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基于生物信息学分析青光眼差异表达基因及潜在干预中药实验研究
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作者 滕丹 李乐 +3 位作者 郭溪女 李如岩 王庆峰 曹晶 《沈阳药科大学学报》 CAS CSCD 2024年第10期1386-1397,1404,共13页
目的通过生物信息学方法分析青光眼发病相关核心差异基因,筛选出对青光眼治疗有干预作用的中药,并进行体外细胞实验验证,为青光眼中药治疗提供新的研究思路和实验依据.方法从GEO数据库中获取包含青光眼全基因组表达的数据集GSE27276,用... 目的通过生物信息学方法分析青光眼发病相关核心差异基因,筛选出对青光眼治疗有干预作用的中药,并进行体外细胞实验验证,为青光眼中药治疗提供新的研究思路和实验依据.方法从GEO数据库中获取包含青光眼全基因组表达的数据集GSE27276,用R语言对其进行差异基因分析,String数据库进行蛋白质-蛋白质相互作用(protein-protein interaction,PPI)分析,Cytoscape软件筛选核心差异基因.利用Python语言,在TCMSP数据库内抓取核心差异表达基因对应的化合物及相关中药,进行体外细胞实验研究.用MTT及MTS检测细胞存活率,采用Western Blot检测Bcl-2、Bax、caspase-3蛋白表达,化学荧光法检测细胞内活性氧(ROS),双抗体夹心法测定肿瘤坏死因子α(TNF-α)及白细胞介素(IL-1β)水平.结果从GSE27276中共获得194个差异表达基因,其中表达下调基因为130个,表达上调基因为64个,通过Cytoscape获得15个上调和15个下调核心差异表达基因.利用Python语言,在TCMSP数据库内共抓取了6048个/频次的化合物,最终共获得了498个中药,出现频次最多的中药为冬瓜皮(2852频次),对其进行的体外实验结果表明,采用MTT及MTS两种检测细胞活力方法,高、中、低3种浓度冬瓜皮水提液均可提高过氧化氢损伤后的细胞存活率.Western Blot检测结果表明冬瓜皮水提液可上调Bcl-2/Bax,下调Bax、Caspase-3蛋白表达;ROS检测结果显示,与过氧化氢模型组相比,冬瓜皮水提液三个浓度组ROS水平均明显降低;ELISA检测结果显示冬瓜皮水提液可降低损伤细胞TNF-α和IL-1β水平.结论通过生物信息学方法可挖掘潜在的抗青光眼中药,实验验证可知其中冬瓜皮水提液对视网膜神经节细胞具有保护作用,其作用机制可能与抗炎和抗氧化损伤相关. 展开更多
关键词 青光眼 生物信息学 视网膜神经节细胞 细胞实验
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Advancing automated pupillometry:a practical deep learning model utilizing infrared pupil images
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作者 Dai Guangzheng Yu Sile +2 位作者 Liu Ziming Yan Hairu He Xingru 《国际眼科杂志》 CAS 2024年第10期1522-1528,共7页
AIM:To establish pupil diameter measurement algorithms based on infrared images that can be used in real-world clinical settings.METHODS:A total of 188 patients from outpatient clinic at He Eye Specialist Shenyang Hos... AIM:To establish pupil diameter measurement algorithms based on infrared images that can be used in real-world clinical settings.METHODS:A total of 188 patients from outpatient clinic at He Eye Specialist Shenyang Hospital from Spetember to December 2022 were included,and 13470 infrared pupil images were collected for the study.All infrared images for pupil segmentation were labeled using the Labelme software.The computation of pupil diameter is divided into four steps:image pre-processing,pupil identification and localization,pupil segmentation,and diameter calculation.Two major models are used in the computation process:the modified YoloV3 and Deeplabv 3+models,which must be trained beforehand.RESULTS:The test dataset included 1348 infrared pupil images.On the test dataset,the modified YoloV3 model had a detection rate of 99.98% and an average precision(AP)of 0.80 for pupils.The DeeplabV3+model achieved a background intersection over union(IOU)of 99.23%,a pupil IOU of 93.81%,and a mean IOU of 96.52%.The pupil diameters in the test dataset ranged from 20 to 56 pixels,with a mean of 36.06±6.85 pixels.The absolute error in pupil diameters between predicted and actual values ranged from 0 to 7 pixels,with a mean absolute error(MAE)of 1.06±0.96 pixels.CONCLUSION:This study successfully demonstrates a robust infrared image-based pupil diameter measurement algorithm,proven to be highly accurate and reliable for clinical application. 展开更多
关键词 PUPIL infrared image algorithm deep learning model
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