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General General

Grading the Severity of Damage to the Perijunctional Actomyosin Ring and Zonula Occludens-1 of the Corneal Endothelium by Ensemble Learning Methods.

In Journal of ocular pharmacology and therapeutics : the official journal of the Association for Ocular Pharmacology and Therapeutics

Purpose: In many epithelia, including the corneal endothelium, intracellular/extracellular stresses break down the perijunctional actomyosin ring (PAMR) and zonula occludens-1 (ZO-1) at the apical junctions. This study aims to grade the severity of damage to PAMR and ZO-1 through machine learning. Methods: Immunocytochemical images of PAMR and ZO-1 were drawn from recent studies on the corneal endothelium subjected to hypothermia and oxidative stress. The images were analyzed for their morphological (e.g., Hu moments) and textural features (based on gray-level co-occurrence matrix [GLCM] and Gabor filters). The extracted features were ranked by SHapley analysis and analysis of variance. Then top features were used to grade the severity of damage using a suite of ensemble classifiers, including random forest, bagging classifier (BC), AdaBoost, extreme gradient boosting, and stacking classifier. Results: A partial set of features from GLCM, along with Hu moments and the number of hexagons, enabled the classification of damage to PAMR into Control, Mild, Moderate, and Severe with the area under the receiver operating characteristics curve (AUC) = 0.92 and F1 score = 0.77 with BC. In contrast, a bank of Gabor filters provided a partial set of features that could be combined with Hu moments, branch length, and sharpness for the classification of ZO-1 images into four levels with AUC = 0.95 and F1 score of 0.8 with BC. Conclusions: We have developed a workflow that enables the stratification of damage to PAMR and ZO-1. The approach can be applied to similar data during drug discovery or pathophysiological studies of epithelia.

Shilpashree Palanahalli S, Ravi Tapanmitra, Thanuja M Y, Anupama Chalimeswamy, Ranganath Sudhir H, Suresh Kaggere V, Srinivas Sangly P

2023-Mar-17

ZO-1, barrier function, corneal endothelium, machine learning, perijunctional actomyosin ring, tight junctions

General General

Deep-Learning-Assisted Underwater 3D Tactile Tensegrity.

In Research (Washington, D.C.)

The growth of underwater robotic applications in ocean exploration and research has created an urgent need for effective tactile sensing. Here, we propose an underwater 3-dimensional tactile tensegrity (U3DTT) based on soft self-powered triboelectric nanogenerators and deep-learning-assisted data analytics. This device can measure and distinguish the magnitude, location, and orientation of perturbations in real time from both flow field and interaction with obstacles and provide collision protection for underwater vehicles operation. It is enabled by the structure that mimics terrestrial animals' musculoskeletal systems composed of both stiff bones and stretchable muscles. Moreover, when successfully integrated with underwater vehicles, the U3DTT shows advantages of multiple degrees of freedom in its shape modes, an ultrahigh sensitivity, and fast response times with a low cost and conformability. The real-time 3-dimensional pose of the U3DTT has been predicted with an average root-mean-square error of 0.76 in a water pool, indicating that this developed U3DTT is a promising technology in vehicles with tactile feedback.

Xu Peng, Zheng Jiaxi, Liu Jianhua, Liu Xiangyu, Wang Xinyu, Wang Siyuan, Guan Tangzhen, Fu Xianping, Xu Minyi, Xie Guangming, Wang Zhong Lin

2023

General General

Rational Design of Organelle-Targeted Fluorescent Probes: Insights from Artificial Intelligence.

In Research (Washington, D.C.)

Monitoring the physiological changes of organelles is essential for understanding the local biological information of cells and for improving the diagnosis and therapy of diseases. Currently, fluorescent probes are considered as the most powerful tools for imaging and have been widely applied in biomedical fields. However, the expected targeting effects of these probes are often inconsistent with the real experiments. The design of fluorescent probes mainly depends on the empirical knowledge of researchers, which was inhibited by limited chemical space and low efficiency. Herein, we proposed a novel multilevel framework for the prediction of organelle-targeted fluorescent probes by employing advanced artificial intelligence algorithms. In this way, not only the targeting mechanism could be interpreted beyond intuitions but also a quick evaluation method could be established for the rational design. Furthermore, the targeting and imaging powers of the optimized and synthesized probes based on this methodology were verified by quantitative calculation and experiments.

Dong Jie, Qian Jie, Yu Kunqian, Huang Shuai, Cheng Xiang, Chen Fei, Jiang Hualiang, Zeng Wenbin

2023

General General

Trends and Potential of Machine Learning and Deep Learning in Drug Study at Single-Cell Level.

In Research (Washington, D.C.)

Cancer treatments always face challenging problems, particularly drug resistance due to tumor cell heterogeneity. The existing datasets include the relationship between gene expression and drug sensitivities; however, the majority are based on tissue-level studies. Study drugs at the single-cell level are perspective to overcome minimal residual disease caused by subclonal resistant cancer cells retained after initial curative therapy. Fortunately, machine learning techniques can help us understand how different types of cells respond to different cancer drugs from the perspective of single-cell gene expression. Good modeling using single-cell data and drug response information will not only improve machine learning for cell-drug outcome prediction but also facilitate the discovery of drugs for specific cancer subgroups and specific cancer treatments. In this paper, we review machine learning and deep learning approaches in drug research. By analyzing the application of these methods on cancer cell lines and single-cell data and comparing the technical gap between single-cell sequencing data analysis and single-cell drug sensitivity analysis, we hope to explore the trends and potential of drug research at the single-cell data level and provide more inspiration for drug research at the single-cell level. We anticipate that this review will stimulate the innovative use of machine learning methods to address new challenges in precision medicine more broadly.

Qi Ren, Zou Quan

2023

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Semi-Self-Supervised Learning for Semantic Segmentation in Images with Dense Patterns.

In Plant phenomics (Washington, D.C.)

Deep learning has shown potential in domains with large-scale annotated datasets. However, manual annotation is expensive, time-consuming, and tedious. Pixel-level annotations are particularly costly for semantic segmentation in images with dense irregular patterns of object instances, such as in plant images. In this work, we propose a method for developing high-performing deep learning models for semantic segmentation of such images utilizing little manual annotation. As a use case, we focus on wheat head segmentation. We synthesize a computationally annotated dataset-using a few annotated images, a short unannotated video clip of a wheat field, and several video clips with no wheat-to train a customized U-Net model. Considering the distribution shift between the synthesized and real images, we apply three domain adaptation steps to gradually bridge the domain gap. Only using two annotated images, we achieved a Dice score of 0.89 on the internal test set. When further evaluated on a diverse external dataset collected from 18 different domains across five countries, this model achieved a Dice score of 0.73. To expose the model to images from different growth stages and environmental conditions, we incorporated two annotated images from each of the 18 domains to further fine-tune the model. This increased the Dice score to 0.91. The result highlights the utility of the proposed approach in the absence of large-annotated datasets. Although our use case is wheat head segmentation, the proposed approach can be extended to other segmentation tasks with similar characteristics of irregularly repeating patterns of object instances.

Najafian Keyhan, Ghanbari Alireza, Sabet Kish Mahdi, Eramian Mark, Shirdel Gholam Hassan, Stavness Ian, Jin Lingling, Maleki Farhad

2023

General General

An Effective Integrated Machine Learning Framework for Identifying Severity of Tomato Yellow Leaf Curl Virus and Their Experimental Validation.

In Research (Washington, D.C.)

Tomato yellow leaf curl virus (TYLCV) dispersed across different countries, specifically to subtropical regions, associated with more severe symptoms. Since TYLCV was first isolated in 1931, it has been a menace to tomato industrial production worldwide over the past century. Three groups were newly isolated from TYLCV-resistant tomatoes in 2022; however, their functions are unknown. The development of machine learning (ML)-based models using characterized sequences and evaluating blind predictions is one of the major challenges in interdisciplinary research. The purpose of this study was to develop an integrated computational framework for the accurate identification of symptoms (mild or severe) based on TYLCV sequences (isolated in Korea). For the development of the framework, we first extracted 11 different feature encodings and hybrid features from the training data and then explored 8 different classifiers and developed their respective prediction models by using randomized 10-fold cross-validation. Subsequently, we carried out a systematic evaluation of these 96 developed models and selected the top 90 models, whose predicted class labels were combined and considered as reduced features. On the basis of these features, a multilayer perceptron was applied and developed the final prediction model (IML-TYLCVs). We conducted blind prediction on 3 groups using IML-TYLCVs, and the results indicated that 2 groups were severe and 1 group was mild. Furthermore, we confirmed the prediction with virus-challenging experiments of tomato plant phenotypes using infectious clones from 3 groups. Plant virologists and plant breeding professionals can access the user-friendly online IML-TYLCVs web server at https://balalab-skku.org/IML-TYLCVs, which can guide them in developing new protection strategies for newly emerging viruses.

Bupi Nattanong, Sangaraju Vinoth Kumar, Phan Le Thi, Lal Aamir, Vo Thuy Thi Bich, Ho Phuong Thi, Qureshi Muhammad Amir, Tabassum Marjia, Lee Sukchan, Manavalan Balachandran

2023