Different Degrees Of Compaction Research Articles

Circulating Tumor Cell cluster phenotype allows monitoring response to treatment and predicts survival

Circulating tumor cells (CTCs) are putative markers of tumor prognosis and may serve to evaluate patient’s response to chemotherapy. CTCs are often detected as single cells but infrequently as clusters and are indicative of worse prognosis. In this study, we developed a short-term culture of nucleated blood cells which was applied to blood samples from breast, lung, esophageal and bladder cancer patients. Clusters of different degrees of compactness, classified as very tight, tight and loose were observed across various cancer types. These clusters show variable expression of cytokeratins. Cluster formation from blood samples obtained during the course of chemotherapy was found to be associated with disease progression and shorter overall survival. The short-term cultures offer a robust and highly reliable method for early prediction of treatment response in different cancer types.

General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins.

Unconstrained atomistic simulations of intrinsically disordered proteins and peptides (IDP) remain a challenge: widely used, "general purpose" water models tend to favor overly compact structures relative to experiment. Here we have performed a total of 93 μs of unrestrained MD simulations to explore, in the context of IDPs, a recently developed "general-purpose" 4-point rigid water model OPC, which describes liquid state of water close to experiment. We demonstrate that OPC, together with a popular AMBER force field ff99SB, offers a noticeable improvement over TIP3P in producing more realistic structural ensembles of three common IDPs benchmarks: 55-residue apo N-terminal zinc-binding domain of HIV-1 integrase ("protein IN"), amyloid β-peptide (Aβ42) (residues 1-42), and 26-reside H4 histone tail. As a negative control, computed folding profile of a regular globular miniprotein (CLN025) in OPC water is in appreciably better agreement with experiment than that obtained in TIP3P, which tends to overstabilize the compact native state relative to the extended conformations. We employed Aβ42 peptide to investigate the possible influence of the solvent box size on simulation outcomes. We advocate a cautious approach for simulations of IDPs: we suggest that the solvent box size should be at least four times the radius of gyration of the random coil corresponding to the IDP. The computed free energy landscape of protein IN in OPC resembles a shallow "tub" - conformations with substantially different degrees of compactness that are within 2 kB T of each other. Conformations with very different secondary structure content coexist within 1 kB T of the global free energy minimum. States with higher free energy tend to have less secondary structure. Computed low helical content of the protein has virtually no correlation with its degree of compactness, which calls into question the possibility of using the helicity as a metric for assessing performance of water models for IDPs, when the helicity is low. Predicted radius of gyration ( R g) of H4 histone tail in OPC water falls in-between that of a typical globular protein and a fully denatured protein of the same size; the predicted R g is consistent with two independent predictions. In contrast, H4 tail in TIP3P water is as compact as the corresponding globular protein. The computed free energy landscape of H4 tail in OPC is relatively flat over a significant range of compactness, which, we argue, is consistent with its biological function as facilitator of internucleosome interactions.

Linking pore network structure derived by microfocus X-ray CT to mass transport parameters in differently compacted loamy soils

Mass transport in soil occurs through the soil pore network, which is highly influenced by pore structural parameters such as pore-size distribution, porosity, pore tortuosity, and coordination number. In this study, we visualised the networks of meso- and macro-pores (typical pore radius r ≥ 10 μm) using microfocus X-ray computed tomography (MFXCT) and evaluated pore structural parameters of two loamy soils from Japan and New Zealand packed at different degrees of compaction. The effect of compaction on pore structural parameters and relationships between pore structural parameters and measured mass transport parameters were examined. Results showed a clear influence of compaction on pore structural parameters, with the MFXCT-derived mean pore radii and pore tortuosities decreasing and the mean pore coordination number increasing with increasing dry bulk density. Especially, pores with r > 80 µm became finer or were not well formed due to compaction. The MFXCT-derived pore structural parameters were not well correlated with the equivalent pore radii from measured water retention curves. However, volumetric surface areas and pore-network connectivity-tortuosity factors derived from MFXCT allowed a fair prediction of several important mass transport parameters such as saturated hydraulic conductivities, soil-gas diffusion coefficients, and soil-air permeabilities. Further studies are needed to link micro-pores with radii smaller than the X-ray CT resolution to meso- and macro-pores visualised by X-ray CT to improve the prediction of mass transport parameters in soil.

Suitability of Boulder Marl and Marsh Clay as Sealing Substrates for Landfill Capping Systems—A Practical Comparison

The effects of compaction on soil shrinkage behavior need to be considered for engineering long-term durable mineral liners of landfill capping systems. For this purpose, a new three-dimensional laser scanning device was coupled with a mathematical-empirical model to simultaneously determine the shrinkage behavior of a boulder marl (bm) and a marsh clay (mc). Therefore, both materials were precompacted in 200 soil cores (100 cm3) on the basis of the Proctor test results with five different degrees of compaction (bm1-bm5; mc1-mc5). Thus, the shrinkage behavior, intensity, and tendency were determined during a standardized drying experiment. The volume shrinkage index was used to describe the pore size dependent shrinkage tendency and was classified as high to very high (11.3–17.7%) for the marsh clay and medium (5.3–9.2%) for the boulder marl. Additionally, only the boulder marl (bm2), compacted up to 88% of Proctor density, could be installed as landfill bottom liner in drier locations if the local matric potentials did not exceed the previously highest observed drying range (i.e. values below −300 hPa), to avoid crack formation and generation.

Changes of structural and physical properties of semi-gel from Alaska pollock surimi during 4 °C storage

This study compared the semi-gel system of Alaska pollock surimi formed at a low temperature with a heat-induced gel system. The cold semi-gel and heat-induced gel were found to have obvious differences in their degrees of protein unfolding, aggregation, and gel network structures. Microscopic observations and an analysis of their fractal dimensions revealed different degrees of compactness and uniformity in the two network structures. Rheological parameters, including the least permanent deformation, equilibrium stress, and frequency exponent, confirmed the non-total aggregation and lower degree of cross-linking in the cold semi-gel. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis showed that the myosin heavy chain (MHC) value gradually decreased, but the light meromyosin (LMM) value remained stable during cold storage. Furthermore, a decrease in the α-helix and an increase in the β-sheet and random coil values, as revealed by Fourier-transform infrared (FT-IR) spectroscopy, indicated that the proteins unfolded differently in the two gel systems. By comparing the times required for the cold semi-gel and heat-induced gel to form, we concluded that the formation process of heat-induced gel is intertwined while it is temporally separated in cold storage. Overall, myosin was selected as the starting point for establishing a schema chart to characterize the gelation processes of the cold semi-gel and heat-induced gel. These findings are helpful for understanding the gelation process of surimi in refrigerated storage.

Tuning the antimicrobial behaviour of Cu85Zr15 thin films in “wet” and “dry” conditions through structural modifications

The antimicrobial behaviour of Cu85Zr15 at.% thin films prepared by magnetron sputtering was studied in both wet and dry conditions. Small variations in key deposition processing parameters (pressure and substrate temperature) enabled the growth of thin films with similar nanostructures but different degrees of compactness, according to the Thornton's structural zone model. This model has proven its effectiveness in providing sensitive structural information to explain significant differences in antimicrobial behaviour of the CuZr thin films, even when processing conditions lie within the same structural zone. The antimicrobial behaviour has been studied for E. coli and S. aureus for up to 4 h of “dry” contact. Structures of lower compactness, grown at higher deposition pressure, are shown to provide higher antimicrobial activity for “dry” conditions than for “wet” conditions. For thin films of CuZr deposited at 0.5 Pa, the reduction percentage of bacteria is 99.47%, which is much higher than the results of 70–80% obtained for the films deposited at 0.1 and 0.3 Pa. Microscopy studies indicate that for 4 h of contact time, bacteria exhibit inner damage and even lysis, however, no morphological changes are detected because of the short timeframes used.

Methods for assessment and identification of dispersive soils

AbstractDispersive clay soils represent a specific type of fine‐grained soils, which can not be determined by the visual classification or using standard identification ‐ classification tests such as granulometric (particle size) analysis, plasticity tests and similar. The paper gives an overview of the results of testing dispersivity of fine‐grained soil using other classification tests: the crumb test, the double hydrometer test and the pinhole test. Tests were conducted on samples: sandy clay embankment dams of “Rovni”, loess from different locations (Zemun, Novi Beograd, Titel, Kelebija, Srbobran, Slankamen, Ruma, Mali Iđoš) and kaolinite sandy clay deposits Grabež ‐ Aranđelovac. In order to improve soil properties, special consideration was given to the influence of soil compaction to dispersion properties. However, dispersion tests obtained with the use of the pinhole method at different degrees of compaction showed that the degree of compaction has no significant effect on the soil behavior, i.e. its class of dispersion.

Abnormal phase-separated state of LixNi0.8Co0.15Al0.05O2 in the first charge: Effect of electrode compaction

A planar electrochemical cell developed for operando/in situ neutron diffraction experiments at time-of-flight diffractometers was used to study a structural state of LixNi0.8Co0.15Al0.05O2 (NCA) electrodes with different degree of compaction. A two-phase-separated state of the NCA electrodes was observed in the first charge cycle. It was established that stronger compaction of the electrodes partially suppresses the phase separation of the cathode material: reduces a state of charge (SOC) range where two phases coexist, and decreases the difference between structural parameters of the phases. X-ray photoelectron spectroscopy has revealed a presence of Li2CO3 film at the surface of the NCA material in the amount that is unlikely to affect the NCA behavior during the first charge. It was suggested that the phase-separated state is caused by the morphology of the NCA material. This observation could be expanded to layered cathode materials with similar microstructures.

Low velocity collisions of porous planetesimals in the early solar system

The ESA Rosetta mission has shown that Comet 67P/Churuymov–Gerasimenko is bi-lobed, has a high average porosity of around 70%, does not have internal cavities on size scales larger than 10 m, the lobes could have individual sets of onion shell-like layering, and the nucleus surface contains 100 m-scale cylindrical pits. It is currently debated whether these properties are consistent with high-velocity collisional evolution or if they necessarily are surviving signatures of low-velocity primordial accretion. We use an Eulerian hydrocode to study collisions between highly porous bodies of different sizes, material parameters and relative velocities with emphasis on 5–100 m/s to characterize the effects of collisions in terms of deformation, compaction, and heating. We find that accretion of 1 km cometesimals by 3 km nuclei at 13.5 m/s flattens and partially buries the cometesimal with ∼ 1% reduction of the bulk porosity. This structure locally becomes more dense but the global effect of compaction is minor, suggesting that low-velocity accretion does not lead to a ‘bunch of grapes’ structure with large internal cavities but a more homogeneous interior, consistent with Rosetta findings. The mild local compaction associated with accretion is potentially the origin of the observed nucleus layering. In 2D axially symmetric impacts hit-and-stick collisions of similarly-sized nuclei are possible at velocities up to 30 m/s where deformation becomes severe. The bulk porosity is reduced significantly, even at 30–50 m/s relative velocity. To avoid hit-and-run collisions the impact angle must be less than 35°–45° from the surface normal at 10 m/s, and even smaller at higher velocities. Impact heating is insignificant. We find that the small cross section of the 67P neck may require a ≤ 5 m/s impact, unless the cohesion exceeds 10 kPa. We conclude that bi-lobe nucleus formation is possible at velocities typically discussed in hierarchical growth scenarios. Impacts of a 7 m projectile at 100–500 m/s create a rimless cylindrical shaft with vertical walls, up to 50 m wide and 70 m deep. These shafts bear some resemblance with the pits on 67P, particularly if the depth-to-width ratio is reduced by nucleus erosion. Collisions between similarly-sized nuclei above 100 m/s lead to complete disintegration, and even small fragments suffer different degrees of compaction. Thus, we strongly doubt that 67P has been subjected to high-velocity collisions by projectiles larger than those that might have formed the pits, or is the fragment of a larger parent body. We suggest that the observed properties of 67P are more consistent with primordial accretion.

Influence of backfill soil shear strength parameters on retaining walls stability

One of the problem of geotechnical engineering is the analysis of the retaining walls stability, where are several uncertainty sources. Some of these uncertainties relate to the inherent variability of fill soil, retained by the retaining wall, strength parameters. This feature can be quantified through a retaining wall stability probabilistic analysis using the Monte Carlo Simulation method (SMC), which enables to determine the wall reliability from collected testing shear strength information of existing soils in the cities of Coquimbo and La Serena, Coquimbo Region, Chile. An application example, the study of a cantilever retaining wall stability filled with silty sand soil (SM) with three different degrees of compaction (DC%: 80, 90 and 95%), with the objective to analyze the wall stability through statistical analysis of safety factors.

Development and Application of an Instantaneous Impulsion-based Detector to Inspect the Degree of Compaction of the Cement-stabilized Macadam

To inspect the degree of compaction of cement-stabilized macadam (CSM), a new detector was developed based on an instantaneous impulsion method. The degree of compaction could be assessed by the acceleration response value (ARV). To achieve the appropriate parameter of device, the gaskets, falling distance, and hammer weight were optimized. The correlation coefficient of degree of compaction and ARV were also improved. The instrument parameters and operability of the instrument were determined by a correlation coefficient and the device operability. The case study on two types of CSM with different degrees of compaction indicated that the ARV showed a highest linking with the degree of compaction when the gasket of DP-4 with a falling distance of 40cm and a hammer weight of 5.7kg. Compared to the falling distance and hammer weight, the type of gasket impacts highly on the correlation coefficient. The case study proves the new developed device with more than 0.8 (correlation coefficient).

Comparison and evaluation of railway subgrade quality detection methods

Subgrade is a critical component of railway systems since it provides a stable platform for the track substructure. The implementation of quality assurance methods is very important during the construction of a new railway subgrade and in monitoring the working performance of operating railways. There are several indicators available to measure the compaction and mechanical performance of a completed subgrade system, including compaction degree ( K), porosity ( n), modulus of subgrade reaction ( K30), basic bearing capacity ([Formula: see text]), strain moduli ( Ev), dynamic modulus of deformation ( Evd), and light dynamic penetration ( N10). The objective of this research was to compare and evaluate the frequently used engineering methods in order to select the important and reliable indicators of field parameters. Four soil models with different degree of compaction were considered in the common laboratory tests and detection methods in China to determine the construction quality. The implementation and test results of these methods were analyzed and compared. The study results indicate that K correlates with n linearly. There is also a good correlation among K30, Ev, and Evd. As a recommendation, K is considered as the controlling indicator for compaction performance, and Ev2 and Evd are considered as the controlling indicators for railway subgrade stiffness evaluation. The bearing capacity or strength indicators may be added to the quality detection work in heavy-haul railway construction.

Xenacoelomorpha: a case of independent nervous system centralization?

Centralized nervous systems (NSs) and complex brains are among the most important innovations in the history of life on our planet. In this context, two related questions have been formulated: How did complex NSs arise in evolution, and how many times did this occur? As a step towards finding an answer, we describe the NS of several representatives of the Xenacoelomorpha, a clade whose members show different degrees of NS complexity. This enigmatic clade is composed of three major taxa: acoels, nemertodermatids and xenoturbellids. Interestingly, while the xenoturbellids seem to have a rather 'simple' NS (a nerve net), members of the most derived group of acoel worms clearly have ganglionic brains. This interesting diversity of NS architectures (with different degrees of compaction) provides a unique system with which to address outstanding questions regarding the evolution of brains and centralized NSs. The recent sequencing of xenacoelomorph genomes gives us a privileged vantage point from which to analyse neural evolution, especially through the study of key gene families involved in neurogenesis and NS function, such as G protein-coupled receptors, helix-loop-helix transcription factors and Wnts. We finish our manuscript proposing an adaptive scenario for the origin of centralized NSs (brains).

Experimental Study of Improved Loess High Embankment Foundation Jointly by Chemical Materials and Electric Field Treatment

Electric field treatment is a kind of new technology that improves and reinforces soil. Proper amounts of lime and sodium sulfate were added to the soil as stabilizers. Compacted the mixture to meet the predetermined dry density and then imposed a certain intensity of electric field on it. After curing, unconfined compression tests, direct shear tests, high pressure compression tests and collapsibility tests were carried out. The results show that the engineering properties of the improved soils, such as its unconfined compressive strength, shear strength, compressibility, are better than that of the backfill compacted loess. Moreover, collapsibility under the different degree of compaction has been removed. The microstructure and improving mechanism of the improved soils are analyzed using scanning electron microscope (SEM), and the results can provide references for further study and engineering application.

Effects of Density and Moisture Variation on Dynamic Deformation Properties of Compacted Lateritic Soil

A series of repeated load triaxial tests were conducted in this study to investigate the influences of compaction density and postcompaction moisture variation on the dynamic elastic modulus (Ed) and plastic permanent strain (PPS) of compacted lateritic soil. Specimens were compacted at optimum moisture content (OMC) and three degrees of compaction (90%, 93%, and 96%). Then the specimens were dried or wetted to different moisture contents (OMC,OMC±3%,OMC±6%, andOMC+9%) prior to testing forEdand PPS. Results show that moisture content has greater influence on theEdand PSS than compaction degree, and the increase in moisture content leads to a decrease ofEdand an increase of PPS. Furthermore, an empirical relationship betweenEdand applied cyclic stress (σd) is developed that incorporates density and moisture variations. Three different evolution types of PPS with number of load cycles, plastic stable, plastic creep, and incremental collapse, are identified as the increase of moisture content. In addition, the critical dynamic stress (σdc) separating stable and unstable deformation is determined based on the shakedown concept. The envelope curves ofσdc-moisture of lateritic soil with different degrees of compaction are also determined to provide reference for the pavement design.

Self-excited regime of sedimentation of partially molten rocks

We consider the phenomenon of sedimentation of partially molten rocks in intrusions. During the sedimentation of the suspension, a stratified structure consisting of zones with different degree of compaction of the solid phase appears. The highest degree of compaction corresponds to a poroviscous medium. With a critical porosity at the boundary, this medium is overlaid by a thin intermediate layer. The supercritical porosity values correspond to the violation in the skeleton’s connectivity. Within the thin layer, the skeleton of the poroviscous medium generally retains its properties, although in a strongly reduced form. The grains bounded by strong hydrodynamical bonds form the structures characterized by instability. During the sedimentation, these structures periodically collapse and recover, which is perceived as periodic self-excited oscillations on the macroscopic level. The self-excited sedimentation regime leads to the formation of a periodical layered structure in the cumulates, which is detectable many millions of years after the solidification of the intrusive chamber. This process is studied in the present paper.

Looping dynamics of a flexible chain with internal friction at different degrees of compactness

In recent times single molecule experiments have shown the importance of internal friction in biopolymer dynamics. Such studies also suggested that the internal friction although independent of solvent viscosity has a strong dependence on denaturant concentration. In addition, recent simulations showed that the weak interactions contribute to the internal friction in proteins. In this work we made an attempt to investigate how a single polymer chain with internal friction undergoes reconfiguration and looping dynamics in a confining potential that accounts for the presence of the denaturant, by using recently proposed “Compacted Rouse with internal friction”. We also incorporated the effect of hydrodynamics by extending this further to “Compacted Zimm with internal friction”. All the calculations are carried out within the Wilemski Fixman framework without invoking excluded-volume effect. By changing the strength of the confinement we mimicked chains with different degrees of compactness at different denaturant concentrations. While compared with experiments our results are found to be in good agreement.

Investigation of soil density effect on suction induced due to root water uptake by Schefflera heptaphylla

AbstractAn increase in soil water suction due to root water uptake is significant for stability of slopes and landfill covers as it increases shear strength of soil by 50%. Coupled effects of soil density changes in soil hydraulic properties [i.e., soil water characteristic curve (SWCC) and hydraulic conductivity] and root characteristics (root depth, vertical root distribution) found in past experimental studies may affect soil water suction, which are not fully understood. The objective of this study is to numerically investigate these coupled effects of soil density by systematically comparing suction profiles under three different scenarios: (1) changes in only soil hydraulic properties, (2) changes in only root characteristics, and (3) changes in both soil properties and root characteristics. Silty sand with two different degrees of compaction (DoC) (i.e., 82% and 89%), which are typically found on man‐made slopes in subtropical regions, is considered. Schefflera heptaphylla is selected as vegetation species, which is commonly used for ecological restoration for man‐made slopes. A laboratory experiment was conducted to quantify suction distribution in silty sand vegetated with Schefflera heptaphylla at DoC of 89%. Vertical root distribution was measured using image analysis, while an axi‐symmetric finite element analysis was conducted to calibrate transpiration rate from measured suction. Root characteristics corresponding to DoC of 82% were then deduced using observations from literature. Richards equation coupled with sink term was numerically solved using Vadose/W to simulate water flow and root uptake on a flat ground (5 m depth, 10 m wide). Soil hydraulic parameters from a completely decomposed granite soil for two different DoCs (82% and 89%) were considered. Simulations assume constant transpiration rate for a period of 10 d. With increase in soil density from DoC of 82% to 89%, computed suction increases by 110% for scenario 1 (only effect on soil hydraulic properties), whereas it decreases by at least 21% for scenarios 2 (only root characteristics) and 3 (coupled effect). Here, a higher unsaturated hydraulic conductivity and a lower actual transpiration rate balance effects of a lower desorption rate of SWCC.

Nondestructive Measurement of Water Content and Moisture Migration of Unsaturated Red Clays in South China

To reveal the moisture migration mechanism of the unsaturated red clays, which are sensitive to water content change and widely distributed in South China, and then rationally use them as a filling material for highway embankments, a method to measure the water content of red clay cylinders using X-ray computed tomography (CT) was proposed and verified. Then, studies on the moisture migrations in the red clays under the rainfall and ground water level were performed at different degrees of compaction. The results show that the relationship between dry density, water content, and CT value determined from X-ray CT tests can be used to nondestructively measure the water content of red clay cylinders at different migration time, which avoids the error reduced by the sample-to-sample variation. The rainfall, ground water level, and degree of compaction are factors that can significantly affect the moisture migration distance and migration rate. Some techniques, such as lowering groundwater table and increasing degree of compaction of the red clays, can be used to prevent or delay the moisture migration in highway embankments filled with red clays.

The conformational response to Zn(II) and Ni(II) binding of Sporosarcina pasteurii UreG, an intrinsically disordered GTPase.

Urease is an essential Ni(II) enzyme involved in the nitrogen metabolism of bacteria, plants and fungi. Ni(II) delivery into the enzyme active site requires the presence of four accessory proteins, named UreD, UreF, UreG and UreE, acting through a complex protein network regulated by metal binding and GTP hydrolysis. The GTPase activity is catalyzed by UreG, which couples this function to a non-enzymatic role as a molecular chaperone. This moonlighting activity is reflected in a flexible fold that makes UreG the first discovered intrinsically disordered enzyme. UreG binds Ni(II) and Zn(II),which in turn modulate the interactions with other urease chaperones. The aim of this study is to understand the structural implications of metal binding to Sporosarcina pasteurii UreG (SpUreG). A combination of light scattering, calorimetry, mass spectrometry, and NMR spectroscopy revealed that SpUreG exists in monomer-dimer equilibrium (K(d)= 45 µM), sampling three distinct folding populations with different degrees of compactness. Binding of Zn(II) ions, occurring in two distinct sites (K(d1) = 3 nM, K(d2) = 0.53 µM), shifts the protein conformational landscape toward the more compact population, while maintaining the overall protein structural plasticity. Differently, binding of Ni(II) ions occurs in three binding sites (K(d1(= 14 µM; K(d2) = 270 µM; K(d3)= 160 µM), with much weaker influence on the protein conformational equilibrium. These distinct conformational responses of SpUreG to Ni(II) and Zn(II) binding suggest that selective metal binding modulates protein plasticity, possibly having an impact on the protein-protein interactions and the enzymatic activity of UreG.