BrainSignals Revisited: Simplifying a Computational Model of Cerebral Physiology

Systemic physiology augmented functional near-infrared spectroscopy: a powerful approach to study the embodied human brain

In this Outlook paper, we explain why an accurate physiological interpretation of functional near-infrared spectroscopy (fNIRS) neuroimaging signals is facilitated when systemic physiological activity (e.g., cardiorespiratory and autonomic activity) is measured simultaneously by employing systemic physiology augmented functional near-infrared spectroscopy (SPA-fNIRS). The rationale for SPA-fNIRS is twofold: (i) SPA-fNIRS enables a more complete interpretation and understanding of the fNIRS signals measured at the head since they contain components originating from neurovascular coupling and from systemic physiological sources. The systemic physiology signals measured with SPA-fNIRS can be used for regressing out physiological confounding components in fNIRS signals. Misinterpretations can thus be minimized. (ii) SPA-fNIRS enables to study the embodied brain by linking the brain with the physiological state of the entire body, allowing novel insights into their complex interplay. We envisage the SPA-fNIRS approach will become increasingly important in the future.

Systems Biology Model of Cerebral Oxygen Delivery and Metabolism During Therapeutic Hypothermia: Application to the Piglet Model

Hypoxic ischaemic encephalopathy (HIE) is a significant cause of death and disability. Therapeutic hypothermia (TH) is the only available standard of treatment, but 45-55% of cases still result in death or neurodevelopmental disability following TH. This work has focussed on developing a new brain tissue physiology and biochemistry systems biology model that includes temperature effects, as well as a Bayesian framework for analysis of model parameter estimation. Through this, we can simulate the effects of temperature on brain tissue oxygen delivery and metabolism, as well as analyse clinical and experimental data to identify mechanisms to explain differing behaviour and outcome. Presented here is an application of the model to data from two piglets treated with TH following hypoxic-ischaemic injury showing different responses and outcome following treatment. We identify the main mechanism for this difference as the Q₁₀ temperature coefficient for metabolic reactions, with the severely injured piglet having a median posterior value of 0.133 as opposed to the mild injury value of 5.48. This work demonstrates the use of systems biology models to investigate underlying mechanisms behind the varying response to hypothermic treatment.

Quantification of the severity of hypoxic-ischemic brain injury in a neonatal preclinical model using measurements of cytochrome-c-oxidase from a miniature broadband-near-infrared spectroscopy system

We describe the development of a miniaturized broadband near-infrared spectroscopy system (bNIRS), which measures changes in cerebral tissue oxyhemoglobin ( [ HbO 2 ] ) and deoxyhemoglobin ([HHb]) plus tissue metabolism via changes in the oxidation state of cytochrome-c-oxidase ([oxCCO]). The system is based on a small light source and a customized mini-spectrometer. We assessed the instrument in a preclinical study in 27 newborn piglets undergoing transient cerebral hypoxia-ischemia (HI). We aimed to quantify the recovery of the HI insult and estimate the severity of the injury. The recovery in brain oxygenation ( Δ [ HbDiff ] = Δ [ HbO 2 ] - Δ [ HHb ] ), blood volume ( Δ [ HbT ] = Δ [ HbO 2 ] + Δ [ HHb ] ), and metabolism ( Δ [ oxCCO ] ) for up to 30 min after the end of HI were quantified in percentages using the recovery fraction (RF) algorithm, which quantifies the recovery of a signal with respect to baseline. The receiver operating characteristic analysis was performed on bNIRS-RF measurements compared to proton ( H 1 ) magnetic resonance spectroscopic (MRS)-derived thalamic lactate/N-acetylaspartate (Lac/NAA) measured at 24-h post HI insult; Lac/NAA peak area ratio is an accurate surrogate marker of neurodevelopmental outcome in babies with neonatal HI encephalopathy. The Δ [ oxCCO ] -RF cut-off threshold of 79% within 30 min of HI predicted injury severity based on Lac/NAA with high sensitivity (100%) and specificity (93%). A significant difference in thalamic Lac/NAA was noticed ( p < 0.0001 ) between the two groups based on this cut-off threshold of 79% Δ [ oxCCO ] -RF. The severe injury group ( n = 13 ) had ∼ 30 % smaller recovery in Δ [ HbDiff ] -RF ( p = 0.0001 ) and no significant difference was observed in Δ [ HbT ] -RF between groups. At 48 h post HI, significantly higher P 31 -MRS-measured inorganic phosphate/exchangeable phosphate pool (epp) ( p = 0.01 ) and reduced phosphocreatine/epp ( p = 0.003 ) were observed in the severe injury group indicating persistent cerebral energy depletion. Based on these results, the bNIRS measurement of the oxCCO recovery fraction offers a noninvasive real-time biomarker of brain injury severity within 30 min following HI insult.

Brain cytochrome-c-oxidase as a marker of mitochondrial function: A pilot study in major depression using NIRS

BACKGROUND

Brain mitochondrial dysfunction is implicated in the pathophysiology of mood disorders. Brain cytochrome-c-oxidase (COX) activity is associated with the mitochondrial function. Near-infrared spectroscopy (NIRS) noninvasively measures oxidized COX (oxCOX) and tissue oxygenation index (TOI) reflecting cerebral blood flow and oxygenation.

METHODS

oxCOX and TOI were assessed in prefrontal cortex (Fp1/2, Brodmann area 10) in patients in a major depressive episode (N = 13) with major depressive disorder (MDD; N = 7) and bipolar disorder (BD; N = 6) compared with the controls (N = 10). One patient with MDD and all the patients with BD were taking medications. Computational modeling estimated oxCOX and TOI related indices of mitochondrial function and cerebral blood flow, respectively.

RESULTS

oxCOX was lower in patients than controls (p = .014) correlating inversely with depression severity (r = -.72; p = .006), driven primarily by lower oxCOX in BD compared with the controls. Computationally modeled mitochondrial parameters of the electron transport chain, such as the nicotinamide adenine dinucleotide ratio (NAD⁺ /NADH; p = .001) and the proton leak rate across the inner mitochondrial membrane (k_lk2 ; p = .008), were also lower in patients and correlated inversely with depression severity. No such effects were found for TOI.

CONCLUSIONS

In this pilot study, oxCOX and related mitochondrial parameters assessed by NIRS indicate an abnormal cerebral metabolic state in mood disorders proportional to depression severity, potentially providing a biomarker of antidepressant effect. Because the effect was driven by the medicated BD group, findings need to be evaluated in a larger, medication-free population.

A Bayesian framework for the analysis of systems biology models of the brain

Systems biology models are used to understand complex biological and physiological systems. Interpretation of these models is an important part of developing this understanding. These models are often fit to experimental data in order to understand how the system has produced various phenomena or behaviour that are seen in the data. In this paper, we have outlined a framework that can be used to perform Bayesian analysis of complex systems biology models. In particular, we have focussed on analysing a systems biology of the brain using both simulated and measured data. By using a combination of sensitivity analysis and approximate Bayesian computation, we have shown that it is possible to obtain distributions of parameters that can better guard against misinterpretation of results, as compared to a maximum likelihood estimate based approach. This is done through analysis of simulated and experimental data. NIRS measurements were simulated using the same simulated systemic input data for the model in a ‘healthy’ and ‘impaired’ state. By analysing both of these datasets, we show that different parameter spaces can be distinguished and compared between different physiological states or conditions. Finally, we analyse experimental data using the new Bayesian framework and the previous maximum likelihood estimate approach, showing that the Bayesian approach provides a more complete understanding of the parameter space.

Systems biology models are mathematical representations of biological processes that reproduce the overall behaviour of a biological system. They are comprised by a number of parameters representing biological information. We use them to understand the behaviour of biological systems, such as the brain. We do this by fitting the model’s parameter to observed or simulated data; and by looking at how these values change during the fitting process we investigate the behaviour of our system. We are interested in understanding differences between a healthy and an injured brain. Here we outline a statistical framework that uses a Bayesian approach during the fitting process that can provide us with a distribution of parameters rather than single parameter number. We apply this method when simulating the physiological responses between a healthy and a vascular compromised brain to a drop in oxygenation. We then use experimental data that demonstrates the healthy brain response to an increase in arterial CO2 and fit our brain model predictions to the measurements. In both instances we show that our approach provides more information about the overlap between healthy and unhealthy brain states than a fitting process that provides a single value parameter estimate.

Multimodality Neuromonitoring in Adult Traumatic Brain Injury: A Narrative Review

Neuromonitoring plays an important role in the management of traumatic brain injury. Simultaneous assessment of cerebral hemodynamics, oxygenation, and metabolism allows an individualized approach to patient management in which therapeutic interventions intended to prevent or minimize secondary brain injury are guided by monitored changes in physiologic variables rather than generic thresholds. This narrative review describes various neuromonitoring techniques that can be used to guide the management of patients with traumatic brain injury and examines the latest evidence and expert consensus guidelines for neuromonitoring.

WeBCMD: A cross-platform interface for the BCMD modelling framework

Multimodal monitoring of the brain generates a great quantity of data, providing the potential for great insight into both healthy and injured cerebral dynamics. In particular, near-infrared spectroscopy can be used to measure various physiological variables of interest, such as haemoglobin oxygenation and the redox state of cytochrome-c-oxidase, alongside systemic signals, such as blood pressure. Interpreting these measurements is a complex endeavour, and much work has been done to develop mathematical models that can help to provide understanding of the underlying processes that contribute to the overall dynamics. BCMD is a software framework that was developed to run such models. However, obtaining, installing and running this software is no simple task. Here we present WeBCMD, an online environment that attempts to make the process simpler and much more accessible. By leveraging modern web technologies, an extensible and cross-platform package has been created that can also be accessed remotely from the cloud. WeBCMD is available as a Docker image and an online service.

Hyperoxia results in increased aerobic metabolism following acute brain injury

Acute brain injury is associated with depressed aerobic metabolism. Below a critical mitochondrial pO₂ cytochrome c oxidase, the terminal electron acceptor in the mitochondrial respiratory chain, fails to sustain oxidative phosphorylation. After acute brain injury, this ischaemic threshold might be shifted into apparently normal levels of tissue oxygenation. We investigated the oxygen dependency of aerobic metabolism in 16 acutely brain-injured patients using a 120-min normobaric hyperoxia challenge in the acute phase (24-72 h) post-injury and multimodal neuromonitoring, including transcranial Doppler ultrasound-measured cerebral blood flow velocity, cerebral microdialysis-derived lactate-pyruvate ratio (LPR), brain tissue pO₂ (p_brO₂), and tissue oxygenation index and cytochrome c oxidase oxidation state (oxCCO) measured using broadband spectroscopy. Increased inspired oxygen resulted in increased p_brO₂ [Δp_brO₂ 30.9 mmHg p < 0.001], reduced LPR [ΔLPR -3.07 p = 0.015], and increased cytochrome c oxidase (CCO) oxidation (Δ[oxCCO] + 0.32 µM p < 0.001) which persisted on return-to-baseline (Δ[oxCCO] + 0.22 µM, p < 0.01), accompanied by a 7.5% increase in estimated cerebral metabolic rate for oxygen ( p = 0.038). Our results are consistent with an improvement in cellular redox state, suggesting oxygen-limited metabolism above recognised ischaemic p_brO₂ thresholds. Diffusion limitation or mitochondrial inhibition might explain these findings. Further investigation is warranted to establish optimal oxygenation to sustain aerobic metabolism after acute brain injury.

Multimodality Neuromonitoring

The monitoring of systemic and central nervous system physiology is central to the management of patients with neurologic disease in the perioperative and critical care settings. There exists a range of invasive and noninvasive and global and regional monitors of cerebral hemodynamics, oxygenation, metabolism, and electrophysiology that can be used to guide treatment decisions after acute brain injury. With mounting evidence that a single neuromonitor cannot comprehensively detect all instances of cerebral compromise, multimodal neuromonitoring allows an individualized approach to patient management based on monitored physiologic variables rather than a generic one-size-fits-all approach targeting predetermined and often empirical thresholds.

Modelling confounding effects from extracerebral contamination and systemic factors on functional near-infrared spectroscopy

Haemodynamics-based neuroimaging is widely used to study brain function. Regional blood flow changes characteristic of neurovascular coupling provide an important marker of neuronal activation. However, changes in systemic physiological parameters such as blood pressure and concentration of CO2 can also affect regional blood flow and may confound haemodynamics-based neuroimaging. Measurements with functional near-infrared spectroscopy (fNIRS) may additionally be confounded by blood flow and oxygenation changes in extracerebral tissue layers. Here we investigate these confounds using an extended version of an existing computational model of cerebral physiology, ‘BrainSignals’. Our results show that confounding from systemic physiological factors is able to produce misleading haemodynamic responses in both positive and negative directions. By applying the model to data from previous fNIRS studies, we demonstrate that such potentially deceptive responses can indeed occur in at least some experimental scenarios. It is therefore important to record the major potential confounders in the course of fNIRS experiments. Our model may then allow the observed behaviour to be attributed among the potential causes and hence reduce identification errors.

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Confounding of fNIRS haemoglobin signals is simulated using a computational model.

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Model is extended to simulate scalp haemodynamics.

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Changes in blood pressure and CO₂ can mimic and mask functional activation.

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Experimental recording of systemic factors is recommended to aid interpretation.

Cerebral blood flow and autoregulation: current measurement techniques and prospects for noninvasive optical methods

Cerebral blood flow (CBF) and cerebral autoregulation (CA) are critically important to maintain proper brain perfusion and supply the brain with the necessary oxygen and energy substrates. Adequate brain perfusion is required to support normal brain function, to achieve successful aging, and to navigate acute and chronic medical conditions. We review the general principles of CBF measurements and the current techniques to measure CBF based on direct intravascular measurements, nuclear medicine, X-ray imaging, magnetic resonance imaging, ultrasound techniques, thermal diffusion, and optical methods. We also review techniques for arterial blood pressure measurements as well as theoretical and experimental methods for the assessment of CA, including recent approaches based on optical techniques. The assessment of cerebral perfusion in the clinical practice is also presented. The comprehensive description of principles, methods, and clinical requirements of CBF and CA measurements highlights the potentially important role that noninvasive optical methods can play in the assessment of neurovascular health. In fact, optical techniques have the ability to provide a noninvasive, quantitative, and continuous monitor of CBF and autoregulation.