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Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats

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Journal of Advanced research 2024年

作者： Matsumoto, Yuki Yik-Lok Chung, Claire Isobe, Sachiko Sakamoto, Mika Lin, Xiao Chan, Ting-Fung Hirakawa, Hideki Ishihara, Genki Lam, Hon-Ming Nakayama, Shinobu Sasamoto, Shigemi Tanizawa, Yasuhiro Watanabe, Akiko Watanabe, Kei Yagura, Masaru Niimura, Yoshihito Nakamura, Yasukazu Research and Development Section Anicom Specialty Medical Institute Inc. Kanagawa Yokohama Japan Data Science Center Azabu University Kanagawa Sagamihara Japan School of Life Sciences and the Center for Soybean Research of the State Key Laboratory of Agrobiotechnology The Chinese University of Hong Kong Shatin Hong Kong Kazusa DNA Research Institute Chiba Kisarazu Japan National Institute of Genetics Research Organization of Information and Systems Shizuoka Mishima Japan Department of Veterinary Sciences Faculty of Agriculture University of Miyazaki Miyazaki Miyazaki Japan

Introduction: Comprehensive genomic resources offer insights into biological features, including traits/disease-related genetic loci. The current reference genome assembly for the domestic cat (Felis catus), Felis_Catus_9.0 (felCat9), derived from sequences of the Abyssinian cat, may inadequately represent the general cat population, limiting the extent of deducible genetic variations. Objectives: The goal was to develop Anicom American Shorthair 1.0 (AnAms1.0), a reference-grade chromosome-scale cat genome assembly. Methods: In contrast to prior assemblies relying on Abyssinian cat sequences, AnAms1.0 was constructed from the sequences of more popular American Shorthair breed, which is related to more breeds than the Abyssinian cat. By combining advanced genomics technologies, including PacBio long-read sequencing and Hi-C- and optical mapping data-based sequence scaffolding, we compared AnAms1.0 to existing Felidae genome assemblies (20 scaffolds, scaffolds N50 > 150 Mbp). Homology-based and ab initio gene annotation through Iso-Seq and RNA-Seq was used to identify new coding genes and splice variants. Results: AnAms1.0 demonstrated superior contiguity and accuracy than existing Felidae genome assemblies. Using AnAms1.0, we identified over 1.5 thousand structural variants and 29 million repetitions compared to felCat9. Additionally, we identified > 1,600 novel protein-coding genes. Notably, olfactory receptor structural variants and cardiomyopathy-related variants were identified. Conclusion: AnAms1.0 facilitates the discovery of novel genes related to normal and disease phenotypes in domestic cats. The analyzed data are publicly accessible on Cats-I (https://***/), which we established as a platform for accumulating and sharing genomic resources to discover novel genetic traits and advance veterinary medicine. © 2024

关键词： Feline genomics Hi-C sequencing Olfactory receptor genes PacBio sequencing Precision medicine Structural variants

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Depth Estimation of the Object of Interest in Challenging Cross-Domain Scenes

SSRN

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SSRN 2023年

作者： Xu, Chenglong Chen, Chu Xing, Wen Herrera-Viedma, Enrique College of Intelligent Systems Science and Engineering Harbin Engineering University Harbin150001 China Qingdao Innovation and Development Center Harbin Engineering University Qingdao266000 China Shenyang SIASUN Robot & Automation Co. LTD Shenyang110168 China Andalusian Research Institute of Data Science and Computational Intelligence Department of Computer Science and AI University of Granada Granada18071 Spain

Depth estimation plays an important role in 3D visual perception, autonomous vehicles, and near-field optical detection. At present, there are mainly learning-based methods and traditional geometric constraint reasoning based methods. However, most learning-based methods have poor cross-domain generalization, the accuracy will be greatly reduced when tested on new scenes. Although the traditional geometric methods have strong scene adaptability, they have more marginal noise in depth discontinuity areas, and require a large amount of memory at a high bandwidth. In order to solve the above problems, we present a disparity confidence propagation and edge smoothing framework, which combines robust semantic mask with tree diffusion model. Compared with those of state-of-the-art fast geometric constraint based methods and learning-based methods, the proposed method has a great improvement in cross-domain adaptability and efficiency. Experiments on multiple data sets verify the effectiveness of the method, and a good balance is achieved between generalization and accuracy. © 2023, The Authors. All rights reserved.

关键词： Semantics

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Artificial intelligence to improve clinical coding practice in Scandinavia: a crossover randomized controlled trial

arXiv

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arXiv 2024年

作者： Chomutare, Taridzo Svenning, Therese Olsen Tejedor Hernández, Miguel Ángel Ngo, Phuong Dinh Budrionis, Andrius Markljung, Kaisa Hind, Lill Irene Torsvik, Torbjørn Mikalsen, Karl Øyvind Babic, Aleksandar Dalianis, Hercules Health Data Analytics Norwegian Centre for E-health Research Tromsø Norway Department of Computer Science UiT The Arctic University of Norway Tromsø Norway Department of Mathematics and Statistics UiT The Arctic University of Norway Tromsø Norway Department of Physics and Technology UiT The Arctic University of Norway Tromsø Norway University Hospital of North Norway Tromsø Norway University Hospital of North Norway Tromsø Norway Department of Computer and Systems Sciences Stockholm University Kista Sweden Group Research and Development DNV Høvik Norway

Trial design Crossover randomized controlled trial. Methods An AI tool, Easy-ICD, was developed to assist clinical coders and was tested for improving both accuracy and time in a user study in Norway and Sweden. Participants were randomly assigned to two groups, and crossed over between coding complex (longer) texts versus simple (shorter) texts, while using our tool versus not using our tool. Results Based on Mann-Whitney U test, the median coding time difference for complex clinical text sequences was 123 seconds (P Copyright © 2024, The Authors. All rights reserved.

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Anisotropic Exchange Spin Model to Investigate the Curie Temperature Dispersion of Finite-Size L10-FePt Magnetic Nanoparticles

arXiv

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arXiv 2025年

作者： Ochiai, Kohei Tsuyama, Tomoyuki Shimizu, Sumera Zhang, Lei Watanabe, Jin Kudo, Fumito Zhu, Jian-Gang Okuno, Yoshishige Resonac Corporation Research Center for Computational Science and Informatics 8 Ebisu-cho Kanagawa-ku Kanagawa. Yokohama221-8517 Japan Resonac Hard Disk Corporation Research & Development Center 5-1 Yawatakaigan-dori Chiba Ichihara290-0067 Japan Data Storage Systems Center Carnegie Mellon University PittsburghPA15213 United States Electrical and Computer Engineering Department Carnegie Mellon University PittsburghPA15213 United States Materials Science and Engineering Department Carnegie Mellon University PittsburghPA15213 United States

We developed an anisotropic spin model that accounts for magnetic anisotropy and evaluated the Curie temperature (Tc) dispersion due to finite size effects in L10-FePt nanoparticles. In heat-assisted magnetic recording (HAMR) media, a next-generation magnetic recording technology, high-density recording is achieved by locally heating L10-FePt nanoparticles near their Tc and rapidly cooling them. However, variations in Tc caused by differences in particle size and shape can compromise recording stability and areal density capacity, making the control of Tc dispersion critical. In this study, we constructed atomistic LLG models to explicitly incorporate the spin exchange anisotropy of L10-FePt, based on parameters determined by first-principles calculations. Using this model, we evaluated the impact of particle size on Tc dispersion. As a result, (1) the Tc dispersion critical to the performance of HAMR can be reproduced, whereas it was previously underestimated by isotropic models and (2) approximately 70% of the experimentally observed Tc dispersion can be attributed to particle size effects. This research highlights the role of exchange anisotropy in amplifying finite-size effects and underscores the importance of size control in HAMR media. Copyright © 2025, The Authors. All rights reserved.

关键词： Curie temperature

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Effusol ameliorates ischemic stroke by targeting NLRP3 protein to regulate NLRP3 inflammasome-mediated pyroptosis

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Phytomedicine 2025年 136卷 156253页

作者： Xu, Libin Li, Siyu Qi, Jiaxin Mi, Yan Zhang, Ying Yang, Yuxin Wang, Yingjie Zhou, Di Li, Ning Hou, Yue Key Laboratory of Bioresource Research and Development of Liaoning Province College of Life and Health Sciences National Frontiers Science Center for Industrial Intelligence and Systems Optimization Key Laboratory of Data Analytics and Optimization for Smart Industry Ministry of Education Northeastern University Shenyang China School of Traditional Chinese Materia Medica Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning province Key Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang City Shenyang Pharmaceutical University Shenyang 110016 China

Background: The significance of pyroptosis as an inflammatory mode of death in ischemic stroke (IS) has attracted much attention in recent years. Effusol is a dihydrophenanthrene component extracted from Juncus effusus L. Previous studies have found that Juncus effusus L. has a good inhibitory effect against microglia activation. However, it is not clear whether effusol inhibits microglia over-activation and attenuates its mediated microglia pyroptosis in the treatment of IS. Purpose: The aim is to examine how effusol influences the initiation and activation stages of pyroptosis, as well as the NLRP3 inflammasome, resulting from microglial over-activation triggered post-IS. Methods: This study investigated the impact of effusol on neurological severity and edema to assess its neuroprotective effects in IS. Mechanistically, immunofluorescence and western blotting were applied to explore the initiation and activation of the NLRP3 inflammasome. Finally, we employed the NLRP3 specific inhibitor, molecular docking, drug affinity responsive target stability (DARTS), and cellular thermal shift assay (CETSA) to further explore the underlying targets of effusol. Results: Effusol mitigated IS-induced damage and downregulated the expression of inflammatory factors at the mRNA level, the protein levels of toll-like receptor 4 (TLR4), nuclear transcription factor NF-κB p65, and key components of the NLRP3 inflammasome. Effusol also mitigated mitochondrial damage by increasing ATP levels and decreasing mitochondrial membrane potential. Importantly, effusol targets NLRP3 protein to inhibit pyroptosis, thereby suppressing the hyperactivation of NLRP3 inflammasome. Conclusions: Effusol may be protective against IS by targeting NLRP3 proteins to inhibit NLRP3 inflammasome activation-mediated pyroptosis. This finding provides a theoretical basis and a prospective drug candidate for the treatment of effusol in IS. © 2024 Elsevier GmbH

关键词： Effusol Ischemic stroke Microglia NLRP3 inflammasome Pyroptosis

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Digital Twin-Enabled Real-Time Optimization System for Traffic and Power Grid Management in 6G-Driven Smart Cities

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IEEE Internet of Things Journal 2025年

作者： Prathiba, Sahaya Beni Krishnamoorthy, Sri Ram Kannan, Karuna Soundari Selvaraj, Arikumar K. Ranganayakulu, Dhanalakshmi Fang, Kai Gadekallu, Thippa Reddy Vellore Institute of Technology Centre for Cyber Physical Systems School of Computer Science and Engineering Chennai600127 India Vellore Institute of Technology School of Electronics Engineering Chennai600127 India College of Engineering and Technology Department of Data Science and Business Systems Kattankulathur603 203 India Zhejiang A and F University College of Mathematics and Computer Science Hangzhou311300 China Zhejiang A and F University Division of Research and Development Lovely Professional University College of Mathematics and Computer Science Hangzhou Phagwara311300 India Chitkara University Center of Research Impact and Outcome Punjab Rajpura140401 India

The advent of 6G-enabled Internet of Everything(IoE) technologies is set to revolutionize urban infrastructures by providing fast, consistent, and low-delay capabilities for communication. 6G connectivity will integrate traffic and power grids for adaptive urban management. However, current traffic networks and power grids face critical challenges such as fragmented data processing, delayed responses, and outdated resource management leading to inefficiencies like traffic congestion and power outages. In 6G-enabled smart grid cities, system complexity and interdependence demand dynamic, real-time solutions, further exacerbating inefficiencies. To address these issues, this study introduces Digital Twin-enabled Real-time Optimization System (DT-ROS), a dynamic framework designed to optimize urban traffic and power grid systems. DT-ROS integrates a dual-tier Digital Twin (DT) and an advanced scheduling framework based on Priority Age of Information Deep Q Scheduler (PAoI-QS). The dual-tier framework builds an elementary and Integrated Digital Twin (IDT) with Auto-Regressive Integrated Moving Average (ARIMA)-based forecasting for accurate real-time traffic and energy demand predictions. The advanced scheduling framework minimizes the Age of Information (AoI), ensuring decision-making relies on the most current and relevant data. By continuously monitoring and processing real-time data, DT-ROS creates virtual models to simulate system behavior and dynamically allocate resources. Simulation results demonstrate the effectiveness of DT-ROS, achieving a 30% reduction in traffic congestion and a 25% improvement in power grid stability compared to existing methods. To create effective, robust, and sustainable urban systems for future smart cities, DT-ROS addresses traffic and electricity problems. © 2014 IEEE.

关键词： Smart power grids

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A Method to Recognize Significant Informative Speech Signal Parameters Relevant to Human Emotional States

A Method to Recognize Significant Informative Speech Signal ...

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Annual Siberian Russian Workshop on Electron Devices and Materials (EDM)

作者： Alan K. Alimuradov Alexander Yu. Tychkov Oksana S. Simakova Anna N. Tychkova Anna A. Mamonova Pyotr P. Churakov Student Research and Production Business Incubator Penza State University Penza Russia Department of Radio Engineering and Radioelectronic Systems Penza State University Penza Russia Department for Comprehensive Development of Inclusive Education Penza State University Penza Russia Department of Scientific and Innovation Penza State University Penza Russia Department of Translation and Translation Theory Penza State University Penza Russia Data Measuring Equipment and Metrology Department Penza State University Penza Russia

ISBN: (数字)9798350389234

ISBN: (纸本)9798350353051

At present, various physiological signals that capture electrical activity from the human body (electrocardiography, electroencephalography, oculography, etc.) are used to detect and classify emotional states. Since the speech apparatus is sensitive to the nervous system disorders, human emotional states and emotions are encoded into relevant speech parameters contingent upon the psychological situation. This paper aims to assess the reliability of recognizing significant informative emotional speech parameters, and the degree of relevance thereof to the emotions experienced by a person. The scientific novelty of the work is to determine the threshold values for critical human emotional states under extreme conditions. The article proposes a method to recognize significant informative speech signal parameters using energy, prosodic, format, spectral, timing, cepstral, and nonlinear Teager energy operator-based analyzes. The method provides the possibility of expanding the information space for speech signal parameters through the use of a mathematical representation model based on the empirical mode decomposition modifications. The proposed method was investigated using a speech signal database of human negative (fear, disgust, anger, and sadness), neutral, and positive (surprise, joy) emotional states recorded in human real-life experiencing emotions. The research results have evidenced that the proposed method provides high-level relevance to human natural emotional states. The research findings have revealed the minimum and maximum recorded changes in the values of significant informative parameters for negative and positive states relative to a conditionally exemplary neutral state (a decrease by 18% and an increase by 40%, respectively).

关键词： Emotion recognition Empirical mode decomposition Psychology Speech recognition Nervous system Physiology Mathematical models

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Linking data Sovereignty and data Economy: Arising Areas of Tension 17

Linking Data Sovereignty and Data Economy: Arising Areas of ...

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17th International Conference on Wirtschaftsinformatik, WI 2022

作者： Lauf, Florian Scheider, Simon Bartsch, Jan Herrmann, Philipp Radic, Marija Rebbert, Marcel Nemat, André T. Schlueter-Langdon, Christoph Konrad, Ralf Sunyaev, Ali Meister, Sven Fraunhofer Institute for Software and Systems Engineering ISST Healthcare Dortmund Germany TU Dortmund Chair of Industrial Information Management Dortmund Germany Department of Economics and Management Karlsruhe Germany Fraunhofer Center for International Management and Knowledge Economy IMW Corporate Development in International Competition Division Leipzig Germany Witten/Herdecke University Institute for Digital Transformation in Healthcare GmbH Witten Germany T-Systems International GmbH Digital Solutions - Data Intelligence Hub Frankfurt Germany Claremont Graduate University Drucker School of Management Claremont United States KASTEL Security Research Labs Karlsruhe Germany Witten/Herdecke University Faculty of Health School of Medicine Witten Germany

In the emerging information economy, data evolves as an essential asset and personal data in particular is used for data-driven business models. However, companies frequently leverage personal data without considering individuals’ data sovereignty. Therefore, we strive to strengthen individuals’ position in data ecosystems by combining concepts of data sovereignty and data economy. Our research design comprises an approach to design thinking iteratively generating, validating, and refining such concepts. As a result, we identified ten areas of tension that arise when linking data sovereignty and data economy. Subsequently, we propose initial solutions to resolve these tensions and thus contribute to knowledge about the development of fair data ecosystems benefiting both individuals’ sovereignty and companies’ access to data. © 2022 17th International Conference on Wirtschaftsinformatik, WI 2022. All rights reserved.

关键词： Ecosystems

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Post-Quantum Blockchain over Lattice

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Computers, Materials & Continua 2020年第5期63卷 845-859页

作者： Xiao Zhang Faguo Wu Wang Yao Wenhua Wang Zhiming Zheng School of Mathematics and Systems Science Beihang Universityand Key Laboratory of MathematicsInformatics and Behavioral SemanticsMinistry of EducationBeijing100191China Peng Cheng Laboratory Shenzhen518055China Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang UniversityBeijing100191China Aviation Industry Development Research Center of China BeijingChina

Blockchain is an emerging decentralized architecture and distributed computing paradigm underlying Bitcoin and other cryptocurrencies,and has recently attracted intensive attention from governments,financial institutions,high-tech enterprises,and the capital *** cryptographic security relies on asymmetric cryptography,such as ECC,***,with the surprising development of quantum technology,asymmetric cryptography schemes mentioned above would become ***,lattice-based cryptography scheme was proposed to be secure against attacks in the quantum *** 2018,with the aid of Bonsai Trees technology,Yin et al.[Yin,Wen,Li et al.(2018)]proposed a lattice-based authentication method which can extend a lattice space to multiple lattice spaces accompanied by the corresponding *** their scheme has theoretical significance,it is unpractical in actual situation due to extremely large key size and signature *** this paper,aiming at tackling the critical issue of transaction size,we propose a post quantum blockchain over *** using SampleMat and signature without trapdoor,we can reduce the key size and signature size of our transaction authentication approach by a significant *** of using a whole set of vectors as a basis,we can use only one vector and rotate it enough times to form a *** on the hardness assumption of Short Integer Solution(SIS),we demonstrate that the proposed anti-quantum transaction authentication scheme over lattice provides existential unforgeability against adaptive chosen-message attacks in the random *** compared to the Yin et al.[Yin,Wen,Li et al.(2018)]scheme,our scheme has better performance in terms of energy consumption,signature size and signing key *** the underlying lattice problem is intractable even for quantum computers,our scheme would work well in the quantum age.

关键词： Blockchain post quantum lattice random oracle

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地理大数据揭示中国主要城市建成环境物质存量的空间格局

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Engineering 2024年第3期34卷 143-153页

作者： Zhou Huang Yi Bao Ruichang Mao Han Wang Ganmin Yin Lin Wan Houji Qi Qiaoxuan Li Hongzhao Tang Qiance Liu Linna Li Bailang Yu Qinghua Guo Yu Liu Huadong Guo Gang Liu Institute of Remote Sensing and Geographical Information Systems School of Earth and Space SciencesPeking UniversityBeijing 100871China International Research Center of Big Data for Sustainable Development Goals Beijing 100094China SDU Life Cycle Engineering Department of Green TechnologyUniversity of Southern DenmarkOdense 5230Denmark Department of Construction Management School of Civil EngineeringTsinghua UniversityBeijing 100084China School of Computer Science China University of GeosciencesWuhan 430074China School of Geographical Sciences East China Normal UniversityShanghai 200062China Land Satellite Remote Sensing Application Center Ministry of Natural ResourcesBeijing 100048China Institute of Geographic Sciences and Natural Resources Research Chinese Academy of SciencesBeijing 100101China Department of Geography California State UniversityLong BeachCA 90840USA Aerospace Information Research Institute Chinese Academy of SciencesBeijing 100094China College of Urban and Environmental Sciences Peking UniversityBeijing 100871China

The patterns of material accumulation in buildings and infrastructure accompanied by rapid urbanization offer an important,yet hitherto largely missing stock perspective for facilitating urban system engineering and informing urban resources,waste,and climate ***,our existing knowledge on the patterns of built environment stocks across and particularly within cities is limited,largely owing to the lack of sufficient high spatial resolution *** study leveraged multi-source big geodata,machine learning,and bottom-up stock accounting to characterize the built environment stocks of 50 cities in China at 500 m fine-grained *** per capita built environment stock of many cities(261 tonnes per capita on average)is close to that in western cities,despite considerable disparities across cities owing to their varying socioeconomic,geomorphology,and urban form *** is mainly owing to the construction boom and the building and infrastructure-driven economy of China in the past ***’s urban expansion tends to be more“vertical”(with high-rise buildings)than“horizontal”(with expanded road networks).It trades skylines for space,and reflects a concentration-dispersion-concentration pathway for spatialized built environment stocks development within cities in *** results shed light on future urbanization in developing cities,inform spatial planning,and support circular and low-carbon transitions in cities.

关键词： Urban system engineering Built environment stock Spatial pattern Urban sustainability Big geodata

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