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arXiv 2024年

作者： Ahmad, Alwani Liyana Sanchez-Bornot, Jose Sotero, Roberto C. Coyle, Damien Idris, Zamzuri Faye, Ibrahima Department of Fundamental and Applied Sciences Faculty of Science and Information Technology Universiti Teknologi PETRONAS Perak Malaysia Department of Neurosciences Hospital Universiti Sains Malaysia Kelantan Malaysia Brain and Behaviour Cluster School of Medical Sciences Universiti Sains Malaysia Kelantan Malaysia Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Magee campus Derry~Londonderry BT48 7JL United Kingdom Department of Radiology Hotchkiss Brain Institute University of Calgary CalgaryAB Canada The Bath Institute for the Augmented Human University of Bath BathBA2 7AY United Kingdom Department of Neurosciences School of Medical Sciences Universiti Sains Malaysia Kelantan Malaysia Universiti Teknologi PETRONAS Perak Malaysia

Background: Magneto/eletro-encephalography (MEG/EEG) are non-invasive neuroimaging techniques that offer excellent temporal and spatial resolution that can be used to study brain functioning. It has been proven effective in research on dementia and Alzheimer's disease (AD), where MEG/EEG analyses can identify changes in brain activity at various stages of AD progression, including preclinical and prodromal. research has shown differences in the power spectrum properties among healthy controls (HC) and individuals with mild cognitive impairment (MCI) or AD. It has also been conjectured that MEG/EEG analyses have the capability to identify pathological changes before first clinical symptoms and may provide biomarkers for interventions designed to reverse or slow the progression of AD. Objective: To conduct a comprehensive analysis by evaluating the performance of various classification techniques using features extracted by following different MEG methodologies. This study will focus on selecting MEG-based biomarkers/features that enhance performance in distinguishing between healthy control (HC) and mild cognitive impairment (MCI) participants from the BioFIND study. Furthermore, we will compare this with the effectiveness of using MRI-based anatomical features extracted from same participants, independently or in combination with the MEG features;thus, extending from previous study where similar analyses were performed using ADNI and OASIS-3 datasets. Methods: MEG and MRI data are obtained from the BioFIND dataset, comprising 324 participants with 158 individuals diagnosed as MCI and 166 HC. Sensor and source-based MEG analyses are performed using custom MATLAB code based on SPM12 and OSL toolboxes, for co-registration, preprocessing including filtering, and automatic artifact rejection. Source-based analyses were applied through different source localization methods as implemented in SPM12 and DAiSS toolboxes. We conducted analogous machine learning analyses on sen

关键词： Neurodegenerative diseases

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intelligent Synthesis of Individual Rehabilitation Plans for Patients after Joint Endoprosthesis Based on Computer Vision Technologies

Intelligent Synthesis of Individual Rehabilitation Plans for...

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International Conference on Information Technologies in engineering Education (Inforino)

作者： D.G Arseniev V.V. Borisov A.E. Misnik E.A Gomzhina M.A. Shalukhova Scientific Innovation Institute “Mathematical Modeling and Intelligent Control Systems” Peter the Great St. Petersburg Polytechnic University St. Petersburg Russian Federation Department of Computer Engineering National Research University “MPEI” Branch in Smolensk Smolensk Russia Information Technology Software Inter-State Educational Institution of Higher Education ‘Belarusian-Russian University” Mogilev Belarus Early Medical Rehabilitation FSBI “FCTOE” of the Ministry of Health of the Russian Federation Smolensk Russian Federation Information Technology Software Inter-State Educational Institution of Higher Education ‘Belarusian-Russian University Peter the Great St. Petersburg Polytechnic University Mogilev Belarus

ISBN: (数字)9798350371369

ISBN: (纸本)9798350371376

The article presents an innovative approach to the rehabilitation process for patients with joint endoprosthetics, focusing on the integration of a specialized software module based on computer vision technologies and the ontological approach. Developed for the Federal centre for Traumatology, Orthopaedics, and Endoprosthesis in Smolensk, Russia, this system is designed to improve the quality of life for patients by offering personalized rehabilitation plans. The core of the study lies in the application of ontological models and meta-associative graphs for synthesizing individual rehabilitation plans, which streamline the recovery process and reduce the workload on healthcare professionals. This method allows for the processing of large amounts of information, providing detailed conclusions and recommendations for functional correction of the musculoskeletal system. The software utilizes computer vision to analyze patient movement and develop tailored rehabilitation strategies, overcoming the limitations of traditional diagnostic tools like MRI, which may not be suitable for all patients. By incorporating artificial intelligence and augmented reality, the system enhances the accuracy of patient assessments and the effectiveness of rehabilitation plans. Furthermore, the article discusses the application of this technology in the educational process at the Belarusian-Russian University, where students are introduced to cutting-edge software tools that assist in creating personalized rehabilitation plans. This educational integration not only enriches the students’ learning experience but also fosters innovation in the development of new applications for computer vision in medical rehabilitation. The ontological approach, combined with modern technology, represents a significant advancement in the management of musculoskeletal system diseases, offering a more efficient, personalized approach to rehabilitation and recovery.

关键词： Computer vision Musculoskeletal system Technological innovation Computational modeling Medical services Propulsion Trajectory

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General-purpose machine-learned potential for 16 elemental metals and their alloys

arXiv

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arXiv 2023年

作者： Song, Keke Zhao, Rui Liu, Jiahui Wang, Yanzhou Lindgren, Eric Wang, Yong Chen, Shunda Xu, Ke Liang, Ting Ying, Penghua Xu, Nan Zhao, Zhiqiang Shi, Jiuyang Wang, Junjie Lyu, Shuang Zeng, Zezhu Liang, Shirong Dong, Haikuan Sun, Ligang Chen, Yue Zhang, Zhuhua Guo, Wanlin Qian, Ping Sun, Jian Erhart, Paul Ala-Nissila, Tapio Su, Yanjing Fan, Zheyong Beijing Advanced Innovation Center for Materials Genome Engineering University of Science and Technology Beijing Beijing100083 China School of Materials Science and Engineering Hunan University Changsha410082 China MSP group QTF Centre of Excellence Department of Applied Physics Aalto University P.O. Box 15600 Aalto EspooFI-00076 Finland Chalmers University of Technology Department of Physics Gothenburg41926 Sweden National Laboratory of Solid State Microstructures School of Physics Collaborative Innovation Center of Advanced Microstructures Nanjing University Nanjing210093 China Department of Civil and Environmental Engineering George Washington University WashingtonDC20052 United States Department of Electronic Engineering and Materials Science and Technology Research Center The Chinese University of Hong Kong N.T. Shatin999077 Hong Kong Department of Physical Chemistry School of Chemistry Tel Aviv University Tel Aviv6997801 Israel Institute of Zhejiang University-Quzhou Quzhou324000 China College of Chemical and Biological Engineering Zhejiang University Hangzhou310027 China State Key Laboratory of Mechanics and Control of Mechanical Structures Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education Institute for Frontier Science Nanjing University of Aeronautics and Astronautics Nanjing210016 China Department of Mechanical Engineering The University of Hong Kong Pokfulam Road Hong Kong School of Science Harbin Institute of Technology Shenzhen518055 China College of Physical Science and Technology Bohai University Jinzhou121013 China Interdisciplinary Centre for Mathematical Modelling Department of Mathematical Sciences Loughborough University Leicestershire LoughboroughLE11 3TU United Kingdom

Machine-learned potentials (MLPs) have exhibited remarkable accuracy, yet the lack of general-purpose MLPs for a broad spectrum of elements and their alloys limits their applicability. Here, we present a feasible approach for constructing a unified general-purpose MLP for numerous elements, demonstrated through a model (UNEP-v1) for 16 elemental metals and their alloys. To achieve a complete representation of the chemical space, we show, via principal component analysis and diverse test datasets, that employing one-component and two-component systems suffices. Our unified UNEP-v1 model exhibits superior performance across various physical properties compared to a widely used embedded-atom method potential, while maintaining remarkable efficiency. We demonstrate our approach's effectiveness through reproducing experimentally observed chemical order and stable phases, and large-scale simulations of plasticity and primary radiation damage in MoTaVW alloys. This work represents a significant leap towards a unified general-purpose MLP encompassing the periodic table, with profound implications for materials science. Copyright © 2023, The Authors. All rights reserved.

关键词： Radiation damage

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Machine Learning Approach for Identifying Anatomical Biomarkers of Early Mild Cognitive Impairment

arXiv

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arXiv 2024年

作者： Ahmad, Alwani Liyana Sanchez-Bornot, Jose Sotero, Roberto C. Coyle, Damien Idris, Zamzuri Faye, Ibrahima Department of Fundamental and Applied Sciences Faculty of Science and Information Technology Universiti Teknologi PETRONAS Perak Malaysia Department of Neurosciences Hospital Universiti Sains Malaysia Kelantan Malaysia Brain and Behaviour Cluster School of Medical Sciences Universiti Sains Malaysia Kelantan Malaysia Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Magee campus Derry LondonderryBT48 7JL United Kingdom Department of Radiology Hotchkiss Brain Institute University of Calgary CalgaryAB Canada The Bath Institute for the Augmented Human University of Bath BathBA2 7AY United Kingdom Department of Neurosciences School of Medical Sciences Universiti Sains Malaysia Kelantan Malaysia Universiti Teknologi PETRONAS Perak Malaysia Universiti Teknologi PETRONAS Perak32610 Malaysia

Background. Alzheimer's Disease (AD) represents a significant challenge in neurodegenerative disorders, necessitating early detection for effective intervention. Among neuroimaging methods, magnetic resonance imaging (MRI) is widely used because it is easy to apply in clinical practice and cost-effective, making it crucial for studying AD. Objective. This study aims to perform a comprehensive analysis of machine learning (ML) methods used in MRI-based biomarker selection and classification analysis. The goal is to study AD-related early cognitive decline by discriminating between healthy control (HC) participants who stayed stable and those unstable (uHC) who developed mild cognitive impairment (MCI) within five years. Methods. We utilized 3-Tesla (3T) MRI data from the Alzheimer's Disease Neuroinformatic Initiative (ADNI) and the Open Access Series of Imaging Studies 3 (OASIS-3), focusing on HC and uHC. Freesurfer’s recon-all, among other tools, was used to extract MRI-based anatomical biomarkers corresponding to semi-automatic segmented subcortical and cortical brain regions. We applied various ML techniques to select features and classify the data. These included methods from preliminary analysis performed in the MATLAB Classification Learner (MCL) app and more sophisticated methods like nested cross-validation and Bayesian optimization implemented in a customized pipeline to enhance classification performance for balanced and imbalanced datasets. Our pipeline was applied to both original imbalanced and randomly balanced datasets within a Monte Carlo analysis. Moreover, we implemented data harmonization approaches based on polynomial regression that enhanced the performance of ML and statistical methods. Complementary performance metrics, such as Accuracy (Acc), area under receiver operating characteristic curve (AROC), F1 score, and Matthew’s correlation coefficient (MCC), were used to evaluate the assessed methodologies. Results. In feature selection analyses,

关键词： Neurodegenerative diseases

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Is the winner really the best? A critical analysis of common research practice in biomedical image analysis competitions

arXiv

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arXiv 2018年

作者： Maier-Hein, Lena Eisenmann, Matthias Reinke, Annika Onogur, Sinan Stankovic, Marko Scholz, Patrick Arbel, Tal Bogunovic, Hrvoje Bradley, Andrew P. Carass, Aaron Carolin Feldmann Frangi, Alejandro F. Ful, Peter M. van Ginneken, Bram Hanbury, Allan Honauer, Katrin Kozubek, Michal Landman, Bennett A. Marz, Keno Maier, Oskar Maier-Hein, Klaus Menze, Bjoern H. Müller, Henning Neher, Peter F. Niessen, Wiro Rajpoot, Nasir Sharp, Gregory C. Sirinukunwattana, Korsuk Speidel, Stefanie Stock, Christian Stoyanov, Danail Taha, Abdel Aziz van der Sommen, Fons Wang, Ching-Wei Weber, Marc-André Zheng, Guoyan Jannin, Pierre Kopp-Schneider, Annette Heidelberg Germany Centre for Intelligent Machines McGill University MontrealQC Canada Christian Doppler Laboratory for Ophthalmic Image Analysis Department of Ophthalmology Medical University Vienna Vienna Austria Science and Engineering Faculty Queensland University of Technology BrisbaneQLD Australia Department of Electrical and Computer Engineering Department of Computer Science Johns Hopkins University Baltimore United States CISTIB Centre for Computational Imaging and Simulation Technologies in Biomedicine University of Sheffield Sheffield United Kingdom Department of Radiology and Nuclear Medicine Medical Image Analysis Radboud University Center Nijmegen Netherlands Institute of Information Systems Engineering TU Wien Vienna Austria Heidelberg University Heidelberg Germany Centre for Biomedical Image Analysis Masaryk University Brno Czech Republic Electrical Engineering Vanderbilt University NashvilleTN United States Institute of Medical Informatics Universität zu Lübeck Lübeck Germany Heidelberg Germany Institute for Advanced Studies Department of Informatics Technical University of Munich Munich Germany Information System Institute HES-SO Sierre Switzerland Departments of Radiology Nuclear Medicine and Medical Informatics Erasmus MC Rotterdam Netherlands Department of Computer Science University of Warwick Coventry United Kingdom Department of Radiation Oncology Massachusetts General Hospital BostonMA United States Institute of Biomedical Engineering University of Oxford Oxford United Kingdom National Center for Tumor Diseases Dresden Dresden Germany Heidelberg Germany Department of Computer Science University College London London United Kingdom Data Science Studio Research Studios Austria FG Vienna Austria Department of Electrical Engineering Eindhoven University of Technology Eindhoven Netherlands AIExplore NTUST Center of Computer Vision and Medical Imaging Graduate Institute of Biomedical Engineering National Ta

International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges has not yet been performed. In this paper, we present a comprehensive analysis of biomedical image analysis challenges conducted up to now. We demonstrate the importance of challenges and show that the lack of quality control has critical consequences. First, reproducibility and interpretation of the results is often hampered as only a fraction of relevant information is typically provided. Second, the rank of an algorithm is generally not robust to a number of variables such as the test data used for validation, the ranking scheme applied and the observers that make the reference annotations. To overcome these problems, we recommend best practice guidelines and define open research questions to be addressed in the future. Copyright © 2018, The Authors. All rights reserved.

关键词： Quality control

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Vehicle Dynamics and Interaction for Trajectory Prediction and Traffic control

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ACM Transactions on Autonomous and Adaptive systems 1000年

作者： Jian Chen Shaorui Zhou Wei Wang Yuzhu Hu Jianqing Li Ben-Guo He Junxin Chen Marwan Omar Ali Kashif Bashir Xiping Hu School of Intelligent Systems Engineering Sun Yat-Sen University China Guangdong-Hong Kong-Macao Joint Laboratory for Emotion Intelligence and Pervasive Computing Artificial Intelligence Research Institute Shenzhen MSU-BIT University China School of Computer Science and Engineering Faculty of Innovation Engineering Macau University of Science and Technology Macao SAR China Key Laboratory of Ministry of Education on Safe Mining of Deep Metal Mines Northeastern University China the School of Software Dalian University of Technology China Information Technology and Management Illinois Institute of Technology USA Department of Computing and Mathematics Manchester Metropolitan University UK Centre for Research Impact & Outcome Chitkara University Institute of Engineering and Technology Chitkara University Rajpura 140401 Punjab India

Trajectory prediction is a crucial challenge in autonomous vehicle motion planning and decision-making techniques. However, existing methods face limitations in accurately capturing vehicle dynamics and interactions. To address this issue, this paper proposes a novel approach to extracting vehicle velocity and acceleration, enabling the learning of vehicle dynamics and encoding them as auxiliary information. The VDI-LSTM model is designed, incorporating graph convolution and attention mechanisms to capture vehicle interactions using trajectory data and dynamic information. Specifically, a dynamics encoder is designed to capture the dynamic information, a dynamic graph is employed to represent vehicle interactions, and an attention mechanism is introduced to enhance the performance of LSTM and graph convolution. To demonstrate the effectiveness of our model, extensive experiments are conducted, including comparisons with several baselines and ablation studies on real-world highway datasets. Experimental results show that VDI-LSTM outperforms other baselines compared, which obtains a 3% improvement on the average RMSE indicator over the five prediction steps.

关键词： Trajectory Prediction Vehicle Dynamics Interaction Perception Graph Convolution Attention Mechanism

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Functional Synthetic Biology

arXiv

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arXiv 2022年

作者： Aldulijan, Ibrahim Beal, Jacob Billerbeck, Sonja Bouffard, Jeff Chambonnier, Gaël Delkis, Nikolaos Guerreiro, Isaac Holub, Martin Ross, Paul Selvarajah, Vinoo Sprent, Noah Vidal, Gonzalo Vignoni, Alejandro Systems Engineering Stevens Institute of Technology 1 Castle Point Terrace HobokenNJ07030 United States Intelligent Software & Systems Raytheon BBN Technologies 10 Moulton Street CambridgeMA02138 United States Molecular Microbiology Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 7 Groningen9747 AG Netherlands Centre for Applied Synthetic Biology Department of Biology Concordia University 7141 Sherbrooke Street West MontréalQCH4B 1R6 Canada Department of Biological Engineering Massachusetts Institute of Technology CambridgeMA02139 United States Plant and Environmental Biotechnology Laboratory Department of Biochemistry and Biotechnology University of Thessaly Viopolis Mezourlo Larissa41500 Greece iGEM Foundation 45 Prospect Street CambridgeMA02139 United States Delft University of Technology Van der Maasweg 9 2629 HZ Netherlands BioStrat Marketing 9965 Harbour Lake Circle Boynton BeachFL33437 United States Department of Chemical Engineering Imperial College London South Kensington Campus Exhibition Road SW7 2AZ United Kingdom Research Group School of Computing Newcastle University Devonshire Building Devonshire Terrace Newcastle Upon TyneNE1 7RU United Kingdom Synthetic Biology and Biosystems Control Lab Instituto de Automatica e Informatica Industrial Universitat Politecnica de Valencia Camino de Vera s/n Valencia46022 Spain

Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradigms in the field entangle sequence and functionality in a manner that makes abstraction difficult, reduces engineering flexibility, and impairs predictability and design reuse. Functional Synthetic Biology aims to overcome these impediments by focusing the design of biological systems on function, rather than on sequence. This reorientation will decouple the engineering of biological devices from the specifics of how those devices are put to use, requiring both conceptual and organizational change, as well as supporting software tooling. Realizing this vision of Functional Synthetic Biology will allow more flexibility in how devices are used, more opportunity for reuse of devices and data, improvements in predictability, and reductions in technical risk and cost. © 2022, CC BY.

关键词： Biological systems

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DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

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Genomics, Proteomics & Bioinformatics 2020年第2期18卷 104-119页

作者： Tiansheng Zhu Yi Zhu Yue Xuan Huanhuan Gao Xue Cai Sander R.Piersma Thang V.Pham Tim Schelfhorst Richard R.G.D.Haas Irene V.Bijnsdorp Rui Sun Liang Yue Guan Ruan Qiushi Zhang Mo Hu Yue Zhou Winan J.Van Houdt Tessa Y.S.Le Large Jacqueline Cloos Anna Wojtuszkiewicz Danijela Koppers-Lalic Franziska Bottger Chantal Scheepbouwer Ruud H.Brakenhoff Geert J.L.H.van Leenders Jan N.M.Ijzermans John W.M.Martens Renske D.M.Steenbergen Nicole C.Grieken Sathiyamoorthy Selvarajan Sangeeta Mantoo Sze S.Lee Serene J.Y.Yeow Syed M.F.Alkaff Nan Xiang Yaoting Sun Xiao Yi Shaozheng Dai Wei Liu Tian Lu Zhicheng Wu Xiao Liang Man Wang Yingkuan Shao Xi Zheng Kailun Xu Qin Yang Yifan Meng Cong Lu Jiang Zhu Jin'e Zheng Bo Wang Sai Lou Yibei Dai Chao Xu Chenhuan Yu Huazhong Ying Tony K.Lim Jianmin Wu Xiaofei Gao Zhongzhi Luan Xiaodong Teng Peng Wu Shi'ang Huang Zhihua Tao Narayanan G.Iyer Shuigeng Zhou Wenguang Shao Henry Lam Ding Ma Jiafu Ji Oi L.Kon Shu Zheng Ruedi Aebersold Connie R.Jimenez Tiannan Guo Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Westlake UniversityHangzhou 310024China Key Laboratory of Structural Biology of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China School of Computer Science Shanghai Key Laboratory of Intelligent Information ProcessingFudan UniversityShanghai 200433China Thermo Fisher Scientific(BREMEN)GmbH Bremen 28195Germany OncoProteomics Laboratory Department of Medical OncologyVU University Medical CenterVU UniversityAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamUrologyCancer Center AmsterdamAmsterdam 1011The Netherlands Thermo Fisher Scientific Shanghai 201206China The Netherlands Cancer Institute Surgical OncologyAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamSurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPediatric Oncology/HematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamHematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamMedical OncologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamNeurosurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPathologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamOtolaryngology/Head and Neck SurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Erasmus MC University Medical Center PathologyRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center SurgeryRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center Medical OncologyRotterdam 1016LVThe Netherlands Department of Anatomical Pathology Singapore General HospitalSingapore 169608Singapore Division of Medical Scie

To address the increasing need for detecting and validating protein biomarkers in clinical specimens,mass spectrometry(MS)-based targeted proteomic techniques,including the selected reaction monitoring(SRM),parallel reaction monitoring(PRM),and massively parallel dataindependent acquisition(DIA),have been *** optimal performance,they require the fragment ion spectra of targeted peptides as prior *** this report,we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue *** build the spectral resource,we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on *** then applied the workflow to generate DPHL,a comprehensive DIA pan-human library,from 1096 data-dependent acquisition(DDA)MS raw files for 16 types of cancer *** extensive spectral resource was then applied to a proteomic study of 17 prostate cancer(PCa)***,PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was *** a second application,the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma(DLBCL)patients and 18 healthy control *** expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by *** data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker *** is freely accessible at https://***/page/***?id=IPX0001400000.

关键词： Data-independent acquisition Parallel reaction monitoring Spectral library Prostate cancer Diffuse large B cell lymphoma

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Using artificial intelligence to document the hidden RNA virosphere

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四川生理科学杂志 2024年第10期46卷 2345-2345页

作者： Xin Hou National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases State Key Laboratory for Biocontrol School of Medicine Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University Shenzhen China Apsara Lab Alibaba Cloud Intelligence Alibaba Group Hangzhou China Wuhan Centers for Disease Control and Prevention Wuhan China Polar Research Institute of China Shanghai China Department of Nursing The Fifth Affiliated Hospital Sun Yat-sen University Zhuhai China School of Geospatial Engineering and Science Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat-sen University Zhuhai China Key Laboratory of Comprehensive Observation of Polar Environment Ministry of Education Sun Yat-sen University Zhuhai China Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary Institute of Biodiversity Science and Institute of Eco-Chongming School of Life Sciences Fudan University Shanghai Shanghai China Centre for Virus Research Westmead Institute for Medical Research Westmead NSW Australia School of Medical Sciences The University of Sydney Sydney NSW 2006 Australia College of Life Sciences Zhejiang University Hangzhou China School of Life Science Guangzhou University Guangzhou China Key Laboratory of Pathogen Infection Prevention and Control (MOE) State Key Laboratory of Respiratory Health and Multimorbidity National Institute of Pathogen Biology Chinese Academy of Medical Sciences & Peking Union Medical College Beijing China School of Public Health (Shenzhen) Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University Shenzhen China Guangzhou National Laboratory Guangzhou International Bio-Island Guangzhou China Department of Infectious Diseases and Public Health Jockey Club College of Veterinary Medicine and Life Sciences City University of Hong Kong Hong Kong SAR China Laboratory of Data Disco

Current metagenomic tools can fail to identify highly divergent RNA *** developed a deep learning algorithm,termed LucaProt,to discover highly divergent RNA-dependent RNA polymerase(RdRP)sequences in 10,487 metatranscriptomes generated from diverse global *** integrates both sequence and predicted structural information,enabling the accurate detection of RdRP *** this approach,we identified 161,979 potential RNA virus species and 180 RNA virus supergroups,including many previously poorly studied groups,as well as RNA virus genomes of exceptional length(up to 47,250 nucleotides)and genomic complexity.

关键词： artificial exceptional integrate

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Mapping the Human Body at Cellular Resolution -- The NIH Common Fund Human BioMolecular Atlas Program

arXiv

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arXiv 2019年

作者： Snyder, Michael P. Lin, Shin Posgai, Amanda Atkinson, Mark Regev, Aviv Rood, Jennifer Rozenblatt-Rosen, Orit Gaffney, Leslie Hupalowska, Anna Satija, Rahul Gehlenborg, Nils Shendure, Jay Laskin, Julia Harbury, Pehr Nystrom, Nicholas A. Bar-Joseph, Ziv Zhang, Kun Börner, Katy Lin, Yiing Conroy, Richard Procaccini, Dena Roy, Ananda L. Pillai, Ajay Brown, Marishka Galis, Zorina S. Cai, Long Shendure, Jay Trapnell, Cole Lin, Shin Jackson, Dana Snyder, Michael P. Nolan, Garry Greenleaf, William James Lin, Yiing Plevritis, Sylvia Ahadi, Sara Lee, Hayan Nevins, Stephanie Esplin, Ed Horning, Aaron Bahmani, Amir Zhang, Kun Sun, Xin Jain, Sanjay Hagood, James Kharchenko, Peter Atkinson, Mark Bodenmiller, Bernd Brusko, Todd Clare-Salzler, Michael Nick, Harry Otto, Kevin Posgai, Amanda Wasserfall, Clive Maffioletti, Sergio Caprioli, Richard M. Spraggins, Jeffrey M. Gutierrez, Danielle Patterson, Nathan Heath Neumann, Elizabeth K. Harris, Raymond deCaestecker, Mark de Plas, Raf Van Lau, Ken Cai, Long Yuan, Guo-Cheng Zhu, Qian Dries, Ruben Yin, Peng Saka, Sinem K. Kishi, Jocelyn Y. Wang, Yu Goldaracena, Isabel Laskin, Julia Ye, DongHye Burnum-Johnson, Kristin E. Piehowski, Paul D. Ansong, Charles Zhu, Ying Harbury, Pehr Desai, Tushar Mulye, Jay Chou, Peter Nagendran, Monica Bar-Joseph, Ziv Teichmann, Sarah A. Paten, Benedict Murphy, Robert F. Ma, Jian Kiselev, Vladimir Yu Kingsford, Carl Ricarte, Allyson Ruffalo, Matthew Gehlenborg, Nils Kharchenko, Peter Vella, Margaret McCallum, Chuck Börner, Katy Cross, Leonard E. Friedman, Samuel H. Heiland, Randy Herr, Bruce Macklin, Paul Quardokus, Ellen M. Record, Lisel Sluka, James P. Weber, Griffin M. Nystrom, Nicholas A. Silverstein, Jonathan C. Blood, Philip D. Ropelewski, Alexander J. Shirey, William E. Mabee, Paula Lenhardt, W. Christopher Robasky, Kimberly Michailidis, Stavros Satija, Rahul Marioni, John Regev, Aviv Butler, Andrew Stuart, Tim Fisher, Eyal Ghazanfar, Shila Rood, Jennifer Gaffney, Leslie Ersalan, Gokcen Biancalani, Tommaso Conroy, Richard Procaccini, Dena Roy, Anan School of Medicine Stanford University 300 Pasteur Drive United States Department of Genetics Stanford School of Medicine StanfordCA94305 United States Department of Medicine University of Washington SeattleWA98195 United States Department of Pathology University of Florida Diabetes Institute GainesvilleFL32610 United States Klarman Cell Observatory Broad Institute of MIT and Harvard CambridgeMA02142 United States Howard Hughes Medical Institute Koch Institute of Integrative Cancer Research Department of Biology Massachusetts Institute of Technology CambridgeMA02140 United States New York Genome Center New York CityNY10013 United States New York University New YorkNY10012 United States Department of Biomedical Informatics Harvard Medical School BostonMA02115 United States Department of Genome Sciences University of Washington SeattleWA98105 United States Department of Chemistry Purdue University West LafayetteIN47907 United States Department of Biochemistry Stanford University School of Medicine StanfordCA94305 United States Pittsburgh Supercomputing Center Carnegie Mellon University PittsburghPA15213 United States Department of Computational Biology School of Computer Science Carnegie Mellon University PittsburghPA15213 United States Department of Bioengineering University of California San Diego La JollaCA92093 United States Department of Intelligent Systems Engineering School of Informatics Computing and Engineering Indiana University BloomingtonIN47408 United States Department of Surgery Washington University School of Medicine St LouisMO63110 United States Division of Program Coordination Planning and Strategic Initiatives National Institutes of Health BethesdaMD20892 United States National Human Genome Research Institute National Institutes of Health BethesdaMD20892 United States National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Caltech-UW TMC Departmen

Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible 3D molecular and cellular atlas of the human body, in health and various disease settings. Copyright © 2019, The Authors. All rights reserved.

关键词： Mapping

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