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Reducing language barriers, promoting information absorption, and communication using fanyi

中华医学杂志(英文版) 2024年第16期137卷 2024 Jul 22页

作者： Wang Difei Chen Guannan Li Lin Wen Shaodi Xie Zijing Luo Xiao Zhan Li xu shuangbin Li Junrui Wang Rui Wang Qianwen Yu Guangchuang Nanfang Hospital Southern Medical University Guangzhou Guangdong China Department of Bioinformatics School of Basic Medical Sciences Southern Medical University Guangzhou Guangdong China Comprehensive Technology Center of Lianyungang Customs Lianyungang Jiangsu China Department of Oncology The Affiliated Cancer Hospital of Nanjing Medical University &amp Jiangsu Cancer Hospital Nanjing Jiangsu China Department of Laboratory Medicine Microbiome Medicine Center Zhujiang Hospital Southern Medical University Guangzhou Guangdong China

Interpreting genes of interest is essential for identifying molecular mechanisms, but acquiring such information typically involves tedious manual retrieval. To streamline this process, thefanyi package offers tools to retrieve gene information from sources like National Center for Biotechnology Information (NCBI), significantly enhancing accessibility. Additionally, understanding the latest research advancements and sharing achievements are crucial for junior researchers. However, language barriers often restrict knowledge absorption and career development. To address these challenges, we developed thefanyi package, which leverages artificial intelligence (AI)-driven online translation services to accurately translate among multiple languages. This dual functionality allows researchers to quickly capture and comprehend information, promotes a multilingual environment, and fosters innovation in academic community. Meanwhile, the translation functions are versatile and applicable beyond biomedicine research to other domains as well. Thefanyi package is freely available at https://***/YuLab-SMU/fanyi.

关键词： Multilingualism Communication barriers Translating Artificial intelligence Single-cell analysis Gene expression profiling Biological markers

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shinyTempSignal:an R shiny application for exploring temporal and other phylogenetic signals

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Journal of Genetics and Genomics 2024年第7期51卷 762-768页

作者： Li Zhan Xiao Luo Wenqin Xie xuan-An Zhu Zijing Xie Jianfeng Lin Lin Li Wenli Tang Rui Wang Lin Deng Yufan Liao Bingdong Liu Yantong Cai Qianwen Wang shuangbin xu Guangchuang Yu Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong 510515China Faculty of Computers Guangdong University of TechnologyGuangzhouGuangdong 510006China Ubigene Biosciences Co. Ltd.GuangzhouGuangdong 510530China State Key Laboratory of Applied Microbiology Southern China Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Open Laboratory of Applied MicrobiologyGuangdong Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

The molecular clock model is fundamental for inferring species divergence times from molecular ***,its direct application may introduce significant biases due to sequencing errors,recombination events,and inaccurately labeled sampling *** accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous ***,while not all branches of a phylogenetic tree may exhibit a clear temporal signal,specific branches may still adhere to the assumptions,with varying evolutionary *** a relaxed molecular clock model better aligns with the complexities of *** root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic *** its utility,there remains a lack of corresponding software implementations for broader *** address this gap,we present shinyTempSignal,an interactive web application implemented with the shiny framework,available as an R package and publicly accessible at https://***/YuLab-SMU/*** tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed *** extending the root-to-tip regression method to diverse signals,shinyTempSignal helps in the detection of evolving features or traits,thereby laying the foundation for deeper insights and subsequent analyses.

关键词： Molecular clock Root-to-tip regression Temporal signal Phylogenetic signal

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MicrobiotaProcess:A comprehensive R package for deep mining microbiome

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The Innovation 2023年第2期4卷 48-58,47页

作者： shuangbin xu Li Zhan Wenli Tang Qianwen Wang Zehan Dai Lang Zhou Tingze Feng Meijun Chen Tianzhi Wu Erqiang Hu Guangchuang Yu Division of Laboratory Medicine Microbiome Medicine CenterZhujiang HospitalSouthern Medical UniversityGuangzhou 510515China Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China

The data output from microbiome research is growing at an accelerating rate,yet mining the data quickly and efficiently remains *** is still a lack of an effective data structure to represent and manage data,as well as flexible and composable analysis *** response to these two issues,we designed and developed the MicrobiotaProcess *** provides a comprehensive data structure,MPSE,to better integrate the primary and intermediate data,which improves the integration and exploration of the downstream *** this data structure,the downstream analysis tasks are decomposed and a set of functions are designed under a tidy *** functions independently perform simple tasks and can be combined to perform complex tasks.

关键词： methods. structure integrate

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clusterProfiler 4.0:A universal enrichment tool for interpreting omics data

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The Innovation 2021年第3期2卷 51-61页

作者： Tianzhi Wu Erqiang Hu shuangbin xu Meijun Chen Pingfan Guo Zehan Dai Tingze Feng Lang Zhou Wenli Tang Li Zhan Xiaocong Fu Shanshan Liu Xiaochen Bo Guangchuang Yu Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China Department of Biotechnology Beijing Institute of Radiation MedicineBeijing 100850China Guangdong Provincial Key Laboratory of Proteomics School of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China Microbiome Medicine Center Department of Laboratory MedicineZhujiang HospitalSouthern Medical UniversityGuangzhou 510515China

Functional enrichment analysis is pivotal for interpreting highthroughput omics data in life *** is crucial for this type of tool to use the latest annotation databases for as many organisms as *** meet these requirements,we present here an updated version of our popular Bioconductor package,clusterProfiler *** package has been enhanced considerably compared with its original version published 9 years *** new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online *** also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and *** new features include gene set enrichment analysis and comparison of enrichment results from multiple gene *** anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms.

关键词： clusterProfiler biological knowledge mining functional analysis enrichment analysis visualization

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Riverine sulfate sources and behaviors in arid environment,Northwest China:Constraints from sulfur and oxygen isotopes

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Journal of Environmental Sciences 2024年第3期137卷 716-731页

作者： Yifu xu Wenjing Liu Bing xu Zhifang xu Key Laboratory of Cenozoic Geology and Environment Institute of Geology and GeophysicsChinese Academy of SciencesBeijing 100029China Innovation Academy for Earth Science Chinese Academy of SciencesBeijing 100029China University of Chinese Academy of Sciences Beijing 100049China

The fate of riverine sulfate ion (SO_(4)^(2-)) and its environmental effects in arid environment are difficult to evaluate due to its complicated sources and strongly coupled behaviors with water cycle which is significantly modified by *** understand the sulfur cycle in aquatic systems in arid environment,the chemical and sulfur and oxygen isotopic compositions (δ^(34)S_(SO4)and δ^(18)O_(SO4)) of major rivers around the Badain Jaran Desert,northwestern China,were *** rivers had averaged SO_(4)^(2-)content at 1336μmol/L,over 10times higher than the global *** δ^(34)S_(SO4)and δ^(18)O_(SO4)values ranged from-5.3‰to+11.8‰and+1.6‰to+12.8‰,*** end-member analysis and the inverse model showed that riverine sulfate was mainly derived from evaporites dissolution (0-87%),sulfide oxidation (13%-100%) and precipitation (0-33%),indicating heterogeneity in sulfur sources and behaviors along the river drainage with the lithology variations and climate *** isotopic tools combining with hydro-chemistry compositions could be applied to reveal sulfur cycle in arid *** on the calculation,sulfide oxidation plays the primary role in the headwater and upstream in the Qilian-Mountains area,where sulfide is widely *** the proportion of evaporites dissolution contributing to riverine sulfate is much higher in downstream in a drier ***,less precipitation and higher temperature can lead to more intensive evaporation,affecting the process of sulfide oxidation and enhancing the rates of evaporites dissolution and sulfate precipitation in the basin.

关键词： Sulfur and oxygen isotopes Source apportionment Inverse model Arid environment Inland rivers Northwestern China

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Laboratory evaluation of high-friction thin overlays for pavement preservation

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Frontiers of Structural and Civil Engineering 2024年第6期18卷 936-948页

作者： Ouming xu Rentao xu Lintong JIN School of Highway Chang’an UniversityXi’an 710064China School of Materials Science and Engineering Chang’an UniversityXi’an 710061China

Traditional asphalt concrete(AC)and stone matrix asphalt(SMA),which are used as thin asphalt overlays,are common maintenance strategies to enhancing ride quality,skid resistance,and ***,several studies have used a novel asphalt mixture known as a high-friction thin overlay(HFTO)to improve surface ***,it remains uncertain whether the laboratory properties of HFTO differ significantly from those of conventional *** study aims to evaluate the laboratory properties of HFTO mixtures and compare them with those of AC and *** mixtures with nominal maximum size of 9.5 mm were produced in the laboratory,and performance tests were conducted,including wheel tracking test,low temperature flexural creep test,moisture susceptibility test,Cantabro Abrasion Test,Marshall Test,sand patch test,British pendulum test,and indoor tire-rollingdown *** results showed that the HFTO exhibited a lower tire/pavement noise than the AC and ***,HFTO had superior high-temperature stability,larger macro texture,and higher skid resistance in comparison to those of AC,but lower than those of ***,HFTO mixtures may be considered a suitable replacement for traditional AC mixtures in regions where skid resistance and noise reduction are concerns.

关键词： road engineering pavement maintenance high friction thin overlay performance skid resistance tire/pavement noise

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Aldehyde oxidase mediated enantioselective metabolic health risk of dinotefuran

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Science China Chemistry 2024年第6期67卷 2079-2091页

作者： Liwei xu Xinxin xu Hua Kuang Chuanlai xu Xiaoling Wu State Key Laboratory of Food Science and Resources Jiangnan UniversityWuxi214122China International Joint Research Laboratory for Biointerface and Biodetection and School of Food Science and Technology Jiangnan UniversityWuxi214122China Collaborative Innovation center of Food Safety and Quality Control in Jiangsu Province Jiangnan UniversityWuxi214122China

Chiral pollutants often pose significant differential environmental health *** this study,the biotransformation of chiral dinotefuran(DIN)and its enantioselective metabolic toxicity mechanisms have been systemically ***,reversedphase chromatography-high resolution mass spectrometry was developed to quantify the content of DIN R/S chiral enantiomer with pg level sensitivity,revealing a lower elimination rate constant(K_(e))of S-DIN(0.730 h^(-1))than R-DIN(0.746 h^(-1)).Secondly,the interaction mechanism between DIN metabolism and important endogenous bioactive molecules,such as aldehyde oxidase(AOX)and neurotransmitters,was *** DIN nitro-group was converted into a guanidine group by the reducing site of nearby flavin adenine dinucleotide(FAD)in AOX with the preferred higher affinity of ***,the endogenous tryptophan(Trp)aldehyde metabolic intermediate,5-hydroxyindoleacetaldehyde(5-HIAL),provides a persistent electron donor for DIN reduction via the oxidation-catalyzed site in AOX,resulting in remarkable up-regulation of monoamine neurotransmitters such as serotonin and ***,the higher level of neurotransmitters further mediated dysregulation of oxylipin homeostasis via the serotonergic pathway,where S-DIN exhibited more pronounced liver lipid damage and environmental health risk with the accumulated lipid biomarkers,oxidized triglyceride(OxTG)and oxidized sphingomyelin(OxSM).This study elucidates the AOX-mediated enantioselectivity metabolic pathway of DIN,providing a new analytical method for chiral pollutants and paves the way for their health risk assessments.

关键词： neonicotinoid dinotefuran enantiomer aldehyde oxidase metabolomics health risk

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Skeletal interoception in osteoarthritis

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Bone Research 2024年第2期12卷 241-254页

作者： Dinglong Yang Jiawen xu Ke xu Peng xu Department of Joint Surgery Honghui HospitalXi’an Jiaotong UniversityXi’an 710054China Department of Orthopedic Surgery and Orthopedic Research Institute West China HospitalSichuan UniversityChengdu 610041China

The interoception maintains proper physiological conditions and metabolic homeostasis by releasing regulatory signals after perceving changes in the internal state of the *** its various forms,skeletal interoception specifically regulates the metabolic homeostasis of ***(OA)is a complex joint disorder involving cartilage,subchondral bone,and *** subchondral bone undergoes continuous remodeling to adapt to dynamic joint *** findings highlight that skeletal interoception mediated by aberrant mechanical loads contributes to pathological remodeling of the subchondral bone,resulting in subchondral bone sclerosis in *** skeletal interoception is also a potential mechanism for chronic synovial inflammation in *** this review,we offer a general overview of interoception,specifically skeletal interoception,subchondral bone microenviroment and the aberrant subchondral *** also discuss the role of skeletal interoception in abnormal subchondral bone remodeling and synovial inflammation in OA,as well as the potential prospects and challenges in exploring novel OA therapies that target skeletal interoception.

关键词： homeostasis inflammation releasing

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Malware Evasion Attacks Against IoT and Other Devices: An Empirical Study

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Tsinghua Science and Technology 2024年第1期29卷 127-142页

作者： Yan xu Deqiang Li Qianmu Li Shouhuai xu School of Computer Science and Engineering Nanjing University of Science and TechnologyNanjing 210094China School of Computer Science Nanjing University of Posts and TelecommunicationsNanjing 210023China Department of Computer Science University of Colorado Colorado SpringsColorado SpringsCO 80918USA

The Internet of Things(loT)has grown rapidly due to artificial intelligence driven edge *** enabling many new functions,edge computing devices expand the vulnerability surface and have become the target of malware ***,attackers have used advanced techniques to evade defenses by transforming their malware into functionality-preserving *** systematically analyze such evasion attacks and conduct a large-scale empirical study in this paper to evaluate their impact on *** specifically,we focus on two forms of evasion attacks:obfuscation and adversarial *** the best of our knowledge,this paper is the first to investigate and contrast the two families of evasion attacks *** apply 10 obfuscation attacks and 9 adversarial attacks to 2870 malware *** obtained findings are as follows.(1)Commercial Off-The-Shelf(COTS)malware detectors are vulnerable to evasion attacks.(2)Adversarial attacks affect COTS malware detectors slightly more effectively than obfuscated malware examples.(3)Code similarity detection approaches can be affected by obfuscated examples and are barely affected by adversarial attacks.(4)These attacks can preserve the functionality of original malware examples.

关键词： Android malware obfuscation adversarial examples

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Granting strength to aerogel fibers through encapsulation

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Science China Materials 2024年第4期67卷 1365-1366页

作者： Wenhui xu Department of Basic Chemistry School of PharmacyJiangxi University of Chinese MedicineNanchang 330004China

Aerogel fibers, distinguished by their lightweight nature, pronounced porosity, large surface area, and superior thermal insulation properties, have diversified applications in thermal management, energy devices, and environmental remediation[1]. However, compared with monolithic ones, these fibershaped aerogels exhibit limited mechanical strength and resilience due to their one-dimensional small size.

关键词： strength fibers thermal

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