Search

A three-dimensional nonhydrostatic coastal model SUNTANS is used to study hyperpycnal plumes on sloping continental shelves with idealized domain setup. The study aims to examine the nonhydrostatic effect of the plunging hyperpycnal plume and the associated flow structures on different shelf slopes. The unstructured triangular grid in SUNTANS allows for local refinement of the grid size for regions in which the flow varies abruptly, while retaining low-cost computation using the coarse grid resolution for regions in which the flow is more uniform. These nonhydrostatic simulations reveal detailed three-dimensional flow structures in both transient and steady states. Via comparison with the hydrostatic simulation, we show that the nonhydrostatic effect is particularly important before plunging, when the plume is subject to significant changes in both the along-shore and vertical directions. After plunging, where the plume becomes an undercurrent that is more spatially uniform, little difference is found between the hydrostatic and nonhydrostatic simulations in the present gentle- and mild-slope cases. A grid-dependence study shows that the nonhydrostatic effect can be seen only when the grid resolution is sufficiently fine that the calculation is not overly diffusive. A depth-integrated momentum budget analysis is then conducted to show that the flow convergence due to plunging is an important factor in the three-dimensional flow structures. Moreover, it shows that the nonhydrostatic effect becomes more important as the slope increases, and in the steep-slope case, neglect of transport of the vertical momentum during plunging in the hydrostatic case further leads to an erroneous prediction for the undercurrent.

Droplet digital loop-mediated isothermal amplification (ddLAMP) is an important assay for pathogen detection due to its high accuracy, specificity, and ability to quantify nucleic acids. However, performing ddLAMP requires expensive instrumentation and the need for highly trained personnel with expertise in microfluidics. To make ddLAMP more accessible, a ddLAMP assay is developed, featuring significantly decreased operational difficulty and instrumentation requirements. The proposed assay consists of three simplified steps: (1) droplet generation step, in which a LAMP mixture can be emulsified just by manually pulling a syringe connected to a microfluidic device. In this step, for the first time, we verify that highly monodispersed droplets can be generated with unstable flow rates or pressures, allowing untrained personnel to operate the microfluidic device and perform ddLAMP assay; (2) heating step, in which the droplets are isothermally heated in a water bath, which can be found in most laboratories; and (3) result analysis step, in which the ddLAMP result can be determined using only a fluorescence microscopy and an open-source analyzing software. Throughout the process, no droplet microfluidic expertise or equipment is required. More importantly, the proposed system enables multiple samples to be processed simultaneously with a detection limit of 10 copies/μL. The test is simple and intuitive to operate in most laboratories for multi-sample detection, significantly enhancing the accessibility and detection throughput of the ddLAMP technique.

Triple-negative breast cancers (TNBCs) are difficult to cure and currently lack of effective treatment strategies. Cancer stem cells (CSCs) are highly associated with the poor clinical outcome of TNBCs. Thoc1 is a core component of the THO complex (THOC) that regulates the elongation, processing and nuclear export of mRNA. The function of thoc1 in TNBC and whether Thoc1 serves as a drug target are poorly understood. In this study, we demonstrated that thoc1 expression is elevated in TNBC cell lines and human TNBC patient tissues. Knockdown of thoc1 decreased cancer stem cell populations, reduced mammosphere formation, impaired THOC function, and downregulated the expression of stemness-related proteins. Moreover, the thoc1-knockdown 4T1 cells showed less lung metastasis in an orthotopic breast cancer mouse model. Overexpression of Thoc1 promoted TNBC malignancy and the mRNA export of stemness-related genes. Furthermore, treatment of TNBC cells with the natural compound andrographolide reduced the expression of Thoc1 expression, impaired homeostasis of THOC, suppressed CSC properties, and delayed tumor growth in a 4T1-implanted orthotopic mouse model. Andrographolide also reduced the activity of NF-κB, an upstream transcriptional regulator of Thoc1. Notably, thoc1 overexpression attenuates andrographolide-suppressed cellular proliferation. Altogether, our results demonstrate that THOC1 promotes cancer stem cell characteristics of TNBC, and andrographolide is a potential natural compound for eliminating CSCs of TNBCs by downregulating the NF-κB-thoc1 axis.

In this study, numerical simulations of the interaction between supersonic crossflow and a side liquid jet were performed. The processes of the liquid jet breakup, flow separation and shock waves r...

The neurotransmitter phenylethylamine (PEA) is highly susceptible to oxidation to produce phenylacetic acid (PA). The fact that PEA and PA are both metabolites of phenylalanine (Phe) in humans makes them important indicators in the diagnosis of phenylketonuria. In this work, three-color whole-cell biosensors were developed to simultaneously detect these analytes (Phe, PEA, and PA). The tyrosine-responsive promoter was used to control the production of green fluorescent protein signals in response to Phe levels. The FeaR regulon was first used to indicate the presence of PEA, whereas the Paa regulon was used for the detection of PA. The combination of three sensor strains together made it possible to semiquantify the three analytes according to unique color outputs without cross-interference. We sought to optimize various modular components (ribosomal binding sites and fluorescent proteins) to ensure the rapid generation of fluorescent signals. Finally, the biosensors were implemented within a microchannel device to reduce sample consumption in point-of-care assays.

We investigate the photonic topological phases in Tellegen metamaterials characterized by the antisymmetric magnetoelectric tensors with real-valued quantities. The underlying medium is considered a photonic analogue of the topological semimetal featured with a displaced Weyl cone in the frequency-wave vector space. As the ’spin’-degenerate condition is satisfied, the photonic system consists of two hybrid modes that are completely decoupled. By introducing the pseudospin states as the basis for the hybrid modes, the photonic system is described by two subsystems in terms of the spin-orbit Hamiltonians with spin 1, which result in nonzero spin Chern numbers that determine the topological properties. Surface modes at the interface between two Tellegen metamaterials with opposite sign of the magnetoelectric parameter exist at their common gap in the wave vector space, which are analytically formulated by algebraic equations. In particular, two types of surface modes are tangent to or wrapping around the Weyl cones, which form a pair of bended and a pair of twisted surface sheets. At the Weyl frequency, the surface modes contain a typical and two open Fermi arc-like states that concatenate to yield an infinite straight line. Topological features of the Tellegen metamaterials are further illustrated with the robust transport of surface modes at an irregular boundary.

We present numerical simulations and laboratory experiments to study bulge formation at the trailing edge of an inclined surface and its inhibitory effect on particle removal during surface cleaning. We investigate the spatial variations in liquid films near the trailing edge and find that the Weber number can be used as a dominant parameter to determine bulge occurrence over the trailing edge. We divide the film region near the trailing edge at which the bulge occurs into two: the region where the surface linearly grows and the surface tension is negligible, and the region where the surface tension force becomes dominant and the film surface is curved. In the investigated cases in which the Reynolds number is O(10) or greater, the viscous forces are negligible, which allows for the derivation of the scaling laws for the length of the two regions according to the condition that the bulge height scales with the capillary length. In the resulting scaling law, the length scales depend on the Froude number and the inclination angle. The proposed scaling law allows for the prediction of the bulge shape and the prediction agrees with the simulation results, particularly at low Weber numbers (i.e., We < 0.5). Moreover, we construct a particle removability map to assess the removal of particles of different sizes at specific locations on the substrate. The map reveals a reduction of the removability for small-size particles or particles located in the bulge.

We study the stability of unsteady particle-laden flows in long, tilted water columns in batch settling mode, where the quasi-steady assumption of base flow no longer holds for the fast settling of particles. For this purpose, we introduce a settling time scale in the momentum and transport equations to solve the unsteady base flow, and utilise non-modal analysis to examine the stability of the disturbance flow field. The base flow increases in magnitude as the settling speed decreases and attains its maximum value when the settling speed becomes infinitesimal. The time evolution of the disturbance flow energy experiences an algebraic growth caused by the lift-up mechanism of the wall-normal disturbance, followed by an exponential growth owing to the shear instability of the base flow. The streamwise and spanwise wavenumbers corresponding to the peak energy gain are identified for both stages. In particular, the flow instability is enhanced as the Prandtl number increases, which is attributed to the sharpening of the particle-laden interface. On the other hand, the flow instability is suppressed by the increase in settling speed, because less disturbance energy can be extracted from the base flow. There exists an optimal tilted angle for efficient sedimentation, where the particle-laden flow is relatively stable and is accompanied by a smaller energy gain of the disturbance.

Aging is the major risk factor for cardiovascular disease, which is the leading cause of mortality worldwide among aging populations. Cisd2 is a prolongevity gene that mediates lifespan in mammals. Previously, our investigations revealed that a persistently high level of Cisd2 expression in mice is able to prevent age-associated cardiac dysfunction. This study was designed to apply a genetic approach that induces cardiac-specific Cisd2 overexpression (Cisd2 icOE) at a late-life stage, namely a time point immediately preceding the onset of old age, and evaluate the translational potential of this approach. Several discoveries are pinpointed. Firstly, Cisd2 is downregulated in the aging heart. This decrease in Cisd2 leads to cardiac dysfunction and impairs electromechanical performance. Intriguingly, Cisd2 icOE prevents an exacerbation of age-associated electromechanical dysfunction. Secondly, Cisd2 icOE ameliorates cardiac fibrosis and improves the integrity of the intercalated discs, thereby reversing various structural abnormalities. Finally, Cisd2 icOE reverses the transcriptomic profile of the aging heart, changing it from an older-age pattern to a younger pattern. Intriguingly, Cisd2 icOE modulates a number of aging-related pathways, namely the sirtuin signaling, autophagy, and senescence pathways, to bring about rejuvenation of the heart as it enters old age. Our findings highlight Cisd2 as a novel molecular target for developing therapies targeting cardiac aging.

We present three-dimensional simulations of sedimentation of suspended solids in inclined vessels using a Eulerian-Lagrangian model developed specifically for the study of solid-liquid mixtures. The simulation results reveal the three-dimensional vortical flow structures that follow the occurrence of flow instability and induce strong mixing between the particle-laden and clear-fluid layers. We show that the tubes exhibit significant spanwise variation due to the presence of wall boundary layers and are subsequently transformed into three-dimensional turbulent structures. The vortices and turbulence result in significant resuspension from the particle-laden layer and weaken the convective effect that enhances sedimentation. We show that for the present flow condition and particle size, particle inertia plays an important role in particle resuspension. Analysis of the release of potential energy is presented to examine the sedimentation efficiency under different flow conditions. We show that the time history for a typical case can be divided into development, convection, and deposition stages. The analysis for cases with different particle sizes shows that the faster settling associated with larger particles stabilizes the flow by reducing the interfacial shear while settling. From simulation results using various angles of inclination, we can find the optimal angle of inclination to achieve the greatest efficiency in settling enhancement. Finally, critical modeling aspects, including the importance of different forcing terms and two- or three-dimensional considerations, are discussed.

Toll-like receptors (TLRs) play crucial roles in host immune defenses. Recently, TLR-mediated autophagy is reported to promote immune responses via increasing antigen processing and presentation in antigen presenting cells. The present study examined whether the synthetic TLR4 activator (CCL-34) could induce autophagy to promote innate and adaptive immunity. In addition, the potential of CCL-34 as an immune adjuvant in vivo was also investigated. Our data using RAW264.7 cells and bone marrow-derived macrophages showed that CCL-34 induced autophagy through a TLR4-NF-κB pathway. The autophagy-related molecules (Nrf2, p62 and Beclin 1) were activated in RAW264.7 cells and bone marrow-derived macrophages under CCL-34 treatment. CCL-34-stimulated macrophages exhibited significant antigen-processing activity and induced the proliferation of antigen-specific CD4+T cells as well as the production of activated T cell-related cytokines, IL-2 and IFN-γ. Furthermore, CCL-34 immunization in mice induced infiltration of monocytes in the peritoneal cavity and elevation of antigen-specific IgG in the serum. CCL-34 treatment in vivo did not cause toxicity based on serum biochemical profiles. Notably, the antigen-specific responses induced by CCL-34 were attenuated by the autophagy inhibitor, 3-methyladenine. In summary, we demonstrated CCL-34 can induce autophagy to promote antigen-specific immune responses and act as an efficient adjuvant.

We conduct Eulerian–Lagrangian simulations to study double-diffusive sedimentation in stratified flows. The results show the pattern of double-diffusive sedimentation and the transition to the pattern of Rayleigh–Taylor instability when the size of particles increases. In cases of double-diffusive sedimentation, our simulation results show little variation in the temperature-to-particle flux ratio among cases with various particle sizes and initial concentrations, which is consistent with previous theoretical derivations and experimental observations. The energy budget is analysed to show that the settling enhancement is a result of the thermal effect combined with shear dissipation and that the thermal contribution decreases as the size increases. Based on the balance of the energy budget, velocity scaling was derived for the quasi-steady state in the thermally controlled region, which can be used to characterize the plumes’ final velocity of double-diffusive sedimentation. Moreover, adopting some values from the simulation results yields a velocity criterion with which to distinguish different sedimentation patterns. Finally, we investigate changes in the particle-laden plumes below the region of the apparent temperature gradient at which secondary instabilities occur in the form of significant horizontal flow motion. We show that the resulting initial shift of the dominant modes can be approximated with the existing theoretical analysis of collective instabilities for salt fingers. A simple scaling argument for the change in the total cross-sectional area of particle-laden plumes is presented, which is then used to scale the resulting enhanced sedimentation.

Lateral flow immunoassays (LFIAs) have wide application in point-of-care testing, particularly in resource-poor settings. To achieve signal amplification in a gold nanoparticle-based lateral flow assay without an additional procedure or the need for complex fabrication, a new and simple method was developed for using a “stacking pad” configuration that adds an additional membrane between the conjugation pad and test pad to the conventional AuNP-based LFIA format. This design helps to accumulate the antibody and antigen on the stacking pad, hence extending the antigen/antibody binding interactions to enhance the test’s detection sensitivity. With the enhanced lateral flow assay, as low as 1 ng/mL of Protein A and 15.5 ng/mL of C-reactive protein can be visualized with the naked eye. We also successfully applied the stacking pad system in the analysis of C-reactive protein in human serum and synovial fluid samples. These results suggest that this stacking pad LFIA can provide sensitive and on-site prognosis for detection in synovial fluid and serum samples in resource-limited settings.

We conduct numerical simulations to investigate the formation and evolution of drops and vortex rings of particle-laden fingers in double-diffusive convection in stably stratified environments. We show that the temporal evolution can be divided into double diffusion, acceleration and deceleration phases. The acceleration phase is a result of the vanishing temperature perturbation in the drop during the descent in the layer of uniform temperature. The drop decelerates because it transforms into a vortex ring. A theoretical drag model is presented to predict the speed of the spherical drop with the low drop Reynolds number. By formulating the boundary condition based on the vorticity, our drag model gives a more general form of the drag coefficient for small spherical drops and shows good agreement in predicting the drag coefficient. Drops with five particle sizes are compared, and it is found that although the greater vertical settling enhances vertical transport, the final state differs little among the various sizes. Comparison of our drag model with the simulation results under various bulk conditions and previous experimental results shows good model predictability. Finally, a comparison with the salt-finger case shows that the diffusive nature of the dissolved scalar field, along with the wake effect, can result in an apparent loss of mass from the drop and a permanent presence of the connection between the drop and its parent finger. This makes the observed detachment of the particle-laden drop much less likely in the salt-finger case.

This paper presents a single-pressure-field two-fluid model with finite-volume discretization to solve the equations of motion of compressible multiphase flows. To capture the discontinuities caused by shock waves and fluid interfaces, we propose a generalized discontinuity sharpening technique that combines the conventional monotonic upstream scheme for conservation law (MUSCL) and tangent of hyperbola interface capturing (THINC) schemes. In addition, a slope ratio-weighted parameter, ζ, is used to control the proportion of values reconstructed by MUSCL and THINC, and we show that the present method can retain sharp interfaces when the value of the parameter β in the THINC scheme is set ranging from 1.6 to 3.0. Fluxes across various interfaces are evaluated using a hybrid AUSMD-type flux algorithm, where the mass flux and pressure induced on the cell faces are calculated using an approximate Riemann solver. The accuracy and robustness of the proposed method are validated by solving a series of one- and two-dimensional single-phase flows. Furthermore, complex wave patterns arising from two-dimensional shock bubble/water-column interactions are examined, which indicate that compared with the existing schemes applied to two-fluid modeling, the proposed scheme significantly sharpens the interfaces and captures more details of the flow features. Finally, simulations of a three-dimensional example of the liquid jet crossflow are conducted. The proposed scheme shows more details of the fluid interface, including the interfacial instabilities on the windward side of the liquid jet and droplet formation due to the breakup phenomenon in the downstream of the crossflow, than the existing schemes.

Heart failure (HF) is a global pandemic public health burden affecting one in five of the general population in their lifetime. For high-risk individuals, early detection and prediction of HF progression reduces hospitalizations, reduces mortality, improves the individual’s quality of life, and reduces associated medical costs. In using an artificial intelligence (AI)-assisted genome-wide association study of a single nucleotide polymorphism (SNP) database from 117 asymptomatic high-risk individuals, we identified a SNP signature composed of 13 SNPs. These were annotated and mapped into six protein-coding genes (GAD2, APP, RASGEF1C, MACROD2, DMD, and DOCK1), a pseudogene (PGAM1P5), and various non-coding RNA genes (LINC01968, LINC00687, LOC105372209, LOC101928047, LOC105372208, and LOC105371356). The SNP signature was found to have a good performance when predicting HF progression, namely with an accuracy rate of 0.857 and an area under the curve of 0.912. Intriguingly, analysis of the protein connectivity map revealed that DMD, RASGEF1C, MACROD2, DOCK1, and PGAM1P5 appear to form a protein interaction network in the heart. This suggests that, together, they may contribute to the pathogenesis of HF. Our findings demonstrate that a combination of AI-assisted identifications of SNP signatures and clinical parameters are able to effectively identify asymptomatic high-risk subjects that are predisposed to HF.

We conduct numerical simulations using the Eulerian–Lagrangian approach to investigate the formation of the leaking, finger, and stable-settling modes in convective sedimentation when a sediment-laden fluid layer descends through a sharply stratified ambient flow. We show that the temporal evolution of the sedimentation process for the leaking mode can be divided into three stages, including (in temporal order) Rayleigh–Taylor instability, convection, and leaking stages. The presence of sheet-like descending plumes of suspended particles is an important characteristic of the leaking mode, which marks the existence of the leaking stage. For larger particles, the motion is more dominated by gravitational settling and less affected by buoyancy-induced flow motion. The resulting lack of the leaking stage for the larger-particle case leads to persistent finger-like plumes of suspended particles, known as the finger mode. The stable-settling mode occurs when the particles are large and the concentration is dilute such that flow motion due to Rayleigh–Taylor instability has no effect on the particle motion, and the convective motion of suspended particles is insignificant. For the third stage of the leaking mode, which is also the final stationary state, we derive the criterion for the occurrence of the leaking pattern from a scaling argument of the viscous boundary layer. The criterion is further confirmed by the present simulation results and previous laboratory experiments. Through analysis of the energy budget and the vertical flux, we show that although the settling of individual particles is accelerated, the presence of the sheet-like descending plumes in the leaking mode does not contribute to an efficient settling enhancement compared with the finger mode and the Rayleigh–Taylor instability, i.e., the cases with no background stratification. This implies a negative effect on the settling enhancement for small suspended particles when a stable background density stratification exists. In addition, simulations using the equilibrium Eulerian description for the suspended particles are also conducted to examine the difference between the present Lagrangian particle approach and the conventional Eulerian model.

CDGSH iron-sulfur domain-containing protein 2 (Cisd2) is pivotal to mitochondrial integrity and intracellular Ca2+ homeostasis. In the heart of Cisd2 knockout mice, Cisd2 deficiency causes intercalated disc defects and leads to degeneration of the mitochondria and sarcomeres, thereby impairing its electromechanical functioning. Furthermore, Cisd2 deficiency disrupts Ca2+ homeostasis via dysregulation of sarco/endoplasmic reticulum Ca2+-ATPase (Serca2a) activity, resulting in an increased level of basal cytosolic Ca2+ and mitochondrial Ca2+ overload in cardiomyocytes. Most strikingly, in Cisd2 transgenic mice, a persistently high level of Cisd2 is sufficient to delay cardiac aging and attenuate age-related structural defects and functional decline. In addition, it results in a younger cardiac transcriptome pattern during old age. Our findings indicate that Cisd2 plays an essential role in cardiac aging and in the heart’s electromechanical functioning. They highlight Cisd2 as a novel drug target when developing therapies to delay cardiac aging and ameliorate age-related cardiac dysfunction., Cardiomyocytes from young mice lacking the mitochondrial iron-sulfur domain-containing protein Cisd2 show signs of premature aging; conversely, cardiomyocytes from old transgenic mice with a persistently high level of Cisd2 appear “young.” This highlights Cisd2 as a novel drug target when developing therapies to delay cardiac aging.

In field-scale modeling, when the resuspension of sediment is modeled using a hydrodynamic model, a standard and common approach is to add a resuspension flux as the bottom boundary condition in the transport model. In this study, we show that the way of simply imposing an empirical bottom erosion formula as the flux is actually unrealistic. Its inability to stabilize the sediment concentration can cause excessive suspension fluxes in some extreme cases. Moreover, we present a modified erosion/deposition formula to model the resuspension of sediment. The formulation is based on volume conservation in the presence of erosion/deposition near the bottom. By taking into account the prescribed dry density of the bed material, the proposed formulation is able to produce realistic near-bed concentrations while ensuring model stability. The formulation is then tested in a one-dimensional vertical model and field modeling cases using a three-dimensional coastal circulation model. We show that the modified formulation is particularly important in modeling mud resuspension subject to the large bottom stress, which can be a result of waves or a strong river discharge.

Chronic myelogenous leukemia (CML) is clinically treated with imatinib, which inhibits the kinase activity of the Bcr-Abl oncoprotein. However, imatinib resistance remains a common clinical issue. Andrographolide, the major compound of the medicinal plant Andrographis paniculata, was reported to exhibit anticancer activity. In this study, we explored the therapeutic potential of andrographolide and its derivative, NCTU-322, against both imatinib-sensitive and imatinib-resistant human CML cell lines. Both andrographolide and NCTU-322 downregulated the Bcr-Abl oncoprotein in imatinib-resistant CML cells through an Hsp90-dependent mechanism similar to that observed in imatinib-sensitive CML cells. In addition, NCTU-322 had stronger effects than andrographolide on downregulation of Bcr-Abl oncoprotein, induction of Hsp90 cleavage and cytotoxicity of CML cells. Notably, andrographolide and NCTU-322 could induce differentiation, mitotic arrest and apoptosis of both imatinib-sensitive and imatinib-resistant CML cells. Finally, the anticancer activity of NCTU-322 against imatinib-resistant CML cells was demonstrated in vivo. In summary, our data demonstrated that andrographolide and NCTU-322 inhibit Bcr-abl function via a mechanism different from that of imatinib, and they induced multiple anticancer effects in both imatinib-sensitive and resistant CML cells. Our findings demonstrate that andrographolide and NCTU-322 are potential therapeutic agents again CML.

In this paper, we present a numerical model to simulate wind waves and hydrodynamics in the estuary. We employ the unstructured-grid SUNTANS model for hydrodynamics, and within this model we implement a spectral wave model which solves for transport of wave action density with the finite-volume formulation. Hydrodynamics is coupled to the wave field through the radiation stress. Based on the unstructured grid and finite-volume formulation of SUNTANS, the radiation stress is implemented in a way that directly calculates the divergence of transport of the wave-induced orbital velocity. A coupled hydrodynamics-wave simulation of San Francisco Bay is then performed. Through the input of wind forcing that is obtained from the reconstructed wind field, the model is capable of predicting wave heights that are in good agreement with the field measurements. We examine the importance of modeling sea bed dissipation in muddy shallow water environments by using a bottom friction model and a bed mud model with different mud layer thicknesses. Moreover, currents driven by wave shoaling and dissipation are investigated in the presence of abrupt bathymetric change. We find that spatially varying wave heights induced by spatially heterogeneous bottom mud dissipation produce wave-driven currents that are stronger than those induced by wave shoaling and can be of the same order as the tidal currents in shallow water. HighlightsAn unstructured-grid model is presented to simulate hydrodynamics under wind-wave and tidal forcing.Simulations are performed to study wave-coupled hydrodynamics in San Francisco Bay.Currents driven by waves are investigated in the presence of abrupt bathymetric change.

This article presents a two-way coupled Euler-Lagrange model to simulate the suspension of fine particles in liquid flows. The goal is to develop a three-dimensional numerical model that is capable of replicating the detailed features of particle-laden turbulent flow. A two-phase fractional-step projection method is developed to ensure mixture incompressibility by solving a modified Poisson equation for pressure, which in turn affects the particle motion through the pressure gradient. An efficient particle-moving algorithm that exchanges particles between Eulerian meshes is developed that automatically retains the necessary particle information at each time step and does not require any Lagrangian particle tracking. A soft-sphere particle collision model is employed to avoid excessive particle overlap and to achieve the random closed packing limit for depositing particles. Since particles are all inherently localized in Eulerian meshes, efficient particle searches can be achieved when calculating particle-particle collision. This model is then used to simulate the gravitational settling of particles, and the results confirm the effect of mixture incompressibility and demonstrate that the model is capable of reaching the random closed packing limit. Numerical examples for the flow problems of particle-induced stratification are conducted, and the model is able to reveal the detailed features of particle-laden flows. Sensitivity on the grid resolution and deviations from the existing single-phase model results are also discussed.

This paper presents a numerical study on the influence of the geometrical arrangement of the hybrid synthetic jet (HSJ) actuators. We study five variants of the HSJ actuators. The laboratory experiment by using water as the working fluid has been conducted for comparison and validation of the numerical simulation. The numerical results reveal the formation and propagation of vortices during the operating cycle in detail. It is identified that the internal vortex within the HSJ actuator plays essential roles on the flow mass exchange during the operating cycle. Our results show that the flow pattern of synthetic jet is highly sensitive to the internal geometrical design, which leads to significant difference in efficiency for different actuators.

In the present study, we develop a three-dimensional two-way coupled Euler–Euler model to simulate the dilute suspensions of fine particles. In addition to the inter-phase drag term, commonly appearing in standard EE formulations, the model formulation includes inter-phase momentum exchange resulting from added mass, which is not negligible in solid–liquid systems. Moreover, through a two-phase pressure projection method, the present numerical model ensures that the incompressibility of the solid–liquid mixture is also taken into consideration. A series of numerical experiments on the particle-induced Rayleigh–Taylor (RT) instability is carried out to investigate bulk mixing attributable to the initial concentration of particles, covering a range of suspension from dilute to dense ( O ( 0.001 - 0.05 ) in volume fraction). This study identifies deviations in the current two-phase simulations by comparing them with single-phase approximations. Our results indicate that the deviations are caused by non-equilibrium particle inertia and mixture incompressibility. In the dilute suspension, it is found that the non-equilibrium particle inertia enhances vertical motion of bubbles and spikes, resulting in a higher efficiency in vertical mixing, compared to the results from single-phase simulations. However, as initial concentration increases, the influence of mixture incompressibility becomes more pronounced and is able to induce a significant suppression of upward-moving motion of bubbles, which in turn decreases the efficiency of vertical mixing.

This paper presents a two-way coupled Euler–Euler model to simulate the dilute suspension of fine particles. The goal is to develop a three-dimensional numerical model that is capable of replicating detailed features of particle-laden turbulent flow. In addition to the terms found in typical two-phase Euler–Euler models, the present formulation also accounts for the effects of added mass and pressure, which are crucial to solid–liquid systems in which densities for each phase are of the same order. This study derives various approximations with which to assess existing model formulations, namely solid–gas equations, equilibrium-state approximation, simplified Euler models, and hindered settling velocity. We then emphasize the deviation of the present simulation results from the equilibrium state, which is simulated by the single-phase approach. We investigate simple examples of the Rayleigh–Taylor instability induced by the suspension of fine particles, the results of which reveals the distribution of non-equilibrium particle inertia. We then examine its influence on the carrier flow. A comparison between the present two-phase model and single-phase approximation demonstrates the importance of the coupled pressure on the evolution of a single bubble induced by the particle-driven Rayleigh Taylor instability.

This paper presents a wave-resolving sediment transport model, which is capable of simulating sediment suspension in the field-scale surf zone. The surf zone hydrodynamics is modeled by the non-hydrostatic model NHWAVE (Ma et al., 2012). The turbulent flow and suspended sediment are simulated in a coupled manner. Three effects of suspended sediment on turbulent flow field are considered: (1) baroclinic forcing effect; (2) turbulence damping effect and (3) bottom boundary layer effect. Through the validation with the laboratory measurements of suspended sediment under nonbreaking skewed waves and surfzone breaking waves, we demonstrate that the model can reasonably predict wave-averaged sediment profiles. The model is then utilized to simulate a rip current field experiment (RCEX) and nearshore suspended sediment transport. The offshore sediment transport by rip currents is captured by the model. The effects of suspended sediment on self-suspension are also investigated. The turbulence damping and bottom boundary layer effects are significant on sediment suspension. The suspended sediment creates a stably stratified water column, damping fluid turbulence and reducing turbulent diffusivity. The suspension of sediment also produces a stably stratified bottom boundary layer. Thus, the drag coefficient and bottom shear stress are reduced, causing less sediment pickup from the bottom. The cross-shore suspended sediment flux is analyzed as well. The mean Eulerian suspended sediment flux is shoreward outside the surf zone, while it is seaward in the surf zone.

A novel bacterial strain, designated a4T, isolated from a sea anemone (Aiptasia pulchella) in Taiwan, was characterized using a polyphasic taxonomic approach. Strain a4T was aerobic, Gram-negative, pale-yellow-pigmented and rod-shaped. It grew optimally at 30-35 degrees C, in the presence of 3-4 % (w/v) NaCl and at pH 8.0. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Tenacibaculum (family Flavobacteriaceae, phylum Bacteroidetes). The closest neighbours were Tenacibaculum lutimaris TF-26T (97.6 % similarity) and Tenacibaculum aestuarii SMK-4T (97.7 % similarity). The novel isolate could be distinguished from all Tenacibaculum species by several phenotypic characteristics. The major fatty acids were summed feature 3 (comprising C16 : 1 omega 7c and/or iso-C15 : 0 2-OH, 19.6 %), iso-C15 : 0 (12.9 %), iso-C16 : 0 3-OH (10.2 %), iso-C17 : 0 3-OH (9.9 %) and iso-C15 : 1 (9.5 %). The DNA G+C content was 35.0 mol%. Hence, genotypic and phenotypic data demonstrate that strain a4(T) should be classified as a representative of a novel species in the genus Tenacibaculum, for which the name Tenacibaculum aiptasiae sp. nov. is proposed. The type strain is a4T (=BCRC 17655T =LMG 24004T).

A bacterium designated strain Liujia-146T was isolated in the Tainan area of southern Taiwan from root nodules of the aquatic legume Neptunia oleracea. 16S rRNA gene sequence analysis indicated that strain Liujia-146T was highly similar to Labrys monachus VKM B-1479T (97.8 %) and Labrys methylaminiphilus JLW10T (95.5 %) and belonged to the order Rhizobiales in the Alphaproteobacteria. On the basis of phylogenetic analysis, DNA–DNA hybridization data, physiological and biochemical characteristics and fatty acid compositions, the organism was shown to belong to the genus Labrys whilst representing a novel species within this genus. We propose to classify strain Liujia-146T (=BCRC 17578T=LMG 23578T) as the type strain of Labrys neptuniae sp. nov.

Twenty Mimosa -nodulating bacterial strains from Brazil and Venezuela, together with eight reference Mimosa -nodulating rhizobial strains and two other β-rhizobial strains, were examined by amplified rRNA gene restriction analysis. They fell into 16 patterns and formed a single cluster together with the known β-rhizobia, Burkholderia caribensis , Burkholderia phymatum , and Burkholderia tuberum . The 16S rRNA gene sequences of 15 of the 20 strains were determined, and all were shown to belong to the genus Burkholderia ; four distinct clusters could be discerned, with strains isolated from the same host species usually clustering very closely. Five of the strains (MAP3-5, Br3407, Br3454, Br3461, and Br3469) were selected for further studies of the symbiosis-related genes nodA , the NodD-dependent regulatory consensus sequences ( nod box), and nifH . The nodA and nifH sequences were very close to each other and to those of B. phymatum STM815, B. caribensis TJ182, and Cupriavidus taiwanensis LMG19424 but were relatively distant from those of B. tuberum STM678. In addition to nodulating their original hosts, all five strains could also nodulate other Mimosa spp., and all produced nodules on Mimosa pudica that had nitrogenase (acetylene reduction) activities and structures typical of effective N 2 -fixing symbioses. Finally, both wild-type and green fluorescent protein-expressing transconjugant strains of Br3461 and MAP3-5 produced N 2 -fixing nodules on their original hosts, Mimosa bimucronata (Br3461) and Mimosa pigra (MAP3-5), and hence this confirms strongly that Burkholderia strains can form effective symbioses with legumes.

The bacterial strain designated I1-1(T) was isolated from a hot spring located in the Pingtung area, southern Taiwan. Cells of this organism were Gram reaction negative rods, motile by a single polar flagellum. Optimum conditions for growth were 55 degrees C and pH 7. Strain I1-1(T) grew well in lower nutrient media such as 5-10% Luria-Bertani broth, and its extracellular products expressed alkaline protease activity. The 16S rRNA gene sequence analysis indicates that strain I1-1(T) is a member of beta-Proteobacteria. On the basis of a phylogenetic analysis of 16S rDNA sequences, DNA-DNA similarity data, whole-cell protein analysis, physiological and biochemical characteristics, as well as fatty acid compositions, the organism belonged to the genus Tepidimonas and represented a novel species within this genus. The predominant cellular fatty acids of strain I1-1(T) were 16:0 (about 41%), 18:1 omega7c (about 13%), and summed feature 3 [16:1 omega7c or 15:0 iso 2OH or both (about 26%)]. Its DNA base ratio was 68.1 mol%. We propose to classify strain I1-1(T) (=BCRC 17406(T)=LMG 22826(T)) as Tepidimonas taiwanensis sp. nov.

Sediment-maintenance flushing flows designed to mimic the action of natural floods in removing the accumulated fine sediments from the channel and loosening the gravel bed have been increasingly proposed as an effective alternative in dam management and a required component of riverine restoration programmes. However, reservoir releases are generally associated with financial and environmental costs, thus it is highly desirable to specify flushing flows as accurately as possible. In this paper we present a simulation approach to evaluating flushing flows and exploring the tradeoffs associated with noninferior flushing options. A two-fraction sediment routing model is used to simulate the gravel-sand bed response to flushing flows. The results reveal that the sand cleansing effect propagates from upstream to downstream and from surface to subsurface. Under a steady gravel supply from upstream, an equilibrium state of gravel transport and bed degradation is eventually reached in the simulation reach. The flushing flow and sediment transport system investigated in this study involves a transient state variable (bed sand content), a decision variable (flushing flow discharge), a flushing goal (ultimate bed sand content), and three outcomes to be minimized (flushing duration, released water volume, and total gravel loss). A series of numerical simulations are carried out with a range of flows and pre-flushing bed sediment conditions. The results reveal that the flushing efficiency is higher for the larger flow. However, for flows greater than � 100 m 3 /s the flushing duration is less sensitive to the flow discharge, thus the system may be simplified as a bi-objective one. The gravel loss and water volume are two conflicting outcomes within the non-inferior flow region. Under a worse bed sediment condition, the feasible flushing options are constrained in a narrower range and also associated with higher costs. The tradeoffs between the conflicting outcomes are quantitatively displayed with the transformed feasible solutions in the objective space. We provide here a general and practical approach permitting a quantitative evaluation of the different flushing options that is appropriate to the level of data typically available. Copyright # 2004 John Wiley & Sons, Ltd.