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AttentionSplice: An Interpretable Multi-Head Self-Attention Based Hybrid Deep Learning Model in Splice Site Prediction

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Chinese Journal of Electronics 2022年第5期31卷 870-887页

作者： YAN Wenjing ZHANG Baoyu ZUO Min ZHANG Qingchuan WANG Hong mao da Division of Chemical Metrology and Analytical Science National Institute of Metrology National Engineering Laboratory for Agri-Product Quality Traceability Beijing Technology and Business University

Pre-mRNA splicing is an essential procedure for gene transcription. Through the cutting of introns and exons, the DNA sequence can be decoded into different proteins related to different biological *** cutting boundaries are defined by the donor and acceptor splice sites. Characterizing the nucleotides patterns in detecting splice sites is sophisticated and challenges the conventional methods. Recently, the deep learning frame has been introduced in predicting splice sites and exhibits high performance. It extracts high dimension features from the DNA sequence automatically rather than infers the splice sites with prior knowledge of the relationships, dependencies, and characteristics of nucleotides in the DNA sequence. This paper proposes the Attention Splice model, a hybrid construction combined with multi-head self-attention, convolutional neural network, bidirectional long short-term memory *** performance of Attention Splice is evaluated on the Homo sapiens(Human) and Caenorhabditis Elegans(Worm) datasets. Our model outperforms state-of-the-art models in the classification of splice sites. To provide interpretability of Attention Splice models, we extract important positions and key motifs which could be essential for splice site detection through the attention learned by the model. Our result could offer novel insights into the underlying biological roles and molecular mechanisms of gene expression.

关键词： pre-mRNA splicing RNA Caenorhabditis Elegans datasets genetics convolutional neural network feature extraction AttentionSplice model acceptor splice sites genomics convolutional neural nets DNA gene expression biological functions splice site detection proteins DNA sequence interpretable multihead self-attention recurrent neural nets splice site prediction gene transcription deep learning (artificial intelligence) molecular mechanisms Homo sapiens bioinformatics bidirectional long short-term memory network cellular biophysics donor splice sites pattern classification hybrid deep learning model molecular biophysics nucleotides patterns

A Computational Study on Water-assisted Ammonolysis of N-Methyl β-Sultam

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Chemical Research in Chinese Universities 2006年第1期22卷 94-98页

作者： HE mao-xia FENG da-cheng YU Ling-juan CAI Zheng-ting Institute of Theoretical Chemistry Shandong University Jinan 250100 P. R. China

The ring opening of β-sultam v/a an H2O-assisted ammonolysis process was studied by using Density Functional Theory（DFT） method at the B3LYP/6-31G level as a further step in the theoretical investigation of the ammonolysis reaction of β-sultams. The calculated pathways are analogous to those previously described for the non-assisted ammonolysis reaction. Solvent effects were assessed by using the polarized continuum model（PCM） method. The results show that mode 1 and pathway a in channel Ⅱ are the most favorable ones in both the cases. The energy barrier of the cleavage of C-S bonds producing P1 is the highest among all the energy barriers. The presence of a solvent in the continuum model disfavors the reaction, whereas the participation of water in the ammonolysis reaction plays a positive role and reduces the active energy greatly. The relative energies of all the transition states in the assisted ammonolysis are 20-80 kJ/mol lower than those for the non-assisted reaction.

关键词： Ammonolysis Water-assisted mechanism Density Functional Theory(DFT) β-Sultam

A Numerical Investigation of the Reduction of Solitary Wave Runup by A Row of Vertical Slotted Piles

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China Ocean Engineering 2020年第1期34卷 10-20页

作者： YAO Yu JIA Mei-jun mao da-wei DENG Zheng-zhi LIU Xiao-jian School of Hydraulic Engineering Changsha University of Science and TechnologyChangsha410114China Hunan Provincial Key Laboratory of Key Technology on Hydropower Development Changsha 410014China Ocean College Zhejiang UniversityZhoushan 316021China Key Laboratory of Water-Sediment Sciences and Water Disaster Prevention of Hunan Province Changsha 410114China

To improve the current understanding of the reduction of tsunami-like solitary wave runup by the pile breakwater on a sloping beach, we developed a 3D numerical wave tank based on the CFD tool OpenFOAM in this study. The Navier Stokes equations were applied to solve the two-phase incompressible flow, combined with an LES model to solve the turbulence and a VOF method to capture the free surface. The adopted model was firstly validated with existing empirical formulas for solitary wave runup on the slope without the pile structure. It is then validated using our new laboratory observations of the free surface elevation, the velocity and the pressure around a row of vertical slotted piles subjected to solitary waves, as well as the wave runup on the slope behind the piles. Subsequently, a set of numerical simulations were implemented to analyze the wave reflection, the wave transmission, and the shoreline runup with various offshore wave heights, offshore water depths, adjacent pile spaces and beach slopes. Finally, an improved empirical equation accounting for the maximum wave runup on the slope was proposed by taking the presence of the pile breakwater into consideration.

关键词： Wave runup solitary wave slotted piles Navier Stokes equations

Effect of long-term fertilization on soil nitrate distribution

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Journal of Environmental Sciences 2001年第1期13卷 58-63页

作者： GUO Li ping ZHANG Fu suo WANG Xing ren mao da ru CHEN Xin ping Department of Plant Nutrition China Agricultural UniversityBeijing 100094China.

A thirteen years long-term field fertilizer experiment was conducted to monitor the effect of different fertilization on soil nitrate distribution. The results showed: (1) Applying relative excessive N fertilizer could result large quantities of NO3- residue and NO3- movement downward in soil profiles; amending phosphate fertilizer or organic manure with nitrogen fertilizer together could significantly improve the status of NO3- leaching downward due to the balanced uptake of nutrients by crops. ( 2) Appropriate amounts of nitrogen fertilizer which was equal or smaller than the optimal fertilization rate could not result in more NO3- leaching in Northern China. (3) Precipitation influenced the amounts and depth of soil NO3- leaching: NO3- could move to 80 cm depth or below at autumn or at the next spring when rainfall was higher during the rainy season through July to September in North China.

关键词： fertilization soil nitrate nitrate leaching long-term experiment nitrogen apparent recovery

A Cross-linked Polyethylene with Recyclability and Mechanical Robustness Enabled by Establishment of Multiple Hydrogen Bonds Network via Reactive Melt Blending

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Chinese Journal of Polymer Science 2023年第7期41卷 1104-1114页

作者： Hong-da mao Ting-Ting Zhang Zhen-You Guo Dong-Yu Bai Jie Wang Hao Xiu Qiang Fu College of Polymer Science and Engineering State Key Laboratory of Polymer Materials EngineeringSichuan UniversityChengdu610065China Chongqing University Key Laboratory of Micro/Nano Materials Engineering and Technology Chongqing University of Arts and SciencesChongqing402160China Hubei Huifu Nanomaterial Co. LTD.Yichang443007China

Physical cross-linking by hydrogen-bonds (H-bonds), providing a good combination of application properties of thermosets and processability of thermoplastics, is a potential strategy to resolve the recycling problem of traditional chemically cross-linked polyethylene. However, ureidopyrimidone (UPy), the most widely used H-bonding motif, is unfavorable for large-scale industrial application due to its poor thermal stability. In this work, H-bonds cross-linked polyethylene was successfully prepared by reactive melt blending maleic anhydride grafted polyethylene (PE-g-MAH) with 3-amino-1,2,4-triazole (ATA) to form amide triazole ring-carboxylic acid units. Triazole ring can easily generate multiple H-bonds with carboxylic acid and amide. More importantly, these units are more thermal stable than UPy due to the absence of unstable urea group of UPy. The introduction of H-bonds cross-linking leads to an obvious improvement in mechanical properties and creep resistance and a good maintain in thermal properties and recyclability. Furthermore, the reinforcement effect monotonically improves with increasing the density of H-bonds. The obtained good properties are mainly attributed to largely enhanced interchain interactions induced by H-bonds cross-linking and intrinsic reversibility of H-bonds. This work develops a novel way for the simple fabrication of H-bonds cross-linked PE with high performance through reactive melt blending.

关键词： Cross-linked polyethylene Hydrogen bonds Recyclability

Enhancement Effect of CpG DNA on the Somatostatin DNA Vaccine in Mice

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Agricultural Sciences in China 2007年第7期6卷 882-889页

作者： XUE Chun-lin mao da-gan YANG Li-guo CHENG Bao College of Animal Science and Technology Huazhong Agricultural University Wuhan 430070 P.R.China Research Institute of Animal Breeding ＆ Reproduction Nanjing Agricultural University Nanjing 210095 P.R.China Yancheng Institute of Animal Husbandry ＆ Veterinary Yancheng 224002 P.R. China

To study the immune effect of CpGDNA on somatostatin （SS） DNA vaccine, the 20-day-old experimental mice were immunized with 20 lag SS eukaryotic expression plasmid pES/2SS with different adjuvants in equal dose, such as the synthetic CpG-ODN, the pE-CpG plasmid, E. coli DNA and the crude liposome. A booster was given two weeks later. The results showed that the body weight gain of female mice in the SS immunized group was higher than that of the control （P 〈0.05）. The levels of antibodies against SS, IgG2a/IgG1, spleen lymphocyte proliferation activity and the concentrations of GH and IGF-Ⅰ in the DNA vaccine groups combined with CpGDNA were significantly increased compared to that of the group immunized with DNA vaccine alone. All these suggested the recombinant SS expression plasmid can stimulate animals to produce antibodies against SS, and CpGDNA adjuvant can enhance the immune effect of DNA vaccine against SS and influence the concentration of GH and IGF-Ⅰ .

关键词： immnostimulatory sequence CpGDNA somatostatin DNA vaccine

Effect of electromagnetic and ultrasonic cast rolling on microstructure and properties of 1050 aluminum substrate for presensitized plate

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Journal of Central South University 2015年第2期22卷 422-429页

作者：石琛毛大恒扶宗礼 School of Materials Science and Engineering (Central South University) State Key Laboratory of High Performance and Complex Manufacturing (Central South University)

The 1050 aluminum alloy strip was prepared by means of electromagnetic and ultrasonic cast rolling on the modified asymmetric twin roll caster, and then the aluminum substrate for presensitized plate was prepared through cold rolling and *** effects of electromagnetic and ultrasonic cast rolling on microstructure, mechanical properties, surface roughness and electrolytic corrosion properties of 1050 aluminum substrate were studied. The results show that electromagnetic and ultrasonic cast rolling can decrease the average crystallite size of aluminum substrate by 5 μm, increase the crystal boundaries with uniform distribution, and make the second-phase particles with smaller size distributed dispersively in the substrate, meanwhile, it can increase the tensile strength, elongation and micro-hardness by 4.58%, 9.85% and HV 2, respectively, reduce the surface roughness, make the surface appearance more even, electrolytic corrosion polarization curve of aluminum substrate more smooth and the surface corrosion pits with regular shape more dispersive.

关键词： 1050 aluminum alloy electromagnetic and ultrasonic cast rolling microstructure mechanical properties electrolytic corrosion property

A protective role of resveratrol against the effects of immobilization stress in corpora lutea of mice in early pregnancy

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Journal of Integrative Agriculture 2020年第7期19卷 1857-1866页

作者： Saif ULLAH Sheeraz MUSTAFA Wael ENNAB Muhammad JAN Muhammad SHAFIQ Ngekure MXKAVITA LU Zeng-peng mao da-gan SHI Fang-xiong College of Animal Science and Technology Nanjing Agricultural UniversityNanjing 210095P.R.China

In the present study,we aimed to investigate a protective role for resveratrol against the effects of immobilization stress on corpora lutea(CL)of mice in early pregnancy.A total of 45 early-pregnant mice were divided into no immobilization stress(NIS)group,immobilization stress(IS)group,and immobilization and resveratrol treatment(IS+RES)group(n=15).Mice were immobilized in plastic tubes(50 mL)for 3 h per day during day 1 to 7 of *** the IS+RES group,5 mg kg-'d-1 of resveratrol was administered just prior to application of *** analyzed apoptotic activity in CL by Western botting analysis(WB),transmission electron microscopy(TEM),and immunohistochemistry(IHC).Serum progesterone levels were examined with radioimmunoassay(RIA).IHC results showed that the intensity of positive staining for Bax was increased,and for BcI-2 was decreased in CL after IS,while resveratrol treatment reversed the positive staining for Bax and *** revealed that immobilization stress up-regulated the expression of Bax and caspase-9,and down-regulated Bcl-2 expression,while resveratrol treatment attenuated the effects of immobilization stress on the expression of Bax,Bcl-2 and *** to our TEM results,apoptosis as defined by chromatin condensation was found in CL after immobilization stress,while resveratrol inhibited the *** also demonstrated that immobilization stress decreased progesterone concentrations and ovarian expression of StAR,while resveratrol restored the concentrations of progesterone and expression of StAR back to *** results indicated that immobilization stress induced luteal regression while resveratrol inhibited luteal regression,suggesting that resveratrol plays a protective role on corpora lutea of mice during early pregnancy.

关键词： immobilization stress apoptosis corpora lutea resveratrol pregnant mice

Application of Nano-tungsten disulfide particulates in green motor oil

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材料科学与工程（中英文版） 2008年第4期2卷 12-19页

作者： SHI Chen mao da-heng School of Mechanical and Electrical Engineering Central South University Changsha 410083 China