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PubMed2000

A kaiC-interacting sensory histidine kinase, SasA, necessary to sustain robust circadian oscillation in cyanobacteria.

Both regulated expression of the clock genes kaiA, kaiB, and kaiC and interactions among the Kai proteins are proposed to be important for circadian function in the cyanobacterium Synechococcus sp. strain PCC 7942. We have identified the histidine kinase SasA as a KaiC-interacting protein. SasA contains a KaiB-like sensory domain, which appears sufficient for interaction with KaiC. Disruption of the sasA gene lowered kaiBC expression and dramatically reduced amplitude of the kai expression rhythms while shortening the period. Accordingly, sasA disruption attenuated circadian expression patterns of all tested genes, some of which became arrhythmic. Continuous sasA overexpression eliminated circadian rhythms, whereas temporal overexpression changed the phase of kaiBC expression rhythm. Thus, SasA is a close associate of the cyanobacterial clock that is necessary to sustain robust circadian rhythms.

Adaptation, Physiological↗

PubMed1999

An algorithm for the assembly of robust physical maps based on a combination of multi-level hybridization data and fingerprinting data.

We have developed an algorithm which combines data obtained from restriction digestion experiments and hybridization experiments to construct robust physical maps of whole chromosomes. The algorithm has been incorporated into a program which accepts hybridization data consisting of an unordered hybridization matrix and fingerprinting data containing band coordinates for each clone. The combined data is used to produce a non-redundant, ordered matrix which can be further reduced to represent a minimum tile coverage of the chromosome. In addition, the method also takes into account multi-level hybridization events which allows for an improved treatment of the hybridization data. The program is evaluated against several other contig building programs using simulated and real data sets. Finally, it is applied to construct a physical map of the 4.1 Mb genome of Ochrobactrum anthropi based on 1387 clones and 70 probes, as well as 624 fingerprints.

Algorithms↗

PubMed2001

A robust GTP-induced shift in alpha(2)-adrenoceptor agonist affinity in tissue sections from rat brain.

A method is presented for monitoring the coupling of the alpha(2)-adrenoceptor, as well as other receptors, to their G proteins using the GTP-induced shift in agonist affinity states. In tissue sections GTP, but not ATP, induces a robust decrease in agonist affinity of greater than 100-fold, which is much larger than previously found in membrane preparations. A sensitive and easy procedure to monitor the extent of coupling is to compare the amount of [(3)H]RX821002 binding remaining in the presence of 100 nM brimonidine in the absence and presence of 100 microM GTP. This method should be especially applicable for determining the extent of coupling of receptors to their G proteins in multiple brain regions using autoradiographic procedures.

Adrenergic alpha-2 Receptor Agonists↗

PubMed2003

A robust, efficient and flexible method for staining myelinated axons in blocks of brain tissue.

Previous studies have demonstrated the utility of the gold chloride method for en bloc staining of a bisected brain in mice and rats. The present study explores several variations in the method, assesses its reliability, and extends the limits of its application. We conclude that the method is very efficient, highly robust, sufficiently accurate for most purposes, and adaptable to many morphometric measures. We obtained acceptable staining of commissures in every brain, despite a wide variety of fixation methods. One-half could be stained 24 h after the brain was extracted and the other half could be stained months later. When staining failed because of an exhausted solution, the brain could be stained successfully in fresh solution. Relatively small changes were found in the sizes of commissures several weeks after initial fixation or staining. A half brain stained to reveal the mid-sagittal section could then be sectioned coronally and stained again in either gold chloride for myelin or cresyl violet for Nissl substance. Uncertainty, arising from pixelation of digitized images was far less than errors arising from human judgments about the histological limits of major commissures. Useful data for morphometric analysis were obtained by scanning the surface of a gold chloride stained block of brain with an inexpensive flatbed scanner.

Animals↗

PubMed1999

The chemokine system: redundancy for robust outputs.

Chemokines are redundant in their action on target cells and promiscuous in receptor usage. Moreover, certain cells concomitantly produce several chemokines with an overlapping spectrum of action. Here, Alberto Mantovani argues that such robustness provides a conceptual framework to understand these intriguing aspects of the chemokine system.

Animals↗

PubMed2002

Stem-loop oligonucleotides: a robust tool for molecular biology and biotechnology.

The specific structural features of stem-loop (hairpin) DNA constructs provide increased specificity of target recognition. Recently, several robust assays have been developed that exploit the potential of structurally constrained oligonucleotides to hybridize with their cognate targets. Here, I review new diagnostic approaches based on the formation of stem-loop DNA oligonucleotides: molecular beacon methodology, suppression PCR approaches and the use of hairpin probes in DNA microarrays. The advantages of these techniques over existing ones for sequence-specific DNA detection, amplification and manipulation are discussed.

Base Sequence↗

PubMed2003

Robust recovery of human motion from video using Kalman filters and virtual humans.

In sport science, as in clinical gait analysis, optoelectronic motion capture systems based on passive markers are widely used to recover human movement. By processing the corresponding image points, as recorded by multiple cameras, the human kinematics is resolved through multistage processing involving spatial reconstruction, trajectory tracking, joint angle determination, and derivative computation. Key problems with this approach are that marker data can be indistinct, occluded or missing from certain cameras, that phantom markers may be present, and that both 3D reconstruction and tracking may fail. In this paper, we present a novel technique, based on state space filters, that directly estimates the kinematical variables of a virtual mannequin (biomechanical model) from 2D measurements, that is, without requiring 3D reconstruction and tracking. Using Kalman filters, the configuration of the model in terms of joint angles, first and second order derivatives is automatically updated in order to minimize the distances, as measured on TV-cameras, between the 2D measured markers placed on the subject and the corresponding back-projected virtual markers located on the model. The Jacobian and Hessian matrices of the nonlinear observation function are computed through a multidimensional extension of Stirling's interpolation formula. Extensive experiments on simulated and real data confirmed the reliability of the developed system that is robust against false matching and severe marker occlusions. In addition, we show how the proposed technique can be extended to account for skin artifacts and model inaccuracy.

Humans↗

PubMed2003

Applying the Taguchi robust design to the optimization of the asymmetric reduction of ethyl 4-chloro acetoacetate by bakers' yeast.

This study examined the characteristics and operational parameters of the asymmetric reduction of ethyl 4-chloro acetoacetate by bakers' yeast in order to produce S-4-chloro-3-hydroxybutyric acid ethyl ester. Eight operational variables were also optimized using the Taguchi method with consideration of the freshness of yeast cells as a noise factor. An L(18) orthogonal array was used to design the experiments. The reaction yield and the product's optical purity were considered as two product quality variables. A desirability function was applied to combine these two qualities as a single objective function. Additionally, the signal-to-noise (SN) ratio was used to estimate the variability in product quality. Optimization was undertaken not only to yield the best performance, but also to minimize the variation in quality. The confirmation experiments indicated that the reaction performance and the robustness of the product quality under the optimized conditions were higher than those obtained in other experiments in this study. Our results further demonstrate that the product's optical purity could be increased to >95% by adjusting the operational level of the main factors.

Acetoacetates↗

PubMed1997

Robust moving averages, with Hopfield neural network implementation, for monitoring evoked potential signals.

This technical note describes a robust version of moving averages, that enables reliable monitoring of the evoked potential (EP) signals. A cluster analysis (CA) procedure is introduced to robustify the signal averaging (SA). It is implemented via a Hopfield neural network (HNN), which performs selection of the trials forming a cluster around the current state of the EP signal. The core of this cluster serves as an estimate of the instantaneous EP. The effectiveness of the method, indicated by application to real data, and its computation efficiency, due to the use of simple matrix operations, makes it very promising for clinical observations.

Electroencephalography↗

PubMed1997

A software program based on robust linear regression methods for instrumental calibration in biochemical analysis.

A microcomputer program written in GWBASIC for conventional least squares regression (LS) and robust linear regression methods (RRMs) such as single median (SM) and repeated median (RM) is described. The main advantages of RRMs is the ability to detect outliers which can cause an inaccurate estimation of the analyzed samples. It requires MS DOS PC version 3.3 or higher and at least 256 kbyte of RAM. The joint application of RRMs and residuals analysis by the studentized method (STRM) allows a more precise biochemical analysis.

Biochemistry↗

PubMed1983

A robust, brief measure of an individual's most preferred level of salt in an ordinary foodstuff.

A single-session procedure to assess an individual's most preferred level of a factor in a product is justified theoretically and illustrated by the results for salt concentration in samples of bread and tomato soup tested on 30 young men who had had no previous experience of the task. Each man rated the saltiness of each sample as a distance below or above his ideal for that food type. Without the rater knowing, his stimulus set was coordinated to his rating responses in order to minimise biases in what other have shown can be a linear response mode. The Weber fraction is constant for the medium range of NaCl solutions when concentration units are used, and so Fechner's principle of direct scaling was applied: mean linear regressions between ideal-relative intensity responses and the logarithm of salt concentrations in each individual were nearly always statistically reliable with only six to 20 ratings of three to six salt levels in bread or soup. Values of the regression intercepts for bread at the initial session and five months later correlated significantly, as also did the regression slopes. Thus, a robust value for each individual's ideal salt level for each food could be interpolated from the regression equation. There was no effect of sequence of bread and soup sessions. Bread and soup salt-ideals were correlated, as were their slopes. A regression slope appears to represent an individual's tolerance of deviations from ideal. The relation of the slope to choice behaviour, and its relative dependence on intensity sensitivity and a preference motivation characteristic of the individual and test situation, remain to be elucidated. This procedure should have wide application in consumer preference measurement.

Adult↗

PubMed2002

Coherent and robust modulation of a metabolic network by cytoskeletal organization and dynamics.

In order to investigate the influence of cytoskeletal organization and dynamics on cellular biochemistry, a mathematical model was formulated based on our own experimental evidence. The model couples microtubular protein (MTP) dynamics to the glycolytic pathway and its branches: the Krebs cycle, ethanolic fermentation, and the pentose phosphate (PP) pathway. Results show that the flux through glycolysis coherently and coordinately increases or decreases with increased or decreased levels of polymerized MTP, respectively. The rates of individual enzymatic steps and metabolite concentrations change with the polymeric status of MTP throughout the metabolic network. Negative control is exerted by the PP pathway on the glycolytic flux, and the extent of inhibition depends inversely on the polymerization state of MTP, i.e. a high degree of polymerization relieves the negative control. The stability of the model's steady state dynamics for a wide range of variation of metabolic parameters increased with the degree of polymerized MTP. The findings indicate that the organization of the cytoskeleton bestows coherence and robustness to the coordination of cellular metabolism.

Cytoskeleton↗

PubMed2003

Sustainability of fisheries through marine reserves: a robust modeling analysis.

Among the many factors that contribute to overexploitation of marine fisheries, the role played by uncertainty is important. This uncertainty includes both the scientific uncertainties related to the resource dynamics or assessments and the uncontrollability of catches. Some recent works advocate for the use of marine reserves as a central element of future stock management. In the present paper, we study the influence of protected areas upon fisheries sustainability through a simple dynamic model integrating non-stochastic harvesting uncertainty and a constraint of safe minimum biomass level. Using the mathematical concept of invariance kernel in a robust and worst-case context, we examine through a formal modeling analysis how marine reserves might guarantee viable fisheries. We also show how sustainability requirement is not necessarily conflicting with optimization of catches. Numerical simulations are provided to illustrate the main findings.

Animals↗

PubMed1999

Characterization of cavitational activity in lithotripsy fields using a robust electromagnetic probe.

A robust electromagnetic probe has been used to investigate cavitational activity in vitro in the fields of two extracorporeal lithotripters and one intracorporeal lithotripter. Some aspects of the electromagnetic probe design and characteristics are described. A series of experiments have been carried out with results indicating that the probe head moves in response to the pressure gradient generated by radial motion of cavitation bubbles. Empirical expressions have been derived for the cavitational force acting on the probe head, and for the low-frequency sawtooth pressure wave generated by inertial cavitation. This is the first time that the existence of a low-frequency sawtooth wave produced by inertial cavitation has been described. A linear relationship exists between the negative pressure amplitude of the sawtooth wave and the lifetime of the bubbles. Close to the cavitation site, substantial negative pressure is maintained throughout bubble expansion. This can easily exceed the tensile strength of urinary calculi, and may be considered to be an important mechanism for disintegrating these relatively weak structures. A pilot study has also been carried out involving three patients treated by extracorporeal lithotripsy. Signals similar to those recorded during the in vitro cavitation experiments were detected. We conclude that the electromagnetic probe is capable of detecting and quantifying aspects of cavitational activity in vitro, and potentially also in vivo. The observation that the probe responds directly to the motion of cavitation bubbles, coupled with its ability to detect cavitation at a distance, give it the potential for use in a range of medical and industrial applications.

Electromagnetic Phenomena↗

PubMed2002

Robustness of MetaNet graph models: predicting control of urea production in humans.

Urea production in human liver was described by a MetaNet graph, a flowchart-like representation of metabolic pathways that includes parameters for the kinetic constants of the constituent enzymes. Formal operations on the graph facilitate the identification of ligand-binding equilibria that participate in feedback regulation in the network of biochemical reactions. The state of the biochemical network is specified by the concentrations of the intermediates. At any particular time, the influence of an identified locus of regulation is proportional to the respective fractional saturation of the corresponding binding site. Enzymes that make or consume the feedback chemicals share in the control of the strength of the feedback signal in proportion to their fractional saturation. This model predicts control of urea production by the processes that deliver amino groups to the urea cycle enzymes more than by the cycle enzymes themselves. Mitochondrial membrane transport processes are important for transmission of information through the network, but irreversible enzymes and processes far from equilibrium control the strength of the feedback signal. Systematic variation of the parameter values by amounts comparable to the expected variability of their measured values indicated a high probability of invariance in the identities of the predicted control points. The properties of the model are consistent with those of error-tolerant scale-free networks. These results demonstrate the robustness of a MetaNet model's predictions with respect to uncertainties in the values of its parameters.

Computer Simulation↗

PubMed1998

Achieving robust behavior by using proprioceptive activity patterns.

This paper proposes a new self-organizing, biologically-inspired control architecture for mobile robots consisting of a controller and a value system. The controller uses activity patterns of visual sensors to determine the motor commands, whereas the value system receives stimuli from proprioceptive sensors. This design decision is justified by the following arguments: (1) the feedback of proprioceptive sensory patterns is omnipresent in biological systems and has been widely neglected in control systems, (2) both components are significantly decoupled by using different sensory modalities, and (3) proprioceptive sensors operate more reliably and can be used more efficiently than visual sensors, such as pixels in a CCD camera. Practical experiments with the Khepera robot show that by using proprioceptive sensor values, the control architecture can adapt to different environments and yield very robust behavior with respect to, for example, sensor failures. Furthermore, the new control architecture can be easily enhanced by further components.

Feedback↗

PubMed2000

Robust localization of the contralateral precentral gyrus in hemiparetic patients using the unimpaired ipsilateral hand: a clinical functional magnetic resonance imaging protocol.

Tumor related contralateral motor deficits complicate preoperative functional magnetic resonance imaging (fMRI). In plegic patients the localization of the sensorimotor cortex is often impossible. In this context we developed a clinical fMRI protocol dedicated to patients with motor deficits using the unaffected ipsilateral hand. Based on the hypothesis that selfpaced finger movements recruit more and larger neuronal populations with rising task complexity, different motor tasks were tested regarding ipsilateral localization in ten right handed volunteers. Complex finger opposition localized the ipsilateral premotor cortex (Brodman area 6) robustly and was introduced to preoperative fMRI in hemiparetic patients as functional landmark to identify the precentral gyrus on the tumors side. Additional contralateral automated tactile stimulation localized the primary somatosensory cortex and completed the protocol.

Adult↗

PubMed2003

Robust localization and lateralization of human language function: an optimized clinical functional magnetic resonance imaging protocol.

An optimized clinical functional magnetic resonance imaging (fMRI) protocol with a total scanning time of 8 min is presented that localizes Broca's and Wernicke's areas robustly and determines hemispheric dominance. Language function was visualized using two different sentence generation (SG) and word generation (WG) tasks. Block designed blood oxygenation level dependent (BOLD) fMRI was applied in 14 right-handed volunteers at 1.5 T during visual stimulation. BOLD-clusters were assessed individually for anatomical localization. Reference data are provided for the maximum correlation of the measured BOLD-signal time course to the applied reference function (r(max)), for the maximum relative signal change (dS%), cluster size and Euklidian coordinates of Broca and Wernicke activation and of the anatomical homologues in the right hemispheres. Statistical means and a lateralization index (LI) were calculated. Broca activation focussed on the inferior frontal gyrus, and Wernicke activation on the superior temporal, supramarginal or middle temporal gyri. Mean BOLD-signals for Broca ranged from 1.53% (SG) to 2.56% (WG), and for Wernicke from 1.47% (SG) to 1.80% (WG). LI indicated left language dominance. The data provided further evidence for the high anatomical variability of language areas, which underlined the relevance of an individual language localization and lateralization prior to brain surgery.

Adult↗