Formation Of Spatial Structure Research Articles

The central regulatory circuit in the gene network controlling the morphogenesis of Drosophila mechanoreceptors: an <i>in silico</i> analysis

The central regulatory circuit in the gene network controlling the morphogenesis of Drosophila mechanoreceptors: an <i>in silico</i> analysis

A Study on the Spatial Pattern of Traditional Villages from the Perspective of Courtyard House Distribution

As clan and blood relations are the essential core of rural social attributes, the rise and fall of the main family names in a village not only affects the spatial arrangement of their internal courtyard houses but also influences the overall spatial pattern of the village. Taking Pei Cheng Village as an example, in this study, quantitative analyses, such as those entailing standard deviation ellipse, kernel density, and space syntax, are incorporated to investigate the changes in rural family names’ courtyard houses and the historical context for these changes to reveal the influence of the evolution of courtyard house distribution under a given social structure on the overall spatial structure of the countryside at the micro- and meso-scales. The results in this study show that there is strong aggregation and bonding associated with the main family surname in a village and that such surnames have an important correlation with the village centre and spatial structure formation. Notably, the distribution of the surname-bearing clan courtyard houses has a certain degree of consistency with the spatial pattern of the village, with the main space corresponding to the main family surname, the secondary space corresponding to the secondary family, and the underdeveloped space corresponding to mixed family surnames. On this basis, the spatial system grading of Pei Cheng Village is summarized, providing a fundamental basis for future planning of Pei Cheng Village facilities and other aspects of planning, such as the selection of locations.

Dynamical mean-field-driven spinor-condensate physics beyond the single-mode approximation

$^{23}\mathrm{Na}$ spin-1 Bose-Einstein condensates are used to experimentally demonstrate that mean-field physics beyond the single-mode approximation can be relevant during the nonequilibrium dynamics. The experimentally observed spin oscillation dynamics and associated dynamical spatial structure formation confirm theoretical predictions that are derived by solving a set of coupled mean-field Gross-Pitaevskii equations [J. Jie et al., Phys. Rev. A 102, 023324 (2020)]. The experiments rely on microwave dressing of the $f=1$ hyperfine states, where $f$ denotes the total angular momentum of the $^{23}\mathrm{Na}$ atom. The fact that physics beyond the single-mode approximation at the mean-field level, i.e., spatial mean-field dynamics that distinguishes the spatial density profiles associated with different Zeeman levels, can, in certain parameter regimes, have a pronounced effect on the dynamics when the spin healing length is comparable to or larger than the size of the Bose-Einstein condensate has implications for using Bose-Einstein condensates as models for quantum phase transitions and spin squeezing studies as well as for nonlinear SU(1,1) interferometers.

Disturbing the Spatial Organization of Biofilm Communities Affects Expression of agr-Regulated Virulence Factors in Staphylococcus aureus.

Staphylococcus aureus uses quorum sensing and nutrient availability to control the expression of agr-regulated virulence factors. Quorum sensing is mediated by autoinducing peptide (AIP), which at a high concentration reduces expression of surface attachment proteins (coa, fnbpA) and increases expression of exotoxins (lukS) and proteases (splA). Nutrient availability can be sensed through the saeS/saeR system. Low nutrients increase expression of saeR, which augments expression of coa and fnbpA, distinct from the activity of AIP. The formation of spatial structure, such as biofilms, can alter quorum sensing and nutrient acquisition. In natural environments, biofilms encounter forces that may alter their spatial structure. These forces may impact quorum sensing and/or nutrient acquisition and thus affect the expression of agr-regulated virulence factors. However, this has not been studied. We show that periodically disturbing biofilms composed of S. aureus using a physical force affected the expression of agr-regulated virulence factors. In nutrient-poor environments, disturbance increased the expression of coa, fnbpA, lukS, and splA. Disturbance in a nutrient-rich environment at low or high disturbance amplitudes moderately reduced expression of coa and fnbpA but increased expression of lukS and splA. Interestingly, at an intermediate amplitude, the overall expression of agr-regulated virulence factors was the lowest; expression of lukS and splA remained unchanged relative to an undisturbed biofilm, while expression of coa and fnbpA significantly decreased. We hypothesize that these changes are a result of disturbance-driven changes in access to AIP and nutrients. Our results may allow the identification of environments where virulence is enhanced, or reduced, owing to a disturbance. IMPORTANCE Bacteria, such as Staphylococcus aureus, integrate signals from the environment to regulate genes encoding virulence factors. These signals include those produced by quorum-sensing systems and nutrient availability. We show that disturbing the spatial organization of S. aureus populations can lead to changes in the expression of virulence factors, likely by altering the ways in which S. aureus detects these signals. Our work may allow us to identify environments that increase or reduce the expression of virulence factors in S. aureus.

Conformational ensemble of amyloid-forming semenogelin 1 peptide SEM1(68–107) by NMR spectroscopy and MD simulations

SEM1(68–107) is a peptide corresponding to the region of semenogelin 1 protein from 68 to 107 amino acid position. SEM1(68–107) is an abundant component of semen, which participates in HIV infection enhanced by amyloid fibrils forming. To understand the causes influencing amyloid fibril formation, it is necessary to determine the spatial structure of SEM1(68–107). It was shown that the determination of SEM1(68–107) structure is complicated by the non-informative NMR spectra due to the high intramolecular mobility of peptides. The complementary approach based on the geometric restrictions of individual peptide fragments and molecular modeling was used for the determination of the spatial structure of SEM1(68–107). The N- (SEM1(68–85)) and C-terminuses (SEM1(86–107)) of SEM1(68–107) were chosen as two individual peptide fragments. SEM1(68–85) and SEM1(86–107) structures were established with NMR and circular dichroism CD spectroscopies. These regions were used as geometric restraints for the SEM1(68–107) structure modeling. Even though most of the SEM1(68–107) peptide is unstructured, our detailed analysis revealed the following structured elements: N-terminus (70His-84Gln) forms an α-helix, (86Asp-94Thr) and (101Gly-103Ser) regions fold into 310-helixes. The absence of a SEM1(68–107) rigid conformation leads to instability of these secondary structure regions. The calculated SEM1(68–107) structure is in good agreement with experimental values of hydrodynamic radius and dihedral angles obtained by NMR spectroscopy. This testifies the adequacy of a combined approach based on the use of peptide fragment structures for the molecular modeling formation of full-size peptide spatial structure.

Spatial Structure Formation by RsmE-Regulated Extracellular Secretions in Pseudomonas fluorescens Pf0-1.

ABSTRACTCells in microbial communities on surfaces live and divide in close proximity, which greatly enhances the potential for social interactions. Spatiogenetic structures are manifested through competitive and cooperative interactions among the same and different genotypes within a shared space, and extracellular secretions appear to function dynamically at the forefront. A previous experimental evolution study utilizing Pseudomonas fluorescens Pf0-1 colonies demonstrated that diverse mutations in the rsmE gene were repeatedly and exclusively selected through the formation of a dominant spatial structure. RsmE’s primary molecular function is translation repression, and its homologs regulate various social and virulence phenotypes. Pseudomonas spp. possess multiple paralogs of Rsm proteins, and RsmA, RsmE, and RsmI are the most prevalent. Here, we demonstrate that the production of a mucoid polymer and a biosurfactant are exclusively regulated through RsmE, contradicting the generalized notion of functional redundancy among the Rsm paralogs. Furthermore, we identified the biosurfactant as the cyclic lipopeptide gacamide A. Competition and microscopy analyses showed that the mucoid polymer is solely responsible for creating a space of low cellular density, which is shared exclusively by the same genotype. Gacamide A and other RsmE-regulated products appear to establish a physical boundary that prevents the encroachment of the competing genotype into the newly created space. Although cyclic lipopeptides and other biosurfactants are best known for their antimicrobial properties and reducing surface tension to promote the spreading of cells on various surfaces, they also appear to help define spatial structure formation within a dense community.IMPORTANCE In densely populated colonies of the bacterium Pseudomonas fluorescens Pf0-1, diverse mutations in the rsmE gene are naturally selected by solving the problem of overcrowding. Here, we show that RsmE-regulated secretions function together to create and protect space of low cell density. A biosurfactant generally promotes the spreading of bacterial cells on abiotic surfaces; however, it appears to function atypically within a crowded population by physically defining genotypic boundaries. Another significant finding is that these secretions are not regulated by RsmE’s paralogs that share high sequence similarity. The experimental pipeline described in this study is highly tractable and should facilitate future studies to explore additional RsmE-regulated products and address why RsmE is functionally unique from its paralogs.

Ecological adaptation shaped the genetic structure of homoploid ferns against strong dispersal capacity.

The formation of spatial genetic structure with the presence of extensive gene flow, an evolutionary force which is generally expected to eliminate population-specific variation and maintain genetic homogeneity, remains poorly understood. Homosporous ferns, which spread by spores through wind and possess long distance dispersal capacity, provide an ideal system to investigate such a process. Here, using a homoploid fern lineage, the Athyrium sinense complex, we used reduced-representation genomic data to examine spatial genetic structure and explored potential driving forces including geographical distance, environment, climatic history and external dispersal constraints. Our findings showed a clear north-south divergence at the genetic, morphological and ecological levels between both sides of 35°N in East Asia. Fluctuant and heterogeneous climatic condition was demonstrated to play a crucial role during the formation of the divergence. Our results suggested that this lineage was able to migrate southward and colonize new habitat as a result of the Quaternary climatic fluctuation. Furthermore, the present genetic structure is attributed to adaptation to heterogeneous environments, especially temperature difference. In addition to ecological adaptation, we found clues showing that canopy density, wind direction as well as habitat continuity were all likely to constrain the effect of gene flow. These results demonstrated a diversification process without ploidy changes in ferns providing new insights for our present knowledge on ferns' spatio-temporal evolutionary pattern. In particular, our study highlights the influence of environmental heterogeneity in driving genetic divergence against strong dispersal capacity.

Spatial structure of natural boxwood and the invasive box tree moth can promote coexistence

In the absence of top-down and bottom-up controls, herbivores eventually drive themselves to extinction by exhausting their host plants. Poorly mobile herbivores may experiment only local disappearance, because they can recolonize intact plant patches elsewhere, leaving time to previously over-exploited patches to regrow. However most herbivores such as winged insects are highly mobile, which may prevent the formation of spatial heterogeneity. We test if long-distance dispersal can preclude coexistence using the invasion of box tree moth (Cydalima perspectalis) in Europe as a model system. We build a lattice model and estimate the parameters with a combination of field measurements, experimental data and literature sources. Space corresponds either to a realistic boxwood landscape in the Alps, or to theoretical landscapes of various sizes. We find that both species persist under a large range of realistic parameter values, despite a severe reduction in boxwood biomass, with an alternation of outbreaks and near-to-extinction moth densities. Large landscapes are necessary for coexistence, allowing the formation of spatial structure. Slow plant regrowth combined with long-distance dispersal could drive moths to extinction, because of resources depletion at the global scale even without a complete synchronization of the local dynamics. The spatial dynamics leads to formation of small plant patches evenly distributed in the landscape, because of a combination of local plant dispersal and global indirect competition between plants through their positive effect on moth population size. Coexistence is favoured by such heterogeneous landscapes, because empty patches increase moth mortality during dispersal: the system thus creates its own stability conditions.

Quantitative Assessment of Chirality of Protein Secondary Structures and Phenylalanine Peptide Nanotubes.

In this study we consider the features of spatial-structure formation in proteins and their application in bioengineering. Methods for the quantitative assessment of the chirality of regular helical and irregular structures of proteins are presented. The features of self-assembly of phenylalanine (F) into peptide nanotubes (PNT), which form helices of different chirality, are also analyzed. A method is proposed for calculating the magnitude and sign of the chirality of helix-like peptide nanotubes using a sequence of vectors for the dipole moments of individual peptides.

Ice needles weave patterns of stones in freezing landscapes

Patterned ground, defined by the segregation of stones in soil according to size, is one of the most strikingly self-organized characteristics of polar and high-alpine landscapes. The presence of such patterns on Mars has been proposed as evidence for the past presence of surface liquid water. Despite their ubiquity, the dearth of quantitative field data on the patterns and their slow dynamics have hindered fundamental understanding of the pattern formation mechanisms. Here, we use laboratory experiments to show that stone transport is strongly dependent on local stone concentration and the height of ice needles, leading effectively to pattern formation driven by needle ice activity. Through numerical simulations, theory, and experiments, we show that the nonlinear amplification of long wavelength instabilities leads to self-similar dynamics that resemble phase separation patterns in binary alloys, characterized by scaling laws and spatial structure formation. Our results illustrate insights to be gained into patterns in landscapes by viewing the pattern formation through the lens of phase separation. Moreover, they may help interpret spatial structures that arise on diverse planetary landscapes, including ground patterns recently examined using the rover Curiosity on Mars.

ARCHITECTURAL-SPATIA PRINCIPLES OF FORMATION OF THE STRUCTURE OF MODERN CULT BUILDINGS OF CHRISTIAN CONFESSIONS IN UKRAINE

The article «Architectural-spatial principles of formation of the structure of modern cult buildings of Christian confessions in Ukraine» acquaints the readers with the percentage of different denominations in Ukraine. The paper reports on the coexistence of different religious denominations in Ukraine, a table with sacred architecture in different areas is given, as it is an important component of national minorities living in our country. The architectural and spatial organization of sacred buildings on the territory of Ukraine is analyzed. The purpose of the study is to identify and analyze the formation of evaluation criteria, sacred buildings of Christian denominations in Ukraine. The main research methods in the article are general scientific methods, which include: review of the literature, study of analogues; theoretical methods: analysis and synthesis, analogy and comparison; empirical methods: description, observation, perception, images. The objects are a selection of the twenty most successful buildings during the period of independence of Ukraine of each denominational unit of Christianity in the country. Discovery the relevance of the study and the basic principles of formation and development of the category of assessment of buildings of Christian denominations. Discovery the basic principles of formation of architectural and spatial structure and development of the category of assessment of buildings of Christian denominations. The analysis of modern Ukrainian church building and the search for ways of its further development in the theory of architecture is carried out mainly from internally Christian positions without taking into account the current theories of development of post-Soviet Orthodoxy. This leads to a biased and religiously involved consideration of a number of aspects of Christian architecture, in particular the Orthodox denomination of Ukraine in the late XX - early XXI century, patterns and principles of development of which cannot be determined, being within the model of post-Soviet Orthodoxy. The paper is supplied with diagrams, tables, figures.

Chronology of the Nizhne-Arkhyz fortified settlement development according to historical, bibliographic and archival sources

This article is devoted to identifying the chronology of the medieval Alania capital architectural and spatial structure formation. The study revealed that the first on the site were erected cross-domed temples, built according to the Byzantine model and dated to the first half of the 10th century. In this regard, the planning structure of the fortified settlement was formed under the influence of the Byzantine Christian topography traditions. The chronological stages of the fortified settlement formation are revealed. The planning structure of the Nizhne-Arkhyz fortified settlement is similar to the planning of Constantinople, the main features of which were laid down at the end of the 5th century. Both cities have similar outlines of plans, inscribed in a triangle, at the eastern peak of which their community centers were located. In the spatial planning scheme of both cities, there are three main streets, the directions of which merge into one main street leading to the community center. Community centers of cities are represented by the squares where Christian churches are located.

Driving factors of formation, development, and change of spatial structure in metropolitan areas: A systematic review

In the last decades, there have been many articles on the spatial structure of metropolitan areas, but a study for explaining driving factors of changes in the spatial structure of metropolitan areas has remained unknown so far. To fill this gap, the article explains the driving factors of these changes using a systematic review method. To this end, 115 peer-reviewed scientific articles published from 1999 to 2019 were carefully analyzed. According to the results, 4 main dimensions including contextual and intrinsic, incentive and disincentive, developmental, and transformative were identified in this regard. This article argues that spatial structure subject to the driving factors have undergone vast changes over the past two decades, and the metropolitan areas have been shifting from concentrated and compact patterns toward decentralized and dispersed patterns.

Spatial genetic structure and historical demography of East Asian wild boar.

Pleistocene climatic fluctuations may have had a profound impact on the evolutionary history of many species. The geographical pattern of European wild boar (Sus scrofa) is clearly studied, and it was greatly influenced by ancient climatic events, especially the Last Glacial Maximum. Previous research on genetic variation has mainly focused on the origin and distribution histories of domestic pigs. However, some questions have not been answered, including those concerning the genetic diversity, geographical pattern and possible historic influence of climate on East Asian wild boar (EAWB). Employing the control region of mtDNA (511bp), we investigated the contributions of historic climate, which possibly shaped the genetic pattern of wild boar. Given that the level of genetic diversity of wild boars is higher in East Asia than in Europe, 172 haplotypes were detected from 680 individuals. Phylogenetic analysis demonstrated the complex phylogeographic structure of EAWB. Mismatch analysis, neutrality tests and the Bayesian Skyline Plot results all retrieved signals of a rapid population expansion, which might have played an important role in driving the formation of complex spatial genetic structure. Genetic data and species distribution modelling showed that the Last Glacial Maximum had weak effect on the distribution of the EAWB. We suggest that, in shaping spatial genetic structure in East Asian, long-term gene flow and population history played more important roles than Pleistocene climate fluctuations.

Do high-speed railways accelerate urban land expansion in China? A study based on the multi-stage difference-in-differences model

High-speed railway (HSR) have become the main transportation mode in China and a crucial contributing factor for the formation and development of urban and regional spatial structure. This study aims to investigate the effects and mechanisms of HSR on urban land expansion in China. The multi-stage difference-in-differences (DID) estimation method is used to explore the cases of 35 mega cities. The main results are presented as follows. 1) Opening HSR can positively influence urban land expansion, as evidenced by the 9.5% increase in the urban land expansion index after such opening. 2) The increase in the number of HSR station and route can accelerate urban land expansion. Each newly added station increases the urban land expansion index by 2.4%, and urban land expansion increases 4.8% when a new HSR route is added. 3) The positive effects of the opening of HSR on urban land expansion generally have a time lag of five years. 4) Compared with cities in the east, the midwestern ones are more vulnerable to the impact of HSR. The net effect of HSR on urban land expansion for midwestern cities is 10.9% higher than that for cities in the east. Furthermore, the mechanisms of the effect of HSR on urban land expansion are the industrial agglomeration effect of HSR and the incentive effect of local governments’ land finance alongside the development of HSR.

TRANSFORMASI TATA RUANG DALEM DI SEKITAR KAWASAN JERON BETENG, YOGYAKARTA

Abstrak- Dalem atau rumah bangsawan adalah rumah yang diberikan oleh Keraton Yogyakarta kepada saudara atau kerabat Sultan. Dalem berada di dalam dan sekitar kawasan Jeron Beteng, Yogyakarta. Saat ini dalem sudah mengalami banyak perubahan terutama dari tata ruang dalem. Perubahan tersebut dipengaruhi dari peningkatan kepadatan penduduk dan perubahan pola pikir masyarakat menjadi lebih modern di lingkungan kawasan Jeron Beteng. Perubahan-perubahan yang muncul pada dalem terutama dalam aspek tata ruanganya menjadi hal yang menarik untuk diteliti. Tujuan penelitian ini adalah untuk memahami perubahan yang terjadi pada tata ruang dalem dan aspek yang mendominasi terjadinya perubahan pada dalem.Penelitian ini menggunakan metode deskriptif dengan pendekatan kualitatif dengan mengkaji dari aspek sejarah kawasan dan budaya masyarakat Jawa. Kedua aspek tersebut menjelaskan adanya adat atau ritual yang dilakukan secara terus menerus dan menjadi dasar pembentukkan tata ruang dengan ruang-ruang yang dibutuhkan pada rumah masayarakat Jawa. Data diperoleh dengan melakukan observasi ke lapangan dan wawancara serta studi literatur. Analisis dalem dikaji dengan mempelajari budaya dan sejarah Yogyakarta serta prinsip arsitektur Yogyakarta.Penelitian ini mencoba mengungkap bagaimana perubahan yang terjadi terhadap tata ruang dalem dengan membandingkan kondisi tata ruang berdasarkan prinsip arsitektur Yogyakarta dengan kondisi dalem saat ini. Aspek tata ruang yang dibahas adalah orientasi, fungsi, bentuk bangunan, zonasi ruang, dan susunan massa dalem. Hasil dari penelitian ini didapatkan bahwa perubahan yang terjadi pada dalem diawali dari peningkatan kepadatan penduduk dan pola pikir modern sehingga terjadinya perubahan fungsi pada dalem untuk pemanfaatan ruang, perubahan bentuk bangunan, perubahan zonasi ruang pada kawasan, dan penambahan massa pada susunan massa.

Influence of mass repatriation factor of Armenians in the first half of the 20th Century on the formation of spatial and planning structure of Yerevan

The article deals with the management of the process of development of the planning and spatial structure of Yerevan, taking into account the factor of mass repatriation of Armenians 20-70th. The specificity of territorial and planning development of the city at different stages of rapid development is analyzed. Data on mass repatriation of Armenians and their resettlement are given. The compositional and planning principles and features of the formation and territorial organization of residential settlements and areas for returnees, which later became the most important planning parts of modern Yerevan, are considered.The provisions and principles outlined in the report can be useful in the study of various aspects of the architectural and spatial development of Yerevan and can be used at all stages of design related to the prospect of further architectural and planning formation of urban systems of Yerevan.

Similar Material Simulation Test of Overlying Strata Characteristics of Isolated Working Face Mining with Thick-Hard Strata

The overlying strata spatial structure of isolated working face under thick-hard strata is complex, and the overlying strata movement is drastic. Rock burst in this kind of isolated working face is easy to occur under the influence of mining depth and geological structure. Aiming at the safety problems caused by the overlying strata movement deformation of the isolated working face under deep mining, one similar model of the thick-hard strata on the working face is built. The overlying strata structure and its evolution characteristics in the mining process of working face are studied by using a similar material simulation test. The results show that the overlying strata structure above the isolated working face is long-arm T-type spatial structure in the vertical section, and the coal body at the corner of isolated working face forms the stress concentration region. In addition, with the increase of the mining range, the coal pillar in the upper and lower sections compress and sink, resulting in the gob range increases, and the overlying strata re-move on both sides of isolated working face, the long-arm T-type overlying strata fracturing after reaching the limit of suspension, causing the isolated working face instability. It can be seen that the long-arm T-type structure is prone to large scale fracture movement of the key strata, and the risk of inducing strong rock burst is high. Therefore, when mining by strip method, the mining range of the working face on both sides of isolated working face should be increased, or the technology of cutting roof and pressure relief should be adopted to avoid the formation of long-arm T-type spatial structure above the isolated working face, so as to reduce the occurrence of rock burst.

Assessment of important environmental factors in formation of spatial structure of phytoplankton in large subarctic rivers (Eastern Siberia)

On the basis of data-array analysis (2000–2011) of phytoplankton in large subarctic rivers; the rivers’ hydrochemical, hydrological, and morphological parameters; and climatic properties of the catchment-basin areas and by using stepwise discriminant analysis and clustering, it was determined that formation of phytoplankton spatial structure is mostly affected by climate rather than by physical-chemical properties of the river waters in northeastern Siberia. Floristic structure of phytoplankton is mostly connected to abiotic factors among phytoplankton-development indicators. The duration of vegetation-growth period is another important environmental factor.

Assessing the Key Environmental Factors in the Formation of Phytoplankton Spatial Structure in Large Subarctic Rivers (East Siberia)

Data of 2000–2011 on phytoplankton of 12 large subarctic rivers, their hydrochemical, hydrological, and morphometric parameters and the climatic characteristics of their drainage basins have been analyzed with the use of step-wise discriminant analysis and clusterization of observations to establish that the formation of phytoplankton spatial structure in rivers in the northeastern Siberia is governed by climate rather than water physicochemical properties. Among the characteristics of phytoplankton development, its floristic structure shows the closest correlation with abiotic factors. An important environmental factor is the duration of growing season .