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Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models

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Chinese Journal of Cancer 2013年第4期32卷 186-194页

作者： Hongyan Wang Xiaobo Zhou Department of radiology the Methodist Hospital Research Institute Department of radiology Weill Cornell Medical College

By altering the electrostatic charge of histones or providing binding sites to protein recognition molecules, Chromatin marks have been proposed to regulate gene expression, a property that has motivated researchers to link these marks to cis-regulatory elements. With the help of next generation sequencing technologies, we can now correlate one specific chromatin mark with regulatory elements (e.g. enhancers or promoters) and also build tools, such as hidden Markov models, to gain insight into mark combinations. However, hidden Markov models have limitation for their character of generative models and assume that a current observation depends only on a current hidden state in the chain. Here, we employed two graphical probabilistic models, namely the linear conditional random field model and multivariate hidden Markov model, to mark gene regions with different states based on recurrent and spatially coherent character of these eight marks. Both models revealed chromatin states that may correspond to enhancers and promoters, transcribed regions, transcriptional elongation, and low-signal regions. We also found that the linear conditional random field model was more effective than the hidden Markov model in recognizing regulatory elements, such as promoter-, enhancer-, and transcriptional elongation-associated regions, which gives us a better choice.

关键词： Epigenetics, histone modification, conditional random field, regulatory elements

Perspectives on Nutrition Needs for the New Millennium for South Asian Regions

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Biomedical and Environmental Sciences 2001年第1期14卷 66-74页

作者： KAMALA KRISHNASWAMY director National Institute of Nutrition Indian Council of Medical Research

South Asia is the most populated region of the world with several nutritional challenges. Though per capita food energy supply, child survival and life expectancy have improved, and even today large segments of the population are below the poverty line with high infant and maternal mortality rates. It is important to recognize the crucial role of nutrition throughout the life cycle from conception to old age. It is very necessary now to move from food security to nutrition security and improve the quality of foods both in macro and micronutrients in order to break the transgenerational effects of malnutrition. The key solutions to the problems should address the issue of social development, population stabilization, environmental degradation and inadequate health and nutritional services. Strategies for empowering women and actuating community participation as sustainable programmes for human development, measures to reduce underweight and stunting in children and prevention of micronutrient malnutrition across the population are required. Enhancing food and nutrition security through innovative diversified agriculture and dietary practices, prevention and control of infection, promotion of food safety and fortification of staples with appropriate attention on emerging chronic disorders are essential. Population control measures to stabilize the fertility rates, biotechnological approaches for genetically modified foods, nutrition surveillance based on assessment, analysis and action to address the logistic, technical and compliance issues with emphasis on promotion of breast feeding and complementary foods with adequate attention on the reproductive needs of adolescent girls, pregnant mothers and lactating women would eliminate low birth weight, stunting, and chronic energy deficiency in vulnerable groups. Focused studies on bioavailability of micronutrients and its enhancement, innovative horticulture interventions, fortifications, social marketing strat

关键词： for South Asian Regions Perspectives on Nutrition Needs for the New Millennium

Storage time affects the level and diagnostic efficacy of plasma biomarkers for neurodegenerative diseases

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Neural Regeneration Research 2025年第8期20卷 2373-2381页

作者： Lifang Zhao Mingkai Zhang Qimeng Li Xuemin Wang Jie Lu Ying Han Yanning Cai Department of Clinical Biobank Xuanwu HospitalCapital Medical UniversityBeijingChina Beijing Geriatric Medical Research Center BeijingChina Department of Neurology Xuanwu HospitalCapital Medical UniversityBeijingChina Department of radiology and Nuclear Medicine Xuanwu HospitalCapital Medical UniversityBeijingChina Beijing Key Laboratory of Magnetic Resonance Imaging and Brain Informatics BeijingChina Key Laboratory of Neurodegenerative diseases Ministry of EducationBeijingChina School of Biomedical Engineering Hainan UniversityHaikouHainan ProvinceChina Center of Alzheimer’s Disease Beijing Institute for Brain DisordersBeijingChina National Clinical Research Center for Geriatric Diseases BeijingChina institute of Biomedical Engineering Shenzhen Bay LaboratoryGaoke Innovation CenterShenzhenGuangdong ProvinceChina Department of Neurobiology Xuanwu HospitalCapital Medical UniversityBeijingChina

Several promising plasma biomarker proteins,such as amyloid-β(Aβ),tau,neurofilament light chain,and glial fibrillary acidic protein,are widely used for the diagnosis of neurodegenerative ***,little is known about the long-term stability of these biomarker proteins in plasma samples stored at-80°*** aimed to explore how storage time would affect the diagnostic accuracy of these biomarkers using a large *** samples from 229 cognitively unimpaired individuals,encompassing healthy controls and those experiencing subjective cognitive decline,as well as 99 patients with cognitive impairment,comprising those with mild cognitive impairment and dementia,were acquired from the Sino Longitudinal Study on Cognitive Decline *** samples were stored at-80°C for up to 6 years before being used in this *** results showed that plasma levels of Aβ42,Aβ40,neurofilament light chain,and glial fibrillary acidic protein were not significantly correlated with sample storage ***,the level of total tau showed a negative correlation with sample storage ***,in individuals without cognitive impairment,plasma levels of total protein and tau phosphorylated protein threonine 181(p-tau181)also showed a negative correlation with sample storage *** was not observed in individuals with cognitive ***,we speculate that the diagnostic accuracy of plasma p-tau181 and the p-tau181 to total tau ratio may be influenced by sample storage ***,caution is advised when using these plasma biomarkers for the identification of neurodegenerative diseases,such as Alzheimer's ***,in cohort studies,it is important to consider the impact of storage time on the overall results.

关键词： Alzheimer’s disease amyloid-β diagnostic ability glial fibrillary acidic protein neurodegeneration neurofilament light chain plasma biomarkers single molecule array storage time tau

IMAGING OF NON-GLANDULAR SUPERFICIAL METASTASES: A COMPARISON OF XERORADIOGRAPHY, ULTRASONO-GRAPHY AND COMPUTED TOMOGRAPHY

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Chinese Journal of Cancer Research 1989年第2期1卷 39-43页

作者： A.Cardinale R.Lagalla A.Guarino institute of radiology University of Palermo Palermo ItalyInstitute of Radiology University of Palermo Palermo ItalyInstitute of Radiology University of Palermo Palermo Italy

Between January 1985 and July 1987, 1,622 cancer patients were evaluated to outline the possible applications and limits of various investigative techniques for evaluating metastases. Seventy-three cases with superficial metastases of the dermal-hypodermal (59) layers, of the muscles (11) and of other target organs (3) were included in the *** non-glandular superficial metastases are a relatively rare occurrence, diagnostic imaging techniques are indicated for evaluating their extent and anatomical connections. Secondary neoplasms were studied using the imaging techniques of sono-graphy, computed tomography and *** diagnostic reliability of these three techniques was evaluated, taking into account their ability to determine the extent of metastases and of assessing *** is considered as a satisfactory screening technique, but CT is an even better tool for evaluating the extent and anatomical connections of such lesions. Xeroradiography has been made obsolete by the introduction of the other two techniques.

关键词： A COMPARISON OF XERORADIOGRAPHY IMAGING OF NON-GLANDULAR SUPERFICIAL METASTASES ULTRASONO-GRAPHY AND COMPUTED TOMOGRAPHY US

Full-scale dynamic testing of response-controlled buildings and their components:concepts,methods,and findings

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Earthquake Engineering and Engineering Vibration 2014年第S1期13卷 167-181页

作者： Kazuhiko Kasai Kazuhiro Matsuda Structural Engineering Research Center Tokyo Institute of Technology director and Professor Assistant Professor

A series of shake-table tests was conducted by inserting and replacing 4 different types of dampers,or by removing them in a full-scale 5-story steel frame building. The objective is to validate response-control technologies that are increasingly adopted for major Japanese buildings without being attested to-date by a major earthquake. Test results are briefly described,and good performance of the dampers and frame demonstrated. The concepts of the full-scale building tests and various contributions are discussed. The difficulty associated with full-scale dynamic testing is explained.

关键词： response-controlled building steel frame steel damper viscous damper oil damper viscoelastic damper

Hydrogen technologies and developments in Japan

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Clean Energy 2019年第2期3卷 105-113页

作者： Shigeki Iida Ko Sakata director The Institute of Applied Energy Executive Research Fellow The Institute of Applied Energy

The successful development of hydrogen-energy technologies has several advantages and ***-energy development could prevent global warming as well as ensure energy security for countries without adequate energy *** successful development of hydrogen would provide energy for transportation and electric *** is a unique energy carrier,as it can be produced from various energy sources such as wind,fossil fuels and biomass and,when it is combusted,it emits no CO_(2)*** other advantage is the wide distribution of resources globally that can be used to produce *** Japan,the Ministry of Economy,Trade and Industry(METI)published a‘Strategic Roadmap for Hydrogen and Fuel Cells’in 2014,with a revised update published in March *** goal of the roadmap is to achieve a hydrogen *** roadmap aims to resolve technical problems and secure economic *** roadmap has been organized into the following three phases:Phase 1-Installation of fuel cells;Phase 2-Hydrogen power plant/mass supply chain;Phase 3-CO_(2)-free *** paper reports on the current status of fuel cells and fuel-cell vehicles in Japan and gives a description and status of the R&D programmes along with the results of global energy model study towards 2050.

关键词： hydrogen and fuel cell energy system and policy energy and environment energy storage

Transarterial chemoembolization in hepatocellular carcinoma treatment: Barcelona clinic liver cancer staging system

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World Journal of Gastroenterology 2015年第36期21卷 10327-10335页

作者： Kichang Han Jin Hyoung Kim Department of radiology and Research institute of radiology Asan Medical CenterUniversity of Ulsan College of Medicine

Hepatocellular carcinoma(HCC),the fifth most common cancer that predominantly occurs in liver cirrhosis patients,requires staging systems to design treatments. The barcelona clinic liver cancer staging system(BCLC) is the most commonly used HCC management guideline. For BCLC stage B(intermediate HCC),transarterial chemoembolization(TACE) is the standard treatment. Many studies support the use of TACE in early and advanced HCC patients. For BCLC stage 0(very early HCC),TACE could be an alternative for patients unsuitable for radiofrequency ablation(RFA) or hepatic resection. In patients with BCLC stage A,TACE plus RFA provides better local tumor control than RFA alone. TACE can serve as bridge therapy for patients awaiting liver transplantation. For patients with BCLC B,TACE provides survival benefits compared with supportive care options. However,because of the substantial heterogeneity in the patient population with this stage,a better patient stratification system is needed to select the best candidates for TACE. Sorafenib represents the first line treatment in patients with BCLC C stage HCC. Sorafenib plus TACE has shown a demonstrable effect in delaying tumor progression. Additionally,TACE plus radiotherapy has yielded better survival in patients with HCC and portal venous thrombosis. Considering these observations together,TACE clearly has a critical role in the treatment of HCC as a stand-alone or combination therapy in each stage of HCC. Diverse treatment modalities should be used for patients with HCC and a better patient stratification system should be developed to select the best candidates for TACE.

关键词： Hepatocellular carcinoma Transarterial chemoemboli

Pyoderma Gangrenosum with Oral Involvement–Case Report and Review of the Literature

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International Journal of Oral Science 2010年第2期2卷 111-116页

作者： Geetha Paramkusam Venkateswarlu Meduri Naresh Gangeshetty Department of Oral Medicine and radiology Kaminein Institute of Dental Sciences

Pyoderma gangrenosum （PG） is a rare, noninfectious neutrophilic dermatosis. Clinically, it begins with sterile pustules that rapidly progress into painful ulcers of variable depth and size with undermined violaceous borders. The diagnosis of PG is based on the history of an underlying disease, a typical clinical presentation, histopathology, and exclusion of other diseases. The peak incidence occurs between the ages of 20 to 50 years with women being more often affected than men. There have been very few reports of pyoderma gangrenosum with oral mucosal involvement. Oral lesions in previously reported cases have included ulcers of varying sizes from a few mm to several cm and have been reported to have been found on the tongue, soft and hard palate, buccal mucosa, and gingiva. Some of these oral lesions have been associated with ulcerative colitis, inflammatory bowel disease, and polycythemia rubra vera. A few cases were reported with biopsy findings, the histological picture being nonspecific, showing ulceration, and necrosis with inflam- matory cell infiltrate. A peculiar case of pyoderma gan- grenosum with an oral lesion is presented here, and the differential diagnosis is discussed.

关键词： pyoderma gangrenosum oral lesion of pyoderma gangrenosum diagnosis

Treatment of hepatocellular carcinoma with portal venous tumor thrombosis: A comprehensive review

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World Journal of Gastroenterology 2016年第1期22卷 407-416页

作者： Kichang Han Jin Hyoung Kim Gi-Young Ko Dong Il Gwon Kyu-Bo Sung Department of radiology and Research institute of radiology Asan Medical CenterUniversity of Ulsan College of Medicine

The natural history of hepatocellular carcinoma(HCC)with portal vein tumor thrombosis(PVTT)is dismal(approximately 2-4 mo),and PVTT is reportedly found in 10%-40%of HCC patients at *** to the Barcelona Clinic Liver Cancer(BCLC)Staging System(which is the most widely adopted HCC management guideline),sorafenib is the standard of care for advanced HCC(i.e.,BCLC stage C)and the presence of PVTT is included in this ***,sorafenib treatment only marginally prolongs patient survival and,notably,its therapeutic efficacy is reduced in patients with *** this context,there have been diverse efforts to develop alternatives to current standard systemic chemotherapies or combination treatment *** date,many studies on transarterial chemoembolization,3-dimensional conformal radiotherapy,hepatic arterial chemotherapy,and transarterial radioembolization report better overall survival than sorafenib therapy alone,but their outcomes need to be verified in future prospective,randomized controlled studies in order to be incorporated into current treatment ***,combination strategies have been applied to treat HCC patients with PVTT,with the hope that the possible synergistic actions among different treatment modalities would provide promising *** narrative review describes the current status of the management options for HCC with PVTT,with a focus on overall survival.

关键词： Hepatocellular carcinoma Portal vein tumorthrombosis Sorafenib Transarterial chemoembolization Transarterial radioembolization Hepatic arterial chemotherapy Radiotherapy