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At least 253 records · Page 14

A compendium of multi-omics data illuminating host responses to lethal human virus infections

Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology.

60 APPLIED LIFE SCIENCES↗

Grain boundary segregation in BCC vanadium-based alloys: Quantum-accurate computed segregation spectra and targeted experimental validations

Grain boundaries are critically important to the material performance of fusion reactor materials such as vanadium, particularly mechanical properties and irradiation resistance. A key challenge to the design and control of grain boundaries in vanadium alloys is the lack of quantitative data on grain boundary segregation. In this study, we combine computational and experimental methods to address this gap. Furthermore, using a machine learning-accelerated quantum mechanics/molecular mechanics approach, we calculated the segregation spectra for 28 transition metal elements in polycrystalline vanadium, and validated these predictions experimentally for a subset of solutes that sample a range of segregation behavior, specifically zirconium, titanium, and tungsten, using analytical transmission electron microscopy. Furthermore, the agreement between experiment and theory highlights the predictive capability of our approach. Critically, this work provides a comprehensive database of quantum-accurate solute segregation enthalpies in vanadium, enabling the development of advanced alloys for fusion reactors applications.

Fusion materials↗

Electrochemical Methods for Assessing Kinetic Factors in the Reduction of CO 2 to Formate: Implications for Improving Electrocatalyst Design

hermochemical insights are often employed in the rationalization of reactivity and in the design of electrocatalysts for CO 2 reduction reactions targeting C–H bond-containing products. This work identifies experimental methods for assessing kinetic aspects of reactivity. These methods are illustrated using [Fe 4 N(CO) 12 ] - , which produces formate from CO 2 at -1.2 V versus SCE in either a MeCN/H 2 O solvent (95:5) or pH 6.5 buffered water. Elementary rates for each reaction step are identified along with the rate-determining step (RDS) as C–H bond formation. Transition state kinetics were determined from an Eyring analysis for the rate-determining C–H bond formation step using temperature-dependent electrochemical measurements. A lower measured Δ G ‡ (298 K, 12.3 ± 0.1 kcal mol –1 ) in a pH 6.5 aqueous solution, compared with a Δ G ‡ (298 K) of 15.0 ± 0.1 kcal mol –1 in a MeCN/H 2 O solvent (95:5), correlates with faster observed reaction rates and provides a kinetic rationalization for the solvent-dependent chemistry. Taken together, the experimentally determined kinetic insights highlight that enhancement of the local concentration of CO 2 at catalyst–hydride sites should be a primary focus of ongoing catalyst design. This will both enhance reaction rates and increase selectivity for C–H bond formation over competing H–H bond formation, because that step is fast in H 2 evolution reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cumulative material damage from train of ultrafast infrared laser pulses

We developed a systematic experimental method to demonstrate that damage threshold fluence (DTF) for fused silica changes with the number of femtosecond laser (800 nm, $65\pm 5~\text{fs}$ , 10 Hz and 600 Hz) pulses. Based on the experimental data, we were able to develop a model which indicates that the change in DTF varies with the number of shots logarithmically up to a critical value. Above this value, DTF approaches an asymptotic value. Both DTF for a single shot and the asymptotic value as well as the critical value where this happens, are extrinsic parameters dependent on the configuration (repetition rate, pressure and geometry near or at the surface). Here these measurements indicate that the power of this dependence is an intrinsic parameter independent of the configuration.

36 MATERIALS SCIENCE↗

Characterization of submillisecond response optical addressing phase modulator based on low light scattering polymer network liquid crystal

Optically addressed conventional nematic liquid crystal spatial light modulator has attracted wide research interests. But the slow response speed limited its further application. In this paper, polymer network liquid crystal (PNLC) was proposed to replace the conventional nematic liquid crystal to enhance the response time to the order of submillisecond. The maximum light scattering of the employed PNLC was suppressed to be less than 2% at 1.064 μm by optimizing polymerization conditions and selecting large viscosity liquid crystal as solvent. The occurrence of phase ripple phenomenon due to electron diffusion and drift in photoconductor was found to deteriorate the phase modulation effect of the optical addressed PNLC phase modulator. The wavelength effect and AC voltage frequency effect on the on state dynamic response of phase change was investigated by experimental methods. These effects were interpreted by electron diffusion and drift theory based on the assumption that free electron was inhomogeneously distributed in accordance with the writing beam intensity distribution along the incident direction. The experimental results indicated that the phase ripple could be suppressed by optimizing the wavelength of the writing beam and the driving AC voltage frequency when varying the writing beam intensity to generate phase change in 2π range. The modulation transfer function was also measured.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

High pressure structural and lattice dynamics study of α-In2Se3

Layered α-In2Se3 has been studied using a combined in situ synchrotron angle-dispersive powder x-ray diffraction and Raman spectroscopy study in a diamond anvil cell up to 60+ GPa, at room temperature. Helium, which remains fairly hydrostatic up to the highest pressure in this study, was used as the pressure-transmitting medium. The results from both experimental methods reveal a pressure-induced structural phase transition from α-In2Se3 to a monoclinic β'-In2Se3 structure at ≈1 GPa, in agreement with previous studies. Based on our detailed measurements using both experimental techniques and the F-f formalism, the β'-In2Se3 structure remains stable up to 45 GPa, without a clear indication of a phase transition toward the previously reported β-In2Se3 phase. Above this pressure, In2Se3 adopts a disordered solid-solution-like orthorhombic structure, phase IV. The results are discussed in comparison with the relevant previous studies of α-In2Se3 under pressure.

Feng, Shiyu↗

Development of a New Method to Investigate the Dynamic Friction Behavior of Interfaces Using a Kolsky Tension Bar

In order to understand interfacial interaction of a bi-material during an impact loading event, the dynamic friction coefficient is one of the key parameters that must be characterized and quantified. In this study, a new experimental method to determine the dynamic friction coefficient between two metals was developed by using a Kolsky tension bar and a custom-designed friction fixture. Polyvinylidene fluoride (PVDF) force sensors were used to measure the normal force applied to the friction tribo pairs and the friction force was measured with conventional Kolsky tension bar method. To evaluate the technique, the dynamic friction coefficient between 4340 steel and 7075-T6 aluminum was investigated at an impact speed of approximately 8 m/s. Additionally, the dynamic friction coefficient of the tribo pairs with varied surface roughness was also investigated. The data suggest that higher surface roughness leads to higher friction coefficients at the same speed of 8 m/s.

36 MATERIALS SCIENCE↗

Determination of the relative orientation between 15 N- 1 H dipolar coupling and 1 H chemical shift anisotropy tensors under fast MAS solid-state NMR

Here, in this work, we have proposed a proton-detected three-dimensional (3D) 15 N- 1 H dipolar coupling (DIP)/ 1 H chemical shift anisotropy (CSA)/ 1 H chemical shift (CS) correlation experiment to measure the relative orientation between the 15 N- 1 H dipolar coupling and the 1 H CSA tensors under fast magic angle spinning (MAS) solid-state NMR. In the 3D correlation experiment, the 15 N- 1 H dipolar coupling and 1 H CSA tensors are recoupled using our recently developed windowless C-symmetry-based $C3^{1}_{3}$-ROCSA (recoupling of chemical shift anisotropy) DIPSHIFT and $C3^{1}_{3}$-ROCSA pulse-based methods, respectively. The 2D 15 N- 1 H DIP/ 1 H CSA powder lineshapes extracted using the proposed 3D correlation method are shown to be sensitive to the sign and asymmetry of the 1 H CSA tensor, a feature that allows the determination of the relative orientation between the two correlating tensors with improved accuracy. The experimental method developed in this study is demonstrated on a powdered U- 15 N L-Histidine.HCl·H 2 O sample.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Frictional Contacts Between Individual Woody Biomass Particles under Wet and Dry Conditions

Friction between wood particles can be a critical property when designing processing equipment for creating cellulosic biofuels and similar natural products. Also, as wood processing is likely to occur year-round, understanding the friction between wet as well as dry wood particles can help design and model equipment, such as screw feeders. Here, a tribo-rheometry method was developed using a commercial rheometer that measured the torque required to rotate two contacting millimeter-scale wood chip particles. First, a range of normal forces were used to find the limits of the experimental method. Torque values were measured for seven pairs of wood chip particles at 1 N normal force under both dry and wet conditions, at both ambient conditions and in a humidity-controlled chamber. The torque required to rotate the wet particles was consistently higher than that of the dry particles, although differences were not quite statistically significant when measurements were performed at ambient conditions. Using humidity control resulted in torque values for wet particles of 1900 uNm and 900 uNm for dry particles. Finally, the friction coefficient was calculated as 0.23 for wet particles and 0.11 for dry particles when humidity was controlled. These frictions coefficients agreed with values for wood reported in the literature. Overall, controlling humidity is strongly recommended to quantify the range of friction for particles that uptake water, including granular systems from biomass to food to powders.

biomass↗

On the consistency of scale among experiments, theory, and simulation

As a tool for addressing problems of scale, we consider an evolving approach known as the thermodynamically constrained averaging theory (TCAT), which has broad applicability to hydrology. We consider the case of modeling of two-fluid-phase flow in porous media, and we focus on issues of scale as they relate to various measures of pressure, capillary pressure, and state equations needed to produce solvable models. We apply TCAT to perform physics-based data assimilation to understand how the internal behavior influences the macroscale state of two-fluid porous medium systems. A microfluidic experimental method and a lattice Boltzmann simulation method are used to examine a key deficiency associated with standard approaches. In a hydrologic process such as evaporation, the water content will ultimately be reduced below the irreducible wetting-phase saturation determined from experiments. This is problematic since the derived closure relationships cannot predict the associated capillary pressures for these states. We demonstrate that the irreducible wetting-phase saturation is an artifact of the experimental design, caused by the fact that the boundary pressure difference does not approximate the true capillary pressure. Using averaging methods, we compute the true capillary pressure for fluid configurations at and below the irreducible wetting-phase saturation. Results of our analysis include a state function for the capillary pressure expressed as a function of fluid saturation and interfacial area.

13 HYDRO ENERGY↗

The usefulness of three-dimensional cell culture in induction of cancer stem cells from esophageal squamous cell carcinoma cell lines

Highlights: •Spheroids were created from esophageal carcinoma cells using NanoCulture® Plates. •The proportion of strongly ALDH-positive cells increased in 3-D culture. •Expression of cancer stem cell-related genes was enhanced in 3-D culture. •CA-9 expression was enhanced, suggesting hypoxia had been induced in 3-D culture. •Drug resistance was increased. 3-D culture is useful for inducing cancer stem cells. -- Abstract: In recent years, research on resistance to chemotherapy and radiotherapy in cancer treatment has come under the spotlight, and researchers have also begun investigating the relationship between resistance and cancer stem cells. Cancer stem cells are assumed to be present in esophageal cancer, but experimental methods for identification and culture of these cells have not yet been established. To solve this problem, we created spheroids using a NanoCulture® Plate (NCP) for 3-dimensional (3-D) cell culture, which was designed as a means for experimentally reproducing the 3-D structures found in the body. We investigated the potential for induction of cancer stem cells from esophageal cancer cells. Using flow cytometry we analyzed the expression of surface antigen markers CD44, CD133, CD338 (ABCG2), CD318 (CDCP1), and CD326 (EpCAM), which are known cancer stem cell markers. None of these surface antigen markers showed enhanced expression in 3-D cultured cells. We then analyzed aldehyde dehydrogenase (ALDH) enzymatic activity using the ALDEFLUOR reagent, which can identify immature cells such as stem cells and precursor cells. 3-D-cultured cells were strongly positive for ALDH enzyme activity. We also analyzed the expression of the stem cell-related genes Sox-2, Nanog, Oct3/4, and Lin28 using RT-PCR. Expression of Sox-2, Nanog, and Lin28 was enhanced. Analysis of expression of the hypoxic surface antigen marker carbonic anhydrase-9 (CA-9), which is an indicator of cancer stem cell induction and maintenance, revealed that CA-9 expression was enhanced, suggesting that hypoxia had been induced. Comparison of cancer drug resistance using cisplatin and doxorubicin in 3-D-cultured esophageal cancer cells showed that cancer drug resistance had increased. These results indicate that 3-D culture of esophageal squamous cell carcinoma lines is a useful method for inducing cancer stem cells.

60 APPLIED LIFE SCIENCES↗

A new route to obtain fluorescence X-ray absorption spectra of compounds and to remove the self-absorption induced nonlinearity in the spectra

A new route to obtain fluorescence X-ray absorption spectra of compounds and to remove the self-absorption induced nonlinearity in the spectra is described. The fluorescent intensity If is linearly proportional to the absorption coefficient μ. For studies of surface structures around an element (κ) the fluorescence detection is often the mode of choice. However, the measurement may suffer from a self-absorption (SA) effect which nonlinearly distorts the spectra. The effect is severe when κ is concentrated or the measurements are carried out in certain geometries. Here, the correlations among emission events in compounds are examined following resonance X-ray core-electron excitation within κ. Under conditions leading to SA, If emitted from κ apparently has a conjugated relationship with the fluorescent intensities simultaneously emitted from other elements (ξ). Normalizing the former (κ) by the latter (ξ) will largely remove SA effects and reduce this nonlinear problem to a tractable linear problem. This does result in a moderate reduction of the spectral amplitude due to the so-called secondary emission from ξ excited by the emission from κ. Nonetheless, the resulting spectra will allow one to accurately determine bond distances and disorder and, in some respects, can be superior to spectra obtained via the absorption channel. For μξ < μκ and grazing incidence geometry, the amplitude reduction can be small and simple normalization is sufficient to restore the spectral integrity with remarkable accuracy. This has been instrumental in unravelling the surface and subsurface structures around cations in amorphous Ga–In–O and Zn–Sn–O films which are otherwise inaccessible due to severe SA effects. This method has also been applied to several samples with μξ ≃ μκ to examine its applicability. For these samples, the amplitude reduction is 12 ± 4% versus their standards for the data measured with the classical 45°/45° geometry. This experimental method is easy to implement. Since If from κ and ξ are measured by the same detector system, it is also superior to other methods in removing systematic errors such as detector system nonlinearity, electronic noise, and some beam instabilities, and in removing spectral imperfections due to, for example, SA effects, diffraction effects and sample inhomogeneity. The distortions resulting from the latter can be severe in the spectra measured in transmission mode.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural maturation of myofilaments in engineered 3D cardiac microtissues characterized using small angle x-ray scattering

Abstract Understanding the structural and functional development of human-induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs) is essential to engineering cardiac tissue that enables pharmaceutical testing, modeling diseases, and designing therapies. Here we use a method not commonly applied to biological materials, small angle x-ray scattering, to characterize the structural development of hiPSC-CMs within three-dimensional engineered tissues during their preliminary stages of maturation. An x-ray scattering experimental method enables the reliable characterization of the cardiomyocyte myofilament spacing with maturation time. The myofilament lattice spacing monotonically decreases as the tissue matures from its initial post-seeding state over the span of 10 days. Visualization of the spacing at a grid of positions in the tissue provides an approach to characterizing the maturation and organization of cardiomyocyte myofilaments and has the potential to help elucidate mechanisms of pathophysiology, and disease progression, thereby stimulating new biological hypotheses in stem cell engineering.

36 MATERIALS SCIENCE↗

BaSn 2 : A wide-gap strong topological insulator

BaSn 2 has been shown to form as layers of buckled stanene intercalated by barium ions. However, despite an apparently straightforward synthesis and significant interest in stanene as a topological material, BaSn 2 has been left largely unexplored, and has only recently been recognized as a potential topological insulator. Belonging to neither the lead nor bismuth chalcogenide families, it would represent a unique manifestation of the topological insulating phase. Here in this paper, we present a detailed investigation of BaSn 2 , using both ab initio and experimental methods. First-principles calculations demonstrate that this overlooked material is indeed a strong, wide-gap topological insulator with a bulk band gap of 200 meV. We characterize the surface state dependence on termination chemistry, providing guidance for experimental efforts to measure and manipulate its topological properties. Additionally, through ab initio modeling and synthesis experiments, we explore the stability and accessibility of this phase, revealing a complicated phase diagram that indicates a challenging path to obtaining single crystals.

36 MATERIALS SCIENCE↗

Computationally Directed Discovery of MoBi 2

Incorporating bismuth, the heaviest element stable to radioactive decay, into new materials enables the creation of emergent properties such as permanent magnetism, superconductivity, and nontrivial topology. Understanding the factors that drive Bi reactivity is critical for the realization of these properties. Using pressure as a tunable synthetic vector, we can access unexplored regions of phase space to foster reactivity between elements that do not react under ambient conditions. Furthermore, combining computational and experimental methods for materials discovery at high-pressures provides broader insight into the thermodynamic landscape than can be achieved through experiment alone, informing our understanding of the dominant chemical factors governing structure formation. Herein, we report our combined computational and experimental exploration of the Mo–Bi system, for which no binary intermetallic structures were previously known. Using the ab initio random structure searching (AIRSS) approach, we identified multiple synthetic targets between 0–50 GPa. Highpressure in situ powder X-ray diffraction experiments performed in diamond anvil cells confirmed that Mo–Bi mixtures exhibit rich chemistry upon the application of pressure, including experimental realization of the computationally predicted CuAl 2 -type MoBi 2 structure at 35.8(5) GPa. Electronic structure and phonon dispersion calculations on MoBi 2 revealed a correlation between valence electron count and bonding in high-pressure transition metal–Bi structures as well as identified two dynamically stable ambient pressure polymorphs. Our study demonstrates the power of the combined computational–experimental approach in capturing highpressure reactivity for efficient materials discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An assessment of CFD-based wall heat transfer models in piston engines

The lack of accurate submodels for in-cylinder heat transfer has been identified as a key shortcoming in developing truly predictive, physics-based computational fluid dynamics (CFD) models that can be used to develop combustion systems for advanced high-efficiency, low-emissions engines. Only recently have experimental methods become available that enable accurate near-wall measurements to enhance simulation capability via advancing models. Initial results show crank-angle dependent discrepancies with respect to previously used boundary-layer models of up to 100%. However, available experimental data is quite sparse (only few data points on engine walls) and limited (available measurements are those of heat flux only). Predictive submodels are needed for medium-resolution ("engineering") LES and for unsteady Reynolds-averaged simulations (URANS). Recently, some research groups have performed DNS studies on engine-relevant conditions using simple geometries. These provide very useful data for benchmarking wall heat transfer models under such conditions. Further, a number of new and more sophisticated models have also become available in the literature which account for these engine-like conditions. Some of these have been incorporated while others of a more complex nature, which include solving additional partial differential equations (PDEs) within the thin boundary layer near the wall, are underway. These models will then be tested against the available DNS/experimental data in both SI (spark-ignition) and CI (compression-ignition) engines.

33 ADVANCED PROPULSION SYSTEMS↗

Efficiency Calculation for an In-situ Beta Nuclide Monitoring System Based on a Plastic Scintillator - 18193

A plastic scintillator performance for an in-situ measurement system was analyzed using both simulation and experimental methods. The measurement results of four major pure beta-emitting radionuclides - namely H-3. C-14, P-32 and Sr-90/Y-90 - were compared with those from a Monte Carlo N-particle (MCNP) code simulation. Good agreement between the simulation and experimental results was observed for P-32 and Sr-90/Y-90. However, due to the short range of their beta particles in water, the efficiency for both H-3 and C-14 was rather low, and these radionuclides could not be detected. The optimal thickness for the plastic scintillator was identified, as was its suggested diameter. The effect of water depth on system performance was also considered. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Experimental characterization and modeling of optical tweezer particle handling dynamics [Modeling and Simulation of Optical Tweezer Particle Handling Dynamics]

Here, we report a new framework for a quantitative understanding of optical trapping (OT) particle handling dynamics. We present a novel three-dimensional particle-based model that includes optical, hydrodynamic, and inter-particle forces. This semi-empirical colloid model is based on an open-source simulation code known as LAMMPS (large-scale atomic/molecular massively parallel simulator) and properly recapitulates the full OT force profile beyond the typical linear approximations valid near the trap center. Simulations are carried out with typical system parameters relevant for our experimental holographic optical trapping (HOT) system, including varied particle sizes, trap movement speeds, and beam powers. Furthermore, we present a new experimental method for measuring both the stable and metastable boundaries of the optical force profile to inform or validate the model’s underlying force profile. We show that our framework is a powerful tool for accurately predicting particle behavior in a practical experimental OT setup and can be used to characterize and predict particle handling dynamics within any arbitrary OT force profile.

36 MATERIALS SCIENCE↗