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Recent advances of microbial metabolism analysis:from metabolic molecules to environments

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Science China Chemistry 2023年第11期66卷 2941-2950页

作者： Na Chen Xiaoming Zhang Jing Xi Yanbing Yang Quan Yuan College of Chemistry and Molecular Sciences Institute of Molecular MedicineRenmin Hospital of Wuhan UniversityWuhan UniversityWuhan 430072China

Microbial metabolism analysis is of great significance to the biosynthesis industries and the diagnosis and treatment of infectious diseases caused by microorganisms.However,it remains a grand challenge to offer deep insight into microbial metabolism due to the particularly complex and dynamic processes.Analytical methods are recognized as the critical bottleneck that constrains the in-depth understanding of microbial metabolism.Specific and real-time analytical tools for microbial metabolic processes have currently drawn increasing attention.Here,we summarized the major advances over the past 5 years focusing on the following three aspects including real-time and dynamic analysis of metabolic molecules,selective analysis of specific metabolic pathways and quantitative analysis of the microbial metabolism.Finally,the remaining challenges and perspectives on microbial analysis are discussed and outlooked.

关键词： microorganism metabolites metabolic pathway real-time quantification

Precore/basal core promoter mutants quantification throughout phases of hepatitis B virus infection by Simpleprobe

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World Journal of Gastroenterology 2015年第21期21卷 6639-6648页

作者： Wen-Hui Tu Ying Lv Yong-Mei Zhang Wei Hou Jin-Yu Wang Yi-Jun Zhang Hong-Yan Liu Hao-Xiang Zhu Yan-Li Qin Ri-Cheng Mao Ji-Ming Zhang Department of Infectious Disease Huashan HospitalFudan University Department of Infectious Disease Taizhou Municipal Hospital Department of Infectious Disease Public Health Clinical Center of ShanghaiFudan University

AIM:To investigate precore/basal core promoter(PC/BCP) mutants throughout hepatitis B virus(HBV) infection and to determine their relationship to hepatitis B early antigen(HBeA g) titers.METHODS:We enrolled 191 patients in various stages of HBV infection at the Huashan Hospital and the Taizhou Municipal Hospital from 2010 to 2012.None of the patients received antiviral therapy.HBV DNA from serum,was quantified by real-time PCR.The HBV genotype was determined by direct sequencing of the S gene.We used the Simpleprobe ultrasensitivequantitative method to detect PC/BCP mutants in each patient.We compared the strain number,percentage,and the changes in PC/BCP mutants in different phases,and analyzed the relationship between PC/BCP mutants and HBe Ag by multiple linear regression and logistic regression.RESULTS:Patients with HBV infection(n = 191) were assigned to groups by phase:Immune tolerance(IT) = 55,Immune clearance(IC) = 67,Low-replicative(LR) = 49,and HBeA g-negative hepatitis(ENH) = 20.Of the patients(male,112; female,79) enrolled,122 were HBe Ag-positive and 69 were HBe Ag-negative.The median age was 33 years(range:18-78 years).PC and BCP mutation detection rates were 84.82%(162/191) and 96.86%(185/191),respectively.In five HBe Ag-negative cases,we detected double mutation G1896A/G1899 A.The logarithm value of PC mutant quantities(log10 PC) significantly differed in IT,IC,and LR phases,as well as in the ENH phase(F = 49.350,P < 0.001).The logarithm value of BCP mutant quantities(log10 BCP) also differed during the four phases(F = 25.530,P < 0.001).Log10 PC and log10 BCP values were high in the IT and IC phases,decreased in the LR phase,and increased in the ENH phase,although the absolute value at this point remained lower than that in the IT and IC phases.PC mutant quantity per total viral load(PC%) and BCP mutant quantity per total viral load(BCP%) differed between phases(F = 20.040,P < 0.001; F = 10.830,P < 0.001),with PC% and BCP% gradually increasing in successive phases.HBeA g titers negatively correlat

关键词： precore mutant basal core promotermutant Hepatitis B virus quantification Hepatitis Bearly antigen titers

Quantifying Electrochemical Processes in Batteries and Beyond

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Energy & Environmental Materials 2022年第4期5卷 1001-1004页

作者： Emma N.Antonio Michael F.Toney Materials Science and Engineering Program University of Colorado BoulderBoulderColorado 80309USA Joint Center for Energy Storage Research(JCESR) University of Colorado BoulderBoulderColorado 80309USA Department of Chemical and Biological Engineering University of Colorado BoulderBoulderColorado 80309USA Renewable and Sustainable Energy Institute University of Colorado BoulderBoulderColorado 80309USA

The correlation of electrochemical measurements with materials characterization has advanced our understanding of operation and degradation mechanisms in electrochemical energy storage and many other fields.Yet,often these correlations are qualitative,preventing the unambiguous identification of both operational principles and the root causes of performance losses.Here we suggest quantitative approaches to define competing mechanisms and determine their relative contributions.We illustrate the importance of quantitative methodologies over a range of electrochemical systems and highlight the need to consider the effect of the experimental design and measurement itself.These approaches will reveal the most detrimental degradation mechanisms and enable the development of strategies to suppress,stabilize or eliminate them,leading to materials and devices with longer lifetimes,reduced environmental impact,and improved performance.

关键词： electrochemistry in situ and operando characterization batteries quantification materials science

Quantitative Calculation of Groundwater Vulnerability Assessment Based on quantification Theory Ⅲ

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Journal of Groundwater Science and Engineering 2014年第1期2卷 78-85页

作者： Liang ZHU Wei-dong KANG Ji-chao SUN Jing-tao LIU Institute of Hydrogeology and Environmental Geology Chinese Academy of Geological Sciences State Key Laboratory of Continental Dynamics Northwest University

There are a lot of key qualitative variables in factors affecting groundwater vulnerability. The processing of qualitative variables of the existing superimposed index method generally relies on experience, so the results are normally subjective. Quantitative theory can handle qualitative variables quantitatively, achieve the unity of quantitative and qualitative indicators, highlight the decisive role of the main factors and reflect the actual situation more objectively. We took Yulin City as the research area to verify the feasibility and applicability of quantitative theory Ⅲ, which is used for the quantitative evaluation of groundwater vulnerability. The results show that it has obvious advantage in the screening of indicators and the groundwater vulnerability partition,so it can be used as a quantitative calculation method of groundwater vulnerability assessment.

关键词： Groundwater Vulnerability assessment Quantitative calculation quantification theory III

Large-scale App privacy governance

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Frontiers of Engineering Management 2022年第4期9卷 640-652页

作者： Zitong LI Zhuoya FAN Junxu LIU Leixia WANG Xiaofeng MENG School of Information Renmin University of ChinaBeijing 100872China

Recently,the problem of mobile applications(Apps)leaking users’private information has aroused wide concern.As the number of Apps continuously increases,effective large-scale App governance is a major challenge.Currently,the government mainly filters out Apps with potential privacy problems manually.Such approach is inefficient with limited searching scope.In this regard,we propose a quantitative method to filter out problematic Apps on a large scale.We introduce Privacy Level(P-Level)to measure an App’s probability of leaking privacy.P-Level is calculated on the basis of Permission-based Privacy Value(P-Privacy)and Usage-based Privacy Value(U-Privacy).The former considers App permission setting,whereas the latter considers App usage.We first illustrate the privacy value model and computation results of both values based on real-world dataset.Subsequently,we introduce the P-Level computing model.We also define the P-Level computed on our dataset as the PL standard.We analyze the distribution of average usage and number of Apps under the levels given in the PL standard,which may provoke insights into the large-scale App governance.Through P-Privacy,U-Privacy,and P-Level,potentially problematic Apps can be filtered out efficiently,thereby making up for the shortcoming of being manual.

关键词： privacy risk Privacy Level quantification large-scale App governance

Flow Cytometer Performance Characterization, Standardization and Calibration against CD4 on T Lymphocytes Enables quantification of Biomarker Expressions for Immunological Applications

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Journal of Biomedical Science and Engineering 2014年第9期7卷 756-768页

作者： Heba Degheidy Steven Bauer Gerald Marti Lili Wang Center for Biologics Evaluation and Research US Food and Drug Administration (FDA) Bethesda Maryland USA Center for Devices and Radiological Health FDA Silver Spring Maryland USA National Institute of Standards and Technology (NIST) Gaithersburg Maryland USA

There is an urgent need for developing a procedure for biomarker standardization and relative quantificationin clinical laboratories. Measuring the expression levels of cell antigens is critical for the diagnosis of many diseases, e.g. leukemia, lymphoma and immunodeficiency diseases. One of the most significant challenges in flow cytometry is obtaining inter-laboratory and intra-laboratory consistent and reproducible results across multiple cytometer platforms and locations longitudinally over time. To obtain measurement consistency, the target flow cytometer voltages should be optimized to segregate the negative population from the electronic noise, and to keep the brightest positive population within the dynamic range of each detector. Then target values should be determined and transferred to selected cytometers. In this study, we optimized a procedure for instrument standardization across three different flow cytometer platforms from the same vendor and in two different locations. The biomarker quantification was implemented on standardized instruments using CD4 expression on T lymphocytes with a known amount of antibody bound per cell as a quantification standard. Our results on blood cell subset typing and CD19 quantification demonstrated that consistent and reliable results could be accomplished between instruments using the developed procedure. Quantitating the expression levels of certain cell biomarkers relative to a known reference marker before, during, and after therapy would provide important information for monitoring antibody-based therapy and could be potentially used to adjust dosing. Presently, we are implementing this protocol to quantify critical disease biomarkers, and making necessary modifications to the procedure to include instruments from different instrument manufacturers.

关键词： Flow Cytometry Biomarker quantification Instrument Standardization Target Median Fluorescence Intensity (MFI)

Comparison Study on Different quantification Methods of Diffuse Myocardial Fibrosis of Dilated Cardiomyopathy Using Myocardial T1 Value

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Open Journal of Radiology 2013年第3期3卷 117-123页

作者： Takeshi Hayashida Eijun Sueyoshi Hiroki Nagayama Ichiro Sakamoto Masataka Uetani Department of Radiology Nagasaki University School of Medicine Nagasaki Japan

Purpose: The purpose is to compare several quantification methods and clarify which quantification method is reliable to estimate diffuse myocardial fibrosis with cardiac MRI in patients with dilated cardiomyopathy (DCM) using myocardial T1 value. Methods and Results: Delayed enhancement imaging was performed in 52 patients with DCM and 10 control subjects to identify fibrosis using an inversion time scout sequence. The mean contrast-enhanced myocardial (M) T1 values of the pre and post contrast-enhanced myocardial and left ventricular lumen (L) of control and dilated cardiomyopathy cases were compared. The calculated post M T1 value, pre M T1 value-post M T1 value, and (pre M TI value-post M T1 value)/(pre L T1 value-post L T1 value) were significantly different between the patient group and the control group (344.5 ± 31.6 vs. 390.4 ± 19.3 msec, 239.9 ± 64.2 msec vs. 134.0 ± 28.9 msec, and 0.50 ± 0.11 vs. 0.30 ± 0.60, respectively). (Pre M T1 value-post M T1 value)/(pre L T1 value-post L T1 value) was significantly the most related to the left ventricular ejection fraction (r = 0.66, p Conclusion: (Pre M T1 value-post M T1 value)/(pre L T1 value-post L T1 value) was the most reliable quantification method to estimate the severity of DCM.

关键词： Inversion Time quantification Methods Myocardial Fibrosis Dilated Cardiomyopathy

Development and Validation of Chiral HPLC Method for Identification and quantification of (R)-Enantiomer in Ezetimibe

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American Journal of Analytical Chemistry 2012年第7期3卷 478-483页

作者： Kameswara Rao Chimalakonda Venkatanarayana Gudala Madhusudhan Gutta Srinivasulu Polisetty Sai Venkata Srinivas Koduri Jawaharlal Nehru Technological University Inogent Laboratory Hyderabad India

A normal phase enantioselective high performance liquid chromatographic method was developed for enantiomeric resolution of Ezetimibe it reduces the overall delivery of cholesterol to the liver. The enantiomers of Ezetimibe were resolved on a Chiral Pak AS-H (250 × 4.6 mm, 5 μm) column using a mobile phase system containing n-Hexane, etha-nol, 2-Propanol and Trifloroacetic acid (84:12:4:0.1 v/v). The resolution between enantiomers was found to be more than 2.0. The limit of detection and limit of quantification of (R)-enantiomer were found to be 0.2 μg/mL and 0.5 μg/mL, respectively, for 10 μL injection volume. The sample solution and mobile phase were found to be stable for at least 48 h. The final optimized method was successfully applied to separate (R)-enantiomer from Ezetimibe and was proven to be reproducible and accurate for the quantitative determination of (R)-enantiomer in bulk drugs.

关键词： Ezetimibe (R)-Enantiomer Identification quantification and Validation

Chaos, Fractal and Recurrence quantification Analysis of Surface Electromyography in Muscular Dystrophy

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World Journal of Neuroscience 2015年第4期5卷 205-257页

作者： Elio Conte Ken Ware Riccardo Marvulli Giancarlo Ianieri Marisa Megna Sergio Conte Leonardo Mendolicchio Enrico Pierangeli School of Advanced International Studies on Applied Theoretical and Non Linear Methodologies of Physics Bari Italy Department of Basic Sciences Neuroscience and Sense Organs University of Bari Aldo Moro Bari Italy The International NeuroPhysics Functional Performance Institute Robina Queensland Australia Department of Physical Medicine and Rehabilitation University of Bari Aldo Moro Bari Italy

We analyze muscular dystrophy recorded by sEMG and use standard methodologies and nonlinear chaotic methods here including the RQA. We reach sufficient evidence that the sEMG signal contains a large chaotic component. We have estimated the correlation dimension (fractal measure), the largest Lyapunov exponent, the LZ complexity and the %Rec and %Det of the RQA demonstrating that such indexes are able to detect the presence of repetitive hidden patterns in sEMG which, in turn, senses the level of MU synchronization within the muscle. The results give also an interesting methodological indication in the sense that it evidences the manner in which nonlinear methods and RQA must be arranged and applied in clinical routine in order to obtain results of clinical interest. We have studied the muscular dystrophy and evidence that the continuous regime of chaotic transitions that we have in muscular mechanisms may benefit in this pathology by the use of the NPT treatment that we have considered in detail in our previous publications.

关键词： Chaos Analysis Correlation Dimension LZ Complexity Recurrence quantification Analysis Muscular Dystrophy Chaos and Fractal Estimation by Surface Electromyography