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YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

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Genomics, Proteomics & Bioinformatics 2015年第1期13卷 25-35页

作者： Christopher M.Colangelo Mark Shifman kei-hoi cheung Kathryn L.Stone Nicholas J.Carriero Erol E.Gulcicek TuKiet T.Lam Terence Wu Robert D.Bjornson Can Bruce Angus C.Nairn Jesse Rinehart Perry L.Miller Kenneth R.Williams W.M.Keck Foundation Biotechnology Resource Laboratory School of Medicine Yale University Department of Molecular Biophysics & Biochemistry Yale University Yale Center for Medical Informatics School of Medicine Yale University Department of Anesthesiology School of Medicine Yale University Department of Emergency Medicine School of Medicine Yale University VA Connecticut Healthcare System W.M. Keck Foundation Biotechnology Resource Laboratory School of Medicine Yale University Department of Computer Science Yale University Yale Center for Genome Analysis West Campus Yale University Yale West Campus Analytical Core West Campus Yale University Yale Bioinformatics Resource School of Medicine Yale University Department of Psychiatry School of Medicine Yale University Department of Cellular & Molecular Physiology School of Medicine Yale University Systems Biology Institute Yale University

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry（LC–MS/MS） database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring（MRM）/selective reaction monitoring（SRM） assay development. We have linked YPED＇s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.

关键词： Proteomics Database Bioinformatics Mass spectrometry Repository Spectral library

Options and survival benefits of conversion therapy for unresectable hepatocellular carcinoma

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World Journal of Gastroenterology 2024年第18期30卷 2479-2481页

作者： Wong hoi She Tan To cheung Department of Surgery The University of Hong KongHong Kong 999077China

In the study by Wu et al,patients with unresectable hepatocellular carcinoma were subjected to transarterial chemoembolization(TACE)as a conversion therapy in order to render their tumors suitable for resection.A nomogram was devised and shown to be effective in predicting the survival of these *** of the results,however,is questionable since the study subjects consisted of patients who had resection after TACE while excluding patients with the same disease but not suitable for *** can be considered to be an option for conversion ***,markers for determining responses to a conversion therapy and for guiding the decision between TACE and sequential immunotherapy have been *** question of whether effective conversion therapy can truly enhance overall survival remains unanswered.

关键词： Conversion therapy Immunotherapy Liver resection Survival Transarterial chemoembolization Unresectable hepatocellular carcinoma

A review on radiofrequency,microwave and high-intensity focused ultrasound ablations for hepatocellular carcinoma with cirrhosis

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Hepatobiliary Surgery and Nutrition 2021年第2期10卷 193-209页

作者： Tan To cheung Ka Wing Ma Wong hoi She Department of Surgery The University of Hong Kong102 Pok Fu Lam RoadHong KongChina

Importance:Hepatocellular carcinoma(HCC)is usually accompanied by liver cirrhosis,which makes treatment of this disease *** transplantation theoretically provides an ultimate solution to the disease,but the maximal surgical stress and the scarcity of liver graft make this treatment option impossible for some *** an ideal situation,a treatment that is safe and effective should provide a better outcome for patients with the ***:This article aims to give a comprehensive review of various types of loco-ablative treatment for *** Review:Loco-ablative treatment bridges the gap between surgical resection and transarterial *** types of ablative therapy have their unique ability,and evidence-based outcome analysis is the most important key to assisting clinicians to choose the most suitable treatment modality for their ***:Radiofrequency ablation(RFA)has a relatively longer history and more evidence to support its *** ablation(MWA)is gaining momentum because of its shorter ablation time and consistent ablation ***-intensity focused ultrasound(HIFU)ablation is a relatively new technology that provides non-invasive treatment for patients with *** has been carried out at centers of excellence and it is a safe and effective treatment option for selected patients with HCC and liver *** and Relevance:Selective use of different loco-ablative therapies will enhance clinicians’treatment options for treatment of HCC.

关键词： High-intensity focused ultrasound(HIFU) hepatocellular carcinoma(HCC) liver cancer radiofrequency ablation(RFA) microwave ablation(MWA) survival non-invasive treatment ablation cirrhosis complication

Molecular Evidence for the Hybrid Origin of Bauhinia blakeana(Caesalpinioideae)

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Journal of Integrative Plant Biology 2008年第1期50卷 111-118页

作者： Chun Yin Mak Ka Shing cheung Pui Ying Yip hoi Shan Kwan Department of Biology The Chinese University of Hong KongShatinHong KongChina

Bauhinia blakeana Dunn is the Hong Kong Special Administrative Region emblem and a popular horticultural species in many Asian countries. It was first described as a new species from Hong Kong almost a century ago. This plant is sterile and has long been considered a hybrid, possibly from two related species, B. purpurea and B. variegata. However, not much evidence based on molecular methods was available to support this hypothesis. In this study, sequences of internal transcribed spacer I （ITS1）, rbcL and atpB-rbcL intergenic spacer for five Bauhinia species and two varieties of one of the species were determined and compared. There were two types of ITS1 sequences in B. blakeana, one indistinguishable from that of B. purpurea and the other one identical to that of B. variegata. This confirmed that B. blakeana was a hybrid of these two species. Chloroplast atpB-rbcL intergenic spacer sequence of B. blakeana was identical to that of B. purpurea, indicating that B. purpurea was the female parent. The hybridization event seemed to occur only recently and was a rare incident. Its occurrence was likely facilitated by interspecific pollen competition. It appeared that human efforts played a crucial role in the preservation and ubiquity of B. blakeana.

关键词： atpB-rbcL intergenic spacer Bauhinia internal transcribed spacer 1 interspecific hybrid interspecific pollen competition.

A functional tacrolimus-releasing nerve wrap for enhancing nerve regeneration following surgical nerve repair

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Neural Regeneration Research 2025年第1期20卷 291-304页

作者： Simeon C.Daeschler Katelyn J.W.So Konstantin Feinberg Marina Manoraj Jenny cheung Jennifer Zhang Kaveh Mirmoeini JPaul Santerre Tessa Gordon Gregory HBorschel SickKids Research Institute Neuroscience and Mental Health ProgramTorontoONCanada Institute of Biomaterials and Biomedical Engineering University of TorontoTorontoONCanada Indiana University School of Medicine IndianapolisINUSA Division of Plastic and Reconstructive Surgery the Hospital for Sick ChildrenTorontoONCanada Translational Biology and Engineering Program Ted Rogers Centre for Heart ResearchInstitute of Biomedical EngineeringFaculty of DentistryUniversity of TorontoTorontoONCanada

Axonal regeneration following surgical nerve repair is slow and often incomplete,resulting in poor functional recovery which sometimes contributes to lifelong ***,there are no FDA-approved therapies available to promote nerve *** accelerates axonal regeneration,but systemic side effects presently outweigh its potential benefits for peripheral nerve *** authors describe herein a biodegradable polyurethane-based drug delivery system for the sustained local release of tacrolimus at the nerve repair site,with suitable properties for scalable production and clinical application,aiming to promote nerve regeneration and functional recovery with minimal systemic drug *** is encapsulated into co-axially electrospun polycarbonate-urethane nanofibers to generate an implantable nerve wrap that releases therapeutic doses of bioactive tacrolimus over 31 *** and drug loading are adjustable for applications in small and large caliber nerves,and the wrap degrades within 120 days into biocompatible *** released from the nerve wrap promotes axon elongation in vitro and accelerates nerve regeneration and functional recovery in preclinical nerve repair models while off-target systemic drug exposure is reduced by 80%compared with systemic *** its surgical suitability and preclinical efficacy and safety,this system may provide a readily translatable approach to support axonal regeneration and recovery in patients undergoing nerve surgery.

关键词： biodegradable local drug delivery nerve injury nerve regeneration nerve wrap tacrolimus

Housing price dispersion in the presale market

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Economic and Political Studies 2020年第1期8卷 65-81页

作者： Siu kei Wong Ka Shing cheung Department of Real Estate and Construction University of Hong Kongthe Hong Kong SARChina The Ronald Coase Centre for Property Rights Research University of Hong Kongthe Hong Kong SARChina Department of Property The University of Auckland Business SchoolAucklandNew Zealand

Sale before completion(***)is a common practice that real estate developers use to sell residential *** presale buyers are unable to inspect uncompleted units,developers may take advantage of asymmetric information and release information about quality to the market *** search theory also suggests that incomplete pricing information,especially for new products,will induce a less competitive market that is characterised by dispersed presale *** price dispersion be reduced if developers were required to provide more quality and pricing information?In this study,we argue that this is not necessarily the *** conduct a natural experiment using a new information disclosure ordinance governing first-hand residential sales in the Hong Kong SAR,*** find that the ordinance reduced the price dispersion of presale units with asymmetric information about property quality,but increased their price dispersion when limited pricing information(*** trading volume)was available in the *** a critical test,we further show that the ordinance increased price dispersion even more after the units were *** suggests that the ordinance has indeed made presale pricing more difficult because developers are no longer allowed to use different strategies to test market demand.

关键词： Price dispersion presale housing market pricing information quality information natural experiment

Stem cell aging in adult progeria

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Cell Regeneration 2015年第1期4卷 75-83页

作者： hoi-Hung cheung Duanqing Pei Wai-Yee Chan CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine School of Biomedical SciencesFaculty of MedicineThe Chinese University of Hong KongShatinHong Kong S.A.R.China Chinese Academy of Sciences(CAS)Guangzhou Institutes of Biomedicine and Health(GIBH) GuangzhouChina The Chinese University of Hong Kong Room G03ALo Kwee-Seong Intergrated Biomedical Science BuildingShatinN.T.Hong Kong S.A.R.China

Aging is considered an irreversible biological process and also a major risk factor for a spectrum of geriatricdiseases. Advanced age-related decline in physiological functions, such as neurodegeneration, development ofcardiovascular disease, endocrine and metabolic dysfunction, and neoplastic transformation, has become thefocus in aging research. Natural aging is not regarded as a programmed process. However, accelerated agingdue to inherited genetic defects in patients of progeria is programmed and resembles many aspects ofnatural aging. Among several premature aging syndromes, Werner syndrome (WS) and Hutchinson–Gilfordprogeria syndrome (HGPS) are two broadly investigated diseases. In this review, we discuss how stem cellaging in WS helps us understand the biology of aging. We also discuss briefly how the altered epigeneticlandscape in aged cells can be reversed to a “juvenile” state. Lastly, we explore the potential application ofthe latest genomic editing technique for stem cell-based therapy and regenerative medicine in the context of aging.

关键词： Werner syndrome Stem cells Aging WRN

Biocomposites:Their multifunctionality

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International Journal of Smart and Nano Materials 2010年第1期1卷 13-27页

作者： Kin-tak Lau Mei-po Ho Chi-ting Au-Yeung hoi-yan cheung Centre of Excellence in Engineered Fibre Composites Faculty of Engineering and SurveyingUniversity of Southern QueenslandQueenslandAustralia Department of Mechanical Engineering The Hong Kong Polytechnic UniversityHung HomKowloonHong KongChina

During the last decade,tissue engineering has shown a considerable promise in providing more viable alternatives to surgical procedures for harvested tissues,implants and *** to the fast development on nano-and biomaterial technologies,it is now possible for doctors to use patients’cells to repair orthopaedic defects such as focal articular cartilage *** order to support the three-dimensional tissue formation,scaffolds made by biocompatible and bioresorbable polymers and composite materials,for providing temporary support of damaged body and cell structures,have been developed *** ceramic and metallic materials have been widely accepted for the development of implants,their non-resorbability and necessity of second surgical operation(like for bone repair),which induce extra pain for the patients,limit their wide *** development of different types of biocomposites for biomedical engineering applications is *** biocomposites include(i)basic biomaterials;(ii)natural fiber-reinforced biocomposites and(iii)nanoparticle-reinforced *** multifunctionality is discussed in terms of the control of mechanical properties,biodegradability and bioresorbability.

关键词： multifunctional materials biocomposite

Supramolecular Self-assembly of Amphiphilic Alkynylplatinum(II)2,6-Bis(N-alkylbenzimidazol-2′-yl)pyridine Complexes

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Chemical Research in Chinese Universities 2021年第5期37卷 1079-1084页

作者： Andy Shun-hoi cheung Sammual Yu-Lut LEUNG Franky Ka-Wah HAU Vivian Wing-Wah YAM Institute of Molecular Functional Materials and Department of Chemistry The University of Hong KongPokfulam RoadHong KongP.R.China

Alkynylplatinum(II)bzimpy complexes of trimethylammoniumbenzylethynyl ligand have been synthesized and *** with long alkyl chains have been found to exhibit interesting self-assembly properties in the acetonitrile *** amphiphilic nature of the complexes has led to the formation of nanorods,as revealed by electron microscopy *** increasing the polarity of the solvent media has given rise to the enhancement of low-energy emission.

关键词： solution. platinum alkyl