Search Results (38)

Large soil pores critically influence water and solute transport in soils. The presence of preferential flow paths created by soil macropores can profoundly impact water quality, underscoring the necessity of accurately assessing the characteristics of these macropores. However, it remains unclear whether variations in macropore structure exist between different altitudes and positions of terraced paddy fields. The primary objective of this research was to utilize X-ray computed tomography (CT) and image analysis techniques to characterize the soil pore structure at both the inner field and ridge positions across different altitude levels (high, medium, and low altitude) within terraced paddy fields. The results indicate that there are significant differences in the distribution of large soil pores at different altitudes, with large pores concentrated in the surface layer (0–10 cm) in low-altitude areas, while in high-altitude areas, the distribution of large pores is more uniform. Additionally, as altitude increases, the porosity of large pores shows an increasing trend. The three-dimensional equivalent diameter and large pore volume are primarily characterized by large pores ranging from 1 to 2 mm and 0 to 5 mm³, respectively, with their morphology predominantly appearing spherical or ellipsoidal. The connectivity of large pores in the surface layer of paddy soil is stronger than that in the bunds. However, this connectivity gradually weakens with increasing soil depth. The findings from this study provide valuable quantitative insights into the unique characteristics of soil macropores that vary according to the altitude and position in terraced paddy fields. Moreover, this study emphasizes the necessity for future research that encompasses a broader range of soil types, altitudes, and terraced paddy locations to validate and further explore the identified relationships between altitude and macropore characteristics. Full article

Despite significant advances in understanding neuronal development, a fully quantitative framework that integrates intracellular mechanisms with environmental cues during axonal growth remains incomplete. Here, we present a unified biophysical model that captures key mechanochemical processes governing axonal extension on micropatterned substrates. In these environments, axons preferentially align with the pattern direction, form bundles, and advance at constant speed. The model integrates four core components: (i) actin–adhesion traction coupling, (ii) lateral inhibition between neighboring axons, (iii) tubulin transport from soma to growth cone, and (iv) orientation dynamics guided by substrate anisotropy. Dynamical systems analysis reveals that a saddle–node bifurcation in the actin adhesion subsystem drives a transition to a high-traction motile state, while traction feedback shifts a pitchfork bifurcation in the signaling loop, promoting symmetry breaking and robust alignment. An exact linear solution in the tubulin transport subsystem functions as a built-in speed regulator, ensuring stable elongation rates. Simulations using experimentally inferred parameters accurately reproduce elongation speed, alignment variance, and bundle spacing. The model provides explicit design rules for enhancing axonal alignment through modulation of substrate stiffness and adhesion dynamics. By identifying key control parameters, this work enables rational design of biomaterials for neural repair and engineered tissue systems. Full article

The migration of radioactive waste in geological environments often exhibits anomalies, such as tailing and early arrival. Fractional derivative models (FADE) can provide a good description of these phenomena. However, developing models for solute transport in unsaturated media using fractional derivatives remains an unexplored area. This study developed a variably saturated fractional derivative model combined with different release scenarios, to capture the abnormal increase observed in monitoring wells at a field site. The model can comprehensively simulate the migration of nuclides in the unsaturated zone (impermeable layer)—saturated zone system. This study fully analyzed the penetration of pollutants through the unsaturated zone (retardation stage), and finally the rapid lateral and rapid diffusion of pollutants along the preferential flow channels in the saturated zone. Comparative simulations indicate that the spatial nonlocalities effect of fractured weathered rock affects solute transport much more than the temporal memory effect. Therefore, a spatial fractional derivative model was selected to simulate the super-diffusive behavior in the preferential flow pathways. The overall fitness of the proposed model is good (R² ≈ 1), but the modeling accuracy will be lower with the increased distance from the waste source. The spatial differences between simulated and observed concentrations reflect the model’s limitations in long-distance simulations. Although the model reproduced the overall temporal variation of solute migration, it does not explain all the variability and uncertainty of the specific sites. Based on the sensitivity analysis, the fractional derivative parameters of the unsaturated zone show higher sensitivity than those of the saturated zone. Finally, the advantages and limitations of the fractional derivative model in radionuclide contamination prediction and remediation are discussed. In conclusion, the proposed FADE model coupled with unsaturated and saturated flow conditions, has significant application prospects in simulating nuclide migration in complex geological and hydrological environments. Full article

The gut–brain axis is increasingly understood to play a role in neuropsychiatric disorders. The probiotic bacterium Lactobacillus (L.) reuteri and products of tryptophan degradation, specifically the neuroactive kynurenine pathway (KP) metabolite kynurenic acid (KYNA), have received special attention in this context. We, therefore, assessed relevant features of KP metabolism, namely, the cellular uptake of the pivotal metabolite kynurenine and its conversion to its primary products KYNA, 3-hydroxykynurenine and anthranilic acid in L. reuteri by incubating the bacteria in Hank’s Balanced Salt solution in vitro. Kynurenine readily entered the bacterial cells and was preferentially converted to KYNA, which was promptly released into the extracellular milieu. De novo production of KYNA increased linearly with increasing concentrations of kynurenine (up to 1 mM) and bacteria (10⁷ to 10⁹ CFU/mL) and with incubation time (1–3 h). KYNA neosynthesis was blocked by two selective inhibitors of mammalian kynurenine aminotransferase II (PF-048559989 and BFF-122). In contrast to mammals, however, kynurenine uptake was not influenced by other substrates of the mammalian large neutral amino acid transporter, and KYNA production was not affected by the presumed competitive enzyme substrates (glutamine and α-aminoadipate). Taken together, these results reveal substantive qualitative differences between bacterial and mammalian KP metabolism. Full article

Mitochondria are most likely descendants of strictly aerobic prokaryotes from the class Alphaproteobacteria. The mitochondrial matrix is surrounded by two membranes according to its relationship with Gram-negative bacteria. Similar to the bacterial outer membrane, the mitochondrial outer membrane acts as a molecular sieve because it also contains diffusion pores. However, it is more actively involved in mitochondrial metabolism because it plays a functional role, whereas the bacterial outer membrane has only passive sieving properties. Mitochondrial porins, also known as eukaryotic porins or voltage-dependent anion-selective channels (VDACs) control the permeability properties of the mitochondrial outer membrane. They contrast with most bacterial porins because they are voltage-dependent. They switch at relatively small transmembrane potentials of 20 to 30 mV in closed states that exhibit different permeability properties than the open state. Whereas the open state is preferentially permeable to anionic metabolites of mitochondrial metabolism, the closed states prefer cationic solutes, in particular, calcium ions. Mitochondrial porins are encoded in the nucleus, synthesized at cytoplasmatic ribosomes, and post-translationally imported through special transport systems into mitochondria. Nineteen beta strands form the beta-barrel cylinders of mitochondrial and related porins. The pores contain in addition an α-helical structure at the N-terminal end of the protein that serves as a gate for the voltage-dependence. Similarly, they bind peripheral proteins that are involved in mitochondrial function and compartment formation. This means that mitochondrial porins are localized in a strategic position to control mitochondrial metabolism. The special features of the role of mitochondrial porins in apoptosis and cancer will also be discussed in this article. Full article

This study highlights the importance of water infiltration in hydrological basin management, emphasizing its role in water services, water quality regulation, and temporal patterns. To measure this crucial function, this study introduces a portable and user-friendly tension infiltrometer designed for easy assembly and data collection. The tension infiltrometer, based on the 2009 design by Spongrová and Kechavarzi, offers a comprehensive characterization of the soil properties related to water flow. It eliminates the influence of preferential flow, providing accurate data. Additionally, it accommodates changes in pore size distribution within the soil, which is crucial for understanding water movement. This study discusses the challenges associated with traditional infiltration measurement tools, like double-ring infiltrometers and single rings, which are not easily transported and can lead to inaccuracies. In response, the proposed infiltrometer simplifies data collection, making it accessible to a broader range of users. This study also explores the use of the VL53L0X distance sensor in the infiltrometer, providing an innovative solution for measuring the water column height. The system’s user interface allows real-time data collection and analysis, significantly reducing the processing time compared to that of the manual methods. Overall, this work demonstrates the potential for advancement in hydrological basin management using user-friendly instrumentation and automated data collection, paving the way for improved research and decision making in environmental services, conservation, and restoration efforts within these ecosystems. Full article

In this study, the effects of topological properties with local variable apertures on fluid flow and solute transport through three-dimensional (3D) discrete fracture networks (DFNs) were investigated. A series of 3D DFNs with different fracture density, length, and aperture distribution were generated. The fluid flow and solute transport through the models were simulated by combining the MATLAB code and COMSOL Multiphysics. The effects of network topology and aperture heterogeneity on fluid flow and transport process were analyzed. The results show that the fluid flow and solute transport exhibit a strong channeling effect even in the DFNs with identical aperture, in which the areas of fast and slow migration fit well with the high- and low-flow regions, respectively. More obvious preferential paths of flow and migration are observed in individual fractures for the DFN with heterogeneous aperture than the model with identical aperture. Increasing the fracture length exponent reduces the available flow and transport paths for sparse fracture networks but does not significantly change the flow and transport channels for dense fracture networks. The breakthrough curves (BTCs) shift towards the right and slightly lag behind as the fracture density decreases or the aperture heterogeneity increases. The advection–diffusion equation (ADE) model cannot properly capture the evolution of BTCs for 3D DFNs, especially the long tails of BTCs. Compared to the ADE model, the mobile-immobile model (MIM) model separating the liquid phase into flowing and stagnate regions is proven to better fit the BTCs of 3D DFNs with heterogeneous aperture. Full article

Cement fractures represent preferential leakage pathways in abandoned wells upon exposure to a CO₂-rich fluid. Understanding fracture alteration resulting from geochemical reactions is critical for assessing well integrity in CO₂ storage. This paper describes a mathematical model used to investigate the physical and the chemical changes in cement properties when CO₂-saturated water is injected into a wellbore. This study examines the flow of a solution of CO₂-saturated water in a two-dimensional fractured cement. In this approach, a micro-continuum equation based on the Darcy–Brinkman–Stokes (DBS) equation is used as the momentum balance equation; in addition, reactive transport equations are used to study the coupled processes of reactant transport and geochemical reactions, and the model for cement porosity alteration and fracture enhancement. This paper focuses on the effects of cement porosity, fracture aperture size, and surface roughness. Mineral dissolution and precipitation mechanisms are also considered. Our simulations show that smaller initial fracture apertures tend to a high mineral precipitation self-sealing. However, a complete sealing of the fracture is not observed due to the continuous flow of CO₂-saturated water. The calcite precipitation mechanism of a rough fracture (random zigzag shape) differs from that of a smooth/flat fracture surface. Full article

Transport and retention of multi-sized suspended granules are common phenomena in fracture media of oil, gas and geothermal reservoirs. It can lead to severe permeability damage and productivity decline, which has a significant impact on the efficient development of underground resources. However, the granule transport and retention behaviors remain not well understood and quantified. The novel stochastic model is proposed for the multi-sized suspended granule transport in naturally fractured reservoirs accounting for granule retention and fracture clogging kinetics. A percolation fracture network is proposed considering fracture connectivity evolution during suspended granule transport. Granule retention and fracture clogging dynamics equations are proposed to account for incomplete fracture clogging by retained granules. The microscale stochastic model is allowed for upscaling to predict the multi-sized granule transport behavior in naturally fractured reservoirs. The model solution exhibits preferential plugging of fractures with sizes equal to or below the granule size. Multi-sized suspended granule shows great advantages over mono-sized suspended granule in the control of permeability damage induced by granule retention and fracture clogging. The retained granule concentration and permeability damage rate decrease with fracture network connectivity improvement. The experimental investigation on size-exclusion suspended granule flow has been performed. The model-based prediction of the retained granule concentration and permeability variation history shows good agreement with the experimental data, which verifies the developed model. Full article

The ionic rare earth (RE) ore body undergoes particle transport and pore structure change during the leaching process, resulting in "uneven percolation, preferential channel, leaching blind area," and other problems, leading to structural changes in the ore body, low leaching efficiency, and waste of resources. The unsaturated infiltration process is also the key stage that causes these problems. The initial pore structure evolution of the ore body plays a decisive role in the permeability coefficient of the ore body, and the direct influencing factor of the permeability coefficient is the distribution of the pore radius. We carried out research through indoor simulated leaching, the filter paper method for determining matrix suction, and nuclear magnetic resonance (NMR) testing. An ionic rare earth ore soil-water characteristic curve within a large matrix suction range was obtained by the filter paper method. With the increase in volumetric water content, the matrix suction presents a sharp downward trend. When the volumetric water content is less than 20%, this rule is particularly obvious. With the increase in matrix suction, the thickness of the adsorbed water film on the particle surface and pore radius show a decreasing power function trend. Under percolation, the porosity of an ionic rare earth ore sample tends to increase linearly with the increase in volumetric water content during the process from non-saturation to saturation; the porosity of a saturated ore sample after seepage expanded by 17.5 times compared to that of an unsaturated ore sample before seepage. The change rule of the internal microstructure of the ore sample is reflected in the gradual disappearance of micro pores and the gradual formation of small, medium, large, and mega pores, which shows a gradual increase trend. In the pore radius distribution, the more large and medium pores, the larger the permeability coefficient; the more micro and small pores, the smaller the permeability coefficient. For some ore bodies with poor permeability, the ore body is infiltrated with clear water under small water pressure before leaching with a leaching solution, which can improve the permeability of the ore body, effectively improve the efficiency of rare earth leaching, and increase the economic benefits. Full article

Bacterial adhesion is the first step in the formation of surface biofilms. The number of bacteria that bind to a surface from the solution depends on how many bacteria can reach the surface (bacterial transport) and the strength of interactions between bacterial adhesins and surface receptors (adhesivity). By using microfluidic channels and video microscopy as well as computational simulations, we investigated how the interplay between bacterial transport and adhesivity affects the number of the common human pathogen Escherichia coli that bind to heterogeneous surfaces with different receptor densities. We determined that gravitational sedimentation causes bacteria to concentrate at the lower surface over time as fluid moves over a non-adhesive region, so bacteria preferentially adhere to adhesive regions on the lower, inflow-proximal areas that are downstream of non-adhesive regions within the entered compartments. Also, initial bacterial attachment to an adhesive region of a heterogeneous lower surface may be inhibited by shear due to mass transport effects alone rather than shear forces per se, because higher shear washes out the sedimented bacteria. We also provide a conceptual framework and theory that predict the impact of sedimentation on adhesion between and within adhesive regions in flow, where bacteria would likely bind both in vitro and in vivo, and how to normalize the bacterial binding level under experimental set-ups based on the flow compartment configuration. Full article

The Yellow River Delta wetlands in the Yellow River Delta National Nature Reserve are facing serious degradation due to water scarcity and soil salinization. This study aims to investigate the mechanism of wetland degradation by analyzing the small-scale distribution of soil nutrients and preferential flow transport patterns in the Robinia Pseudoacacia community, which is a typical vegetation community in degraded wetlands. Soil physical and chemical properties based on field staining experiments were analyzed, and indoor solute penetration experiments were conducted to investigate the distribution of soil nutrients and hydrological characteristics. The results showed that the contents of soil organic carbon, organic matter, total nitrogen, and available phosphorus decreased with increasing soil depth, with higher contents in the preferential flow area than in the matrix flow area. Soil organic carbon, organic matter, total nitrogen, total phosphorus, and available phosphorus showed positive correlations with each other, while soil pH and conductivity exhibited negative correlations with the above nutrients. The efflux rate of the Acacia community exhibited a gradual decline as soil depth increased, and the relative concentration of the solution exhibited a non-monotonic pattern of decrease, increase, and subsequent decrease with increasing soil depth. The findings could provide valuable guidance for the restoration and management of degraded wetlands in the Yellow River Delta. Full article

Malignant melanoma is the most fatal form of skin cancer worldwide, and earlier diagnosis and more effective therapies are required to improve prognosis. As a possible solution, near-infrared fluorescent heptamethine cyanine dyes have been shown to be useful for tumor diagnosis and treatment. Here, we synthesized a novel theranostic agent, IR-817, a multifunctional bioactive small-molecule that has near-infrared emission, targets mitochondria in cancer cells, and has selective anti-cancer effects. In in vitro experiments, IR-817 preferentially accumulated in melanoma cells through organic anion transporting polypeptide transporters but also selectively inhibited the growth of tumor cells by inducing mitochondrial-dependent intrinsic apoptosis. Mechanistically, IR-817 caused G0/G1 cell cycle arrest by targeting the E2F/Cyclin/CDK pathway. Finally, IR-817 significantly suppressed the growth of xenograft tumors in zebrafish and mice. Immunohistochemical staining and hematoxylin and eosin staining revealed that IR-817 induced apoptosis and inhibited tumor cell proliferation without notable side effects. Therefore, mitochondrial-targeting theranostic agent IR-817 may be promising for accurate tumor diagnosis, real-time monitoring, and safe anti-cancer treatments. Full article

Soil preferential flow is an essential process that affects the movement and relocation of soil water and solutes. This study was conducted on cropland in an arid and semi-arid area in Zhongning County, Ningxia. According to the different cracks, rain intensity, rainfall duration, and slope, there were three groups, and 17 dye tracer experiments were conducted in the field. We quantified the characteristics of soil preferential flow by investigating and analyzing the infiltration depth, dyeing area, saturation, runoff coefficient, and rainfall infiltration coefficient using the dye tracer method. The results showed that increasing the rainfall or irrigation intensity could promote the activation of the fracture channel as the preferential flow channel, which is advantageous to the preferential flow formation. The fractures dominated the formation of the preferential flow. The fractures slowed the formation of runoff, reduced the velocity of slope flow, reduced the flow of the slope, and increased the amount of soil water infiltration. These results have theoretical and practical significance for understanding soil water transportation, especially for agricultural irrigation management and improving cropland water use efficiency in arid and semi-arid areas. Full article

Preferential solute transport is a common phenomenon in soil, and it is of great significance to accurately describe the mechanism of pollutant transport and water and soil environmental governance. However, the description of preferential solutes still relies on applying solute breakthrough curves for model parameters fitting. At present, most of the solute breakthrough curves are obtained indoors, and with some limitations. Therefore, this study established a method for securing solute breakthrough curves based on the electrical resistivity method. The research results show that the change in soil concentration during the tracer infiltration process can be captured by establishing the fitting relationship between soil resistivity and solute concentration. Then the solute breakthrough curve can be found. Through a time moment analysis, the difference between the breakthrough curve parameters obtained by the traditional method and the resistivity method is slight; the average error is less than 10%. On this basis, the sensitive response of the parameters of the “mobile–immobile” model to concentration was elucidated through different concentration tracer experiments, among which β and D are more sensitive, and w is less sensitive. The suitable tracer concentration range should be 50–120 mg/L. Therefore, the established method could obtain the breakthrough curves and describe the transport of preferential solutes at the field scale. Full article