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TSUNAMI:Translational Bioinformatics Tool Suite for Network Analysis and Mining

Genomics, Proteomics & Bioinformatics 2021年第6期19卷 1023-1031页

作者： Zhi Huang Zhi Han Tongxin Wang Wei Shao shunian xiang Paul Salama Maher Rizkalla Kun Huang Jie Zhang School of Electrical and Computer Engineering Purdue UniversityWest LafayetteIN 47907USA Department of Electrical and Computer Engineering Indiana University-Purdue University IndianapolisIndianapolisIN 46202USA Department of Medicine Indiana University School of MedicineIndianapolisIN 46202USA Department of Computer Science Indiana UniversityBloomingtonIN 47405USA Department of Medical and Molecular Genetics Indiana University School of MedicineIndianapolisIN 46202USA Department of Biostatistics and Health Data Science Indiana University School of MedicineIndianapolisIN 46202USA

Gene co-expression network(GCN)mining identifies gene modules with highly correlated expression profiles across samples/*** enables researchers to discover latent gene/molecule interactions,identify novel gene functions,and extract molecular features from certain disease/condition groups,thus helping to identify disease ***,there lacks an easy-to-use tool package for users to mine GCN modules that are relatively small in size with tightly connected genes that can be convenient for downstream gene set enrichment analysis,as well as modules that may share common *** address this need,we developed an online GCN mining tool package:TSUNAMI(Tools SUite for Network Analysis and MIning).TSUNAMI incorporates our state-of-the-art lmQCM algorithm to mine GCN modules for both public and user-input data(microarray,RNA-seq,or any other numerical omics data),and then performs downstream gene set enrichment analysis for the identified *** has several features and advantages:1)a user-friendly interface and real-time co-expression network mining through a web server;2)direct access and search of NCBI Gene Expression Omnibus(GEO)and The Cancer Genome Atlas(TCGA)databases,as well as user-input gene ex-pression matrices for GCN module mining;3)multiple co-expression analysis tools to choose from,all of which are highly flexible in regards to parameter selection options;4)identified GCN modules are summarized to eigengenes,which are convenient for users to check their correlation with other clinical traits;5)integrated downstream Enrichr enrichment analysis and links to other gene set enrichment tools;and 6)visualization of gene loci by Circos plot in any step of the *** web service is freely accessible through URL:https://***/.Source code is available at https://***/huangzhii/TSUNAMI/.

关键词： Network mining Gene co-expression network Transcriptomic data analysis lmQCM Web server Survival analysis

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MRI在三阴性乳腺癌新辅助化疗疗效评价中的研究进展

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磁共振成像 2024年第7期15卷 191-195页

作者：李书念谭红娜郑州大学人民医院河南省人民医院医学影像科郑州450003

三阴性乳腺癌(triple-negative breast cancer, TNBC)是一种具有高度异质性及侵袭性的乳腺癌亚型,并且由于缺乏有效的治疗靶点,对内分泌治疗及靶向治疗均不敏感,预后较差。目前新辅助化疗(neoadjuvant chemotherapy, NAC)是其标准治疗... 详细信息

三阴性乳腺癌(triple-negative breast cancer, TNBC)是一种具有高度异质性及侵袭性的乳腺癌亚型,并且由于缺乏有效的治疗靶点,对内分泌治疗及靶向治疗均不敏感,预后较差。目前新辅助化疗(neoadjuvant chemotherapy, NAC)是其标准治疗策略之一,但个体差异及肿瘤异质性使得不同患者的疗效差别较大,故早期准确客观评估NAC疗效对TNBC患者后续治疗的方案制订及预后判断尤为重要。磁共振成像(magnetic resonance imaging, MRI)因具有较高的软组织分辨率及定量成像技术,可准确反映肿瘤实质以及其微环境的变化,是目前监测肿瘤治疗疗效最常用的影像学检查方法之一。基于MRI的影像组学能够深度挖掘NAC前后TNBC的影像特征,获取更全面的肿瘤信息并应用于NAC疗效的评价。近年来,国内外研究人员就影像组学在TNBC NAC疗效评价方面进行了大量探索。本文就MRI及影像组学在TNBC患者NAC疗效评价的临床应用及研究进展做一综述,旨在为TNBC精准化和个体化治疗策略的制订提供参考。

关键词：乳腺肿瘤三阴性乳腺癌磁共振成像新辅助化疗疗效预测

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nc2Cancer:一个研究与癌症相关人类非编码RNA的数据库

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生物信息学 2015年第2期13卷 77-81页

作者：程卓刘珂严章明向书念孙之荣清华大学生命科学学院教育部生物信息学重点实验室北京100084

伴随着高通量测序技术的飞速发展,许多新型的非编码RNA陆续被发现,比如长链非编码RNA(lncRNA)和环状RNA(Circular RNA)。先前的研究已经表明这些非编码RNA在基因表达调控过程中起着很重要的作用,并且与癌症的发生有着很密切的联系。但是... 详细信息

伴随着高通量测序技术的飞速发展,许多新型的非编码RNA陆续被发现,比如长链非编码RNA(lncRNA)和环状RNA(Circular RNA)。先前的研究已经表明这些非编码RNA在基因表达调控过程中起着很重要的作用,并且与癌症的发生有着很密切的联系。但是,由于研究者们仍然对它们行使何种功能知之甚少,鉴定这些非编码RNA是否与人类癌症存在密切的相互关系仍然是一个巨大的挑战。为了促进这一领域的研究,这篇文章的作者分析了大规模的RNA相互作用数据,然后建立了数据库nc2Cancer(http://***/nc2Cancer/***)。这个数据库的目标便是提供非编码RNA与癌症之间的全面关系。现在,该nc2Cancer数据库包括了三种类型的非编码RNA分子:长链非编码RNA,环状RNA以及由假基因转录而成的RNA。这项研究将有助于研究者更好地去理解非编码RNA的功能以及它们在人类癌症发生过程中所起到的作用。

关键词：非编码RNA 癌症 MicroRNA RNA相互作用网络

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Differential pressure reset strategy based on reinforcement learning for chilled water systems

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Building Simulation 2022年第2期15卷 233-248页

作者： Xinfang Zhang Zhenhai Li Zhengwei Li shunian Qiu Hai Wang School of Mechanical Engineering Tongji UniversityShanghaiChina Key Laboratory of Performance Evolution and Control for Engineering Structures of Ministry of Education Tongji UniversityShanghaiChina

Air conditioning water systems account for a large proportion of building energy *** a pressure-controlled water system,one of the key measures to save energy is to adjust the differential pressure setpoints during ***,such adjustments are based either on certain rules,which rely on operator experience,or on complicated models that are not easy to *** this paper,a data-driven control method based on reinforcement learning is *** main idea is to construct an agent model that adapts to the researched *** of directly being told how to react,the agent must rely on its own experiences to *** with traditional control strategies,reinforcement learning control(RLC)exhibits more accurate and steady performances while maintaining indoor air temperature within a limited range.A case study shows that the RLC strategy is able to save substantial amounts of energy.

关键词： water system differential pressure reset reinforcement learning control energy saving

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Optimum linear array of an optical aperture synthesis telescope

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Chinese Science Bulletin 2002年第23期47卷 1964-1968页

作者： WEN Jianguo JIN Shengzhen NING shunian National Astronomical Observatory Chinese Academy of SciencesBeijing 100012China China University of Mining and Technology Beijing 100083China

Measuring out successively the degree of coherence of the source produced by any couple of the small apertures via rotating an array composed of the small aperture telescopes, and synthesizing them into the (u, v) coverage of the source, the brightness distribution of the source can be obtained by the inverse Fourier transform of the degree of coherence with much higher resolution than from a single telescope. This article discusses the arrangements of the small apertures in the linear array, and found a method to decide the quality of the arrangements, the judgment factorε is introduced to calculate the arrangements in quantity. There are 1.5x1011 possibilities for 11 apertures. Therefore, the computer procedures are programmed to select the optimum arrangements. The effect of the simulation of the aperture synthesis is given for the linear array. The simulation method can also be used in the nonlinear arrays.

关键词： optical aperture synthesis optimum linear array judgment factor (u v)-spectrum sampling point spread function.

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An improvement in stability of delay difference systems

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Chinese Science Bulletin 1998年第7期43卷 544-547页

作者： ZHANG shunian Department of Applied Mathematics, Shanghai Jiaotong University, Shanghai 200240, China Department of Applied Mathematics Shanghai Jiaotong University Shanghai China

A new result on the stability of delay difference equations is established, in which a kind of weighted norm for x is adopted in order to estimate the upper bound of Liapunov functional.

关键词： delay difference systems uniform asymptotic stability in terms of two measures Liapunov functionals.

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A fast compound direct iterative algorithm for solving transient line contact elastohydrodynamic lubrication problems

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Frontiers of Mechanical Engineering 2014年第2期9卷 156-167页

作者： Jian LIU Yuxue CHEN Zhenzhi HE shunian YANG School of Mechanical Science & Engineering Huazhong University of Science and Technology Wuhan 430074 China

A fast compound direct iterative algorithm for solving transient line contact elastohydrodynamic lubrication （EHL） problems is presented. First, by introducing a special matrix splitting iteration method into the traditional compound direct iterative method, the full matrices for the linear systems of equations are transformed into sparse banded ones with any half-bandwidth; then, an extended Thomas method which can solve banded linear systems with any half-bandwidth is derived to accelerate the computing speed. Through the above two steps, the computational complexity of each iteration is reduced approximately from O（N^3/3） to O（β^2N）, where N is the total number of nodes, and β is the half-bandwidth. Two kinds of numerical results of transient EHL line contact problems under sinusoidal excitation or pure normal approach process are obtained. The results demonstrate that the new algorithm increases computing speed several times more than the traditional compound direct iterative method with the same numerical precision. Also the results show that the new algorithm can get the best computing speed and robustness when the ratio, half-bandwidth to total number of nodes, is about 7.5% 10.0% in moderate load cases.

关键词： elastohydrodynamic lubrication transient line contact matrix splitting iteration method the Thomas method

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Almost periodic solutions of difference systems

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Chinese Science Bulletin 1998年第24期43卷 2041-2046页

作者： ZHANG shunian Department of Applied Mathematics, Shanghai Jiaotong University, Shanghai 200240, China Department of Applied Mathematics Shanghai Jiaotong University Shanghai China

For linear difference systems, a rather general result on the existence of almost periodic solutions is established, which also gives the explicit expression of the almost periodic solution in terms of the coefficient matrix and the nonhomogeneous term. The obtained result confirms not only the existence, but also the uniqueness as well as the uniform asymptotic stability of the almost periodic solution. As an application, a criterion on the existence of almost periodic solutions of the second order difference equations is derived.

关键词： difference systems mean values of almost periodic sequences almost periodic solutions existence uniqueness uniform asymptotic stability

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ON UNIFORM ASYMPTOTIC STABILITY OF INFINITE DELAY DIFFERENCE EQUATIONS

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Chinese Annals of Mathematics,Series B 2001年第4期22卷 495-502页

作者： ZHANG shunian Department of Applied Mathematics, Shanghai Jiaotong University Shanghai 200030, China. E-mail: snzhang@*** Department of Applied Mathematics Shanghai Jiaotong University Shanghai 200030 China

For the infinite delay difference equations of the general form, two new uniform asymptotic stability criteria are established in terms of the discrete Liapunov functionals.

关键词： Infinite delay difference equations Uniform asymptotic stability g-uniform asymptotic stability Discrete Liapunov functionals

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A NEW APPROACH TO STABILITY THEORY OF FUNCTIONAL DIFFERENTIAL EQUATIONS

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Annals of Differential Equations 1995年第4期11卷 495-503页

作者： Zhang shunian (Shanghai Jiaotong University)

In this work, a new approach to stability theory of functional differential equations is proposed. Instead of putting all components of the state variable x in one Liapunov-Razumikhin function, several functions of partial components of x, which can be much easier constructed. are used so that the conditions ensuring that stability are simpler and less restrictive. Also, an example is given to illustrate the advantages of the obtained results.

关键词： Functional differential equations uniform stability uniform asymptotic stability. Liapunov-Razumikhin functions.

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