Experimental System Research Articles

Ventilation does not affect close-range transmission of influenza virus in a ferret playpen setup

Sustained community spread of influenza viruses relies on efficient person-to-person transmission. Current experimental transmission systems do not mimic environmental conditions (e.g., air exchange rates, flow patterns), host behaviors, or exposure durations relevant to real-world settings. Therefore, results from these traditional systems may not be representative of influenza virus transmission in humans. To address this pitfall, we developed a close-range transmission setup that implements a play-based scenario and used it to investigate the impact of ventilation rates on transmission. In this setup, four immunologically naive recipient ferrets were exposed to a donor ferret infected with a genetically barcoded 2009 H1N1 virus (H1N1pdm09) for 4 h. The ferrets interacted in a shared space that included toys, similar to a childcare setting. Transmission efficiency was assessed under low and high ventilation, with air exchange rates of ~1.3 h −1 and 23 h −1 , respectively. Transmission efficiencies observed in three independent replicate studies were similar between ventilation conditions. The presence of infectious virus or viral RNA on surfaces and in air throughout the exposure area was also not impacted by the ventilation rate. While high viral genetic diversity in donor ferret nasal washes was maintained during infection, recipient ferret nasal washes displayed low diversity, revealing a narrow transmission bottleneck regardless of ventilation rate. Examining the frequency and duration of ferret physical touches revealed no link between these interactions and a successful transmission event. Our findings indicate that exposures characterized by frequent, close-range interactions and the presence of fomites can overcome the benefits of increased ventilation.

A Novel Method for Measuring Three-Axis Dynamic Centrifugal Acceleration Field: the Matrix Transformation Method

Abstract When a three-axis dynamic centrifuge is used to test the performance of inertial equipment (accelerometer, gyroscope, gyro-accelerometer, etc.), accurate estimating of the acceleration at the sensing position of the tested sensors is a key step. To solve the problem of the lack of relevant suitable methods, first, the principle of rigid body kinematics is used to prove that the acceleration of each point on a rigid body changes linearly with respect to the position. Subsequently, a matrix transformation method for accurately measuring the acceleration field on the three-axis dynamic centrifuge is presented. In this method, the distribution law (expressed by a 3×3 matrix) of the acceleration field is calculated based on the measured acceleration at multiple positions. After that the acceleration estimation value at any point on the centrifuge can be calculated. Finally, the uncertainty of the estimated acceleration value is analysed, and a verification experiment is carried out. The results show that the accuracy of this method is mainly limited by the accuracy of the acceleration measurements. The preliminary verification experiment system shows that the mean deviation of the estimated value error obtained by this method is less than 0.024 g, the standard uncertainty is less than 0.015 g, the left and right endpoints of the 95% probability inclusion interval are less than -0.026 g and 0.036 g, respectively, and the half width of the interval is less than 0.028 g. In all, this paper provides a powerful tool for examining the precision performance of inertial equipment on a three-axis dynamic centrifuge, and can also be used for calibration of this kind of centrifuge.

Investigating 3D microbial community dynamics of the rhizosphere using quantitative phase and fluorescence microscopy

Microbial interactions in the rhizosphere contribute to soil health, making understanding these interactions crucial for sustainable agriculture and ecosystem management. Yet it is difficult to understand what we cannot see; among the limitations in rhizosphere imaging are challenges associated with rapidly and noninvasively imaging microbial cells over field depths relevant to plant roots. Here, we present a bimodal imaging technique called complex-field and fluorescence microscopy using the aperture scanning technique (CFAST) that addresses these limitations. CFAST integrates quantitative phase imaging using synthetic aperture imaging based on Kramers–Kronig relations, along with three-dimensional (3D) fluorescence imaging using an engineered point spread function. We showcase CFAST’s practicality and versatility in two ways. First, by harnessing its depth of field of more than 100 μm, we significantly reduce the number of captures required for 3D imaging of plant roots and bacteria in the rhizoplane. This minimizes potential photobleaching and phototoxicity issues. Second, by leveraging CFAST’s phase sensitivity and fluorescence specificity, we track microbial growth, competition, and gene expression at early stages of colony biofilm development. Specifically, we resolve bacterial growth dynamics of mixed populations without the need for genetically labeling environmental isolates. Moreover, we find that gene expression related to phosphorus sensing and antibiotic production varies spatiotemporally within microbial populations that are surface attached and appears distinct from their expression in planktonic cultures. Together, CFAST’s attributes overcome commercial imaging platform limitations and enable insights to be gained into microbial behavioral dynamics in experimental systems of relevance to the rhizosphere.

The characteristics of CTCF binding sequences contribute to enhancer blocking activity.

While the elements encoding enhancers and promoters have been relatively well studied, the full spectrum of insulator elements which bind the CCCTC binding factor (CTCF), is relatively poorly characterized. This is partly due to the genomic context of CTCF sites greatly influencing their roles and activity. Here we have developed an experimental system to determine the ability of minimal, consistently sized, individual CTCF elements to interpose between enhancers and promoters and thereby reduce gene expression during differentiation. Importantly, each element is tested in the identical location thereby minimising the effect of genomic context. We found no correlation between the ability of CTCF elements to block enhancer-promoter activity with the degree of evolutionary conservation; their resemblance to the consensus core sequences; or the number of CTCF core motifs harboured in the element. Nevertheless, we have shown that the strongest enhancer-promoter blockers include a previously described bound element lying upstream of the CTCF core motif. In addition, we found other uncharacterised DNaseI footprints located close to the core motif that may affect function. We have developed an assay of CTCF sequences which will enable researchers to sub-classify individual CTCF elements in a uniform and unbiased way.

A Hierarchical Model for Complex Adaptive System: From Adaptive Agent to AI Society

As complex adaptive system involves human and social factors (e.g., changing demands, competition and collaboration among agents), accurately modeling the complex features of adaptive agents and AI society is crucial for the effective analysis and governance of complex adaptive systems. However, existing modeling methods struggle to accurately represent these complex features, there is a gap between existing technologies and complex features modeling. In this context, this paper proposes a hierarchical model based on the computational experiments method, which consists of four layers (i.e., L1, L2, L3 and L4) modeling the autonomous, evolutionary, interactive, and emergent features respectively from adaptive agent to AI society. Additionally, taking intelligent transportation system as an example, a computational experiments system is constructed to demonstrate the effectiveness of the proposed model. This model builds a bridge between complex feature modeling and various technologies, thereby offering theoretical support for further research in complex adaptive systems.

Identification of specific IgG class antibodies to certain flaviviruses in the population of the Republic of Guinea

One of the most common arboviruses in the world are representatives of the genus Orthoflavivirus (family Flaviviridae). On the territory of the Republic of Guinea, the circulation of such representatives of this family as the yellow fever virus (YFV), West Nile virus (WNV) and dengue virus (DENV) has been confirmed. The aim of the study was to determine the level of specific IgG class antibodies to YFV, DENV and WNV in residents of various landscape– geographical zones of the Republic of Guinea by the ELISA method. Materials and methods. For the study, a panel of 1559 blood serums from practically healthy people was compiled, which were collected in all landscape and geographical zones of the Republic of Guinea. The detection of specific IgG class antibodies to DENV and WNV was carried out with commercial diagnostic drugs, and for YFV — with an experimental ELISA test system based on an analogue of the third domain of protein E obtained at the State Research Center for Virology and Biotechnology “Vector” of Rospotrebnadzor. Results. When testing blood sera in 28.5% (95% CI: 26.3–30.7) of cases, IgG antibodies to YFV, to DENV — in 11.8%, (95% CI: 10.3–13.5) and to WNV — in 27.0% (95% CI: 24.8–29.3) were detected. Antibodies to three viruses simultaneously (YFV, DENV and WNV) were detected in 30 cases, to YFV and DENV — 14, YFV and WNV — 44, DENV and WNV — 56. Conclusion. The detection of antibodies to WNV and DENV confirms the fact of the continued circulation of these pathogens in the territory of the Republic of Guinea, which poses a health risk to the local population. A detailed study of the molecular genetic and antigenic properties of flaviviruses circulating in this area will allow the development of more specific diagnostic tools.

Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation

Hybridization has been recognized to play important roles in evolution, however studies of the genetic consequence are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the genus Xiphophorus are proposed to have evolved with multiple ancient and ongoing hybridization events. They have served as an informative research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genomic resource including annotations for all described 26 Xiphophorus species and three undescribed taxa and resolve all uncertain phylogenetic relationships. We investigate the molecular evolution of genes related to cancers such as melanoma and for the genetic control of puberty timing, focusing on genes that are predicted to be involved in pre-and postzygotic isolation and thus affect hybridization. We discovered dramatic size-variation of some gene families. These persisted despite reticulate evolution, rapid speciation and short divergence time. Finally, we clarify the hybridization history in the entire genus settling disputed hybridization history of two Southern swordtails. Our comparative genomic analyses revealed hybridization ancestries that are manifested in the mosaic fused genomes and show that hybridization often preceded speciation.

Experimental analysis of bow flare slamming and whipping responses in a ship at different sailing speeds

This study conducted an experimental investigation using a segmented model to determine bow flare slamming loads and whipping responses of a ship in regular waves. The model simulated the distribution of the vertical and horizontal bending stiffnesses of the hull. A continuous wavelet transform was employed to capture temporal variations in the harmonic components. The influences of sailing speeds on the temporal and spatial variations in the slamming pressures in the bow flare were analyzed. Subsequently, the time-frequency characteristics and asymmetry of the global responses under different test conditions are discussed. The random errors in the experimental system were investigated through repeated testing. The findings revealed that a higher sailing speed could significantly influence the magnitude and distribution of slamming pressures on the bow flare, while playing an important role in inducing asymmetric slamming loads under oblique waves. The slamming-induced whipping responses under regular waves caused considerable periodic changes in the strengths of the harmonic components around the wet natural frequency of the model. At high sailing speeds, the whipping responses significantly increased the asymmetry of the vertical bending moment (VBM) at midship.

Experimental study on the evolution of shock waves in the near field of cylindrical charge explosion

Cylindrical charges are frequently used in blasting engineering and military operations, often detonated very close to target structures. Obtaining the characteristics of the flow field distribution in the near field of explosions through experimentation consistently poses challenges. These challenges constrain efforts to elucidate the evolutionary processes of explosive shock waves. Employing the explosive schlieren experimental system yields a clearer depiction of the near field flow than previous studies, thereby facilitating a more comprehensive understanding of the characteristics of cylindrical charge explosions. The overall flow field adopts a droplet shape, with the interface of the detonation products and the shock wave front forming continuous concave shapes. The detonation process in cylindrical charges can be conceptualized as the detonation wave propelling the detonation products at supersonic speeds. The formation of explosive shock waves can be elucidated through the dynamics of oblique shock waves generated by two-dimensional curved surfaces. This mechanism influences the relationship between the deflection angles of detonation products and the shock wave angles resulting from different detonation velocities. Theoretical calculations of shock wave positions align with experimental images. Significant variations in shock wave velocities at different positions within cylindrical charges are observed, identifying patterns of these variations. The research findings clarify the formation mechanisms of explosive shock waves in cylindrical charges and deepen the understanding of shock wave evolution in the near field.

Experimental and numerical investigation on detection of BVID in CFRP composite plates using vibro-acoustic modulation

ABSTRACT Carbon fibre reinforced plastic (CFRP) composite has gained popularity due to the advantages such as its high strength-to-weight ratio and high corrosion resistance, but susceptibility to barely visible impact damage limits their use in engineering. This study experimentally and numerically investigates the detection of BVID in CFRP composite plates using Vibro-acoustic modulation (VAM) technique. An experimental system of VAM was constructed for measuring sidebands induced by the nonlinear effects of BVID. An integrated finite element (FE) model is developed to further explore the nonlinear interaction between the BVID, low-frequency pump, and high-frequency probe waves. To address this issue of the mesh size and computational time step mismatch caused by the large difference in frequency between the pump and probe waves, a regionally refined mesh was employed at the BVID region. Furthermore, the effects of BVID’s size and depth on the modulation were discussed. Through the Hilbert-Huang Transform (HHT), the amplitude modulation (AM) and frequency modulation (FM) indexes were extracted from the VAM responses to quantitatively characterise the impact damages. The results demonstrate that the MIA index increases steadily with the exciting voltage and damage degree, making it a suitable indicator to accurately assess the impact damage in CFRP composites.

Where in the tissues of Danio rerio is more H2O2 produced during acute hypoxia?

The lack of oxygen (O2) causes changes in the cell functioning. Modeling hypoxic conditions in vitro is challenging given that different cell types exhibit different sensitivities to tissue O2 levels. We present an effective in vivo platform for assessing various tissue and organ parameters in Danio rerio larvae under acute hypoxic conditions. Our system allows simultaneous positioning of multiple individuals within a chamber where O2 level in the water can be precisely and promptly regulated, all while conducting microscopy. We applied this approach in combination with a genetically encoded pH-biosensor SypHer3s and a highly H2O2-sensitive Hyper7 biosensor. Hypoxia causes H2O2 production in areas of brain, heart and skeletal muscles, exclusively in the mitochondrial matrix; it is noteworthy that H2O2 does not penetrate into the cytosol and is neutralized in the matrix upon reoxygenation. Hypoxia causes pronounced tissue acidosis, expressed by a decrease in pH by 0.4-0.6 units everywhere. Using imaging photoplethysmography, we measured in D.rerio fry real-time heart rate decrease under conditions of hypoxia and subsequent reoxygenation. Our observations in this experimental system lead to the hypothesis that mitochondria are the only source of H2O2 in cells of D.rerio under hypoxia.

New Physically-Based Mathematical Model and Experiments for a Recently Invented Solar Pot

The studied solar pot is a recent invention, which is made for environmentally friendly cooking or heating (by utilizing solar energy) of foods and liquids. Its structure is similar to a double pipe heat exchanger, it has an outer mantle and an inner cooking tank. The goals of the paper are proposing a new physically-based mathematical model describing the solar pot and carrying out computer experiments with it, assembling an experimental system of the pot connected with a solar collector and performing measurements on it. Based on the results, the solar pot can successfully be used for cooking or sterilizing foods or liquids during the studied time period, in Hungary. In particular, based on measured data, the temperature level needed for heat treatment (75 °C) can be maintained in the cooking tank for several hours (~5 h, on the average) in a typical day in May.

Design of subsurface defect detection system based on two channels

With the continuous improvement of quality requirements for optical components, the detection of subsurface defects in optical components has become a key technology. However, there is a problem with existing detection techniques, which is that they cannot simultaneously and independently detect subsurface defects at the micrometer and nanometer levels. This article analyzes the scattering field model of subsurface scratches and conducts simulation experiments on the relationship between scattering light intensity and system aperture. Based on the simulation results, a dual channel experimental system with adjustable spot size was designed to achieve automated measurement of subsurface defects. The narrow channel was used to detect micrometer-level subsurface defects and the wide channel was used to detect nanometer-level subsurface defects. The experimental results verified the correctness of the simulation experiment. In order to improve the sensitivity of the system, we designed an aperture based on the scattering field distribution of surface and subsurface defects, which is used to block the interference signal on the sample surface and improve the signal-to-noise ratio of the subsurface defect signal. The experimental results show that this aperture plays an important role, and the detection sensitivity of the system reaches 100 nm. We used four algorithms for data processing and found that the IQR algorithm is most suitable for this system. Finally, the detection results were compared under different spot sizes, and it was found that small spot sizes have better detection effects on nanoscale subsurface defects. In practice, the spot size can be dynamically adjusted according to the detection needs to achieve the optimal configuration of detection speed and sensitivity.

Dynamic response characteristics of microchannel evaporator in a mechanically pumped two-phase loop under hypergravity environment

The unique hypergravity environment and severe heat-dissipation requirements of modern fighter aircrafts pose serious challenges to the potential utilization of mechanically pumped two-phase loops (MPTLs), which are an efficient cooling technology. The microchannel evaporator is a key component of the MPTL system, and understanding its startup and operation characteristics is of great significance for design and optimization. In this context, an experimental MPTL system is built and fixed on a rotating platform, which is designed to generate hypergravity ranging from 0 g0 to 15.0 g0 (g0 = 9.8 m·s−2). The dynamic-response characteristics of the temperature, pressure, and flow rates during the startup and operation of the microchannel evaporator under various hypergravity conditions are investigated. The results indicate that different startup modes, namely gradual startup under low hypergravity and overshoot startup under high hypergravity, are achieved on the microchannel evaporator, even if the flow rate and heat flux are not changed, which is completely different from that under normal gravity. These two startup modes can be quantitatively recognized by two dimensionless numbers: the boiling number (Bo) and Froude number (Fr). A larger Bo or 1/Fr, which corresponds to a larger heat flux or hypergravity; both conditions contribute to the startup mode of the microchannel evaporator shifting from gradual to overshoot startup. During the operation of a microchannel evaporator, the competition between the elevated saturation temperature of the fluid and the induced Coriolis and centrifugal forces caused by hypergravity determines the wall-temperature variation of the evaporator. The dynamic wall temperature decreases under hypergravity below 2.5 g0, is stable with small fluctuations under hypergravity from 4.7 g0 to 7.5 g0, and increases for hypergravity larger than 11.0 g0.

Evaluation of Seasonal Reservoir Water Treatment Processes in Southwest Florida: Protection of the Caloosahatchee River Estuary

In southwest Florida, the Caloosahatchee River flows from Lake Okeechobee into a biologically productive tidal estuarine system. A combination of excess water during the wet season, insufficient fresh water in the dry season, and poor quality of the river water are damaging the estuarine ecosystem. To better control the quality and quantity of the water entering the estuary, reservoirs are being constructed to store excess, poor quality water during the wet season and return it to the river for discharge into the estuary at an appropriate time. This stored water is enriched in nutrients and organic carbon. Because of the subtropical nature of the climate in southwest Florida and potential increases in temperature in the future, the return flow of water from the reservoirs must be treated before it can be returned to the river. Hence, an experimental water treatment system was developed and operated to compare biological treatment processes consisting of solely wetland plants versus adding some engineered processes, including slow sand filtration and a combination of slow sand filtration and ultraviolet (UV) treatment. These three treatment trains were operated and monitored through a seasonal cycle in 2021–2022. All three treatment methods significantly reduced the concentrations of nutrients and total organic carbon. While the enhanced engineered wetlands’ treatment trains did slightly outperform the wetland train, a comparison of the three process trains showed no statistically significant difference. It was concluded that upscaling of the slow sand filtration and UV process could improve the treatment efficiency, but this change would have to be evaluated within a framework of long-term economic benefits. It was also concluded that the Caloosahatchee River water quality is quite enriched in nutrients so that reservoir storage would increase the organic carbon concentrations, making it imperative that it be treated before being returned to the river. It was also discovered that the green alga Cladophora sp. grew rapidly in the biological treatment tubs and will present a significant challenge for the treatment of the reservoir discharge water using the currently proposed alum treatment.

Investigation of typical behavioral characteristics of the dynamic separation of bauxite using vibration table tests

With the Bulk Jupiter accident, the dynamic separation behavior of solid bulk cargoes in sea transportation, which is different from the usual liquefaction of cargoes, has gradually come to people’s attention and is an almost empty field that urgently needs to be researched. In this work, we first conducted vibration table tests for bauxite, replaced bauxite with transparent soil with the same particle size distribution and moisture content, and combined image processing and analysis techniques to complete the detailed visualization of the dynamic separation process. Through the above research, this article reveals the essential characteristics of dynamic separation, including the changing rules of layer-wise water content, pore water pressure, particle motion, and pore water migration. It is concluded that the most apparent feature of the dynamic separation process is the generation of a free liquid surface containing fine particles in the upper layer. The article concludes with a systematic study of the dynamic separation of typical mineral soil. The novel experimental system developed in this study contributes to elucidating the mechanism of dynamic separation of minerals and soil from a precise perspective.

Twisted hyperbolic-sine-correlated beams

In this study, a novel class of spatially non-uniformly correlated beams called twisted hyperbolic-sine-correlated (THSC) beams is introduced. The coherence structure of such beam sources is characterized by a hyperbolic sine function with a high-order twist phase embedded in its argument. The propagation properties of the THSC beams are numerically examined in detail. Our results reveal that the order numbers and twist factor of the twist phase has a significant effect on the spectral density and orbital angular momentum (OAM) flux density upon propagation, and they can be used to control the formation of certain specific far-field intensity profiles such as doughnut shape, rectangular window shape, and dumbbell-like shape, as well as the OAM flux distributions such as windmill-like shape. In addition, the THSC beams under certain order numbers may possess peculiar propagation characteristics such as diffraction-effect suppression, lateral shift of intensity maxima and beam spot rotation. Further, we have established a flexible yet compact experimental system to synthesize such kind of beam sources. The evolution properties of the intensity distribution are investigated and analyzed in the experiment.

Stable isotope-resolved metabolomics analyses of metabolic phenotypes reveal variable glutamine metabolism in different patient-derived models of non-small cell lung cancer from a single patient.

Stable isotope tracers have been increasingly used in preclinical cancer model systems, including cell culture and mouse xenografts, to probe the altered metabolism of a variety of cancers, such as accelerated glycolysis and glutaminolysis and generation of oncometabolites. Comparatively little has been reported on the fidelity of the different preclinical model systems in recapitulating the aberrant metabolism of tumors. We have been developing several different experimental model systems for systems biochemistry analyses of non-small cell lung cancer (NSCLC1) using patient-derived tissues to evaluate appropriate models for metabolic and phenotypic analyses. To address the issue of fidelity, we have carried out a detailed Stable Isotope-Resolved Metabolomics study of freshly resected tissue slices, mouse patient derived xenografts (PDXs), and cells derived from a single patient using both 13C6-glucose and 13C5,15N2-glutamine tracers. Although we found similar glucose metabolism in the three models, glutamine utilization was markedly higher in the isolated cell culture and in cell culture-derived xenografts compared with the primary cancer tissue or direct tissue xenografts (PDX). This suggests that caution is needed in interpreting cancer biochemistry using patient-derived cancer cells in vitro or in xenografts, even at very early passage, and that direct analysis of patient derived tissue slices provides the optimal model for ex vivo metabolomics. Further research is needed to determine the generality of these observations.

An enhancement filtering method based on CEEMDAN-EP-WTD for TDLAS gas sensing

In tunable diode laser absorption spectroscopy (TDLAS) gas detection, the accuracy of the detection system is reduced due to the impact of nonlinear noise on the second harmonic. In this paper, a noise reduction method CEEMDAN-EP-WTD was proposed. Combining wavelet threshold method and complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) via evaluation parameter (EP) and sample entropy (SE). The CEEMDAN-EP-WTD can evaluate the noise level of the (intrinsic mode function) IMF component. It calculates the unknown noise standard deviation of the IMF component in the actual signal, which is related to the wavelet threshold. Based on simulation and experimental analysis, the signal-to-noise ratio of the harmonic signal is improved from 4.41 to 28.8596. The minimum detection limit of the experimental system is 4.72 ppm and the detection accuracy is 4.4 %. The results confirm that the algorithm successfully suppresses system noise and enhances the performance of the detection system.

Dynamically generated decoherence-free subspaces and subsystems on superconducting qubits.

Decoherence-free subspaces and subsystems (DFS) preserve quantum information by encoding it into symmetry-protected states unaffected by decoherence. An inherent DFS of a given experimental system may not exist; however, through the use of dynamical decoupling (DD), one can induce symmetries that support DFSs. Here, we provide the first experimental demonstration of DD-generated decoherence-free subsystem logical qubits. Utilizing IBM Quantum superconducting processors, we investigate two and three-qubit DFS codes comprising up to six and seven noninteracting logical qubits, respectively. Through a combination of DD and error detection, we show that DFS logical qubits can achieve up to a 23\% improvement in state preservation fidelity over physical qubits subject to DD alone. This constitutes a beyond-breakeven fidelity improvement for DFS-encoded qubits. Our results showcase the potential utility of DFS codes as a pathway toward enhanced computational accuracy via logical encoding on quantum processors.