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PubMed2002

Neural networks applied to the prediction of fed-batch fermentation kinetics of Bacillus thuringiensis.

This paper proposes using a new recurrent neural network model (RNNM) to predict and control fed batch fermentations of Bacillus thuringiensis. The control variables are the limiting substrate and the feeding conditions. The multi-input multi-output RNNM proposed has twelve inputs, seven outputs, nineteen neurons in the hidden layer, and global and local feedbacks. The weight update learning algorithm designed is a version of the well known backpropagation through time algorithm directed to the RNNM learning. The error approximation for the last epoch of learning is 2% and the total learning time is 51 epochs, where the size of an epoch is 162 iterations. The RNNM generalization was carried out reproducing a B. thuringiensis fermentation not included in the learning process. It attains an error approximation of 1.8%.

Journal Article↗

PubMed1982

Sleep apnea considered as a control system instability.

In the present study a mathematical model of the chemical control of respiration is described which attempts to simulate periodic breathing during sleep. The model is an extension of an earlier model which has been shown to successfully reproduce the transient effects of CO2 inhalation on breathing, controlled changes in ventilation on arterial gas tension, and Cheyne-Stokes breathing. Included in the extended model are the effects of chemical stimuli during sleep on both chest wall and upper airway muscle activity. Data is presented indicating that simulations from the model reproduce reasonably well the essential features of the results obtained in eight subjects with periodic respiration during sleep when breathing room air, O2, or low concentrations of CO2. Simulations from the model and the experimental data suggest that periodic breathing during sleep results from unstable operation in the respiratory control system analogous to that seen during instabilities in physical control systems. The model indicates that obstructive as well as central apneas can be produced by control system instability. Furthermore, central apneas increase the likelihood of obstructive apneas while obstructive apneas tend to aggravate the control instability. The model results predict that the characteristics of the periodic breathing seen during sleep, such as apnea length, will depend on circulation time and the sensitivity of both upper airway and chest wall muscles to hypercapnia and hypoxia.

Air↗

PubMed2003

Comparison of several well-known controllers used in process control.

In this paper, several well-known design methods, PID control, Smith predictor, inferential control, internal model control, Dahlin controller, deadbeat control, and predictive control, are studied. A suboptimal Smith predictor is derived. The relationship among these methods is investigated. It is shown that these methods are equivalent to each other on certain premises. This explains why they are widely used in process control and provides insight into the work of bringing these techniques together to control system design. Examples are given to illustrate the result.

Journal Article↗

PubMed2003

Fighting a virus with a virus: a dynamic model for HIV-1 therapy.

A mathematical model examined a potential therapy for controlling viral infections using genetically modified viruses. The control of the infection is an indirect effect of the selective elimination by an engineered virus of infected cells that are the source of the pathogens. Therefore, this engineered virus could greatly compensate for a dysfunctional immune system compromised by AIDS. In vitro studies using engineered viruses have been shown to decrease the HIV-1 load about 1000-fold. However, the efficacy of this potential treatment for reducing the viral load in AIDS patients is unknown. The present model studied the interactions among the HIV-1 virus, its main host cell (activated CD4+ T cells), and a therapeutic engineered virus in an in vivo context; and it examined the conditions for controlling the pathogen. This model predicted a significant drop in the HIV-1 load, but the treatment does not eradicate HIV. A basic estimation using a currently engineered virus indicated an HIV-1 load reduction of 92% and a recovery of host cells to 17% of their normal level. Greater success (98% HIV reduction, 44% host cells recovery) is expected as more competent engineered viruses are designed. These results suggest that therapy using viruses could be an alternative to extend the survival of AIDS patients.

CD4-Positive T-Lymphocytes↗

PubMed2003

Silica reduces the toxicity of aluminium to a tropical freshwater fish (Mogurnda mogurnda).

The toxicity of aluminium (Al) to fish in acidic waters has been well documented. It was therefore expected that Al toxicity would be significant in fish communities in Gadjarrigamarndah (Gadji) Creek, a seasonally flowing stream in tropical northern Australia. This creek receives acidic groundwater containing elevated concentrations of Al from earlier land irrigation of treated mine tailings water from the former Nabarlek uranium mine. It was hypothesised that Al toxicity was reduced by high levels of silica (Si) in the water, and the subsequent formation of Al-silicate complexes. This prompted a laboratory assessment of the toxicity of Gadji Creek water to sac-fry of the native fish, Mogurnda mogurnda, followed by more detailed investigation of the toxicity of Al and the influence of Si in reducing Al toxicity. No mortality of M. mogurnda sac-fry was observed in two toxicity tests using Gadji Creek water collected in August 1997 and September 1998. The majority of Al (80-95%) was calculated to be complexed with humic substances and sulfate, with < 1% being complexed with silicate. Assessment of the influence of silica on the acute toxicity of Al in the absence of natural organic complexants (i.e. in reconstituted freshwater, pH 5) revealed that Si reduced Al toxicity. As the molar ratio of Si:Al was increased, the percent survival of M. mogurnda sac-fry increased until there was no significant (P > 0.05) difference from the controls. However, speciation modelling again predicted that little (< 3%) Al complexed with silicate, with the speciation and bioavailability of Al remaining constant as the molar ratio of Si:Al increased. Therefore, the original hypothesis that Al-silicate complexes in solution reduced the toxicity of Al to M. mogurnda could not be supported. This potential mechanism, and an alternative hypothesis, that Si competes with Al for binding sites at the fish gill surface, requires further investigation.

Aluminum↗

PubMed1980

The structure of transposable yeast mating type loci.

A recombinant plasmid containing a MAT alpha mating type locus of Saccharomyces cerevisiae has been isolated by its ability to complement a sterile mat alpha mutation. The plasmid hybridizes to restriction fragments containing both active mating type loci (MATa and MAT alpha) and both silent mating type loci (HMRa and HML alpha). All loci therefore have common sequences. Recombinant lambda clones of the locihave been isolated by plaque hybridization and their structures have been compared by a heteroduplex analysis. At its center, each locus contains one of two apparently nonhomologous sequences. Loci concerned with the alpha phenotype (MAT alpha and HML alpha) contain and 850 bp alpha-specific sequence, whereas loci concerned with the a phenotype (MATa and HMRa) contain a 700 bp a-specific sequence. The a- or alpha-specific sequences are surrounded by DNA sequences that are common to all loci. These homologous sequences extend for 230 bp on the left and 700 bp on the right. They appear to be unrelated to each other. Surprisingly, HML alpha and HMRa differ in their extent of homology to MATa and MAT alpha outside the above regions. HMRa lacks an extensive (700 bp) DNA sequence to the right of the large right-hand homologous region, and possibly also a small (90 bp) sequence to the left of the small left-hand homologous region, both of which are present at HML alpha, MATa and MAT alpha. Hybridization studies have shown that the 700 bp sequence is present at HMLa but absent at HMR alpha alleles. It is therefore characteristic of HML, irrespective of whether it contains a- or alpha-specific sequences. The results imply that mating type interconversion is effected by transposition of DNA sequences from HML or HMR to MAT, as predicted by the controlling element model of Oshima and Takano (1971) and the Cassette model of Hicks, Strathern and Herskowitz (1977).

Base Sequence↗

PubMed1989

Transduction heats in retinal rods: tests of the role of cGMP by pyroelectric calorimetry.

The sensory dark current of vertebrate retinal rods is believed to be controlled by light activation of a chain of coupled biochemical cycles that finally regulate the cationic conductance of the plasma membrane by hydrolytically reducing the level of cGMP in rod outer segment cytoplasm. The scheme has been tested by measuring heat production by live frog retinas when stimulated with sequences of light flashes of progressively increasing energy. Using pyroelectric poly(vinylidene 1,1-difluoride) detectors that simultaneously measure transretinal voltage and retinal temperature change, four heat effects assignable to known biochemical cycles in rods have been found. As the dark current shuts down after a flash causing 180-1800 rhodopsin photoisomerizations per rod, a heat burst, q1, raises the retinal temperature 1-2 microK. q1 is closely regulated in size and slightly precedes dark current shutdown. Isobutylmethylxanthine slows and enlarges q1, delaying the dark-current response. Increasing cytoplasmic Ca2+ stops the dark current without affecting q1. Although rod heat production is consistent with splitting of 1-3 microM of free cytoplasmic cGMP during transduction, the kinetics of the two processes do not match the predictions of current cGMP control models.

Animals↗

PubMed1998

Time course of reactions controlled and gated by intramolecular dynamics of proteins: predictions of the model of random walk on fractal lattices.

Computer simulations of random walk on the Sierpinski gasket and percolation clusters demonstrate that the short, initial condition-dependent stage of protein involving reactions can dominate the progress of the reaction over the main stage described by the standard kinetics. This phenomenon takes place if the intramolecular conformational transition dynamics modeled by the stochastic process is slow enough and the initial conformational substate of the protein already belongs to the transition state of the reaction. Both conditions are realized in two kinds of experiments: small ligand rebinding to protein after laser flash photolysis and direct recording of single protein channel activity. The model considered suggests simple analytical formulae that can explain the time behavior of the processes observed and its variation with temperature. The initial condition-dependent stage, and not the stage described by the standard kinetics, is expected as responsible for the coupling of component reactions in the complete catalytic cycles and more complex processes of biological free energy transduction.

Journal Article↗

PubMed1998

The folly of effort: ironic effects in the mental control of pain.

During exposure to pain, participants who were engaged in hypnotic analgesia or stress inoculation provided pain reports every 5 s and 45 s, respectively. It was found that the frequency of pain reporting had a significant effect on participants' level of experienced pain. This finding is discussed in the context of important methodological implications for laboratory investigations of analgesia. Furthermore, preliminary evidence was obtained suggesting that high hypnotizables in hypnotic analgesia remained relatively undisrupted by frequent pain reporting. Based on Wegner's (1994) ironic process theory, it is argued that this pattern of results is inconsistent with theories of hypnosis that propose that hypnotized individuals intentionally engender responses while remaining unaware of their sustained, deliberate effort. The obtained pattern of results was, however, predicted from the dissociated control model of hypnosis (Bowers, 1990, 1992).

Adult↗

PubMed1993

Domain I of 23S rRNA competes with a paused transcription complex for ribosomal protein L4 of Escherichia coli.

Ribosomal protein L4 of Escherichia coli regulates expression of its own eleven gene S10 operon both by inhibiting translation and by stimulating premature termination of transcription. Both regulatory processes presumably involve L4 recognition of the S10 leader RNA. To help define L4's regulatory target, we have investigated the protein's cognate target on 23S rRNA. Binding of L4 to various fragments of the 23S rRNA was monitored by determining their ability to sequester L4 in an in vitro transcription system and thereby eliminate the protein's effect on transcription. Using this approach we identified a region of about 110 bases within domain I of 23S rRNA which binds L4. A two base deletion within this region, close to the base to which L4 has been cross-linked in intact 50S subunits, eliminates L4 binding. These results also confirm the prediction of the autogenous control model, that L4 bound to its target on rRNA is not active in regulating transcription of the S10 operon.

Bacterial Proteins↗

PubMed2002

Three-dimensional modeling of acoustic backscattering from fluid-like zooplankton.

Scattering models that correctly incorporate organism size and shape are a critical component for the remote detection and classification of many marine organisms. In this work, an acoustic scattering model has been developed for fluid-like zooplankton that is based on the distorted wave Born approximation (DWBA) and that makes use of high-resolution three-dimensional measurements of the animal's outer boundary shape. High-resolution computerized tomography (CT) was used to determine the three-dimensional digitizations of animal shape. This study focuses on developing the methodology for incorporating high-resolution CT scans into a scattering model that is generally valid for any body with fluid-like material properties. The model predictions are compared to controlled laboratory measurements of the acoustic backscattering from live individual decapod shrimp. The frequency range used was 50 kHz to 1 MHz and the angular characteristics of the backscattering were investigated with up to a 1 degree angular resolution. The practical conditions under which it is necessary to make use of high-resolution digitizations of shape are assessed.

Journal Article↗

PubMed2005

Caregiver psychological adjustment and institutionalization of persons with Alzheimer's disease.

UNLABELLED: This prospective study examines the relationship between caregiver psychological adjustment and institutionalization of persons with Alzheimer's disease (AD). METHOD: A 3-year longitudinal study was conducted with a clinic-based cohort of 396 persons with AD and their respective family caregivers. Caregiver adjustment was sequentially measured in 3-month intervals using standard scales of appraisal (perceived burden and satisfaction) and emotion (depressive symptoms and positive affect). RESULTS: In multivariable proportional hazards regression models predicting time to institutionalization controlling for AD severity, hazard ratios were significant for appraisal measures of caregiver adjustment, perceived burden (1.053; 95% confidence interval [CI], 1.014, 1.093), and satisfaction (.929; 95% CI, .883, .977). In contrast, levels of caregivers' positive and negative emotion did not reliably predict institutionalization. DISCUSSION: The findings highlight the importance of caregiver appraisals in decisions to institutionalize persons with a dementia syndrome, but the limited impact of caregiver emotion was unexpected and requires further study.

Adaptation, Psychological↗

PubMed2006

Signal dynamics in Sonic hedgehog tissue patterning.

During development, secreted signaling factors, called morphogens, instruct cells to adopt specific mature phenotypes. However, the mechanisms that morphogen systems employ to establish a precise concentration gradient for patterning tissue architecture are highly complex and are typically analyzed only at long times after secretion (i.e. steady state). We have developed a theoretical model that analyzes dynamically how the intricate transport and signal transduction mechanisms of a model morphogen, Sonic hedgehog (Shh), cooperate in modular fashion to regulate tissue patterning in the neural tube. Consistent with numerous recent studies, the model elucidates how the dynamics of gradient formation can be a key determinant of cell response. In addition, this work yields several novel insights into how different transport mechanisms or ;modules' control pattern formation. The model predicts that slowing the transport of a morphogen, such as by lipid modification of the ligand Shh, by ligand binding to proteoglycans, or by the moderate upregulation of dedicated transport molecules like Dispatched, can actually increase the signaling range of the morphogen by concentrating it near the secretion source. Furthermore, several transcriptional targets of Shh, such as Patched and Hedgehog-interacting protein, significantly limit its signaling range by slowing transport and promoting ligand degradation. This modeling approach elucidates how individual modular elements that operate dynamically at various times during patterning can shape a tissue pattern.

Animals↗

PubMed2002

The influence of visual landscape on the free flight behavior of the fruit fly Drosophila melanogaster.

To study the visual cues that control steering behavior in the fruit fly Drosophila melanogaster, we reconstructed three-dimensional trajectories from images taken by stereo infrared video cameras during free flight within structured visual landscapes. Flies move through their environment using a series of straight flight segments separated by rapid turns, termed saccades, during which the fly alters course by approximately 90 degrees in less than 100 ms. Altering the amount of background visual contrast caused significant changes in the fly's translational velocity and saccade frequency. Between saccades, asymmetries in the estimates of optic flow induce gradual turns away from the side experiencing a greater motion stimulus, a behavior opposite to that predicted by a flight control model based upon optomotor equilibrium. To determine which features of visual motion trigger saccades, we reconstructed the visual environment from the fly's perspective for each position in the flight trajectory. From these reconstructions, we modeled the fly's estimation of optic flow on the basis of a two-dimensional array of Hassenstein-Reichardt elementary motion detectors and, through spatial summation, the large-field motion stimuli experienced by the fly during the course of its flight. Event-triggered averages of the large-field motion preceding each saccade suggest that image expansion is the signal that triggers each saccade. The asymmetry in output of the local motion detector array prior to each saccade influences the direction (left versus right) but not the magnitude of the rapid turn. Once initiated, visual feedback does not appear to influence saccade kinematics further. The total expansion experienced before a saccade was similar for flight within both uniform and visually textured backgrounds. In summary, our data suggest that complex behavioral patterns seen during free flight emerge from interactions between the flight control system and the visual environment.

Animals↗

PubMed1994

Optimal control of antagonistic muscle stiffness during voluntary movements.

This paper presents a study on the control of antagonist muscle stiffness during single-joint arm movements by optimal control theory with a minimal effort criterion. A hierarchical model is developed based on the physiology of the neuromuscular control system and the equilibrium point hypothesis. For point-to-point movements, the model provides predictions on (1) movement trajectory, (2) equilibrium trajectory, (3) muscle control inputs, and (4) antagonist muscle stiffness, as well as other variables. We compared these model predictions to the behavior observed in normal human subjects. The optimal movements capture the major invariant characteristics of voluntary movements, such as a sigmoidal movement trajectory with a bell-shaped velocity profile, an 'N'-shaped equilibrium trajectory, a triphasic burst pattern of muscle control inputs, and a dynamically modulated joint stiffness. The joint stiffness is found to increase in the middle of the movement as a consequence of the triphasic muscle activities. We have also investigated the effects of changes in model parameters on movement control. We found that the movement kinematics and muscle control inputs are strongly influenced by the upper bound of the descending excitation signal that activates motoneuron pools in the spinal cord. Furthermore, a class of movements with scaled velocity profiles can be achieved by tuning the amplitude and duration of this excitation signal. These model predictions agree with a wide body of experimental data obtained from normal human subjects. The results suggest that the control of fast arm movements involves explicit planning for both the equilibrium trajectory and joint stiffness, and that the minimal effort criterion best characterizes the objective of movement planning and control.

Arm↗

PubMed2003

Relationship between refractive error and monochromatic aberrations of the eye.

PURPOSE: To examine the relationship between ametropia and optical aberrations in a population of 200 normal human eyes with refractive errors spanning the range from +5.00 to -10.00 D. METHODS: Using a reduced-eye model of ametropia, we tested the hypothesis that the optical system of the eye is uncorrelated with the degree of ametropia. These predictions were evaluated experimentally with a Shack-Hartmann aberrometer that measured the monochromatic aberrations across the central 6 mm of the dilated pupil in well-corrected, cyclopleged eyes. RESULTS: Optical theory predicted, and control experiments on a model eye verified, that Shack-Hartmann measurements of spherical aberration will vary with axial elongation of the eye even if the dioptric components of the eye are fixed. Contrary to these predictions, spherical aberration was not significantly different from emmetropic eyes. Root mean square of third-order aberrations, fourth-order aberrations, and total higher aberrations (third to 10th) in myopic and hyperopic eyes were also uncorrelated with refractive error. Astigmatic eyes tended to have larger total higher-order aberrations than nonastigmatic eyes. CONCLUSIONS: We conclude that a reduced-eye model of myopia assuming fixed optical parameters and variable axial length is not tenable.

Accommodation, Ocular↗

PubMed2005

Dynamic modeling of the ratio volatile fatty acids/bicarbonate alkalinity in a UASB reactor for potato processing wastewater treatment.

In this work, dynamic mathematical model for the prediction of the operational parameter volatile fatty acids/bicarbonate alkalinity (VFA/ALK) in a UASB reactor was developed. The dynamic modeling technique was applied successfully to a two-year data record from an industrial wastewater treatment plant of a potato processing industry. The technique used included regression analysis by residuals. Seventeen parameters were examined including the following: wastewater's flow rate, reactor's temperature and pH, total and soluble influent COD, wastewater's temperature and pH, total and soluble effluent COD, volatile fatty acids, alkalinity, biogas production rate and each parameter with a time lag of up to 10 days. Finally, after all parameters and all time lag trials the best fitted model was developed. The model's adequacy was checked by chi2 test for a data record of the same UASB reactor but at a different time period and proved to be satisfactory. Additionally, the model's ability to predict and to control the plant's operation via VFA/ALK was examined. Through this model, in contrary to steady state models, various aspects of the process can be enlighten, such as the fact that the hydrolysis of starch requires at least a resident time of seven days.

Bicarbonates↗

PubMed1984

Attributional style: degree of depression, respondent's sex, and nature of the attributional event.

Attributional responses made to both good and bad events by male and female Ss (N = 117) differing in degree of clinical depression were examined in light of the reformulated learned helplessness model of depression. Data comparison with control Ss provided support for the model's prediction. Clinically depressed Ss assumed more personal responsibility than control Ss for their life outcomes, especially the negative ones. While significant main effects were demonstrated in the clinical sample for all three variables, the significant two and three-way interaction effects revealed a complex relationship between causal attribution and depression.

Adaptation, Psychological↗