[Design and realization of a microarray data analysis platform].

OBJECTIVE: To design a platform for microarray data analysis and processing in the browser/server mode running in Linux operating system. METHODS: Based on the Apache HTTP server, the platform, programmed with Perl language, integrated R language and Bioconductor packages for processing and analysis of the input data of oligonucleotide arrays and two-color spotted arrays. Users were allowed to submit data and parameter configurations to the platform via the web page, and the results of analysis were also returned via the web page. RESULTS: With an easy operation and high performance, the platform fulfilled the functions of processing, quality assessment, biological annotation and statistical analysis of the data from oligonucleotide arrays and two-color spotted arrays. Using the platform, we analyzed the gene expression profiles in Mtb-stimulated macrophages of three clinical phenotypes, namely latent TB (LTB), pulmonary (PTB) and meningeal (TBM), and obtained valuable clues for identifying tuberculosis susceptibility genes. We also analyzed the effect of INH treatment on Mycobacterium tuberculosis gene expression in various dormancy models, such as hypoxia and KatG mutant, and found that a set of genes responded to INH treatment during exponential growth but not in dormancy, and that the overall number of differentially regulated genes was reduced in the cells in low metabolic state. CONCLUSION: The platform we have constructed integrates comprehensive resources, and with a user-friendly interface, allows direct result visualization to facilitate microarray data analysis.

[Design and construction of the platform for comparative genomics].

OBJECTIVE: To design a versatile genome comparison and visualization platform based on browser/server mode supported by a local server. METHODS: The server of the platform was Apache HTTP server. Perl was used to integrate such genome alignment package and algorithms as MUMmer, LAGAN, and Mauve for different comparison purposes, and the users could submit data and parameters to the platform via the web page. The results of analysis were also returned via the web page. RESULTS: The platform could handle multiple data input formats, compare complete and draft genome sequence, alignment pair-wise or multi genome of more divergent species, identify regions of high similarity, locate local nucleotide mutations and large-scale recombination, and display the results by visualization interface. Analysis of the homology of 10 new strains of influenza A virus indicated that PB1 gene might evolve from human H3N2 viruses, PB2 and PA genes from avian H3N2 viruses, and HA and NS genes from swine H1N1 viruses. Alignment of Mycobacterium tuberculosis (H37Rv, CDC1551) and Mycobacterium bovis (AF2122/97) genomes revealed that sequence insertion/deletion and duplication were the major source of genomic differences. CONCLUSION: The platform integrate comprehensive resources with a user-friendly interface and intuitive result visualization to facilitate conventional study of comparative genomics.

[A novel respiratory detecting system based on bio-impedance].

This paper introduces the design and implementation of a novel respiratory detecting system based on bio-impedance method. By increasing electrodes in space, the system make multi-channel respiratory signals be superpositioned and filtered (SNR); Traditional filter methods by both hardware and software are also used to further increase anti-interference ability. A low consumption and portable instrument is designed based on MSP430 Micro Controller Unit (MCU), The experiment shows a better performance in the reduction of interference noises of heartbeat and blood flow especially the motion artifact. Also the system works stably.

[A study on the individual adaptability of electronic sphygmomanometer].

This paper analyzed the limitation of electronic sphygmomanometer based on oscillometry, and according to the characteristics of pulse signal, the author proposed a new method of the characteristic parameter detection based on wavelet transform, and improved its recognition ability on fixed-scale, via resampling rate according to the heartbeat. And the prototype test has been proved that this method is more adaptability for individuals and stability for operation.

Differential expression profiles of microRNAs in NIH3T3 cells in response to UVB irradiation.

MicroRNAs (miRNAs) are known as a kind of small, noncoding RNA, which play an important role in mediating many biological processes such as development, cell proliferation and differentiation in plants and animals. Here we report the differential expression profiles of miRNAs and characterized putative target genes in NIH3T3 cells at a series of different time points after UVB irradiation (compared with no UVB irradiation). The relative expression of mature miRNA genes was determined by miRNA microarray technique and the results were confirmed by real-time reverse transcriptase polymerase chain reaction (qRT-PCR). Potential target genes of these miRNAs were classified into different function categories with the GOstat software (http://gostat.wehi.edu.au/cgi-bin/goStat.pl). Several miRNAs in this study expressed highly at different time points, especially mmu-miR-365 and mmu-miR-21. Three miRNAs were lowly expressed, of which mmu-miR-465 showed low levels of expression at all time points, whereas after 50 J m(-2) UVB irradiation mmu-miR-296 and mmu-miR-376c showed low levels of expression at 6 and 12 h, respectively. Our study provided a basis for the global characterization of UV-regulated miRNA expression.

Evidence of gene conversion in the evolutionary process of the codon 41/42 (-CTTT) mutation causing beta-thalassemia in southern China.

The 4-bp deletion (-CTTT) at codon 41/42 (CD41/42) of the human beta-globin gene represents one of the most common beta-thalassemia mutations in East Asia and Southeast Asia, which is historically afflicted with endemic malaria, thus hypothetically evolving under natural selection by malaria infection. To understand the evolutionary process of generating the beta(CD41/42) allele and its maintenance, including the effect of natural selection on the pattern of linkage disequilibrium (LD), we sequenced a 15.933-kb region spanning 20.693 kb of the beta-globin cluster surrounding the 4-bp deletion using a sample from a Chinese population consisting of 24 normal individuals and 16 heterozygotes for the deletion. Forty-nine polymorphic sites were found. Analysis of the data, using a variety of methods including formal population genetics analysis and visual approaches, suggests that the spread of the CD41/42 (-CTTT) deletion is most likely mediated by interallelic gene conversion, although independent deletions in different lineages are also possible. The neutrality test resulted in a significant positive Tajima's D for the beta-globin locus, which is consistent with the existence of balancing selection. This suggests that the 4-bp deletion that occurred at this locus may be an event that is subject to natural selection, due to malaria, which leads to the heterozygote advantage, spread widely with further help by conversion and migration. The evolutionary process of this mutant through gene conversion that could conceivably take place between the 4-bp deletion and the normal sequence in the respective region is discussed in detail.

[A novel model of the medical instrumentation--an overview of wearable sensors and systems].

The traditional medical instrumentation is now not suited for the transformation of the present healthcare model. It's an attempt to make a breakthrough on traditions to develop wearable sensors/systems. Five articles about wearable technology are selected by this special topic. And our aim is to inspire the designers of medical devices to grasp the chance and to take a vigorous action on innovatory developments, so as to satisfy the huge requirements of the healthcare market, and to open a new era of the medical device industry.

[The design of a wearable ECG and respiration sensor vest and its monitoring system].

This article describes the design of a sensor vest and its corresponding measuring and transfering system which can be used for ECG and respiration monitoring in mobile and noninvasive conditions. The electric conduction textile is sutured in the inside of the vest in its specific position to be detecting electrodes, which are connected to the vest edge. The signal is then connected to the measuring and transferring system. in which the microcontroller and circuits monitor the ECG, heart rate and respiration data. The data are transmitted through the serial communication to a PC, and then are received and displayed with Visual Basic program.

Mathematical model of phosphatidylinositol-4,5-bisphosphate hydrolysis mediated by epidermal growth factor receptor generating diacylglycerol.

Phosphatidylinositol-4,5-bisphosphate (PIP2) is hydrolyzed in response to the tyrosine phosphorylation of the epidermal growth factor receptor (EGFR) and plays an important role in regulating cell proliferation and differentiation through the generation of second messengers diacylglycerol (DAG) and trisphosphate inositol (IP3) which lead to the activation of protein kinase C (PKC) and increased levels of intracellular calcium, respectively. In the paper, a mathematical model was established to simulate the accumulation of DAG due to PIP2 hydrolysis mediated by EGFR. Molecular mechanisms between DAG, PIP2, EGFR and phosphatidylinositol transfer protein (PITP) were explained successfully, and positive cooperativity which existed between phospholipase C-gamma1 (PLC-gamma1) and PIP2 was also explained. In the model the effects of parameters on simulation of PIP2 hydrolysis were analyzed and the efficacies of some molecular intervention strategies were predicted. To test the coherence between the model and the biological response to epidermal growth factor (EGF) in cells, the levels of DAG and the tyrosine phosphorylation-EGFRs in NIH3T3 mouse embryonic fibroblast (MEF) were determined by biochemical experiments which showed that the accumulation of DAG was a sigmoidal function of phosphorylation-EGFR concentration, and the consistency between the mathematical model and experimental results was confirmed. In brief, this mathematical model provided a new idea for the further study of the dynamic change of biological characteristics in inositol phospholipid hydrolysis, predicting the efficacy of molecular intervention and the relationship between the metabolisms of inositol phospholipid and other signal transduction pathways.

[Analysis and realization of the method for predicting physical pathways of allosteric communication in a protein family].

A fundamental goal in signal transduction study is to understand allosteric communication. The authors present hereby a statistical coupling analysis method (developed by Steve W. Lockless etc.) for quantitative mapping of the global network of amino acid positions in a protein and predicting a set of energetically coupled positions, which may constitute the physical pathways of allosteric communication in a protein family. Based on MATLAB, the authors realized this method and created histograms of amino acid distributions for all 63 395 entries (as of April 2004) in the Swiss-Prot database of eukaryotic proteins and calculated the mean values. The result was similar to that calculated by Steve W. Lockless in October 1998.

[Value of galvanic skin response in assessment of diabetic autonomic neuropathy].

OBJECTIVE: To explore a method for early detection of diabetic autonomic neuropathy (DAN) on the basis of analysis of galvanic skin response (GSR). METHODS: In 25 randomly selected diabetic inpatients (14 with clinical DAN symptoms), GSR signals were collected from the fingers of both hands based on Virtual Instrumental WorkBench-LabVIEW and compared with those acquired from normal subjects. RESULTS: The GSR indices of patients either with or without DAN were different from those of normal subjects, and even in the same patients, the changes of these indices after clinical treatment were also obvious. CONCLUSION: GSR detection and analysis can help understand the impairment of the autonomic system and facilitate DAN assessment.

[Mathematical model of epidermal growth factor receptor-mediated lipid phosphatidylinositol(4,5)-bisphosphate hydrolyzation by phospholipase C-gamma1 activity].

OBJECTIVE: To investigate the dynamic characteristics of lipid phosphatidylinositol (4,5)-bisphosphate (PIP(2)) in plasma membrane hydrolyzed by phospholipase C-gamma1 in epidermal growth factor receptor(EGFR)-mediated signal pathway. METHODS: A mathematical model based on the law of mass action was established with differential equations to simulate metabolizable pathway of PIP(2). RESULTS: Differential equations of the key product concentration during hydrolysis of PIP(2) were formulated, and the effects of the parameters on these hydrolyzed products analyzed. CONCLUSION: This mathematical model provides foundation for further investigation of the dynamic changes of biological characteristics and the relations between the key product concentrations in PIP2 hydrolysis.

[A new approach for exploring the essence of meridian].

The paper includes a brief review and evaluation of the progress in the research of the essence of meridian in China in the last two decades, in which the author suggests that more effort at all levels involving multiple disciplines needs to be investigated in the pursuit of this issue after the failure of prolonged research in the fields of histological anatomy. Microcosmic investigation, in particular, should be pursued making full use of the available achievement in molecular cell biology, genome research, biophysics and biochemistry and so forth, so as to build a solid plateform for making a breakthrough. The author urges the importance of research in the information carrier that regulates the meridian physiological network of the body. Based on the theories in cellular signal transduction and relevant experimental data, the author points out that the signal amplitude and frequency of intracellular Ca(2+) oscillations and intercellular Ca(2) wave elicited by specific acupuncture may contain information of the meridian routes and physiological function regulations. Through its binding proteins, Ca(2+) participates in almost all the physiological processes such as reproduction, metabolism, muscle contraction to cognition and memory. It is therefore hypothetically believed that Ca(2+) and inositol trisphosphate (IP(3), which is required for the propagation of intercellular Ca(2+) waves) can be the long-quested information carriers of the meridian physiological network, and they in conjunction with the gap-junction protein (connexon) build the material bases of the meridian. The author also specifies some possible directions of further study and experimental methods.

[Nonlinear dynamic analysis of heart rate variability in patients with diabetic autonomic neuropathy].

OBJECTIVE: To explore earlier detection methods for diabetic autonomic neuropathy (DAN) by heart rate variability (HRV) analysis. METHODS: Thirty-four diabetic patients (including 22 with explicit clinical DAN symptoms) were randomly selected for this study from the in-patient department of endocrinology. On the basis of Virtual Instrumental WorkBench- LabVIEW and using several nonlinear dynamic analysis measures, including Allan factor, lyapunov exponent, approximate entropy, fractal dimension, complexity, wavelet-transform standard deviation and nonlinear energy operator, the analysis of the HRV in these diabetic patients was performed in comparison with normal subjects. RESULTS: The nonlinear indices of both DAN patients and patients without obvious DAN were significantly different from those of the normal subjects, especially in terms of Lyapunov exponent, approximate entropy, and nonlinear energy operator. CONCLUSION: Nonlinear dynamic methods of HRV analysis can provide assistance in assessing the status and impairment of the autonomic system, and can be used to efficiently detect diabetic neuropathy in early stages.

[A method for transfering physiological data through GSM wireless communication network].

This article describes a method for transfering physiological data through GSM wireless communication network. The data of heart rate and body temperature are collected by a microcontroller and transmitted through serial ports to the GSM data module, which then transmits the data to a remote terminal through GSM network. This method ensures cheap and stable long-distance data transfer within the coverage of the GSM network.

[Development of apparatus for remote personal vital status monitoring and positioning].

OBJECTIVE: To develop a wireless apparatus for remote physiological monitoring and positioning of the personnel which can be utilized in searching and implementing emergency care for the wounded in the battlefield. METHODS: The heart rate was obtained from electrocardiogram, and body temperature was measured by using a temperature crystal. Positioning of the personnel was realized with the assistance of global positioning system, and wireless transmission of physiological and position data accomplished by way of spread spectrum communication chip set. RESULTS: Data transmission by spread spectrum communication covered a distance as far as 1 kilometer, and the error was controlled below 100 m in positioning. In the span of 30 to 250 beats/min, the heart rate error was less than 1 beat/min, and the body temperature error less than 0.1 degrees celsius in the span of 25 to 45 degrees celsius. CONCLUSIONS: This wireless device meets the demands of spread spectrum transfer of physiological and position data at the distance of 1 kilometer.