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Viral integration detection strategies and a technical update on Virus-Clip

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BIOCELL 2021年第6期45卷 1495-1500页

作者： DANIEL WAI-HUng HO XUEYIng LYU irene oi-lin ng Department of Pathology The University of Hong KongHong KongChina State Key Laboratory of Liver Research The University of Hong KongHong KongChina

Oncovirus infection is crucial in human *** oncoviruses can lead to structural variations in the human genome known as viral genomic integration,which can contribute to *** viral integration detection tools differ in their underlying algorithms pinpointing different aspects or features of viral integration *** discuss about major procedures in performing viral integration *** importantly,we provide a technical update on Virus-Clip to facilitate its usage on the latest human genome builds(hg19 and hg38)and the adoption of multi-thread mode for faster initial read *** comparing the execution of Virus-Clip using single-thread and multi-thread modes of read alignment on targeted-panel sequencing data of HBV-associated hepatocellular carcinoma patients,we demonstrate the marked improvement of multi-thread mode in terms of significantly reduced execution time,while there is negligible difference in memory *** together,with the current update of Virus-Clip,it will continue supporting the in silico detection of oncoviral integration for better understanding of various human malignancies.

关键词： Oncovirus Viral genomic integration In silico detection Tumorigenesis Human malignancies

TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways in hepatocellular carcinoma

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Frontiers of Medicine 2015年第3期9卷 322-330页

作者： Daniel Wai-Hung Ho Alan Ka-Lun Kai irene oi-lin ng Department of Pathology and State Key Laboratory for Liver Research The University of Hong Kong ttong Kong SAR China

This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma （HCC） by comparing the global gene expression profiles between tumors and their corresponding non- tumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated （CENPF and FOXM1） and downregulated （CLEC4G, CRHBP, and CLEC1B） genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.

关键词： TCGA whole-transcriptome sequencing HCC liver cancer

The impact of hypoxia in hepatocellular carcinoma metastasis

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Frontiers of Medicine 2014年第1期8卷 33-41页

作者： Carmen Chak-Lui Wong Alan Ka-Lun Kai irene oi-lin ng The State Key Laboratory for Liver Research and Department of Pathology The Universi(v of Hong Kong Hong Kong China

Hypoxia is a common phenomenon in hepatocellular carcinoma （HCC）. Hypoxia stabilizes transcription factor, hypoxia-inducible factor （HIF）, to activate gene transcription. Expression of HIF is closely associated with metastasis and poor prognosis in HCC. HIF mediates expression of genes that are involved in every step of HCC metastasis including epithelial-mesenchymal transition, invasion of the extracellular matrix, intravasation, extravasation, and secondary growth of the metastases. Because HIF is the central regulator of HCC metastasis, HIF inhibitors are attractive tools when used alone or as combined treatment to curb HCC metastasis. This review will summarize the current findings on the impact of hypoxia/HIF in HCC, with a particular focus on cancer metastasis.

关键词： hypoxia hepatocellular carcinoma (HCC) metastasis hypoxia-inducible factor (HIF)

Single cell analysis informing therapy response in hepatocellular carcinoma and intrahepatic cholangiocarcinoma

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Hepatobiliary Surgery and Nutrition 2022年第1期11卷 126-128页

作者： Daniel Wai-Hung Ho irene oi-lin ng Department of Pathology The University of Hong KongHong KongChina State Key Laboratory of Liver Research The University of Hong KongHong KongChina

Liver cancer is known to have significant degree of intra-tumoral heterogeneity(ITH)(1).Hepatocellular carcinoma(HCC)and intrahepatic cholangiocarcinoma(ICC)are major forms of primary liver cancer,accounting for>95%of *** is linked,as least in part,to the aggressiveness and refractoriness of liver cancer,rendering its high lethality among human malignancies(2).The complex tumor microenvironment promotes tumor progression and contributes to poor treatment ***,it is vital to address the biological mechanisms underlying liver cancer progression and treatment response analyzing the cells in high resolution rather than the mixture of many cell *** advances in single-cell RNA sequencing(scRNA-seq)provide an avenue to dissect liver cancer in an unprecedented degree of high resolution to characterize the underlying pathogenesis and heterogeneity.

关键词： cancer intrahepatic Liver

MicroRNA-142-3p and microRNA-142-5p are downregulated in hepatocellular carcinoma and exhibit synergistic effects on cell motility

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Frontiers of Medicine 2015年第3期9卷 331-343页

作者： Felice Ho-Ching Tsang Sandy Leung-Kuen Au Lai Wei Dorothy ngo-Yin Fan Joyce Man-Fong Lee Carmen Chak-Lui Wong irene oi-lin ng Chun-Ming Wong State Key Laboratory for Liver Research and Department of Pathology Li Ka Shing Faculty of Medicine The University of Hong Kong HongKong SAR China

MicroRNAs （miRNAs）, an important class of small non-coding RNAs, regulate gene expression at the post-transcriptional level, miRNAs are involved in a wide range of biological processes and implicated in different diseases, including cancers. In this study, miRNA profiling and qRT-PCR validation revealed that miR-142-3p and miR-142-5p were significantly downregulated in hepatocellular carcinoma （HCC） and their expression levels decreased as the disease progressed. The ectopic expression of miR-142 significantly reduced HCC cell migration and invasion. Overexpression of either miR-142-3p or miR-142-5p suppressed HCC cell migration, and overexpression of both synergistically inhibited cell migration, which indicated that miR-142-3p and miR-142-5p may cooperatively regulate cell movement, miR-142-3p and miR-142-5p, which are mature miRNAs derived from the 3＇- and 5＇-strands of the precursor miR-142, target distinct pools of genes because of their different seed sequences. Pathway enrichment analysis showed a strong association of the putative gene targets of miR-142-3p and miR-142-5p with several cell motility-associated pathways, including those regulating actin cytoskeleton, adherens junctions, and focal adhesion. Importantly, a number of the putative gene targets were also significantly upregulated in human HCC cells. Moreover, overexpression of miR-142 significantly abrogated stress fiber formation in HCC cells and led to cell shrinkage. This study shows that mature miR-142 pairs collaboratively regulate different components of distinct signaling cascades and therefore affects the motility of HCC cells.

关键词： hepatocellular carcinoma microRNA metastasis cytoskeletal reorganization

Analytic Regularity for a Singularly Perturbed Reaction-Convection-Diffusion Boundary Value Problem with Two Small Parameters

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Communications in Mathematical Research 2024年第2期40卷 125-153页

作者： irene Sykopetritou Christos Xenophontos Department of Mathematics and Statistics University of CyprusPo Box 20537Nicosia 1678Cyprus.

We consider a second order,two-point,singularly perturbed boundary value problem,of reaction-convection-diffusion type with two small parameters,and we obtain analytic regularity results for its solution,under the assumption of analytic input ***,we establish classical differentiability bounds that are explicit in the order of differentiation and the singular perturbation ***,for small values of these parameters we show that the solution can be decomposed into a smooth part,boundary layers at the two endpoints,and a negligible *** estimates are obtained for each component of the solution,which again are explicit in the differentiation order and the singular perturbation parameters.

关键词： Singularly perturbed problem reaction-convection-diffusion boundary layers analytic regularity.

Quantitative assessment of self-management in patients with nonalcoholic fatty liver disease: An unmet clinical need

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World Journal of Gastroenterology 2024年第25期30卷 3143-3146页

作者： Raffaele Borriello Giorgio Esposto irene Mignini Antonio Gasbarrini Maria Assunta Zocco CEMAD Digestive Disease Center Fondazione Policlinico Universitario A.Gemelli IRCCSCatholic University of RomeRome 00168Italy

In this editorial we comment on the article titled“Establishment and validation of an adherence prediction system for lifestyle interventions in non-alcoholic fatty liver disease”by Zeng et al published in a recent issue of the World Journal of ***-alcoholic fatty liver disease(NAFLD)represents one of the current challenges in hepatology and public health,due to its continuous growing prevalence and the rising incidence of NAFLD-related fibrosis,non-alcoholic steatohepatitis and *** only effective therapeutic strategy for this dis-ease is represented by encouraging patients to improve their lifestyle through the modification of dietary intake and increased physical exercise,but the effective application of such modifications is often limited by various factors such as lack of information,psychological barriers or poor social *** poor adherence to a healthy lifestyle can be decisive in determining the clinical outcome,in daily practice there is a lack of quantitative instruments aimed at identifying patients with the lowest adherence to lifestyle changes and higher risk of disease progre-ssion in the course of *** this article,Zeng et al propose a quantitative scale to assess the grade of adherence of patients with NAFLD to hea-lthy lifestyle intervention,called the Exercise and Diet Adherence Scale(EDAS).This scale,consisting of 33 items divided into 6 dimensions which relates to six subjective aspects in the self-management of NAFLD,has shown a good correlation with the identification of the sub-cohort of patients with the highest reduction in caloric intake,increase in physical exercise,probability of a reduction in liver stiffness measurement and alanine aminotransferase *** cor-relation among clinical outcomes and specific dimensions of this scale also highlights the pivotal role of a good and confidential doctor-patient relationship and of an effective *** is an urgent need for practical and e

关键词： Non-alcoholic fatty liver disease Non-alcoholic steatohepatitis Liver cirrhosis Metabolic associated fatty liver disease Metabolic associated steatohepatitis Insulin resistance Self-management Self-management measurement Patient education

Targeted ngS analysis reveals a complex genetic background of idiopathic erythrocytosis in a large Venetian family

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Genes & Diseases 2024年第2期11卷 561-563页

作者： Bertozzi irene Benetti Andrea Regazzo Daniela Polese Francesca Biagetti Giacomo Ceolotto Giulio Randi Maria Luigia First Medical Clinic University of Padua Department of Medicine – DIMEDVia Giustiniani 2Padova 35123Italy Transfusion Medicine Department Ospedale dell'Angelo - Venezia MestreVia Paccagnella 1Venice 30174Italy Emergency Medicine University of Padua Department of Medicine – DIMEDVia Giustiniani 2Padova 35123Italy

Absolute erythrocytosis,due to an increased production of red blood cells,becomes manifest with hemoglobin(Hb)levels above 165 or 160 g/L or with a hematocrit(HCT)above 51%and 48%in males and females,respectively.1 A minority of patients have polycythemia vera(PV);acquired secondary erythrocytosis frequently occurs due to appropriate or inappropriate erythropoietin(EPO)excess,while congenital secondary erythrocytosis may derive from genetic defects causing tissue *** erythrocytosis occurs in patients with genetic mutations of the oxygen-sensing pathway(VHL,PHD2,_HIF-1-alpha)or the erythropoietin receptor(EPOR)genes.2 Recently,HFE gene variants have been described in sporadic erythrocytoses.3 In a high proportion(about 70%)of patients with erythrocytosis,a specific etiology remains elusive despite extensive testing,and the diagnosis of idiopathic erythrocytosis(IE)is ruled out.

关键词： diagnosis patients congenital

Environmental drivers of long-term variations in the abundance of the red hocicudo mouse (Oxymycterus rufus) in Pampas agroecosystems

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Integrative Zoology 2024年第1期19卷 37-51页

作者： Laura Mariel CALFAYAN Regino CAVIA Jimena FRASCHINA Juan Santiago GUIDOBONO irene Laura GOROSITO María BUSCH Laboratorio de Ecología de Poblaciones Departamento de EcologíaGenética y EvoluciónFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires and Instituto de EcologíaGenética y Evolución de Buenos Aires(IEGEBA)Buenos AiresArgentina

During the 20th century,there has been an ongoing agricultural expansion and global warming,two of the main determinants influencing biodiversity changes in *** red hocicudo mouse(Oxymycterus rufus)inhabits subtropical grasslands and riparian habitats and has increased its abundance in recent years in central Argentina *** paper describes the long-term temporal changes in *** abundance in Exaltación de la Cruz department,Buenos Aires province,Argentina,in relation to weatherfluctuations and landscape features,as well as analyzes the spatio-temporal structure of captures of *** used generalized liner models,semi-variograms,the Mantel test,and autocorrelation functions for the analysis of rodent data obtained from trappings conducted between 1984 and *** showed an increase in abundance across the years of study,with its distribution depending on landscape features,such as habitat types and the distance *** rates showed a spatio-temporal aggregation,suggesting expansion from previously occupied *** was more abundant at lower minimum temperatures in summer,higher precipitation in spring and summer,and lower precip-itations in *** conditions affected *** abundance,but there was local variation that differed from global patterns of climate change.

关键词： agroecosystems climate change linear habitats Oxymycterus rufus rodent