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Explainable artificial intelligence in breast cancer detection and risk prediction:A systematic scoping review

Cancer Innovation 2024年第5期3卷 1-22页

作者： Amirehsan Ghasemi Soheil Hashtarkhani David L.Schwartz Arash Shaban‐Nejad Department of Pediatrics Center for Biomedical InformaticsCollege of MedicineUniversity of Tennessee Health Science CenterMemphisTennesseeUSA The Bredesen Center for interdisciplinary Research and Graduate Education University of TennesseeKnoxvilleTennesseeUSA Department of Radiation Oncology College of MedicineUniversity of Tennessee Health Science CenterMemphisTennesseeUSA

With the advances in artificial intelligence(AI),data‐driven algorithms are becoming increasingly popular in the medical ***,due to the nonlinear and complex behavior of many of these algorithms,decision‐making by such algorithms is not trustworthy for clinicians and is considered a blackbox ***,the scientific community has introduced explainable artificial intelligence(XAI)to remedy the *** systematic scoping review investigates the application of XAI in breast cancer detection and risk *** conducted a comprehensive search on Scopus,IEEE Explore,PubMed,and Google Scholar(first 50 citations)using a systematic search *** search spanned from January 2017 to July 2023,focusing on peer‐reviewed studies implementing XAI methods in breast cancer *** studies met our inclusion criteria and were included in the *** results revealed that SHapley Additive exPlanations(SHAP)is the top model‐agnostic XAI technique in breast cancer research in terms of usage,explaining the model prediction results,diagnosis and classification of biomarkers,and prognosis and survival ***,the SHAP model primarily explained tree‐based ensemble machine learning *** most common reason is that SHAP is model agnostic,which makes it both popular and useful for explaining any model ***,it is relatively easy to implement effectively and completely suits performant models,such as tree‐based *** AI improves the transparency,interpretability,fairness,and trustworthiness of AI‐enabled health systems and medical devices and,ultimately,the quality of care and outcomes.

关键词： breast cancer deep learning explainable artificial intelligence interpretable AI machine learning XAI

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Analysis of finite-time regulation property of biomolecular PI controller

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Control Theory and Technology 2020年第2期18卷 135-142页

作者： Peng RONG Takashi NAKAKUKI major of interdisciplinary informatics Kyushu Institute of TechnologyFukuoka 820-8502Japan ZDepartment of Intelligent and Control Systems Kyushu Institute of TechnologyFukuoka 820-8502Japan

In practical applications of dynamic DNA nanotechnology,a biomolecular controller is required for maintaining the operation of the molecular actuator at a desired condition based on the information from molecular *** making use of the DNA strand displacement mechanism as a"programming language"in the controller design,a biomolecular PI controller has been ***,this PI control system has been verified only at the simulation level,and a theoretical regulation analysis is still ***,in this study,we perform a rigorous regulation analysis of the biomolecular PI control ***,we theoretically prove that the output signal approaches the target level at a quasi-steady *** this end,we apply the concept of finite-time regulation property to the biomolecular PI control system.

关键词： Molecular robotics biomolecular reaction system PI controller finite-time regulation property

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An effective pharmacological hydrogel induces optic nerve repair and improves visual function

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Science China(Life Sciences) 2024年第3期67卷 529-542页

作者： Lipeng Wang Shan Zhang Yawen Han Shuo Tang Jiarui Li Lina Bu Dongyu Zhao Hongkui Deng Department of Cell Biology Schoolof Basic Medical SciencesPeking University Stem Cell Research CenterStateKey Laboratoryof Naturaland Biomimetic DrugsPeking University Health Science Center Beijing 100191China MOE Key Laboratory of Cell Proliferation and Differentiation College of Life SciencesPeking-Tsinghua Center for Life SciencesPeking UniversityBeijing 100871China Academy for Advanced interdisciplinary Studies Peking UniversityBeijing 100871China Changping Laboratory Beijing 102206China Department of Ophthalmology Peking University People's Hospital Eye Diseases and Optometry InstituteBeijing 100871China Department of Biomedical informatics School of Basic Medical SciencesPeking UniversityBeijing 100191China

Irreversible eye lesions, such as glaucoma and traumatic optic neuropathy, can cause blindness;however, no effective treatments exist. The optic nerve, in particular, lacks the capacity to spontaneously regenerate, requiring the development of an effective approach for optic nerve repair, which has proven challenging. Here, we demonstrate that a combination of the small molecules 3BDO and trichostatin A(TSA)—which regulate mTOR and HDAC, respectively—packaged in thermosensitive hydrogel for 4-week-sustained release after intravitreal injection, effectively induced optic nerve regeneration in a mouse model of optic nerve crush injury. Moreover, this combination of 3BDO and TSA also protected axon projections and improved visual responses in an old mouse model(11 months old) of glaucoma. Taken together, our data provide a new, local small molecule-based treatment for the effective induction of optic nerve repair, which may represent a foundation for the development of pharmacological methods to treat irreversible eye diseases.

关键词： retinal ganglion cell axon regeneration old-age glaucoma small molecules pharmacological hydrogel visual function repair

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High-Efficiency Photo-Induced Charge Transfer for SERS Sensing in N-Doped 3D-Graphene on Si Heterojunction

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Energy & Environmental Materials 2024年第2期7卷 268-276页

作者： Guanglin Zhang Jie Sun Genwang Wei Shan Zhang Zhengyi He Huijuan Wu Bingkun Wang Siwei Yang Guqiao Ding Zhiduo Liu Zhiwen Jin Caichao Ye Gang Wang Department of Microelectronic Science and Engineering School of Physical Science and TechnologyNingbo UniversityNingbo 315211China Department of Biochemistry and Molecular Biology School of Basic Medical SciencesShenzhen UniversityShenzhen 518071China Academy for Advanced interdisciplinary Studies&Department of Materials Science and Engineering Guangdong Provincial Key Laboratory of Computational Science and Material DesignSouthern University of Science and TechnologyShenzhen 518055China State Key Laboratory of Functional Materials for informatics Shanghai Institute of Microsystem and Information TechnologyChinese Academy of SciencesShanghai 200050China Centre for Quantum Physics Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement(MOE)School of PhysicsBeijing Institute of TechnologyBeijing 100081China School of Physical Science and Technology&Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education Lanzhou UniversityLanzhou 730000China

Nitrogen-doped three-dimensional graphene(N-doped 3D-graphene)is a graphene derivative with excellent adsorption capacity,large specific surface area,high porosity,and optoelectronic ***,N-doped 3D-graphene/Si heterojunctions were grown in situ directly on silicon(Si)substrates via plasma-assisted chemical vapor deposition(PACVD),which is promising for surface-enhanced Raman scattering(SERS)substrates *** analyses of theoretical simulation,incorporating N atoms in 3D-graphene are beneficial to increase the electronic state density of the system and enhance the charge transfer between the substrate and the target *** enhancement of the optical and electric fields benefits from the stronger light-matter interaction improved by the natural nano-resonator structure of N-doped *** as-prepared SERS substrates based on N-doped 3D-graphene/Si heterojunctions achieve ultra-low detection for various molecules:10^(-8)M for methylene blue(MB)and 10^(-9)M for crystal violet(CRV)with rhodamine(R6G)of 10^(10)*** practical detected,10^(-8)M thiram was precisely detected in apple peel *** results indicate that N-doped 3D-graphene/Si heterojunctions based-SERS substrates have promising applications in low-concentration molecular detection and food safety.

关键词： charge transfer DFT simulation N-doped 3D-graphene SERS Thiram detection

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Necessary prerequisites for evidence-based practice:results of investigating nurses'informatics competency and information literacy skills

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Frontiers of Nursing 2024年第1期11卷 67-76页

作者： Jamileh Farokhzadian Somayeh Jouparinejad Mahdieh Montazeri Elham Bakhshipour Amirreza Sabzi Fatemeh Falahati-Marvast Nursing Research Center Kerman University of Medical SciencesKermanIran Coronary Care Unit Shafa HospitalKerman University of Medical SciencesKermanIran Department of Health Information Sciences Faculty of Management and Medical Information SciencesKerman University of Medical SciencesKermanIran Medical informatics Research Center Institute for Futures Studies in HealthKerman University of Medical SciencesKermanIran Biomechanics and Movement Sciences interdisciplinary Program University of DelawareNewarkDEUSA Student Research Committee Shiraz University of Medical SciencesShirazIran Department of Health Technology Assessment School of Public HealthShahid Sadoughi University of Medical SciencesYazdIran

This study aimed to evaluate the correlation between nursing informatics(NI)competency and information literacy skills for evidencebased practice(EBP)among intensive care *** cross-sectional study was conducted on 184 nurses working in intensive care units(ICUs).The study data were collected through demographic information,Nursing informatics Competency Assessment Tool(NICAT),and information literacy skills for EBP *** intensive care nurses received competent and low-moderate levels for the total scores of NI competency and information literacy skills,*** received a moderate score for the use of different information resources but a low score for information searching skills,different search features,and knowledge about search operators,and only 31.5%of the nurses selected the most appropriate *** competency and related subscales had a significant direct bidirectional correlation with information literacy skills for EBP and its subscales(P<0.05).Nurses require a high level of NI competency and information literacy for EBP to obtain up-to-date information and provide better care and *** planners and policymakers should develop interventions to enhance NI competency and information literacy skills among nurses and motivate them to use EBP in clinical settings.

关键词： evidence-based practice nursing informatics nursing informatics competency information literacy critical care nursing

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Early development and the point of no return in pikeperch( Sander lucioperca L.) larvae

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Chinese Journal of Oceanology and Limnology 2017年第6期35卷 1493-1500页

作者：许郑超李彩娟凌去非 GAUGHAN Sarah 王国成韩晓飞 School of Biology and Basic Medical Sciences Soochow University Department of Biology & School of interdisciplinary informatics University of Nebraska at Omaha

The objectives of the present study were to evaluate the yolk-sac and oil globule absorption and point of no return （PNR） ofpikeperch （Sander lucioperca L.） larvae. Artificial propagation ofpikeperch was performed at （15±2）℃. Yolk-sac absorption, oil globule absorption, larval growth and the first initial feeding rate were observed to analyze the early growth and to determine the PNR of pikeperch larvae. The total length of newly hatched （0 day after hatching, DAH） pikeperch larvae was （4.25±0.22） mm and the volume of the yolk-sac and the oil globule was （0.30±0.12）mm^3 and （5.14±2.28） 10-2 mm^3 respectively. The yolk-sac and the oil globule were exhausted at 11 DAH and 14 DAH, respectively. Pikeperch larvae began feeding at 8 DAH with an initial feeding rate about 10.0%. From 9 to 14 DAH, the initial feeding rate increased rapidly, and reached its highest （about 82.7%） at 14 DAH. It declined thereafter, 48.9% at 15 DAH and 35.6% at 16 DAH, thus the pikeperch larvae reached PNR by 15-16 DAH. The appropriate first feeding time for the pikeperch larvae is 11-12 DAH, when the initial feeding rate is higher than half of the maximum initial feeding rate.

关键词： growth initial feeding rate pikeperch (Sander lucioperca) larvae Point of No Return

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High resolution aerosol optical thickness retrieval over the Pearl River Delta region with improved aerosol modelling

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Science China Earth Sciences 2009年第10期52卷 1641-1649页

作者： WONG ManSing NICHOL Janet LEE Kwon Ho Department of Land Surveying and Geo-informatics The Hong Kong Polytechnic University Earth System Science interdisciplinary Center University of Maryland (UMD)

Aerosol retrieval algorithms for the MODerate Resolution Imaging Spectroradiometer (MODIS) have been developed to estimate aerosol and microphysical properties of the atmosphere, which help to address aerosol climatic issues at global scale. However, higher spatial resolution aerosol products for urban areas have not been well researched mainly due to the difficulty of differentiating aerosols from bright surfaces in urban areas. Here, a new aerosol retrieval algorithm using the MODIS 500 m resolution images is described, to retrieve aerosol properties over Hong Kong and the Pearl River Delta region. The rationale of our technique is to first estimate the aerosol reflectance by decomposing the top-of-atmosphere reflectance from surface reflectance and Rayleigh path reflectance. For the determination of surface reflectance, a modified Minimum Reflectance Technique (MRT) is used, and MRT images are computed for different seasons. A strong correlation is shown between the surface reflectance of MRT images and MODIS land surface reflectance products (MOD09), with a value of 0.9. For conversion of aerosol reflectance to Aerosol Optical Thickness (AOT), comprehensive Look Up Tables (LUT) are constructed, in which aerosol properties and sun-viewing geometry in the radiative transfer calculations are taken into account. Four aerosol types, namely mixed urban, polluted urban, dust, and heavy pollution, were derived using cluster analysis on three years of AERONET measurements in Hong Kong. Their aerosol properties were input for LUT calculation. The resulting 500 m AOT images are highly correlated (r = 0.89) with AERONET sunphotometer observations in Hong Kong. This study demonstrates the applicability of aerosol retrieval at fine resolution scale in urban areas, which can assist the study of aerosol loading distribution and the impact of localized and transient pollution on urban air quality. In addition, the MODIS 500 m AOT images can be used to study cross-boundary aeroso

关键词： aerosol retrieval aerosol optical thickness AERONET MODIS satellite image

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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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Biomolecular condensates and disease pathogenesis

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Science China(Life Sciences) 2024年第9期67卷 1792-1832页

作者： Ke Ruan Ge Bai Yanshan Fang Dan Li Tingting Li Xingguo Liu Boxun Lu Qing Lu Zhou Songyang Shuguo Sun Zheng Wang Xin Zhang Wen Zhou Hong Zhang The First Affiliated Hospital&School of Life Sciences Ministry of Education Key Laboratory for Membrane-less Organelles&Cellular DynamicsHefei National Research Center for Interdisciplinary Sciences at the MicroscaleCenter for Advanced Interdisciplinary Science and Biomedicine of IHMDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230027China Nanhu Brain-computer Interface Institute Hangzhou 311100China Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine Zhejiang University School of MedicineHangzhou 310058China interdisciplinary Research Center on Biology and Chemistry Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai 201210China University of Chinese Academy of Sciences Beijing 100049China Bio-X Institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders(Ministry of Education)Shanghai Jiao Tong UniversityShanghai 200030China Department of Biomedical informatics School of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China CAS Key Laboratory of Regenerative Biology Joint School of Life SciencesGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China Joint School of Life Sciences Guangzhou Medical UniversityGuangzhou 510000China Neurology Department at Huashan Hospital State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceInstitutes of Brain ScienceSchool of Life SciencesFudan UniversityShanghai 200433 China Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of EducationBio-X InstitutesShanghai Jiao Tong UniversityShanghai 200030China State Key Laboratory of Biocontrol MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging ResearchSchool of Life SciencesSun Yat-sen Memorial HospitalSun Yat-sen UniversityGuangzhou 510275China Department of Human Anatomy Hist

Biomolecular condensates or membraneless organelles(MLOs)formed by liquid-liquid phase separation(LLPS)divide intracellular spaces into discrete compartments for specific *** of LLPS or aberrant phase transition that disturbs the formation or material states of MLOs is closely correlated with neurodegeneration,tumorigenesis,and many other pathological ***,we summarize the recent progress in development of methods to monitor phase separation and we discuss the biogenesis and function of MLOs formed through phase *** then present emerging proof-of-concept examples regarding the disruption of phase separation homeostasis in a diverse array of clinical conditions including neurodegenerative disorders,hearing loss,cancers,and immunological ***,we describe the emerging discovery of chemical modulators of phase separation.

关键词： liquid-liquid phase separation biomolecular condensate membraneless organelle

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Single-cell omics:experimental workflow,data analyses and applications

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Science China Life Sciences 2024年

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biology the Institute of Biomedical Sciences and School of Life Sciences East China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Center for Quantitative Biology (CQB) Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for major Gynecological Diseases Women’s Hospital Zhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of Statistics East China Normal University Shanghai 200062 China Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical informatics Institute College of Pharmaceutical Sciences Zhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of Education Orthopaedic Department Tongji Hospital Bioinformatics Department School of Life Sciences and Technology Tongji University Frontier Science Center for Stem Cells School of Life Sciences and Technology Tongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East Hospital Bioinformatics Department School of Life Sciences and Technology Tongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public Health Shanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River Delta Zhejiang University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

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