Robust and Fast Markov Chain Monte Carlo Sampling of Diffusion MRI Microstructure Models

Machine learning with multiple modalities of brain magnetic resonance imaging data to identify the presence of bipolar disorder

BACKGROUND

Bipolar disorder (BD) is a chronic psychiatric mood disorder that is solely diagnosed based on clinical symptoms. These symptoms often overlap with other psychiatric disorders. Efforts to use machine learning (ML) to create predictive models for BD based on data from brain imaging are expanding but have often been limited using only a single modality and the exclusion of the cerebellum, which may be relevant in BD.

METHODS

In this study, we sought to improve ML classification of BD by combining information from structural, functional, and diffusion-weighted imaging. Participants (108 BD I, 78 control) with BD type I and matched controls were recruited into an imaging study. This dataset was randomly divided into training and testing sets. For each of the three modalities, a separate ML model was selected, trained, and then used to generate a prediction of the class of each test subject. Majority voting was used to combine results from the three models to make a final prediction of whether a subject had BD. An independent replication sample was used to evaluate the ability of the ML classification to generalize to data collected at other sites.

RESULTS

Combining the three machine learning models through majority voting resulted in an accuracy of 89.5 % for classification of the test subjects as being in the BD or control group. Bootstrapping resulted in a 95 % confidence interval of 78.9 %-97.4 % for test accuracy. Performance was reduced when only using 2 of the 3 modalities. Analysis of feature importance revealed that the cerebellum and nodes of the emotional control network were among the most important regions for classification. The machine learning model performed at chance on the independent replication sample.

CONCLUSION

BD I could be identified with high accuracy in our relatively small sample by combining structural, functional, and diffusion-weighted imaging data within a single site but not generalize well to an independent replication sample. Future studies using harmonized imaging protocols may facilitate generalization of ML models.

On the optimization of 3D inflow-based vascular-space-occupancy (iVASO) MRI for the quantification of arterial cerebral blood volume (CBVa)

PURPOSE

The inflow-based vascular-space-occupancy (iVASO) MRI was originally developed in a single-slice mode to measure arterial cerebral blood volume (CBVa). When vascular crushers are applied in iVASO, the signals can be sensitized predominantly to small pial arteries and arterioles. The purpose of this study is to perform a systematic optimization and evaluation of a 3D iVASO sequence on both 3 T and 7 T for the quantification of CBVa values in the human brain.

METHODS

Three sets of experiments were performed in three separate cohorts. (1) 3D iVASO MRI protocols were compared to single-slice iVASO, and the reproducibility of whole-brain 3D iVASO MRI was evaluated. (2) The effects from different vascular crushers in iVASO were assessed. (3) 3D iVASO MRI results were evaluated in arterial and venous blood vessels identified using ultrasmall-superparamagnetic-iron-oxides-enhanced MRI to validate its arterial origin.

RESULTS

3D iVASO scans showed signal-to-noise ratio (SNR) and CBVa measures consistent with single-slice iVASO with reasonable intrasubject reproducibility. Among the iVASO scans performed with different vascular crushers, the whole-brain 3D iVASO scan with a motion-sensitized-driven-equilibrium preparation with two binomial refocusing pulses and an effective TE of 50 ms showed the best suppression of macrovascular signals, with a relatively low specific absorption rate. When no vascular crusher was applied, the CBVa maps from 3D iVASO scans showed large CBVa values in arterial vessels but well-suppressed signals in venous vessels.

CONCLUSION

A whole-brain 3D iVASO MRI scan was optimized for CBVa measurement in the human brain. When only microvascular signals are desired, a motion-sensitized-driven-equilibrium-based vascular crusher with binomial refocusing pulses can be applied in 3D iVASO.

Deconvolution and Analysis of the 1H NMR Spectra of Crude Reaction Mixtures

Nuclear magnetic resonance (NMR) spectroscopy is an important analytical technique in synthetic organic chemistry, but its integration into high-throughput experimentation workflows has been limited by the necessity of manually analyzing the NMR spectra of new chemical entities. Current efforts to automate the analysis of NMR spectra rely on comparisons to databases of reported spectra for known compounds and, therefore, are incompatible with the exploration of new chemical space. By reframing the NMR spectrum of a reaction mixture as a joint probability distribution, we have used Hamiltonian Monte Carlo Markov Chain and density functional theory to fit the predicted NMR spectra to those of crude reaction mixtures. This approach enables the deconvolution and analysis of the spectra of mixtures of compounds without relying on reported spectra. The utility of our approach to analyze crude reaction mixtures is demonstrated with the experimental spectra of reactions that generate a mixture of isomers, such as Wittig olefination and C-H functionalization reactions. The correct identification of compounds in a reaction mixture and their relative concentrations is achieved with a mean absolute error as low as 1%.

Modeling gene expression cascades during cell state transitions

During cellular processes such as differentiation or response to external stimuli, cells exhibit dynamic changes in their gene expression profiles. Single-cell RNA sequencing (scRNA-seq) can be used to investigate these dynamic changes. To this end, cells are typically ordered along a pseudotemporal trajectory which recapitulates the progression of cells as they transition from one cell state to another. We infer transcriptional dynamics by modeling the gene expression profiles in pseudotemporally ordered cells using a Bayesian inference approach. This enables ordering genes along transcriptional cascades, estimating differences in the timing of gene expression dynamics, and deducing regulatory gene interactions. Here, we apply this approach to scRNA-seq datasets derived from mouse embryonic forebrain and pancreas samples. This analysis demonstrates the utility of the method to derive the ordering of gene dynamics and regulatory relationships critical for proper cellular differentiation and maturation across a variety of developmental contexts.

Age-Related Alterations in Gray Matter Microstructure in Older People With Remitted Major Depression at Risk for Dementia

Background

Major depressive disorder (MDD) in late life is a risk factor for mild cognitive impairment (MCI) and Alzheimer's disease. However, studies of gray matter changes have produced varied estimates of which structures are implicated in MDD and dementia. Changes in gray matter volume and cortical thickness are macrostructural measures for the microstructural processes of free water accumulation and dendritic spine loss.

Methods

We conducted multishell diffusion imaging to assess gray matter microstructure in 244 older adults with remitted MDD (n = 44), MCI (n = 115), remitted MDD+MCI (n = 61), or without psychiatric disorders or cognitive impairment (healthy control participants; n = 24). We estimated measures related to neurite density, orientation dispersion, and free water (isotropic volume fraction) using a biophysically plausible model (neurite orientation dispersion and density imaging).

Results

Results showed that increasing age was correlated with an increase in isotropic volume fraction and a decrease in orientation dispersion index, which is consistent with neuropathology dendritic loss. In addition, this relationship between age and increased isotropic volume fraction was more disrupted in the MCI group than in the remitted MDD or healthy control groups. However, the association between age and orientation dispersion index was similar for all 3 groups.

Conclusions

The findings suggest that the neurite orientation dispersion and density imaging measures could be used to identify biological risk factors for Alzheimer's disease, signifying both conventional neurodegeneration observed with MCI and dendritic loss seen in MDD.

Multishell diffusion MRI reveals whole-brain white matter changes in HIV

Diffusion tensor imaging (DTI) and diffusion kurtosis imaging (DKI) have been previously used to explore white matter related to human immunodeficiency virus (HIV) infection. While DTI and DKI suffer from low specificity, the Combined Hindered and Restricted Model of Diffusion (CHARMED) provides additional microstructural specificity. We used these three models to evaluate microstructural differences between 35 HIV-positive patients without neurological impairment and 20 healthy controls who underwent diffusion-weighted imaging using three b-values. While significant group effects were found in all diffusion metrics, CHARMED and DKI analyses uncovered wider involvement (80% vs. 20%) of all white matter tracts in HIV infection compared with DTI. In restricted fraction (FR) analysis, we found significant differences in the left corticospinal tract, middle cerebellar peduncle, right inferior cerebellar peduncle, right corticospinal tract, splenium of the corpus callosum, left superior cerebellar peduncle, left superior cerebellar peduncle, pontine crossing tract, left posterior limb of the internal capsule, and left/right medial lemniscus. These are involved in language, motor, equilibrium, behavior, and proprioception, supporting the functional integration that is frequently impaired in HIV-positivity. Additionally, we employed a machine learning algorithm (XGBoost) to discriminate HIV-positive patients from healthy controls using DTI and CHARMED metrics on an ROIwise basis, and unique contributions to this discrimination were examined using Shapley Explanation values. The CHARMED and DKI estimates produced the best performance. Our results suggest that biophysical multishell imaging, combining additional sensitivity and built-in specificity, provides further information about the brain microstructural changes in multimodal areas involved in attentive, emotional and memory networks often impaired in HIV patients.

Machine learning classification of chronic traumatic brain injury using diffusion tensor imaging and NODDI: A replication and extension study

Individuals with acute and chronic traumatic brain injury (TBI) are associated with unique white matter (WM) structural abnormalities, including fractional anisotropy (FA) differences. Our research group previously used FA as a feature in a linear support vector machine (SVM) pattern classifier, observing high classification between individuals with and without acute TBI (i.e., an area under the curve [AUC] value of 75.50%). However, it is not known whether FA could similarly classify between individuals with and without history of chronic TBI. Here, we attempted to replicate our previous work with a new sample, investigating whether FA could similarly classify between incarcerated men with (n = 80) and without (n = 80) self-reported history of chronic TBI. Additionally, given limitations associated with FA, including underestimation of FA values in WM tracts containing crossing fibers, we extended upon our previous study by incorporating neurite orientation dispersion and density imaging (NODDI) metrics, including orientation dispersion (ODI) and isotropic volume (Viso). A linear SVM based classification approach, similar to our previous study, was incorporated here to classify between individuals with and without self-reported chronic TBI using FA and NODDI metrics as separate features. Overall classification rates were similar when incorporating FA and NODDI ODI metrics as features (AUC: 82.50%). Additionally, NODDI-based metrics provided the highest sensitivity (ODI: 85.00%) and specificity (Viso: 82.50%) rates. The current study serves as a replication and extension of our previous study, observing that multiple diffusion MRI metrics can reliably classify between individuals with and without self-reported history of chronic TBI.

Neurodevelopmental patterns of early postnatal white matter maturation represent distinct underlying microstructure and histology

Cerebral white matter undergoes a rapid and complex maturation during the early postnatal period. Prior magnetic resonance imaging (MRI) studies of early postnatal development have often been limited by small sample size, single-modality imaging, and univariate analytics. Here, we applied nonnegative matrix factorization, an unsupervised multivariate pattern analysis technique, to T2w/T1w signal ratio maps from the Developing Human Connectome Project (n = 342 newborns) revealing patterns of coordinated white matter maturation. These patterns showed divergent age-related maturational trajectories, which were replicated in another independent cohort (n = 239). Furthermore, we showed that T2w/T1w signal variations in these maturational patterns are explained by differential contributions of white matter microstructural indices derived from diffusion-weighted MRI. Finally, we demonstrated how white matter maturation patterns relate to distinct histological features by comparing our findings with postmortem late fetal/early postnatal brain tissue staining. Together, these results delineate concise and effective representation of early postnatal white matter reorganization.

Structural and diffusion-weighted brain imaging predictors of attention-deficit/hyperactivity disorder and its symptomology in very young (4- to 7-year-old) children

The current study aimed to identify the key neurobiology of attention-deficit/hyperactivity disorder (ADHD), as it relates to ADHD diagnostic category and symptoms of hyperactive/impulsive behaviour and inattention. To do so, we adapted a predictive modelling approach to identify the key structural and diffusion-weighted brain imaging measures and their relative standing with respect to teacher ratings of executive function (EF) (measured by the Metacognition Index of the Behavior Rating Inventory of Executive Function [BRIEF]) and negativity and emotion regulation (ER) (measured by the Emotion Regulation Checklist [ERC]), in a critical young age range (ages 4 to 7, mean age 5.52 years, 82.2% Hispanic/Latino), where initial contact with educators and clinicians typically take place. Teacher ratings of EF and ER were predictive of both ADHD diagnostic category and symptoms of hyperactive/impulsive behaviour and inattention. Among the neural measures evaluated, the current study identified the critical importance of the largely understudied diffusion-weighted imaging measures for the underlying neurobiology of ADHD and its associated symptomology. Specifically, our analyses implicated the inferior frontal gyrus as a critical predictor of ADHD diagnostic category and its associated symptomology, above and beyond teacher ratings of EF and ER. Collectively, the current set of findings have implications for theories of ADHD, the relative utility of neurobiological measures with respect to teacher ratings of EF and ER, and the developmental trajectory of its underlying neurobiology.

Frontal grey matter microstructure is associated with sleep slow waves characteristics in late midlife

STUDY OBJECTIVES

The ability to generate slow waves (SW) during non-rapid eye movement (NREM) sleep decreases as early as the 5th decade of life, predominantly over frontal regions. This decrease may concern prominently SW characterized by a fast switch from hyperpolarized to depolarized, or down-to-up, state. Yet, the relationship between these fast and slow switcher SW and cerebral microstructure in ageing is not established.

METHODS

We recorded habitual sleep under EEG in 99 healthy late midlife individuals (mean age = 59.3 ± 5.3 years; 68 women) and extracted SW parameters (density, amplitude, frequency) for all SW as well as according to their switcher type (slow vs. fast). We further used neurite orientation dispersion and density imaging (NODDI) to assess microstructural integrity over a frontal grey matter region of interest (ROI).

RESULTS

In statistical models adjusted for age, sex, and sleep duration, we found that a lower SW density, particularly for fast switcher SW, was associated with a reduced orientation dispersion of neurites in the frontal ROI (p = 0.018, R2β* = 0.06). In addition, overall SW frequency was positively associated with neurite density (p = 0.03, R2β* = 0.05). By contrast, we found no significant relationships between SW amplitude and NODDI metrics.

CONCLUSIONS

Our findings suggest that the complexity of neurite organization contributes specifically to the rate of fast switcher SW occurrence in healthy middle-aged individuals, corroborating slow and fast switcher SW as distinct types of SW. They further suggest that the density of frontal neurites plays a key role for neural synchronization during sleep.

TRIAL REGISTRATION NUMBER

EudraCT 2016-001436-35.

Analysis of non-pharmaceutical interventions and their impacts on COVID-19 in Kerala

In the absence of an effective vaccine or drug therapy, non-pharmaceutical interventions are the only option for control of the outbreak of the coronavirus disease 2019, a pandemic with global implications. Each of the over 200 countries affected has followed its own path in dealing with the crisis, making it difficult to evaluate the effectiveness of measures implemented, either individually, or collectively. In this paper we analyse the case of the south Indian state of Kerala, which received much attention in the international media for its actions in containing the spread of the disease in the early months of the pandemic, but later succumbed to a second wave. We use a model to study the trajectory of the disease in the state during the first four months of the outbreak. We then use the model for a retrospective analysis of measures taken to combat the spread of the disease, to evaluate their impact. Because of the differences in the trajectory of the outbreak in Kerala, we argue that it is a model worthy of a place in the discussion on how the world might best handle this and other, future, pandemics.

Adverse childhood experiences predict neurite density differences in young children with and without attention deficit hyperactivity disorder

Adverse childhood experiences (ACEs) put millions of children at risk for later health problems. As childhood represents a critical developmental period, it is important to understand how ACEs impact brain development in young children. In addition, children with attention-deficit/hyperactivity disorder (ADHD) are more likely than typically developing (TD) peers to experience ACEs. Therefore, the current study examined the impact of ACEs on early brain development, using a cumulative risk approach, in a large sample of children with and without ADHD. We examined 198 young children (M_age  = 5.45, 82.3% Hispanic/Latino; 52.5% ADHD) across measures of brain volume, cortical thickness, neurite density index (NDI), and orientation dispersion index (ODI). For the NDI measure, there was a significant interaction between group and cumulative risk (ß = .18, p = .048), such that for children with ADHD, but not TD children, greater cumulate risk was associated with increased NDI in corpus callosum. No other interactions were detected. Additionally, when examining across groups, greater cumulative risk was associated with reduced ODI and volume in the cerebellum, although these findings did not survive a correction for multiple comparisons. Our results highlight the role early cumulative ACEs play in brain development across TD and children with ADHD.

Biophysical compartment models for single-shell diffusion MRI in the human brain: a model fitting comparison

Clinically oriented studies commonly acquire diffusion MRI (dMRI) data with a single non-zero b-value (i.e. single-shell) and diffusion weighting ofb=1000 s/mm². To produce microstructural parameter maps, the tensor model is usually used, despite known limitations. Although compartment models have demonstrated improved fits in multi-shell dMRI data, they are rarely used for single-shell parameter maps, where their effectiveness is unclear from the literature. Here, various compartment models combining isotropic balls and symmetric tensors were fitted to single-shell dMRI data to investigate model fitting optimization and extract the most information possible. Full testing was performed in 5 subjects, and 3 subjects with multi-shell data were included for comparison. The results were tested and confirmed in a further 50 subjects. The Markov chain Monte Carlo (MCMC) model fitting technique outperformed non-linear least squares. Using MCMC, the 2-fibre-orientation mono-exponential ball & stick model (BS_ME²) provided artifact-free, stable results, in little processing time. The analogous ball & zeppelin model (BZ²) also produced stable, low-noise parameter maps, though it required much greater computing resources (50 000 burn-in steps). In single-shell data, the gamma-distributed diffusivity ball & stick model (BS_GD²) underperformed relative to other models, despite being an often-used software default. It produced artifacts in the diffusivity maps even with extremely long processing times. Neither increased diffusion weighting nor a greater number of gradient orientations improved BS_GD²fits. In white matter (WM), the tensor produced the best fit as measured by Bayesian information criterion. This result contrasts with studies using multi-shell data. However, in crossing fibre regions the tensor confounded geometric effects with fractional anisotropy (FA): the planar/linear WM FA ratio was 49%, while BZ²and BS_ME²retained 76% and 83% of restricted fraction, respectively. As a result, the BZ²and BS_ME²models are strong candidates to optimize information extraction from single-shell dMRI studies.

Compartmental models for diffusion weighted MRI reveal widespread brain changes in HIV-infected patients

Diffusion tensor imaging (DTI) has been used to explore changes in the brain of subjects with human immunodeficiency virus (HIV) infection. However, DTI notoriously suffers from low specificity. Neurite orientation dispersion and density imaging (NODDI) is a compartmental model able to provide specific microstructural information with additional sensitivity/specificity. In this study we use both the NODDI and the DTI models to evaluate microstructural differences between 35 HIV-positive patients and 20 healthy controls. Diffusion-weighted imaging was acquired using three b-values (0, 1000 and 2500 s/mm²). Both DTI and NODDI models were fitted to the data, obtaining estimates for fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), axial diffusivity (AD), neurite density index (NDI) and orientation dispersion index (ODI), after which we performed group comparisons using Tract-based spatial statistics (TBSS). While significant group effects were found in in FA, MD, RD, AD and NDI, NDI analysis uncovered a much wider involvement of brain tissue in HIV infection as compared to DTI. In region-of interest (ROI)-based analysis, NDI estimates from the right corticospinal tract produced excellent performance in discriminating the two groups (AUC = 0.974, sensitivity = 90%; specificity =97%).

Indices of callosal axonal density and radius from diffusion MRI relate to upper and lower limb motor performance

Understanding the relationship between human brain structure and functional outcome is of critical importance in systems neuroscience. Diffusion MRI (dMRI) studies show that fractional anisotropy (FA) is predictive of motor control, underscoring the importance of white matter (WM). However, as FA is a surrogate marker of WM, we aim to shed new light on the structural underpinnings of this relationship by applying a multi-compartment microstructure model providing axonal density/radius indices. Sixteen young adults (7 males / 9 females), performed a hand/foot tapping task and a Multi Limb Reaction Time task. Furthermore, diffusion (STEAM &HARDI) and fMRI (localizer hand/foot activations) data were obtained. Sphere ROIs were placed on activation clusters with highest t value to guide interhemispheric WM tractography. Axonal radius/density indices of callosal parts intersecting with tractography were calculated from STEAM, using the diffusion-time dependent AxCaliber model, and correlated with behavior. Results indicated a possible association between larger apparent axonal radii of callosal motor fibers of the hand and higher tapping scores of both hands, and faster selection-related processing (normalized reaction) times (RTs) on diagonal limb combinations. Additionally, a trend was present for faster selection-related processing (normalized reaction) times for lower limbs being related with higher axonal density of callosal foot motor fibers, and for higher FA values of callosal motor fibers in general being related with better tapping and faster selection-related processing (normalized reaction) times. Whereas FA is sensitive in demonstrating associations with motor behavior, axon radius/density (i.e., fiber geometry) measures are promising to explain the physiological source behind the observed FA changes, contributing to deeper insights into brain-behavior interactions.

A Bayesian approach to model the trends and variability in urban stormwater quality associated with catchment and hydrologic parameters

Stormwater runoff pollution has become a key environmental issue in urban areas. Reliable estimation of stormwater pollutant discharge is important for implementing robust water quality management strategies. Even though significant attempts have been undertaken to develop water quality models, deterministic approaches have proven inappropriate as they do not address the variability in stormwater quality. Due to the random nature of rainfall characteristics and the differences in catchment characteristics, it is difficult to generate the runoff pollutographs to a desired level of certainty. Bayesian hierarchical modelling is an effective tool for developing complex models with a large number of sources of variability. A Bayesian model does not look for a single value of the model parameters, but rather determines a distribution of the model parameters from which all inference is drawn. This study introduces a Bayesian hierarchical linear regression model to describe a catchment specific runoff pollutograph incorporating the associated uncertainties in the model parameters. The model incorporates catchment and rainfall characteristics including the effective impervious area, time of concentration, rain duration, average rainfall intensity and the antecedent dry period as the contributors to random effects.

Challenges for biophysical modeling of microstructure

The biophysical modeling efforts in diffusion MRI have grown considerably over the past 25 years. In this review, we dwell on the various challenges along the journey of bringing a biophysical model from initial design to clinical implementation, identifying both hurdles that have been already overcome and outstanding issues. First, we describe the critical initial task of selecting which features of tissue microstructure can be estimated using a model and which acquisition protocol needs to be implemented to make the estimation possible. The model performance should necessarily be tested in realistic numerical simulations and in experimental data - adapting the fitting strategy accordingly, and parameter estimates should be validated against complementary techniques, when/if available. Secondly, the model performance and validity should be explored in pathological conditions, and, if appropriate, dedicated models for pathology should be developed. We build on examples from tumors, ischemia and demyelinating diseases. We then discuss the challenges associated with clinical translation and added value. Finally, we single out four major unresolved challenges that are related to: the availability of a microstructural ground truth, the validation of model parameters which cannot be accessed with complementary techniques, the development of a generalized standard model for any brain region and pathology, and the seamless communication between different parties involved in the development and application of biophysical models of diffusion.