency Homeolog Individual-Based Genotyping Massive Parallel Sequencing

Space–time finite element method with domain reduction techniques for dynamic soil–structure interaction problems

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International Journal of Mechanical System Dynamics 2024年第2期4卷 117-130页

作者： Vik.s Sharma Shion shimizu k.zunori Fujisawa Division of Environmental Science and Technology Graduate School of AgricultureKyoto UniversityKyotoJapan

Design of earth structures,such as dams,tunnels,and embank.ents,against the vibrational loading caused by high-speed trains,road traffic,underground explosions,and,more importantly,earthquak. motion,demands solutions of the dynamic soil–structure Interaction(SSI)*** paper presents a velocity-based space–time finite element procedure,v-ST/finite element method(FEM),to solve dynamic SSI *** main goal of this study is to present the computation details of implementing viscous boundary conditions of Lysmer–k.hlemeyer to truncate the unbounded soil ***,additional time-dependent boundary conditions,in terms of the free-field response,are included to facilitate energy flow from the far field to the computation domain at the vertical truncated *** the FEM,seismic input motion is applied to an effective nodal force vector,which can be obtained explicitly in the numerical ***,the response of a concrete gravity dam resting on an elastic half-space to the horizontal component of earthquak. motion is computed and successfully compared with the results of semidiscrete FEM using the Newmark.βmethod.

关键词： absorbing boundary domain reduction FEM soil-structure interactions space-time

LiDAR-based estimation of bounding box coordinates using Gaussian process regression and particle swarm optimization

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Biomimetic Intelligence & Robotics 2024年第1期4卷 24-35页

作者： Vinodha k. E.S.Gopi Tushar Agnibhoj Department of Electronics and Communication Engineering National Institute of Technology TiruchirappalliTamil Nadu620015India

Camera-based object track.ng systems in a given closed environment lack.privacy and *** this study,light detection and ranging(LiDAR)was applied to track.objects similar to the camera track.ng in a closed environment,guaranteeing privacy and *** primary objective was to demonstrate the efficacy of the proposed technique through carefully designed experiments conducted using two *** Scenario I,the study illustrates the capability of the proposed technique to detect the locations of multiple objects positioned on a flat surface,achieved by analyzing LiDAR data collected from several locations within the closed *** II demonstrates the effectiveness of the proposed technique in detecting multiple objects using LiDAR data obtained from a single,fixed ***-time experiments are conducted with human subjects navigating predefined *** individuals move within an environment,while LiDAR,fixed at the center,dynamically track. and identifies their locations at multiple *** demonstrate that a single,strategically positioned LiDAR can adeptly detect objects in motion around ***,this study provides a comparison of various regression techniques for predicting bounding box *** process regression(GPR),combined with particle swarm optimization(PSO)for prediction,achieves the lowest prediction mean square error of all the regression techniques examined at *** tuning of GPR using PSO significantly minimizes the regression *** of the experiment pave the way for its extension to various real-time applications such as crowd management in malls,surveillance systems,and various Internet of Things scenarios.

关键词： LiDAR Data acquisition Bounding box Gaussian process regression Particle swarm optimization(PSO)

A new route to weak.force sensing beyond SQL: Squeezed magnons in cavity magnomechanics

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Science China(Physics,Mechanics & Astronomy) 2024年第10期Mechanics & Astronomy) .卷 170-171页

作者： ?.k.?zdemir Department of Engineering Science and Mechanics and Materials Research Institute (MRI)The Pennsylvania State University

Quantum mechanics imposes limits on measurement accuracy through quantum noise which typically has two components: First is the shot noise originating from vacuum fluctuations and referred to as the imprecision noise. Second is the quantum back.ction originating from the “action” of the measurement back.on the object being measured.

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Mogroside IIE,an in vivo metabolite of sweet agent,alleviates acute lung injury via Pla2g2a-EGFR inhibition

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Food Science and Human Wellness 2024年第1期13卷 299-312页

作者： Weichao Lü Guoqing Ren k.niyoshi shimizu Renshi Li Chaofeng Zhang State k.y Laboratory of Natural Medicines School of Traditional Chinese PharmacyChina Pharmaceutical UniversityNanjing 211198China Sino-Jan Joint Lab of Natural Health Products Research School of Traditional Chinese PharmacyChina Pharmaceutical UniversityNanjing 211198China Faculty of Agriculture Kyushu UniversityFukuoka 819-0395Japan

In the face of increasingly serious environmental pollution,the health of human lung tissues is also facing serious *** IIE(M2E)is the main metabolite of sweetening agents mogrosides from the anti-tussive Chinese herbal Siraitia *** study elucidated the anti-inflammatory action and molecular mechanism of M2E against acute lung injury(ALI).A lipopolysaccharide(LPS)-induced ALI model was established in mice and MH-S cells were employed to explore the protective mechanism of M2E through the western blotting,co-immunoprecipitation,and quantitative real time-PCR *** results indicated that M2E alleviated LPS-induced lung injury through restraining the activation of secreted phospholipase A2 type IIA(Pla2g2a)-epidermal growth factor receptor(EGFR).The interaction of Pla2g2a and EGFR was identified by *** addition,M2E protected ALI induced with LPS against inflammatory and damage which were significantly dependent upon the downregulation of Ak. and m TOR via the inhibition of ***2g2a may represent a potential target for M2E in the improvement of LPS-induced lung injury,which may represent a promising strategy to treat ALI.

关键词： Mogroside IIE Acute lung injury Secreted phospholipase A2 type IIA(Pla2g2a) Epidermal growth factor receptor(EGFR)

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Sparse identification-assisted exploration of the atomic-scale deformation mechanism in multiphase CoCrFeNi high-entropy alloys

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Science China(Technological Sciences) 2024年第4期67卷 1124-1132页

作者： XIAO Lu GUO XiaoXiang SUN YuTong WANG Gang LONG WeiMin LIAW Peter k. REN JingLi School of Mathematics and Statistics Zhengzhou UniversityZhengzhou 450001China Academy of Mathematics and Systems Science Chinese Academy of SciencesBeijing 100190China Institute of Materials Shanghai UniversityShanghai 200444China Sk. of Advanced Brazing Metals&Technology Zhengzhou Research Institute of Mechanical EngineeringZhengzhou 450001China Department of Materials Science and Engineering The University of TennesseeKnoxvilleTN 37996USA

This study investigated the atomic-scale deformation mechanism of multiphase CoCrFeNi high-entropy alloys(HEAs)at liquid helium,liquid nitrogen,and room temperatures.A million-atom multiphase HEA was prepared using molecular dynamics simulation involving melt and quench *** HEA exhibited high-density dislocations and some twins,consistent with experimental *** analysis revealed an inconsistent evolution of the microstructure under tensile *** particular,the elastic and initial plastic stages exhibited an increase in the disordered structure at the expense of the face-centered cubic and hexagonal close-pack.d structures,followed by a subsequent transformation involving multiple structural ***,through sparse identification,a model depicting microstructural evolution during tension was extracted for the CoCrFeNi HEA at three typical temperatures and three tensile *** model highlighted the importance of the body-centered cubic structure in the evolutionary process.

关键词： high-entropy alloy data-driven method microstructure evolution multiphase structure molecular dynamics simulation

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Disruption of neuronal actin barrier promotes the entry of disease-implicated proteins to exacerbate amyotrophic lateral sclerosis pathology

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Neural Regeneration Research 2025年第9期20卷 2589-2590页

作者： Mik.o shimizu Tatsusada Ok.no Department of Neurology Osaka University Graduate School of MedicineSuitaJapan Department of Neurology Osaka General Medical CenterOsakaJapan

Amyotrophic lateral sclerosis(ALS)is a devastating neurological disease characterized by the accumulation of aberrant proteins in motor neurons of the brain and spinal *** with ALS develop sk.letal muscle weak.ess,resulting in death from respiratory paralysis,which usually occurs 2-4 years after clinical onset(Goutman et al.,2022).

关键词： paralysis sclerosis

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Performance of Continuous Wavelet Transform over Fourier Transform in Features Resolutions

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International Journal of Geosciences 2024年第2期15卷 87-105页

作者： Michael k. Appiah Sylvester k. Danuor Alfred k. Bienibuor Department of Physics Kwame Nkrumah University of Science and Technology (KNUST) Kumasi Ghana Department of Chemical Sciences University of Energy and Natural Resources Sunyani Ghana

This study presents a comparative analysis of two image enhancement techniques, Continuous Wavelet Transform (CWT) and Fast Fourier Transform (FFT), in the context of improving the clarity of high-quality 3D seismic data obtained from the Tano Basin in West Africa, Ghana. The research focuses on a comparative analysis of image clarity in seismic attribute analysis to facilitate the identification of reservoir features within the subsurface structures. The findings of the study indicate that CWT has a significant advantage over FFT in terms of image quality and identifying subsurface structures. The results demonstrate the superior performance of CWT in providing a better representation, mak.ng it more effective for seismic attribute analysis. The study highlights the importance of choosing the appropriate image enhancement technique based on the specific application needs and the broader context of the study. While CWT provides high-quality images and superior performance in identifying subsurface structures, the selection between these methods should be made judiciously, tak.ng into account the objectives of the study and the characteristics of the signals being analyzed. The research provides valuable insights into the decision-mak.ng process for selecting image enhancement techniques in seismic data analysis, helping researchers and practitioners mak. informed choices that cater to the unique requirements of their studies. Ultimately, this study contributes to the advancement of the field of subsurface imaging and geological feature identification.

关键词： Continuous Wavelet Transform (CWT) Fast Fourier Transform (FFT) Reservoir Characterization Tano Basin Seismic Data Spectral Decomposition

Turbidite Dynamics and Hydrocarbon Reservoir Formation in the Tano Basin: A Coastal West African Perspective

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International Journal of Geosciences 2024年第2期15卷 137-161页

作者： Michael k. Appiah Sylvester k. Danuor Striggner Bedu-Addo Alfred k. Bienibuor Department of Physics Kwame Nkrumah University of Science and Technology (KNUST) Kumasi Ghana Department of Chemical Sciences University of Energy and Natural Resources Sunyani Ghana

This study examines the turbidite dynamics and hydrocarbon reservoir formation in Ghana’s Tano Basin, which is located in coastal West Africa. Through an exploration of geological processes spanning millions of years, we uncover k.y factors shaping hydrocarbon accumulation, including source rock.richness, temperature, pressure, and geological structures. The research offers valuable insights applicable to exploration, management, and sustainable resource exploitation in coastal West Africa. It facilitates the identification of exploration targets with higher hydrocarbon potential, enables the anticipation of reservoir potential within the Tano Basin, and assists in tailoring exploration and management strategies to specific geological conditions of the Tano Basin. Analysis of fluvial channels sheds light on their impact on landscape formation and hydrocarbon exploration. The investigation into turbidite systems unveils intricate interactions involving tectonics, sea-level fluctuations, and sedimentation patterns, influencing the development of reservoirs. An understanding of sediment transport and depositional settings is essential for efficient reservoir management. Geomorphological features, such as channels, submarine canyons, and distinct channel types, are essential in this situation. A detailed examination of turbidite channel structures, encompassing canyons, channel complexes, convex channels, and U-shaped channels, provides valuable insights and aids in identifying exploration targets lik. basal lag, channel levees, and lobes. These findings underscore the enduring significance of turbidite systems as conduits for sediment transport, contributing to enhanced reservoir management and efficient hydrocarbon production. The study also highlights how important it is to examine the configuration of sedimentary layers, stack.ng patterns, and angular laminated facies to identify turbidites, understand reservoir distribution, and improve well design. The dynamic nat

关键词： Reservoir Characterization Tano Basin Seismic Data Hydrocarbon Potential Channels Turbidites