Modular Complex Research Articles

Sex Differences in Hierarchical and Modular Organization of Functional Brain Networks: Insights from Hierarchical Entropy and Modularity Analysis.

Existing studies have demonstrated significant sex differences in the neural mechanisms of daily life and neuropsychiatric disorders. The hierarchical organization of the functional brain network is a critical feature for assessing these neural mechanisms. But the sex differences in hierarchical organization have not been fully investigated. Here, we explore whether the hierarchical structure of the brain network differs between females and males using resting-state fMRI data. We measure the hierarchical entropy and the maximum modularity of each individual, and identify a significant negative correlation between the complexity of hierarchy and modularity in brain networks. At the mean level, females show higher modularity, whereas males exhibit a more complex hierarchy. At the consensus level, we use a co-classification matrix to perform a detailed investigation of the differences in the hierarchical organization between sexes and observe that the female group and the male group exhibit different interaction patterns of brain regions in the dorsal attention network (DAN) and visual network (VIN). Our findings suggest that the brains of females and males employ different network topologies to carry out brain functions. In addition, the negative correlation between hierarchy and modularity implies a need to balance the complexity in the hierarchical organization of the brain network, which sheds light on future studies of brain functions.

Техническое обслуживание и ремонт цапф барабанной мельницы плавучего комплекса горного оборудования

Introduction. In order to develop promising deposits of non-ferrous metals in the Arctic zone, in particular the Pavlovskoye lead-zinc deposit on Novaya Zemlya, it is necessary to develop climate-saving geo-technologies for mining. In this connection, a concept of conservation geo-technology has been developed and proposed through the use of a specially designed floating complex of mining equipment, included together with the quarry equipment in a single technological chain for the extraction of ore raw materials and its processing into concentrate. However, for the full functioning of the concept of this geo-technology, it is necessary to carry out preventive maintenance and repair of mining equipment at the site of its operation on a floating complex. Research methods and materials. The methodological basis of the work is a systematic approach to the studied means of carrying out repair and restoration works of mining machinery and equipment, which includes both theoretical analysis and generalization of the results of fundamental and applied works of domestic and foreign authors, including methods and theories of designing technology for repairing metalworking and mining processing complexes, multicriteria analysis and simulation modeling. Research results. The article proposes a new technology for the implementation of repair work to restore the working surfaces of hollow loading and unloading support trunnions of hydrostatic sliding bearing units of a drum mill in cramped deck conditions of a floating complex of mining equipment for the development of deposits in the Arctic zone. The structure of the built-in mechanized modular machine tool complex is developed and presented, with the help of which the hollow support trunnions of the drum mill are directly machined according to the patented repair technology. Conclusion. It is shown that the use of the described repair technology by means of an embedded mechanized modular complex will reduce the complexity of the overhaul of the trunnions without the need to perform dismantling work to disconnect the mill drum body from the hollow trunnion caps, which has a positive effect on the accuracy of processing the working surfaces of hollow trunnions.

Community Detection in Modular Complex Networks Using an Improved Particle Swarm Optimization Algorithm

Community detection is an important and interesting topic for better understanding and analyzing complex network structures. Detecting hidden partitions in complex networks is proven to be an NP-hard problem that may not be accurately resolved using traditional methods. So it is solved using evolutionary computation methods and modeled in the literature as an optimization problem. In recent years, many researchers have directed their research efforts toward addressing the problem of community structure detection by developing different algorithms and making use of single-objective optimization methods. In this study, we have continued that research line by improving the Particle Swarm Optimization (PSO) algorithm using a local improvement operator to effectively discover community structure in the modular complex networks when employing the modularity density metric as a single-objective function. The framework of the proposed algorithm consists of three main steps: an initialization strategy, a movement strategy based on perturbation genetic operators, and an improvement operator. The key idea behind the improvement operator is to determine and reassign the complex network nodes that are located in the wrong communities if the majority of their topological links do not belong to their current communities, making it appear that these nodes belong to another community. The performance of the proposed algorithm has been tested and evaluated when applied to publicly-available modular complex networks generated using a flexible and simple benchmark generator. The experimental results showed the effectiveness of the suggested method in discovering community structure over modular networks of different complexities and sizes.

Parametric nonlinear modelling of 3D masonry arch bridges

Detailed modelling of masonry arch bridges and viaducts presents unique computational challenges. Not only do such structures exhibit complex nonlinear behaviour, but they are also difficult to describe within a consistent computational framework for high-fidelity simulations, due to the range of interactive components with varying geometric characteristics. This paper presents a novel parametric model design tool for the generation of detailed 3D FE meshes of realistic masonry arch bridges and viaducts. This tool has been developed according to a modular description as an add-on component within the Rhino – Grasshopper environment. It allows for modular complex bridge assemblages with independent definition of the key viaduct parts, including arch barrels, spandrel walls, piers as well as multi-layered fill. Moreover, new parts can be seamlessly introduced into the framework due to its modular nature. Notably, as all components are geometrically addressable, it is possible to further enhance the model generation tool by adding non-standard routines to create more complex geometry than that allowed by the current parametric definition. Importantly, the developed strategy enables variable fidelity model generation, where different segments of an analysed viaduct can be represented by meso‑ and/or macro-scale masonry descriptions at different levels of detail. This approach further enables the consideration of initial damage in the brick/blockwork, which is a very common feature of many existing masonry bridges and viaducts.

Alternating chimera states in complex networks with modular structures.

Chimera, the coexistence state of synchronization and non-synchronization, widely exists in complex networks. It has a great potentially explanatory power for the unihemispheric sleep of birds and some mammals, in which the synchronizations of the hemispheres of the cerebral cortex are evolving alternately. In this study, a coupled nonlinear oscillator system with a topology of the modular complex network was constructed to simulate the left and right hemispheres of the brain. The results showed that a stable chimera, an alternating chimera, and a breathing chimera were produced when the coupling strength and connection probability of the left and right hemispheres were changed. Further, we studied the effect of noise on rich synchronous patterns and found that the alternating chimera was robust to Gaussian white noise when the strength was not very large. Finally, our study was extended to a complex network with three sub-networks, and an alternating chimera could exist in two or three sub-networks. Our research provides a deeper insight into the mechanism of brain function like unihemispheric sleep.

Complexity of modular neuromuscular control increases and variability decreases during human locomotor development

When does modular control of locomotion emerge during human development? One view is that modularity is not innate, being learnt over several months of experience. Alternatively, the basic motor modules are present at birth, but are subsequently reconfigured due to changing brain-body-environment interactions. One problem in identifying modular structures in stepping infants is the presence of noise. Here, using both simulated and experimental muscle activity data from stepping neonates, infants, preschoolers, and adults, we dissect the influence of noise, and identify modular structures in all individuals, including neonates. Complexity of modularity increases from the neonatal stage to adulthood at multiple levels of the motor infrastructure, from the intrinsic rhythmicity measured at the level of individual muscles activities, to the level of muscle synergies and of bilateral intermuscular network connectivity. Low complexity and high variability of neuromuscular signals attest neonatal immaturity, but they also involve potential benefits for learning locomotor tasks.

Three-State Opinion Model on Complex Topologies.

We investigate opinion diffusion on complex networks and the interplay between the existence of neutral opinion states and non-trivial network structures. For this purpose, we apply a three-state opinion model based on magnetic-like interactions to modular complex networks, both synthetic and real networks extracted from Twitter. The model allows for tuning the contribution of neutral agents using a neutrality parameter. We also consider social agitation, encoded as a temperature, that accounts for random opinion changes that are beyond the agent neighborhood opinion state. Using this model, we study which topological features influence the formation of consensus, bipartidism, or fragmentation of opinions in three parties, and how the neutrality parameter and the temperature interplay with the network structure.

A novel connection between Trypanosoma brucei mitochondrial proteins TbTim17 and TbTRAP1 is discovered using Biotinylation Identification (BioID)

The protein translocase of the mitochondrial inner membrane in Trypanosoma brucei, TbTIM17, forms a modular complex in association with several other trypanosome-specific proteins. To identify transiently interacting proximal partner(s) of TbTim17, we used Biotinylation Identification (BioID) by expressing a modified biotin ligase-TbTim17 (BirA∗-TbTim17) fusion protein in T.brucei. BirA∗-TbTim17 was targeted to mitochondria and assembled in the TbTIM complex. In the presence of biotin, BirA∗-TbTim17 biotinylated several mitochondrial proteins. Interestingly, TbHsp84/TbTRAP1, a mitochondrial Hsp90 homolog, was identified as the highest enriched biotinylated proteins. We validated that interaction and colocalization of TbTim17 and TbHsp84 in T.brucei mitochondria by coimmunoprecipitation analysis and confocal microscopy, respectively. TbTim17 association with TbTRAP1 increased several folds during denaturation/renaturation of mitochondrial proteins invitro, suggesting TbTRAP1 acts as a chaperone for TbTim17 refolding. We demonstrated that knockdown of TbTRAP1 reduced cell growth and decreased the levels of the TbTIM17, TbTim62, and mitochondrial (m)Hsp70 complexes. However, ATPase, VDAC, and Atom69 complexes were minimally affected. Additionally, the steady state levels of TbTim17, TbTim62, and mHsp70 were reduced significantly, but Atom69, ATPase β, and RBP16 were mostly unaltered due to TbTRAP1 knockdown. Quantitative proteomics analysis also showed significant reduction of TbTim62 along with a few other mitochondrial proteins due to TbTRAP1 knockdown. Finally, TbTRAP1 depletion did not hamper the import of the ectopically expressed TbTim17-2xMyc into mitochondria but reduced its assembly into the TbTIM17 complex, indicating TbTRAP1 is critical for assembly of TbTim17. This is the first report showing the role of TRAP1 in the TIM complex assembly in eukaryotes.

Cytosolic Protein Delivery Using Modular Biotin-Streptavidin Assembly of Nanocomposites.

Current strategies for the delivery of proteins into cells face general challenges of endosomal entrapment and concomitant degradation of protein cargo. Efficient delivery directly to the cytosol overcomes this obstacle: we report here the use of biotin-streptavidin tethering to provide a modular approach to the generation of nanovectors capable of a cytosolic delivery of biotinylated proteins. This strategy uses streptavidin to organize biotinylated protein and biotinylated oligo(glutamate) peptide into modular complexes that are then electrostatically self-assembled with a cationic guanidinium-functionalized polymer. The resulting polymer-protein nanocomposites demonstrate efficient cytosolic delivery of six biotinylated protein cargos of varying size, charge, and quaternary structure. Retention of protein function was established through efficient cell killing via delivery of the chemotherapeutic enzyme granzyme A. This platform represents a versatile and modular approach to intracellular delivery through the noncovalent tethering of multiple components into a single delivery vector.

Proton-controlled Action of an Imidazole as Electron Relay in a Photoredox Triad.

Electron relays play a crucial role for efficient light-induced activation by a photo-redox moiety of catalysts for multi-electronic transformations. Their insertion between the two units reduces detrimental energy transfer quenching while establishing at the same time unidirectional electron flow. This rectifying function allows charge accumulation necessary for catalysis. Mapping these events in photophysical studies is an important step towards the development of efficient molecular photocatalysts. Three modular complexes comprised of a Ru-chromophore, an imidazole electron relay function, and a terpyridine unit as coordination site for a metal ion were synthesized and the light-induced electron transfer events studied by laser flash photolysis. In all cases, formation of an imidazole radical by internal electron transfer to the oxidized chromophore was observed. The effect of added base evidenced that the reaction sequence depends strongly on the possibility for deprotonation of the imidazole function in a proton-coupled electron transfer process. In the complex with MnII present as a proxy for a catalytic site, a strongly accelerated decay of the imidazole radical together with a decreased rate of back electron transfer from the external electron acceptor to the oxidized complex was observed. This transient formation of an imidazolyl radical is clear evidence for the function of the imidazole group as an electron relay. The implication of the imidazole proton and the external base for the kinetics and energetics of the electron trafficking is discussed.

Abstract 2129: Usp22 controls multiple signaling pathways in development and disease

Abstract Our research is focused on defining the functions of histone-modifying enzymes in normal cells so that we can understand how alterations in these activities contribute to tumor development or progression. The highly conserved SAGA complex plays important roles at multiple steps of gene transcription in yeast, flies, and mammalian cells. This modular complex houses two enzymatic activities, the GCN5 histone acetyltransferase, and the USP22 deubiquitinase. USP22 is overexpressed in highly aggressive, therapy-resistant cancers, but the normal functions of this deubiquitinase are not well defined. Our detailed analysis of the embryonic lethality observed in the Usp22-/- mouse model we generated highlighted a critical role for Usp22 in the developing placenta. We found that Usp22 deletion in mice results in embryonic lethality due to defects in the formation and organization of extra-embryonic placental tissues, culminating in failure to establish proper vascular interactions with the maternal circulatory system. These phenotypes arise from abnormal gene expression patterns that reflect defective kinase signaling, including TGFß and several receptor tyrosine kinase (RTK) pathways. Interestingly, overexpression of USP22 in mice leads to an over branching phenotype of the mammary gland, which is linked to the deregulation of the signaling pathways described above. Our results provide insights to potential angiogenic functions of the SAGA complex, indicate that Usp22 is critical for the proper execution of multiple signaling pathways important for normal development, and provide new clues towards Usp22 contributions to cancer and other disease states. Citation Format: Evangelia Koutelou, Xianghong Kuang, Sharon Y. Dent. Usp22 controls multiple signaling pathways in development and disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2129.

A Fully Symmetrical High Performance Modular Milling Cutter

Milling cutters belong to a widely used category of cutting tools. In this category, modular milling cutters are a narrow niche, less studied, and developed. Usually, they are symmetrical cutting tools. A milling cutting tool that can be reconfigured due to its modularity and still keeps its symmetry becomes more interesting and useful for machining. The paper presents such a new concept in a computer aided design (CAD) model of a cutting tool based on some novel features. The tool itself is designed as a modular complex. The way the torque is transmitted from the shaft to the elementary cutters is an original one, as they are joined together based on a profiled assembling. The profile is one formed of filleted circular sectors and segments. The reaming of the elementary cutters has two sections each of them assuming a task: transmitting the torque, and precisely centring, respectively. The cooling system, which is a component of the tool, provides the cutting area with coolant both on the front and side face of the cutting tool. Some nozzles placed around the cutting tool send jets or curtains of coolant towards the side surface of the cutter, instead of parallel, as some existing solutions do. The source of the coolant supply is the inner cooling system of the machine tool. This provides the tool with coolant having proper features: high enough flow and pressure. The output of the research is a CAD-based model of the modular milling cutter with a high performance cooling system. All of this model’s elements were designed taking into account the design for manufacturing principles, so it will be possible to easily manufacture this tool. Several variants of milling cutters obtained by reconfiguring the complex tool are presented. Even if the tool is usually a symmetric complex, it can process asymmetric parts. Symmetry is intensively used to add some advantages to the modular cutting tool: balanced forces in the cutting process, the possibility of controlling the direction of the axial cutting force, and a good machinability of the grooves used to assemble the main parts of the cutting tool.

Experimental laboratory complex for studying the physical properties of artificially formed gas-hydrate-containing sediments

Physical properties of gas hydrate-containing sediments (HCS) are extremely important information for the development of methods for their search and exploration. The presence of gas hydrates in marine bottom sediments significantly changes their physical properties, so they can be detected by marine remote geophysical observations. The physical properties of HCS are very important for detecting the presence of these compounds, estimating the amount of captured gas hydrates by sediments, as well as developing methods for using this resource. Currently, the study of physical properties concerned mainly artificial gas hydrates in the process of formation and decomposition under various thermodynamic conditions in their pure form. Therefore, very little is known about the physical properties of HCS, which makes their detection by remote geophysical surveys too difficult. Development and creation of experimental laboratory modular complex for formation of artificial methane gas hydrates in various lithological-granulometric matrices (sandstones, argillites, siltstones, etc.) and measurement of their physical properties in thermodynamic conditions of bottom sediments of the Black Sea, will increase efficiency technology of methane hydrate deposits development. Under experimental conditions, along with the thermal conductivity and velocities of longitudinal and transverse waves of artificial HCS, the parameters of elastic deformation, strength, and decay characteristics will be measured, which will allow performing theoretical analysis to build models based on different hypotheses of their genesis. At the S.I. Subbotin Institute of Geophysics of the National Academy of Sciences of Ukraine created a model of the installation for the formation and study of the physical properties of HCS. The development is based on the modern technological level of research in the field of thermobaric petro- physical experimental modeling of geological environments, as well as on the use of modern software and hardware laboratory research to obtain physical properties of bottom sediments of various lithological and particle size distribution.

Empty Pericarp24 and Empty Pericarp25 Are Required for the Splicing of Mitochondrial Introns, Complex I Assembly, and Seed Development in Maize

RNA splicing is an essential post-transcriptional regulation in plant mitochondria and chloroplasts. As the mechanism of RNA splicing remains obscure, identification and functional elucidation of new splicing factors are necessary. Through a characterization of two maize mutants, we cloned Empty pericarp 24 (Emp24) and Empty pericarp 25 (Emp25). Both Emp24 and Emp25 encode mitochondrion-targeted P-type PPR proteins. EMP24 is required for the splicing of nad4 introns 1 and 3, which was reported (Ren Z. et al., 2019), and EMP25 functions in the splicing of nad5 introns 1, 2, and 3. Absence of either Nad4 or Nad5 proteins blocks the assembly of mitochondrial complex I, resulting in the formation of a sub-sized complex I of similar size in both mutants. Mass spectrometry identification revealed that the subcomplexes in both mutants lack an identical set of proteins of complex I. These results indicate that EMP24 and EMP25 function in the splicing of nad4 and nad5 introns, respectively, and are essential to maize kernel development. The identification of the subcomplexes provides genetic and molecular insights into the modular complex I assembly pathway in maize.

Extracting backbones in weighted modular complex networks

Network science provides effective tools to model and analyze complex systems. However, the increasing size of real-world networks becomes a major hurdle in order to understand their structure and topological features. Therefore, mapping the original network into a smaller one while preserving its information is an important issue. Extracting the so-called backbone of a network is a very challenging problem that is generally handled either by coarse-graining or filter-based methods. Coarse-graining methods reduce the network size by grouping similar nodes, while filter-based methods prune the network by discarding nodes or edges based on a statistical property. In this paper, we propose and investigate two filter-based methods exploiting the overlapping community structure in order to extract the backbone in weighted networks. Indeed, highly connected nodes (hubs) and overlapping nodes are at the heart of the network. In the first method, called “overlapping nodes ego backbone”, the backbone is formed simply from the set of overlapping nodes and their neighbors. In the second method, called “overlapping nodes and hubs backbone”, the backbone is formed from the set of overlapping nodes and the hubs. For both methods, the links with the lowest weights are removed from the network as long as a backbone with a single connected component is preserved. Experiments have been performed on real-world weighted networks originating from various domains (social, co-appearance, collaboration, biological, and technological) and different sizes. Results show that both backbone extraction methods are quite similar. Furthermore, comparison with the most influential alternative filtering method demonstrates the greater ability of the proposed backbones extraction methods to uncover the most relevant parts of the network.

Epidemic spreading on modular networks: The fear to declare a pandemic.

In the past few decades, the frequency of pandemics has been increased due to the growth of urbanization and mobility among countries. Since a disease spreading in one country could become a pandemic with a potential worldwide humanitarian and economic impact, it is important to develop models to estimate the probability of a worldwide pandemic. In this paper, we propose a model of disease spreading in a structural modular complex network (having communities) and study how the number of bridge nodes n that connect communities affects disease spread. We find that our model can be described at a global scale as an infectious transmission process between communities with global infectious and recovery time distributions that depend on the internal structure of each community and n. We find that near the critical point as n increases, the disease reaches most of the communities, but each community has only a small fraction of recovered nodes. In addition, we obtain that in the limit n→∞, the probability of a pandemic increases abruptly at the critical point. This scenario could make the decision on whether to launch a pandemic alert or not more difficult. Finally, we show that link percolation theory can be used at a global scale to estimate the probability of a pandemic since the global transmissibility between communities has a weak dependence on the global recovery time.

Innovation in online higher-education services: building complex systems

ABSTRACT Digitization is increasing the complexity and variety of educational services supplied and demanded. However, there is a lack of a systematic treatment of this phenomenon from the perspective of innovation and entrepreneurship. This paper employs the complex adaptive systems approach to explore how digitization changes the characteristics, generativity (combinatorial possibilities) and architecture of online educational services. Our main claims are that: (a) online courses (OCs) are modular complex hierarchical systems; (b) the development of new OCs is a significant type of innovation (not limited merely to technological change) brought about by entrepreneurial reconfiguration of modules that create new combinations in the design space of new educational services; (c) these new combinations generate new OC systems; and (d) OCs are embedded in broader institutional and social structures (e.g. universities) that co-evolve with technological change. By means of a formal combinatorial model, we examine the computational mechanism and the principles of connection-making that govern how new OCs are created and adapted.

Exploring Hubs and Overlapping Nodes Interactions in Modular Complex Networks

Exploring Hubs and Overlapping Nodes Interactions in Modular Complex Networks

Mechanisms and Regulation of Neuronal GABAB Receptor-Dependent Signaling.

γ-Aminobutyric acid B receptors (GABABRs) are broadly expressed throughout the central nervous system where they play an important role in regulating neuronal excitability and synaptic transmission. GABABRs are G protein-coupled receptors that mediate slow and sustained inhibitory actions via modulation of several downstream effector enzymes and ion channels. GABABRs are obligate heterodimers that associate with diverse arrays of proteins to form modular complexes that carry out distinct physiological functions. GABABR-dependent signaling is fine-tuned and regulated through a multitude of mechanisms that are relevant to physiological and pathophysiological states. This review summarizes the current knowledge on GABABR signal transduction and discusses key factors that influence the strength and sensitivity of GABABR-dependent signaling in neurons.

In-depth Analysis of the Lid Subunits Assembly Mechanism in Mammals

The 26S proteasome is a key player in the degradation of ubiquitinated proteins, comprising a 20S core particle (CP) and a 19S regulatory particle (RP). The RP is further divided into base and lid subcomplexes, which are assembled independently from each other. We have previously demonstrated the assembly pathway of the CP and the base by observing assembly intermediates resulting from knockdowns of each proteasome subunit and the assembly chaperones. In this study, we examine the assembly pathway of the mammalian lid, which remains to be elucidated. We show that the lid assembly pathway is conserved between humans and yeast. The final step is the incorporation of Rpn12 into the assembly intermediate consisting of two modular complexes, Rpn3-7-15 and Rpn5-6-8-9-11, in both humans and yeast. Furthermore, we dissect the assembly pathways of the two modular complexes by the knockdown of each lid subunit.