CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network

The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ruminant multi-chambered stomach innovation.We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific genes via batteries of active-RSCNEs during development.Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules.Notably,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the esophagus.Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.

Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes

Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms.Many conserved non-coding sequences(CNSs)function as cis-regulatory elements.They control the development of various lineages.How-ever,predicting clade-wide cis-regulatory elements across several closely related species remains challenging.Based on the relationship between CNSs and cis-regulatory elements,we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes.Using 12-way whole-genome alignment,we first obtained 632112 CNSs in Cucurbitaceae.Next,we identified 16552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants.Furthermore,we predicted 3271 potential regulatory pairs in the cucumber genome,of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages.The CNSs,Cucurbitaceae-wide cis-regulatory elements,and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/.These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.

A modified discrete element method for concave granular materials based on energy-conserving contact model

The development of a general discrete element method for irregularly shaped particles is the core issue of the simulation of the dynamic behavior of granular materials.The general energy-conserving contact theory is used to establish a universal discrete element method suitable for particle contact of arbitrary shape.In this study,three dimentional(3D)modeling and scanning techniques are used to obtain a triangular mesh representation of the true particles containing typical concave particles.The contact volumebased energy-conserving model is used to realize the contact detection between irregularly shaped particles,and the contact force model is refined and modified to describe the contact under real conditions.The inelastic collision processes between the particles and boundaries are simulated to verify the robustness of the modified contact force model and its applicability to the multi-point contact mode.In addition,the packing process and the flow process of a large number of irregular particles are simulated with the modified discrete element method(DEM)to illustrate the applicability of the method of complex problems.

Conserved sequences identify the closest living relatives of primates

Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.

Ultraconvergence for averaging discontinuous finite elements and its applications in Hamiltonian system

This paper discusses the k-degree averaging discontinuous finite element solution for the initial value problem of ordinary differential equations. When k is even, the averaging numerical flux （the average of left and right limits for the discontinuous finite element at nodes） has the optimal-order ultraconvergence 2k ＋ 2. For nanlinear Hamiltonian systems （e.g., SchrSdinger equation and Kepler system） with momentum conservation, the discontinuous finite element methods preserve momentum at nodes. These properties are confirmed by numerical experiments.

SPACE-TIME FINITE ELEMENT METHOD FOR SCHRDINGER EQUATION AND ITS CONSERVATION

Energy conservation of nonlinear Schrodinger ordinary differential equation was proved through using continuous finite element methods of ordinary differential equation; Energy integration conservation was proved through using space-time continuous fully discrete finite element methods and the electron nearly conservation with higher order error was obtained through using time discontinuous only space continuous finite element methods of nonlinear Schrodinger partial equation. The numerical results are in accordance with the theory.

SPECTRAL/HP ELEMENT METHOD WITH HIERARCHICAL RECONSTRUCTION FOR SOLVING NONLINEAR HYPERBOLIC CONSERVATION LAWS

The hierarchical reconstruction （HR） [Liu, Shu, Tadmor and Zhang, SINUM ＇07] has been successfully applied to prevent oscillations in solutions computed by finite volume, Runge-Kutta discontinuous Galerkin, spectral volume schemes for solving hyperbolic conservation laws. In this paper, we demonstrate that HR can also be combined with spectral/hp element method for solving hyperbolic conservation laws. An orthogonal spectral basis written in terms of Jacobi polynomials is applied. High computational efficiency is obtained due to such matrix-free algorithm. The formulation is conservative, and essential nomoscillation is enforced by the HR limiter. We show that HR preserves the order of accuracy of the spectral/hp element method for smooth solution problems and generate essentially non-oscillatory solutions profiles for capturing discontinuous solutions without local characteristic decomposition. In addition, we introduce a postprocessing technique to improve HR for limiting high degree numerical solutions.

Spectral Element Viscosity Methods for Nonlinear Conservation Laws on the Semi-Infinite Interval

In this paper we propose a spectral element: vanishing viscosity (SEW) method for the conservation laws on the semi-infinite interval. By using a suitable mapping, the problem is first transformed into a modified conservation law in a bounded interval, then the well-known spectral vanishing viscosity technique is generalized to the multi-domain case in order to approximate this trarsformed equation more efficiently. The construction details and convergence analysis are presented. Under a usual assumption of boundedness of the approximation solutions, it is proven that the solution of the SEW approximation converges to the uniciue entropy solution of the conservation laws. A number of numerical tests is carried out to confirm the theoretical results.

Development of endemicity and conservation importance indices for tropical forests and the floral diversity assessment of Mt.Natoo in Benguet,Philippines

The scientific community faces the challenge of measuring progress toward biodiversity targets and indices have been traditionally used.However,recent inventories in secondary tropical mountain forests using traditional biodiversity indices have yielded results that are indistinct with primary ones.This shows the need to develop complementary indices that goes beyond species count but integrates the distribution and conservation status of the species.This study developed endemicity and conservation importance index for tropical forest that incorporated the distribution and conservation status of the species.These indices were applied to Mt.Natoo,a remnant primary mossy forest in Buguias,Benguet,Philippines,that resulted to endemicity index of 81.07 and conservation importance index of 42.90.Comparing these with secondary forest sites with comparable Shannon-Wiener,Simpson,Evenness and Margalef’s indices,our endemicity and conservation indices clearly differentiates primary forest(our study site)with higher values from secondary forests with much lower values.Thus,we are proposing these indices for a direct but scientifically-informed identification of specific sites for conservation and protection in tropical forests.Additionally,our study documented a total of 168 vascular plant species(79 endemic and 12 locally threatened species)in Mt.Nato-o.Majority are of tropical elements for both generic and species levels with some temperate elements that could be attributed to the site's high elevation and semi-temperate climate.These are important baseline information for conservation plans and monitoring of tropical mossy forests.

Floristic Characteristics of the Rare and Endangered Plants and the Conservation Countermeasures in Tibet, China

The floristic elements and the geographical distribution are analyzed in thispaper based on statistics of elements of rare and endangered plants in Tibet. The results have beengained as following: (1) According to 'the National Important Wild Conservative Plants List (List1)' and 'the National Important Wild Conservative Plants List (List 1)', there are a total of 54plant species (48 genera and 33 families); (2) The geographical elements are very complicated inTibet with 12 of 15 distribution patterns of genera classified by academician Wu; (3) There areobvious temperate genera with 28 genera accounting for 60. 4% of the total genera; (4) There areabundant endemic species accounting for 18. 52% of total species but poor endemic genera; (5) Thegeographical distribution is uneven and a great of species distribute in the areas between 1 000 mand 3 500 m above sea level; (6) To protect the rare and endangered plants efficiently, sixconservation measures are proposed, and 35 species are suggested for the conservative plants of theautonomous conservation level.

DNA Damage-Induced Transcription of Transposable Elements and Long Non-coding RNAs in Arabidopsis Is Rare and ATM-Dependent

Induction and mobilization of transposable elements （TEs） following DNA damage or other stresses has been reported in prokaryotes and eukaryotes. Recently it was discovered that eukaryotic TEs are frequently associated with long non-coding RNAs （IncRNAs）, many of which are also upregulated by stress. Yet, it is unknown whether DNA damage-induced transcriptional activation of TEs and IncRNAs occurs sporadically or is a synchronized, genome-wide response. Here we investigated the transcriptome of Arabidopsis wild- type （WT） and ataxia telangiectasia mutated （atm） mutant plants 3 h after induction of DNA damage. In WT, expression of 5.2% of the protein-coding genes is 〉 2-fold changed, whereas in atm plants, only 2.6% of these genes are regulated, and the response of genes associated with DNA repair, replication, and cell cy- cle is largely lost. In contrast, only less than 0.6% of TEs and IncRNAs respond to DNA damage in WT plants, and the regulation of 〉95% of them is ATM-dependent. The ATM-downstream factors BRCA1, DRM1, JMJ30, AGO2, and the ATM-independent AGO4 participate in the regulation of individual TEs and IncRNAs. Remarkably, protein-coding genes located adjacent to DNA damage-responsive TEs and IncRNAs are frequently coexpressed, which is consistent with the hypothesis that TEs and IncRNAs located close to genes commonly function as controlling elements.

CONSERVATION LAWS IN FINITE MICROCRACKING BRITTLE SOLIDS

This paper addresses the conservation laws in finite brittle solids with microcracks. The discussion is limited to the 2-D cases. First, after considering the combination of the Pseudo-Traction Method and the indirect Boundary Element Method, a versatile method for solving multi-crack interacting problems in finite plane solids is proposed, by which the fracture parameters （SIF and path-independent integrals） can be calculated with a desirable accuracy. Second, with the aid of the method proposed, the roles the conservation laws play in the fracture analysis for finite microcracking solids are studied. It is concluded that the conservation laws do play important roles in not only the fracture analysis but also the analysis of damage and stability for the finite microcracking system. Finally, the physical interpretation of the M-integral is discussed further. An explicit relation between the M-integral and the crack face area, i.e., M = GS, has been discovered using the analytical method, which can shed some light on the Damage Mechanics issues from a different perspective.

Continuous finite element methods for Hamiltonian systems

By applying the continuous finite element methods of ordinary differential equations, the linear element methods are proved having second-order pseudo-symplectic scheme and the quadratic element methods are proved having third-order pseudo- symplectic scheme respectively for general Hamiltonian systems, and they both keep energy conservative. The finite element methods are proved to be symplectic as well as energy conservative for linear Hamiltonian systems. The numerical results are in agree-ment with theory.

ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor

Background:Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau.This extreme living env ironment makes it a great model to study animal adaptation to hypoxia,low temperature,and high carbon dioxide concentration.Methods:We provide an integrated resource,ZokorDB,for tissue specific regulatory network annotation for zokor.ZokorDB is based on a high-quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain,heart,liver,kidney,and lung.The conserved non-coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites.Results:ZokorDB provides a general draft gene regulatory network(GRN),Le?potential transcription factor(TF)binds to non-coding regulatory elements and regulates the expression of target genes(TG).Furthermore,we refined the GRN by incorporating matched RNA-seq and DNase-seq data from mouse ENCODE project and reconstructed five tissue-specific regulatory networks.Conclusions:A web-based,open-access database is developed for easily searching,visualizing,and downloading the annotation and data.The pipeline of non-coding region annotation for zokor will be useful for other non-model species.ZokorDB is free available at the website(bigd.big.ac.cn/zokordb/).

CONVERGENCE ANALYSIS OF MIXED VOLUME ELEMENT-CHARACTERISTIC MIXED VOLUME ELEMENT FOR THREE-DIMENSIONAL CHEMICAL OIL-RECOVERY SEEPAGE COUPLED PROBLEM

The physical model is described by a seepage coupled system for simulating numerically three-dimensional chemical oil recovery, whose mathematical description includes three equations to interpret main concepts. The pressure equation is a nonlinear parabolic equation, the concentration is defined by a convection-diffusion equation and the saturations of different components are stated by nonlinear convection-diffusion equations. The transport pressure appears in the concentration equation and saturation equations in the form of Darcy velocity, and controls their processes. The flow equation is solved by the conservative mixed volume element and the accuracy is improved one order for approximating Darcy velocity. The method of characteristic mixed volume element is applied to solve the concentration, where the diffusion is discretized by a mixed volume element method and the convection is treated by the method of characteristics. The characteristics can confirm strong computational stability at sharp fronts and it can avoid numerical dispersion and nonphysical oscillation. The scheme can adopt a large step while its numerical results have small time-truncation error and high order of accuracy. The mixed volume element method has the law of conservation on every element for the diffusion and it can obtain numerical solutions of the concentration and adjoint vectors. It is most important in numerical simulation to ensure the physical conservative nature. The saturation different components are obtained by the method of characteristic fractional step difference. The computational work is shortened greatly by decomposing a three-dimensional problem into three successive one-dimensional problems and it is completed easily by using the algorithm of speedup. Using the theory and technique of a priori estimates of differential equations, we derive an optimal second order estimates in 12 norm. Numerical examples are given to show the effectiveness and practicability and the method is testified as a powerful tool to solve the important problems.

Finite Element Methods for Coupled Stokes and Darcy Problems

We derived and analyzed a new numerical scheme for the coupled Stokes and Darcy problems by using H（div） conforming elements in the entire domain. The approach employs the mixed finite element method for the Darcy equations and a stabilized H（div） finite element method for the Stokes equations. Optimal error estimates for the fluid velocity and pressure are derived. The finite element solutions from the new scheme not only feature a full satisfaction of the continuity equation, which is highly demanded in scientific computing, but also satisfy the mass conservation.

A Posteriori Error Estimates for Finite Element Methods for Systems of Nonlinear,Dispersive Equations

The present study regards the numerical approximation of solutions of systems of Korteweg-de Vries type,coupled through their nonlinear terms.In our previous work[9],we constructed conservative and dissipative finite element methods for these systems and presented a priori error estimates for the semidiscrete schemes.In this sequel,we present a posteriori error estimates for the semidiscrete and fully discrete approximations introduced in[9].The key tool employed to effect our analysis is the dispersive reconstruction devel-oped by Karakashian and Makridakis[20]for related discontinuous Galerkin methods.We conclude by providing a set of numerical experiments designed to validate the a posteriori theory and explore the effectivity of the resulting error indicators.

贫数据小型水利工程结构安全分析

我国小型水库数量多,溃坝多发,运行风险大。为了保障水库的安全稳定运行,有必要对小型水库的结构安全分析和评估进行深入研究。由于小型水库大多建于20世纪50—70年代,各类工程资料匮乏,难以进行结构安全分析工作。以北京地区一小型拱坝为例,采用地面三维激光扫描测绘技术对大坝进行扫描,将所得点云数据集进行编辑、配准、拼接处理,生成三维模型导入有限元分析计算软件进行结构稳定分析。坝体建模网格及单元划分质量高,满足计算精度的要求,分析计算成果与客观规律一致,这为资料匮乏的小型水利工程结构安全分析提供了一种新思路。

基于能量守恒的空间旋转目标消旋力矩计算方法

针对空间旋转目标电磁消旋技术,提出一种计算空间旋转目标消旋力矩的新方法。首先,介绍了电磁消旋的常用计算方法;然后,介绍了能量守恒法的基本思想,从系统能量守恒的角度出发,从整体考虑电磁消旋过程中各物理场之间的相互作用,提出了一种基于能量守恒的消旋力矩计算方法,并通过球壳模型消旋力矩的计算过程对能量守恒法进行阐述。最后,进行了地面消旋实验,对比了实验结果和有限元法、电磁张量法和能量守恒法的计算结果。实验及仿真结果表明,本文提出的基于能量守恒的空间旋转目标消旋力矩计算方法有效。

潜蚀的局部守恒有限元和有限体积交替解法

潜蚀的模拟需要计算土中的渗流过程以及土中细粒随孔隙水流的运移过程。常规有限元法在求解纯运移方程时存在稳定性问题,为此提出了一个采用有限元法求解渗流方程、有限体积法求解细粒运移方程的交替方法。鉴于常规有限元法不能给出满足有限体积法输入要求的流速场,给出了一个基于单元不平衡流量总体再平衡修正单元边界流速的算法。利用该算法对有限元计算的单元边界流速进行局部守恒处理,即可实现在同一有限元网格上利用有限体积法求解细粒运移方程,因此可以方便地和现有的有限元计算程序结合。算例验证表明,所提出的局部守恒处理算法及交替解法计算效率高且具有可接受的精度,是模拟潜蚀问题的一条简单实用的途径。