Gene expression profile analysis of human hepatocellular carcinoma using SAGE and LongSAGE

<p>Abstract</p> <p>Background</p> <p>Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and the second cancer killer in China. The initiation and malignant transformation of cancer result from accumulation of genetic changes in the sequences or expression level of cancer-related genes. It is of particular importance to determine gene expression profiles of cancers on a global scale. SAGE and LongSAGE have been developed for this purpose.</p> <p>Methods</p> <p>We performed SAGE in normal liver and HCC samples as well as the liver cancer cell line HepG2. Meanwhile, the same HCC sample was simultaneously analyzed using LongSAGE. Computational analysis was carried out to identify differentially expressed genes between normal liver and HCC which were further validated by real-time quantitative RT-PCR.</p> <p>Results</p> <p>Approximately 50,000 tags were sequenced for each of the four libraries. Analysis of the technical replicates of HCC indicated that excluding the low abundance tags, the reproducibility of SAGE data is high (R = 0.97). Compared with the gene expression profile of normal liver, 224 genes related to biosynthesis, cell proliferation, signal transduction, cellular metabolism and transport were identified to be differentially expressed in HCC. Overexpression of some transcripts selected from SAGE data was validated by real-time quantitative RT-PCR. Interestingly, sarcoglycan-ε (SGCE) and paternally expressed gene (PEG10) which is a pair of close neighboring genes on chromosome 7q21, showed similar enhanced expression patterns in HCC, implicating that a common mechanism of deregulation may be shared by these two genes.</p> <p>Conclusion</p> <p>Our study depicted the expression profile of HCC on a genome-wide scale without the restriction of annotation databases, and provided novel candidate genes that might be related to HCC.</p

Controlled Synthesis of Hollow α-Fe2O3 Microspheres Assembled With Ionic Liquid for Enhanced Visible-Light Photocatalytic Activity

Porous self-assembled α-Fe2O3 hollow microspheres were fabricated via an ionic liquid-assisted solvothermal reaction and sequential calcinations. The concentration of the ionic liquid (1-butyl-3-methylimidazolium tetrafluoroborate [C4Mim]BF4) was found to play a crucial role in the control of these α-Fe2O3 hollow structures. Trace amounts ionic liquid was used as the soft template to synthesize α-Fe2O3 hollow spheres with a large specific surface (up to 220 m2/g). Based on time-dependent experiments, the proposed formation mechanisms were presented. Under UV light irradiation, the as-synthesized α-Fe2O3 hollow spheres exhibited excellent photocatalysis in Rhodamine B (RhB) photodegradation and the rate constant was 2–3 times higher than α-Fe2O3 particles. The magnetic properties of α-Fe2O3 hollow structures were found to be closely associated with the shape anisotropy

SYSTEMIC VISION TOWARD THE STUDIES OF WU-LI SHI-LI REN-LI SYSTEM APPROACH

Since the Wu-li Shi-li Ren-li system approach proposed by Jifa Gu and Zhichang Zhu at the University of Hull in November of 1994, the studies on WSR system approach undergo continual development. As an oriental system approach, WSR is mainly based on systems practice in China. With a collection of literatures relevant to WSR system approach, we apply the iView, a supporting technology toward qualitative meta-synthesis, to those literatures to show a systemic vision towards the studies on WSR system approach. The scopes, especially the practical areas are detected. Moreover, the main themes and expansions of topics are detected at different periods. The results are based on computing and visualized for better understanding and exploratory analysis. Such a study not only shows the development of WSR studies, but also exhibits that the iView analysis is an effective technology to support such kind of qualitative study

TOWARDS META-SYNTHETIC SUPPORT TO UNSTRUCTURED PROBLEM SOLVING

Decision support system (DSS) aims to provide effective support to solve unstructured, ill-structured or wicked problems as its initial claim in the late 1960s. Great as those technology achievements, "people problems" are key reasons of unimplemented goals of DSS, and sometimes increase uncertainties to decision making process. Meta-synthesis system approach (MSA) is oriented to complexities in those problems. In this paper, we adopt a paradigm of decision making in a DSS context, which emphasizes the synthesis of perspectives towards problems description and analysis, to explain the meta-synthetic support to unstructured problem solving. After very brief introduction of basic ideas of MSA and its testbed, Hall of Workshop on Meta-Synthetic Engineering (HWMSE), which is regarded as a knowledge creating ba, we address computerized supports to expose problem structure by collaborative activities for qualitative meta-synthesis. A practical tool and its visualization of humans' ideas are introduced.Meta-synthesis, decision support systems, problem structuring, idea visualization

Stimuli strategy and learning dynamics promote the wisdom of crowds

Collective wisdom is the ability of a group to perform more effectively than any individual alone. Through an evolutionary game-theoretic model of collective prediction, we investigate the role that reinforcement learning stimulus may play the role in enhancing collective voting accuracy. And collective voting bias can be dismissed through self-reinforcing global cooperative learning. Numeric simulations suggest that the provided method can increase collective voting accuracy. We conclude that real-world systems might seek reward-based incentive mechanism as an alternative to surmount group decision error

This is the final version for KEST’2004. Computerized Support for Idea Generation during Knowledge Creating Process 1

Knowledge is regarded as the most important capital for organizations in the 21st century. And knowledge creation is as one of most effective methods to enhance industrial competitiveness especially along the global trend and increasing complexities in the socioeconomic development. In this paper, we combine an organizational knowledge creating model proposed by a Japanese social scientist I. Nonaka and framework of Hall for Workshop of Meta-synthetic Engineering proposed by Chinese system scientist Qian Xuesen (Tsien HsueShen) to explore how to effectively facilitate knowledge creating process using computerized supports, especially during group working context, where group discussion and debates are usual activities during idea/alternative generation and evaluations. We focus on one kind of group activities, group thinking, especially group brainstorming for idea generation, which is very basic and also convenient way to collect opinion and acquire knowledge for new alternatives or solutions towards difficult decision problems. A computerized support tool for idea generation has been developed and a simple example is demonstrated

Metasynthesis and Knowledge Creation

The metasynthesis system approach (MSA) proposed by Qian et al has closely related to the knowledge creation. When we run a major project related to the realizing the MSA supported by National Natural Science foundation from 1999 to 2004, we found the knowledge creation process has been materalized also in this project. We have used the Wuli-Shili-Renli system approach to explain the Renli aspect for creation and used the complex network, especially social network analysis to describe the creation process in this major project quantitatively.The original publication is available at JAIST Press http://www.jaist.ac.jp/library/jaist-press/index.htmlIFSR 2005 : Proceedings of the First World Congress of the International Federation for Systems Research : The New Roles of Systems Sciences For a Knowledge-based Society : Nov. 14-17, 2062, Kobe, JapanSymposium 1, Session 4 : Technology Creation Based on Knowledge Science Knowledge/Technology Management(1

A New Efficient Algorithm for Solving Systems of Multivariate Polynomial Equations

The security of many recently proposed cryptosystems is based on the difficulty of solving large systems of quadratic multivariate polynomial equations. The classical algorithm for solving such a system is Buchberger&apos;s algorithm for constructing Gröbner bases. Another algorithm for solving such a system is XL algorithm. For sparse system, Buchberger&apos;s algorithm benefits from sparsity of the system, but its complexity is impractical and hard to determine. XL could not make a good use of sparse structure of the system, since XL has no good strategy of choosing the multiply monomials. In this paper, based on..

Dynamics of Online Collective Attention as Hawkes Self-exciting Process

Understanding the dynamic formation mechanism of online collective attention has been attracted diversified interests such as Internet memes, viral videos, or social media platforms and Web-based businesses, and has practical application in the area of marketing and advertising, propagation of information. Bulletin Board System, or BBS can be regarded as an ecosystem of digital resources connected and shaped by collective successive behaviors of users. Clicks and replies of the posts quantify the degree of collective attention. For example, the collective clicking behavior of users on BBS gives rise to the up and down of focus on posts, and transporting attention between topics, the ratio between clicks and replies measure the heat degree of a post. We analyzed the dynamics of collective attention millions of users on an interactive Tianya Zatan BBS. By analyzing the dynamics of clicks we uncovered a non-trivial Hawkes process self-exciting regularity concerning the impact of novelty exponential decay mechanism. Here, it able to explain the empirical data of BBS remarkably well, such as popular topics are observed in time frequently cluster, asymptotic normality of clicks. Our findings indicate that collective attention among large populations decays with a exponential decaying law, suggest the existence of a natural time scale over novelty fades. Importantly, we show that self-exciting point processes can be used for the purpose of collective attention modeling