Oxygen tension modulates cell function in an in vitro three-dimensional glioblastoma tumor model

Hypoxia is a typical feature of the tumor microenvironment,one of the most critical factors affecting cell behavior and tumor progression.However,the lack of tumor models able to precisely emulate natural brain tumor tissue has impeded the study of the effects of hypoxia on the progression and growth of tumor cells.This study reports a three-dimensional(3D)brain tumor model obtained by encapsulating U87MG(U87)cells in a hydrogel containing type I collagen.It also documents the effect of various oxygen concentrations(1%,7%,and 21%)in the culture environment on U87 cell morphology,proliferation,viability,cell cycle,apoptosis rate,and migration.Finally,it compares two-dimensional(2D)and 3D cultures.For comparison purposes,cells cultured in flat culture dishes were used as the control(2D model).Cells cultured in the 3D model proliferated more slowly but had a higher apoptosis rate and proportion of cells in the resting phase(G0 phase)/gap I phase(G1 phase)than those cultured in the 2D model.Besides,the two models yielded significantly different cell morphologies.Finally,hypoxia(e.g.,1%O2)affected cell morphology,slowed cell growth,reduced cell viability,and increased the apoptosis rate in the 3D model.These results indicate that the constructed 3D model is effective for investigating the effects of biological and chemical factors on cell morphology and function,and can be more representative of the tumor microenvironment than 2D culture systems.The developed 3D glioblastoma tumor model is equally applicable to other studies in pharmacology and pathology.

Prediction of three-dimensional ocean temperature in the South China Sea based on time series gridded data and a dynamic spatiotemporal graph neural network

Ocean temperature is an important physical variable in marine ecosystems,and ocean temperature prediction is an important research objective in ocean-related fields.Currently,one of the commonly used methods for ocean temperature prediction is based on data-driven,but research on this method is mostly limited to the sea surface,with few studies on the prediction of internal ocean temperature.Existing graph neural network-based methods usually use predefined graphs or learned static graphs,which cannot capture the dynamic associations among data.In this study,we propose a novel dynamic spatiotemporal graph neural network(DSTGN)to predict threedimensional ocean temperature(3D-OT),which combines static graph learning and dynamic graph learning to automatically mine two unknown dependencies between sequences based on the original 3D-OT data without prior knowledge.Temporal and spatial dependencies in the time series were then captured using temporal and graph convolutions.We also integrated dynamic graph learning,static graph learning,graph convolution,and temporal convolution into an end-to-end framework for 3D-OT prediction using time-series grid data.In this study,we conducted prediction experiments using high-resolution 3D-OT from the Copernicus global ocean physical reanalysis,with data covering the vertical variation of temperature from the sea surface to 1000 m below the sea surface.We compared five mainstream models that are commonly used for ocean temperature prediction,and the results showed that the method achieved the best prediction results at all prediction scales.

Three-dimensional structural models,evolution and petroleum geological significances of transtensional faults in the Ziyang area,central Sichuan Basin,SW China

With drilling and seismic data of Transtensional(strike-slip)Fault System in the Ziyang area of the central Sichuan Basin,SW China plane-section integrated structural interpretation,3-D fault framework model building,fault throw analyzing,and balanced profile restoration,it is pointed out that the transtensional fault system in the Ziyang 3-D seismic survey consists of the northeast-trending F_(I)19 and F_(I)20 fault zones dominated by extensional deformation,as well as 3 sets of northwest-trending en echelon normal faults experienced dextral shear deformation.Among them,the F_(I)19 and F_(I)20 fault zones cut through the Neoproterozoic to Lower Triassic Jialingjiang Formation,presenting a 3-D structure of an“S”-shaped ribbon.And before Permian and during the Early Triassic,the F_(I)19 and F_(I)20 fault zones underwent at least two periods of structural superimposition.Besides,the 3 sets of northwest-trending en echelon normal faults are composed of small normal faults arranged in pairs,with opposite dip directions and partially left-stepped arrangement.And before Permian,they had formed almost,restricting the eastward growth and propagation of the F_(I)19 fault zone.The F_(I)19 and F_(I)20 fault zones communicate multiple sets of source rocks and reservoirs from deep to shallow,and the timing of fault activity matches well with oil and gas generation peaks.If there were favorable Cambrian-Triassic sedimentary facies and reservoirs developing on the local anticlinal belts of both sides of the F_(I)19 and F_(I)20 fault zones,the major reservoirs in this area are expected to achieve breakthroughs in oil and gas exploration.

A three-dimensional semi-implicit unstructured grid finite volume ocean model

A new three-dimensional semi-implicit finite-volume ocean model has been developed for simulating the coastal ocean circulation, which is based on the staggered C-unstructured non-orthogonal grid in the hor- izontal direction and z-level grid in the vertical direction. The three-dimensional model is discretized by the semi-implicit finite-volume method, in that the free-surface and the vertical diffusion are semi-implicit, thereby removing stability limitations associated with the surface gravity wave and vertical diffusion terms. The remaining terms in the momentum equations are discretized explicitly by an integral method. The partial cell method is used for resolving topography, which enables the model to better represent irregular topography. The model has been tested against analytical cases for wind and tidal oscillation circulation, and is applied to simulating the tidal flow in the Bohal Sea. The results are in good agreement both with the analytical solutions and measurement results.

A THREE-DIMENSIONAL COASTAL BAROTROPIC MODEL IN GENERALIZED CURVILINEAR GRIDS

The method of automatically generating generalized curvilinear meshes has many advantages and is beginning to be used in ocean simulations. This three dimensional (3 D) coastal barotropic model in generalized curvilinear grids was developed to simulate the M 2, S 2, K 1 and O 1 tidal waves in the Bohai Sea, China. The numerical results agreeing with observations showed that the method is an effective tool for improving accuracy of simulations in shallow shelf seas, especially in the near coast region, if the pseudo effect there usually caused by rectangular grids can be removed.

Modelling Three-Dimensional Winds on a NW Pacific Region of Mexico Using Boundary-Fitted Grids

In this study, the momentum equations describing an atmospheric flow over a NW Pacific region of Mexico are solved numerically. In order to capture the complex flow-topography interactions with detail, a combination of a numerical wind model in full 3D curvilinear coordinates, along with a high resolution boundary-fitted grid is used. Boundary conditions were obtained from ten years (2002-2012) of measured offshore wind data. Prevailing winds from April to September during that period of observations were selected for the simulations. For the cases analyzed, it was found that at the points of the study region (PSS, PSM, PM), wind speed increased about 10% to 20% of its offshore values, while inland they decreased about 86% to 96%. This spatial behavior agreed very well with the observed local winds. A coastal jet (CJ), 35 km long with speeds about 1.5 - 2 m/s, emanating from PSS was found for NNW winds. Modeled winds were also used to compute wind stresses, wind stress curl, and CUI fields. Wind stress values agreed very well to those reported in the literature. High values of wind stress curl, and CUI were found at the lee of the points (PSS, PSM, PM). Indirect estimations of sea surface currents were about 15 - 20 cm/s offshore and 5 - 10 cm/s at the coast.

DEVELOPMENT OF A HYBRID MODEL FOR THREE-DIMENSIONAL GIS

This paper presents a hybrid model for three-dimensional Geographical Information Systems which is an integration of surface- and volume-based models. The Triangulated Irregular Network (TIN) and octree models are integrated in this hybrid models. The TIN model works as a surface-based model which mainly serves for surface presentation and visualization. On the other hand, the octree encoding supports volumetric analysis. The designed data structure brings a major advantage in the three-dimensional selective retrieval. This technique increases the efficiency of three-dimensional data operation.

Three-dimensional numerical modeling of gravity anomalies based on Poisson equation in spacewavenumber mixed domain

In gravity-anomaly-based prospecting, the computational and memory requirements for practical numerical modeling are potentially enormous. Achieving an efficient and precise inversion for gravity anomaly imaging over large-scale and complex terrain requires additional methods. To this end, we have proposed a new topography-capable By performing a two-dimensional Fourier transform in the horizontal directions, threedimensional partial differential equations in the spatial domain were transformed into a group of independent, one-dimensional differential equations engaged with different wave numbers. These independent differential equations are highly parallel across different wave numbers. differential equations with different wave numbers, and the efficiency of solving fixedbandwidth linear equations was further improved by a chasing method. In a synthetic test, a prism model was used to verify the accuracy and reliability of the proposed algorithm by comparing the numerical solution with the analytical solution. We studied the computational precision and efficiency with and without topography using different Fourier transform methods. The results showed that the Guass-FFT method has higher numerical precision, while the standard FFT method is superior, in terms of computation time, for inversion and quantitative interpretation under complicated terrain.

Three-dimensional tidal current numerical model of the Oujiang Estuary

The characteristics of three-dimensional （3-D） tidal current in the Oujiang Estuary are investigated according to in situ observations. The Oujiang Estuary has features of irregular coastline, complex topography, many islands, moveable boundary, and submerged dyke, therefore, σ 3-D numerical model oil an unstructured triangular grid has been degeloped. The σ coordinate transforination, the moveable boundary and submerged dyke treatment techniques were employed in the model so it is suitable for the tidal simulations in the Oujing Estuary with submerged dyke and moveable boundary problems. The model is evaluated with the in situ data, and the results show that the calculated water elevations at 19 stations and currents at 19 profiler stations are in good agreement with measured data both in magnitude and phase. This numerical model is applied to the 3-D tidal circulation simulations of experiments in stopping flow transport through the South Branch of the Oujiang Estuary, and the feasibility to cutoff the flow in the South Branch of the Oujiang Estuary is demonstrated by numerical simulation experiments. The developed numerical model simulated the 3-D tidal current circulations in complicated coastal and estuarine waters very well.

Three-dimensional cell culture systems as an in vitro platform for cancer and stem cell modeling

Three-dimensional(3D)culture systems are becoming increasingly popular due to their ability to mimic tissue-like structures more effectively than the monolayer cultures.In cancer and stem cell research,the natural cell characteristics and architectures are closely mimicked by the 3D cell models.Thus,the 3D cell cultures are promising and suitable systems for various proposes,ranging from disease modeling to drug target identification as well as potential therapeutic substances that may transform our lives.This review provides a comprehensive compendium of recent advancements in culturing cells,in particular cancer and stem cells,using 3D culture techniques.The major approaches highlighted here include cell spheroids,hydrogel embedding,bioreactors,scaffolds,and bioprinting.In addition,the progress of employing 3D cell culture systems as a platform for cancer and stem cell research was addressed,and the prominent studies of 3D cell culture systems were discussed.

Three-Dimensional Tidal Model and Its Application to Numerical Simulation of Water Quality in Coastal Waters

The turbulence mechanism plays an important part in the mixing process and momentum transfer of turbulence. A three-dimensional Prandtl mixing length tidal model has been developed to simulate tidal flows and water quality. The eddy viscosities and diffusivities are computed from the Prandtl mixing length model. In order to model the water quality of an estuary or coastal area many interdependent processes need to be simulated. These may be conveniently separated into three main groups: transport and mixing processes, biochemical interaction of water quality variables and the utilization and re-cycling of nutrients by living matter. The model simulates full oxygen and nutrient balance, primary productivity and the transport, reaction mechanism and fate of pollutants over tidal time-scales. The model is applied to numerical simulation of tidal flows and water quality in Dalian Bay. The model has been calibrated against a limited data set of historical water quality observations and in general demonstrates excellent agreement with all available data.

Three-dimensional land FD-CSEM forward modeling using edge finite-element method

A modeling tool for simulating three-dimensional land frequency-domain controlled-source electromagnetic surveys,based on a finite-element discretization of the Helmholtz equation for the electric fields,has been developed.The main difference between our modeling method and those previous works is edge finite-element approach applied to solving the three-dimensional land frequency-domain electromagnetic responses generated by horizontal electric dipole source.Firstly,the edge finite-element equation is formulated through the Galerkin method based on Helmholtz equation of the electric fields.Secondly,in order to check the validity of the modeling code,the numerical results are compared with the analytical solutions for a homogeneous half-space model.Finally,other three models are simulated with three-dimensional electromagnetic responses.The results indicate that the method can be applied for solving three-dimensional electromagnetic responses.The algorithm has been demonstrated,which can be effective to modeling the complex geo-electrical structures.This efficient algorithm will help to study the distribution laws of3-D land frequency-domain controlled-source electromagnetic responses and to setup basis for research of three-dimensional inversion.

The study on three-dimensional numerical model and fronts of the Jiulong Estuary and the Xiamen Bay

Applying the methods of on-site observation and dynamic model, the research on the fronts at the Jiulong Estuary has been carried out, during which spatial and temporal distribution, dynamic characteristics and formation mechanism of salinity fronts are analyzed and discussed. The research shows that the estuarine fronts mainly lie in the area from the Jiyu Islet to the Haimen Island, outside of Yuweizai to Hulishan cross-section, the near coast of Yuweizai and the south of the Songyu-Gulangyu Channel. The fronts in the former two regions are formed directly by plume, while the one near the coast of Yuweizai is a tidal intrusion front caused by flood current and the one at the south of the Songyu-Gulangyu Channel is the result of current shear transformation. Under normal circumstances, fresh water of the Jiulong River mainly influences the inside of the Xiamen Bay, and when it is in typhoon seasons, plume front can affect the Taiwan Strait and has an effect on the biogeochemical Drocesses in the strait.

Microstructure modeling and virtual test of asphalt mixture based on three-dimensional discrete element method

The objective of this work is to model the microstructure of asphalt mixture and build virtual test for asphalt mixture by using Particle Flow Code in three dimensions(PFC^(3D))based on three-dimensional discrete element method.A randomly generating algorithm was proposed to capture the three-dimensional irregular shape of coarse aggregate.And then,modeling algorithm and method for graded aggregates were built.Based on the combination of modeling of coarse aggregates,asphalt mastic and air voids,three-dimensional virtual sample of asphalt mixture was modeled by using PFC^(3D).Virtual tests for penetration test of aggregate and uniaxial creep test of asphalt mixture were built and conducted by using PFC^(3D).By comparison of the testing results between virtual tests and actual laboratory tests,the validity of the microstructure modeling and virtual test built in this study was verified.Additionally,compared with laboratory test,the virtual test is easier to conduct and has less variability.It is proved that microstructure modeling and virtual test based on three-dimensional discrete element method is a promising way to conduct research of asphalt mixture.

Assessment of Crop Yield in China Simulated by Thirteen Global Gridded Crop Models

Global gridded crop models(GGCMs) have been broadly applied to assess the impacts of climate and environmental change and adaptation on agricultural production. China is a major grain producing country, but thus far only a few studies have assessed the performance of GGCMs in China, and these studies mainly focused on the average and interannual variability of national and regional yields. Here, a systematic national-and provincial-scale evaluation of the simulations by13 GGCMs [12 from the GGCM Intercomparison(GGCMI) project, phase 1, and CLM5-crop] of the yields of four crops(wheat, maize, rice, and soybean) in China during 1980–2009 was carried out through comparison with crop yield statistics collected from the National Bureau of Statistics of China. Results showed that GGCMI models generally underestimate the national yield of rice but overestimate it for the other three crops, while CLM5-crop can reproduce the national yields of wheat, maize, and rice well. Most GGCMs struggle to simulate the spatial patterns of crop yields. In terms of temporal variability, GGCMI models generally fail to capture the observed significant increases, but some can skillfully simulate the interannual variability. Conversely, CLM5-crop can represent the increases in wheat, maize, and rice, but works less well in simulating the interannual variability. At least one model can skillfully reproduce the temporal variability of yields in the top-10 producing provinces in China, albeit with a few exceptions. This study, for the first time, provides a complete picture of GGCM performance in China, which is important for GGCM development and understanding the reliability and uncertainty of national-and provincial-scale crop yield prediction in China.

A Three-dimensional Heterogeneous Mass Transfer Model for the Absorption of Gas into Multiphase System

A three-dimensional heterogeneous mass transfer model was proposed to investigate the enhancement of dispersed particles on gas absorption. The strategy to calculate local and overall enhancement factors is proposed. Instead of a global grid, the composite overlapping grid is adopted, which simplifies the setup and solution of the three-dimensional model equations. It is found that dispersed particle hold-up, particle size, liquid-solid partition coefficient of transported component, characteristic contact time, and the shortest distance between particles and gas-liquid interface have major influence on absorption enhancement factor. The particle-particle interaction on gas absorption and the lateral diffusion of transported component in liquid film were studied with the multi-particle simulation. The proposed model predicted the experimental data from the literature reasonably well.

Three-dimensional forward modeling for magnetotelluric sounding by finite element method

A finite element algorithm combined with divergence condition was presented for computing three-dimensional(3D) magnetotelluric forward modeling. The finite element equation of three-dimensional magnetotelluric forward modeling was derived from Maxwell's equations using general variation principle. The divergence condition was added forcedly to the electric field boundary value problem, which made the solution correct. The system of equation of the finite element algorithm was a large sparse, banded, symmetric, ill-conditioned, non-Hermitian complex matrix equation, which can be solved using the Bi-CGSTAB method. In order to prove correctness of the three-dimensional magnetotelluric forward algorithm, the computed results and analytic results of one-dimensional geo-electrical model were compared. In addition, the three-dimensional magnetotelluric forward algorithm is given a further evaluation by computing COMMEMI model. The forward modeling results show that the algorithm is very efficient, and it has a lot of advantages, such as the high precision, the canonical process of solving problem, meeting the internal boundary condition automatically and adapting to all kinds of distribution of multi-substances.

A Novel Three-Dimensional Mouse Embryonic Implantation Model In Vitro

To regenerate three-dimensional endometrium in vitro as a novel model for studying the mechanism of implantation of embryos, the luminal epithelial cells and stromal cells of the rabbit uterus were separated and cultured in vitro. The type Ⅰ mouse tail collagen was used as scaffolding material. The stromal cells were inoculated in the type I mouse tail collagen, and the luminal epithelial cells were inoculated on the type i mouse tall collagen to regenerate the endometrium in vitro. The regenerated endometrium was cultured in DMEM-F/12 media containing 100 nmol L^-1 progesterone, 10 nM β-estradiol, and 10% fetal bovine serum （FBS） for 3 d. The media were then replaced with CZB containing 100 nM progesterone, 10 nmol L-1 β-estradiol, and 10% FBS, and the mouse blastulas were co-cultured with it. The results of scanning electronic micrography showed that the epithelial cells on the surface of the reconstructed endometrium were covered with numerous slender microvilli and some epithelial cells protruded pinopodes. After culturing for 12 h with the mouse blastula, the shedding, attachment, and implantation of the blastula were observed. The blastula can escape from zona pellucida and attach to the three-dimensional endometrium and is then implanted into it. This study showed that the reconstructed three-dimensional endometrium can serve as a robust embryo implantation model in vitro.

A Three-Dimensional Water Quality Model and Its Application to Jiaozhou Bay, China

A three-dimensional coupled physical and water quality model was developed and applied to the Jiaozhou Bay to study water quality involving nutrients, biochemical oxygen demand, dissolved oxygen, and phytoplankton that are closely related to eutrophication process. The physical model is a modified ECOM-si version with inclusion of flooding/draining processes over the intertidal zone. The water quality model is based on WASP5 which quantifies processes governing internal nutrients cycling, dissolved oxygen balance and phytoplankton growth. The model was used to simulate the spatial distribution and the temporal variation of water quality in the Jiaozhou Bay for the period of May 2005 to May 2006. In addition, the effect of reduction of riverine nutrients load was simulated and evaluated. The simulated results show that under the influence of nutrients discharged from river, the concentrations of nutrients and phytoplankton were higher in the northwest and northeast of the bay, and decreased from the inner bay to the outer. Affected by strong tidal mixing, the concentrations of all state variables were vertically homogeneous except in the deeper regions where a small gradient was found. Obvious seasonal variation of phytoplankton biomass was found, which exhibited two peaks in March and July, respectively. The variation of riverine waste loads had remarkable impact on nutrients concentration in coastal areas, but slightly altered the distribution in the center of the bay.

Single-phase Computational Fluid Dynamics Applicability for the Study of Three-dimensional Flow in 5×5 Rod Bundles with Spacer Grids

Spacer grids play an important role in pressurized water reactor（PWR） fuel assembly in that they have significant influence on the thermal-hydraulic characteristics of the reactor core.But so far,the numerical studies are performed without regarding dimple and spring of spacer grids,just considering mixing vane.Moreover,these studies use k-ε turbulence model without considering the suitability of the other turbulence models upon the different spacer grids flow.A study is carried out to understand the 3-D single-phase flow in AFA-2G 5×5 rod bundles with spacer grids based on numerical method.In order to investigate the suitability of different turbulence models,k-ε model and k-ω model,the influence of different parts of spacer grid on the fluid flow is also predicted.By using second-order upwind scheme,hybrid grids technique,and improved SIMPLEC algorithm,the Reynolds averaged mass conservation and momentum conservation equations are solved,and the pressure and velocity field of flow are obtained.The numerical simulation results are compared with experiment results and the agreement is satisfactory.The simulation results show the influences of the spring,dimple and mixing vane,and the different characteristics of the k-ε model and k-ω model.Comparing with the experiment results,the simulation results suggest that the k-ω model is suitable for the simulation of the rod bundle flow with spacer grids;the spring and dimple are the main causes of the pressure loss in the spacer grid channel.The friction coefficient of the channel with spring and dimple is 1.5 times the coefficient of the channel with the vane.These results are beneficial to enhance the simulation ability of spacer grids flow and optimization design ability of spaces grid.