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Sex and APOE genotype-specific white matter changes in Alzheimer’s disease

Alzheimer's & Dementia 2021年第S1期17卷

作者： Emrin Horgusluoglu-Moloch Minghui Wang Xianxiao Zhou Qi Zeng Bin Zhang Icahn Institute of Genomics and Multiscale Biology New York NY USA Icahn School of Medicine at Mount Sinai New York NY USA Icahn Institute for Data Science and Genomic Technology New York NY USA Mount Sinai Center for Transformative Disease Modeling New York NY USA Ronald M. Loeb Center for Alzheimer's Disease New York NY USA

Background APOE ε4 genotype and sex difference represent strong risk factors for Alzheimer’s Disease (AD) that also lead to white matter (WM) microstructural changes. However, it is still not clear which brain regions have the strongest changes with APOE ε3 and ε4 allele carrier status and sex difference, and what are the key drivers and biological pathways underlying WM abnormality during disease progression. In this study, we present a new comprehensive framework to identify sex- and APOE genotype-specific WM changes in specific brain regions with AD severity using the data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI-GO/2). Method DTI-derived features including fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (L1), radial diffusivity (RD) were calculated from ADNIGO/2 (N = 232). ADNI participants were classified depending on their sex and APOE genotype status as female APOE ε3/3, male APOE ε3/3, female APOE ε4 positive, and male APOE ε4 positive. Through correlating DTI features with the clinical/cognitive traits, we systematically rank-ordered 176 brain regions in relation to disease severity for each group. Multiscale Embedded Gene co-Expression Network Analysis (MEGENA) was performed using processed expression data to identify clusters of highly correlated genes and DTI-features as modules. Gene Set Enrichment Analysis (GSEA) was carried out to annotate each module with enriched pathways for each group. Result The parahippocampal gyrus (PHG)-right, posterior thalamic radiation (PTR)-left, hippocampus (HIPPO)-left, and the superior temporal gyrus (STG)-right were top-ranked regions with sex and APOE ε3 and ε4 alleles carrier status (Figure 1A-D). WM changes in PTR-right are the only specific for the male APOE ε4+ group compared to the other groups. PHG-right is highly associated with worse AD clinical outcomes in APOE ε4 allele carriers regardless of sex difference. DTI features in MTWM-left is significantly correlated with onl

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Fast Positioning of Rotating Center Based on Correction of Finite Angle Deviation of CT System

Fast Positioning of Rotating Center Based on Correction of F...

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IEEE data Driven Control and Learning Systems Conference

作者： Deyu Duan Fahui Zhai Yuqin Cao Huaqiong Hou Shuguo Yang Research Center for Mathematical Modeling School of Mathematics and Physics Qingdao University of Science and Technology Institute of Intelligence Science & Data Technology School of Mathematics and Physics Qingdao University of Science and Technology

ISBN: (纸本)9781538626191

Note that it is very important to determine accurately the position of the Center of Rotation (COR) to the image reconstruction in the CT scanning system, in this paper, we establish the model of fast determining COR by using the correction of finite angle deviation, moreover apply certain algorithms to achieve the center of rotation calibration. By simulating original signal or the original signal with noise, we obtain that the artifact of the reconstructed image is significantly less and the image quality is also raised, thus the center of rotation can be accurately determined. Compared with the known algorithms, the model in this paper has a small amount of calculation and strong resistance to random noise. Consequently, our model and algorithm are helpful for determining COR.

关键词： 2D-CT Finite Angle Deviation Improved Inverse Transformation of Radon Least Square Method White Gaussian Noise

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Study on Stumbles of the Elderly from a Depth Perception Dependency Test

Study on Stumbles of the Elderly from a Depth Perception Dep...

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2019 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)

作者： Emiko Uchiyama Toshihiro Mino Hiroki Obara Tomoki Tanaka Wataru Takano Yoshihiko Nakamura Katsuya Iijima graduate school of information science and technology university of Tokyo Hongo 7-3-1 Bunkyo-ku Tokyo Japan graduate school of medicine university of Tokyo Hongo 7-3-1 Bunkyo-ku Tokyo Japan center for mathematical modeling and data science Osaka University Japan institute of gerontology university of Tokyo Hongo 7-3-1 Bunkyo-ku Tokyo Japan

In this paper, we investigate the relationship between the depth perception and an approaching motion toward an object. We propose the depth perception dependency test, which is the combination of tests of a motion and depth perception based on the situation that an object is placed on the human's pathway. Firstly, as the motion test, we set the ball approach motion and asked elderly participants to approach and contact a ball by their foot, because this motion is easy to measure and requires localization skill and motion planning skill. The swing/support legs positions at the toeoff time of the swing leg just before contacting the ball was analyzed. Secondly, as the depth perception test, the pseudo3D image test was proposed. The coordinate transformation model for the calculation of the depth perception ability was also proposed. Through the proposed test and the proposed model, it was clarified that the participants who are regarded as perceiving the strong visual illusion perceive the objects closer than its real position, and their swing leg toe off positions in the ball approaching motion were significantly farther than other participants. Thus, it can be concluded that there was a relationship between the depth perception and the approaching motion that is thought to be a higher risk of stumbles.

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modeling the Tertiary Structure of a Multi-domain Protein: Structure Prediction of Multi-domain Proteins 18

Modeling the Tertiary Structure of a Multi-domain Protein: S...

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9th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2018

作者： Almsned, Fahad Gogovi, Gideon Bracci, Nicole Kehn-Hall, Kylene Blaisten-Barojas, Estela Shehu, Amarda Krasnow Institute for Advanced School of Systems Biology George Mason University United States Center for Simulation and Modeling Dept of Computational and Data Sciences George Mason University United States National Center for Biodefense and Infectious Diseases School of Systems Biology George Mason University United States Dept of Computer Science Dept of Bioengineering Center for Simulation and Modeling School of Systems Biology George Mason University United States

ISBN: (纸本)9781450357944

Due to the central role that tertiary structure plays in determining protein function, resolving protein tertiary structures is an integral research thrust in both wet and dry laboratories. Dry laboratories have primarily focused on small- to medium-size proteins. However, proteins central to human biology and human health are often quite complex, containing multiple domains and consisting of thou- sands of amino acids. Such proteins are challenging for various reasons, including the inability to crystallize. We present a case study of structure determination for the Rift Valley fever virus L-protein, a a large, multi-domain protein with currently no available tertiary structure. We employ this case study as an emerging paradigm and demonstrate how to leverage the rich and diverse landscape of bioinformatics tools for building tertiary structure models for multi-domain proteins with thousands of amino acids. © 2018 ACM.

关键词： Proteins

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Correction to: On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments

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BMC genomics 2020年第1期21卷 384页

作者： Alemu Takele Assefa Jo Vandesompele Olivier Thas Department of Data Analysis and Mathematical Modeling Ghent University 9000 Ghent Belgium. alemutakele.assefa@UGent.be. Department of Biomolecular Medicine Ghent University 9000 Ghent Belgium. Cancer Research Institute Ghent Ghent University Ghent Belgium. Center for Medical Genetics Ghent University Ghent Belgium. Department of Data Analysis and Mathematical Modeling Ghent University 9000 Ghent Belgium. National Institute for Applied Statistics Research Australia (NIASRA) University of Wollongong Wollongong Australia. Data Science Institute I-BioStat Hasselt University Hasselt Belgium.

An amendment to this paper has been published and can be accessed via the original article.

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data-based Parameter Calibration Method of the Computed Tomography System

Data-based Parameter Calibration Method of the Computed Tomo...

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第37届中国控制会议

作者： Zhang Ruikun Shan Zhengduo Duan Deyu Xu Guangwei Zhang Xinli School of Mathematics and Physics Qingdao University of Science and Technology Big Data Research Center of School of Mathematics and Physics Qingdao University of Science and Technology Center for Mathematical Modeling Research Qingdao University of Science and Technology

This paper mainly studies data-based parameter calibration of the computed tomography（CT） system. By establishing a least squares algorithm model, CT system parameters were calibrated. First, the attenuation coefficient is calculated from the known data, and the relationship between the received information and the pitch of the X-ray transmission template is obtained by using the Lambert-beers principle. Then, by using the geometric relationship between the ray and the two-dimensional graph, the relationship model between the pitch and the variable to be sought is established. On this basis, we can get the multivariate linear equations which present the received information and the variables to be solved. Finally, the least square method is used to establish the target programming model which is based on the minimum square sum of the fitting value and the actual value of the received information. By using the genetic algorithm, the multiple linear equations are solved. Meanwhile, the deflection center and receiver unit spacing can be obtained.

关键词： Parameter Calibration data-based CT system Least Square Method Genetic Algorithm

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Corrigendum to “Oscillation-free source term inversion of atmospheric radionuclide releases with joint model bias corrections and non-smooth competing priors” [J. Hazard. Mater. 440 (2022) 129806]

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Journal of Hazardous Materials 2023年 445卷

作者： Sheng Fang Xinwen Dong Shuhan Zhuang Zhijie Tian Tianfeng Chai Yuhan Xu Yungang Zhao Li Sheng Xuan Ye Wei Xiong Institute of Nuclear and New Energy Technology Collaborative Innovation Centre of Advanced Nuclear Energy Technology Key Laboratory of Advanced Reactor Engineering and Safety of Ministry of Education Tsinghua University Beijing 100084 China China Institute for Radiation Protection Taiyuan 030006 China NOAA Air Resources Laboratory (ARL) NOAA Center for Weather and Climate Prediction 5830 University Research Court College Park MD 20740 USA Cooperative Institute for Climate and Satellites University of Maryland College Park MD 20740 USA Key Laboratory of Beam Technology of Ministry of Education College of Nuclear Science and Technology Beijing Normal University Beijing 100875 China CTBT Beijing National Data Centre and Beijing Radionuclide Laboratory Beijing 100085 China CMA Earth System Modeling and Prediction Center (CEMC) Beijing 100081 China

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Blow up analysis for boltzmann-poisson equation in onsager's theory for point vortices with multi-intensities

arXiv

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arXiv 2018年

作者： Suzuki, Takashi Toyota, Yohei Center for Mathematical Modeling and Data Science Osaka University Osaka560-8531 Japan Department of Systems Innovation Graduate School of Engineering Science Osaka University Osaka560-8531 Japan

In this paper we consider the minimizing sequence for some energy functional of an elliptic equation associated with the mean field limit of the point vortex distribution one-sided Borel probability measure. If such a sequence blows up, we derive some estimate which is related to the behavior of solution near the blow-up point. Moreover, we study the two-intensities case to consider the suficient condition for this estimate. Our main results are new for the standard mean field equation as well. Copyright © 2018, The Authors. All rights reserved.

关键词： Poisson equation

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DeePMD-kit v2: A software package for Deep Potential models

arXiv

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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

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Climatic and Biotic Controls of Evapotranspiration Across Grassland Ecosystems on the Tibetan Plateau

SSRN

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SSRN 2025年

作者： Peng, Siyuan Yang, Yue Luo, Dengnan Zeng, Xiang Liang, Minqi Tao, Long Zhang, Guangru Li, Pan Liao, Weijie Guo, Qun Cao, Ruochen Li, Yuzhe Zhang, Weirong Hu, Zhongmin Hainan Baoting Tropical Rainforest Ecosystem Observation and Research Station School of Ecology Hainan University Haikou570228 China Department of Geography Faculty of Arts and Sciences Beijing Normal University Zhuhai519087 China Facility of Geographical Science Beijing Normal University Beijing100875 China Zhuhai Branch of State Key Laboratory of Earth Surface Processes and Resource Ecology Beijing Normal University Zhuhai519087 China School of Geography South China Normal University Shipai Campus Guangzhou510631 China School of Atmospheric Sciences Guangdong Province Data Center of Terrestrial and Marine Ecosystems Carbon Cycle Sun Yat-sen University Guangdong Zhuhai510245 China Key Lab of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Beijing100101 China College of Resources and Environment University of Chinese Academy of Sciences Beijing101408 China International Institute for Earth System Sciences Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application Nanjing University Jiangsu210023 China Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology Key Laboratory for Land Satellite Remote Sensing Applications of Ministry of Natural Resources School of Geography and Ocean Science Nanjing University Jiangsu210023 China Key Laboratory of Land Surface Pattern and Simulation Institute of Geographical Sciences and Natural Resources Research Chinese Academy of Sciences Beijing China

Study region: The Tibetan Plateau in China, the Third Pole of the *** focus: Accurate descriptions of spatial variation in evapotranspiration (ET) and its components on the Tibetan Plateau (TP) are crucial for understanding the dynamics of the regional water cycle and energy balance. However, how various environmental factors affect ET and its components remains unclear. This study addresses this gap using observational data from 14 sites and employing the Shuttleworth-Wallace-Hu (SWH) model to examine the spatial relationships between ET, its components, and underlying *** hydrological insights for the region: The SWH model parameters were optimized using the Monte Carlo method, achieving a satisfactory model performance with an average R² of 0.75. The ratio of transpiration to ET was generally higher in alpine meadows (0.55) than alpine steppes (0.39). Across the TP, precipitation and the leaf area index together shaped spatial variation in ET and transpiration. Precipitation emerged as the primary driver of interannual variation in ET, while the leaf area index strongly regulated the proportion of ET accounted for by transpiration. Furthermore, above aridity index values of 0.73, grassland ecosystems transitioned from water to energy. This finding is significant as it challenges the common application of an aridity index value of 0.65 to distinguish arid from humid regions. It suggests that TP grasslands, with an AI of 0.65-0.73, remain primarily water-limited. © 2025, The Authors. All rights reserved.

关键词： Monte Carlo methods

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