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PDDD-PreTrain:A Series of Commonly Used Pre-Trained Models Support Image-Based Plant Disease Diagnosis

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Plant Phenomics 2023年第2期5卷 313-332页

作者： Xinyu Dong Qi Wang Qianding Huang Qinglong Ge Kejun Zhao Xingcai Wu Xue Wu Liang Lei Gefei Hao State Key Laboratory of Public Big Data College of Computer Science and TechnologyGuizhou UniversityGuiyang 550025China The School of Physics and Optoelectronic Engineering Guangdong University of TechnologyGuangzhou 510006China National Key Laboratory of Green Pesticide Key Laboratory of Green Pesticide and Agricultural BioengineeringMinistry of EducationGuizhou UniversityGuiyang 550025China

Plant diseases threaten global food security by reducing crop yield;thus,diagnosing plant diseases is critical to agricultural production.Artificial intelligence technologies gradually replace traditional plant disease diagnosis methods due to their time-consuming,costly,inefficient,and subjective disadvantages.As a mainstream AI method,deep learning has substantially improved plant disease detection and diagnosis for precision agriculture.In the meantime,most of the existing plant disease diagnosis methods usually adopt a pre-trained deep learning model to support diagnosing diseased leaves.However,the commonly used pre-trained models are from the computer vision dataset,not the botany dataset,which barely provides the pre-trained models sufficient domain knowledge about plant disease.Furthermore,this pre-trained way makes the final diagnosis model more difficult to distinguish between different plant diseases and lowers the diagnostic precision.To address this issue,we propose a series of commonly used pre-trained models based on plant disease images to promote the performance of disease diagnosis.In addition,we have experimented with the plant disease pre-trained model on plant disease diagnosis tasks such as plant disease identification,plant disease detection,plant disease segmentation,and other subtasks.The extended experiments prove that the plant disease pre-trained model can achieve higher accuracy than the existing pre-trained model with less training time,thereby supporting the better diagnosis of plant diseases.In addition,our pre-trained models will be open-sourced at https://***/and Zenodo platform https://***/10.5281/zenodo.7856293.

关键词： diagnosis Plant thereby

De novo serine synthesis regulates chondrocyte proliferation during bone development and repair

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Bone Research 2022年第2期10卷 274-285页

作者： Steve Stegen Shauni Loopmans Ingrid Stockmans Karen Moermans Peter Carmeliet Geert Carmeliet Laboratory of Clinical and Experimental Endocrinology Department of Chronic Diseases and MetabolismKU Leuven3000 LeuvenBelgium Laboratory of Angiogenesis and Vascular Metabolism VIB Center for Cancer Biology3000 LeuvenBelgium Laboratory of Angiogenesis and Vascular Metabolism Department of Oncology and Leuven Cancer InstituteKU Leuven3000 LeuvenBelgium State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat-Sen UniversityGuangzhou 510080China

The majority of the mammalian skeleton is formed through endochondral ossification starting from a cartilaginous template.Cartilage cells, or chondrocytes, survive, proliferate and synthesize extracellular matrix in an avascular environment, but the metabolic requirements for these anabolic processes are not fully understood. Here, using metabolomics analysis and genetic in vivo models, we show that maintaining intracellular serine homeostasis is essential for chondrocyte function. De novo serine synthesis through phosphoglycerate dehydrogenase(PHGDH)-mediated glucose metabolism generates nucleotides that are necessary for chondrocyte proliferation and long bone growth. On the other hand, dietary serine is less crucial during endochondral bone formation, as serine-starved chondrocytes compensate by inducing PHGDH-mediated serine synthesis.Mechanistically, this metabolic flexibility requires ATF4, a transcriptional regulator of amino acid metabolism and stress responses.We demonstrate that both serine deprivation and PHGDH inactivation enhance ATF4 signaling to stimulate de novo serine synthesis and serine uptake, respectively, and thereby prevent intracellular serine depletion and chondrocyte dysfunction. A similar metabolic adaptability between serine uptake and de novo synthesis is observed in the cartilage callus during fracture repair.Together, the results of this study reveal a critical role for PHGDH-dependent serine synthesis in maintaining intracellular serine levels under physiological and serine-limited conditions, as adequate serine levels are necessary to support chondrocyte proliferation during endochondral ossification.

关键词： synthesis starting thereby

Generation of functional oligopeptides that promote osteogenesis based on unsupervised deep learning of protein IDRs

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Bone Research 2022年第2期10卷 354-366页

作者： Mingxiang Cai Baichuan Xiao Fujun Jin Xiaopeng Xu Yuwei Hua Junhui Li Pingping Niu Meijing Liu Jiaqi Wu Rui Yue Yong Zhang Zuolin Wang Yongbiao Zhang Xiaogang Wang Yao Sun Department of Oral Implantology School of StomatologyTongji UniversityShanghai Engineering Research Center of Tooth Restoration and RegenerationShanghai 200072China The First Affiliated Hospital of Jinan University School of StomatologyClinical Research Platform for Interdiscipline of StomatologyJinan UniversityGuangzhou 510630China Key Laboratory of Big Data-Based Precision Medicine School of Engineering MedicineBeihang UniversityBeijing 100191China Guangzhou Laboratory Bioland LaboratoryGuangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangzhou 510320China Institute for Regenerative Medicine Shanghai East HospitalShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China

Deep learning(DL)is currently revolutionizing peptide drug development due to both computational advances and the substantial recent expansion of digitized biological data.However,progress in oligopeptide drug development has been limited,likely due to the lack of suitable datasets and difficulty in identifying informative features to use as inputs for DL models.Here,we utilized an unsupervised deep learning model to learn a semantic pattern based on the intrinsically disordered regions of~171 known osteogenic proteins.Subsequently,oligopeptides were generated from this semantic pattern based on Monte Carlo simulation,followed by in vivo functional characterization.A five amino acid oligopeptide(AIB5P)had strong bone-formation-promoting effects,as determined in multiple mouse models(e.g.,osteoporosis,fracture,and osseointegration of implants).Mechanistically,we showed that AIB5P promotes osteogenesis by binding to the integrinα5 subunit and thereby activating FAK signaling.In summary,we successfully established an oligopeptide discovery strategy based on a DL model and demonstrated its utility from cytological screening to animal experimental verification.

关键词： functional thereby utilized

RIOX1-demethylated cGAS regulates ionizing radiation-elicited DNA repair

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Bone Research 2022年第2期10卷 367-377页

作者： Yanxuan Xiao Jingyi Li Xiaoyu Liao Yumin He Tao He Cuiping Yang Lu Jiang So Mi Jeon Jong-Ho Lee Yongbin Chen Rui Liu Qianming Chen State Key Laboratory of Oral Diseases National Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduSichuan 610041China The Second Affiliated Hospital of Chengdu Medical College China National Nuclear Corporation 416 HospitalChengduSichuan 610051China School of Biological Sciences and Technology Chengdu Medical CollegeChengdu 610599China Department of Cardio-thoracic Surgery the Second Affiliated Hospital of Chengdu Medical CollegeChina National Nuclear Corporation 416 HospitalChengduSichuan 610051China Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences Yunnan Province Kunming Institute of ZoologyKunmingYunnan 650223China Department of Health Sciences The Graduate School of Dong-A UniversityBusan 49315Republic of Korea Department of Biological Sciences Dong-A UniversityBusan 49315Republic of Korea Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China

Exposure to radiation causes DNA damage;hence, continuous surveillance and timely DNA repair are important for genome stability. Epigenetic modifications alter the chromatin architecture, thereby affecting the efficiency of DNA repair. However, how epigenetic modifiers coordinate with the DNA repair machinery to modulate cellular radiosensitivity is relatively unknown. Here, we report that loss of the demethylase ribosomal oxygenase 1(RIOX1) restores cell proliferation and reduces cell death after exposure to ionizing radiation. Furthermore, RIOX1 depletion enhances homologous recombination(HR) repair but not nonhomologous endjoining(NHEJ) repair in irradiated bone marrow cells and oral mucosal epithelial cells. Mechanistic study demonstrates that RIOX1 removes monomethylation at K491 of cyclic GMP-AMP synthase(c GAS) to release c GAS from its interaction with the methyl-lysine reader protein SAGA complex-associated factor 29(SGF29), which subsequently enables c GAS to interact with poly(ADP-ribosyl)ated poly(ADP-ribose) polymerase 1(PARP1) at DNA break sites, thereby blocking PARP1-mediated recruitment of Timeless. High expression of RIOX1 maintains c GAS K491 me at a low level, which impedes HR repair and reduces cellular tolerance to ionizing radiation. This study highlights a novel RIOX1-dependent mechanism involved in the non-immune function of c GAS that is essential for the regulation of ionizing radiation-elicited HR repair.

关键词： thereby repair remove

De novo creation of popcorn-like fragrant foxtail millet

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Journal of Integrative Plant Biology 2023年第11期65卷 2412-2415页

作者： Yanyan Zhang Qiang He Shihui Zhang Xinyu Man Yi Sui Guanqing Jia Sha Tang Hui Zhi Chuanyin Wu Xianmin Diao Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China Zhongyuan Research Center Chinese Academy of Agricultural SciencesXinxiang 453000China

Aroma plays a crucial role in the sensory appeal and enjoyment of food,and it significantly impacts the grain quality of cereals,thereby influencing the value and consumption of agricultural products.For example,aromatic rice varieties like Basmati and Jasmine are renowned for their distinct aroma and command almost double the price of regular rice in the market.

关键词： cereal corn thereby

Functional in vivo assessment of stem cell-secreted pro-oligodendroglial factors

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Neural Regeneration Research 2022年第10期17卷 2194-2196页

作者： Jessica Schira-Heinen Iria Samper Agrelo Veronica Estrada Patrick Küry Department of Neurology Neuroregeneration LaboratoryMedical FacultyHeinrich-Heine-UniversityDüsseldorfGermany

The role of adult neural stem cells(NSCs)in demyelinating diseases of the central nervous system(CNS):Multipotent NSCs hold great potential for cell replacement in diseases and upon injury of the CNS.Originating from radial glial cells during nervous system development,adult NSCs are localized in the subgranular zone of the hippocampus and the subventricular zone(SVZ)of the lateral brain ventricles,the main neurogenic zones of the adult brain.Hippocampal precursor cells(type 1 cells)exhibiting properties of radial glial cells give rise to granule neurons through distinct intermediate precursor cells,and integrate into the hippocampal circuitry[reviewed by Kempermann et al.(2015)].Likewise,under physiological conditions,neuron generation by mouse SVZ-derived NSCs(also known as type B cells)is the predominant cell fate,which thereby results in large numbers of transient amplifying precursor cells(also known as type C cells)which in turn differentiate into neuroblasts(type A cells).These cells migrate along the rostral migratory stream into the olfactory bulb where they undergo maturation into local interneurons.The structure of the rodent SVZ differs from that of the human SVZ since the proliferative capacity is reduced,and migration of neuroblasts is a rare event in adult humans[reviewed by Lim and Alvarez-Buylla(2016)].

关键词： thereby migrate predominant

Old dog,new trick:The PHR-SPX system regulates arbuscular mycorrhizal symbiosis

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Molecular Plant 2022年第2期15卷 225-227页

作者： Debatosh Das Caroline Gutjahr CUHK Shenzhen Research Institute No.10 Yuexing 2nd RoadNanshanShenzhenChina Plant Genetics TUM School of Life SciencesTechnical University of Munich(TUM)Emil Ramann Strasse 485354 FreisingGermany

Plant growth depends on the continuous availability of the macro-nutrient phosphate(Pi).However,in most soils,Pi is only poorly accessible to plants,resulting in Pi deficiency and triggering a number of Pi starvation responses.One strategy of plants to over-come Pi limitation is to form a symbiosis with arbuscular mycor-rhizal(AM)fungi(Smith et al.,2011),which occurs with approximately 80%of land plants.AM fungi improve the uptake of Pi and other mineral nutrients and thereby increase plant performance and stress tolerance.They collect these minerals with an extraradical hyphal network from the soil and release them from highly branched structures,called arbuscules,into root cortex cells.Interestingly,Pi sufficiency causes inhibition of internal root colonization(Balzergue et al.,2011;Breuillin et al.,2010).The mechanistic basis for this has long remained obscure.Two studies have now solved this long-standing mystery and demonstrated that a canonical Pi-response regulatory module regulates AM symbiosis in accordance with the plant Pi status(Shi et al.,2021;Das et al.,2022).

关键词： thereby symbiosis release

Sustainable Laboratory Capacity Building in Sierra Leone:From Ebola to COVID-19

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China CDC weekly 2023年第28期5卷 632-636页

作者： Lili Wang Alie Brima Tia Bing Xu Xiaopeng Qi Doris Harding Center for Global Public Health Chinese Center for Disease Control and PreventionBeijingChina Sierra Leone-China Friendship Biological Safety Laboratory Ministry of Health and SanitationFreetownSierra Leone Ministry of Health and Sanitation FreetownSierra Leone

The onset of the Ebola outbreak in 2014 originated in Guinea and proceeded to swiftly reach Sierra Leone and Liberia(1).Unfortunately,these nations were critically deficient in their capacity for pathogenic testing and diagnostics,the availability of healthcare workers,and their supply of epidemic prevention materials,thereby impeding their ability to address the outbreak efficiently(2).This grave scenario underscored the need for support from the worldwide community.

关键词： Ebola prevention thereby

RNA modifications:importance in immune cell biology and related diseases

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Signal Transduction and Targeted Therapy 2022年第10期7卷 3811-3836页

作者： Lian Cui Rui Ma Jiangluyi Cai Chunyuan Guo Zeyu Chen Lingling Yao Yuanyuan Wang Rui Fan Xin Wang Yuling Shi Department of Dermatology Shanghai Skin Disease HospitalTongji University School of Medicine1278 Baode RoadJing’an DistrictShanghai 200443China Institute of Psoriasis Tongji University School of MedicineShanghaiChina Department of Respiratory and Critical Care Medicine Shanghai Pulmonary HospitalTongji University School of MedicineShanghai 200433China

RNA modifications have become hot topics recently.By influencing RNA processes,including generation,transportation,function,and metabolization,they act as critical regulators of cell biology.The immune cell abnormality in human diseases is also a research focus and progressing rapidly these years.Studies have demonstrated that RNA modifications participate in the multiple biological processes of immune cells,including development,differentiation,activation,migration,and polarization,thereby modulating the immune responses and are involved in some immune related diseases.In this review,we present existing knowledge of the biological functions and underlying mechanisms of RNA modifications,including N6-methyladenosine(m^(6)A),5-methylcytosine(m^(5)C),N1-methyladenosine(m1 A),N7-methylguanosine(m^(7)G),N4-acetylcytosine(ac^(4)C),pseudouridine(Ψ),uridylation,and adenosine-to-inosine(A-to-I)RNA editing,and summarize their critical roles in immune cell biology.Via regulating the biological processes of immune cells,RNA modifications can participate in the pathogenesis of immune related diseases,such as cancers,infection,inflammatory and autoimmune diseases.We further highlight the challenges and future directions based on the existing knowledge.All in all,this review will provide helpful knowledge as well as novel ideas for the researchers in this area.

关键词： diseases thereby modification