DEM study on the mechanical behaviours of methane hydrate sediments: hydrate growth patterns and hydrate bonding strength

Natural methane hydrate soil sediments attract worldwide interest, as there is huge commercial potential in the immense global deposits of natural gas hydrate that lies under deep seabeds and permafrost regions. However, the geomechanical behaviour of methane hydrate soil is poorly understood. In this study, Discrete Element Method (DEM) was employed to provide insights into the mechanical behaviour of hydrate-bearing sediments with different hydrate patterns in the pores: the pore-filling case and the cementation case. A series of drained triaxial compressional tests were performed, and the results were analyzed in terms of stress-strain response and volumetric response. In both pore-filling and cementation cases, the presence of hydrates caused an increase in the strength and dilative tendency of the simulated hydrate-bearing soil samples, and the strength and dilation both increased with hydrate saturation (or amount of hydrates in the pores). In addition, at the same hydrate saturation, the cementation case showed higher values of strength and dilation than the pore-filling case. In the cementation case, two typical hydrate growth patterns were considered: soil surface coating (hydrates form around the grain surface) and soil-soil contact gathering (hydrates preferentially form at the grain contacts). Results showed that hydrate growth patterns greatly influenced the mechanical behaviour of the simulated hydrate-bearing samples, especially when the bonding strength and hydrate saturation were increased. In both patterns, strength and dilation were enhanced as bonding strength increased, and the enhancement was greater in the soil-soil contact model than in the soil surface gathering model. At high hydrate saturation, as bonding strength increased, a larger axial strain was needed to reach the peak strength, and the development of dilation was delayed

Exploration of the Survival Probability and Shape Evolution of Crushable Particles during One-Dimensional Compression Using Dyed Gypsum Particles

Observing the fragmentation of individual particles within granular assemblies is a subject of evident theoretical and practical importance. A new technique using dyed gypsum particles (DGPs) to match the broken particles to their parents was adopted in this study. An image-based method of acquiring the shape information of particles from two orthogonal views was proposed. The mass survival probability and shape characteristics of the children particles were analyzed after a series of one-dimensional compression tests on the DGPs. It was found that medium-sized particles in the polydisperse samples underwent more breakage than the other particles, and this might have been attributed to the combined effects of the particle crushing strength and the coordination number. The shape evolution of broken particles and surviving particles showed opposite trends. Because the particles after the test within a given size range consisted of both the broken and surviving particles, their overall shape characteristics did not show a consistent trend. Furthermore, individual particle crushing tests on the children particles suggested that the breakage-induced shape irregularity did not change the Weibull modulus, but had a substantial effect on the magnitude of the survival probability

Quantifying the effects of elevated CO<inf>2</inf> on water budgets by combining FACE data with an ecohydrological model

© 2014 John Wiley & Sons, Ltd. Response of leaf area index (LAI) is the key determinant for predicting impacts of the elevated CO 2 (eCO 2 ) on water budgets. Importance of the changes in functional attributes of vegetation associated with eCO 2 for predicting responses of LAI has rarely been addressed. In this study, the WAter Vegetation Energy and Solute (WAVES) model was applied to simulate ecohydrological effects of the eCO 2 at two free-air CO 2 enrichment (FACE) experimental sites with contrasting vegetation. One was carried out by the Oak Ridge National Laboratory on the forest (ORNL FACE). The other one was conducted by the University of Minnesota on the grass (BioCON FACE). Results demonstrated that changes in functional attributes of vegetation (including reduction in specific leaf area, changes in carbon assimilation and allocation characteristics) and availability of nutrients are important for reproducing the responses of LAI, transpiration and soil moisture at both sites. Predicted LAI increased slightly at both sites because of fertilization effects of the eCO 2 . Simulated transpiration decreased 10·5% at ORNL site and 13·8% at BioCON site because of reduction in the stomatal conductance. Predicted evaporation from interception and soil surface increased slightly ( < 1·0mmyear -1 ) at both sites because of increased LAI and litter production, and increased soil moisture resulted from reduced transpiration. All components of run-off were predicted to increase because of significant decrease in transpiration. Simulated mean annual evapotranspiration decreased about 8·7% and 10·8%, and mean annual run-off increased about 11·1% (59·3mmyear -1 ) and 9·5% (37·6mmyear -1 ) at the ORNL and BioCON FACE sites, respectively

In situ loading and delivery of short single- And double-stranded dna by supramolecular organic frameworks

Short DNA represents an important class of biomacromolecules that are widely applied in gene therapy, editing, and modulation. However, the development of simple and reliable methods for their intracellular delivery remains a challenge. Herein, we describe that seven water-soluble, homogeneous supramolecular organic frameworks (SOFs) with a well-defined pore size and high stability in water that can accomplish in situ inclusion of single-stranded (ss) and double-stranded (ds) DNA (21, 23, and 58 nt) and effective intracellular delivery (including two noncancerous and six cancerous cell lines). Fluorescence quenching experiments for single and double endlabeled ss- and ds-DNA support that the DNA sequences can be completely enveloped by the SOFs. Confocal laser scanning microscopy and flow cytometry reveal that five of the SOFs exhibit excellent delivery efficiencies that, in most of the studied cases, outperform the commercial standard Lipo2000, even at low SOF-nucleic acid ratios. In addition to high delivery efficiencies, the watersoluble, self-assembled SOF carriers have a variety of advantages, including convenient preparation, high stability, and in situ DNA inclusion, which are all critical for practical applications in nucleic acid delivery

Impacts of elevated CO<inf>2</inf>, climate change and their interactions on water budgets in four different catchments in Australia

© 2014 Elsevier B.V. Future water availability is affected directly by climate change mainly through changes in precipitation and indirectly by the biological effects of climate change and elevated atmospheric CO2 concentration (eCO2) through changes in vegetation water use. Previous studies of climate change impact on hydrology have focused on the direct impact and little has been reported in the literature on catchment-scale the indirect impact. In this study, we calibrated an ecohydrological model (WAVES) and used this model to estimate the direct and indirect effects and the interactive effect between climate change and eCO2 on water availability in four different catchments in Australia with contrasting climate regime and vegetation cover. These catchments were: a water-limited forest catchment and an energy-limited forest catchment, a water-limited grass catchment and an energy-limited grass catchment. The future meteorological forcing was projected from 12 GCMs representing a period centred on 2050s and future CO2 concentration was set as 550ppm. Modelling experiments show that impacts of eCO2 and projected climate change on vegetation growth, evapotranspiration (ET) and runoff were in the same magnitude but opposite directions in all four catchments, except for the effects on runoff in the energy-limited grass catchment. Predicted responses of runoff to eCO2 indicate that eCO2 increased runoff in the energy-limited forest catchment by ~2% but decreased runoff in other three catchments from 1% to 18%. This study indicates that rising CO2 increases ecosystem water use efficiency but it does not necessarily result in increased runoff because elevated CO2 also stimulates vegetation growth and increases ET. Elevated CO2 was proved to have greater impacts on runoff than climate change in the forest catchments. Modelling experiments also suggest that interactive effects between climate and CO2 are important, especially for predicting leaf area index (LAI) and ET in grassland catchments or runoff in water-limited catchments, where interactive effects were 1-6%. It implies that the assumption that linear combination of individual effects in most of previous studies is not appropriate. This study highlights the importance of considering elevated CO2 in assessing climate change impacts on catchment-scale water balance and failure to account for direct eCO2 effect or its interactive effects can lead to large bias in the predictions of future water budgets, especially for the water-limited catchments in Australia

Hydrodynamics, erosion and accretion of intertidal mudflats in extremely shallow waters

© 2019 Elsevier B.V. Intertidal flats are shallow-water environments that undergo cyclical variations in water depth, leading to a frequent occurrence of extremely shallow water stages (ESWS; water depths 0.2 m), and the rate of change was an order of magnitude faster than during RDWS. This larger and faster bed-level change occurred even though the ESWS duration only accounted for 10% of the entire tidal cycle. This result occurred because the bed shear stress due to combined current–wave action during ESWS, was, on average, two times higher than during RDWS at the flood stage causing more extensive erosion. Whereas during the ebb stage, this shear stress during ESWS was only half of that during RDWS resulting in greater accretion. The main implications of these results are that, because ESWS occur frequently (twice every tide) and are associated with large bed shear stress and bed-level changes, these conditions are likely to play an important role in morphological changes of intertidal flats. Our study shows that ESWS have a key influence on intertidal flat hydrodynamics and sediment dynamics. Thus our results are the basis for an improved understanding of the coastal morphodynamic processes on intertidal flats

Proteome profiling of cadmium-induced apoptosis by antibody array analyses in human bronchial epithelial cells

Protein array technology is a powerful platform for the simultaneous determination of the expression levels of a number of proteins as well as post-translational modifications such as phosphorylation. Here, we screen and report for the first time, the dominant signaling cascades and apoptotic mediators during the course of cadmium (Cd)-induced cytotoxicity in human bronchial epithelial cells (BEAS-2B) by antibody array analyses. Proteins from control and Cd-treated cells were captured on Proteome Profiler™ Arrays for the parallel determination of the relative levels of protein phosphorylation and proteins associated with apoptosis. Our results indicated that the p38 MAPK- and JNK-related signal transduction pathways were dramatically activated by Cd treatment. Cd potently stimulates the phosphorylations of p38α (MAPK14), JNK1/2 (MAPK8/9), and JUN; while the phosphorylations of Akt1, ERK1/2 (MAPK3/1), GSK3β, and mTOR were suppressed. Moreover, there was an induction of proapoptotic protein BAX, release of cytochrome c (CYCS) from mitochondria, activation of caspase-3/9 (CASP3/9); as well as decreased expression of cell cycle checkpoint proteins (TP53, p21, and p27) and several inhibitors of apoptosis proteins (IAPs) [including cIAP-1/2 (BIRC2/3), XIAP (BIRC4), and survivin (BIRC5)]. Pretreatment of cells with the thiol antioxidant glutathione or p38 MAPK/JNK inhibitors before Cd treatment effectively abrogated ROS activation of p38 MAPK/JNK pathways and apoptosis-related proteins. Taken together, our results demonstrate that Cd causes oxidative stress-induced apoptosis; and the p38 MAPK/JNK and mitochondrial pathways are more importantly participated for signal transduction and the induction of apoptosis in Cd-exposed human lung cells.published_or_final_versio

Discrete element modelling of methane hydrate soil sediments using elongated soil particles

In this discrete element modelling research, triaxial compression tests of particle assemblies were simulated to study the mechanical behaviour of methane hydrate sediments with two different hydrate formation patterns: pore-filling and cementation. The soil particles were modelled using spherical or elongated particles (two aspect ratios 1.5 and 2.0). Hydrates were modelled as smaller particles and were placed either inside the pores in a random manner (the pore-filling case) or around the soil particle contacts (the cementation case). Compared to the pure soil samples, the hydrates essentially influenced the mechanical behaviour of the hydrate-bearing soil samples, and the behaviours varied due to the different hydrate growth patterns. The behaviour with elongated soil particles is much closer to that of the natural hydrate-bearing sandy sediments retrieved from the Nankai Trough than the behaviour with spherical particles. The observed macroscopic strength behaviour is also explained by the microscopic contact-type related contributions (soil-soil contact, soil-hydrate contact and hydrate-hydrate contact) to the deviatoric stresses

High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using affymetrix cytoscan HD chip

Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis. Our analysis showed a 91% overlap between CNV detection by microarray with FFPE tissues and chromosomal abnormality detection by karyotyping with fresh tissues on 8 cases of lymphoma samples. The CNV overlap between matched frozen and FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The analysis was further validated by Fluorescence In Situ Hybridization on these samples using probes specific for BRAF and CITED2. The results suggested that the modified method using Affymetrix Cytoscan HD chip gave rise to a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE microarray methodology may hold promise for broad application of CNV analysis on clinical samples. © 2014 Yu et al

Protective effect of wild Corni fructus methanolic extract against acute alcoholic liver injury in mice

Background: In Chinese folk medicine, Corni fructus (C. fructus) has traditionally been used to improve liver function, although the mechanism underlying its activity remains unclear. The aim of the present study was to evaluate the protective effects of wild C. fructus methanolic extract against acute alcoholic liver injury.Methods: Alcohol was administered to mice for three consecutive days, either alone or in combination with C. fructus methanolic extract (50, 100, or 200mg/kg body weight/d). Serum and liver tissue were collected from the animals and subjected to biochemical and histopathological analyses.Results:C. fructus significantly alleviated alcohol-induced liver injury by reducing serum alanine aminotransferase, aspartate aminotransferase, and thiobarbituric acid reactive species, inhibiting hydroxyl radicals (center dot OH), and increasing total superoxide dismutase, glutathione peroxidase, and glutathione in the liver (P<0.05). In addition, the C. fructus treatment inhibited the expression and activity of cytochrome P450 2E1 (P<0.05)Conclusions:C. fructus could be a promising natural substance for ameliorating acute alcohol-induced oxidative stress and hepatic injury.- This work was supported by the Construction Project of Shaanxi Collaborative Innovation Center (2015, Shaanxi Sci-tech University); High-End Foreign Experts Recruitment Program [Grant GDW20146100228]; and Key Construction Program of International Cooperation Base in S&T Shaanxi Province, China [Grant 2015SD0018].info:eu-repo/semantics/publishedVersio