Mindfulness meditation changes the boundary and configuration of the primary functional networks in the brain

Research has shown that mindfulness meditation not only improves our cognitive and motivational functioning (e.g., attention, mental health), it influences the way how our brain networks [e.g., default mode network (DMN), front-parietal network (FPN), and sensory-motor network (SMN)] function and operate. However, surprisingly little attention has been paid to the possibility that mindfulness meditation alters the structure (composition) of these functional brain networks. Here, using a single-case experimental design with longitudinal intensive data, we examined the effect of mindfulness mediation on intra-individual changes in the composition of whole-brain networks. The results showed that mindfulness meditation (1) changed the community size (with a number of regions in the FPN being merged into the DMN after mindfulness meditation), (2) changed the brain regions composing the SMN community without changing its size, and (3) led to instability in the community allegiance of the regions in the FPN. These results suggest that, in addition to altering specific functional connectivity, mindfulness meditation leads to reconfiguration of whole-brain network structure. The reconfiguration of community structure in the brain provides fruitful information about the neural mechanisms of mindfulness meditation. Author Summary Training to focus on present-moment experiences, i.e., mindfulness meditation, is known to produce significant beneficial outcomes, such as improved attention and mental health. It is important to understand how these beneficial effects are produced at the neural level; however, previous research investigating this question almost exclusively employed a pre-post design (i.e. assessing brain functioning only once or twice) or comparison between beginners and experts. The current study takes a fundamentally different approach ---- we repeatedly assess the brain function of a single person over many days (intensive longitudinal design) and show that mindfulness mediation significantly changes the size, composition, and variability of the brain networks that are related to sensory processing, executive control, or spontaneous thoughts and self-referential processing. These results highlight the importance of investigating intraindividual changes for understanding the neural mechanisms of mindfulness meditation and suggest that such changes may be used as a biomarker to reflect the efficacy and progress of mindfulness meditation.


Introduction 1
Mindfulness meditation is a cognitive practice aimed to enhance one's core psychological 2 capacities, such as attentional and emotional self-regulation (1). It involves focused attention to 3 present-moment experiences without emotional reaction and judgment and has been found to 4 produce significant beneficial outcomes, such as stress reduction (2) and improvements in attention 5 processing (3). 6 Past research indicates that mindfulness meditation is primarily related to three brain 7 networks: the fronto-parietal network (FPN), sensory-motor network (SMN), and default mode 8 network (DMN) (1). The FPN mainly consists of the rostro-and dorso-lateral prefrontal cortex 9 (lPFC), anterior insula, dorsal anterior cingulate cortex (dACC), and anterior inferior parietal lobule 10 (aIPL); all of these brain areas are critical for cognitive control functions, such as regulation of 11 attention and emotion (4-7). Mindfulness meditation, especially in the early stages of long-term 12 practice, increases activation of FPN regions (8-11), which is consistent with the general observation 13 that focusing on the present moment requires effortful attentional control.
14 Mindfulness meditation also alters sensory experiences through the SMN (12, 13), 15 consisting of motor cortices, primary somatosensory cortex, and insula. In a previous study, these 16 brain areas showed reduced activation in a four-day mindfulness meditation when beginners 17 meditated in the presence of noxious stimulation causing pain (14). This change in brain activity may 1 be associated with enhanced body awareness, as mindfulness meditation requires individuals to focus 2 on a body part or internal experiences, such as breathing (15). 3 The DMN, mainly consisting of the anterior medial prefrontal cortex (amPFC), posterior 4 cingulate cortex (PCC), and posterior inferior parietal lobule (pIPL), is the network supporting 5 spontaneous thoughts and self-referential processing (16-18). Because mindfulness meditation aims 6 to shut out task-irrelevant thoughts by directing one's attention to an anchoring object such as one's 7 breath, the DMN is expected to be suppressed during mindfulness meditation. In fact, the mPFC and 8 PCC showed less activity during mindfulness meditation, and functional connectivity between the 9 PCC, dACC, and dlPFC was stronger in meditators compared to meditation-naive controls (19). 10 Increased functional connectivity between the PCC and task-positive regions was also observed in a 11 different study (20). These results indicate that mindfulness meditation may increase cognitive 12 control over the DMN functioning (19). 13 Although the previous work has provided various insights into how mindfulness 14 meditation influences the functional network of the brain, there are two critical limitations in the 15 current literature. First, the brain networks were defined a priori in the previous studies, precluding 16 the possibility that mindfulness meditation practice can alter the structure of the primary brain 17 6 networks themselves (i.e. FPN, SMN, and DMN). Because recent studies have shown that 1 mindfulness meditation can change functional connectivity across brain regions (10,19,21,22), the 2 whole-brain composition of the FPN, SMN, and DMN may be altered as a consequence of 3 mindfulness meditation. 4 Second, most of the previous research has employed a one-shot pre-post or 5 nonmeditator-meditator comparison design (23,24), and compared the conditions after aggregating 6 the data across heterogeneous participants. This inter-individual aggregation approach is useful to 7 examine the effects of meditation averaged across participants. However, given the large individual 8 differences in the whole-brain functional connectivity pattern (25,26), there is danger that the 9 approach potentially masks important intra-individual changes in the composition of the brain 10 networks (e.g., some participant-specific network structures may be canceled out by inter-individual 11 aggregation). Therefore, adopting a design that allows us to focus on the intra-individual change may 12 provide novel insights into how mindfulness meditation alters the structure of the brain networks. 13 The current research aims to expand our understanding of mindfulness meditation by 14 addressing these two critical issues. For that purpose, we will examine the effects of mindfulness 15 meditation using a single-case experimental design with intensive longitudinal data. Single-case 16 experimental designs have a long tradition in psychology (27,28), and in later years, they have been 17 7 applied to intensive longitudinal data (for a systematic review, see (29)). Single-case experimental 1 designs are effective in reliably detecting intra-individual changes in outcome variables in response 2 to intervention (29). However, this design has rarely been implemented in neuroimaging studies (for 3 an exception without experimental manipulation, see (30)). Based on this design, we scanned a 4 single participant repeatedly over a long period of time (65 days), employing mindfulness meditation 5 intermittently, and examined whether and how the whole-brain composition of the FPN, SMN, and 6 DMN were altered on the days of mindfulness meditation.

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Similarity of the functional connectivity across time 10 To examine variability of the functional connectivity over time, we calculated correlation 11 of functional connectivity between days (Fig. 1). The correlation value ranged from 0.429 to 0.780, 12 suggesting that the functional connectivity of a single person varies on a daily basis. This result is 13 consistent with previous longitudinal scanning data from a single participant (30).

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Finding community structure 16 To detect the community structure in the time-varying functional connectivity 17 8 across the 58 days, we applied a generalized Louvain method (31) (Fig. 2). We defined the dominant 1 community for each ROI for each condition as the community to which the ROI belonged for the 2 largest number of days under the given condition. To label the four communities detected in the 3 current study, we assessed how these communities overlapped with the template communities  Metrics that quantify the changes in community structure 9 We examined the effect of meditation practice on intra-individual changes in the 10 composition of the whole-brain networks with three metrics: community size, community coherence, 11 and flexibility.   The community size is one way of examining the change in the composition of the brain 2 network across the two conditions. In fact, even if the relative community size is the same between 3 the two conditions, the constituent ROIs of each community may be substantially different in the two 4 conditions. Therefore, for each community, we examined the extent to which the community as  Previous studies have provided accumulating evidence that mindfulness meditation 16 changes activation and connectivity patterns between specific brain regions (19-21,23,24,33,34).

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Extending previous work, we employed a whole-brain graph theoretic analysis with a single-case 1 experimental design using intensive longitudinal data to reveal that mindfulness meditation provokes 2 the reconfiguration of the community structure of the whole-brain functional network. 3 We found that the size of the FPN decreased and that of the DMN increased as a 4 consequence of mindfulness meditation. This result is consistent with the previously shown  Although the SMN showed a change in coherence across the two conditions, as the FPN 9 and DMN did, the size and flexibility of the SMN were intact. In this sense, mindfulness meditation 10 influenced the SMN but to a lesser extent than it influenced the FPN and DMN. This weaker 11 alteration in the SMN might be because awareness of the body sensation that recruits the SMN (14) 12 is not a primary target of mindfulness meditation in contrast to the attentional enhancement, which is 13 associated with the FPN, and reduction of mind wandering, which is associated with the DMN. One 14 can test this possibility in future research by using an external stimulus (e.g., a fixation) as an object 15 on which attention should be focused during mindfulness meditation rather than a body sensation. 16 The present study demonstrated the value of a single-case experimental design with 17 intensive longitudinal data. It allows us to detect intra-individual changes in the whole-brain network 1 composition without being influenced by the large heterogeneity of individuals' brain functional 2 networks (26). Previous studies on mindfulness meditation heavily relied on the expert-beginner 3 and/or pre-post comparison design (1). Future research should be encouraged to adopt the single-case 4 research design more frequently to seek further insights into intra-individual changes in patterns of 5 brain networks as a consequence of mindfulness meditation. One obvious limitation of the current 6 research design is that the data were collected from a single participant, which makes it impossible to 7 examine potential individual differences in our findings. However, although research in cognitive 8 neuroscience typically collects data from multiple participants, for the majority of studies, their main 9 focus is on the aggregated pattern of the brain activation/connectivity (but see person-centered 10 research, e.g., (25)), and individual differences have been typically treated as random noise 11 (sampling error). Therefore, in our view, this limitation is superseded by the strength of the current 12 design: sensitivity to the nuanced intra-individual changes in brain signals and functional 13 connectivity. Nevertheless, the potential of the current intensive longitudinal design would be 14 considerably improved by data obtained from multiple participants in future studies. Another 15 limitation of the present study is that the participant performed mindfulness mediation only for three 16 months, which is considerably shorter than the previous studies with experts (e.g., more than one year of regular practice) (10). Future research should collect data for a more prolonged period of 1 time to examine how the progress of practice induces long-term changes in the community structure. The study was approved by the local institutional review board (UREC 16/28). study. In 18 out of the 58 days (Fig. 1), the participant underwent a 15-min session of mindfulness meditation practice a few minutes before scanning. In the practice, the participant tried to focus on 1 his breathing, specifically on sensations of the breath on the nostrils, and attempted to suppress 2 spontaneously upcoming thoughts (10). Before the data collection, the participant studied the 3 mindfulness meditation several times from an auditory instruction developed by a professional 4 trainer (36). In the following text, the "mindfulness meditation (MM) condition" refers to the days on 5 which scanning followed the mindfulness meditation practice. The "no mindfulness meditation 6 (NoMM) condition" refers to the days on which there was no MM practice prior to scanning.        Given the similarity matrix for a community, we compared the coherence of the 12 community within and across the practice conditions. Specifically, we adapted a permutation test, where I represents the number of days (NoMM condition, 40; MM condition, 18), and Ii represents 1 the number of days in which the ROI belonged to community i (i = 1, 2, 3, 4). The IPR is equal to 2 0.75, which is the largest possible value, when a ROI belongs to all the communities with the same 3 probability. In this case, the ROI is the most flexible in terms of the community membership. The 4 IPR is equal to 0, which is the smallest possible value, when the ROI belongs to the same single 5 community in all the days. In this case, the ROI is the least flexible. To investigate whether the 6 mindfulness meditation affects the community-wide flexibility of ROIs, for each community, we 7 applied a paired sample t-test to test the mean difference in the flexibility between the two 8 conditions. In this particular analysis, we defined each community i by its core members, i.e., the 9 ROIs that belonged to community i as the dominant community under both conditions.    Figure 5. Changes in flexibility of ROIs between two conditions. Histograms for each community show the 2 distribution of the values of ROIs that belonged to the corresponding community in both conditions.