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ABSTRACT: Genome-wide association study is a powerful approach to identify disease risk loci. However, the molecular regulatory mechanisms for most complex diseases are still not well understood. Therefore, further investigating the interplay between genetic factors and biological networks is important for elucidating the molecular mechanisms of complex diseases. Here, we proposed a novel framework to identify susceptibility gene modules and disease risk genes by combining network topological properties with support vector regression from single nucleotide polymorphism (SNP) level. We assigned risk SNPs to genes using the University of California at Santa Cruz (UCSC) genome database, and then mapped these genes to protein-protein interaction (PPI) networks. The gene modules implicated by hub genes were extracted using the PPI networks and the topological property was analyzed for these gene modules. For each gene module, risk feature genes were determined by topological property analysis and support vector regression. As a result, five shared risk feature genes, CD80, EGFR, FN1, GSK3B and TRAF6 were found and proven to be associated with rheumatoid arthritis by previous reports. Our approach showed a good performance in comparison with other approaches and can be used for prioritizing candidate genes associated with complex diseases.
Journal of Theoretical Biology 09/2011; 289:225-36. · 2.21 Impact Factor
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ABSTRACT: A satisfied glaucoma model is absent now. The aim of this study was to evaluate the effect of a combination of intracameral injection of silicone oil and electrocoagulation of corneal limbal vessels and episcleral veins in the rats to establish glaucoma model.
Operation was performed in each of the left eyes of 90 adult male rats. Right eyes were used as controls. Measurement of intraocular pressure (IOP) was performed with an applanation tonometer (Tono-Pen). Retinal ganglion cells (RGCs) were retrogradely labeled by applying FluoroGold onto the bilateral superior colliculus.
During the follow-up (24 weeks), the IOP of the study eyes was significantly higher (P < 0.05) than the control eyes (at final examination, IOP of control eyes was (13.4 ± 1.0) mmHg and IOP of study eyes was (16.1 ± 1.8) mmHg). Correspondingly, at 24 weeks after operation, the RGCs density of the study eyes (2286.11 ± 290.45/mm(2)) was significantly lower than the control eyes (2626.46 ± 164.85/mm(2), P < 0.01). In the operated eyes, histological examination showed excavation of optic disc and increased neuroglial cells in the optic nerve, reduced thickness of retina and diminution of retinal ganglion cells, and atrophy of ciliary body and iris. Notably, the anterior chamber angle of the operated eye remained open.
A combination of intracameral injection of silicone oil and electrocoagulation of corneal limbal vessels and episcleral veins may establish a reliable glaucoma model for further research.
Chinese medical journal 01/2011; 124(2):309-14. · 0.86 Impact Factor
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ABSTRACT: There is great interest in chromosome- and pathway-based techniques for genomics data analysis in the current work in order to understand the mechanism of disease. However, there are few studies addressing the abilities of machine learning methods in incorporating pathway information for analyzing microarray data. In this paper, we identified the characteristic pathways by combining the classification error rates of out-of-bag (OOB) in random forests with pathways information. At each characteristic pathway, the correlation of gene expression was studied and the co-regulated gene patterns in different biological conditions were mined by Mining Attribute Profile (MAP) algorithm. The discovered co-regulated gene patterns were clustered by the average-linkage hierarchical clustering technique. The results showed that the expression of genes at the same characteristic pathway were approximate. Furthermore, two characteristic pathways were discovered to present co-regulated gene patterns in which one contained 108 patterns and the other contained one pattern. The results of cluster analysis showed that the smallest similarity coefficient of clusters was more than 0.623, which indicated that the co-regulated patterns in different biological conditions were more approximate at the same characteristic pathway. The methods discussed in this paper can provide additional insight into the study of microarray data.
Journal of Theoretical Biology 09/2010; 266(2):242-9. · 2.21 Impact Factor
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Yi-sen Zhang,
Xin-jian Yang,
Sheng-zhang Wang,
Ai-ke Qiao,
Jia-liang Chen,
Kun-ya Zhang, Zhi-cheng Liu,
Yu-jing Zhao,
Ying Zhang,
Bin Luo,
Chuan-hui Li
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ABSTRACT: Stent placement has been widely used to assist coiling in cerebral aneurysm treatments. The present study aimed to investigate the hemodynamic effects of stenting on wide-necked intracranial aneurysms.
Three idealized plexiglass aneurismal models with different geometries before and after stenting were created, and their three-dimensional computational models were constructed. Flow dynamics in stented and unstented aneurismal models were studied using in vitro flow visualization and computational fluid dynamics (CFD) simulations. In addition, effects of stenting on flow dynamics in a patient-specific aneurysm model were also analyzed by CFD.
The results of flow visualization were consistent with those obtained with CFD simulations. Stent deployment reduced vortex inside the aneurysm and its impact on the aneurysm sac, and decreased wall shear stress on the sac. Different aneurysm geometries dictated fundamentally different hemodynamic patterns and outcomes of stenting.
Stenting across the neck of aneurysms improves local blood flow profiles. This may facilitate thrombus formation in aneurysms and decrease the chance of recanalization.
Chinese medical journal 08/2010; 123(15):1999-2003. · 0.86 Impact Factor
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ABSTRACT: Lessons from organophosphorus pesticides, which could be bioaccumulated in non-target organisms at different trophic levels and caused unexpected negative impacts, necessitate a study of the possibility of biotransfer and bioaccumulation of Bacillus thuringiensis (Bt) insecticidal toxin(s) expressed in Bt plants. Using ELISA, we evaluated the transfer of Cry1Ab toxin in a food chain of Bt rice (KMD1 and KMD2), the target insect, Cnaphalocrocis medinalis, and its predator, Pirata subpiraticus. Cry1Ab was detected in C. medinalis and P. subpiraticus. However, the concentration of Cry1Ab detected from C. medinalis and P. subpiraticus did not increase as feeding or preying time increased. A binding study of Cry1Ab to the brush border membrane vesicle of C. medinalis and P. subpiraticus indicated that P. subpiraticus does not have binding receptors in its midgut to Cry1Ab, while C. medinalis does. Survivorship and fecundity of P. subpiraticus preying on Bt rice-fed C. medinalis were not significantly different from those preying on non-Bt rice-fed C. medinalis. Developmental time of P. subpiraticus was significantly longer when it preyed on Bt rice-fed C. medinalis than on non-Bt rice-fed prey. However, a 3-year field trial indicated that Bt rice did not significantly affect the density of P. subpiraticus.
Ecotoxicology 12/2008; 18(2):230-8. · 2.36 Impact Factor
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ABSTRACT: To investigate the effects and outcomes of four procedures for hysterectomy.
Retrospectively, we analyzed the clinical characteristics of 756 cases who respectively received hysterectomy by total abdominohysterectomy (TAH, 260 cases), modified abdominohysterectomy (MAH, 180 cases), transvaginal hysterectomy (TVH, 106 cases), or laparoscopic assisted vaginal hysterectomy (LAVH) (210 cases) and compared their effects and outcomes.
The average operation time of TAH (98 +/- 23) minutes, MAH (67 +/- 18) minutes, TVH (63 +/- 19) minutes and LAVH (99 +/- 35) minutes. The average operation time of LAVH and TAH groups was significantly longer than that of TVH and MAH groups (P < 0.05). The volume of hemorrhage during operation in TAH group (180 +/- 49) ml was much more than that of other three groups significantly [MAH (102 +/- 43) ml, TVH (93 +/- 31) ml, LAVH (111 +/- 39) ml]. The average time of antibiotic administration and bowel function recovery in TAH group [(5.2 +/- 2.6) days, (36 +/- 9) hours] was significantly longer than that of TVH [(3.2 +/- 1.6) days, (21 +/- 4) hours], LAVH [(3.5 +/- 1.9) days, (23 +/- 6) hours] and MAH [(3.3 +/- 1.7) days, (23 +/- 7) hours] (P < 0.05). The incidence of fever in TAH group was significantly higher than that of other three groups also. The average hospital stay after operation in TVH [(3.3 +/- 1.2) days] and LAVH [(3.6 +/- 1.1) days] groups was significantly shorter than that of MAH [(5.6 +/- 1.9) days] or TAH [(5.4 +/- 2.3) days] groups (P < 0.05).
Different procedures for total hysterectomy have their own advantages and disadvantages. Microinvasive surgery by laparoscopy for hysterectomy will be mainstream in the future.
Zhonghua fu chan ke za zhi 11/2005; 40(10):652-5.
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ABSTRACT: To investigate the clinic characteristics and efficacy of combined multi-disciplinary laparoscopic surgery.
Combined laparoscopic surgery was performed in 46 gynecological patients who concomitantly had gastrointestinal and urinary tract diseases as study group, and single gynecologic laparoscopic surgery in 40 patients as control group. The complications and mean time of operations, bowel function restoration, and hospitalization length were observed.
The surgery of every patient was successful. None of the cases was transferred to open laparotomy. No complications occurred. The mean time of operations was significantly increased in study group (127 +/- 91) min compared with control group (100 +/- 80) min (P < 0.05). The recovery time of bowel function, as well as the mean time of hospitalization was not different between study group (20 +/- 10) h, (3.7 +/- 1.5) d and control group (19 +/- 10) h, (3.5 +/- 1.3) d (both P > 0.05).
Combined multi-disciplinary laparoscopic surgery can be performed safely and effectively for gynecological patients complicated with gastrointestinal or urinary tract diseases.
Zhonghua fu chan ke za zhi 11/2004; 39(10):690-2.
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ABSTRACT: Transgenic rice containing insecticidal protein(s) from Bt (Bacillus thuringiensis) effectively control lepidopteran pests under laboratory and field conditions. However, Bt rice has not been widely commercialized. A major concern regarding the deployment of Bt rice is its potential impact on non-target arthropods, including herbivorous insect pests and biological control agents (predators and parasitoids) in the rice ecosystem. A 2-year field study was conducted at 3 sites in Zhejiang Province, China to assess the impacts of a homozygous transgenic japonica rice line KMD1 (Bt rice) containing a synthetic cry1Ab gene from Bacillus thuringiensis Berliner. The impacts on three planthoppers (Homoptera: Delphacidae), Sogatella furcifera (Horváth), Nilaparvata lugens (Stål) and Laodelphax striatellus (Fallén), and the natural enemy, Cyrtorhinus lividipennis (Reuter) (Hemiptera: Miridae), were evaluated using two sampling methods: vacuum-suction and Malaise trap. Population densities of planthoppers and C. lividipennis were not significantly affected by rice type (Bt/non-Bt) over the season at any of the 3 sites in each year, regardless of sampling methods. Both in Bt rice and non-Bt rice plots, S. furcifera was the predominant species of planthoppers as determined by either of the two sampling methods, and comprised >50% of the planthoppers at each site. No consistent effects of Bt rice and Bt rice × sampling date interaction on population dynamics of the predominant planthopper species, S. furcifera, and the predator, C. lividipennis, were observed throughout the sampling period. Overall, this 2-year field study indicates that, in comparison with non-Bt rice, Bt rice did not lead to higher planthopper populations and did not negatively affect the predator C. lividipennis. These results suggest that use of Bt rice may provide control of the key lepidopteran pests while promoting the key biological control agent of planthopppers, C. lividipennis.
Biological Control.
