Ideal internal kink modes in a differentially rotating cylindrical plasma

The Velikhov effect leading to magnetorotational instability (MRI) is incorporated into the theory of ideal internal kink modes in a differentially rotating cylindrical plasma column. It is shown that this effect can play a stabilizing role for suitably organized plasma rotation profiles, leading to suppression of MHD (magnetohydrodynamic) instabilities in magnetic confinement systems. The role of this effect in the problem of the Suydam and the m = 1 internal kink modes is elucidated, where m is the poloidal mode number. Published in Russian in Fizika Plazmy, 2008, Vol. 34, No. 7, pp. 589–597. The text was submitted by the authors in English.     

Gain control in a proprioceptive feedback loop as a prerequisite for working close to instability

In the artificially closed femur-tibia control system of stick insects oscillations were induced in 3 different ways: Increasing the phase-shift by introducing an electronic delay, afference sign reversal and coupling the tibia to an inert mass. In all 3 cases the oscillations stopped after some time. The gain of the open-loop system was significantly smaller after the oscillations. Afference sign reversal by surgically crossing of the receptor apodeme of the femoral chordotonal organ for 25–85 days does not lead to altered characteristics of the control loop. When sinusoidal passive movements are forced upon the intact femur-tibia joint the forces resisting these movements do not decrease with time. In contrast to direct stimulation of the femoral chordotonal organ, these passive movements also influence the contralateral leg. The experiments show that the gain-control system of the femur-tibia control loop of stick insects consists of at least two components: A sensitization system (with inputs from many kinds of stimuli indicating some kind of disturbance) increases the gain of all reflex loops. A specific habituation-like system decreases the gain with repetitive stimulation only of one control system.Abbreviations fCO femoral chordotonal organ - SETi slow extensor tibiae motor neuron     

RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn

The kink turn is a widespread RNA motif that introduces an acute kink into the axis of duplex RNA, typically comprising a bulge followed by a G?A and A?G pairs. The kinked conformation is stabilized by metal ions, or the binding of proteins including L7Ae. We now demonstrate a third mechanism for the stabilization of k-turn structure, involving tertiary interactions within a larger RNA structure. The SAM-I riboswitch contains an essential standard k-turn sequence that kinks a helix so that its terminal loop can make?a?long-range interaction. We find that some sequence variations in the k-turn within the riboswitch do not prevent SAM binding, despite preventing the folding of the k-turn in isolation. Furthermore, two crystal structures show that the sequence-variant k-turns are conventionally folded within the riboswitch. This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure.     

Closed loop control of oxgenation and ventilation

Closed loop control of oxygenation and ventilation during mechanical ventilatory support is essential for remote medical care in an austere environment. Closed loop control allows for expert systems to provide the current standard of care in the absence of on-site expertise. Ventilation may be controlled by simple systems incorporating patient height or by advanced systems incorporating measurements of end-tidal carbon dioxide (ETCO2) and pulmonary impedance. Oxygenation may be controlled by adjustments of inspired oxygen concentrations (FIO2) and positive end-expiratory pressure (PEEP) using pulse oximetry (SpO2) as the input. Control of oxygenation can prevent hypoxemia and has the potential to reduce oxygen requirements. A double closed loop system of oxygenation control including control of FIO2 via SpO2 and control of oxygen generation by a portable oxygen generator (POG) based on FIO2 and minute ventilation (VE) promises safety and efficiency. Remote control of ventilation and oxygenation is possible using existing technology.     

UKF-based closed loop iterative learning control of epileptiform wave in a neural mass model

A novel closed loop control framework is proposed to inhibit epileptiform wave in a neural mass model by external electric field, where the unscented Kalman filter method is used to reconstruct dynamics and estimate unmeasurable parameters of the model. Specifically speaking, the iterative learning control algorithm is introduced into the framework to optimize the control signal. In the proposed method, the control effect can be significantly improved based on the observation of the past attempts. Accordingly, the proposed method can effectively suppress the epileptiform wave as well as showing robustness to noises and uncertainties. Lastly, the simulation is carried out to illustrate the feasibility of the proposed method. Besides, this work shows potential value to design model-based feedback controllers for epilepsy treatment.     

Proline affects oligomerization of a coiled coil by inducing a kink in a long helix

The structural effect of a proline in a helix in trifluoroethanol (TFE)/water medium was examined on a 29-mer peptide and its proline analog derived from the leucine zipper (LZ)-like motif of gp41 (the transmembrane glycoprotein of HIV-1) by NMR and circular dichroism (CD) spectroscopies. Lower helical content was found for the proline mutant from the CD study. NMR data show that distortion of the helix by proline is local and occurs mainly on the N-terminal side of the substitution site. Molecular dynamics computation exhibits a bending of the helical axis of 30 degrees +/- 10 degrees, in agreement with X-ray diffraction results. Light-scattering experiments indicated that the average aggregation number of the proline-substituted mutant is substantially lower than that of the wild-type peptide. From the ratio of dissociation constants of the wild-type and the proline mutant peptides, the difference in free energy of trimeric formation is calculated to be 2.1 kcal/mol. Thermal stability, helicity, and the average aggregation number for the helix oligomers were found to be correlated. The structural alteration and the reduced coiled coil stability may account for the deficiency in the biological functions of the proline mutants of gp41 and in the inhibitory action of proline-substituted peptides. These effects may also be important in unraveling the roles played by proline in transmembrane proteins.     

Extracellular pH is under circadian control in Gonyaulax polyedra and forms a metabolic feedback loop

This study investigates the relationship between the circadian clock and metabolism based on recordings of the extracellular pH in cultures of the marine dinoflagellate, Gonyaulax polyedra. In light-dark cycles, pH of the medium rises during the light phase and declines in the dark. The amplitude of this pH-rhythm correlates with light intensity, indicating photosynthesis (and respiration) as the driving force. The recorded extracellular pH changes probably reflect the need to control intracellular pH in spite of pH-modifying reactions. The daily pH-changes are under control of the circadian clock because they continue to oscillate with a circa-24 h period in constant light, albeit with a smaller amplitude. Similar to other circadian output rhythms, the pH rhythm depends (amplitude and phase) on nitrate levels in the medium. Both the bioluminescence and the pH rhythm can also be shifted by extracellular pH-changes although Gonyaulax is rarely exposed to significant pH changes in its marine ecosystems (except for highly dense algal blooms). Because intracellular proton levels are both affecting circadian input and output they form a feedback loop with the Gonyaulax circadian system indicating complex interactions between metabolism and the circadian clock.     

Information processing in the femur-tibia control loop of stick insects

The complicated response characteristics of the identified nonspiking interneuron type E4 upon elongation stimuli to the femoral chordotonal organ (fCO) can be obtained by a computer simulation using the neuronal network simulator BioSim, if the following assumptions were introduced: (1) The interneurons receive direct excitatory input from position- and velocity-sensitive fCO afferents but also, in parallel delayed inhibition from the same velocity-sensitive afferents. (2) Position-sensitive afferents in part show adaptation with a rather long time-constant. A subsequent experimental analysis demonstrated that all these assumptions fit the reality: (1) Interneurons of type E4 receive direct excitatory input from fCO afferents. (2) Interneurons of type E4 are affected by velocity dependent delayed inhibitory inputs from the fCO. (3) The fCO does contain adapting position-sensitive sensory neurons, which have not been described before. The described principle of the information processing is also able to generate the response in interneurons of type E6 with less steep amplitude-velocity characteristic due to a different weighting of the direct excitation and delayed inhibition.Abbreviations EPSP excitatory postsynaptic potential - FETi fast extensor tibiae motor neuron - fCO femoral chordotonal organ - FT-control loop femur-tibia control loop - IPSP inhibitory postsynaptic potential - SETi slow extensor tibiae motor neuron     

Closed loop control of human body temperature: results from a one-dimensional model

A one-dimensional model of human thermoregulation is used to solve a variety of basic problems in determining an adequate structure of the controller for metabolic heat production, skin blood flow and sweat production. Assuming one integrated central and one integrated peripheral afferent signal the controller parameters are evaluated by analysis of the control performance. Based on a validation by experimental results this allows the determination of a first optimized set of values for controller gains and weight of skin temperature feedback. Furthermove we analyse the effect of inhomogeneous distribution of heat production and blood flow, the influence of body fat content, of controller gains, of weight of skin temperature feedback and of depth of peripheral receptors on the dynamic performance. Increase of peripheral blood flow in particular evokes essentially both an increase of energy requirement in the cold and a quicker system response. Differing rates of increase of metabolic heat production are the consequence of differing body fat content. The weight of skin temperature feedback can be limited to 5...20%, because values outside this range evoke dynamic responses incompatible with the experiments. The actual value can only be determined if there is a correct assumption for the depth of the skin receptors. The use of measured superficial skin temperatures brings about an underestimation of the peripheral afferent signal. Of the controller gains it is primarily the gain of the metabolic controller which affects the dynamic response of the system. The experimental fact of a delayed onset of sweat production after a transition from cold to heat is the consequence of a high gain of the vasomotor system.     

Peculiar features of kink dynamics in inhomogeneous DNA

A mathematical model was constructed for studies of the peculiar features of the dynamics of local conformational distortions (kinks) in inhomogeneous DNA. General formulas were obtained that determine the dependence of the main dynamic characteristics of kinks: size, energy, energy density and velocity, on DNA composition. Quantitative estimates were made for the characteristics of kinks activated in polynucleotide chains analogous to promoter sequences A₁, A₂, and A₃ of bacteriophage T7.     

Persistent propensities: Portrait of a familiar controversy

Susan Mills and John Beatty's propensity interpretation of fitness encountered very different philosophical criticisms by Alexander Rosenberg and Kenneth Waters. These criticisms and the rejoinders to them are both predictable and important. They are predictable as raisingkinds of issues typically associated with disposition concepts (this is established through a systematic review of the problems generated by Carnap's dispositional interpretation of all scientific terms). They are important as referring the resolution of these issues to the development of evolutionary biology. This historical approach to the propensity interpretation of fitness draws attention to the precarious relation between philosophical clarification of scientific concepts and any given state of the empirical arts.