Self-organized Structures Research Articles

Evolution of Nanodomains and Formation of Self-Organized Structures during Local Switching in X-Cut LNOI

The features of nanodomain growth during local switching in X-cut lithium niobate on insulator (LNOI) were comprehensively studied using the biased tip of a scanning probe microscope. The obtained results were discussed in terms of the kinetic approach. The revealed differences in domain growth in bulk LN and LNOI were attributed to the higher bulk conductivity of LNOI. The obtained influence of humidity on the shape and growth of isolated domains was attributed to the water meniscus. Analysis of the transition between the “forward growth” and “sideways growth” stages was performed by switching to the stripe electrode. A sand-glass-shaped domain was formed due to growth in the opposite direction after the domain touched the electrode. Stable periodical domain structures down to 300 nm were created and characterized in LNOI. Highly ordered comb-like domains of various alternating lengths, including four- and eight-fold increase periods, were produced by performing biased tip scanning along the Y axis. The obtained knowledge is important for the future development of nanodomain engineering methods in monocrystalline ferroelectric thin films on insulators.

Adult mouse kidney stem cells orchestrate the de novo assembly of a nephron via Sirt2‐ modulated canonical Wnt/β‐catenin signaling

End‐stage renal disease affects an estimated 2.4 million people annually worldwide. With cases increasing 8% every year, regenerative strategies are needed to help alleviate, and potentially replace, the increasing demand for kidney transplants. An important question remains whether stem cells reside in the adult mammalian kidney. Here we developed a methodology for isolation of kidney stem cells from adult mouse kidney by using Sca1 and Oct4 stem cell markers. Using these cells, we generated three types of kidney‐like structures. First, we observed the assembly of self‐organizing three‐dimensional kidney organoids. These kidney organoids show characteristic of kidney structures and contain podocytes and endothelial cells that form networks of capillary loop‐like structures. We also observed the de novogeneration of a self‐organizing nephron (and its associated collecting duct) from monolayer cultures. Comma‐ and S‐shaped bodies that expressed activated Notch1 were present during this formation, suggesting that Notch signaling played a key role in driving nephrogenesis. This is consistent with our current knowledge of nephron formation in the mouse embryo. Furthermore, we observed the differentiation of monolayer cells into functionally mature tubules and self‐organizing kidney‐shaped structures that selectively endocytose dextran. Finally, we demonstrated that expression of Sirt2 was upregulated, which modulated the dynamics of canonical Wnt/β‐catenin signaling during kidney organoid development. Altogether, our observations provide the first evidence for the existence of stem cells in the adult mouse kidney. These findings offer powerful tools for future applications, including drug screening, disease modelling, cell therapy, and kidney regeneration.

Monensin and its analogues show anti‐glioblastoma activity in an organoid model of cancer

Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. Despite numerous clinical trials, the standard of care therapy has remained unchanged for the last decade. One of the main problems contributing to the limited effective treatment options and poor overall survival is the lack of models which can reliably recapitulate tumor heterogeneity. Organoids are 3D self‐organized structures which mimic tumor architecture, microenvironment, and cellular interactions which makes them an improved model for anti‐cancer drug discovery.Monensin (MON) is a polyether ionophore antibiotic characterized by wide range of biological properties including anti‐cancer activity. In order to identify more potent compounds based on the scaffold of MON, we investigated the anti‐GBM activity of 14 novel esters and urethanes of MON. In 3D mini‐ring cell viability assays, we identified seven analogues (IC50 = 91.5 ± 54.4 ‐ 291.7 ± 68.8 nM) more potent towards GBM than the parental MON (IC50 = 612.6 ± 184.4 nM). These analogues induced DNA fragmentation in an organoid model of GBM, suggestive of apoptotic cell death. Furthermore, the most potent analog, compound 1, significantly reduced GBM cell migration, induced PARP cleavage and degradation, increased ɣH2AX signaling and increased expression of the autophagy marker LCII. To investigate the activity of these novel compounds in a tumor microenvironment, we have developed a host:tumor hybrid 3D organoid system. For host tissue, we generated human cerebral organoids (COs) from hiPSCs. The COs displayed multiple neural rosettes with a proliferative zone of neural stem cells (Nestin+), neurons (TUJ1+), primitive ventricular system (SOX2+/Ki67+), intermediate zone (TBR2+) and cortical plate (MAP2+). These findings suggest the level of differentiation and development of our COs as equivalent to early stage human fetal brain. We then co‐cultured RFP‐labeled U87MG cells with fully formed COs. After establishing U87MG tumor formation, hybrid organoids were treated with MON or compound 1. Compound 1 significantly reduced U87MG tumor size after four days of treatment. Our findings highlight the therapeutic potential of MON analogues towards GBM and support further research and clinical development of these compounds.

The Influence of the Synergistic Effects of Sodium Bis(2-ethylhexyl)sulfosuccinate and Lecithin at the Water/Liquid Paraffin–Oil Interface on the Properties of Self-Organizing Structures

The Influence of the Synergistic Effects of Sodium Bis(2-ethylhexyl)sulfosuccinate and Lecithin at the Water/Liquid Paraffin–Oil Interface on the Properties of Self-Organizing Structures

Control of the wetting properties of stainless steel by ultrashort laser texturing using multi-parallel beam processing

The laser surface microtexturing is increasingly used for the production of surfaces with desired wetting characteristics (i.e., superhydrophobicity). For this not only precise but also fast laser processing is needed. Microtextures not based entirely on laser induced material self-organization require relatively tight focusing of the laser beam which can not be achieved using fast beam scanning systems. Therefore, in this work, the possibility to use parallel laser processing by multi-beam array for control of the EN 1.4301 (AISI 304) stainless steel surface was investigated. High-energy picosecond laser pulses were used to pattern the polished steel surface using 8 × 8 beam array with two different patterning strategies: mesh and dot. The multi-beam patterning inevitably brings some irregularities due to variation of properties of the beams in the array. However, after the investigation of the influence of laser patterning parameters on the wetting properties of the steel surface, it was determined that multi-beam mesh patterning allows obtaining superhydrophobic surface properties through the right combination of texture depth, surface chemical properties and laser induced surface ripples. The dot patterning was even more promising and was found suitable for obtaining a broad spectrum of wetting states ranging from superhydrophobic to superhydrophilic, when appropriate patterning parameters were used, mostly by controlling self-organized surface structure shape by changing texture period (laser spot overlap).

Spatial Dissipative Solitons in Graphene-Based Active Random Metamaterials

We investigate dissipative nonlinear dynamics in graphene-based active metamaterials composed of randomly dispersed graphene nanoflakes embedded within an externally pumped gain medium. We observe that graphene saturable nonlinearity produces a subcritical bifurcation of nonlinear modes, enabling self-organization of the emitted radiation into several dissipative soliton structures with distinct topological charges. We systematically investigate the existence domains of such nonlinear waves and their spatial dynamics, finding that soliton vortices are unstable, thus enabling self-organization into single dissipative structures with vanishing topological charge, independently of the shape of the graphene nanoflakes. Our results shed light on self-organization of coherent radiation structures in disordered systems and are relevant for future cavity-free lasers and amplifier designs.

Evaluation of the Effect of Taheri Consciousness Field 1 on Nanostructured Lipid Carriers in the Treatment of UV-irradiated Human Hair Keratin

Self-organizing nanostructured lipid carriers (NLCs) that are nanoemulsions composed of a dispersed phase of a mixture of solid and liquid lipids have been used in drug delivery systems. Research on NLCs has shown that these carriers have advantages for drug treatments over conventional carriers, including increased solubility, stability, and shelf life and improved permeability and bioavailability. Also, self-assembly has attracted much research attention because of its possible role at the beginning of life. Moreover, it is known that solar ultraviolet waves play two contradictory roles in the prebiotic and biotic atmosphere in the process of life initiating: The constructive role in providing primary energy for effective reactions in the formation of organic molecules and the destructive role in breaking of biomolecules formed in the ozone-depleted early atmosphere and full of disturbing waves. Considering the importance of self-organizing structures in the category of life initiation and drug delivery, as well as the significant effects of the Taheri Consciousness Field 1 on the structure and function of enzymes, biomimetic molecules, and biological cells that have been observed in several studies, this research aimed to study effects of Taheri Consciousness Field on UV irradiated human hair keratin. According to the results of the present study, using Faradarmani CF treated synthetic NLCs, a remarkable repair and improvement of the UV-irradiated keratin protein have been achieved.

Self-Organized Space Charge Structure Formations in DC Glow Discharge

Experimental investigations of a hollow cathode discharge through the controlled variation of anode potential inside a hollow cylindrical cavity, in the absence and presence of the magnetic field, reveal the self-organization of uniform complex space charge structure formation around the spherical anode into concentrated localized anode spots. The discharge current&#x2013;voltage (<inline-formula> <tex-math notation="LaTeX">$I$ </tex-math></inline-formula>&#x2013;<inline-formula> <tex-math notation="LaTeX">$V$ </tex-math></inline-formula>) characteristic along with the electrostatic floating potential and discharge current fluctuations measured during the glow discharge regime suggest that the initial stable multiple sheath formation around the anode dissociates into intermittent multiple localized anode spot formations while passing through transient states during anode potential variation. On introducing a magnetic field, the localized concentrated anode spot formations on the anode surface undergo random distribution through self-organized criticality (SOC) and pronounced low-frequency oscillations (&#x007E;52.4 kHz). These oscillations gradually develop into harmonics of 100 kHz on further increasing the anode potential in the presence of the external magnetic field. Various discharge regimes are investigated through the time-resolved floating potential variation measurements using a cylindrical Langmuir probe (LP). We report on the relation between the discharge variations with the nonlinear time series analysis of the discharge current and floating potential fluctuations through the reconstructed phase space in different time domains to analyze the dynamics of complex structure formations and the existence of SOC behavior during the present hollow cathode discharge regime. The study of self-organized pattern formations and SOC behavior is vital for understanding the complex behavior of plasmas in the field of strongly coupled plasmas, plasma-based surface treatments, and thrusters for further development.

Mass spectrometry-based proteomics of 3D cell culture: A useful tool to validate culture of spheroids and organoids

Worldwide obesity, defined as abnormal or excessive fat accumulation that may result in different comorbidities, is considered a pandemic condition that has nearly tripled in the last 45 years. Most studies on obesity use animal models or adipocyte monolayer cell culture to investigate adipose tissue. However, besides monolayer cell culture approaches do not fully recapitulate the physiology of living organisms, there is a growing need to reduce or replace animals in research. In this context, the development of 3D self-organized structures has provided models that better reproduce the in vitro aspects of the in vivo physiology in comparison to traditional monolayer cell culture. Besides, recent advances in omics technologies have allowed us to characterize these cultures at the proteome, metabolome, transcription factor, DNA-binding and transcriptomic levels. These two combined approaches, 3D culture and omics, have provided more realistic data about determined conditions. Thereby, here we focused on the development of an obesity study pipeline including proteomic analysis to validate adipocyte-derived spheroids. Through the combination of collected mass spectrometry data from differentiated 3T3-L1 spheroids and from murine white adipose tissue (WAT), we identified 1732 proteins in both samples. By using a comprehensive proteomic analysis, we observed that the in vitro 3D culture of differentiated adipocytes shares important molecular pathways with the WAT, including expression of proteins involved in central metabolic process of the adipose tissue. Together, our results show a combination of an orthogonal method and an image-based analysis that constitutes a useful pipeline to be applied in 3D adipocyte culture.

Hydrogen isotope effect on self-organized electron internal transport barrier criticality and role of radial electric field in toroidal plasmas

Self-organized structure formation in magnetically confined plasmas is one of the most attractive subjects in modern experimental physics. Nonequilibrium media are known to often exhibit phenomena that cannot be predicted by superposition of linear theories. One representative example of such phenomena is the hydrogen isotope effect in fusion plasmas, where the larger the mass of the hydrogen isotope fuel is the better the plasma confinement becomes, contrary to what simple scaling models anticipate. In this article, threshold condition of a plasma structure formation is shown to have a strong hydrogen isotope effect. To investigate the underlying mechanism of this isotope effect, the electrostatic potential is directly measured by a heavy ion beam probe. It is elucidated that the core electrostatic potential transition occurs with less input power normalized by plasma density in plasmas with larger isotope mass across the structure formation. This observation is suggestive of the isotope effect in the radial electric field structure formation.

Мусульманская умма в Индонезии в 2021 г.: участники, процессы и противоречия развития

The author analyzes the features of development and the main vectors of transformation of the moderate trends of Indonesian political Islam in 2021. It is assumed that the COVID-19 pandem-ic has become an incentive for the technical modernization of Islam in the context of its virtualization. The article deals with the problems of activation of the oldest, “historical” organizations of In-donesian Muslims, including Muhammadiyah and Nahdatul Ulama. The author provides the materi-als of their congresses held in 2021. The role of political parties in the contemporary history of Indonesian political Islam is considered. The author believes that modern Indonesian political Islam is looking for new forms of structural self-organization. Therefore, it is shown that moderate political Islam seeks to use the resources of modernization and is active also in the development and use of virtual space.

Human Intestinal Organoids: Promise and Challenge.

The study of human intestinal biology in healthy and diseased conditions has always been challenging. Primary obstacles have included limited tissue accessibility, inadequate in vitro maintenance and ethical constrains. The development of three-dimensional organoid cultures has transformed this entirely. Intestinal organoids are self-organized three-dimensional structures that partially recapitulate the identity, cell heterogeneity and cell behaviour of the original tissue in vitro. This includes the capacity of stem cells to self-renew, as well as to differentiate towards major intestinal lineages. Therefore, over the past decade, the use of human organoid cultures has been instrumental to model human intestinal development, homeostasis, disease, and regeneration. Intestinal organoids can be derived from pluripotent stem cells (PSC) or from adult somatic intestinal stem cells (ISC). Both types of organoid sources harbour their respective strengths and weaknesses. In this mini review, we describe the applications of human intestinal organoids, discussing the differences, advantages, and disadvantages of PSC-derived and ISC-derived organoids.

Molecular modelling and computational studies of peptide diphenylalanine nanotubes, containing waters: structural and interactions analysis.

The work is devoted to computer studies of the structural and physical properties of such self-organizing structures as peptide nanotubes (PNT) based on diphenylalanine (FF) dipeptide with different initial isomers of the left (L-FF) and right (D-FF) chiralities of these dipeptides. The structures under study are considered both with empty anhydrous and with internal cavities filled with water molecules. Molecular models of both chiralities are investigated using quantum-chemical DFT and semi-empirical methods, which are in consistent with the known experimental data. To study the effect of nano-sized clusters of water molecules embedded in the inner hydrophilic cavity on the properties of nanotubes (including the changes in their dipole moments and polarizations), as well as the changes in the structure and properties of water clusters themselves (their own dipole moments and polarizations), the surfaces of internal cavities of nanotubes and outer surfaces of water cluster structures for both types of chirality are analyzed. A specially developed method of visual differential analysis of structural features of (bio)macromolecular structures is applied for these studies. The results obtained of a number of physical properties (interacting energies, dipole moments, polarization values) are given for various cases and analyzed in comparison with the known data. These data are necessary for analyzing the interactions of water molecules with hydrophilic parts of nanotube molecules based on FF, such as COO- and NH3 + , since they determine many properties of the structures under study. The data obtained are useful for further analysis of the possible adhesion and capture of medical molecular components by active layers of FF-based PNT, which can be designed for creating capsules for targeted delivery of pharmaceuticals and drugs on their basis.

Spontaneous patterning method utilizing transformation of UV-curable emulsion

A self-organizing structure is important for imparting functions and simplifying the manufacturing process. The development of spontaneous structures with a roll-to-roll process capability is a challenging task. We propose a novel patterning method utilizing the destruction of the emulsion structure. An oil-in-water (O/W) UV-curable emulsion liquid film was partially exposed to UV, resulting in aggregation and immobilization of the emulsion in the medium. Emulsion droplets in the unexposed area are coalesced by removing water. Coalesced emulsion droplets expand and spontaneously permeate into the pores formed in the aggregated structure of UV-cured emulsion particles, causing an uneven structure. An uneven pattern can be formed by direct UV exposure of the liquid film and the subsequent drying process without requiring a development process.

Design of stabilized fuzzy relation-based neural networks driven to ensemble neurons/layers and multi-optimization

In this study, a design methodology based on fuzzy relation-based neural networks for stabilized network structure is introduced to cope with over-fitting as well as multi-collinearity problems which generally appear in conventional fuzzy neural networks. The design method of the proposed self-organizing network structure provides an efficient solution to construct the stabilized Fuzzy Relation-based Neural Networks (FRNN) through a synergy of multi-techniques such as ensemble neurons/layers, L2-norm regularization, compromise technique, and multi-optimization, in order to generate the structure of the multi-layered self-organizing network designed with the aid of the learning as well as novel structural design.The overall network structure is realized with the aid of parallel network structure with newly added layers as well as effective node selection method through the combination technique of both a sum of squared coefficients (SSC) and performance index (PI) as a node selection criterion for each layer in FRNN. Ensemble neurons consist of the current inputs and the original inputs, and they serve to reduce the bias of the proposed FRNN by maintaining the information of the original inputs. Also, ensemble layers stand for the combination of the current layer and the front layer, and they play a role for control the variance of the model by taking into account the output of the previous layers. The least square error estimation (LSE)-based learning method with L2-norm regularization is used for constructing the stabilized network architecture, and their ensuring design methodologies result in alleviating the overfitting phenomenon and also enhancing the generalization ability. For the performance enhancement of FRNN directly affected by some parameters such as the number of input variables, collocation of the specific subset of input variables, the number of membership functions per each variable, and the order of polynomial in the consequent parts of the fuzzy rules, multi-particle swarm optimization (MPSO) is exploited for the effectively structural as well as parametric optimization of the proposed networks. That is, the multi-optimization helps achieve a compromise between the better generation performance and the alleviated over-fitting leading to the stabilization of the proposed multi-layered self-organizing network structure realized with the aid of synergistic multi-techniques and ensemble structures such as a) L2-norm regularization-based LSE learning, b) combination technique for effective node selection through the combination of SSC and PI, and c) a novel parallel network structure including newly added layers and node selection method. The performance of the proposed network structure is quantified by comprehensive experiments and comparative analysis.

The effect of elastic anisotropy on the symmetry selection of irradiation-induced void superlattices in cubic metals

Self-organized microstructures and patterns have been widely observed in non-equilibrium physical systems. In particular, irradiation in metals creates far-from-equilibrium environments, in which the competing dynamics of defect production and annihilation can lead to unique self-organized superlattice structures, e.g., void and gas bubble superlattices. From a physical point of view, the superlattice structures are dictated by the intrinsic symmetry breaking in the metals, i.e., anisotropy caused by the breaking of continuous rotational symmetry. In the literature, two distinctive anisotropies, elastic anisotropy and diffusion anisotropy of interstitials, have been proposed to be the origins of superlattice formation. However, it is still unclear which anisotropy dominates the symmetry selection of superlattice structures. In this paper, we study elastic anisotropy and its effect on the symmetry of void superlattices. By using theoretical analyses and phase field simulations, we show that elastic anisotropy in cubic metals can lead to either face-centered cubic or simple cubic superlattices depending on the Zener anisotropy ratio. The superlattices formed under this elastic anisotropy mechanism must form under the influence of spinodal decomposition, as the mechanism requires perturbations in the vacancy concentration field to develop into spatially-static concentration waves. We compare to existing work on symmetry selection in superlattices via diffusion anisotropy and to experimental observations, and we suggest that concentration wave development under the influence of elastic anisotropy is not the mechanism for symmetry selection during the formation of irradiation-induced void superlattices, but that diffusion anisotropy could be the dominant mechanism.

Self-Organization of Diverse Directional Hierarchical Networks in Simple Coupled Maps with Connection Changes

We comprehensively studied the morphology of the self-organized effective network structures that form in simple coupled maps with interelement synchronization-dependent connection changes. Based on the parameter values, the spontaneous formation of four types of directional hierarchical networks, named pair-driven networks, loop-driven networks, hidden trio-driven networks, and hidden community-driven networks, was observed. This study provides novel insights into the self-organized complex networks that form in neural networks, various other biological networks, and social networks.

On the Nature of Functional Differentiation: The Role of Self-Organization with Constraints.

The focus of this article is the self-organization of neural systems under constraints. In 2016, we proposed a theory for self-organization with constraints to clarify the neural mechanism of functional differentiation. As a typical application of the theory, we developed evolutionary reservoir computers that exhibit functional differentiation of neurons. Regarding the self-organized structure of neural systems, Warren McCulloch described the neural networks of the brain as being “heterarchical”, rather than hierarchical, in structure. Unlike the fixed boundary conditions in conventional self-organization theory, where stationary phenomena are the target for study, the neural networks of the brain change their functional structure via synaptic learning and neural differentiation to exhibit specific functions, thereby adapting to nonstationary environmental changes. Thus, the neural network structure is altered dynamically among possible network structures. We refer to such changes as a dynamic heterarchy. Through the dynamic changes of the network structure under constraints, such as physical, chemical, and informational factors, which act on the whole system, neural systems realize functional differentiation or functional parcellation. Based on the computation results of our model for functional differentiation, we propose hypotheses on the neuronal mechanism of functional differentiation. Finally, using the Kolmogorov–Arnold–Sprecher superposition theorem, which can be realized by a layered deep neural network, we propose a possible scenario of functional (including cell) differentiation.

Yb-doped Y–Al–O thin films with a self-organized columnar structure and their anti-Stokes photoluminescence properties

We fabricated ytterbium-doped yttrium aluminum oxide (Yb:Y–Al–O) thin films by radio-frequency magnetron sputtering and evaluated their crystallinity and anti-Stokes photoluminescence (PL) properties for optical refrigeration. The Yb:Y–Al–O films that were grown on c-sapphire substrates had better transparency than the films deposited on fused-quartz substrates. The better transparency is considered to be a result of the smaller mismatch between the thermal expansion coefficients of Yb:Y–Al–O and c-sapphire. We found that the thin films on the c-sapphire substrates consist of densely packed sub-micron columnar crystals that are aligned perpendicular to the substrate. In these films, we confirmed the existence of perovskite, garnet, and monoclinic phases despite using a single-phase sputtering target. The excitation wavelength dependence of anti-Stokes PL is used to investigate the energy transfer process between trivalent Yb ions in neighboring columnar crystals. The data indicate that the resonant energy transfer from Yb3+ ions at a specific seven-coordinated site of the monoclinic phase to Yb3+ ions in neighboring columnar crystals is faster than the radiative relaxation at the energy-donor site.

Organoid Technology and Clinical Applications in Digestive System Cancer

Abstract Cancers of the digestive system (DS), including esophageal, gastric, colorectal, liver, and pancreatic cancers, have a high incidence and mortality worldwide. Current cancer models cannot faithfully recapitulate the critical features of the original tumor, resulting in the failure of translation from basic research into clinical practice. More advanced cancer models are in urgent need of pathogenesis exploration and anticancer medicine development. Organoids are in vitro cultured three dimensional (3D) self-organizing organotypic structures derived from tissues and pluripotent stem cells, which faithfully mimic the histological features and preserve the genetic heterogeneity of the original tissues. Both normal and malignant organoids can now be efficiently established from the DS tissues of patients. In this review, we summarize the general methods to generate human DS organoids and their applications as a novel model in basic cancer research, preclinical medical practice, and precision medicine.