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structure-oriented methods for protein NMR data analysis

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010年第4期56卷 311-328页

作者： Bermejo, Guillermo A. Llinas, Miguel Carnegie Mellon Univ Dept Chem Pittsburgh PA 15213 USA

The review of Progress in Nuclear Magnetic Resonance Spectroscopy focuses on structure-oriented strategies for solution NMR structure determination of proteins. The review considers those methods that rely on a structure-oriented stage to compensate for sparseness of conventionally generated assignments. ITAS and FastNMR are two of these methods that rely on partial chemical shift assignment information to calculate the initial structure' of a subsequent structure-oriented step. There are a number of direct methods that aim at obtaining protein structures directly from NMR data without prior assignments by translating the spectral information into distances between pairs of atoms. It has been found that direct methods supplement the NOE-derived distances with antidistance constraints (ADCs, or non-NOEs).

关键词： Automated protein NMR structure determination Direct NMR methods Clouds structure-oriented Top-down protein NMR structure

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structure-oriented Electrochemical Synthesis of Layered Double Hydroxide Electrocatalytic Materials for 5-Hydroxymethylfurfural Oxidation

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ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2024年第46期12卷 16905-16913页

作者： Feng, Yixuan Smith Jr, Richard L. Shen, Feng Qi, Xinhua Nankai Univ Coll Environm Sci & Engn Tianjin 300350 Peoples R China Tohoku Univ Grad Sch Environm Studies Sendai 9808572 Japan Chinese Acad Agr Sci Agroenvironm Protect Inst Tianjin 300191 Peoples R China

Quantitative conversion of biomass-derived 5-hydroxymethylfurfural (HMF) to downstream chemicals at room temperature is a critical milestone in sustainable chemistry. Herein, conversion of metal-organic framework (MOF) structures into layered double hydroxide (LDH) electrocatalytic materials (NiFe-LDH/MOF) was fabricated using NiFe-MOF as a structure-oriented sacrificial template via an in situ electrochemical strategy. Results showed that the electrochemical method to convert the material structures not only overcame inherent limitations of MOF structures (inaccessible sites and low conductivity) but also eliminated LDH self-stacking. Hierarchical NiFe-LDH/MOF exhibited high catalytic activity and selectivity in the electrooxidation of 5-hydroxymethylfurfural (HMF) to 2,5-furandicarboxylic acid (FDCA), which is due to the increased number of catalytically active sites and the extended electron transport channels of uniformly dispersed LDH nanosheets. Optimized Ni2Fe1-LDH/MOF materials achieved FDCA yields of 99% with Faraday efficiencies of 99% in 1 M KOH with 50 mM HMF at an applied potential of 1.40 V vs reversible hydrogen electrode at ambient temperature. This work demonstrates a promising method for fabricating LDH electrocatalytic materials from MOF structures and shows a proof of principle for selective oxidation of HMF to FDCA.

关键词： MOF LDH structure-oriented electrooxidationof HMF FDCA

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structure-oriented DTGV Regularization for Random Noise Attenuation in Seismic Data

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IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING 2021年第2期59卷 1757-1771页

作者： Wang, Dehua Gao, Jinghuai Liu, Naihao Jiang, Xiudi Xian Technol Univ Sch Sci Xian 710021 Peoples R China Univ Elect Sci & Technol China Sch Math Sci Chengdu 611731 Peoples R China Xi An Jiao Tong Univ Sch Informat & Commun Engn Xian 710049 Peoples R China Natl Engn Lab Offshore Oil Explorat Xian 710049 Peoples R China China Natl Offshore Oil Corp CNOOC Res Inst Technol Res & Dev Ctr Geophys Key Lab Beijing 100029 Peoples R China

Noise attenuation is a very important step in seismic data processing, which facilitates accurate geologic interpretation. Random noise is one of the main factors that lead to reductions in the signal-to-noise ratio (SNR) of seismic data. It is necessary for seismic data, including complex geological structures, to develop a number of new noise attenuation technologies. In this article, we concern with a new variational regularization method for random noise attenuation of seismic data. Considering that seismic reflection events often have spatially varying directions, we first employ the gradient structure tensor (GST) to estimate the spatially varying dips point by point and propose the structure-oriented directional total generalized variation (DTGV) (SODTGV) functional. Then, we employ the SODTGV as a regularizer to establish an $\ell _structure-oriented$ -SODTGV model and develop the primal-dual algorithm for solving this model. Next, the choice of the model parameters is discussed. Finally, the proposed model is applied to restore noisy synthetic and field data to verify the effectiveness of the proposed workflow. For contrastive methods, we select the structure adaptive median filtering (SAMF), anisotropic total variation (ATV), total generalized variation (TGV), DTGV, median filtering, KL transform, SVD transform, and curvelet transform. The synthetic and real seismic data examples indicate that our proposed method can preferably improve the vertical resolution of seismic profiles, enhance the lateral continuity of reflection events, and preserve local geologic features while improving the SNR. Moreover, the proposed regularization method can also be applied to other inverse problems, such as image processing, medical imaging, and remote sensing.

关键词： TV Attenuation Transforms Oils Geology Data models Signal to noise ratio Gradient structure tensor (GST) Noise attenuation primal-dual algorithm structure-oriented variational regularization

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structure-oriented GAUSSIAN FILTER FOR SEISMIC DETAIL PRESERVING SMOOTHING

STRUCTURE-ORIENTED GAUSSIAN FILTER FOR SEISMIC DETAIL PRESER...

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16th IEEE International Conference on Image Processing

作者： Wang, Wei Gao, Jinghuai Li, Kang Ma, Ke Zhang, Xia Xi An Jiao Tong Univ Sch Elect & Informat Engn Xian 710049 Peoples R China China Satellite Maritime Tracking & Control Dept Jiangyin 214431 Peoples R China

ISBN: (纸本)9781424456536

This paper presents a structure-oriented Gaussian (SOG) filter for reducing noise in 3D reflection seismic data while preserving relevant details such as structural and stratigraphic discontinuities and lateral heterogeneity. The Gaussian kernel is anisotropically constructed based on two confidence measures, both of which take into account the regularity of the local seismic structures. So that, the filter shape is well adjusted according to different local geological features. Then, the anisotropic Gaussian is steered by local orientations of the geological features (layers) provided by the Gradient structure Tensor. The potential of our approach is presented through a comparative experiment with seismic fault preserving diffusion (SFPD) filter on synthetic blocks and an application to real 3D seismic data.

关键词： Anisotropic Gaussian filter structure-oriented Gradient structure Tensor Confidence Measure Seismic Data

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structure-oriented Edge-Preserving Smoothing in the Frequency Domain: Application to Enhance 3D Seismic Data Volumes 17

Structure-Oriented Edge-Preserving Smoothing in the Frequenc...

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17th Workshop on Information Processing and Control (RPIC)

作者： Gomez, Julian L. Velis, Danilo R. Univ Nacl La Plata Fac Ciencias Astron & Geofis Grp METIS Metodos Especializados Tratamiento Info La Plata Buenos Aires Argentina Consejo Nacl Invest Cient & Tecn Buenos Aires DF Argentina

ISBN: (纸本)9789875447547

We present a structure-oriented and edge-preserving algorithm for denoising seismic exploration poststack data volumes in the frequency domain. After transforming the 3D data into frequency-space domain we apply, for each frequency slice, a 1D edge-preserving smoothing filter which is guided spatially by the so-called gradient structure tensor. The algorithm can be efficiently implemented using linear convolutions to compute the gradient structure tensor and simple operations for the 1D edge-preserving filters. Examples using 3D seismic field data volumes show that random as well as coherent footprint noise can be significantly reduced with no loss of important structural information.

关键词： image enhancement structure-oriented denoising footprint seismic data

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On structure-oriented hybrid two-stage iteration methods for the large and sparse blocked system of linear equations

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JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS 2010年第8期234卷 2367-2376页

作者： Zheng, Yi Guo, Wenbin Zhao, Jianli Wang, Nan Liaocheng Univ Sch Math Sci Liaocheng 252059 Shandong Peoples R China

In this paper, we first present a class of structure-oriented hybrid two-stage iteration methods for solving the large and sparse blocked system of linear equations, as well as the saddle point problem as a special case. And the new methods converge to the solution under suitable restrictions, for instance, when the coefficient matrix is positive stable matrix generally. Numerical experiments for a model generalized saddle point problem are given, and the results show that our new methods are feasible and efficient, and converge faster than the Classical Uzawa Method. (C) 2010 Elsevier B.V. All rights reserved.

关键词： Blocked systems of linear equations structure-oriented Two-stage iteration method Matrix multisplitting Saddle point problem The classical Uzawa method

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Search-based Multi-paths Test Data Generation for structure-oriented Testing 09

Search-based Multi-paths Test Data Generation for Structure-...

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World Summit on Genetic and Evolutionary Computation (GEC 09)

作者： Cao, Yang Hu, Chunhua Li, Luming Tsinghua Univ Sch Aerosp Beijing 100084 Peoples R China

ISBN: (纸本)9781605583266

This paper presents a new fitness function to generate test data for a specific single path, which is different from the predicate distance applied by most test data generators based on genetic algorithms (GAs). We define a similarity between the target path and execution path to evaluate the quality of the populations. The problem of the most existing generators is to search only one target data a time, wasting plenty of available interim data. We construct another fitness function combined with the single path function, which can drive GA to complete covering multi-paths to avoid the reduplicate searching and utilize the interim populations for different paths. Several experiments are taken to examine the effectiveness of both the single path and multi-path fitness functions, which evaluate the functions' performance with the convergence ability and consumed time. Results show that the two functions perform well compared with other two typical path-oriented functions and the multi-paths approach retrenches the searching actually.

关键词： Software testing structure-oriented Path testing Genetic algorithms Automation test

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Multitrace Seismic Impedance Inversion With structure-oriented Minimum Entropy Stabilizer

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IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING 2024年 62卷

作者： Geng, Weiheng Lu, Wenkai Li, Jingye Chen, Xiaohong Xue, Yaru Song, Cao Zhang, Yuanpeng Tsinghua Univ Beijing Natl Res Ctr Informat Sci & Technol BNRist Dept Automat Beijing 100084 Peoples R China China Univ Petr State Key Lab Petr Resources & Prospecting Natl Engn Lab Offshore Oil Explorat Beijing 102249 Peoples R China China Univ Petr State Key Lab Petr Resources & Prospecting CNPC Key Lab Geophys Prospecting Beijing 102249 Peoples R China China Univ Petr Coll Informat Sci & Engn Beijing 102249 Peoples R China Inst Geophys & Geochem Explorat CAGS Langfang 065000 Hebei Peoples R China

As an important elastic parameter, seismic acoustic impedance is usually obtained through poststack inversion. However, there are usually two problems that limit the quality of the inversion results. First, conventional inversion methods typically use regularization terms to enhance the stability of the inversion results, and effective regularization terms are particularly important for accurately inverting seismic impedance. Second, most inversion methods adopt a trace-by-trace inversion strategy, resulting in poor lateral continuity when connecting the inversion results of all traces into a 2-D profile, especially for processing noisy data. To address these two problems, we propose a structure-oriented minimum entropy stabilizer for acoustic impedance inversion that enhances the lateral continuity of the inversion results while restoring the blocky structures of the strata and improving the resolution of the inversion results. The stabilizer consists of a structure-oriented regularization (SOR) operator and the minimum entropy norm. The SOR operator is constructed using the local dip estimated from the seismic data by the plane-wave destruction (PWD) algorithm and constrains the inverted impedance along the structural trend, making it more consistent with geological features. The minimum entropy norm restores the blocky structures and enhances resolution by imposing sparse constraints on the temporal and spatial derivatives of the impedance. Based on synthetic and field seismic data, we compare the inversion results of the proposed method with those of conventional Tikhonov regularization and total variation (TV) regularization methods. The results show that the proposed method exhibits superior performance, especially in processing noisy data.

关键词： Impedance Entropy Acoustics TV Geology Mathematical models Reservoirs Blocky minimum entropy stabilizer poststack inversion seismic acoustic impedance structure-oriented

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Calculation method of the signal-to-noise ratio attribute of seismic data based on structural orientation

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Applied Geophysics 2019年第4期16卷 455-462,560页

作者： Zhao Yan Mao Ning-Bo Chen Xu Key Laboratory of Exploration Technologies for Oil and Gas Resources(Yangtze University) Ministry of EducationWuhanHubei 430100China School of Geophysics and Oil Resources Yangtze UniversityWuhanHubei 430100China Institute of Mud Logging Technology and Engineering Yangtze UniversityJingzhou 434023China.

At present,most signal-to-noise ratio(SNR)estimation methods can only calculate the global and not the local SNR of seismic *** paper proposes a calculation method of a structure-oriented-based seismic SNR *** purpose is to characterize the temporal and spatial variation of the seismic data ***,the local slope parameters of the seismic events are calculated using a plane wave decomposition ***,the singular value decomposition method is used to calculate the local seismic data SNR,thereby obtaining it in time and *** proposed method overcomes the insufficiency of a conventional global SNR to characterize any local seismic data features and uses the SNR as an attribute of seismic data to more accurately describe the signal-noise energy distribution characteristics of seismic data in time and *** results of a theoretical model test and real data processing show that the SNR attribute can be used not only for seismic data quality evaluation but also for analysis and evaluation of denoising methods.

关键词： Seismic data signal-to-noise ratio attribute local slope singular value decomposition structure-oriented

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Use of chemical labeling-assisted liquid chromatography-mass spectrometry for discovering derivatives of brassinosteroids

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JOURNAL OF CHROMATOGRAPHY A 2022年 1685卷 463639页

作者： Xiong, Cai-Feng Bai, Ya-Li Yin, Xiao-Ming Ye, Tian-Tian Feng, Yu-Qi Wuhan Univ Dept Chem Wuhan 430072 Peoples R China Fourth Mil Med Univ Natl Translat Sci Ctr Mol Med Dept Cell Biol Xian 710032 Shaanxi Peoples R China Wuhan Univ Sch Publ Hlth Wuhan 430073 Peoples R China Wuhan Univ Frontier Sci Ctr Immunol & Metab Wuhan 430073 Peoples R China

Brassinosteroids (BRs) are plant steroid hormones that are involved in the regulation of plant growth and development as well as environmental adaptation. The discovery of new BR derivatives is beneficial to their biosynthesis and regulation mechanisms research. However, there are few reports on the methods for exploring new BRs, and the existing methods tend to lack coverage. In this work, we established a comprehensive, highly sensitive and selective structure-oriented method for the screening and structural identification of potential BRs in plants using chemical isotope labeling-assisted liquid chromatography -high resolution mass spectrometry (CL-LC-HRMS). The potential BRs were speculated according to the structural features of the reported BRs, and those speculated BRs containing cis-diol groups were la-beled by isotope reagents of 2-methyl-4-phenylaminomethylphenylboronic acid (2-methyl-4-PAMBA) and 2-methyl-4-PAMBA-d5 to improve the sensitivity and selectivity of MS detection. In addition, the fragmen-tation of 2-methyl-4-PAMBA-labeled BRs via collision-induced dissociation (CID) led to the generation of reporter ions, which contributed to specific screening of potential BRs. In-depth structure of potential BRs was elucidated by analyzing multistage MS (MS n ) fragmentation patterns. Using our proposed method, a total of 16 potential BRs were detected from plant samples including 5 new ones, of which one new BR derivative was identified as 2-deoxy-3-epi-6-deoxy-dolichosterone, and this new BR may be involved in the biosynthesis of BRs as precursor of 6-deoxo-dolichosterone. The method developed in this work is promising for screening and identifying new BR derivatives in plants, thereby supplementing the biosyn-thesis pathway of BRs. (c) 2022 Elsevier B.V. All rights reserved.

关键词： Brassinosteroids structure-oriented Chemical labeling Liquid chromatography-mass spectrometry

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