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Gao S.,University of Aarhus | Gao S.,BGI Co. | Zou D.,BGI Co. | Zou D.,National University of Defense Technology | And 15 more authors.
Bioinformatics | Year: 2015

Sodium bisulfite conversion followed by sequencing (BS-Seq, such as whole genome bisulfite sequencing or reduced representation bisulfite sequencing) has become popular for studying human epigenetic profiles. Identifying single nucleotide polymorphisms (SNPs) is important for quantification of methylation levels and for study of allele-specific epigenetic events such as imprinting. However, SNP calling in such data is complex and time consuming. Here, we present an ultrafast and memory-efficient package named BS-SNPer for the exploration of SNP sites from BS-Seq data. Compared with Bis-SNP, a popular BS-Seq specific SNP caller, BS-SNPer is over 100 times faster and uses less memory. BS-SNPer also offers higher sensitivity and specificity compared with existing methods. © The Author 2015. Published by Oxford University Press. All rights reserved.


Wang Z.,Shantou University | Chen J.,Peking University | Wang S.,Fourth Peoples Hospital of Shenzhen | Chen Z.,Shantou University
Journal of Luminescence | Year: 2013

Oridonin is an effective anticancer drug which has high potency and low systemic toxicity. In this study, the interaction between oridonin and bovine serum albumin (BSA) was investigated by several spectroscopic approaches for the first time. The binding characteristics of oridonin and BSA were determined by fluorescence emission spectra and resonance light scattering spectra. It is showed that the oridonin quenches the fluorescence of BSA and the static quenching constant KSV is 1.30×104 L mol -1 at 298 K. Moreover, oridonin and BSA form a 1:1 complex with a binding constant of 0.62×104 L mol-1. On the other hand, the thermodynamic parameters indicate that the binding process was a spontaneous molecular interaction procedure, in which hydrophobic forces played a major role. The structure analysis indicates that oridonin binding results in an increased hydrophobicity around the tryptophan residues of BSA. Additionally, as shown by the UV-vis absorption, synchronous fluorescence and three-dimensional fluorescence results, oridonin could lead to conformational and some microenvironmental changes of BSA. The work provides accurate and full basic data for clarifying the binding mechanism of oridonin with BSA in vitro and is helpful for understanding its effect on protein function during its transportation and distribution in blood. © 2012 Elsevier B.V. All rights reserved.


Zhang W.,Fujian Medical University | Jia N.,Fourth Peoples Hospital of Shenzhen | Su J.,Fujian Medical University | Lin J.,Fujian Medical University | And 2 more authors.
PLoS ONE | Year: 2014

Objective: To examine in what aspects and to what extent robotic ablation is superior over manual ablation, we sought to design a meta-analysis to compare clinical outcomes between the two ablations in the treatment of atrial fibrillation. Methods and Results: A literature search was conducted of PubMed and EMBASE databases before December 1, 2013. Data were extracted independently and in duplicate from 8 clinical articles and 792 patients. Effect estimates were expressed as weighted mean difference (WMD) or odds ratio (OR) and the accompanied 95% confidence interval (95% CI). Pooling the results of all qualified trials found significant reductions in fluoroscopic time (minutes) (WMD; 95% CI; P: -8.9; -12.54 to -5.26; <0.0005) and dose-area product (Gyxcm2) (WMD; 95% CI; P: -1065.66; -1714.36 to -416.96; 0.001) for robotic ablation relative to manual ablation, with evident heterogeneity (P<0.0005) and a low probability of publication bias. In subgroup analysis, great improvement of fluoroscopic time in patients with robotic ablation was consistently presented in both randomized and nonrandomized clinical trials, particularly in the former (WMD; 95% CI; P: -12.61; -15.13 to -10.09; <0.0005). Success rate of catheter ablation was relatively higher in patients with robotic ablation than with manual ablation (OR; 95% CI; P: 3.45; 0.24 to 49.0; 0.36), the difference yet exhibiting no statistical significance. Conclusions: This study confirmed and extended previous observations by quantifying great reductions of fluoroscopic time and dose-area product in patients referred for robotic ablation than for manual ablation in the treatment of atrial fibrillation, especially in randomized clinical trials. © 2014 Zhang et al.


Xu J.,Fuzhou General Hospital of Nanjing Command | Xu J.,Fujian Medical University | Huang Y.,Fujian Medical University | Cai H.,Fujian Medical University | And 7 more authors.
PLoS ONE | Year: 2014

Objective: Currently radiofrequency and cryoballoon ablations are the two standard ablation systems used for catheter ablation of atrial fibrillation; however, there is no universal consensus on which ablation is the optimal choice. We therefore sought to undertake a meta-analysis with special emphases on comparing the efficacy and safety between cryoballoon and radiofrequency ablations by synthesizing published clinical trials. Methods and Results: Articles were identified by searching the MEDLINE and EMBASE databases before September 2013, by reviewing the bibliographies of eligible reports, and by consulting with experts in this field. Data were extracted independently and in duplicate. There were respectively 469 and 635 patients referred for cryoballoon and radiofrequency ablations from 14 qualified clinical trials. Overall analyses indicated that cryoballoon ablation significantly reduced fluoroscopic time and total procedure time by a weighted mean of 14.13 (95% confidence interval [95% CI]: 2.82 to 25.45; P = 0.014) minutes and 29.65 (95% CI: 8.54 to 50.77; P = 0.006) minutes compared with radiofrequency ablation, respectively, whereas ablation time in cryoballoon ablation was nonsignificantly elongated by a weighted mean of 11.66 (95% CI: 210.71 to 34.04; P = 0.307) minutes. Patients referred for cryoballoon ablation had a high yet nonsignificant success rate of catheter ablation compared with cryoballoon ablation (odds ratio; 95% CI; P: 1.34; 0.53 to 3.36; 0.538), and cryoballoon ablation was also found to be associated with the relatively low risk of having recurrent atrial fibrillation (0.75; 0.3 to 1.88; 0.538) and major complications (0.46; 0.11 to 1.83; 0.269). There was strong evidence of heterogeneity and low probability of publication bias. Conclusion: Our findings demonstrate greater improvement in fluoroscopic time and total procedure duration for atrial fibrillation patients referred for cryoballoon ablation than those for radiofrequency ablation. © 2014 Xu et al.


Han W.-D.,Fourth Peoples Hospital of Shenzhen | Huang A.-J.,Fourth Peoples Hospital of Shenzhen | Chen L.-P.,Second Peoples Hospital of Futian District
Chinese Journal of Tissue Engineering Research | Year: 2013

Background: Bone cement injection is one of the commonly used methods for the treatment of thoracolumbar osteoporotic fractures. Objective: To evaluate biomechanical properties and fixed effects of bone cement injection for the treatment of thoracolumbar osteoporotic fractures. Methods: The specimens of thoracolumbar osteoporotic fractures were selected, and used to measure the mechanical properties of bone mineral density, maximum pressure load, displacement and stiffness. The bone model was established, and after bone cement injection, the maximum pressure load, displacement and stiffness were measured again. The mechanical properties before and after bone cement injection were compared, and compared with those in the treatment of thoracolumbar osteoporotic fractures with pedicle screw fixation. The patients received bone cement injection for the treatment of thoracolumbar osteoporotic fractures were followed-up, and the treatment effect of bone cement injection was determined through evaluating the pain relief degree, thoracolumbar vertebral height restoration, amount of bone cement injection and bone cement extravasation. Results and Conclusion: The biomechanical experiment determined that the maximum load was 2 285 N after thoracolumbar osteoporotic fractures treated with bone cement injection, which increased almost by 16.9% than 1 954 N before fracture; the stiffness was 427 N after thoracolumbar osteoporotic fractures treated with bone cement injection, which increased almost by 22.1% than 349 N before fracture, and showed good biological properties. The thoracolumbar osteoporotic fractures patients treated with bone cement injection and closed reduction combined with bone cement injection were followed-up, and found that both these two methods could relieve the pain of the patients. But closed reduction combined with bone cement injection for the treatment of thoracolumbar osteoporotic fractures was better than bone cement injection in the amount of bone cement injection, local kyphosis angle and vertebral height restoration. The results indicate that closed reduction combined with bone cement injection is a safe and effective method for the treatment of thoracolumbar osteoporotic fractures.

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