Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering

Shanghai, China

Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering

Shanghai, China

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Yang Y.,Shanghai JiaoTong University | Yang Y.,Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering | Wu Z.,Shanghai JiaoTong University | Kong W.,Shanghai Maritime University | Kong W.,Shanghai JiaoTong University
Current Bioinformatics | Year: 2017

Background: MicroRNAs (miRNAs) are short non-coding RNAs that serve as key regulators at post-transcriptional level in many important biological processes. In recent years, miRNA expression profiles have been largely investigated and demonstrated to be promising biomarkers for discriminating subtypes of complex human diseases and measuring treatment effects. Most of the analysis approaches for DNA microarray data can be applied to miRNA microarray data, such as statistical test for differential expression analysis, and clustering for co-regulation analysis. Benefitting from the comprehensive annotation available for protein-coding genes, gene expression analysis is usually guided by prior biological knowledge in order to obtain more biologically meaningful results. However, functional annotation of miRNAs is relatively few, thus the prior knowledge-based methods are hard to be applied to miRNAs. Results: In this paper, we incorporate gene ontology information of the target genes of miRNAs for the clustering of miRNAs, and propose a combined similarity measure. The experiments were conducted on two public miRNA microarray data sets. Experimental results show that the new similarity measure can improve the quality of clustering with regard to the classification accuracy and functional enrichment significance of clusters. Conclusion: The clustering of microRNA expression profiles can be improved by incorporating domain knowledge, thus resulting in more functionally compact clusters, which are the basis for the identification of potential miRNA biomarkers and the construction of miRNA co-regulation networks. © 2017 Bentham Science Publishers.


Yang Y.,Shanghai JiaoTong University | Yang Y.,Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering | Yang Y.,Shanghai Center for Systems Biomedicine | Huang N.,Shanghai JiaoTong University | And 2 more authors.
BMC Genomics | Year: 2017

Background: MicroRNAs (miRNAs) have great potential serving as tumor biomarkers and therapeutic targets. As the rapid development of high-throughput experimental technology, gene expression experiments have become more and more specialized and diversified. The complex data structure has brought great challenge for the identification of biomarkers. In the meantime, current statistical and machine learning methods for detecting biomarkers have the problem of low reliability and biased criteria. Results: This study aims to select combinatorial miRNA biomarkers, which have higher sensitivity and specificity than single-gene biomarkers. In order to avoid exhaustive search and redundant information, miRNAs are firstly clustered, then the combinations of representative cluster members are assessed as potential biomarkers. Both the criteria for the partition of clusters and selection of representative members are based on Fisher linear discriminant analysis (FDA). The FDA-based criterion has been demonstrated to be superior to three other criteria in selecting representative members, and also good at refining clusters. In the comparison with eight common feature selection methods, this clustering-based method performs the best with regard to the discriminative ability of selected biomarkers. Conclusions: Our experimental results demonstrate that the clustering-based method can identify microRNA combinatorial biomarkers with high accuracy and efficiency. Our method and data are available to the public upon request. © 2017 The Author(s).


Peng H.-L.,National Key Laboratory of Science and Technology on Micro Nano Fabrication | Peng H.-L.,Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering | Peng H.-L.,Shanghai JiaoTong University | Liu J.-Q.,National Key Laboratory of Science and Technology on Micro Nano Fabrication | And 18 more authors.
Sensors and Actuators, A: Physical | Year: 2015

A novel flexible dry electrode based on carbon nanotube (CNT) and polydimethylsiloxane (PDMS) is proposed for recording biopotentials. Because the homogeneous dispersion of CNTs in PDMS is challenge due to the high viscosity of PDMS and aggregation of CNTs, a novel process is developed through addition of an organic solvent to disentangle CNTs and reduce the viscosity of PDMS. The electrical performance of the composite of CNTs and PDMS as the function of CNT concentration was characterized. The optimized 10 wt% MWCNTs is dispersed in PDMS as the material of flexible dry electrode. In order to apply for long-term, wearable biopotential recording devices, the flexible dry electrode with micropillar array is designed and fabricated by MEMS process. The testing result shows that the skin-electrode contact impedance of the flexible mciropillar electrode is lower an order magnitude than that of the flexible flat electrode without micropillar array structures. Moreover, the contact impedance of this fabricated electrode was stable during two-day continuous testing, which indicates the flexible dry electrode is suitable for long-term measurement. In order to investigate the effect of motion artifact on the ECG signal, ECG signals are recording under two statuses of resting and walking. The ECG signals measured by the fabricated micropillar electrode were good fidelity, and did not degrade because of the motion. © 2015 Published by Elsevier B.V.


Peng H.-L.,National Key Laboratory of Science and Technology on Micro Nano Fabrication | Peng H.-L.,Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering | Peng H.-L.,Shanghai JiaoTong University | Liu J.-Q.,National Key Laboratory of Science and Technology on Micro Nano Fabrication | And 13 more authors.
Sensors and Actuators, B: Chemical | Year: 2016

In this paper, we present a novel passive electrode based on porous titanium (Ti) for electroencephalography (EEG) recording. There was a reservoir with a capacity of 200 μl on the passive electrode. When the slight pressure was applied on the reservoir, the electrolyte in the reservoir permeated from micro-holes of the porous Ti onto the skin. The liquid could provide continuous wet interface between electrode and skin to maintain low and stable contact impedance. After the pressure was removed, the liquid withdrew into the reservoir to make the skin keep clean. Meanwhile, the amount of the permeated liquid was too little to form short circuit of adjacent electrodes. We used physiological saline as the electrolyte because it was not different from conductive gel of the conventional silver/silver chloride (Ag/AgCl) electrode and didn't cause skin irritations or allergic reactions. The testing results indicated that the passive electrode had a relatively low skin-electrode contact impedance. The alpha rhythm and N100 auditory evoked potential were measured to evaluate the electrode performance for EEG recording. © 2015 Elsevier B.V. All rights reserved.


Peng H.-L.,National Key Laboratory of Science and Technology on Micro Nano Fabrication | Peng H.-L.,Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering | Peng H.-L.,Shanghai JiaoTong University | Liu J.-Q.,National Key Laboratory of Science and Technology on Micro Nano Fabrication | And 12 more authors.
Sensors and Actuators, B: Chemical | Year: 2016

The conventional wet silver/silver chloride (Ag/AgCl) electrode is used to record biopotential mostly due to its potential reproducibility, excellent signal to noise ratio (SNR), reliability and biocompatibility. However, this type of electrode only works with conductive gel, and the conductive gel would result in irritation and injury of the skin. Furthermore, the conductive gel would dehydrate over time and thus the quality of biopotential signal degrades. In this paper, a new novel flexible dry electrode with thousands of AgCl micro-pads is proposed for biopotential recording. As the radius of AgCl pad was only 50 μm, the moisture of the skin could be used as the electrolyte of the flexible dry electrode during the biopotentail recording. The fabricated electrode was thin and flexible, so that it attached conformably onto the skin. As a consequence, the contact impedance of electrode-skin interface was relatively stable. The experimental results indicated that the SNR (23.8 dB) of the fabricated electrode was higher than that of conventional dry Ag electrode (20.6 dB). The flexible dry electrode was suitable for long-term biopotential recording and further used in wearable systems for human health monitoring. © 2016 Elsevier B.V. All rights reserved.


Yang Y.,Shanghai JiaoTong University | Yang Y.,Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering | Xu Z.,Shanghai JiaoTong University | Song D.,Beijing Institute of Technology
BMC Bioinformatics | Year: 2016

Background: Missing values are commonly present in microarray data profiles. Instead of discarding genes or samples with incomplete expression level, missing values need to be properly imputed for accurate data analysis. The imputation methods can be roughly categorized as expression level-based and domain knowledge-based. The first type of methods only rely on expression data without the help of external data sources, while the second type incorporates available domain knowledge into expression data to improve imputation accuracy. In recent years, microRNA (miRNA) microarray has been largely developed and used for identifying miRNA biomarkers in complex human disease studies. Similar to mRNA profiles, miRNA expression profiles with missing values can be treated with the existing imputation methods. However, the domain knowledge-based methods are hard to be applied due to the lack of direct functional annotation for miRNAs. With the rapid accumulation of miRNA microarray data, it is increasingly needed to develop domain knowledge-based imputation algorithms specific to miRNA expression profiles to improve the quality of miRNA data analysis. Results: We connect miRNAs with domain knowledge of Gene Ontology (GO) via their target genes, and define miRNA functional similarity based on the semantic similarity of GO terms in GO graphs. A new measure combining miRNA functional similarity and expression similarity is used in the imputation of missing values. The new measure is tested on two miRNA microarray datasets from breast cancer research and achieves improved performance compared with the expression-based method on both datasets. Conclusions: The experimental results demonstrate that the biological domain knowledge can benefit the estimation of missing values in miRNA profiles as well as mRNA profiles. Especially, functional similarity defined by GO terms annotated for the target genes of miRNAs can be useful complementary information for the expression-based method to improve the imputation accuracy of miRNA array data. Our method and data are available to the public upon request. © 2015 Yang et al.


Tian H.-C.,Shanghai JiaoTong University | Liu J.-Q.,Shanghai JiaoTong University | Liu J.-Q.,Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering | Kang X.-Y.,Shanghai JiaoTong University | And 4 more authors.
Sensors and Actuators, A: Physical | Year: 2015

Biomedical microelectrodes play a significant role in motor paralysis recovery caused by spinal cord injury (SCI). As most researchers focused on implantable microelectrodes with multiple functions for neural studies and application, we developed flexible intramuscular microelectrodes integrated wire electrodes for functional electrical stimulation (FES) and electromyogram (EMG) recording with micro tube channels for fluidic drug delivery. The electrodes were electrochemically deposited with conducting polymer (PEDOT/pTS) coating to improve the electrode performance including electrochemical impedance and charge storage capacity (CSC). Moreover, the excellent mechanical and electrochemical stability of PEDOT/pTS coated electrodes was verified by withstanding ultrasonic bath and experiencing repeated cyclic voltammetry (CV) scan. Furthermore, the fluidic property of the micro channels of electrodes was investigated to be suitable for intramuscular drug delivery. In addition, electrophysiological experiments in vivo comprising FES and EMG recording were performed to evaluate the practical application of flexible intramuscular microelectrodes. As a consequence, the developed multi-functional intramuscular microelectrodes are suitable for intramuscular implantation and electrophysiological application, and open a new gate for future researchers on intramuscular motor prostheses for paralysis recovery. © 2015 Elsevier B.V. All rights reserved.


Yu K.,Shanghai JiaoTong University | Yu K.,Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering | Chen L.,Shanghai JiaoTong University | Chen L.,Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering | And 6 more authors.
Jisuanji Xuebao/Chinese Journal of Computers | Year: 2015

Human-machine dialogue system is a human-machine interaction system which treats the machine as a cognitive agent. With the advances of computing hardware and software as well as the booming of mobile internet, cognitive dialogue system, which can deal with uncertain interactive information, attracts great interest. The paper argues that task-oriented dialogue system consists of three layers: physical layer, control layer and application layer. IO technology, cognitive technology and knowledge management are corresponding techniques. Cognitive technology is a new middle ware technology recently emerging with the need of instant natural human-machine conversation. Its goal is to make machine a cognitive agent capable of understanding, learning, guiding and adapting. For this purpose, deep and robust understanding, inference based on uncertain information, policy optimization, adaptation and influential information generation are required. This paper is a position paper of cognitive technology. The scope and content of cognitive technology in dialogue systems is introduced. Relevant techniques are reviewed and future research direction are also discussed. © 2015, Science Press. All right reserved.

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