Technical note: GAMMORA,a free,open-source,and validated GATE-based model for Monte-Carlo simulations of the Varian TrueBeam

PurposeMonte Carlo (MC) is the reference computation method for medical physics. In radiotherapy, MC computations are necessary for some issues (such as assessing figures of merit, double checks, and dose conversions). A tool based on GATE is proposed to easily create full MC simulations of the Varian TrueBeam STx.MethodsGAMMORA is a package that contains photon phase spaces as a pre-trained generative adversarial network (GAN) and the TrueBeam’s full geometry. It allows users to easily create MC simulations for simple or complex radiotherapy plans such as VMAT. To validate the model, the characteristics of generated photons are first compared to those provided by Varian (IAEA format). Simulated data are also compared to measurements in water and heterogeneous media. Simulations of 8 SBRT plans are compared to measurements (in a phantom). Two examples of applications (a second check and interplay effect assessment) are presented.ResultsThe simulated photons generated by the GAN have the same characteristics (energy, position, and direction) as the IAEA data. Computed dose distributions of simple cases (in water) and complex plans delivered in a phantom are compared to measurements, and the Gamma index (3%/3mm) was always superior to 98%. The feasibility of both clinical applications is shown.ConclusionsThis model is now shared as a free and open-source tool that generates radiotherapy MC simulations. It has been validated and used for five years. Several applications can be envisaged for research and clinical purposes.     

牙周组织再生术联合无托槽隐形矫治对牙周炎患者龈沟液炎症因子的影响

目的探讨牙周组织再生术(PTR)联合无托槽隐形矫治对牙周炎患者龈沟液炎症因子的影响,为该类患者的治疗提供参考。方法选取2017年3月至2019年3月我院收治的120例牙周炎患者为研究对象,依据随机数字表分为再隐组和再直组,每组60例。再隐组患者给予PTR联合无托槽隐形矫治,再直组患者给予PTR联合直丝弓矫治。比较两组患者龈沟液炎症因子[白介素6(IL-6)、C反应蛋白(CRP)、肿瘤坏死因子α(TNF-α)]水平、牙周健康状况[牙周探诊深度(PD)、牙龈指数(GI)、龈沟出血指数(SBI)、牙菌斑指数(PLI)、临床附着丧失(CAL)]、治疗疗效和并发症情况。结果再隐组和再直组患者治疗后龈沟液IL-6、CRP、TNF-α水平及PD、GI、SBI、PLI、CAL明显低于治疗前,再隐组患者治疗后龈沟液IL-6、CRP、TNF-α水平及PD、GI、SBI、PLI、CAL明显低于再直组,差异均有统计学意义(均P0.05)。再隐组患者治疗有效率为95.00%,明显高于再直组的80.00%,差异有统计学意义(χ~2=6.171,P=0.013)。再隐组患者并发症发生率为5.00%,明显低于再直组的16.67%,差异有统计学意义(χ~2=4.227,P=0.040)。结论 PTR联合无托槽隐形矫治可有效改善牙周炎患者龈沟液炎症因子水平及牙周健康状况,有利于提高疗效和减少并发症,值得临床推广。     

基孔肯雅病毒非结构蛋白基因合成中多位点缺失突变的校正方法

目的:建立一种PCR方法,以快速校正基孔肯雅病毒非结构蛋白基因合成过程中发生的多位点缺失突变。方法:用PCR方法合成基孔肯雅病毒非结构蛋白基因;对测序的克隆进行序列比对,分析不同克隆上缺失突变发生的位置,以保守区域互相重叠的寡核苷酸为上下游引物、以该区域测序正确的克隆为模板进行PCR扩增,得到所需片段,再将这些片段用PCR方法进一步组装成完整的基因序列并进行测序。结果:测序结果表明,经过2次PCR扩增,校正了基孔肯雅病毒非结构蛋白基因合成过程中发生的5个位点缺失突变。结论:得到序列正确的基孔肯雅病毒非结构蛋白基因。在进行基因合成过程中如发生多位点缺失突变,可利用该方法同时对以上突变进行校正,无须再合成引物,降低了实验操作难度,并提高了实验效率。     

Enhancement of Hounsfield unit distribution in cone-beam CT images for adaptive radiation therapy: Evaluation of a hybrid correction approach

PurposeThis study aims to evaluate the accuracy of a hybrid approach combining the histogram matching (HM) and the multilevel threshold (MLT) to correct the Hounsfield Unit (HU) distribution in cone-beam CT (CBCT) images.Methods and MaterialsCBCT images acquired for ten prostate cancer patients were processed by matching their histograms to those of deformed planning CT (pCT) images obtained after applying a deformable registration (DR) process. Then, HU values corresponding to five tissue types in the pCT were assigned to the obtained CBCT images (CBCT_HM-MLT). Finally, the CBCT_HM-MLT images were compared to the deformed pCT visually and using different statistical metrics.ResultsThe visual assessment and the profiles comparison showed that the high discrepancies in the CBCT images were significantly reduced when using the proposed approach. Furthermore, the correlation values indicated that the CBCT_HM-MLT were in good agreement with the deformed pCT with correlation values ranging from 0.9893 to 0.9962. In addition, the root mean squared error (RMSE) over the entire volume was reduced from 64.15 ± 9.50 to 51.20 ± 6.76 HU. Similarly, the mean absolute error in specific tissue classes was significantly reduced especially in the soft tissue-air interfaces. These results confirmed that applying MLT after HM worked better than using only HM for which the correlation values were ranging from 0.9878 to 0.9955 and the RMSE was 55.95 ± 10.43 HU.ConclusionEvaluation of the proposed approach showed that the HM + MLT correction can improve the HU distribution in the CBCT images and generate corrected images in good agreement with the pCT.     

Enhancement of soft-tissue contrast in cone-beam CT using an anti-scatter grid with a sparse sampling approach

PurposeAnti-scatter grids suppress the scatter substantially thus improving image contrast in radiography. However, its active use in cone-beam CT for the purpose of improving contrast-to-noise ratio (CNR) has not been successful mainly due to the increased noise related to Poisson statistics of photons. This paper proposes a sparse-view scanning approach to address the above issue.MethodCompared to the conventional cone-beam CT imaging framework, the proposed method reduces the number of projections and increases exposure in each projection to enhance image quality without an additional cost of radiation dose to patients. For image reconstruction from sparse-view data, an adaptive-steepest-descent projection-onto-convex-sets (ASD POCS) algorithm regularized by total-variation (TV) minimization was adopted. Contrast and CNR with various scattering conditions were evaluated in projection domain by a simulation study using GATE. Then we evaluated contrast, resolution, and image uniformity in CT image domain with Catphan phantom. A head phantom with soft-tissue structures was also employed for demonstrating a realistic application. A virtual grid-based estimation and reduction of scatter has also been implemented for comparison with the real anti-scatter grid.ResultsIn the projection domain evaluation, contrast and CNR enhancement was observed when using an anti-scatter grid compared to the virtual grid. In the CT image domain, the proposed method produced substantially higher contrast and CNR of the low-contrast structures with much improved image uniformity.ConclusionWe have shown that the proposed method can provide high-quality CBCT images particularly with an increased contrast of soft-tissue at a neutral dose for image-guidance.     

Diet estimation in California sea lions,Zalophus californianus

We performed a captive feeding experiment using California sea lions to assess biases associated with estimating pinniped diet using scats and spews. Sea lions were fed nine of their natural prey species: anchovy, sardine, Pacific mackerel, jack mackerel, hake, steelhead smolts, shortbelly rockfish, pink salmon, and market squid. Recovery percentages varied among prey species using otoliths and were improved for adult salmon and sardine using the all‐structure method. Numerical and graded length correction factors provided better estimates of number and size of prey consumed. Four models used to determine the proportions of prey species consumed by a sea lion population were tested. The all‐structure method and variable biomass reconstruction model, in conjunction with numerical and graded length correction factors, provided more accurate estimates than without. We provide numerical correction factors for all prey species, including correction factors for specific salmon bones: vertebrae, branchials, radials, teeth, gill rakers, and hypurals.     

Computational analysis of RNA editing sites in plant mitochondrial genomes reveals similar information content and a sporadic distribution of editing sites

A computational analysis of RNA editing sites was performedon protein-coding sequences of plant mitochondrial genomes fromArabidopsis thaliana, Beta vulgaris, Brassica napus, and Oryzasativa. The distribution of nucleotides around edited and uneditedcytidines was compared in 41 nucleotide segments and included1481 edited cytidines and 21,390 unedited cytidines in the 4genomes. The distribution of nucleotides was examined in 1,2, and 3 nucleotide windows by comparison of nucleotide frequencyratios and relative entropy. The relative entropy analyses indicatethat information is encoded in the nucleotide sequences in the5 prime flank (–18 to –14, –13 to –10,–6 to –4, –2/–1) and the immediate 3prime flanking nucleotide (+1), and these regions may be importantin editing site recognition. The relative entropy was largewhen 2 or 3 nucleotide windows were analyzed, suggesting thatseveral contiguous nucleotides may be involved in editing siterecognition. RNA editing sites were frequently preceded by 2pyrimidines or AU and followed by a guanidine (HYCG) in themonocot and dicot mitochondrial genomes, and rarely precededby 2 purines. Analysis of chloroplast editing sites from a dicot,Nicotiana tabacum, and a monocot, Zea mays, revealed a similardistribution of nucleotides around editing sites (HYCA). Thesimilarity of this motif around editing sites in monocots anddicots in both mitochondria and chloroplasts suggests that amechanistic basis for this motif exists that is common in thesedifferent organelle and phylogenetic systems. The preferredsequence distribution around RNA editing sites may have an importantimpact on the acquisition of editing sites in evolution becausethe immediate sequence context of a cytidine residue may rendera cytidine editable or uneditable, and consequently determinewhether a T to C mutation at a specific position may be correctedby RNA editing. The distribution of editing sites in many protein-codingsequences is shown to be non-random with editing sites clusteredin groups separated by regions with no editing sites. The sporadicdistribution of editing sites could result from a mechanismof editing site loss by gene conversion utilizing edited sequenceinformation, possibly through an edited cDNA intermediate.     

不同光谱类型对银川平原土壤含盐量反演精度的影响与校正

土壤盐渍化是导致土壤质量下降、耕地减产的重要因素之一。为准确快速评价银川平原土壤含盐量,本研究对野外高光谱数据和室内高光谱数据进行一阶微分(FDR)变换,逐步回归(SR)筛选特征波段,利用偏最小二乘回归(PLSR)与支持向量机(SVM)进行建模,明确适用于本地区土壤含盐量准确反演的光谱类型,并对较差光谱类型进行分段校正与全局校正,尝试提高土壤含盐量反演精度。结果表明: 基于野外光谱的土壤含盐量反演模型精度比室内光谱平均高58.9%;对室内光谱进行分段校正、全局校正后反演精度均有提高,其中,PLSR以分段校正精度更高,建模决定系数(R_c²)、验证决定系数(R_p²)和相对分析误差(RPD)分别为0.790、0.633和1.64,而SVM以全局校正精度更高,R_c²、R_p²和RPD分别为0.927、0.947和3.87;SVM模型的反演精度高于PLSR,其中,野外光谱建模效果最佳,室内全局校正光谱与室内分段校正光谱次之,室内光谱最差。因此,野外高光谱可实现对银川平原土壤表层含盐量的定量反演,经校正的室内光谱对土壤含盐量反演精度显著提升,均可为粮食安全与生态环境高质量发展提供保障。     

基于GIS技术的城市开敞空间适宜性布局

依托GIS技术平台,通过“开敞空间分级—指标体系建立—理想模型建构—理想模型修正—系统建构与分级导控”5个步骤,建立开敞空间适宜性布局的普适性思路框架,以理想模型建构和理想模型修正为核心环节。并以福建省武夷山市总体城市设计为例对此思路框架进行实际应用,以期对上位规划的城市开敞空间适宜性布局评估及优化提供思路和方法。     

Quantification of collagen fiber structure using second harmonic generation imaging and two‐dimensional discrete Fourier transform analysis: Application to the human optic nerve head

Second harmonic generation (SHG) microscopy is widely used to image collagen fiber microarchitecture due to its high spatial resolution, optical sectioning capabilities and relatively nondestructive sample preparation. Quantification of SHG images requires sensitive methods to capture fiber alignment. This article presents a two‐dimensional discrete Fourier transform (DFT)–based method for collagen fiber structure analysis from SHG images. The method includes integrated periodicity plus smooth image decomposition for correction of DFT edge discontinuity artefact, avoiding the loss of peripheral image data encountered with more commonly used windowing methods. Outputted parameters are as follows: the collagen fiber orientation distribution, aligned collagen content and the degree of collagen fiber dispersion along the principal orientation. We demonstrate its application to determine collagen microstructure in the human optic nerve head, showing its capability to accurately capture characteristic structural features including radial fiber alignment in the innermost layers of the bounding sclera and a circumferential collagen ring in the mid‐stromal tissue. Higher spatial resolution rendering of individual lamina cribrosa beams within the nerve head is also demonstrated. Validation of the method is provided in the form of correlative results from wide‐angle X‐ray scattering and application of the presented method to other fibrous tissues.