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BioTreasury:a community-based repository enabling indexing and rating of bioinformatics tools

Science China(Life Sciences) 2024年第2期67卷 221-229页

作者： Qi Zhao Xin Zhou Jingxing Wu Jieyi Cai Xiaoqiong Bao Lin Tang Chaoye Wang Chunlei Liu Yukai Wang Yuyan Teng Mohan Zheng Weiping Mu Zhixiang Zuo Yubin Xie Xiaotong Luo Jian Ren School of Life Sciences State Key Laboratory of Oncology in South ChinaCancer CenterGuangdong Provincial Clinical Research Center for CancerSun Yat-sen UniversityGuangzhou 510060China Institute of Precision Medicine The First Affiliated HospitalSun Yat-sen UniversityGuangzhou 510080China guangdong Institute of Gastroenterology Department of General SurgeryGuangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat-sen UniversityGuangzhou 510275China

The exponential growth of bioinformatics tools in recent years has posed challenges for scientists in selecting the most suitable one for their data analysis assignments.Therefore,to aid scientists in making informed choices,a community-based platform that indexes and rates bioinformatics tools is urgently needed.In this study,we introduce Bio Treasury(http://***),an integrated communitybased repository that provides an interactive platform for users and developers to share their experiences in various bioinformatics tools.Bio Treasury offers a comprehensive collection of well-indexed bioinformatics software,tools,and databases,totaling over 10,000 entries.In the past two years,we have continuously improved and maintained Bio Treasury,adding several exciting features,including creating structured homepages for every tool and user,a hierarchical category of bioinformatics tools and classifying tools using large language model(LLM).Bio Treasury streamlines the tool submission process with intelligent auto-completion.Additionally,Bio Treasury provides a wide range of social features,for example,enabling users to participate in interactive discussions,rate tools,build and share tool collections for the public.We believe Bio Treasury can be a valuable resource and knowledge-sharing platform for the biomedical community.It empowers researchers to effectively discover and evaluate bioinformatics tools,fostering collaboration and advancing bioinformatics research.

关键词： bioinformatics tools index tool database rating system large language model tool collections shari

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Metagenomics analysis identifies oral Streptococcus as potential biomarkers for nasopharyngeal carcinoma

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Journal of Genetics and Genomics 2024年第3期51卷 363-366页

作者： Yanmin Liu Chengtao Wang Lixiang Xie Shuling Du Li Ding Ying Cui Runzhi Chen Jingxiang Zhang Wan Wang Xi Liu Yan Wang Shiyan Chen Tian Tan Qiaochu Zhao Limei Yin Chunwei Li Yong Chen Tao Ding Department of Immunology and Microbiology Zhongshan School of MedicineSun Yat-sen UniversityGuangzhouGuangdong 510080China key laboratory of Tropical Disease Control(sun yat-sen university) Ministry of EducationGuangzhouGuangdong 510080China Department of Radiation Oncology The First Affiliated HospitalSun Yat-sen UniversityGuangzhouGuangdong 510080China Department of Infectious Diseases The Fifth Affiliated HospitalSun Yat-sen UniversityZhuhaiGuangdong 519000China Department of Endocrinology&Metabolism The Fifth Affiliated HospitalSun Yat-sen UniversityZhuhaiGuangdong 519000China Department of Otolaryngology The First Affiliated HospitalSun Yat-sen UniversityGuangzhouGuangdong 510080China

Nasopharyngeal carcinoma(NPC)is a malignancy originating from the nasopharyngeal epithelial cells.Although some studies have identified potential biomarkers for early diagnosis of NPC based on metabolomics data(Chen et al.,2023;Zhou et al.,2023)and Epstein-Barr virus subtypes(Xu et al.,2019),their effectiveness and applicability need further investigation,particularly when consideringthe roles of oral microbiota.

关键词： al. nasopharyngeal diagnosis

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Classification of congenital cataracts based on multidimensional phenotypes and its association with visual outcomes

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International Journal of Ophthalmology(English edition) 2024年第3期17卷 473-479页

作者： Yuan Tan Ying-Shi Zou Ying-Lin Yu Le-Yi Hu Ting Zhang Hui Chen Ling Jin Duo-Ru Lin Yi-Zhi Liu Hao-Tian Lin Zhen-Zhen Liu State key laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat-sen UniversityGuangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangdong Provincial Clinical Research Center for Ocular DiseasesGuangzhou 510060Guangdong ProvinceChina

●AIM:To establish a classification for congenital cataracts that can facilitate individualized treatment and help identify individuals with a high likelihood of different visual outcomes.●METHODS:Consecutive patients diagnosed with congenital cataracts and undergoing surgery between January 2005 and November 2021 were recruited.data on visual outcomes and the phenotypic characteristics of ocular biometry and the anterior and posterior segments were extracted from the patients’medical records.A hierarchical cluster analysis was performed.The main outcome measure was the identification of distinct clusters of eyes with congenital cataracts.●RESULTS:A total of 164 children(299 eyes)were divided into two clusters based on their ocular features.Cluster 1(96 eyes)had a shorter axial length(mean±SD,19.44±1.68 mm),a low prevalence of macular abnormalities(1.04%),and no retinal abnormalities or posterior cataracts.Cluster 2(203 eyes)had a greater axial length(mean±SD,20.42±2.10 mm)and a higher prevalence of macular abnormalities(8.37%),retinal abnormalities(98.52%),and posterior cataracts(4.93%).Compared with the eyes in Cluster 2(57.14%),those in Cluster 1(71.88%)had a 2.2 times higher chance of good best-corrected visual acuity[<0.7 logMAR;OR(95%CI),2.20(1.25–3.81);P=0.006].●CONCLUSION:This retrospective study categorizes congenital cataracts into two distinct clusters,each associated with a different likelihood of visual outcomes.This innovative classification may enable the personalization and prioritization of early interventions for patients who may gain the greatest benefit,thereby making strides toward precision medicine in the field of congenital cataracts.

关键词： classification congenital cataract phenotype visual acuity cluster analysis

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Distribution of per-and polyfluoroalkyl substances in blood,serum,and urine of patients with liver cancer and associations with liver function biomarkers

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Journal of Environmental Sciences 2024年第5期139卷 418-427页

作者： Cao Dai Lin Peng Yanjie Li Zhendong Li Da Chen Fei Wang Nan Lin Department of Hepatobiliary Surgery The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630China School of Environment Guangdong Key Laboratory of Environmental Pollution and HealthJinan UniversityGuangzhou 510632China State key laboratory of Environmental and Biological analysis Department of ChemistryHong Kong Baptist UniversityHong Kong 999077China South China Institute of Environmental Sciences MEEGuangzhou 510655China

Studies have shown that per-and polyfluoroalkyl substances(PFASs)may be hepatotoxic in animals or humans.However,data on clinical epidemiology are very limited.In this study,21PFASs were determined in patients with liver diseases,with the highest median concentrations detected in the serum sample(26.7 ng/mL),followed by blood(10.7 ng/mL)and urine(5.02 ng/mL).Higher total PFAS concentrations were found in hepatocellular carcinoma(HCC)patients compared to non-HCC patients,with significant discrepancies in serum and blood samples.Besides,significant correlations were also found among PFAS concentrations and age,gender,body mass index(BMI),and liver function biomarkers levels.For example,PFAS concentrations are significantly higher in males than in females;Several serum PFASs concentrations increase with age and BMI,while the serum perfluorohexane sulfonic acid(PFHxS)concentrations are negatively correlated with age.In addition,multiple regression models adjusted for age,gender and BMI found that increased serum perfluorobutane sulfonic acid(PFBS),perfluoroheptane sulfonic acid(PFHpS)and perfluorohexylphosphonic acid(PFHxPA)conentrations are correlated with elevated alkaline phosphatase(ALP),aspartate aminotransferase(AST),and alpha-fetoprotein(AFP)(p<0.05).Our results provide epidemiological support for the future study on the potential clinical hepatotoxicity of PFAS.

关键词： Per-and polyfluoroalkyl substances(PFASs) Liver cancer Serum Blood Urine Liver function biomarkers

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Bureaucratic Culture and Innovation

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China & World Economy 2024年第3期32卷 31-66页

作者： Shigang Li Kexin She Li Zhang International School of Business and Finance Sun Yat-sen UniversityChina National School of Development Peking UniversityChina International School of Business and Finance Key Laboratory of Mesoeconomics and Coordinated Development of Regions and IndustriesSun Yat-sen UniversityChina

This study explores the effects of bureaucratic culture on innovation.We define bureaucratic culture as a culture in which power and officials are held in the highest regard.Using panel data of publicly listed Chinese manufacturing firms from 2007 to 2015,we found that bureaucratic culture negatively correlated with firms'patent output.A mechanism analysis shows that bureaucratic culture hindered corporate innovation by reducing firms'research and development inputs and decreasing innovation efficiency.Furthermore,we provided evidence that anti-corruption campaigns and the development of formal institutions could neutralize the negative impact of bureaucratic culture on corporate innovation.This study is the first to investigate quantitatively the causal effect of bureaucratic culture on corporate innovation and it can deepen the understanding of the relationship between culture and innovation in China.We speculate that promoting a creative culture,particularly one that fosters entrepreneurial spirit,is of utmost importance.

关键词： bureaucratic culture corporate innovation economic growth talent allocation

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Slowing down of the summer Southern Hemisphere Annular Mode trend against the background of ozone recovery

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Atmospheric and Oceanic Science Letters 2024年第1期17卷 1-8页

作者： Fei Zheng School of Atmospheric Sciences Key Laboratory of Tropical Atmosphere-Ocean SystemMinistry of EducationSun Yat-sen UniversityZhuhaiChina Southern Marine Science and Engineering guangdong laboratory ZhuhaiChina

20世纪末期,南半球热带外地区经历了显著的气候变化,包括夏季南半球环状模(SAM)的显著上升趋势,伴随着南极半岛的增暖和别林斯高晋海的海冰融化.这些趋势主要是由20世纪末期南极平流层臭氧消耗所驱动的.本文发现,自2001年左右以来,在南... 详细信息

20世纪末期,南半球热带外地区经历了显著的气候变化,包括夏季南半球环状模(SAM)的显著上升趋势,伴随着南极半岛的增暖和别林斯高晋海的海冰融化.这些趋势主要是由20世纪末期南极平流层臭氧消耗所驱动的.本文发现,自2001年左右以来,在南极平流层臭氧恢复的背景下,观测到的夏季SAM的上升趋势已经趋于平缓,验证了前人利用数值模拟预测的夏季SAM上升趋势减缓现象,与SAM在臭氧恢复后趋势只减缓但没有逆转不同,南极地表气温和海冰的趋势发生了逆转.南极半岛由变暖趋势转为降温趋势,别林斯高晋海域的海冰由融化趋势转为增多趋势.

关键词：南半球环状模南极臭氧损耗南极臭氧恢复

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RSPSSL:A novel high-fidelity Raman spectral preprocessing scheme to enhance biomedical applications and chemical resolution visualization

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Light(Science & Applications) 2024年第2期13卷 366-386页

作者： Jiaqi Hu Gina Jinna Chen Chenlong Xue Pei Liang Yanqun Xiang Chuanlun Zhang Xiaokeng Chi Guoying Liu Yanfang Ye Dongyu Cui De Zhang Xiaojun yu Hong Dang Wen Zhang Junfan Chen Quan Tang Penglai Guo Ho-Pui Ho Yuchao Li Longqing Cong Perry Ping Shum State key laboratory of Optical Fiber and Cable Manufacture Technology Guangdong Key Laboratory of Integrated Optoelectronics IntellisenseDepartment of EEESouthern University of Science and TechnologyShenzhen 518055China College of Optical and Electronic Technology China Jiliang UniversityHangzhou 310018China Department of Nasopharyngeal Carcinoma Sun Yat-sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou 510060China Department of Ocean Science and Engineering Southern University of Science and TechnologyShenzhen 518055China Department of Nephrology Chaozhou People’s HospitalChaozhou 521011China Clinical Research Design Division Sun Yatsen Memorial HospitalGuangzhouGuangdong 510120China School of Automation Northwestern Polytechnical UniversityXi’anShaanxi 710072China Department of Biomedical Engineering The Chinese University of Hong KongHong KongChina guangdong Provincial key laboratory of Nanophotonic Manipulation Institute of NanophotonicsJinan UniversityGuangzhou 511443China

Raman spectroscopy has tremendous potential for material analysis with its molecular fingerprinting capability in many branches of science and technology.It is also an emerging omics technique for metabolic profiling to shape precision medicine.However,precisely attributing vibration peaks coupled with specific environmental,instrumental,and specimen noise is problematic.Intelligent Raman spectral preprocessing to remove statistical bias noise and sample-related errors should provide a powerful tool for valuable information extraction.Here,we propose a novel Raman spectral preprocessing scheme based on self-supervised learning(RSPSSL)with high capacity and spectral fidelity.It can preprocess arbitrary Raman spectra without further training at a speed of~1900 spectra per second without human interference.The experimental data preprocessing trial demonstrated its excellent capacity and signal fidelity with an 88%reduction in root mean square error and a 60%reduction in infinite norm(L__(∞))compared to established techniques.With this advantage,it remarkably enhanced various biomedical applications with a 400%accuracy elevation(ΔAUC)in cancer diagnosis,an average 38%(few-shot)and 242%accuracy improvement in paraquat concentration prediction,and unsealed the chemical resolution of biomedical hyperspectral images,especially in the spectral fingerprint region.It precisely preprocessed various Raman spectra from different spectroscopy devices,laboratories,and diverse applications.This scheme will enable biomedical mechanism screening with the label-free volumetric molecular imaging tool on organism and disease metabolomics profiling with a scenario of high throughput,cross-device,various analyte complexity,and diverse applications.

关键词： spectral scheme resolution

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NHE7 upregulation potentiates the uptake of small extracellular vesicles by enhancing maturation of macropinosomes in hepatocellular carcinoma

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Cancer Communications 2024年第2期44卷 251-272页

作者： Yue Yao Yi Xu Liang Yu Ting-Mao Xue Zhi-Jie Xiao Pui-Chi Tin Hiu-Ling Fung Hoi-Tang Ma Jing-Ping Yun Judy Wai Ping Yam Department of Pathology School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongP.R.China Department of Endocrinology and Metabolism Second Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjingP.R.China Department of Hepatopancreatobiliary Surgery Second Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjingP.R.China State key laboratory of Oncology in South China Cancer Center of Sun Yat-sen UniversityGuangzhouGuangdongP.R.China Department of Hepatobiliary Surgery II Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongP.R.China Scientific Research Center The Seventh Affiliated HospitalSun Yat-sen UniversityShenzhenGuangdongP.R.China State key laboratory of Liver Research The University of Hong KongHong KongP.R.China Department of Pathology Cancer Center of Sun Yat-sen UniversityGuangzhouGuangdongP.R.China

Background:Small extracellular vesicles(sEVs)mediate intercellular commu-nication that contributes to hepatocellular carcinoma(HCC)progression via multifaceted pathways.The success of cell entry determines the effect of sEV on recipient cells.Here,we aimed to delineate the mechanisms underlying the uptake of sEV in HCC.Abbreviations:AF,Alexa Fluor;ANOVA,analysis of variance;ATP9A,ATPase Phospholipid Transporting 9A;BCECF-AM,2’,7’-bis-(2-barboxyethyl)-5-(and-6)-carboxyfluorescein,acetoxymethyl ester;BSA,bovine serum albumin;CCMR,Centre for Comparative Medicine Research;CRISPR,clustered regularly interspaced short palindromic repeats;CTL,ctrl;CXCR4,C-X-C Chemokine Receptor Type 4;DAPI,4′,6-diamidino-2-phenylindole;DFS,disease-free survival;DMEM,Dulbecco’s Modified Eagle Medium;DMSO,dimethyl sulfoxide;Dox,doxycycline;EEA1,early endosome antigen 1;EIPA,5-(N-ethyl-N-isopropyl)-amiloride;FBS,fetal bovine serum;FITC,fluorescein isothiocyanate;GAPDH,glyceraldehyde-3-phosphate dehydrogenase;GM130,Golgi matrix protein 130;HCC,hepatocellular carcinoma;HEPES,4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid;HPRT1,hypoxanthine phosphoribosyltransferase 1;H-score,histoscore;IAA,indole-3-acetic acid;KD,knockdown;KO,knockout;mAID,mini-auxin-inducible degron;MTT,3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide;NHE7,Na(+)/H(+)exchanger 7;ns,non-significant;OD,optical density;OS,overall survival;PBS,phosphate-buffered saline;PCR,polymerase chain reaction;pHe,endosomal pH;pHi,intracellular pH;PKH67,Paul Karl Horan 67;Rab21,Ras-associated binding protein 21;RIPA,radioimmunoprecipitation assay;SAM,synergistic activation mediator;SEMs,standard error of the means;sEVs,small extracellular vesicles;sgRNA,single-guide RNA;shRNA,short-hairpin RNA;SLC9,solute carrier gene 9;SLiCE,Seamless Ligation Cloning Extract;TCGA,The Cancer Genome Atlas;TCL,total cell lysates;TGN,trans-Golgi network;TMA,tissue microarray;TMR,tetramethyl rhodamine;TSG101,tumor susceptibility gene 101.Yue Yao and Yi Xu contributed equally to this work.Methods

关键词： hepatocellular carcinoma small extracellular vesicles macropinocytosis pH regulation sodium-hydrogen exchanger

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analysis of light propagation characteristic in the aero-optic flow field of cone-headed vehicle with side window

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Optoelectronics Letters 2024年第1期20卷 58-64页

作者： XU Liang ZHOU Liye WANG Luyang ZHAO Shiwei WANG Tao Tianjin key laboratory of Complex Control Theory and Application School of Electrical Engineering and AutomationTianjin University of TechnologyTianjin 300384China School of Intelligent Engineering Sun Yat-sen UniversityGuangzhou 510275China Southern Marine Science and Engineering guangdong laboratory(Zhuhai) Zhuhai 519000China

Aero-optic imaging deviation research is carried out for infrared-guided vehicle with cone-head side window,with a focus on the propagation characteristics of light in an aero-optic flow field.When the light entering the aero-optic flow field from the free-stream should be close to the normal,numerous data indicate that the light is refracted away from the normal.This paper divides the aero-optic flow field into two parts and uses the gas density distribution in the aero-optic flow field to propose the hypothesis that there are two modes of refraction when light propagates through the flow field.The results show that light propagates from the optically denser medium to the optically thinner medium after passing through the shock wave and eventually leads to refraction away from the normal when the light enters the aero-optic flow field.

关键词： flow propagation light

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Understanding Urban Vitality from the Economic and Human Activities Perspective:A Case Study of Chongqing,China

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Chinese Geographical Science 2024年第1期34卷 52-66页

作者： YANG Fiona Fan LIN Geng LEI Yubing WANG Ying YI Zheng School of Geography and Planning Sun Yat-sen UniversityGuangzhou510006China Southern Marine Science and Engineering guangdong laboratory(Zhuhai) Zhuhai519100China Chongqing Planning and Design Institute Chongqing401147China

The literature on urban vitality tends to focus on the built environment.This paper argues that some important processes in shaping vitality may be overlooked without examining the intensity and diversity of economic and human activities.Using newly developed spatial big data and adopting the methods of multi-indicator measurement and spatial analysis methods,we analyzed the pattern of urban vitality in Chongqing,a provincial city in western China and,on this basis,evaluated the creation and maintenance of urban vitality from the economic and human activities perspective.Our findings indicate that the impacts of economic and human activities are positive and significant.Among the three intensity and diversity indicators,economic intensity and population density show an effect on urban vitality stronger than that of economic diversity.However,economic diversity has the strongest superposition or interactive effect,and is thus an important foundation dynamic.The positive effect of population density on urban vitality is largely a result of Chongqing’s jobs-housing balance.The case of Chongqing highlights the importance of topographic features,historical inheritance,large-scale migration,and cultural activities in shaping the distinctive vitality pattern of a city.This study contends that the creation and maintenance of urban vitality can not be fully explained without incorporating the impacts of economic and human activities.It contributes to a comprehensive measurement of urban vitality and enriches its connotations.

关键词： urban vitality economic diversity economic intensity population density Chongqing,China

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