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A Novel Method of Gene Regulatory Network Structure Inference from Gene Knock-Out Expression Data

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Tsinghua science and Technology 2019年第4期24卷 446-454页

作者： Xiang Chen Min Li Ruiqing Zheng Siyu Zhao Jianxin Wang Fang-Xiang Wu Yaohang Li the school of Computer science and Engineering Central South University the Department of Mechanical Engineering and Division of biomedical Engineering University of Saskatchewan the Department of Computer science Old Dominion University

Inferring Gene Regulatory Networks(GRNs) structure from gene expression data has been a challenging problem in systems biology. It is critical to identify complicated regulatory relationships among genes for understanding regulatory mechanisms in cells. Various methods based on information theory have been developed to infer GRNs. However, these methods introduce many redundant regulatory relationships in the network inference process due to external noise in the original data, topology sparseness in the network structure, and non-linear dependency among genes. Especially as the network size increases, the performance of these methods decreases dramatically. In this paper, a novel network structure inference method named Loc-PCA-CMI is proposed that first identifies local overlapped gene clusters, and then infers the local network structure for each cluster by a Path Consistency Algorithm based on Conditional Mutual Information(PCA-CMI). The final structure of the GRN is denoted as dependence among genes by an ensemble of the obtained local network structures. Loc-PCA-CMI was evaluated on DREAM3 knock-out datasets, and its performance was compared to other information theorybased network inference methods including ARACNE, MRNET, PCA-CMI, and PCA-PMI. Experimental results demonstrate our novel method Loc-PCA-CMI outperforms the other four methods in DREAM3 datasets especially in size 50 and 100 networks.

关键词： gene regulatory networks network inference path consistency algorithm

MULTI-SOURCE QUANTITATIVE PHOTOACOUSTIC TOMOGRAPHY WITH DETECTOR RESPONSE FUNCTION AND LIMITED-VIEW SCANNING

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Journal of Computational Mathematics 2016年第6期34卷 590-609页

作者： Jing Feng Weifeng Zhou Hao Gao school of biomedical Engineering Shanghai Jiao Tong University Shanghai China school of Mathematics and Physics Qingdao University of Science and Technology Qingdao Shandong China Department of Mathematics and school of biomedical Engineering Shanghai Jiao Tong University Shanghai China

A practical image reconstruction method for multi-source quantitative photoacoustic tomography （QPAT） is proposed in this work with the consideration of detector response function and limited-view scanning. First, the correct detector response function, i.e., spa- tim impulse response （SIR） and acousto-electric impulse response （EIR）, is considered for the ultrasonic transducer to accurately model the acoustic measurement; second, acoustic data is only measured near optical sources with meaningful signal-to-noise ratio （SNR）, i.e., the limited-view scanning, which also reduces the data acquisition time for point trans- ducer. However, due to the incomplete limited-view data, a two-step image reconstruction method （i.e., to first reconstruct initial acoustic pressure and then reconstruct optical coef- ficients） no longer applies, since it is neither possible nor necessary to robustly reconstruct initial acoustic pressure with limited-view data. Therefore, here we propose a direct image reconstruction method that incorporates SIR, EIR and limited-view scanning in a coupled opto-acoustic forward model, regularizes the framelet sparsity, and then solves the QPAT alternating direction method of multipliers. nonlinear QPAT data fidelity with tensor problem with Quasi-Newton method based

关键词： Quantitative photoacoustic tomography Alternating direction method of mul-tipliers Image reconstruction.

Cascade Human Activity Recognition Based on Simple Computations Incorporating Appropriate Prior Knowledge

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Computers, Materials & Continua 2023年第10期77卷 79-96页

作者： Jianguo Wang Kuan Zhang Yuesheng Zhao Xiaoling Wang Muhammad Shamrooz Aslam school of biomedical Engineering Capital Medical UniversityBeijing100054China school of Automation Guangxi University of Science and TechnologyLiuzhou545006China

The purpose of Human Activities Recognition(HAR)is to recognize human activities with sensors like accelerometers and *** normal research strategy is to obtain better HAR results by finding more efficient eigenvalues and classification *** this paper,we experimentally validate the HAR process and its various algorithms *** the base of which,it is further proposed that,in addition to the necessary eigenvalues and intelligent algorithms,correct prior knowledge is even more *** prior knowledge mentioned here mainly refers to the physical understanding of the analyzed object,the sampling process,the sampling data,the HAR algorithm,***,a solution is presented under the guidance of right prior knowledge,using Back-Propagation neural networks(BP networks)and simple Convolutional Neural Networks(CNN).The results show that HAR can be achieved with 90%–100%*** analysis shows that intelligent algorithms for pattern recognition and classification problems,typically represented by HAR,require correct prior knowledge to work effectively.

关键词： Human activities recognition prior knowledge physical understanding sensors HAR algorithms

Methods of calibration to optical trapping force upon non-spherical cells

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Chinese Optics Letters 2006年第12期4卷 722-724页

作者：喻有理张镇西李政王小力 The Key Laboratory of biomedical Information Engineering of Ministry of Education and Institute of Biomedical EngineeringXi'an Jiaotong UniversityXi'an 710049 School of ScienceXi'an Jiaotong UniversityXi'an 710049 The Key Laboratory of biomedical Information Engineering of Ministry of Education and Institute of Biomedical EngineeringXi'an Jiaotong UniversityXi'an 710049 school of science Xi'an Jiaotong UniversityXi'an 710049

The dynamical equation of a trapping cell is solved to find calibration methods for the trapping force, and two methods are compared by synthetic experiment data. Results indicate that： Boltzmann distribution method （BDM） is available for the force calibration of non-spherical or anisotropic cells in arbitrary trap potential; the mean square displacement method （MSDM） is available only for a symmetric harmonic optical trap. The spatial resolution requirement of the calibration system is about a nanometer. The results agree with the reported experiments.

关键词： Light measurement Optical devices Optical resolving power

De Novo Assembly Methods for Next Generation Sequencing Data

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Tsinghua science and Technology 2013年第5期18卷 500-514页

作者： Yiming He Zhen Zhang Xiaoqing Peng Fangxiang Wu Jianxin Wang the school of Information science and Engineering Central South University the Morehouse school of Medicine the Department of Mechanical Engineering and Division of biomedical Engineering University of Saskatchewan

The recent breakthroughs in next-generation sequencing technologies, such as those of Roche 454,Illumina/Solexa, and ABI SOLID, have dramatically reduced the cost of producing short reads of the genome of new species. The huge volume of reads, along with short read length, high coverage, and sequencing errors, poses a great challenge to de novo genome assembly. However, the paired-end information provides a new solution to these problems. In this paper, we review and compare some current assembly tools, including Newbler, CAP3, Velvet,SOAPdenovo, AllPaths, Abyss, IDBA, PE-Assembly, and Telescoper. In general, we compare the seed extension and graph-based methods that use the overlap/lapout/consensus approach and the de Bruijn graph approach for assembly. At the end of the paper, we summarize these methods and discuss the future directions of genome assembly.

关键词： next-generation sequencing genome assembly overlap/lapout/consensus de Bruijn graph

Aminoacyl tRNA synthetases and their relationships with peripheral nerve degeneration and regeneration

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Neural Regeneration Research 2015年第8期10卷 1237-1238页

作者： Junyang Jung Department of Anatomy and Neurobiology School of MedicineBiomedical Science Institution Kyung Hee University

Following damage resulting from mechanical injury,viral infection,or autoimmunity,peripheral nerves degenerate and a variety of complications,including sensory loss,muscular paralysis,skin thinning,and a loss of tendon reflexes,can *** these complications persist,they can cause a number of debilitating personal and/or social *** example,

关键词： degeneration regeneration muscular persist thinning Schwann paralysis tendon degenerate nerves

Short- and medium-term reproducibility of gastric emptying of a solid meal determined by a low dose of ^(13)C-octanoic acid and nondispersive isotope-selective infrared spectrometry

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World Journal of Gastroenterology 2006年第8期12卷 1243-1248页

作者： Anna Kasicka-Jonderko Magdalena Kami■ska Krzysztof Jonderko Olga Setera Barbara Blo■ska-Fajfrowska Department of Basic biomedical science.school of Pharmacy Medical University of SilesiaSosnowiecPoland Department of Basic biomedical science.school of Pharmacy Medical University of SilesiaSosnowiecPoland Department of PhysiologyInstitute of Occupational Medicine and Environmental HealthSosnowiecPoland

AIM： To evaluate the reproducibility of a modified 13^C breath test-based measurement of solid phase gastric emptying （GE） within the frames of a simple-repeated measure study protocol. METHODS： Twelve healthy subjects （6 females and 6 males, mean age 24.9＋0.7 years） were recruited to undergo three identical GE examinations. In six subjects the first two examinations were performed 2 d apart, and the third session was carried out at a median interval of 19.5 d （range 18 - 20 d） from the second one. In another six subjects the first two measurements were taken 20 d apart （median, range： 17-23 d）, whereas the third session took place 2 d after the second one. Probes of expiratory air collected before and during six hours after intake of a solid meal （378 kcal） labelled with 75 μL （68 mg） 13^C-octanoic acid, were measured for 13^CO2 enrichment with the nondispersive isotopeselective infrared spectrometry NDIRS apparatus. RESULTS： Taking coefficients of variation for paired examinations into account, the short-term reproducibility of the GE measurement was slightly but not significantly better than the medium-term one： 7.7% and 11.2% for the lag phase （T-Lag）, 7.3% and 10.9% for the gastric half emptying time （T1/2）. The least differences in GE parameters detectable at P= 0.05 level in the 12 paired examinations were 9.6 and 15.6 min for T-Lag, 11.6 and 19.7 min for T1/2 by a two-day or two to three-week time gap, respectively CONCLUSION： The low-cost modification of the breath test involving a lower dose of 13^C-octanoic acid and NDIRS, renders good short- and medium-term reproducibility, as well as sensitivity of the measurement of gastric emptying of solids.

关键词： 13^C breath test Gastric emptying Nondispersive isotope-selective infrared spectrometry 13^C-octanoic acid Reproducibility

Robust and Self-healable Antibiofilm Multilayer Coatings

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Chinese Journal of Polymer science 2021年第4期39卷 425-440,I0005页

作者： Chao Zhou Jun-Tao Zhou Cheng-Ju Sheng Dicky Pranantyo Yan Pan Xiao-Jia Huang Institute of biomedical Engineering and Health sciences Changzhou UniversityChangzhou 213164China Department of Chemical and biomolecular Engineering National University of Singapore117585Singapore

The infection induced by implantation of biomedical materials may result from the biofilm formation after bacteria ***,the antibiofilm surface coating represents a novel technique to improve the antibacterial activity of biomedical *** traditional antibiofilm surface coatings exhibited some disadvantages and provided a limited service *** this work,we used polyethyleneimine grafted 3-maleimidopropionic acid(PEIM)and poly(acrylic acid)grafted 2-furfurylamine(PAAF)to achieve robust and self-healable crosslinked multilayer coatings,employing Layer-by-Layer(LbL)self-assembly technique and Diels-Alder ***,thiol-terminated poly((3-acrylamidopropyl)trimethylammonium chloride)(PAMPTMA-SH)was grafted onto the crosslinked multilayer coating by thiol-ene click reaction to form a novel multilayer coating(PEIM/PAAF)_(10)-*** found that this coating showed robust and self-healable activity,and significantly inhibited the bacterial growth and biofilm formation after infection with Escherichia coli(***)and Staphylococcus aureus(***)by in vitro and in vivo assays for 120 *** addition,the multilayer coating did not induce significant hemolysis or affect the cell viability of red blood *** vivo studies also showed that(PEIM/PAAF)_(10)-PAMPTMA coating efficiently blocked the infiltration of inflammatory cells and gene expression in the mouse skin challenged with E coli or *** together,these results showed that the prepared multilayer coating exhibited strong antibiofilm activity and provided a new strategy for the application of highly efficient antibiofilm surface coating of biomedical materials.

关键词： Layer-by-Layer assembly Diels-Alder reaction Self-healable Antibiofilm coating Thiol-ene click reaction

Fe-porphyrin:A redox-related biosensor of hydrogen molecule

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Nano Research 2023年第2期16卷 2020-2025页

作者： Zhaokui Jin Penghe Zhao Wanjun Gong Wenjiang Ding Qianjun He Center of Hydrogen science School of Materials Science and EngineeringShanghai Jiao Tong University800 Dongchuan RoadShanghai 200240China school of biomedical Engineering Health Science CenterShenzhen University1066 Xueyuan RoadShenzhen 518060China

Hydrogen molecule(H_(2))exhibits broad-spectrum but microenvironment-dependent biomedical effects in varied oxidation stress-related diseases,but its molecular mechanism is unclear and its targeting molecule is unknown so ***,we originally reveal that Fe-porphyrin is a H_(2)-targeted *** have demonstrated that the oxidized Fe-porphyrin in both free and protein-confining states can self-catalyze the hydrogenation/reduction by reacting with H_(2)to catalytically scavenge∙OH,and can also catalytically hydrogenate to reduce CO_(2)into CO in the hypoxic microenvironment of in vitro simulation and in vivo tumor,confirming that Fe-porphyrin is a redox-related biosensor of H_(2)and H_(2)is an upstream signaling molecule of *** discoveries are favorable for deep understanding and exploration of profound biomedical effects of H2,and helpful for development of innovative drugs and hydrogen energy/agricultural materials.

关键词： hydrogen molecule molecular mechanism molecular target hydrogen medicine porphyrin catalysis carbon monoxide