Biochemical systems consist of numerous elementary reactions governed by the law of mass action. However, experimentally characterizing all the elementary reactions is nearly impossible. Thus, over a ...century, their deterministic models that typically contain rapid reversible bindings have been simplified with non-elementary reaction functions (e.g., Michaelis-Menten and Morrison equations). Although the non-elementary reaction functions are derived by applying the quasi-steady-state approximation (QSSA) to deterministic systems, they have also been widely used to derive propensities for stochastic simulations due to computational efficiency and simplicity. However, the validity condition for this heuristic approach has not been identified even for the reversible binding between molecules, such as protein-DNA, enzyme-substrate, and receptor-ligand, which is the basis for living cells. Here, we find that the non-elementary propensities based on the deterministic total QSSA can accurately capture the stochastic dynamics of the reversible binding in general. However, serious errors occur when reactant molecules with similar levels tightly bind, unlike deterministic systems. In that case, the non-elementary propensities distort the stochastic dynamics of a bistable switch in the cell cycle and an oscillator in the circadian clock. Accordingly, we derive alternative non-elementary propensities with the stochastic low-state QSSA, developed in this study. This provides a universally valid framework for simplifying multiscale stochastic biochemical systems with rapid reversible bindings, critical for efficient stochastic simulations of cell signaling and gene regulation. To facilitate the framework, we provide a user-friendly open-source computational package, ASSISTER, that automatically performs the present framework.
A catastrophic displacement of a waste dump occurred on December 20, 2015, in Guangming New District, Shenzhen, China. During this event, approximately 2.51 × 106 m3 of construction waste slid out of ...the dump site affecting approximately 0.38 km2, destroying 33 buildings and killing 77 people. This study tries to reconstruct the dump structure prior to the failure event, including evolution of dump geometry, geotechnical profile, hydrogeological conditions, and physical properties of fill materials. The dumpsite had been an abandoned quarry before receiving construction wastes beginning in February 2014. Within 22 months, 5.83 × 106 m3 of construction wastes, some of which had high water content, filled the dumpsite forming a 110-m-high loose fill. The dominant component of the fill was completely decomposed granite (CDG) excavated from the adjacent underground construction. The dumping operation at the site was characterized by rapid filling, inadequate compaction and poor water drainage. Poor compaction on the fill materials resulted in low compactness. The measurements of soil density showed that over 80% of the collected CDG samples had a relative density (Dr) from 4% to 67%. The dynamic penetration tests conducted on the landslide bed indicated that the fill materials were loose to slightly dense at most of the penetration depth. No effective drainage facilities were provided at the dump site. A large quantity of water from a catchment area of 0.51 km2 readily poured into the dump, resulting in a significant rise in the phreatic surface. The rapid filling rate of 5–7 m/month was very likely to have caused a build-up of excessive pore-water pressure in the lower poorly drained fill, which was verified by borehole exposure of the confined groundwater and the evaluation of consolidation degree based on the measurements of soil density. The fill materials within the landslide bed were found to have a consolidation degree of 33% on average. A deep-seated translational failure occurred on the lower poorly consolidated fill layer, forming a very-fast-moving flow slide.
•The evolution of dump geometry and the geotechnical profile were reconstructed.•The dumping operation was revealed to be fast with inadequate compaction.•Most of the fill materials samples had a relative density less than 67%.•Excessive pore-water pressure in the lower poorly-drained fill was verified.•A deep-seated translational failure occurred on the poorly consolidated fill layer.
With the rapid development of stretchable and wearable technologies, stretchable interconnection technology also demanded along it. Stretchable interconnections should have high stretchability and ...stable conductivity for use as an electrode. In addition, to develop to commercialization scale from research scale, a simple fabrication process that can be scaled up, and the stretchable interconnection should be able to be electrically connected to devices or modules directly. To date, printable conductor inks, liquid metals and stretchable structured interconnections have been reported for stretchable interconnections. These approaches have demonstrated high stretchability and conductivity, but in aspect of scale, it is appropriate to apply in micro-scale devices. For requirements of stretchability, conductivity and direct integration into meso- or centimeter-scale electronic devices or modules, here we introduce stretchable interconnections with a textile structure composed of metal fibers. The stretchable woven and knitted textiles show 67% strain and stable conductivity, and the cylindrical textile shows more than 700% strain with high strength. The stretchable textiles were fabricated using a weaving, knitting and braiding machine that can be used to produce textiles without any limit to length or area. These textiles exhibit high and stable conductivity even under deformation, and can be directly integrated into devices or modules by soldering. These high-performance stretchable textiles have great potential for commercial applications.
This paper presents a computational sand model based on the well-known pressure dependent multi-surface constitutive model to solve the necessity of employing a separate set of model parameters for ...each soil relative density change. The proposed model correlates the original model parameters with the soil relative density through critical-state-based soil mechanics formulations to provide a single set of model constants that adapt to different soil states. Model formulation updates are performed for the flow rules, material moduli calculations, and the computation of stress ratios at the phase transformation and failure stages. The model parameters are calibrated for Ottawa F-65 sand against cyclic soil element tests with different stress levels and various soil densities. Thereafter, numerical simulations are conducted for centrifuge experiments of gently sloped grounds to validate the proposed model. Throughout numerical simulations, the proposed model accurately replicates the sand cyclic undrained behavior as similar to laboratory-measured responses for different soil relative densities with a single calibrated set of model parameters and provides reliable numerical predictions in finite element simulations of the engaged centrifuge experiments. Overall, the proposed model robustly simulates the saturated sand seismic response, which can improve the numerical prediction accuracy of liquefaction-induced damage in different engineering applications.
Chitosan is a well-known excellent adsorbent for a number of organics and metal ions, but its mechanical properties and specific gravity should be enhanced for practical operation. In this study, ...activated clay was added in chitosan slurry to prepare composite beads. The adsorption isotherms and kinetics of two organic acids (tannic acid, humic acid) and two dyes (methylene blue, reactive dye RR222) using composite beads, activated clay, and chitosan beads were compared. With composite beads as an adsorbent, all the isotherms were better fitted by the Freundlich equation. The adsorption capacities with composite beads were generally comparable to those with chitosan beads but much larger than those with activated clay. The pseudo-first-order and pseudo-second-order equations were then screened to describe the adsorption processes. It was shown that the adsorption of larger molecules such as tannic acid (MW, 1700 g
mol
−1), humic acid, and RR222 from water onto composite beads was better described by the pseudo-first-order kinetic model. The rate parameters of the intraparticle diffusion model for adsorption onto such adsorbents were also evaluated and compared to identify the adsorption mechanisms.
The 2008 Wenchuan earthquake caused widespread liquefaction of gravelly soils (i.e., gravelly sands and sandy gravels), which phenomena show many differences compared to those of typical sands. To ...study the liquefaction mechanism and triggering evaluation of gravelly soils during this event, comprehensive case studies with measurement of shear wave velocity on both liquefied and non-liquefied sites were carried out according to a suite of recommended procedures for site investigation, field testing and data processing. Three typical cases were provided to illustrate the distinct characteristics of ground motion, liquefaction manifestation, soil profiles and field testing, and explore the possible mechanisms of liquefaction. Eighty-one well identified case histories were obtained, which feature the updated estimation of ground motion parameters from the USGS ShakeMap and the probabilistic treatment of the datasets. The preliminary analyses on liquefaction triggering boundary curves, shear wave velocities of these case histories and the applicability of the Ishihara criterion (1985) indicate that the gravel content plays a key role in the liquefaction mechanism and the consequences of gravelly soil deposits, and the liquefaction evaluation of gravelly sands and sandy gravels should be treated separately.
•Eighty-one Vs-based liquefaction case histories are compiled from the 2008 Wenchuan earthquake.•Liquefaction consequences of sand-gravel mixtures are not as severe as that of typical sands.•Shear wave velocity of gravelly soils increases with gravel content at an increasing rate.•Liquefaction triggering curve for gravelly soils shifts to the right-hand side considerably.•Liquefaction evaluation of gravelly sands and sandy gravels should be treated separately.
We present new Atacama Large Millimeter Array (ALMA) dust continuum observations of 101 galaxies in the COSMOS field to study the effect of the environment on the interstellar medium at z ∼ 0.7. At ...this redshift, our targets span a wide range of environments allowing for a diverse sample of galaxies with densities of = 0.16-10.5 Mpc−2 (per Δz = 0.024). Using the ALMA observations, we calculate the total interstellar medium (ISM) mass (MISM) and look for depletion as a function of galaxy density in order to understand the quenching or triggering of star formation in galaxies in different environments. MISM is found to have a small dependence on the environment, while the depletion timescale remains constant (∼200 Myr) across all environments. We find elevated MISM values at intermediate densities and lower values at high densities compared to low (field) densities. Our observed evolution in gas fraction with density in this single redshift slice is equivalent to the observed evolution with cosmic time over 2-3 Gyr. To explain the change in the gas mass fraction seen in galaxies in intermediate and high densities, these results suggest environmental processes such as mergers and ram pressure stripping are likely playing a role in dense filamentary cluster environments.
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne viral disease caused by the SFTS virus (SFTSV) from Bunyaviridae that is endemic in East Asia. However, the genetic and ...evolutionary characteristics shared between tick- and human-derived Korean SFTSV strains are still limited.
In this study we identify, for the first time, the genome sequence of a tick (Haemaphysalis longicornis)-derived Korean SFTSV strain (designated as KAGWT) and compare this virus with recent human SFTSV isolates to identify the genetic variations and relationships among SFTSV strains. The genome of the KAGWT strain is consistent with the described genome of other members of the genus Phlebovirus with 6,368 nucleotides (nt), 3,378 nt, and 1,746 nt in the Large (L), Medium (M) and Small (S) segments, respectively. Compared with other completely sequenced human-derived Korean SFTSV strains, the KAGWT strain had highest sequence identities at the nucleotide and deduced amino acid level in each segment with the KAGWH3 strain which was isolated from SFTS patient within the same region, although there is one unique amino acid substitution in the Gn protein (A66S). Phylogenetic analyses of complete genome sequences revealed that at least four different genotypes of SFTSV are co-circulating in South Korea, and that the tick- and human-derived Korean SFTSV strains (genotype B) are closely related to one another. Although we could not detect reassortant, which are commonly observed in segmented viruses, further large-scale surveillance and detailed genomic analysis studies are needed to better understand the molecular epidemiology, genetic diversity, and evolution of SFTSV.
Full-length sequence analysis revealed a clear association between the genetic origins of tick- and human-derived SFTSV strains. While the most prevalent Korean SFTSV is genotype B, at least four different genotypes of SFTSV strains are co-circulating in South Korea. These findings provide information regarding the molecular epidemiology, genetic diversity, and evolution of SFTSV in East Asia.
DNA metabarcoding analysis for gut contents has been shown to compensate the disadvantage of traditionally morphological identification and offer higher resolution of prey items in an efficient way. ...Holland's carp (Spinibarbus hollandi) is a freshwater fish native to southern and eastern Taiwan. In the past two decades, this species has been introduced as a sport fish into the river basins of northern and western Taiwan. The large body size and active predation make it a potential threat for native fishes, but which native species are preyed by Holland's carp remains unknown. In this study, the diet from the gut contents of Holland's carp from the Zhonggang River, an invaded basin, was examined using DNA metabarcoding from 51 individuals and by morphological examinations on 140 samples. Detritus of plants were found in 83.6% samples (117 individuals). Twenty fish species of seven families were identified by DNA metabarcoding, including species of all water layers. Taiwan torrent carp (Acrossocheilus paradoxus) and Rhinogobius spp. are the most common prey items. Based on the results of this study, Holland's carp is considered an opportunistic omnivore because of its diverse diet items, which is an important trait for successful invasive fish species. The population decline of Opsariichthys pachycephalus may not result from the invasion of Holland's carps. Nonetheless, the time lag between successful invasion and the samplings of this study may be a concern because the population size of O. pachycephalus may have declined and become difficult to prey. The Holland's carps consumed the least species in winter; nonetheless, the occurrence frequencies of preys among seasons were not significantly different probably because of limited temperature fluctuation. The smallest Holland's carps consumed the least prey species compared to other size categories, similar to the relationship of prey species number to size of invasive largemouth bass (Micropterus salmoides).
Geotechnical engineers face several challenges when constructing embankments over soft soils. These include potential bearing failure, intolerable settlement, and global or local instability. Piled ...embankments provide an economic and effective method to construct roads on soft soils. Soil arching developed within such embankments has significant influence on its behavior. A total of 15 model tests were conducted to evaluate the effects of pile–subsoil relative displacement, embankment height, cap beam width and clear spacing, and geosynthetics with different tensile strengths on stress concentration ratios and settlements in the embankments. The test results indicate that stress concentration ratio varies with pile–subsoil relative displacement and has upper and lower bounds. A higher ratio of embankment height to cap beam clear spacing, as well as a higher ratio of cap beam width to clear spacing, would result in a higher stress concentration ratio. The inclusion of a geosynthetic membrane can increase the stress concentration ratio. When the embankment height to the cap beam clear spacing ratio,
h/
s, is less than 1.4, apparent differential settlements may occur on the surface of embankment. When
h/
s is greater than 1.6, however, no apparent differential settlements will occur on the embankment surface. In addition, experimental results were also compared to several current design methods.
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