Abnormalities of white matter network properties in middle-aged and elderly patients with functional constipation

Purpose

To explore white matter network topological properties changes in middle-aged and elderly patients with functional constipation (Functional Constipation, FC) by diffusion tensor imaging (DTI), and to evaluate the correlation between the abnormal changes and clinical data.

Methods

29 FC patients and 31 age- and sex-matched healthy controls (HC) were recruited. Magnetic resonance imaging and clinical data were collected. The white matter network changes in FC patients were analyzed using deterministic fiber tracking methods, graph theory algorithms, and partial correlation analysis with clinical data.

Results

The nodal clustering coefficient and nodal local efficiency of FC patients in the right orbital inferior frontal gyrus, right medial superior frontal gyrus, right rectus muscle, right hippocampus, left paracentral lobule and left temporal pole, and the nodal clustering coefficient in right orbital superior frontal gyrus, left cuneus lobe and right superior occipital gyrus, the nodal local efficiency in the right medial and paracingulate gyrus, right precuneus and right dorsolateral superior frontal gyrus of FC patients are lower than that of HC. The nodal local efficiency and clustering coefficient of FC patients in left hippocampus, left amygdala, right parietal inferior limbic angular gyrus and right angular gyrus, the nodal local efficiency in the right fusiform gyrus, left supplementary motor cortex and the nodal efficiency in the left lateral temporal gyrus and right orbital middle frontal gyrus (ORBmid.R) of FC patients are higher than that of HC. The nodal efficiency of ORBmid.R in FC was positively correlated with the Patient Assessment of Constipation quality of life questionnaire (PAC-QoL).

Conclusion

Middle-aged and elderly FC patients have differences in the nodal level properties in the limbic system, supplementary motor cortex, and default mode network brain regions, and the nodal efficiency of ORBmid.R was positively correlated with the PAC-QoL score, revealing that FC may be related to the abnormal processing of visceral sensorimotor in ORBmid.R and providing potential imaging diagnostic markers and therapeutic targets for middle-aged and elderly FC patients.

In patients with mild disability NMOSD: is the alteration in the cortical morphological or functional network topological properties more significant

Objective

To assess the alteration of individual brain morphological and functional network topological properties and their clinical significance in patients with neuromyelitis optica spectrum disorder (NMOSD).

Materials and methods

Eighteen patients with NMOSD and twenty-two healthy controls (HCs) were included. The clinical assessment of NMOSD patients involved evaluations of disability status, cognitive function, and fatigue impact. For each participant, brain images, including high-resolution T1-weighted images for individual morphological brain networks (MBNs) and resting-state functional MR images for functional brain networks (FBNs) were obtained. Topological properties were calculated and compared for both MBNs and FBNs. Then, partial correlation analysis was performed to investigate the relationships between the altered network properties and clinical variables. Finally, the altered network topological properties were used to classify NMOSD patients from HCs and to analyses time- to-progression of the patients.

Results

The average Expanded Disability Status Scale score of NMOSD patients was 1.05 (range from 0 to 2), indicating mild disability. Compared to HCs, NMOSD patients exhibited a higher normalized characteristic path length (λ) in their MBNs (P = 0.0118, FDR corrected) but showed no significant differences in the global properties of FBNs (p: 0.405-0.488). Network-based statistical analysis revealed that MBNs had more significantly altered connections (P< 0.01, NBS corrected) than FBNs. Altered nodal properties of MBNs were correlated with disease duration or fatigue scores (P< 0.05/6 with Bonferroni correction). Using the altered nodal properties of MBNs, the accuracy of classification of NMOSD patients versus HCs was 96.4%, with a sensitivity of 93.3% and a specificity of 100%. This accuracy was better than that achieved using the altered nodal properties of FBNs. Nodal properties of MBN significantly predicted Expanded Disability Status Scale worsening in patients with NMOSD.

Conclusion

The results indicated that patients with mild disability NMOSD exhibited compensatory increases in local network properties to maintain overall stability. Furthermore, the alterations in the morphological network nodal properties of NMOSD patients not only had better relevance for clinical assessments compared with functional network nodal properties, but also exhibited predictive values of EDSS worsening.

Altered cortical thickness-based structural covariance networks in type 2 diabetes mellitus

Cognitive impairment is a common complication of type 2 diabetes mellitus (T2DM), and early cognitive dysfunction may be associated with abnormal changes in the cerebral cortex. This retrospective study aimed to investigate the cortical thickness-based structural topological network changes in T2DM patients without mild cognitive impairment (MCI). Fifty-six T2DM patients and 59 healthy controls underwent neuropsychological assessments and sagittal 3-dimensional T1-weighted structural magnetic resonance imaging. Then, we combined cortical thickness-based assessments with graph theoretical analysis to explore the abnormalities in structural covariance networks in T2DM patients. Correlation analyses were performed to investigate the relationship between the altered topological parameters and cognitive/clinical variables. T2DM patients exhibited significantly lower clustering coefficient (C) and local efficiency (Elocal) values and showed nodal property disorders in the occipital cortical, inferior temporal, and inferior frontal regions, the precuneus, and the precentral and insular gyri. Moreover, the structural topological network changes in multiple nodes were correlated with the findings of neuropsychological tests in T2DM patients. Thus, while T2DM patients without MCI showed a relatively normal global network, the local topological organization of the structural network was disordered. Moreover, the impaired ventral visual pathway may be involved in the neural mechanism of visual cognitive impairment in T2DM patients. This study enriched the characteristics of gray matter structure changes in early cognitive dysfunction in T2DM patients.

Topological properties analysis and identification of mild cognitive impairment based on individual morphological brain network connectome

Mild cognitive impairment is considered the prodromal stage of Alzheimer's disease. Accurate diagnosis and the exploration of the pathological mechanism of mild cognitive impairment are extremely valuable for targeted Alzheimer's disease prevention and early intervention. In all, 100 mild cognitive impairment patients and 86 normal controls were recruited in this study. We innovatively constructed the individual morphological brain networks and derived multiple brain connectome features based on 3D-T1 structural magnetic resonance imaging with the Jensen-Shannon divergence similarity estimation method. Our results showed that the most distinguishing morphological brain connectome features in mild cognitive impairment patients were consensus connections and nodal graph metrics, mainly located in the frontal, occipital, limbic lobes, and subcortical gray matter nuclei, corresponding to the default mode network. Topological properties analysis revealed that mild cognitive impairment patients exhibited compensatory changes in the frontal lobe, while abnormal cortical-subcortical circuits associated with cognition were present. Moreover, the combination of multidimensional brain connectome features using multiple kernel-support vector machine achieved the best classification performance in distinguishing mild cognitive impairment patients and normal controls, with an accuracy of 84.21%. Therefore, our findings are of significant importance for developing potential brain imaging biomarkers for early detection of Alzheimer's disease and understanding the neuroimaging mechanisms of the disease.

Topological transport properties of highly oriented Bi2Te3thin film deposited by sputtering

Topological insulators (TIs) are the promising materials for next-generation technology due to their exotic features such as spin momentum locking, conducting surface states, etc. However, the high-quality growth of TIs by sputtering technique, which is one of the foremost industrial requirements, is extremely challenging. Also, the demonstration of simple investigation protocols to characterize topological properties of TIs using electron-transport methods is highly desirable. Here, we report the quantitative investigation of non-trivial parameters employing magnetotransport measurements on a prototypical highly textured Bi2Te3 TI thin film prepared by sputtering. Through the systematic analyses of the temperature and magnetic field dependent resistivity, all topological parameters associated with TIs, such as coherency factor (α), Berry phase (Φ_B), mass term (m), the dephasing parameter (p), slope of temperature dependent conductivity correction (κ) and the surface state penetration depth (λ) are estimated by using the modified 'Hikami-Larkin-Nagaoka', 'Lu-Shen' and 'Altshuler-Aronov' models. The obtained values of topological parameters are well comparable to those reported on molecular beam epitaxy grown TIs. The epitaxial growth of Bi2Te3 film using sputtering, and investigation of the non-trivial topological states from its electron-transport behaviour are important for their fundamental understanding and technological applications.

Altered topological properties of functional brain networks in patients with first episode, late-life depression before and after antidepressant treatment

Objectives

To preliminarily explore the functional activity and information integration of the brains under resting state based on graph theory in patients with first-episode, late-life depression (LLD) before and after antidepressant treatment.

Methods

A total of 50 patients with first-episode LLD and 40 non-depressed controls (NCs) were recruited for the present research. Participants underwent the RBANS test, the 17-item Hamilton depression rating scale (HAMD-17) test, and resting-state functional MRI scans (rs-fMRI). The RBANS test consists of 12 sub-tests that contribute to a total score and index scores across the five domains: immediate memory, visuospatial/constructional, language, attention, and delayed memory. Escitalopram or sertraline was adopted for treating depression, and the dosage of the drug was adjusted by the experienced psychiatrists. Of the 50 LLD patients, 27 cases who completed 6-month follow-ups and 27 NCs matched with age, sex, and education level were included for the final statistical analysis.

Results

There were significant differences in RBANS total score, immediate memory, visuospatial/constructional, language, attention, and delayed memory between LLD baseline group and NCs group (P < 0.05). Considering the global attribute indicators, the clustering coefficient of global indicators was lower in the LLD baseline group than in the NCs group, and the small-world attribute of functional brain networks existed in all three groups. The degree centrality and node efficiency of some brains were lower in the LLD baseline group than in the NCs group. After 6 months of antidepressant therapy, the scores of HAMD-17, immediate memory, language, and delayed memory in the LLD follow-up group were higher than those in the LLD baseline group. Compared with the LLD baseline group, the degree centrality and node efficiency of some brains in the cognitive control network were decreased in the LLD follow-up group.

Conclusions

The ability to integrate and divide labor of functional brain networks declines in LLD patients and linked with the depression severity. After the relief of depressive symptoms, the small-world attribute of functional brain networks in LLD patients persists. However, the information transmission efficiency and centrality of some brain regions continue to decline over time, perhaps related to their progressive cognitive impairment.

Construction and comprehensive analysis of the biological network related to rheumatoid arthritis-related interstitial lung disease

OBJECTIVE

Interstitial lung disease (ILD) is a severe manifestation of rheumatoid arthritis (RA), which is characterized by low survival time post-diagnosis. Thus, it is important to explore the role of gene regulation related with ILD.

METHOD

Constructed a RA-ILD-related long chain noncoding RNA - messenger RNA (lncRNA-mRNA) network (ILD-LMN), based on ILD- and RA-related genes. We analyzed the topological properties of the resulting network.

RESULT

The results for network modularization and functional analysis showed that ILD-LMN performed basic and specific functions in ILD pathology. Furthermore, differential expression and correlation analysis of hub nodes revealed highly correlated competitive endogenous RNA regulatory relationships with important roles in pathological regulation. Following this, statistical analysis of disease-related single nucleotide polymorphisms (SNPs) in hub lncRNAs revealed that some of transcription factor-related SNPs were significantly associated with the expression of lncRNA. In fact, these SNPs exhibited significant differential expression in disease and normal samples.

CONCLUSION

These results suggest that ILD-LMN has important implications in the study of disease. Altogether, the study of RA- and ILD-related lncRNA and genes on the basis of biological network would assist in providing better treatment opportunities for ILD patients. Additionally, it would promote further research on treatment of the disease.

Understanding Hazardous Materials Transportation Accidents Based on Higher-Order Network Theory

In hazardous materials transportation systems, accident causation analysis is important to transportation safety. Complex network theory can be effectively used to understand the causal factors of and their relationships within accidents. In this paper, a higher-order network method is proposed to establish a hazardous materials transportation accident causation network (HMTACN), which considers the sequences and dependences of causal factors. The HMTACN is composed of 125 first- and 118 higher-order nodes that represent causes, and 545 directed edges that denote complex relationships among causes. By analyzing topological properties, the results show that the HMTACN has the characteristics of small-world networks and displays the properties of scale-free networks. Additionally, critical causal factors and key relationships of the HMTACN are discovered. Moreover, unsafe tank or valve states are important causal factors; and leakage, roll-over, collision, and fire are most likely to trigger chain reactions. Important higher-order nodes are discovered, which can represent key relationships in the HMTACN. For example, unsafe distance and improper operation usually lead to collision and roll-over. These results of higher-order nodes cannot be found by the traditional Markov network model. This study provides a practical way to extract and construct an accident causation network from numerous accident investigation reports. It also provides insights into safety management of hazardous materials transportation.

Geometric Phase and Localized Heat Diffusion

Many unusual wave phenomena in artificial structures are governed by their topological properties. However, the topology of diffusion remains almost unexplored. One reason is that diffusion is fundamentally different from wave propagation because of its purely dissipative nature. The other is that the diffusion field is mostly composed of modes that extend over wide ranges, making it difficult to be rendered within the tight-binding theory as commonly employed in wave physics. Here, the above challenges are overcome and systematic studies are performed on the topology of heat diffusion. Based on a continuum model, the band structure and geometric phase are analytically obtained without using the tight-binding approximation. A deterministic parameter is found to link the geometric phase with the edge state, thereby proving the bulk-boundary correspondence for heat diffusion. The topological edge state is experimentally demonstrated as localized heat diffusion and its dependence on the boundary conditions is verified. This approach is general, rigorous, and able to reveal rich knowledge about the system with great accuracy. The findings set up a solid foundation to explore the topology in novel thermal management applications.

Increasing nodal vulnerability and nodal efficiency implied recovery time prolonging in patients with supplementary motor area syndrome

Supplementary motor area (SMA) syndrome is a surgery‐related complication that commonly occurs after removing SMA glioma, and needs weeks to recover. However, susceptible factors of patients suffering from SMA syndrome remain unknown. Graphic theory was applied to reveal topological properties of sensorimotor network (SMN) by processing resting‐state functional magnetic resonance images in 66 patients with SMA gliomas. Patients were classified into SMA and non‐SMA groups based on whether they suffered from SMA syndrome. We collected recovery time and used causal mediation analysis to find association between topological properties and recovery time. Compared with the non‐SMA group, higher vulnerability (left: p = .0018; right: p = .0033) and lower fault tolerance (left: p = .0022; right: p = .0248) of the whole SMN were found in the SMA group. Moreover, higher nodal properties of lesional‐hemispheric cingulate cortex (nodal efficiency: left, p = .0389; right, p = .0169; nodal vulnerability: left, p = .0185; right, p = .0085) and upper limb region of primary motor cortex (PMC; nodal efficiency: left, p = .0132; right, p = .0001; nodal vulnerability: left, p = .0091; right, p = .0209) were found in the SMA group. Nodal efficiency and nodal vulnerability of cingulate cortex and upper limb region of PMC were important predictors for SMA syndrome occurring and recovery time prolonging. Neurosurgeons should carefully deal with upper limb region of PMC and cingulate cortex, and protect them if these two region were unnecessary to damage during SMA glioma resection.

Network medicine in ovarian cancer: topological properties to drug discovery

Network medicine provides network theoretical tools, methods and properties to study underlying laws governing human interactome to identify disease states and disease complexity leading to drug discovery. Within this framework, we investigated the topological properties of ovarian cancer network (OCN) and the roles of hubs to understand OCN organization to address disease states and complexity. The OCN constructed from the experimentally verified genes exhibits fractal nature in the topological properties with deeply rooted functional communities indicating self-organizing behavior. The network properties at all levels of organization obey one parameter scaling law which lacks centrality lethality rule. We showed that $\langle k\rangle $ can be taken as a scaling parameter, where, power law exponent can be estimated from the ratio of network diameters. The betweenness centrality $C_B$ shows two distinct behaviors one shown by high degree hubs and the other by segregated low degree nodes. The $C_B$ power law exponent is found to connect the exponents of distributions of high and low degree nodes. OCN showed the absence of rich-club formation which leads to the missing of a number of attractors in the network causing formation of weakly tied diverse functional modules to keep optimal network efficiency. In OCN, provincial and connector hubs, which includes identified key regulators, take major responsibility to keep the OCN integrity and organization. Further, most of the key regulators are found to be over expressed and positively correlated with immune infiltrates. Finally, few potential drugs are identified related to the key regulators.

Developing Graphene-Based Moiré Heterostructures for Twistronics

Graphene-based moiré heterostructures are strongly correlated materials, and they are considered to be an effective platform to investigate the challenges of condensed matter physics. This is due to the distinct electronic properties that are unique to moiré superlattices and peculiar band structures. The increasing research on strongly correlated physics via graphene-based moiré heterostructures, especially unconventional superconductors, greatly promotes the development of condensed matter physics. Herein, the preparation methods of graphene-based moiré heterostructures on both in situ growth and assembling monolayer 2D materials are discussed. Methods to improve the quality of graphene and optimize the transfer process are presented to mitigate the limitations of low-quality graphene and damage caused by the transfer process during the fabrication of graphene-based moiré heterostructures. Then, the topological properties in various graphene-based moiré heterostructures are reviewed. Furthermore, recent advances regarding the factors that influence physical performances via a changing twist angle, the exertion of strain, and regulation of the dielectric environment are presented. Moreover, various unique physical properties in graphene-based moiré heterostructures are demonstrated. Finally, the challenges faced during the preparation and characterization of graphene-based moiré heterostructures are discussed. An outlook for the further development of moiré heterostructures is also presented.

Emerging properties of carbon based 2D material beyond graphene

Graphene turns out to be the pioneering material for setting up boulevard to a new zoo of recently proposed carbon based novel two dimensional (2D) analogues. It is evident that their electronic, optical and other related properties are utterly different from that of graphene because of the distinct intriguing morphology. For instance, the revolutionary emergence of Dirac cones in graphene is particularly hard to find in most of the other 2D materials. As a consequence the crystal symmetries indeed act as a major role for predicting electronic band structure. Since tight binding calculations have become an indispensable tool in electronic band structure calculation, we indicate the implication of such method in graphene's allotropes beyond hexagonal symmetry. It is to be noted that some of these graphene allotropes successfully overcome the inherent drawback of the zero band gap nature of graphene. As a result, these 2D nanomaterials exhibit great potential in a broad spectrum of applications, viz nanoelectronics, nanooptics, gas sensors, gas storages, catalysis, and other specific applications. The miniaturization of high performance graphene allotrope based gas sensors to microscopic or even nanosized range has also been critically discussed. In addition, various optical properties like the dielectric functions, optical conductivity, electron energy loss spectra reveal that these systems can be used in opto-electronic devices. Nonetheless, the honeycomb lattice of graphene is not superconducting. However, it is proposed that the tetragonal form of graphene can be intruded to form new hybrid 2D materials to achieve novel superconducting device at attainable conditions. These dynamic experimental prospects demand further functionalization of these systems to enhance the efficiency and the field of multifunctionality. This topical review aims to highlight the latest advances in carbon based 2D materials beyond graphene from the basic theoretical as well as future application perspectives.

Disrupted Brain Connectivity Networks in Aphasia Revealed by Resting-State fMRI

Aphasia is characterized by the disability of spontaneous conversation, listening, understanding, retelling, naming, reading, or writing. However, the neural mechanisms of language damage after stroke are still under discussion. This study aimed to investigate the global and nodal characterization of the functional networks in patients with aphasic stroke based on resting-state functional MRI (fMRI). Twenty-four right-handed patients with aphasia after stroke and 19 healthy controls (HC) underwent a 3-TfMRI scan. A whole-brain large-scale functional connectivity network was then constructed based on Power's atlas of 264 functional regions of interest, and the global and nodal topological properties of these networks were analyzed using graph theory approaches. The results showed that patients with aphasia had decreased in small-worldness (sigma), normalized clustering coefficient (gamma), and local efficiency (E_loc) values. Furthermore, E_loc was positively correlated with language ability, retelling, naming, and listening comprehension in patients with aphasia. Patients with aphasia also had decreased nodal degree and decreased nodal efficiency in the left postcentral gyrus, central opercular cortex, and insular cortex. Our results suggest that the global and local topology attributes were altered by injury in patients with aphasic stroke. We argue that the local efficiency of brain networks might be used as a potential indicator of basic speech function in patients with aphasia.

Altered Functional Topological Organization in Type-2 Diabetes Mellitus With and Without Microvascular Complications

Microvascular complications can accelerate cognitive impairment in patients with type 2 diabetes mellitus (T2DM) and have a high impact on their quality of life; however, the underlying mechanism is still unclear. The complex network in the human brain is the physiological basis for information processing and cognitive expression. Therefore, this study explored the relationship between the functional network topological properties and cognitive function in T2DM patients with and without microvascular complications (T2DM-C and T2DM-NC, respectively). Sixty-seven T2DM patients and 41 healthy controls (HCs) underwent resting-state functional MRI and neuropsychological assessment. Then, graph theoretical network analysis was performed to explore the global and nodal topological alterations in the functional whole brain networks of T2DM patients. Correlation analyses were performed to investigate the relationship between the altered topological parameters and cognitive/clinical variables. The T2DM-C group exhibited significantly higher local efficiency (Eloc), normalized cluster coefficient (γ), and small-world characteristics (σ) than the HCs. Patients with T2DM at different clinical stages (T2DM-C and T2DM-NC) showed varying degrees of abnormalities in node properties. In addition, compared with T2DM-NC patients, T2DM-C patients showed nodal properties disorders in the occipital visual network, cerebellum and middle temporal gyrus. The Eloc metrics were positively correlated with HbA1c level (P = 0.001, r = 0.515) and the NE values in the right paracentral lobule were negatively related with serum creatinine values (P = 0.001, r = −0.517) in T2DM-C patients. This study found that T2DM-C patients displayed more extensive changes at different network topology scales. The visual network and cerebellar may be the central vulnerable regions of T2DM-C patients.

Anab initiostudy of topological and transport properties of YAuPb

In the last few decades, the study of topological materials has been carried out on an extensive scale. Half-Heusler alloys are well known for their topological behaviours. In this work, we present a detailed study of topological properties of a ternary half-Heusler alloy, YAuPb, using the tight-binding approach. We have calculated some important topological properties which includes-finding nodes and their chiralities, Berry curvature (Ω) and the surface-states. Five pairs of characteristic nodes with equal and opposite chiralities are obtained. Based on the study of these properties, we categorise the material as non-trivial topological semimetal. Besides the topological behaviours, we present a comparative study of temperature dependent transport properties corresponding to the chemical potential (μ) of the Fermi level and the node points. The temperature range chosen for the study is 50-300 K. The results obtained from the calculations of electrical conductivity per unit relaxation time (σ/τ) and the electronic part of thermal conductivity per unit relaxation time (κ₀) indicates the conducting nature of the material to both the heat and electricity. At the Fermi level, the value of Seebeck coefficient (S) is found to be ∼-9.07(-35.95) μV K^-1at 50(300) K. The negative value ofSindicates the n-type behaviour of the compound. The calculated value of electronic specific heat (Pauli magnetic susceptibility) corresponding to Fermi level is ∼0.03(0.18) × 10^-2 J mol^-1 K^-1(∼1.21(1.14) × 10^-10 m³ mol^-1) at 50(300) K. This work suggests that YAuPb is a promising candidate of non-trivial topological semimetals which can be employed in transmission of heat and electricity, and as n-type material within the temperature range of 50-300 K.

Competition between spin density wave and charge density wave driven by interactions of spinful Haldane model on honeycomb lattices

We investigate the interacting spinful Haldane model with on-site and nearest-neighbor repulsions on honeycomb lattices. Interactions drive spin-density and charge-density waves competing with each other. This competition enriches the phase diagram of the system greatly, where both topological and non-topological coexistence phases emerge with spin-density and charge-density wave orders. Moreover, the topological phase transition accompanied by the energy gap closure in coexistence phases is of third order. Finally, we study the topological properties consisting ofChernnumbers and edge states for different phases.

Shared and Distinct Topologically Structural Connectivity Patterns in Autism Spectrum Disorder and Attention-Deficit/Hyperactivity Disorder

Background

Previous neuroimaging studies have described shared and distinct neurobiological mechanisms between autism spectrum disorders (ASDs) and attention-deficit/hyperactivity disorder (ADHD). However, little is known about the similarities and differences in topologically structural connectivity patterns between the two disorders.

Methods

Diffusion tensor imaging (DTI) and deterministic tractography were used to construct the brain white matter (WM) structural networks of children and adolescents (age range, 6–16 years); 31 had ASD, 34 had ADHD, and 30 were age- and sex-matched typically developing (TD) individuals. Then, graph theoretical analysis was performed to investigate the alterations in the global and node-based properties of the WM structural networks in these groups. Next, measures of ASD traits [Social Responsiveness Scale (SRS)] and ADHD traits (Swanson, Nolan, and Pelham, version IV scale, SNAP-IV) were correlated with the alterations to determine the functional significance of such changes.

Results

First, there were no significant differences in the global network properties among the three groups; moreover, compared with that of the TD group, nodal degree (Ki) of the right amygdala (AMYG.R) and right parahippocampal gyrus (PHG.R) were found in both the ASD and ADHD groups. Also, the ASD and ADHD groups shared four additional hubs, including the left middle temporal gyrus (MTG.L), left superior temporal gyrus (STG.L), left postcentral gyrus (PoCG.L), and right middle frontal gyrus (MFG.R) compared with the TD group. Moreover, the ASD and ADHD groups exhibited no significant differences regarding regional connectivity characteristics. Second, the ADHD group showed significantly increased nodal betweenness centrality (Bi) of the left hippocampus (HIP.L) compared with the ASD group; also, compared with the ADHD group, the ASD group lacked the left anterior cingulate gyrus (ACG.L) as a hub. Last, decreased nodal efficiency (Enodal) of the AMYG.R, Ki of the AMYG.R, and Ki of the PHG.R were associated with higher SRS scores in the ASD group. Decreased Ki of the PHG.R was associated with higher SRS scores in the full sample, whereas decreased Bi of the PHG.R was associated with lower oppositional defiance subscale scores of the SNAP-IV in the ADHD group, and decreased Bi of the HIP.L was associated with lower inattention subscale scores of the SNAP-IV in the full sample.

Conclusion

From the perspective of the topological properties of brain WM structural networks, ADHD and ASD have both shared and distinct features. More interestingly, some shared and distinct topological properties of WM structures are related to the core symptoms of these disorders.

Comparing equilibration schemes of high-molecular-weight polymer melts with topological indicators

Recent theoretical studies have demonstrated that the behaviour of molecular knots is a sensitive indicator of polymer structure. Here, we use knots to verify the ability of two state-of-the-art algorithms-configuration assembly and hierarchical backmapping-to equilibrate high-molecular-weight (MW) polymer melts. Specifically, we consider melts with MWs equivalent to several tens of entanglement lengths and various chain flexibilities, generated with both strategies. We compare their unknotting probability, unknotting length, knot spectra, and knot length distributions. The excellent agreement between the two independent methods with respect to knotting properties provides an additional strong validation of their ability to equilibrate dense high-MW polymeric liquids. By demonstrating this consistency of knotting behaviour, our study opens the way for studying topological properties of polymer melts beyond time and length scales accessible to brute-force molecular dynamics simulations.

The relationships between the topological properties of the whole-brain white matter network and the severity of autism spectrum disorder: A study from monozygotic twins

Twins provide a valuable perspective for exploring the pathological mechanism of autism spectrum disorder (ASD). We aim to analyze differences in the topological properties of the white matter (WM) network between monozygotic twins with ASD (MZCo-ASD) and children with typical development (TD). We enrolled 67 subjects aged 2-9 years. Twenty-three pairs of MZCo-ASD and 21 singleton children with TD completed clinical assessments and diffusion tensor imaging (DTI). Graph theory was used to compare the topological properties of the WM network between the two groups, and analyzed their correlations with the severity of clinical symptoms. We found that the global efficiency (Eg) of MZCo-ASD is weaker than that of TD children, while the shortest path length (Lp) of MZCo-ASD is longer than that of TD children, and MZCo-ASD have three unique hubs (the bilateral dorsolateral superior frontal gyrus and right insula). Eg and Lp were both correlated with the repetitive behavior scores of the Autism Diagnostic Interview-Revised (ADI-R) in the MZCo-ASD group, and the nodal efficiency of the dorsal superior frontal gyrus (SFGdor) was correlated with the ADI-R scores of repetitive behaviors. Left SFGdor nodal efficiency was correlated with Repetitive Behavior and Communication, two core symptoms of autism. The results implicated that MZCo-ASD had atypical brain structural network attributes and node distributions. Using MZCo-ASD, we found that the WM topological properties that correlate with the severity of ASD core symptoms were Eg, Lp, and the nodal efficiency of the SFGdor.

Analysis of Air Mean Temperature Anomalies by Using Horizontal Visibility Graphs

The last decades have been successively warmer at the Earth’s surface. An increasing interest in climate variability is appearing, and many research works have investigated the main effects on different climate variables. Some of them apply complex networks approaches to explore the spatial relation between distinct grid points or stations. In this work, the authors investigate whether topological properties change over several years. To this aim, we explore the application of the horizontal visibility graph (HVG) approach which maps a time series into a complex network. Data used in this study include a 60-year period of daily mean temperature anomalies in several stations over the Iberian Peninsula (Spain). Average degree, degree distribution exponent, and global clustering coefficient were analyzed. Interestingly, results show that they agree on a lack of significant trends, unlike annual mean values of anomalies, which present a characteristic upward trend. The main conclusions obtained are that complex networks structures and nonlinear features, such as weak correlations, appear not to be affected by rising temperatures derived from global climate conditions. Furthermore, different locations present a similar behavior and the intrinsic nature of these signals seems to be well described by network parameters.

On the Use of Topological Features of Metabolic Networks for the Classification of Cancer Samples

BACKGROUND

The increasing availability of omics data collected from patients affected by severe pathologies, such as cancer, is fostering the development of data science methods for their analysis.

INTRODUCTION

The combination of data integration and machine learning approaches can provide new powerful instruments to tackle the complexity of cancer development and deliver effective diagnostic and prognostic strategies.

METHODS

We explore the possibility of exploiting the topological properties of sample-specific metabolic networks as features in a supervised classification task. Such networks are obtained by projecting transcriptomic data from RNA-seq experiments on genome-wide metabolic models to define weighted networks modeling the overall metabolic activity of a given sample.

RESULTS

We show the classification results on a labeled breast cancer dataset from the TCGA database, including 210 samples (cancer vs. normal). In particular, we investigate how the performance is affected by a threshold-based pruning of the networks by comparing Artificial Neural Networks, Support Vector Machines and Random Forests. Interestingly, the best classification performance is achieved within a small threshold range for all methods, suggesting that it might represent an effective choice to recover useful information while filtering out noise from data. Overall, the best accuracy is achieved with SVMs, which exhibit performances similar to those obtained when gene expression profiles are used as features.

CONCLUSION

These findings demonstrate that the topological properties of sample-specific metabolic networks are effective in classifying cancer and normal samples, suggesting that useful information can be extracted from a relatively limited number of features.

Sex Differences in Anatomical Rich-Club and Structural-Functional Coupling in the Human Brain Network

Structural and functional differences between the brains of female and male adults have been well documented. However, potential sex differences in the patterns of rich-club organization and the coupling between their structural connectivity (SC) and functional connectivity (FC) remain to be determined. In this study, functional magnetic resonance imaging and diffusion tensor imaging techniques were combined to examine sex differences in rich-club organization. Females had a stronger SC-FC coupling than males. Moreover, stronger SC-FC coupling in the females was primarily located in feeder connections and non-rich-club nodes of the left inferior frontal gyrus and inferior parietal lobe and the right superior frontal gyrus and superior parietal gyrus, whereas higher coupling strength in males was primarily located in rich-club connections and rich-club node of the right insula, and non-rich-club nodes of the left hippocampus and the right parahippocampal gyrus. Sex-specific patterns in correlations were also shown between SC-FC coupling and cognitive function, including working memory and reasoning ability. The topological changes in rich-club organization provide novel insight into sex-specific effects on white matter connections that underlie a potential network mechanism of sex-based differences in cognitive function.

Alteration in topological properties of brain functional network after 2-year high altitude exposure: A panel study

INTRODUCTION

High altitude (HA) exposure leads to cognitive impairment while the underlying mechanism is still unclear. Brain functional network is crucial for advanced functions, and its alteration is implicated in cognitive decline in multiple diseases. The aim of current study was to investigate the topological changes in HA-exposed brain functional network.

METHODS

Based on Shaanxi-Tibet immigrant cohort, neuropsychological tests and resting-state functional MRI were applied to evaluate the participants' cognitive function and functional connection (FC) changes, respectively. GRETNA toolbox was used to construct the brain functional network. The gray matter was parcellated into 116 anatomically defined regions according to Automated Anatomical Labeling atlas. Subsequently, the mean time series for each of the 116 regions were extracted and computed for Pearson's correlation coefficients. The relation matrix was further processed and seen as brain functional network. Correlation between functional network changes and neuropsychological results was also examined.

RESULTS

The cognitive performance was impaired by HA exposure as indicated by neuropsychological test. HA exposure led to alterations of degree centrality and nodal efficiency in multiple brain regions. Moreover, two subnetworks were extracted in which the FCs significantly decreased after exposure. In addition, the alterations in FCs within above two subnetworks were significantly correlated with changes of memory and reaction time.

CONCLUSIONS

Our results suggest that HA exposure modulates the topological property of functional network and FCs of some important regions, which may impair the attention, perception, memory, motion ignition, and modulation processes, finally decreasing cognitive performance in neuropsychological tests.

Altered Topological Properties of Brain Structural Covariance Networks in Patients With Cervical Spondylotic Myelopathy

Background

Brain structural alterations play an important role in patients with cervical spondylotic myelopathy (CSM). However, while there have been studies on regional brain structural alterations, only few studies have focused on the topological organization of the brain structural covariance network. This work aimed to describe the structural covariance network architecture alterations that are possibly linked to cortex reorganization in patients with CSM.

Methods

High-resolution anatomical images of 31 CSM patients and 31 healthy controls (HCs) were included in the study. The images were acquired using a sagittal three-dimensional T1-weighted BRAVO sequence. Firstly, the gray matter volume of 90 brain regions of automated anatomical labeling atlas were computed using a VBM toolbox based on the DARTEL algorithm. Then, the brain structural covariance network was constructed by thresholding the gray matter volume correlation matrices. Subsequently, the network measures and nodal property were calculated based on graph theory. Finally, the differences in the network metrics and nodal property between groups were compared using a non-parametric test.

Results

Patients with CSM showed larger global efficiency and smaller local efficiency, clustering coefficient, characteristic path length, and sigma values than HCs. Patients with CSM had greater betweenness in the left superior parietal gyrus (SPG.L) and the left supplementary motor area (SMA.L) than HCs. Besides, patients with CSM had smaller betweenness in right middle occipital gyrus. The brain structural covariance networks of CSM patients exhibited equal resilience to random failure as those of HCs. However, the maximum relative size of giant connected components was approximately 10% larger in HCs than in CSM patients, upon removal of 44 nodes in targeted attack.

Conclusion

These observed alternations in global network measures in CSM patients reflect that the brain structural covariance network in CSM exhibits the less optimal small-world model compared to that in HCs. Increased betweenness in SPG.L and SMA.L seems to be related to cortex reorganization to recover multiple sensory functions after spinal cord injury in CSM patients. The network resilience of patients with CSM exhibiting a relative mild vulnerability, compared to HCs, is probably attributable to the balance and interplay between cortex reorganization and ongoing degeneration.

Direct protein-protein interaction network for insecticide resistance based on subcellular localization analysis in Drosophila melanogaster

In present study, we constructed the direct protein-protein interaction network of insecticide resistance based on subcellular localization analysis. Totally 177 of 528 resistance proteins were identified and they were located in 11 subcellular localizations. We further analyzed topological properties of the network and the biological characteristics of resistance proteins, such as k-core, neighborhood connectivity, instability index and aliphatic index. They can be used to predict the key proteins and potential mechanisms from macro-perspective. The problem of resistance has not been solved fundamentally, because the development of new insecticides can't keep pace with the development speed of resistance, and the lack of understanding of molecular mechanism of resistance. As the further analysis to reduce data noise, we constructed the direct protein-protein interaction network of insecticide resistance based on subcellular localization analysis. The interaction between proteins located at the same subcellular location belongs to direct interactions, thus eliminating indirect interaction. Totally 177 of 528 resistance proteins were identified and they were located in 11 subcellular localizations. We further analyzed topological properties of the network and the biological characteristics of resistance proteins, such as k-core, neighborhood connectivity, instability index and aliphatic index. They can be used to predict the hub proteins and potential mechanisms from macro-perspective. This is the first study to explore the insecticide resistance molecular mechanism of Drosophila melanogaster based on subcellular localization analysis. It can provide the bioinformatics foundation for further understanding the mechanisms of insecticide resistance. It also provides a reference for the study of molecular mechanism of insecticide resistance of other insects.

Brain Functional Networks in Type 2 Diabetes Mellitus Patients: A Resting-State Functional MRI Study

Background

Previous diabetes mellitus studies of cognitive impairments in the early stages have focused on changes in brain structure and function, and more recently the focus has shifted to the relationships between encephalic regions and diversification of network topology. However, studies examining network topology in diabetic brain function are still limited.

Methods

The study included 102 subjects; 55 type 2 diabetes mellitus (T2DM) patients plus 47 healthy controls. All subjects were examined by resting-state functional magnetic resonance imaging (rs-fMRI) scan. According to Automated Anatomical Labeling, the brain was divided into 90 anatomical regions, and every region corresponds to a brain network analysis node. The whole brain functional network was constructed by thresholding the correlation matrices of the 90 brain regions, and the topological properties of the network were computed based on graph theory. Then, the topological properties of the network were compared between different groups by using a non-parametric test. Finally, the associations between differences in topological properties and the clinical indicators were analyzed.

Results

The brain functional networks of both T2DM patients and healthy controls were found to possess small-world characteristics, i.e., normalized clustering coefficient (γ) > 1, and normalized characteristic path length (λ) close to 1. No significant differences were found in the small-world characteristics (σ). Second, the T2DM patient group displayed significant differences in node properties in certain brain regions. Correlative analytic results showed that the node degree of the right inferior temporal gyrus (ITG) and the node efficiencies of the right ITG and superior temporal gyrus of T2DM patients were positively correlated with body mass index.

Conclusion

The brain network of T2DM patients has the same small-world characteristics as normal people, but the normalized clustering coefficient is higher and the normalized characteristic path length is lower than that of the normal control group, indicating that the brain function network of the T2DM patients has changed. The changes of node properties were mostly concentrated in frontal lobe, temporal lobe and posterior cingulate gyrus. The abnormal changes in these indices in T2DM patients might be explained as a compensatory behavior to reduce cognitive impairments, which is achieved by mobilizing additional neural resources, such as the excessive activation of the network and the efficient networking of multiple brain regions.

Age Related Changes in Topological Properties of Brain Functional Network and Structural Connectivity

Introduction: There are still uncertainties about the true nature of age related changes in topological properties of the brain functional network and its structural connectivity during various developmental stages. In this cross- sectional study, we investigated the effects of age and its relationship with regional nodal properties of the functional brain network and white matter integrity.

Method: DTI and fMRI data were acquired from 458 healthy Chinese participants ranging from age 8 to 81 years. Tractography was conducted on the DTI data using FSL. Graph Theory analyses were conducted on the functional data yielding topological properties of the functional network using SPM and GRETNA toolbox. Two multiple regressions were performed to investigate the effects of age on nodal topological properties of the functional brain network and white matter integrity.

Result: For the functional studies, we observed that regional nodal characteristics such as node betweenness were decreased while node degree and node efficiency was increased in relation to increasing age. Perversely, we observed that the relationship between nodal topological properties and fasciculus structures were primarily positive for nodal betweenness but negative for nodal degree and nodal efficiency. Decrease in functional nodal betweenness was primarily located in superior frontal lobe, right occipital lobe and the global hubs. These brain regions also had both direct and indirect anatomical relationships with the 14 fiber bundles. A linear age related decreases in the Fractional anisotropy (FA) value was found in the callosum forceps minor.

Conclusion: These results suggests that age related differences were more pronounced in the functional than in structural measure indicating these measures do not have direct one-to-one mapping. Our study also indicates that the fiber bundles with longer fibers exhibited a more pronounced effect on the properties of functional network.

Topological Dirac States beyond π-Orbitals for Silicene on SiC(0001) Surface

The discovery of intriguing properties related to the Dirac states in graphene has spurred huge interest in exploring its two-dimensional group-IV counterparts, such as silicene, germanene, and stanene. However, these materials have to be obtained via synthesizing on substrates with strong interfacial interactions, which usually destroy their intrinsic π(p_z)-orbital Dirac states. Here we report a theoretical study on the existence of Dirac states arising from the p_x,y orbitals instead of p_z orbitals in silicene on 4H-SiC(0001), which survive in spite of the strong interfacial interactions. We also show that the exchange field together with the spin-orbital coupling give rise to a detectable band gap of 1.3 meV. Berry curvature calculations demonstrate the nontrivial topological nature of such Dirac states with a Chern number C = 2, presenting the potential of realizing quantum anomalous Hall effect for silicene on SiC(0001). Finally, we construct a minimal effective model to capture the low-energy physics of this system. This finding is expected to be also applicable to germanene and stanene and imply great application potentials in nanoelectronics.

Disrupted structural and functional connectivity networks in ischemic stroke patients

Local lesions caused by stroke may result in extensive structural and functional reorganization in the brain. Previous studies of this phenomenon have focused on specific brain networks. Here, we aimed to discover abnormalities in whole-brain networks and to explore the decoupling between structural and functional connectivity in patients with stroke. Fifteen ischemic stroke patients and 23 normal controls (NCs) were recruited in this study. A graph theoretical analysis was employed to investigate the abnormal topological properties of structural and functional brain networks in patients with stroke. Both patients with stroke and NCs exhibited small-world organization in brain networks. However, compared to NCs, patients with stroke exhibited abnormal global properties characterized by a higher characteristic path length and lower global efficiency. Furthermore, patients with stroke showed altered nodal characteristics, primarily in certain motor- and cognition-related regions. Positive correlations between the nodal degree of the inferior parietal lobule and the Fugl-Meyer Assessment (FMA) score and between the nodal betweenness centrality of the posterior cingulate gyrus (PCG) and immediate recall were observed in patients with stroke. Most importantly, the strength of the structural-functional connectivity network coupling was decreased, and the coupling degree was related to the FMA score of patients, suggesting that decoupling may provide a novel biomarker for the assessment of motor impairment in patients with stroke. Thus, the topological organization of brain networks is altered in patients with stroke, and our results provide insights into the structural and functional organization of the brain after stroke from the viewpoint of network topology.

Disrupted small-world brain functional network topology in male patients with severe obstructive sleep apnea revealed by resting-state fMRI

PURPOSE

Obstructive sleep apnea (OSA) is a common sleep-related breathing disorder that can damage cognitive function. However, the functional network organization remains poorly understood. The aim of this study was to investigate the topological properties of OSA patients using a graph theoretical analysis.

PATIENTS AND METHODS

A total of 30 male patients with untreated severe OSA and 25 male education- and age-matched good sleepers (GSs) underwent functional magnetic resonance imaging (MRI) examinations. Clinical and cognitive evaluations were conducted by an experienced psychologist. GRETNA (a toolbox for topological analysis of imaging connectomics) was used to construct the brain functional network and calculate the small-world properties (γ, λ, σ, E_glob, and E_loc). Relationships between these small-world properties and clinical and neuropsychological assessments were investigated in OSA patients.

RESULTS

The networks of both OSA patients and GSs exhibited efficient small-world topology over the sparsity range of 0.05-0.40. Compared with GSs, the OSA group had significantly decreased γ, but significantly increased λ and σ. The OSA group's brain network showed significantly decreased E_glob (P<0.05) over the sparsity range of 0.09-0.15, but significantly increased E_loc over the sparsity range of 0.23-0.40. In OSA patients, γ was significantly negatively correlated with apnea-hypopnea index (AHI; r=-0.326, P=0.015) and Epworth Sleepiness Scale (ESS; r=-0.274, P=0.043), λ was significantly positively correlated with AHI (r=0.373, P=0.005) and ESS (r=0.269, P=0.047), and σ was significantly negatively correlated with AHI (r=-0.363, P=0.007) and ESS (r=-0.295, P=0.029).

CONCLUSION

Our results suggest that the high degree of local integration and integrity of the brain connections in OSA patients may be disrupted. The topological alterations of small-world properties may be the mechanism of cognitive impairment in OSA patients. In addition, σ, γ, and λ could be used as a quantitative physiological index for auxiliary clinical diagnoses.

The drug target genes show higher evolutionary conservation than non-target genes

Although evidence indicates that drug target genes share some common evolutionary features, there have been few studies analyzing evolutionary features of drug targets from an overall level. Therefore, we conducted an analysis which aimed to investigate the evolutionary characteristics of drug target genes. We compared the evolutionary conservation between human drug target genes and non-target genes by combining both the evolutionary features and network topological properties in human protein-protein interaction network. The evolution rate, conservation score and the percentage of orthologous genes of 21 species were included in our study. Meanwhile, four topological features including the average shortest path length, betweenness centrality, clustering coefficient and degree were considered for comparison analysis. Then we got four results as following: compared with non-drug target genes, 1) drug target genes had lower evolutionary rates; 2) drug target genes had higher conservation scores; 3) drug target genes had higher percentages of orthologous genes and 4) drug target genes had a tighter network structure including higher degrees, betweenness centrality, clustering coefficients and lower average shortest path lengths. These results demonstrate that drug target genes are more evolutionarily conserved than non-drug target genes. We hope that our study will provide valuable information for other researchers who are interested in evolutionary conservation of drug targets.

Topological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM)

Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T approximately 20 K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (l(max) = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C-C, C-N and C-O bonds, and for hydrogen bonds together with covalent C-H and N-H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H...O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997). An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead to the correct characterization of chemical bonding. Our results do not confirm suggestions in the literature that the promolecule density might be sufficient for a characterization of hydrogen bonds.