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Ning Z, Tan G. [Cancer metabolism: a novel perspective on precision diagnosis and treatment for liver cancer]. ZHONGHUA WAI KE ZA ZHI [CHINESE JOURNAL OF SURGERY] 2020; 58:31-36. [PMID: 31902167 DOI: 10.3760/cma.j.issn.0529-5815.2020.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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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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] [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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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: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [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]
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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] [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] [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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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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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] [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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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Indexed: 01/16/2023]
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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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] [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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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/06/2018] [Indexed: 02/05/2023]
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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] [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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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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Shi Z, Meng Z, Han Y, Cao C, Tan G, Wang L. The involvement of galectin-3 in skin injury in systemic lupus erythematosus patients. Lupus 2017; 27:621-627. [PMID: 29058991 DOI: 10.1177/0961203317736144] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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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] [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: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [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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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. 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] [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] [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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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] [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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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] [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] [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: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [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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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] [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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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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