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A novel model-free approach for reconstruction of time-delayed gene regulatory networks

中国科学：生命科学英文版 2006年第2期49卷 190-200页

作者： JIANG Wei1,2, LI Xia1,2,3,4. GUO Zheng1,2,3, LI Chuanxing1, WANG Lihong1 & RAO Shaoqi1,5 1. Department of Bioinformatics, Harbin medical university, Harbin 150086, china 2. Department of Computer Science, Harbin institute of Technology, Harbin 150080, china 3. School of Life Science and Technology, Tongji university, Shanghai 200092, china 4. biomedical engineering institute, capital university of medical sciences, beijing 100054, china 5. Departments of Cardiovascular Medicine and Molecular Cardiology, Cleveland Clinic Foundation, Cleveland, Ohio 4.195, USA Department of Bioinformatics Harbin Medical University Harbin China Department of Computer Science Harbin Institute of Technology Harbin China School of Life Science and Technology Tongji University Shanghai China Departments of Cardiovascular Medicine and Molecular Cardiology Cleveland Clinic Foundation Cleveland USA

Reconstruction of genetic networks is one of the key scientific challenges in functional genomics. This paper describes a novel approach for addressing the regulatory dependencies be-tween genes whose activities can be delayed by multiple units of time. The aim of the proposed ap-proach termed TdGRN (time-delayed gene regulatory networking) is to reversely engineer the dy-namic mechanisms of gene regulations, which is realized by identifying the time-delayed gene regu-lations through supervised decision-tree analysis of the newly designed time-delayed gene expres-sion matrix, derived from the original time-series microarray data. A permutation technique is used to determine the statistical classification threshold of a tree, from which a gene regulatory rule(s) is ex-tracted. The proposed TdGRN is a model-free approach that attempts to learn the underlying regula-tory rules without relying on any model assumptions. Compared with model-based approaches, it has several significant advantages: it requires neither any arbitrary threshold for discretization of gene transcriptional values nor the definition of the number of regulators (k). We have applied this novel method to the publicly available data for budding yeast cell cycling. The numerical results demonstrate that most of the identified time-delayed gene regulations have current biological knowledge supports.

关键词： gene regulatory networks, time delayed, decision tree.

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Chinese Guidelines for the Diagnosis and Management of Atrial Fibrillation

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Journal of Geriatric Cardiology 2024年第3期21卷 251-314页

作者： Chang-Sheng MA Shu-Lin WU Shao-Wen LIU Ya-Ling HAN Chinese Society of Cardiology Chinese medical Association Heart Rhythm Committee of Chinese Society of biomedical engineering beijing Anzhen Hospital Capital Medical University Guandong Provincial People’s Hospital Shanghai First People’s Hospital General Hospital of Northern Theater Command 不详

Atrial fibrillation(AF)is the most common sustained cardiac arrhythmia,significantly impacting patients’quality of life and increasing the risk of death,stroke,heart failure,and *** the past two decades,there have been significant breakthroughs in AF risk prediction and screening,stroke prevention,rhythm control,catheter ablation,and integrated *** this period,the scale,quality,and experience of AF management in china have greatly improved,providing a solid foundation for the development of guidelines for the diagnosis and management of *** further promote standardized AF management,and apply new technologies and concepts to clinical practice in a timely and comprehensive manner,the Chinese Society of Cardiology of the Chinese medical Association and the Heart Rhythm Committee of the Chinese Society of biomedical engineering have jointly developed the Chinese Guidelines for the Diagnosis and Management of Atrial *** guidelines have comprehensively elaborated on various aspects of AF management and proposed the CHA2DS2-VASc-60 stroke risk score based on the characteristics of AF in the Asian *** guidelines have also reevaluated the clinical application of AF screening,emphasized the significance of early rhythm control,and highlighted the central role of catheter ablation in rhythm control.

关键词： prevention sustained diagnosis

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Application of synchrotron source based DEI method in guinea pig cochleae imaging

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Progress in Natural Science:Materials International 2007年第1期17卷 59-67页

作者： YIN Hongxia, LIU Bo, GAO Xin, GAO Xiulai and LUO Shuqian ( College of biomedical engineering, capital university of medical sciences, beijing 100069,{4. Department of Anatomy, capital university of medical sciences, beijing 100069,{4.) College of biomedical engineering Capital University of Medical Sciences Beijing 100069 China Department of Anatomy Capital University of Medical Sciences Beijing 100069 China

Hard X-ray diffraction enhanced imaging (DEI), which is based on a synchrotron source and monochromator-analyzer-crystal system, is an effective method for imaging X-ray phase shift. Utilizing an analyzer crystal with high angular sensitivity of micro-radian, DEI can measure the transmitted, refracted and scattered X-rays when projecting onto a sample. It dramatically improves the contrast and spatial resolution of the resultant images. At the topography station of beijing Synchrotron Radiation Facilities (BSRF), we implemented DEI method in guinea pig cochleae imaging and acquired a series of DEI images. Based on these images, the apparent absorption and refraction images were calculated. The DEI images revealed the holistic spiral structures and inner details of guinea pig cochleae clearly, even including the structures at the cellular level, such as the static cilia of hairy cells and the limbus of Hansen cell. Due to the advantages of high contrast, high spatial resolution and distinct edge-enhanced effect, DEI method promises extensive applications in biology, medicine and clinic in the near future.

关键词： diffraction enhanced imaging hard X-ray imaging phase-contrast imaging cochlea micro-structure synchrotron source.

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Spinal processing of bee venom-induced pain and hyperalgesia

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生理学报 2008年第5期60卷 645-652页

作者： Jun CHEN institute for biomedical sciences of Pain and institute for Functional Brain Disorders,Tangdu Hospital,the Fourth Military {4. university,Xi’an 710038,china institute for biomedical sciences of Pain,capital {4. university,beijing 100069,china institute for biomedical sciences of Pain and institute for Functional Brain Disorders Tangdu Hospital the Fourth Military Medical University Xi'an 710038

Subcutaneous injection of bee venom causes long-term neural activation and hypersensitization in the dorsal horn of the spinal cord,which contributes to the development and maintenance of various pain-related *** unique behavioral 'phenotypes' of nociception and hypersensitivity identified in the rodent bee venom test are believed to reflect a complex pathological state of inflammatory pain and might be appropriate to the study of phenotype-based mechanisms of pain and *** this review,the spinal processing of the bee venom-induced different 'phenotypes' of pain and hyperalgesia will be *** accumulative electrophysiological,pharmacological,and behavioral data strongly suggest that different 'phenotypes' of pain and hyperalgesia are mediated by different spinal signaling *** the phenotype-based mechanisms of pain might be useful in development of novel therapeutic drugs against complex clinic pathological pain.

关键词：脊髓痛觉过敏蜂毒疼痛治疗方法

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Studies on repairing of hemisected thoracic spinal cord of adult rats by using a chitosan tube filled with alginate fibers

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Progress in Natural Science:Materials International 2006年第10期16卷 1051-1055页

作者： LI Xiaoguang, YANG Zhaoyang and YANG Yi ( beijing Center for Neural Regeneration and Repairing, capital university of medical sciences, beijing 100054, china Department of Bio{4., beijing university of Aeronautics and Astronautics, beijing 100083, china National Center of biomedical Analysis, beijing 100850, china) beijing Center for Neural Regeneration and Repairing Capital University of Medical Sciences Beijing 100054 China Department of Bioengineering Beijing University of Aeronautics and Astronautics Beijing 100083 China National Center of biomedical Analysis Beijing 100850 China

A chitosan tube filled with alginate fibers was implanted into the injured spinal cord of a rat for repairing the damaged tissue. Twelve months after the operation, the morphological observation demonstrated that this chitosan tube could induce regeneration of myelinated and non-myelinated axons and blood vessels. The Basso-Beattie-Bresnahan (BBB) behavioral evaluation confirmed that the implants played a key role in the long-term restoration of rats motor functions. It is a promising start in the treatment of the patients with the injury of the spinal cord.

关键词： spinal cord injury regeneration function recovery chitosan alginate behavioral evaluation.

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Information extraction and CT reconstruction of liver images based on diffraction enhanced imaging

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Progress in Natural Science:Materials International 2009年第8期19卷 955-962页

作者： Chunhong Hua,b, Tao Zhao a, Lu Zhanga, Hui Lia, Xinyan Zhao c, Shuqian Luoa, a College of biomedical engineering, capital medical {4., beijing 100069, china b National Laboratory of Pattern Recognition, institute of Automation, Chinese Academy of sciences, beijing 100080, china c Liver Research Center, beijing Friendship Hospital, capital medical {4., beijing 100050, china College of biomedical engineering Capital Medical University Beijing 100069 China National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Sciences Beijing 100080 China Liver Research Center Beijing Friendship Hospital Capital Medical University Beijing 100050 China

X-ray phase-contrast imaging (PCI) is a new emerging imaging technique that generates a high spatial resolution and high contrast of biological soft tissues compared to conventional radiography. Herein a biomedical application of diffraction enhanced imaging (DEI) is presented. As one of the PCI methods, DEI derives contrast from many different kinds of sample information, such as the sample’s X-ray absorption, refraction gradient and ultra-small-angle X-ray scattering (USAXS) properties, and the sample information is expressed by three parametric images. Combinedwith computed tomography (CT), DEI-CT can produce 3D volumetric images of the sample and can be used for investigating micro-structures of biomedical samples. Our DEI experiments for liver samples were implemented at the topography station of beijing Synchrotron Radiation Facility (BSRF). The results show that by using our provided information extraction method and DEI-CT reconstruction approach, the obtained parametric images clearly display the inner structures of liver tissues and the morphology of blood vessels. Furthermore, the reconstructed 3D view of the liver blood vessels exhibits the micro blood vessels whose minimum diameter is on the order of about tens of microns, much better than its conventional CT reconstruction at a millimeter resolution. In conclusion, both the information extraction method and DEI-CT have the potential for use in biomedical micro-structures analysis.

关键词： Diffraction enhanced imaging Computed tomography Information extraction X-ray Liver

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Mutagenicity and Induction of Drug-metabolizing Enzyme Activity by LPG Combustion Particulates in Rats

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biomedical and Environmental sciences 1994年第4期7卷 346-356页

作者： YIN XUE-JUN LIU JUN-ZHUO LI YONG-SHUN KONG XIANG-HUAN AND LIU HONG(Department of Environmental Health, capital university of medical sciences, beijing 100054, china Department of Environmental Health, beijing {4. university, beijing, china) Department of Environmental Health Capital University of Medical Sciences Beijing China.

Methylene chloride extracts of particulates from liquefied petroleum gas (LPG) combustion appliance were studied by using Ames test, micronucleus test and inducibility of pulmonary and hepatic aryl hydrocarbon hydroxylase (AHH) and glutathione S-transferase (GST) in rats. The extracts showed mutagenicity for Salmonella typhimurium strain TA98 and its derivatives TA98NR and TA98/1,8-DNP6 with or without S9 mix. The revertants in strains TA98NR and TA98/1,8-DNP6 were less than 4.% and 50% of that in strain TA98 without S9 mix, respectively. Positive results were obtained in mouse bone marrow micronucleus assay. Intratracheal instillation of the extracts led to increase in pulmonary (but not hepatic) AHH and GST activities in rats. It was seen that AHH was more sensitive than GST to induction by the extracts

关键词： Activity Mutagenicity and Induction of Drug-metabolizing Enzyme Activity by LPG Combustion Particulates in Rats DNP LPG

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Analysis of a 2D “liquid”plasma lattice

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Science china(Physics,Mechanics & Astronomy) 2004年第1期47卷 129-136页

作者： HUA Jianjun1, LIU Yanhong1 & ZHANG Zhihe2 1. institute of Physics, Chinese Academy of sciences, beijing 100080, china 2. College of {4. engineering, capital university of medical sciences, beijing 100054, china Correspondence should be addressed to Hua Jianjun (email: jj_hua@***) Received September 20, 2003 institute of Physics Chinese Academy of Sciences Beijing China College of biomedical engineering Capital University of Medical Sciences Beijing China

To study the structural and dynamical properties of a 2D dusty plasma lattice, a set of experiments were performed in an environment of radio frequency discharge. Based on the results of one of the experiments, pair correlation function, bond-orientational correlation function and mean square displacement of such a system were computed and analyzed. The bond-orientational correlation function is found to fit in with the law of e?r , and the mean square displacement is found to increase monotonously with time, both of which, together with the pair correlation function, indicate that the two-dimensional dusty plasma lattice formed in the experiment stayed in a “liquid” state.

关键词： plasma lattice, pair correlation function, bond-orientational correlation function, mean square displacement.

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Patterns of platinum-group elements in mantle peridotite, granulite xenoliths and basalt in Hannuoba

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Chinese Science Bulletin 1999年第18期44卷 1676-1681页

作者： CHU Xuelei, LI Xiaolin, XU Jiuhua and LIU Jianming1. The Research Center of Mineral Resources Exploration , Chinese Academy of sciences , beijing 100101, china 2. institute of Geology , Chinese Academy of sciences , beijing 100029, china 3. institute of High Energy Physics , Chinese Academy of sciences , beijing 100817 , china 4. beijing university of Science and engineering , beijing 100083, china Corresponding author The Research Center of Mineral Resources Exploration Chinese Academy of Sciences Beijing China institute of Geology Chinese Academy of Sciences Beijing China institute of High Energy Physics Chinese Academy of Sciences Beijing China beijing university of Science and engineering Beijing China

Neutron activation analysis after preconcentration of nickel sulfide fire assay was used in measurement of Ru, Ph, Pd, Os, Ir, Pt (i.e. PGE elements) and Au concentrations for basalt, mantle and granulite xenoliths in Hannuoba. The chondrite- and primitive mantle-normalized PGE patterns generally exhibit flat (for Iherzolite), negative slope (for harzburgite),

关键词： mantle xenolith granulite xenolith basalt platinum-group element Hannuoba.

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Simulation study and function analysis of the dynamic aortic valve

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Progress in Natural Science:Materials International 2006年第5期16卷 512-517页

作者： XIA Dongdong and BAI Jing (Department of biomedical engineering, Tsinghua university, beijing 100084.{4.) Department of biomedical engineering Tsinghua University Beijing 100084 China

The dynamic aortic valve (DAV) is a new left ventricular assist device, a micro-axial blood pump implemented at the position of the aortic valve, pumping blood from the left ventricle into the aortic artery. The present dynamic aortic valve operates at 7 different rotation speeds, ranging from 3000 r/min (speed 1) to 9000 r/min (speed 7). Because in vivo experiments need a lot of live animals and take a long period of time, modeling and simulation have been widely used to simulate and analyze hydra-dynamic property of the DAV and its assisting effects. With the measurements from the mock circulatory loop, a mathematic model of the DAV is established and embedded into the previously developed canine circulatory system. Using this model, the effect of the DAV on the failing heart at each rotation speed level is investigated. The vital cardiac variables are computed and compared with in vivo experimental results, which are in good agreement with an acceptable difference mostly 15%. The establishment of the DAV model and its simulation are useful for further improvement of the DAV device.

关键词： dynamic aortic valve mathematic model computer simulation.

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