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Two intestinal microbiota-derived metabolites, deoxycholic acid and butyrate, synergize to enhance host defense peptide synthesis and alleviate necrotic enteritis

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Journal of Animal Science and Biotechnology 2024年第3期15卷 1158-1172页

作者： Dohyung M.Kim Jing Liu Melanie A.Whitmore Isabel Tobin Zijun Zhao Guolong Zhang department of Animal and Food Sciences Oklahoma State UniversityStillwaterOKUSA

Background Necrotic enteritis(NE)is a major enteric disease in poultry,yet effective mitigation strategies remain *** acid(DCA)and butyrate,two major metabolites derived from the intestinal microbiota,have independently been shown to induce host defense peptide(HDP)***,the potential synergy between these two compounds remains *** To investigate the possible synergistic effect between DCA and butyrate in regulating HDP synthesis and barrier function,we treated chicken HD11 macrophage cells and jejunal explants with DCA and sodium butyrate(NaB),either individually or in combination,for 24 ***,we performed RNA isolation and reverse transcrip-tion-quantitative PCR to analyze HDP genes as well as the major genes associated with barrier *** further determine the synergy between DCA and NaB in enhancing NE resistance,we conducted two independent trials with Cobb broiler *** each trial,the diet was supplemented with DCA or NaB on the day-of-hatch,followed by NE induction through sequential challenges with Eimeria maxima and Clostridium perfringens on d 10 and 14,*** recorded animal mortality after infection and assessed intestinal lesions on d *** impact of DCA and NaB on the microbiota in the ileum and cecum was evaluated through bacterial 16S rRNA gene *** We found that the combination of DCA and NaB synergistically induced multiple HDP genes in both chicken HD11 cells and jejunal ***,the gene for claudin-1,a major tight junction protein,also exhibited synergistic induction in response to DCA and ***,dietary supplementation with a combination of 0.75 g/kg DCA and 1 g/kg NaB led to a significant improvement in animal survival and a reduction in intestinal lesions compared to either compound alone in a chicken model of ***,the cecal microbiota of NE-infected chickens showed a marked decrease in SCFA-producing bacteria such as Bacteroides,F

关键词： Bile acids Host defense peptides Metabolites Microbiome Necrotic enteritis Short-chain fatty acids

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Recurrent Neural Network Inspired Finite-Time Control Design

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IEEE/CAA Journal of Automatica Sinica 2024年第6期11卷 1527-1529页

作者： Jianan Liu Shihua Li Rongjie Liu School of Automation Southeast UniversityNanjing 210096China department of statistics Florida State UniversityFL 32304 USA IEEE

Dear Editor,This letter is concerned with the role of recurrent neural networks(RNNs)on the controller design for a class of nonlinear *** by the architectures of RNNs,the system states are stacked according to the dynamic along with time while the controller is represented as the neural network *** build the bridge between RNNs and finite-time controller,a novel activation function is imposed on RNNs to drive the convergence of states at finite-time and propel the overall control process *** stability proof is briefly provided for the convergence of the proposed finite-time *** last,a numerical simulation example is presented to illustrate the efficiency of the proposed *** networks can be classified as static(feedforward)and dynamic(recurrent)nets[1].The former nets do not perform well in dealing with training data and using any information of the local data structure[2].In contrast to the feedforward neural networks,RNNs are constituted by high dimensional hidden states with dynamics.

关键词： dynamics finite proof

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Mesenchymal stem cell-based TRAIL delivery inhibits the metastatic state of clinical therapy-resistant progressive neuroblastoma

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World Journal of Pediatrics 2024年第3期20卷 287-293页

作者： Dinesh Babu Somasundaram Andrew Maher Sheeja Aravindan Zhongxin Yu Brian MBesch Natarajan Aravindan department of Radiation Oncology University of Oklahoma Health Sciences CenterOklahoma CityOKUSA Stephenson Cancer Center Oklahoma CityOKUSA department of Pathology University of Oklahoma Health Sciences CenterOklahoma CityOKUSA Radiation Biology Laboratory University of Oklahoma Health Sciences CenterBSEB 302F941 Stanton L.Young BoulevardOklahoma CityOK 73104USA

Progressive neuroblastomas(pNBs)that defy current intensive multimodal clinical therapy(IMCT)are a significant contributor to overall childhood cancer deaths[l].Neuroblastomas(NBs)that survive first-line IMCT actively evolve to acquire genetic and molecular rearrangements and display unparalleled plasticity and evolution,which causes frequent relapses in a rapidly accelerating timeline[2-4].

关键词： neuroblastoma clinical evolve

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DiffGR:Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 143-155页

作者： Huiling Liu Wenxiu Ma department of statistics University of California RiversideRiversideCA 92521USA

Recent advances in high-throughput chromosome conformation capture(Hi-C)techniques have allowed us to map genome-wide chromatin interactions and uncover higher-order chromatin structures,thereby shedding light on the principles of genome architecture and ***,statistical methods for detecting changes in large-scale chromatin organization such as topologically associating domains(TADs)are still ***,we proposed a new statistical method,DiffGR,for detecting differentially interacting genomic regions at the TAD level between Hi-C contact *** utilized the stratum-adjusted correlation coefficient to measure similarity of local TAD *** then developed a nonparametric approach to identify statistically significant changes of genomic interacting *** simulation studies,we demonstrated that DiffGR can robustly and effectively discover differential genomic regions under various ***,we successfully revealed cell type-specific changes in genomic interacting regions in both human and mouse Hi-C datasets,and illustrated that DiffGR yielded consistent and advantageous results compared with state-of-the-art differential TAD detection *** DiffGR R package is published under the GNU General Public License(GPL)≥2 license and is publicly available at https://***/wmalab/DiffGR.

关键词： Hi-C Differential analysis Topologically associating domain Stratum-adjusted correlation coefficient Nonparametric method

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Iterative Subregion Correction Preconditioners with Adaptive Tolerance for Problems with Geometrically Localized Stiffness

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Communications on Applied Mathematics and Computation 2024年第2期6卷 811-836页

作者： Michael Franco Per-Olof Persson Will Pazner department of Mathematics University of CaliforniaBerkeleyBerkeleyCA 94720-3840USA Fariborz Maseeh department of Mathematics and statistics Portland State UniversityPortlandOR 97201USA

We present a class of preconditioners for the linear systems resulting from a finite element or discontinuous Galerkin discretizations of advection-dominated *** preconditioners are designed to treat the case of geometrically localized stiffness,where the convergence rates of iterative methods are degraded in a localized subregion of the *** convergence may be caused by a number of factors,including the mesh size,anisotropy,highly variable coefficients,and more challenging *** approach taken in this work is to correct well-known preconditioners such as the block Jacobi and the block incomplete LU(ILU)with an adaptive inner subregion *** goal of these preconditioners is to reduce the number of costly global iterations by accelerating the convergence in the stiff region by iterating on the less expensive reduced *** tolerance for the inner iteration is adaptively chosen to minimize subregion-local work while guaranteeing global convergence *** present analysis showing that the convergence of these preconditioners,even when combined with an adaptively selected tolerance,is independent of discretization parameters(e.g.,the mesh size and diffusion coefficient)in the *** demonstrate significant performance improvements over black-box preconditioners when applied to several model convection-diffusion ***,we present performance results of several variations of iterative subregion correction preconditioners applied to the Reynolds number 2.25×10^(6)fluid flow over the NACA 0012 airfoil,as well as massively separated flow at 30°angle of attack.

关键词： Subregion correction Nested Krylov Geometrically localized stiffness

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An efficient and safe strategy for germ cell-specific automatic excision of foreign DNA in F1 hybrid transgenic silkworms

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Insect Science 2024年第1期31卷 28-46页

作者： Dingpei Long Rongpeng Liu Yang Huang Anyao Fu Yuli Zhang Zhanzhang Hao Qiang Li Hanfu Xu Zhonghuai Xiang Aichun Zhao state Key Laboratory of Resource Insects Institute of Sericulture and Systems BiologySouthwest UniversityChongqingChina department of Biology Georgia State UniversityAtlantaGeorgiaUSA Guangxi Institute of Sericulture Science NanningGuangxiChina department of Mathematics and statistics Georgia State UniversityAtlantaGeorgiaUSA

The safety of transgenic technology is a major obstacle in the popularization and use of transgenic silkworms and their *** sericulture,only the first filial generation(F1)hybrid eggs produced by cross-breeding Japanese and Chinese original strains are usually used for the large-scale breeding of silkworms,but this may result in uncontrolled transgene dispersal during the popularization and application of the F1 hybrid transgenic *** address this issue,we developed a safe and efficient strategy using the GAL4/Upstream activating sequence(UAS)system,the FLP/flippase recognition target(FRT)system,and the gonad-specific expression gene promoters(RSHP1p and Nanosp)for the germ cell-specific automatic excision of foreign DNA in the F1 hybrid transgenic *** established 2 types of activator strains,R1p::GAL4-Gr and Nsp::GAL4-Gr,containing the testis-specific GAL4 gene expression cassettes driven by RSHP1p or Nanosp,respectively,and 1 type of effector strain,UAS::FLP-Rg,containing the UAS-linked FLP gene expression *** FLP recombinase-mediated sperm-specific complete excision of FRT-flanked target DNA in the F1 double-transgenic silkworms resulting from the hybridization of R1p::GAL4-Gr and UAS::FLP-Rg was 100%,whereas the complete excision efficiency resulting from the hybridization of Nsp::GAL4-Gr and UAS::FLP-Rg ranged from 13.73%to 80.3%.Additionally,we identified a gene,sw11114,that is expressed in both testis and ovary of Bombyx mori,and can be used to establish novel gonad-specific expression systems in transgenic *** strategy has the potential to fundamentally solve the safety issue in the production of F1 transgenic silkworm eggs and provides an important reference for the safety of transgenic technology in other insect species.

关键词： Bombyx mori FLP/FRT system GAL4/UAS system germ cell-specific excision safety of transgenic technology transgenic silkworm

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Adaptive Sparse Grid Discontinuous Galerkin Method:Review and Software Implementation

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Communications on Applied Mathematics and Computation 2024年第1期6卷 501-532页

作者： Juntao Huang Wei Guo Yingda Cheng department of Mathematics and statistics Texas Tech UniversityLubbockTX79409USA department of Computational Mathematics Science and EngineeringMichigan State UniversityEast LansingMI48824USA department of Mathematics Michigan State UniversityEast LansingMI48824USA

This paper reviews the adaptive sparse grid discontinuous Galerkin(aSG-DG)method for computing high dimensional partial differential equations(PDEs)and its software *** C++software package called AdaM-DG,implementing the aSG-DG method,is available on GitHub at https://***/JuntaoHuang/*** package is capable of treating a large class of high dimensional linear and nonlinear *** review the essential components of the algorithm and the functionality of the software,including the multiwavelets used,assembling of bilinear operators,fast matrix-vector product for data with hierarchical *** further demonstrate the performance of the package by reporting the numerical error and the CPU cost for several benchmark tests,including linear transport equations,wave equations,and Hamilton-Jacobi(HJ)equations.

关键词： Adaptive sparse grid Discontinuous Galerkin High dimensional partial differential equation Software development

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The TaGW2‐TaSPL14 module regulates the trade‐off between tiller number and grain weight in wheat

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Journal of Integrative Plant Biology 2024年第9期66卷 1953-1965页

作者： Chao Jian Yuxue Pan Shujuan Liu Mengjiao Guo Yilin Huang Lina Cao Weijun Zhang Liuling Yan Xueyong Zhang Jian Hou Chenyang Hao Tian Li state Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Crop Research Institute Ningxia Academy of Agriculture and Forestry SciencesYinchuan 750002China department of Plant and Soil Sciences Oklahoma State UniversityStillwaterOklahoma 74078USA

IDEAL PLANT ARCHITECTURE1(IPA1)is a pivotal gene controlling plant architecture and grain ***,little is known about the effects of Triticum aestivum SQUAMOSA PROMOTER‐BINDING‐LIKE 14(TaSPL14),an IPA1 ortholog in wheat,on balancing yield traits and its regulatory mechanism in wheat(*** L.).Here,we determined that the *** GRAIN WIDTH2(TaGW2)‐TaSPL14 module influences the balance between tiller number and grain weight in *** of TaSPL14 resulted in a reduced tiller number and increased grain weight,whereas its knockout had the opposite effect,indicating that TaSPL14 negatively regulates tillering while positively regulating grain *** further identified TaGW2 as a novel interacting protein of TaSPL14 and confirmed its ability to mediate the ubiquitination and degradation of *** on our genetic evidence,TaGW2 acts as a positive regulator of tiller number,in addition to its known role as a negative regulator of grain weight,which is opposite to ***,combinations of TaSPL14‐7A and TaGW2‐6A haplotypes exhibit significantly additive effects on tiller number and grain weight in wheat *** findings provide insight into how the TaGW2‐TaSPL14 module regulates the trade‐off between tiller number and grain weight and its potential application in improving wheat yield.

关键词： grain weight TaGW2 TaSPL14 tiller number wheat

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VARIABLE STEP-SIZE BDF3 METHOD FOR ALLEN-CAHN EQUATION

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Journal of Computational Mathematics 2024年第5期42卷 1380-1406页

作者： Minghua Chen Fan Yu Qingdong Zhang Zhimin Zhang School of Mathematics and statistics Gansu Key Laboratory of Applied Mathematics and Complex SystemsLanzhou UniversityLanzhou 730000China department of Mathematics Wayne State UniversityDetroitMI 48202USA

In this work,we analyze the three-step backward differentiation formula(BDF3)method for solving the Allen-Cahn equation on variable *** BDF2 method,the discrete orthogonal convolution(DOC)kernels are positive,the stability and convergence analysis are well established in[Liao and Zhang,***.,90(2021),1207–1226]and[Chen,Yu,and Zhang,arXiv:2108.02910,2021].However,the numerical analysis for BDF3 method with variable steps seems to be highly nontrivial due to the additional degrees of freedom and the non-positivity of DOC *** developing a novel spectral norm inequality,the unconditional stability and convergence are rigorously proved under the updated step ratio restriction rk:=τk/τk−1≤1.405 for BDF3 ***,numerical experiments are performed to illustrate the theoretical *** the best of our knowledge,this is the first theoretical analysis of variable steps BDF3 method for the Allen-Cahn equation.

关键词： Variable step-size BDF3 method Allen-Cahn equation Spectral norm inequality Stability and convergence analysis

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Nonlinear Extrapolation Estimates of π

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Acta Mathematicae Applicatae Sinica 2024年第1期40卷 91-108页

作者： Wen-qing Xu Sha-sha Wang Da-chuan Xu Beijing Institute for Scientific and Engineering Computing Beijing University of TechnologyBeijing100124China department of Mathematics and statistics California State UniversityLong BeachCalifornia90840USA department of Mathematics and Physics Shijiazhuang Tiedao UniversityShijiazhuang050043China

The classical Archimedean approximation of π uses the semiperimeter or area of regular polygons inscribed in or circumscribed about a unit circle in R~2 and it is well-known that by using linear combinations of these basic estimates,modern extrapolation techniques can greatly speed up the approximation ***,when n vertices are randomly selected on the circle,the semiperimeter and area of the corresponding random inscribed and circumscribing polygons are known to converge to π almost surely as n→∞,and by further applying extrapolation processes,faster convergence rates can also be achieved through similar linear combinations of the semiperimeter and area of these random *** this paper,we further develop nonlinear extrapolation methods for approximating π through certain nonlinear functions of the semiperimeter and area of such *** focus on two types of extrapolation estimates of the forms χ_n=S_n~αA_n~β and Y_n(p)=(αS_n~p+βA_n~p)~(1/p) where α+β=1,p≠0,and Sn and An respectively represents the semiperimeter and area of a random n-gon inscribed in the unit circle in R~2,and Xn may be viewed as the limit of Y_n(p) when p→*** deriving probabilistic asymptotic expansions with carefully controlled error estimates for Xn and Y_n(p),we show that the choice α=4/3,β=-1/3 minimizes the approximation error in both cases,and their distributions are also asymptotically normal.

关键词： Archimedean polygons random polygons approximations ofπ extrapolation processes asymptotic convergence

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