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Free form deformation and symmetry constraint‐based multimodal brain image registration using generative adversarial nets

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CAAI Transactions on Intelligence Technology 2023年第4期8卷 1492-1506页

作者： Xingxing Zhu Mingyue Ding Xuming Zhang Department of Biomedical Engineering School of Life Science and TechnologyMinistry of Education Key Laboratory of Molecular BiophysicsHuazhong University of Science and TechnologyWuhanChina

Multi‐modal brain image registration has been widely applied to functional localisation,neurosurgery and computational anatomy.The existing registration methods based on the dense deformation fields involve too many parameters,which is not conducive to the exploration of correct spatial correspondence between the float and reference images.Meanwhile,the unidirectional registration may involve the deformation folding,which will result in the change of topology during registration.To address these issues,this work has presented an unsupervised image registration method using the free form deformation(FFD)and the symmetry constraint‐based generative adversarial networks(FSGAN).The FSGAN utilises the principle component analysis network‐based structural representations of the reference and float images as the inputs and uses the generator to learn the FFD model parameters,thereby producing two deformation fields.Meanwhile,the FSGAN uses two discriminators to decide whether the bilateral registration have been realised simultaneously.Besides,the symmetry constraint is utilised to construct the loss function,thereby avoiding the deformation folding.Experiments on BrainWeb,high grade gliomas,IXI and LPBA40 show that compared with state‐of‐the‐art methods,the FSGAN provides superior performance in terms of visual comparisons and such quantitative indexes as dice value,target registration error and computational efficiency.

关键词： Free‐form deformation Generative adversarial nets Multi‐modal brain image registration Structural representation Symmetry constraint

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Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants

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Journal of Integrative Plant Biology 2022年第12期64卷 2252-2274页

作者： Yutong Liu Jie Wang Bao Liu Zheng-Yi Xu key laboratory of molecular Epigenetics of the ministry of education(MOE) Northeast Normal UniversityChangchun 130024China

DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants.Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications.In the last two decades,how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied.Here,based on recent publications,we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought,abscisic acid,high salt,extreme temperature,nutrient deficiency or toxicity,and ultraviolet B exposure.We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory.We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or-resilient crops,which is essential for coping with global warming and extreme environments.

关键词： abiotic stress DNA methylation histone modification transcriptional regulation

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Ferroelectric hybrid organic-inorganic perovskites and their structural and functional diversity

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National Science Review 2023年第2期10卷 242-259页

作者： Tie Zhang Ke Xu Jie Li Lei He Da-Wei Fu Qiong Ye Ren-Gen Xiong Jiangsu key laboratory for Science and Applications of molecular Ferroelectrics Southeast University Institute for Science and Applications of molecular Ferroelectrics Key Laboratory of the Ministry of Education for Advanced Catalysis MaterialsZhejiang Normal University

molecular ferroele ctrics have gradually aroused great interest in both fundamental scientific research and te chnological applications because of their easy processing,light weight and mechanical flexibility.Hybrid organic-inorganic perovskite ferroelectrics(HOIPFs),as a class of molecule-based ferroelectrics,have diverse functionalities owing to their unique structure and have become a hot spot in molecular ferroelectrics research.Therefore,they are extremely attractive in the field of ferroelectrics.However,there seems to be a lack of systematic review of their design,performance and potential applications.Herein,we review the recent development of HOIPFs from lead-base d,lead-free and metal-free perovskites,and outline the vers atility of these ferroelectrics,including piezoelectricity for mechanical energy-harvesting and optoelectronic properties for photovoltaics and light detection.Furthermore,a perspective view of the challenges and future directions of HOIPFs is also highlighted.

关键词： ferroelectrics hybrid perovskite molecular design photoelectric effect piezoelectricity

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Stereotypes About Enterotype: the Old and New Ideas

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Genomics, Proteomics & Bioinformatics 2019年第1期17卷 4-12页

作者： Mingyue Cheng Kang Ning key laboratory of molecular biophysics of the ministry of education Hubei Key Laboratory of Bioinformatics and Molecular-imaging Department of Bioinformatics and Systems Biology College of Life Science and TechnologyHuazhong University of Science and Technology

In 2011, the term ‘‘enterotype" first appeared to the general public in Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of view.We firstly illustrated the definition of the enterotype and various factors influencing enterotypes,such as diet, administration of antibiotics, and age. Then we summarized lines of evidence that pose the concept against the enterotype, and described the current methods for enterotype analysis.Finally, we showed that the concept of enterotype has been extended to other ecological niches.Based on current studies on enterotypes, it has been clear that more studies with larger sample sizes are needed to characterize the enterotypes. Improved computational methods are also required to build sophisticated models, reflecting the dynamics and resilience of enterotypes.

关键词： Enterotype Gut microbiome Biomarker Continuity Computational methods

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K_(2)S_(2)O_(8)-mediated acylarylation of unactivated alkenes via acyl radical addition/C–H annulation cascade of N-allyl-indoles with silver cocatalysis

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Organic Chemistry Frontiers 2022年第1期9卷 32-38页

作者： Jitan Zhang Manyi Wu Hu Ju Haitao Yang Baiyang Qian Ke Ding Jiaping Wu Meihua Xie key laboratory of Functional molecular Solids(ministry of education) Anhui Key Laboratory of Molecular Based MaterialsCollege of Chemistry and Materials ScienceAnhui Normal UniversityWuhu 241002China.

A silver-catalyzed,K_(2)S_(2)O_(8)-mediated protocol to access regioselective acylarylation of unactivated alkenes was developed.The reaction between N-allyl-indoles andα-oxocarboxylic acids proceeded smoothly and involved an acyl radical addition/C–H cyclization cascade.The protocol showed a broad substrate scope and good tolerance of functional groups.The reaction proceeded with both internal and terminal alkenes to furnish many functional pyrrolo[1,2-a]indoles bearing the ketone carbonyl group,and this feature also provides the potential to construct structurally complex N-containing heterocycles.

关键词： silver allyl radical

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Gut health benefit and application of postbiotics in animal production

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Journal of Animal Science and Biotechnology 2022年第4期13卷 999-1010页

作者： Yifan Zhong Shanshan Wang Hanqiu Di Zhaoxi Deng Jianxin Liu Haifeng Wang College of Animal Science Zhejiang UniversityThe Key Laboratory of Molecular Animal NutritionMinistry of EducationHangzhou 310058China

Gut homeostasis is of importance to host health and imbalance of the gut usually leads to disorders or diseases for both human and animal.Postbiotics have been applied in manipulating of gut health,and utilization of postbiotics threads new lights into the host health.Compared with the application of probiotics,the characteristics such as stability and safety of postbiotics make it a potential alternative to probiotics.Studies have reported the beneficial effects of components derived from postbiotics,mainly through the mechanisms including inhibition of pathogens,strengthen gut barrier,and/or regulation of immunity of the host.In this review,we summarized the characteristics of postbiotics,main compounds of postbiotics,potential mechanisms in gut health,and their application in animal production.

关键词： Animal production Gut health Postbiotics

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Preparation of π-extended fullerene derivatives through addition of phenylenediamine to opencage fullerene derivatives

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Organic Chemistry Frontiers 2022年第2期9卷 320-328页

作者： Zeyu Liu Zhen Liu Rui Gao Jie Su Yi Qiu Liangbing Gan Beijing National laboratory for molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China

Open-cage fullerenes with carbonyl functional groups on the rim of the orifice are ideal precursors for the extension of fullerene π-systems.Unlike isopropylphenylaniline,which reacts selectively with the lactone moiety on the rim of the orifice,phenylenediamine reacts with the adjacent carbonyl and imino groups on a pentagon to form a quinoxaline moiety.Further dehydroxylative aromatization connects the fullerene cage π-system with the quinoxaline π-system.Both the NMR and UV-Vis spectra revealed an evident effect after the extension of the fullerene cage π-system.

关键词： moiety carbonyl react

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Synthesis and structural analysis of titanium-μ-dinitrogen complex supported by di-anionic guanidinate ligands

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Science China Chemistry 2023年第3期66卷 755-759页

作者： Botao Wu Rui Feng Zhu-Bao Yin Haihan Yan Xueli Wang Gao-Xiang Wang Junnian Wei Zhenfeng Xi key laboratory of Bioorganic Chemistry and molecular Engineering Ministry of Education and Beijing National Laboratory for Molecular ScienceCollege of ChemistryPekingUniversityBeijing100871China

The synthesis,characterization,and theoretical studies of titanium-μ-N_(2) complexes with di-anionic guanidinate ligands were reported as the first example of its kind.Thus,with(Me_(3)Si)_(2)N-guanidinate ligands,the mono-anionic guanidinate-supported titanium-μ-N2complex 1 was obtained.Then,reduction of 1 with potassium afforded the di-anionic guanidinate-supported titanium-μ-N_(2) complex 2 via cleavage of one N–Si bond of the(Me3Si)2N substituents in 1,changing the guanidinate ligands automatically from mono-anionic to di-anionic and remarkably lengthening the bond length of theμ-N_(2).Characteristic studies and DFT calculations were performed to reveal that the di-anionic guanidinate ligands stabilized the geometry of 2 and increased the charge density on the bridging dinitrogen.

关键词： dinitrogen complex di-anionic guanidinate ligand titanium

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Prediction of RNA secondary structure with pseudoknots using coupled deep neural networks

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biophysics Reports 2020年第4期6卷 146-154页

作者： Kangkun Mao Jun Wang Yi Xiao School of Physics and key laboratory of molecular biophysics of the ministry of education Huazhong University of Science and Technology

Noncoding RNAs play important roles in cell and their secondary structures are vital for understanding their tertiary structures and functions. Many prediction methods of RNA secondary structures have been proposed but it is still challenging to reach high accuracy, especially for those with pseudoknots.Here we present a coupled deep learning model, called 2 dRNA, to predict RNA secondary structure. It combines two famous neural network architectures bidirectional LSTM and U-net and only needs the sequence of a target RNA as input. Benchmark shows that our method can achieve state-of-the-art performance compared to current methods on a testing dataset. Our analysis also shows that 2 dRNA can learn structural information from similar RNA sequences without aligning them.

关键词： RNA secondary structure prediction Deep learning Minimum free energy

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A practical guide for fast implementation of SNARE-mediated liposome fusion

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biophysics Reports 2024年第1期10卷 31-40页

作者： Shen Wang Cong Ma key laboratory of molecular biophysics of the ministry of education Huazhong University of Science and Technology College of Life Science and Technology

Soluble N-ethylmaleimide-sensitive factor attachment protein receptor(SNAER) family proteins are the engines of most intra-cellular and exocytotic membrane fusion pathways(Jahn and Scheller 2006).Over the past two decades, in-vitro liposome fusion has been proven to be a powerful tool to reconstruct physiological SNARE-mediated membrane fusion processes(Liu et al. 2017). The reconstitution of the membrane fusion process not only provides direct evidence of the capability of the cognate SNARE complex in driving membrane fusion but also allows researchers to study the functional mechanisms of regulatory proteins in related pathways(Wickner and Rizo 2017). Heretofore, a variety of delicate methods for in-vitro SNARE-mediated liposome fusion have been established(Bao et al. 2018;Diao et al. 2012; Duzgunes 2003; Gong et al. 2015; Heo et al. 2021; Kiessling et al. 2015; Kreye et al.2008; Kyoung et al. 2013; Liu et al. 2017; Scott et al. 2003). Although technological advances have made reconstitution more physiologically relevant, increasingly elaborate experimental procedures, instruments, and data processing algorithms nevertheless hinder the non-experts from setting up basic SNARE-mediated liposome fusion assays. Here, we describe a low-cost, timesaving, and easy-to-handle protocol to set up a foundational in-vitro SNARE-mediated liposome fusion assay based on our previous publications(Liu et al. 2023; Wang and Ma 2022). The protocol can be readily adapted to assess various types of SNARE-mediated membrane fusion and the actions of fusion regulators by using appropriate alternative additives(e.g., proteins, macromolecules, chemicals, etc.). The total time required for one round of the assay is typically two days and could be extremely compressed into one day.

关键词： Liposome fusion SNARE In-vitro reconstitution Protocol

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