A high-resolution anatomical rat atlas

This paper reports the availability of a high-resolution atlas of the adult rat. The atlas is composed of 9475 cryosectional images captured in 4600 x 2580 x 24-bit TIFF format, constructed using serial cryosection-milling techniques. Cryosection images were segmented, labelled and reconstructed into three-dimensional (3D) computerized models. These images, 3D models, technical details, relevant software and further information are available at our website, http://vchibp.vicp.net/vch/mice/.     

Target volume delineation variation in radiotherapy for early stage rectal cancer in the Netherlands

Purpose

The aim of this study was to measure and improve the quality of target volume delineation by means of national consensus on target volume definition in early-stage rectal cancer.

Methods and materials

The CTV’s for eight patients were delineated by 11 radiation oncologists in 10 institutes according to local guidelines (phase 1). After observer variation analysis a workshop was organized to establish delineation guidelines and a digital atlas, with which the same observers re-delineated the dataset (phase 2). Variation in volume, most caudal and cranial slice and local surface distance variation were analyzed.

Results

The average delineated CTV volume decreased from 620 to 460 cc (p < 0.001) in phase 2. Variation in the caudal CTV border was reduced significantly from 1.8 to 1.2 cm SD (p = 0.01), while it remained 0.7 cm SD for the cranial border. The local surface distance variation (cm SD) reduced from 1.02 to 0.74 for anterior, 0.63 to 0.54 for lateral, 0.33 to 0.25 for posterior and 1.22 to 0.46 for the sphincter region, respectively.

Conclusions

The large variation in target volume delineation could significantly be reduced by use of consensus guidelines and a digital delineation atlas. Despite the significant reduction there is still a need for further improvement.     

Rapid and automatic localization of the anterior and posterior commissure point landmarks in MR volumetric neuroimages

RATIONALE AND OBJECTIVE: Accurate identification of the anterior commissure (AC) and posterior commissure (PC) is critical in neuroradiology, functional neurosurgery, human brain mapping, and neuroscience research. Moreover, major stereotactic brain atlases are based on the AC and PC. Our goal is to provide an algorithm for a rapid, robust, accurate and automatic identification of AC and PC. MATERIALS AND METHOD: The method exploits anatomical and radiological properties of AC, PC and surrounding structures, including morphological variability. The localization is done in two stages: coarse and fine. The coarse stage locates the AC and PC on the midsagittal plane by analyzing their relationships with the corpus callosum, fornix, and brainstem. The fine stage refines the AC and PC in a well-defined volume of interest, analyzing locations of lateral and third ventricles, interhemispheric fissure, and massa intermedia. RESULTS: The algorithm was developed using simple operations, like histogramming, thresholding, region growing, 1D projections. It was tested on 94 diversified T1W and SPGR datasets. After the fine stage, 71 (76%) volumes had an error between 0-1 mm for the AC and 55 (59%) for the PC. The mean errors were 1.0 mm (AC) and 1.0 mm (PC). The accuracy has improved twice due to fine stage processing. The algorithm took about 1 second for coarse and 4 seconds for fine processing on P4, 2.5 GHz. CONCLUSION: The use of anatomical and radiological knowledge including variability in algorithm formulation aids in localization of structures more accurately and robustly. This fully automatic algorithm is potentially useful in clinical setting and for research.     

Generic head models for atlas-based EEG source analysis

We describe a method for using a generic head model, in the form of an anatomical atlas, to produce EEG source localizations. The atlas is fitted to the subject by a nonrigid warp using a set of surface landmarks. The warped atlas is used to compute a finite element model (FEM) of the forward mapping or lead-fields between neural current generators and the EEG electrodes. These lead-fields are used to localize current sources from the subject's EEG data and the sources are then mapped back to the anatomical atlas. This approach provides a mechanism for comparing source localizations across subjects in an atlas-based coordinate system, which can be used in the large fraction of EEG studies in which MR images are not available. The Montreal brain atlas was used as the reference anatomical atlas and 10 individual MR volumes were used to evaluate the method. The atlas was fitted to each subject's head by a thin-plate-spline (TPS) warp. The spatial locations of a generic 155-electrode configuration were used to constrain the warp. For the purposes of evaluation, dipolar sources were placed on the inner cortical surface in the atlas geometry and transferred to each subject's brain space using a polynomial warp. The parameters of the warp were computed using an intensity-based matching of the atlas and subject brains, thus ensuring that the sources were placed at approximately the same anatomical location in each case. Data were simulated in the subject geometry and a dipole fit was performed on these data using an FEM of the TPS warped atlas. The source positions found in the warped atlas were transferred back to the original atlas and compared to the original position. Sources were simulated at 972 locations evenly distributed over the inner cortical surface of the atlas. The mean error over all 10 subjects was 8.1 mm in the subject space and 15.2 mm in the atlas space. In comparison, using an affine transformation of the electrodes into atlas space and an FEM model generated from the atlas produced mean errors of 22.3 mm in subject space and 19.6 mm in atlas space. With a standard three-shell spherical model the errors were 27.2 mm in the subject space and 34.7 mm when mapped to atlas space.     

Signature of prognostic epithelial–mesenchymal transition related long noncoding RNAs (ERLs) in hepatocellular carcinoma

Reliable biomarkers are of great significance for the treatment and diagnosis of hepatocellular carcinoma (HCC). This study identified potential prognostic epithelial–mesenchymal transition related lncRNAs (ERLs) by the cancer genome atlas (TCGA) database and bioinformatics.The differential expression of long noncoding RNA (lncRNA) was obtained by analyzing the lncRNA data of 370 HCC samples in TCGA. Then, Pearson correlation analysis was carried out with EMT related genes (ERGs) from molecular signatures database. Combined with the univariate Cox expression analysis of the total survival rate of hepatocellular carcinoma (HCC) patients, the prognostic ERLs were obtained. Then use “step” function to select the optimal combination of constructing multivariate Cox expression model. The expression levels of ERLs in HCC samples were verified by real-time quantitative polymerase chain reaction.Finally, we identified 5 prognostic ERLs ({"type":"entrez-nucleotide","attrs":{"text":"AC023157.3","term_id":"6980118","term_text":"AC023157.3"}}AC023157.3, {"type":"entrez-nucleotide","attrs":{"text":"AC099850.3","term_id":"25046596","term_text":"AC099850.3"}}AC099850.3, AL031985.3, {"type":"entrez-nucleotide","attrs":{"text":"AL365203.2","term_id":"9743577","term_text":"AL365203.2"}}AL365203.2, CYTOR). The model showed that these prognostic markers were reliable independent predictors of risk factors (P value <.0001, hazard ratio [HR] = 2.400, 95% confidence interval [CI] = 1.667–3.454 for OS). In the time-dependent receiver operating characteristic analysis, this prognostic marker is a good predictor of HCC survival (area under the curve of 1 year, 2 years, 3 years, and 5 years are 0.754, 0.720, 0.704, and 0.662 respectively). We analyzed the correlation of clinical characteristics of these prognostic markers, and the results show that this prognostic marker is an independent factor that can predict the prognosis of HCC more accurately. In addition, by matching with the Molecular Signatures Database, we obtained 18 ERLs, and then constructed the HCC prognosis model and clinical feature correlation analysis using 5 prognostic ERLs. The results show that these prognostic markers have reliable independent predictive value. Bioinformatics analysis showed that these prognostic markers were involved in the regulation of EMT and related functions of tumor occurrence and migration.Five prognostic types of ERLs identified in this study can be used as potential biomarkers to predict the prognosis of HCC.     

Craniofacial imaging informatics and technology development

Author– Vannier MW Purpose – ‘Craniofacial imaging informatics’ refers to image and related scientific data from the dentomaxillofacial complex, and application of ‘informatics techniques’ (derived from disciplines such as applied mathematics, computer science and statistics) to understand and organize the information associated with the data. Method – Major trends in information technology determine the progress made in craniofacial imaging and informatics. These trends include industry consolidation, disruptive technologies, Moore's law, electronic atlases and on‐line databases. Each of these trends is explained and documented, relative to their influence on craniofacial imaging. Results – Craniofacial imaging is influenced by major trends that affect all medical imaging and related informatics applications. The introduction of cone beam craniofacial computed tomography scanners is an example of a disruptive technology entering the field. An important opportunity lies in the integration of biologic knowledge repositories with craniofacial images. Conclusion – The progress of craniofacial imaging will continue subject to limitations imposed by the underlying technologies, especially imaging informatics. Disruptive technologies will play a major role in the evolution of this field.     

几种常见真菌的RAPD指纹图谱的建立

目的 建立常见真菌的随机引物扩增多态DNA(RAPD)指纹图谱。方法 以标准株真菌的基因组DNA为模板,采用(AC)_(10),(GTG)_5,AP_3和M_(13)等4种RAPD引物扩增产物条带组合,建立特征性指纹图谱,并与常规真菌培养结果进行验证比较。结果 单独一种引物往往不能够产生特征性的基因指纹,但是4种产物的组合,却可以形成肉眼直观的、足以区分常见真菌型别的指纹图谱。此图谱与门诊真菌培养结果比较,一致率达95％。结论 皮肤科真菌RAPD指纹图谱的建立和不断扩大将有望成为传统真菌检测的一个快速、可靠的补充。