1.ACtriplet: An improved deep learning model for activity cliffs prediction by in tegrating triplet loss and pre-training.
Xinxin YU ; Yimeng WANG ; Long CHEN ; Weihua LI ; Yun TANG ; Guixia LIU
Journal of Pharmaceutical Analysis 2025;15(8):101317-101317
Activity cliffs (ACs) are generally defined as pairs of similar compounds that only differ by a minor structural modification but exhibit a large difference in their binding affinity for a given target. ACs offer crucial insights that aid medicinal chemists in optimizing molecular structures. Nonetheless, they also form a major source of prediction error in structure-activity relationship (SAR) models. To date, several studies have demonstrated that deep neural networks based on molecular images or graphs might need to be improved further in predicting the potency of ACs. In this paper, we integrated the triplet loss in face recognition with pre-training strategy to develop a prediction model ACtriplet, tailored for ACs. Through extensive comparison with multiple baseline models on 30 benchmark datasets, the results showed that ACtriplet was significantly better than those deep learning (DL) models without pre-training. In addition, we explored the effect of pre-training on data representation. Finally, the case study demonstrated that our model's interpretability module could explain the prediction results reasonably. In the dilemma that the amount of data could not be increased rapidly, this innovative framework would better make use of the existing data, which would propel the potential of DL in the early stage of drug discovery and optimization.
2.Regulatory roles of JAZ in the growth and development of horticultural plants.
Xinxin ZHANG ; Tao TAO ; Hangchun LI ; Zhi QIAO ; Qinglin TANG ; Dayong WEI ; Yang YANG ; Zhimin WANG
Chinese Journal of Biotechnology 2025;41(2):530-545
Jasmonic acid (JA) is a common plant hormone with regulatory effects on plant growth and development. The jasmonate ZIM-domain (JAZ) proteins (JAZs), as key regulators in the JA signaling pathway, are involved in multiple biological processes such as anthocyanin accumulation, flowering time modulation, and secondary metabolite synthesis in plants. JAZs are essential components of many regulatory signaling networks. The JAZ genes, members of the plant-specific TIFY family, have been identified in the genomes of a variety of horticultural plants. Here, we summarized the research progress in the roles of JAZs in horticultural plants, aiming to give insights into the further study of the biological functions and regulatory networks of JAZ genes in plants.
Horticulture
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Repressor Proteins/metabolism*
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Plant Proteins/metabolism*
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Cyclopentanes/metabolism*
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Oxylipins/metabolism*
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Plants/metabolism*
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Plant Development
3.The regulatory role of the RUS family in plant growth and development.
Yao HU ; Sirui LI ; Xinxin ZHANG ; Qinglin TANG ; Dayong WEI ; Shibing TIAN ; Yang YANG ; Zhimin WANG
Chinese Journal of Biotechnology 2024;40(1):81-93
The chloroplast genome encodes many key proteins involved in photosynthesis and other metabolic processes, and metabolites synthesized in chloroplasts are essential for normal plant growth and development. Root-UVB (ultraviolet radiation B)-sensitive (RUS) family proteins composed of highly conserved DUF647 domain belong to chloroplast proteins. They play an important role in the regulation of various life activities such as plant morphogenesis, material transport and energy metabolism. This article summarizes the recent advances of the RUS family proteins in the growth and development of plants such as embryonic development, photomorphological construction, VB6 homeostasis, auxin transport and anther development, with the aim to facilitate further study of its molecular regulation mechanism in plant growth and development.
Female
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Pregnancy
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Humans
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Ultraviolet Rays
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Biological Transport
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Chloroplasts/genetics*
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Embryonic Development
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Plant Development/genetics*
4.Effect of printing orientation on physical and mechanical properties of 3D printing prosthodontic base resin materials
Xinxin ZHAN ; Lulu CAO ; Dong XIANG ; Hao TANG ; Dandan XIA ; Hong LIN
Journal of Peking University(Health Sciences) 2024;56(2):345-351
Objective:To analyze the influence of forming direction on the surface characteristics,elastic modulus,bending strength and fracture toughness of printed parts and the relationship between forming direction and force direction,and to provide scientific basis and guidance for the clinical applica-tion of oral denture base resin materials.Methods:The 3D printing technology was used to print denture base resin samples.The shape and size of the samples referred to the current standard for testing conven-tional denture base materials.The samples used for physical performance testing were cylindrical(with a diameter of 15 mm and a thickness of 1 mm)and printed at different angles along the Z axis(0°,45°,90°).Scanning electron microscope was used to observe the microscopic topography of the different sam-ples.The color stability of different samples was observed by color stabilizer.The surface roughness of the samples was analyzed by using surface roughness tester.The Vickers hardness was measured to ana-lyze the hardness of the samples.The samples used for mechanical performance testing were rectangular(elastic modulus and bending strength:A length of 64 mm,a width of 10 mm,and a height of 3.3 mm;fracture toughness:A length of 39 mm,a width of 8 mm,and a height of 4 mm),divided into two groups:W group and H group.The W group was printed from the bottom up along the Z axis with the length × width as the bottom surface parallel to the X,Y axis plane,while the H group printed from the bottom up along the Z axis with the length × height as the bottom surface parallel to the X,Y axis plane.The forming angles of both groups were equally divided into 0°,45°,and 90°.The elastic modulus,bending strength and fracture toughness of different samples were studied through universal mechanical testing machine.SPSS 22.0 software was used for statistical analysis.Results:The microscopic topogra-phy and roughness of different samples were closely related to the printing direction,with significant differences between the 0°,45°,and 90° specimens.The 0° specimens had the smoothest surface(roughness<1 μm).The surface of the 45 ° specimen was the roughest(roughness>3 μm).The microhardness of the 0° sample was the best[(196.13±0.20)MPa],with a significant difference com-pared with the 90° sample[(186.62±4.81)MPa,P<0.05].The mechanical properties of different samples were also closely related to the printing direction.The elastic modulus,bending strength,and fracture toughness of the 45° samples in the W group were the highest compared with the other groups.The results of elastic modulus showed that in the H group,the 45° specimens had the highest elastic mo-dulus,which was significantly different from the 0° and 90° specimens(P<0.05).The elastic modulus of 0° and 45° specimens in the W group were higher than those in 90° specimens(P<0.05).The bending strength results showed that there was no significant difference between the specimens from dif-ferent angles in the H group.The bending strength of the 90° specimens in the W group was the smallest,and there was a significant difference between 90° and the 0° and 45° specimens(P<0.05);And the bendind strength of the 0° and 45° specimens in the W group was significantly higher than that of the 0° and 45° specimens in the H group(P<0.05).The fracture toughness results showed that the fracture toughness of the H group specimens was lower than 1.9 MPa m1/2,which was specified in the denture base standard.The 45° samples in the W group were the highest,with significant differences compared with the 0° and 90° samples(P<0.05).And the 90° samples of the W group specimens were lower than 1.9 MPa m1/2.And the fracture toughness of the 45° specimen in the W group was significantly higher than that of all the specimens in the H group(P<0.05).Conclusion:The 0° samples had rela-tively better physical properties.The 45° samples had the best mechanical properties.But the fracture toughness of specimens(H group and 90° samples of W group)did not yet meet clinical requirements.That indicated that the characteristics of the 3D printing denture base resin were affected by the printing direction.Only when the performance of the printed samples in all directions met the minimum require-ments of the standard,they could be used in clinical practice.
5.Integration model of management, teaching and research for general practice talent training in community teaching bases
Yan LI ; Wei SONG ; Yiming LI ; Xinxin ZHAO ; Qi XU ; Fang CHENG ; Lan TANG ; Shanzhu ZHU
Chinese Journal of General Practitioners 2024;23(1):65-69
The community teaching bases play an important role in training of general practice talents. To raise the training quality, the development of their own capacity is crucial, but community medical institutions also need close cooperation with the departments of general practice in medical schools and the higher-level general hospitals. This article discusses the integration model of management, teaching and research in general practice talent training based on the cooperation of community teaching bases with relevant governmental departments, professional societies/associations, general hospitals and medical schools.
6.Breast imaging reporting and data system classification combined with mammography radiomics for differentiating breast benign and malignant amorphous calcification lesions
Xinxin LI ; Xiuting CHEN ; Jie LI ; Li YANG ; Xiaomin TANG ; Jing YAN ; Chengcheng MA ; Zhizhen GAO
Chinese Journal of Medical Imaging Technology 2024;40(10):1519-1523
Objective To observe the value of breast imaging reporting and data system(BI-RADS)classification combined with mammography(MG)radiomics for differentiating breast benign and malignant amorphous calcification lesions.Methods A total of 217 breast amorphous calcification lesions in 206 female patients,including 43 malignant and 174 benign ones were retrospectively enrolled and randomly divided into training set(n=151)and validation set(n=66)at the ratio of 7∶3.Then radiomics features were screened based on breast MG images.BI-RADS model,radiomics model and combined model were established,and the value of each model for distinguishing benign and malignant lesions was observed.Results Eight optimal radiomics features were selected.The area under the curve(AUC)of BI-RADS model,radiomics model and combined model for differentiating breast benign and malignant amorphous calcification lesions was 0.821,0.763 and 0.897 in training set,0.800,0.746 and 0.893 in validation set,respectively,AUC of combined model was significantly higher than that of the other two(both P<0.05).Conclusion BI-RADS classification combined with MG radiomics was helpful for differential diagnosis of breast benign and malignant amorphous calcification lesions,with efficacy higher than that of each alone.
7.Genetic analysis of a child with mos 46, X, psu idic(X)(q21.3)40/45, X3
Ting YIN ; Fang ZHANG ; Xinxin TANG ; Minmin ZHU ; Anshun ZHENG ; Qin ZHENG ; Xiaoxi WANG ; Leilei WANG
Chinese Journal of Medical Genetics 2024;41(8):977-981
Objective:To explore the correlation between structural chromosomal abnormality and clinical characteristics of a child featuring gonadal dysplasia.Methods:A 13-year-old child who was admitted to Lianyungang Maternal and Child Health Care Hospital on February 7, 2023 for primary amenorrhoea and occasional abdominal pain was selected as the study subject. Clinical data of the child was collected, and peripheral blood samples of the child and her parents were collected. G-banding chromosomal karyotyping and copy number variation sequencing (CNV-seq) were carried out. "Pseudodual centromere isochromosome X" and "psu idic(X)" were used as keywords to search the CNKI, Wanfang and PubMed databases, and the search period was set as from January 1, 2002 to June 1, 2023. Relevant literature on the structural abnormality of X chromosome was searched and analyzed retrospectively.Results:The child has a height of 153 cm and weighed 45 kg. She has no obvious facial dysmorphism. Laboratory tests showed that she had higher FSH and luteinizing hormone, and lower E2. Ultrasonography showed that she had small ovaries and rudimentary uterus. She was found to have a karyotype of 46, X, psu idic(X)(q21.3)[40]/mos 45, X[3], whilst both of her parents had a normal karyotype. CNV-seq showed that she had a 63.27 Mb deletion in Xq21.32q28 and a 91.59 Mb duplication in Xp22.33q21.32 (mosaicism rate = 74%). A total of 11 relevant literature were retrieved. Clinical phenotypes of patients with similar structural chromosomal abnormalities were diverse, which was closely related to the mosaicism rate of the 45, X karyotype and the location of the breaking point.Conclusion:46, X, psu idic(X)(q21.3)/45, X probably underlay the dysplasia of uterus and ovary and sex hormone abnormalities in this child, while her height was spared. Deletion of Xq21.32q28 is a key factor leading to Turner syndrome-like phenotype such as rudimentary uterus and ovarian dysplasia.
8.Caries experience and its correlation with caries activity of 4-year-old children in Miyun District of Beijing
Xinxin CHEN ; Zhe TANG ; Yanchun QIAO ; Wensheng RONG
Journal of Peking University(Health Sciences) 2024;56(5):833-838
Objective:To investigate the prevalence of dental caries of 4-year-old children in Miyun District of Beijing by international caries detection and assessment system(ICDAS),to detect the caries activity Cariostat value and to analyze the correlation between the Cariostat value and dental caries.Methods:Totally 815 children aged 4 years in 7 kindergartens in Miyun District of Beijing were recrui-ted.The clinical examination of all children was conducted by one examiner using ICDAS.The oral de-birs and plaques were collected by one doctor who recorded the Cariostat scores.The results of clinical examination were compared between genders.At the same time,the prevalence of dental caries,the mean d3-6ft/d3_6fs and d1-6ft/d1-6fs among high Cariostat scores group(2.0-3.0),medium Cariostat scores group(1.5)and low Cariostat scores group(0-1.0)were compared.The distributions of incipi-ent caries in different Cariostat scores groups were compared among children with incipient caries only.Results:All the children had incipient caries,and 78.3%of the children had cavitated caries with ICDAS score of 3 or above.The mean d1-2t scores were 9.76±3.65,the mean d3-6ft scores was 4.64±4.43 and the mean d1-6ft scores were 14.41±3.42.The incipient caries with ICDAS score of 1-2 were widely distributed,accounting for 67.7%of the total numbers of caries.There was no significant diffe-rence in caries prevalence and caries experience between genders(P>0.05).The proportion of children with high Cariostat scores in boys(43.6%)was higher than that in girls(33%)and the difference was statistically significant(P<0.05).With the increase of Cariostat scores,the prevalence of cavitated caries,the mean d3-6ft/d3-6fs and d1-6ft/d,_6fs scores in children was on the increase and the difference among the three groups was statistically significant(P<0.05).For children with incipient caries only,the distribution of incipient caries in different Cariostat scores groups was no significant difference(P>0.05).Conclusion:ICDAS can detect early enamel demineralization of deciduous teeth in children.The prevalence of dental caries among 815 4-year-old children in Miyun District of Beijing is more serious,and incipient caries is widely distributed in children.Cariostat value reflects the status of cavi-tated caries and has no correlation with the distribution of incipient caries.Therefore,the combined ap-plication of ICDAS and Cariostat caries activity detection method is helpful for the detection of incipient caries and screening of caries high-risk children,which has great significance for the comprehensive ma-nagement of caries in children and the formulation of early preventive measures.
9.Prediction of benign and malignant amorphous calcifications in the breast based on clinical and mammographic features
Xinxin LI ; Huiyu DUAN ; Xiaomin TANG ; Dawei ZHOU ; Xiuting CHEN ; Chengcheng MA ; Jing YAN ; Zhizhen GAO
Journal of Practical Radiology 2024;40(8):1276-1280
Objective To investigate the risk factors affecting the malignancy of amorphous calcifications in the breast and to establish a predictive nomogram.Methods Patients with amorphous calcifications detected by mammography were retrospectively collected,clinical data were obtained from electronic medical record(EMR),and the mammographic features of the patients were assessed by diagnostic physicians.The risk factors affecting the malignancy of amorphous calcifications were analyzed to develop a predictive model and to assess the performance of the model.Results A total of 153 amorphous calcifications in 144 patients were included in the study,and the overall malignancy rate of calcifications was 20.92%.Patient's age ≥45 years,linear distribution of calcifications,unilateral single or unilateral multiple calcifications,and a larger maximum ratio of calcification extent all predicted a higher probability of malignancy,establishing a nomogram based on these 4 risk factors,with a 3.65%predicted probability of malig-nancy as the cut-off,33.99%(52/153)of patients were allowed to be spared biopsy.Conclusion Patient's age and the distribution,number,and maximum ratio of calcifications may be the risk predictors of malignancy for amorphous calcifications,with nomogram con-struction for distinguishing benignity from malignancy of amorphous calcifications via combining with mammographic features and clinical data.
10.A CRISPR activation screen identifies genes that enhance SARS-CoV-2 infection.
Fei FENG ; Yunkai ZHU ; Yanlong MA ; Yuyan WANG ; Yin YU ; Xinran SUN ; Yuanlin SONG ; Zhugui SHAO ; Xinxin HUANG ; Ying LIAO ; Jingyun MA ; Yuping HE ; Mingyuan WANG ; Longhai TANG ; Yaowei HUANG ; Jincun ZHAO ; Qiang DING ; Youhua XIE ; Qiliang CAI ; Hui XIAO ; Chun LI ; Zhenghong YUAN ; Rong ZHANG
Protein & Cell 2023;14(1):64-68

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