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Theoretical and experimental biology in one —A symposium in honour of Professor Kuo-Chen Chou’s 50th anniversary and Professor Richard Giegé’s 40th anniversary of their scientific careers

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Journal of Biomedical Science and Engineering 2013年第4期6卷 435-442页

作者： Sheng-Xiang Lin Jacques Lapointe Department of Biochemistry Microbiology and Bioinformatics and PROTEO Laval University Quebec Canada Laboratory of Molecular Endocrinology and Oncology Research Center of Laval University Hospital Center (CHUQ-CHUL) and PROTEO Laval University Quebec Canada

It has been a dream that theoretical biology can be extensively applied in experimental biology to accelerate the understanding of the sophiscated movements in living organisms. A brave assay and an excellent example were represented by enzymology, in which the well-established physico-chemistry is used to describe, to fit, to predict and to improve enzyme reactions. Before the modern bioinformatics, the developments of the combination of theoretical biology and experimental biology have been mainly limited to various classic formulations. The systematic use of graphic rules by Prof. Kuo-Chen Chou and his co-workers has significantly facilitated to deal with complicated enzyme systems. With the recent fast progress of bioinformatics, prediction of protein structures and various protein attributes have been well established by Chou and co-workers, stimulating the experimental biology. For example, their recent method for predicting protein subcellular localization (one of the important attributes of proteins) has been extensively applied by scientific colleagues, yielding many new results with thousands of citations. The research by Prof. Chou is characterized by introducing novel physical concepts as well as powerful and elegant mathematical methods into important biomedical problems, a focus throughout his career, even when facing enormous difficulties. His efforts in 50 years have greatly helped us to realize the dream to make “theoretical and experimental biology in one”. Prof. Richard Giege is well known for his multi-disciplinary research combining physics, chemistry, enzymology and molecular biology. His major focus of study is on the identity of tRNAs and their interactions with aminoacyl-tRNA synthetases (aaRS), which are of critical importance to the fidelity of protein biosynthesis. He and his colleagues have carried out the first crystallization of a tRNA/aaRS complex, that between tRNAAsp and AspRS from yeast. The determination of the complex structure contributed significantly to under- stand the int

关键词： Theoretical Biology Experimental Biology Chou’s Graphic Rules in Enzymology Prediction of Protein Attributes Chou’s Invariance Theorem Macromolecular Crystallogenesis tRNA Identity on Aminoacylation Specificity Physico-Biochemistry

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A Comparison of Statistical Methods for Analyzing Discrete Hierarchical Data: A Case Study of Family Data on Alcohol Abuse

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Open Journal of Statistics 2013年第4期3卷 1-6页

作者： Yuanyuan Liang Keumhee Chough Carriere Department of Epidemiology and Biostatistics University of Texas Health Science Center at San Antonio San Antonio USA Department of Mathematical and Statistical Sciences University of Alberta Edmonton Canada

Although hierarchical correlated data are increasingly available and are being used in evidence-based medical practices and health policy decision making, there is a lack of information about the strengths and weaknesses of the methods of analysis with such data. In this paper, we describe the use of hierarchical data in a family study of alcohol abuse conducted in Edmonton, Canada, that attempted to determine whether alcohol abuse in probands is associated with abuse in their first-degree relatives. We review three methods of analyzing discrete hierarchical data to account for correlations among the relatives. We conclude that the best analytic choice for typical correlated discrete hierarchical data is by nonlinear mixed effects modeling using a likelihood-based approach or multilevel (hierarchical) modeling using a quasilikelihood approach, especially when dealing with heterogeneous patient data.

关键词： Non-Linear Mixed Effects Model Multilevel Model Generalized Estimating Equations Mantel-Haenszel Odds Ratio Specificity Sensitivity

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FRACTAL APPROACH FOR THE INVESTIGATION OF THE ENZYME MODEL

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Chinese Science Bulletin 1991年第15期36卷 1319-1320页

作者：李后强陈淑华赵华明 Department of Chemistry Sichuan University Chengdu 610064 PRC

In general, an enzyme is a protein. The enzyme model implies the small organic molecule or molecular cluster which can imitate the Specificity and function of the enzyme. The fractal features of proteins were firstly found by H. J. Stapleton and his coworkers. Recently, a new method for calculating the fractal dimension of protein has been proposed by the authors based on the knowledge of molecular structures. This letter reports the fractal principles for studying the enzyme models.

关键词： fractal calculating implies letter dimensions Specificity chains 介卿 contained conformation

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The diagnostic accuracy of the usage of the Fetal Medicine Foundation’s (FMF) on-line risk calculator with first-trimester ultrasound for screening for preeclampsia in high-risk pregnant Brazilian population

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Open Journal of Obstetrics and Gynecology 2012年第3期2卷 298-303页

作者： Ernesto Antonio Figueiró-Filho Maithe Vendas Galhardo Bruno Areco de Souza Faculty of Medicine University Hospital Federal University of Mato Grosso do Sul Campo Grande Brazil

To evaluate the sensitivity and Specificity of the usage of the FMF On-Line Risk Calculator with first-trimester ultrasound, in screening assessment for preeclampsia (PE), without serum markers. To define the best risk cut-off values for early, intermediate and late preeclampsia. Diagnostic accuracy study of pregnant women who had first-trimester ultrasounds between 11 and 13 weeks. The index test was the first-trimester ultrasound scan plus the FMF On-Line Risk Calculator to assess the risk for PE. The reference standard was the confirmation of actual development of early, intermediate or late PE. For calculations of sensitivity and Specificity to determine the best cut-off values for early, intermediate and late PE, all the information was processed into ROC curves. The assessment of preeclampsia risk in the first trimester using an ultrasound plus the FMF On-Line Risk Calculator demonstrated a significant (p < 0.05) area under the ROC curve for early, intermediate and late preeclampsia. The best risk cut-off values were defined as 2.1% for early, 2.5% for intermediate and 3.5% for late preeclampsia. The first trimester US plus the FMF On-Line Risk Calculator tool was useful and applicable when assessing the risk for preeclampsia in a specific pregnant Brazilian population.

关键词： Accuracy Sensitivity Specificity Preeclampsia First Trimester Risk

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Tissue-specific isoenzyme variations in Arabian camel, Camelus dromedaries

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Advances in Bioscience and Biotechnology 2012年第7期3卷 863-868页

作者： Mohammed S. AL-Harbi Sayed A. M. Amer Department of Biology Faculty of Science Taif University Taif Saudi Arabia

Malate dehydrogenase, α-esterase and β-esterase isoenzymes have been analyzed by native polyacryla-mide gel electrophoresis in different tissues (liver, kidney, muscle and hump) of the Arabian Camel, Camelus dromedaries in order to study the tissue Specificity of these isoenzymes. Malate dehy-drogenase recorded three fractions while both este-rases recorded two fractions in different studied tissues. Malate dehydrogenase was considered as a key isoenzyme in discriminating among the different studied tissues. The percentage amount of both Mdh-1 and Mdh-2 showed significant difference among the different tissues while Mdh-3 recorded significant variation between muscle and hump tissues. The significant variation in the amount of Mdh isoenzyme (on the level of either total or fractions) among the different studied tissues may reflect the role of this enzyme for energy production in this desert animal. With respect to esterases, the percentage amount for both fractions and the total enzyme did not show significant difference among different tissues except β-Est-2 which was significantly higher in hump than in muscle. This enzyme showed higher thickness and intensity in both liver and kidney than in the muscle and hump indicating its greater activity in both liver and kidney.

关键词： Electrophoresis Esterase Malate Dehydrogenase Tissue Specificity Arabian Camel

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Enzyme-Linked Immunosorbent Assay for Pasteurella Multocida in Rabbits and Serotypes of the Isolates

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中国医科大学学报 1989年第S2期18卷 60-66页

作者：戴显声 Dale L.Brooks Laboratory Animal Centre China Medical University Animal Resources Service University of California Davis USA

The control and prevention of pasteurellosis in rabbits which makes the hosts unsuitable for experimental use raised the needs to improve and simplify the procedures of Enzyme-Linked Immunosorbent Assay (ELISA) for detect of antibody against P.multocida. A comparison on the sensitivity and Specificity of bacterial culture of antemortem and postmortem samples, complement fixation test and enzyme-linked immunosorbent assay of 11 apparently healthy adult rabbits was conducted. The incidence rates showed 45.45%,54.54% and 72.73% respectively. The sensitivity for the three methods were 0.63, 0.67,and 1.00,and Specificity for them were 1.00, 0.67 and 1.00 respectively. Somatic serotypes of isolates of P.multocida from rabbits of three groups (rabbits of group 2 were with clinic signs, those of groups 1 and 3 were apparently healthy) revealed no remarkable differences,and the predominant types were type 3 and type 3, 4. This was somewhat different from the reports derived from other states. As the antigen of different serotype used in ELISA may have different sensitivity and Specificity, which is affected also by different preparation method, a type non-specific antigen should be selected to meet such request. The trial of accomplishment of ELISA without positive and negative controls was presented for discussion.

关键词： Pasteurella multocida serotype Specificity apparently accomplishment postmortem somewhat immunosorbent complement

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Analytical consideration of the selectivity of oligonucleotide hybridization

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Journal of Biophysical Chemistry 2011年第2期2卷 75-91页

作者： M. R. Kabilov D. V. Pyshnyi Institute of Chemical Biology and Fundamental Medicine SB RAS Novosibirsk Russia

Systematic analysis of factors determining efficiency in discrimination of a point substitution (SNP) within specific DNA sequences was carried out in the context of hybridization approach. There are two types of selectivity that are critical for the rational design of highly specific oligonucleotides probes. The first type is the real selectivity of hybridization (fa) that is the ratio of association degrees of targets with an oligonucleotide probe upon the perfect and imperfect complex formation. This type of selectivity reflects the level of discrimination between matched and mismatched signals, which is determined both by experimental conditions and the thermodynamics of oligonucleotide hybridization. The second parameter characterizing the efficiency of SNP discrimination is the limit selectivity of hybridization, which determines the utmost value of fa at a given temperature. This value can be calculated as the ratio of corresponding equilibrium association constants of perfect and imperfect complex formation determined purely by thermodynamics. We have shown that the fa function is the most reliable characteristic describing the hybridization selectivity. For the analytical system designed to reveal any type of perturbation in DNA (e.g. SNP or modification), there is usually a temperature at which fa has its maximum value. The dependency of the fa maximum on different experimental parameters as well as the structural characteristics of a probe are described in details. The results allowed us to postulate points of principle to rationally design the most selective probes on the basis of oli- gonucleotides or their derivatives.

关键词： Allele Specific Hybridization Duplex Stability Oligonucleotide Probes SNP Discrimination Specificity Thermodynamics

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Electrolytes,water,acid-base imbalance

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China Medical Abstracts(Internal Medicine) 2010年第3期27卷 145-145页

2010296 Utility of clinical exercise test in diagnosis of hypokalaemic periodic paralysis. LIU Mingsheng(刘明生),et al. Dept Neurol,PUMC & CAMS,Beijing l00730. Chin J Neurol 2010;43(5):328-330. Objective To assess the utility of changes of muscle strength and compound muscle action potential (CMAP) of abductor digiti minimi (ADM) muscle after the exercise

关键词： paralysis exercise CAMS imbalance utility Neurol minutes Specificity muscles suspected

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CLINICAL APPLICATION OF THE TINGGONG POINT

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Journal of Traditional Chinese Medicine 1989年第2期9卷 97-99页

作者：贺普仁 Department of Acupuncture Beijing Hospital of Traditional Chinese Medicine

Accurate and comprehensive understandingof the relative Specificity of individual pointsand their combination is the essential basis ofacupuncture treatment.Through practice,theauthor studied the therapeutic effect of... 详细信息

关键词： tongue yellow deafness tense feeling hearing Specificity suddenly weakness mania

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Characteristic sites in the internal proteins of avian and human influenza viruses

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Journal of Biomedical Science and Engineering 2010年第10期3卷 943-955页

作者： David King Zachary Miller Wesley Jones Wei Hu Department of Computer Science Houghton College

The capacity of zoonotic influenza to cross species boundaries to infect humans poses a global health threat. A previous study identified sites in 10 influenza proteins that characterize the host shifts from avian to human influenza. Here, we used seven feature selection algorithms based on machine learning techniques to generate a novel and extensive selection of diverse sites from the nine internal proteins of influenza based on statistically importance to differentiating avian from human viruses. A set of 131 sites was generated by processing each protein independently, and a selection of 113 sites was found by analyzing a concatenation of sequences from all nine proteins. These new sites were analyzed according to their annual mutational trends. The correlation of each site with all other sites (one-to-many) and the connectivity within groups of specific sites (one-to-one) were identified. We compared the performance of these new sites evaluated by four classifiers against those recorded in previous research, and found our sites to be better suited to host distinction in all but one protein, validating the significance of our site selection. Our findings indicated that, in our selection of sites, human influenza tended to mutate more than avian influenza. Despite this, the correlation and connectivity between the avian sites was stronger than that of the human sites, and the percentage of sites with high connectivity was also greater in avian influenza.

关键词： Connectivity Correlation Feature Selection Host Specificity Influenza Machine Learning Mutation

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