26
|
Owens MJ, Horbury TS, Wicks RT, McGregor SL, Savani NP, Xiong M. Ensemble downscaling in coupled solar wind-magnetosphere modeling for space weather forecasting. SPACE WEATHER : THE INTERNATIONAL JOURNAL OF RESEARCH & APPLICATIONS 2014; 12:395-405. [PMID: 26213518 PMCID: PMC4508929 DOI: 10.1002/2014sw001064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/06/2014] [Indexed: 06/07/2023]
Abstract
UNLABELLED Advanced forecasting of space weather requires simulation of the whole Sun-to-Earth system, which necessitates driving magnetospheric models with the outputs from solar wind models. This presents a fundamental difficulty, as the magnetosphere is sensitive to both large-scale solar wind structures, which can be captured by solar wind models, and small-scale solar wind "noise," which is far below typical solar wind model resolution and results primarily from stochastic processes. Following similar approaches in terrestrial climate modeling, we propose statistical "downscaling" of solar wind model results prior to their use as input to a magnetospheric model. As magnetospheric response can be highly nonlinear, this is preferable to downscaling the results of magnetospheric modeling. To demonstrate the benefit of this approach, we first approximate solar wind model output by smoothing solar wind observations with an 8 h filter, then add small-scale structure back in through the addition of random noise with the observed spectral characteristics. Here we use a very simple parameterization of noise based upon the observed probability distribution functions of solar wind parameters, but more sophisticated methods will be developed in the future. An ensemble of results from the simple downscaling scheme are tested using a model-independent method and shown to add value to the magnetospheric forecast, both improving the best estimate and quantifying the uncertainty. We suggest a number of features desirable in an operational solar wind downscaling scheme. KEY POINTS Solar wind models must be downscaled in order to drive magnetospheric models Ensemble downscaling is more effective than deterministic downscaling The magnetosphere responds nonlinearly to small-scale solar wind fluctuations.
Collapse
|
27
|
Chen F, Zhou J, Xue Y, Yang S, Xiong M, Li Y, Liu Q. A single nucleotide polymorphism of the TNRC9 gene associated with breast cancer risk in Chinese Han women. GENETICS AND MOLECULAR RESEARCH 2014; 13:182-7. [DOI: 10.4238/2014.january.10.9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
28
|
Sun CC, Shen ZY, Xiong M, Ma FB, Li YY, Chen L, Liu RM. Trend of dissolved inorganic nitrogen at stations downstream from the Three-Gorges Dam of Yangtze River. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2013; 180:13-18. [PMID: 23727562 DOI: 10.1016/j.envpol.2013.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 04/27/2013] [Accepted: 05/01/2013] [Indexed: 06/02/2023]
Abstract
The TRAMO/SEATS program, combined with the Hodrick-Prescott (HP) filter, was used to detect trends and potential change points in time series of dissolved inorganic nitrogen (DIN) at three stations along the Yangtze River. The trend components were extracted, and two change points were successfully detected. The components revealed that DIN has been increasing at all the stations since the 1990s, although variations exist. Changes visible before 2002 illustrate the differences in agriculture development among regions upstream from the stations. The Three-Gorges Dam (TGD), which began to impound in 2003, led to years of different trends. The DIN concentration, which had been trending upward prior to that date, began a slightly downward trend because of NH4(+) depletion. Readings at the Yichang station revealed this trend most strongly; those at the Hankou station less so. The Datong station was far enough away from the TGD so that no obvious effects were seen.
Collapse
|
29
|
Yao J, Xiong M, Tang B, Chen G, Liang M, Ma X, Wang Z, Wu Z. Simvastatin attenuates pulmonary vascular remodelling by down-regulating matrix metalloproteinase-1 and -9 expression in a carotid artery-jugular vein shunt pulmonary hypertension model in rats. Eur J Cardiothorac Surg 2012; 42:e121-7. [DOI: 10.1093/ejcts/ezs445] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
30
|
Zhou SQ, Wen P, Fang L, Jiang L, Xiong M, Zhang FF, Yang JW. The association between RhEPO and FN expression in glomerular mesangial cells. Panminerva Med 2012; 54:205-209. [PMID: 22801437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
AIM Erythropoietin (rhEPO) is increasingly being used in the treatment of anemia caused by miscellaneous reasons. The aim of our research is to investigate the effects of recombinant human erythropoietin (rhEPO) on cellular growth and fibronectin (FN) expression in glomerular mesangial cells. METHODS Western blot was used to detect the expression of FN induced by rhEPO (1, 10, 100 and 1000U/mL). In vivo studies, male CD-1 mice were administered rhEPO subcutaneously at a single dose of 1000U/Kg. The cellular hypertrophy was quantified by counting cell number and calculating the ratio of cell protein to cell number. RESULTS 1) Compared with the control group, the results of mesangial cells' growth stimulated by rhEPO were not significantly different; 2) RhEPO lead to hypertrophy of mesangial cells; 3) rhEPO induced FN expression of mesangial cell in a dose-dependent way. Compared to control, 100U/mL rhEPO enhanced the expression of FN significantly; 4) indirect immunofluorescence showed that rhEPO induced large amount deposition of FN in the intercellular space of mesangial cells; 5) in vivo studies, there were markedly increase of FN expression in mice received the injection of rhEPO. CONCLUSION RhEPO could up-regulated the expression of FN and induced glomerular mesangial cells hypertrophy. These results suggested rhEPO could induce dysfunction of renal glomerulus through its influence on the function of mesangial cells.
Collapse
|
31
|
Fan R, Zhong M, Wang S, Zhang Y, Andrew A, Karagas M, Chen H, Amos CI, Xiong M, Moore JH. Entropy-based information gain approaches to detect and to characterize gene-gene and gene-environment interactions/correlations of complex diseases. Genet Epidemiol 2011; 35:706-21. [PMID: 22009792 PMCID: PMC3384547 DOI: 10.1002/gepi.20621] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
For complex diseases, the relationship between genotypes, environment factors, and phenotype is usually complex and nonlinear. Our understanding of the genetic architecture of diseases has considerably increased over the last years. However, both conceptually and methodologically, detecting gene-gene and gene-environment interactions remains a challenge, despite the existence of a number of efficient methods. One method that offers great promises but has not yet been widely applied to genomic data is the entropy-based approach of information theory. In this article, we first develop entropy-based test statistics to identify two-way and higher order gene-gene and gene-environment interactions. We then apply these methods to a bladder cancer data set and thereby test their power and identify strengths and weaknesses. For two-way interactions, we propose an information gain (IG) approach based on mutual information. For three-ways and higher order interactions, an interaction IG approach is used. In both cases, we develop one-dimensional test statistics to analyze sparse data. Compared to the naive chi-square test, the test statistics we develop have similar or higher power and is robust. Applying it to the bladder cancer data set allowed to investigate the complex interactions between DNA repair gene single nucleotide polymorphisms, smoking status, and bladder cancer susceptibility. Although not yet widely applied, entropy-based approaches appear as a useful tool for detecting gene-gene and gene-environment interactions. The test statistics we develop add to a growing body methodologies that will gradually shed light on the complex architecture of common diseases.
Collapse
|
32
|
McCabe K, Shobeiri N, Beseau D, Adams M, Holden R, Shobeiri N, Adams M, Holden R, Maio T, McCabe K, Laverty K, Beseau D, Pang J, Jozefacki A, Shobeiri N, Holden R, Adams M, Salem S, Jankowski V, Passlick-Deetjen J, Peter M, Zidek W, Jankowski J, Riser B, Barreto F, Valaitis P, Cook C, White J, Drueke T, Holmes C, Massy Z, Mizobuchi M, Ogata H, Kumata C, Nakazawa A, Koiwa F, Kinugasa E, Akizawa T, Lopez I, Aguilera-Tejero E, Guerrero F, Pineda C, Raya AI, Peralta A, Rodriguez M, Ciceri P, Volpi E, Brenna I, Brancaccio D, Cozzolino M, Bozic M, deRoij J, Parisi E, Ruiz-Ortega M, Fernandez E, Valdivielso JM, Lee CT, Ng HY, Tsai YC, Yang YK, Niwa T, Adijiang A, Shimizu H, Nishijima F, Okamoto T, Kamata K, Naito S, Aoyama T, Tazaki H, Yamanaka N, Koenigshausen E, Ohlsson S, Woznowski M, Quack I, Potthoff SA, Rump LC, Sellin L, Maquigussa E, Pereira L, Arnoni C, Boim M, Lee KW, Jeong JY, Jang WI, Chung S, Choi DE, Na KR, Shin YT, Slabiak-Blaz N, Adamczak M, Ritz E, Wiecek A, Uz E, Uz B, Sahin Balcik O, Kaya A, Akdeniz D, Bavbek Ruzgaresen N, Uz E, Turgut FH, Bayrak R, Carlioglu A, Akcay A, Galichon P, Vittoz N, Cornaire E, Baugey E, Vandermeersch S, Verpont MC, Mesnard L, Xu-Dubois YC, Hertig A, Rondeau E, Kokeny G, Fekeshazy O, Fang L, Rosivall L, Mozes MM, Duggan K, Hodge G, Ha H, Chen J, Lee L, Tay C, Macdonald G, Wang PHM, Tamouza H, Chemouny J, Monsinjon E, Tiwari M, Vende F, Vrtovsnik F, Camara NO, Benhamou M, Monteiro RC, Moura IC, Rigothier C, Saleem M, Ripoche J, Mathieson P, Combe C, Welsh G, Duwel A, Munoz-Felix JM, Lopez-Novoa JM, Martinez-Salgado C, Koutroutsos K, Kassimatis T, Nomikos A, Giannopoulou I, Papadakis J, Nakopoulou L, Nakamichi T, Mori T, Sato T, Sato H, Ito S, Neudecker S, Heilmann M, Kramer P, Wolf I, Sticht C, Schock-Kusch D, Gubhaju L, Kriz W, Bertram JF, Schad LR, Gretz N, Munoz-Felix JM, Fuentes-Calvo I, Lopez-Novoa JM, Martinez-Salgado C, Kimura T, Takabatake Y, Takahashi A, Kaimori JY, Matsui I, Namba T, Kitamura H, Niimura F, Matsusaka T, Soga T, Rakugi H, Isaka Y, Shin SJ, Kim KS, Kim WK, Rampanelli E, Teske G, Leemans J, Florquin S, Small D, Bennett N, Roy S, Gobe G, Blazquez-Medela AM, Garcia-Sanchez O, Lopez-Hernandez FJ, Lopez-Novoa JM, Martinez-Salgado C, Deibel A, Cheng J, Warner G, Knudsen B, Gray C, Lien K, Juskewitch J, Grande J, Wang N, Wang X, Zeng M, Sun B, Xing C, Zhao X, Xiong M, Yang J, Cao K, Priante G, Musacchio E, Sartori L, Valvason C, Baggio B, Pitlovanciv EDON, Reis LA, Pessoa EA, Teixeira L, Borges FT, Simoes MJ, Schor N, Munoz-Felix JM, Duwel A, Lopez-Novoa JM, Martinez-Salgado C, Doustar Y, Mohajeri D, Smirnov AV, Kucher AG, Ivanova GT, Berseneva ON, Parastaeva MM, Zarajsky MI, Saburova IJ, Kaukov IG, Koppe L, Fouque D, Dugenet Y, Soulage C, Wan J, Yang X, Cui J, Zou Z. Experimental pathology. Clin Kidney J 2011. [DOI: 10.1093/ndtplus/4.s2.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
33
|
Xiong M, Li S, Peng X, Feng Y, Yu G, Xin Q, Gong Y. Adipogenesis in ducks interfered by small interfering ribonucleic acids of peroxisome proliferator-activated receptor gamma gene. Poult Sci 2010; 89:88-95. [PMID: 20008806 PMCID: PMC7107157 DOI: 10.3382/ps.2009-00289] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Peroxisome proliferator-activated receptor γ (PPARγ) participates in adipocyte differentiation and maintenance, including the promotion of lipid storage in mammals. In the present study, 3 duck PPARγ small interfering RNA (siRNA) expression plasmids were constructed to investigate the effect of downregulating the expression of PPARγ on adipogenesis and fat accumulation in ducks. The results indicate that the 3 siRNA specific for conserved regions of PPARγ can effectively inhibit expression of PPARγ. It was demonstrated that the expression of lipoprotein lipase and adipocyte fatty acid-binding protein in duck adipose tissue is repressed when the expression of PPARγ is downregulated by siRNA. At the same time, the weight of abdominal fat at 21 and 35 d of age is decreased significantly (P < 0.05) compared with the control. However, the triglyceride levels in serum and muscle are not affected when the mRNA of PPARγ is repressed. The current study indicates that the suppression of PPARγ reduces abdominal fat deposition and regulates adipogenesis in ducks.
Collapse
|
34
|
Chu X, Dong C, Lei R, Sun L, Wang Z, Dong Y, Shen M, Wang Y, Wang B, Zhang K, Yang L, Li Y, Yuan W, Wang Y, Song H, Jin L, Xiong M, Huang W. Polymorphisms in the interleukin 3 gene show strong association with susceptibility to Graves' disease in Chinese population. Genes Immun 2009; 10:260-6. [PMID: 19262575 DOI: 10.1038/gene.2009.3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Graves' disease (GD) is a common organ-specific autoimmune disorder, which is multifactorial and develops in genetically susceptible individuals. We had earlier mapped a susceptibility locus for GD to chromosome 5q31-33 in a linkage study. Here we used tag single-nucleotide polymorphisms (SNPs) to search for genetic variants associated with GD, and examined 19 functional candidate genes in this chromosomal region. We identified 192 polymorphisms by re-sequencing the candidate genes, and selected 51 tagSNPs to genotype in a case-control collection of 1118 south Han Chinese subjects (428 cases and 690 controls). Initial analysis suggested that a non-synonymous SNP rs40401 (P27S) of interleukin 3 (IL3) was associated with GD, and further fine-mapping showed that rs40401, or its perfect proxy SNP rs31480 in the 5' flanking region of IL3, fully accounted for the association signal at this locus. We replicated significant association of rs40401 with GD in an independent sample collection of 839 north Han Chinese subjects. A combined analysis revealed strong validation of this association (odds ratio (OR(common))=1.63, combined P (P(comb))=4 x 10(-6) in the Recessive disease model). This study provides convincing evidence that the IL3 gene is a susceptibility locus for GD in the Chinese population.
Collapse
|
35
|
Xiong M. Editorial: Selected papers from the First International Conference on Computational Systems Biology (ICCSB). IET Syst Biol 2007. [DOI: 10.1049/iet-syb:20079025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
36
|
Jiao Z, Qu Z, Ge X, Ao Q, Xiong M. Protective role of tretinoin and N-acetyl-L-cysteine from antiproliferative action of cigarette smoke extract on alveolar epithelial cells. DIE PHARMAZIE 2007; 62:539-43. [PMID: 17718197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
To investigate the mechanisms by which tretinoin and N-acetyl-L-cysteine (NAC) reverse the growth inhibition of alveolar epithelial cells induced by cigarette smoke extract (CSE), MTT assay was used to evaluate cell viability. It was observed that both tretinoin and NAC could restore the viability of CSE-inhibited A549 cells. By incubation with fluorescent indicator H2DCFDA, it was documented that CSE-stimulated accumulation of intracellular reactive oxygen species (ROS) was obviously decreased by tretinoin or NAC. Furthermore, using semi-quantitative and real-time quantitative RT-PCR as well as western blot methods, high expression of insulin-like growth factor binding protein-2 (IGFBP-2) in A549 cells treated with CSE was found at both transcriptional and protein levels, and concomitant with the restoration of cell growth after treatment with tretinoin or NAC, down regulation of IGFBP-2 was observed. From the present study, it is concluded that both RA and NAC can antagonize CSE-induced growth arrest of alveolar epithelial cells and that down regulation of IGFBP-2 may play an important role in the process.
Collapse
|
37
|
Yuan Y, Che D, Xiong M. Effects of DDPH on HECCM-induced proliferation and immunophenotypes of the pulmonary vascular pericytes. JOURNAL OF TONGJI MEDICAL UNIVERSITY = TONG JI YI KE DA XUE XUE BAO 2004; 21:184-7. [PMID: 12539571 DOI: 10.1007/bf02886424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In order to study the effects of 1-(2, 6-dimethylphenoxy)-2-(3, 4-dimethoxyphenylethylamino) propane hydrochloride (DDPH) on proliferation and immunophenotypes of newborn rat pulmonary vascular pericytes induced by hypoxic endothelial cell conditioned medium (HECCM) from porcine pulmonary arteries, the cultured pericytes were divided into 4 groups according to the endothelial cell conditioned medium (ECCM) used: normoxic ECCM (NECCM) group, NECCM + DDPH group, HECCM group and HECCM + DDPH group. Cell culture, immunocytochemical staining, image analysis and flow cytometric method were used to investigate the effects of HECCM and DDPH on the expression of alpha-smooth muscle actin (alpha-SM-Actin) antigen, CD34 antigen, S-100 antigen and proliferating cell nuclear antigen (PCNA) and cell cycle in pericytes. The results showed that the alpha-SM-Actin antigen in the pericytes in HECCM group was stronger positively expressed than in the other three groups, but CD34 antigen and S-100 antigen were negatively expressed. The expression of alpha-SM-Actin antigen, CD34 antigen and S-100 antigen was positive in the groups of NECCM, NECCM + DDPH and HECCM + DDPH; The expression of alpha-SM-Actin and PCNA in HECCM group was 1.32 times (P < 0.01) and 1.24 times (P < 0.05) that in NECCM group, 1.30 times (P < 0.01) and 1.21 times (P < 0.05) that in HECCM + DDPH group, respectively. The percentage of the cells in the GO-G1 phase in the HECCM group was lower by 11.7% and 9.1%, in S phase higher by 5.6% and 4.2%, in G2-M phase higher by 6.1% and 4.9% than in the groups of NECCM, HECCM + DDPH, respectively. The inhibitory rate of DDPH on the increased alpha-SM-Actin and PCNA syntheses in pericytes induced by HECCM were 23.4% and 17.1% respectively. The inhibitory rate on the increased pericytes from GO-G1 phase to S phase was 8.3%. These results suggest that DDPH can directly inhibit pericytes from proliferation and immunophenotypical transformation of smooth muscle-like cells induced by HECCM.
Collapse
|
38
|
Zhang Y, Xiong M, Che D, Yuan Y. Establishment of the culture technique of pulmonary vascular pericytes and its identification in rats. JOURNAL OF TONGJI MEDICAL UNIVERSITY = TONG JI YI KE DA XUE XUE BAO 2003; 19:23-6. [PMID: 12840869 DOI: 10.1007/bf02895588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In order to study the cellular origin of muscularization in non-muscular arterioles of the lung, the pulmonary vascular pericytes-culture was established. The terminal lung tissue of the rat was taken out and minced. Then 0.5% of type IV collagenase solution was added for digestion and the microvascular segments were obtained by screening. The targeted cells were cultured by "selective conditioned media". Under phase-contrast microscope, the cultured cells were large in size with ragged margin and numerous pseudopodia, which imparted tubule-like structure. There was no contact inhibition in growing cells, so multiple layers developed. When they were confluent, there were morphologically no "hillock and dale" growth pattern as in smooth muscle cells or "weave-like" pattern as in fibroblasts. The ultrastructure of cultured cells showed numerous digital processes, moderate amount of rough and smooth endoplasmic reticulum, rich Golgi's apparatus, microfilaments, few lysosomes without myofilaments and dense bodies. Immunohistochemical staining revealed that the cultured pericytes had same kind of cellular skeletal protein, alpha-SM-actin, like smooth muscle cells. The cultured cells also exhibited positive reaction to CD34 antigen and S-100 antigen, which were negative in smooth muscle cells and fibroblasts. The cell growth pattern, ultrastructure and immunological phenotype suggested that the cultured cells had characteristics of vascular pericytes. Pericytes are one of the components of microvascular cells, and the establishment of in vitro culture technique of pericytes is of significance for further exploration of the muscularization of non-muscular arterioles in lung and the mechanism of structural remodeling of pulmonary vessels.
Collapse
|
39
|
Fan R, Floros J, Xiong M. Models and tests of linkage and association studies of quantitative trait locus for multi-allele marker Loci. Hum Hered 2003; 53:130-45. [PMID: 12145549 DOI: 10.1159/000064975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In this paper, we explore models and tests for association and linkage studies of a quantitative trait locus (QTL) linked to a multi-allele marker locus. Based on the difference between an offspring's conditional trait means of receiving and not receiving an allele from a parent at marker locus, we propose three statistics T(m), T(m,row) and T(m,col) to test association or linkage disequilibrium between the marker locus and the QTL. These tests are composite tests, and use the offspring marginal sample means including offspring data of both homozygous and heterozygous parents. For the linkage study, we calculate the offspring's conditional trait mean given the allele transmission status of a heterozygous parent at the marker locus. Based on the difference between the conditional means of a transmitted and a nontransmitted allele from a heterozygous parent, we propose statistics T(parsi), T(satur), T(gen) and T(m,het) to perform composite tests of linkage between the marker locus and the quantitative trait locus in the presence of association. These tests only use the offspring data that are related to the heterozygous parents at the marker locus. T(parsi) is a parsimonious or allele-wise statistic, T(satur) and T(gen )are satured or genotype-wise statistics, and T(m,het) compares the row and column sample means for offspring data of heterozygous parents. After comparing the powers and the sample sizes, we conclude that T(parsi) has higher power than those of the bi-allele tests, T(satur), T(gen), and T(m,het). If there is tight linkage between the marker and the trait locus, T(parsi) is powerful in detecting linkage between the marker and the trait locus in the presence of association. By investigating the goodness-of-fit of T(parsi), we find that T(satur) does not gain much power compared to that of T(parsi). Moreover, T(parsi) takes into account the pattern of the data that is consistent with linkage and linkage disequilibrium. As the number of alleles at the marker locus increases, T(parsi) is very conservative, and can be useful even for sparse data. To illustrate the usefulness and the power of the methods proposed in this paper, we analyze the chromosome 6 data of the Oxford asthma data, Genetic Analysis Workshop 12.
Collapse
|
40
|
Xiong M, Fan R, Jin L. Linkage disequilibrium mapping of quantitative trait loci under truncation selection. Hum Hered 2003; 53:158-72. [PMID: 12145552 DOI: 10.1159/000064978] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
As a dense map of single nucleotide polymorphism (SNP) markers are available, population-based linkage disequilibrium (LD) mapping or association study is becoming one of the major tools for identifying quantitative trait loci (QTL) and for fine gene mapping. However, in many cases, LD between the marker and trait locus is not very strong. Approaches that maximize the potential of detecting LD will be essential for the success of LD mapping of QTL. In this paper, we propose two strategies for increasing the probability of detecting LD: (1) phenotypic selection and (2) haplotype LD mapping. To provide the foundations for LD mapping of QTL under selection, we develop analytic tools for assessing the impact of phenotypic selection on allele and haplotype frequencies, and LD under three trait models: single trait locus, two unlinked trait loci, and two linked trait loci with or without epistasis. In addition to a traditional chi(2) test, which compares the difference in allele or haplotype frequencies in the selected sample and population sample, we present multiple regression methods for LD mapping of QTL, and investigate which methods are effective in employing phenotypic selection for QTL mapping. We also develop a statistical framework for investigating and comparing the power of the single marker and multilocus haplotype test for LD mapping of QTL. Finally, the proposed methods are applied to mapping QTL influencing variation in systolic blood pressure in an isolated Chinese population.
Collapse
|
41
|
Rastsvetaeva RK, Khomyakov AP, Rozenberg KA, Ma Z, Xiong M, Shi N. Doklady Chemistry 2003; 388:9-13. [DOI: 10.1023/a:1022136432069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
42
|
Gu J, Märker-Hermann E, Baeten D, Tsai WC, Gladman D, Xiong M, Deister H, Kuipers JG, Huang F, Song YW, Maksymowych W, Kalsi J, Bannai M, Seta N, Rihl M, Crofford LJ, Veys E, De Keyser F, Yu DTY. A 588-gene microarray analysis of the peripheral blood mononuclear cells of spondyloarthropathy patients. Rheumatology (Oxford) 2002; 41:759-66. [PMID: 12096225 DOI: 10.1093/rheumatology/41.7.759] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To identify genes which are more highly expressed in the peripheral blood mononuclear cells (PBMC) of patients with spondyloarthropathy (SpA), rheumatoid arthritis (RA) and psoriatic arthritis (PsA), in comparison to normal subjects. METHODS A 588-gene microarray was used as a screening tool to select a panel of such genes from PBMC of these subjects and of normal subjects. Results were then validated by reverse transcription-polymerase chain reaction (RT-PCR). RESULTS The following genes were more highly expressed in arthritis patients than in normal subjects: macrophage differentiation marker MNDA (myeloid nuclear differentiation antigen), MRP8 and MRP14 (migratory inhibitory factor-related proteins); signalling molecules JAK3 (janus kinase 3) and MAP kinase p38 (mitogen-activated protein kinase); receptors TNFR2/p75, C-C-chemokine receptor type 1 (CCR1), C-X-C-chemokine receptor type 4 (CXCR4) and integrin beta1; and the cytokines/chemokines interleukin (IL) 1beta and IL-8. Expression of CXCR4 was unexpectedly high among all arthritis subjects. Using RT-PCR, ELISA and immunohistology, expression of stromal cell-derived factor 1 (SDF-1) was demonstrated in arthritis joints. CONCLUSIONS The CXCR4/SDF-1 is a potential pro-inflammatory axis for RA, PsA and SpA.
Collapse
MESH Headings
- Adolescent
- Adult
- Aged
- Antigens, Differentiation/blood
- Antigens, Differentiation/genetics
- Arthritis, Psoriatic/blood
- Arthritis, Psoriatic/genetics
- Arthritis, Rheumatoid/blood
- Arthritis, Rheumatoid/genetics
- Chemokine CXCL12
- Chemokines, CXC/blood
- Chemokines, CXC/genetics
- DNA/analysis
- Female
- Genetic Markers
- Humans
- Leukocytes, Mononuclear/metabolism
- Male
- Middle Aged
- Oligonucleotide Array Sequence Analysis
- Receptors, CXCR4/blood
- Receptors, CXCR4/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Spondylitis, Ankylosing/blood
- Spondylitis, Ankylosing/genetics
- Spondylitis, Ankylosing/pathology
- Synovial Membrane/metabolism
- Synovial Membrane/pathology
Collapse
|
43
|
Zhao J, Li W, Xiong M. Population based linkage disequilibrium mapping of QTL: an application to simulated data in an isolated population. Genet Epidemiol 2002; 21 Suppl 1:S655-9. [PMID: 11793756 DOI: 10.1002/gepi.2001.21.s1.s655] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Despite successes in mapping and cloning genes involved in rare Mendelian diseases, genetic dissection of quantitative traits into single Mendelian factors still remains a challenging task. As the dense map of single nucleotide polymorphism (SNP) markers becomes available in the near future, linkage disequilibrium (LD) mapping will become one of major tools for mapping and identifying quantitative trait loci (QTL). In this report, we present a population-based linkage disequilibrium mapping of QTL. This method unifies the analysis of mapping QTL in humans and in model organisms and can be used for randomly sampled individuals. The proposed method is applied to search for polymorphism sites within the candidate genes 2 and 6, which influence quantitative traits Q1 and Q2 or Q5, in a simulated data set in an isolated population.
Collapse
|
44
|
Zhou X, Tan FK, Xiong M, Milewicz DM, Feghali CA, Fritzler MJ, Reveille JD, Arnett FC. Systemic sclerosis (scleroderma): specific autoantigen genes are selectively overexpressed in scleroderma fibroblasts. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 167:7126-33. [PMID: 11739535 DOI: 10.4049/jimmunol.167.12.7126] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The pathogenesis of systemic sclerosis (SSc) involves complex interactions between activated fibroblasts eventually leading to fibrosis, and impaired immune tolerance characterized by a variety of circulating SSc-specific autoantibodies. The expression of autoantigens in fibroblasts, a key target tissue in SSc, may play an important role in this process. To obtain a global view of this process, we examined gene expression profiles of SSc dermal fibroblasts using cDNA microarrays. The results show that dermal fibroblasts from SSc patients obtained from either affected or unaffected skin displayed a characteristic pattern of increased SSc autoantigen gene expression compared with that from normal controls. In particular, fibrillarin (p = 0.028), centromeric protein B (p = 0.01), centromeric autoantigen P27 (p = 0.042), and RNA polymerase II (220 kDa; p = 0.02) were significantly overexpressed in SSc fibroblasts. Quantitative RT-PCR confirmed overexpression of these autoantigens and also revealed increased levels of DNA topoisomerase I transcripts in SSc fibroblasts compared with normal control fibroblasts (p = 0.0318). The polymyositis/scleroderma autoantigen gene was overexpressed in some SSc patients (p = 0.09). To examine the specificity of these overexpressed autoantigen genes for SSc and its tissue specificity for fibroblasts, cDNA microarrays of dermal fibroblasts from patients with eosinophilic fasciitis and scleromyxedema were studied as well as PBMC and muscle biopsies from SSc patients. None of these tissues showed significant alterations in gene expression of SSc-specific autoantigens. Therefore, SSc-associated autoantigen genes are selectively overexpressed in SSc dermal fibroblasts, a major tissue involved in disease pathogenesis.
Collapse
|
45
|
Abstract
Gene expression studies bridge the gap between DNA information and trait information by dissecting biochemical pathways into intermediate components between genotype and phenotype. These studies open new avenues for identifying complex disease genes and biomarkers for disease diagnosis and for assessing drug efficacy and toxicity. However, the majority of analytical methods applied to gene expression data are not efficient for biomarker identification and disease diagnosis. In this paper, we propose a general framework to incorporate feature (gene) selection into pattern recognition in the process to identify biomarkers. Using this framework, we develop three feature wrappers that search through the space of feature subsets using the classification error as measure of goodness for a particular feature subset being "wrapped around": linear discriminant analysis, logistic regression, and support vector machines. To effectively carry out this computationally intensive search process, we employ sequential forward search and sequential forward floating search algorithms. To evaluate the performance of feature selection for biomarker identification we have applied the proposed methods to three data sets. The preliminary results demonstrate that very high classification accuracy can be attained by identified composite classifiers with several biomarkers.
Collapse
|
46
|
Wang D, Zhang W, Xiong M, Yu M, Xu J. CT virtual endoscopy of the auditory ossicular chain: clinical applications. Chin Med J (Engl) 2001; 114:1015-8. [PMID: 11677756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
OBJECTIVE To evaluate the clinical applications and limitations of CT virtual endoscopy (CTVE) in the auditory ossicular chain. METHODS CTVE of the auditory ossicular chain was performed with 1.0 mm collimation at pitch 1.0, bone algorithm, 9.6 cm field of view, and 0.1-0.2 mm reconstruction interval in 40 patients with middle ear diseases. 30 cases were confirmed by surgery. Results were compared with the findings of axial high resolution CT (HRCT) and multiplanar reformation (MPR) images and surgery. RESULTS The accuracy of CTVE images in detecting ossicular destruction was 92.6%, significantly higher than that of axial HRCT (83.9%) and multiplanar reformation (76.5%) images. CTVE could also clearly reveal the postoperative condition and congenital dysplasia of the auditory ossicular chain. CONCLUSIONS CTVE can clearly demonstrate a three-dimensional image of the auditory ossicular chain and is useful in evaluating diseases of the ear, especially the auditory ossicles. CTVE could not clearly demonstrate abnormal soft tissue within the tympanic cavity, abnormal changes of the tympanic membrane and tympanic walls, and could be easily influenced by artificial factors.
Collapse
|
47
|
Han A, Xiong M, Gu Y, Lin S, Xiong M. [Clinicopathologic features and prognosis of lymphoepithelioma-like carcinoma of the lung]. ZHONGHUA BING LI XUE ZA ZHI = CHINESE JOURNAL OF PATHOLOGY 2001; 30:328-31. [PMID: 11769726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
OBJECTIVE To analyze the clinicopathologic features and prognosis of lymphoepithelioma-like carcinoma (LELC) of the lung. METHODS 26 cases of pulmonary LELC with available long-term follow-up information were compared with 84 cases of pulmonary non-LELC(33 cases of squamous cell carcinoma, 36 cases of adenocarcinoma, 6 cases of adeno-squamous carcinoma and 9 cases of large cell carcinoma) with available long-term follow-up information using Kaplan-Meier method and the generalized Wilcoxon test. RESULTS LELC of the lung had a better prognosis than non-LELC (P < 0.05). Further study showed that pulmonary LELC had a significantly better prognosis than adeno-squamous carcinoma and large cell carcinoma. However, there was no significant prognostic differences between pulmonary LELC and squamous cell carcinoma and adenocarcinoma. Tumor recurrence and necrosis (> or = 5% of tumor) were associated with poor prognosis. CONCLUSION Pulmonary LELC, which is a very rare and unique entity, has a better prognosis after therapy.
Collapse
|
48
|
Han AJ, Xiong M. [Gene chip technology and its advances in medical science]. ZHONGGUO YI XUE KE XUE YUAN XUE BAO. ACTA ACADEMIAE MEDICINAE SINICAE 2001; 23:528-31. [PMID: 12905878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Gene (DNA) chip or DNA microarray is a new technique developed during human genomic research programs. When DNA chip containing thousands of DNA or oligonucleotide are hybridized to labeled samples, gene expression, DNA sequencing as well as DNA mutation and polymorphism can be analyzed with high efficiency in large scale. We are able to perform this technique on dozens of specimens at once in tumor differentiation, tumor typing, tumor diagnosis, tumorigenesis, and new tumor-associated genes discovery.
Collapse
|
49
|
Xiong M, Xu H, Che D. [Study on the rat airway epithelial cell injury induced by bacterial infection and its pathogenesis]. ZHONGHUA BING LI XUE ZA ZHI = CHINESE JOURNAL OF PATHOLOGY 2001; 30:353-6. [PMID: 11769732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
OBJECTIVE To explore the rat airway, especially small airway epithelium injury induced by Klebsiella pneumoniae infection and its pathogenesis. METHODS A rat airway inflammation and COPD model was induced by repeated intranasal infection with Klebsiella pneumoniae. The injury changes were dynamically observed under SEM, TEM and LM. Actin, TNF-alpha, Fos, Jun protein and their mRNA expression levels in small airway epithelium were analyzed by immunohistochemistry and in situ hybridization. The changes of lung TNF-alpha content were examined by radioimmunoassay. RESULTS 1 week after Klebsiella pneumoniae infection the epithelial cilia cohered, fell down, partially fell off and the tight intercellular connection destroyed. 2 and 4 weeks after the infection, the injury of bronchus epithelia worsened with pronounced chronic inflammation in all bronchi. The bronchioles walls became thickened, lumen narrowed and emphysema was noted. Compared with control group, TNF-alpha mRNA expression was higher (P < 0.01) in the 2nd and 4th week while TNF-alpha protein was higher at 4 weeks (P < 0.01). From 1st week after the infection, Fos protein and mRNA expression began to elevate (P < 0.01). TNF-alpha content of lung began to increase (P < 0.01) and kept at a higher level until the 8th week. CONCLUSIONS Repeated intranasal injection of a certain amount of Klebsiella pneumoniae can induce airway inflammation and emphysema. The main features of early airway epithelia injury are damage of cilia and intercellular junctions, the cause of which may be associated with changes in microfilament arrangement of epithelia. High expression of TNF-alpha protein in the airway epithelia and lung parallels with epithelium injury. Fos and Jun proteins may also play important roles in up-regulating the TNF-alpha protein.
Collapse
|
50
|
Han AJ, Xiong M, Rao HL, Zhang X. [Primary giant cell malignant fibrous histiocytoma of the lung]. ZHONGGUO YI XUE KE XUE YUAN XUE BAO. ACTA ACADEMIAE MEDICINAE SINICAE 2001; 23:406-7. [PMID: 12940089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
A case of primary giant cell malignant fibrous histiocytoma (MFH) of the lung was reported. Gross findings showed two well demarcated isolated nodules located in the right lower lobe of the lung appeared yellowish-gray and gray-red on gross section with areas of focal calcifications, hemorrhage and necrosis. Microscopic findings showed that the tumor consisted of diffuse neoplastic histiocytes and spindle-shaped fibroblasts arranged in a prominent storiform pattern intermingled with numerous multinucleated tumor giant cells and osteoclast-like multinucleated giant cells. Focal osteoid tissue was mainly located at the periphery of the tumor. In addition, a number of scattered apoptotic multinucleated giant cells were observed. Tumor cells were positive for vimentin, alpha-1-antitrypsin, lysozyme and mac387, but negative for cytokeratin, actin, S-100, NSE, and NF. Primary giant cell MFH of the lung is a very rare malignant tumor. This tumor should be treated by prompt radical surgery.
Collapse
|