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Expression quantitative trait loci(eQTL):from population genetics to precision medicine

Journal of Genetics and Genomics 2025年第4期52卷 449-459页

作者： Zhi Qi Wong Lian Deng Alvin Cengnata Thuhairah Abdul Rahman Aletza Mohd Ismail Renee Lay Hong Lim Shuhua Xu Boon-Peng Hoh Faculty of Applied Sciences UCSI UniversityKuala Lumpur 56000Malaysia State Key Laboratory of Genetic Engineering Center for Evolutionary BiologyCollaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesFudan UniversityShanghai 200433China Clinical Pathology Diagnostic Centre Research Laboratory Faculty of MedicineUniversiti Teknologi MARA47000Malaysia Key Laboratory of Computational Biology Shanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Department of Liver Surgery and Transplantation Liver Cancer Institute Zhongshan HospitalFudan UniversityShanghai 200433China Ministry of Education Key Laboratory of Contemporary Anthropology School of Life SciencesHuman Phenome InstituteFudan UniversityShanghai 200433China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life SciencesJiangsu Normal UniversityXuzhouJiangsu 221008China Henan Institute of Medical and Pharmaceutical Sciences Zhengzhou UniversityZhengzhouHenan 450001China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China Division of Applied Biomedical Sciences and Biotechnology School of Health SciencesIMU UniversityKuala Lumpur 57000Malaysia

Evidence has shown that differential transcriptomic profiles among human populations from diverse ancestries,supporting the role of genetic architecture in regulating gene expression alongside environmental *** variants that regulate gene expression,known as expression quantitative trait loci(eQTL),are primarily shaped by human migration history and evolutionary forces,likewise,regulation of gene expression in principle could have been influenced by these ***,a comprehensive understanding of how human evolution impacts eQTL offers important insights into how phenotypic diversity is *** studies,however,suggest that eQTL is enriched in genes that are selectively *** eQTL is minimally affected by selective pressures remains an open question and requires comprehensive *** addition,such studies are primarily dominated by the major populations of European ancestry,leaving many marginalized populations *** observations indicate there exists a fundamental knowledge gap in the role of genomics variation on phenotypic diversity,which potentially hinders precision *** article aims to revisit the abundance of eQTL across diverse populations and provide an overview of their impact from the population and evolutionary genetics perspective,subsequently discuss their influence on phenomics,as well as challenges and opportunities in the applications to precision medicine.

关键词： eQTL Transcriptomics Genomics Phenomics Population genetics Precisionmedicine

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Effect of anharmonicity on the thermal conductivity of amorphous silica

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Physical Review B 2022年第1期106卷 014305-014305页

作者： Xueyan Zhu Cheng Shao CAEP Software Center for High Performance Numerical Simulation Beijing 100088 China Institute of Applied Physics and Computational Mathematics Beijing 100088 China Thermal Science Research Center Shandong Institute of Advanced Technology Jinan Shandong Province 250103 China Department of Mechanical Engineering The University of Tokyo 7-3-1 Hongo Bunkyo Tokyo 113-8656 Japan

Proper consideration of anharmonicity is important for the calculation of thermal conductivity. However, how the anharmonicity influences the thermal conduction in amorphous materials is still an open question. In this work, we uncover the role of anharmonicity on the thermal conductivity of amorphous silica (a−SiO2) by comparing the thermal conductivity predicted from the harmonic theory and the anharmonic theory. Moreover, we explore the effect of anharmonicity-induced frequency shift on the prediction of thermal conductivity. It is found that the thermal conductivity calculated by the recently developed anharmonic theory (quasi-harmonic Green-Kubo approximation) is higher than that calculated by the harmonic theory developed by Allen and Feldman. The use of anharmonic vibrational frequencies also leads to a higher thermal conductivity compared with that calculated using harmonic vibrational frequencies. The anharmonicity-induced frequency shift is a mechanism for the positive temperature dependence of the thermal conductivity of a−SiO2 at higher temperatures. Further investigation on the mode diffusivity suggests that although anharmonicity has a larger influence on locons than diffusons, the increase in thermal conductivity due to anharmonicity is mainly contributed by the anharmonicity-induced increase of the diffusivity of diffusons. Finally, it is found that the cross-correlations between diffusons and diffusons contribute most to the thermal conductivity of a−SiO2, and the locons contribute to the thermal conductivity mainly through collaboration with diffusons. These results offer new insights into the nature of the thermal conduction in a−SiO2.

关键词： Anharmonic lattice dynamics Heat transfer Lattice thermal conductivity Phonons Transport phenomena Glasses Molecular dynamics

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Few-photon single ionization of cold rubidium in the over-the-barrier regime

arXiv

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arXiv 2023年

作者： Ma, Huanyu Wang, Xincheng Zhang, Linxuan Zou, Zhihan Yuan, Junyang Ma, Yixuan Lv, Rujin Shen, Zhenjie Yan, Tianmin Weidemüller, Matthias Ye, Difa Jiang, Yuhai Center for Transformative Science School of Physical Science and Technology ShanghaiTech University Shanghai201210 China Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai201210 China University of Chinese Academy of Sciences Beijing100049 China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing100088 China Graduate School China Academy of Engineering Physics Beijing100193 China Physikalisches Institut Universität Heidelberg Im Neuenheimer Feld 226 Heidelberg69120 Germany

Photoionization of the rubidium (Rb) atoms cooled in a magneto-optical trap, characterized by the coexistence of the ground 5S1/2 and the excited 5P3/2 states, is investigated experimentally and theoretically with the 400 nm femtosecond laser pulses at intensities of I = 3×109 W/cm2 −4.5×1012 W/cm2. Recoil-ion momentum distribution (RIMD) of Rb+ exhibits rich ring-like structures and their energies correspond to one-photon ionization of the 5P3/2 state, two-photon and three-photon ionizations of the 5S1/2 state, respectively. With the increasing of I, we find that experimental signals near zero-momentum (NZM) in RIMDs resulted from the 5P3/2 state enhance dramatically and its peaked Rb+ momenta dwindle obviously while that from the 5S1/2 state is maintained. Meanwhile, the ion-yield ratio of the 5S1/2 over the 5P3/2 states varies from I to I1.5 as I increases. These features indicate a transition from perturbative ionization to strong-perturbative ionization for the 5P3/2 state. Numerical simulations by solving the time-dependent Schrödinger equation (TDSE) can qualitatively explain the measurements of RIMD, photoion angular distributions, as well as ion-yield ratio. However, some discrepancies still exist, especially for the NZM dip, which could stem from the electron-electron correlation that is neglected in the present TDSE simulations since we have adopted the single-active-electron approximation. Copyright © 2023, The Authors. All rights reserved.

关键词： Photons

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Existence and regularity of inverse problem for the nonlinear fractional Rayleigh-Stokes equations

Existence and regularity of inverse problem for the nonlinea...

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作者： Tran Bao, Ngoc Nguyen Hoang, Luc Vo Van, Au Nguyen, Huy Tuan Zhou, Yong Institute of Research Development Duy Tan University Da Nang550000 Viet Nam Department of Mathematics and Computer Science University of Science Ho Chi Minh City Viet Nam Vietnam National University Ho Chi Minh City Viet Nam Applied Analysis Research Group Faculty of Mathematics Statistics Ton Duc Thang University Ho Chi Minh City Viet Nam Faculty of Information Technology Macau University of Science Technology 999078 China Faculty of Mathematics Computational Science Xiangtan University Hunan411105 China

This paper investigates an inverse problem for fractional Rayleigh-Stokes equations with nonlinear source. The fractional derivative in time is taken in the sense of Riemann-Liouville. The proposed problem has many applications in some non-Newtonian fluids. We obtain some results on the existence and regularity of mild solutions. © 2020 John Wiley & Sons, Ltd.

关键词： Inverse problems

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Prediction of methylene blue dye sorption to sulfonated date palm kernel biochar using statistical regression and machine learning methods and DFT studies

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Journal of Molecular Liquids 2025年 429卷

作者： Aigbe, Uyiosa Osagie Ukhurebor, Kingsley Eghonghon Onyancha, Robert Birundu Osibote, Adelaja Otolorin Hassaan, Mohamed A. ElKatory, Marwa R. Nemr, Ahmed El Center for Space Research North-West University Private Bag X6001 Potchefstroom2531 South Africa National Institute of Theoretical and Computational Science Johannesburg2000 South Africa School of Chemistry & Physics University of KwaZulu-Natal Pietermaritzburg Campus Private Bag X01 Scottsville3209 South Africa Department of Physics Faculty of Science Edo State University Uzairue Edo State Nigeria School of Physics and Earth Science Faculty of Applied Science and Technology Technical University of Kenya Nairobi Kenya College of Graduate Studies School of Interdisciplinary Research and Graduate Studies Muckleneuk Campus University of South Africa Pretoria0003 South Africa Department of Mathematics and Physics Cape Peninsula University of Technology Cape Town South Africa Kayet Bey Alexandria Elanfoushy Egypt Advanced Technology and New Materials Research Institute SRTA-City New Borg El-Arab City 21934 Alexandria Egypt

In this study, methylene blue (MB) dye adsorption to synthesised sulfonated date palm kernel biochar (SDPKB) was predicted and optimized using statistical-based regression approach (response surface methodology (RSM), machine-learning algorithms (artificial-neural-network (ANN), and adaptive-neuro-fuzzy-inference-system (ANFIS) models), and quantum chemistry calculations performed using density function theory (DFT) to link the electrical properties of the MB dye with the experimental findings. The percentage (%) of MB dye removed using SDPKB was found to be proportional to the biosorbent dosage and interaction time and inversely proportional to the solution pH and initial concentrations based on different used models results. It was observed that these models were accurate and comparable for the prediction of the removal of MB with coefficient of regression (R2) values of 0.9174, 0.9742, and 0.9999, mean square error (MSE) values of 181.71, 94.50, and 0.00000049, and root MSE (RMSE) values of 13.48, 9.72, and 0.0007 for the RSM, ANN, and ANFIS, respectively. The ANFIS model was found to be more effective in the prediction of MB sorption to SDPKB than the other models (ANFIS > ANN > RSM), and it was highly applicable in the sorption process. This study has revealed that the SDPKB can serve as a better biosorbent for MB adsorption. Therefore, this study will serve as a first reference point data that will be of great assistance in industrial effluent management as well as decision-making on the adoption of statistical and machine learning models for adsorption study. © 2025 Elsevier B.V.

关键词： Adversarial machine learning

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Phonon-mediated Migdal effect in semiconductor detectors

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Physical Review D 2022年第4期106卷 043004-043004页

作者： Zheng-Liang Liang Chongjie Mo Fawei Zheng Ping Zhang College of Mathematics and Physics Beijing University of Chemical Technology Beijing 100029 China Beijing Computational Science Research Center Beijing 100193 China Centre for Quantum Physics Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement(MOE) School of Physics Beijing Institute of Technology Beijing 100081 China School of Physics and Physical Engineering Qufu Normal University Qufu 273165 China Institute of Applied Physics and Computational Mathematics Beijing 100088 China

The Migdal effect inside detectors provides a new possibility of probing the sub-GeV dark matter (DM) particles. While there has been well-established methods treating the Migdal effect in isolated atoms, a coherent and complete description of the valence electrons in a semiconductor is still absent. The bremstrahlunglike approach is a promising attempt, but it turns invalid for DM masses below a few tens of MeV. In this paper, we lay out a framework where phonon is chosen as an effective degree of freedom to describe the Migdal effect in semiconductors. In this picture, a valence electron is excited to the conduction state via exchange of a virtual phonon, accompanied by a multiphonon process triggered by an incident DM particle. Under the incoherent approximation, it turns out that this approach can effectively push the sensitivities of the semiconductor targets further down to the MeV DM mass region.

关键词： Particle dark matter Ab initio calculations Dark matter detectors Solid-state detectors

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Magnetic phase diagram of Eu1−xCaxCo2P2 determined using muon spin rotation and relaxation

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Physical Review B 2024年第14期109卷 144408-144408页

作者： Izumi Umegaki Kodai Moriyama Kohei Yoshinaga Kazuki Ohishi Frank Elson Ugne Miniotaite Rasmus Palm Martin Månsson Ola Kenji Forslund Yasmine Sassa Soh Sugiyama Gerald D. Morris Bassam Hitti Chishiro Michioka Hiroaki Ueda Kazuyoshi Yoshimura Jun Sugiyama Institute of Materials Structure Science High Energy Accelerator Research Organization (KEK) Tokai Ibaraki 319-1106 Japan Materials and Life Science Experimental Facility (MLF) Division J-PARC Center Tokai Ibaraki 319-1195 Japan Department of Materials Structure Science The Graduate University for Advanced Studies (SOKENDAI) Tsukuba Ibaraki 305-0801 Japan Department of Chemistry Graduate School of Science Kyoto University Kyoto 606-8502 Japan The Institute for Solid State Physics The University of Tokyo Kashiwa Chiba 277-8581 Japan Neutron Science and Technology Center Comprehensive Research Organization for Science and Society (CROSS) Tokai Ibaraki 319-1106 Japan Department of Applied Physics KTH Royal Institute of Technology SE-106 91 Stockholm Sweden Physik-Institut Universität Zürich Winterthurerstrasse 190 CH-8057 Zürich Switzerland Department of Physics and Astronomy Uppsala University Box 516 SE-75120 Uppsala Sweden Department of Physics Nagoya University Nagoya Aichi 464-8602 Japan Centre for Molecular and Materials Science TRIUMF 4004 Wesbrook Mall Vancouver British Columbia Canada V6T 2A3 Institute for Advanced Materials Research and Development Shimane University Shimane 690-8504 Japan Department of Energy and Hydrocarbon Chemistry Graduate School of Engineering Kyoto University Kyoto 615-8510 Japan Advanced Science Research Center Japan Atomic Energy Agency Tokai Ibaraki 319-1195 Japan

The present study investigated the magnetic nature of a solid solution system consisting of EuCo2P2 and CaCo2P2 using a muon spin rotation and relaxation (μ+SR) technique, which is sensitive to local magnetic environments. The former compound EuCo2P2 is known to enter an incommensurate helical antiferromagnetic (AF) phase below 66 K with neutrons, which was confirmed by the present μ+SR. The magnitude of the ordered Eu moments proposed with neutrons was found to be consistent with that estimated by μ+SR. Furthermore, the latter lattice-collapsed tetragonal phase compound CaCo2P2 is known to enter an A-type AF phase below 90 K, and μ+SR measurements on single crystals revealed the presence of a spin reorientation transition at around 40 K, below which the A-type AF order is likely to be completed. Although all Eu1−xCaxCo2P2 compounds were found to enter a magnetic phase at low temperatures regardless of x, a static ordered state was formed only at the vicinity of the two end compounds, i.e., 0≤x≤0.4 and 0.9≤x≤1. Instead, a disordered state, i.e., a random spin-glass state, short-range ordered state, or highly fluctuating state was found in the x range between 0.4 and 0.9, even at the lowest measured temperature (2 K). Together with the magnetization data, our findings clarified the magnetic phase diagram of Eu1−xCaxCo2P2, where a ferromagnetic exchange interaction between Co ions through the Eu2+ ion competes with a direct AF interaction among the Co ions, particularly in the x range between 0.57 and 0.9. This competition yielded multiple phases in Eu1−xCaxCo2P2.

关键词： Magnetic order Magnetic phase transitions Phase diagrams Muon spin relaxation & rotation

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Nucleon form factors in Nf = 2 + 1 lattice QCD at the physical point: finite lattice spacing effect on the root-mean-square radii

arXiv

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arXiv 2023年

作者： Tsuji, Ryutaro Aoki, Yasumichi Ishikawa, Ken-Ichi Kuramashi, Yoshinobu Sasaki, Shoichi Sato, Kohei Shintani, Eigo Watanabe, Hiromasa Yamazaki, Takeshi Department of Physics Tohoku University Sendai980-8578 Japan RIKEN Center for Computational Science Kobe650-0047 Japan Core of Research for the Energetic Universe Graduate School of Advanced Science and Engineering Hiroshima University Higashi-Hiroshima739-8526 Japan Center for Computational Sciences University of Tsukuba Ibaraki Tsukuba305-8577 Japan Degree Programs in Pure and Applied Sciences Graduate School of Science and Technology University of Tsukuba Ibaraki305-8571 Japan Yukawa Institute for Theoretical Physics Kyoto University Kyoto606-8502 Japan Institute of Pure and Applied Sciences University of Tsukuba Ibaraki Tsukuba305-8571 Japan

We present results for the nucleon form factors: electric (GE), magnetic (GM), axial (FA), induced pseudoscalar (FP) and pseudoscalar (GP) form factors, using the second PACS10 ensemble that is one of three sets of 2+1 flavor lattice QCD configurations at physical quark masses in large spatial volumes (exceeding (10 fm)3). The second PACS10 gauge configurations are generated by the PACS Collaboration with the six stout-smeared O(a) improved Wilson quark action and Iwasaki gauge action at the second gauge coupling β = 2.00 corresponding to the lattice spacing of a = 0.063 fm. We determine the isovector electric, magnetic and axial radii and magnetic moment from the corresponding form factors, as well as the axial-vector coupling gA. Combining our previous results for the coarser lattice spacing [E. Shintani et al., Phys. Rev. D99 (2019) 014510;Phys. Rev. D102 (2020) 019902 (erratum)], the finite lattice spacing effects on the isovector radii, magnetic moment and axial-vector coupling are investigated using the difference between the two results. It was found that the effect on gA is kept smaller than the statistical error of 2% while the effect on the isovector radii was observed as a possible discretization error of about 10%, regardless of the channel. We also report the partially conserved axial vector current (PCAC) relation using a set of nucleon three-point correlation functions in order to verify the effect by O(a)-improvement of the axial-vector current. Copyright © 2023, The Authors. All rights reserved.

关键词： Magnetic moments

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High-performance descriptor for magnetic materials: Accurate discrimination of magnetic structure

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Physical Review B 2023年第1期108卷 014403-014403页

作者： Michi-To Suzuki Takuya Nomoto Eiaki V. Morooka Yuki Yanagi Hiroaki Kusunose Center for Computational Materials Science Institute for Materials Research Tohoku University Sendai Miyagi 980-8577 Japan Center for Spintronics Research Network Graduate School of Engineering Science Osaka University Toyonaka Osaka 560-8531 Japan Research Center for Advanced Science and Technology University of Tokyo Komaba Meguro-ku Tokyo 153-8904 Japan Department of Applied Physics Aalto University P.O. Box 11100 00076 Aalto Espoo Finland Liberal Arts and Sciences Toyama Prefectural University Imizu Toyama 939-0398 Japan Department of Physics Meiji University Kawasaki 214-8571 Japan Quantum Research Center for Chirality Institute for Molecular Science Okazaki 444-8585 Japan

The magnetic structure is crucial in determining the physical properties inherent in magnetic compounds. We present an adequate descriptor for magnetic structure with proper magnetic symmetry and high discrimination performance, which does not depend on artificial choices for coordinate origin, axis, and magnetic unit cell in crystal. We extend the formalism called “smooth overlap of atomic positions” (SOAP), providing a numerical representation of atomic configurations to that of magnetic moment configurations. We introduce the descriptor in terms of the vector spherical harmonics to describe a magnetic moment configuration and partial spectra from the expansion coefficients. We discuss that the lowest-order partial spectrum is insufficient to discriminate the magnetic structures with different magnetic anisotropy, and a higher-order partial spectrum is required in general to differentiate detailed magnetic structures on the same atomic configuration. We then introduce the fourth-order partial spectrum and evaluate the discrimination performance for different magnetic structures, mainly focusing on the difference in magnetic symmetry. The modified partial spectra that are defined not to reflect the difference of magnetic anisotropy are also useful in evaluating magnetic structures obtained from the first-principles calculations performed without spin-orbit coupling. We apply the present method to the symmetry-classified magnetic structures for the crystals of Mn3Ir and Mn3Sn, which are known to exhibit anomalous transport under the antiferromagnetic order, and examine the discrimination performance of the descriptor for different magnetic structures on the same crystal.

关键词： Magnetic order Magnetism Spin-orbit coupling

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Symmetry-Based Phenomenological Model for Magnon Transport in a Multiferroic

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Physical Review Letters 2025年第1期134卷 016703-016703页

作者： Isaac A. Harris Sajid Husain Peter Meisenheimer Maya Ramesh Hyeon Woo Park Lucas Caretta Darrell G. Schlom Zhi Yao Lane W. Martin Department of Physics University of California Berkeley California USA Materials Science Division Lawrence Berkeley National Laboratory Berkeley California USA Department of Materials Science and Engineering University of California Berkeley California USA Department of Materials Science and Engineering Cornell University Ithaca New York USA Department of Physics Korea Advanced Institute of Science and Technology Daejon Korea School of Engineering Brown University Providence Rhode Island USA Kavli Institute at Cornell for Nanoscale Science Ithaca New York 14853 USA Leibniz-Institut für Kristallzüchtung Max-Born-Straße 2 12489 Berlin Germany Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA Department of Materials Science and NanoEngineering Rice University Houston Texas USA Department of Physics and Astronomy Rice University Houston Texas USA Department of Chemistry Rice University Houston Texas USA Rice Advanced Materials Institute Rice University Houston Texas USA

Magnons—carriers of spin information—can be controlled by electric fields in the multiferroic BiFeO3 (BFO), a milestone that brings magnons closer to application in future devices. The origin of magnon-spin currents in BFO, however, is not fully understood due to BFO’s complicated magnetic texture. In this Letter, we present a phenomenological model to elucidate the existence of magnon spin currents in generalized multiferroics by examining the symmetries inherent to their magnetic and polar structures. This model is grounded in experimental data obtained from BFO and its derivatives, which informs the symmetry operations and resultant magnon behavior. By doing so, we address the issue of symmetry-allowed, switchable magnon spin transport in multiferroics, thereby establishing a critical framework for comprehending magnon transport within complex magnetic textures.

关键词： Electric fields

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