Receive a weekly summary and discussion of the top papers of the week by leading researchers in the field.
2023-03-24 00:00:00 +0000
General
Coronaviruses induce severe upper respiratory tract infections, which can spread to the lungs. The nucleocapsid protein (N protein) plays an important role in genome replication, transcription, and virion assembly in SARS-CoV-2, the virus causing COVID-19, and in other coronaviruses. Glycogen synthase kinase 3 (GSK3) activation phosphorylates the viral N protein. To combat COVID-19 and future coronavirus outbreaks, interference with the dependence of N protein on GSK3 may be a viable strategy. Toward this end, this study aimed to construct robust machine learning models to identify GSK3 inhibitors from Food and Drug Administration-approved and investigational drug libraries using the quantitative structure-activity relationship approach. A non-redundant dataset consisting of 495 and 3070 compounds for GSK3α and GSK3β, respectively, was acquired from the ChEMBL database. Twelve sets of molecular descriptors were used to define these inhibitors, and machine learning algorithms were selected using the LazyPredict package. Histogram-based gradient boosting and light gradient boosting machine algorithms were used to develop predictive models that were evaluated based on the root mean square error and R-squared value. Finally, the top two drugs (selinexor and ruboxistaurin) were selected for molecular dynamics simulation based on the highest predicted activity (negative log of the half-maximal inhibitory concentration, pIC50 value) to further investigate the structural stability of the protein-ligand complexes. This artificial intelligence-based virtual high-throughput screening approach is an effective strategy for accelerating drug discovery and finding novel pharmacological targets while reducing the cost and time.
2023-03-24 00:00:00 +0000
General
Genomic selection (GS), a strategy to use genotypes to predict phenotypes via statistical or machine learning models, has become a routine practice in plant breeding programs. GS can speed up the genetic gain by reducing phenotyping costs and/or shortening the breeding cycles. GS analysis is complicated involving data clean up and formatting, training and test population analysis, model selection and evaluation, and parameter optimization. In addition, GS analysis also requires some programming skills and knowledge of statistical modeling. Thus, we need a more practical GS tools for breeders. To alleviate this difficulty, we developed the web-based platform IP4GS (https://ngdc.cncb.ac.cn/ip4gs/), which offers a user-friendly interface to perform GS analysis simply through point-and-click actions. IP4GS currently includes seven commonly used models, eleven evaluation metrics, and visualization modules, offering great convenience for plant breeders with limited bioinformatics knowledge to apply GS analysis.
2023-03-24 00:00:00 +0000
General
Identifying available farmland suitable for agricultural machinery is the most promising way of optimizing agricultural production and increasing agricultural mechanization. Farmland consolidation suitable for agricultural machinery (FCAM) is implemented as an effective tool for increasing sustainable production and mechanized agriculture. By using the machine learning approach, this study assesses the suitability of farmland for agricultural machinery in land consolidation schemes based on four parameters, i.e., natural resource endowment, accessibility of agricultural machinery, socioeconomic level, and ecological limitations. And based on "suitability" and "potential improvement in farmland productivity", we classified land into four zones: the priority consolidation zone, the moderate consolidation zone, the comprehensive consolidation zone, and the reserve consolidation zone. The results showed that most of the farmland (76.41%) was either basically or moderately suitable for FCAM. Although slope was often an indicator that land was suitable for agricultural machinery, other factors, such as the inferior accessibility of tractor roads, continuous depopulation, and ecological fragility, contributed greatly to reducing the overall suitability of land for FCAM. Moreover, it was estimated that the potential productivity of farmland would be increased by 720.8 kg/ha if FCAM were implemented. Four zones constituted a useful basis for determining the implementation sequence and differentiating strategies for FCAM schemes. Consequently, this zoning has been an effective solution for implementing FCAM schemes. However, the successful implementation of FCAM schemes, and the achievement a modern and sustainable agriculture system, will require some additional strategies, such as strengthening farmland ecosystem protection and promoting R&D into agricultural machinery suitable for hilly terrain, as well as more financial support.
2023-03-24 00:00:00 +0000
Surgery
The current guidelines for the ascending aortic aneurysm (AsAA) treatment recommend surgery mainly according to the maximum diameter assessment. This criterion has already proven to be often inefficient in identifying patients at high risk of aneurysm growth and rupture. In this study, we propose a method to compute a set of local shape features that, in addition to the maximum diameter D, are intended to improve the classification performances for the ascending aortic aneurysm growth risk assessment. Apart from D, these are the ratio DCR between D and the length of the ascending aorta centerline, the ratio EILR between the length of the external and the internal lines and the tortuosity T. 50 patients with two 3D acquisitions at least 6 months apart were segmented and the growth rate (GR) with the shape features related to the first exam computed. The correlation between them has been investigated. After, the dataset was divided into two classes according to the growth rate value. We used six different classifiers with input data exclusively from the first exam to predict the class to which each patient belonged. A first classification was performed using only D and a second with all the shape features together. The performances have been evaluated by computing accuracy, sensitivity, specificity, area under the receiver operating characteristic curve (AUROC) and positive (negative) likelihood ratio LHR+ (LHR-). A positive correlation was observed between growth rate and DCR (r = 0.511, p = 1.3e-4) and between GR and EILR (r = 0.472, p = 2.7e-4). Overall, the classifiers based on the four metrics outperformed the same ones based only on D. Among the diameter-based classifiers, k-nearest neighbours (KNN) reported the best accuracy (86%), sensitivity (55.6%), AUROC (0.74), LHR+ (7.62) and LHR- (0.48). Concerning the classifiers based on the four shape features, we obtained the best accuracy (94%), sensitivity (66.7%), specificity (100%), AUROC (0.94), LHR+ (+∞) and LHR- (0.33) with support vector machine (SVM). This demonstrates how automatic shape features detection combined with risk classification criteria could be crucial in planning the follow-up of patients with ascending aortic aneurysm and in predicting the possible dangerous progression of the disease.
2023-03-24 00:00:00 +0000
General
Fetal distress is a symptom of fetal intrauterine hypoxia, which is seriously harmful to both the fetus and the pregnant woman. The current primary clinical tool for the assessment of fetal distress is Cardiotocography (CTG). Due to subjective variability, physicians often interpret CTG results inconsistently, hence the need to develop an auxiliary diagnostic system for fetal distress. Although the deep learning-based fetal distress-assisted diagnosis model has a high classification accuracy, the model not only has a large number of parameters but also requires a large number of computational resources, which is difficult to deploy to practical end-use scenarios. Therefore, this paper proposes a lightweight fetal distress-assisted diagnosis network, LW-FHRNet, based on a cross-channel interactive attention mechanism. The wavelet packet decomposition technique is used to convert the one-dimensional fetal heart rate (FHR) signal into a two-dimensional wavelet packet coefficient matrix map as the network input layer to fully obtain the feature information of the FHR signal. With ShuffleNet-v2 as the core, a local cross-channel interactive attention mechanism is introduced to enhance the model's ability to extract features and achieve effective fusion of multichannel features without dimensionality reduction. In this paper, the publicly available database CTU-UHB is used for the network performance evaluation. LW-FHRNet achieves 95.24% accuracy, which meets or exceeds the classification results of deep learning-based models. Additionally, the number of model parameters is reduced many times compared with the deep learning model, and the size of the model parameters is only 0.33 M. The results show that the lightweight model proposed in this paper can effectively aid in fetal distress diagnosis.
2023-03-24 00:00:00 +0000
General
Objective: To characterize a socially active humanoid robot's therapeutic interaction as a therapeutic assistant when providing arm rehabilitation (i.e., arm basis training (ABT) for moderate-to-severe arm paresis or arm ability training (AAT) for mild arm paresis) to stroke survivors when using the digital therapeutic system Evidence-Based Robot-Assistant in Neurorehabilitation (E-BRAiN) and to compare it to human therapists' interaction. Methods: Participants and therapy: Seventeen stroke survivors receiving arm rehabilitation (i.e., ABT [n = 9] or AAT [n = 8]) using E-BRAiN over a course of nine sessions and twenty-one other stroke survivors receiving arm rehabilitation sessions (i.e., ABT [n = 6] or AAT [n = 15]) in a conventional 1:1 therapist-patient setting. Analysis of therapeutic interaction: Therapy sessions were videotaped, and all therapeutic interactions (information provision, feedback, and bond-related interaction) were documented offline both in terms of their frequency of occurrence and time used for the respective type of interaction using the instrument THER-I-ACT. Statistical analyses: The therapeutic interaction of the humanoid robot, supervising staff/therapists, and helpers on day 1 is reported as mean across subjects for each type of therapy (i.e., ABT and AAT) as descriptive statistics. Effects of time (day 1 vs. day 9) on the humanoid robot interaction were analyzed by repeated-measures analysis of variance (rmANOVA) together with the between-subject factor type of therapy (ABT vs. AAT). The between-subject effect of the agent (humanoid robot vs. human therapist; day 1) was analyzed together with the factor therapy (ABT vs. AAT) by ANOVA. Main results and interpretation: The overall pattern of the therapeutic interaction by the humanoid robot was comprehensive and varied considerably with the type of therapy (as clinically indicated and intended), largely comparable to human therapists' interaction, and adapted according to needs for interaction over time. Even substantially long robot-assisted therapy sessions seemed acceptable to stroke survivors and promoted engaged patients' training behavior. Conclusion: Humanoid robot interaction as implemented in the digital system E-BRAiN matches the human therapeutic interaction and its modification across therapies well and promotes engaged training behavior by patients. These characteristics support its clinical use as a therapeutic assistant and, hence, its application to support specific and intensive restorative training for stroke survivors.
General
Modeling structure-activity relationships with machine learning to identify GSK3-targeted small molecules as potential COVID-19 therapeutics.
In Frontiers in endocrinology ; h5-index 55.0
Pirzada Rameez Hassan, Ahmad Bilal, Qayyum Naila, Choi Sangdun
2023
GSK3, QSAR, coronaviruses, machine learning, molecular descriptors
General
IP4GS: Bringing genomic selection analysis to breeders.
In Frontiers in plant science
Li Tong, Jiang Shan, Fu Ran, Wang Xiangfeng, Cheng Qian, Jiang Shuqin
2023
R shiny, bioinformatics, genomic selection, genotype-to-phenotype prediction, web-based platform
General
Assessing farmland suitability for agricultural machinery in land consolidation schemes in hilly terrain in China: A machine learning approach.
In Frontiers in plant science
Yang Heng, Ma Wenqiu, Liu Tongxin, Li Wenqing
2023
farmland consolidation suitable for agricultural machinery, hilly terrain, machine learning approach (MLA), potential of farmland productivity, suitability assessment, zoning
Surgery
Assessment of shape-based features ability to predict the ascending aortic aneurysm growth.
In Frontiers in physiology
Geronzi Leonardo, Haigron Pascal, Martinez Antonio, Yan Kexin, Rochette Michel, Bel-Brunon Aline, Porterie Jean, Lin Siyu, Marin-Castrillon Diana Marcela, Lalande Alain, Bouchot Olivier, Daniel Morgan, Escrig Pierre, Tomasi Jacques, Valentini Pier Paolo, Biancolini Marco Evangelos
2023
aorta, ascending aorta aneurysm, biomechanical features, cardiovascular diseases, classification, growth rate, machine learning, risk assessment
General
A lightweight fetal distress-assisted diagnosis model based on a cross-channel interactive attention mechanism.
In Frontiers in physiology
Deng Yanjun, Zhang Yefei, Zhou Zhixin, Zhang Xianfei, Jiao Pengfei, Zhao Zhidong
2023
attention mechanism, fetal distress, fetal heart rate, lightweight model, wavelet packet coefficient
General
Analysis of the therapeutic interaction provided by a humanoid robot serving stroke survivors as a therapeutic assistant for arm rehabilitation.
In Frontiers in robotics and AI
Platz Thomas, Pedersen Ann Louise, Deutsch Philipp, Umlauft Alexandru-Nicolae, Bader Sebastian
2023
arm, artificial intelligence, interaction, robot, social, stroke, training
Weekly Summary
Receive a weekly summary and discussion of the top papers of the week by leading researchers in the field.