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Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in hepatocellular carcinoma:the PLANET study

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National Science Review 2022年第3期9卷 96-109页

作者： Weiwei Zhai Hannah Lai Neslihan Arife Kaya Jianbin Chen Hechuan Yang Bingxin Lu Jia Qi Lim Siming Ma Sin Chi Chew Khi Pin Chua Jacob Josiah Santiago Alvarez Pauline Jieqi Chen Mei Mei Chang Lingyan Wu Brian K.P.Goh Alexander Yaw-Fui Chung Chung Yip Chan Peng Chung Cheow Ser Yee Lee Juinn Huar Kam Alfred Wei-Chieh Kow Iyer Shridhar Ganpathi Rawisak Chanwat Jidapa Thammasiri Boon Koon Yoong Diana Bee-Lan Ong Vanessa H.de Villa Rouchelle D.Dela Cruz Tracy Jiezhen Loh Wei Keat Wan Zeng Zeng Anders Jacobsen Skanderup Yin Huei Pang Krishnakumar Madhavan Tony Kiat-Hon Lim Glenn Bonney Wei Qiang Leow Valerie Chew Yock Young Dan Wai Leong Tam Han Chong Toh Roger Sik-Yin Foo Pierce Kah-Hoe Chow Genome Institute of Singapore Agency for Science Technology and Research Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences School of Biological Sciences Nanyang Technological University Division of Biosciences Faculty of Life Sciences Division of Surgery and Surgical Oncology National Cancer Centre Department of Hepato-Pancreato-Biliary and Transplant Surgery Singapore General Hospital Division of Hepatobiliary and Pancreatic Surgery Department of Surgery University Surgical Cluster National University Health System Hepato-Pancreato-Biliary Surgery Unit Department of Surgery National Cancer Institute Division of Pathology National Cancer Institute Department of Surgery Faculty of Medicine University of Malaya Department of Surgery and Center for Liver Disease Management and Transplantation The Medical City Department of Laboratories The Medical City Department of Pathology Singapore General Hospital Institute for Infocomm Research ASTAR Department of Pathology National University Health System Translational Immunology Institute (TII) Sing Health Duke-NUS Academic Medical Centre Division of Gastroenterology and Hepatology University Medicine Cluster National University Hospital Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore Cancer Science Institute of Singapore National University of Singapore Division of Medical Oncology National Cancer Center Singapore Cardiovascular Research Institute National University of Singapore National University Healthcare System Singhealth-Duke-NUS Academic Surgery Program Duke-NUS Graduate Medical School Institute of Molecular and Cell Biology Agency for Science Technology and Research

Intra-tumor heterogeneity(ITH) is a key challenge in cancer treatment, but previous studies have focused mainly on the genomic alterations without exploring phenotypic(transcriptomic and immune)heterogeneity. Using one of the largest prospective surgical cohorts for hepatocellular carcinoma(HCC)with multi-region sampling, we sequenced whole genomes and paired transcriptomes from 67 HCC patients(331 samples). We found that while genomic ITH was rather constant across stages, phenotypic ITH had a very different trajectory and quickly diversified in stage Ⅱ patients. Most strikingly, 30% of patients were found to contain more than one transcriptomic subtype within a single tumor. Such phenotypic ITH was found to be much more informative in predicting patient survival than genomic ITH and explains the poor efficacy of single-target systemic therapies in HCC. Taken together, we not only revealed an unprecedentedly dynamic landscape of phenotypic heterogeneity in HCC, but also highlighted the importance of studying phenotypic evolution across cancer types.

关键词： NADH oxidase H2O2 production oxidative phosphorylation

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Electron Acceleration in Carbon Nanotubes

arXiv

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arXiv 2025年

作者： Bonţoiu, Cristian Bonatto, Alexandre Apsimon, Öznur Bandiera, Laura Cavoto, Gianluca Drebot, Illya Gatti, Giancarlo Giner-Navarro, Jorge Lei, Bifeng Martín-Luna, Pablo Rago, Ilaria Pérez, Juan Rodríguez Nunes, Bruno Silveira Sytov, Alexei Valagiannopoulos, Costas Welsch, Carsten P. Xia, Guoxing Resta-López, Javier Department of Physics University of Liverpool Oxford Street LiverpoolL69 7ZE United Kingdom Graduate Program in Information Technology and Healthcare Management the Beam Physics Group Federal University of Health Sciences of Porto Alegre RS Porto Alegre90050-170 Brazil Department of Physics and Astronomy University of Manchester Oxford Road ManchesterM13 9PL United Kingdom Cockroft Institute Keckwick Lane Daresbury WarringtonWA4 4AD United Kingdom INFN Sezione di Ferrara Via Saragat 1 Ferrara44122 Italy Dipartimento di Fisica Sapienza Università di Roma Piazzale Aldo Moro 2 Roma00185 Italy INFN Sezione di Roma Piazzale Aldo Moro 2 Rome00185 Italy INFN Sezione di Milano Via G. Celoria 16 Milano20133 Italy Centro de Láseres Pulsados Building M5 Science Park Calle Adaja 8 Salamanca Villamayor37185 Spain Universidad de Valencia Paterna46071 Spain Universidad de Valencia CSIC Paterna46980 Spain Nuclear and Energy Research Institute IPEN–CNEN SP São Paulo Brazil National Technical University of Athens School of Electrical and Computer Engineering Zografou157 73 Greece Departamento de Física Aplicada y Electromagnetismo Universidad de Valencia Burjassot46100 Spain

Laser wakefield acceleration (LWFA) may achieve TeV/m gradients using high-density solid-state plasmas as accelerating media. However, the application of bulk solid materials requires attosecond laser pulses, such as X-ray lasers, to drive wakefields at these high densities. Additionally, the short wakefield wavelengths associated with solid-state plasmas greatly limit the accelerating length. An alternative approach employs 2D carbon-based nanomaterials, like graphene or carbon nanotubes (CNTs), configured into structured targets. These nanostructures are designed with voids or low-density regions to effectively reduce the overall plasma density. This reduction enables the use of longer-wavelength lasers and also extends the plasma wavelength and the acceleration length. In this study, we present, to our knowledge, the first numerical demonstration of electron acceleration via self-injection into a wakefield bubble driven by an infrared laser pulse in structured CNT targets, similar to the behavior observed in gaseous plasmas for LWFA in the nonlinear (or bubble) regime. Using the PIConGPU code, bundles of CNTs are modeled in a 3D geometry as 25 nm-thick carbon tubes with an initial density of 1022 cm−3. The carbon plasma is ionized by a three-cycle, 800 nm wavelength laser pulse with a peak intensity of 1021 W cm−2, achieving an effective plasma density of 1020 cm−3. The same laser also drives the wakefield bubble, responsible for the electron self-injection and acceleration. Simulation results indicate that fs-long electron bunches with hundreds of pC charge can be self-injected and accelerated at gradients exceeding 1 TeV/m. Both charge and accelerating gradient figures are unprecedented when compared with LWFA in gaseous plasma. © 2025, CC BY-NC-ND.

关键词： X ray lasers

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Characterization of halotolerant phosphate-solubilizing rhizospheric bacteria from mangrove (Avicennia sp.) with biotechnological potential in agriculture and pollution mitigation

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Biocatalysis and Agricultural Biotechnology 2024年 55卷

作者： Dey, Gobinda Maity, Jyoti Prakash Banerjee, Pritam Sharma, Raju Kumar Etesami, Hassan Bastia, Tapan Kumar Rath, Prasanta Sukul, Uttara Huang, Hsien-Bin Huang, Kuo-Wei Chen, Chien-Yen Department of Agricultural Chemistry National Taiwan University Taipei 106319 Taiwan Department of Biomedical Sciences Graduate Institute of Molecular Biology National Chung Cheng University 168 University Road Chiayi County Ming-Shung 62102 Taiwan Doctoral Program in Science Technology Environment and Mathematics Department of Earth and Environmental Sciences National Chung Cheng University 168 University Rd. Chiayi County Min-Hsiung 62102 Taiwan Environmental Science Laboratory Department of Chemistry Biological Laboratory School of Applied Sciences KIIT Deemed to Be University Odisha Bhubaneswar 751024 India Department of Environmental Science Policy and Management University of California Berkeley CA United States Department of Chemistry and Biochemistry National Chung Cheng University 168 University Road Chiayi County Min-Hsiung 62102 Taiwan Department of Soil Science University of Tehran Tehran 31587-77871 Iran Environmental Science Laboratory Department of Chemistry School of Applied Sciences KIIT Deemed to Be University Odisha Bhubaneswar 751024 India Department of Otolaryngology Ditmanson Medical Foundation Chia-Yi Christian Hospital Taiwan Center for Nano Bio-Detection Center for Innovative Research on Aging Society AIM-HI National Chung Cheng University Chiayi 62102 Taiwan

Mangroves represent intricate and ever-changing ecosystems, exhibiting fluctuations in water level, salinity, and nutrient (such as NPK) availability as well as a wide array of unique bacterial communities. Microbial interactions in different components (e.g., tree roots) of the mangrove ecosystem are crucial to understand the ecosystem functioning for potential application in pollution mitigation and agricultural production. This study aimed to isolate phosphate-solubilizing bacteria (PSB) from the rhizosphere sediment of mangrove (Avicennia sp.) in terms of heavy metals (HMs) and salinity tolerance as well as plant growth promoting (PGP) traits, where the effective PSB were used on Brassica chinensis for their seed priming and growth under salinity stress. The effective two PSB isolates were identified by 16S rRNA, where JKD01 and JKD02 were closely related (99%) to Enterobacter cloacae (OQ271412) and Kocuria rhizophila (OQ271413), respectively. Both the strains exhibited phosphate solubilization, IAA, NH_3, and EPS production ability as well as HMs resistant ability where, E. cloacae (OQ271412) and K. rhizophila (OQ271413), are effectively remove the Cu from the water with 33.23% and 27.54%, respectively. The FTIR results showed functional group shifts (carboxyl, phosphate, and amino) in Cu-treated bacterial biomass and intracellular Cu presence, indicating the involvement of Cu in the bio-sorption and intracellular bioaccumulation process, respectively. The findings suggested PSB tolerance to salinity and HMs are present in mangroves, making them a valuable source for isolating effective bacteria to reduce stress in plants, lower HMs accumulation in mangroves, and aid in the bioremediation of HMs-contaminated environments. © 2023

关键词： Bio-priming Copper remediation Heavy metal tolerant Mangrove Phosphate-solubilizing bacteria Salt tolerant

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Erratum: “Exploring ultra-high-intensity wakefields in carbon nanotube arrays: An effective plasma-density approach” [Phys. Plasmas 30, 033105 (2023)]

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Physics of Plasmas 2023年第4期30卷

作者： A. Bonatto G. Xia O. Apsimon C. Bontoiu E. Kukstas V. Rodin M. Yadav C. P. Welsch J. Resta-López Graduate Program in Information Technology and Healthcare Management and the Beam Physics Group Federal University of Health Sciences of Porto Alegre Porto Alegre RS 90050-170 Brazil Department of Physics and Astronomy The University of Manchester Manchester M13 9PL United Kingdom and The Cockcroft Institute Sci-Tech Daresbury Warrington WA4 4AD United Kingdom Department of Physics The University of Liverpool Liverpool L69 3BX United Kingdom ICMUV Instituto de Ciencia de los Materiales Universidad de Valencia 46071 Valencia Spain

This erratum is being issued to correct an error that affects Fig. 7 in Ref. 1. This error was caused by a problem with the processing of the PDF file. Specific

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A robotic dating coaching system leveraging online communities posts

arXiv

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arXiv 2020年

作者： Jo, Sihyeon Joung, Eun Gyo So, Minseob Jung, Donghwi Nespoli, Giulia Seo, Seung-Woo Kim, Keonwoo Yoo, Seungryong Kim, Seong-Woo Department of Electrical and Computer Engineering Seoul National University Seoul Korea Republic of Technology Management Economics and Policy Program Seoul National University Seoul Korea Republic of Department of Industrial Engineering Seoul National University Seoul Korea Republic of Department of Civil and Environmental Engineering Seoul National University Seoul Korea Republic of Department of Industrial Design Seoul National University Seoul Korea Republic of Graduate School of Engineering Practice Seoul National University Seoul Korea Republic of

Can a robot be a personal dating coach? Even with the increasing amount of conversational data on the internet, the implementation of conversational robots remains a challenge. In particular, a detailed and professional counseling log is expensive and not publicly accessible. In this paper, we develop a robot dating coaching system leveraging corpus from online communities. We examine people’s perceptions of the dating coaching robot with a dialogue module. 97 participants joined to have a conversation with the robot, and 30 of them evaluated the robot. The results indicate that participants thought the robot could become a dating coach while considering the robot is entertaining rather than helpful. © 2020, CC-BY.

关键词： Social networking (online)

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Optimal Design of Hybrid Renewable Energy Generation Sources Integrated with Battery Energy Storage System;A Case Study of Nongplathao Park, Chaiyaphum Provincial Administration Organization, Thailand

Optimal Design of Hybrid Renewable Energy Generation Sources...

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2018 2nd International Conference on Electrical Engineering and Automation（ICEEA2018）

作者： Montre Chaleekure Terapong Boonraksa Nitikorn Junhuathon Boonruang Marungsri Graduate Student in Energy Management Engineering Program Suranaree University of Technology School of Electrical Engineering Suranaree University of Technology

Hybrid renewable energy began to play an essential role after the fossil energy is gradually reduced. In Thailand, the government is very interested in renewable energy, and there are many potential areas in countries where renewable energy sources such as wind energy and solar energy are available. This paper presents the study results of the optimal design of hybrid renewable energy generation sources integrated with battery storage system in a case study of Nongplathao Park, Chaiyaphum Provincial Administration Organization in Thailand. In this study, the On-Grid and the Off-Grid hybrid renewable generation systems were designed, and Homer version 3.11.2 software was used as an analytical tool. The simulation results show that On-Grid renewable energies system can produce electricity supplied to the load and there is also electricity that is sold to the system. The Off-Grid system used renewable energy sources to generate power integrating with the energy storage system for supply electricity to the selection area. Although, an Off-Grid system has expensive installation costs, in the future there is a tendency for lower system equipment costs. This simulation can be used as a case study to promote to other appropriate areas. The simulation results show that On-Grid renewable energies system can produce electricity supplied to the load and there is also electricity that is sold to the system. The Off-Grid system used renewable energy sources to generate power integrating with the energy storage system for supply electricity to the selection area. Although, an Off-Grid system has expensive installation costs, in the future there is a tendency for lower system equipment costs. This simulation can be used as a case study to promote to other appropriate areas.

关键词： hybrid renewable energy battery storage system solar energy wind energy

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Numerical analysis of general-vibration-based method for structural health monitoring

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AIP Conference Proceedings 2020年第1期2227卷

作者： Fergyanto E. Gunawan Benfano Soewito Nico Surantha Tuga Mauritsius Nobumasa Sekishita 1Industrial Engineering Department BINUS Graduate Program - Master of Industrial Engineering Bina Nusantara University Jakarta Indonesia 11480 2Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480 3Information Systems Management Department BINUS Graduate Program - Master of Information Systems Management Bina Nusantara University Jakarta Indonesia 11480 4Department of Mechanical Engineering Toyohashi University of Technology Toyohashi Aichi 441-8580 Japan

For damage detection, this research article discusses an easy-to-compute damage index derived from the governing dynamic of the structure that has potential practical application in Structural Health Monitoring (SHM). The research uses simplified structural models to explore the sensitivity of the index to damages, to compare the index performance with a traditional but popular damage detection method, and to understand the local/global predictive capability of the index. The research uses two simple models, namely, single- and two-degree-of-freedom systems. The results suggest that the damage index is local, that can only monitor damages occurring near the points of measurements, but it is sensitive to damages, unlike the natural frequency, which is global but less sensitive.

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The accuracy of the F statistic for structural health monitoring

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AIP Conference Proceedings 2020年第1期2227卷

作者： Fergyanto E. Gunawan Benfano Soewito Nico Surantha Tuga Mauritsius Nobumasa Sekishita 1Industrial Engineering Department BINUS Graduate Program – Master of Industrial Engineering Bina Nusantara University Jakarta Indonesia 11480 2Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480 3Information Systems Management Department BINUS Graduate Program – Master of Information Systems Management Bina Nusantara University Jakarta Indonesia 11480 4Department of Mechanical Engineering Toyohashi University of Technology Toyohashi Aichi 441-8580 Japan

Understanding the reliability of engineering methods is crucial for its adoption and deployment. This research focuses on the reliability of the Power Spectral Density (PSD) method via the use of the F statistic for damage detection. To the author best knowledge, the method is rather classic but its realibility has not been discussed in the context of a large data size. Priory, the research anticipates that the accuracy is a function of the damage level. In this study, we evaluate 3500 cases with five levels of structural integrity, namely, healthy condition and damaged conditions with 1%, 5%, 10%, and 20% damage levels. The dataset is established via a numerical analysis of a seven degree-of-freedom system loaded with a concentrated dynamic force with random magnitude. A spring on the system is reduced in its stiffness to simulate damages. Our significant findings are the following: it is challenging for the PSD-based method to differentiate the healthy condition from the damaged conditions when the damage level is small. However, the reliability is high at 95% probability when the structural integrity has dropped by five percent.

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Bridge Sub Structure Defect Inspection Assistance by using Deep Learning

Bridge Sub Structure Defect Inspection Assistance by using D...

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IEEE International Conference on Awareness Science and technology

作者： Pravee Kruachottikul Kittikul Kovitanggoon Nagul Cooharojananone Donnaphat Trakulwaranont Gridsada Phanomchoeng Kanokwan Atchariyachanvanich Thira Chavarnakul Technopreneurship and Innovation Management Program Graduate School Chulalongkorn University Bangkok Thailand Department of Mathematics and Computer Science Chulalongkorn University Bangkok Thailand Department of Mechanical Engineering Chulalongkorn University Bangkok Thailand Department of Commerce Chulalongkorn University Bangkok Thailand Faculty of Information Technology King Mongkut’s Institute of Technology Ladkrabang Bangkok Thailand

Road transportation is the most popular transportation in Thailand, which the top two highest traffic are the region-to-region highways;and then inter-city highways. Therefore, the regular maintenance is required to maintain the good condition due to road safety. The most significant process of bridge inspection procedures is sub structure inspection, which requires visual inspection as an initial step. This process is used to quick determine the damage severity i.e. appearance and crack that may cause damage to the structure strength. The current process requires that the experienced maintenance engineer to be on the field in order to visual inspect and estimate whether the maintenance is required. Yet, due to the limitation of number of expert engineers to be on the field, the photo verification is introduced to assist them so that they are no need on every inspection site. However, using human to verify has no standard and uncontrollable. They need to have experience and good knowledge. As well as it is highly depended on individual decisionmaking skill. Thus, in this paper, the deep learning technique will be presented to assist the expert for quality inspection process of bridge sub structure images. That is using image enhancement and then image splitting and overlapping for image pre-processing. After that applying CNNs for object classification. As a result, the total accuracy is 89% based on 3926 dataset.

关键词： Bridges Inspection Machine learning Maintenance engineering Convolution Training Concrete

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Use of machine learning algorithms to determine the relationship between air pollution and cognitive impairment in Taiwan

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Ecotoxicology and environmental safety 2024年 284卷 116885页

作者： Cheng-Hong Yang Chih-Hsien Wu Kuei-Hau Luo Huang-Chih Chang Sz-Chiao Wu Hung-Yi Chuang Department of Information Management Tainan University of Technology Tainan 71002 Taiwan Department of Electronic Engineering National Kaohsiung University of Science and Technology Kaohsiung 80778 Taiwan Ph. D. Program in Biomedical Engineering Kaohsiung Medical University Kaohsiung 80708 Taiwan School of Dentistry Kaohsiung Medical University Kaohsiung 80708 Taiwan Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung 80708 Taiwan. Electronic address: chyang@nkust.edu.tw. Department of Electronic Engineering National Kaohsiung University of Science and Technology Kaohsiung 80778 Taiwan. Electronic address: F108152123@nkust.edu.tw. Graduate Institute of Medicine College of Medicine Kaohsiung Medicine University Kaohsiung 80708 Taiwan. Electronic address: u107800007@kmu.edu.tw. Divisions of Pulmonary & Critical Care Medicine Department of Internal Medicine Kaohsiung Chang Gung Memorial Hospital Chang Gung University College of Medicine Kaohsiung 83341 Taiwan Ph.D Program in Environmental and Occupational Medicine and Research Center for Environmental Medicine College of Medicine Kaohsiung Medical University Kaohsiung 80708 Taiwan. Electronic address: kuan2101@yahoo.com.tw. Epidemiology in the Public Health Program College of Health Oregon State University Oregon 97331 USA. Electronic address: wusz550@***. Graduate Institute of Medicine College of Medicine Kaohsiung Medicine University Kaohsiung 80708 Taiwan Ph.D Program in Environmental and Occupational Medicine and Research Center for Environmental Medicine College of Medicine Kaohsiung Medical University Kaohsiung 80708 Taiwan Department of Public Health and Environmental Medicine School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung 80708 Taiwan Department of Occupational and Environmental Medicine Kaohsiung Medicine University Hospital Kaohsiung Medicine University Kaohsiung 80708 Taiwan. Electronic address: ericch@kmu.edu.tw.

Air pollution has become a major global threat to human health. Urbanization and industrialization over the past few decades have increased the air pollution. Plausible connections have been made between air pollutants and dementia. This study used machine learning algorithms (k-nearest neighbors, random forest, gradient-boosted decision trees, eXtreme gradient boosting, and CatBoost) to investigate the association between cognitive impairment and air pollution. Data from the Taiwan Biobank and 75 air-pollution-monitoring stations in Taiwan were analyzed to determine individual levels of exposure to air pollutants. The pollutants examined were particulate matter with a diameter of ≤ 2.5 μm (PM), nitrogen dioxide, nitric oxide, carbon monoxide, and ozone. The results revealed that the most strongly correlated with cognitive impairment were ozone, PM, and carbon monoxide levels with adjustment of educational level, age, and household income. The model based on these factors achieved accuracy as high as 0.97 for detecting cognitive impairment, indicating a positive association between air pollutions and cognitive impairment.

关键词： Air pollution Carbon monoxide Cognitive impairment Dementia Ozone PM(2.5)

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