A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

Chen, Han,Li, Chunyan,Peng, Xinxin,Zhou, Zhicheng,Weinstein, John N.,Caesar-Johnson, Samantha J.,Demchok, John A.,Felau, Ina,Kasapi, Melpomeni,Ferguson, Martin L.,Hutter, Carolyn M.,Sofia, Heidi J.,Ta Elsevier 2018 Cell Vol.173 No.2

<P><B>Summary</B></P> <P>The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on “chromatin-state” to explain their interplay. Integrating eQTL, mRNA co-expression, and Hi-C data analysis, we developed a computational method to infer causal enhancer-gene interactions, revealing enhancers of clinically actionable genes. Having identified an enhancer ∼140 kb downstream of PD-L1, a major immunotherapy target, we validated it experimentally. This study provides a systematic view of enhancer activity in diverse tumor contexts and suggests the clinical implications of enhancers.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Systematic analysis of enhancer expression across ∼9,000 samples of 33 cancer types </LI> <LI> Global enhancer activation positively correlates with aneuploidy but not mutations </LI> <LI> A computational method that infers causal enhancer-target-gene relationships </LI> <LI> Enhancers as key regulators of therapeutic targets, including PD-L1 </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>

Research on Bending Stiffness of the New Sprayer Joint

Ren Li,Zhicheng Xiao,Hui-jun Li,Baohui Li 한국강구조학회 2024 International Journal of Steel Structures Vol.24 No.2

The socket joint are commonly employed in large-span spatial structures; however, its bending stiff ness is limited. Based on the socket joint, this paper proposes an improved and novel sprayer joint that features a more rational force transmission mechanism and have larger bending stiff ness. Firstly, the joint is designed, followed by verifi cation of numerical model and bending stiff ness comparison with socket joint. Secondly, the bending performance of the sprayer joints with various surrounding bolt radii under load conditions is investigated, and the resulting bending moment-rotation curves are obtained. The research fi ndings demonstrate that the force transmission mechanism of the sprayer joint with larger bending stiff ness is more rational. When the surrounding bolt radius is excessively small or the axial tension is excessively high, the bolt prematurely yields, leading to a signifi cant decrease in joint stiff ness. Despite a mere 15% increase in material cost, the bending stiff ness of the new joint is 21.71 times higher than that of the traditional socket joint, and the ultimate bending moment is 5.42 times higher.

An active learning method with difficulty learning mechanism for crack detection

Zhicheng Zhang,Jiangpeng Shu,Jun Li,Jiawei Zhang,Weijian Zhao,Yuanfeng Duan 국제구조공학회 2022 Smart Structures and Systems, An International Jou Vol.29 No.1

Crack detection is essential for inspection of existing structures and crack segmentation based on deep learning is asignificant solution. However, datasets are usually one of the key issues. When building a new dataset for deep learning, laborious and time-consuming annotation of a large number of crack images is an obstacle. The aim of this study is to develop an approach that can automatically select a small portion of the most informative crack images from a large pool in order to annotate them, not to label all crack images. An active learning method with difficulty learning mechanism for crack segmentation tasks is proposed. Experiments are carried out on a crack image dataset of a steel box girder, which contains 500 images of 320 × 320 size for training, 100 for validation, and 190 for testing. In active learning experiments, the 500 images for training are acted as unlabeled image. The acquisition function in our method is compared with traditional acquisition functions, i.e., Query-By-Committee (QBC), Entropy, and Core-set. Further, comparisons are made on four common segmentation networks: U-Net, DeepLabV3, Feature Pyramid Network (FPN), and PSPNet. The results show that when training occurs with 200 (40%) of the most informative crack images that are selected by our method, the four segmentation networks can achieve 92%-95% of the obtained performance when training takes place with 500 (100%) crack images. The acquisition function in our method shows more accurate measurements of informativeness for unlabeled crack images compared to the four traditional acquisition functions at most active learning stages. Our method can select the most informative images for annotation from many unlabeled crack images automatically and accurately. Additionally, the dataset built after selecting 40% of all crack images can support crack segmentation networks that perform more than 92% when all the images are used.

A Visual Video Synthesis Tool Based on Video Materials

Zhicheng Jiang,Ruofeng Tong,Jinlong Li (사)한국CDE학회 2010 한국CAD/CAM학회 국제학술발표 논문집 Vol.2010 No.8

Video matting is the process of extracting the foreground of a video and compositing it with another background to generate a new video. Currently, there are many ways to edit foreground image, yet we lack of an effective way to edit foreground video and merge it with a new background, forming a new, meaningful, realistic video. In this paper, we present a new video editing tool which fulfills this function effectively. Using this tool, we can easily edit the appearance of extracted object by resizing, rotation and recoloration. We provide a path specification tool to locate the object in an appropriate position at specified frame. Finally, by an illumination blending procedure, we generate a desired video with the objects composed realistically.

Improved Ultra-Low Cycle Fatigue Fracture Models for Structural Steels Considering the Dependence of Cyclic Damage Degradation Parameters on Stress Triaxiality

Shuailing Li,Xu Xie,Qin Tian,Cheng Cheng,Zhicheng Zhang 한국강구조학회 2021 International Journal of Steel Structures Vol.21 No.1

The ultra-low cycle fatigue (ULCF) fracture initiation caused by cyclic large plastic strain in structural steels is often the governing limit state in steel structures when subjected to strong earthquake actions. Based on the author’s previous work, this paper presents the improved cyclic void growth model (CVGM) and degraded signifi cant plastic strain (DSPS) model considering the dependence of cyclic damage degradation parameters on stress triaxiality. To this end, tests on circular notched specimens and coupon specimens made of Q345qC steel were conducted, and scanning electron microscopy studies were performed on fracture surfaces of specimens, analysis results of which show that the ULCF fracture of Q345qC steel exhibits the typical behaviour of “void nucleation, growth, and coalescence.” The cyclic damage degradation parameters of CVGM and DSPS model were calibrated at diff erent stress triaxialities based on experimental results of specimens and complementary fi nite element analysis, and empirical formulas were subsequently established between cyclic damage degradation parameters and stress triaxiality. Finally, detailed fi nite element analysis results demonstrate that the improved CVGM and DSPS model can predict ULCF fracture behaviour with higher accuracy in comparison with original models.

Improvement of comprehensive performance of compound green soil in sponge city

Lei Zhang,Zhicheng Li,Tianliang Yang,Ping Yang 대한환경공학회 2021 Environmental Engineering Research Vol.26 No.5

Large-scale constructions of urbanization increase the impervious areas of city, leading to the urban hydrological effects such as urban waterlogging and rainwater runoff pollution. To this end, China proposed to adopt the measure to build sponge cities. However, the existing green soil cannot meet the comprehensive needs of sponge city. In order to quickly evaluate the comprehensive performance of the soil in sponge city, a comprehensive evaluation criterion was designed, which is related to the characteristics of greening soil permeability, porosity, pH, salinity and fertility. Based on the criterion, a new type of composite green soil was obtained with the silt soil: medium sand: sawdust ratio of 72.5%: 20%: 7.5%. Finally, compared with the existing soil, the new green soil not only meets the comprehensive performance requirements of the green soil’s fertility, pH, permeability and other factors, but also has higher permeability and water retention. It was proved that the new green soil has apparent advantages in the control of rainwater.

Direct Electrodeposition to Fabricate a Graphene Nanosheet-Modified Electrode for Imidacloprid Determination

Liang Yan,Zhicheng Li,Shaojun Zhang 성균관대학교(자연과학캠퍼스) 성균나노과학기술원 2016 NANO Vol.11 No.7

In this study, a film of electrochemically reduced graphene oxide (ERGO) deposited onto a glassy carbon electrode (GCE) was prepared through the pulse potential method (PPM). The asprepared film was characterized via scanning electron microscopy (SEM) and cyclic voltammetry (CV). The ERGO film was applied for the first time to develop a highly sensitive electrochemical sensor for imidacloprid determination. Results revealed that the ERGO film can effectively increase response towards imidacloprid reduction by significantly enhancing the reduction peak currents and decreasing the over potential of imidacloprid. Under optimum conditions, the modified electrode showed a linear voltammetric response to imidacloprid at concentrations ranging from 3.0 x 10-8 mol L-1 to 1.1 x 10-6 mol L-1, with a detection limit of 1.0 x 10-8 mol L-1. The developed electrode is potentially a good candidate for imidacloprid determination. The proposed method provides a good recovery rate of imidacloprid in spiked practical samples, such as lake water and tap water.

Efficiency of gerAa, tupA and ca transformation in Bacillus subtilis for self-healing of concrete cracks

Hanxing He,Gefei Li,Jiantao Zhang,Jinlong Zhang,Mingyue Luo,Wenkai Hu,Yamin Lin,Ziyu Deng,Zhicheng Liu,Weizhao Chen,Xu Deng 한양대학교 세라믹연구소 2019 Journal of Ceramic Processing Research Vol.20 No.5

A genetic approach was proposed to modify the characteristics of Bacillus subtilis strain WB800 (B. subtilis WB800) for selfhealing of concrete cracks. Three genes, namely gerAa which encodes germination receptors activated by L-alanine, tupA which is responsible for the synthesis of teichuronopeptide, and ca which encodes carbonic anhydrase (CA) catalyzing the synthesis of carbonate ion, were separately transformed into WB800. To protect bacterial cells from being squeezed, microspheres were produced with microcrystal cellulose (MCC) before the introduction of bacteria into the specimens. The results showed that the modified B. subtilis expressing GerA achieved 39.9% of germination ratio compared to 17% by the original host cells. With the transformation of tupA, the modified strain demonstrated higher resistance to alkaline environments, tolerating pH as high as 11, while the original strain only tolerated pH 9. The modified strain expressing CA induced more calcium carbonate than the original cells. Energy dispersive spectroscopy (EDS) identified the produced precipitate to be calcite (CaCO3). Moreover, a mathematical model was developed to optimize the influential factors of calcium precipitation process. Finally, based on the above results, an effective self-healing of concrete crack was achieved. This study may provide a promising strategy to improve the efficiency of bacterial self-healing of concrete cracks.

An adaptive marine predator algorithm based optimization method for hood lightweight design

Zhang Chenglin,He Zhicheng,Li Qiqi,Chen Yong,Chen Shaowei,NIE XINYU 한국CDE학회 2023 Journal of computational design and engineering Vol.10 No.3

The lightweight design of the hood is crucial for the structural optimization of an entire vehicle. However, traditional high-fidelity-based lightweight methods are time-consuming due to the complex structures of the hood, and the lightweight results heavily rely on engineering experiences. To this end, an improved adaptive marine predator algorithm (AMPA) is proposed to solve this problem. Compared to the original marine predator algorithm (MPA), the proposed AMPA adapts to optimization problems through three enhancements, including chaotic theory-based initialization, a mixed search strategy, and dynamic partitioning of iteration phases. Experimental comparisons of AMPA, MPA, and eight state-of-the-art algorithms are conducted on IEEE CEC2017 benchmark functions. AMPA outperforms the others in both 30- and 50-dimensional experiments. Friedman and Wilcoxon’s sign-rank tests further confirm AMPA’s superiority and statistical significance. An implicit parametric model of the hood is generated, and the critical design variables are determined through global sensitivity analysis to realize hood lightweight. The stacking method is employed to construct a surrogate meta-model of the hood to accelerate the optimization efficiency of the vehicle hood. Utilizing the meta-model and the proposed AMPA, the hood mass is reduced by 7.43% while all six static and dynamic stiffness metrics are enhanced. The effectiveness of the proposed optimization method is validated through finite element analysis.

Strength, deformation and failure behavior of bolted rock-like specimen with multiple cracks under uniaxial compression by particle flow simulation

Wendong Yang,Yiwei Li,Ling Wang,Kaicheng Zhang,Zhicheng Gong 한국지질과학협의회 2023 Geosciences Journal Vol.27 No.6

Most of the rock mass in nature contains a large number of joints, faults and other defects, which make the rock mass have the characteristics of discontinuity and anisotropy, and easily lead to instability and failure of rock engineering. A great quantity of engineering practices show that the bolt has a significant supporting effect on jointed rock mass. Therefore, it is of great significance to study the deformation and failure characteristics of jointed rock mass and the crack arrest effect of bolt for the safety and stability of engineering. A reasonable numerical model of bolted rock samples with non-persistent joints is established by using a three-dimensional Particle Flow Code (PFC) based on the laboratory rock specimens, and the uniaxial compression numerical test is carried out. The results indicate that (1) the numerical simulation results are in good agreement with the laboratory test results, and the variation trend of strength is basically consistent; (2) the different joint angles and anchorage angles result in variations in the mechanical properties of bolted specimens with non-persistent joints; (3) the joint angle has a significant effect on the failure mode of the specimen; (4) the existence of bolts can effectively limit the initiation and propagation process of micro-cracks, and greatly improve the mechanical properties of the specimen containing non-persistent joints.