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Asadollahi R, Delvendahl I, Muff R, Tan G, Rodríguez DG, Turan S, Russo M, Oneda B, Joset P, Boonsawat P, Masood R, Mocera M, Ivanovski I, Baumer A, Bachmann-Gagescu R, Schlapbach R, Rehrauer H, Steindl K, Begemann A, Reis A, Winkler J, Winner B, Müller M, Rauch A. Pathogenic SCN2A variants cause early-stage dysfunction in patient-derived neurons. Hum Mol Genet 2023; 32:2192-2204. [PMID: 37010102 PMCID: PMC10281746 DOI: 10.1093/hmg/ddad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/23/2023] [Accepted: 03/19/2023] [Indexed: 04/04/2023] Open
Abstract
Pathogenic heterozygous variants in SCN2A, which encodes the neuronal sodium channel NaV1.2, cause different types of epilepsy or intellectual disability (ID)/autism without seizures. Previous studies using mouse models or heterologous systems suggest that NaV1.2 channel gain-of-function typically causes epilepsy, whereas loss-of-function leads to ID/autism. How altered channel biophysics translate into patient neurons remains unknown. Here, we investigated iPSC-derived early-stage cortical neurons from ID patients harboring diverse pathogenic SCN2A variants [p.(Leu611Valfs*35); p.(Arg937Cys); p.(Trp1716*)] and compared them with neurons from an epileptic encephalopathy (EE) patient [p.(Glu1803Gly)] and controls. ID neurons consistently expressed lower NaV1.2 protein levels. In neurons with the frameshift variant, NaV1.2 mRNA and protein levels were reduced by ~ 50%, suggesting nonsense-mediated decay and haploinsufficiency. In other ID neurons, only protein levels were reduced implying NaV1.2 instability. Electrophysiological analysis revealed decreased sodium current density and impaired action potential (AP) firing in ID neurons, consistent with reduced NaV1.2 levels. In contrast, epilepsy neurons displayed no change in NaV1.2 levels or sodium current density, but impaired sodium channel inactivation. Single-cell transcriptomics identified dysregulation of distinct molecular pathways including inhibition of oxidative phosphorylation in neurons with SCN2A haploinsufficiency and activation of calcium signaling and neurotransmission in epilepsy neurons. Together, our patient iPSC-derived neurons reveal characteristic sodium channel dysfunction consistent with biophysical changes previously observed in heterologous systems. Additionally, our model links the channel dysfunction in ID to reduced NaV1.2 levels and uncovers impaired AP firing in early-stage neurons. The altered molecular pathways may reflect a homeostatic response to NaV1.2 dysfunction and can guide further investigations.
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Affiliation(s)
- R Asadollahi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
- Faculty of Engineering and Science, University of Greenwich London, Medway Campus, Chatham Maritime ME4 4TB, UK
| | - I Delvendahl
- Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich 8057, Switzerland
| | - R Muff
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - G Tan
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - D G Rodríguez
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - S Turan
- Department of Stem Cell Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - M Russo
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - B Oneda
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - P Joset
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - P Boonsawat
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - R Masood
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - M Mocera
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - I Ivanovski
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - A Baumer
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - R Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - R Schlapbach
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - H Rehrauer
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - K Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - A Begemann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - A Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - J Winkler
- Department of Molecular Neurology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
- Center for Rare Diseases Erlangen, University Hospital Erlangen, Erlangen 91054, Germany
| | - B Winner
- Department of Stem Cell Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
- Center for Rare Diseases Erlangen, University Hospital Erlangen, Erlangen 91054, Germany
| | - M Müller
- Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich 8057, Switzerland
- University of Zurich Clinical Research Priority Program (CRPP) Praeclare – Personalized prenatal and reproductive medicine, Zurich 8006, Switzerland
- University of Zurich Research Priority Program (URPP) AdaBD: Adaptive Brain Circuits in Development and Learning, Zurich 8006, Switzerland
| | - A Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich 8057, Switzerland
- University of Zurich Clinical Research Priority Program (CRPP) Praeclare – Personalized prenatal and reproductive medicine, Zurich 8006, Switzerland
- University of Zurich Research Priority Program (URPP) AdaBD: Adaptive Brain Circuits in Development and Learning, Zurich 8006, Switzerland
- University of Zurich Research Priority Program (URPP) ITINERARE: Innovative Therapies in Rare Diseases, Zurich 8006, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich 8057, Switzerland
- University Children's Hospital Zurich, University of Zurich, Zurich 8032, Switzerland
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2
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Zhu Z, Liu Z, Tan G, Qi J, Zhou Y, Li J. Interlayered Interface of a Thin Film Composite Janus Membrane for Sieving Volatile Substances in Membrane Distillation. Environ Sci Technol 2023; 57:7612-7623. [PMID: 37104662 DOI: 10.1021/acs.est.3c00093] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Hypersaline wastewater treatment using membrane distillation (MD) has gained significant attention due to its ability to completely reject nonvolatile substances. However, a critical limitation of current MD membranes is their inability to intercept volatile substances owing to their large membrane pores. Additionally, the strong interaction between volatile substances and MD membranes underwater tends to cause membrane wetting. To overcome these challenges, we developed a dual-layer thin film composite (TFC) Janus membrane through electrospinning and sequential interfacial polymerization of a polyamide (PA) layer and cross-linking a polyvinyl alcohol/polyacrylic acid (PP) layer. The resulting Janus membrane exhibited high flux (>27 L m-2 h-1), salt rejection of ∼100%, phenol rejection of ∼90%, and excellent resistance to wetting and fouling. The interlayered interface between the PA and PP layer allowed the sieve of volatile substances by limiting their dissolution-diffusion, with the increasing hydrogen bond network formation preventing their transport. In contrast, small water molecules with powerful dynamics were permeable through the TFC membrane. Both experimental and molecular dynamics simulation results elucidated the sieving mechanism. Our findings demonstrate that this type of TFC Janus membrane can serve as a novel strategy to design next-generation MD membranes against volatile and non-volatile contaminants, which can have significant implications in the treatment of complex hypersaline wastewater.
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Affiliation(s)
- Zhigao Zhu
- Key Laboratory of New Membrane Materials, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Zhu Liu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Guangming Tan
- Key Laboratory of New Membrane Materials, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Junwen Qi
- Key Laboratory of New Membrane Materials, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yujun Zhou
- Key Laboratory of New Membrane Materials, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jiansheng Li
- Key Laboratory of New Membrane Materials, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
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Parsons ES, Liu F, Kaushik A, Lee A, Schuetz J, Dunham D, Seastedt H, Ogulur I, Heider A, Tan G, Shah A, Cao S, Smith E, Kost L, Acharya S, Prunicki M, Rothenberg M, Sindher S, Leib R, Akdis CA, Nadeau K, Lejeune S. Detection of gut and mucosal peptides through TOMAHAQ in healthy individuals. Allergy 2023. [PMID: 36872560 DOI: 10.1111/all.15698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Affiliation(s)
- E S Parsons
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - F Liu
- Mass Spectrometry Center, Stanford University, Palo Alto, California, USA
| | - A Kaushik
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - A Lee
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - J Schuetz
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - D Dunham
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - H Seastedt
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - I Ogulur
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - A Heider
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - G Tan
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - A Shah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - S Cao
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - E Smith
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - L Kost
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - S Acharya
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - M Prunicki
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA
| | - M Rothenberg
- Department of Pediatrics, Department of Allergy and Immunology, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - S Sindher
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA.,Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, Stanford, California, USA
| | - R Leib
- Mass Spectrometry Center, Stanford University, Palo Alto, California, USA
| | - C A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - K Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA.,Department of Environmental Health Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - S Lejeune
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Palo Alto, California, USA.,INSERM U1019, CNRS UMR 9017, Center for infection and immunity of Lille (CIIL), Univ. Lille, CHU Lille, Institut Pasteur de Lille, Lille, France
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4
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Sun W, Tan G, Yan BP. RISK OF THROMBOEMBOLIC AND HEMORRHAGIC EVENTS ASSOCIATED WITH SWITCHING ORAL ANTICOAGULATION THERAPIES AMONG 89,455 PATIENTS WITH NON-VALVULAR ATRIAL FIBRILLATION: HONG KONG-WIDE OBSERVATIONAL STUDY. J Am Coll Cardiol 2023. [DOI: 10.1016/s0735-1097(23)02293-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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5
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Nkonde C, Bell B, Tait A, Tan G, El-Zebdeh H, Yoshimatsu Y, Smithard DG. 1182 THE PREVALENCE OF ORAL FRAILTY AND ITS ASSOCIATION WITH DYSPHAGIA, FRAILTY AND FORMAL CARE NEEDS. Age Ageing 2023. [DOI: 10.1093/ageing/afac322.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Abstract
Introduction
Oral frailty (OF), gradual loss of oral function combined associated with presbyphagia often in conjunction with cognitive and physical decline, has been recommended to be considered as a geriatric giant. DENTAL has been suggested as a possible screening tool for OF. We have looked at the prevalence of OF and its association with dysphagia, frailty and formal care, amongst people admitted acutely to the acute medical/frailty wards in our hospital.
Methods
OF, dysphagia and frailty were screened for as part of the routine clinical assessment of patients during the usual clinical ward round. Screening tools used were DENTAL for OF, Rockwood Score for frailty and 4QT for dysphagia. Age, sex comorbidities and the need for formal care was documented.
Results
101 people were assessed over a 4-week period. Mean age was 84 years (65-99), 58 (57.4%) were female, 31(30.7%) were independent, 33 (32.6%) dementia, 57 (56.4%) frail, 54 (53.4%) had swallowing problems, and 34 (33.6%) OF. Of those with OF 97% had dysphagia, 88% were frail and 85% required formal care support (85%). OF was associated with dysphagia (p<0.0001), frailty (p< 0.0001), formal care support (p<0.05) and dementia (p<0.05). There was an association between needing care and frailty (p<0.01).
Conclusions
OF is associated with dysphagia, frailty and the need for formal care. OF may result in poor oral health and contribute to dysphagia and frailty, conversely frailty and dysphagia may result in poor oral health due to dependency and poor nutrition and dehydration. The associations are most likely be bidirectional. Further work is required to elucidate this. Clinical staff need to be aware of OF and oral health and include oral screening in their clinical assessment of an older adult.
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Affiliation(s)
- C Nkonde
- Queen Elizabeth Hospital, Lewisham and Greenwich NHS Trust
| | - B Bell
- Queen Elizabeth Hospital, Lewisham and Greenwich NHS Trust
| | - A Tait
- Queen Elizabeth Hospital, Lewisham and Greenwich NHS Trust
| | - G Tan
- Queen Elizabeth Hospital, Lewisham and Greenwich NHS Trust
| | - H El-Zebdeh
- Queen Elizabeth Hospital, Lewisham and Greenwich NHS Trust
| | - Y Yoshimatsu
- Queen Elizabeth Hospital, Lewisham and Greenwich NHS Trust
- University of Greenwich Centre for Exercise Activity and Rehabilitation,
| | - D G Smithard
- Queen Elizabeth Hospital, Lewisham and Greenwich NHS Trust
- University of Greenwich Centre for Exercise Activity and Rehabilitation,
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6
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Zhang C, Zhong X, Yi L, Zhao Z, Zhang Y, Tan G, Zhang Y, Zhang Y, Xu Y, Wu N. Exploring the Associations between Alzheimer's Disease and GBM Mediated by Microglia Based on Network Analysis. J Prev Alzheimers Dis 2023; 10:267-275. [PMID: 36946454 DOI: 10.14283/jpad.2023.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Previous studies have revealed that there existed epidemic associations between Alzheimer's disease (AD) and many types of tumors, however, the inner biological mechanism connecting these diseases was not clear currently. In this study, we explored the transcriptome associations between AD and glioblastoma multiforme (GBM) that both originate in the brain, using microglia as a bridge, from gene and network levels. Firstly, we extracted human scRNA sequencing datasets from Gene Expression Omnibus (GEO) database, and identified differentially expressed genes within microglia after cell annotation. It was observed that there were 11 common genes shared by AD and GBM dys-regulated genes. Next, we utilized DIAMOnD and Flow Centrality algorithms to identify microglia modules and mediating pathways connecting these two diseases based on global network topology. Among these candidate pathways, the mediating genes FURIN and BACE1 (from SPIKN5 to CSNK1A1) were not only related to the formation of amyloid beta plaques that accumulate in the brain of AD patients, but also involved in cancer biology. Furthermore, the biological explorations of mediating pathways connecting AD and GBM modules reveal inflammatory response, lipid metabolism disorder, and cell proliferation terms. Finally, novel signatures for early AD detection as well as risk models for glioma prognosis were identified based on mediating genes involved in these pathways. In conclusion, this study provided a novel network-based strategy for exploring microglia mediation between AD and GBM and identified candidate signatures for disease detection and prognosis.
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Affiliation(s)
- C Zhang
- Chunlong Zhang, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China, ; Nan Wu, , Yanjun Xu,
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7
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Tan G, Kraft M. ASYMPTOMATIC EOSINOPHILIA WITH REACTIVE HYPERGAMMAGLOBULINEMIA. Ann Allergy Asthma Immunol 2022. [DOI: 10.1016/j.anai.2022.08.976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Akdis D, Tan G, Wilzeck V, Costa S, Gasperetti A, Matter CM, Ruschitzka F, Brunckhorst C, Akdis CA, Saguner AM, Duru F. Identifying proteomic profiles as indicators of disease severity in arrhythmogenic cardiomyopathy. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Introduction
Arrhythmogenic cardiomyopathy (ACM) is an inherited heart muscle disease characterized by progressive fibrofatty replacement of the myocardium and ventricular arrhythmias. Biventricular (BiV) involvement may lead to heart failure. This study aimed to investigate characteristic proteomic patterns in plasma of ACM patients, and correlated them with clinical outcome as well as physical exercise, to assess if key soluble molecules may serve as specific biomarkers for ACM, and whether mechanical stress induced by physical exercise may alter proteomic patterns in ACM patients.
Methods
In 38 ACM patients clinical parameters and major adverse cardiovascular events (MACE defined as presence of sustained ventricular tachycardia, ventricular fibrillation, appropriate therapy from implantable cardioverter defibrillator, sudden cardiac death, death related to end-stage heart failure or cardiac transplant) were obtained prospectively during a mean follow-up period of 36 months. All patients received genetic testing using next generation DNA sequencing. Plasma protein expression was analysed using the Proximity Extension Assay (PEA) technology, where a pair of oligonucleotide-labelled antibody probe binds to each targeted protein. In a subgroup of 11 patients blood was drawn immediately before and 3 hours after standardised bicycle exercise testing, and plasma protein expression was compared.
Results
12 patients had ACM with BiV involvement, and 26 patients had isolated right ventricular (RV) involvement. During the follow-up period, 34 patients had a MACE (30% with RV and 14% with BiV). Over 360 proteins were assessed in all ACM patients and compared to 24 healthy controls. The proteomic signature of ACM patients differed significantly compared to controls, and 32 proteins were upregulated in ACM (Figure 1). The proteomic profiles of patients with RV involvement also differed from those with BiV involvement. Most importantly, after exercise, over 40 proteins were upregulated specifically in ACM patients compared to controls, including key pro-inflammatory, adipogenic molecules and also markers of cardiac fibrosis.
Conclusion
Our study shows that ACM patients with RV and BiV involvement have different plasma proteomic profiles compared to healthy controls. Furthermore we were able to demonstrate that, specifically in ACM patients, several pro-inflammatory pathways are upregulated after exercise compared to healthy controls, further elucidating the molecular pathways associated with arrhythmogenicity and disease progression and highlighting the key role of physical stress. Our results may enable the identification of potential future biomarkers for diagnosis and risk stratification and may pave the way for personalized patient specific treatments.
Funding Acknowledgement
Type of funding sources: Foundation. Main funding source(s): Baugarten Foundation ZurichSwiss National Foundation
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Affiliation(s)
- D Akdis
- University Heart Center, Cardiology , Zurich , Switzerland
| | - G Tan
- Swiss Institute of Allergy and Asthma Research , Davos , Switzerland
| | - V Wilzeck
- University Heart Center, Cardiology , Zurich , Switzerland
| | - S Costa
- University Heart Center, Cardiology , Zurich , Switzerland
| | - A Gasperetti
- Johns Hopkins University , Baltimore , United States of America
| | - C M Matter
- University Heart Center, Cardiology , Zurich , Switzerland
| | - F Ruschitzka
- University Heart Center, Cardiology , Zurich , Switzerland
| | - C Brunckhorst
- University Heart Center, Cardiology , Zurich , Switzerland
| | - C A Akdis
- Swiss Institute of Allergy and Asthma Research , Davos , Switzerland
| | - A M Saguner
- University Heart Center, Cardiology , Zurich , Switzerland
| | - F Duru
- University Heart Center, Cardiology , Zurich , Switzerland
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Tan G, Xu D, Zhu Z, Zhang X, Li J. Tailoring pore size and interface of superhydrophobic nanofibrous membrane for robust scaling resistance and flux enhancement in membrane distillation. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.120751] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Xu D, Zhu Z, Tan G, Xue X, Li J. Mechanism insight into gypsum scaling of differently wettable membrane surfaces with antiscalants in membrane distillation. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.120499] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Cheng M, Liu H, Han M, Li SC, Bu D, Sun S, Hu Z, Yang P, Wang R, Liu Y, Chen F, Peng J, Peng H, Song H, Xia Y, Chu L, Zhou Q, Guan F, Wu J, Tan G, Ning K. Microbiome Resilience and Health Implications for People in Half-Year Travel. Front Immunol 2022; 13:848994. [PMID: 35281043 PMCID: PMC8907539 DOI: 10.3389/fimmu.2022.848994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
Travel entail change in geography and diet, both of which are known as determinant factors in shaping the human gut microbiome. Additionally, altered gut microbiome modulates immunity, bringing about health implications in humans. To explore the effects of the mid-term travel on the gut microbiome, we generated 16S rRNA gene and metagenomic sequencing data from longitudinal samples collected over six months. We monitored dynamic trajectories of the gut microbiome variation of a Chinese volunteer team (VT) in their whole journey to Trinidad and Tobago (TAT). We found gut microbiome resilience that VT’s gut microbial compositions gradually transformed to the local TAT’s enterotypes during their six-month stay in TAT, and then reverted to their original enterotypes after VT’s return to Beijing in one month. Moreover, we identified driven species in this bi-directional plasticity that could play a role in immunity modulation, as exemplified by Bacteroides dorei that attenuated atherosclerotic lesion formation and effectively suppressed proinflammatory immune response. Another driven species P. copri could play a crucial role in rheumatoid arthritis pathogenesis, a chronic autoimmune disease. Carbohydrate-active enzymes are often implicated in immune and host-pathogen interactions, of which glycoside hydrolases were found decreased but glycosyltransferases and carbohydrate esterases increased during the travel; these functions were then restored after VT’ returning to Beijing. Furthermore, we discovered these microbial changes and restoration were mediated by VT people’s dietary changes. These findings indicate that half-year travel leads to change in enterotype and functional patterns, exerting effects on human health. Microbial intervention by dietary guidance in half-year travel would be conducive to immunity modulation for maintaining health.
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Affiliation(s)
- Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Dongbo Bu
- Key Lab of Intelligent Information Processing, State Lab of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,School of Computer and Control, University of Chinese Academy of Sciences, Beijing, China
| | - Shiwei Sun
- Key Lab of Intelligent Information Processing, State Lab of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,School of Computer and Control, University of Chinese Academy of Sciences, Beijing, China
| | - Zhiqiang Hu
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Wang
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yawen Liu
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Feng Chen
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jianjun Peng
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hong Peng
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hongxing Song
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yang Xia
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Liqun Chu
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Quan Zhou
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Feng Guan
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jing Wu
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Guangming Tan
- Key Lab of Intelligent Information Processing, State Lab of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,School of Computer and Control, University of Chinese Academy of Sciences, Beijing, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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12
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Tan G, Ong C, Kainth G. 10 Tip-Apex Distance in DHS & IM Nail Fixations for Hip Fractures. Br J Surg 2022. [DOI: 10.1093/bjs/znac039.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Aim
Dynamic hip screws (DHS) and intramedullary nail (IMN) fixations have been successful in treating extracapsular hip fractures. Tip to apex distance (TAD) is defined as the total sum of distance from tip of the lag screw to the femoral head tip on both AP and lateral radiographs. Baumgartner et al. defined TAD<25 mm to be predictive of a successful result, with reduced rates of metalwork failure. Therefore, this study aims to assess if TAD principles are practiced during DHS and IMN fixations.
Method
102 patients were identified between December 2019 and February 2020. The distance was measured on AP and lateral radiographs to calculate the TAD. Patients were followed up for 1 year where the fractures either united or failed.
Results
Patients recruited had age ranges between 19–103 years old, of which 36% are male and 64% are female. 68% had underwent DHS while 32% underwent IM nail. In the DHS group, 13 patients had TAD of >25 mm, 28 with TAD of 20–25 mm, 18 with TAD of 15–20mm and 6 with TAD of <15 mm. For the IM nail group, there are 7 with TAD of 20–25 mm, 13 with TAD of 15–20mm and 10 with TAD of <15 mm.
Conclusions
There were no IM nails that exceeded TAD of 25mm, but 13 DHS fixations were >25mm. 12/13 DHS fixations >25mm TAD were performed by trainees. We advocate emphasis on the TAD principle and re-enforcing to orthopaedic trainees to improve the outcome of DHS in patients with neck of femur fractures.
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Affiliation(s)
- G. Tan
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - C.T. Ong
- Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool, United Kingdom
| | - G. Kainth
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
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13
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Tan G, Dunning J. 11 Robotic Left Lower Sleeve Lobectomy with Bronchoplasty for the Removal of a Carcinoid Tumour. Br J Surg 2022. [DOI: 10.1093/bjs/znac039.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Lung carcinoid tumours constitute approximately 1–2% of all pulmonary tumours. They are derived from enterochromaffin cells, which are also known as ‘Kulchitsky cells' and generally have indolent growth and development patterns. Carcinoid tumours are categorized as typical or atypical, depending on the number of mitoses per high power field and the presence of necrosis. In terms of management, surgical resection has been recognized to be the standard treatment for pulmonary carcinoid tumours. To our knowledge, the da Vinci system and robotic surgery have not been applied in sleeve lobectomies and bronchoplasty for the removal of carcinoid tumours in the United Kingdom. Therefore, we present a case of a sleeve lobectomy with bronchoplasty procedure for the removal of a carcinoid tumour located in the left lower lobe of the patient. The bronchus was repaired using a V-lock suture & Prolene sutures with the surgery performed using the da Vinci robotic surgical system.
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Affiliation(s)
- G. Tan
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - J. Dunning
- James Cook University Hospital, Middlesbrough, United Kingdom
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14
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Gomar JJ, Tan G, Halpern J, Gordon ML, Greenwald B, Koppel J. Increased retention of tau PET ligand [ 18F]-AV1451 in Alzheimer's Disease Psychosis. Transl Psychiatry 2022; 12:82. [PMID: 35217635 PMCID: PMC8881582 DOI: 10.1038/s41398-022-01850-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/04/2022] [Accepted: 02/09/2022] [Indexed: 11/09/2022] Open
Abstract
Psychosis in Alzheimer's disease (AD) represents a distinct disease subtype with a more rapid progression of illness evidenced by an increased velocity of cognitive decline and a hastened mortality. Previous biomarker and post-mortem studies have implicated tau neuropathology as a possible mediator of the accelerated decline in AD psychosis. Tau positron emission tomography (PET) neuroimaging provides the opportunity to evaluate tau pathology in-vivo, so that clinical symptomatology can be correlated with disease pathology. [18F]-AV1451 (Flortaucipir) is a PET ligand with high affinity for insoluble paired-helical filaments (PHFs) of hyperphosphorylated tau. In order to determine whether the development of psychosis and worsened prognosis in AD is associated with an increased burden of tau pathology that can be identified with tau imaging, we identified subjects within the Alzheimer's disease neuroimaging initiative (ADNI) who had [18F]-AV1451 imaging at baseline and became psychotic over the course of the study (N = 17) and matched them 1:3 for gender, age, and education to subjects who had [18F]-AV1451 imaging at baseline and did not become psychotic (N = 50). We compared baseline [18F]-AV1451 retention, in addition to cognitive and functional baseline and longitudinal change, in those who became psychotic over the course of participation in ADNI with those who did not. Results suggest that increases in tau pathology in frontal, medial temporal, and occipital cortices, visualized with [18F]-AV1451 binding, are associated with psychosis and a more rapid cognitive and functional decline.
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Affiliation(s)
- J. J. Gomar
- grid.250903.d0000 0000 9566 0634Feinstein Institutes for Medical Research, Manhassett, NY USA
| | - G. Tan
- grid.250903.d0000 0000 9566 0634Feinstein Institutes for Medical Research, Manhassett, NY USA
| | - J. Halpern
- grid.250903.d0000 0000 9566 0634Feinstein Institutes for Medical Research, Manhassett, NY USA
| | - M. L. Gordon
- grid.250903.d0000 0000 9566 0634Feinstein Institutes for Medical Research, Manhassett, NY USA ,grid.416477.70000 0001 2168 3646Department of Psychiatry, Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY USA
| | - B. Greenwald
- grid.416477.70000 0001 2168 3646Department of Psychiatry, Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY USA
| | - J. Koppel
- grid.250903.d0000 0000 9566 0634Feinstein Institutes for Medical Research, Manhassett, NY USA ,grid.416477.70000 0001 2168 3646Department of Psychiatry, Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY USA
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15
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Zhu Z, Tan G, Lei D, Yang Q, Tan X, Liang N, Ma D. Omniphobic membrane with process optimization for advancing flux and durability toward concentrating reverse-osmosis concentrated seawater with membrane distillation. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2021.119763] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Xue X, Tan G, Zhu Z. All-Polymer and Self-Roughened Superhydrophobic PVDF Fibrous Membranes for Stably Concentrating Seawater by Membrane Distillation. ACS Appl Mater Interfaces 2021; 13:45977-45986. [PMID: 34523328 DOI: 10.1021/acsami.1c12775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Novel specially wettable membranes have been attracting significant attention for durable membrane distillation (MD). However, constructing a superhydrophobic interface often has to undergo complex modification procedures including roughness construction and hydrophobic modification. Herein, all-polymer and self-roughened superhydrophobic poly(vinylidene fluoride) fibrous membranes (PVDF FMs) with robustly stable pores were successfully constructed via electrospinning of fluorinated polyhedral oligomeric silsesquioxanes/PVDF (F-POSS/PVDF) emulsion solution in combination with hot-pressing. The comparative experiment reveals that proper hot-pressing, including adequate temperature and pressure, can help improve membrane pore stability by welding the intersecting fibers and increase the membrane surface hydrophobicity by transferring the inner fluorine chains to the outer fiber surface, simultaneously advancing membrane scaling and fouling resistance. Nevertheless, excessive temperature or pressure will destroy the interconnected pores and surface wettability of the PVDF FM. Significantly, the hot-pressing-treated F-POSS/PVDF FM shows a high water recovery (∼90%) and robust stability after five rounds of the concentration process toward concentrating natural seawater as a target. Thus, the all-polymer and self-roughened superhydrophobic PVDF FMs constructed via electrospinning combined with the thermal treatment have potential applications in concentrating hypersaline brines, which make up for the other membrane technology, including reverse osmosis and nanofiltration technologies that failed to concentrate hypersaline solutions.
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Affiliation(s)
- Xiangyang Xue
- Key Laboratory of New Membrane Materials, Ministry of Industry and Information Technology, School of Environment and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Guangming Tan
- Key Laboratory of New Membrane Materials, Ministry of Industry and Information Technology, School of Environment and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Zhigao Zhu
- Key Laboratory of New Membrane Materials, Ministry of Industry and Information Technology, School of Environment and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
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17
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Yang M, Fan Y, Wu ZY, Gu J, Feng Z, Zhang Q, Han S, Zhang Z, Li X, Hsueh YC, Ni Y, Li X, Li J, Hu M, Li W, Gao H, Yang C, Zhang C, Zhang L, Zhu T, Cheng M, Ji F, Xu J, Cui H, Tan G, Zhang MQ, Liang C, Liu Z, Song YQ, Niu G, Wang K. DAGM: A novel modelling framework to assess the risk of HER2-negative breast cancer based on germline rare coding mutations. EBioMedicine 2021; 69:103446. [PMID: 34157485 PMCID: PMC8220579 DOI: 10.1016/j.ebiom.2021.103446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 05/20/2021] [Accepted: 06/03/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Breast cancers can be divided into HER2-negative and HER2-positive subtypes according to different status of HER2 gene. Despite extensive studies connecting germline mutations with possible risk of HER2-negative breast cancer, the main category of breast cancer, it remains challenging to obtain accurate risk assessment and to understand the potential underlying mechanisms. METHODS We developed a novel framework named Damage Assessment of Genomic Mutations (DAGM), which projects rare coding mutations and gene expressions into Activity Profiles of Signalling Pathways (APSPs). FINDINGS We characterized and validated DAGM framework at multiple levels. Based on an input of germline rare coding mutations, we obtained the corresponding APSP spectrum to calculate the APSP risk score, which was capable of distinguish HER2-negative from HER2-positive cases. These findings were validated using breast cancer data from TCGA (AUC = 0.7). DAGM revealed that HER2 signalling pathway was up-regulated in germline of HER2-negative patients, and those with high APSP risk scores had exhibited immune suppression. These findings were validated using RNA sequencing, phosphoproteome analysis, and CyTOF. Moreover, using germline mutations, DAGM could evaluate the risk for HER2-negative breast cancer, not only in women carrying BRCA1/2 mutations, but also in those without known disease-associated mutations. INTERPRETATION The DAGM can facilitate the screening of subjects at high risk of HER2-negative breast cancer for primary prevention. This study also provides new insights into the potential mechanisms of developing HER2-negative breast cancer. The DAGM has the potential to be applied in the prevention, diagnosis, and treatment of HER2-negative breast cancer. FUNDING This work was supported by the National Key Research and Development Program of China (grant no. 2018YFC0910406 and 2018AAA0103302 to CZ); the National Natural Science Foundation of China (grant no. 81202076 and 82072939 to MY, 81871513 to KW); the Guangzhou Science and Technology Program key projects (grant no. 2014J2200007 to MY, 202002030236 to KW); the National Key R&D Program of China (grant no. 2017YFC1309100 to CL); Shenzhen Science and Technology Planning Project (grant no. JCYJ20170817095211560 574 to YN); and the Natural Science Foundation of Guangdong Province (grant no. 2017A030313882 to KW and S2013010012048 to MY); Hefei National Laboratory for Physical Sciences at the Microscale (grant no. KF2020009 to GN); and RGC General Research Fund (grant no. 17114519 to YQS).
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Affiliation(s)
- Mei Yang
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yanhui Fan
- Phil Rivers Technology, Beijing, China; Phil Rivers Technology, Shenzhen, China
| | - Zhi-Yong Wu
- Diagnosis and Treatment Centre of Breast Diseases, Shantou Central Hospital, Shantou, Guangdong, China
| | - Jin Gu
- BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing, China
| | | | | | - Shunhua Han
- Phil Rivers Technology, Beijing, China; Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Zhonghai Zhang
- State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Xu Li
- State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | | | - Yanxiang Ni
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, China
| | - Xiaoling Li
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jieqing Li
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Meixia Hu
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Weiping Li
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Hongfei Gao
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Ciqiu Yang
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Chunming Zhang
- Phil Rivers Technology, Beijing, China; State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Liulu Zhang
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Teng Zhu
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Minyi Cheng
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Fei Ji
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Juntao Xu
- Phil Rivers Technology, Beijing, China
| | | | - Guangming Tan
- State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Centre for Synthetic & Systems Biology, TNLIST; School of Medicine, Tsinghua University, Beijing, China
| | - Changhong Liang
- Department of Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zaiyi Liu
- Department of Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - You-Qiang Song
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Gang Niu
- Phil Rivers Technology, Beijing, China; Western Institute of Advanced Technology, Chinese Academy of Science, Chongqing, China.
| | - Kun Wang
- Department of Breast Cancer, Cancer Centre, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China.
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18
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Yang M, Fan Y, Wu ZY, Feng Z, Zhang Q, Han S, Zhang Z, Li X, Xue Y, Li X, Hu M, Li J, Li W, Gao H, Yang C, Zhang C, Zhang L, Zhu T, Cheng M, Ji F, Xu J, Cui H, Tan G, Zhang MQ, Liang C, Liu Z, Song YQ, Niu G, Wang K. Abstract PS8-29: Rare variants in the germline genome holistically determine receptor-independent Her2 signaling pathway activation and immune suppression, shaping pathological type and risk of HER2-negative breast cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-ps8-29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Pathogenic factors embedded in the germline genome are widely recognized as being crucial to breast cancer development. However, current knowledge is either concentrated on the pathogenic variants of a few individual genes or SNPs distributed sparsely across the genome in non-coding regions. Methods: We developed a multi-layered framework, DAGG, which converts somatic mutations or germline rare coding variants (gRCVs) into a functional spectrum of dozens of cellular functions and signaling pathways to identify potential pathogenic factors.Findings: We analyzed whole-exome sequencing (WES) data of 726 germline DNA samples and 169 breast tumor DNA samples from breast cancer patients with various pathological types and cancer-free female subjects, we found that germline pathogens of breast cancers were (1) mainly distributed in HER2-negative subtypes, and (2) involved Her2 signaling pathway activation and immune suppression. These computational discoveries were experimentally validated and can provide digital features to explain the germline differences between diseased and healthy genome (AUC = 0.76). Furthermore, an individual’s risk for breast cancer can be estimated by calculating the combined effects of these identified germline pathogens. Carriers of BRCA1/2 pathogenic variants were found to have a significantly higher average risk (p = 0.02). Interpretation: The results demonstrated that the identified pathogenic mechanisms by DAGG were compatible with our current understanding of the causes of breast cancer. Moreover, DAGG provides improved performance over currently used polygenic risk score method of measuring complex disease risks. Our framework promises possible future applications for the prevention, diagnosis, and treatment of breast cancer.
Citation Format: Mei Yang, Yanhui Fan, Zhi-Yong Wu, Zhendong Feng, Qiangzu Zhang, Shunhua Han, Zhonghai Zhang, Xu Li, Yiqing Xue, Xiaoling Li, Meixia Hu, Jieqing Li, Weiping Li, Hongfei Gao, Ciqiu Yang, Chunming Zhang, Liulu Zhang, Teng Zhu, Minyi Cheng, Fei Ji, Juntao Xu, Hening Cui, Guangming Tan, Michael Q Zhang, Changhong Liang, Zaiyi Liu, You-Qiang Song, Gang Niu, Kun Wang. Rare variants in the germline genome holistically determine receptor-independent Her2 signaling pathway activation and immune suppression, shaping pathological type and risk of HER2-negative breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS8-29.
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Affiliation(s)
- Mei Yang
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | | | - Zhi-Yong Wu
- 3Shantou Affiliated Hospital, Sun Yat-sen University, Shantou, China
| | | | | | | | - Zhonghai Zhang
- 4Institute of Computing Technology, Chinese Academy of Sciences, Beijing, Beijing, China
| | - Xu Li
- 4Institute of Computing Technology, Chinese Academy of Sciences, Beijing, Beijing, China
| | | | - Xiaoling Li
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | - Meixia Hu
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | - Jieqing Li
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | - Weiping Li
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | - Hongfei Gao
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | - Ciqiu Yang
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | | | - Liulu Zhang
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | - Teng Zhu
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | - Minyi Cheng
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | - Fei Ji
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | - Juntao Xu
- 2Phil Rivers Technology, Beijing, China
| | | | - Guangming Tan
- 4Institute of Computing Technology, Chinese Academy of Sciences, Beijing, Beijing, China
| | | | | | - Zaiyi Liu
- 1Guangdong Provincial People's Hospital, Guangzhou, China
| | - You-Qiang Song
- 6School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Gang Niu
- 2Phil Rivers Technology, Beijing, China
| | - Kun Wang
- 1Guangdong Provincial People's Hospital, Guangzhou, China
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Ji X, Tan W, Zhang C, Zhai Y, Hsueh Y, Zhang Z, Zhang C, Lu Y, Duan B, Tan G, Na R, Deng G, Niu G. TWIRLS, a knowledge-mining technology, suggests a possible mechanism for the pathological changes in the human host after coronavirus infection via ACE2. Drug Dev Res 2020; 81:1004-1018. [PMID: 32657473 PMCID: PMC7404951 DOI: 10.1002/ddr.21717] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/05/2020] [Accepted: 06/27/2020] [Indexed: 12/12/2022]
Abstract
Faced with the current large-scale public health emergency, collecting, sorting, and analyzing biomedical information related to the "SARS-CoV-2" should be done as quickly as possible to gain a global perspective, which is a basic requirement for strengthening epidemic control capacity. However, for human researchers studying viruses and hosts, the vast amount of information available cannot be processed effectively and in a timely manner, particularly if our scientific understanding is also limited, which further lowers the information processing efficiency. We present TWIRLS (Topic-wise inference engine of massive biomedical literatures), a method that can deal with various scientific problems, such as liver cancer, acute myeloid leukemia, and so forth, which can automatically acquire, organize, and classify information. Additionally, this information can be combined with independent functional data sources to build an inference system via a machine-based approach, which can provide relevant knowledge to help human researchers quickly establish subject cognition and to make more effective decisions. Using TWIRLS, we automatically analyzed more than three million words in more than 14,000 literature articles in only 4 hr. We found that an important regulatory factor angiotensin-converting enzyme 2 (ACE2) may be involved in host pathological changes on binding to the coronavirus after infection. On triggering functional changes in ACE2/AT2R, the cytokine homeostasis regulation axis becomes imbalanced via the Renin-Angiotensin System and IP-10, leading to a cytokine storm. Through a preliminary analysis of blood indices of COVID-19 patients with a history of hypertension, we found that non-ARB (Angiotensin II receptor blockers) users had more symptoms of severe illness than ARB users. This suggests ARBs could potentially be used to treat acute lung injury caused by coronavirus infection.
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Affiliation(s)
- Xiaoyang Ji
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Inner Mongolia Autonomous Region College of Animal ScienceInner Mongolia Agricultural UniversityHohhotChina
- Joint Turing‐Darwin Laboratory of Phil Rivers Technology Ltd. and Institute of Computing TechnologyChinese Academy of SciencesBeijingChina
- Department of Computational Biology, Phil Rivers Technology LtdBeijingChina
| | - Wenting Tan
- Department of Infectious DiseasesSouthwest Hospital, Third Military Medical University (Army Medical University)ChongqingChina
| | - Chunming Zhang
- Joint Turing‐Darwin Laboratory of Phil Rivers Technology Ltd. and Institute of Computing TechnologyChinese Academy of SciencesBeijingChina
- Department of Computational Biology, Phil Rivers Technology LtdBeijingChina
- Institute of Computing TechnologyChinese Academy of SciencesBeijingChina
- West Institute of Computing TechnologyChinese Academy of SciencesChongqingChina
| | - Yubo Zhai
- Institute of Computing TechnologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yiching Hsueh
- Joint Turing‐Darwin Laboratory of Phil Rivers Technology Ltd. and Institute of Computing TechnologyChinese Academy of SciencesBeijingChina
- Department of Computational Biology, Phil Rivers Technology LtdBeijingChina
| | - Zhonghai Zhang
- Institute of Computing TechnologyChinese Academy of SciencesBeijingChina
| | - Chunli Zhang
- Department of Computational Biology, Phil Rivers Technology LtdBeijingChina
| | - Yanqiu Lu
- Department of Infectious DiseasesChongqing Public Health Medical CenterChongqingChina
| | - Bo Duan
- Institute of Computing TechnologyChinese Academy of SciencesBeijingChina
- West Institute of Computing TechnologyChinese Academy of SciencesChongqingChina
| | - Guangming Tan
- Institute of Computing TechnologyChinese Academy of SciencesBeijingChina
- West Institute of Computing TechnologyChinese Academy of SciencesChongqingChina
| | - Renhua Na
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Inner Mongolia Autonomous Region College of Animal ScienceInner Mongolia Agricultural UniversityHohhotChina
| | - Guohong Deng
- Department of Infectious DiseasesSouthwest Hospital, Third Military Medical University (Army Medical University)ChongqingChina
| | - Gang Niu
- Joint Turing‐Darwin Laboratory of Phil Rivers Technology Ltd. and Institute of Computing TechnologyChinese Academy of SciencesBeijingChina
- Department of Computational Biology, Phil Rivers Technology LtdBeijingChina
- West Institute of Computing TechnologyChinese Academy of SciencesChongqingChina
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20
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Ren W, Gan D, Tan G, Xue H, Li N, Xu Z. CHANGES OF WNT/B-CATENIN SIGNALING AND DIFFERENTIATION POTENTIAL OF BONE MARROW MESENCHYMAL STEM CELLS IN PROCESS OF BONE LOSS IN OVARIECTOMIZED RATS. Acta Endocrinol (Buchar) 2020; 16:156-164. [PMID: 33029231 DOI: 10.4183/aeb.2020.156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background In vitro studies of the changes about osteoblastogenesis and adipogenesis potential of BMSCs were not clear. As it is the critical pathway for osteogenic differentiation and bone formation, whether or not Wnt/β-catenin signalling is involved in the changes of osteogenic and adipogenic potential of BMSCs and participates in bone content decrease of ovariectomized (OVX)osteoporosis rats has been rarely reported. Material/Methods BMSCs from femurs of ovariectomzed rats were isolated and cultured in vitro. The proliferation potential of BMSCs was analysed by CCK-8 assays . Osteoblastic and adipogenic differentiation potential of the BMSCs was assessed by ALP activity assay, Alizarin red S staining, Oil red O staining and RT-PCR analysis. Results The results demonstrated that BMSCs from bilateral ovariectomization rats were endowed with lower proliferation and osteoblastic differentiation potential but higher adipogenic potential than the control group in vitro. In addition, β-catenin was found to have been decreased in OVX BMSCs, indicating that Wnt/β-catenin signalling pathways were suppressed in OVX BMSCs . Conclusions Results suggested that changes in the Wnt canonical signalling pathway may be related to imbalances of osteogenic and adipogenic potential of BMSCs, and this may be an important factor related to bone content decrease in ovariectomized osteoporosis rats.
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Lang CCV, Masenga J, Semango G, Kaderbhai H, Li N, Tan G, Heider A, Guttman-Yassky E, Grimm F, Schmid-Grendelmeier P, Brüggen MC. Evidence for different immune signatures and sensitization patterns in sub-Saharan African vs. Central European atopic dermatitis patients. J Eur Acad Dermatol Venereol 2020; 35:e140-e142. [PMID: 32780875 DOI: 10.1111/jdv.16871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- C C V Lang
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland.,Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - J Masenga
- Regional Dermatology Training Center at Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - G Semango
- Regional Dermatology Training Center at Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - H Kaderbhai
- Regional Dermatology Training Center at Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - N Li
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland.,Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - G Tan
- Swiss Institute of Allergy and Asthma Research (SIAF), Davos, Switzerland.,Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - A Heider
- Swiss Institute of Allergy and Asthma Research (SIAF), Davos, Switzerland
| | - E Guttman-Yassky
- Department of Dermatology, Mount Sinai Hospital New York, New York, USA
| | - F Grimm
- Institute for Parasitology, University of Zurich, Zurich, Switzerland
| | - P Schmid-Grendelmeier
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland.,Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - M C Brüggen
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland.,Faculty of Medicine, University of Zurich, Zurich, Switzerland.,Hochgebirgsklinik Davos, Davos, Switzerland
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Lloyd TD, Neal‐Smith G, Fennelly J, Claireaux H, Bretherton C, Carr AJ, Murphy M, Kendrick BJ, Palmer AJR, Wong J, Sharma P, Osei‐Bonsu PK, Ashcroft G, Baigent T, Shirland E, Espey R, Stokes M, Liew I, Dhawal A, Watchorn D, Lum J, Qureshi M, Khaled AS, Kauser S, Hodhody G, Rogers S, Haywood‐Alexander B, Sheikh G, Mahapatra P, Twaij H, Chicco M, Arnaout F, Atherton T, Mutimer J, Sinha P, Oliver E, Stedman T, Gadd R, Kutuzov V, Sattar M, Robiati L, Plastow R, Howe T, Hassan A, Lau B, Collins J, Doshi A, Tan G, Baskaran D, Hari Sunil Kumar K, Agarwal R, Horner M, Gwyn R, Masud S, Beaumont O, Pilarski A, Lebe M, Dawson‐Bowling S, Nolan D, Tsitskaris K, Beamish RE, Jordan C, Alsop S, Hibbert E, Deshpande G, Gould A, Briant‐Evans T, Kilbane L, Crowther I, Ingoe H, Naisbitt A, Gourbault L, Muscat J, Goh EL, Gill J, Elbashir M, Modi N, Archer J, Ismael S, Petrie M, O'Brien H, McCormick M, Koh NP, Lloyd T, King A, Ikram A, Peake J, Yoong A, Rye DS, Newman M, Naraen A, Myatt D, Kapur R, Sgardelis P, Kohli S, Culverhouse‐Mathews M, Haynes S, Boden H, Purmah A, Shenoy R, Raja S, Koh NP, Donovan R, Yeomans D, Ritchie D, Larkin R, Aladwan R, Hughes K, Unsworth R, Cooke R, Samra I, Barrow J, Michael K, Byrne F, Anwar R, Karatzia L, Drysdale H, Wilson H, Jones R, Dass D, Liaw F, Aujla R, Kheiran A, Bell K, Ramavath AL, Telfer R, Nachev K, Lawrence H, Garg V, Shenoy P, Lacey A, Byrom I, Simons M, Manning C, Cheyne N, Williams J. Peri‐operative administration of tranexamic acid in lower limb arthroplasty: a multicentre, prospective cohort study. Anaesthesia 2020; 75:1050-1058. [DOI: 10.1111/anae.15056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2020] [Indexed: 12/20/2022]
Affiliation(s)
- T. D. Lloyd
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK
- Oxford Surgical Collaborative for Audit and Research Oxford UK
| | - G. Neal‐Smith
- Oxford Surgical Collaborative for Audit and Research Oxford UK
| | - J. Fennelly
- Oxford Surgical Collaborative for Audit and Research Oxford UK
| | - H. Claireaux
- Oxford Surgical Collaborative for Audit and Research Oxford UK
| | - C. Bretherton
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK
- Oxford Surgical Collaborative for Audit and Research Oxford UK
| | - A. J. Carr
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK
| | - M. Murphy
- University of Oxford UK
- NHS Blood and Transplant Oxford UK
| | - B. J. Kendrick
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK
| | - A. J. R. Palmer
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK
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23
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Toliman P, Phillips S, de Jong S, O'Neill T, Tan G, Brotherton J, Saville M, Kaldor J, Vallely A, Tabrizi S. Evaluation of p16/Ki-67 dual-stain cytology performed on self-collected vaginal and clinician-collected cervical specimens for the detection of cervical pre-cancer. Clin Microbiol Infect 2020; 26:748-752. [DOI: 10.1016/j.cmi.2019.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 10/05/2019] [Accepted: 10/16/2019] [Indexed: 12/19/2022]
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24
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Zhuang K, Patel A, Tay K, Irani F, Matchar D, Sivapragasam N, Pua U, Sum L, Tze Tec C, Tan G, Chan E, Win H, Burgmans M, Gogna A, Damodharan K, Chan S, Too C, Karaddi Venkatanarasimha N, Quek L, Gummalla K, Siew Ping C, Tan B. 4:12 PM Abstract No. 50 Quality of life outcomes from a randomized controlled trial comparing drug-eluting balloon to conventional balloon angioplasty for below-the-knee arteries in patients with critical limb ischemia. J Vasc Interv Radiol 2020. [DOI: 10.1016/j.jvir.2019.12.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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25
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Abstract
Metabolic reprogramming has been identified as a hallmark of cancer. Liver is an essential hub in the body for the metabolism of three major nutrients including glucose, lipids and amino acids. Hepatocellular carcinoma(HCC) usually presents a variety of changes in characteristic metabolism, such as increased aerobic glycolysis, enhanced de novo lipid synthesis, glutamine depletion, and oxidative metabolism imbalance, which can provide energy and bio-macromolecular raw materials for rapidly growing and proliferating tumor cells. The process of tumor metabolic reprogramming is regulated by multiple factors, such as alterations in metabolic enzyme activity, abnormal gene expression, and signaling pathway disturbance. Advances in high-throughout metabolomics technology have provided a powerful platform for discovering the novel biomarkers and metabolic targets of HCC. Therefore, in-depth study of the metabolic characteristics and regulatory mechanisms of HCC is critical for the development of novel antimetabolites.
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Affiliation(s)
- Z Ning
- Department of Hepatobiliary Surgery, the First Affiliated Hospital, Dalian Medical University, Dalian 116000, China
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26
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Chen P, Tan G, Deng J, Xu Q, Tang R. Mutation analysis of annual sediment discharge at Wu Long station in Wu Jiang River Basin from 1960 to 2016. PLoS One 2019; 14:e0225935. [PMID: 31841541 PMCID: PMC6913992 DOI: 10.1371/journal.pone.0225935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/16/2019] [Indexed: 11/18/2022] Open
Abstract
This article introduces a new method for mutation detection, the approximate entropy method, which is based on the complexity of time series. The mutation of average annual sediment discharge in Wu Jiang River Basin from 1960 to 2016 is detected by the introduced approximate entropy method, and compared with the results of double cumulative curve method and B-G segmentation algorithm. The mutation physical mechanism of the sediment discharge is discussed from the aspects of sediment source, annual distribution and interannual variation, climate change, impact of water conservancy and water conservation projects on sediment transport. The results show that mutation points occurred at 1984 and 2008 at Wu Long station, and the sediment discharge has a significant change after 2008. The mutation of average annual sediment discharge in Wu Jiang River Basin is caused by both climate change and human activity. Sediment reduction effect of the hydraulic engineerings built since 1990s climate is main and direct, and the climate change have secondary effect on sediment discharge change.
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Affiliation(s)
- Peng Chen
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, China
- Key Lab. of River Regulation and Flood Control of Ministry of Water Resources, Changjiang River Scientific Research Inst., Wuhan, China
| | - Guangming Tan
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, China
| | - Jinyun Deng
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, China
| | - Quanxi Xu
- Bureau of Hydrology, Yangtze River Water Resources Commission, Wuhan, China
| | - Rouxin Tang
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, China
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27
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Liu H, Han M, Li SC, Tan G, Sun S, Hu Z, Yang P, Wang R, Liu Y, Chen F, Peng J, Peng H, Song H, Xia Y, Chu L, Zhou Q, Guan F, Wu J, Bu D, Ning K. Resilience of human gut microbial communities for the long stay with multiple dietary shifts. Gut 2019; 68:2254-2255. [PMID: 30420399 PMCID: PMC6872438 DOI: 10.1136/gutjnl-2018-317298] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/18/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Hong Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China,Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Guangming Tan
- Key Lab of Intelligent Information Processing, State Lab of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China,School of Computer and Control Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Shiwei Sun
- Key Lab of Intelligent Information Processing, State Lab of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China,School of Computer and Control Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Zhiqiang Hu
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Wang
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yawen Liu
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Feng Chen
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jianjun Peng
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hong Peng
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hongxing Song
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yang Xia
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Liqun Chu
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Quan Zhou
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Feng Guan
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jing Wu
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Dongbo Bu
- Key Lab of Intelligent Information Processing, State Lab of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China,School of Computer and Control Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Budacan AM, Tan G, Cheeseman M, Mofidi R, Wong P. Patients Turned Down for Non-Emergency Abdominal Aortic Aneurysm (AAA) Surgery: Are We Doing The Right Thing? Factors that Influence Decision Making and the Long-term outcome – A Single Centre Experience. Eur J Vasc Endovasc Surg 2019. [DOI: 10.1016/j.ejvs.2019.06.898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Tan G, Chen P, Deng J, Xu Q, Tang R, Feng Z, Yi R. Review and improvement of conventional models for reservoir sediment trapping efficiency. Heliyon 2019; 5:e02458. [PMID: 31687559 PMCID: PMC6819860 DOI: 10.1016/j.heliyon.2019.e02458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 05/15/2019] [Accepted: 09/06/2019] [Indexed: 11/08/2022] Open
Abstract
Sediment accumulation has been the most important factor influencing the comprehensive benefit of reservoirs. A quantitative investigation of the sediment trapping efficiencies of reservoirs is a key to understanding the impact of sedimentation on reservoirs. Generally, the simplest method to assess sediment accumulation ratio is adopting sediment concentration curve with trap efficiency (TE) of the reservoir. Many empirical and semi-empirical models have been proposed to determine this term related to the average annual inflow, features and characteristics of the reservoir watershed area. In this article four different empirical models decided by capacity to inflow ratio (C/I), capacity to watershed ratio (C/W) were used. These different models were summarized and utilized to determine TE of large reservoirs on the Upper Yangtze River for recent decades. Based on these conventional models, an improved model to estimate sediment trapping efficiency is proposed, and experimental data from other 18 reservoirs come from different basins were used to validate the model. The results indicate that the sediment trapping efficiencies that were estimated by the four empirical model were similar to the measured efficiencies for reservoirs on the Upper Yangtze River. Among the the Brune and Siyam empirical models were the most reliable and can be applied to estimate sediment trapping efficiency for reservoirs on the Upper Yangtze River. The improved model takes the capacity/annual inflow ratio and capacity/watershed area ratio into account comprehensively, the effect of particle size and settling velocity of the sediment are also considered, it is more applicable and accuracy to predict large reservoir sediment trapping efficiency. The results of this study provide a valuable reference for predicting large reservoir sedimentation and sediment regulation.
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Affiliation(s)
- Guangming Tan
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China
| | - Peng Chen
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China
| | - Jinyun Deng
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China
| | - Quanxi Xu
- Bureau of Hydrology, Yangtze River Water Resources Commission, Wuhan 430010, China
| | - Rouxin Tang
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China
| | - Zhiyong Feng
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China
| | - Ran Yi
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem, Institute of Hydroecology, MWR & CAS, Wuhan 430079, China
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30
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Shi Z, Tan G, Wang L. 032 Il-1b is essential for anti-galectin3 antibody induced cutaneous vasculitis in systemic lupus erythematosus. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.03.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Chi WK, Tan G, Yan B. PROGNOSTIC NUTRITIONAL INDEX AS A PREDICTOR OF PROGNOSIS IN PATIENTS WITH CRITICAL LIMB ISCHEMIA WHO UNDERWENT ENDOVASCULAR REVASCULARIZATION THERAPY. J Am Coll Cardiol 2019. [DOI: 10.1016/s0735-1097(19)32670-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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32
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Toliman PJ, Kaldor JM, Badman SG, Phillips S, Tan G, Brotherton JML, Saville M, Vallely AJ, Tabrizi SN. Evaluation of self-collected vaginal specimens for the detection of high-risk human papillomavirus infection and the prediction of high-grade cervical intraepithelial lesions in a high-burden, low-resource setting. Clin Microbiol Infect 2018; 25:496-503. [PMID: 29906593 DOI: 10.1016/j.cmi.2018.05.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 05/08/2018] [Accepted: 05/12/2018] [Indexed: 12/20/2022]
Abstract
OBJECTIVES To compare the performance of self-collected vaginal (V) specimens with clinician-collected cervical (C) specimens for detection of high-risk human papillomavirus (hrHPV) and cervical disease using the Cepheid Xpert HPV, Roche Cobas 4800 HPV and Hologic Aptima HPV assays. METHODS Women aged 30-59 years (n = 1005) were recruited at two clinics in Papua New Guinea, and they provided specimens for testing at point-of-care using the Xpert HPV Test, and for subsequent testing using the Cobas HPV (n = 981) and Aptima HPV (n = 983) assays. Liquid-based cytology was performed on C specimens to predict underlying high-grade squamous intraepithelial lesions (HSIL). V specimen results of each assay were evaluated against a constructed reference standard and for detection of HSIL or worse. RESULTS There was substantial (κ >0.6) agreement in hrHPV detection between V and C specimens across all three assays. The sensitivity, specificity, and positive and negative predictive values of Xpert HPV using self-collected V specimens for the detection of HPV type 16 according to the constructed reference standard were 92.1%, 93.1%, 63.6% and 98.9%, respectively; compared with 90.4%, 94.3%, 67.8% and 98.7% for Cobas 4800 HPV; and 63.2%, 97.2%, 75.0% and 95.3% for Aptima HPV. Similar results were observed for all hrHPV types (combined) and for HPV types 18/45, on all three assays. The detection of any hrHPV using self-collected specimens had high sensitivity (86%-92%), specificity (87%-94%) and negative predictive value (>98%) on all assays for HSIL positivity. CONCLUSIONS Xpert HPV, using self-collected vaginal specimens, has sufficient accuracy for use in point-of-care 'test-and-treat' cervical screening strategies in high-burden, low-resource settings.
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Affiliation(s)
- P J Toliman
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea; The Kirby Institute, University of New South Wales, Sydney, NSW, Australia.
| | - J M Kaldor
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - S G Badman
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - S Phillips
- Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, Vic., Australia; Murdoch Children's Research Institute, Parkville, Vic., Australia
| | - G Tan
- Victorian Cytology Service, Melbourne, Vic., Australia
| | | | - M Saville
- Victorian Cytology Service, Melbourne, Vic., Australia
| | - A J Vallely
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea; The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - S N Tabrizi
- Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, Vic., Australia; Murdoch Children's Research Institute, Parkville, Vic., Australia; Department of Obstetrics and Gynaecology, University of Melbourne, Vic., Australia
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33
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Lee ZJ, Chia SL, Tan G, Soo KC, Teo CCM. Cost Effectiveness of Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy for Management of Colorectal Peritoneal Carcinomatosis. Ann Surg Oncol 2018; 25:2340-2346. [DOI: 10.1245/s10434-018-6508-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Indexed: 01/16/2023]
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34
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Chandran N, Tan G, Chia C, Teo M. Prognostic factors for early recurrences following cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) for colorectal and appendiceal peritoneal metastases. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy151.288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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35
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Tan G, Kaya M, Tevlek A, Sargin I, Baran T. Antitumor activity of chitosan from mayfly with comparison to commercially available low, medium and high molecular weight chitosans. In Vitro Cell Dev Biol Anim 2018; 54:366-374. [PMID: 29654403 DOI: 10.1007/s11626-018-0244-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/15/2018] [Indexed: 11/29/2022]
Abstract
Insects' cuticles have a potential to be evaluated as a chitin source. Especially adults of aquatic insects like mayflies (order Ephemeroptera) swarm in enormous numbers in artificially lit areas while mating in spring and then die by leaving huge amounts of dead insects' bodies. Here in this study, mayfly corpses were harvested and used for production of low MW chitosan. Dried mayfly bodies had 10.21% chitin content; mayfly chitin was converted into chitosan with efficiency rate of 78.43% (deacetylation degree, 84.3%; MW, 3.69 kDa). Cytotoxicity and anti-proliferative activity of mayfly and commercially available shrimp chitosans (low, medium, and high MW) were determined on L929 fibroblast and three different cancer types including HeLa, A549, and WiDr. Apoptosis and necrosis stimulating potential of mayfly and commercial chitosans were also evaluated on A549 and WiDr cells using acridine orange and propidium iodide dual staining to observe morphological changes in nuclei and thus to reveal the predominant cell death mechanism. The effects of chitosans have varied depending on cell types, concentration, and chitosan derivatives. Mayfly and low MW chitosans had a cytotoxic effect at a concentration of 500 μg mL-1 on non-cancer cells. At concentrations below this value (250 μg mL-1), mayfly and commercial chitosans except high MW one exhibited strong inhibitory activity on cancer cells especially A549 and WiDr cells. Mayfly chitosan induced early and late apoptosis in A549 cells, but late apoptosis and necrosis in WiDr cells. This study suggests that dead bodies of mayflies can be used for production of low MW chitosan with anti-proliferative activity.
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Affiliation(s)
- G Tan
- Department of Biology, Faculty of Science and Letters, Aksaray University, TR-68100, Aksaray, Turkey.
| | - M Kaya
- Department of Biotechnology and Molecular Biology, Faculty of Science and Letters, Aksaray University, TR-68100, Aksaray, Turkey
| | - A Tevlek
- Bioengineering Division, Institute of Science and Engineering, Hacettepe University, TR-06800, Ankara, Turkey
| | - I Sargin
- Department of Biotechnology and Molecular Biology, Faculty of Science and Letters, Aksaray University, TR-68100, Aksaray, Turkey
| | - T Baran
- Department of Chemistry, Faculty of Science and Letters, Aksaray University, TR-68100, Aksaray, Turkey
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Wei CC, Zhang ST, Tan G, Zhang SH, Liu M. Impact of anemia on in-hospital complications after ischemic stroke. Eur J Neurol 2018; 25:768-774. [PMID: 29431886 DOI: 10.1111/ene.13595] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/06/2018] [Indexed: 02/05/2023]
Affiliation(s)
- C.-C. Wei
- Department of Neurology; West China Hospital; Sichuan University; Chengdu Sichuan Province China
| | - S.-T. Zhang
- Department of Neurology; West China Hospital; Sichuan University; Chengdu Sichuan Province China
| | - G. Tan
- Department of Neurology; West China Hospital; Sichuan University; Chengdu Sichuan Province China
| | - S.-H. Zhang
- Department of Neurology; West China Hospital; Sichuan University; Chengdu Sichuan Province China
| | - M. Liu
- Department of Neurology; West China Hospital; Sichuan University; Chengdu Sichuan Province China
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37
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Xu S, Liang Z, Du Q, Li Z, Tan G, Nie C, Yang Y, Lv X, Zhang C, Luo X. A systematic study on the prevention and treatment of retinopathy of prematurity in China. BMC Ophthalmol 2018; 18:44. [PMID: 29444655 PMCID: PMC5813392 DOI: 10.1186/s12886-018-0708-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 02/06/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND To identify the prevention situation, the main factors influencing prevention effects and to develop control measures over retinopathy of prematurity in China. METHODS Using stratified random sampling method, we randomly selected 23 provincial and ministerial hospitals (8 in Guangdong province, 5 in Hunan province and 10 in Shaanxi province), 81 municipal hospitals (38 in Guangdong province, 19 in Hunan province and 24 in Shaanxi province), 180 district and county hospitals (76 in Guangdong province, 57 in Hunan province and 47 in Shaanxi province) in China. A total of 284 hospitals were enrolled in the study, with questionnaires distributed investigating the status and constrain factors of ROP presentation. Significant outcomes were analyzed thereafter by SPSS 19.0. RESULTS The screening rate of ROP in medical institutions from eastern, central and western China were 84.6%, 35.0% and 56.7%, respectively. The screening rate of tertiary and secondary medical institutions were 84.6% and 25.7% in the eastern, 35.0% and 4.9% in the central, 56.7% and 5.9% in the western region. Screening was carried out better in the tertiary than that in the secondary and primary institutions. Treatment for ROP was available in 15.7% of all the tertiary hospitals surveyed. Lack of professionals, equipments and technologies were considered to be major restrain factors for screening. CONCLUSIONS The ROP screening and treatment status have demonstrated significant regional diversity due to uneven distribution of medical resources in China. Developed areas had established intraregional cooperation models, whereas less-developed areas should consider set up a large-scale, three-level ROP prevention network. It is of paramount importance that education and training towards ophthalmologists should be vigorously strengthened. It is strongly recommended that implement ROP telemedicine and integrated ROP prevention and management platforms through the Internet should be established.
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Affiliation(s)
- Shuman Xu
- Guangdong Women and Children Hospital, 521 Xingnan Road, Guangzhou, Guangdong 511442 People’s Republic of China
| | - Zhijiang Liang
- Guangdong Women and Children Hospital, 521 Xingnan Road, Guangzhou, Guangdong 511442 People’s Republic of China
| | - Qiyun Du
- Hunan Women and Children Hospital, Changsha, Hunan People’s Republic of China
| | - Zhankui Li
- Shaanxi Women and Children Hospital, Xi’an, Shaanxi People’s Republic of China
| | - Guangming Tan
- Guangdong Women and Children Hospital, 521 Xingnan Road, Guangzhou, Guangdong 511442 People’s Republic of China
| | - Chuan Nie
- Guangdong Women and Children Hospital, 521 Xingnan Road, Guangzhou, Guangdong 511442 People’s Republic of China
| | - Yang Yang
- Guangdong Women and Children Hospital, 521 Xingnan Road, Guangzhou, Guangdong 511442 People’s Republic of China
| | - Xuzai Lv
- Guangdong Women and Children Hospital, 521 Xingnan Road, Guangzhou, Guangdong 511442 People’s Republic of China
| | - Chunyi Zhang
- Guangdong Women and Children Hospital, 521 Xingnan Road, Guangzhou, Guangdong 511442 People’s Republic of China
| | - Xianqiong Luo
- Guangdong Women and Children Hospital, 521 Xingnan Road, Guangzhou, Guangdong 511442 People’s Republic of China
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Huang M, Tan G, Lu S, Huang D, Fu L. Evaluation of effect for obstructive sleep apnea patients treated with soft-hard plastic mandibular advancing oral appliance. Sleep Med 2017. [DOI: 10.1016/j.sleep.2017.11.400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Affiliation(s)
- Z Shi
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Z Meng
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Guangzhou, China
- Institute of Dermatology, Guangzhou Medical University, Guangzhou, China
| | - Y Han
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - C Cao
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Guangzhou, China
- Department of Dermatology, Guangzhou Red Cross Hospital, Guangzhou, China
| | - G Tan
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - L Wang
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Guangzhou, China
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Shi Z, Tan G, Han Y, Cao C, Wang L. 327 Galectin-3 in keratinocytes participates psoriasis development by recruiting neutrophils into epidermis. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Yin Z, Lan H, Tan G, Lu M, Vasilakos AV, Liu W. Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges. Comput Struct Biotechnol J 2017; 15:403-411. [PMID: 28883909 PMCID: PMC5581845 DOI: 10.1016/j.csbj.2017.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 06/30/2017] [Accepted: 07/28/2017] [Indexed: 12/25/2022] Open
Abstract
The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics.
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Affiliation(s)
- Zekun Yin
- Shandong University, Jinan, Shandong, China
| | | | - Guangming Tan
- Institute of Computing Technology, Chinese Academy of Sciences, China
| | - Mian Lu
- Huawei Singapore Research Centre, Singapore
| | - Athanasios V Vasilakos
- Department of Computer Science, Electrical and Space Engineering, Luleå University of Technology, Skellefteå SE-931 87, Sweden
| | - Weiguo Liu
- Shandong University, Jinan, Shandong, China
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Dokainish H, Teo K, Zhu J, Roy A, AlHabib KF, ElSayed A, Palileo-Villaneuva L, Lopez-Jaramillo P, Karaye K, Yusoff K, Orlandini A, Sliwa K, Mondo C, Lanas F, Prabhakaran D, Badr A, Elmaghawry M, Damasceno A, Tibazarwa K, Belley-Cote E, Balasubramanian K, Islam S, Yacoub MH, Huffman MD, Harkness K, Grinvalds A, McKelvie R, Bangdiwala SI, Yusuf S, Campos R, Chacón C, Cursack G, Diez F, Escobar C, Garcia C, Vilamajo OG, Hominal M, Ingaramo A, Kucharczuk G, Pelliza M, Rojas A, Villani A, Zapata G, Bourke P, Lanas F, Nahuelpan L, Olivares C, Riquelme R, Ai F, Bai X, Chen X, Chen Y, Gao M, Ge C, He Y, Huang W, Jiang H, Liang T, Liang X, Liao Y, Liu S, Luo Y, Lu L, Qin S, Tan G, Tan H, Wang T, Wang X, Wei F, Xiao F, Zhang B, Zheng T, Mendoza JA, Anaya MB, Gomez E, de Salazar DM, Quiroz F, Rodríguez M, Sotomayor MS, Navas AT, León MB, Montalvo LF, Jaramillo ML, Patiño EP, Perugachi C, Trujillo Cruz F, Elmaghawry M, Wagdy K, Bhardwaj A, Chaturvedi V, Gokhale GK, Gupta R, Honnutagi R, Joshi P, Ladhani S, Negi P, Roy A, Reddy N, Abdullah A, Hassan MA, Balasinga M, Kasim S, Tan W, Yusoff K, Damasceno A, Banze R, Calua E, Novela C, Chemane J, Akintunde A, Ansa V, Gbadamosi H, Karaye K, Mbakwem A, Mohammed S, Nwafor E, Ojji D, Olunuga T, Sa'idu BOH, Umuerri E, Alcaraz J, Palileo-Villanueva L, Palomares E, Timonera MR, Badr A, Alghamdi S, Alhabib K, Almasood A, Alsaif S, Elasfar A, Ghabashi A, Mimish L, Bester F, Kelbe D, Klug E, Sliwa K, Tibarzawa K, Abdalla O, Dimitri M, Mustafa H, Osman O, Saad A, Mondo C. Global mortality variations in patients with heart failure: results from the International Congestive Heart Failure (INTER-CHF) prospective cohort study. The Lancet Global Health 2017; 5:e665-e672. [DOI: 10.1016/s2214-109x(17)30196-1] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/10/2017] [Accepted: 04/26/2017] [Indexed: 12/13/2022]
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Tan G, Seeliger M, Cohen J. Abstract P1-08-12: p53 status and 17q21.3 amplicon formation in HER2-positive breast cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p1-08-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Breast cancers that overexpress HER2/neu are associated with poor clinical outcome. Treatment of HER2-positive breast cancers with trastuzumab, a monoclonal antibody that antagonizes HER2 receptor signaling, increases patient overall and disease-free survival. While targeted therapy is reasonably effective, resistance to trastuzumab remains a problem, particularly in the case of metastatic disease. Tumor suppressor p53 is the most commonly mutated gene in human cancer and mutations that lead to the stabilization and accumulation of p53 in HER2-positive breast cancers are associated with worse clinical outcome. Another feature of HER2-enriched breast cancers are amplifications of the HER2 locus on chromosome 17q21.3.
Table 1 Wildtype p53Mutated p53No amplification12.8%63.9%17q21.3 amplification13.1%8.7%Table 1: Among 58 cases, Her2-positive tumors with mutated p53 (n=37, 63.9%) occurred at a 4.9-fold higher frequency than amplification of the 17q21.3 gene set (n=8, 13.1%), with significant mutual exclusivity (p=0.005), The patient genomic data set was obtained from the Breast Invasive Carcinoma Study conducted by the TCGA Network (Nature, 2012) and visualized using cBioPortal (MSKCC), Copy alterations of genes were assessed using GISTIC2.0 (Broad Institute) via cBioPortal.
We studied the genomic profiles of 58 HER2-positive breast tumor samples using cBioPortal to determine p53 mutation status. 74.1% of samples expressed mutant p53 and a large fraction of mutations occurred in the key DNA binding domain. We assessed the amplification status of 24 genes within the chromosome 17q21.3 locus as an indicator of amplicon formation, and found that 21.8% of breast tumors demonstrated copy number amplification (Table 2). Mutant p53 tumors with no amplicon formation occurred 5 times more frequently than tumors with only 17q21.3 amplicon formation. These alterations tended to occur exclusive of one another (p=0.005, Table 1). Separately, using gene expression data from Kaplan-Meier Plotter, we observed that alterations in gene expression within the 17q21.3 amplicon can have differential effects on the survival of HER2-positive breast cancer patients (Table 2).
Table 217q21.3 Gene SetHazard RatioP-valueCOL1A11.760.01MBTD10.530.01SPATA200.650.04UBE2Z0.680.07EME10.650.08Table 2: List of relevant genes within the chromosome 17q21.3 amplicon. Genes in this amplicon can influence both beneficial and hazardous survival outcomes in HER2-positive breast cancer patients (n=208). Hazard ratios (HR) were determined from gene expression data available through Kaplan-Meier Plotter (Gyorffy, 2010).
Our data shows that HER2-positive breast cancers can be divided into p53 mutant and non-mutant subsets with p53 mutations relatively exclusive to 17q21.3 gene amplification. However, p53 mutation status and 17q21.3 copy number have a variety of effects on patient outcome. We are interested in understanding the interaction between these two genetic alterations and whether subdividing HER2-positive breast cancer into these subtypes will improve our ability to provide effective therapy to patients.
Citation Format: Tan G, Seeliger M, Cohen J. p53 status and 17q21.3 amplicon formation in HER2-positive breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-08-12.
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Affiliation(s)
- G Tan
- Stony Brook University, Stony Brook, NY
| | | | - J Cohen
- Stony Brook University, Stony Brook, NY
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Yu X, Huang Y, Guo Q, Wang Y, Ma H, Zhao Y, Wang Y, Yu X, Tan G, Ma S, Wu X, Xu M, Zhang S, Shang H, Xin S, Zhang X, Wang J, Li L, Wu S, Zhao S, Yang J, Wen H, Sun H, Xiong Y, Wang Y, He J, Liu Q, Li J, Jiang J, Xue F, Han W, Wang Z, Wang Y, Hu Y, Wang L. Clinical motivation and the surgical safety checklist. Br J Surg 2017; 104:472-479. [PMID: 28158915 DOI: 10.1002/bjs.10446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/09/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
Abstract
Background
Although the surgical safety checklist (SSC) has been adopted worldwide, its efficacy can be diminished by poor clinical motivation. Systematic methods for improving implementation are lacking.
Methods
A multicentre prospective study was conducted in 2015 in four academic/teaching hospitals to investigate changes during revision of the SSC for content, staffing and workflow. All modifications were based on feedback from medical staff. Questionnaires were used to monitor dynamic changes in surgeons', nurses' and anaesthetists' perceptions.
Results
Complete information was obtained from 30 654 operations in which the newly developed SSC system was used. Implementation quality was evaluated in 1852 operations before, and 1822 after the changes. The revised SSC content was simplified from 34 to 22 items. Anaesthetists achieved widespread recommendation as SSC coordinators. Completion rates of all stages reached over 80·0 per cent at all sites (compared with 10·2–59·5 per cent at the sign-out stage in the baseline survey). There was a significant change in doctors who participated (for example, surgeon: from 24·6 to 64·5 per cent at one site). The rates of hasty (15·1–33·7 per cent) or casual (0·4–4·4 per cent) checking decreased to less than 6·0 per cent overall. Perceptions about the SSC were studied from 2211 forms. They improved, with a converging trend among the three different professions, to a uniform 80·0 per cent agreeing on the need for its regular use.
Conclusion
Medical staff members are both the users and owners of the SSC. High-quality SSC implementation can be achieved by clinically motivated adaptation.
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Affiliation(s)
- X Yu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Y Huang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Q Guo
- Xiangya Hospital, Central South University, Changsha, China
| | - Y Wang
- Qinghai Provincial People's Hospital, Xining, China
| | - H Ma
- First Hospital of China Medical University, Shenyang, China
| | - Y Zhao
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Y Wang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - X Yu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - G Tan
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - S Ma
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - X Wu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - M Xu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - S Zhang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - H Shang
- First Hospital of ChinaMedical University, Shenyang, China
| | - S Xin
- First Hospital of ChinaMedical University, Shenyang, China
| | - X Zhang
- First Hospital of ChinaMedical University, Shenyang, China
| | - J Wang
- First Hospital of ChinaMedical University, Shenyang, China
| | - L Li
- First Hospital of ChinaMedical University, Shenyang, China
| | - S Wu
- Qinghai Provincial People's Hospital, Xining, China
| | - S Zhao
- Qinghai Provincial People's Hospital, Xining, China
| | - J Yang
- Qinghai Provincial People's Hospital, Xining, China
| | - H Wen
- Qinghai Provincial People's Hospital, Xining, China
| | - H Sun
- Xiangya Hospital, Central South University, Changsha, China
| | - Y Xiong
- Xiangya Hospital, Central South University, Changsha, China
| | - Y Wang
- Xiangya Hospital, Central South University, Changsha, China
| | - J He
- Xiangya Hospital, Central South University, Changsha, China
| | - Q Liu
- Xiangya Hospital, Central South University, Changsha, China
| | - J Li
- Xiangya Hospital, Central South University, Changsha, China
| | - J Jiang
- Institute of Basic Medicine Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - F Xue
- Institute of Basic Medicine Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - W Han
- Institute of Basic Medicine Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Z Wang
- Institute of Basic Medicine Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Y Wang
- Institute of Basic Medicine Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Y Hu
- Institute of Basic Medicine Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - L Wang
- Institute of Basic Medicine Sciences, Chinese Academy of Medical Sciences, Beijing, China
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Dawn L, Smith C, Tan G, Henry G. 195 Molecular Analysis using PCR to Amplify Extracted 16S Ribosomal DNA Appears to Identify Biofilm on Penile Prosthesis In-Vivo. J Sex Med 2017. [DOI: 10.1016/j.jsxm.2016.12.183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Smith C, Dawn L, Tan G, Henry G. 203 Molecular Analysis Using PCR to Amplify Extracted 16S Ribosomal DNA Appears to Identify Antibiotic Sensitivities / Resistance to Biofilm Found on Penile Prosthesis In-Vivo. J Sex Med 2017. [DOI: 10.1016/j.jsxm.2016.12.191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kolder ICRM, van der Plas-Duivesteijn SJ, Tan G, Wiegertjes GF, Forlenza M, Guler AT, Travin DY, Nakao M, Moritomo T, Irnazarow I, den Dunnen JT, Anvar SY, Jansen HJ, Dirks RP, Palmblad M, Lenhard B, Henkel CV, Spaink HP. A full-body transcriptome and proteome resource for the European common carp. BMC Genomics 2016; 17:701. [PMID: 27590662 PMCID: PMC5009708 DOI: 10.1186/s12864-016-3038-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/24/2016] [Indexed: 12/01/2022] Open
Abstract
Background The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies. Results Here we have used 19 different tissues from an F1 hybrid strain of the common carp to perform transcriptome analyses using RNA-Seq. For a subset of the tissues we also have performed deep proteomic studies. As a reference, we updated the European common carp genome assembly using low coverage Pacific Biosciences sequencing to permit high-quality gene annotation. These annotated gene lists were linked to zebrafish homologs, enabling direct comparisons with published datasets. Using clustering, we have identified sets of genes that are potential selective markers for various types of tissues. In addition, we provide a script for a schematic anatomical viewer for visualizing organ-specific expression data. Conclusions The identified transcriptome and proteome data for carp tissues represent a useful resource for further translational studies of tissue-specific markers for this economically important fish species that can lead to new markers for organ development. The similarity to zebrafish expression patterns confirms the value of common carp as a resource for studying tissue-specific expression in cyprinid fish. The availability of the annotated gene set of common carp will enable further research with both applied and fundamental purposes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3038-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- I C R M Kolder
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, RA, Leiden, The Netherlands.,Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333, CA, Leiden, The Netherlands
| | | | - G Tan
- Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - G F Wiegertjes
- Cell Biology and Immunology group, Department of Animal Sciences, Wageningen University, P.O. Box 338, 6700, AH, Wageningen, The Netherlands
| | - M Forlenza
- Cell Biology and Immunology group, Department of Animal Sciences, Wageningen University, P.O. Box 338, 6700, AH, Wageningen, The Netherlands
| | - A T Guler
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300, RC, Leiden, The Netherlands
| | - D Y Travin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, GSP-1, Moscow, Russia
| | - M Nakao
- Laboratory of Marine Biochemistry, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, 812-8581, Japan
| | - T Moritomo
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Kameino 1866, Fujisawa, Kanagawa, 252-0880, Japan
| | - I Irnazarow
- Polish Academy of Sciences, Ichthyobiology and Aquaculture Unit, Gołysz Zaborze, Kalinowa 2, 43-520, Chybie, Poland
| | - J T den Dunnen
- Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - S Y Anvar
- Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - H J Jansen
- ZF-screens B.V., J.H, Oortweg 19, 2333, CH, Leiden, The Netherlands
| | - R P Dirks
- ZF-screens B.V., J.H, Oortweg 19, 2333, CH, Leiden, The Netherlands
| | - M Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300, RC, Leiden, The Netherlands
| | - B Lenhard
- Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - C V Henkel
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, RA, Leiden, The Netherlands
| | - H P Spaink
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, RA, Leiden, The Netherlands.
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Tan G, Shimada K, Nozawa Y, Kaneko S, Urakami T, Koyama K, Komura M, Matsuda A, Yoshimoto M. Atomic step-and-terrace surface of polyimide sheet for advanced polymer substrate engineering. Nanotechnology 2016; 27:295603. [PMID: 27284690 DOI: 10.1088/0957-4484/27/29/295603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Typical thermostable and flexible polyimide polymers exhibit many excellent properties such as strong mechanical and chemical resistance. However, in contrast to single-crystal substrates like silicon or sapphire, polymers mostly display disordered and rough surfaces, which may result in instability and degradation of the interfaces between thin films and polymer substrates. As a step toward the development of next-generation polymer substrates, we here report single-atom-layer imprinting onto the polyimide sheets, resulting in an ultrasmooth 0.3 nm high atomic step-and-terrace surface on the polyimides. The ultrasmooth polymer substrates are expected to be applied to the fabrication of nanostructures such as superlattices, nanowires, or quantum dots in nanoscale-controlled electronic devices. We fabricate smooth and atomically stepped indium tin oxide transparent conducting oxide thin films on the imprinted polyimide sheets for future use in organic-based optoelectronic devices processed with nanoscale precision. Furthermore, toward 2D polymer substrate nanoengineering, we demonstrate nanoscale letter writing on the atomic step-and-terrace polyimide surface via atomic force microscopy probe scratching.
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Affiliation(s)
- G Tan
- Department of Innovative & Engineered Materials, Tokyo Institute of Technology, Yokohama 226-8502, Japan
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Goh W, Teh Y, Tan S, Yong S, Sairi A, Soo K, Tan M, Chan M, Selvaraja S, Sittampalam K, Teh J, Chin F, Sethi V, Ong J, Tan G, Chia C, Teo M, Quek R, Farid M. Treatment and outcomes of melanoma in Asia: Results from National Cancer Centre Singapore. Eur J Cancer 2016. [DOI: 10.1016/j.ejca.2016.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Tan G, Sun Chan JY. MATERNAL OUTCOMES AND RISK ASSESSMENT IN PREGNANCIES ASSOCIATED WITH STRUCTURAL HEART DISEASES: A SINGLE TERTIARY CENTRE EXPERIENCE. J Am Coll Cardiol 2016. [DOI: 10.1016/s0735-1097(16)30953-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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