Joint estimation in batch culture by using unscented kalman filter

The disturbances caused by uncertain factors are inevitable in microbial fermentation. In this paper, we study the joint estimation problem for state and parameter in the bio-dissimulation process of glycerol to 1,3-PD in batch culture. Based on the nonlinear stochastic dynamic system model, we establish the corresponding iteration equations of Joint Unscented Kalman Filter (UKF) by referring to the Extended Kalman Filter (EKF), which is generally applied in microbial fermentation. Through numerical computation, both the state estimations and the uncertain model parameter estimations are obtained. Furthermore, the results of different parameter identification methods are compared. The results show that Joint UKF is more feasible for the process of controlling the glycerol fermentation.     

On-line parameter and state estimation of continuous cultivation by extended Kalman filter

Summary The on-line estimation of biomass concentration and of three variable parameters of the non-linear model of continuous cultivation by an extended Kalman filter is demonstrated. Yeast growth in aerobic conditions on an ethanol substrate is represented by an unstructured non-linear stochastic t-variant dynamic model. The filter algorithm uses easily accessible data concerning the input substrate concentration, its concentration in the fermentor and dilution rate, and estimates the biomass concentration, maximum specific growth rate, saturation constant and substrate yield coefficient. The microorganismCandida utilis, strain Vratimov, was cultivated on the ethanol substrate. The filter results obtained with the real data from one cultivation experiment are presented. The practical possibility of using this method for on-line estimation of biomass concentration, which is difficult to measure, is discussed.Nomenclature D dilution rate (h^-1) - DO₂ dissolved oxygen concentration (%) - E identity matrix - F Jacobi matrix of the deterministic part of the system equations g - g continuousn-vector non-linear real function - h m-vector non-linear real function - K Kalman filter gain matrix - K _S saturation constant (kgm^-3) - K_S expectation of the saturation constant estimate - M Jacobi matrix of the deterministic part of the measurement equations h - P(t₀) co-variance matrix of the initial values of the state - P(t_k/t_k) c-variance matrix of the error in (t _k|t _k) - P(t_k+1/t_k) co-variance matrix of the error in (t _k+1|t _k - Q co-variance matrix of the state noise - R co-variance matrix of the output noise - S substrate concentration (kgm^-3) - S _i input substrate concentration - t time - t _k discrete time instant with indexk=0, 1, 2,... - u(t) input vector - v(t_k) measurement (output) noise sequence - w(t) n-vector white Gaussian random process - x(t₀) initial state of the system - (t₀) expectation of the initial state values - x(t) n-dimensional state vector - x(t_k) state vector at the time instantt _k - (t_k|t_k) expectation of the state estimate at timet _k when measurements are known to the timet _k - (t_k+1|t_k) expectation of the state prediction - X biomass concentration (kgm^-3) - expectation of the biomass concentration estimate - y(t_k) m-dimensional output vector at the time instantt _k - Y _XIS substrate yield coefficient - _X|S expectation of the substrate yield coefficient estimate - specific growth rate (h^-1) - _M maximum specific growth rate (h^-1) - expectation of the maximum specific growth rate estimate - state transition matrix     

Bisintercalators of DNA with a rigid linker in an extended configuration.

A new class of DNA bisintercalators is reported in which phenanthridinium or acridinium rings are connected by rigid and extended linkers of varied length. Cross-linking of DNA by bisintercalation is inferred from the unwinding and folding of linear DNA induced by the compound; after ligation and removal of the bisintercalator, superhelical circles, catenanes, and knots that bear an imprint of the bisintercalator are observed. These novel bisintercalators are of interest because they can be used to probe the organization of DNA in three-dimensional space, especially near sites of replication, recombination, or topoisomerase action, where two duplexes must be in close proximity.     

The estimation of absorbed dose rates for non-human biota: an extended intercomparison

An exercise to compare 10 approaches for the calculation of unweighted whole-body absorbed dose rates was conducted for 74 radionuclides and five of the ICRP's Reference Animals and Plants, or RAPs (duck, frog, flatfish egg, rat and elongated earthworm), selected for this exercise to cover a range of body sizes, dimensions and exposure scenarios. Results were analysed using a non-parametric method requiring no specific hypotheses about the statistical distribution of data. The obtained unweighted absorbed dose rates for internal exposure compare well between the different approaches, with 70% of the results falling within a range of variation of?±20%. The variation is greater for external exposure, although 90% of the estimates are within an order of magnitude of one another. There are some discernible patterns where specific models over- or under-predicted. These are explained based on the methodological differences including number of daughter products included in the calculation of dose rate for a parent nuclide; source-target geometry; databases for discrete energy and yield of radionuclides; rounding errors in integration algorithms; and intrinsic differences in calculation methods. For certain radionuclides, these factors combine to generate systematic variations between approaches. Overall, the technique chosen to interpret the data enabled methodological differences in dosimetry calculations to be quantified and compared, allowing the identification of common issues between different approaches and providing greater assurance on the fundamental dose conversion coefficient approaches used in available models for assessing radiological effects to biota.     

Using mass distribution information to model the human thigh for body segment parameter estimation

Accurate estimations of body segment inertial parameters (BSPs) are required to calculate the kinetics of motion. The purpose of this study was to develop a geometric model of the human thigh segment based on mass distribution properties determined from dual energy x ray absorptiometry (DEXA). One hundred subjects from four populations underwent a DEXA scan and anthropometric measurements were taken. The mass distribution properties of the thigh segment were determined for 20 subjects, a geometric model was developed, and the model was applied to the remaining 80 subjects. The model was validated by comparing to benchmark DEXA measurements. Four other popular models in the literature were also evaluated in the same manner No one set of predictors performed best for a particular group or BSP, however modeling the mass distribution properties of the segment allows the assumption of constant density while still accurately representing the inertial properties of the segment and provides promise for future development of BSP models.     

Analysis and implementation of a neural extended Kalman filter for target tracking

Having a better motion model in the state estimator is one way to improve target tracking performance. Since the motion model of the target is not known a priori, either robust modeling techniques or adaptive modeling techniques are required. The neural extended Kalman filter is a technique that learns unmodeled dynamics while performing state estimation in the feedback loop of a control system. This coupled system performs the standard estimation of the states of the plant while estimating a function to approximate the difference between the given state-coupling function model and the behavior of the true plant dynamics. At each sample step, this new model is added to the existing model to improve the state estimate. The neural extended Kalman filter has also been investigated as a target tracking estimation routine. Implementation issues for this adaptive modeling technique, including neural network training parameters, were investigated and an analysis was made of the quality of performance that the technique can have for tracking maneuvering targets.     

Calculation of the instantaneous centre of rotation for a rigid body

The mathematical procedure presented is used for the calculation of the instantaneous centre of rotation for a rigid body based on kinematic measurement data. For every rotation angle interval observed an average centre of rotation is calculated by an appropriate optimizing calculation similar to data approximation by moving average. Practical applicability of this procedure has been proved by means of two planar and one three-dimensional test measurements of known movements (pure rotation, rolling motion and motion of a ball-and-socket joint.     

The discriminative bilateral filter: an enhanced denoising filter for electron microscopy data

Advances in three-dimensional (3D) electron microscopy (EM) and image processing are providing considerable improvements in the resolution of subcellular volumes, macromolecular assemblies and individual proteins. However, the recovery of high-frequency information from biological samples is hindered by specimen sensitivity to beam damage. Low dose electron cryo-microscopy conditions afford reduced beam damage but typically yield images with reduced contrast and low signal-to-noise ratios (SNRs). Here, we describe the properties of a new discriminative bilateral (DBL) filter that is based upon the bilateral filter implementation of Jiang et al. (Jiang, W., Baker, M.L., Wu, Q., Bajaj, C., Chiu, W., 2003. Applications of a bilateral denoising filter in biological electron microscopy. J. Struc. Biol. 128, 82-97.). In contrast to the latter, the DBL filter can distinguish between object edges and high-frequency noise pixels through the use of an additional photometric exclusion function. As a result, high frequency noise pixels are smoothed, yet object edge detail is preserved. In the present study, we show that the DBL filter effectively reduces noise in low SNR single particle data as well as cellular tomograms of stained plastic sections. The properties of the DBL filter are discussed in terms of its usefulness for single particle analysis and for pre-processing cellular tomograms ahead of image segmentation.     

Combining syndromic surveillance and ILI data using particle filter for epidemic state estimation

Designing effective mitigation strategies against influenza outbreak requires an accurate prediction of a disease’s future course of spreading. Real time information such as syndromic surveillance data and influenza-like-illness (ILI) reports by clinicians can be used to generate estimates of the current state of spreading of a disease. Syndromic surveillance data are immediately available, in contrast to ILI reports that require data collection and processing. On the other hand, they are less credible than ILI data because they are essentially behavioral responses from a community. In this paper, we present a method to combine immediately-available-but-less-reliable syndromic surveillance data with reliable-but-time-delayed ILI data. This problem is formulated as a non-linear stochastic filtering problem, and solved by a particle filtering method. Our experimental results from hypothetical pandemic scenarios show that state estimation is improved by utilizing both sets of data compared to when using only one set. However, the amount of improvement depends on the relative credibility and length of delay in ILI data. An analysis for a linear, Gaussian case is presented to support the results observed in the experiments.     

Feedback models allowing estimation of thresholds for self-promoting body weight gain

Objective: Most people maintain almost constant body weight over long time with varying physical activity and food intake. This indicates the existence of a regulation that works well for most individuals. Yet some people develop obesity, indicating that this regulation sometimes fails. The difference between the two situations is typically an energy imbalance of about 1% over a long period of time.Theory: Weight gain increases basal metabolic rate. Weight gain is often associated with a decrease in physical activity, although not to such an extent that it prevents an increase in total energy expenditure and energy intake. Dependent on the precise balance between these effects of weight gain, they may make the body weight unstable and tend to further promote weight gain. With the aim of identifying the thresholds beyond which such self-promoting weight gain may take place, we develop a simple mathematical model of the body as an energy-consuming machine in which the changes in physical activity and food intake are described as feedback effects in addition to the effect of the weight gain on basal metabolic rate. The feedback parameters of the model may differ between individuals and only in some cases do they take values that make weight gain self-promoting.Results: We determine the quantitative conditions under which body weight gain becomes self-promoting. We find that these conditions can easily be met, and that they are so small that they are not observable with currently available techniques. This phenomenon encourages emphasis on even minor changes in food intake and physical activity to abate or stop weight gain.     

The control of glucose concentration during yeast fed-batch cultivation using a fast measurement complemented by an extended Kalman filter

In this contribution results are presented from the control of glucose during a yeast fed-batch cultivation. For glucose measurements a special flow injection analysis (FIA) system was employed, which uses a glucose oxidase solution instead of immobilized enzymes. To avoid the large delay time caused by probing systems samples containing cells, i.e., samples containing the ordinary culture broth, are injected into the FIA system. Based on a special evaluation method the glucose concentration can be measured with a delay time of about 60 s. Employing an extended Kalman filter, the biomass, the glucose concentration as well as the w_max (Monod model) are estimated. Based on the estimation a feed forward and a PI-control with a set point of 0.5 g/l was carried out. The mean deviation of the set point and the estimated value as well as the set point and the measured value were 0.05 and 0.11 g/l respectively for a control period of 8 h producing a cell dry mass of more than 6 g/l.     

Formula and scale for body surface area estimation in high-risk infants

Advances in medical technology and the health sciences have lead to a rapid increase in the prevalence and morbidity of high-risk infants with chronic or permanent sequels such as the birth of early preterm infants. A suitable formula is therefore needed for body surface area (BSA) estimation for high-risk infants to more accurately devise therapeutic regimes in clinical practice. A cohort study involving 5014 high-risk infants was conducted to develop a suitable formula for estimating BSA using four of the existing formulas in the literature. BSA of high-risk infants was calculated using the four BSA equations (Boyd-BSA, Dubois-BSA, Meban-BSA, Mosteller-BSA), from which a new calculation, Mean-BSA, was arithmetically derived as a reference BSA measure. Multiple-regression was performed using nonlinear least squares curve fitting corresponding to the trend line and the new equation, Neo-BSA, developed using Excel and SPSS 17.0. The Neo-BSA equation was constructed as follows: Neo-BSA = 5.520 x W(0.5526) x L(0.300). With the assumption of the least square root relation between weight and length, a BSA scale using only weight was fabricated specifically for clinical applications where weight is more available in high-risk infant populations than is length. The validity of Neo-BSA was evaluated against Meban-BSA, the best of the four equations for high-risk infants, as there is a similarity of subjects in the two studies. The other formulas revealed substantial variances in BSA compared to Neo-BSA. This study developed a new surface area equation, Neo-BSA, as the most suitable formula for BSA measurement of high-risk infants in modern-day societies, where an emerging population of newborns with shorten gestational ages are becoming more prevalent as a result of new advances in the health sciences and new development of reproductive technologies. In particular, a scale for 400-7000 g body weight babies derived from the Neo-BSA equation has the clinical advantage of using only weight as a measurement, since length is often not feasible as a measurement due to the newborn's body posture. Further studies are required to confirm our findings for the application of Neo-BSA and the BSA scale (based on weight) for various populations and ethnicities under different clinical conditions.     

Evidence for cross-linking DNA by bis-intercalators with rigid and extended linkers is provided by knotting and catenation.

A new series of DNA bis-intercalators is reported in which acridine moieties are connected by rigid and extended pyridine-based linkers of varied length. Cross-linking of DNA by bis-intercalation is inferred from the unwinding and folding of linear DNA induced by the compounds; after ligation and removal of the bis-intercalator, superhelical circles, catenanes and knots that bear a residual imprint of the bis-intercalator are observed. These novel bis-intercalators are of interest because they can be used to probe the spatial organization of DNA, especially near sites of replication, recombination or topoisomerase action where two duplexes must be in close proximity. Preliminary results on the effects of the various compounds on the cloning efficiency of bacteria and replication by permeabilized human cells are also presented.     

Gamma-H2AX-based dose estimation for whole and partial body radiation exposure

Most human exposures to ionising radiation are partial body exposures. However, to date only limited tools are available for rapid and accurate estimation of the dose distribution and the extent of the body spared from the exposure. These parameters are of great importance for emergency triage and clinical management of exposed individuals. Here, measurements of γ-H2AX immunofluorescence by microscopy and flow cytometry were compared as rapid biodosimetric tools for whole and partial body exposures. Ex vivo uniformly X-irradiated blood lymphocytes from one donor were used to generate a universal biexponential calibration function for γ-H2AX foci/intensity yields per unit dose for time points up to 96 hours post exposure. Foci--but not intensity--levels remained significantly above background for 96 hours for doses of 0.5 Gy or more. Foci-based dose estimates for ex vivo X-irradiated blood samples from 13 volunteers were in excellent agreement with the actual dose delivered to the targeted samples. Flow cytometric dose estimates for X-irradiated blood samples from 8 volunteers were in excellent agreement with the actual dose delivered at 1 hour post exposure but less so at 24 hours post exposure. In partial body exposures, simulated by mixing ex vivo irradiated and unirradiated lymphocytes, foci/intensity distributions were significantly over-dispersed compared to uniformly irradiated lymphocytes. For both methods and in all cases the estimated fraction of irradiated lymphocytes and dose to that fraction, calculated using the zero contaminated Poisson test and γ-H2AX calibration function, were in good agreement with the actual mixing ratios and doses delivered to the samples. In conclusion, γ-H2AX analysis of irradiated lymphocytes enables rapid and accurate assessment of whole body doses while dispersion analysis of foci or intensity distributions helps determine partial body doses and the irradiated fraction size in cases of partial body exposures.     

Dwarf bamboo as an ecological filter for forest regeneration

Quantitative relationships between the aboveground biomass of dwarf bamboo, Sasa nipponica, and the survivorship and emergence of seedlings of Abies homolepis, Fraxinus lanuginosa f. serrata, and Fagus crenata were estimated. We show that dwarf bamboo acts as an ecological filter since the responses of tree species differ according to the biomass of dwarf bamboo. Deer exclusion without management of dwarf bamboo would make it impossible for any tree species to regenerate due to rapid increases in the biomass of dwarf bamboo.     

Fault detection filter design for an anaerobic digestion process

In this paper, a Fault Detection and Isolation observer based method has been applied to biological wastewater treatment process. The method is designed with a dynamic model and the observer is determined using the eigenstructure assignment approach. The efficiency of the method is demonstrated for both detection and isolation of an actuator and a sensor failure using experimental data from a pilot scale anaerobic digestion process for the treatment of an industrial wine distillery vinasses.