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Artificial Immune System is a rapidly growing field of information processing and computing based upon immune inspired paradigns of nonlinear dynamics. This paper introduces stochastic models which mimic the phenomenology of basic functions of immune systems such as self-nonself discrimination, self-repair, predator-prey pursuit, and reproduction.
A study is in progress comparing Airborne Synthetic Aperture Radar (AIRSAR) backscatter from coniferous forest plots containing gaps to backscatter from adjacent gap-free plots. Issues discussed are how do gaps in the range of 400 to 1600 sq m (approximately 4-14 pixels at intermediate incidence angles) affect forest backscatter statistics and what incidence angles, wavelengths, and polarizations are most sensitive to forest gaps. In order to visualize the slant-range imaging of forest and gaps, a simple conceptual model is used. This strictly qualitative model has led us to hypothesize that forest radar returns at short wavelengths (eg., C-band) and large incidence angles (e.g., 50 deg) should be most affected by the presence of gaps, whereas returns at long wavelengths and small angles should be least affected. Preliminary analysis of 1989 AIRSAR data from forest near Mt. Shasta supports the hypothesis. Current forest backscatter models such as MIMICS and Santa Barbara Discontinuous Canopy Backscatter Model have in several cases correctly predicted backscatter from forest stands based on inputs of measured or estimated forest parameters. These models do not, however, predict within-stand SAR scene texture, or 'intrinsic scene variability' as Ulaby et al. has referred to it. For instance, the Santa Barbara model, which may be the most spatially coupled of the existing models, is not truly spatial. Tree locations within a simulated pixel are distributed according to a Poisson process, as they are in many natural forests, but tree size is unrelated to location, which is not the case in nature. Furthermore, since pixels of a simulated stand are generated independently in the Santa Barbara model, spatial processes larger than one pixel are not modeled. Using a different approach, Oliver modeled scene texture based on an hypothetical forest geometry. His simulated scenes do not agree well with SAR data, perhaps due to the simple geometric model used. Insofar as texture is the expression of biological forest processes, such as succession and disease, and physical ones, such as fire and wind-throw, it contains useful information about the forest, and has value in image interpretation and classification. Forest gaps are undoubtedly important contributors to scene variance. By studying the localized effects of gaps on forest backscatter, guided by our qualitative model, we hope to understand more clearly the manner in which spatial heterogeneities in forests produce variations in backscatter, which collectively give rise to scene texture.
The dynamics of group affiliation and group dispersion is a concept that is most often studied in order for political candidates to better understand the most efficient way to conduct their campaigns. While political campaigning in the United States is a very hot topic that most politicians analyze and study, the concept of group/party affiliation presents its own area of study that producers very interesting results. One tool for examining party affiliation on a large scale is agent-based modeling (ABM), a paradigm in the modeling and simulation (M&S) field perfectly suited for aggregating individual behaviors to observe large swaths of a population. For this study agent based modeling was used in order to look at a community of agents and determine what factors can affect the group/party affiliation patterns that are present. In the agent-based model that was used for this experiment many factors were present but two main factors were used to determine the results. The results of this study show that it is possible to use agent-based modeling to explore group/party affiliation and construct a model that can mimic real world events. More importantly, the model in the study allows for the results found in a smaller community to be translated into larger experiments to determine if the results will remain present on a much larger scale.
Abstract Nutrient limitation is widespread in terrestrial ecosystems. Accordingly, representations of nitrogen (N) limitation in land models typically dampen rates of terrestrial carbon (C) accrual, compared with C‐only simulations. These previous findings, however, rely on soil biogeochemical models that implicitly represent microbial activity and physiology. Here we present results from a biogeochemical model testbed that allows us to investigate how an explicit versus implicit representation of soil microbial activity, as represented in the MIcrobial‐MIneral Carbon Stabilization (MIMICS) and Carnegie‐Ames‐Stanford Approach (CASA) soil biogeochemical models, respectively, influence plant productivity, and terrestrial C and N fluxes at initialization and over the historical period. When forced with common boundary conditions, larger soil C pools simulated by the MIMICS model reflect longer inferred soil organic matter (SOM) turnover times than those simulated by CASA. At steady state, terrestrial ecosystems experience greater N limitation when using the MIMICS‐CN model, which also increases the inferred SOM turnover time. Over the historical period, however, warming‐induced acceleration of SOM decomposition over high latitude ecosystems increases rates of N mineralization in MIMICS‐CN. This reduces N limitation and results in faster rates of vegetation C accrual. Moreover, as SOM stoichiometry is an emergent property of MIMICS‐CN, we highlight opportunities to deepen understanding of sources of persistent SOM and explore its potential sensitivity to environmental change. Our findings underscore the need to improve understanding and representation of plant and microbial resource allocation and competition in land models that represent coupled biogeochemical cycles under global change scenarios.
An artificial convolutional neural network was created to efficiently mimic a micromechanics model, the High Fidelity Generalized Method of Cells, for use in multi-scale structural finite element analysis. The network was found to quickly and accurately replicate the stiffness predicted by the micromechanics model using a 2D image of an idealized representative volume element of a fiber/matrix microstructure. The long-term goal of this work is to efficiently apply multi-scale methods for predicting the damage progression of a composite structure.
An agent-based simulation model hierarchy emulating disease states and behaviors critical to progression of diabetes type 2 was designed and implemented in the DEVS framework. The models are translations of basic elements of an established system dynamics model of diabetes. In this model hierarchy, which mimics diabetes progression over an aggregated U.S. population, was dis-aggregated and reconstructed bottom-up at the individual (agent) level. Four levels of model complexity were defined in order to systematically evaluate which parameters are needed to mimic outputs of the system dynamics model. Moreover, the four estimated models attempted to replicate stock counts representing disease states in the system dynamics model, while estimating impacts of an elderliness factor, obesity factor and health-related behavioral parameters. Health-related behavior was modeled as a simple realization of the Theory of Planned Behavior, a joint function of individual attitude and diffusion of social norms that spread over each agent s social network. Although the most complex agent-based simulation model contained 31 adjustable parameters, all models were considerably less complex than the system dynamics model which required numerous time series inputs to make its predictions. In all three elaborations of the baseline model provided significantly improved fits to the output of the system dynamics model. The performances of the baseline agent-based model and its extensions illustrate a promising approach to translate complex system dynamics models into agent-based model alternatives that are both conceptually simpler and capable of capturing main effects of complex local agent-agent interactions.
One of the primary tools foreseen for heating, current drive (CD) and q-profile control in future fusion reactors such as ITER and a Fusion Nuclear Science Facility is the neutral beam injection (NBI). However, fast ions from NBI may also provide the drive for energetic particle-driven instabilities (e.g. Alfvénic modes (AEs)), which in turn redistribute fast ions in both space and energy, thus hampering the control capabilities and overall efficiency of NB-driven current. Based on experiments on the NSTX tokamak (M. Ono et al 2000 Nucl. Fusion 40 557), the effects of AEs and other low-frequency magneto-hydrodynamic instabilities on NB-CD efficiency are investigated. When looking at the new fast ion transport model, which accounts for particle transport in phase space as required for resonant AE perturbations, is utilized to obtain consistent simulations of NB-CD through the tokamak transport code TRANSP. It is found that instabilities do indeed reduce the NB-driven current density over most of the plasma radius by up to ~50%. Moreover, the details of the current profile evolution are sensitive to the specific model used to mimic the interaction between NB ions and instabilities. Finally, implications for fast ion transport modeling in integrated tokamak simulations are briefly discussed.
Pattern recognition algorithms such as artificial neural networks (NNs) and convolution neural networks (CNNs) are prime candidates to perform automated gamma-ray spectroscopy. The way these models train and operate mimic how trained spectroscopists identify spectra. These models have shown promise in identifying gamma-ray spectra with large calibration drift and unknown background radiation fields. In this work, two algorithms for mixtures of radioisotopes based on NN and CNN are presented and evaluated.
In this study, development of compact photocurrent models is currently dominated by analytical techniques that rely on physical assumptions to render the governing equations solvable in a closed form. Violation of these assumptions can reduce the accuracy of the models and/or limit their scope. In this paper we show that system identification of nonlinear state-space systems can serve as an alternative numerical basis for non-intrusive reduced order modeling of photocurrent effects. To that end we develop a compact gray box photocurrent model (GBPM) by using a state-space representation with a low-dimensional latent state equation that mimics a mathematical model for the response of an idealized class of devices to ionizing radiation. In so doing we obtain a model that learns the dynamics of a quantity of interest directly from its measurements without requiring snapshots of the internal device state or its discretized model, and can be inferred from very small data sets. To demonstrate the approach we train the GBPM using a small experimental data set for a Z5236 Zener diode and a small synthetic data set obtained by simulating a synthetic pn-junction device. We then compare the GBPMs with black box models trained on the same data and show that performance of the latter is limited by the size of the data set, while the former are able to achieve excellent performance in both the reproductive and the predictive regimes.
A model of the spatial and temporal distribution of rainfall is described that produces random spatial rainfall patterns with these characteristics: (1) the model is defined on a grid with each grid point representing the average rain rate over the surrounding grid box, (2) rain occurs at any one grid point, on average, a specified percentage of the time and has a lognormal probability distribution, (3) spatial correlation of the rainfall can be arbitrarily prescribed, and (4) time stepping is carried out so that large-scale features persist longer than small-scale features. Rain is generated in the model from the portion of a correlated Gaussian random field that exceeds a threshold. The portion of the field above the threshold is rescaled to have a lognormal probability distribution. Sample output of the model designed to mimic radar observations of rainfall during the Global Atmospheric Research Program Atlantic Tropical Experiment (GATE), is shown. The model is intended for use in evaluating sampling strategies for satellite remote-sensing of rainfall and for development of algorithms for converting radiant intensity received by an instrument from its field of view into rainfall amount.
Motivated by a triaxial coreflood experiment with a sample of Utica shale where an abrupt jump in permeability was observed, possibly due to the creation of a percolating fracture network through the sample, we perform numerical simulations based on the experiment to characterize how the effective permeability of otherwise low-permeability porous media depends on fracture formation, connectivity, and the contrast between the fracture and matrix permeabilities. While a change in effective permeability due to fracture formation is expected, the dependence of its magnitude upon the contrast between the matrix permeability and fracture permeability and the fracture network structure is poorly characterized. We use two different high-fidelity fracture network models to characterize how effective permeability changes as percolation occurs. The first is a dynamic two-dimensional fracture propagation model designed to mimic the laboratory settings of the experiment. The second is a static three-dimensional discrete fracture network (DFN) model, whose fracture and network statistics are based on the fractured sample of Utica shale. Once the network connects the inflow and outflow boundaries, the effective permeability increases non-linearly with network density. In most networks considered, a jump in the effective permeability was observed when the embedded fracture network percolated. We characterize how the magnitude of the jump, should it occur, depends on the contrast between the fracture and matrix permeabilities. For small contrasts between the matrix and fracture permeabilities the change is insignificant. However, for larger contrasts, there is a substantial jump whose magnitude depends non-linearly on the difference between matrix and fracture permeabilities. A power-law relationship between the size of the jump and the difference between the matrix and fracture permeabilities is observed. In conclusion, the presented results underscore the importance of fracture network topology on the upscaled properties of the porous medium in which it is embedded.
In models with an extended Higgs sector there exists an alignment limit, in which the lightest CP-even Higgs boson mimics the Standard Model Higgs. The alignment limit is commonly associated with the decoupling limit, where all non-standard scalars are significantly heavier than the Z boson. However, alignment can occur irrespective of the mass scale of the rest of the Higgs sector. In this work we discuss the general conditions that lead to “alignment without decoupling”, therefore allowing for the existence of additional non-standard Higgs bosons at the weak scale. The values of tan β for which this happens are derived in terms of the effective Higgs quartic couplings in general two-Higgs-doublet models as well as in supersymmetric theories, including the MSSM and the NMSSM. In addition, we study the information encoded in the variations of the SM Higgs-fermion couplings to explore regions in the m A – tan β parameter space.
Although parallel alignment of fibroblasts to the tension lines of scar has been evidenced in vivo, how scar contracture generates directional contraction remains largely unclear due to the lack of effective in vitro model. Fibroblast populated collagen lattice (FPCL), a widely used in vitro model, fails to mimic scar contracture since it produces concentric contraction with the random orientation of fibroblast. We hypothesized that a novel FPCL model with fibroblast alignment might produce directional contraction and then simulate scar contracture better. Here, we showed that although direct current electric fields (DCEFs) enabled fibroblasts aligned perpendicularly to the field vector, it also promoted electrotactic migration of fibroblast in FPCL. By contrast, biphasic pulse direct current electric fields (BPDCEFs), featured by reversal of the EF direction periodically, abolished the electrotactic migration, but induced fibroblast alignment in a pulse frequency dependent manner. Specifically, BPDCEF at a pulse frequency of 0.0002 Hz induced fibroblast alignment comparable to that induced by DCEF under the same field strength (300 mV/mm), leading to an enhanced contraction of FPCL along the direction of cell alignment. FPCL pretreated by BPDCEF showed an elliptical contraction whereas it was concentric in control FPCL. Further study revealed that F-actin redistributions acted as a key mechanism for the induction of fibroblasts alignment by BPDCEF. Cytochalasin D, an inhibitor of actin dynamics, abolished F-actins redistribution, and significantly suppressed the fibroblasts alignment and the directional contraction of FPCL. Importantly, BPDCEF significantly increased RhoA activity in fibroblasts, while this response was attenuated by C3 transferase pre-treatment, a potent inhibitor of RhoA, caused F-actin depolymerization and actin filament bundle randomly distributed. Taken together, our study suggests a crucial role for fibroblast orientation in scar contracture, and provides a novel FPCL model that may be feasible and effective for investigating scar contracture in vitro.
Inflammatory bowel disease (IBD) is a set of immunological disorders which can generate chronic pain and fatigue associated with the inflammatory symptoms. The treatment of IBD remains a significant hurdle with current therapies being only partially effective or having significant side effects, suggesting that new therapies that elicit different modes of action and delivery strategies are required. TGM1 is a TGF-β mimic that was discovered from the intestinal helminth parasite Heligmosomoides polygyrus and is thought to be produced by the parasite to suppress the intestinal inflammation response to help evade host immunity, making it an ideal candidate to be developed as a novel anti-inflammatory bio-therapeutic. Here we utilized the expression system of the edible green algae Chlamydomonas reinhardtii in order to recombinantly produce active TGM1 in a form that could be ingested. C. reinhardtii robustly expressed TGM1, and the resultant recombinant protein is biologically active as measured by regulatory T cell induction. When delivered orally to mice, the algal expressed TGM1 is able to ameliorate weight loss, lymphadenopathy, and disease symptoms in a mouse model of DSS-induced colitis, demonstrating the potential of this biologic as a novel treatment of IBD.
Abstract Quantifying the temperature sensitivity of methane (CH 4 ) production is crucial for predicting how wetland ecosystems will respond to climate warming. Typically, the temperature sensitivity (often quantified as a Q 10 value) is derived from laboratory incubation studies and then used in biogeochemical models. However, studies report wide variation in incubation-inferred Q 10 values, with a large portion of this variation remaining unexplained. Here we applied observations in a thawing permafrost peatland (Stordalen Mire) and a well-tested process-rich model ( ecosys ) to interpret incubation observations and investigate controls on inferred CH 4 production temperature sensitivity. We developed a field-storage-incubation modeling approach to mimic the full incubation sequence, including field sampling at a particular time in the growing season, refrigerated storage, and laboratory incubation, followed by model evaluation. We found that CH 4 production rates during incubation are regulated by substrate availability and active microbial biomass of key microbial functional groups, which are affected by soil storage duration and temperature. Seasonal variation in substrate availability and active microbial biomass of key microbial functional groups led to strong time-of-sampling impacts on CH 4 production. CH 4 production is higher with less perturbation post-sampling, i.e. shorter storage duration and lower storage temperature. We found a wide range of inferred Q 10 values (1.2–3.5), which we attribute to incubation temperatures, incubation duration, storage duration, and sampling time. We also show that Q 10 values of CH 4 production are controlled by interacting biological, biochemical, and physical processes, which cause the inferred Q 10 values to differ substantially from those of the component processes. Terrestrial ecosystem models that use a constant Q 10 value to represent temperature responses may therefore predict biased soil carbon cycling under future climate scenarios.
Respiratory syncytial virus and parainfluenza virus cause severe respiratory disease, especially in infants, children and the elderly. An in vitro model that accurately mimics infection of the human respiratory epithelium (HRE) would facilitate vaccine development greatly. Monolayer cultures traditionally used to study these viruses do not accurately and precisely differentiate the replication efficiencies of wild type and attenuated viruses. Therefore, we engineered novel three-dimensional (3D) tissue-like assemblies (TLAs) of human broncho-epithelial (HBE) cells to produce a more physiologically relevant in vitro model of the HRE. TLAs resemble HRE structurally and by expression of differentiated epithelial cell markers. Most significantly, wild type viruses exhibited a clear growth advantage over attenuated strains in TLAs unlike monolayer cultures. In addition, the TLAs responded to virus infection by secreting pro-inflammatory mediators similar to the respiratory epithelia of infected children. These characteristics make the TLA model a valuable platform technology to develop and evaluate live, attenuated respiratory virus vaccine candidates for human use. Respiratory virus diseases, the most frequent and least preventable of all infectious diseases, range in severity from the common cold to severe bronchiolitis and pneumonia . Two paramyxoviruses, respiratory syncytial virus (RSV) and parainfluenza virus type 3 (PIV3), are responsible for a majority of the most severe respiratory diseases of infants and young children. RSV causes 70% of all bronchiolitis cases and is a major cause of morbidity and mortality worldwide, especially in infants. PIV3 causes 10-15% of bronchiolitis and pneumonia during infancy, second only to RSV, and 40% of croup in infants To date, licensed vaccines are not available to prevent these respiratory diseases. At present, traditional monkey kidney (Vero and LLC-MK2) and human (HEp-2) tissue culture cells and small animal models (mouse, cotton rat, guinea pig, ferret, and hamster) fail to accurately imitate viral replication and human disease states (8). Lacking an authentic model has impeded the development and evaluation of live, attenuated vaccine candidates. Development of a physiologically relevant in vitro tissue culture model that reproduces characteristics of the HRE, the primary target of RSV and PIV3, would aid in predicting clinical attenuation and safety of vaccine candidates. Successful tissue engineering of a 3D human intestinal model using novel NASA technology inspired the development of a tri-culture 3D model for the HRE. Sequential layering of primary mesenchymal cells (comprised of normal human fibroblasts and endothelial cells) followed by BEAS-2B epithelial cells derived from human bronchi and tracheae were recapitulated on Cultisphere and/or cytodex3 microcarriers in cylindrical vessels that rotate horizontally creating an organized epithelial structure. Horizontal rotation randomizes the gravity vector modeling aspects of microgravity. Mesenchymal and epithelial cells grown under these conditions reproduce the structural organization, multi-cellular complexity, and differentiation state of the HRE. The opportunity to study respiratory viruses in a nasal epithelium model is invaluable because the most promising respiratory virus vaccine candidates are live attenuated viruses for intranasal administration. Here we characterize the interactions of respiratory viruses and epithelial cells grown under modeled microgravity in comparison to gravity-ladened monolayers. 3D HBE TLAs and traditional monolayers (2D) are infected at 35 C, the upper temperature of the upper HRE, to simulate in vivo infection conditions. Growth kinetics of wild type (wt) RSV and PIV3 viruses were compared in 2D and 3D cells to that of strains attenuated in humans or rhesus macaques. This novel 3D HBE model also offers an opportunity to study whether the epithelial cell function, especially in host defenses recapitulated by mimicking the structural organization of the HRE. In vivo, airway epithelial cells play a significant and dynamic role in host defense by blocking paracellular permeability and modulating airway function through cellular interactions or tight junctions. As regulators of the innate immune response, epithelial cells constitutively express cytokines, chemokines, and colony stimulating factors including RANTES, IL-8, IL-6, GM-CSF, and G-CSF for proactive host defense. In response to viral infection, epithelial cells induce potent immuno-modulatory and pro-inflammatory cytokines that recruit phagocytic and inflammatory cells to clear the virus and enhance protection. Although disease pathogenesis is classically attributed to the cytopathic effects of the pathogen, severe disease states associated with RSV and PIV3 are attributed to the inflammatory response, especially in infants. RSV is a potent inducer of cytokines and pro-inflammatory mediators in epithelial cells in vivo. A differentiated human epithelial model independent of the complete functional immune system will help elucidate the role of epithelial cells in respiratory disease. We reported here, virus and host cell interactions in 3D HBE TLAs are similar to that in vivo. Because the epithelial cell organization of the TLAs impacts not only the expression of airway epithelial characteristics, but also cellular communication, the TLAs represent a more physiologically relevant model of the HRE than BEAS-2B or other non-tumour monolayer models of respiratory disease. As a result, wild type respiratory viruses have a clear growth advantage over attenuated viruses in TLAs unlike traditional monolayers. In addition, the TLAs respond to wild type virus infection by secreting pro-inflammatory mediators characteristic of infected HRE. TLAs expressing microbial defense mechanisms provide an excellent model to study the interactions of respiratory pathogens with their host and to identify the innate immunity mediators. Therefore, 3D HBE TLAs offer advantages for the study of respiratory viruses and the development of viral vaccine candidates.
We show that very general scalar-tensor theories of gravity (including, e.g., Horndeski models) are generically invariant under disformal transformations. However there is a special subset, when the transformation is not invertible, that yields new equations of motion which are a generalization of the so-called 'mimetic' dark matter theory recently introduced by Chamsedinne and Mukhanov. These conclusions hold true irrespective of whether the scalar field in the action of the assumed scalar-tensor theory of gravity is the same or different than the scalar field involved in the transformation. The new equations of motion for our general mimetic theory can also be derived from an action containing an additional Lagrange multiplier field. The general mimetic scalar-tensor theory has the same number of derivatives in the equations of motion as the original scalar-tensor theory. As an application we show that the simplest mimetic scalar-tensor model is able to mimic the cosmological background of a flat FLRW model with a barotropic perfect fluid with any constant equation of state.
We present results from several connected efforts to apply machine learning methods to estimates of seasonal agricultural production anomalies around the world. First, we apply the XGBoost Random Forest method to fit emulators that mimic global crop models participating in the Agricultural Model Intercomparison and Improvement Project (AgMIP) Global Gridded Crop Model Intercomparison (GGCMI). These are the same models used in the agricultural sector simulations of the Inter-Sectoral Impacts Model Intercomparison Project (ISIMIP). These emulators use 8 climate variables split across 5 sub-seasonal representations of the growing season for each ½ degree grid cell around the world for maize, wheat, rice and soybeans. Emulators are useful for estimating conditions that have not already been simulated by GGCMI (e.g., in a seasonal prediction model) and also to diagnose model differences and capabilities. For example, emulators of the pDSSAT maize model tend to be more reliant on mean temperatures than the LPJmL model, and few models have strong responses to cold extremes. Second, we use a similar XGBoost approach to fit empirical models for national production data for the top 20 producing countries according to the United Nations Food and Agricultural Organization (FAO). Models utilize both climate observations and the GGCM models as predictors, resulting in skillful models for many (but not all) top producing-countries. The patterns of climate and crop model features selected indicate regions and systems that are better or worse simulated by the GGCMs. For example, information in cold extreme predictors is often combined with GGCM output predictors to provide sensitivity that models may underrepresent.