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PubMed1995

Three-dimensional structure of halorhodopsin at 7 A resolution.

Two-dimensional crystalline patches containing the light-driven chloride pump, halorhodopsin, appear to form spontaneously in the cell membrane of an overproducing strain of Halobacterium. The three-dimensional structure (space group p42(1)2, a = 102 A) has been analysed by electron cryo-microscopy of tilted specimens. The map shows that halorhodopsin (HR) has an arrangement of seven transmembrane helices similar to that found in the related proton pump bacteriohodopsin (BR). The orientation of the polypeptide framework of HR in the membrane is rotated by 3 degrees relative to BR about an axis in the plane and the intramolecular space between the helices BC FG, which line the cytoplasmic half channel, appears slightly larger in HR than in BR, as would be expected for a chloride channel. The crystals of HR were too small for electron diffraction analysis of tilted specimens, so both the amplitudes and the phases of the Fourier components were obtained from images. This required anisotropic scaling of the image amplitudes in addition to correction for the defocus phase contrast transfer function. The procedure of rescaling the data (in this case roughly equivalent to sharpening with a temperature factor of-490) to compensate for a variety of image and crystal defects may also prove useful in the analysis of other structures for which no prior knowledge of a homologous structure exists and for which only small crystals can be obtained.

Amino Acid Sequence↗

PubMed2001

Conformation and rigidity of DNA microcircles containing waf1 response element for p53 regulatory protein.

The tumor-suppressor activity of p53 is closely related to its DNA-binding properties. It binds a number of DNA response-elements and it is likely that these share a common structural feature. Here, we present a new, general method to determine the absolute twist of flexible DNA promoter sequences based on direct imaging of the topology of microcircles containing the sequences. We have used magnetically driven dynamic force microscopy ("MacMode" AFM) to observe, in solution, the conformation of 168 base-pair DNA microcircles, each containing four equally spaced copies of the waf1/cip1/p21 p53 response-element. Analysis of the images showed that the microcircles are markedly puckered with a small excess of negatively writhed molecules. The average measured values of writhe are 0.109+/-0.013 (for 60 positively writhed molecules) and -0.098+/-0.011 (for 65 negatively writhed molecules). These values lead directly to a difference in linking number for the positively and negatively writhed molecules prior to ligation, from which we derive a twist mismatch of 178 degrees (overtwist). This is 44.5 degrees for each 42-mer precursor containing a single waf1/cip1/p21 p53 response-element, in good agreement with the range of values deduced by indirect biochemical techniques. The two values of writhe may also be used to determine the ratio of the bending (B) to twisting (C) rigidity, yielding B/C=0.23. This is about one-third of the value for long, random-sequence DNA, suggesting that the waf1/cip1/p21 p53 response-element is extremely flexible, a result that is also consistent with indirect biochemical experiments. These results support the idea, proposed by us earlier, that torsional stress may play a role in the regulation of p53 binding through modulation of twist at the binding site.

Aluminum Silicates↗

PubMed1991

The use of a new laser particle sizer and shape analyser to detect and evaluate gelatinous microparticles suspended in reconstituted anthracycline infusion solutions.

The anthracyclines are an important group of antitumour drugs: the best known anthracyclines are doxorubicin (Adriamycin) and epirubicin (Pharmorubicin), both of which are very active against a wide range of solid tumours and haematological malignancies. They are marketed as lyophilized formulations that need to be reconstituted for administration with water for injections or sodium chloride injection. With the aim of reducing the risks of contamination during reconstitution (spillage, spray formation, etc.) and of enhancing the rate of dissolution (that is otherwise slow because of the formation of conglomerates and gelatinous masses), a new formulation (rapid dissolution formula, RDF) containing parabens (hydroxybenzoate esters) as anti-aggregants has been developed; the formulation is a freeze-dried product and is characterized by a practically instantaneous and complete reconstitution. A valid estimate of the completeness of dissolution has been objectively achieved by means of an instrument (Galai CIS-1) that acts both as a particle sizer and a shape analyser; the instrument is equipped with a rotating laser system that defines a toroidal-cylindrical space inside the solution in which every moving particle is measured and, at the same time, visualized on a monitor by an electronically driven video microscope. The instrument has been applied with very satisfactory results to the visualization of the reconstitutional behaviour of commercial lots of Adriamycin and Pharmorubicin lyophilized products, reconstituted at a concentration of 2 mg ml-1 with sodium chloride injection.

Doxorubicin↗

PubMed2001

Biocomplexity: adaptive behavior in complex stochastic dynamical systems.

Existing methods of complexity research are capable of describing certain specifics of bio systems over a given narrow range of parameters but often they cannot account for the initial emergence of complex biological systems, their evolution, state changes and sometimes-abrupt state transitions. Chaos tools have the potential of reaching to the essential driving mechanisms that organize matter into living substances. Our basic thesis is that while established chaos tools are useful in describing complexity in physical systems, they lack the power of grasping the essence of the complexity of life. This thesis illustrates sensory perception of vertebrates and the operation of the vertebrate brain. The study of complexity, at the level of biological systems, cannot be completed by the analytical tools, which have been developed for non-living systems. We propose a new approach to chaos research that has the potential of characterizing biological complexity. Our study is biologically motivated and solidly based in the biodynamics of higher brain function. Our biocomplexity model has the following features, (1) it is high-dimensional, but the dimensionality is not rigid, rather it changes dynamically; (2) it is not autonomous and continuously interacts and communicates with individual environments that are selected by the model from the infinitely complex world; (3) as a result, it is adaptive and modifies its internal organization in response to environmental factors by changing them to meet its own goals; (4) it is a distributed object that evolves both in space and time towards goals that is continually re-shaping in the light of cumulative experience stored in memory; (5) it is driven and stabilized by noise of internal origin through self-organizing dynamics. The resulting theory of stochastic dynamical systems is a mathematical field at the interface of dynamical system theory and stochastic differential equations. This paper outlines several possible avenues to analyze these systems. Of special interest are input-induced and noise-generated, or spontaneous state-transitions and related stability issues.

Adaptation, Physiological↗

PubMedDate not supplied

Long-term in vivo left ventricular assist device study with a titanium centrifugal pump.

A totally implantable centrifugal artificial heart has been developed. The plastic prototype, Gyro PI 601, passed 2 day hemodynamic tests as a functional total artificial heart, 2 week screening tests for antithrombogenicity, and 1 month system feasibility. Based on these results, a metallic prototype, Gyro PI 702, was subjected to in vivo left ventricular assist device (LVAD) studies. The pump system employed the Gyro PI 702, which has the same inner dimensions and the same characteristics as the Gyro PI 601, including an eccentric inlet port, a double pivot bearing system, and a magnet coupling system. The PI 702 is driven with the Vienna DC brushless motor actuator. For the in vivo LVAD study, the pump actuator package was implanted in the preperitoneal space in two calves, from the left ventricular apex to the descending aorta. Case 1 achieved greater than 9 month survival without any complications, at an average flow rate of 6.6 L/min with 10.2 W input power. Case 2 was killed early due to the excessive growth of the calf, which caused functional obstruction of the inlet port. There was no blood clot inside the pump. During these periods, neither case exhibited any physiologic abnormalities. The PI 702 pump gives excellent results as a long-term implantable LVAD.

Equipment Design↗

PubMed2000

Ideal glass transitions for hard ellipsoids

For hard ellipsoids of revolution we calculate the phase diagram for the idealized glass transition. Our equations cover the glass physics in the full phase space, for all packing fractions and all aspect ratios X0. With increasing aspect ratio we find the idealized glass transition to become primarily driven by orientational degrees of freedom. For needlelike or platelike systems the transition is strongly influenced by a precursor of a nematic instability. We obtain three types of glass transition line. The first one (straight phi((B))(c)) corresponds to the conventional glass transition for spherical particles which is driven by the cage effect. At the second one (straight phi((B'))(c)), which occurs for rather nonspherical particles, a glass phase is formed that consists of domains. Within each domain there is a nematic order where the center of mass motion is quasiergodic, whereas the interdomain orientations build an orientational glass. The third glass transition line (straight phi((A))(c)) occurs for nearly spherical ellipsoids where the orientational degrees of freedom with odd parity, e.g., 180 degrees flips, freeze independently from the positions.

Journal Article↗

PubMed2005

The corticospinal system: from development to motor control.

The corticospinal system is the principal motor system for controlling movements that require the greatest skill and flexibility. It is the last motor system to develop. The pattern of termination of corticospinal axons, as they grow into the spinal gray matter, bears little resemblance to the pattern later in development and in maturity. Refinement of corticospinal terminations occurs during a protracted postnatal period and includes both elimination of transient terminations and growth to new targets. This refinement is driven by neural activity in the motor cortical areas and by limb motor experience. Developing corticospinal terminals compete with each other for synaptic space on spinal neurons. More active terminals are more competitive and are able to secure more synaptic space than their less active counterparts. Corticospinal terminals can activate spinal neurons from very early in development. The importance of this early synaptic activity appears to be more for refining corticospinal connections than for transmitting signals to spinal motor circuits for movement control. The motor control functions of the corticospinal system are not expressed until development of connectional specificity with spinal cord neurons, a strong capacity for corticospinal synapses to facilitate spinal motor circuits, and the formation of the cortical motor map.

Animals↗

PubMed1996

Periodontal repair in dogs: evaluation of rhBMP-2 carriers.

This study evaluated candidate carriers for recombinant human bone morphogenetic protein-2 (rhBMP-2)-driven periodontal regeneration. Previous experiments indicated the ability of rhBMP-2 in a particulate delivery system to result in substantial regeneration of bone and periodontal regeneration. In the present study, canine demineralized bone matrix (DBM), bovine deorganified crystalline bone matrix (Bio-Oss), an absorbable collagen sponge (ACS) of type I bovine collagen, poly(D,L-lactide-co-glycolide) microparticles (PLGA), and polylactic acid granules (Drilac) were tested for their ability to support rhBMP-2 (0.2 mg/mL implant volume)-driven periodontal regeneration. The implants were tested in routine critical size canine supra-alveolar periodontal defects with transgingival tooth positioning. Contralateral defects in six beagle dogs were semirandomly assigned to receive: DBM/rhBMP-2, DBM (no rhBMP-2), Bio-Oss/rhBMP-2, ACS/rhBMP-2, PLGA/rhBMP-2, or Drilac/rhBMP-2. Animals were sacrificed 8 weeks postsurgery, and block sections of the defects were processed for light microscopy. Substantial bone regeneration was observed in all defects implanted with rhBMP-2. Other measures of periodontal healing, including cementum regeneration and presence of ankylosis, were more variable between the implants. DBM and Bio-Oss performed well as carriers for rhBMP-2-driven periodontal regeneration, although other impediments to their clinical use exist. This study indicates that qualities of the carrier system, including its space-maintaining capacity can affect the ability of rhBMP-2 to regenerate both alveolar bone and periodontal attachment.

Alveolar Bone Loss↗

PubMed2004

An embedded network approach for scale-up of fluctuation-driven systems with preservation of spike information.

To address computational "scale-up" issues in modeling large regions of the cortex, many coarse-graining procedures have been invoked to obtain effective descriptions of neuronal network dynamics. However, because of local averaging in space and time, these methods do not contain detailed spike information and, thus, cannot be used to investigate, e.g., cortical mechanisms that are encoded through detailed spike-timing statistics. To retain high-order statistical information of spikes, we develop a hybrid theoretical framework that embeds a subnetwork of point neurons within, and fully interacting with, a coarse-grained network of dynamical background. We use a newly developed kinetic theory for the description of the coarse-grained background, in combination with a Poisson spike reconstruction procedure to ensure that our method applies to the fluctuation-driven regime as well as to the mean-driven regime. This embedded-network approach is verified to be dynamically accurate and numerically efficient. As an example, we use this embedded representation to construct "reverse-time correlations" as spiked-triggered averages in a ring model of orientation-tuning dynamics.

Cerebral Cortex↗

PubMed2006

Anisotropic rupture of polymer strips driven by Rayleigh instability.

We demonstrate that the separated polymer strips of micro- and sub-micro-length-scales rupture anisotropically along the strip direction, resulting in the formation of distinctly observable, regularly spaced polymer drops. The wavelength of the polymer drops and the surface tension dependence of the rupture behavior are found to be well represented by a relationship derived on the basis of Rayleigh instability. The period is proportional to the square root of the cross-sectional area of the strip and the proportionality constant depends on the contact angle. The rupture of polymer strips into polymer blocks instead of drops, which result when annealed with physically confining walls in place, is found to be well described by the same relationship.

Journal Article↗

PubMed1992

An experimental system for determining the influence of microgravity on B lymphocyte activation and cell fusion.

The influence of microgravity on lymphocyte activation is central to the understanding of immunological function in space. Moreover, the adaptation of groundbased technologies to microgravity conditions presents opportunities for biotechnological applications including high efficiency production of antibody forming hybridomas. Because the emerging technology of microgravity hybridoma generation is dependent upon activation and cultivation of B lymphocytes during flight, we have adapted mitogen-driven B lymphocyte stimulation and culture that allows for the in vitro generation of large numbers of antibody forming cells suitable for cell fusion over a period of 1-2 weeks. We believe that this activation and cultivation system can be flown on near-term space flights to test fundamental hypotheses about mammalian cell activation, cell fusion, metabolism, secretion, growth, and bio-separation.

Animals↗

PubMed2004

Effects of housing density and cage floor space on C57BL/6J mice.

The Guide for the Care and Use of Laboratory Animals (the Guide) is widely accepted as the housing standard by most Institutional Animal Care and Use Committees. The recommendations are based on best professional judgment rather than experimental data. Current efforts are directed toward replacing these guidelines with data-driven, species-appropriate standards. Our studies were undertaken to determine the optimum housing density for C57BL/6J mice, the most commonly used inbred mouse strain. Four-week-old mice were housed for 8 weeks at four densities (the recommended approximately 12 in2 [ca. 77.4 cm2]/mouse down to 5.6 in2 [ca. 36.1 cm2]/mouse) in three cage types with various amounts of floor space. Housing density did not affect a variety of physiologic parameters but did affect certain micro-environmental parameters, although these remained within accepted ranges. A second study was undertaken housing C57BL/6J mice with as little as 3.2 in2/mouse (ca. 20.6 cm2). The major effect was elevated ammonia concentrations that exceeded limits acceptable in the workplace at increased housing densities; however, the nasal passages and eyeballs of the mice remained microscopically normal. On the basis of these results, we conclude that C57BL/6J mice as large as 29 g may be housed with 5.6 in2 of floor space per mouse. This area is approximately half the floor space recommended in the Guide. The role of the Guide is to ensure that laboratory animals are well treated and housed in a species-appropriate manner. Our data suggest that current policies could be altered in order to provide the optimal habitation conditions matched to this species' social needs.

Age Factors↗

PubMed2005

Evaluation of ionic air purifiers for reducing aerosol exposure in confined indoor spaces.

UNLABELLED: Numerous techniques have been developed over the years for reducing aerosol exposure in indoor air environments. Among indoor air purifiers of different types, ionic emitters have gained increasing attention and are presently used for removing dust particles, aeroallergens and airborne microorganisms from indoor air. In this study, five ionic air purifiers (two wearable and three stationary) that produce unipolar air ions were evaluated with respect to their ability to reduce aerosol exposure in confined indoor spaces. The concentration decay of respirable particles of different properties was monitored in real time inside the breathing zone of a human manikin, which was placed in a relatively small (2.6 m3) walk-in chamber during the operation of an ionic air purifier in calm air and under mixing air condition. The particle removal efficiency as a function of particle size was determined using the data collected with a size-selective optical particle counter. The removal efficiency of the more powerful of the two wearable ionic purifiers reached about 50% after 15 min and almost 100% after 1.5 h of continuous operation in the chamber under calm air conditions. In the absence of external ventilation, air mixing, especially vigorous one (900 CFM), enhanced the air cleaning effect. Similar results were obtained when the manikin was placed inside a partial enclosure that simulated an aircraft seating configuration. All three stationary ionic air purifiers tested in this study were found capable of reducing the aerosol concentration in a confined indoor space. The most powerful stationary unit demonstrated an extremely high particle removal efficiency that increased sharply to almost 90% within 5-6 min, reaching about 100% within 10-12 min for all particle sizes (0.3-3 microm) tested in the chamber. For the units of the same emission rate, the data suggest that the ion polarity per se (negative vs. positive) does not affect the performance but the ion emission rate does. The effects of particle size (within the tested range) and properties (NaCl, PSL, Pseudomonas fluorescens bacteria) as well as the effects of the manikin's body temperature and its breathing on the ionic purifier performance were either small or insignificant. The data suggest that the unipolar ionic air purifiers are particularly efficient in reducing aerosol exposure in the breathing zone when used inside confined spaces with a relatively high surface-to-volume ratio. PRACTICAL IMPLICATIONS: Ionic air purifiers have become increasingly popular for removing dust particles, aeroallergens and airborne microorganisms from indoor air in various settings. While the indoor air cleaning effect, resulting from unipolar and bipolar ion emission, has been tested by several investigators, there are still controversial claims (favorable and unfavorable) about the performance of commercially available ionic air purifiers. Among the five tested ionic air purifiers (two wearable and three stationary) producing unipolar air ions, the units with a higher ion emission rate provided higher particle removal efficiency. The ion polarity (negative vs. positive), the particle size (0.3-3 microm) and properties (NaCl, PSL, Pseudomonas fluorescens bacteria), as well as the body temperature and breathing did not considerable affected the ionization-driven particle removal. The data suggest that the unipolar ionic air purifiers are particularly efficient in reducing aerosol exposure in the breathing zone when they are used inside confined spaces with a relatively high surface-to-volume ratio (such as automobile cabins, aircraft seating areas, bathrooms, cellular offices, small residential rooms, and animal confinements). Based on our experiments, we proposed that purifiers with a very high ion emission rate be operated in an intermittent mode if used indoors for extended time periods. As the particles migrate to and deposit on indoor surfaces during the operation of ionic air purifiers, some excessive surface contamination may occur, which introduces the need of periodic cleaning these surfaces.

Aerosols↗

PubMed2006

Partitioning the phase space in a natural way for scattering systems.

In this paper, we demonstrate a recent procedure for the construction of a symbolic dynamics for open systems by applying it to a model potential, the driven inverted Gaussian, which has proven very useful in describing laser-atom interaction. The symbolic dynamics and the corresponding partition of the Poincaré map are natural from the point of view of an asymptotic observer since the resulting branching tree coincides with the one extracted from the scattering functions. In general, the whole procedure is approximate because it only describes the globally unstable part of the chaotic invariant set, that is, the part that can be seen by an asymptotic observer in scattering data. It ignores Kolmogorov-Arnold-Moser islands and their fractal surroundings.

Journal Article↗

PubMed1996

Cooperative relaxation of supercoils and periodic transcriptional initiation within polymerase batteries.

Transcription and DNA supercoiling are known to be linked by a cause-effect relationship that operates in both directions. It is proposed here that this two-way relationship may be exploited by the E. coli genome to facilitate constitutive transcription of supercoil-sensitive genes by polymerase batteries made up of uniformly spaces RNA polymerase elongation complexes. Specifically, it is argued that (1) polymerases transcribing DNA in tandem cooperate to relax each other's transcription-driven positive supercoils; and (2) negative supercoils driven upstream by elongation complexes tend to be 'harnessed' and used to cooperatively (and periodically) initiate fresh transcription from promoters. Harnessing of transcription-driven negative supercoils is thought to be achieved through the erection of protein barriers to the rotational upstream propagation of supercoils from transcription events. The possible relevance of such cooperation amongst polymerases to the activation of transcription by DNA-binding protein factors is emphasized. Some testable predictions are made and implications are discussed.

DNA Topoisomerases, Type I↗

PubMed1989

Lateral coherence of the electrocorticogram: a new measure of brain synchrony.

As one test of the idea that compound field potentials in higher centers have a fine structure, the horizontal extent of coherence (C) was studied on the brain surface, with many closely spaced semimicroelectrodes in rabbits and rats. On the average C tends to fall with distance (D) in the 0.5-10 mm range; apart from driven rhythms, C usually falls to noise level at D greater than 10 mm. A useful measure is D (mm) where C has fallen to 0.5 (DC = 0.5); for most F bands within the range 1-50 Hz this is usually 2.5-5 mm, averaging over the neocortex in both species. Synchrony for neural tissue should mean a degree of congruence in a population (not a 2-point correlation); decline of C with D can measure synchrony by reflecting the volume at or above a specified C. Sleeping and waking mammals, an invertebrate (Aplysia), a ray, and a reptile were compared in degrees of synchrony; this cannot be judged by eye and is found sometimes hardly different between high-voltage-slow and low-voltage-fast states. Aplysia has negligible synchrony; the ray and lizard may be intermediate. C maps show patchiness superimposed on the general decline with D; no obvious pattern between parts of the cortex is consistent among individuals. Factors influencing variance, repeatability and extent of significant C are assessed. Brain size, passive spread, electrode size (at least 1-100 microns) and closeness of contact with pia mater rarely contribute materially, even within 1 mm. C commonly falls moderately with frequency (F) from a maximum between 1 and 8 Hz, usually without consistent peaks except for special cases of driving rhythms, such as theta. Intracortically the distribution of C is more local, both radially and horizontally. Although it was not possible to say when the two electrodes were in the same lamina, most laminae are highly coherent with all others. One or two sharp radial discontinuities in C are common, often but not consistently in the middle layers. C shows no simple relation to distance. In spite of the prevalent high coherence between laminae, radially, C varies widely horizontally from low to high in the 0.1-1 mm range. C is regarded as one aspect of cooperativity in a cellular dynamic system with fine structure in the fractional millimeter and second range; so far we are observing it with severely distorting smoothing procedures.

Animals↗

PubMed2002

Inducible expression of vascular endothelial growth factor in adult mice causes severe proliferative retinopathy and retinal detachment.

Transgenic mice with vascular endothelial growth factor (VEGF) driven by the rhodopsin promoter (rho/VEGF mice) develop neovascularization that originates from the deep capillary bed of the retina and grows into the subretinal space. In rho/VEGF mice, VEGF expression in photoreceptors begins between postnatal days 5 and 7, the period when the deep capillary bed is developing. An important question is whether or not the developmental stage of the deep capillary bed is critical for occurrence of neovascularization. Also, although rho/VEGF mice are extremely useful for the study of ocular neovascularization, there are some applications for which the early onset of VEGF expression is a disadvantage. In this study, we used the reverse tetracycline transactivator (rtTA) inducible promoter system coupled to either the rhodopsin or interphotoreceptor retinoid-binding protein (IRBP) promoter to control the time of onset of VEGF transgene expression in photoreceptors. In the absence of doxycycline, adult double-transgenic rho/rtTA-TRE/VEGF or IRBP/rtTA-TRE/VEGF mice showed little VEGF transgene expression and no phenotype. The addition of doxycycline to the drinking water resulted in prominent transgene expression and evidence of neovascularization within 3 to 4 days. Like rho/VEGF mice, the neovascularization originated from the deep capillary bed of the retina, but it was more extensive and caused outer retinal folds followed by total retinal detachment. Real-time polymerase chain reaction and enzyme-linked immunosorbent assay demonstrated that the mice with inducible expression of VEGF that developed retinal detachment had much higher ocular levels of VEGF mRNA and protein compared to rho/VEGF mice that manifest a much milder phenotype. These data demonstrate that regardless of developmental stage of the vascular bed, increased expression of VEGF in the retina is sufficient to cause neovascularization, and high levels of expression cause severe neovascularization and traction retinal detachment. Mice with inducible expression of VEGF in the retina provide a valuable new model of ocular neovascularization.

Animals↗

PubMed2001

Mode locking in a periodically forced integrate-and-fire-or-burst neuron model.

The minimal "integrate-and-fire-or-burst" (IFB) neuron model reproduces the salient features of experimentally observed thalamocortical relay neuron response properties, including the temporal tuning of both tonic spiking (i.e., conventional action potentials) and post-inhibitory rebound bursting mediated by the low-threshold Ca2+ current, I(T). In previous work focusing on experimental and IFB model responses to sinusoidal current injection, large regions of stimulus parameter space were observed for which the response was entrained to periodic applied current, resulting in repetitive burst, tonic, or mixed (i.e., burst followed by tonic) responses. Here we present an exact analysis of such mode-locking in the integrate-and-fire-or-burst model under the influence of arbitrary periodic forcing that includes sinusoidally driven responses as one case. In this analysis, the instabilities of mode-locked states are identified as both smooth bifurcations of an associated firing time map and nonsmooth bifurcations of the underlying discontinuous flow. The explicit construction of borders in parameter space that define the instabilities of mode-locked zones is used to build up the Arnol'd tongue structure for the model. The zones for mode-locking are shown to be in excellent agreement with numerical simulations and are used to explore the observed stimulus dependence of burst versus tonic response of the IFB neuron model.

Action Potentials↗