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Identifying common signatures and potential therapeutic biomarkers in COPD and lung cancer using miRNA-mRNA co-expression networks

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Informatics in Medicine Unlocked 2022年 34卷

作者： Fathinavid, Amirhossein Mousavian, Zaynab Najafi, Ali Nematzadeh, Sajjad Salimi, Mahdieh Masoudi-Nejad, Ali Department of Computer Engineering College of Engineering Hamedan Branch Islamic Azad University Hamedan Iran Laboratory of Systems Biology and Bioinformatics (LBB) Institute of Biochemistry and Biophysics University of Tehran Tehran Iran Department of Computer Science School of Mathematics Statistics and Computer Science University of Tehran Tehran Iran Molecular Biology Research Center System Biology and Poisoning Institute Tehran Iran Computer Engineering Department Architecture and Engineering Faculty Nisantasi University Istanbul Turkey Department of Medical Genetics Institute of Medical Biotechnology National Institute of Genetic Engineering and Biotechnology (NIGEB) Tehran Iran

The association between non-small cell lung cancer (NSCLC) and chronic obstructive pulmonary disease (COPD) is now well established, as people with COPD are more likely to develop lung carcinoma. However, the evidence for this relationship is inconclusive and there is currently little information on the underlying molecular mechanisms. MicroRNAs (miRNAs) are one of the regulatory factors in NSCLC and COPD that their functions are widely studied in many chronic diseases and cancers. In this study, we applied systems biology approaches to identify and predict miRNAs that potentially play regulatory roles between COPD and NSCLC. We performed differential expression analysis on public miRNA and mRNA expression datasets, for both of diseases, and then we reconstructed two miRNA-mRNA co-expression networks and merged these two co-expression networks into a community co-expression network. Results indicated the existence of very common miRNAs (ex. hsa-miR-326 and hsa-miR-1293) and mRNAs (such as FAT2, ALOX5AP, and LDB2) between the two mentioned diseases. Moreover, we discovered specific miRNAs (hsa-miR-574-3p) that targeted common mRNAs. We utilized drug-target interaction networks to identify candidate drugs for common mRNAs, which can be considered in the treatment of two diseases (e.g. iloperidone). Generally, our study highlighted common miRNAs between COPD and NSCLC that as new signatures or biomarkers for therapeutic purposes. Investigating the miRNA biomarkers in this study improves our understanding about the shared mechanisms between COPD and NSCLC. © 2022

关键词： Co-expression networks Community networks COPD miRNA-mRNA network Non-small cell lung cancer

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A Survey on Indoor Visible Light Positioning systems: Fundamentals, Applications, and Challenges

arXiv

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arXiv 2024年

作者： Zhu, Zhiyu Yang, Yang Chen, Mingzhe Guo, Caili Cheng, Julian Cui, Shuguang The Beijing Key Laboratory of Network System Architecture and Convergence School of Information and Communication Engineering Beijing University of Posts and Telecommunications Beijing100876 China The Department of Electrical and Computer Engineering Institute for Data Science and Computing University of Miami Coral GablesFL33146 United States The Beijing Laboratory of Advanced Information Networks School of Information and Communication Engineering Beijing University of Posts and Telecommunications Beijing100876 China The Faculty of Applied Science School of Engineering The University of British Columbia KelownaBCV1V 1V7 Canada The Chinese University of Hong Kong Shenzhen518172 China

The growing demand for location-based services in areas like virtual reality, robot control, and navigation has intensified the focus on indoor localization. Visible light positioning (VLP), leveraging visible light communications (VLC), becomes a promising indoor positioning technology due to its high accuracy and low cost. This paper provides a comprehensive survey of VLP systems. In particular, since VLC lays the foundation for VLP, we first present a detailed overview of the principles of VLC. Then, we provide an in-depth overview of VLP algorithms. The performance of each positioning algorithm is also compared in terms of various metrics such as accuracy, coverage, and orientation limitation. Beyond the physical layer studies, the network design for a VLP system is also investigated, including multi-access technologies, resource allocation, and light-emitting diode (LED) placements. Next, the applications of the VLP systems are overviewed. Finally, this paper outlines open issues, challenges, and opportunities for the research field. In a nutshell, this paper constitutes the first holistic survey on VLP from state-of-the-art studies to practical uses. Copyright © 2024, The Authors. All rights reserved.

关键词： Resource allocation

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Federated Edge Learning via Integrated Sensing, Computation, and Communication

Federated Edge Learning via Integrated Sensing, Computation,...

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IEEE International Conference on Communications (ICC)

作者： Peixi Liu Guangxu Zhu Shuai Wang Miaowen Wen Wu Luo H. Vincent Poor Shuguang Cui State Key Laboratory of Advanced Optical Communication Systems and Networks Peking University Shenzhen Research Institute of Big Data Chinese Academy of Sciences Shenzhen Institute of Advanced Technology School of Electronic and Information Engineering South China University of Technology Department of Electrical and Computer Engineering Princeton University the Guangdong Provincial Key Laboratory of Future Networks of Intelligence School of Science and Engineering (SSE) Future Network of Intelligence Institute (FNii) the Chinese University of Hong Kong Shenzhen

Sensing, computation, and communication (SC 2 ) are highly coupled processes in federated edge learning (FEEL) and need to be jointly designed in a task-oriented manner for pursuing the best FEEL performance under the stringent resource constraints at edge devices. However, this remains an open problem as there is a lack of theoretical understanding on how the SC 2 resources jointly affect the FEEL performance. In this paper, we address the problem of joint SC 2 resource allocation for FEEL via a concrete case study of human motion recognition based on wireless sensing. Specifically, the joint SC 2 resource allocation problem is cast to maximize the convergence speed of FEEL, under the constraints on training time and energy supply of each edge device. Solving this problem entails solving two subproblems in order: the first one reduces to determining a joint sensing and communication resource allocation that maximizes the total number of samples sensed during the entire training process; the second one concerns the partition of the total number of sensed samples over communication rounds to determine the batch size at each round for convergence speed maximization. Finally, extensive simulation results are provided to validate the superiority of the proposed scheme over several baseline schemes.

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Student Loss: Towards the Probability Assumption in Inaccurate Supervision

TechRxiv

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TechRxiv 2023年

作者： Zhang, Shuo Li, Jianqing Fujita, Hamido Li, Yuwen Wang, Dengbao Zhu, Tingting Zhang, Minling Liu, Chengyu The School of Instrument Science and Engineering The State Key Laboratory of Bioelectronics The School of Biological Science and Medical Engineering Southeast University Nanjing210096 China The State Key Laboratory of Bioelectronics School of Instrument Science and Engineering Southeast University Nanjing210096 China HUTECH University Ho Chi Minh City Viet Nam University of Granada Granada Spain Regional Research Center Iwate Prefectural University Iwate Japan The School of Computer Science and Engineering Southeast University Nanjing210096 China The Key Laboratory of Computer Network and Information Integration Southeast University Ministry of Education China The Department of Engineering Science University of Oxford OxfordOX3 7DQ United Kingdom

Noisy labels are often encountered in datasets, but learning with them is challenging. Although natural discrepancies between clean and mislabeled samples in a noisy category exist, most techniques in this field still gather them indiscriminately, which leads to their performances being partially robust. In this paper, we reveal both empirically and theoretically that the learning robustness can be improved by assuming deep features with the same labels follow a student distribution, resulting in a more intuitive method called student loss. By embedding the student distribution and exploiting the sharpness of its curve, our method is naturally data-selective. This ability makes clean samples aggregate tightly in the center, while mislabeled samples scatter, even if they share the same label. Additionally, we employ the metric learning strategy and develop a large-margin student (LT) loss for better capability. It should be noted that our approach is the first work that adopts the prior probability assumption in feature representation to decrease the contributions of mislabeled samples. This strategy can enhance various losses to join the student loss family, even if they have been robust losses. Experiments demonstrate that our approach is more effective in inaccurate supervision. Enhanced LT losses significantly outperform various state-of-the-art methods in most cases. Even huge improvements of over 50% can be obtained under certain conditions. An implementation of the main codes is available at https://***/Zhangshuojackpot/Student-Loss. © 2023, CC BY.

关键词： Students

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Enhancing Tilapia Harvesting through Semi-automated Fish Pen Elevating system and Single-input-multiple-output Aquaculture Pump system 14

Enhancing Tilapia Harvesting through Semi-automated Fish Pen...

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14th IEEE International Conference on Humanoid, Nanotechnology, Information Technology, Communication and Control, Environment, and Management, HNICEM 2022

作者： Bejar, Althea Tiffanie A. Ouyang, Jon Kinsly T. Villabroza, Vince Miguel D. Correa, Aurelle Mikael Concepcion, Ronnie Palconit, Maria Gemel Vicerra, Ryan Rhay Duarte, Bernardo Fonseca, Vanessa F. De la Salle University Department of Manufacturing Engineering and Management Manila Philippines De la Salle University Department of Electronics and Computer Engineering Manila Philippines Faculdade de Ciências da Universidade de Lisboa MARE - Marine and Environmental Sciences Centre ARNET - Aquatic Research Infrastructure Network Laboratory Lisbon1749-016 Portugal Universidade de Lisboa Faculdade de Ciências Departamento de Biologia Vegetal Lisbon Portugal Universidade de Lisboa Faculdade de Ciências Departamento de Biologia Animal Lisbon Portugal

ISBN: (纸本)9781665464932

Fish is a staple in the diet of nations globally and is cultured and harvested using various practices such as open sea fishing and aquaculture. In fact, the fisheries and aquaculture industry are valued at 250 billion as a whole and contribute to almost 2% of the Philippines' Gross Domestic Product;therefore, it is an industry with constant great demand. Aquaculture practice is where fish, shellfish, and other consumable marine species are cultivated by fishermen using traditional methods and experience typically manually operated via fish pens. However, occupational hazards exposed to fishermen in the industry often result in injury and long-term health effects. Thus, there is a need to semi-automate the labour-intensive task of fish harvesting by applying concepts from common current aquaculture practices and control systems engineering. This study develops two systems, namely: a fish pen elevating system and a single-input-multiple-output aquaculture pump system, for harvesting of tilapia in the Laguna de Bay, Philippines, based on the vastness of the lake, the quantity of open water fish pens located in the area, and the species being the most produced in this type of fish pen as a whole. The discussion of existing aquacultures around the world is also included in this study to show advancements in technology when it comes to this industry. The two proposed systems presented integrate the automation of the process where fish is brought to the surface via raising the base frame of the fish pen or its surrounding poles. The proper application of each system should result in more efficient harvests, fewer injuries to fishermen, and improved production volumes. © 2022 IEEE.

关键词： Fish

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Tunable unidirectional surface plasmon-polaritons at the interface between gyrotropic and isotropic conductors 22

Tunable unidirectional surface plasmon-polaritons at the int...

引用

22nd International Conference on Electromagnetics in Advanced Applications, ICEAA 2021

作者： Liang, Y. Pakniyat, S. Xiang, Y. Chen, J. Shi, F. Hanson, G.W. Cen, C. West Virginia University Department of Physics and Astronomy MorgantownWV26506 United States University of Wisconsin-Milwaukee Department of Electrical Engineering MilwaukeeWI53211 United States University of Pittsburgh Peterson Institute of Nano Science and Engineering Department of Electrical and Computer Engineering PittsburghPA15261 United States Guangxi Key Lab for Relativistic Astrophysics Center on Nanoenergy Research School of Physical Science and Technology Guangxi University Nanning Guangxi530004 China Key Laboratory of Computer Vision and System of Ministry of Education Tianjin University of Technology Tianjin300384 China

ISBN: (纸本)9781665413862

The propagation of SPPs in solid state systems is usually reciprocal, which means that a forward-traveling SPP wave can be easily backscattered by disorders. Since such backscattering is detrimental for SPP-based information processing applications, the development of nonreciprocal plasmonic platforms that enforce unidirectional SPP propagations is of great importance. © 2021 IEEE.

关键词： Electromagnetic wave polarization

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The Deep-Time Digital Earth program: data-driven discovery in geosciences

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National Science Review 2021年第9期8卷 156-166页

作者： Chengshan Wang Robert M.Hazen Qiuming Cheng Michael H.Stephenson Chenghu Zhou Peter Fox Shu-zhong Shen Roland Oberhansli Zengqian Hou Xiaogang Ma Zhiqiang Feng Junxuan Fan Chao Ma Xiumian Hu Bin Luo Juanle Wang Craig M.Schiffries State Key Laboratory of Biogeology and Environmental Geology China University of Geosciences School of the Earth Science and Resources China University of Geosciences Earth and Planets Laboratory Carnegie Institution for Science State Key Laboratory of Geological Processes and Mineral Resources China University of Geosciences British Geological Survey State Key Laboratory of Resources and Environment Information System Institute of Geographical Science and Natural Resources Chinese Academy of Sciences Tetherless World Constellation Rensselaer Polytechnic Institute School of Earth Sciences and Engineering Nanjing University Institute of Earth and Environmental Sciences University of Potsdam Institute of Geology Chinese Academy of Geological Sciences Department of Computer Science University of Idaho Petroleum Exploration and Production Research Institute SINOPEC DDE Center of Excellence(Suzhou)

Current barriers hindering data-driven discoveries in deep-time Earth(DE) include: substantial volumes of DE data are not digitized; many DE databases do not adhere to FAIR(findable, accessible, interoperable and reusable) principles; we lack a systematic knowledge graph for DE; existing DE databases are geographically heterogeneous; a significant fraction of DE data is not in open-access formats; tailored tools are needed. These challenges motivate the Deep-Time Digital Earth(DDE) program initiated by the International Union of Geological Sciences and developed in cooperation with national geological surveys,professional associations, academic institutions and scientists around the world. DDE's mission is to build on previous research to develop a systematic DE knowledge graph, a FAIR data infrastructure that links existing databases and makes dark data visible, and tailored tools for DE data, which are universally accessible. DDE aims to harmonize DE data, share global geoscience knowledge and facilitate data-driven discovery in the understanding of Earth's evolution.

关键词： Deep-Time Digital Earth data-driven discovery big data Earth evolution cyberinfrastructure

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Protocol for the fabrication of self-standing (nano)cellulose-based 3D scaffolds for tissue engineering

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STAR Protocols 2025年第1期6卷 103583页

作者： Mohan, Tamilselvan Bračič, Matej Bračič, Doris Lackner, Florian Nagaraj, Chandran Štiglic, Andreja Dobaj Kargl, Rupert Kleinschek, Karin Stana Graz University of Technology Institute for Chemistry and Technology of Biobased System (IBioSys) Stremayrgasse 9 Graz 8010 Austria University of Maribor Faculty of Mechanical Engineering Laboratory for Characterization and Processing of Polymers Smetanova Ulica 17 Maribor 2000 Slovenia Department of Internal Medicine Division of Pulmonology Medical University of Graz Graz Austria Institute of Automation Faculty of Electrical Engineering and Computer Science University of Maribor Maribor Slovenia Members of the European Polysaccharide Network of Excellence (EPNOE) Austria

Three-dimensional (3D) and porous scaffolds made from nanocellulosic materials hold significant potential in tissue engineering (TE). Here, we present a protocol for fabricating self-standing (nano)cellulose-based 3D scaffolds designed for in vitro testing of cells from skin and cartilage tissues. We describe steps for preparation of nanocellulose ink, scaffold formation using 3D printing, and freeze-drying. We then detail post-processing procedures to enhance mechanical properties, stability, and biocompatibility. This protocol offers researchers a framework for developing versatile and sustainable biomaterials for regenerative medicine. For complete details on the use and execution of this protocol, please refer to Mohan et al.¹ and Štiglic et al.² © 2025 The Authors

关键词： Biotechnology and bioengineering Chemistry Material sciences Tissue engineering

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Optical Intelligent Reflecting Surface Assisted MIMO VLC: Channel Modeling and Capacity Characterization

arXiv

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arXiv 2023年

作者： Sun, Shiyuan Mei, Weidong Yang, Fang An, Nan Song, Jian Zhang, Rui The Department of Electronic Engineering Tsinghua University Beijing100084 China The Key Laboratory of Digital TV System of Shenzhen City Research Institute of Tsinghua University in Shenzhen Shenzhen518057 China The Shenzhen International Graduate School Tsinghua University Shenzhen518055 China The Department of Electrical and Computer Engineering National University of Singapore Singapore117583 Singapore The Chinese University of Hong Kong Shenzhen China Shenzhen Research Institute of Big Data Shenzhen518172 China

Although the multi-antenna or so-called multiple-input multiple-output (MIMO) transmission has been the enabling technology for the past generations of radio-frequency (RF)-based wireless communication systems, its application to the visible light communication (VLC) still faces a critical challenge as the MIMO spatial multiplexing gain can be hardly attained in VLC channels due to their strong spatial correlation. In this paper, we tackle this problem by deploying the optical intelligent reflecting surface (OIRS) in the environment to boost the capacity of MIMO VLC. Firstly, based on the extremely near-field channel condition in VLC, we propose a new channel model for OIRS-assisted MIMO VLC and reveal its peculiar "no crosstalk" property, where the OIRS reflecting elements can be respectively configured to align with one pair of transmitter and receiver antennas without causing crosstalk to each other. Next, we characterize the OIRS-assisted MIMO VLC capacities under different practical power constraints and then proceed to maximize them by jointly optimizing the OIRS element alignment and transmitter emission power. In particular, for optimizing the OIRS element alignment, we propose two algorithms, namely, location-aided interior-point algorithm and log-det-based alternating optimization algorithm, to balance the performance versus complexity trade-off;while the optimal transmitter emission power is derived in closed form. Numerical results are provided, which validate the capacity improvement of OIRS-assisted MIMO VLC against the VLC without OIRS and demonstrate the superior performance of the proposed algorithms compared to baseline schemes. Copyright © 2023, The Authors. All rights reserved.

关键词： Visible light communication

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A Risk-Averse Just-In-Time Scheme for Learning-Based Operation of Microgrids with Coupled Electricity-Hydrogen-Ammonia under Uncertainties

arXiv

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arXiv 2024年

作者： Li, Longyan Ning, Chao Pan, Guangsheng Zhang, Leiqi Gu, Wei Zhao, Liang Du, Wenli Shahidehpour, Mohammad Department of Automation Shanghai Jiao Tong University Shanghai200240 China Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China School of Electrical Engineering Southeast University Nanjing210096 China Zhejiang Key Laboratory of Distributed Generations and Microgrid Technology State Grid Zhejiang Electric Power Research Institute Hangzhou310014 China Key Laboratory of Smart Manufacturing in Energy Chemical Process Ministry of Education East China University of Science and Technology China Department of Electrical and Computer Engineering Illinois Institute of Technology ChicagoIL60616 United States

This paper proposes a Risk-Averse Just-In-Time (RAJIT) operation scheme for Ammonia-Hydrogen-based Micro-Grids (AHMGs) to boost electricity-hydrogen-ammonia coupling under uncertainties. First, an off-grid AHMG model is developed, featuring a novel multi-mode ammonia synthesis process and a hydrogen-ammonia dual gas turbine with tunable feed-in ratios. Subsequently, a state-behavior mapping strategy linking hydrogen storage levels with the operation modes of ammonia synthesis is established to prevent cost-ineffective shutdowns. The proposed model substantially improves operational flexibility but results in a challenging nonlinear fractional program. Based upon this model, a data-driven RAJIT scheme is developed for the real-time rolling optimization of AHMGs. Unlike conventional one-size-fits-all schemes using one optimization method throughout, the data-driven RAJIT intelligently switches between cost-effective deterministic optimization and risk-averse online-learning distributionally robust optimization depending on actual risk profiles, thus capitalizing on the respective strengths of these two optimization methods. To facilitate the solution of the resulting nonlinear program, we develop an equivalent-reformulation-based solution methodology by leveraging a constraint-tightening technique. Numerical simulations demonstrate that the proposed scheme guarantees safety and yields an overall cost reduction up to 14.6% compared with several state-of-the-art methods. © 2024, CC BY.

关键词： Ammonia

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