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shinyTempSignal:an R shiny application for exploring temporal and other phylogenetic signals

Journal of Genetics and Genomics 2024年第7期51卷 762-768页

作者： Li Zhan Xiao Luo Wenqin Xie Xuan-An Zhu Zijing Xie Jianfeng lin lin Li Wenli Tang Rui Wang lin deng Yufan Liao Bingdong Liu Yantong Cai Qianwen Wang Shuangbin Xu Guangchuang Yu Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong 510515China Faculty of Computers Guangdong University of TechnologyGuangzhouGuangdong 510006China Ubigene Biosciences Co. Ltd.GuangzhouGuangdong 510530China State Key Laboratory of Applied Microbiology Southern China Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Open Laboratory of Applied MicrobiologyGuangdong Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

The molecular clock model is fundamental for inferring species divergence times from molecular ***,its direct application may introduce significant biases due to sequencing errors,recombination events,and inaccurately labeled sampling *** accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous ***,while not all branches of a phylogenetic tree may exhibit a clear temporal signal,specific branches may still adhere to the assumptions,with varying evolutionary *** a relaxed molecular clock model better aligns with the complexities of *** root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic *** its utility,there remains a lack of corresponding software implementations for broader *** address this gap,we present shinyTempSignal,an interactive web application implemented with the shiny framework,available as an R package and publicly accessible at https://***/YuLab-SMU/*** tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed *** extending the root-to-tip regression method to diverse signals,shinyTempSignal helps in the detection of evolving features or traits,thereby laying the foundation for deeper insights and subsequent analyses.

关键词： Molecular clock Root-to-tip regression Temporal signal Phylogenetic signal

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Regulation of 2-acetyl-1-pyrroline and grain quality in early-season indica fragrant rice by nitrogen and silicon fertilization under different plantation methods

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Journal of Integrative Agriculture 2024年第2期23卷 511-535页

作者： yongjian Chen Lan Dai Siren Cheng yong Ren Huizi deng Xinyi Wang Yuzhan Li Xiangru Tang Zaiman Wang Zhaowen Mo State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of AgricultureSouth China Agricultural UniversityGuangzhou 510642China Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology Yulin Normal UniversityYulin 537000China Key Laboratory for Conservation and Utilization of Subtropical Bio-Resources Education Department of Guangxi Zhuang Autonomous Region/College of Biology and PharmacyYulin Normal UniversityYulin 537000China Scientific Observing and Experimental Station of Crop Cultivation in South China Ministry of Agriculture and Rural AffairsGuangzhou 510642China Guangzhou Key Laboratory for Science and Technology of Fragrant Rice Guangzhou 510642China Key Laboratory of Key Technology for South Agricultural Machine and Equipment Ministry of Education/College of EngineeringSouth China Agricultural UniversityGuangzhou 510642China

Fragrant rice has a high market value,and it is a popular rice type among consumers owing to its pleasant *** methods,nitrogen(N)fertilizers,and silicon(Si)fertilizers can affect the grain yield and fragrance of fragrant ***,the core commercial rice production attributes,namely the head rice yield(HRY)and 2-acetyl-1-pyrroline(2-AP)content of fragrant rice,under various nitrogen and silicon(N-Si)fertilization levels and different plantation methods remain *** field experiment in this study was performed in the early seasons of 2018 and 2019 with two popular indica fragrant rice cultivars(Yuxiangyouzhan and Xiangyaxiangzhan).They were grown under six N-Si fertilization treatments(combinations of two levels of Si fertilizer,0 kg Si ha^(−1)(Si0)and 150 kg Si ha^(−1)(Si1),and three levels of N fertilizer,0 kg N ha^(−1)(N0),150 kg N ha^(−1)(N1),and 220 kg N ha^(−1)(N2))and three plantation methods(artificial transplanting(AT),mechanical transplanting(MT),and mechanical direct-seeding(MD)).The results showed that the N-Si fertilization treatments and all the plantation methods significantly affected the HRY and 2-AP content and related parameters of the two different fragrant rice *** with the Si0N0 treatment,the N-Si fertilization treatments resulted in higher HRY and 2-AP *** rates of brown rice,milled rice,head rice,and chalky rice of the fragrant rice also improved with the N-Si fertilization *** N-Si fertilization treatments increased the activities of N metabolism enzymes and the accumulation of N and Si in various parts of the fragrant rice,and affected their antioxidant response *** key parameters for the HRY and 2-AP content were assessed by redundancy ***,the structural equation model revealed that the Si and N accumulation levels indirectly affected the HRY by affecting the N metabolism enzyme activity,N use efficiency,and grain quality of fragrant ***,high N

关键词： fragrant rice 2-AP content head rice yield mechanical planting nitrogen silicon

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Deterministic and Robust Volt-var Control Methods of Power System Based on Convex Deep Learning

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Journal of Modern Power Systems and Clean Energy 2024年第3期12卷 719-729页

作者： Qing Ma Changhong deng the School of Electrical Engineering and Automation Wuhan UniversityWuhanChina

Volt-var control(VVC)is essentially a non-convex optimization problem due to the non-convexity of power flow(PF)constraints,resulting in the difficulty in obtaining the optimum without convexity *** existing second-order cone method for the convexity conversion often leads to a sharp increase in PF constraints and optimization variables,which in turn increases the optimization difficulty or even leads to optimization *** paper first proposes a deterministic VVC method based on convex deep learning power flow(DLPF).This method uses the input convex neural network(ICNN)to establish a single convex mapping between state parameters and node voltage to complete the convexity conversion while the optimization variables only correspond to reactive power equipment,which can ensure the global optimum with extremely fast computation *** cope with the impact brought by the uncertainty of distributed energy and omit the additional worst scenario search of traditional robust VVC,this paper proposes robust VVC method based on convex deep learning interval power flow(DLIPF),which continues to adopt ICNN to establish another convex mapping between state parameters and node voltage *** DLIPF with DLPF,this method decreases the modeling and optimization difficulty of robust VVC *** results on 30-bus,118-bus,and 200-bus systems prove the correctness and rapidity of the proposed methods.

关键词： Volt-var control convexity conversion convex deep learning power flow

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Pediatric liver transplantation in 31 consecutive children

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Chinese Medical Journal 2008年第20期121卷 2001-2003页

作者： SHEN Zhong-yang WANG Zi-fa ZHU Zhi-jun ZANG Yun-jin ZHENG Hong deng yong-lin PAN Cheng CHEN Xin-guo Liver Transplantation Institute General Hospital of Chinese People's Armed Police Force Beijing 100039 China Oriental Organ Transplantation Center Tianjin First Central Hospital Tianjin 300192 China

Background Although liver transplantation has become a standard therapy for end-stage liver diseases, the experience of pediatric liver transplantation is limited in China. In this article we report our experience in pediatric liver transplantation, and summarize its characters in their indications, surgical techniques, and postoperative managements. Methods Thirty-one children （≤18 years old） underwent liver transplantation in our centers. The mean age at transplantation was 12.4 years old （ranged from 5 months to 18 years） with 7 children being less than 4 years of age at transplantation. The most common diagnosis of patients who underwent liver transplantation were biliary atresia, Wilson＇s disease, primary biliary cirrhosis, glycogen storage disease, hepatoblastoma, urea cycle defects, fulminant hepatic failure, etc. The surgical procedures included 12 standard （without venovenous bypass）, 6 pigyback, 6 reduced-size, 3 split, 3 living donor liver transplantation, and 1 Domino liver transplantation. The triple-drug （FK506, steroid, and mycophenolate mofetil） immunosuppressive regimen was used in most of patients. Patients were followed up for a mean of 21.8 months. Results Five of the 31 patients died during perioperative time; mortality rate was 16.1%. The reasons of death were infections, primary non-function, heart failure, and hypovolemic shock. Postoperative complications in 10 patients included biliary leakage, acute rejection, abdominal infection, hepatitis B virus （HBV） or hepatitis C virus （HCV） infection, and pulmonary infection. Overall patient cumulative survival rate at 1-, 3-, and 5-year was 78.1%, 62.6%, 62.6%, respectively. Conclusions The most common indications of pediatric liver transplantation were congenital end-stage liver diseases. According to patients＇ age and body weight, standard, piggyback, reduced-size, split, or living donor liver transplantation should be performed. Pediatric liver transplantation especially requires higher su

关键词： pediatric liver transplantation indications complications

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Scattering of Water Waves by Dual Symmetric Inclined Floating Porous Barriers Using the DBEM

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China Ocean Engineering 2024年第1期38卷 156-168页

作者： WANG Li-xian deng Yan-wen YE Yang-sha deng Zheng-zhi Key Laboratory of High Performance Ship Technology(Wuhan University of Technology) Ministry of EducationWuhan 430063China School of Naval Architecture Ocean and Energy Power EngineeringWuhan University of TechnologyWuhan 430063China Key Laboratory of Water-Sediment Sciences and Water Disaster Prevention of Hunan Province Changsha 410114China Institute of Port Coastal and Offshore EngineeringZhejiang UniversityZhoushan 316021China

The scattering of normally incident water waves by two surface-piercing inclined perforated barriers in water with a uniform finite depth is investigated within the framework of linear water wave *** that thin barriers are zero-thickness,a novel numerical method involving the the coupling of the dual boundary element method(DBEM)with damping layers is *** order to effectively damp out the reflected waves,two damping layers,instead of pseudoboundaries are implemented near the two side boundaries of the computational ***,the modified linearized free surface boundary conditions are formulated and used for solving both the ordinary boundary integral equation as well as the hypersingular boundary integral equation for degenerate *** newly developed numerical method is validated against analytical methods using the matched eigenfunction expansion method for the special case of two vertical barriers or the inclined angle to the vertical being *** influence of the length of the two damping layers has been ***,these findings are also validated against previous results for several *** validation,the numerical results for the reflection coefficient,transmission coefficient and dissipation coefficient are obtained by varying the inclination angle and porosity-effect *** effects of both the inclination angle and the porosity on the amplitudes of wave forces acting on both the front and rear barriers are also *** is found that the effect of the inclination angle mainly shifts the location of the extremal values of the reflection and the transmission ***,a moderate value of the porosity-parameter is quite effective at dissipating wave energy and mitigating the wave loads on dual barriers.

关键词： dual boundary element method inclined perforated floating breakwater reflection coefficient transmission coefficient damping layer

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Mulberry leaf supplementation inhibits skatole deposition by regulating gut microbiota and upregulating liver cytochrome P4501A1 expression in finishing pigs

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Animal Nutrition 2024年第1期16卷 34-44页

作者： Yuqing Sun Xiaoming Men Tianbao lin Bo deng Shi Zhong Jinxi Huo Kaipeng Qin Zhiqiang Lv Ziwei Xu Yougui Li Institute of Sericulture and Tea Zhejiang Academy of Agricultural Sciences298 Deshengzhong RoadShangchengHangzhou 310021China Institute of Animal Husbandry and Veterinary Science Zhejiang Academy of Agricultural Sciences298 Deshengzhong RoadShangchengHangzhou 310021China

Skatole,a strong fecal odor substance,is generated through microbial degradation of tryptophan in the animal *** easily accumulates in adipose tissue and affects meat *** this study,the effect of mulberry leaf supplementation on skatole in finishing pigs was *** a 35-day trial,20 finishing pigs(barrows and gilts)were fed with a basal diet or basal diet with 6%mulberry *** performance of the pigs(n=10)was automatically recorded by a performance-testing feeder system and 8 pigs in each treatment were slaughtered and sampled for the remaining *** and short-chain fatty acids were detected using HPLC and gas chromatography,*** microbiota were analyzed using 16S r RNA gene *** metabolomics analysis of feces and serum was performed with UHPLC-MS/*** major cytochrome P450(CYP)enzymes that catalyze skatole degradation in the liver were tested by using RT-PCR and Western *** of major bioactive compounds in mulberry leaves on the CYP genes were verified in the hepatic cell line Hep G2 in an in vitro test(n=3).In finishing pigs,mulberry leaf supplementation had no significant effect on the average daily gain,average daily feed intake,and feed conversion ratio(P>0.05),but reduced skatole levels in feces,serum,and backfat(P<0.05),and increased acetic acid levels in feces(P=0.027).Mulberry leaf supplementation decreased the relative abundance of the skatole-producing bacteria Megasphaera and Olsenella(P<0.05).Indole-3acetic acid,the intermediate that is essential for skatole production,was significantly reduced in feces by mulberry leaf supplementation(P<0.05)and was positively correlated with skatole content in feces(P=0.004).In pigs treated with mulberry leaves,liver CYP1A1 expression was increased(P<0.05)and was negatively correlated with skatole content in backfat(P=0.045).The in vitro test demonstrated that mulberry leaf polyphenols and polysaccharides could directly stimulate CYP1A1 expression in

关键词： Pig Skatole Mulberry leaf Microbiota Cytochrome P450

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Quantitative characterizations of anisotropic dynamic properties in organic-rich shale with different kerogen content

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Petroleum Science 2024年第2期21卷 855-865页

作者： Jian-yong Xie Yan-Ping Fang Xing-Hua Wu Jian'er Zhao Jun-Cheng Dai Jun-Xing Cao Ji-Xin deng State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation Chengdu University of TechnologyChengdu610059SichuanChina Key Lab of Earth Exploration&Information Techniques of Ministry of Education Geophysical InstituteChengdu University of TechnologyChengdu610059SichuanChina PetroChina Southwest Oil&Gasfield Company Chengdu610017SichuanChina

Understanding the quantitative responses of anisotropic dynamic properties in organic-rich shale with different kerogen content(KC)is of great significance in hydrocarbon exploration and *** controlled experiments with a single variable is challenging for natural shales due to their high variations in components,diagenesis conditions,or pore *** employed the hot-pressing technique to construct 11 well-controlled artificial shale with varying *** artificial shale samples were successive machined into prismatic shape for ultrasonic measurements along different *** revealed bedding perpendicular P-wave velocities are more sensitive to the increasing KC than bedding paralleling velocities due to the preferential alignments of *** elastic stiffnesses except C_(13)are generally decreasing with the increasing KC,the variation of C_(1) and C_(33)on kerogen content are more sensitive than those of C_(44)and C_(66).Apparent dynamic mechanical parameters(v and E)were found to have linear correlation with the true ones from complete anisotropic equations independent of KC,which hold value towards the interpretation of well logs consistently across formations,Anisotropic mechanical parameters(ΔE and brittlenessΔB)tend to decrease with the reducing KC,withΔB showing great sensitivity to KC *** the range of low KC(linearly negative correlation with KC,and the V_(P)/V_(S) ratio magnitude of less than 1.75may serve as a significant characterization for highly organic-rich(>10%)shale,compilation of data from natural organic rich-shales globally verified the similar systematic relationships that can be empirically used to predict the fraction of KC in shales.

关键词： Elastic properties Organic shale Anisotropy Kerogen content Physical modeling

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INVARIANTS-PRESERVING DU FORT-FRANKEL SCHEMES AND THEIR ANALYSES FOR NONlinEAR SCHRÖDINGER EQUATIONS WITH WAVE OPERATOR

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Journal of Computational Mathematics 2024年第3期42卷 814-850页

作者： Dingwen deng Zhijun Li College of Mathematics and Information Science Nanchang Hangkong UniversityNanchang 330063China

Du Fort-Frankel finite difference method(FDM)was firstly proposed for linear diffusion equations with periodic boundary conditions by Du Fort and Frankel in *** is an explicit and unconditionally von Neumann stable ***,there has been no research work on numerical solutions of nonlinear Schrödinger equations with wave operator by using Du Fort-Frankel-type finite difference methods(FDMs).In this study,a class of invariants-preserving Du Fort-Frankel-type FDMs are firstly proposed for one-dimensional(1D)and two-dimensional(2D)nonlinear Schrödinger equations with wave *** using the discrete energy method,it is shown that their solutions possess the discrete energy and mass conservative laws,and conditionally converge to exact solutions with an order of for ofο(T^(2)+h_(x)^(2)+(T/h_(x))^(2))1D problem and an order ofο(T^(2)+h_(x)^(2)+h_(Y)^(2)+(T/h_(X))^(2)+(T/h_(y))^(2))for 2D problem in ***,τdenotes time-step size,while,hx and hy represent spatial meshsizes in x-and y-directions,***,by introducing a stabilized term,a type of stabilized invariants-preserving Du Fort-Frankel-type FDMs are *** not only preserve the discrete energies and masses,but also own much better stability than original ***,numerical results demonstrate the theoretical analyses.

关键词： Nonlinear Schrodinger equations with wave operator Du Fort-Frankel finite difference methods Discrete energy and mass conservative laws Numerical convergence

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Non-intrusive Load Monitoring Based on Graph Total Variation for Residential Appliances

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Journal of Modern Power Systems and Clean Energy 2024年第3期12卷 947-957页

作者： Xiaoyang Ma Diwen Zheng Xiaoyong deng Ying Wang Dawei deng Wei Li the College of Electrical Engineering Sichuan UniversityChengdu 610065China State Grid Chongqing Electric Power Company Chongqing 400014China State Grid Sichuan Electric Power Company Chengdu 610095China State Grid Hubei Electric Power Company Limited Research Institute Wuhan 430077China

Non-intrusive load monitoring is a technique for monitoring the operating conditions of electrical appliances by collecting the aggregated electrical information at the household power *** several studies on the mining of unique load characteristics,few studies have extensively considered the high computational burden and sample *** on lowfrequency sampling data,a non-intrusive load monitoring algorithm utilizing the graph total variation(GTV)is proposed in this *** algorithm can effectively depict the load state without the need for prior ***,the combined Kmeans clustering algorithm and graph signals are used to build concise and accurate graph structures as load *** GTV representing the internal structure of the graph signal is introduced as the optimization model and solved using the augmented Lagrangian iterative *** introduction of the difference operator reduces the computing cost and addresses the inaccurate reconstruction of the graph *** low-frequency sampling data,the algorithm only requires a little prior data and no training,thereby reducing the computing *** conducted using the reference energy disaggregation dataset and almanac of minutely power dataset demonstrated the stable superiority of the algorithm and its low computational burden.

关键词： Non-intrusive load monitoring graph total variation augmented Lagrangian function smart grid

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Genetically modified pigs with CD163 point mutation are resistant to HP-PRRSV infection

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Zoological Research 2024年第4期45卷 833-844页

作者： Ying Liu lin Yang Hong-yong Xiang Ming Niu Jia-Cheng deng Xue-Yuan Li Wen-Jie Hao Hong-Sheng Ou-Yang Tong-Yu Liu Xiao-Chun Tang Da-Xin Pang Hong-Ming Yuan State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Animal Genome Editing Technology Innovation CenterCollege of Animal SciencesJilin UniversityChangchunJilin 130062China Chifeng Best Genetics Technology Co. Ltd.ChifengNei Mongol 024000China Chongqing Jitang Biotechnology Research Institute Co. Ltd.Chongqing 400015China

Porcine reproductive and respiratory syndrome(PRRS)is a globally prevalent contagious disease caused by the positive-strand RNA PRRS virus(PRRSV),resulting in substantial economic losses in the swine *** the CD163 SRCR5 domain,either through deletion or substitution,can eff1ectively confer resistance to PRRSV infection in ***,large fragment modifications in pigs inevitably raise concerns about potential adverse effects on growth *** the impact of genetic modifications on normal physiological functions is a promising direction for developing PRRSV-resistant *** the current study,we identified a specific functional amino acid in CD163 that influences PRRSV *** infection experiments conducted on Marc145 and PK-15CD163 cells illustrated that the mE535G or corresponding pE529G mutations markedly inhibited highly pathogenic PRRSV(HP-PRRSV)proliferation by preventing viral binding and ***,individual viral challenge tests revealed that pigs with the E529G mutation had viral loads two orders of magnitude lower than wild-type(WT)pigs,confirming effective resistance to *** of the physiological indicators and scavenger function of CD163 verified no significant differences between the WT and E529G *** findings suggest that E529G pigs can be used for breeding PRRSV-resistant pigs,providing novel insights into controlling future PRRSV outbreaks.

关键词： PRRSV CD163 Point mutation E529G Pigs

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