reproducible-computational-workflow-for-drug-discovery-to-standardize

Reproducible Computational Workflow for Drug Discovery to Standardize Network Pharmacology and Molecular Docking Analyses

Network pharmacology and molecular docking are widely applied in drug discovery, yet fragmented workflows and inconsistent operations frequently undermine ...

Beijing University of Chinese Medicine

: To assess the performance of elastography (ES) and ultrasound (US) in predicting the malignancy of breast lesions and to compare their combined diagnostic value with that of magnetic resonance imaging (MRI). : The study prospectively enrolled 242 female patients with dense breasts treated in 35 heath care facilities in China between November 2018 and October 2019. Based on conventional US and elastography, radiologists classified the degree of suspicion of breast lesions according to the US Breast Imaging Reporting and Data System (BI-RADS) criteria. The diagnostic value was compared between US BI-RADS and MRI BI-RADS, with pathological results used as the reference standard. : The results demonstrated that irregular tumor shape, a nonparallel growth orientation, indistinct margins, angular contours, microcalcifications, color Doppler flow and ES score on US imaging were significantly related to breast cancer in dense breasts (P=0.001; P=0.001; P=0.008; P<0.001; P=0.019; P=0.008; P=0.002, respectively). The sensitivity, specificity, PPV, NPV, accuracy and AUC of US BI-RADS category were 94.7%, 90.7%, 95.8%, 88.0%, 93.4% and 0.93 (95%CI, 0.88-0.97), respectively, while those of MRI BI-RADS category were 98.2%, 57.5%, 84.3%, 83.3%, 86.0% and 0.78 (95%CI, 0.71-0.85), respectively. MRI BI-RADS showed a significantly higher sensitivity than US BI-RADS (98.2% vs 94.7%, P=0.043), whereas US BI-RADS showed significantly higher specificity (90.7% vs 57.5%, P<0.001). US BI-RADS showed better diagnostic efficiency in differentiating nodules in dense breasts than MRI BI-RADS (AUC 0.93 vs 0.78, P<0.001). : By combining the use of ES and conventional US, US BI-RADS had better diagnostic efficiency in differentiating nodules in dense breasts than MRI. For the diagnosis of malignant tumors in patients with dense breasts, MRI and US BI-RADS can be used as supplemental diagnostic tools to detect lesions, with US BI-RADS considered the preferred adjunctive resource.

Can Combined Screening of Ultrasound and Elastography Improve Breast Cancer Identification Compared with MRI in Women with Dense Breasts-a Multicenter Prospective Study.

 To develop and to validate a risk-predicted nomogram for downgrading Breast Imaging Reporting and Data System (BI-RADS) category 4a breast lesions.  We enrolled 680 patients with breast lesions that were diagnosed as BI-RADS category 4a by conventional ultrasound from December 2018 to June 2019. All 4a lesions were randomly divided into development and validation groups at the ratio of 3:1. In the development group consisting of 499 cases, the multiple clinical and ultrasound predicted factors were extracted, and dual-predicted nomograms were constructed by multivariable logistic regression analysis, named clinical nomogram and ultrasound nomogram, respectively. Patients were twice classified as either "high risk" or "low risk" in the two nomograms. The performance of these dual nomograms was assessed by an independent validation group of 181 cases. Receiver Operating Characteristic (ROC) curve and diagnostic value were calculated to evaluate the applicability of the new model.  After multiple logistic regression analysis, the clinical nomogram included 2 predictors: age and the first-degree family members with breast cancer. The area under the curve (AUC) value for the clinical nomogram was 0.661 and 0.712 for the development and validation groups, respectively. The ultrasound nomogram included 3 independent predictors (margins, calcification and strain ratio), and the AUC value in this nomogram was 0.782 and 0.747 in the development and validation groups, respectively. In the development group of 499 patients, approximately 50.90% (254/499) of patients were twice classified "low risk", with a malignancy rate of 1.18%. In the validation group of 181 patients, approximately 47.51% (86/181) of patients had been twice classified as "low risk", with a malignancy rate of 1.16%.  A dual-predicted nomogram incorporating clinical factors and imaging characteristics is an applicable model for downgrading the low-risk lesions in BI-RADS category 4a and shows good stability and accuracy, which is useful for decreasing the rate of invasive examinations and surgery.

Risk-predicted dual nomograms consisting of clinical and ultrasound factors for downgrading BI-RADS category 4a breast lesions - A multiple centre study.

Plant hormone brassinosteroids (BRs) play key roles in plant adaptation to biotic stresses, including various pathogen infections. As a core factor in BR signaling, the transcription factor BRI1-EMS-SUPPRESSOR 1 (BES1) activates BR responses  regulating the expression of target genes. However, the molecular mechanism of BRs in regulating plant immunity is unclear, and the key components are not identified. In this study, we found that BR biosynthesis and signaling transduction are essential for plant resistance to pathogen infection, and BR biosynthesis or BR signaling-deficient mutants displayed susceptibility to  pv.  DC3000 ( DC3000) infection [including more serious symptoms and more photosystem II (PSII) photochemistry damage]. We identified a callose synthase gene  () as a direct target of BES1, and its expression was induced by BRs/BES1. Meanwhile, BRs induced callose accumulation after  DC3000 infection. Moreover, BES1 gain-of-function mutant  showed promoted  DC3000 resistance.  T-DNA insertion mutant  was susceptible to DC3000, while brassinolide (BL) treatment partially rescued  susceptible phenotypes. Our study suggests that BR-induced pathogen resistance partly depends on the BR-induced BES1-GSL8 cascade to mediate callose accumulation.

Brassinosteroids Positively Regulate Plant Immunity  BRI1-EMS-SUPPRESSOR 1-Mediated  Transcription.

Studies on deep learning (DL)-based models in breast ultrasound (US) remain at the early stage due to a lack of large datasets for training and independent test sets for verification. We aimed to develop a DL model for differentiating benign from malignant breast lesions on US using a large multicenter dataset and explore the model's ability to assist the radiologists.

Deep learning based on ultrasound images assists breast lesion diagnosis in China: a multicenter diagnostic study.

An organized cervical cancer screening program is an effective method to prevent and control cervical cancer. This study aims to find barriers and facilitators in the implementation process of National Cervical Cancer Screening Program in Rural Areas (NACCSPRA) in China through program evaluation, and thus propose suggestions for optimization of the program.

Status quo and problem analysis of cervical cancer screening program in China: Based on RE-AIM framework.

The incidence of depression has been steadily rising in recent years, making it one of the most prevalent mental illnesses. As the pursuit of novel antidepressant drugs captivates the pharmaceutical field, the therapeutic efficacy of Traditional Chinese Medicine (TCM) has been widely explored. Chaihu () has been traditionally used for liver conditions such as hepatitis, liver inflammation, liver fibrosis, and liver cancer. It is believed to have hepatoprotective effects, promoting liver cell regeneration and protecting against liver damage. In addition,  has also been used as a Jie Yu (depression-relieving) medicine in China, Japan, Republic of Korea, and other Asian countries for centuries. This review article aims to summarize the research conducted on the antidepressant properties and mechanisms of , as well as discuss the potential of TCM formulas containing . This review highlights various antidepressant ingredients isolated from , including saikosaponin A, saikosaponin D, rutin, puerarin, and quercetin, each with distinct mechanisms of action. Additionally, Chinese herb prescriptions and extracts containing , such as Chaihu Shugansan, Xiaoyaosan, and Sinisan, are also included due to their demonstrated antidepressant effects. This review reveals that these  compounds exhibit antidepressant effects through the regulation of neurotransmitter mechanisms (such as 5-HT and DA), the NMDA (N-methyl-D-aspartate) system, brain-derived neurotrophic factor (BDNF), and other intracellular signaling pathways. Collectively, this comprehensive review provides insights into the multiple applications of  in the treatment of depression and highlights its potential as an alternative or complementary approach to traditional therapies. However, it is essential to consider the potential adverse effects and clinical restrictions of  despite its promising potential. Further research is needed to elucidate its specific mechanisms of action and evaluate its effectiveness in human subjects.

 in Treatment of Depression Disorder: A Comprehensive Review.

The global rise in mental disorders presents a significant public health challenge, highlighting the need for a deeper understanding of their underlying risk factors. Existing studies on obesity and brain health primarily rely on metrics such as body mass index and waist-to-hip ratio, which inadequately capture central obesity, a fat distribution strongly associated with increased health risks. This underscores the need for more precise metrics, with the body roundness index (BRI) emerging as a promising option. 321,596 UK Biobank participants were analyzed in this study. Cox regression models assessed associations between BRI and incident mental disorders, while logistic and multiple linear regression models explored relationships with psychiatric symptoms and white matter integrity, respectively. Results indicated that higher BRI was significantly associated with increased risks of incident overall mental disorders (HR [95% CI] = 1.12 [1.09, 1.15]), as well as specific high-prevalence disorders including substance use disorder (1.05 [1.01, 1.11]), depressive disorder (1.34 [1.24, 1.45]), and anxiety disorder (1.09 [1.03, 1.15]). An overall positive association was also observed between elevated BRI and adverse psychiatric symptoms and reduced white matter integrity. These findings highlighted BRI as a potential indicator of mental health. BRI's association with clinical and subclinical psychiatric outcomes emphasized its relevance in understanding the interplay between central adiposity and brain health.

Body roundness index and mental health in middle-aged and elderly adults: a prospective cohort study.

To elucidate the possible mechanism of Jiawei Erzhi pill (, JWEZP) in the treatment of atherosclerosis (AS).

Network pharmacology combined with experiments to explore the molecular mechanism of Jiawei Erzhi pill protects against atherosclerosis by inhibiting ferroptosis.

Article	Year
Can Combined Screening of Ultrasound and Elastography Improve Breast Cancer Identification Compared with MRI in Women with Dense Breasts-a Multicenter Prospective Study. Journal of Cancer\| PubMed ID: 32328194	2020
Risk-predicted dual nomograms consisting of clinical and ultrasound factors for downgrading BI-RADS category 4a breast lesions - A multiple centre study. Journal of Cancer\| PubMed ID: 33391426	2021
Brassinosteroids Positively Regulate Plant Immunity BRI1-EMS-SUPPRESSOR 1-Mediated Transcription. Frontiers in plant science\| PubMed ID: 35401617	2022
Deep learning based on ultrasound images assists breast lesion diagnosis in China: a multicenter diagnostic study. Insights into imaging\| PubMed ID: 35900608	2022
Status quo and problem analysis of cervical cancer screening program in China: Based on RE-AIM framework. Frontiers in public health\| PubMed ID: 36311598	2022
in Treatment of Depression Disorder: A Comprehensive Review. Pharmaceuticals (Basel, Switzerland)\| PubMed ID: 38675471	2024
Body roundness index and mental health in middle-aged and elderly adults: a prospective cohort study. Scientific reports\| PubMed ID: 40593122	2025
Network pharmacology combined with experiments to explore the molecular mechanism of Jiawei Erzhi pill protects against atherosclerosis by inhibiting ferroptosis. Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan\| PubMed ID: 41376225	2025

Jiawei Ran

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