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Yong He

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JBHI Journal 2025 Journal Article

Preoperative Prediction of Microvascular Invasion in Hepatocellular Carcinoma From Multi-Sequence Magnetic Resonance Imaging Based on Deep Fusion Representation Learning

  • Haishu Ma
  • Lili Wang
  • Lingzhi Sun
  • Shinan Wang
  • Lulu Lu
  • Chaoyang Zhang
  • Yong He
  • Yuan Zhu

Recent studies have identified microvascular invasion (MVI) as the most vital independent biomarker associated with early tumor recurrence. With advancements in medical technology, several computational methods have been developed to predict preoperative MVI using diverse medical images. These existing methods rely on human experience, attribute selection or clinical trial testing, which is often time-consuming and labor-intensive. Leveraging the advantages of deep learning, this study presents a novel end-to-end algorithm for predicting MVI prior to surgery. We devised a series of data preprocessing strategies to fully extract multi-view features from the data while preserving peritumoral information. Notably, a new multi-branch deep fused feature algorithm based on ResNet (DFFResNet) is introduced, which combines Magnetic Resonance Images (MRI) from different sequences to enhance information complementarity and integration. We conducted prediction experiments on a dataset from the Radiology Department of the First Hospital of Lanzhou University, comprising 117 individuals and seven MRI sequences. The model was trained on 80% of the data using 10-fold cross-validation, and the remaining 20% were used for testing. This evaluation was processed in two cases: CROI, containing samples with a complete region of interest (ROI), and PROI, containing samples with a partial ROI region. The robustness results from repeated experiments at both image and patient levels demonstrate the superior performance and improved generalization of the proposed method compared to alternative models. Our approach yields highly competitive prediction results even when the ROI region outline is incomplete, offering a novel and effective multi-sequence fused strategy for predicting preoperative MVI.

YNIMG Journal 2024 Journal Article

Segregation of the regional radiomics similarity network exhibited an increase from late childhood to early adolescence: A developmental investigation

  • Lei Chu
  • Debin Zeng
  • Yirong He
  • Xiaoxi Dong
  • Qiongling Li
  • Xuhong Liao
  • Tengda Zhao
  • Xiaodan Chen

Brain development is characterized by an increase in structural and functional segregation, which supports the specialization of cognitive processes within the context of network neuroscience. In this study, we investigated age-related changes in morphological segregation using individual Regional Radiomics Similarity Networks (R2SNs) constructed with a longitudinal dataset of 494 T1-weighted MR scans from 309 typically developing children aged 6.2 to 13 years at baseline. Segertation indices were defined as the relative difference in connectivity strengths within and between modules and cacluated at the global, system and local levels. Linear mixed-effect models revealed longitudinal increases in both global and system segregation indices, particularly within the limbic and dorsal attention network, and decreases within the ventral attention network. Superior performance in working memory and inhibitory control was associated with higher system-level segregation indices in default, frontoparietal, ventral attention, somatomotor and subcortical systems, and lower local segregation indices in visual network regions, regardless of age. Furthermore, gene enrichment analysis revealed correlations between age-related changes in local segregation indices and regional expression levels of genes related to developmental processes. These findings provide novel insights into typical brain developmental changes using R2SN-derived segregation indices, offering a valuable tool for understanding human brain structural and cognitive maturation.

TMLR Journal 2024 Journal Article

Transfer Learning for High-dimensional Quantile Regression with Statistical Guarantee

  • Sheng Qiao
  • Yong He
  • Wenxin Zhou

The task of transfer learning is to improve estimation/inference of a target model by migrating data from closely related source populations. In this article, we propose transfer learning algorithms for high-dimensional Quantile Regression (QR) models with the technique of convolution-type smoothing. Given the transferable source populations, we derive $\ell_1/\ell_2$-estimation error bounds for the estimators of the target regression coefficients under mild conditions. Theoretical analysis shows that the upper bounds are improved over those of the classical penalized QR estimator with only the target data, as long as the target and the sources are sufficiently similar to each other. When the set of informative sources is unknown, a transferable source detection algorithm is proposed to detect informative sources from all available sources. Thorough simulation studies justify our theoretical analysis.

YNICL Journal 2023 Journal Article

Resting-state functional connectivity of the raphe nuclei in major depressive Disorder: A Multi-site study

  • Yajuan Zhang
  • Chu-Chung Huang
  • Jiajia Zhao
  • Yuchen Liu
  • Mingrui Xia
  • Xiaoqin Wang
  • Dongtao Wei
  • Yuan Chen

Accumulating evidence showed that major depressive disorder (MDD) is characterized by a dysfunction of serotonin neurotransmission. Raphe nuclei are the sources of most serotonergic neurons that project throughout the brain. Incorporating measurements of activity within the raphe nuclei into the analysis of connectivity characteristics may contribute to understanding how neurotransmitter synthesized centers are involved in thepathogenesisof MDD. Here, we analyzed the resting-state functional magnetic resonance imaging (RS-fMRI) dataset from 1,148 MDD patients and 1,079 healthy individuals recruited across nine centers. A seed-based analysis with the dorsal raphe and median raphe nuclei was performed to explore the functional connectivity (FC) alterations. Compared to controls, for dorsal raphe, the significantly decreased FC linking with the right precuneus and median cingulate cortex were found; for median raphe, the increased FC linking with right superior cerebellum (lobules V/VI) was found in MDD patients. In further exploratory analyzes, MDD-related connectivity alterations in dorsal and median raphe nuclei in different clinical factors remained highly similar to the main findings, indicating these abnormal connectivities are a disease-related alteration. Our study highlights a functional dysconnection pattern of raphe nuclei in MDD with multi-site big data. These findings help improve our understanding of the pathophysiology of depression and provide evidence of the theoretical foundation for the development of novel pharmacotherapies.

YNIMG Journal 2022 Journal Article

A deep learning-based multisite neuroimage harmonization framework established with a traveling-subject dataset

  • Dezheng Tian
  • Zilong Zeng
  • Xiaoyi Sun
  • Qiqi Tong
  • Huanjie Li
  • Hongjian He
  • Jia-Hong Gao
  • Yong He

The accumulation of multisite large-sample MRI datasets collected during large brain research projects in the last decade has provided critical resources for understanding the neurobiological mechanisms underlying cognitive functions and brain disorders. However, the significant site effects observed in imaging data and their derived structural and functional features have prevented the derivation of consistent findings across multiple studies. The development of harmonization methods that can effectively eliminate complex site effects while maintaining biological characteristics in neuroimaging data has become a vital and urgent requirement for multisite imaging studies. Here, we propose a deep learning-based framework to harmonize imaging data obtained from pairs of sites, in which site factors and brain features can be disentangled and encoded. We trained the proposed framework with a publicly available traveling subject dataset from the Strategic Research Program for Brain Sciences (SRPBS) and harmonized the gray matter volume maps derived from eight source sites to a target site. The proposed framework significantly eliminated intersite differences in gray matter volumes. The embedded encoders successfully captured both the abstract textures of site factors and the concrete brain features. Moreover, the proposed framework exhibited outstanding performance relative to conventional statistical harmonization methods in terms of site effect removal, data distribution homogenization, and intrasubject similarity improvement. Finally, the proposed harmonization network provided fixable expandability, through which new sites could be linked to the target site via indirect schema without retraining the whole model. Together, the proposed method offers a powerful and interpretable deep learning-based harmonization framework for multisite neuroimaging data that can enhance reliability and reproducibility in multisite studies regarding brain development and brain disorders.

YNIMG Journal 2022 Journal Article

Quantitative mapping of the brain’s structural connectivity using diffusion MRI tractography: A review

  • Fan Zhang
  • Alessandro Daducci
  • Yong He
  • Simona Schiavi
  • Caio Seguin
  • Robert E Smith
  • Chun-Hung Yeh
  • Tengda Zhao

Diffusion magnetic resonance imaging (dMRI) tractography is an advanced imaging technique that enables in vivo reconstruction of the brain's white matter connections at macro scale. It provides an important tool for quantitative mapping of the brain's structural connectivity using measures of connectivity or tissue microstructure. Over the last two decades, the study of brain connectivity using dMRI tractography has played a prominent role in the neuroimaging research landscape. In this paper, we provide a high-level overview of how tractography is used to enable quantitative analysis of the brain's structural connectivity in health and disease. We focus on two types of quantitative analyses of tractography, including: 1) tract-specific analysis that refers to research that is typically hypothesis-driven and studies particular anatomical fiber tracts, and 2) connectome-based analysis that refers to research that is more data-driven and generally studies the structural connectivity of the entire brain. We first provide a review of methodology involved in three main processing steps that are common across most approaches for quantitative analysis of tractography, including methods for tractography correction, segmentation and quantification. For each step, we aim to describe methodological choices, their popularity, and potential pros and cons. We then review studies that have used quantitative tractography approaches to study the brain's white matter, focusing on applications in neurodevelopment, aging, neurological disorders, mental disorders, and neurosurgery. We conclude that, while there have been considerable advancements in methodological technologies and breadth of applications, there nevertheless remains no consensus about the "best" methodology in quantitative analysis of tractography, and researchers should remain cautious when interpreting results in research and clinical applications.

YNIMG Journal 2022 Journal Article

Structural insight into the individual variability architecture of the functional brain connectome

  • Lianglong Sun
  • Xinyuan Liang
  • Dingna Duan
  • Jin Liu
  • Yuhan Chen
  • Xindi Wang
  • Xuhong Liao
  • Mingrui Xia

Human cognition and behaviors depend upon the brain's functional connectomes, which vary remarkably across individuals. However, whether and how the functional connectome individual variability architecture is structurally constrained remains largely unknown. Using tractography- and morphometry-based network models, we observed the spatial convergence of structural and functional connectome individual variability, with higher variability in heteromodal association regions and lower variability in primary regions. We demonstrated that functional variability is significantly predicted by a unifying structural variability pattern and that this prediction follows a primary-to-heteromodal hierarchical axis, with higher accuracy in primary regions and lower accuracy in heteromodal regions. We further decomposed group-level connectome variability patterns into individual unique contributions and uncovered the structural-functional correspondence that is associated with individual cognitive traits. These results advance our understanding of the structural basis of individual functional variability and suggest the importance of integrating multimodal connectome signatures for individual differences in cognition and behaviors.

YNIMG Journal 2021 Journal Article

A large-scale structural and functional connectome of social mentalizing

  • Yin Wang
  • Athanasia Metoki
  • Yunman Xia
  • Yinyin Zang
  • Yong He
  • Ingrid R Olson

Humans have a remarkable ability to infer the mind of others. This mentalizing skill relies on a distributed network of brain regions but how these regions connect and interact is not well understood. Here we leveraged large-scale multimodal neuroimaging data to elucidate the brain-wide organization and mechanisms of mentalizing processing. Key connectomic features of the mentalizing network (MTN) have been delineated in exquisite detail. We found the structural architecture of MTN is organized by two parallel subsystems and constructed redundantly by local and long-range white matter fibers. We uncovered an intrinsic functional architecture that is synchronized according to the degree of mentalizing, and its hierarchy reflects the inherent information integration order. We also examined the correspondence between the structural and functional connectivity in the network and revealed their differences in network topology, individual variance, spatial specificity, and functional specificity. Finally, we scrutinized the connectome resemblance between the default mode network and MTN and elaborated their inherent differences in dynamic patterns, laterality, and homogeneity. Overall, our study demonstrates that mentalizing processing unfolds across functionally heterogeneous regions with highly structured fiber tracts and unique hierarchical functional architecture, which make it distinguishable from the default mode network and other vicinity brain networks supporting autobiographical memory, semantic memory, self-referential, moral reasoning, and mental time travel.

YNIMG Journal 2021 Journal Article

Development of the default-mode network during childhood and adolescence: A longitudinal resting-state fMRI study

  • Fengmei Fan
  • Xuhong Liao
  • Tianyuan Lei
  • Tengda Zhao
  • Mingrui Xia
  • Weiwei Men
  • Yanpei Wang
  • Mingming Hu

The default-mode network (DMN) is a set of functionally connected regions that play crucial roles in internal cognitive processing. Previous resting-state fMRI studies have demonstrated that the intrinsic functional organization of the DMN undergoes remarkable reconfigurations during childhood and adolescence. However, these studies have mainly focused on cross-sectional designs with small sample sizes, limiting the consistency and interpretations of the findings. Here, we used a large sample of longitudinal resting-state fMRI data comprising 305 typically developing children (6-12 years of age at baseline, 491 scans in total) and graph theoretical approaches to delineate the developmental trajectories of the functional architecture of the DMN. For each child, the DMN was constructed according to a prior parcellation with 32 brain nodes. We showed that the overall connectivity increased in strength from childhood to adolescence and became spatially similar to that in the young adult group (N = 61, 18-28 years of age). These increases were primarily located in the midline structures. Global and local network efficiency in the DMN also increased with age, indicating an enhanced capability in parallel information communication within the brain system. Based on the divergent developmental rates of nodal centrality, we identified three subclusters within the DMN, with the fastest rates in the cluster mainly comprising the anterior medial prefrontal cortex and posterior cingulate cortex. Together, our findings highlight the developmental patterns of the functional architecture in the DMN from childhood to adolescence, which has implications for the understanding of network mechanisms underlying the cognitive development of individuals.

I&C Journal 2021 Journal Article

Extremal synchronizing circular automata

  • Yong He
  • Xueping Chen
  • Gang Li
  • Shiyuan Sun

An n-state synchronizing automaton is said to be extremal if it has the reset threshold ( n − 1 ) 2. An extremal synchronizing automaton is specially called an extreme synchronizing automaton if it is no longer an extremal synchronizing automaton after the removal of at least one letter. The Černý automata provide an infinite sequence of extreme synchronizing automata. Besides this, up to isomorphism, only eight isolated examples of extreme synchronizing automata on at least three states have been found. Since the Černý automata and one of the eight isolated examples are circular, one may say that almost all known extreme synchronizing automata are circular. In 2006, Trahtman conjectured that no other extreme synchronizing automaton on at least three states exists. In this paper, all extremal synchronizing circular automata and all extreme synchronizing circular automata are determined. As a consequence, Trahtman's conjecture is confirmed for circular automata.

YNIMG Journal 2021 Journal Article

The coupling of BOLD signal variability and degree centrality underlies cognitive functions and psychiatric diseases

  • Jintao Sheng
  • Liang Zhang
  • Junjiao Feng
  • Jing Liu
  • Anqi Li
  • Wei Chen
  • Yuedi Shen
  • Jinhui Wang

Brain signal variability has been consistently linked to functional integration; however, whether this coupling is associated with cognitive functions and/or psychiatric diseases has not been clarified. Using multiple multimodality datasets, including resting-state functional magnetic resonance imaging (rsfMRI) data from the Human Connectome Project (HCP: N = 927) and a Beijing sample (N = 416) and cerebral blood flow (CBF) and rsfMRI data from a Hangzhou sample (N = 29), we found that, compared with the existing variability measure (i. e. , SDBOLD), the mean-scaled (standardized) fractional standard deviation of the BOLD signal (mfSDBOLD) maintained very high test-retest reliability, showed greater cross-site reliability and was less affected by head motion. We also found strong reproducible couplings between the mfSDBOLD and functional integration measured by the degree centrality (DC), both cross-voxel and cross-subject, which were robust to scanning and preprocessing parameters. Moreover, both mfSDBOLD and DC were correlated with CBF, suggesting a common physiological basis for both measures. Critically, the degree of coupling between mfSDBOLD and long-range DC was positively correlated with individuals’ cognitive total composite scores. Brain regions with greater mismatches between mfSDBOLD and long-range DC were more vulnerable to brain diseases. Our results suggest that BOLD signal variability could serve as a meaningful index of local function that underlies functional integration in the human brain and that a strong coupling between BOLD signal variability and functional integration may serve as a hallmark of balanced brain networks that are associated with optimal brain functions.

YNIMG Journal 2020 Journal Article

The spatial organization of the chronnectome associates with cortical hierarchy and transcriptional profiles in the human brain

  • Jin Liu
  • Mingrui Xia
  • Xindi Wang
  • Xuhong Liao
  • Yong He

The chronnectome of the human brain represents dynamic connectivity patterns of brain networks among interacting regions, but its organization principle and related transcriptional signatures remain unclear. Using task-free fMRI data from the Human Connectome Project (681 participants) and microarray-based gene expression data from the Allen Institute for Brain Science (1791 brain tissue samples from six donors), we conduct a transcriptome-chronnectome association study to investigate the spatial configurations of dynamic brain networks and their linkages with transcriptional profiles. We first classify the dynamic brain networks into four categories of nodes according to their time-varying characteristics in global connectivity and modular switching: the primary sensorimotor regions with large global variations, the paralimbic/limbic regions with frequent modular switching, the frontoparietal cortex with both high global and modular dynamics, and the sensorimotor association cortex with limited dynamics. Such a spatial layout reflects the cortical functional hierarchy, microarchitecture, and primary connectivity gradient spanning from primary to transmodal areas, and the cognitive spectrum from perception to abstract processing. Importantly, the partial least squares regression analysis reveals that the transcriptional profiles could explain 28% of the variation in this spatial layout of network dynamics. The top-related genes in the transcriptional profiles are enriched for potassium ion channel complex and activity and mitochondrial part of the cellular component. These findings highlight the hierarchically spatial arrangement of dynamic brain networks and their coupling with the variation in transcriptional signatures, which provides indispensable implications for the organizational principle and cellular and molecular functions of spontaneous network dynamics.

YNIMG Journal 2019 Journal Article

Graph theoretical modeling of baby brain networks

  • Tengda Zhao
  • Yuehua Xu
  • Yong He

The human brain undergoes explosive growth during the prenatal period and the first few postnatal years, establishing an early infrastructure for the later development of behaviors and cognitions. Revealing the developmental rules during the early phase is essential for understanding the emergence of brain functions and the origin of developmental disorders. Graph-theoretical network modeling in combination with multiple neuroimaging probes provides an important research framework to explore the early development of the topological wiring and organizational paradigms of the brain. Here, we reviewed studies that employed neuroimaging and graph-theoretical modeling to investigate brain network development from approximately 20 gestational weeks to 2 years of age. Specifically, the structural and functional brain networks have evolved to highly efficient topological architectures in the early stage; where the structural network remains ahead and paves the way for the development of the functional network. The brain network develops in a heterogeneous order, from primary to higher-order systems and from a tendency of network segregation to network integration in the prenatal and postnatal periods. The early brain network topologies show abilities in predicting certain cognitive and behavior performance in later life, and their impairments are likely to continue into childhood and even adulthood. These macroscopic topological changes may be associated with possible microstructural maturations, such as axonal growth and myelinations. Collectively, this review provides a detailed delineation of the early changes in the baby brains in a graph-theoretical modeling framework, which opens up a new avenue for understanding the developmental principles of the connectome.

YNIMG Journal 2019 Journal Article

Network analysis reveals disrupted functional brain circuitry in drug-naive social anxiety disorder

  • Xun Yang
  • Jin Liu
  • Yajing Meng
  • Mingrui Xia
  • Zaixu Cui
  • Xi Wu
  • Xinyu Hu
  • Wei Zhang

Social anxiety disorder (SAD) is a common and disabling condition characterized by excessive fear and avoidance of public scrutiny. Psychoradiology studies have suggested that the emotional and behavior deficits in SAD are associated with abnormalities in regional brain function and functional connectivity. However, little is known about whether intrinsic functional brain networks in patients with SAD are topologically disrupted. Here, we collected resting-state fMRI data from 33 drug-naive patients with SAD and 32 healthy controls (HC), constructed functional networks with 34 predefined regions based on previous meta-analytic research with task-based fMRI in SAD, and performed network-based statistic and graph-theory analyses. The network-based statistic analysis revealed a single connected abnormal circuitry including the frontolimbic circuit (termed the “fear circuit”, including the dorsolateral prefrontal cortex, ventral medial prefrontal cortex and insula) and posterior cingulate/occipital areas supporting perceptual processing. In this single altered network, patients with SAD had higher functional connectivity than HC. At the global level, graph-theory analysis revealed that the patients exhibited a lower normalized characteristic path length than HC, which suggests a disorder-related shift of network topology toward randomized configurations. SAD-related deficits in nodal degree, efficiency and participation coefficient were detected in the parahippocampal gyrus, posterior cingulate cortex, dorsolateral prefrontal cortex, insula and the calcarine sulcus. Aspects of abnormal connectivity were associated with anxiety symptoms. These findings highlight the aberrant topological organization of functional brain network organization in SAD, which provides insights into the neural mechanisms underlying excessive fear and avoidance of social interactions in patients with debilitating social anxiety.

YNIMG Journal 2019 Journal Article

Regional excitation-inhibition balance predicts default-mode network deactivation via functional connectivity

  • Hong Gu
  • Yuzheng Hu
  • Xi Chen
  • Yong He
  • Yihong Yang

Deactivation of the default mode network (DMN) is one of the most reliable observations from neuroimaging and has significant implications in development, aging, and various neuropsychiatric disorders. However, the neural mechanism underlying DMN deactivation remains elusive. As the coordination of regional neurochemical substrates and interregional neural interactions are both essential in support of brain functions, a quantitative description of how they impact DMN deactivation may provide new insights into the mechanism. Using an n-back working memory task fMRI and magnetic resonance spectroscopy, we probed the pairwise relationship between task-induced deactivation, interregional functional connectivity and regional excitation-inhibition balance (evaluated by glutamate/GABA ratio) in the posterior cingulate cortex/precuneus (PCC/PCu). Task-induced PCC/PCu deactivation correlated with its excitation-inhibition balance and interregional functional connectivity, where participants with lower glutamate/GABA ratio, stronger intra-DMN connections and stronger antagonistic DMN-SN (salience network)/ECN (executive control network) inter-network connections had greater PCC/PCu deactivation. Mediation analyses revealed that the DMN-SN functional interactions partially mediated the relationship between task-induced deactivation and the excitation-inhibition balance at the PCC/PCu. The triple-relationship discovered in the present study has the potential to bridge DMN-deactivation related findings from various neuroimaging modalities and may provide new insights into the neural mechanism of DMN deactivation. Moreover, this finding may have significant implications for neuropsychiatric disorders related to the DMN dysfunction and suggests an integrated application of pharmacological and neuromodulation-based strategies for rescuing DMN deactivation deficits.

YNIMG Journal 2019 Journal Article

Reproducibility of functional brain alterations in major depressive disorder: Evidence from a multisite resting-state functional MRI study with 1,434 individuals

  • Mingrui Xia
  • Tianmei Si
  • Xiaoyi Sun
  • Qing Ma
  • Bangshan Liu
  • Li Wang
  • Jie Meng
  • Miao Chang

Resting-state functional MRI (R-fMRI) studies have demonstrated widespread alterations in brain function in patients with major depressive disorder (MDD). However, a clear and consistent conclusion regarding a repeatable pattern of MDD-relevant alterations is still limited due to the scarcity of large-sample, multisite datasets. Here, we address this issue by including a large R-fMRI dataset with 1434 participants (709 patients with MDD and 725 healthy controls) from five centers in China. Individual functional activity maps that represent very local to long-range connections are computed using the amplitude of low-frequency fluctuations, regional homogeneity and distance-related functional connectivity strength. The reproducibility analyses involve different statistical strategies, global signal regression, across-center consistency, clinical variables, and sample size. We observed significant hypoactivity in the orbitofrontal, sensorimotor, and visual cortices and hyperactivity in the frontoparietal cortices in MDD patients compared to the controls. These alterations are not affected by different statistical analysis strategies, global signal regression and medication status and are generally reproducible across centers. However, these between-group differences are partially influenced by the episode status and the age of disease onset in patients, and the brain-clinical variable relationship exhibits poor cross-center reproducibility. Bootstrap analyses reveal that at least 400 subjects in each group are required to replicate significant alterations (an extent threshold of P <. 05 and a height threshold of P <. 001) at 50% reproducibility. Together, these results highlight reproducible patterns of functional alterations in MDD and relevant influencing factors, which provides crucial guidance for future neuroimaging studies of this disorder.

YNIMG Journal 2019 Journal Article

Unbiased age-specific structural brain atlases for Chinese pediatric population

  • Tengda Zhao
  • Xuhong Liao
  • Vladimir S. Fonov
  • Qiushi Wang
  • Weiwei Men
  • Yanpei Wang
  • Shaozheng Qin
  • Shuping Tan

In magnetic resonance (MR) imaging studies of child brain development, structural brain atlases usually serve as important references for the pediatric population, in which individual images are spatially normalized into a common or standard stereotactic space. However, the popular existing pediatric brain atlases (e. g. , National Institutes of Health pediatric atlases, NIH-PD) are mostly based on MR images obtained from Caucasian populations and thus are not ideal for the characterization of the brains of Chinese children due to neuroanatomical differences related to genetic and environmental factors. Here, we use an unbiased template construction algorithm to create a set of age-specific Chinese pediatric (CHN-PD) atlases based on high-quality T1-and T2-weighted MR images from 328 cognitively normal Chinese children aged 6–12 years. The CHN-PD brain atlases include asymmetric and symmetric templates, sex-specific templates and tissue probability templates, and contain multiple age-specific templates at one-year intervals. A direct comparison of the CHN-PD and NIH-PD atlases reveals dramatic anatomical differences mainly in the bilateral frontal and parietal regions. After applying the CHN-PD and NIH-PD atlases to two independent Chinese pediatric datasets (N = 114 and N = 71), we find that the CHN-PD atlases result in significantly higher accuracy than the NIH-PD atlases in both predicting “brain age” and guiding brain tissue segmentation. These results suggest that the CHN-PD brain atlases are necessary for studies of the typical and atypical development of the Chinese pediatric population. These CHN-PD atlases have been released on the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) website (https: //www. nitrc. org/projects/chn-pd).

YNIMG Journal 2017 Journal Article

Functional connectomics from a “big data” perspective

  • Mingrui Xia
  • Yong He

In the last decade, explosive growth regarding functional connectome studies has been observed. Accumulating knowledge has significantly contributed to our understanding of the brain's functional network architectures in health and disease. With the development of innovative neuroimaging techniques, the establishment of large brain datasets and the increasing accumulation of published findings, functional connectomic research has begun to move into the era of “big data”, which generates unprecedented opportunities for discovery in brain science and simultaneously encounters various challenging issues, such as data acquisition, management and analyses. Big data on the functional connectome exhibits several critical features: high spatial and/or temporal precision, large sample sizes, long-term recording of brain activity, multidimensional biological variables (e. g. , imaging, genetic, demographic, cognitive and clinic) and/or vast quantities of existing findings. We review studies regarding functional connectomics from a big data perspective, with a focus on recent methodological advances in state-of-the-art image acquisition (e. g. , multiband imaging), analysis approaches and statistical strategies (e. g. , graph theoretical analysis, dynamic network analysis, independent component analysis, multivariate pattern analysis and machine learning), as well as reliability and reproducibility validations. We highlight the novel findings in the application of functional connectomic big data to the exploration of the biological mechanisms of cognitive functions, normal development and aging and of neurological and psychiatric disorders. We advocate the urgent need to expand efforts directed at the methodological challenges and discuss the direction of applications in this field.

YNIMG Journal 2017 Journal Article

Individual differences and time-varying features of modular brain architecture

  • Xuhong Liao
  • Miao Cao
  • Mingrui Xia
  • Yong He

Recent studies have suggested that human brain functional networks are topologically organized into functionally specialized but inter-connected modules to facilitate efficient information processing and highly flexible cognitive function. However, these studies have mainly focused on group-level network modularity analyses using “static” functional connectivity approaches. How these extraordinary modular brain structures vary across individuals and spontaneously reconfigure over time remain largely unknown. Here, we employed multiband resting-state functional MRI data (N=105) from the Human Connectome Project and a graph-based modularity analysis to systematically investigate individual variability and dynamic properties in modular brain networks. We showed that the modular structures of brain networks dramatically vary across individuals, with higher modular variability primarily in the association cortex (e. g. , fronto-parietal and attention systems) and lower variability in the primary systems. Moreover, brain regions spontaneously changed their module affiliations on a temporal scale of seconds, which cannot be simply attributable to head motion and sampling error. Interestingly, the spatial pattern of intra-subject dynamic modular variability largely overlapped with that of inter-subject modular variability, both of which were highly reproducible across repeated scanning sessions. Finally, the regions with remarkable individual/temporal modular variability were closely associated with network connectors and the number of cognitive components, suggesting a potential contribution to information integration and flexible cognitive function. Collectively, our findings highlight individual modular variability and the notable dynamic characteristics in large-scale brain networks, which enhance our understanding of the neural substrates underlying individual differences in a variety of cognition and behaviors.

TCS Journal 2016 Journal Article

Conjugacy relations of prefix codes

  • Yong He
  • Zhenhe Cui
  • Zihan Yuan

It is shown that, if X and Y are prefix codes and Z is a non-empty language satisfying the condition X Z = Z Y, then Z is the union of a non-empty family { P n } i ∈ I of pairwise disjoint prefix sets such that X P i = P i Y for all i ∈ I. Consequently, the conjugacy relations of prefix codes are explored and, under the restriction that both of X and Y are prefix codes, the solutions of the conjugacy equation X Z = Z Y for languages are determined. Also, the decidability of the conjugacy problem for finite prefix codes is confirmed.

YNIMG Journal 2016 Journal Article

Intrinsic functional network architecture of human semantic processing: Modules and hubs

  • Yangwen Xu
  • Qixiang Lin
  • Zaizhu Han
  • Yong He
  • Yanchao Bi

Semantic processing entails the activation of widely distributed brain areas across the temporal, parietal, and frontal lobes. To understand the functional structure of this semantic system, we examined its intrinsic functional connectivity pattern using a database of 146 participants. Focusing on areas consistently activated during semantic processing generated from a meta-analysis of 120 neuroimaging studies (Binder et al. , 2009), we found that these regions were organized into three stable modules corresponding to the default mode network (Module DMN), the left perisylvian network (Module PSN), and the left frontoparietal network (Module FPN). These three dissociable modules were integrated by multiple connector hubs—the left angular gyrus (AG) and the left superior/middle frontal gyrus linking all three modules, the left anterior temporal lobe linking Modules DMN and PSN, the left posterior portion of dorsal intraparietal sulcus (IPS) linking Modules DMN and FPN, and the left posterior middle temporal gyrus (MTG) linking Modules PSN and FPN. Provincial hubs, which converge local information within each system, were also identified: the bilateral posterior cingulate cortices/precuneus, the bilateral border area of the posterior AG and the superior lateral occipital gyrus for Module DMN; the left supramarginal gyrus, the middle part of the left MTG and the left orbital inferior frontal gyrus (IFG) for Module FPN; and the left triangular IFG and the left IPS for Module FPN. A neuro-functional model for semantic processing was derived based on these findings, incorporating the interactions of memory, language, and control.

EAAI Journal 2015 Journal Article

Coordinated learning based on time-sharing tracking framework and Gaussian regression for continuous multi-agent systems

  • Xin Chen
  • Penghuan Xie
  • Yong He
  • Min Wu

Applying multi-agent reinforcement learning (MARL) in continuous distributed control system is an attractive issue, because it entitles agents adaptively to construct a cooperative behavior, even if the dynamics of such distributed system is unknown a priori. However the implementation of MARL always suffers from dimension explosion, nonstationary learning, and generalization in continuous systems. This paper presents a continuous coordinated learning algorithm with time-sharing tracking framework (CCL-TT) to deal with these problems, in which the value function is dimension reduced to lighten dimension explosion, the time-sharing tracking framework (TTF) is developed to solve nonstationary learning, and Gaussian regression modeling is applied to realize generalization. With TTF, a macroscopic concurrent learning is set up to meet the requirements of temporal stationary condition in value learning and generalization. Finally the simulation illustrates how CCL-TT realizes cooperative learning without knowledge about the dynamics of the system, even with disturbance.

YNIMG Journal 2015 Journal Article

Cortisol awakening response predicts intrinsic functional connectivity of the medial prefrontal cortex in the afternoon of the same day

  • Jianhui Wu
  • Shen Zhang
  • Wanqing Li
  • Shaozheng Qin
  • Yong He
  • Zhi Yang
  • Tony W. Buchanan
  • Chao Liu

Cortisol awakening response (CAR) is the cortisol secretory activity in the first 30–60min immediately after awakening in the morning. Alterations in CAR as a trait have been associated with changes in the brain structure and function. CAR also fluctuates over days. Little, however, is known about the relationship between CAR as a state and brain activity. Using resting-state functional magnetic resonance imaging (fMRI), we investigated whether the CAR predicts intrinsic functional connectivity (FC) of the brain in the afternoon of the same day. Data from forty-nine healthy participants were analyzed. Salivary cortisol levels were assessed immediately after awakening and 15, 30 and 60min after awakening, and resting-state fMRI data were obtained in the afternoon. Global FC strength (FCS) of each voxel was computed to provide a whole-brain characterization of intrinsic functional architecture. Correlation analysis was used to examine whether CAR predicts the intrinsic FC of core brain networks. We observed that the CAR was positively correlated with the FCS of the medial prefrontal cortex (mPFC). Further analysis revealed that higher CAR predicted stronger positive mPFC connectivity with regions in the default mode network. Our findings suggest that the HPA activity after awakening in the early morning may predict intrinsic functional connectivity of mPFC at rest in the afternoon of the same day.

YNIMG Journal 2015 Journal Article

Dynamic brain architectures in local brain activity and functional network efficiency associate with efficient reading in bilinguals

  • Gangyi Feng
  • Hsuan-Chih Chen
  • Zude Zhu
  • Yong He
  • Suiping Wang

The human brain is organized as a dynamic network, in which both regional brain activity and inter-regional connectivity support high-level cognitive processes, such as reading. However, it is still largely unknown how the functional brain network organizes to enable fast and effortless reading processing in the native language (L1) but not in a non-proficient second language (L2), and whether the mechanisms underlying local activity are associated with connectivity dynamics in large-scale brain networks. In the present study, we combined activation-based and multivariate graph-theory analysis with functional magnetic resonance imaging data to address these questions. Chinese–English unbalanced bilinguals read narratives for comprehension in Chinese (L1) and in English (L2). Compared with L2, reading in L1 evoked greater brain activation and recruited a more globally efficient but less clustered network organization. Regions with both increased network efficiency and enhanced brain activation in L1 reading were mostly located in the fronto-temporal reading-related network (RN), whereas regions with decreased global network efficiency, increased clustering, and more deactivation in L2 reading were identified in the default mode network (DMN). Moreover, functional network efficiency was closely associated with local brain activation, and such associations were also modulated by reading efficiency in the two languages. Our results demonstrate that an economical and integrative brain network topology is associated with efficient reading, and further reveal a dynamic association between network efficiency and local activation for both RN and DMN. These findings underscore the importance of considering interregional connectivity when interpreting local BOLD signal changes in bilingual reading.

YNIMG Journal 2014 Journal Article

3D BrainCV: Simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution

  • Jingpeng Wu
  • Yong He
  • Zhongqin Yang
  • Congdi Guo
  • Qingming Luo
  • Wei Zhou
  • Shangbin Chen
  • Anan LI

Systematic cellular and vascular configurations are essential for understanding fundamental brain anatomy and metabolism. We demonstrated a 3D brainwide cellular and vascular (called 3D BrainCV) visualization and quantitative protocol for a whole mouse brain. We developed a modified Nissl staining method that quickly labeled the cells and blood vessels simultaneously in an entire mouse brain. Terabytes 3D datasets of the whole mouse brains, with unprecedented details of both individual cells and blood vessels, including capillaries, were simultaneously imaged at 1-μm voxel resolution using micro-optical sectioning tomography (MOST). For quantitative analysis, we proposed an automatic image-processing pipeline to perform brainwide vectorization and analysis of cells and blood vessels. Six representative brain regions from the cortex to the deep, including FrA, M1, PMBSF, V1, striatum, and amygdala, and six parameters, including cell number density, vascular length density, fractional vascular volume, distance from the cells to the nearest microvessel, microvascular length density, and fractional microvascular volume, had been quantitatively analyzed. The results showed that the proximity of cells to blood vessels was linearly correlated with vascular length density, rather than the cell number density. The 3D BrainCV made overall snapshots of the detailed picture of the whole brain architecture, which could be beneficial for the state comparison of the developing and diseased brain.

YNIMG Journal 2014 Journal Article

Different topological organization of human brain functional networks with eyes open versus eyes closed

  • Pengfei Xu
  • Ruiwang Huang
  • Jinhui Wang
  • Nicholas T. Van Dam
  • Teng Xie
  • Zhangye Dong
  • Chunping Chen
  • Ruolei Gu

Opening and closing the eyes are fundamental behaviors for directing attention to the external versus internal world. However, it remains unclear whether the states of eyes-open (EO) relative to eyes-closed (EC) are associated with different topological organizations of functional neural networks for exteroceptive and interoceptive processing (processing the external world and internal state, respectively). Here, we used resting-state functional magnetic resonance imaging and neural network analysis to investigate the topological properties of functional networks of the human brain when the eyes were open versus closed. The brain networks exhibited higher cliquishness and local efficiency, but lower global efficiency during the EO state compared to the EC state. These properties suggest an increase in specialized information processing along with a decrease in integrated information processing in EO (vs. EC). More importantly, the “exteroceptive” network, including the attentional system (e. g. , superior parietal gyrus and inferior parietal lobule), ocular motor system (e. g. , precentral gyrus and superior frontal gyrus), and arousal system (e. g. , insula and thalamus), showed higher regional nodal properties (nodal degree, efficiency and betweenness centrality) in EO relative to EC. In contrast, the “interoceptive” network, composed of visual system (e. g. , lingual gyrus, fusiform gyrus and cuneus), auditory system (e. g. , Heschl's gyurs), somatosensory system (e. g. , postcentral gyrus), and part of the default mode network (e. g. , angular gyrus and anterior cingulate gyrus), showed significantly higher regional properties in EC vs. EO. In addition, the connections across sensory modalities were altered by volitional eye opening. The synchronicity between the visual system and the motor, somatosensory and auditory systems, characteristic of EC, was attenuated in EO. Further, the connections between the visual system and the attention, arousal and subcortical systems were increased in EO. These results may indicate that EO leads to a suppression of sensory modalities (other than visual) to allocate resources to exteroceptive processing. Our findings suggest that the topological organization of human brain networks dynamically switches corresponding to the information processing modes as we open or close our eyes.

YNIMG Journal 2013 Journal Article

Brain anatomical networks in world class gymnasts: A DTI tractography study

  • Bin Wang
  • Yuanyuan Fan
  • Min Lu
  • Shumei Li
  • Zheng Song
  • Xiaoling Peng
  • Ruibin Zhang
  • Qixiang Lin

The excellent motor skills of world class gymnasts amaze everyone. People marvel at the way they precisely control their movements and wonder how the brain structure and function of these elite athletes differ from those of non-athletes. In this study, we acquired diffusion images from thirteen world class gymnasts and fourteen matched controls, constructed their anatomical networks, and calculated the topological properties of each network based on graph theory. From a connectivity-based analysis, we found that most of the edges with increased connection density in the champions were linked to brain regions that are located in the sensorimotor, attentional, and default-mode systems. From graph-based metrics, we detected significantly greater global and local efficiency but shorter characteristic path length in the anatomical networks of the champions compared with the controls. Moreover, in the champions we found a significantly higher nodal degree and greater regional efficiency in several brain regions that correspond to motor and attention functions. These included the left precentral gyrus, left postcentral gyrus, right anterior cingulate gyrus and temporal lobes. In addition, we revealed an increase in the mean fractional anisotropy of the corticospinal tract in the champions, possibly in response to long-term gymnastic training. Our study indicates that neuroanatomical adaptations and plastic changes occur in gymnasts' brain anatomical networks either in response to long-term intensive gymnastic training or as an innate predisposition or both. Our findings may help to explain gymnastic skills at the highest levels of performance and aid in understanding the neural mechanisms that distinguish expert gymnasts from novices.

YNIMG Journal 2013 Journal Article

Functional brain hubs and their test–retest reliability: A multiband resting-state functional MRI study

  • Xu-Hong Liao
  • Ming-Rui Xia
  • Ting Xu
  • Zheng-Jia Dai
  • Xiao-Yan Cao
  • Hai-Jing Niu
  • Xi-Nian Zuo
  • Yu-Feng Zang

Resting-state functional MRI (R-fMRI) has emerged as a promising neuroimaging technique used to identify global hubs of the human brain functional connectome. However, most R-fMRI studies on functional hubs mainly utilize traditional R-fMRI data with relatively low sampling rates (e. g. , repetition time [TR]=2s). R-fMRI data scanned with higher sampling rates are important for the characterization of reliable functional connectomes because they can provide temporally complementary information about functional integration among brain regions and simultaneously reduce the effects of high frequency physiological noise. Here, we employed a publicly available multiband R-fMRI dataset with a sub-second sampling rate (TR=645ms) to identify global hubs in the human voxel-wise functional networks, and further examined their test–retest (TRT) reliability over scanning time. We showed that the functional hubs of human brain networks were mainly located at the default-mode regions (e. g. , medial prefrontal and parietal cortex as well as the lateral parietal and temporal cortex) and the sensorimotor and visual cortex. These hub regions were highly anatomically distance-dependent, where short-range and long-range hubs were primarily located at the primary cortex and the multimodal association cortex, respectively. We found that most functional hubs exhibited fair to good TRT reliability using intraclass correlation coefficients. Interestingly, our analysis suggested that a 6-minute scan duration was able to reliably detect these functional hubs. Further comparison analysis revealed that these results were approximately consistent with those obtained using traditional R-fMRI scans of the same subjects with TR=2500ms, but several regions (e. g. , lateral frontal cortex, paracentral lobule and anterior temporal lobe) exhibited different TRT reliability. Finally, we showed that several regions (including the medial/lateral prefrontal cortex and lateral temporal cortex) were identified as brain hubs in a high frequency band (0. 2–0. 3Hz), which is beyond the frequency scope of traditional R-fMRI scans. Our results demonstrated the validity of multiband R-fMRI data to reliably detect functional hubs in the voxel-wise whole-brain networks, which motivated the acquisition of high temporal resolution R-fMRI data for the studies of human brain functional connectomes in healthy and diseased conditions.

YNIMG Journal 2013 Journal Article

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

  • Xi-Nian Zuo
  • Ting Xu
  • Lili Jiang
  • Zhi Yang
  • Xiao-Yan Cao
  • Yong He
  • Yu-Feng Zang
  • F. Xavier Castellanos

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 ReHo's 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 5min 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).

YNIMG Journal 2013 Journal Article

Where color rests: Spontaneous brain activity of bilateral fusiform and lingual regions predicts object color knowledge performance

  • Xiaoying Wang
  • Zaizhu Han
  • Yong He
  • Alfonso Caramazza
  • Luping Song
  • Yanchao Bi

Knowledge of the physical attributes of objects is commonly assumed to be distributed near their respective modality-specific brain regions. The exact neural correlates for such knowledge, especially how it is maintained in the resting state, are largely unknown. In the current study, we explored the intrinsic neural basis related to a specific type of object knowledge — color — by investigating the relationship between spontaneous brain activity and color knowledge behavioral performance. We correlated the regional amplitude of spontaneous low-frequency fluctuations (ALFF, a resting-state fMRI parameter) with healthy participants' performance on two object color knowledge tasks (object color verification and color attribute judgment). We found that ALFF in bilateral lingual and fusiform gyri and right inferior occipital gyrus reliably predicted participants' color knowledge performance (correlation coefficients=0. 55–0. 70), and that calcarine cortex showed a similar trend, although less stable. Furthermore, the ALFF-behavior correlations for other types of object knowledge (i. e. form, motion and sound) in these regions were minimal and significantly lower than those for color knowledge, suggesting that the effects in the observed regions were not merely due to general object processing. Furthermore, we showed that functional connectivity strengths of the lingual/fusiform and inferior occipital regions are significantly associated with color knowledge performance, indicating that they work as a network to support color knowledge processing or the acquisition of such knowledge. Our findings show the critical role of ventral medial occipito-temporal regions in processing or acquiring color knowledge and highlight the behavioral significance of spontaneous brain activity in the resting state.

YNIMG Journal 2012 Journal Article

Convergence and divergence of thickness correlations with diffusion connections across the human cerebral cortex

  • Gaolang Gong
  • Yong He
  • Zhang J. Chen
  • Alan C. Evans

Cortical thickness correlation across individuals has been observed. So far, it remains unclear to what extent such a correlation in thickness is a reflection of underlying fiber connection. Here we explicitly compared the patterns of cortical thickness correlation and diffusion-based fiber connection across the entire cerebral cortex, in 95 normal adults. Interregional thickness correlations were extracted by using computational neuroanatomy algorithms based on structural MRI, and diffusion connections were detected by using diffusion probabilistic tractography. Approximately 35–40% of thickness correlations showed convergent diffusion connections across the cerebral cortex. Intriguingly, the observed convergences between thickness correlation and diffusion connection are mostly focused on the positive thickness correlations, while almost all of the negative correlations (>90%) did not have a matched diffusion connection, suggesting different mechanisms behind the positive and negative thickness correlations, the latter not being mediated by a direct fiber pathway. Furthermore, graph theoretic analysis reveals that the thickness correlation network has a more randomized overall topology, whereas the nodal characteristics of cortical regions in these two networks are statistically correlated. These findings indicate that thickness correlations partly reflect underlying fiber connections but they contains exclusive information, and therefore should not be simply taken as a proxy measure for fiber connections.

YNIMG Journal 2012 Journal Article

Discriminative analysis of early Alzheimer's disease using multi-modal imaging and multi-level characterization with multi-classifier (M3)

  • Zhengjia Dai
  • Chaogan Yan
  • Zhiqun Wang
  • Jinhui Wang
  • Mingrui Xia
  • Kuncheng Li
  • Yong He

Increasing attention has recently been directed to the applications of pattern recognition and brain imaging techniques in the effective and accurate diagnosis of Alzheimer's disease (AD). However, most of the existing research focuses on the use of single-modal (e. g. , structural or functional MRI) or single-level (e. g. , brain local or connectivity metrics) biomarkers for the diagnosis of AD. In this study, we propose a methodological framework, called multi-modal imaging and multi-level characteristics with multi-classifier (M3), to discriminate patients with AD from healthy controls. This approach involved data analysis from two imaging modalities: structural MRI, which was used to measure regional gray matter volume, and resting-state functional MRI, which was used to measure three different levels of functional characteristics, including the amplitude of low-frequency fluctuations (ALFF), regional homogeneity (ReHo) and regional functional connectivity strength (RFCS). For each metric, we computed the values of ninety regions of interest derived from a prior atlas, which were then further trained using a multi-classifier based on four maximum uncertainty linear discriminant analysis base classifiers. The performance of this method was evaluated using leave-one-out cross-validation. Applying the M3 approach to the dataset containing 16 AD patients and 22 healthy controls led to a classification accuracy of 89. 47% with a sensitivity of 87. 50% and a specificity of 90. 91%. Further analysis revealed that the most discriminative features for classification are predominantly involved in several default-mode (medial frontal gyrus, posterior cingulate gyrus, hippocampus and parahippocampal gyrus), occipital (fusiform gyrus, inferior and middle occipital gyrus) and subcortical (amygdale and pallidum of lenticular nucleus) regions. Thus, the M3 method shows promising classification performance by incorporating information from different imaging modalities and different functional properties, and it has the potential to improve the clinical diagnosis and treatment evaluation of AD.

YNIMG Journal 2011 Journal Article

Age-related alterations in the modular organization of structural cortical network by using cortical thickness from MRI

  • Zhang J. Chen
  • Yong He
  • Pedro Rosa-Neto
  • Gaolang Gong
  • Alan C. Evans

Normal aging is accompanied by various cognitive functional declines. Recent studies have revealed disruptions in the coordination of large-scale functional brain networks such as the default mode network in advanced aging. However, organizational alterations of the structural brain network at the system level in aging are still poorly understood. Here, using cortical thickness, we investigated the modular organization of the cortical structural networks in 102 young and 97 normal aging adults. Brain networks for both cohorts displayed a modular organization overlapping with functional domains such as executive and auditory/language processing. However, compared with the modular organization of young adults, the aging group demonstrated a significantly reduced modularity that might be indicative of reduced functional segregation in the aging brain. More importantly, the aging brain network exhibited reduced intra-/inter-module connectivity in modules corresponding to the executive function and the default mode network of young adults, which might be associated with the decline of cognitive functions in aging. Finally, we observed age-associated alterations in the regional characterization in terms of their intra/inter-module connectivity. Our results indicate that aging is associated with an altered modular organization in the structural brain networks and provide new evidence for disrupted integrity in the large-scale brain networks that underlie cognition.

YNIMG Journal 2011 Journal Article

Age-related changes in the surface morphology of the central sulcus

  • Shuyu Li
  • Mingrui Xia
  • Fang Pu
  • Deyu Li
  • Yubo Fan
  • Haijun Niu
  • Baoqing Pei
  • Yong He

We utilized a sulcus-based computational approach to investigate the relationship between the three-dimensional (3D) morphology of the central sulcus (CS) and age. The anterior and posterior walls of the CS were manually outlined using high-resolution magnetic resonance images of 295 right-handed healthy participants (age range: 18~94years). Surface reconstruction and parameterization methods were employed to create anatomical correspondence of surface locations across participants. Four surface metrics, including average sulcal length (SL), surface area, fractal dimension (FD) and sulcal span, were used to represent the 3D morphology of the CS. We found significant age-related decreases in the surface area for all walls of the CS, the SL for posterior walls of the CS and the FD for posterior wall of right CS. Age-related increases were found in the sulcal spans between the anterior and posterior walls. These surface metrics (except FD) exhibited leftward asymmetries. Specifically, age-related changes in surface morphology progressed more rapidly in the posterior than in the anterior walls. Finally, sex differences were found only in the FD of the right anterior wall of the CS. Taken together, our results show age-related changes in the surface morphology of the CS and therefore provide insights into the normal aging process.

YNIMG Journal 2011 Journal Article

Characterizing dynamic functional connectivity in the resting brain using variable parameter regression and Kalman filtering approaches

  • Jin Kang
  • Liang Wang
  • Chaogan Yan
  • Jinhui Wang
  • Xia Liang
  • Yong He

The cognitive activity of the human brain benefits from the functional connectivity of multiple brain regions that form specific, functional brain networks. Recent studies have indicated that the relationship between brain regions can be investigated by examining the temporal interaction (known as functional connectivity) of spontaneous blood oxygen level-dependent (BOLD) signals derived from resting-state functional MRI. Most of these studies plausibly assumed that inter-regional interactions were temporally stationary. However, little is known about the dynamic characteristics of resting-state functional connectivity (RSFC). In this study, we thoroughly examined this question within and between multiple functional brain networks. Twenty-two healthy subjects were scanned in a resting state. Several of the RSFC networks observed, including the default-mode, motor, attention, memory, auditory, visual, language and subcortical networks, were first identified using a conventional voxel-wise correlation analysis with predefined region of interests (ROIs). Then, a variable parameter regression model combined with the Kalman filtering method was employed to detect the dynamic interactions between each ROI and all other brain voxels within each of the RSFC maps extracted above. Experimental results revealed that the functional interactions within each RSFC map showed time-varying properties, and that approximately 10–20% of the voxels within each RSFC map showed significant functional connectivity to each ROI during the scanning session. This dynamic pattern was also observed for the interactions between different functional networks. In addition, the spatial pattern of dynamic connectivity maps obtained from neighboring time points had a high similarity. Overall, this study provides insights into the dynamic properties of resting-state functional networks.

YNIMG Journal 2011 Journal Article

Frequency-dependent changes in the amplitude of low-frequency fluctuations in amnestic mild cognitive impairment: A resting-state fMRI study

  • Ying Han
  • Jinhui Wang
  • Zhilian Zhao
  • Baoquan Min
  • Jie Lu
  • Kuncheng Li
  • Yong He
  • Jianping Jia

Here we utilized resting-state functional magnetic resonance imaging (R-fMRI) to measure the amplitude of low-frequency fluctuations (ALFF) and fractional ALFF (fALFF) in 24 patients with amnestic mild cognitive impairment (aMCI) and 24 age- and sex-matched healthy controls. Two different frequency bands (slow-5: 0. 01–0. 027 Hz; slow-4: 0. 027–0. 073 Hz) were analyzed. We showed that there were widespread differences in ALFF/fALFF between the two bands in many brain regions, predominantly including the medial prefrontal cortex (MPFC), posterior cingulate cortex/precuneus (PCC/PCu), basal ganglia, and hippocampus/parahippocampal gyrus (PHG). Compared to controls, the aMCI patients had decreased ALFF/fALFF values in the PCC/PCu, MPFC, hippocampus/PHG, basal ganglia, and prefrontal regions, and increased ALFF/fALFF values mainly in several occipital and temporal regions. Specifically, we observed that the ALFF/fALFF abnormalities in the PCC/PCu, PHG, and several occipital regions were greater in the slow-5 band than in the slow-4 band. Finally, our results of functional analysis were not significantly influenced by the gray matter loss in the MCI patients, suggesting that the results reflect functional differences between groups. Together, our data suggest that aMCI patients have widespread abnormalities in intrinsic brain activity, and the abnormalities depend on the studied frequency bands of R-fMRI data.

YNIMG Journal 2011 Journal Article

Hemisphere- and gender-related differences in small-world brain networks: A resting-state functional MRI study

  • Lixia Tian
  • Jinhui Wang
  • Chaogan Yan
  • Yong He

We employed resting-state functional MRI (R-fMRI) to investigate hemisphere- and gender-related differences in the topological organization of human brain functional networks. Brain networks were first constructed by measuring inter-regional temporal correlations of R-fMRI data within each hemisphere in 86 young, healthy, right-handed adults (38 males and 48 females) followed by a graph-theory analysis. The hemispheric networks exhibit small-world attributes (high clustering and short paths) that are compatible with previous results in the whole-brain functional networks. Furthermore, we found that compared with females, males have a higher normalized clustering coefficient in the right hemispheric network but a lower clustering coefficient in the left hemispheric network, suggesting a gender–hemisphere interaction. Moreover, we observed significant hemisphere-related differences in the regional nodal characteristics in various brain regions, such as the frontal and occipital regions (leftward asymmetry) and the temporal regions (rightward asymmetry), findings that are consistent with previous studies of brain structural and functional asymmetries. Together, our results suggest that the topological organization of human brain functional networks is associated with gender and hemispheres, and they provide insights into the understanding of functional substrates underlying individual differences in behaviors and cognition.

YNIMG Journal 2010 Journal Article

Age-related changes in topological patterns of large-scale brain functional networks during memory encoding and recognition

  • Liang Wang
  • Yanfang Li
  • Paul Metzak
  • Yong He
  • Todd S. Woodward

In this study we used functional magnetic resonance imaging to investigate age-related changes in large-scale brain functional networks during memory encoding and recognition in 12 younger and 16 older adults. For each participant, functional brain networks were constructed by computing temporal correlation matrices of 90 brain regions and analyzed using graph theoretical approaches. We found the age-related changes mainly in the long-range connections with widespread reductions associated with aging in the fronto-temporal and temporo-parietal regions, and a few age-related increases in the posterior parietal regions. Graph theoretical analysis revealed that the older adults had longer path lengths linking different regions in the functional brain networks as compared to the younger adults. Further analysis indicated that the increases in shortest path length in the networks were combined with the loss of long-range connections. Finally, we showed that for older adults, frontal areas played reduced roles in the network (reduced regional centrality), whereas several default-mode regions played increased roles relative to younger subjects (increased regional centrality). Together, our results suggest that normal aging is associated with disruption of large-scale brain systems during the performance of memory tasks, which provides novel insights into the understanding of age-related decline in multiple cognitive functions.

TCS Journal 2009 Journal Article

Two semi-online scheduling problems on two uniform machines

  • C.T. Ng
  • Zhiyi Tan
  • Yong He
  • T.C.E. Cheng

This paper considers two semi-online scheduling problems, one with known optimal value and the other with known total sum, on two uniform machines with a machine speed ratio of s ≥ 1. For the first problem, we provide an optimal algorithm for s ∈ [ 1 + 3 2, 1 + 21 4 ], and improved algorithms or/and lower bounds for s ∈ [ 1 + 21 4, 3 ], over which the optimal algorithm is unknown. As a result, the largest gap between the competitive ratio and the lower bound decreases to 0. 02192. For the second problem, we also present algorithms and lower bounds for s ≥ 1. The largest gap between the competitive ratio and the lower bound is 0. 01762, and the length of the interval over which the optimal algorithm is unknown is 0. 47382. Our algorithms and lower bounds for these two problems provide insights into their differences, which are unusual from the viewpoint of the known results on these two semi-online scheduling problems in the literature.

YNIMG Journal 2008 Journal Article

Fisher discriminative analysis of resting-state brain function for attention-deficit/hyperactivity disorder

  • Chao-Zhe Zhu
  • Yu-Feng Zang
  • Qing-Jiu Cao
  • Chao-Gan Yan
  • Yong He
  • Tian-Zi Jiang
  • Man-Qiu Sui
  • Yu-Feng Wang

In this study, a resting-state fMRI based classifier, for the first time, was proposed and applied to discriminate children with attention-deficit/hyperactivity disorder (ADHD) from normal controls. On the basis of regional homogeneity (ReHo), a mapping of brain function at resting state, PCA-based Fisher discriminative analysis (PC-FDA) was trained to build a linear classifier. Permutation test was then conducted to identify the brain areas with the most significant contribution to the final discrimination. Experimental results showed a correct classification rate of 85% using a leave-one-out cross-validation. Moreover, some highly discriminative brain regions, like the prefrontal cortex and anterior cingulate cortex, well confirmed the previous findings on ADHD. Interestingly, some important but less reported regions such as the thalamus were also identified. We conclude that the classifier, using resting-state brain function as classification feature, has potential ability to improve current diagnosis and treatment evaluation of ADHD.

YNIMG Journal 2007 Journal Article

Regional coherence changes in the early stages of Alzheimer’s disease: A combined structural and resting-state functional MRI study

  • Yong He
  • Liang Wang
  • Yufeng Zang
  • Lixia Tian
  • Xinqing Zhang
  • Kuncheng Li
  • Tianzi Jiang

Recent functional imaging studies have indicated that the pathophysiology of Alzheimer’s disease (AD) can be associated with the changes in spontaneous low-frequency (<0. 08 Hz) blood oxygenation level-dependent fluctuations (LFBF) measured during a resting state. The purpose of this study was to examine regional LFBF coherence patterns in early AD and the impact of regional brain atrophy on the functional results. Both structural MRI and resting-state functional MRI scans were collected from 14 AD subjects and 14 age-matched normal controls. We found significant regional coherence decreases in the posterior cingulate cortex/precuneus (PCC/PCu) in the AD patients when compared with the normal controls. Moreover, the decrease in the PCC/PCu coherence was correlated with the disease progression measured by the Mini-Mental State Exam scores. The changes in LFBF in the PCC/PCu may be related to the resting hypometabolism in this region commonly detected in previous positron emission tomography studies of early AD. When the regional PCC/PCu atrophy was controlled, these results still remained significant but with a decrease in the statistical power, suggesting that the LFBF results are at least partly explained by the regional atrophy. In addition, we also found increased LFBF coherence in the bilateral cuneus, right lingual gyrus and left fusiform gyrus in the AD patients. These regions are consistent with previous findings of AD-related increased activation during cognitive tasks explained in terms of a compensatory-recruitment hypothesis. Finally, our study indicated that regional brain atrophy could be an important consideration in functional imaging studies of neurodegenerative diseases.

TCS Journal 2007 Journal Article

Semi-online scheduling problems on two identical machines with inexact partial information

  • Zhiyi Tan
  • Yong He

In semi-online scheduling problems, we always assume that some partial additional information is exactly known in advance. This may not be true in some applications. This paper considers semi-online scheduling problems on two identical machines with inexact partial information. Three versions are considered, where we know in advance that the total size of all jobs, the optimal value, and the largest job size are in given intervals, respectively, while their exact values are unknown. We give both lower bounds of the problems and competitive ratios of algorithms as functions of a so-called disturbance parameter r ∈ [ 1, ∞ ). We establish for which r the inexact partial information is useful to improve the performance of a semi-online algorithm with respect to its pure online problem. Optimal or near optimal algorithms are then obtained.

I&C Journal 2006 Journal Article

Bin packing problems with rejection penalties and their dual problems

  • György Dósa
  • Yong He

In this paper we consider the following problems: we are given a set of n items {u 1, …, u n } and a number of unit-capacity bins. Each item u i has a size w i ∈(0, 1] and a penalty p i ⩾0. An item can be either rejected, in which case we pay its penalty, or put into one bin under the constraint that the total size of the items in the bin is no greater than 1. No item can be spread into more than one bin. The objective is to minimize the total number of used bins plus the total penalty paid for the rejected items. We call the problem bin packing with rejection penalties, and denote it as BPR. For the on-line BPR problem, we present an algorithm with an absolute competitive ratio of 2. 618 while the lower bound is 2. 343, and an algorithm with an asymptotic competitive ratio arbitrarily close to 1. 75 while the lower bound is 1. 540. For the off-line BPR problem, we present an algorithm with an absolute worst-case ratio of 2 while the lower bound is 1. 5, and an algorithm with an asymptotic worst-case ratio of 1. 5. We also study a closely related bin covering version of the problem. In this case p i means some amount of profit. If an item is rejected, we get its profit, or it can be put into a bin in such a way that the total size of the items in the bin is no smaller than 1. The objective is to maximize the number of covered bins plus the total profit of all rejected items. We call this problem bin covering with rejection (BCR). For the on-line BCR problem, we show that no algorithm can have absolute competitive ratio greater than 0, and present an algorithm with asymptotic competitive ratio 1/2, which is the best possible. For the off-line BCR problem, we also present an algorithm with an absolute worst-case ratio of 1/2 which matches the lower bound.

YNIMG Journal 2006 Journal Article

Changes in hippocampal connectivity in the early stages of Alzheimer's disease: Evidence from resting state fMRI

  • Liang Wang
  • Yufeng Zang
  • Yong He
  • Meng Liang
  • Xinqing Zhang
  • Lixia Tian
  • Tao Wu
  • Tianzi Jiang

A selective distribution of Alzheimer's disease (AD) pathological lesions in specific cortical layers isolates the hippocampus from the rest of the brain. However, functional connectivity between the hippocampus and other brain regions remains unclear in AD. Here, we employ a resting state functional MRI (fMRI) to examine changes in hippocampal connectivity comparing 13 patients with mild AD versus 13 healthy age-matched controls. Hippocampal connectivity was investigated by examination of the correlation between low frequency fMRI signal fluctuations in the hippocampus and those in all other brain regions. We found that functional connectivity between the right hippocampus and a set of regions was disrupted in AD; these regions are: medial prefrontal cortex (MPFC), ventral anterior cingulate cortex (vACC), right inferotemporal cortex, right cuneus extending into precuneus, left cuneus, right superior and middle temporal gyrus and posterior cingulate cortex (PCC). We also found increased functional connectivity between the left hippocampus and the right lateral prefrontal cortex in AD. In addition, rightward asymmetry of hippocampal connectivity observed in elderly controls was diminished in AD patients. The disrupted hippocampal connectivity to the MPFC, vACC and PCC provides further support for decreased activity in “default mode network” previously shown in AD. The decreased connectivity between the hippocampus and the visual cortices might indicate reduced integrity of hippocampus-related cortical networks in AD. Moreover, these findings suggest that resting-state fMRI might be an appropriate approach for studying pathophysiological changes in early AD.

TCS Journal 2006 Journal Article

Improved algorithms for two single machine scheduling problems

  • Yong He
  • Weiya Zhong
  • Huikun Gu

In this paper, we investigate two single machine scheduling problems. The first problem addresses a class of the two-stage scheduling problems in which the first stage is job production and the second stage is job delivery. For the case that jobs are processed on a single machine and delivered by a single vehicle to one customer area, with the objective of minimizing the time when all jobs are completed and delivered to the customer area and the vehicle returns to the machine, an approximation algorithm with a worst-case ratio of 5 3 is known and no approximation can have a worst-case of 3 2 unless P = NP. We present an improved approximation algorithm with a worst-case ratio of 53 35, which only leaves a gap of 1 70. The second problem is a single machine scheduling problem subject to a period of maintenance. The objective is to minimize the total completion time. The best known approximation algorithm has a worst-case ratio of 20 17. We present a polynomial time approximation scheme.

TCS Journal 2006 Journal Article

Scheduling linear deteriorating jobs with an availability constraint on a single machine

  • Min Ji
  • Yong He
  • T.C.E. Cheng

We consider a single machine scheduling problem in which the processing time of a job is a simple linear increasing function of its starting time and the machine is subject to an availability constraint. We consider the non-resumable case. The objectives are to minimize the makespan and the total completion time. We show that both problems are NP-hard and present pseudo-polynomial time optimal algorithms to solve them. Furthermore, for the makespan problem, we present an optimal approximation algorithm for the on-line case, and a fully polynomial time approximation scheme for the off-line case. For the total completion time problem, we provide a heuristic and evaluate its efficiency by computational experiments.

I&C Journal 2005 Journal Article

Optimal on-line algorithms for the uniform machine scheduling problem with ordinal data

  • Zhiyi Tan
  • Yong He
  • Leah Epstein

In this paper, we consider an ordinal on-line scheduling problem. A sequence of n independent jobs has to be assigned non-preemptively to two uniformly related machines. We study two objectives which are maximizing the minimum machine completion time, and minimizing the l p norm of the completion times. It is assumed that the values of the processing times of jobs are unknown at the time of assignment. However it is known in advance that the processing times of arriving jobs are sorted in a non-increasing order. We are asked to construct an assignment of all jobs to the machines at time zero, by utilizing only ordinal data rather than actual magnitudes of jobs. For the problem of maximizing the minimum completion time we first present a comprehensive lower bound on the competitive ratio, which is a piecewise function of machine speed ratio s. Then, we propose an algorithm which is optimal for any s ⩾1. For minimizing the l p norm, we study the case of identical machines (s =1) and present tight bounds as a function of p.

TCS Journal 2005 Journal Article

Optimal semi-online preemptive algorithms for machine covering on two uniform machines

  • Yong He
  • Yiwei Jiang

In this paper, we consider the semi-online preemptive scheduling problem with decreasing job sizes on two uniform machines. Our goal is to maximize the continuous period of time (starting from time zero) when both machines are busy, which is equivalent to maximizing the minimum machine completion time if idle time is not introduced before all the jobs are completed. We design optimal deterministic semi-online algorithms for every machine speed ratio s ∈ [ 1, ∞ ), and show that idle time is required during the assignment procedure of algorithms for any s > 6 / 2. The competitive ratios of the algorithms match the randomized lower bound for every 1 ⩽ s ⩽ 3. The problem of whether randomization still does not help for the discussed preemptive scheduling problem remains open.

YNIMG Journal 2004 Journal Article

Regional homogeneity approach to fMRI data analysis

  • Yufeng Zang
  • Tianzi Jiang
  • Yingli Lu
  • Yong He
  • Lixia Tian

Kendall's coefficient concordance (KCC) can measure the similarity of a number of time series. It has been used for purifying a given cluster in functional MRI (fMRI). In the present study, a new method was developed based on the regional homogeneity (ReHo), in which KCC was used to measure the similarity of the time series of a given voxel to those of its nearest neighbors in a voxel-wise way. Six healthy subjects performed left and right finger movement tasks in event-related design; five of them were additionally scanned in a rest condition. KCC was compared among the three conditions (left finger movement, right finger movement, and the rest). Results show that bilateral primary motor cortex (M1) had higher KCC in either left or right finger movement condition than in rest condition. Contrary to prediction and to activation pattern, KCC of ipsilateral M1 is significantly higher than contralateral M1 in unilateral finger movement conditions. These results support the previous electrophysiologic findings of increasing ipsilateral M1 excitation during unilateral movement. ReHo can consider as a complementary method to model-driven method, and it could help reveal the complexity of the human brain function. More work is needed to understand the neural mechanism underlying ReHo.

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