L. L. Jiang

Toward reliable characterization of functional homogeneity in the human brain: preprocessing, scan duration, imaging resolution and computational space.

While researchers have extensively characterized functional connectivity between brain regions, the characterization of functional homogeneity within a region of the brain connectome is in early stages of development. Several functional homogeneity measures were proposed previously, among which regional homogeneity (ReHo) was most widely used as a measure to characterize functional homogeneity of resting state fMRI (R-fMRI) signals within a small region (Zang et al., 2004). Despite a burgeoning literature on ReHo in the field of neuroimaging brain disorders, its test-retest (TRT) reliability remains unestablished. Using two sets of public R-fMRI TRT data, we systematically evaluated the ReHos TRT reliability and further investigated the various factors influencing its reliability and found: 1) nuisance (head motion, white matter, and cerebrospinal fluid) correction of R-fMRI time series can significantly improve the TRT reliability of ReHo while additional removal of global brain signal reduces its reliability, 2) spatial smoothing of R-fMRI time series artificially enhances ReHo intensity and influences its reliability, 3) surface-based R-fMRI computation largely improves the TRT reliability of ReHo, 4) a scan duration of 5 min can achieve reliable estimates of ReHo, and 5) fast sampling rates of R-fMRI dramatically increase the reliability of ReHo. Inspired by these findings and seeking a highly reliable approach to exploratory analysis of the human functional connectome, we established an R-fMRI pipeline to conduct ReHo computations in both 3-dimensions (volume) and 2-dimensions (surface).

Topological organization of the human brain functional connectome across the lifespan

Graphical abstract

Logarithmic Sensing in Escherichia coli Bacterial Chemotaxis

We studied the response of swimming Escherichia coli (E. coli) bacteria in a comprehensive set of well-controlled chemical concentration gradients using a newly developed microfluidic device and cell tracking imaging technique. In parallel, we carried out a multi-scale theoretical modeling of bacterial chemotaxis taking into account the relevant internal signaling pathway dynamics, and predicted bacterial chemotactic responses at the cellular level. By measuring the E. coli cell density profiles across the microfluidic channel at various spatial gradients of ligand concentration grad[L] and the average ligand concentration [L] near the peak chemotactic response region, we demonstrated unambiguously in both experiments and model simulation that the mean chemotactic drift velocity of E. coli cells increased monotonically with grad [L]/[L] or approximately grad(log[L])--that is E. coli cells sense the spatial gradient of the logarithmic ligand concentration. The exact range of the log-sensing regime was determined. The agreements between the experiments and the multi-scale model simulation verify the validity of the theoretical model, and revealed that the key microscopic mechanism for logarithmic sensing in bacterial chemotaxis is the adaptation kinetics, in contrast to explanations based directly on ligand occupancy.

Toward neurobiological characterization of functional homogeneity in the human cortex: regional variation, morphological association and functional covariance network organization

Local functional homogeneity of the human cortex indicates the boundaries between functionally heterogeneous regions and varies remarkably across the cortical mantle. It is unclear whether these variations have the neurobiological and structural basis. We employed structural and resting-state functional magnetic resonance imaging scans from 482 healthy subjects and computed the vertex-wise regional homogeneity of low-frequency fluctuations (2dReHo) and five measures of cortical morphology. We then used these metrics to examine regional variation, morphological association and functional covariance network of 2dReHo. Within the ventral visual stream, increases of 2dReHo reflect reduced complexity of information processing or functional hierarchies. Along the divisions of the prefrontal cortex and posteromedial cortex, the gradients of 2dReHo revealed the hierarchical organization within the two association areas, respectively. Individual differences in 2dReHo are associated with those of cortical morphology, and their whole-brain inter-regional covariation is organized into a functional covariance network, comprising five hierarchically organized modules with hubs of both primary sensory and high-order association areas. These highly reproducible observations suggest that local functional homogeneity has neurobiological relevance that is likely determined by anatomical, developmental and neurocognitive factors and should serve as a neuroimaging marker to investigate the human brain function.

Connectivity trajectory across lifespan differentiates the precuneus from the default network

The default network of the human brain has drawn much attention due to its relevance to various brain disorders, cognition, and behavior. However, its functional components and boundaries have not been precisely defined. There is no consensus as to whether the precuneus, a hub in the functional connectome, acts as part of the default network. This discrepancy is more critical for brain development and aging studies: it is not clear whether age has a stronger impact on the default network or precuneus, or both. We used Generalized Ranking and Averaging Independent Component Analysis by Reproducibility (gRAICAR) to investigate the lifespan trajectories of intrinsic functional networks. By estimating individual-specific spatial components and aligning them across subjects, gRAICAR measures the spatial variation of component maps across a population without constraining the same components to appear in every subject. In a cross-lifespan fMRI dataset (N=126, 7-85years old), we observed stronger age dependence in the spatial pattern of a precuneus-dorsal posterior cingulate cortex network compared to the default network, despite the fact that the two networks exhibit considerable spatial overlap and temporal correlation. These results remained even when analyses were restricted to a subpopulation with very similar head motion across age. Our analyses further showed that the two networks tend to merge with increasing age. Post-hoc analyses of functional connectivity confirmed the distinguishable cross-lifespan trajectories between the two networks. Based on these observations, we proposed a dynamic model of cross-lifespan functional segregation and integration between the two networks, suggesting that the precuneus network may have a different functional role than the default network, which declines with age. These findings have implications for understanding the functional roles of the default network, gaining insight into its dynamics throughout life, and guiding interpretation of alterations in brain disorders.

Can Taichi Reshape the Brain? A Brain Morphometry Study

Although research has provided abundant evidence for Taichi-induced improvements in psychological and physiological well-being, little is known about possible links to brain structure of Taichi practice. Using high-resolution MRI of 22 Tai Chi Chuan (TCC) practitioners and 18 controls matched for age, sex and education, we set out to examine the underlying anatomical correlates of long-term Taichi practice at two different levels of regional specificity. For this purpose, parcel-wise and vertex-wise analyses were employed to quantify the difference between TCC practitioners and the controls based on cortical surface reconstruction. We also adopted the Attention Network Test (ANT) to explore the effect of TCC on executive control. TCC practitioners, compared with controls, showed significantly thicker cortex in precentral gyrus, insula sulcus and middle frontal sulcus in the right hemisphere and superior temporal gyrus and medial occipito-temporal sulcus and lingual sulcus in the left hemisphere. Moreover, we found that thicker cortex in left medial occipito-temporal sulcus and lingual sulcus was associated with greater intensity of TCC practice. These findings indicate that long-term TCC practice could induce regional structural change and also suggest TCC might share similar patterns of neural correlates with meditation and aerobic exercise.

Quantitative Modeling of Escherichia coli Chemotactic Motion in Environments Varying in Space and Time

Escherichia coli chemotactic motion in spatiotemporally varying environments is studied by using a computational model based on a coarse-grained description of the intracellular signaling pathway dynamics. We find that the cells chemotaxis drift velocity vd is a constant in an exponential attractant concentration gradient [L]∝exp(Gx). vd depends linearly on the exponential gradient G before it saturates when G is larger than a critical value GC. We find that GC is determined by the intracellular adaptation rate kR with a simple scaling law: . The linear dependence of vd on G = d(ln[L])/dx directly demonstrates E. colis ability in sensing the derivative of the logarithmic attractant concentration. The existence of the limiting gradient GC and its scaling with kR are explained by the underlying intracellular adaptation dynamics and the flagellar motor response characteristics. For individual cells, we find that the overall average run length in an exponential gradient is longer than that in a homogeneous environment, which is caused by the constant kinase activity shift (decrease). The forward runs (up the gradient) are longer than the backward runs, as expected; and depending on the exact gradient, the (shorter) backward runs can be comparable to runs in a spatially homogeneous environment, consistent with previous experiments. In (spatial) ligand gradients that also vary in time, the chemotaxis motion is damped as the frequency ω of the time-varying spatial gradient becomes faster than a critical value ωc, which is controlled by the cells chemotaxis adaptation rate kR. Finally, our model, with no adjustable parameters, agrees quantitatively with the classical capillary assay experiments where the attractant concentration changes both in space and time. Our model can thus be used to study E. coli chemotaxis behavior in arbitrary spatiotemporally varying environments. Further experiments are suggested to test some of the model predictions.

Local-to-remote cortical connectivity in early- and adulthood-onset schizophrenia.

Schizophrenia is increasingly thought of as a brain network or connectome disorder and is associated with neurodevelopmental processes. Previous studies have suggested the important role of anatomical distance in developing a connectome with optimized performance regarding both the cost and efficiency of information processing. Distance-related disturbances during development have not been investigated in schizophrenia. To test the distance-related miswiring profiles of connectomes in schizophrenia, we acquired resting-state images from 20 adulthood-onset (AOS) and 26 early-onset schizophrenia (EOS) patients, as well as age-matched healthy controls. All patients were drug naive and had experienced their first psychotic episode. A novel threshold-free surface-based analytic framework was developed to examine local-to-remote functional connectivity profiles in both AOS and EOS patients. We observed consistent increases of local connectivity across both EOS and AOS patients in the right superior frontal gyrus, where the connectivity strength was correlated with a positive syndrome score in AOS patients. In contrast, EOS but not AOS patients exhibited reduced local connectivity within the right postcentral gyrus and the left middle occipital cortex. These regions’ remote connectivity with their interhemispheric areas and brain network hubs was altered. Diagnosis–age interactions were detectable for both local and remote connectivity profiles. The functional covariance between local and remote homotopic connectivity was present in typically developing controls, but was absent in EOS patients. These findings suggest that a distance-dependent miswiring pattern may be one of the key neurodevelopmental features of the abnormal connectome organization in schizophrenia.

A Mechanism for Precision-Sensing via a Gradient-Sensing Pathway: A Model of Escherichia coli Thermotaxis

Thermotaxis is the phenomenon where an organism directs its movement toward its preferred temperature. So far, the molecular origin for this precision-sensing behavior remains a puzzle. We propose a model of Escherichia coli thermotaxis and show that the precision-sensing behavior in E. coli thermotaxis can be carried out by the gradient-sensing chemotaxis pathway under two general conditions. First, the thermosensor response to temperature is inverted by its internal adaptation state. For E. coli, chemoreceptor Tar changes from a warm sensor to a cold sensor on increase of its methylation level. Second, temperature directly affects the adaptation kinetics. The adapted activity in E. coli increases with temperature in contrast to the perfect adaptation to chemical stimuli. Given these two conditions, E. coli thermotaxis is achieved by the cryophilic and thermophilic responses for temperature above and below a critical temperature Tc, which is encoded by internal pathway parameters. Our model results are supported by both experiments with adaptation-disabled mutants and the recent temperature impulse response measurements for wild-type cells. Tc is predicted to decrease with the background attractant concentration. This mechanism for precision sensing in an adaptive gradient-sensing system may apply to other organisms, such as Dictyostelium discoideum and Caenorhabditis elegans.

Examination of Local Functional Homogeneity in Autism

Increasing neuroimaging evidence suggests that autism patients exhibit abnormal brain structure and function. We used the Autism Brain Imaging Data Exchange (ABIDE) sample to analyze locally focal (~8 mm) functional connectivity of 223 autism patients and 285 normal controls from 15 international sites using a recently developed surface-based approach. We observed enhanced local connectivity in the middle frontal cortex, left precuneus, and right superior temporal sulcus, and reduced local connectivity in the right insular cortex. The local connectivity in the right middle frontal gyrus was positively correlated with the total score of the autism diagnostic observation schedule whereas the local connectivity within the right superior temporal sulcus was positively correlated with total subscores of both the communication and the stereotyped behaviors and restricted interests of the schedule. Finally, significant interactions between age and clinical diagnosis were detected in the left precuneus. These findings replicated previous observations that used a volume-based approach and suggested possible neuropathological impairments of local information processing in the frontal, temporal, parietal, and insular cortices. Novel site-variability analysis demonstrated high reproducibility of our findings across the 15 international sites. The age-disease interaction provides a potential target region for future studies to further elucidate the neurodevelopmental mechanisms of autism.