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Hao H, Fujii K, Shibuya M, Imanaka T, Takagi Y, Kawakami R, Hirota S. The true character of lipid rich plaque by intravascular imaging: message from pathologist to cardiologist. Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht309.2676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Imanaka T, Hao H, Fujii K, Shibuya M, Fukunaga M, Miki K, Tamaru H, Masutani M, Ohyanagi M, Masuyama T. Analysis of atherosclerosis plaques by measuring attenuation coefficients in optical coherence tomography: thin-cap fibroatheroma or foam cells accumulation without necrotic core? Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht310.p5482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bian L, Zhao H, Hao H, Yin Q, Wu S, Gong J, Dong W. Novel Glutaric Acid Cocrystal Formation via Cogrinding and Solution Crystallization. Chem Eng Technol 2013. [DOI: 10.1002/ceat.201200720] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Duan H, Luo Y, Hao H, Feng L, Zhang Y, Lu D, Xing S, Feng J, Yang D, Song L, Yan X. Soluble CD146 in cerebrospinal fluid of active multiple sclerosis. Neuroscience 2013; 235:16-26. [DOI: 10.1016/j.neuroscience.2013.01.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 12/20/2012] [Accepted: 01/02/2013] [Indexed: 11/28/2022]
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Salman Z, Ofer O, Radovic M, Hao H, Ben Shalom M, Chow KH, Dagan Y, Hossain MD, Levy CDP, Macfarlane WA, Morris GM, Patthey L, Pearson MR, Saadaoui H, Schmitt T, Wang D, Kiefl RF. Nature of weak magnetism in SrTiO3/LaAlO3 multilayers. PHYSICAL REVIEW LETTERS 2012; 109:257207. [PMID: 23368496 DOI: 10.1103/physrevlett.109.257207] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 09/20/2012] [Indexed: 06/01/2023]
Abstract
We report the observation of weak magnetism in superlattices of LaAlO(3)/SrTiO(3) using β-detected nuclear magnetic resonance. The spin lattice relaxation rate of ^{8}Li in superlattices with a spacer layers of 8 and 6 unit cells of LaAlO(3) exhibits a strong peak near ~35 K, whereas no such peak is observed in a superlattice with spacer layer thickness of 3 unit cells. We attribute the observed temperature dependence to slowing down of weakly coupled electronic moments at the LaAlO(3)/SrTiO(3) interface. These results show that the magnetism at the interface depends strongly on the thickness of the spacer layer, and that a minimal thickness of ~4-6 unit cells is required for the appearance of magnetism. A simple model is used to determine that the observed relaxation is due to small fluctuating moments (~0.002μ(B)) in the two samples with a larger LaAlO(3) spacer thickness.
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Egger ME, Gomez-Gutierrez J, Hao H, Zhou H, McMasters KM. Viral-mediated gene therapy in combination with temozolomide in melanoma. J Am Coll Surg 2012. [DOI: 10.1016/j.jamcollsurg.2012.06.319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Huang Y, Chuang A, Hao H, Talbot C, Sen T, Trink B, Sidransky D, Ratovitski E. Phospho-ΔNp63α is a key regulator of the cisplatin-induced microRNAome in cancer cells. Cell Death Differ 2011; 18:1220-30. [PMID: 21274007 DOI: 10.1038/cdd.2010.188] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) cells exposed to cisplatin (CIS) displayed a dramatic ATM-dependent phosphorylation of ΔNp63α that leads to the transcriptional regulation of downstream mRNAs. Here, we report that phospho (p)-ΔNp63α transcriptionally deregulates miRNA expression after CIS treatment. Several p-ΔNp63α-dependent microRNA species (miRNAs) were deregulated in HNSCC cells upon CIS exposure, including miR-181a, miR-519a, and miR-374a (downregulated) and miR-630 (upregulated). Deregulation of miRNA expression led to subsequent modulation of mRNA expression of several targets (TP53-S46, HIPK2, ATM, CDKN1A and 1B, CASP3, PARP1 and 2, DDIT1 and 4, BCL2 and BCL2L2, TP73, YES1, and YAP1) that are involved in the apoptotic process. Our data support the notion that miRNAs are critical downstream targets of p-ΔNp63α and mediate key pathways implicated in the response of cancer cells to chemotherapeutic drugs.
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Zhong-Ran Z, Hai-Qin T, Jie-Hua L, Lin-Lin Y, Hao H. e0332 Tongxinluo capsule for coronary heart disease: a systematic review. BRITISH HEART JOURNAL 2010. [DOI: 10.1136/hrt.2010.208967.332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Hao H, Hai-Qin T, Jie-Hua L, Lin-Lin Y, Wen-Juan T, Zhong-Ran Z. e0331 Effects of Shen Song Yang xin capsule for treatment of cardiac arrhythmia: a systematic review. BRITISH HEART JOURNAL 2010. [DOI: 10.1136/hrt.2010.208967.331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Ekinci EI, Thomas G, MacIsaac RJ, Johnson C, Houlihan C, Panagiotopoulos S, Premaratne E, Hao H, Finch S, O'Callaghan C, Jerums G. Salt supplementation blunts the blood pressure response to telmisartan with or without hydrochlorothiazide in hypertensive patients with type 2 diabetes. Diabetologia 2010; 53:1295-303. [PMID: 20372874 DOI: 10.1007/s00125-010-1711-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2009] [Accepted: 01/27/2010] [Indexed: 12/21/2022]
Abstract
AIMS/HYPOTHESIS We assessed the effects of sodium chloride (NaCl) supplementation on the blood pressure response to treatment with telmisartan with or without hydrochlorothiazide in hypertensive patients with type 2 diabetes and habitually high (HDS, sodium excretion >200 mmol/24 h on two out of three consecutive occasions) or low (LDS, sodium excretion <100 mmol/24 h on two out of three consecutive occasions) salt intake. METHODS Patients received 4 weeks of telmisartan followed by 4 weeks of telmisartan plus hydrochlorothiazide. In a double-blind randomised fashion, patients received sodium chloride (NaCl, 100 mmol/24 h) or placebo capsules in addition to their habitual salt intake during the last 2 weeks of telmisartan and telmisartan plus hydrochlorothiazide therapy. The protocol was repeated with NaCl and placebo capsules administered in reverse order to allow each participant to act as his or her own control. At 0, 4, 8, 14, 18 and 22 weeks, 24 h ambulatory blood pressure (ABP) and 24 h urine collections were performed. RESULTS No statistically significant differences were seen in the ABP response in the LDS vs HDS groups to any of the interventions (p = 0.58). NaCl supplementation reduced the effect of telmisartan with or without hydrochlorothiazide on systolic BP by approximately 50% (-5.8 mmHg during NaCl supplementation vs -11.3 mmHg during placebo, mean difference 5.6 mmHg [95% CI 1.7-9.4 mmHg], p = 0.005), irrespective of habitual salt intake. By contrast, addition of hydrochlorothiazide increased the antihypertensive effect of telmisartan on systolic BP by approximately 35% (p = 0.048) in both groups of patients. CONCLUSIONS/INTERPRETATION NaCl supplementation blunts the effectiveness of telmisartan with or without hydrochlorothiazide in hypertensive patients with type 2 diabetes, independently of habitual low or high salt intake.
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Lin G, Chang S, Hao H, Tathireddy P, Orthner M, Magda J, Solzbacher F. Osmotic Swelling Pressure Response of Smart Hydrogels Suitable for Chronically-Implantable Glucose Sensors. SENSORS AND ACTUATORS. B, CHEMICAL 2010; 144:332. [PMID: 20161690 PMCID: PMC2821116 DOI: 10.1016/j.snb.2009.07.054] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In the last few years, a new type of glucose-sensitive hydrogel (GSH) has been developed that shrinks with increasing glucose concentration due to the formation of reversible crosslinks The first osmotic swelling pressure results measured for any member of this new class of GSH are reported, so that their suitability for use in sensors combining pressure transducers and smart gels can be evaluated. Comparison is also made with results obtained for an older type of GSH that expands with increasing glucose concentration due to an increase in the concentration of counterions within the gel. The newer type of GSH exhibits both faster kinetics and weaker fructose interference, and therefore is more suitable for in vivo glucose sensing.
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Yin BL, Hao H, Wang YY, Jiang YJ, Xue S. Downregulating osteopontin reduces angiotensin II-induced inflammatory activation in vascular smooth muscle cells. Inflamm Res 2009; 58:67-73. [DOI: 10.1007/s00011-009-8034-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Tu X, Miao L, Kang Y, Xia H, Tu JW, Wang Q, Tu Q, Wang JM, Hao H. Effects of dl-praeruptorin a on cultured neonatal rat ventricular cardiomyocytes with hypertrophy induced by endothelin-1. ACTA ACUST UNITED AC 2009; 31:231-6. [DOI: 10.1358/mf.2009.31.4.1371199] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Zhou X, Li L, Wang M, Zhang L, Zhang X, Zhong W, Hao H, Wang S, Lin P, Xu J. Circulating tumor cells (CTC) as a prognostic and predictive factor in Lung Cancer Patients–a pilot study in PUMCH. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.22201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Nakai N, Ishikawa T, Nishitani A, Liu NN, Shincho M, Hao H, Isozaki K, Kanda T, Nishida T, Fujimoto J, Hirota S. A mouse model of a human multiple GIST family with KIT-Asp820Tyr mutation generated by a knock-in strategy. J Pathol 2008; 214:302-11. [PMID: 18098338 DOI: 10.1002/path.2296] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Several families exhibiting multiple gastrointestinal stromal tumours (GISTs) and germline c-kit gene mutations at exons 8, 11, 13, or 17 have been reported. These patients also exhibit diffuse hyperplasia of the interstitial cells of Cajal (ICCs) as a pre-existing lesion of multiple GISTs. We generated a mouse model of a family with germline c-kit gene mutation at exon 17, and compared the phenotypes between the mice and humans. The mouse counterpart (KIT-Asp818Tyr) of the human KIT-Asp820Tyr mutation was transmitted into germline by a knock-in strategy. Mating of male and female heterozygotes (KIT-Asp818Tyr/+) resulted in the generation of homozygotes (KIT-Asp818Tyr/KIT-Asp818Tyr). Histological examination revealed that all heterozygotes had both a small KIT-positive mesenchymal tumour at the caecum, consistent with GIST, and KIT-positive diffuse spindle-shaped cell proliferation in the distal oesophagus, stomach, proximal duodenum, and colon consistent with ICC hyperplasia. All homozygotes exhibited a larger caecal tumour and more prominent spindle-shaped cell proliferation compared with the heterozygous mice, and they usually died within 10 weeks after birth, likely due to ileus. The small intestine of both genotypes showed no apparent morphological abnormality, and autonomous contraction of the ileal segments appeared normal. Western blotting demonstrated that the caecal tumours expressed phosphorylated KIT, MAPK, Stat1, and Stat5. These mutant mice are considered to be useful for further investigation of the mechanism of GIST development as a result of ICC hyperplasia and for assessment of the in vivo effects of drugs against molecular targets.
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Xu J, Liu X, Jiang Y, Chu L, Hao H, Liua Z, Verfaillie C, Zweier J, Gupta K, Liu Z. MAPK/ERK signalling mediates VEGF-induced bone marrow stem cell differentiation into endothelial cell. J Cell Mol Med 2008; 12:2395-406. [PMID: 18266967 PMCID: PMC4514117 DOI: 10.1111/j.1582-4934.2008.00266.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Multi-potent adult progenitor cells (MAPCs) differentiate into endothelial cells (ECs) in the presence of vascular endothelial growth factor (VEGF). The mechanism(s) of VEGF-induced differentiation of MAPCs to ECs are not yet known. We, therefore, examined the role of mitogen-activated protein kinase/extracellular signal-regulated kinase (p42/44-MAPK/ERK1/2) signalling in endothelial differentiation from bone marrow stem cells. We observed that VEGF stimulation of MAPCs for 14 days results in a significant expression of endothelial-specific gene and/or proteins including von Willebrand factor (vWF), vascular endothelial-cadherin (VE-cadherin), VEGF receptor-2 (VEGFR2), and CD31. Up-regulation of EC-specific markers was accompanied by a cobblestone morphology, expression of endothelial nitric oxide synthase (eNOS), and Dil-Ac-LDL uptake, typical for EC morphology and function. VEGF induced a sustained activation of p42 MAPK/ERK, but not that of p44 MAPK/ERK during the course of MAPCs differentiation in a time-dependent manner up to 14 days. VEGF-induced activation of p42 MAPK/ERK also led to the nuclear translocation of MAPK/ERK1/2. Incubation of MAPCs with MAPK/ERK1/2 phosphorylation inhibitor PD98059 blocked the sustained VEGF-induced MAPK/ERK1/2 phosphorylation as well as its nuclear translocation in the differentiating MAPCs. Inhibition of MAPK/ERK1/2 phosphorylation by PD98059 also blocked the expression of EC-specific genes in these cells and their differentiation to ECs. These data suggest that VEGF induces MAPC differentiation into EC via a. MAPK/ERK1/2 signalling pathway-mediated mechanism in vitro.
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Hao H, d'Alincourt-Salazar M, Kelley KMM, Shatnawi A, Mukherjee S, Shah YM, Ratnam M. Estrogen-induced and TAFII30-mediated gene repression by direct recruitment of the estrogen receptor and co-repressors to the core promoter and its reversal by tamoxifen. Oncogene 2007; 26:7872-84. [PMID: 17599049 DOI: 10.1038/sj.onc.1210592] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Estradiol (E2) acts through the estrogen receptor (ER) to downregulate many genes, and tamoxifen (Tam) largely reverses this repression but the underlying mechanisms are unclear. Repression of the folate receptor (FR)-alpha P4 core promoter by ER is enhanced by E2 and reversed by Tam. This effect was unaffected by inhibition of new protein synthesis and required the E/F and the DNA-binding domains of ER without direct binding of ER to DNA. The repression by E2/ER was not specific for either Sp1 or TATA elements but was loosely selective for the initiator and flanking sequence. Insertion of a response element or a relatively strong Sp1 cluster to recruit ER upstream of the core promoters caused a switch to activation by E2/ER that was inhibited by Tam. In nuclear extracts, association of ER with a biotinylated core promoter fragment was promoted by E2 but Tam blocked this effect. Repression/de-repression of the P4 promoter and endogenous FR-alpha expression by E2/Tam required SMRT and/or NCoR. ER associated with the chromosomal P4 promoter and SMRT and NCoR associated with it in an ER-dependent manner; these associations were favored by E2 but disrupted by Tam, in the short term, without changes in ER expression. TAFII30 was required for optimal P4 promoter activity and for the repressive association of ER. E2 may thus maintain a low transcriptional status of genes by favoring direct TAFII30-dependent association of ER with the core promoter in a co-repressor complex containing SMRT and/or NCoR; this repression is overridden in target genes containing an upstream element that strongly recruits ER. In addition to suppressing the activation of classical E2 target genes, Tam may upregulate genes by passively dissociating the ER co-repressor complex.
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Hao H, Iihara K, Ishibashi-Ueda H, Hirota S. PO14-368 RELATION BETWEEN PATHOLOGY OF CAROTID ARTERY PLAQUE AND PATIENT RISK FACTOR FOR ENDARTERECTOMY. ATHEROSCLEROSIS SUPP 2007. [DOI: 10.1016/s1567-5688(07)71378-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Hao H, Xin T, Nancai Y, Yanxia W, Qian L, Wei M, Yandong Y, Hanju H. Short-interfering RNA-mediated silencing of proliferating cell nuclear antigen inhibit proliferation and induce apoptosis in HeLa cells. Int J Gynecol Cancer 2007; 18:36-42. [PMID: 17466038 DOI: 10.1111/j.1525-1438.2007.00955.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is an important protein for DNA polymerase delta in the nucleus, and shown to have a fundamental role in cellular proliferation. It is overexpressed to support cell growth in cervical carcinoma. To study its role in stress response, we design and use short hairpin RNA (shRNA) to inhibit PCNA expression in HeLa cells and validate its effect on cell proliferation. In this study, three PCNA-shRNA expression vectors are constructed and introduced into HeLa cells, and the cell cycle is analyzed by flow cytometry. Apoptotic cell is detected by single cell gel electrophoresis assay (comet assay), and caspase cleavage is studied also. Expression of PCNA is assessed by real-time reverse transcription-polymerase chain reaction and Western blot analysis. Upon transient transfection with plasmid encoding shRNA, it is found that expression of PCNA decreased in shRNA-transfected cells, downregulation of PCNA inhibit cell growth and induce apoptosis in HeLa cells. PCNA downregulation also increase cell population in the G0-G1 phase. In conclusion, our findings demonstrate that shRNA can inhibit the DNA replication and induce apoptosis in HeLa cells effectively and, therefore, could be used as a new potential anticancer tool for therapy of human cervical carcinoma.
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Brisset A, Bacchetta M, Geinoz A, Chaponnier C, Hao H, Camenzind E, Gabbiani G, Bochaton-Piallat ML. S100A4: A marker for activated smooth muscle cells in atherosclerosis and restenosis. Vascul Pharmacol 2006. [DOI: 10.1016/j.vph.2006.08.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Qing L, Lv J, Li H, Tan Y, Hao H, Chen Z, Zhao J, Chen H. The recombinant nonstructural polyprotein NS1 of porcine parvovirus (PPV) as diagnostic antigen in ELISA to differentiate infected from vaccinated pigs. Vet Res Commun 2006; 30:175-90. [PMID: 16400603 DOI: 10.1007/s11259-006-3212-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2004] [Indexed: 11/28/2022]
Abstract
To differentiate pigs infected with porcine parvovirus (PPV) from those vaccinated with inactivated whole-virus vaccine, an enzyme-linked immunosorbent assay (ELISA) based on detection of a nonstructural polyprotein 1 (NS1) was developed. A threshold of 0.23 optical density units was established and the assay had high specificity (100), sensitivity (88), accuracy (90) and positive predictive value (100) using haemagglutination inhibition as the standard method. A reproducibility test revealed that the coefficients of variation of sera within-plates and between-run were less than 10%. The assay showed no cross-reactivity with antibodies to porcine reproductive respiratory syndrome virus, pseudorabies virus, foot and mouth disease virus, Actinobacillus pleuropneumoniae, Toxoplasma or Chlamydia. Sera obtained from pigs infected with PPV reacted with recombinant NS1 protein in the ELISA. Sera from pigs vaccinated with inactivated whole virus did not recognize this protein in the ELISA. In contrast, antibodies against PPV whole virus were present in both PPV-infected and vaccinated animals. Serum conversion against NS1 was first detected 10 days after infection and NS1-specific antibodies were detectable up to half a year post infection. In conclusion, the PPV-NS1 ELISA can differentiate PPV-infected versus inactivated PPV-vaccinated pigs and could be applied in disease diagnosis and surveillance.
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Hatakeyama K, Azuma Y, Hao H, Imamura T, Nishihira K, Shirai M, Ogawa H, Asada Y. Tu-P7:279 Lack of association between chlamydia pneumoniae infection and plaque instability or restenosis in coronary atherosclerotic lesions. ATHEROSCLEROSIS SUPP 2006. [DOI: 10.1016/s1567-5688(06)80982-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Robertson G, Bilenky M, Lin K, He A, Yuen W, Dagpinar M, Varhol R, Teague K, Griffith OL, Zhang X, Pan Y, Hassel M, Sleumer MC, Pan W, Pleasance ED, Chuang M, Hao H, Li YY, Robertson N, Fjell C, Li B, Montgomery SB, Astakhova T, Zhou J, Sander J, Siddiqui AS, Jones SJM. cisRED: a database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Res 2006; 34:D68-73. [PMID: 16381958 PMCID: PMC1347438 DOI: 10.1093/nar/gkj075] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2005] [Revised: 10/08/2005] [Accepted: 10/08/2005] [Indexed: 11/30/2022] Open
Abstract
We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (www.cisred.org). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools. Motifs are predicted in promoter regions using multiple discovery methods applied to sequence sets that include corresponding sequence regions from vertebrates. We estimate motif significance by applying discovery and post-processing methods to randomized sequence sets that are adaptively derived from target sequence sets, retain motifs with p-values below a threshold and identify groups of similar motifs and co-occurring motif patterns. The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally.
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Hao H, Gabbiani G, Camenzind E, Virmani R, Bochaton-Piallat ML. Smooth Muscle Cells of Fatal Coronary Artery Lesions Exhibit a Myofibroblastic Phenotype. Wound Repair Regen 2005. [DOI: 10.1111/j.1067-1927.2005.130117d.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Hao H, Yutani C, Kanmatsuse K, Gabbiani G, Bochaton-Piallat ML. 3P-0696 Heterogeneity of smooth muscle cell populations cultured from pig coronary artery. ATHEROSCLEROSIS SUPP 2003. [DOI: 10.1016/s1567-5688(03)90915-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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