Understanding brain networks and brain organization

“Communities are determined by subdividing a network into groups of nodes, often by maximizing the number of within-group links, and minimizing the number of between-group links [142].”

“In the past decade, graph-theoretical analysis of functional neuroimaging data has focused almost exclusively on characterizing the large-scale properties of resting-state data [122,123].”

“For detailed treatments, please see [62]; for applications to brain data, please see [66].”

“It is noteworthy, for instance, that the task-positive network and the task-negative network display fairly complementary profiles, matching the intuition that these networks are at times “anti-correlated”[158, 159].”

“Using a similar approach, Postuma and Dagher [120] identified patterns of co-activation between the cortex and striatum that appear to reflect the cortico-striatal loops proposed by Alexander and colleagues [67].”

“One such case is the proposal that the fusiform gyrus in ventral visual cortex of the right hemisphere acts as a “face module” [13].”

“6 Resting-state connectivity refers to methods that evaluate functional connectivity across brain areas during conditions that do not involve overt tasks, that is, during “rest” [110].”

“As another example, Menon, Uddin, and colleagues suggest that a salience network including the anterior insula and the anterior cingulate cortex is involved in attention to external and internal worlds [44,45].”

“They preserve a high degree of connectivity within local neighborhoods while allowing all nodes of the network to be linked by surprisingly short paths (that is, connection steps), thus creating a “small world” within the network – as in the famous “six degrees of separation” [32].”

“Although prevalent, in general, this approach is inadequate given that in many complex systems, elements naturally belong to multiple communities [140,141].”

“In network research, assortative networks are those in which highly connected nodes are themselves preferentially connected to high-degree nodes [164].”

“Consequently, the structurefunction mapping is not a static property, but a dynamic one [48].”

“Some regions are best characterized as “provincial” hubs because they occupy a central position within a single functional cluster [63].”

“Counter intuitively, however, in some circumstances influence does not correspond to the most highly connected nodes of a network ([128]; see also [129]).”

“Counter intuitively, as described by Estrada and Hatano [134], “information” can in fact spread along non-shortest paths (see also [135,136]).”

“It is defined also as the “temporal correlation between spatially remote neurophysiological events” [98].”

“The prospect of simpler structure-function relationships (hence less context dependent) is discussed by Buckner and colleagues ([57], pp.”

“Along these lines, recent work has suggested that task-negative networks can be subdivided in a number of ways [165].”

“11Though Mesulam [46] also discussed network overlap.”

“Counter intuitively, as described by Estrada and Hatano [134], “information” can in fact spread along non-shortest paths (see also [135,136]).”

“In early work [25], he suggested that a network involving the posterior parietal cortex, frontal cortex, and cingulate cortex, contribute sensory, motor, and motivational representations to attentional processes, respectively.”

“Based on structural human brain data, van den Heuvel and Sporns[36] (p. 15784) proposed that “the aggregation of hubs [i.e., regions of high connectivity] into a rich club suggests that the communication hubs of the brain do not operate as individual entities, but instead act as a strongly interlinked collective” (see…”

“1 See Pessoa [4] for examples concerning emotion and cognition; Cisek [5] for examples concerning perception and action; and Schultz [6] for discussion related to dopamine function.”

“One reason is that a process is suggested to emerge from the interactions between regions – it is thus an emergent property (see [44]).”

“Poldrack RA.”

“In a similar vein, most real-world networks have multiple plausible hierarchical representations of roughly equal likelihood [146, 147].”

“Algorithms of community detection for multirelational networks offer exciting new avenues to explore network structure [152].”

“This means that, counter intuitively, highly overlapping communities can have more external than internal connections [141].”

“For instance, Dosenbach and colleagues [43] have proposed that goal-directed executive control can be understood in terms of two networks, a cingulate-operculum2 network responsible for “set maintenance” (such as maintaining task focus over relatively extended periods of time) and a frontal-parietal network responsibl…”

“To illustrate the idea, consider the insular cortex, a functionally diverse brain region that has been characterized by its involvement in somatic and visceral sensory processes, autonomic regulation, as well as motor processing [167].”

“Also, cortical networks involved in executive control can be decomposed into “stable set control” and “rapid adaptive control” subnetworks, as previously mentioned [145].”

“Also relevant, the amygdala receives signals from all sensory modalities [79].”

“Schneidman and colleagues [137] recorded simultaneously from 40 cells in the salamander retina.”

“Such dynamics are not only important for extending the repertoire of lateral PFC computations but they also influence the precise form of functional connectivity that the lateral PFC entertains with other regions [49].”

“Jones EG, Powell TP.”

“For example, Bassett and colleagues [51] studied the dynamic reconfiguration of human brain networks during learning and uncovered several clusters of brain regions that remained integrated with one another by a complex pattern of weak functional interconnections.”

“Many other examples of this dynamic affiliation idea exist, including the fronto-parietal cortex, whose regions affiliate with others based on current needs [52].”

“Romanski LM, Giguere M, Bates JF, Goldman-Rakic PS. Topographic organization of medial pulvinar connections with the prefrontal cortex in the rhesus monkey.”

“Schultz W. Behavioral theories and the neurophysiology of reward.”

“1 See Pessoa [4] for examples concerning emotion and cognition; Cisek [5] for examples concerning perception and action; and Schultz [6] for discussion related to dopamine function.”

“Degeneracy refers to the ability of structurally different elements to perform the same function or yield the same output [3] – or to be able to complete a task.”

“In early studies, robust interhemispheric correlation of functional MRI signals was observed between cortical regions that have few direct connections, such as those of the left and right hand representation in primary motor cortex [110] and those of spatial representations in left and right primary visual cortex [111…”

“Several studies have suggested that the cortical connectivity of the macaque exhibits small-world properties [33].”

“In one study of resting-state activity [121], the pattern of co-activations between 90 regions (involving major cortical gyri and subcortical nuclei) were submitted to hierarchical clustering, which identified six major systems corresponding approximately to four cortical lobes, a medial temporal cluster, and a cluste…”

“The dual competition model [126] proposes that the effects of reward during perception and cognition depend in part on interactions between valuation regions and fronto-parietal regions important for attention and executive control.”

“The notion of a network is thus extended to incorporate other physiological events, for instance, the state of a given neurotransmitter (as in the beautiful work by Marder and colleagues; see [59]).”

“Indeed, multiple measure of centrality have been proposed [66] and generate different results [132].”

“For example, visual area V4 is highly connected with other visual regions, and can thus be considered to be a visual hub [65] – a type of provincial hub.”

“In this regard, the pattern of connectivity between the amygdala and prefrontal cortex [80] is of particular interest given the latter’s role in cognitive functions.”

“For example, the functional connectivity between two regions with known (or presumed) structural connections can increase or decrease as a function of several variables, including task performance [103], motivation [104], and emotion [105].”

“network, and not necessarily as a fixed internal computation implemented by the network [53-55].”

“concept that was initially devised to characterize how neurons interact and was defined as the “temporal coherence” among the activity of different neurons, as measured by crosscorrelating their spike trains [94-96].”

“To understand the impact of a region on behavior, its connectivity pattern should be considered [61].”

“By recording simultaneously in the pulvinar and cortical visual areas V4 and TEO (the latter in inferior temporal cortex), Saalmann and colleagues [76] reported that maintaining attention in the absence of visual stimulation (during a delay”

“A related concept is that of a rich-club, namely a dominant cluster of highly influential nodes [35].”

“A variant of the third scenario was illustrated by He and colleagues [100].”

“046106-10, [147]): “There are typically an exponential number of structurally diverse alternative partitions with modularities very close to the optimum (the degeneracy problem).”

“However, networks are often multirelational (also called multiplex), like when several types of information define the interactions between two individuals in social networks [151].”

“For example, the functional connectivity between two regions with known (or presumed) structural connections can increase or decrease as a function of several variables, including task performance [103], motivation [104], and emotion [105].”

“A growing number of studies is seeking to explore the relationship between functional and structural connectivity [107].”

“global level, Markov, Kennedy and colleagues injected a retrograde tracer into 29 cortical areas distributed relatively evenly across the macaque cortex [40], allowing them to determine connectivity for a complete 29 × 29 connectivity graph.”

“The hypothalamus is probably the largest source of nonthalamic direct input to cortex, as reviewed in detail by Larry Swanson and colleagues [29, 83].”

“In addition to substantial connections between the amygdala and both medial and orbital aspects of prefrontal cortex, recent findings indicate that bidirectional connectivity is present also along the lateral surface [81] – although the connections are relatively weak.”

“Poldrack RA.”

“where S = 20 was the number of task domains and pi corresponded to the ith domain proportion (for an improved Shannon index, see [158]).”

“Damasio A.”

“11 Some researchers have suggested that hierarchical information can be resolved once laminar information is established for the regions involved (thus presumably helping determine “feedforward” and “feedback” connections”) [150].”

“Counter intuitively, as described by Estrada and Hatano [133], “information” can in fact spread along non-shortest paths (see also [134]; [135]).”

“In this context, Power and colleagues [132] discuss the shortcomings of using the measure of degree to define node importance and suggest other measures instead.”

“For instance, Swanson and colleagues reported that on the order of 600 connections of the amygdala were known at the time of their publication [30], and estimated that the total would likely be closer to 1000.”

“Cacioppo JT, Tassinary LG. Inferring psychological significance from physiological signals.”

“In recent computational analyses, Markov and colleagues [42] suggest the intriguing possibility that, at higher densities, rewiring (i.”

“21 Hermundstad and colleagues [39], who averaged the values of several network diagnostics across one hundred partitions.”

“Using a similar approach, Postuma and Dagher [120] identified patterns of co-activation between the cortex and striatum that appear to reflect the cortico-striatal loops proposed by Alexander and colleagues [67].”

“One suggestion [74] is that the pulvinar participates in cortical communication, with direct cortical connections between two areas supplemented by an indirect pathway coursing through the pulvinar or other higher-order thalamic nuclei (Fig.”

“Koch and colleagues compared anatomical and functional connectivity between cortical patches on adjacent cortical gyri [113].”

“What determines a region’s affiliation? Here, the importance of the context within which a brain region is operating must be considered [47].”

“In particular, the existence of two or more degenerate systems that do not overlap precludes the existence of a single necessary area for a given function [7].”

“By comparison, the volume of the human neocortex is 24% larger than expected for a primate of our brain size [92], whereas the human frontal lobe, frequently assumed to be enlarged, is approximately the size expected for an ape of human brain size [93].”

“8 One way to evaluate this is to use k-shell decomposition [131].”

“An analysis of MEG data has suggested that greater cognitive effort is associated with the emergence of a less modular network topology [127].”

“5) [63,64] (“importance” will be further refined in a later section).”

“concept that was initially devised to characterize how neurons interact and was defined as the “temporal coherence” among the activity of different neurons, as measured by crosscorrelating their spike trains [94-96].”

“Indeed, sites in the dorsal pulvinar may be connected with relatively distal parts of the brain, such as parietal and frontal cortex [70].”

“By comparison, the volume of the human neocortex is 24% larger than expected for a primate of our brain size [92], whereas the human frontal lobe, frequently assumed to be enlarged, is approximately the size expected for an ape of human brain size [93].”

“[119] identified three functional networks: a fronto-parietal attention network, a resting-state network, and a motor network.”

“The importance of networks also was emphasized by Barbas in the domain of emotion and cognition [27].”

“[75], “corticothalamocortical information transfer may represent an important addition to, or even replacement of, the current dogma that corticocortical transfer of primary information exclusively involves direct corticocortical pathways.”

“For example, the functional connectivity between two regions with known (or presumed) structural connections can increase or decrease as a function of several variables, including task performance [103], motivation [104], and emotion [105].”

“The hypothalamus is probably the largest source of nonthalamic direct input to cortex, as reviewed in detail by Larry Swanson and colleagues [29,83].”

“, regions of high connectivity] into a rich club suggests that the communication hubs of the brain do not operate as individual entities, but instead act as a strongly interlinked collective” (see also [37]).”

“For instance, we could describe the amygdala as emotional given its contributions to fear conditioning, and the dorsal-medial PFC as cognitive given its role in the processing of response conflict [2].”

“The pulvinar complex, as this set of related nuclei is sometimes called, is the largest nuclear mass in the primate thalamus and thought to have expanded in size as it evolved in primates [68,69].”

“Notably, many extensive fronto-parietal cortical connections are mirrored by overlapping fields in the pulvinar [72,73]: where regions in frontal and parietal cortex are interconnected in the cortex, their projection sites in the pulvinar typically coincide (and the connections are bidirectional between pulvinar and c…”

“Another illustration is given by a study of patients with multiple sclerosis, a pathology that compromises central white matter in a diffuse manner [101].”

“For instance, the left posterior fusiform gyrus in temporal cortex, which has been implicated in the processing of word forms, animal structures, and so on, can be described by a single, more abstract label of “sensori-motor integration” [8].”

“Furthermore, in the network analysis by Modha and Singh [34] discussed previously, several amygdala nuclei (e.”

“Indeed, the idea of cortical inhibition of subcortex has a long history dating to early researchers, such as Hughlings–Jackson (see [85]).”

“However, the boundary between anatomy and function becomes blurred very quickly once one starts considering factors that characterize the anatomy [94].”

“In the patients, functional connectivity increased in the face of a concomitant reduction of anatomical connectivity (see also [102]).”

“One way to restate the discussion thus far is to consider psychological events (for instance, “functions”, “behaviors”) and physiological events (for instance, brain regions), which can be denoted Ψ and φ, respectively [9].”

“[115] compared existing data on structural connectivity in macaques (data collated in the CoComac database) and functional connectivity obtained during MRI scanning of macaques under anesthesia.”

“Nevertheless, I believe that insisting on a non-overlapping partitioning scheme provides a poor characterization of brain organization (see [142, 143]).”

“The amygdala receives highly processed sensory information [21,78], which is important for value representation since it often depends not on superficial sensory properties, but on those showing some “invariance.”

“Recently, we employed a data-driven approach to investigate the functional repertoire of brain regions based on a large set of functional MRI studies [154].”

“A striking example of structure-function dissociation was reported by Tyszka and colleagues [114] who investigated an unusual population of adults without the corpus callosum, which provides the major communication pathway between the two hemispheres.”

“Based on these assumptions, Hilgetag and colleagues [149] investigated the organization of the visual system and concluded that “the information in the anatomical constraints cannot be expressed satisfactorily by any single hierarchical ordering” [149].”

“Although this introduces outstanding problems, the availability of data repositories containing the results of thousands of neuroimaging studies provides novel opportunities for the investigation of human brain function [153].”

“Based on the available data at the time, analysis of amygdala pathways by Young and colleagues [21] revealed that, of the 72 cortical areas included in their study, it was connected to all but eight (see also [27,77]).”

“In a recent study, we sought instead to understand the network properties of a focused set of brain regions during task conditions engaging them [124].”

“Functional connectivity is at times contrasted with effective connectivity, which attempts to explain the origins of the observed functional relationship and, by definition, assumes a model [99].”

“Given this type of organization, patterns of impairment in perceptual and memory functions following brain damage reflect the demand that each task places (at specific brain locations) rather than dissociable cognitive modules [14,15].”

“Chareyron and colleagues [89] found that the lateral, basal, and accessory basal subregions are dramatically more “developed” in monkeys than in rats (based on morphological characteristics, such as cell counts and the volume of subregions).”

“In the emotion task [125], participants viewed an initial cue that determined whether they were in a threat or safe trial; in the motivation task [104], they viewed an initial cue that indicated whether they were in a reward or control trial.”

“Averbeck and Seo [38] proposed an interesting strategy to tackle this problem.”

“How should one define the domain structure? One hope is that cognitive ontologies can be defined that meaningfully carve the “mental” into stable categories [8,166].”

“To contrast brain networks to each other in terms of the functional fingerprints of the component regions, we employed a multivariate test based on “statistical energy” [161].”

“A few years later, Jouve and colleagues [41] updated the data set analyzed by Felleman and Van Essen and revised those figures to 37% (observed) and 58% (predicted).”

“Work by Barger and colleagues [91] have shown that the lateral nucleus of the amygdala in humans is significantly larger than predicted for an ape of human brain size.”

“Given this type of organization, patterns of impairment in perceptual and memory functions following brain damage reflect the demand that each task places (at specific brain locations) rather than dissociable cognitive modules [14,15].”

“The pulvinar complex, as this set of related nuclei is sometimes called, is the largest nuclear mass in the primate thalamus and thought to have expanded in size as it evolved in primates [68,69].”

“In one study, the functional connectivity pattern between early visual areas was investigated during affective and neutral contexts [106].”

“For example, all twenty to thirty known visual cortical areas connect with the pulvinar, sometimes in a relatively topographic fashion [70,71].”

“Here, I build upon a recent discussion by Vlachos and colleagues [128], who considered this question in the context of neurons.”

“…of nervous systems since 2006, as evidenced by rapid growth in research articles, reviews and citations related to“brain graphs” and “connectomes” [20–22]; by the publication of several textbooks [23, 24]; and by the recent launch of new specialist journals for network neuroscience [25].”

“…approaches have opened new avenues toward studying the neural mechanisms underlying human cognition and behavior from the view of interregional brain interactions (Park and Friston, 2013; Pessoa, 2014; Sporns, 2014; Medaglia et al., 2015; Petersen and Sporns, 2015; Kriegeskorte and Douglas, 2018).”

“…these phenomenological dimensions and activity in specific brain regions is plausible because studies concerning emotion and cognition have shown that brain regions’ functions are inherently multidimensional, and that structurally different regions can perform the same function (Pessoa, 2014).”