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Protein Residue Contact Prediction Based on Deep Learning and Massive Statistical Features from Multi-Sequence Alignment

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Tsinghua Science and Technology 2022年第5期27卷 843-854页

作者： Huiling Zhang Min Hao Hao Wu hing-fung ting Yihong Tang Wenhui Xi Yanjie Wei Shenzhen Institutes of Advanced Technology Chinese Academy of SciencesShenzhen 518055China University of Chinese Academy of Sciences Beijing 100049China College of Electronic and Information Engineering Southwest UniversityChongqing 400715China School of Software Engineering University of Science and Technology of ChinaHefei 230051China Department of Computer Science The University of Hong KongHong Kong 999077China School of Computer Science Beijing University of Posts and TelecommunicationsBeijing 100876China

Sequence-based protein tertiary structure prediction is of fundamental importance because the function of a protein ultimately depends on its 3 D *** accurate residue-residue contact map is one of the essential elements for current ab initio prediction protocols of 3 D structure ***,with the combination of deep learning and direct coupling techniques,the performance of residue contact prediction has achieved significant ***,a considerable number of current Deep-Learning(DL)-based prediction methods are usually time-consuming,mainly because they rely on different categories of data types and third-party *** this research,we transformed the complex biological problem into a pure computational problem through statistics and artificial *** have accordingly proposed a feature extraction method to obtain various categories of statistical information from only the multi-sequence alignment,followed by training a DL model for residue-residue contact prediction based on the massive statistical *** proposed method is robust in terms of different test sets,showed high reliability on model confidence score,could obtain high computational efficiency and achieve comparable prediction precisions with DL methods that relying on multi-source inputs.

关键词： multi-sequence alignment residue-residue contact prediction feature extraction statistical information Deep Learning(DL) high computational efficiency

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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 *** success of cell entry determines the effect of sEV on recipient ***,we aimed to delineate the mechanisms underlying the uptake of sEV in ***: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 *** Yao an

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

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Toward haplotype studies in polyploid plants to assist breeding

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Molecular Plant 2021年第12期14卷 1969-1972页

作者： Yuxuan Yuan Armin Scheben David Edwards ting-fung Chan School of Life Sciences and State Key Laboratory of Agrobiotechnology The Chinese University of Hong KongHong Kong SARChina Simons Center for Quantitative Biology Cold Spring Harbor LaboratoryCold Spring HarborNYUSA School of Biological Sciences and Institute of Agriculture The University of Western AustraliaPerthAustralia

THE IMPORTANCE OF POLYPLOIDS Polyploids are typically classified as either autopolyploids or allo-polyploids(Figure 1).Autopolyploids result from whole-genome duplication within the same species,while allopolyploids derive from the hybridization of different species followed by chromo-some ***,plant allopolyploids are thought to be the most common polyploids,although autopolyploid plants and allopolyploid plants might be at parity in numbers(Barker et al.,2016).During speciation,polyploidization allows plants to adapt to different environments(Soltis et al.,2009).Mutation and hybridization increase the heterozygosity of the genome,while genome rearrangements during polyploidization lead to the formation of new chromosomes and new chromosome rearrangements,which complicate polyploid genomes and the following studies.

关键词： breeding Figure

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Psychometrics of the chronic liver disease questionnaire for Southern Chinese patients with chronic hepatitis B virus infection

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World Journal of Gastroenterology 2009年第26期15卷 3288-3297页

作者： Elegance ting Pui Lam Cindy Lo Kuen Lam Ching Lung Lai Man fung Yuen Daniel Yee Tak Fong Department of Medicine The University of Hong Kong Department of Nursing Studies The University of Hong Kong

AIM： To test the psychometric properties of a Chinese [（Hong Kong） HK] translation of the chronic liver disease questionnaire （CLDQ）. METHODS： A Chinese （HK） translation of the CLDQ was developed by iterative translation and cognitive debriefing. It was then administered to 72 uncomplicated and 78 complicated chronic hepatitis B （CriB） patients in Hong Kong together with a structured questionnaire on service utilization, and the Chinese （HK） SF-36 Health Survey Version 2 （SF-36v2）. RESULTS： Scaling success was ≥ 80% for all but three items. A new factor assessing sleep was found and items of two （Fatigue and Systemic Symptoms） subscales tended to load on the same factor. Internal consistency and test-retest reliabilities ranged from 0.58-0.90 for different subscales. Construct validity was confirmed by the expected correlations between the SF-36v2 Health Survey and CLDQ scores. Mean scores of CLDQ were significantly lower in complicated compared with uncomplicated CHB, supporting sensitivity in detecting differences between groups.CONCLUSION： The Chinese （HK） CLDQ is valid, reliable and sensitive for patients with CHB. Some modifications to the scaling structure might further improve its psychometric properties,

关键词： Chronic liver disease Health-related quality of life Hepatitis B Southern Chinese Validity

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Seropharmacological Study on Osteogenic Effects of Post-Absorption Ingredients of An Osteoprotective Herbal Formula

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Chinese Journal of Integrative Medicine 2017年第1期23卷 25-32页

作者： SIU Wing-sum KO Chun-hay WONG hing-lok GAO Si SHUM Wai-ting LAU Clara Bik-san HUNG Lung-kim LEUNG Ping-chung Institute of Chinese Medicine Chinese University of Hong KongHong KongChina State Key Laboratory of Phytochemistry and Plant Resources in West China Chinese University of Hong KongHong KongChina Department of Orthopaedics and Traumatology Chinese University of Hong KonqHong KongChina

Objective： To further investigate the in vitro effects of an osteoprotective herbal formula ＂ELP＂（Herba Epimedii, Fructus Ligustri Lucidi and Fructus Psora/eae） using seropharmacological approach. Methods： Rats were fed with ELP or its individual component herbs for 2 days. The serum containing the post-absorbed ingredients of the herbal items were collected for cell culture using UMR106 cell, RAW264.7 cell and mesenchymal stem cell （MSC） isolated from the bone marrow of the rats. The effects of the herbal-containing serum on cell toxicity were detected by 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide assay; bromodeoxyuridine assay was conducted to measure the cell proliferation of UMR106 cell and MSC; cell activity was measured using colorimetric method, and mRNA expression of runt-related transcription factor 2 （Runx2）, alkaline phosphatase （ALP） and osteopontin （OPN） of UMR106 and MSC as well as matrix metalloproteinase 9 （MMP-9）, tartrate-resistant acid phosphatase （TRAP） and cathepsin K of RAW264.7 were analyzed using real-time reverse-transcription polymerase chain reaction. Results： ELP and its component serum exhibited no cytotoxic effects on the cells. The ELP-containing serum increased the proliferation of UMR106 cell and MSC by 25.7% and 14.4%, respectively and the alkaline phosphatase activity of MSC was increased by 42.6%. On the contrary, it inhibited the RAW264.7 cell differentiation by 29.2%. ELP serum upregulated the Runx2 expression of UMR and MSC by 1.18 fold and 1.27 fold, respectively. It also upregulated ALP and OPN expression in MSC by 1.69- and 2.12-fold, respectively. On the other hand, ELP serum down-regulated MMP-9 and cathepsin K expression of RAW264.7 cell by 0.46- and 0.36-fold, respectively. Conclusions： The serum of the animals fed with ELP contains active ingredients which are effective in promoting osteogenesis and inhibiting osteoclastogenesis.

关键词： osteoporosis seropharmacology osteogenesis herbal formula

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Enhancing the graphene photocurrent using surface plasmons and a p-n junction

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Light(Science & Applications) 2020年第1期9卷 793-802页

作者： Di Wang Andres E.Llacsahuanga Allcca ting-fung Chung Alexander V.Kildishev Yong P.Chen Alexandra Boltasseva Vladimir M.Shalaev School of Electrical and Computer Engineering Purdue UniversityWest LafayetteIN 47907USA Birck Nanotechnology Center Purdue UniversityWest LafayetteIN 47907USA Department of Physics and Astronomy Purdue UniversityWest LafayetteIN 47907USA Purdue Quantum Science and Engineering Institute(PQSEI) Purdue UniversityWest LafayetteIN 47907USA

The recently proposed concept of graphene photodetectors offers remarkable properties such as unprecedented compactness,ultrabroadband detection,and an ultrafast response ***,owing to the low optical absorption of pristine monolayer graphene,the intrinsically low responsivity of graphene photodetectors significantly hinders the development of practical *** address this issue,numerous efforts have thus far been made to enhance the light–graphene interaction using plasmonic *** approaches,however,can be significantly advanced by leveraging the other critical aspect of graphene photoresponsivity enhancement-electrical junction *** has been reported that the dominant photocarrier generation mechanism in graphene is the photothermoelectric(PTE)***,the two energy conversion mechanisms involved in the graphene photodetection process are light-to-heat and heat-to-electricity *** this work,we propose a meticulously designed device architecture to simultaneously enhance the two conversion ***,a gap plasmon structure is used to absorb a major portion of the incident light to induce localized heating,and a pair of split gates is used to produce a p-n junction in graphene to augment the PTE current *** gap plasmon structure and the split gates are designed to share common key components so that the proposed device architecture concurrently realizes both optical and electrical *** experimentally demonstrate the dominance of the PTE effect in graphene photocurrent generation and observe a 25-fold increase in the generated photocurrent compared to the un-enhanced *** further photocurrent enhancement can be achieved by applying a DC bias,the proposed device concept shows vast potential for practical applications.

关键词： electrical plasmon hinder

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Techno-economic Analysis of Distributed Hydrogen Production from Natural Gas

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Chinese Journal of Chemical Engineering 2012年第3期20卷 489-496页

作者： LUK Ho ting LEI Ho Man NG Wai Yee LAM Koon fung Department of Chemical and Biomolecular Engineering the Hong Kong University of Science and TechnologyHong KongChina

It is well established that hydrogen has the potential to make a significant contribution to the world energy *** U.S.,majority of hydrogen production plants implement steam methane reforming(SMR) for centralized hydrogen ***,there is a wide lack of agreement on the nascent stage of using hydrogen as fuel in vehicles industry because of the difficulty in delivery and *** performing technological and economic analysis,this work aims to establish the most feasible hydrogen production pathway for automotives in near *** the evaluation,processes such as thermal cracking of ammonia and centralized hydrogen production followed by bulk delivery are eliminated while on-site steam reforming of methanol and natural gas are the most technologically feasible *** two processes are further evaluated by comprehensive economic *** results showed that the steam reforming(SR) of natural gas has a shorter payback time and a higher return on investment(ROI) and internal rate of return(IRR).Sensitivity analysis has also been constructed to evaluate the impact of variables like NG feedstock price,capital of investment and operating capacity factor on the overall production cost of *** on this study,natural gas is prompted to be the most economically and technologically available raw material for short-term hydrogen production before the transition to renewable energy source such as solar energy,biomass and wind power.

关键词： gas station cost analysis steam reforming ammonia cracking

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Factors Affecting Mesenchymal Stromal Cells Yield from Bone Marrow Aspiration

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Chinese Journal of Cancer Research 2011年第1期23卷 43-48页

作者： Jing Li Wilfred hing-Sang Wong Shing Chan James Chor-San Chim Kenneth Man-Chee Cheung Tsz-Leung Lee Wing-Yan Au Shau-Yin Ha Albert Kwok-Wei Lie Yu-Lung Lau Raymond Hin-Suen Liang Godfrey Chi-fung Chan China Oxford Centre for International Health Research Cardiovascular Institute ＆ Fuwai HospitalChinese Academy of Medical Sciences ＆ Peking Union Medical CollegeBeijing 100037China Department of Paediatrics and Adolescent Medicine Department of Medicine Department of Orthopaedics ＆Traumatology the University of Hong KongHKSARChina

Objective：This study was to investigate the variables in bone marrow harvesting procedure and individual donor factors which can potentially affect the yield of mesenchymal stromal cells（MSC）.Methods：We determined the yield of MSC from bone marrow under different clinical conditions by comparing the MSC colony numbers from：（1） donors of different ages;（2） healthy donors and patients with leukemia;（3） bone marrow aspirated at different time points during marrow harvesting;（4） bone marrow harvested by different ***：During the process of harvesting,the number of MSC significantly decreased with increase number of aspiration,from 675/ml at the initial decreased to 60/ml after 100 ml bone marrow aspirated,and 50/ml after 200 ml bone marrow *** number of MSC retrieved from leukemia patients（99/ml bone marrow） was significantly lower than that of healthy donors（708/ml bone marrow）.However,there was no significant difference in growth *** was no significant age-related difference of MSC yielded from donors 55 *** there was no significant difference in MSC number between the samples from single end-holed needle and those from multiple-side-hole ***：The optimal bone marrow samples for MSC collection should be obtained earlier in the process of harvesting *** marrow from donors 55 years was equally good as MSC *** autologous MSC from leukemia patients can be utilized for in-vitro MSC expansion.

关键词： Mesenchymal stromal cell CFU-F Bone marrow aspiration Leukemia

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Outcomes of radical prostatectomy in a 20-year localized prostate cancer single institution series in China

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Asian Journal of Andrology 2023年第3期25卷 345-349页

作者： Xiao-Hao Ruan Tsun Tsun Stacia Chun Da Huang Hoi-Lung Wong Brian Sze-Ho Ho Chiu-fung Tsang Terence Chun-ting Lai Ada Tsui-Lin Ng Rong Na James Hok-Leung Tsu Division of Urology Department of SurgeryThe University of Hong KongHong KongChina Department of Urology Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghai 200025China Division of Urology Department of SurgeryQueen Mary HospitalHong KongChina

The long-term survival outcomes of radical prostatectomy(RP)in Chinese prostate cancer(PCa)patients are poorly *** conducted a single-center,retrospective analysis of patients undergoing RP to study the prognostic value of pathological and surgical *** April 1998 to February 2022,782 patients undergoing RP at Queen Mary Hospital of The University of Hong Kong(Hong Kong,China)were included in our *** Cox regression analysis and Kaplan–Meier analysis with stratification were *** 5-year,10-year,and 15-year overall survival(OS)rates were 96.6%,86.8%,and 70.6%,respectively,while the 5-year,10-year,and 15-year PCa-specific survival(PSS)rates were 99.7%,98.6%,and 97.8%,*** International Society of Urological Pathology PCa grades(ISUP Grade Group)≥4 was significantly associated with poorer PSS(hazard ratio[HR]=8.52,95%confidence interval[CI]:1.42–51.25,P=0.02).Pathological T3 stage was not significantly associated with PSS or OS in our *** node invasion and extracapsular extension might be associated with worse PSS(HR=20.30,95%CI:1.22–336.38,P=0.04;and HR=7.29,95%CI:1.22–43.64,P=0.03,respectively).Different surgical approaches(open,laparoscopic,or robotic-assisted)had similar outcomes in terms of PSS and *** conclusion,we report the longest timespan follow-up of Chinese PCa patients after RP with different approaches.

关键词： China oncologic outcome prostate cancer radical prostatectom

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Feasibility of gallbladder preservation during robotic left hepatectomy:A retrospective comparative study

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Laparoscopic, Endoscopic and Robotic Surgery 2022年第3期5卷 100-105页

作者： Kit-Fai Lee Andrew KY.fung Hon-ting Lok Janet WC.Kung Eugene YJ.Lo Charing CN.Chong John Wong Kelvin KC.Ng Division of Hepatobiliary and Pancreatic Surgery Department of SurgeryPrince of Wales HospitalThe Chinese University of Hong KongHong KongChina

Objective:Traditionally,gallbladder is routinely removed during left hepatectomy even if there is no gallbladder ***,adverse consequence after cholecystectomy,though rare,still occa-sionally *** study aims to evaluate the feasibility of gallbladder preservation during robotic left ***:All consecutive robotic left hepatectomy cases between December 2010 and January 2022 in Prince of Wales Hospital,the Chinese University of Hong Kong were retrieved from a prospectively collected *** gallbladder was preserved by moving the liver transection line just away from the gallbladder *** were divided into two groups:gallbladder preservation(GBP)and non-gallbladder preservation(NGBP).Operative results and long-term outcomes were compared between these two ***:There were 11 cases in the GBP group and 25 cases in the NGBP *** two groups were comparable in terms of the patient demographics and disease *** was no operative *** was no difference between the two groups in operative time(GBP 270 min *** 332 min,p=0.132),blood loss(GBP 50 mL *** 150 mL,p=0.115)or complication rate(GBP 27.3%*** 24.0%,p>0.999).There was also no difference in 5-year overall *** the GBP group,no patient developed specific symptoms or complications related to the preserved ***-up ultrasound or computed tomography revealed a normal appearance of the preserved gallbladders except in one patient who developed a 3-mm gallbladder *** the other hand,one(4%)patient in the NGBP group developed troublesome diarrhoea after ***:Gallbladder preservation is safe and feasible during robotic left *** preserved gallbladder does not lead to any symptoms,while postcholecystectomy diarrhoea can be avoided.

关键词： Robotic left hepatectomy Gallbladder preservation Cholecystectomy

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