肿瘤核仁形成区形态定量诊断的误差及规范化分析

本文采用包括自动图象分析技术在内的ＡｇＮＯＲ形态定量学方法,以大肠肿瘤为模型,进行了ＡｇＮＯＲ定量形态学研究的误差分析,以探讨肿瘤ＡｇＮＯＲ定量诊断规范化的可能。结果表明,染色条件、视场目标选择和细胞计数量是引起ＡｇＮＯＲ定量诊断的主要误差;恒定染色环境,正确选择欲测细胞及测定足够量的细胞是使ＡｇＮＯＲ形态定量诊断规范化的途径。     

基于时频分析检测EEG中癫痫样棘/尖波的方法

提出了一种基于Ｃｈｏｉ－Ｗｉｌｌｉａｍｓ分布检测ＥＥＧ中癫痫样棘波／尖波的方法。该方法通过计算ＥＥＧ信号的时频分布,得到一段信号在各个时刻上沿频率方向上的能量分布。这种能量分布相当于一种瞬时频谱,反映了ＥＥＧ信号在局部时间范围里的波形特征。以一段ＥＥＧ信号在各个时刻的瞬时频谱的平均作为这段脑电的背景信号频谱,通过计算每一时刻的瞬时频谱与背景信号频谱之间的频谱差,检测这段信号中的棘波／尖波。对临床Ｅ     

Deep learning dose prediction for IMRT of esophageal cancer: The effect of data quality and quantity on model performance

PurposeTo investigate the effect of data quality and quantity on the performance of deep learning (DL) models, for dose prediction of intensity-modulated radiotherapy (IMRT) of esophageal cancer.Material and methodsTwo databases were used: a variable database (VarDB) with 56 clinical cases extracted retrospectively, including user-dependent variability in delineation and planning, different machines and beam configurations; and a homogenized database (HomDB), created to reduce this variability by re-contouring and re-planning all patients with a fixed class-solution protocol.Experiment 1 analysed the user-dependent variability, using 26 patients planned with the same machine and beam setup (E26-VarDB versus E26-HomDB). Experiment 2 increased the training set by groups of 10 patients (E16, E26, E36, E46, and E56) for both databases.Model evaluation metrics were the mean absolute error (MAE) for selected dose-volume metrics and the global MAE for all body voxels.ResultsFor Experiment 1, E26-HomDB reduced the MAE for the considered dose-volume metrics compared to E26-VarDB (e.g. reduction of 0.2 Gy for D95-PTV, 1.2 Gy for Dmean-heart or 3.3% for V5-lungs). For Experiment 2, increasing the database size slightly improved performance for HomDB models (e.g. decrease in global MAE of 0.13 Gy for E56-HomDB versus E26-HomDB), but increased the error for the VarDB models (e.g. increase in global MAE of 0.20 Gy for E56-VarDB versus E26-VarDB).ConclusionA small database may suffice to obtain good DL prediction performance, provided that homogenous training data is used. Data variability reduces the performance of DL models, which is further pronounced when increasing the training set.     

Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies

We present an RNA-As-Graphs (RAG) based inverse folding algorithm, RAG-IF, to design novel RNA sequences that fold onto target tree graph topologies. The algorithm can be used to enhance our recently reported computational design pipeline (Jain et al., NAR 2018). The RAG approach represents RNA secondary structures as tree and dual graphs, where RNA loops and helices are coarse-grained as vertices and edges, opening the usage of graph theory methods to study, predict, and design RNA structures. Our recently developed computational pipeline for design utilizes graph partitioning (RAG-3D) and atomic fragment assembly (F-RAG) to design sequences to fold onto RNA-like tree graph topologies; the atomic fragments are taken from existing RNA structures that correspond to tree subgraphs. Because F-RAG may not produce the target folds for all designs, automated mutations by RAG-IF algorithm enhance the candidate pool markedly. The crucial residues for mutation are identified by differences between the predicted and the target topology. A genetic algorithm then mutates the selected residues, and the successful sequences are optimized to retain only the minimal or essential mutations. Here we evaluate RAG-IF for 6 RNA-like topologies and generate a large pool of successful candidate sequences with a variety of minimal mutations. We find that RAG-IF adds robustness and efficiency to our RNA design pipeline, making inverse folding motivated by graph topology rather than secondary structure more productive.     

特异性三重PCR快速检测副溶血性弧菌

【目的】建立同时检测副溶血性弧菌gyrase、tdh、trh基因的三重PCR快速检测方法。【方法】将已报道的这3种基因的引物加入一个PCR反应管中,对引物浓度和退火温度进行优化,找到最佳引物比例和扩增条件。通过特异性验证、灵敏度验证以及方法间对比进行方法确认,其PCR产物使用全自动毛细管电泳分析系统进行分析。【结果】仅在91、269、485 bp处分别出现预期DNA扩增条带;纯培养条件下,扩增gyrase、tdh、trh的菌浓度检测限分别为6.6×101、6.6×102和6.6×101 CFU/mL;本底干扰物存在时,扩增gyrase、tdh、trh的菌浓度检测限分别为6.6×103、6.6×104和6.6×103 CFU/mL;模板DNA浓度检测限为1.36μg/L。检测进境海产品时,检测结果和FDA 2004标准结果一致,且更易辨认和判断。【结论】此检测方法的成功建立,为副溶血性弧菌及携带tdh和/或trh基因的致病性副溶血性弧菌的检测提供了一种准确、高效、便捷的分子技术手段。     

MALDI-Mass Spectrometric Imaging for the Investigation of Metabolites in Medicago truncatula Root Nodules

Most techniques used to study small molecules, such as pharmaceutical drugs or endogenous metabolites, employ tissue extracts which require the homogenization of the tissue of interest that could potentially cause changes in the metabolic pathways being studied¹. Mass spectrometric imaging (MSI) is a powerful analytical tool that can provide spatial information of analytes within intact slices of biological tissue samples^1-5. This technique has been used extensively to study various types of compounds including proteins, peptides, lipids, and small molecules such as endogenous metabolites. With matrix-assisted laser desorption/ionization (MALDI)-MSI, spatial distributions of multiple metabolites can be simultaneously detected. Herein, a method developed specifically for conducting untargeted metabolomics MSI experiments on legume roots and root nodules is presented which could reveal insights into the biological processes taking place. The method presented here shows a typical MSI workflow, from sample preparation to image acquisition, and focuses on the matrix application step, demonstrating several matrix application techniques that are useful for detecting small molecules. Once the MS images are generated, the analysis and identification of metabolites of interest is discussed and demonstrated. The standard workflow presented here can be easily modified for different tissue types, molecular species, and instrumentation.     

不同全自动凝血仪检测结果的分析研究

目的:探讨不同全自动凝血分析仪检测结果是否具有可比性,同时对其检测结果临床可接受性进行评估,使不同全自动凝血分析仪检测结果标准化.方法:连续30天用SYSMEX CA- 1500及CA-7000全自动凝血分析仪同时检测并比对仪器配套定值质控物的PT、INR、APTT、FIB、TT值;同时连续30天利用两台仪器检测并对比新鲜血标本的PT、INR、APTT、FIB、TT值.结果:SYSMEX CA- 1500及CA-7000日间质控物各检测项目:PT、INR、APTT、FIB、TT变异系数均小于5％.CA- 1500及CA-7000全自动凝血分析仪检测新鲜血标本:PT、INR、APTT、FIB、TT统计分析结果,t检验其P值均＞0.05;相关系数r在0.993-0.999之间;两台仪器的偏差均符合1/2美国CLIA’88能力验证分析质量要求.结论:两台仪器PT、INR、APTT、FIB、TT的检测结果具有很好的相关性,经统计分析两台仪器检测结果无统计学意义.对不同凝血分析仪进行比对分析,不仅能够及时发现仪器存在的系统误差.而且使其检测结果具有很好的一致性,给临床可提供一个准确、可靠一致的实验室检测结果,使临床对疾病的诊断、疗效观察有一个统一的评判标准.     

MR 脑图像海马自动分割法在AD 早期诊断中的应用研究

目的:研究磁共振(Magnetic resonance,MR)脑图像中海马的自动分割方法及海马的形态学分析方法,为阿尔茨海默病(Alzheimer’s disease,AD)的早期诊断提供依据。方法:对20例AD患者和60名正常对照者行MRI T1 WI 3D容积扫描,建立海马的三维主动表观模型,并以此模型对每个个体脑部磁共振图像上的海马进行自动识别和三维分割,分别建立正常对照组和AD组的海马统计形状模型,比较AD组与正常对照组间海马形状的差异性。结果:海马三维分割方法与手动分割方法在海马体积测量上无统计学差别(P>0.05);AD患者海马头部发生萎缩(P<0.05)。结论:基于主动表观模型的MR脑图像海马自动识别和三维分割法是准确可靠的;海马头部萎缩可作为AD诊断的依据之一。     

全自动核酸分子诊断系统的现状与发展

分子诊断是预测诊断的主要方法,广泛用于血液筛查和传染性疾病的诊断中,也用于个体遗传病的诊断和产前诊断。如今,随着各种新发突发传染病频发,以及精准医疗发展的需要,快速、精确、简便的全自动化集成式分子诊断系统越来越受到全世界的关注。对当前国际致力于全自动化集成式分子诊断系统的公司及其产品进行综述,并对全自动化集成式分子诊断系统的未来发展进行了展望。     

An automatic device for in vivo absorption spectra acquisition and chlorophyll estimation in phytoplankton cultures

In order to aid the study of photoacclimation, a new programmable deviceis described which provides automatic on-line acquisition of in vivo cellabsorption in phytoplankton cultures. The system was used for a long-termstudy of Rhodomonas salina grown at constant photon flux density ina nitrate-limited continuous culture with different dilution rates. Particulate absorption measured at the red chlorophyll a (Chl a)maximum was not a good proxy of biomass, because of the large variabilityof cellular chlorophyll induced by nitrogen limitation. However, thedevice is well suited to automatic assessment of Chl a andphycoerythrin (PE) concentrations in phytoplankton cultures, if algal cellsize and concentration are measured in parallel to correct the packagingeffect. The effects of nitrogen limitation on Chl a and PE contentsand particle absorbance are discussed.