The association between single nucleotide polymorphism and disease is a typical representation of genetic association studies. Compared with the traditional dichotomous data, single nucleotide polymorphism data has its own characteristics, and 5 genetic models are commonly performed in meta-analysis. In this paper, we show how to use the " meta” package in R software to conduct meta-analysis of single nucleotide polymorphism research through examples.
Stata is statistical software that combines programming and un-programming, which is easy to operate, of high efficiency and good expansibility. In performing meta-analysis, Stata software also presents powerful function. The mvmeta package of Stata software is based on a multiple regression model to conduct network meta-analysis, and it also processes "multiple outcomes-multivariate" data. Currently, the disadvantages of mvmeta package include relatively cumbersome process, poor interest-risk sorting, and lack of drawing function in the process of conducting network meta-analysis. In this article, we introduce how to implement network meta-analysis using this package based on cases.
ObjectiveTo investigate the clinical effect of 3D computed tomography bronchial bronchography and angiography (3D-CTBA) and guidance of thoracoscopic anatomic pulmonary segmentectomy by Mimics software system. MethodsA retrospective analysis was performed on patients who underwent thoracoscopic segmentectomy in the Department of Thoracic Surgery of Affiliated People's Hospital of Jiangsu University from June 2020 to December 2022. The patients who underwent preoperative 3D-CTBA using Materiaise's interactive medical image control system (Mimics) were selected as an observation group, and the patients who did not receive 3D-CTBA were selected as a control group. The relevant clinical indicators were compared between the two groups. ResultsA total of 59 patients were included, including 29 males and 30 females, aged 25-79 years. There were 37 patients in the observation group, and 22 patients in the control group. The operation time (163.0±48.7 min vs. 188.8±43.0 min, P=0.044), intraoperative blood loss [10.0 (10.0, 20.0) mL vs. 20.0 (20.0, 35.0) mL, P<0.001], and preoperative puncture localization rate (5.4% vs. 31.8%, P=0.019) in the observation group were better than those in the control group. There was no statistically significant difference in the thoracic tube placement time, thoracic fluid drainage volume, number of intraoperative closure nail bin, postoperative hospital stay, or postoperative air leakage incidence (P>0.05) between the two groups. ConclusionFor patients who need to undergo anatomical pulmonary segmentectomy, using Mimics software to produce 3D-CTBA before surgery can help accurately identify pulmonary arteriovenous anatomy, reduce surgical time and intraoperative blood loss, help to determine the location of nodules and reduce invasive localization before surgery, and alleviate patients' pain, which is worthy of clinical promotion.
R Software is an open, free of use and charge statistical software which has a powerful graphic capability; however, it requires more complex codes and commands to perform network meta-analysis, which causes errors and difficulties in operation. WinBUGS software is based on Bayesian theory, which has a powerful data processing capability, and especially its codes are simple and easy to operate for dealing with network meta-analysis. However, its function of illustrating statistical results is very poor. In order to fully integrate the advantages of R software and WinBUGS software, an R2WinBUGS package based on R software has been developed which builds a “bridge” across two of them, making network meta-analysis process conveniently, quickly and result illustration more beautiful. In this article, we introduced how to use the R2WinBUGS package for performing network meta-analysis using examples.
ObjectiveTo fabricate the bionic scaffolds of rat spinal cord by combining three dimensional (3D) printer and 3D software, so as to lay the foundation of theory and technology for the manufacture of scaffolds by using biomaterials. MethodsThree female Sprague Dawley rats were scanned by 7.0T MRI to obtain the shape and position data of the cross section and gray matter of T8 to T10 spinal cord. Combined with data of position and shape of nerve conduction beam, the relevant data were obtained via Getdata software. Then the 3D graphics were made and converted to stereolithography (STL) format by using SolidWorks software. Photosensitive resin was used as the materials of spinal cord scaffolds. The bionic scaffolds were fabricated by 3D printer. ResultsMRI showed that the section shape of T8 to T10 segments of the spinal cord were approximately oval with a relatively long sagittal diameter of (2.20±0.52) mm and short transverse diameter of (2.05±0.24) mm, and the data of nerve conduction bundle were featured in the STL format. The spinal cord bionic scaffolds of the target segments made by 3D printer were similar to the spinal cord of rat in the morphology and size, and the position of pores simulated normal nerve conduction of rat spinal cord. ConclusionSpinal cord scaffolds produced by 3D printer which have similar shape and size of normal rat spinal cord are more bionic, and the procedure is simple. This technology combined with biomaterials is also promising in spinal cord repairing after spinal cord injury.
ObjectiveTo introduce the method of meta-analysis for effect combination of regression coefficient conducted with the metafor package in R software. MethodsBy using the data of a published meta-analysis as an example, the detailed process of meta-analysis for regression coefficient was presented with metafor package in R. ResultsThe results of meta-analysis conducted with metaphor package in R were the same as the published literature. ConclusionAs a completely free open source software for statistical analysis, R can conduct meta-analysis for effect combination of regression coefficient flexibly and precisely, and should be expanded in the future meta-analysis.
ITC (Indirect Treatment Comparison) software and indirect procedure of Stata software are especially used for indirect comparison nowadays, both of which possess the characteristics of friendly concise interface and support for menu operation. ITC software needs the application of other software to yield effect estimation and its confidence interval of direct comparison firstly; while Stata-indirect procedure can complete direct comparison internally and also operate using commands, which simplifies complicated process of indirect comparison. However, both of them only perform "single-pathway" of data transferring and pooling, which is a common deficiency. From the results, their results are of high-degree similarity.
The "bnma" package is a Bayesian network meta-analysis software package developed based on the R programming language. The network meta-analysis was performed utilizing JAGS software, which yielded relevant results and visual graphs. Moreover, this software package provides support for various data structures and types, while also providing the advantages of flexible utilization, user-friendly operation, and deliver of rich and accurate outcomes. In this paper, using a network meta-analysis example of different therapies for androgenetic alopecia, the operational process of conducting network meta-analysis using the "bnma" package is briefly introduced.
The metacor, which is developed based on the classical frequentist theory, is a specified package for performing meta-analysis of correlation coefficients in R software. This package was officially launched in 2011. Based on the DerSimonian-Laird method and Olkin-Pratt method, correlation coefficients can be directly pooled by using this package. The metacor package also can be used to draw the forest plot and is easy to use; however, it still needs to be improved. This paper briefly introduced how to perform a meta-analysis of correlation coefficients using the metacor package in R software through an example.
Objective To study digitize design of custom-made radial head prosthesis and to verify its matching precision by the surgery of preoperative three-dimensional (3-D) virtual replacement. Methods Six healthy adult volunteers (3 males and 3 females, aged 25-55 years with an average of 33 years) received slice scan of bilateral elbow by Speed Light 16-slice spiral CT. The CT Dicom data were imported into Mimics 10.0 software individually for 3-D reconstruction image, and the left proximal radial 3-D image was extracted, the mirror of the image was generated and it was split into 2 pieces: the head and the neck. The internal diameter and the length of the radial neck were obtained by Mimics 10.0 software measurement tools. In Geomagic Studio 12 software, the radial head was simulated to cover the cartilage surface (1 mm thickness) and generated to an entity. In UG NX 8.0 software, the stem of prosthesis was designed according to the parameters above and assembled head entity. Each custom-made prosthesis was performed and verified its matching precision by the surgery of preoperative 3-D virtual replacement. Results Comparing the morphology of 6 digitize custom-made prostheses with ipsilateral radial heads by the 3-D virtual surgery, the error was less than 1 mm. The radial head prosthesis design on basis of the contralateral anatomy was verified excellent matching. Conclusion The 3-D virtual surgery test and the digitized custom-made radial head prosthesis will be available for clinical accurate replacement.