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A Simple Method for Peak Alignment Using Relative Retention Time Related to an Inherent Peak in Liquid Chromatography-Mass Spectrometry-Based Metabolomics

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JOURNAL OF CHROMATOGRAPHIC SCIENCE 2019年第1期57卷 9-16页

作者： Wang, Yang Ma, Li Zhang, Mengliu Chen, Meiwan Li, Peng He, Chengwei Yan, Chunyan Wan, Jian-Bo Univ Macau Inst Chinese Med Sci State Key Lab Qual Res Chinese Med Macau Peoples R China Jinan Univ Atmospher Environm Inst Safety & Pollut Control Guangzhou Guangdong Peoples R China Guangdong Pharmaceut Univ Coll Pharm Guangzhou 510006 Guangdong Peoples R China

Retention time (RT) shifts are inevitable in liquid chromatography-mass spectrometry (LC-MS)-based metabolomics studies. RT alignment, aligning peaks originating from the same feature to an identical RT, is a necessary step prior to multivariate data analysis. Many RT alignment software packages and various algorithms have been developed. In the present study, a simple method for peak alignment was proposed using relative RT related to an inherent peak in the chromatogram, and its performance on RT alignment in untargeted metabolomics was evaluated using an LC-MS dataset acquired from plasma samples from osteoporotic rats, and compared with the common MarkerLynx XS method using different RT window. RT alignment accuracy and relative standard deviation (RSD) value of the intensity of 79 selected ions in a chromatogram were employed to assess the alignment effectiveness of Method I (0.2 RT window), Method II (0.5 RT window) and Method III (relative RT). The overall RT alignment accuracy of these three methods was 67.7%, 77.2% and 90.9%, and 44.3%, 72.2% and 82.3% of the ions had intensity RSD values <30%, respectively. The results demonstrated that Method III using relative RT significantly reduced the influence caused by RT shifts in LC-MS-based metabolomics. Furthermore, Method I and Method III were applied to discover plasma biomarkers for osteoporosis in rats. Thirteen and nineteen ions were selected as potential biomarkers, respectively. Among them, only eight common ions were found, which demonstrated that different sets of biomarkers were obtained using those two RT alignment methods. The relative RT method exhibited fewer missing values, a lower RSD of peak intensity and better performance in pattern recognition, thereby showing the great potential in future metabolomics studies.

关键词： LIQUID chromatography-mass spectrometry OSTEOPOROSIS diagnosis METABOLOMICS computer algorithms ACCURACY

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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

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BIOPOLYMERS 2003年第1期68卷 91-109页

作者： Pande, VS Baker, I Chapman, J Elmer, SP Khaliq, S Larson, SM Rhee, YM Shirts, MR Snow, CD Sorin, EJ Zagrovic, B Stanford Univ Dept Chem Stanford CA 94305 USA Stanford Univ Stanford Synchrotron Radiat Lab Stanford CA 94305 USA Stanford Univ Biophys Program Stanford CA 94305 USA Stanford Univ Dept Comp Sci Stanford CA 94305 USA Stanford Univ Dept Biol Struct Stanford CA 94305 USA

Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds of atomistic molecular dynamics. This has allowed us to directly simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide alpha-helices, a beta-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins. (C) 2002 Wiley Periodicals, Inc.

关键词： atomistic protein folding microsecond time scale computer hardware computer algorithms molecular dynamics distributed computing villin beta hairpin

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A criterion for atomicity revisited

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ACTA INFORMATICA 2007年第2期44卷 123-151页

作者： Hesselink, Wim H. Univ Groningen Dept Math & Comp Sci NL-9700 AV Groningen Netherlands

Concurrent and reactive programs are specified by their behaviours in the presence of a nondeterministic environment. In a natural way, this gives a specification (ARW) of an atomic variable in the style of Abadi and Lamport. Several implementations of atomic variables by lower level primitives are known. A few years ago, we formulated a criterion to prove the correctness of such implementations. The proof of correctness of the criterion itself was based on Lynch's definition of atomicity by serialization points. Here, this criterion is reformulated as a specification HRW in the formal sense. Simulations from HRW to ARW and vice versa are constructed. These now serve as a constructive proof of correctness of the criterion. Eternity variables are used in the simulation from HRW to ARW. We propose so-called gliding simulations to deal with the problems that appear when occasionally the concrete implementation needs fewer steps than the abstract specification.

关键词： PROGRAMMING languages (Electronic computers) VARIABLES (Mathematics) MATHEMATICAL programming algorithms computer algorithms

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A Comparison of algorithms for Handheld Wand Tracking

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APPLIED ARTIFICIAL INTELLIGENCE 2014年第9期28卷 888-915页

作者： Wolfe, Britton Gloudemans, Monica Indiana Univ Purdue Univ Ft Wayne IPFW Dept Comp Sci Ft Wayne IN 46805 USA

We examine several algorithms for tracking a handheld wand in a 3D virtual reality system: extended Kalman filters (EKFs), interacting multiple models (IMMs), and support vector machines (SVMs). The IMMs consist of several EKF models, each of which is tuned for one particular type of user motion. For determining the types of motion, we compare hand-created rules with an automatic clustering algorithm, with mixed results. The mode-specific EKFs within the IMM are more accurate than one overall EKF. However, the IMM is comparable to a single EKF, because of the overhead of predicting the current component EKF. SVMs with a one-frame lookahead perform the best, cutting the error in half. Aside from those SVMs, different model types were best for the different dimensions of tracking (x, y, z, and rotation).

关键词： computer algorithms Cluster analysis (Statistics) Artificial intelligence Kalman filtering Virtual reality Support vector machines

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Experimental study on dominant sets clustering

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IET computer VISION 2015年第2期9卷 208-215页

作者： Hou, Jian Xia, Qi Qi, Nai-Ming Bohai Univ Sch Informat Sci & Technol Jinzhou 121013 Peoples R China Harbin Inst Technol Sch Astronaut Harbin 150001 Peoples R China

Based on a graph-theoretic concept of a cluster, dominant sets clustering has been shown to be an attractive clustering algorithm with many useful properties. In this study, the authors conduct a comprehensive study of related issues in dominant sets clustering, in an endeavour to explore the potential of this algorithm and obtain the best clustering results. Specifically, they empirically investigate how similarity parameters, similarity measures and game dynamics influence the dominant sets clustering results. From experiments on eight datasets, they conclude that distance-based similarity measures perform evidently better than cosine and histogram intersection similarity measures potentially, and they need to find the best-performing similarity parameter to make use of this advantage. They then study the effect of similarity parameter on dominant sets clustering results and induce the range of the best-performing similarity parameters. Furthermore, they find that the recently proposed infection and immunisation dynamics performs better than the replicator dynamics in most cases while being much more efficient than the latter. These observations are helpful in applying dominant sets clustering to practical problems, and also indicate directions for further improvement of this algorithm.

关键词： GRAPH theory CLUSTER analysis (Statistics) computer algorithms SET theory GAME theory

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Common problems in delay-based congestion control algorithms: a gallery of solutions

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EUROPEAN TRANSACTIONS ON TELECOMMUNICATIONS 2011年第4期22卷 168-178页

作者： Rodriguez-Perez, M. Herreria-Alonso, S. Fernandez-Veiga, M. Lopez-Garcia, C. EI Telecomunicac Dept Telemat Engn Vigo 36310 Spain

Although delay-based congestion control protocols such as FAST Transmission Control Protocol (TCP) promise to deliver better performance than traditional TCP Reno, they have not yet been widely incorporated to the Internet. Several factors have contributed to their lack of deployment. Probably, the main contributing factor is that they are not able to compete fairly against loss-based congestion control protocols. In fact, the transmission rate in equilibrium of delay-based approaches is always less than their fair share when they share the network with traditional TCP Reno derivatives that employ packet losses as their congestion signal. There are also other performance impairments caused by the sensitivity to errors in the measurement of the congestion signal (queuing delay) that reduce the efficiency and the intra-protocol fairness of the algorithms. In this paper, we report, analyse and discuss some recent proposals in the literature to improve the dynamic behaviour of delay-based congestion control algorithms, FAST in particular. The coexistence of sources reacting differently to congestion, the identification of congestion appearance in the reverse path and the persistent congestion problem are the issues specifically addressed. Copyright (C) 2011 John Wiley & Sons, Ltd.

关键词： Packet loss Solutions Error measure control protocol Transmission control protocol Tritolyl Phosphates computer algorithms tactical command post

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Observer Evaluation of a Metal Artifact Reduction Algorithm Applied to Head and Neck Cone Beam Computed Tomographic Images

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INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS 2016年第4期96卷 897-904页

作者： Korpics, Mark Surucu, Murat Mescioglu, Ibrahim Alite, Fiori Block, Alec M. Choi, Mehee Emami, Bahman Harkenrider, Matthew M. Solanki, Abhishek A. Roeske, John C. Loyola Univ Med Ctr Dept Radiat Oncol 2160 S First Ave Maywood IL 60153 USA

Purpose and Objectives: To quantify, through an observer study, the reduction in metal artifacts on cone beam computed tomographic (CBCT) images using a projection-interpolation algorithm, on images containing metal artifacts from dental fillings and implants in patients treated for head and neck (H&N) cancer. Methods and Materials: An interpolation-substitution algorithm was applied to H&N CBCT images containing metal artifacts from dental fillings and implants. Image quality with respect to metal artifacts was evaluated subjectively and objectively. First, 6 independent radiation oncologists were asked to rank randomly sorted blinded images (before and after metal artifact reduction) using a 5-point rating scale (1 = severe artifacts;5 = no artifacts). Second, the standard deviation of different regions of interest (ROI) within each image was calculated and compared with the mean rating scores. Results: The interpolation-substitution technique successfully reduced metal artifacts in 70% of the cases. From a total of 60 images from 15 H&N cancer patients undergoing image guided radiation therapy, the mean rating score on the uncorrected images was 2.3 +/- 1.1, versus 3.3 +/- 1.0 for the corrected images. The mean difference in ranking score between uncorrected and corrected images was 1.0 (95% confidence interval: 0.9-1.2, P<.05). The standard deviation of each ROI significantly decreased after artifact reduction (P<.01). Moreover, a negative correlation between the mean rating score for each image and the standard deviation of the oral cavity and bilateral cheeks was observed. Conclusion: The interpolation-substitution algorithm is efficient and effective for reducing metal artifacts caused by dental fillings and implants on CBCT images, as demonstrated by the statistically significant increase in observer image quality ranking and by the decrease in ROI standard deviation between uncorrected and corrected images. (C) 2016 Elsevier Inc. All rights reserved.

关键词： HEAD & neck cancer diagnosis COMPUTED tomography computer algorithms THREE-dimensional imaging IMAGE quality analysis

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Scheduling algorithms for real-time computing systems admitting simulation models

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PROGRAMMING AND computer SOFTWARE 2013年第5期39卷 255-267页

作者： Kostenko, V. A. Moscow MV Lomonosov State Univ Fac Computat Math & Cybernet Moscow 119992 Russia

A major requirement imposed on the operation of a real-time computing (RTC) system is that the deadlines for the operation of application programs must be met. The violation of an operational deadline leads to a failure of an RTC system. In this context, the problem arises of ensuring the required accuracy of estimating the execution time of application programs. An approach is developed for the design of iterative scheduling algorithms in which the execution times of application programs are estimated using simulation models with a different degree of detail, which ensures the required accuracy of estimating the execution time of programs. The approach can be used to design iterative algorithms of the following classes: genetic, evolutionary, simulated annealing, random-search, and locally optimal algorithms.

关键词： computer scheduling computer algorithms REAL-time computing computer simulation APPLICATION software ITERATIVE methods (Mathematics)

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New automatic forward and backward blind sources separation algorithms for noise reduction and speech enhancement

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computerS & ELECTRICAL ENGINEERING 2014年第7期40卷 2072-2088页

作者： Djendi, Mohamed Zoulikha, Meriem Univ Blida 1 Signal Proc & Image Lab LATSI Blida 09000 Algeria

In this paper, we consider the speech enhancement problem in a moving car through a blind source separation (BSS) scheme involving two spaced microphones. The forward and backward blind source separation structures often use manual voice activity detector (MVAD) systems to control the adaptation of the separating adaptive filters. In this paper, we propose two new automatic voice activity detector (AVAD) systems that allow adapting the original forward and backward BSS structures automatically. The proposed AVAD systems are based on the use of the forward BSS structure to estimate the optimal values of the separating adaptive filters step-sizes. Moreover, the new proposed algorithms are stable and could be used even in very noisy conditions. Intensive experiments are carried out with these two new proposed algorithms to validate their good performances in speech enhancement and noise reduction applications. The presented experiments are based on the system mismatch, the cepstral distance and the output signal-to-noise ratio criteria evaluations. The obtained results show the good performances of the proposed algorithms in comparison with their original versions, where manual VAD systems are used. (C) 2014 Elsevier Ltd. All rights reserved.

关键词： SIGNAL denoising BLIND source separation ADAPTIVE filters computer algorithms SIGNAL-to-noise ratio

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BASIC ARRAY THEORY

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PROCEEDINGS OF THE IEEE 1992年第1期80卷 127-140页

作者： KUMMER, WH W.H. Kummer Inc. Santa Monica CA

This paper outlines basic antenna array theory with major emphasis on pattern analysis and synthesis for periodic linear and planar arrays, phased arrays, and conformal arrays. Extension is made to synthesis techniques which use computer algorithms. These include arbitrary side lobe control, shaped beams, and phase-only null steering. The subjects of random errors and phased array quantization errors are outlined.

关键词： antenna array theory antenna arrays antenna radiation patterns antenna theory arbitrary sidelobe control computer algorithms conformal arrays errors pattern analysis phase-only null steering phased array quantization errors phased arrays planar arrays random errors shaped beams synthesis techniques

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