49 research outputs found

    A prognostic index model for assessing the prognosis of ccRCC patients by using the mRNA expression profiles of AIF1L, SERPINC1 and CES1

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    Background: Kidney carcinoma is a major cause of carcinoma-related death, with the prognosis for advanced or metastatic renal cell carcinoma still very poor. The aim of this study was to investigate feasible prognostic biomarkers that can be used to construct a prognostic index model for clear cell renal cell carcinoma (ccRCC) patients. Methods: The mRNA expression profiles of ccRCC samples were downloaded from the The Cancer Genome Atlas (TCGA) dataset and the correlation of AIF1L with malignancy, tumor stage and prognosis were evaluated. Differentially expressed genes (DEGs) between AIF1L-low and AIF1L-high expression groups were selected. Those with prognostic value as determined by univariate and multivariate Cox regression analysis were then used to construct a prognostic index model capable of predicting the outcome of ccRCC patients. Results: The expression level of AIF1L was lower in ccRCC samples than in normal kidney samples. AIF1L expression showed an inverse correlation with tumor stage and a positive association with better prognosis. ccRCC samples were divided into high- and low-expression groups according to the median value of AIF1L expression. In the AIF1L-high expression group, 165 up-regulated DEGs and 601 down-regulated DEGs were identified. Three genes (AIF1L, SERPINC1 and CES1) were selected following univariate and multivariate Cox regression analysis. The hazard ratio (HR) and 95% confidence intervals (CI) for these genes were: AIF1L (HR = 0.83, 95% CI: 0.76–0.91), SERPINC1 (HR = 1.33, 95% CI: 1.12–1.58), and CES1 (HR = 0.87, 95% CI: 0.78–0.97). A prognostic index model based on the expression level of the three genes showed good performance in predicting ccRCC patient outcome, with an area under the ROC curve (AUC) of 0.671. Conclusion: This research provides a better understanding of the correlation between AIF1L expression and ccRCC. We propose a novel prognostic index model comprising AIF1L, SERPINC1 and CES1 expression that may assist physicians in determining the prognosis of ccRCC patients

    Robust estimation of bacterial cell count from optical density

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    Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

    Investigating the effectiveness of monitoring relevant variations during IMRT and VMAT treatments by EPID-based 3D in vivo verification performed using planning CTs.

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    PURPOSE:The goal of this study was to investigate the effectiveness of monitoring relevant variations during treatments for electronic portal imaging device (EPID)-based 3D in vivo verification performed using planning CTs. METHODS:Experiments on two simple phantoms (uniform and nonuniform phantoms) and a thoracic phantom were analyzed in this study, and six relevant variations including the machine output, planning target volume (PTV) deformation, multileaf collimator (MLC) and Phantom shift (set-up errors), and gantry and couch angle shifts were evaluated. 3D gamma and dose-volume histogram (DVH) methods were used to evaluate the detection sensitivity of the EPID-based 3D in vivo dosimetry and the dose accuracy of the EPID reconstruction, respectively, as affected by the variations, and the results were validated by determining the consistency with TPS simulated results. RESULTS:The results of the simple phantoms showed that the gamma failure rates and DVH trend of EPID reconstructions were consistent with the results of TPS simulations for machine output and MLC shifts and inconsistent for phantom shift, gantry/couch angle shift and PTV deformation variations. The results of the thoracic phantom showed that CBCT-guided EPID reconstruction sensitively detected 3-mm Phantom shift in thoracic phantom and its gamma failure rates and DVH trend were consistent with the results of TPS simulations. CONCLUSION:The variations, such as machine output and MLC shift, that are phantom unrelated and cause changes in the beam of the linear accelerator can be sensitively detected by EPID-based 3D in vivo dosimetry and do not affect the accuracy of the EPID reconstruction dose. Planning CT will limit the detection sensitivity and the accuracy of the reconstruction dose of the EPID-based 3D in vivo dosimetry for phantom-related variations (such as Phantom shift and gantry/couch angle shift). EPID reconstruction combined with IGRT technology is a more effective method to monitor phantom shift variations

    The combination of the error correction methods of GAFCHROMIC EBT3 film

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    <div><p>Purpose</p><p>The aim of this study was to combine a set of methods for use of radiochromic film dosimetry, including calibration, correction for lateral effects and a proposed triple-channel analysis. These methods can be applied to GAFCHROMIC EBT3 film dosimetry for radiation field analysis and verification of IMRT plans.</p><p>Methods</p><p>A single-film exposure was used to achieve dose calibration, and the accuracy was verified based on comparisons with the square-field calibration method. Before performing the dose analysis, the lateral effects on pixel values were corrected. The position dependence of the lateral effect was fitted by a parabolic function, and the curvature factors of different dose levels were obtained using a quadratic formula. After lateral effect correction, a triple-channel analysis was used to reduce disturbances and convert scanned images from films into dose maps. The dose profiles of open fields were measured using EBT3 films and compared with the data obtained using an ionization chamber. Eighteen IMRT plans with different field sizes were measured and verified with EBT3 films, applying our methods, and compared to TPS dose maps, to check correct implementation of film dosimetry proposed here.</p><p>Results</p><p>The uncertainty of lateral effects can be reduced to ±1 cGy. Compared with the results of Micke A et al., the residual disturbances of the proposed triple-channel method at 48, 176 and 415 cGy are 5.3%, 20.9% and 31.4% smaller, respectively. Compared with the ionization chamber results, the difference in the off-axis ratio and percentage depth dose are within 1% and 2%, respectively. For the application of IMRT verification, there were no difference between two triple-channel methods. Compared with only corrected by triple-channel method, the IMRT results of the combined method (include lateral effect correction and our present triple-channel method) show a 2% improvement for large IMRT fields with the criteria 3%/3 mm.</p></div

    Comparison of isodose maps for a large field IMRT plan.

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    <p>(a) Isodose maps of the present method, (b) isodose maps of the method of Micke et al.; (c) and (d) show horizontal and vertical profiles.</p

    The scanned pixel values of the red channel and their second-order polynomial fits at different constant dose values.

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    <p>The scanned pixel values of the red channel and their second-order polynomial fits at different constant dose values.</p