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pepgrep:A Tool for Peptide MS/MS Pattern Matching

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Genomics, Proteomics & Bioinformatics 2013年第2期11卷 127-132页

作者： Igor Chernukhin school of Biological Sciences University of Essex

Typically, detection of protein sequences in collision-induced dissociation （CID） tandem MS （MS2） dataset is performed by mapping identified peptide ions back to protein sequence by using the protein database search （PDS） engine. Finding a particular peptide sequence of interest in CID MS2 records very often requires manual evaluation of the spectrum, regardless of whether the peptide-associated MS2 scan is identified by PDS algorithm or not. We have developed a com- pact cross-platform database-free command-line utility, pepgrep, which helps to find an MS2 finger- print for a selected peptide sequence by pattern-matching of modelled MS2 data using Peptide-to- MS2 scoring algorithm, pepgrep can incorporate dozens of mass offsets corresponding to a variety of post-translational modifications （PTMs） into the algorithm. Decoy peptide sequences are used with the tested peptide sequence to reduce false-positive results. The engine is capable of screening an MS2 data file at a high rate when using a cluster computing environment. The matched MS2 spectrum can be displayed by using built-in graphical application programming interface （API） or optionally recorded to file. Using this algorithm, we were able to find extra peptide sequences in studied CID spectra that were missed by PDS identification. Also we found pepgrep especially useful for examining a CID of small fractions of peptides resulting from, for example, affinity puri- fication techniques. The peptide sequences in such samples are less likely to be positively identified by using routine protein-centric algorithm implemented in PDS. The software is freely available at http：//***：8080/data/download/pepgrep- ***.

关键词： Collision-induced dissociation Tandem MSTandem MS Protein database search Peptide identification

Cooperative Localization of AUVs Using Moving Horizon Estimation

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IEEE/CAA Journal of Automatica Sinica 2014年第1期1卷 68-76页

作者： Sen Wang Ling Chen Dongbing Gu Huosheng Hu the school of Computer Science and Electronic Engineering University of Essex

This paper studies the localization problem of autonomous underwater vehicles(AUVs) constrained by limited size, power and payload. Such AUVs cannot be equipped with heavy sensors which makes their underwater localization problem difficult. The proposed cooperative localization algorithm is performed by using a single surface mobile beacon which provides range measurement to bound the localization error. The main contribution of this paper is twofold: 1) The observability of single beacon based localization is first analyzed in the context of nonlinear discrete time system, deriving a sufficient condition on observability. It is further compared with observability of linearized system to verify that a nonlinear state estimation is necessary. 2) Moving horizon estimation is integrated with extended Kalman filter(EKF) for three dimensional localization using single beacon, which can alleviate the computational complexity,impose various constraints and make use of several previous range measurements for each estimation. The observability and improved localization accuracy of the localization algorithm are verified by extensive numerical simulation compared with EKF.

关键词： Kalman filters Radio frequency Robots Sensors Vehicles Acoustic measurements Underwater vehicles

Using light to improve commercial value

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Horticulture Research 2018年第1期5卷 332-344页

作者： Matthew Alan Jones school of Biological Sciences University of EssexWivenhoe ParkEssexColchesterCO43SQUK

The plasticity of plant morphology has evolved to maximize reproductive fitness in response to prevailing environmental *** architecture elaborates to maximize light harvesting,while the transition to flowering can either be accelerated or delayed to improve an individual’s *** of the most important environmental signals is light,with plants using light for both photosynthesis and as an environmental *** perceive different wavelengths of light using distinct *** advances in LED technology now enable light quality to be manipulated at a commercial scale,and as such opportunities now exist to take advantage of plants’developmental plasticity to enhance crop yield and quality through precise manipulation of a crops’lighting *** review will discuss how plants perceive and respond to light,and consider how these specific signaling pathways can be manipulated to improve crop yield and quality.

关键词： harvesting plasticity prevailing

EPR spectroscopy of whole blood and blood components:can we diagnose abnormalities?

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The Journal of Biomedical Research 2021年第4期35卷 294-300页

作者： Dimitri A.Svistunenko school of Life Sciences University of EssexColchesterEssex CO43SQUK.

This mini-review gives a brief account of the emergence of the electron paramagnetic resonance(EPR)spectroscopy in the second half of the 20th century and reports the continuous wave EPR spectroscopy studies on human and animal *** question posed by this review is whether the EPR spectroscopy in the form it appeared 70 years ago is still able to provide useful information about different pathological conditions in humans,particularly in the area of diagnosis.

关键词： EPR spectroscopy biological tissues paramagnetic metals protein free radicals human blood animal blood

Using Echo Ultrasound from schooling Fish to Detect and Classify Fish Types

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Journal of Bionic Engineering 2009年第3期6卷 264-269页

作者： Yeffry Handoko Yul.Y.Nazaruddin Huosheng Hu Department of Engineering Physics Bandung Institute of Technology school of Computer Science and Electronic Engineering University of Essex

Fish finders have already been widely available in the fishing market for a number of ***,the sizes of these fish finders are too big and their prices are expensive to suit for the research of robotic fish or *** goal of this research is to propose a low-cost fish detector and classifier which suits for underwater robot or submarine as a proximity sensor. With some pre-condition in hardware and algorithms,the experimental results show that the proposed design has good per- formance,with a detection rate of 100 % and a classification rate of 94 %.Both the existing type of fish and the group behavior can be revealed by statistical interpretations such as hovering passion and sparse swimming mode.

关键词： fish detection classincation artificial neural network ultrasound sensor

Joint user grouping and resource allocation for uplink virtual MIMO systems

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Science China(Information Sciences) 2016年第2期59卷 60-73页

作者： Xiaofeng LU Kun YANG Wenna LI Shaojun QIU Hailin ZHANG State Key Laboratory of Integrated Service Networks Xidian University school of Computer Science and Electrical Engineering University of Essex

MIMO has become a core technology of 5G network to largely improve system throughput. Due to the cost and size of the user equipment(UE), the application of MIMO uplink is limited by the difficulty in practical implementation at the user side. Virtual MIMO has been widely investigated to solve this problem for wireless uplink systems. However, virtual MIMO transmission leads to performance degradation due to the multiuser interference. To obtain good trade-off between the system throughput and transmission performance,we investigate joint user grouping and resource allocation under the consideration of system throughput and average mean squared error(MSE) performance in SC-FDMA uplink systems. Based on linear MIMO detection,we first develop MSE-oriented user grouping criteria for evaluation of transmission performance, then establish dynamic user grouping and optimal resource allocation problems for hard and elastic average MSE *** proposed joint resource allocation algorithm is evaluated in SC-FDMA uplink scenarios and the results show that it achieves maximum system throughput with average MSE guaranteed for the hard MSE constraint algorithms and the alterable trade-off between system throughput and average MSE for the elastic MSE constraint algorithms.

关键词： virtual MIMO user grouping average MSE system throughput resource allocation

Linear perspective shape-from-shading method with two images

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Journal of Systems Engineering and Electronics 2015年第5期26卷 1080-1087页

作者： Lei Yang Ning Zhang Yanyun Ren Huosheng Hu Shanghai Key Laboratory of Power Station Automation Technology School of Mechatronics Engineering and AutomationShanghai University school of Computer Science and Electrical Engineering University of Essex

Shape-from-shading(SFS) is one of the important approaches of 3-D surface reconstruction in computer vision. Since reflectance map equation in SFS is a nonlinear partial differential equation(PDE) with two unknown variables, SFS with one image is ill-posed in mathematical sense. A linear perspective SFS method with two images is proposed to deal with the problem. We assume that two images with different light source directions are captured firstly. Orthogonal projection is not as accurate as perspective one to simulate imaging processes. Two reflectance map equations are established based on the Lambertian model under perspective projection, and the equations are further transformed into one linear PDE. Then the iterative semi-Lagrangian algorithm is used to approximate the solution. Finally, 3-D height values of pixel points in imaging planes are solved by the numerical interpolation method. Experimental results of both hemisphere and complex surfaces show that the proposed method can reconstruct surfaces accurately.

关键词： shape-from-shading(SFS) perspective projection semi-Lagrangian algorithm numerical interpolation method

Bio-signal based control in assistive robots:a survey

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Digital Communications and Networks 2015年第2期1卷 85-101页

作者： Ericka Janet Rechy-Ramirez Huosheng Hu school of Computer Science & Electronic Engineering University of Essex

Recently, bio-signal based control has been gradually deployed in biomedical devices and assistive robots for improving the quality of life of disabled and elderly people, among which electromyography(EMG) and electroencephalography(EEG) bio-signals are being used *** paper reviews the deployment of these bio-signals in the state of art of control *** main aim of this paper is to describe the techniques used for(i) collecting EMG and EEG signals and diving these signals into segments(data acquisition and data segmentation stage),(ii) dividing the important data and removing redundant data from the EMG and EEG segments(feature extraction stage), and(iii) identifying categories from the relevant data obtained in the previous stage(classification stage). Furthermore, this paper presents a summary of applications controlled through these two bio-signals and some research challenges in the creation of these control systems. Finally, a brief conclusion is summarized.

关键词： Assistive robots EMG EEG Feature extraction and classification

A General Linguistic Steganalysis Framework Using Multi-Task Learning

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Computer Systems Science & Engineering 2023年第8期46卷 2383-2399页

作者： Lingyun Xiang Rong Wang Yuhang Liu Yangfan Liu Lina Tan school of Computer and Communication Engineering Changsha University of Science and TechnologyChangsha410114China school of Computer Science and Electronic Engineering University of EssexColchesterCO43SQUK school of Computer Science Hunan University of Technology and BusinessChangsha410205China

Prevailing linguistic steganalysis approaches focus on learning sensitive features to distinguish a particular category of steganographic texts from non-steganographic texts,by performing binary *** it remains an unsolved problem and poses a significant threat to the security of cyberspace when various categories of non-steganographic or steganographic texts *** this paper,we propose a general linguistic steganalysis framework named LS-MTL,which introduces the idea of multi-task learning to deal with the classification of various categories of steganographic and non-steganographic ***-MTL captures sensitive linguistic features from multiple related linguistic steganalysis tasks and can concurrently handle diverse tasks with a constructed *** the proposed framework,convolutional neural networks(CNNs)are utilized as private base models to extract sensitive features for each steganalysis ***,a shared CNN is built to capture potential interaction information and share linguistic features among all ***,LS-MTL incorporates the private and shared sensitive features to identify the detected text as steganographic or *** results demonstrate that the proposed framework LS-MTL outperforms the baseline in the multi-category linguistic steganalysis task,while average Acc,Pre,and Rec are increased by 0.5%,1.4%,and 0.4%,*** ablation experimental results show that LS-MTL with the shared module has robust generalization capability and achieves good detection performance even in the case of spare data.

关键词： Linguistic steganalysis multi-task learning convolutional neural network(CNN) feature extraction detection performance