The relationship between structure and ecosystem services of forest and grassland based on pattern analysis method: A case study of the Mongolian Plateau.

Global warming has led to severe land desertification on the Mongolian plateau. It puts great environmental pressure on vegetation communities. This pressure leads to fragmentation of land use and landscape patterns, thus triggering changes in the spatial distribution patterns of vegetation. The spatial distribution pattern of vegetation is crucial for the performance of its ecosystem services. However, there is not enough research on the relationship between large-scale spatial distribution patterns of vegetation and ecosystem services. Therefore, this study is to construct an ecological spatial network on the Mongolian Plateau based on landscape ecology and complex network theory. Combining pattern analysis methods to analyze the network, we obtained the spatial and temporal trends of forest and grass spatial distribution patterns from 2000 to 2100, and explored the relationship between the topological properties of source patches and ecosystem services in different patterns. It was found that there are four basic patterns of spatial distribution of forest and grass in the Mongolian Plateau. The Core-Linked Ring pattern accounts for 40.74 % and exhibits the highest stability. Under the SSP5-RCP8.5 scenario, source patches are reduced by 22.76 % in 2100. Topological indicators of source patches showed significant correlations with ecosystem services. For example, the CUE of grassland patches in the Centralized Star pattern was positively correlated with betweeness centrality. The most significant improvement in WUE after optimization is 19.90 % compared to pre-optimization. The conclusion of the study shows that the spatial distribution pattern of vegetation can be used to enhance the stability of ecological spatial network and improve ecosystem services at a larger scale. It can provide a certain reference for the study of spatial patterns of vegetation distribution in arid and semi-arid areas.

Individual-based morphological brain network changes in children with Rolandic epilepsy.

OBJECTIVE: To investigate the local cortical morphology and individual-based morphological brain networks (MBNs) changes in children with Rolandic epilepsy (RE). METHODS: Based on the structural MRI data of 56 children with RE and 56 healthy controls (HC), we constructed four types of individual-based MBNs using morphological indices (cortical thickness [CT], fractal dimension [FD], gyrification index [GI], and sulcal depth [SD]). The global and nodal properties of the brain networks were analyzed using graph theory. The between-group difference in local morphology and network topology was estimated, and partial correlation analysis was further analyzed. RESULTS: Compared with the HC, children with RE showed regional GI increases in the right posterior cingulate gyrus and SD increases in the right anterior cingulate gyrus and medial prefrontal cortex. Regarding the network level, RE exhibited increased characteristic path length in CT-based and FD-based networks, while decreased FD-based network node efficiency in the right inferior frontal gyrus. No significant correlation between altered morphological features and clinical variables was found in RE. CONCLUSIONS: These findings indicated that children with RE have disrupted morphological brain network organization beyond local morphology changes. SIGNIFICANCE: The present study could provide more theoretical basis for exploring the neuropathological mechanisms in RE.

Electroacupuncture modulates abnormal brain connectivity after ischemia reperfusion injury in rats: A graph theory-based approach.

BACKGROUND: Electroacupuncture (EA) has been shown to facilitate brain plasticity-related functional recovery following ischemic stroke. The functional magnetic resonance imaging technique can be used to determine the range and mode of brain activation. After stroke, EA has been shown to alter brain connectivity, whereas EA's effect on brain network topology properties remains unclear. An evaluation of EA's effects on global and nodal topological properties in rats with ischemia reperfusion was conducted in this study. METHODS AND RESULTS: There were three groups of adult male Sprague-Dawley rats: sham-operated group (sham group), middle cerebral artery occlusion/reperfusion (MCAO/R) group, and MCAO/R plus EA (MCAO/R + EA) group. The differences in global and nodal topological properties, including shortest path length, global efficiency, local efficiency, small-worldness index, betweenness centrality (BC), and degree centrality (DC) were estimated. Graphical network analyses revealed that, as compared with the sham group, the MCAO/R group demonstrated a decrease in BC value in the right ventral hippocampus and increased BC in the right substantia nigra, accompanied by increased DC in the left nucleus accumbens shell (AcbSh). The BC was increased in the right hippocampus ventral and decreased in the right substantia nigra after EA intervention, and MCAO/R + EA resulted in a decreased DC in left AcbSh compared to MCAO/R. CONCLUSION: The results of this study provide a potential basis for EA to promote cognitive and motor function recovery after ischemic stroke.

Disrupted topological properties of structural brain networks present a glutamatergic neuropathophysiology in people with narcolepsy.

STUDY OBJECTIVES: Growing evidences have documented various abnormalities of the white matter bundles in people with narcolepsy. We sought to evaluate topological properties of brain structural networks, and their association with symptoms and neuropathophysiological features in people with narcolepsy. METHODS: Diffusion tensor imaging was conducted for people with narcolepsy (n = 30) and matched healthy controls as well as symptoms assessment. Structural connectivity for each participant was generated to analyze global and regional topological properties and their correlations with narcoleptic features. Further human brain transcriptome was extracted and spatially registered for connectivity vulnerability. Genetic functional enrichment analysis was performed and further clarified using in vivo emission computed tomography data. RESULTS: A wide and dramatic decrease in structural connectivities was observed in people with narcolepsy, with descending network degree and global efficiency. These metrics were not only correlated with sleep latency and awakening features, but also reflected alterations of sleep macrostructure in people with narcolepsy. Network-based statistics identified a small hyperenhanced subnetwork of cingulate gyrus that was closely related to rapid eye movement sleep behavior disorder (RBD) in narcolepsy. Further imaging genetics analysis suggested glutamatergic signatures were responsible for the preferential vulnerability of connectivity alterations in people with narcolepsy, while additional PET/SPECT data verified that structural alteration was significantly correlated with metabotropic glutamate receptor 5 (mGlutR5) and N-methyl-D-aspartate receptor (NMDA). CONCLUSIONS: People with narcolepsy endured a remarkable decrease in the structural architecture, which was not only closely related to narcolepsy symptoms but also glutamatergic signatures.

Topological properties of brain functional networks in adolescents with major depressive disorder / 中华神经医学杂志

Objective:To investigate the topological properties of whole-brain functional networks in first-episode drug-na?ve adolescents with major depressive disorder (MDD).Methods:Seventy-six first-episode drug-na?ve adolescents with MDD admitted to Department of Neurology, Xiangyang No.1 Hospital Affilated to Hubei University of Medicince from January 2022 to January 2023 were selected as study subjects; 66 gender- and age-matched healthy controls (HCs) were recruited via advertisement. All subjects underwent resting-state functional MRI. The whole-brain functional networks were constructed for each subject; and then, the global topological metrics (global efficiency, local efficiency, clustering coefficient, characteristic path length, normalized clustering coefficient, normalized characteristic path length, and small-worldness properties) and local topological metrics (nodal degree centrality, nodal efficiency and nodal betweenness centrality) of the functional brain networks were analyzed between the two groups using graph-theory methods. Network-based statistics were used to examine between-group differences in functional connectivity strength of whole brain networks. Results:Small-worldness properties were demonstrated in both MDD group and HC group. MDD patients showed significantly higher global efficiency (0.129[0.124, 0.132] vs. 0.131[0.128, 0.133]), significantly lower clustering coefficient and characteristic path length (0.143[0.139, 0.146] vs. 0.139[0.135, 0.144]; 0.457[0.446, 0.734] vs. 0.451[0.440, 0.463]), and significantly increased nodal centralities in the right inferior parietal lobule, bilateral caudate nucleus and bilateral thalamus of brain functional networks compared with HCs ( P<0.05, FDR-corrected). Compared with HCs, MDD patients exhibited obviously lower functional connectivity strength in the orbitofrontal-temporal and anterior cingulate-limbic-temporal circuits. Conclusion:Abnormal alterations of topological properties of the brain functional networks are found in adolescents with MDD, which may be the underlying neuropathologic basis for MDD.

Topological properties of Xene tuned by perpendicular electric field and exchange field in the presence of Rashba spin-orbit coupling.

Xene (X=Si, Ge, Sn) is a typical and promising two-dimensional topological insulator with many novel topological properties. Here, we investigate the topological properties of Xene tuned by a perpendicularly applied electric field, exchange field, and Rashba spin-orbit coupling (RSOC) using the tight-binding (TB) method. We show that in the presence of RSOC, the system can be converted from a quantum spin Hall (QSH) insulator into a conventional band insulator (BI) by a weak perpendicular electric field or into a quantum anomalous Hall (QAH) insulator by a weak exchange field. Additionally, a suitable combination of electric and exchange fields can give rise to a valley-polarized metallic (VPM) state. Furthermore, we explore the competition between the electric field and exchange field in tuning the topological states owing to the Rashba coupling effect. When the electric field is stronger than the exchange field, the system tends to be in a topologically trivial BI state; otherwise, it will be a QAH insulator. More intriguingly, for a fixed exchange field and RSOC, as the perpendicular electric field increase continuously from zero, the system undergoes multiphase (e.g. QSH-VPM-BI) transitions. This paves the way for designing multiphase transition devices through external single-field regulation.

Different Dynamic Nodal Properties Contribute to Cognitive Impairment in Patients with White Matter Hyperintensities.

White matter hyperintensities (WMHs) are commonly observed in older adults and are associated with cognitive impairment. Although previous studies have found abnormal functional connectivities in patients with WMHs based on static functional magnetic resonance imaging (fMRI), the topological properties in the context of brain dynamics remain relatively unexplored. Herein, we explored disrupted dynamic topological properties of functional network connectivity in patients with WMHs and its relationship with cognitive impairment. We included 36 healthy controls (HC) and 104 patients with mild WMHs (n = 39), moderate WMHs (n = 37), and severe (n = 28) WMHs. The fMRI data of all participants were analyzed using Anatomical Automatic Labeling (AAL) and a sliding-window approach to generate dynamic functional connectivity matrics. Then, graph theory methods were applied to calculate the topological properties. Comprehensive neuropsychological scales were used to assess cognitive functions. Relationships between cognitive functions and abnormal dynamic topological properties were evaluated by Pearson's correlation. We found that the patients with WMHs had higher temporal variability in regional properties, including betweenness centrality, nodal efficiencies, and nodal clustering coefficient. Furthermore, we found that the degree of centrality was related to executive function and memory, and the local coefficient correlated to executive function. Our results indicate that patients with WMHs have higher temporal variabilities in regional properties and are associated with executive and memory function.

Disrupted Brain Structural Network Connection in de novo Parkinson's Disease With Rapid Eye Movement Sleep Behavior Disorder.

Objective: To explore alterations in white matter network topology in de novo Parkinson's disease (PD) patients with rapid eye movement sleep behavior disorder (RBD). Materials and Methods: This study included 171 de novo PD patients and 73 healthy controls (HC) recruited from the Parkinson's Progression Markers Initiative (PPMI) database. The patients were divided into two groups, PD with probable RBD (PD-pRBD, n = 74) and PD without probable RBD (PD-npRBD, N = 97), according to the RBD screening questionnaire (RBDSQ). Individual structural network of brain was constructed based on deterministic fiber tracking and analyses were performed using graph theory. Differences in global and nodal topological properties were analyzed among the three groups. After that, post hoc analyses were performed to explore further differences. Finally, correlations between significant different properties and RBDSQ scores were analyzed in PD-pRBD group. Results: All three groups presented small-world organization. PD-pRBD patients exhibited diminished global efficiency and increased shortest path length compared with PD-npRBD patients and HCs. In nodal property analyses, compared with HCs, the brain regions of the PD-pRBD group with changed nodal efficiency (Ne) were widely distributed mainly in neocortical and paralimbic regions. While compared with PD-npRBD group, only increased Ne in right insula, left middle frontal gyrus, and decreased Ne in left temporal pole were discovered. In addition, significant correlations between Ne in related brain regions and RDBSQ scores were detected in PD-pRBD patients. Conclusions: PD-pRBD patients showed disrupted topological organization of white matter in the whole brain. The altered Ne of right insula, left temporal pole and left middle frontal gyrus may play a key role in the pathogenesis of PD-RBD.

Contralesional Sensorimotor Network Participates in Motor Functional Compensation in Glioma Patients.

Background: Some gliomas in sensorimotor areas induce motor deficits, while some do not. Cortical destruction and reorganization contribute to this phenomenon, but detailed reasons remain unclear. This study investigated the differences of the functional connectivity and topological properties in the contralesional sensorimotor network (cSMN) between patients with motor deficit and those with normal motor function. Methods: We retrospectively reviewed 65 patients (32 men) between 2017 and 2020. The patients were divided into four groups based on tumor laterality and preoperative motor status (deficit or non-deficit). Thirty-three healthy controls (18 men) were enrolled after matching for sex, age, and educational status. Graph theoretical measurement was applied to reveal alterations of the topological properties of the cSMN by analyzing resting-state functional MRI. Results: The results for patients with different hemispheric gliomas were similar. The clustering coefficient, local efficiency, transitivity, and vulnerability of the cSMN significantly increased in the non-deficit group and decreased in the deficit group compared to the healthy group (p < 0.05). Moreover, the nodes of the motor-related thalamus showed a significantly increased nodal efficiency and nodal local efficiency in the non-deficit group and decreased in the deficit group compared with the healthy group (p < 0.05). Conclusions: We posited the existence of two stages of alterations of the preoperative motor status. In the compensatory stage, the cSMN sacrificed stability to acquire high efficiency and to compensate for impaired motor function. With the glioma growing and the motor function being totally damaged, the cSMN returned to a stable state and maintained healthy hemispheric motor function, but with low efficiency.

Alterations of white matter tracts and topological properties of structural networks in hemifacial spasm.

Hemifacial spasm (HFS) is characterized by involuntary and paroxysmal muscle contractions on the hemiface. It is generally believed that HFS is caused by neurovascular compression at the root exit zone of the facial nerve. In recent years, the structural alterations of brains with HFS have aroused growing concern. However, little attention has been directed towards the possible involvement of specific white matter (WM) tracts and the topological properties of structural networks in HFS. In the present study, diffusion magnetic resonance imaging tractography was utilized to construct structural networks and perform tractometric analysis. The diffusion tensor imaging scalar parameters along with the WM tracts, and the topological parameters of global networks and subnetworks, were assessed in 62 HFS patients and 57 demographically matched healthy controls (HCs). Moreover, we investigated the correlation of these parameters with disease-clinical-level (DCL) and disease-duration-time (DDT) of HFS patients. Compared with HCs, HFS patients had additional hub regions including the amygdala, ventromedial putamen, lateral occipital cortex, and rostral cuneus gyrus. Furthermore, HFS patients showed significant alternations with specific topological properties in some structural subnetworks, including the limbic, default mode, dorsal attention, somato-motor, and control networks, as well as diffusion properties in some WM tracts, including the superior longitudinal fasciculus, cingulum bundle, thalamo-frontal, and corpus callosum. These subnetworks and tracts were associated with the regulation of emotion, motor function, vision, and attention. Notably, we also found that the parameters with subnetworks and tracts exhibited correlations with DCL and DDT. In addition to corroborating previous findings in HFS, this study demonstrates the changed microstructures in specific locations along with the fiber tracts and changed topological properties in structural subnetworks.

Pressure-Induced Superconductivity in HgTe Single-Crystal Film.

HgTe film is widely used for quantum Hall well studies and devices, as it has unique properties, like band gap inversion, carrier-type switch, and topological evolution depending on the film thickness modulation near the so-called critical thickness (63.5 Å), while its counterpart bulk materials do not hold these nontrivial properties at ambient pressure. Here, much richer transport properties emerging in bulk HgTe crystal through pressure-tuning are reported. Not only the above-mentioned abnormal properties can be realized in a 400 nm thick bulk HgTe single crystal, but superconductivity is also discovered in a series of high-pressure phases. Combining crystal structure, electrical transport, and Hall coefficient measurements, a p-n carrier type switching is observed in the first high-pressure cinnabar phase. Superconductivity emerges after the semiconductor-to-metal transition at 3.9 GPa and persists up to 54 GPa, crossing four high-pressure phases with an increased upper critical field. Density functional theory calculations confirm that a surface-dominated topologic band structure contributes these exotic properties under high pressure. This discovery presents broad and efficient tuning effects by pressure on the lattice structure and electronic modulations compared to the thickness-dependent critical properties in 2D and 3D topologic insulators and semimetals.

Brain Network Topology and Structural-Functional Connectivity Coupling Mediate the Association Between Gut Microbiota and Cognition.

Increasing evidence indicates that gut microbiota can influence cognition via the gut-brain axis, and brain networks play a critical role during the process. However, little is known about how brain network topology and structural-functional connectivity (SC-FC) coupling contribute to gut microbiota-related cognition. Fecal samples were collected from 157 healthy young adults, and 16S amplicon sequencing was used to assess gut diversity and enterotypes. Topological properties of brain structural and functional networks were acquired by diffusion tensor imaging (DTI) and resting-state functional magnetic resonance imaging (fMRI data), and SC-FC coupling was further calculated. 3-Back, digit span, and Go/No-Go tasks were employed to assess cognition. Then, we tested for potential associations between gut microbiota, complex brain networks, and cognition. The results showed that gut microbiota could affect the global and regional topological properties of structural networks as well as node properties of functional networks. It is worthy of note that causal mediation analysis further validated that gut microbial diversity and enterotypes indirectly influence cognitive performance by mediating the small-worldness (Gamma and Sigma) of structural networks and some nodal metrics of functional networks (mainly distributed in the cingulate gyri and temporal lobe). Moreover, gut microbes could affect the degree of SC-FC coupling in the inferior occipital gyrus, fusiform gyrus, and medial superior frontal gyrus, which in turn influence cognition. Our findings revealed novel insights, which are essential to provide the foundation for previously unexplored network mechanisms in understanding cognitive impairment, particularly with respect to how brain connectivity participates in the complex crosstalk between gut microbiota and cognition.

The large-scale spatial patterns of ecological networks between phytoplankton and zooplankton in coastal marine ecosystems.

Although autotrophic phytoplankton and heterotrophic zooplankton both play important roles in the food web of marine ecosystem, their comprehensive interactions and spatial patterns at continental scale remain poorly studied. Here, we collected 251 seawater samples along 13,000 km of Chinese coastline, and microscopically investigated the latitudinal gradients of planktonic diversities. In total, 307 phytoplanktonic and 311 zooplanktonic species were visually identified. Using the newly developed Inter-Domain Ecological Networks (IDENs) approach, the phytoplankton-zooplankton interaction networks were constructed. We found that the phyto-zooplankton network structure was varied across three regions, more complex and numerous connections along the southern coast than in the north. In addition, some particular associations between zooplanktonic and phytoplanktonic groups were found to be localized in specific regions. Furthermore, the seawater temperature and salinity were the major driving force for shaping planktonic interaction networks. These results provide a deeper understanding of planktonic biogeography and phytoplankton-zooplankton interaction patterns.

Systematic analysis of olfactory protein-protein interactions network of fruitfly, Drosophila melanogaster.

Olfaction is one of the physiological traits of insect behavior. Insects have evolved a sophisticated olfactory system and use a combined coding strategy to process general odor. Drosophila melanogaster is a powerful model to reveal the molecular and cellular mechanisms of odor detection. Identifying new olfactory targets through complex interactions will contribute to a better understanding of the functions, interactions, and signaling pathways of olfactory proteins. However, the mechanism of D. melanogaster olfaction is still unclear, and more olfactory proteins are required to be discovered. In this study, we tried to explore essential proteins in the olfactory system of D. melanogaster and conduct protein-protein interactions (PPIs) analysis. We constructed the PPIs network of the olfactory system of D. melanogaster, consisting of 863 proteins and 18,959 interactions. Various methods were used to perform functional enrichment analysis, topological analysis and cluster analysis. Our results confirmed that Class B scavenger receptors (SR-Bs), glutathione S-transferases (GSTs), and UDP-glycosyltransferases (UGTs) play an essential role in olfaction of D. melanogaster. The proteins obtained in this study can be used for subsequent functional identification in D. melanogaster olfactory.

Age-related alterations of brain metabolic network based on [18F]FDG-PET of rats.

Using animal models to study the underlying mechanisms of aging will create a critical foundation from which to develop new interventions for aging-related brain disorders. Aging-related reorganization of the brain network has been described for the human brain based on functional, metabolic and structural connectivity. However, alterations in the brain metabolic network of aging rats remain unknown. Here, we submitted young and aged rats to [18F]fluorodeoxyglucose with positron emission tomography (18F-FDG PET) and constructed brain metabolic networks. The topological properties were detected, and the network robustness against random failures and targeted attacks was analyzed for age-group comparison. Compared with young rats, aged rats showed reduced betweenness centrality (BC) in the superior colliculus and a decreased degree (D) in the parietal association cortex. With regard to network robustness, the brain metabolic networks of aged rats were more vulnerable to simulated damage, which showed significantly lower local efficiency and clustering coefficients than those of the young rats against targeted attacks and random failures. The findings support the idea that aged rats have similar aging-related changes in the brain metabolic network to the human brain and can therefore be used as a model for aging studies to provide targets for potential therapies that promote healthy aging.

Structure-Property Relationships of 2D Ga/In Chalcogenides.

Two-dimensional MX (M = Ga, In; X = S, Se, Te) homo- and heterostructures are of interest in electronics and optoelectronics. Structural, electronic and optical properties of bulk and layered MX and GaX/InX heterostructures have been investigated comprehensively using density functional theory (DFT) calculations. Based on the quantum theory of atoms in molecules, topological analyses of bond degree (BD), bond length (BL) and bond angle (BA) have been detailed for interpreting interatomic interactions, hence the structure-property relationship. The X-X BD correlates linearly with the ratio of local potential and kinetic energy, and decreases as X goes from S to Te. For van der Waals (vdW) homo- and heterostructures of GaX and InX, a cubic relationship between microscopic interatomic interaction and macroscopic electromagnetic behavior has been established firstly relating to weighted absolute BD summation and static dielectric constant. A decisive role of vdW interaction in layer-dependent properties has been identified. The GaX/InX heterostructures have bandgaps in the range 0.23-1.49 eV, absorption coefficients over 10-5 cm-1 and maximum conversion efficiency over 27%. Under strain, discordant BD evolutions are responsible for the exclusively distributed electrons and holes in sublayers of GaX/InX. Meanwhile, the interlayer BA adjustment with lattice mismatch explains the constraint-free lattice of the vdW heterostructure.

Resting-state brain network properties mediate the association between the oxytocin receptor gene and interdependence.

While an increasing number of behavioral findings have provided gene-culture coevolution accounts of human development, whether and how the brain mediates gene-culture associations remain unresolved. Based on the Culture-Behavior-Brain-Loop Model and the recent finding of associations between the oxytocin receptor gene (OXTR, rs53576) and a cultural trait (i.e., interdependence) across populations, we tested the hypothesis that resting-state brain network properties mediate the relationship between OXTR rs53576 and interdependence. G and A allele carriers of OXTR rs53576 were scanned during a resting state using functional magnetic resonance imaging (fMRI) and completed questionnaires to estimate their interdependence cultural values. We identified significant genotype effects on the local network metrics of the right hippocampus and its functional connectivity with the medial prefrontal cortex, dorsal anterior cingulate cortex, amygdala, basal ganglia and thalamus. The local network metrics of the right hippocampus and its functional connectivity with the basal ganglia and thalamus were correlated with interdependence. Moreover, both the degree of the right hippocampus and its functional connectivity with the basal ganglia and thalamus mediated the relationship between OXTR and interdependence. Our results provide brain imaging evidence for a key function of the brain in mediating the relationship between genes and culture.

Perceptual load modulates contour integration in conscious and unconscious states.

Previous research has documented that contour detection and integration may either be affected by local features such as the distances between elements or by high-level cognitive factors such as attention in our visual system. Less is known about how low and high level factors interact to influence contour integration. In this paper, we investigated how attention modulates contour integration through saliency (different element spacing) and topological propert ies (circle or S-shaped) when the state of conscious awareness is manipulated. A modified inattentional blindness (IB) combined with the Posner cuing paradigm was adopted in our three-phased experiment (unconscious-training-conscious). Attention was manipulated with high or low perceptual load for a foveal go/no-go task. Cuing effects were utilized to assess the covert processing of contours prior to a peripheral orientation discrimination task. We found that (1) salient circles and S-contours induced different cuing effects under low perceptual load but not with high load; (2) no consistent pattern of cuing effects was found for non-salient contours in all the conditions; (3) a positive cuing effect was observed for salient circles either consciously or unconsciously while a negative cuing effect occurred for salient S-contours only consciously. These results suggest that conscious awareness plays a pivotal role in coordinating a closure effect with the level of perceptual load. Only salient circles can be successfully integrated in an unconscious state under low perceptual load although both salient circles and S-contours can be done consciously. Our findings support a bi-directional mechanism that low-level sensory features interact with high-level cognitive factors in contour integration.

Protein-protein interaction network analysis of insecticide resistance molecular mechanism in Drosophila melanogaster.

The problem of resistance has not been solved fundamentally at present, because the development speed of new insecticides can not keep pace with the development speed of resistance, and the lack of understanding of molecular mechanism of resistance. Here we collected seed genes and their interacting proteins involved in insecticide resistance molecular mechanism in Drosophila melanogaster by literature mining and the String database. We identified a total of 528 proteins and 13514 protein-protein interactions. The protein interaction network was constructed by String and Pajek, and we analyzed the topological properties, such as degree centrality and eigenvector centrality. Proteasome complexes and drug metabolism-cytochrome P450 were an enrichment by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. This is the first time to explore the insecticide resistance molecular mechanism of D. melanogaster by the methods and tools of network biology, it can provide the bioinformatic foundation for further understanding the mechanisms of insecticide resistance.

ce-Subpathway: Identification of ceRNA-mediated subpathways via joint power of ceRNAs and pathway topologies.

Competing endogenous RNAs (ceRNAs) represent a novel mechanism of gene regulation that may mediate key subpathway regions and contribute to the altered activities of pathways. However, the classical methods used to identify pathways fail to specifically consider ceRNAs within the pathways and key regions impacted by them. We proposed a powerful strategy named ce-Subpathway for the identification of ceRNA-mediated functional subpathways. It provided an effective level of pathway analysis via integrating ceRNAs, differentially expressed (DE) genes and their key regions within the given pathways. We respectively analysed one pulmonary arterial hypertension (PAH) and one myocardial infarction (MI) data sets and demonstrated that ce-Subpathway could identify many subpathways whose corresponding entire pathways were ignored by those non-ceRNA-mediated pathway identification methods. And these pathways have been well reported to be associated with PAH/MI-related cardiovascular diseases. Further evidence showed reliability of ceRNA interactions and robustness/reproducibility of the ce-Subpathway strategy by several data sets of different cancers, including breast cancer, oesophageal cancer and colon cancer. Survival analysis was finally applied to illustrate the clinical application value of the ceRNA-mediated functional subpathways using another data sets of pancreatic cancer. Comprehensive analyses have shown the power of a joint ceRNAs/DE genes and subpathway strategy based on their topologies.