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Characterization of macropore structure of Malan loess in NW China based on 3d pipe models constructed by using computed tomography technology

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JOURNAL OF ASIAN EARTH SCIENCES 2018年 154卷 271-279页

作者： Li, Yanrong He, Shengdi deng, Xiaohong Xu, Yongxin Taiyuan Univ Technol Dept Earth Sci & Engn Taiyuan 030024 Shanxi Peoples R China Taiyuan Univ Technol Coll Water Resources Sci & Engn Taiyuan 030024 Shanxi Peoples R China Univ Western Cape Dept Earth Sci Cape Town South Africa

Malan loess is a grayish yellow or brownish yellow, elastic, highly porous and brittle late Quaternary sediment formed by the accumulation of windblown dust. The present-day pore structure of Malan loess is crucial for understanding the loessification process in history, loess strengths and mechanical behavior. This study employed a modern computed tomography (CT) device to scan Malan loess samples, which were obtained from the east part of the Loess Plateau of China. A sophisticated and efficient workflow for processing the CT images and constructing 3d pore models was established by selecting and programming relevant mathematical algorithms in MATLAB, such as the maximum entropy method, medial axis method, and node recognition algorithm. Individual pipes within the Malan loess were identified and constructed by partitioning and recombining links in the 3d pore model. The macropore structure of Malan loess was then depicted using quantitative parameters. The parameters derived from 2d images of CT scanning included equivalent radius, length and aspect ratio of pores, porosity, and pore distribution entropy, whereas those derived from the constructed 3d structure models included porosity, coordination number, node density, pipe radius, length, length density, dip angle, and dip direction. The analysis of these parameters revealed that Malan loess is a strongly anisotropic geomaterial with a dense and complex network of pores and pipes. The pores discovered on horizontal images, perpendicular to the vertical direction, were round and relatively uniform in shape and size and evenly distributed, whereas the pores discovered on vertical images varied in shape and size and were distributed in clusters. The pores showed good connectivity in vertical direction and formed vertically aligned pipes but displayed weak connectivity in horizontal directions. The pipes in vertical direction were thick, long, and straight compared with those in horizontal directions. These results

关键词： Malan loess Macropore structure 3d structure model Anisotropy CT technique

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modeling ECM fiber formation: structure information extracted by analysis of 2d and 3d image sets

Modeling ECM fiber formation: Structure information extracte...

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Conference on 3-dimensional and Multidimensional Microscopy: Image Acquisition and Processing IX

作者： Wu, J Voytik-Harbin, SL Filmer, dL Hoffmann, CM Yuan, B Chiang, CS Sturgis, J Robinson, JP Purdue Univ Sch Vet Med Dept BMS W Lafayette IN 47907 USA

ISBN: (纸本)0819443603

Recent evidence supports the notion that biological functions of extracellular matrix (ECM) are highly correlated to its structure. Understanding this fibrous structure is very crucial in tissue engineering to develop the next generation of biomaterials for restoration of tissues and organs. In this paper, we integrate confocal microscopy imaging and image-processing techniques to analyze the structural properties of ECM. We describe a 2d fiber middle-line tracing algorithm and apply it via Euclidean distance maps (EdM) to extract accurate fibrous structure information, such as fiber diameter, length, orientation, and density, from single slices. Based on a 2d tracing algorithm, we extend our analysis to 3d tracing via Euclidean distance maps to extract 3d fibrous structure information. We use computer simulation to construct the 3d fibrous structure which is subsequently used to test our tracing algorithms. After further image processing, these models are then applied to a variety of ECM constructions from which results of 2d and 3d traces are statistically analyzed.

关键词： extracellular matrix (ECM) 3d structure model tracing software computer simulation confocal microscopy

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Advancing neogene-quaternary reservoir characterization in offshore Nile delta, Egypt: high-resolution seismic insights and 3d modeling for new prospect identification

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ENVIRONMENTAL EARTH SCIENCES 2024年第20期83卷 581页

作者： Reda, Mohamed El-Gendy, Nader H. Raef, Abdelmoniem El Mashaly, Mohamed M. Alarifi, Nasir Barakat, Moataz Kh. Al Azhar Univ Fac Sci Geol Dept POB 11884 Nasr City Cairo Egypt Tanta Univ Fac Sci Geol Dept Tanta 31527 Egypt Kansas State Univ Dept Geol Manhattan KS USA ECS Elect Construct Serv POB 8Kattamia New Cairo Egypt King Saud Univ Coll Sci Geol & Geophys Dept Riyadh Saudi Arabia

This study presents a comprehensive characterization of the Neogene-Quaternary formations within the offshore Temsah gas field, which is approximately 65 km NNW of Port Said offshore the Nile delta Basin. By integrating seismic and well log data, we constructed a detailed static reservoir model to address the complex geological structures and evaluate hydrocarbon potential. The Temsah offshore gas field has a complex geological structure characterized by numerous normal faults aligned in the two fault systems one northeast-southwest and another northwest-southeast trending. The predominance of clastic rocks and petroleum system setting in the Nile delta Basin make this location favourable for hydrocarbon accumulations. Utilizing data from four wells and twenty-nine seismic lines, an in-depth interpretation was conducted to overcome the challenge of precise seismic feature delineation. Static reservoir model incorporates detailed three-dimensional visualizations of sandstones and shale layers, with a particular focus on the Upper Sandstone of Kafr El-Sheikh and Sidi Salem formations. detailed three-dimensional model illustrated the structural impact on the studied reservoirs. Shale volume, water saturation property distribution grids complemented a constructed 3d model depicting the spatial distribution of rock facies and petrophysical parameters within the Temsah gas field. The integrated approach facilitated the identification and evaluation of three hydrocarbon prospect locations with estimated Gas Initially In Place (GIIP) ranging from approximately 2,856,782 Billion Cubic Feet [BCF] to 5,332,660 [BCF]. These findings underscore the substantial potential for advancing field development in the Temsah gas field.

关键词： High resolution seismic interpretation 3d structure model 3d property models Facies interpretation New prospect definition Temsah field

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B-factor-saturation mutagenesis as a strategy to increase the thermostability of α-L-rhamnosidase from Aspergillus terreus

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JOURNAL OF BIOTECHNOLOGY 2018年 275卷 17-23页

作者： Ge, Lin Li, dongdong Wu, Tao Zhao, Linguo ding, Gang Wang, Zhenzhong Xiao, Wei Nanjing Forestry Univ Coinnovat Ctr Sustainable Forestry Southern China 159 Long Pan Rd Nanjing 210037 Jiangsu Peoples R China Nanjing Forestry Univ Coll Chem Engn 159 Long Pan Rd Nanjing 210037 Jiangsu Peoples R China Jiangsu Kan Pharmaceut Co Ltd 58 Haichang South Rd Lianyungang 222001 Jiangsu Peoples R China

The alpha-L-Rhamnosidase is an important enzyme with applications in the food and pharmaceutical industries because it can release terminal L-rhamnose residues from various natural products. In this study, the B-factor-saturation mutagenesis strategy was used to increase the thermostability of alpha-L-rhamnosidase from Aspergillus terreus. The d594Q and G827K/d594Q mutant enzymes were obtained by screening a series of mutants;they prolonged the half-life of the enzyme at 70 degrees C by 2.1-fold and 2.3-fold, respectively. Analysis of the 3d structure showed that in the thermostable variants the number of hydrogen bonds and salt bridges was increased, explaining the enhanced thermostability. Kinetic studies showed that the KM values for the d594Q and G827K/d594Q mutant enzymes decreased by 4.0% and 3.8%, respectively. Additionally, the kcat/K-M values for the d594Q and G827K/d594Q mutant enzymes increased by 15.5% and 9.2%, respectively. Moreover, the d594Q and G827K/d594Q mutant enzymes exhibited markedly improved isoquercitrin yield at 70 degrees C that increased by 13.5% and 11.0%, respectively. Therefore, the d594Q and G827K/d594Q mutant enzymes are more suitable for the industrial processes of isoquercitrin preparation.

关键词： Thermostability alpha-L-rhamnosidase B-factor-saturation mutagenesis 3d structure model Isoquercitrin yield

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Complete genome analysis of a Staphylococcus aureus phage (vBSM-A1)

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ARCHIVES OF MICROBIOLOGY 2020年第7期202卷 1617-1626页

作者： Geng, Huijun Zhang, Meixia Li, Xiaoyu Wang, Lili Cong, Cong Cui, Huijing Wang, Linhui Xu, Yongping Dalian Univ Technol Sch Bioengn Dalian 116024 Peoples R China Aimei Hissen Vaccine Dalian Co Ltd Dalian Peoples R China Minist Educ Ctr Food Safety Anim Origin Dalian 116600 Peoples R China

In this study, the genome of a new strain of lytic Staphylococcus aureus Herelleviridae, vBSM-A1, was characterized and annotated. The phage was isolated from sewage samples collected in Xinjiang Province, China. The genome of vBSM-A1 was found to comprise a linear double-stranded dNA of 140,654 bp length, with a G + C content of 30.33%. A total of 215 ORFs were detected in the phage dNA, 74 of which were functionally assigned. The 3d structure model of endolysin LysK (ORF 143) was created using Phyre2.

关键词： Staphylococcus aureus Genome analysis 3d structure model

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digital Twin of Piezoelectric Effect at Microscale and Macroscale PVdF Film 18

Digital Twin of Piezoelectric Effect at Microscale and Macro...

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18th IEEE/ASME International Conference on Mechatronic and Embedded Systems and Applications (MESA)

作者： Huang, Yu-Hsiang Huang, Tsung-Han Hung, Wei-Song Chang, Ching-Yuan Natl Taipei Univ Technol Dept Mech Engn Taipei Taiwan Natl Taiwan Univ Sci & Technol Grad Inst Applieed Sci & Technol Taipei Taiwan

ISBN: (纸本)9781665455701

This study uses computer tomography (CT) and a finite element method (FEM) criterion to establish a digital twin (dT) model for Polyvinylidene fluoride (PVdF) film. The CT provides sliced images of the PVdF film with 50 mu m, and we have developed a standard procedure to rebuild the stereo and interior model of the PVdF film. We also use a d33 meter to measure the piezoelectric effect of the PVdF film and utilize the value in the FEM model. The primary material of the piezoelectric film is polyvinylidene fluoride, which has a unique dielectric effect, piezoelectric effect, and pyroelectric effect. In this study, computer tomography was used to establish the microstructure model of the film, and ANSYS software was used to establish the microstructure model. The primary purpose of simulating the piezoelectric effect of the self-made piezoelectric film is to compare the small holes contained in the film structure and the forward and reverse piezoelectric responses of different structures in the same environment. This study has established three different dT-FEM models and simulated the piezoelectric effect of the thin film. The dT-FEM model contributes to the emerging technology of material science and helps scientists to investigate the piezoelectric effect at the micro- and macro-scale.

关键词： Piezoelectric Electromechanical coupling properties PVdF thin films 3d structure model Numerical simulation

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Three-dimensional reservoir modeling of the pliocene reservoir based on seismic data advances for new prospect assessment

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MARINE GEORESOURCES & GEOTECHNOLOGY 2024年

作者： Elgendy, Nader H. Reda, Mohamed Elmashaly, Mohamed M. Raef, Abdelmoneam Al-Hashim, Mansour H. Barakat, Moataz Kh. Tanta Univ Fac Sci Geol Dept Tanta Egypt Al Azhar Univ Fac Sci Geol Dept POB 11884 Nasr City Cairo Egypt ECS Elect construct Serv Kattamia New Cairo Egypt Kansas State Univ Coll Arts & Sci Dept Geol Manhattan KS USA King Saud Univ Coll Sci Dept Geol & Geophys Riyadh Saudi Arabia

This study presents a comprehensive characterization of the Pliocene reservoir formation in the Temsah gas field, located 65 km NNW of Port Said in the northeastern Nile delta Basin. The research integrates seismic data with well log analysis to enhance reservoir characterization. The Temsah gas field is distinguished by its intricate geological structure, featuring numerous normal faults oriented along northeast-southwest and northwest-southeast trends. The field's stratigraphy is predominantly composed of sandstone and shale facies, which are considered highly prospective for hydrocarbon accumulation. A full geological field analysis was conducted to identify key prospects for enhancing productivity. To accurately delineate seismic features, data from four wells and twenty-nine 2d seismic lines were interpreted. depth maps of the reservoir layers were constructed, highlighting critical transitions between sandstone and shale facies, which are pivotal for future exploration efforts. A detailed 3d static model was developed to illustrate the impact of lithological composition on reservoir characteristics, with a specific focus on the Upper Sand of Kafr El-Sheikh Formation. Petrophysical properties, including effective porosity (13-23%), shale content (7-31%), and water saturation (30-45%), were meticulously evaluated to inform the creation of a robust 3d property model. This model provides a detailed spatial distribution of rock facies and petrophysical parameters within the Temsah gas field. The integration of these studies identified two promising areas, with estimated original gas in place (OGIP) ranging from 2.86 to 4.04 stock cubic feet (SCF), indicating significant potential for field development and enhancement.

关键词： Seismic interpretation 3d structure model 3d property model prospect assessment Temsah field offshore Nile delta

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Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids

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HUMAN GENOMICS 2021年第1期15卷 18-18页

作者： Fang, Ke-Ying Cao, Wen-Chao Xie, Tian-Ao Lv, Jie Chen, Jia-Xin Cao, Xun-Jie Li, Zhong-Wei deng, Shu-Ting Guo, Xu-Guang Guangzhou Med Univ Affiliated Hosp 3 Dept Clin Lab Med Guangzhou 510150 Peoples R China Guangzhou Med Univ Clin Sch 3 Dept Clin Med Guangzhou 511436 Peoples R China Guangzhou Med Univ Affiliated Hosp 3 Key Lab Major Obstet Dis Guangdong Prov Guangzhou 510150 Peoples R China Guangzhou Med Univ Affiliated Hosp 3 Key Lab Reprod & Genet Guangdong Higher Educ Inst Guangzhou 510150 Peoples R China

Background In the novel coronavirus pandemic, the high infection rate and high mortality have seriously affected people's health and social order. To better explore the infection mechanism and treatment, the three-dimensional structure of human bronchus has been employed in a better in-depth study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methods We downloaded a separate microarray from the Integrated Gene Expression System (GEO) on a human bronchial organoids sample to identify differentially expressed genes (dEGS) and analyzed it with R software. After processing with R software, Gene Ontology (GO) and Kyoto PBMCs of Genes and Genomes (KEGG) were analyzed, while a protein-protein interaction (PPI) network was constructed to show the interactions and influence relationships between these differential genes. Finally, the selected highly connected genes, which are called hub genes, were verified in CytoHubba plug-in. Results In this study, a total of 966 differentially expressed genes, including 490 upregulated genes and 476 downregulated genes were used. Analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways related to immune response and cytokines. We construct protein-protein interaction network and identify 10 hub genes, including IL6, MMP9, IL1B, CXCL8, ICAM1, FGF2, EGF, CXCL10, CCL2, CCL5, CXCL1, and FN1. Finally, with the help of GSE150728, we verified that CXCl1, CXCL8, CXCL10, CCL5, EGF differently expressed before and after SARS-CoV-2 infection in clinical patients. Conclusions In this study, we used mRNA expression data from GSE150819 to preliminarily confirm the feasibility of hBO as an in vitro model to further study the pathogenesis and potential treatment of COVId-19. Moreover, based on the mRNA differentiated expression of this model, we found that CXCL8, CXCL10, and EGF are hub genes in the process of SARS-COV-2 infection, and we emphasized their key roles in SARS-CoV-

关键词： Immune response Human bronchial organoids Novel coronavirus infection Bioinformatics analysis 3d structure model

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