Surrogate Systems Research Articles

648: Consequences of couch sag and couch movement for optical surrogate systems in respiratory guided CT

648: Consequences of couch sag and couch movement for optical surrogate systems in respiratory guided CT

Chaotic attractor reconstruction using small reservoirs—the influence of topology

Abstract Forecasting timeseries based upon measured data is needed in a wide range of applications and has been the subject of extensive research. A particularly challenging task is the forecasting of timeseries generated by chaotic dynamics. In recent years reservoir computing has been shown to be an effective method of forecasting chaotic dynamics and reconstructing chaotic attractors from data. In this work strides are made toward smaller and lower complexity reservoirs with the goal of improved hardware implementability and more reliable production of adequate surrogate models. We show that a reservoir of uncoupled nodes more reliably produces long term timeseries predictions than more complex reservoir topologies. We then link the improved attractor reconstruction of the uncoupled reservoir with smaller spectral radii of the resulting surrogate systems. These results indicate that, the node degree plays an important role in determining whether the desired dynamics will be stable in the autonomous surrogate system which is attained via closed-loop operation of the trained reservoir. In terms of hardware implementability, uncoupled nodes would allow for greater freedom in the hardware architecture because no complex coupling setups are needed and because, for uncoupled nodes, the system response is equivalent for space and time multiplexing.

Exploring Potential Surrogate Systems for Studying the Early Steps of the Sporisorium scitamineum Pathogenesis.

Despite its global importance as a primary source of table sugar and bioethanol, sugarcane faces a significant threat to its production due to diseases. One of these diseases, sugarcane smut, involves the emergence of a whip-like structure from the host apical shoot. The slow onset of this pathogenesis is the most substantial challenge for researchers to investigate the molecular events leading to resistance or susceptibility. In this study, we explored the early interaction between the smut fungus Sporisorium scitamineum and foliar tissues of the model plants Arabidopsis thaliana and Nicotiana benthamiana. Upon inoculation with the fungus, A. thaliana showed a compatible reaction, producing lesions during fungus colonization, whereas N. benthamiana showed signs of nonhost resistance. In addition, we propose a sugarcane detached leaf assay using plants cultivated in vitro to reveal sugarcane smut response outcomes. We used two sugarcane genotypes with known contrasting reactions to smut in the field. Although there is no evidence of sugarcane smut fungus infecting host leaves naturally, the sugarcane detached leaf assay enabled a rapid assessment of disease outcomes. Different symptoms in the detached leaves after inoculation distinguished smut-susceptible and smut-resistant sugarcane genotypes. Microscopic observations and gene expression analysis of S. scitamineum candidate effectors confirmed the fungal growth and its restriction on the compatible and incompatible interactions, respectively. These findings offer new prospects into the disease phenotyping of S. scitamineum, which could greatly expedite the comprehension of the initial stages of the pathogenesis and predict smut resistance in sugarcane genotypes.

Boosting genome editing in plants with single transcript unit surrogate reporter systems

CRISPR–Cas-based genome editing holds immense promise for advancing plant genomics and crop enhancement. However, the challenge of low editing activity complicates the identification of editing events. In this study, we introduce multiple single transcript unit surrogate reporter (STU-SR) systems to enhance the selection of genome-edited plants. These systems use the same single guide RNAs designed for endogenous genes to edit reporter genes, establishing a direct link between reporter gene editing activity and that of endogenous genes. Various strategies are used to restore functional reporter genes after genome editing, including efficient single-strand annealing (SSA) for homologous recombination in STU-SR–SSA systems. STU-SR–base editor systems leverage base editing to reinstate the start codon, enriching C-to-T and A-to-G base editing events. Our results showcase the effectiveness of these STU-SR systems in enhancing genome editing events in the monocot rice, encompassing Cas9 nuclease-based targeted mutagenesis, cytosine base editing, and adenine base editing. The systems exhibit compatibility with Cas9 variants, such as the PAM-less SpRY, and are shown to boost genome editing in Brassica oleracea, a dicot vegetable crop. In summary, we have developed highly efficient and versatile STU-SR systems for enrichment of genome-edited plants.

Early interferon lambda production is induced by double-stranded RNA in iPS-derived hepatocyte-like cells.

Hepatotropic viruses are amongst the most ubiquitous pathogens worldwide, causing significant morbidity and mortality. As hepatocytes are among the primary targets of these viruses, their ability to mount early effective innate defence responses is of major research interest. Interferon lambda (IFNL) is produced early in response to viral stimulation in other cell types, but hepatocyte production of this interferon is little investigated. Due to the difficulty and significant costs in obtaining and culturing human primary hepatocytes, surrogate systems are widely sought. Here we used induced pluripotent stem (iPS)-derived hepatocyte-like cells (HLCs) to investigate hepatic IFNL expression in response to viral-like ligands. We demonstrate that hepatocytes rely on cytoplasmic pattern recognition receptors (PRRs) such as Protein Kinase RNA-dependent (PKR) and retinoic acid-inducible gene-I (RIG-I)-like receptors (RLR) for the detection of double stranded RNA. Stimulation of HLCs by viral-like RNA ligands activating cytosolic RNA sensors resulted in thousand fold increase of type III interferon gene expression. These results are in contrast with type I IFN expression, which was induced to a lower extent. Concomitant induction of interferon stimulated genes, such as interferon-stimulated gene 15 (ISG15) and CXCL10, indicated the ability of HLCs to activate interferon-dependent activity. These results demonstrate that HLCs mount an innate antiviral response upon stimulation with viral-like RNA characterized by the induction of type III IFN.

POD-Galerkin FSI Analysis for Flapping Motion.

FSI simulations of flapping motions have been widely investigated to develop a flapping-wing micro air vehicle. Because an intensive parametric study is important for the product design, a computationally efficient model is required. The purpose of the present study was to develop a reduced-order model of flapping motion. Among the various methods available to solve FSI problems, we employed the Dirichlet-Neumann partitioned iterative method, in which three sub-systems (fluid mesh update, fluid analysis, and structural analysis) are executed. In the proposed analysis system, first, snapshot data of structural displacement, fluid velocity, fluid pressure, and displacement for the fluid mesh update were collected from a high-fidelity FSI analysis. Then, the snapshot data were used to create low-dimensional surrogate systems of the above three sub-systems based on the POD under Galerkin projection (i.e., the POD-Galerkin method). In numerical examples, we considered a two-dimensional FSI problem of simplified flapping motion. The problem was described via two parameters: frequency and amplitude of flapping motion. We demonstrated the effectiveness of the presented reduced-order model in significantly reducing computational time while preserving the desired accuracy.

Optimized CRISPR/Cas9 system for gene knockout in chicken DF1 cells

The editing efficiency primarily hinders the utility of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology in poultry. For a better understanding of the factors that influence the efficiency of gene knockout mediated by CRISPR/Cas9 in chicken DF1 cells, the single or dual single guide RNA (sgRNA) targeted exon regions of genes (taking anti-Müllerian hormone, TGF-beta receptor type-2 and Peroxisome proliferator-activated receptor gamma as examples) were designed. The sgRNA-CRISPR/Cas9 vectors with corresponding reporter vectors were transfected into DF1 cells. T7 endonuclease 1 (T7E1) and amplicon sequencing assay were compared for evaluating genome editing efficiency and the indel profiles were analyzed based on the data of amplicon sequencing. Meanwhile, to evaluate the precision of Cas9 cleavage, we also analyzed the homology of small insertion with the nucleotides of upstream and downstream of cleave sties. The surrogate reporter systems showed strong enrichment function, and the indel percentages were increased after puromycin selection. The indel ratios of T7E1 assay were lower than amplicon sequencing assay, which indicated T7E1 isn't fit to be used as the sole evaluation criterion for the targeting efficiency of CRISPR/Cas9. Based on the amplicon sequencing analysis, the editing efficiency showed noticeable differences among cells treated with different sgRNAs. However, the variety of indel efficiencies was not related to the GC content of sgRNA or chromosome types of targeted genes. The results showed that the dual sgRNA might not raise the indel ratios compared with individual sgRNA, but they could increase the ratios of the fragment deletions. The present study suggested that the surrogate reporter was an effective method to promote the editing efficiencies of CRISPR/Cas9 in chicken cells. The dual sgRNA could increase the fragment deletions, and the sensitivity of amplicon sequencing to detect cleavage was higher than the T7 endonuclease 1 assay. These results are essential to improve the application of CRISPR/Cas9 technology in chicken cells.

The long-run effects of health aid in low-income countries.

Whether health aid has a positive, negative, or no effect on the health status of recipient countries is controversial. The current paper examines the long-run effect of health aid on health status in low-income countries. The long-run health function was estimated using infant mortality as a proxy for health status and panel data constructed from 34 low-income countries from 2000 to 2017. For the estimation, fixed effect, random effect, and Hausman-Taylor estimators were employed. The estimation results indicate that health aid has a beneficial and statistically significant long-run effect on the health status of low-income countries. Doubling health aid saves the lives of 44 infants per 1000 live births in the long run. This study shows that health aid could be one of the best interim tools with which the health status of low-income groups could get improved and helps meet the target of universal health coverage. Despite the favorable effect of health aid observed in this study, recipient countries need to find ways of promoting surrogate domestic health financing systems, as external assistance cannot be an everlasting means of improving population health.

A literature review of bench top and pilot lead corrosion assessment studies.

Bench top and pilot lead corrosion studies are gaining more interest, considering revisions and upcoming improvements to the Lead and Copper Rule. This literature review identified studies ranging from simpler month(s)-long bench top dump-and-fill stagnant water tests (coupon tests/standing pipe tests) to more complicated year(s)-long intermittent flow pilot studies (recirculating pipe loops/once through pipe rigs). With increasing complexity in design and operation, studies more closely approximated real plumbing conditions (e.g., by incorporating harvested lead pipes and intermittent flow regimes) at increased cost, footprint, and duration. Comparison of bench top and pilot designs (in terms of lead test piece age/dimensions/configuration/replicates, study duration, sample collection, and other factors) can assist drinking water utilities, consultants, academics, and others to select a design that matches their needs and constraints. No matter the choice, surrogate systems cannot replace actual system water testing and are best complemented by other corrosion assessment tools.

A review of the oxygen vacancy ordering in surrogate structures simulating Pu-based nuclear ceramics

Advanced nuclear power systems and nuclear fuel cycles will require nuclear fuels capable of higher burnup and with higher transuranic concentrations than those previously developed for current nuclear power plants. Expensive qualification tests are required to validate the thermal and mechanical performance of fuels in normal and accident-scenario operations. Research of surrogate systems with specific properties and characteristics of advanced nuclear fuels can be an effective way to frame the problem, reduce costs, and support the technical development of future research. From this perspective, lanthanide counterparts like mixed oxides of Ce and Nd can provide replica systems for many technological properties of the actual fuels. These ceramic systems can lead to a better understanding of the fundamental irradiation processes responsible for the evolution of their microstructures, the interplay with charge and defect localisation, and the evolution of their mechanical properties. In non-stoichiometric MO2−x binary systems (M = Ce, Pr, and Tb), there is evidence of systematic ordering of vacancies resulting in a deviation from the ideal fluorite structure and the formation of several intermediate fluorite-related phases. Substitution of the 4+ cations with 3+ cations in these systems drives the formation of oxygen vacancies as a charge compensation mechanism. By analogy with MO2−x systems, a variety of similar intermediate phases would also be expected to form in the MO2:Ln2O3 (Ln = La, Nd, Gd … etc). However, in order to achieve chemical homogeneity and charge ordering, prolonged annealing just above the charge ordering transition temperature is required, covering a time-scale determined by the chemical diffusion coefficient. Achieving these conditions with powder metallurgy techniques, commonly employed in literature, is practically impossible. This paper reviews the transport properties and structural features found in these surrogate systems which may be helpful in addressing challenges facing advanced nuclear fuels. We present results of a recent diffraction experiment investigating the structure of neodymium doped ceria synthesised using soft chemical methods. The sample shows a deviation from previous literature as the diffraction data is best described by a monoclinic Ln6O11-type structure (SG P21/c), often referred to as “β phase” in PrO2−x.

Caveats of Using Bacterial Type Three Secretion Assays for Validating Fungal Avirulence Effectors in Wheat.

Functional characterization of effector proteins of fungal obligate biotrophic pathogens, especially confirmation of avirulence (Avr) properties, has been notoriously difficult, due to the experimental intractability of many of these organisms. Previous studies in wheat have shown promising data suggesting the type III secretion system (T3SS) of bacteria may be a suitable surrogate for delivery and detection of Avr properties of fungal effectors. However, these delivery systems were tested in the absence of confirmed Avr effectors. Here, we tested two previously described T3SS-mediated delivery systems for their suitability when delivering two confirmed Avr effectors from two fungal pathogens of wheat, Puccinia graminis f. sp. tritici and Magnaporthe oryzae pathotype tritici. We showed that both effectors (AvrSr50 and AvrRmg8) were unable to elicit a hypersensitive response on wheat seedlings with the corresponding resistance gene when expressed by the Pseudomonas fluorescens "Effector to Host Analyser" (EtHAn) system. Furthermore, we found the utility of Burkholderia glumae for screening Avr phenotypes is severely limited, as the wild-type strain elicits nonhost cell death in multiple wheat accessions. These results provide valuable insight into the suitability of these systems for screening fungal effectors for Avr properties that may help guide further development of surrogate bacterial delivery systems in wheat. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Spectroscopic characterization of rare events in colloidal particle stochastic thermodynamics.

Given the remarkable developments in synthetic control over chemical and physical properties of colloidal particles, it is interesting to see how stochastic thermodynamics studies may be performed with new, surrogate, or hybrid model systems. In the present work, we apply stochastic dynamics and nonlinear optical light-matter interaction simulations to study nonequilibrium trajectories of individual Yb (III):Er (III) colloidal particles driven by two-dimensional dynamic optical traps. In addition, we characterize the role of fluctuations at the single-particle level by analyzing position trajectories and time-dependent upconversion emission intensities. By integrating these two complementary perspectives, we show how the methods developed here can be used to characterize rare events.

Surrogate Models for the Prediction of Damping Ratios in Coupled Acoustoelastic Rotor-Cavity Systems

Abstract Centrifugal compressors are versatile machines that many industries employ for a wide range of different applications, including the production of highly compressed gases. During the last decades, comprehensive research was conducted on the impact of high-pressure operating conditions on the vibrational behavior of radial compressors. In various studies, acoustic modes building up in the side cavities were found to be a potential source of high cycle fatigue. Nowadays, it is well-known that an increase in gas pressure levels leads to a more pronounced fluid–structure interaction between the side cavities and the impeller resulting in a frequency shift of the acoustic and structural modes. In a recently published paper, the authors presented a generalized model which can predict this behavior. As it is not always possible to avoid operating close to or accelerating through a resonance, it is crucial to know the damping present within the system. Currently, only few publications concentrate on the damping of radial impellers. Therefore, the authors present measurement data acquired from a test rig at the University of Duisburg-Essen, which reveals the damping behavior of a disk under varying operating conditions. Two surrogate models are proposed to predict the identified damping behavior. The first one is based solely on a one-dimensional piston model and the second approach uses an enhanced version of the generalized method. Finally, the measurement data are used to validate both surrogate systems.

Multiplex precision gene editing by a surrogate prime editor in rice

Multiplex precision gene editing by a surrogate prime editor in rice

Bereaved Caregiver Perspectives on Implantation and End of Life in Pediatric Ventricular Assist Device Patients

<h3>Purpose</h3> Ventricular assist devices (VADs) are increasingly used in pediatric patients with heart failure as a bridge to heart transplant, though approximately 3-12% will die on support. The patient and family perspectives of pediatric VAD implantation, deactivation, and end-of-life experience are not well described. <h3>Methods</h3> Semi-structured interviews were performed with caregivers of pediatric VAD patients who died from 2014-2020. Analysis was performed using a grounded theory framework: interviews were coded by two independent readers using Dedoose software, and themes derived from codes were discussed in iterative meetings using established qualitative analysis methods. Caregivers were screened for adverse psychological reactions by a psychologist during interviews and at one-week follow up. <h3>Results</h3> Six of 18 eligible families participated in interviews at a median 2.4 years after their child died. Four major themes emerged. Five of six families did not regret their decision for VAD implant despite the child's death. Caregiver-child accord (via verbal consent or cues from the child's physical state) at implant and end of life was associated with lack of regret. Perceived cues from the child about readiness to die were often more impactful in families' decisions for VAD deactivation than medical provider recommendation. Moreover, the development of a surrogate local "family" composed of the medical team (VAD providers, nurses, social workers) and other patient families provided powerful support to these families, equal or above that of the extended family or palliative care service. Though caregiver coping styles differed widely, they did not spontaneously report persistent symptoms of post-traumatic stress or depression. <h3>Conclusion</h3> This qualitative study of bereaved caregivers of pediatric VAD patients demonstrates that accord between the child and family is an important component of caregiver decision-making in VAD implantation and deactivation. Local surrogate support systems and longitudinal medical providers often play a meaningful role for caregivers at a child's end of life, sometimes more so than remote families or palliative care. A better understanding of the caregiver perspective should inform VAD programs' approach to implantation and end-of-life conversations to promote quality decision-making and bereavement.

A predictive viscosity model for aqueous electrolytes and mixed organic–inorganic aerosol phases

Abstract. Aerosol viscosity is determined by mixture composition and temperature, with a key influence from relative humidity (RH) in modulating aerosol water content. Aerosol particles frequently contain mixtures of water, organic compounds, and inorganic ions, so we have extended the thermodynamics-based group-contribution model AIOMFAC-VISC to predict viscosity for aqueous electrolyte solutions and aqueous organic–inorganic mixtures. For aqueous electrolyte solutions, our new, semi-empirical approach uses a physical expression based on Eyring's absolute rate theory, and we define activation energy for viscous flow as a function of temperature, ion activities, and ionic strength. The AIOMFAC-VISC electrolyte model's ion-specific expressions were simultaneously fitted, which arguably makes this approach more predictive than that of other models. This also enables viscosity calculations for aqueous solutions containing an arbitrary number of cation and anion species, including mixtures that have never been studied experimentally. These predictions achieve an excellent level of accuracy while also providing physically meaningful extrapolations to extremely high electrolyte concentrations, which is essential in the context of microscopic aqueous atmospheric aerosols. For organic–inorganic mixtures, multiple mixing approaches were tested to couple the AIOMFAC-VISC electrolyte model with its existing aqueous organic model. We discuss the best-performing mixing models implemented in AIOMFAC-VISC for reproducing viscosity measurements of aerosol surrogate systems. We present advantages and drawbacks of different model design choices and associated computational costs of these methods, of importance for use of AIOMFAC-VISC in dynamic simulations. Finally, we demonstrate the capabilities of AIOMFAC-VISC predictions for phase-separated organic–inorganic particles equilibrated to observed temperature and relative humidity conditions from atmospheric balloon soundings. The predictions for the studied cases suggest liquid-like viscosities for an aqueous electrolyte-rich particle phase throughout the troposphere, yet a highly viscous or glassy organic-rich phase in the middle and upper troposphere.

Uncertainty Reduction in Logistic Growth Regression Using Surrogate Systems Carrying Capacities: a COVID-19 Case Study

Logistic growth regressions present high uncertainties when data are not past their inflection points. In such conditions, the uncertainty in the estimated carrying capacity K, for example, can be of the order of K. Here, we present a method for uncertainty reduction in logistic growth regression using data from a surrogate logistic growth process. We illustrate the method using Richards’ growth function to predict the inflection points of COVID-19 first-wave accumulated causalities in Brazilian cities. First waves of epidemics are known to be reasonably well modeled a posteriori by Richard’s growth function. Yet, we make predictions using early data that end before or around the inflection point. For that goal, we estimate K by logistic growth regression using data from surrogate international cities where the epidemics are clearly past their inflection points. The constraint stabilizes the logistic growth regression for the Brazilian cities, reducing the uncertainty in the prediction parameters even when the surrogate K is a rough estimate. The predictions for COVID-19 first-wave peaks in Brazilian cities agree with official data. The method may be used for other logistic models and logistic processes, in areas such as economics and biology, when surrogate populations or systems are identified.

Functional Severe Acute Respiratory Syndrome Coronavirus 2 Virus-Like Particles From Insect Cells.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a major epidemic threat since the beginning of 2020. Efforts to combat the virus and the associated coronavirus disease 2019 (COVID-19) disease are being undertaken worldwide. To facilitate the research on the virus itself, a number of surrogate systems have been developed. Here, we report the efficient production of SARS-CoV-2 virus-like particles (VLPs) in insect cells. Contrary to widely used pseudovirus particles, where only one coronaviral protein is displayed within a heterologous scaffold, developed VLPs are structurally similar to the native virus and allow for more throughput studies on the biology of the infection. On the other hand, being devoid of the viral genome, VLPs are unable to replicate and thus safe to work with. Importantly, this is the first report showing that SARS-CoV-2 VLPs can be efficiently produced in insect cells and purified using scalable affinity chromatography.

Terahertz Wireless Communications: Co-Sharing for Terrestrial and Satellite Systems Above 100 GHz

This letter demonstrates how spectrum up to 1 THz will support mobile communications beyond 5G in the coming decades. Results of rooftop surrogate satellite/tower base station measurements at 140 GHz show the natural isolation between terrestrial networks and surrogate satellite systems, as well as between terrestrial mobile users and co-channel fixed backhaul links. These first-of-their-kind measurements and accompanying analysis show that by keeping the energy radiated by terrestrial emitters on the horizon (e.g., elevation angles ≤ 15°), there will not likely be interference in the same or adjacent bands between passive satellite sensors and terrestrial terminals, or between mobile links and terrestrial backhaul links at frequencies above 100 GHz.

Nonlinear random vibration analysis: A Bayesian nonparametric approach

Random vibration analysis aims to estimate the response statistics of dynamical systems subject to stochastic excitations. Stochastic differential equations (SDEs) that govern the response of general nonlinear systems are often complicated, and their analytical solutions are scarce. Thus, a range of approximate methods and simulation techniques have been developed. This paper develops a hybrid approach that approximates the governing SDE of nonlinear systems using a small number of response simulations and information available a priori. The main idea is to identify a set of surrogate linear systems such that their response probability distributions collectively estimate the response probability distribution of the original nonlinear system. To identify the surrogate linear systems, the proposed method integrates the simulated responses of the original nonlinear system with information available a priori about the number and parameters of the surrogate linear systems. There will be epistemic uncertainty in the number and parameters of the surrogate linear systems because of the limited data. This paper proposes a Bayesian nonparametric approach, called a Dirichlet Process Mixture Model, to capture these uncertainties. The Dirichlet process models the uncertainty over an infinite-dimensional parameter space, representing an infinite number of potential surrogate linear systems. Specifically, the proposed method allows the number of surrogate linear systems to grow indefinitely as the nonlinear system observed dynamic unveil new patterns. The quantified uncertainty in the estimates of the unknown model parameters propagates into the response probability distribution. The paper then shows that, under some mild conditions, the estimated probability distribution approaches, as close as desired, to the original nonlinear system’s response probability distribution. As a measure of model accuracy, the paper provides the convergence rate of the response probability distribution. Because the posterior distribution of the unknown model parameters is often not analytically tractable, a Gibbs sampling algorithm is presented to draw samples from the posterior distribution. Variational Bayesian inference is also introduced to derive an approximate closed-form expression for the posterior distribution. The paper illustrates the proposed method through the random vibration analysis of a nonlinear elastic and a nonlinear hysteretic system.