DeepLabCut increases markerless tracking efficiency in X-ray video analysis of rodent locomotion.

Despite the prevalence of rat models to study human disease and injury, existing methods for quantifying behavior through skeletal movements are problematic owing to skin movement inaccuracies associated with optical video analysis, or require invasive implanted markers or time-consuming manual rotoscoping for X-ray video approaches. We examined the use of a machine learning tool, DeepLabCut, to perform automated, markerless tracking in bi-planar X-ray videos of locomoting rats. Models were trained on 590 pairs of video frames to identify 19 unique skeletal landmarks of the pelvic limb. Accuracy, precision and time savings were assessed. Machine-identified landmarks deviated from manually labeled counterparts by 2.4±0.2 mm (n=1710 landmarks). DeepLabCut decreased analysis time by over three orders of magnitude (1627×) compared with manual labeling. Distribution of these models may enable the processing of a large volume of accurate X-ray kinematics locomotion data in a fraction of the time without requiring surgically implanted markers.

Core Competencies for Undergraduates in Bioengineering and Biomedical Engineering: Findings, Consequences, and Recommendations.

This paper provides a synopsis of discussions related to biomedical engineering core curricula that occurred at the Fourth BME Education Summit held at Case Western Reserve University in Cleveland, Ohio in May 2019. This summit was organized by the Council of Chairs of Bioengineering and Biomedical Engineering, and participants included over 300 faculty members from 100+ accredited undergraduate programs. This discussion focused on six key questions: QI: Is there a core curriculum, and if so, what are its components? QII: How does our purported core curriculum prepare students for careers, particularly in industry? QIII: How does design distinguish BME/BIOE graduates from other engineers? QIV: What is the state of engineering analysis and systems-level modeling in BME/BIOE curricula? QV: What is the role of data science in BME/BIOE undergraduate education? QVI: What core experimental skills are required for BME/BIOE undergrads? s. Indeed, BME/BIOI core curricula exists and has matured to emphasize interdisciplinary topics such as physiology, instrumentation, mechanics, computer programming, and mathematical modeling. Departments demonstrate their own identities by highlighting discipline-specific sub-specialties. In addition to technical competence, Industry partners most highly value our students' capacity for problem solving and communication. As such, BME/BIOE curricula includes open-ended projects that address unmet patient and clinician needs as primary methods to prepare graduates for careers in industry. Culminating senior design experiences distinguish BME/BIOE graduates through their development of client-centered engineering solutions to healthcare problems. Finally, the overall BME/BIOE curriculum is not stagnant-it is clear that data science will become an ever-important element of our students' training and that new methods to enhance student engagement will be of pedagogical importance as we embark on the next decade.

Challenges associated with nerve conduction block using kilohertz electrical stimulation.

Neuromodulation therapies, which electrically stimulate parts of the nervous system, have traditionally attempted to activate neurons or axons to restore function or alleviate disease symptoms. In stark contrast to this approach is inhibiting neural activity to relieve disease symptoms and/or restore homeostasis. One potential approach is kilohertz electrical stimulation (KES) of peripheral nerves-which enables a rapid, reversible, and localized block of conduction. This review highlights the existing scientific and clinical utility of KES and discusses the technical and physiological challenges that must be addressed for successful translation of KES nerve conduction block therapies.

Kilohertz Electrical Stimulation Nerve Conduction Block: Effects of Electrode Material.

Kilohertz electrical stimulation (KES) has enabled a novel new paradigm for spinal cord and peripheral nerve stimulation to treat a variety of neurological diseases. KES can excite or inhibit nerve activity and is used in many clinical devices today. However, the impact of different electrode materials on the efficacy of KES is unknown. We investigated the effect of different electrode materials and their respective charge injection mechanisms on KES nerve block thresholds using 20- and 40-kHz current-controlled sinusoidal KES waveforms. We evaluated the nerve block threshold and the power requirements for achieving an effective KES nerve block. In addition, we evaluated potential effects on the onset duration and recovery of normal conduction after delivery of KES. We found that thresholds and the onset and recovery of KES nerve block are not a function of the electrode material. In contrast, the power dissipation varies among electrode materials and is a function of the materials' properties at high frequencies. We conclude that materials with a proven track record of chronic stability, both for the tissue and electrode, are suitable for developing KES nerve block therapies.

Corrigendum: Kilohertz frequency nerve block enhances anti-inflammatory effects of vagus nerve stimulation.

This corrects the article DOI: 10.1038/srep39810.

Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI).

The ability to experimentally perturb biological systems has traditionally been limited to static pre-programmed or operator-controlled protocols. In contrast, real-time control allows dynamic probing of biological systems with perturbations that are computed on-the-fly during experimentation. Real-time control applications for biological research are available; however, these systems are costly and often restrict the flexibility and customization of experimental protocols. The Real-Time eXperiment Interface (RTXI) is an open source software platform for achieving hard real-time data acquisition and closed-loop control in biological experiments while retaining the flexibility needed for experimental settings. RTXI has enabled users to implement complex custom closed-loop protocols in single cell, cell network, animal, and human electrophysiology studies. RTXI is also used as a free and open source, customizable electrophysiology platform in open-loop studies requiring online data acquisition, processing, and visualization. RTXI is easy to install, can be used with an extensive range of external experimentation and data acquisition hardware, and includes standard modules for implementing common electrophysiology protocols.

Kilohertz Electrical Stimulation Nerve Conduction Block: Effects of Electrode Surface Area.

Kilohertz electrical stimulation (KES) induces repeatable and reversible conduction block of nerve activity and is a potential therapeutic option for various diseases and disorders resulting from pathological or undesired neurological activity. However, successful translation of KES nerve block to clinical applications is stymied by many unknowns, such as the relevance of the onset response, acceptable levels of waveform contamination, and optimal electrode characteristics. We investigated the role of electrode geometric surface area on the KES nerve block threshold using 20- and 40-kHz current-controlled sinusoidal KES. Electrodes were electrochemically characterized and used to characterize typical KES waveforms and electrode charge characteristics. KES nerve block amplitudes, onset duration, and recovery of normal conduction after delivery of the KES were evaluated along with power requirements for effective KES nerve block. Results from this investigation demonstrate that increasing electrode geometric surface area provides for a more power-efficient KES nerve block. Reductions in block threshold by increased electrode surface area were found to be KES-frequency-dependent, with block thresholds and average power consumption reduced by greater than two times with 20-kHz KES waveforms and greater than three times for 40-kHz KES waveforms.

Kilohertz frequency nerve block enhances anti-inflammatory effects of vagus nerve stimulation.

Efferent activation of the cervical vagus nerve (cVN) dampens systemic inflammatory processes, potentially modulating a wide-range of inflammatory pathological conditions. In contrast, afferent cVN activation amplifies systemic inflammatory processes, leading to activation of the hypothalamic-pituitary-adrenal (HPA) axis, the sympathetic nervous system through the greater splanchnic nerve (GSN), and elevation of pro-inflammatory cytokines. Ideally, to clinically implement anti-inflammatory therapy via cervical vagus nerve stimulation (cVNS) one should selectively activate the efferent pathway. Unfortunately, current implementations, in animal and clinical investigations, activate both afferent and efferent pathways. We paired cVNS with kilohertz electrical stimulation (KES) nerve block to preferentially activate efferent pathways while blocking afferent pathways. Selective efferent cVNS enhanced the anti-inflammatory effects of cVNS. Our results demonstrate that: (i) afferent, but not efferent, cVNS synchronously activates the GSN in a dose-dependent manner; (ii) efferent cVNS enabled by complete afferent KES nerve block enhances the anti-inflammatory benefits of cVNS; and (iii) incomplete afferent KES nerve block exacerbates systemic inflammation. Overall, these data demonstrate the utility of paired efferent cVNS and afferent KES nerve block for achieving selective efferent cVNS, specifically as it relates to neuromodulation of systemic inflammation.

Stochastic slowly adapting ionic currents may provide a decorrelation mechanism for neural oscillators by causing wander in the intrinsic period.

Oscillatory neurons integrate their synaptic inputs in fundamentally different ways than normally quiescent neurons. We show that the oscillation period of invertebrate endogenous pacemaker neurons wanders, producing random fluctuations in the interspike intervals (ISI) on a time scale of seconds to minutes, which decorrelates pairs of neurons in hybrid circuits constructed using the dynamic clamp. The autocorrelation of the ISI sequence remained high for many ISIs, but the autocorrelation of the ΔISI series had on average a single nonzero value, which was negative at a lag of one interval. We reproduced these results using a simple integrate and fire (IF) model with a stochastic population of channels carrying an adaptation current with a stochastic component that was integrated with a slow time scale, suggesting that a similar population of channels underlies the observed wander in the period. Using autoregressive integrated moving average (ARIMA) models, we found that a single integrator and a single moving average with a negative coefficient could simulate both the experimental data and the IF model. Feeding white noise into an integrator with a slow time constant is sufficient to produce the autocorrelation structure of the ISI series. Moreover, the moving average clearly accounted for the autocorrelation structure of the ΔISI series and is biophysically implemented in the IF model using slow stochastic adaptation. The observed autocorrelation structure may be a neural signature of slow stochastic adaptation, and wander generated in this manner may be a general mechanism for limiting episodes of synchronized activity in the nervous system.

Microneedle cuff electrodes for extrafascicular peripheral nerve interfacing.

OBJECTIVE: The work presented here describes a new tool for peripheral nerve interfacing, called the microneedle cuff (µN-cuff) electrode. APPROACH: µN arrays are designed and integrated into cuff electrodes for penetrating superficial tissues while remaining non-invasive to delicate axonal tracts. MAIN RESULTS: In acute testing, the presence of 75 µm height µNs decreased the electrode-tissue interface impedance by 0.34 kΩ, resulting in a 0.9 mA reduction in functional stimulation thresholds and increased the signal-to-noise ratio by 9.1 dB compared to standard (needle-less) nerve cuff electrodes. Preliminary acute characterization suggests that µN-cuff electrodes provide the stability and ease of use of standard cuff electrodes while enhancing electrical interfacing characteristics. SIGNIFICANCE: The ability to stimulate, block, and record peripheral nerve activity with greater specificity, resolution, and fidelity can enable more precise spatiotemporal control and measurement of neural circuits.

Differential fiber-specific block of nerve conduction in mammalian peripheral nerves using kilohertz electrical stimulation.

Kilohertz electrical stimulation (KES) has been shown to induce repeatable and reversible nerve conduction block in animal models. In this study, we characterized the ability of KES stimuli to selectively block specific components of stimulated nerve activity using in vivo preparations of the rat sciatic and vagus nerves. KES stimuli in the frequency range of 5-70 kHz and amplitudes of 0.1-3.0 mA were applied. Compound action potentials were evoked using either electrical or sensory stimulation, and block of components was assessed through direct nerve recordings and muscle force measurements. Distinct observable components of the compound action potential had unique conduction block thresholds as a function of frequency of KES. The fast component, which includes motor activity, had a monotonically increasing block threshold as a function of the KES frequency. The slow component, which includes sensory activity, showed a nonmonotonic block threshold relationship with increasing KES frequency. The distinct trends with frequency of the two components enabled selective block of one component with an appropriate choice of frequency and amplitude. These trends in threshold of the two components were similar when studying electrical stimulation and responses of the sciatic nerve, electrical stimulation and responses of the vagus nerve, and sensorimotor stimulation and responses of the sciatic nerve. This differential blocking effect of KES on specific fibers can extend the applications of KES conduction block to selective block and stimulation of neural signals for neuromodulation as well as selective control of neural circuits underlying sensorimotor function.

Dynamic clamp in cardiac and neuronal systems using RTXI.

The injection of computer-simulated conductances through the dynamic clamp technique has allowed researchers to probe the intercellular and intracellular dynamics of cardiac and neuronal systems with great precision. By coupling computational models to biological systems, dynamic clamp has become a proven tool in electrophysiology with many applications, such as generating hybrid networks in neurons or simulating channelopathies in cardiomyocytes. While its applications are broad, the approach is straightforward: synthesizing traditional patch clamp, computational modeling, and closed-loop feedback control to simulate a cellular conductance. Here, we present two example applications: artificial blocking of the inward rectifier potassium current in a cardiomyocyte and coupling of a biological neuron to a virtual neuron through a virtual synapse. The design and implementation of the necessary software to administer these dynamic clamp experiments can be difficult. In this chapter, we provide an overview of designing and implementing a dynamic clamp experiment using the Real-Time eXperiment Interface (RTXI), an open-source software system tailored for real-time biological experiments. We present two ways to achieve this using RTXI's modular format, through the creation of a custom user-made module and through existing modules found in RTXI's online library.

Slow noise in the period of a biological oscillator underlies gradual trends and abrupt transitions in phasic relationships in hybrid neural networks.

In order to study the ability of coupled neural oscillators to synchronize in the presence of intrinsic as opposed to synaptic noise, we constructed hybrid circuits consisting of one biological and one computational model neuron with reciprocal synaptic inhibition using the dynamic clamp. Uncoupled, both neurons fired periodic trains of action potentials. Most coupled circuits exhibited qualitative changes between one-to-one phase-locking with fairly constant phasic relationships and phase slipping with a constant progression in the phasic relationships across cycles. The phase resetting curve (PRC) and intrinsic periods were measured for both neurons, and used to construct a map of the firing intervals for both the coupled and externally forced (PRC measurement) conditions. For the coupled network, a stable fixed point of the map predicted phase locking, and its absence produced phase slipping. Repetitive application of the map was used to calibrate different noise models to simultaneously fit the noise level in the measurement of the PRC and the dynamics of the hybrid circuit experiments. Only a noise model that added history-dependent variability to the intrinsic period could fit both data sets with the same parameter values, as well as capture bifurcations in the fixed points of the map that cause switching between slipping and locking. We conclude that the biological neurons in our study have slowly-fluctuating stochastic dynamics that confer history dependence on the period. Theoretical results to date on the behavior of ensembles of noisy biological oscillators may require re-evaluation to account for transitions induced by slow noise dynamics.

Electrical polarization of titanium surfaces for the enhancement of osteoblast differentiation.

Electrical stimulation has been used clinically to promote bone regeneration in cases of fractures with delayed union or nonunion, with several in vitro and in vivo reports suggesting its beneficial effects on bone formation. However, the use of electrical stimulation of titanium (Ti) implants to enhance osseointegration is less understood, in part because of the few in vitro models that attempt to represent the in vivo environment. In this article, the design of a new in vitro system that allows direct electrical stimulation of osteoblasts through their Ti substrates without the flow of exogenous currents through the media is presented, and the effect of applied electrical polarization on osteoblast differentiation and local factor production was evaluated. A custom-made polycarbonate tissue culture plate was designed to allow electrical connections directly underneath Ti disks placed inside the wells, which were supplied with electrical polarization ranging from 100 to 500 mV to stimulate MG63 osteoblasts. Our results show that electrical polarization applied directly through Ti substrates on which the cells are growing in the absence of applied electrical currents may increase osteoblast differentiation and local factor production in a voltage-dependent manner.

Contentious problems in bioscience and biotechnology: a pilot study of an approach to ethics education.

This manuscript describes a pilot study in ethics education employing a problem-based learning approach to the study of novel, complex, ethically fraught, unavoidably public, and unavoidably divisive policy problems, called "fractious problems," in bioscience and biotechnology. Diverse graduate and professional students from four US institutions and disciplines spanning science, engineering, humanities, social science, law, and medicine analyzed fractious problems employing "navigational skills" tailored to the distinctive features of these problems. The students presented their results to policymakers, stakeholders, experts, and members of the public. This approach may provide a model for educating future bioscientists and bioengineers so that they can meaningfully contribute to the social understanding and resolution of challenging policy problems generated by their work.

Dynamics of neuromodulatory feedback determines frequency modulation in a reduced respiratory network: a computational study.

Neuromodulators, such as amines and neuropeptides, alter the activity of neurons and neuronal networks. In this work, we investigate how neuromodulators, which activate G(q)-protein second messenger systems, can modulate the bursting frequency of neurons in a critical portion of the respiratory neural network, the pre-Bötzinger complex (preBötC). These neurons are a vital part of the ponto-medullary neuronal network, which generates a stable respiratory rhythm whose frequency is regulated by neuromodulator release from the nearby Raphe nucleus. Using a simulated 50-cell network of excitatory preBötC neurons with a heterogeneous distribution of persistent sodium conductance and Ca(2+), we determined conditions for frequency modulation in such a network by simulating interaction between Raphe and preBötC nuclei. We found that the positive feedback between the Raphe excitability and preBötC activity induces frequency modulation in the preBötC neurons. In addition, the frequency of the respiratory rhythm can be regulated via phasic release of excitatory neuromodulators from the Raphe nucleus. We predict that the application of a G(q) antagonist will eliminate this frequency modulation by the Raphe and keep the network frequency constant and low. In contrast, application of a G(q) agonist will result in a high frequency for all levels of Raphe stimulation. Our modeling results also suggest that high [K(+)] requirement in respiratory brain slice experiments may serve as a compensatory mechanism for low neuromodulatory tone.

High-frequency stimulation selectively blocks different types of fibers in frog sciatic nerve.

Conduction block using high-frequency alternating current (HFAC) stimulation has been shown to reversibly block conduction through various nerves. However, unlike simulations and experiments on myelinated fibers, prior experimental work in our lab on the sea-slug, Aplysia, found a nonmonotonic relationship between frequency and blocking thresholds in the unmyelinated fibers. To resolve this discrepancy, we investigated the effect of HFAC waveforms on the compound action potential of the sciatic nerve of frogs. Maximal stimulation of the nerve produces a compound action potential consisting of the A-fiber and C-fiber components corresponding to the myelinated and unmyelinated fibers' response. In our study, HFAC waveforms were found to induce reversible block in the A-fibers and C-fibers for frequencies in the range of 5-50 kHz and for amplitudes from 0.1-1 mA. Although the A-fibers demonstrated the monotonically increasing threshold behavior observed in published literature, the C-fibers displayed a nonmonotonic relationship, analogous to that observed in the unmyelinated fibers of Aplysia. This differential blocking behavior observed in myelinated and unmyelinated fibers during application of HFAC waveforms has diverse implications for the fields of selective stimulation and pain management.

Conflicting effects of excitatory synaptic and electric coupling on the dynamics of square-wave bursters.

Using two-cell and 50-cell networks of square-wave bursters, we studied how excitatory coupling of individual neurons affects the bursting output of the network. Our results show that the effects of synaptic excitation vs. electrical coupling are distinct. Increasing excitatory synaptic coupling generally increases burst duration. Electrical coupling also increases burst duration for low to moderate values, but at sufficiently strong values promotes a switch to highly synchronous bursts where further increases in electrical or synaptic coupling have a minimal effect on burst duration. These effects are largely mediated by spike synchrony, which is determined by the stability of the in-phase spiking solution during the burst. Even when both coupling mechanisms are strong, one form (in-phase or anti-phase) of spike synchrony will determine the burst dynamics, resulting in a sharp boundary in the space of the coupling parameters. This boundary exists in both two cell and network simulations. We use these results to interpret the effects of gap-junction blockers on the neuronal circuitry that underlies respiration.

Synaptic and intrinsic determinants of the phase resetting curve for weak coupling.

A phase resetting curve (PRC) keeps track of the extent to which a perturbation at a given phase advances or delays the next spike, and can be used to predict phase locking in networks of oscillators. The PRC can be estimated by convolving the waveform of the perturbation with the infinitesimal PRC (iPRC) under the assumption of weak coupling. The iPRC is often defined with respect to an infinitesimal current as z(i)(ϕ), where ϕ is phase, but can also be defined with respect to an infinitesimal conductance change as z(g)(ϕ). In this paper, we first show that the two approaches are equivalent. Coupling waveforms corresponding to synapses with different time courses sample z(g)(ϕ) in predictably different ways. We show that for oscillators with Type I excitability, an anomalous region in z(g)(ϕ) with opposite sign to that seen otherwise is often observed during an action potential. If the duration of the synaptic perturbation is such that it effectively samples this region, PRCs with both advances and delays can be observed despite Type I excitability. We also show that changing the duration of a perturbation so that it preferentially samples regions of stable or unstable slopes in z(g)(ϕ) can stabilize or destabilize synchrony in a network with the corresponding dynamics.

Effects of heterogeneity in synaptic conductance between weakly coupled identical neurons.

A significant degree of heterogeneity in synaptic conductance is present in neuron to neuron connections. We study the dynamics of weakly coupled pairs of neurons with heterogeneities in synaptic conductance using Wang-Buzsaki and Hodgkin-Huxley model neurons which have Types I and II excitability, respectively. This type of heterogeneity breaks a symmetry in the bifurcation diagrams of equilibrium phase difference versus the synaptic rate constant when compared to the identical case. For weakly coupled neurons coupled with identical values of synaptic conductance a phase locked solution exists for all values of the synaptic rate constant, α. In particular, in-phase and anti-phase solutions are guaranteed to exist for all α. Heterogeneity in synaptic conductance results in regions where no phase locked solution exists and the general loss of the ubiquitous in-phase and anti-phase solutions of the identically coupled case. We explain these results through examination of interaction functions using the weak coupling approximation and an in-depth analysis of the underlying multiple cusp bifurcation structure of the systems of coupled neurons.