Brain-wide inferiority and equivalence tests in fMRI group analyses: Selected applications

Statistical Testing for Protein Equivalence Identifies Core Functional Modules Conserved across 360 Cancer Cell Lines and Presents a General Approach to Investigating Biological Systems

Quantitative proteomics has enhanced our capability to study protein dynamics and their involvement in disease using various techniques, including statistical testing, to discern the significant differences between conditions. While most focus is on what is different between conditions, exploring similarities can provide valuable insights. However, exploring similarities directly from the analyte level, such as proteins, genes, or metabolites, is not a standard practice and is not widely adopted. In this study, we propose a statistical framework called QuEStVar (Quantitative Exploration of Stability and Variability through statistical hypothesis testing), enabling the exploration of quantitative stability and variability of features with a combined statistical framework. QuEStVar utilizes differential and equivalence testing to expand statistical classifications of analytes when comparing conditions. We applied our method to an extensive data set of cancer cell lines and revealed a quantitatively stable core proteome across diverse tissues and cancer subtypes. The functional analysis of this set of proteins highlighted the molecular mechanism of cancer cells to maintain constant conditions of the tumorigenic environment via biological processes, including transcription, translation, and nucleocytoplasmic transport.

Amygdala-related electrical fingerprint is modulated with neurofeedback training and correlates with deep-brain activation: proof-of-concept in borderline personality disorder

BACKGROUND

The modulation of brain circuits of emotion is a promising pathway to treat borderline personality disorder (BPD). Precise and scalable approaches have yet to be established. Two studies investigating the amygdala-related electrical fingerprint (Amyg-EFP) in BPD are presented: one study addressing the deep-brain correlates of Amyg-EFP, and a second study investigating neurofeedback (NF) as a means to improve brain self-regulation.

METHODS

Study 1 combined electroencephalography (EEG) and simultaneous functional magnetic resonance imaging to investigate the replicability of Amyg-EFP-related brain activation found in the reference dataset (N = 24 healthy subjects, 8 female; re-analysis of published data) in the replication dataset (N = 16 female individuals with BPD). In the replication dataset, we additionally explored how the Amyg-EFP would map to neural circuits defined by the research domain criteria. Study 2 investigated a 10-session Amyg-EFP NF training in parallel to a 12-weeks residential dialectical behavior therapy (DBT) program. Fifteen patients with BPD completed the training, N = 15 matched patients served as DBT-only controls.

RESULTS

Study 1 replicated previous findings and showed significant amygdala blood oxygenation level dependent activation in a whole-brain regression analysis with the Amyg-EFP. Neurocircuitry activation (negative affect, salience, and cognitive control) was correlated with the Amyg-EFP signal. Study 2 showed Amyg-EFP modulation with NF training, but patients received reversed feedback for technical reasons, which limited interpretation of results.

CONCLUSIONS

Recorded via scalp EEG, the Amyg-EFP picks up brain activation of high relevance for emotion. Administering Amyg-EFP NF in addition to standardized BPD treatment was shown to be feasible. Clinical utility remains to be investigated.

Utilizing fMRI to Guide TMS Targets: the Reliability and Sensitivity of fMRI Metrics at 3 T and 1.5 T

US Food and Drug Administration (FDA) cleared a Transcranial Magnetic Stimulation (TMS) system with functional Magnetic Resonance Imaging-guided (fMRI) individualized treatment protocol for major depressive disorder, which employs resting state-fMRI (RS-fMRI) functional connectivity (FC) to pinpoint the target individually to increase the accuracy and effeteness of the stimulation. Furthermore, task activation-guided TMS, as well as the use of RS-fMRI local metrics for targeted the specific abnormal brain regions, are considered a precise scheme for TMS targeting. Since 1.5 T MRI is more available in hospitals, systematic evaluation of the test-retest reliability and sensitivity of fMRI metrics on 1.5 T and 3 T MRI may provide reference for the application of fMRI-guided individualized-precise TMS stimulation. Twenty participants underwent three RS-fMRI scans and one scan of finger-tapping task fMRI with self-initiated (SI) and visual-guided (VG) conditions at both 3 T and 1.5 T. Then the location reliability derived by FC (with three seed regions) and peak activation were assessed by intra-individual distance. The test-retest reliability and sensitivity of five RS-fMRI local metrics were evaluated using intra-class correlation and effect size, separately. The intra-individual distance of peak activation location between 1.5 T and 3 T was 15.8 mm and 19 mm for two conditions, respectively. The intra-individual distance for the FC derived targets at 1.5 T was 9.6-31.2 mm, compared to that of 3 T (7.6-31.1 mm). The test-retest reliability and sensitivity of RS-fMRI local metrics showed similar trends on 1.5 T and 3 T. These findings hasten the application of fMRI-guided individualized TMS treatment in clinical practice.

Infants' sex affects neural responses to affective touch in early infancy

Social touch is closely related to the establishment and maintenance of social bonds in humans, and the sensory brain circuit for gentle brushing is already active soon after birth. Brain development is known to be sexually dimorphic, but the potential effect of sex on brain activation to gentle touch remains unknown. Here, we examined brain activation to gentle skin stroking, a tactile stimulation that resembles affective or social touch, in term-born neonates. Eighteen infants aged 11-36 days, recruited from the FinnBrain Birth Cohort Study, were included in the study. During natural sleep, soft brush strokes were applied to the skin of the right leg during functional magnetic resonance imaging (fMRI) at 3 cm/s velocity. We examined potential differences in brain activation between males (n = 10) and females (n = 8) and found that females had larger blood oxygenation level dependent (BOLD) responses (brushing vs. rest) in bilateral orbitofrontal cortex (OFC), right ventral striatum and bilateral inferior striatum, pons, and cerebellum compared to males. Moreover, the psychophysiological interactions (PPI) analysis, setting the left and right OFC as seed regions, revealed significant differences between males and females. Females exhibited stronger PPI connectivity between the left OFC and posterior cingulate or cuneus. Our work suggests that social touch neural responses are different in male and female neonates, which may have major ramifications for later brain, cognitive, and social development. Finally, many of the sexually dimorphic brain responses were subcortical, not captured by surface-based neuroimaging, indicating that fMRI will be a relevant technique for future studies.

Structural brain changes in emotion recognition across the adult lifespan

Emotion recognition (ER) declines with increasing age, yet little is known whether this observation is based on structural brain changes conveyed by differential atrophy. To investigate whether age-related ER decline correlates with reduced grey matter (GM) volume in emotion-related brain regions, we conducted a voxel-based morphometry analysis using data of the Human Connectome Project-Aging (N = 238, aged 36-87) in which facial ER was tested. We expected to find brain regions that show an additive or super-additive age-related change in GM volume indicating atrophic processes that reduce ER in older adults. The data did not support our hypotheses after correction for multiple comparisons. Exploratory analyses with a threshold of P < 0.001 (uncorrected), however, suggested that relationships between GM volume and age-related general ER may be widely distributed across the cortex. Yet, small effect sizes imply that only a small fraction of the decline of ER in older adults can be attributed to local GM volume changes in single voxels or their multivariate patterns.

No evidence from a negative mood induction fMRI task for frontal functional asymmetry as a suitable neurofeedback target

Frontal functional asymmetry (FA) has been proposed as a potential target for neurofeedback (NFB) training for mental disorders but most FA NFB studies used electroencephalography while the investigations of FA NFB in functional magnetic resonance imaging (fMRI) are rather limited. In this study, we aimed at identifying functional asymmetry effects in fMRI and exploring its potential as a target for fMRI NFB studies by re-analyzing an existing data set containing a resting state measurement and a sad mood induction task of n = 30 participants with remitted major depressive disorder and n = 30 matched healthy controls. We applied low-frequency fluctuations (ALFF), fractional ALFF, and regional homogeneity and estimated functional asymmetry in both a voxel-wise and regional manner. We assessed functional asymmetry during rest and negative mood induction as well as functional asymmetry changes between the phases, and associated the induced mood change with the change in functional asymmetry. Analyses were conducted within as well as between groups. Despite extensive analyses, we identified only very limited effects. While some tests showed nominal significance, our results did not contain any clear identifiable patterns of effects that would be expected if a true underlying effect would be present. In conclusion, we do not find evidence for FA effects related to negative mood in fMRI, which questions the usefulness of FA measures for real-time fMRI neurofeedback as a treatment approach for affective disorders.

Using preregistration as a tool for transparent fNIRS study design

Significance

The expansion of functional near-infrared spectroscopy (fNIRS) methodology and analysis tools gives rise to various design and analytical decisions that researchers have to make. Several recent efforts have developed guidelines for preprocessing, analyzing, and reporting practices. For the planning stage of fNIRS studies, similar guidance is desirable. Study preregistration helps researchers to transparently document study protocols before conducting the study, including materials, methods, and analyses, and thus, others to verify, understand, and reproduce a study. Preregistration can thus serve as a useful tool for transparent, careful, and comprehensive fNIRS study design.

Aim

We aim to create a guide on the design and analysis steps involved in fNIRS studies and to provide a preregistration template specified for fNIRS studies.

Approach

The presented preregistration guide has a strong focus on fNIRS specific requirements, and the associated template provides examples based on continuous-wave (CW) fNIRS studies conducted in humans. These can, however, be extended to other types of fNIRS studies.

Results

On a step-by-step basis, we walk the fNIRS user through key methodological and analysis-related aspects central to a comprehensive fNIRS study design. These include items specific to the design of CW, task-based fNIRS studies, but also sections that are of general importance, including an in-depth elaboration on sample size planning.

Conclusions

Our guide introduces these open science tools to the fNIRS community, providing researchers with an overview of key design aspects and specification recommendations for comprehensive study planning. As such it can be used as a template to preregister fNIRS studies or merely as a tool for transparent fNIRS study design.

The precuneus as a central node in declarative memory retrieval

Both, the hippocampal formation and the neocortex are contributing to declarative memory, but their functional specialization remains unclear. We investigated the differential contribution of both memory systems during free recall of word lists. In total, 21 women and 17 men studied the same list but with the help of different encoding associations. Participants associated the words either sequentially with the previous word on the list, with spatial locations on a well-known path, or with unique autobiographical events. After intensive rehearsal, subjects recalled the words during functional magnetic resonance imaging (fMRI). Common activity to all three types of encoding associations was identified in the posterior parietal cortex, in particular in the precuneus. Additionally, when associating spatial or autobiographical material, retrosplenial cortex activity was elicited during word list recall, while hippocampal activity emerged only for autobiographically associated words. These findings support a general, critical function of the precuneus in episodic memory storage and retrieval. The encoding-retrieval repetitions during learning seem to have accelerated hippocampus-independence and lead to direct neocortical integration in the sequentially associated and spatially associated word list tasks. During recall of words associated with autobiographical memories, the hippocampus might add spatiotemporal information supporting detailed scenic and contextual memories.

Neural cue reactivity is not stronger in male than in female patients with alcohol use disorder

BACKGROUND

Males consume more alcohol than females, and alcohol use disorder (AUD) is more prevalent in males than females. However, females progress faster to AUD. Sex differences in neural alcohol cue reactivity were previously observed in young social drinkers, indicating a role of hypersensitivity to alcohol-related cues in very early stages of addiction. To our knowledge, this is the first study on patients diagnosed with AUD to test sex differences in neural reactivity to alcohol cues in order to widen previous findings.

METHODS

We analyzed data from previous studies, using a well-established functional magnetic resonance imaging (fMRI) paradigm to compare neural reactivity to alcohol cues between 42 female and 124 male patients with AUD (mean age 45 and 46 years) in predefined regions of interest that were implicated by previous studies (ventral and dorsal striatum as well as caudate, putamen, amygdala, hippocampus, insula, anterior cingulate cortex, and medial prefrontal cortex) using independent samples t-tests. Post-hoc, effect size calculations were performed.

RESULTS

Throughout all nine regions of interest, we found no statistically significant sex differences in neural reactivity toward alcoholic pictures alone or in comparison to neutral pictures (p > 0.05, FDR-corrected). Post-hoc effect size estimates indicated a magnitude between 0.137 and 0.418 (Hedge's g) on alcohol reactivity to alcohol cues compared to neutral cues and indicate very small to less than medium effect sizes in the direction of higher cue reactivity in female patients.

CONCLUSION

Previous studies showed sex differences in neural alcohol cue reactivity in younger social and problematic alcohol drinkers, i.e., stronger striatal cue-reactivity in males. After correction for multiple comparisons, we did not observe significant sex differences in a cohort of middle-aged females and males with AUD. Sex differences that are present during early phases of addiction development might disappear at later stages of AUD and might thus be considered as clinically less relevant in patients with more severe AUD.

Altered neural correlates of episodic memory for food and non-food cues in females with overweight/obesity

Episodic memory formation is fundamental to cognition and plays a key role in eating behaviors, indirectly promoting the maintenance and acceleration of weight gain. Impaired episodic memory function is a hallmark of people with overweight/obesity, nevertheless, little research has been conducted to explore the effects of overweight/obesity on neural networks associated with episodic memory. The current study aimed to unravel the behavioral responses and neurocognitive mechanisms underlying the episodic memory for food and non-food cues in females with overweight/obesity. To explore this issue, a group of females with overweight/obesity (n = 26) and a group of age-matched females with healthy weight (n = 28) participated in a functional magnetic resonance imaging (fMRI) event-related episodic memory paradigm, during which pictures of palatable food and pictures of neutral daily necessities were presented. Whole-brain analyses revealed differential engagement in several neural regions between the groups during an episodic memory task. Specifically, compared to the healthy weight controls, females with overweight/obesity exhibited reduced brain activity in the temporal, parietal, and frontal regions during episodic memory encoding and successful retrieval of both food and non-food cues. Additionally, activation patterns in the left hippocampus and right olfactory cortex of females with and without overweight/obesity suggested that item memory changed according to the type of stimuli presented during item memory. Specifically, females with overweight/obesity showed greater engagement of the left hippocampus and right olfactory cortex when processing food cues, but less activation of the left hippocampus and right olfactory cortex when presented with non-food cues. Consistent with the obesity and suboptimal food-related decision theoretical model, these findings provide evidence of dissociation of the neural underpinnings of episodic memory in females with overweight/obesity and underline important effects of overweight/obesity on brain functions related to episodic memory.

Evidence for the Normalization Effects of Medication for Opioid Use Disorder on Functional Connectivity in Neonates with Prenatal Opioid Exposure

Altered functional connectivity has been reported in infants with prenatal exposure to opioids, which significantly interrupts and influences endogenous neurotransmitter/receptor signaling during fetal programming. Better birth outcomes and long-term developmental outcomes are associated with medication for opioid use disorder (MOUD) during pregnancy, but the neural mechanisms underlying these benefits are largely unknown. We aimed to characterize effects of prenatal opioid/other drug exposure (PODE) and the neural basis for the reported beneficial effects of MOUD by examining neonatal brain functional organization. A cohort of 109 human newborns, 42 PODE, 39 with prenatal exposure to drugs excluding opioids (PDE), 28 drug-free controls (males and females) underwent resting-state fMRI at 2 weeks of age. To examine neural effects of MOUD, PODE infants were separated into subgroups based on whether mothers received MOUD (n = 31) or no treatment (n = 11). A novel heatmap analysis was designed to characterize PODE-associated functional connectivity alterations and MOUD-related effects, and permutation testing identified regions of interest with significant effects. PODE neonates showed alterations beyond those associated with PDE, particularly in reward-related frontal-sensory connectivity. MOUD was associated with a significant reduction of PODE-related alterations in key regions of endogenous opioid pathways including limbic and frontal connections. However, significant residual effects in limbic and subcortical circuitry were observed. These findings confirm altered brain functional organization associated with PODE. Importantly, widespread normalization effects associated with MOUD reveal, for the first time, the potential brain basis of the beneficial effects of MOUD on the developing brain and underscore the importance of this treatment intervention for better developmental outcomes.SIGNIFICANCE STATEMENT This is the first study to reveal the potential neural mechanisms underlying the beneficial effects on the neonate brain associated with MOUD during pregnancy. We identified both normalization and residual effects of MOUD on brain functional architecture by directly comparing neonates prenatally exposed to opioids with MOUD and those exposed to opioids but without MOUD. Our findings confirm altered brain functional organization associated with prenatal opioid exposure and demonstrate that although significant residual effects remain in reward circuitry, MOUD confers significant normalization effects on functional connectivity of regions associated with socioemotional development and reward processing. Together, our results highlight the importance of MOUD intervention for better neurodevelopmental outcomes.

Ghani ARIG, Wan Mohamad WNA, Mohamed Mustafar MF, Hanafi MH, Reza MF, Umar H, Mohd Zulkifly MF, Ang SY, Zakaria Z, Musa KI, Othman A, Embong Z, Sapiai NA, Kandasamy R, Ibrahim H, Abdullah MZ, Amaruchkul K, Valdes-Sosa P, Luisa-Bringas M, Biswal B, Songsiri J, Yaacob HS, Sumari P, Jamir Singh PS, Azman A, Abdullah JM. Alteration in the Functional Organization of the Default Mode Network Following Closed Non-severe Traumatic Brain Injury

The debilitating effect of traumatic brain injury (TBI) extends years after the initial injury and hampers the recovery process and quality of life. In this study, we explore the functional reorganization of the default mode network (DMN) of those affected with non-severe TBI. Traumatic brain injury (TBI) is a wide-spectrum disease that has heterogeneous effects on its victims and impacts everyday functioning. The functional disruption of the default mode network (DMN) after TBI has been established, but its link to causal effective connectivity remains to be explored. This study investigated the differences in the DMN between healthy participants and mild and moderate TBI, in terms of functional and effective connectivity using resting-state functional magnetic resonance imaging (fMRI). Nineteen non-severe TBI (mean age 30.84 ± 14.56) and twenty-two healthy (HC; mean age 27.23 ± 6.32) participants were recruited for this study. Resting-state fMRI data were obtained at the subacute phase (mean days 40.63 ± 10.14) and analyzed for functional activation and connectivity, independent component analysis, and effective connectivity within and between the DMN. Neuropsychological tests were also performed to assess the cognitive and memory domains. Compared to the HC, the TBI group exhibited lower activation in the thalamus, as well as significant functional hypoconnectivity between DMN and LN. Within the DMN nodes, decreased activations were detected in the left inferior parietal lobule, precuneus, and right superior frontal gyrus. Altered effective connectivities were also observed in the TBI group and were linked to the diminished activation in the left parietal region and precuneus. With regard to intra-DMN connectivity within the TBI group, positive correlations were found in verbal and visual memory with the language network, while a negative correlation was found in the cognitive domain with the visual network. Our results suggested that aberrant activities and functional connectivities within the DMN and with other RSNs were accompanied by the altered effective connectivities in the TBI group. These alterations were associated with impaired cognitive and memory domains in the TBI group, in particular within the language domain. These findings may provide insight for future TBI observational and interventional research.

Feasibility of training the dorsolateral prefrontal-striatal network by real-time fMRI neurofeedback

Real-time fMRI neurofeedback (rt-fMRI NF) is a promising non-invasive technique that enables volitional control of usually covert brain processes. While most rt-fMRI NF studies so far have demonstrated the ability of the method to evoke changes in brain activity and improve symptoms of mental disorders, a recently evolving field is network-based functional connectivity (FC) rt-fMRI NF. However, FC rt-fMRI NF has methodological challenges such as respirational artefacts that could potentially bias the training if not controlled. In this randomized, double-blind, yoke-controlled, pre-registered FC rt-fMRI NF study with healthy participants (N = 40) studied over three training days, we tested the feasibility of an FC rt-fMRI NF approach with online global signal regression (GSR) to control for physiological artefacts for up-regulation of connectivity in the dorsolateral prefrontal-striatal network. While our pre-registered null hypothesis significance tests failed to reach criterion, we estimated the FC training effect at a medium effect size at the end of the third training day after rigorous control of physiological artefacts in the offline data. This hints at the potential of FC rt-fMRI NF for the development of innovative transdiagnostic circuit-specific interventional approaches for mental disorders and the effect should now be confirmed in a well-powered study.

Brain-wide inferiority and equivalence tests in fMRI group analyses: Selected applications

Null hypothesis significance testing is the major statistical procedure in fMRI, but provides only a rather limited picture of the effects in a data set. When sample size and power is low relying only on strict significance testing may lead to a host of false negative findings. In contrast, with very large data sets virtually every voxel might become significant. It is thus desirable to complement significance testing with procedures like inferiority and equivalence tests that allow to formally compare effect sizes within and between data sets and offer novel approaches to obtain insight into fMRI data. The major component of these tests are estimates of standardized effect sizes and their confidence intervals. Here, we show how Hedges' g, the bias corrected version of Cohen's d, and its confidence interval can be obtained from SPM t maps. We then demonstrate how these values can be used to evaluate whether nonsignificant effects are really statistically smaller than significant effects to obtain “regions of undecidability” within a data set, and to test for the replicability and lateralization of effects. This method allows the analysis of fMRI data beyond point estimates enabling researchers to take measurement uncertainty into account when interpreting their findings.