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CGPS:A machine learning-based approach integrating multiple gene set analysis tools for better prioritization of biologically relevant pathways

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Journal of Genetics and Genomics 2018年第9期45卷 489-504页

作者： chen ai Lei Kong Center for Bioinformatics State Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking University

Gene set enrichment（GSE） analyses play an important role in the interpretation of large-scale transcriptome datasets. Multiple GSE tools can be integrated into a single method as obtaining optimal results is challenging due to the plethora of GSE tools and their discrepant performances. Several existing ensemble methods lead to different scores in sorting pathways as integrated results; furthermore, it is difficult for users to choose a single ensemble score to obtain optimal final results. Here, we develop an ensemble method using a machine learning approach called Combined Gene set analysis incorporating Prioritization and Sensitivity（CGPS） that integrates the results provided by nine prominent GSE tools into a single ensemble score（R score） to sort pathways as integrated results. Moreover, to the best of our knowledge, CGPS is the first GSE ensemble method built based on a priori knowledge of pathways and phenotypes. Compared with 10 widely used individual methods and five types of ensemble scores from two ensemble methods, we demonstrate that sorting pathways based on the R score can better prioritize relevant pathways, as established by an evaluation of 120 simulated datasets and 45 real ***, CGPS is applied to expression data involving the drug panobinostat, which is an anticancer treatment against multiple myeloma. The results identify cell processes associated with cancer, such as the p53 signaling pathway（hsa04115）; by contrast, according to two ensemble methods（EnrichmentBrowser and EGSEA）, this pathway has a rank higher than 20, which may cause users to miss the pathway in their analyses. We show that this method, which is based on a priori knowledge, can capture valuable biological information from numerous types of gene set collections, such as KEGG pathways, GO terms, Reactome, and BioCarta. CGPS is publicly available as a standalone source code at ftp：//***/pub/CGPS_download/***.

关键词： Gene expression Differential expression Gene set enrichment Support vector machine

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Bio-screening and quantification of methyl paraben in vinegar and coconut juice separated by HPTLC

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Food Science and Human Wellness 2024年第3期13卷 1602-1607页

作者： Yisheng chen xingjun xi College of Food Science and Engineering Shanxi Agricultural UniversityTaigu 030801China Insitute of Food Nutrition and Safety Shanxi Agricultural UniversityTaiyuan 030031China Institute of Agricultural Food Standardization China National Institute of StandardizationBeijing 100191China

As a widely used food preservative,methyl paraben was experimentally evidenced with serious hormonelike adverse ***,a high performance thin-layer chromatography platformed bioluminescent bioautography and image analysis for the selective quantification and confirmation of methyl paraben was proposed and validated in vinegar and coconut ***,the detectability of the bioautography to the analyte on different layer materials was estimated,revealing that normal silica gel was the best *** that,the liquid of sample extract and working solution were separated to overcome the background noises due to co-extracted *** separation result was then coupled to the optimized bioautography,enabling instant and straightforward screening of the targeted *** accurate quantification,bioluninescent inhibition pattern caused by the analyte was processed by image analysis,giving useful sensitivity(LOD>16 mg/kg),precision(RSD<10.1%)and accuracy(spike-recovery rate 76.9%-112.2%).Finally,the suspected result was confirmed by determining its MS fingerprint,further strengthening the reliability of screening.

关键词： High performance thin-layer chromatography Bio-screening Bioluminescence Image analysis Methyl paraben

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Analytic prediction for planar turbulent boundary layers

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Science China(Physics,Mechanics & Astronomy) 2016年第11期59卷 51-57页

作者： xi chen Zhen-Su She State Key Laboratory for Turbulence and Complex Systems and Department of Mechanics College of EngineeringPeking University

Analytic predictions of mean velocity profile(MVP) and streamwise(x) development of related integral quantities are presented for flows in channel and turbulent boundary layer(TBL), based on a symmetry analysis of eddy length and total stress. Specific predictions include the relations for momentum Reynolds number(Reθ) with friction Reτ and streamwise Re_x: Re_θ≈ 3.27Re_τ,and Re_x/Re_θ = 4.94(lnRe_θ + 1.88)~2 + 1; the streamwise development of the friction velocity u_τ: U_e/u_τ≈ 2.22 lnRe_x + 2.86. 3.83ln(lnRe_x), and of the boundary layer thickness δ_e: x/δ_e ≈ 7.27 lnRe_x.5.***.12.52ln(lnRe_x), which are fully validated by recent reliable data.

关键词： turbulent boundary layer symmetry analysis eddy length log law

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Carrier-Envelope-Phase Control of Single-Electron Transport in Coupled Quantum Dots

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Chinese Physics Letters 2013年第11期30卷 102-105页

作者： YANG Wen-xing chen ai-xi Bai Yan-Feng LU Jia-Wei Department of Physics Southeast UniversityNanjing 210096 Department of Applied Physics School of Basic ScienceEast China Jiaotong UniversityNanchang 330013

We propose a scheme for controlling the coherent transport of a single electron through a closed three-level structure in coupled quantum *** coherent transport is externally controlled by applying a weak few-cycle pulse with an adjustable carrier-envelope phase(CEP).It is revealed numerically that there exists a significant dependence of the electron transport on the *** results illustrate the potential to utilize few-cycle pulses for the excitation in coupled quantum dot systems through control of the CEP,as well providing guidance in the design for possible experimental implementations.

关键词： coherent quantum utilize

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Synthesis of Dendritic-Linear Block Copolymers by Atom Transfer Radical Polymerization

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Chinese Chemical Letters 2001年第7期12卷 595-596页

作者： You Liang ZHAO ai Jun GONG Jing JIANG Hong Wei LIU Chuan Fu chen Fu xi State Key Laboratory of Polymer Physics and Chemistry Center of Molecular ScienceInstitute of ChemistryChinese Academy of SciencesBeijing 100080

The dendritic polyarylether 2-bromoisobutyrate as the macromolecular initiator for the controlled free radical polymerization of styrene was investigated. The polymerization was carried out with CuBr/2,2 ' -bipyridine catalyst at 110 degreesC. It is found that the hybrid dendritic-linear block copolymers possess well-defined molecular weights and low polydispersities.

关键词： Atom transfer radical polymerization dendrimer polystyrene block copolymer

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L1 adaptive control of a generic hypersonic vehicle model with a blended pneumatic and thrust vectoring control strategy

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Science China(Information Sciences) 2017年第3期60卷 139-152页

作者： Qi chen Jing WAN Jianliang ai Department of Aeronautics and Astronautics Fudan University Institute of Vehicle Design Fudan University

The extreme aeroheating at hypersonic regime and the insufficient dynamic pressure in the near space limit the achievable performance of the hypersonic vehicles using aerosurfaces alone. In this paper, an integrated pneumatic and thrust vectoring control strategy is employed to design a control scheme for the longitudinal dynamics of a hypersonic vehicle model. The methodology reposes upon a division of the model dynamics, and an L1adaptive control architecture is applied to the design of the inner-loop and outer-loop controllers. Further, a control allocation algorithm is developed to coordinate pneumatic and thrust vectoring control. Simulation results demonstrate that the allocation algorithm is effective in control coordination, and the proposed control scheme achieves excellent tracking performance in spite of aerodynamic uncertainties.

关键词： hypersonic flight control L1 adaptive control thrust vectoring control allocation parametric uncertainty

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L_1 adaptive controller design for hypersonic formation flight

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Science China(Technological Sciences) 2016年第10期59卷 1597-1608页

作者： chen Qi WAN Jing ai JianLiang Department of Aeronautics and Astronautics Fudan University Institute of Vehicle Design Fudan University

The design of an L_1 adaptive controller for hypersonic formation flight is presented. The traditional leader/wingman formation control problem is considered, with focused attention on dealing with the input disturbance and parametric variations, both of which are intrinsic properties of the system that result in undesired control performance. A proportional-derivative control scheme based on nonlinear dynamic inversion is implemented as the baseline controller, and an L_1 adaptive controller is augmented to the baseline controller to attenuate the effects of input disturbance and parametric variations. Simulation results illustrate the effectiveness of the proposed control scheme.

关键词： hypersonic flight control nonlinear dynamic inversion L1 adaptive control input disturbance parametric variation

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Bioengineered miR-124-3p prodrug selectively alters the proteome of human carcinoma cells to control multiple cellular components and lung metastasis in vivo

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Acta Pharmaceutica Sinica B 2021年第12期11卷 3950-3965页

作者： Linglong Deng Hannah Petrek Mei-Juan Tu Neelu Batra ai-xi Yu ai-Ming Yu Department of Orthopaedic Trauma and Microsurgery Zhongnan Hospital of Wuhan UniversityWuhan 430072China Department of Biochemistry and Molecular Medicine UC Davis School of MedicineSacramentoCA 95817USA

With the understanding of microRNA(miRNA or miR) functions in tumor initiation,progression,and metastasis,efforts are underway to develop new miRNA-based *** recently,we demonstrated effectiveness of a novel humanized bioengineered miR-124-3 p prodrug in controlling spontaneous lung metastasis in mouse *** study was to investigate the molecular and cellular mechanisms by which miR-124-3 p controls tumor *** study identified a set of proteins selectively and significantly downregulated by bioengineered miR-124-3 p in A549 cells,which were assembled into multiple cellular components critical for metastatic *** them,plectin(PLEC) was verified as a new direct target for miR-124-3 p that links cytoskeleton components and *** miR-124-3 p-treated lung cancer and osteosarcoma cells,protein levels of vimentin,talin 1(TLN1),integrin beta-1(ITGB1),IQ motif containing GTPase activating protein 1(IQGAP1),cadherin2 or N-cadherin(CDH2),and junctional adhesion molecule A(F11 R or JAMA or JAM1) decreased,causing remodeling of cytoskeletons and disruption of cell-cell ***,miR-124-3 p sharply suppressed the formation of focal adhesion plaques,leading to reduced cell adhesion ***,efficacy and safety of biologic miR-124-3 p therapy was established in an aggressive experimental metastasis mouse model in *** results connect miR-124-3 p-PLEC signaling to other elements in the control of cytoskeleton,cell junctions,and adhesion essential for cancer cell invasion and extravasation towards metastasis,and support the promise of miR-124 therapy.

关键词： RNA therapy MiR-124-3p Metastasis Proteomics Junctions Cell adhesion Bioengineer Imaging

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Distribution and seasonal variation of estrogenic endocrine disrupting compounds,N-nitrosodimethylamine, and N-nitrosodimethylamine formation potential in the Huangpu River, China

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Journal of Environmental Sciences 2014年第5期26卷 1023-1033页

作者： ai Zhang Yongmei Li Ling chen State Key Laboratory of Pollution Control and Resources Reuse College of Environmental Science and Engineering Tongji University

Detection of estrogenic endocrine disrupting compounds （EDCs） and N-nitrosodimethylamine （NDMA） in drinking water has led to rising concerns. There are, however, a paucity of studies on the distribution and seasonal variation of NDMA and NDMA formation potential （NDMA-FP） in natural waters, especially in China. For EDCs, limited studies have investigated the distribution and seasonal variation of estrone （El）, 1713-estradiol （E2）, estriol （E3）, 17a-ethinylestradiol （EE2）, technical-nonylphenols （t-NP）, and bisphenol A （BPA） in Shanghai. In this study, water samples were collected from 11 sampling sites along the Huangpu River in 2012. The distribution and seasonal variation of EDCs, NDMA, and NDMA-FP were investigated. The results showed that all of the 11 sampling sites were contaminated by the target compounds. Compared with E2 and EE2, higher E1 and E3 concentrations were usually detected in the Huangpu River. The values of 17β- estradiol equivalents （EEQ） suggest a high possibility of endocrine effects on exposed organisms in the Huangpu River. NDMA-FP and t-NP were the dominant contaminants among the eight target compounds. The detection rates of the target compounds and their concentrations were both higher in dry seasons than in wet seasons. Higher concentrations of target compounds were observed in urban sampling sites near drainage outlets, and also in suburban sampling sites where intensive livestock farming and farmlands were located.

关键词： EDCs NDMA NDMA-FP seasonal variation spatial distribution

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An extended numerical model of the first exothermic peak for three dimensional printed cement-based materials

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Frontiers of Structural and Civil Engineering 2024年第1期18卷 80-88页

作者： Wei JIANG Wenqian LI xi chen School of Materials Science and Engineering Tongji UniversityShanghai 200092China School of Civil Engineering Tongji UniversityShanghai 200092China

The first exothermic peak of cement-based material occurs a few minutes after mixing,and the properties of three dimensional(3D)printed concrete,such as setting time,are very sensitive to *** this background,based on the classical Park cement exothermic model of hydration,we propose and construct a numerical model of the first exothermic peak,taking into account the proportions of C_(3)S,C_(3)A and quicklime in *** calculated parameters are calibrated by means of relevant published exothermic test *** is found that this developed model offers a good simulation of the first exothermic peak of hydration for C_(3)S and C_(3)A proportions from 0 to 100% of cement clinker and reflects the effect of quicklime content at 8%-10%.The unique value of this research is provision of an important computational tool for applications that are sensitive to the first exothermic peak of hydration,such as 3D printing.

关键词： 3D printed cement-based materials cement hydration the first exothermic peak liquid quick-setting agent numerical model

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