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Decomposition of dynamic transcriptomic responses during effector-triggered immunity reveals conserved responses in two distinct plant cell populations

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Plant Communications 2024年第8期5卷 1-17页

作者： Xiaotong Liu Daisuke Igarashi Rachel A.Hillmer Thomas Stoddard You Lu Kenichi Tsuda Chad L.Myers Fumiaki Katagiri Department of Plant and Microbial Biology University of Minnesota-Twin CitiesSt PaulMN 55108USA Department of Computer Science and Engineering University of Minnesota-Twin CitiesMinneapolisMN 55455USA Bioinformatics and Computational Biology Graduate Program University of Minnesota-Twin CitiesMinneapolisMN 55455USA Institute for Innovation Ajinomoto Co.Inc.KawasakiJapan State Key Laboratory of Agricultural Microbiology Hubei Hongshan LaboratoryHubei Key Lab of Plant PathologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Present address:225 S 6th St MinneapolisMN 55402USA Present address:Biotalys Inc.2520 Meridian Parkway Suite 480DurhamNC 27713USA Present address:Life Sciences Institute and Department of Cell and Developmental Biology University of Michigan Medical SchoolAnn ArborMI 48109USA

Rapid plant immune responses in the appropriate cells are needed for effective defense against *** transcriptome analysis is often used to describe overall immune responses,collection of transcriptome data with sufficient resolution in both space and time is *** reanalyzed public Arabidopsis time-course transcriptome data obtained after low-dose inoculation with a Pseudomonas syringae strain expressing the effector AvrRpt2,which induces effector-triggered immunity in ***-peak time-course patterns are prevalent among thousands of upregulated *** implemented a multicompartment modeling approach to decompose the double-peak pattern into two single-peak patterns for each *** decomposed peaks reveal an“echoing”pattern:the peak times of the first and second peaks correlate well across most upregulated *** demonstrated that the two peaks likely represent responses of two distinct cell populations that respond either cell autonomously or indirectly to ***,the peak decomposition has extracted spatial information from the time-course *** echoing pattern also indicates a conserved transcriptome response with different initiation times between the two cell populations despite different elicitor types.A gene set highly overlapping with the conserved gene set is also upregulated with similar kinetics during pattern-triggered *** of a WRKY network via different entry-point WRKYs can explain the similar but not identical transcriptome responses elicited by different elicitor *** discuss potential benefits of the properties of the WRKY activation network as an immune signaling network in light of pressure from rapidly evolving pathogens.

关键词： Arabidopsis Pseudomonas syringae plant immune response multi-compartment model WRKY transcription factors resilient immune signaling network

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Spatially differentiated life cycle assessment of Thailand's transport: The implications from country-specific factors and alternative technologies

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Sustainable Production and Consumption 2025年 57卷 319-340页

作者： Vitoon Chotanapund Shabbir H. Gheewala Vladimir Strezov Nazmul Huda Jitti Mungkalasiri Trakarn Prapaspongsa Graduate Program in Environmental and Water Resources Engineering Department of Civil and Environmental Engineering Faculty of Engineering Mahidol University Nakhon Pathom Thailand School of Natural Sciences Faculty of Science and Engineering Macquarie University NSW 2109 Australia The Joint Graduate School of Energy and Environment (JGSEE) King Mongkut's University of Technology Thonburi Bangkok Thailand Center of Excellence on Energy Technology and Environment Ministry of Higher Education Science Research and Innovation Ministry of Education Bangkok Thailand School of Engineering Faculty of Science and Engineering Macquarie University NSW 2109 Australia Technology and Informatics Institute for Sustainability (TIIS) National Metal and Materials Technology Center (MTEC) National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand

This study proposed country-specific characterisation factors (CFs) for Thailand by modifying the Thai Spatially Differentiated Life Cycle Impact Assessment (ThaiSD) method and introducing monetary conversion factors to express environmental impacts in Thai Baht. Five impact categories were fully parameterised, including fine particulate matter formation (PMF), human toxicity (both cancer and non-cancer) (HT c and HT nc ), freshwater ecotoxicity (FET), and water scarcity (WS). Other spatialised CFs were selected from regionalisation models in ReCiPe2016 and IMPACT World+. When comparing the use of country-specific CFs with global average, the impact scores for PMF, HT c , HT nc , FET, photochemical ozone formation and terrestrial acidification demonstrated notably different levels, ranging from ±25 to ±50 %. The developed method was then applied to assess environmental impacts and costs of Thailand's transport sector, encompassing freight and passenger transport across roadway, railway, waterway, and aviation. Climate change (CC) was significantly attributed to human health and ecosystem quality impacts, while the major contributor to resource scarcity impact was fossil resource scarcity (FS). In some scenarios, non-exhaust emissions, particularly from freight trucks, accounted for 40–60 % of the total PMF impacts. Environmental costs of freight and passenger transport in Thailand were 0.08–3.64 Thai Baht per tonne-kilometre and 0.01–0.81 Thai Baht per passenger-kilometre, respectively. Among transport modes, trains were found to be the most environmentally favourable option for both passenger and freight transport, while aviation had the highest environmental impact for freight transport. In contrast, passenger aviation had a comparable environmental burden to passenger cars due to optimised occupancy rates. Despite the efficiency of modern internal combustion engine vehicles (ICEVs), particularly Euro 5 and 6, employing blended biodiesel was less effective in comp

关键词： Life cycle assessment Thai Spatially Differentiated Life Cycle Impact Assessment Freight transport Passenger transport Transport technologies

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Benefits and drawbacks of radiofrequency ablation via percutaneous or minimally invasive surgery for treating hepatocellular carcinoma

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World Journal of Gastrointestinal Surgery 2024年第11期16卷 3400-3407页

作者： Ching-Lung Hsieh Cheng-Ming Peng Chun-Wen Chen Chang-Hsien Liu Chih-Tao Teng Yi-Jui Liu Department of Computer Science and Information Engineering Feng Chia UniversityTaichung 40724Taiwan Department of Surgery Chung Shan Medical University HospitalTaichung 40201Taiwan School of Medicine Chung Shan Medical UniversityTaichung 40201Taiwan Department of Radiology Taichung Armed Forces General HospitalTaichung 406Taiwan Department of Medical Imaging and Radiological Sciences Central Taiwan University of Science and TechnologyTaichung 406Taiwan Department of Radiology School of MedicineNational Defense Medical CenterTaipei 11490Taiwan Department of Medical Imaging China Medical University Hsinchu Hospital and China Medical UniversityHsinchu 302Taiwan Institute of Nuclear Engineering and Science National Tsing Hua UniversityHsinchu 300Taiwan Department of Radiology Nantou Hospital of the Ministry of Health and WelfareNantou 540Taiwan Master’s Program of Biomedical Informatics and Biomedical Engineering Feng Chia UniversityTaichung 407Taiwan Department of Automatic Control Engineering Feng Chia UniversityTaichung 407Taiwan

The management of early stage hepatocellular carcinoma(HCC)presents significant *** radiofrequency ablation(RFA)has shown safety and effectiveness in treating HCC,with lower mortality rates and shorter hospital stays,its high recurrence rate remains a significant ***,achieving improved survival solely through RFA is challenging,particularly in retrospective studies with inherent *** is commonly used for guiding percutaneous RFA,but its low contrast can lead to missed tumors and the risk of HCC *** enhance the efficiency of ultrasound-guided percutaneous RFA,various techniques such as artificial ascites and contrast-enhanced ultrasound have been developed to facilitate complete tumor *** invasive surgery(MIS)offers advantages over open surgery and has gained traction in various surgical *** studies suggest that laparoscopic intraoperative RFA(IORFA)may be more effective than percutaneous RFA in terms of survival for HCC patients unsuitable for surgery,highlighting its ***,combining MIS-IORFA with these enhanced percutaneous RFA techniques may hold greater significance for HCC treatment using the MIS-IORFA *** article reviews liver resection and RFA in HCC treatment,comparing their merits and proposing a trajectory involving their combination in future therapy.

关键词： Percutaneous radiofrequency ablation Minimally invasive surgery Hepatocellular carcinoma Intraoperative radiofrequency ablation Contrast-enhanced ultrasound

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Digital Nomads during the COVID-19 Pandemic: Evidence from Narratives on Reddit discussions 25

Digital Nomads during the COVID-19 Pandemic: Evidence from N...

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25th IEEE International Conference on Computer Supported Cooperative Work in Design, CSCWD 2022

作者： De Almeida, Marcos Antonio Correia, Antonio De Souza, Jano Moreira Schneider, Daniel Systems Engineering and Computer Science Program PESC/COPPE/UFRJ Rio de Janeiro Brazil Inesc Tec University of Trás-os-Montes e Alto Douro Vila Real Portugal Postgraduate Program in Informatics PPGI/UFRJ Rio de Janeiro Brazil Tércio Pacitti Institute of Computer Applications and Research NCE/UFRJ Rio de Janeiro Brazil

ISBN: (纸本)9781665405270

In this paper, we report on new findings about the results of an empirical study which aims to investigate how the COVID-19 pandemic has been shaping nomadic work practices and also challenging the lifestyles of digital nomads (DN). To do this, we collected textual data from posts in a Reddit community. We argue that, in order to understand how to design technical solutions for the so-called 'new normal' working conditions, one way to approach this is to understand how digital nomads are being impacted in their work practices and routines, and also how they are seeing the future of their technology-mediated work-life space. Finally, we show how evidence collected from DNs about their experiences and difficulties perceived during the pandemic period can inform CSCW researchers worldwide about future design-oriented strands. © 2022 IEEE.

关键词： COVID-19

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Meta-EHR: A meta-learning approach for electronic health records with a high imbalanced ratio and missing rate

Meta-EHR: A meta-learning approach for electronic health rec...

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Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Hsu-Hsiang Chang Te-Cheng Hsu Yi-Hsien Hsieh Che Lin Graduate Institute of Communication Engineering National Taiwan University (NTU) Taipei Taiwan Institute of Communications Engineering National Tsing Hua University (NTHU) Hsinchu Taiwan Department of Electrical Engineering National Taiwan University (NTU) Taipei Taiwan Center for Computational and Systems Biology and Center for Biotechnology NTU Taipei Taiwan Smart Medicine and Health Informatics Program NTU Taipei Taiwan

Data imbalance is a practical and crucial issue in deep learning. Moreover, real-world datasets, such as electronic health records (EHR), often suffer from high missing rates. Both issues can be understood as noises in data that may lead to bad generalization results for standard deep-learning algorithms. This paper introduces a novel meta-learning approach to deal with these noise issues in an EHR dataset for a binary classification task. This meta-learning approach leverages the information from a selected subset of balanced, low-missing rate data to automatically assign proper weight to each sample. Such weights would enhance the informative samples and suppress the opposites during training. Furthermore, the meta-learning approach is model-agnostic for deep learning-based architectures that simultaneously handle the high imbalanced ratio and high missing rate problems. Through experiments, we demonstrate that this meta-learning approach is better in extreme cases. In the most extreme one, with an imbalance ratio of 172 and a 74.6% missing rate, our method outperforms the original model without meta-learning by as much as 10.3% of the area under the receiver-operating characteristic curve (AUROC) and 3.2% of the area under the precision-recall curve (AUPRC). Our results mark the first step towards training a robust model for extremely noisy EHR datasets.

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Glucose-mediated mitochondrial reprogramming by cholesterol export at TM4SF5-enriched mitochondria-lysosome contact sites

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Cancer Communications 2024年第1期44卷 47-75页

作者： Ji Eon Kim So-Young Park Chulhwan Kwak Yoonji Lee Dae-Geun Song Jae Woo Jung Haesong Lee Eun-Ae Shin Yangie Pinanga Kyung-hee Pyo Eun Hae Lee Wonsik Kim Soyeon Kim Chang-Duck Jun Jeanho Yun Sun Choi Hyun-Woo Rhee Kwang-Hyeon Liu Jung Weon Lee Department of Pharmacy College of PharmacySeoul National UniversitySeoulRepublic of Korea Research Institute of Pharmaceutical Sciences College of PharmacySeoul National UniversitySeoulRepublic of Korea BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit College of Pharmacy and Research Institute of Pharmaceutical SciencesKyungpook National UniversityDaeguRepublic of Korea Department of Chemistry Seoul National UniversitySeoulRepublic of Korea College of Pharmacy Chung-Ang UniversitySeoulRepublic of Korea Natural Product Informatics Research Center Korea Institute of Science and Technology(KIST)Gangneung-siGangwon-doRepublic of Korea School of Life Sciences Gwangju Institute of Science and Technology(GIST)GwangjuRepublic of Korea Department of Biochemistry College of MedicineDong-A UniversityBusanRepublic of Korea Global AI Drug Discovery Center College of Pharmacy and Graduate School of Pharmaceutical SciencesEwha Womans UniversitySeoulRepublic of Korea Interdisciplinary Program in Genetic Engineering Seoul National UniversitySeoulRepublic of Korea

Background:Transmembrane 4 L six family member 5(TM4SF5)translocates subcellularly and functions metabolically,although it is unclear how intracellu-lar TM4SF5 translocation is linked to metabolic *** is thus of interests to understand how the traffic dynamics of TM4SF5 to subcellular endosomal membranes are correlated to regulatory roles of ***:Here,we explored the metabolic significance of TM4SF5 localization at mitochondria-lysosome contact sites(MLCSs),using in vitro cells and in vivo animal systems,via approaches by immunofluorescence,proximity labelling based proteomics analysis,organelle reconstitution ***:Upon extracellular glucose repletion following depletion,TM4SF5 became enriched at MLCSs via an interaction between mitochondrial FK506-binding protein 8(FKBP8)and lysosomal *** labeling showed molecular clustering of phospho-dynamic-related protein I(DRP1)and certain mitophagy receptors at TM4SF5-enriched MLCSs,leading to mitochondrial fis-sion and ***4SF5 bound NPC intracellular cholesterol transporter 1(NPC1)and free cholesterol,and mediated export of lysosomal cholesterol to mitochondria,leading to impaired oxidative phosphorylation but intact tri-carboxylic acid(TCA)cycle andβ-*** mouse models,hepatocyte Tm4sf5 promoted mitophagy and cholesterol transport to mitochondria,both with positive relations to liver ***:Our findings suggested that TM4SF5-enriched MLCSs regu-late glucose catabolism by facilitating cholesterol export for mitochondrial reprogramming,presumably while hepatocellular carcinogenesis,recapitulating aspects for hepatocellular carcinoma metabolism with mitochondrial repro-gramming to support biomolecule synthesis in addition to glycolytic energetics.

关键词： cholesterol fluorescent imaging glucose catabolism hepatocellular carcinogenesis mem-brane contact sites mitochondria function mitophagy oxidative phosphorylation protein-protein interaction tetraspanin

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The Implementation of TOGAF for Enterprise System Planning on XYZ Campus

The Implementation of TOGAF for Enterprise System Planning o...

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Networking, Electrical engineering, Computer science, and Technology (IConNECT), International Conference on

作者： Tamsir Hasudungan Sirait Ford Lumban Gaol Suhono Harso Supangkat Benny Ranti Binus Graduate Program Computer Science Bina Nusantara University Jakarta Indonesia Computer Science Department Bina Nusantara University Jakarta Indonesia School of Electrical Engineering and Informatics Bandung Institute of Technology Bandung Indonesia Computer Science Department Universitas Indonesia Jakarta Indonesia

Universities can employ information technology as one means of achieving their goals and objectives. Universities can get advantages from information technology, such as effective resource management and information management for decision-making. However, don't forget that the campus must consider what technology is appropriate to assist them achieve their goals, particularly in the current industrial era 4.0 where technology is available with many different choices. The campus requires an enterprise architecture in order to design, manage, and coordinate information technology infrastructure, applications, and processes strategically and thoroughly. The adoption of enterprise information system architecture (EA) is also intended to improve the quality of services provided to internal and external stakeholders. In this case, Enterprise Architecture can help an organization to match its information technology resources with business processes and strategies to achieve their goals. This research was conducted using TOGAF ADM, also known as the Open Group Architecture Framework Architecture Development Method. This method offers best practices for creating enterprise architecture and emphasizes several steps that include creating an architectural vision, information systems, business architecture modeling to help XYZ campus manage all their information technology.

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Classification of Breast Thermal Images into Healthy/Cancer Group Using Pre-Trained Deep Learning Schemes

Classification of Breast Thermal Images into Healthy/Cancer ...

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2022 International Conference on Machine Learning and Data engineering, ICMLDE 2022

作者： Kadry, Seifedine Crespo, Rubén González Herrera-Viedma, Enrique Krishnamoorthy, Sujatha Rajinikanth, Venkatesan Faculty of Applied Computing and Technology Noroff University College Kristiansand94612 Norway Computer Science Department School of Engineering and Technology Universidad Internacional de la Rioja Andalusia26006 Spain Research Institute in Data Science and Computational Intelligence University of Granada Granada Spain Zhejiang Bioinformatics International Science and Technology Cooperation Center Wenzhou-Kean University Zhejiang Province China Wenzhou Municipal Key Lab of Applied Biomedical and Biopharmaceutical Informatics Wenzhou-Kean University Zhejiang Province China Department of Computer Science and Engineering Saveetha School of Engineering SIMATS Tamil Nadu Chennai602105 India

In the women's community, Breast Cancer (BC) is a severe disease. The World Health Organization reported in 2020 that 2.26 million deaths occur due to BC. BC is curable if detected early. Since thermal imaging is non-invasive and supports disease detection, it is commonly used in clinics. Compared to other methods, it keeps BC early and accurate. The proposed work aims to evaluate the performance of the Pretrained Deep-Learning Methods (PDLM) in detecting BC using the thermal images collected from the benchmark dataset. It includes the following stages: primary image processing, deep feature mining, handcrafted feature mining, feature optimization using Firefly-Algorithm (FA), classification and validation. Visual Lab thermal images were used in the study. The investigational outcome of this study authenticates that the VGG16, along with the DT, provides better detection accuracy (95.5%) compared to other classifiers used in this study. To justify the significance of the implemented technique, the proposed work not only improved accuracy, but also improved precision, sensitivity, specificity, and F1-Scores. © 2023 The Authors. Published by Elsevier B.V.

关键词： Classification (of information)

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When data disappear: public health pays as US policy strays

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The Lancet Digital Health 2025年 100874页

作者： McAndrew, Thomas Lover, Andrew A Hoyt, Garrik Majumder, Maimuna S Department of Biostatistics and Health Data Science College of Health Lehigh University BethlehemPA United States Department of Biostatistics and Epidemiology School of Public Health and Health Sciences University of Massachusetts Amherst AmherstMA United States Department of Computer Science and Engineering PC Rossin College of Engineering and Applied Sciences Lehigh University BethlehemPA United States Department of Pediatrics Harvard Medical School BostonMA United States Computational Health Informatics Program Boston Children's Hospital BostonMA United States

Presidential actions on Jan 20, 2025, by President Donald Trump, including executive orders, have delayed access to or led to the removal of crucial public health data sources in the USA. The continuous collection and maintenance of health data support public health, safety, and security associated with diseases such as seasonal influenza. To show how public health data surveillance enhances public health practice, we analysed data from seven US Government-maintained sources associated with seasonal influenza. We fit two models that forecast the number of national incident influenza hospitalisations in the USA: (1) a data-rich model incorporating data from all seven Government data sources;and (2) a data-poor model built using a single Government hospitalisation data source, representing the minimal required information to produce a forecast of influenza hospitalisations. The data-rich model generated reliable forecasts useful for public health decision making, whereas the predictions using the data-poor model were highly uncertain, rendering them impractical. Thus, health data can serve as a transparent and standardised foundation to improve domestic and global health. Therefore, a plan should be developed to safeguard public health data as a public good. © 2025 The Author(s)

关键词： Health insurance

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Near-Optimal Pilot Assignment in Cell-Free Massive MIMO

arXiv

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arXiv 2023年

作者： Guedes, Raphael M. de Rezende, José F. Barbosa, Valmir C. Informatics and Computer Science Department State University of Rio de Janeiro RJ Rio de Janeiro20550-900 Brazil Systems Engineering and Computer Science Program Federal University of Rio de Janeiro RJ Rio de Janeiro21941-914 Brazil Graduate Program in Computational Sciences State University of Rio de Janeiro RJ Rio de Janeiro20550-900 Brazil

Cell-free massive MIMO systems are currently being considered as potential enablers of future (6G) technologies for wireless communications. By combining distributed processing and massive MIMO, they are expected to deliver improved user coverage and efficiency. A possible source of performance degradation in such systems is pilot contamination, which contributes to causing interference during uplink training and affects channel estimation negatively. Contamination occurs when the same pilot sequence is assigned to more than one user. This is in general inevitable, as the number of mutually orthogonal pilot sequences corresponds to only a fraction of the coherence interval. We introduce a new algorithm for pilot assignment and analyze its performance both from a theoretical perspective and in computational experiments. We show that it has an approximation ratio close to 1 for a plausibly large number of orthogonal pilot sequences, as well as low computational complexity under massive parallelism. We also show that, on average, it outperforms other methods in terms of per-user SINR and throughput on the uplink. Copyright © 2023, The Authors. All rights reserved.

关键词： Channel estimation

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