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Pretreating and normalizing metabolomics data for statistical analysis

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Genes & Diseases 2024年第3期11卷 188-205页

作者： Jun sun Yinglin Xia Division of Gastroenterology and Hepatology Department of MedicineDepartment of Microbiology/ImmunologyUIC Cancer CenterUniversity of Illinois ChicagoJesse Brown VA Medical Center Chicago(537)ChicagoIL 60612USA Division of Gastroenterology and Hepatology Department of MedicineUniversity of Illinois ChicagoChicagoIL 60612USA

Metabolomics as a research field and a set of techniques is to study the entire small molecules in biological samples.Metabolomics is emerging as a powerful tool generally for pre-cision medicine.Particularly,integration of microbiome and metabolome has revealed the mechanism and functionality of microbiome in human health and disease.However,metabo-lomics data are very complicated.Preprocessing/pretreating and normalizing procedures on metabolomics data are usually required before statistical analysis.In this review article,we comprehensively review various methods that are used to preprocess and pretreat metabolo-mics data,including MS-based data and NMR-based data preprocessing,dealing with zero and/or missing values and detecting outliers,data normalization,data centering and scaling,data transformation.We discuss the advantages and limitations of each method.The choice for a suitable preprocessing method is determined by the biological hypothesis,the characteristics of the data set,and the selected statistical data analysis method.We then provide the perspective of their applications in the microbiome and metabolome research.

关键词： Data centering and scaling Data normalization Data transformation Missing values MS-Baseddata preprocessing NMRData preprocessing Outliers Preprocessing/pretreatment

Fossil Equidae in the Linxia Basin with Biostratigraphic and Paleozoogeographic Significance

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Acta Geologica Sinica(English Edition) 2024年第1期98卷 1-9页

作者： sun Boyang Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China

The Linxia Basin is characterized by an abundance of Cenozoic sediments,that contain exceptionally rich fossil resources.Equids are abundant in the Linxia Basin,the fossil record of equids in this region including 16 species that represent 10 genera.In comparison to other classic late Cenozoic areas in China,the Linxia Basin stands out,because the fauna and chronological data accompanying Linxia equids render them remarkably useful for biostratigraphy.The anchitheriines in the region,such as Anchitherium and Sinohippus,represent early equids that appeared in the late stages of the middle and late Miocene,respectively.Among the equines,most species of Chinese hipparions have been identified in the Linxia Basin and some species of the genera Hipparion and Hippotherium have FAD records for China.Furthermore,Equus eisenmannae is one of the earliest known species of Equus in the Old World and is well-represented at the Longdan locality.Some species with precise geohistorical distributions can serve as standards for high-resolution chronological units within this framework.Located at the eastern margin of the Tibetan Plateau and subject to considerable uplift,the Linxia Basin has served as a biogeographic transition area for equids throughout the late Cenozoic.

关键词： Equidae Cenozoic biostratigraphy paleozoogeography Linxia Basin

NADPH oxidase 4(NOX4)as a biomarker and therapeutic target in neurodegenerative diseases

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Neural Regeneration Research 2024年第9期19卷 1961-1966页

作者： Napissara Boonpraman sun Shin Yi BK21 four Program Department of Medical SciencesSoonchunhyang UniversityAsanSouth Korea Department of Biomedical Laboratory Science Soonchunhyang UniversityAsanSouth Korea iConnectome Co.Ltd.CheonanSouth Korea

Diseases like Alzheimer’s and Parkinson’s diseases are defined by inflammation and the damage neurons undergo due to oxidative stress. A primary reactive oxygen species contributor in the central nervous system, NADPH oxidase 4, is viewed as a potential therapeutic touchstone and indicative marker for these ailments. This in-depth review brings to light distinct features of NADPH oxidase 4, responsible for generating superoxide and hydrogen peroxide, emphasizing its pivotal role in activating glial cells, inciting inflammation, and disturbing neuronal functions. Significantly, malfunctioning astrocytes, forming the majority in the central nervous system, play a part in advancing neurodegenerative diseases, due to their reactive oxygen species and inflammatory factor secretion. Our study reveals that aiming at NADPH oxidase 4 within astrocytes could be a viable treatment pathway to reduce oxidative damage and halt neurodegenerative processes. Adjusting NADPH oxidase 4 activity might influence the neuroinflammatory cytokine levels, including myeloperoxidase and osteopontin, offering better prospects for conditions like Alzheimer’s disease and Parkinson’s disease. This review sheds light on the role of NADPH oxidase 4 in neural degeneration, emphasizing its drug target potential, and paving the path for novel treatment approaches to combat these severe conditions.

关键词： Alzheimer’s disease astrocytes mitochondrial dysfunction myeloperoxidase NADPH oxidase 4 NADPH oxidase 4 inhibitors neurodegenerative diseases osteopontin Parkinson’s disease reactive oxygen species

Lupenone improves motor dysfunction in spinal cord injury mice through inhibiting the inflammasome activation and pyroptosis in microglia via the nuclear factor kappa B pathway

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Neural Regeneration Research 2024年第8期19卷 1802-1811页

作者： Fudong Li Xiaofei sun Kaiqiang sun Fanqi Kong Xin Jiang Qingjie Kong Department of Orthopedics Shanghai General HospitalShanghai Jiao Tong University School of MedicineShanghaiChina Department of Orthopedic Surgery Spine CenterShanghai Changzheng HospitalNaval Medical UniversityShanghaiChina Department of Orthopedic Surgery Naval Medical CenterNaval Medical UniversityShanghaiChina Department of Anesthesiology Shanghai Changzheng HospitalNaval Medical UniversityShanghaiChina

Spinal cord injury-induced motor dysfunction is associated with neuroinflammation.Studies have shown that the triterpenoid lupenone,a natural product found in various plants,has a remarkable anti-inflammatory effect in the context of chronic inflammation.However,the effects of lupenone on acute inflammation induced by spinal cord injury remain unknown.In this study,we established an impact-induced mouse model of spinal cord injury,and then treated the injured mice with lupenone(8 mg/kg,twice a day)by intrape ritoneal injection.We also treated BV2 cells with lipopolysaccharide and adenosine5’-triphosphate to simulate the inflammatory response after spinal cord injury.Our res ults showed that lupenone reduced IKBa activation and p65 nuclear translocation,inhibited NLRP3 inflammasome function by modulating nuclear factor kappa B,and enhanced the conve rsion of proinflammatory M1 mic roglial cells into anti-inflammatory M2 microglial cells.Furthermore,lupenone decreased NLRP3 inflammasome activation,NLRP3-induced mic roglial cell polarization,and microglia pyroptosis by inhibiting the nuclear factor kappa B pathway.These findings suggest that lupenone protects against spinal cord injury by inhibiting inflammasomes.

关键词： inflammasome inflammation lupenone microglia polarization pyroptosis spinal cord injury

Rational surface charge engineering of haloalkane dehalogenase for boosting the enzymatic performance in organic solvent solutions

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Chinese Journal of Chemical Engineering 2024年第1期65卷 276-285页

作者： Yin Wu Yan sun Department of Biochemical Engineering School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology(Ministry of Education)Tianjin UniversityTianjin 300350China

Biocatalysis in organic solvents(OSs)has numerous important applications,but native enzymes in OSs often exhibit limited catalytic performance.Herein,we proposed a computation-aided surface charge engineering strategy to improve the catalytic performance of haloalkane dehalogenase DhaA in OSs based on the energetic analysis of substrate binding to the DhaA surface.Several variants with enhanced OS resistance were obtained by replacing negative charged residues on the surface with positive charged residue(Arg).Particularly,a four-substitution variant E16R/E93R/E121R/E257R exhibited the best catalytic performance(five-fold improvement in OS resistance and seven-fold half-life increase in 40%(vol)dimethylsulfoxide).As a result,the overall catalytic performance of the variant could be at least 26 times higher than the wild-type DhaA.Fluorescence spectroscopy and molecular dynamics simulation studies revealed that the residue substitution mainly enhanced OS resistance from four aspects:(a)improved the overall structural stability,(b)increased the hydrophobicity of the local microenvironment around the catalytic triad,(c)enriched the hydrophobic substrate around the enzyme molecule,and(d)lowered the contact frequency between OS molecules and the catalytic triad.Our findings validate that computationaided surface charge engineering is an effective and ingenious rational strategy for tailoring enzyme performance in OSs.

关键词： Surface charge engineering Organic solvent resistance Molecular dynamics simulation Haloalkane dehalogenase

Study on Coded Permutation Entropy of Finite Length Gaussian White Noise Time Series

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Chinese Journal of Electronics 2024年第1期33卷 185-194页

作者： Huihui sun Xiaofeng ZHANG School of Physics and Information Technology Shaanxi Normal University

As an extension of permutation entropy(PE), coded permutation entropy(CPE) improves the performance of PE by making a secondary division for ordinal patterns defined in PE. In this study, we provide an exploration of the statistical properties of CPE using a finite length Gaussian white noise time series theoretically. By means of the Taylor series expansion, the approximate expressions of the expected value and variance of CPE are deduced and the Cramér-Rao low bound(CRLB) is obtained to evaluate the performance of the CPE estimator. The results indicate that CPE is a biased estimator, but the bias only depends on relevant parameters of CPE and it can be easily corrected for an arbitrary time series. The variance of CPE is related to the encoding patterns distribution,and the value converges to the CRLB of the CPE estimator when the time series length is large enough. For a finitelength Gaussian white noise time series model, the predicted values can match well with the actual values, which further validates the statistic theory of CPE. Using the theoretical expressions of CPE, it is possible to better understand the behavior of CPE for most of the time series.

关键词： Coded permutation entropy Gaussian white noise Finite-length time series Cramér-Rao low bound

Complex adaptive system theory,agent-based modeling,and simulation in dominant technology formation

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Journal of Systems Engineering and Electronics 2024年第1期35卷 130-153页

作者： ZHANG Ruihan sun Bing Glorious sun School of Business and Management Donghua UniversityShanghai 200051China School of Economics and Management Harbin Engineering UniversityHarbin 150001China

Dominant technology formation is the key for the hightech industry to“cross the chasm”and gain an established foothold in the market(and hence disrupt the regime).Therefore,a stimulus-response model is proposed to investigate the dominant technology by exploring its formation process and mechanism.Specifically,based on complex adaptive system theory and the basic stimulus-response model,we use a combination of agent-based modeling and system dynamics modeling to capture the interactions between dominant technology and the socio-technical landscape.The results indicate the following:(i)The dynamic interaction is“stimulus-reaction-selection”,which promotes the dominant technology’s formation.(ii)The dominant technology’s formation can be described as a dynamic process in which the adaptation intensity of technology standards increases continuously until it becomes the leading technology under the dual action of internal and external mechanisms.(iii)The dominant technology’s formation in the high-tech industry is influenced by learning ability,the number of adopting users and adaptability.Therein,a“critical scale”of learning ability exists to promote the formation of leading technology:a large number of adopting users can promote the dominant technology’s formation by influencing the adaptive response of technology standards to the socio-technical landscape and the choice of technology standards by the socio-technical landscape.There is a minimum threshold and a maximum threshold for the role of adaptability in the dominant technology’s formation.(iv)The socio-technical landscape can promote the leading technology’s shaping in the high-tech industry,and different elements have different effects.This study promotes research on the formation mechanism of dominant technology in the high-tech industry,presents new perspectives and methods for researchers,and provides essential enlightenment for managers to formulate technology strategies.

关键词： complex adaptive system theory agent-based modeling and simulation dominant technology socio-technical landscape adaptation-choice

AI for Supporting the Freedom of Drawing

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Machine Intelligence Research 2024年第1期21卷 63-88页

作者： Xiaohua sun Juexiao Qin College of Design and Innovation Tongji UniversityShanghai 200082China

Artificial intelligence(AI)has recently been developing rapidly in image processing and generation.AI is not only starting to take over repetitive and tedious tasks but is also involved in creative activities.Drawing is one of the areas with the greatest potential for collaboration between humans and AI.It is an important approach to express various information,but due to the lack of appropriate knowledge and skills,ordinary people without long-time training are unable to draw freely.Although there have been various attempts at human-AI collaboration in drawing,it is difficult for researchers to consider the wide variety of specific problems and develop univer-sal methods due to the openness,improvisation,and individuality of drawing.In this paper,we first analysed the contents of drawing and the general creation process in detail.Second,we have described a mechanism for using AI to enable people to regain the freedom of drawing collaboratively.Finally,we have developed a framework that describes methods for analysing specific problems and quickly finding solutions by building connections between the influencing factors in drawing,the demands of humans,and possible implementa-tion options.The framework also reveals a broad scope of possibilities for applying AI to support people in drawing.

关键词： Intention understanding drawing support drawing art human-artificial intelligence(AI)collaboration

Multi-Sensor Fusion Adaptive Estimation for Nonlinear Under-observed System with Multiplicative Noise

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Chinese Journal of Electronics 2024年第1期33卷 282-292页

作者： Yongpeng CUI Xiaojun sun School of Electronic Engineering Heilongjiang University Key Laboratory of Information Fusion Estimation and Detection

The adaptive fusion estimation problem was studied for the multi-sensor nonlinear under-observed systems with multiplicative noise. A one-step predictor with state update equations was designed for the virtual state with virtual noise first of all. An extended incremental Kalman filter(EIKF) was then proposed for the nonlinear under-observed systems. Furthermore, an adaptive filtering method was given for optimization. The fusion adaptive incremental Kalman filter weighted by scalar was finally proposed. The comparison analysis was made to verify the optimization of the state estimation using adaptive filtering method in the filtering process.

关键词： Information fusion Multiplicative noise Under-observed systems Adaptive filtering Incremental filtering