Spatial Organization Research Articles

The role of compartmentalized β-AR/cAMP signaling in the regulation of lipolysis in white and brown adipocytes.

White and brown adipocytes are central mediators of lipid metabolism and thermogenesis, respectively. Their function is tightly regulated by all three β-adrenergic receptor (β-AR) subtypes which are coupled to the production of the second messenger 3',5'-cyclic adenosine monophosphate (cAMP). While known for decades in other cell types, compartmentation of adipocyte β-AR/cAMP signaling by spatial organization of the pathway and by cAMP degrading phosphodiesterases (PDEs) as well as its role in the regulation of lipolysis is only beginning to emerge. Here, we provide a short overview of recent findings which shed light on compartmentalized signaling using live cell imaging of cAMP in adipocytes and discuss possible future directions of research which could open up new avenues for the treatment of metabolic disorders.

The sustainable potential of the architectural and urban heritage of the Algerian ksour

ABSTRACT This paper aims to assess the sustainability potential of Algerian desert Ksour's architectural and urban heritage. It identifies systems aligning with the 17 sustainable development goals (SDGs), categorized into formal, spatial organization, and architectonic aspects. The approach correlates Ksour's architectural features with SDGs defined by the International Union of Architects, yielding 40 passive features applicable for achieving SDGs. Notably, features like high windows (architectural) and strategic siting (urban) remain relevant for energy efficiency and carbon footprint reduction. This research gives us the opportunity to improve our strategies for rehabilitating and adapting built heritage so that it can meet current environmental challenges, but also opens up the possibility in the future of continuing to identify more sustainable systems by extending the study of heritage examples, but also and above all of developing a reflection on the adaptation of these passive systems in the design of contemporary architectural and urban projects.

Quantifying 3′UTR length from scRNA-seq data reveals changes independent of gene expression

Although more than half of all genes generate transcripts that differ in 3′UTR length, current analysis pipelines only quantify the amount but not the length of mRNA transcripts. 3′UTR length is determined by 3′ end cleavage sites (CS). We map CS in more than 200 primary human and mouse cell types and increase CS annotations relative to the GENCODE database by 40%. Approximately half of all CS are used in few cell types, revealing that most genes only have one or two major 3′ ends. We incorporate the CS annotations into a computational pipeline, called scUTRquant, for rapid, accurate, and simultaneous quantification of gene and 3′UTR isoform expression from single-cell RNA sequencing (scRNA-seq) data. When applying scUTRquant to data from 474 cell types and 2134 perturbations, we discover extensive 3′UTR length changes across cell types that are as widespread and coordinately regulated as gene expression changes but affect mostly different genes. Our data indicate that mRNA abundance and mRNA length are two largely independent axes of gene regulation that together determine the amount and spatial organization of protein synthesis.

Tropical cyclone low-level wind speed, shear, and veer: sensitivity to the boundary layer parametrization in the Weather Research and Forecasting model

Abstract. Mesoscale modeling can be used to analyze key parameters for wind turbine load assessment in a large variety of tropical cyclones. However, the modeled wind structure of tropical cyclones is known to be sensitive to the boundary layer scheme. We analyze modeled wind speed, shear, and wind veer across a wind turbine rotor plane in the eyewall and outer cyclone. We further assess the sensitivity of wind speed, shear, and veer to the boundary layer parametrization. Three model realizations of Typhoon Megi are analyzed over the open ocean using three frequently used boundary layer schemes in the Weather Research and Forecasting (WRF) model. All three typhoon simulations reasonably reproduce the cyclone track and structure. The boundary layer parametrization causes up to 15 % differences in median wind speed at hub height between the simulations. The simulated wind speed variability also depends on the boundary layer scheme. The modeled median wind shear is smaller than or equal to 0.11 used in the current IEC (International Electrotechnical Commission) standard regardless of the boundary layer scheme for the eyewall and outer cyclone region. However, up to 43.6 % of the simulated wind profiles in the eyewall region exceed 0.11. While the surface inflow angle is sensitive to the boundary layer scheme, wind veer in the lowest 400 m of the atmospheric boundary layer is less affected by the boundary layer scheme. Simulated median wind veer reaches values up to 1.7×10-2° m−1 (1.2×10-2° m−1) in the eyewall region (outer cyclone region) and is relatively small compared to moderate-wind-speed regimes. On average, simulated wind speed shear and wind veer are highest in the eyewall region. Yet strong spatial organization of wind shear and veer along the rainbands may increase wind turbine loads due to rapid changes in the wind profile at the turbine location.

Practice-induced SNARC: evidence from a null-SNARC sample.

The mental representation of numbers inherently involves a spatial organization, often positioning smaller numbers to the left and larger numbers to the right. The SNARC effect, characterized by faster responses to small numbers using the left hand and vice versa for large numbers, is typically attributed to this left-to-right oriented mental number line (MNL). However, the direction of the SNARC effect seems to rely on reading direction, with most research exploring these mechanisms conducted within left-to-right reading cultures where the SNARC effect is prevalent. This study takes advantage of a sample from a left-to-right reading culture that does not exhibit the SNARC effect, allowing us to isolate and elucidate the stand-alone effects of recent experiences on SNARC. Therefore, the current study aims to investigate how MNL-compatible and MNL-incompatible practices induce an effect within a sample lacking the SNARC effect. To accomplish this, we reinvited the individuals from the sample which had previously shown no SNARC, and retested those who agreed to take part in the current study after an MNL-compatible or MNL-incompatible practice manipulation. The findings revealed an absence of the SNARC effect with MNL-compatible practices. Conversely, MNL-incompatible practices yielded a reverse SNARC effect. These results prompt a discussion on SNARC mechanisms within the framework of practice effects.

Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and obesity

The hepatocytes within the liver present an immense capacity to adapt to changes in nutrient availability. Here, by using high resolution volume electron microscopy, we map how hepatic subcellular spatial organization is regulated during nutritional fluctuations and as a function of liver zonation. We identify that fasting leads to remodeling of endoplasmic reticulum (ER) architecture in hepatocytes, characterized by the induction of single rough ER sheet around the mitochondria, which becomes larger and flatter. These alterations are enriched in periportal and mid-lobular hepatocytes but not in pericentral hepatocytes. Gain- and loss-of-function in vivo models demonstrate that the Ribosome receptor binding protein1 (RRBP1) is required to enable fasting-induced ER sheet-mitochondria interactions and to regulate hepatic fatty acid oxidation. Endogenous RRBP1 is enriched around periportal and mid-lobular regions of the liver. In obesity, ER-mitochondria interactions are distinct and fasting fails to induce rough ER sheet-mitochondrion interactions. These findings illustrate the importance of a regulated molecular architecture for hepatocyte metabolic flexibility.

IMMERSIVE ANALYTICS

Immersive Analytics focuses on the benefits and challenges of using immersive environments for data analysis, and developing designs to improve efficiency. Although immersive technologies are widely available, practical solutions have not gained widespread acceptance in real- world applications. Research in this field focuses on abstract 3D visualization, immersive environments, paper sampling and use case evaluation. 03 Related Works • Brooks early review of VR applications found it effective in specific domains like flight simulators, automotive engineering, and astronaut training. • Van Dam et al. highlighted VR applications for SciVis, benefiting archaeology and medical fields. • Laha and Bowman reviewed VR techniques for visualizing volume data, highlighting the need for controlled experiments to explore individual components of immersion. • Reda et al. summarized research for hybrid reality environments like the CAVE2, emphasizing the possibility of collaborative data analysis. • Brath collected evidence that 3D visualizations offer advantages beyond 2D, focusing on immersive displays. 05 Result • Overall, immersive analytics can lead to better data comprehension, better decision-making, more engagement and teamwork, effective big data exploration, creative data visualization methods, non-technical users' empowerment, and applications in a variety of fields. • These results add to the increasing importance of immersive analytics as an efficient tool for decision support and data analysis. Introduction • To facilitate data-driven analytical reasoning, immersive analytics leverages interactive technology like as virtual reality glasses, big flat screen displays, and even the internet of things. • Immersion refers to an experience that creates a genuine sense of presence in a virtual environment. • A person experiences a shift in awareness from their immediate real environment to another reality. • Immersion analytics is still a relatively new field that has mostly been studied in use cases and workshops. • The notion remains extremely difficult, even within the small community of immersive analytics practitioners. Methodology 4.1 Immersive environments • The study focuses on immersive environments leading to a mixed reality experience. • Abstract 3D visualizations must be presented in a mixed or VR environment where hardware and user interact closely. 4.2 Abstract 3D visualizations • Data that lacks a physical representation or intrinsic spatial organization is referred to as abstract data. • In visualization, abstraction is obtained by using colors and shapes that are not directly associated with the object. 4.3 Paper sampling • Paper sampling in immersive analytics refers to the process of selecting and gathering relevant research papers and publications related to immersive analytics. Conclusion and future scope • In conclusion, immersive analytics has the potential to completely transform how we work with data by facilitating deeper understanding, better decision-making, and improved teamwork. • Immersion analytics will develop further and contribute significantly to data analysis and decision support in the future by tackling issues and seizing opportunities in technological innovation, domain-specific applications, ethical issues, and user experience design.

EXPRESS:Spatial Organisation in the Human Mind as a Function of the Distance Between Stimuli.

Studies investigating serial order in working memory have shown that participants from Western cultures are faster at responding to items presented at the beginning of a sequence using their left hand and faster at responding to items at the end with their right hand. This is known as the spatial positional association of response codes (SPoARC) effect. The SPoARC effect provides evidence that recently presented information is spatially organised in the cognitive system along a horizontal axis. This study investigated the flexibility of spatialisation by testing the effect that distance between items presented on a screen has on the magnitude of the SPoARC effect. It was hypothesised that by increasing the distance between items on a screen a larger SPoARC effect would be found. We used three conditions: central, narrow, and wide. In central, four random letters were presented sequentially at the centre of the screen, in narrow the letters were presented from left to right on the screen, wide was the same as narrow but the separation between the letters was larger. Participants consisted of 64 adults aged 18-55 years old. Participants were presented with four random letters, followed by single probe letter, participants had to indicate, by pressing a key on a normal keyboard, if the probe had been in the sequence. We analysed the data with multilevel modelling. We found evidence for the SPoARC effect in all three conditions. But no evidence that the effect varied between conditions.

Bio‐Inspired Crystalline Core‐Shell Guanine Spherulites

AbstractSpherical particles with diameters within the wavelength of visible light, known as spherulites, manipulate light uniquely due to their spatial organization and their structural birefringence. Most of the known crystalline spherulites are branched, and composed of metals, alloys, and semi‐crystalline polymers. Recently, a different spherulite architecture was discovered in the vision systems of decapod crustaceans ‐ core‐shell spherulites composed of highly birefringent (Δn ∼ 30%) organic single‐crystal platelets, with exceptional optical properties. These metastructures, which efficiently scatter light even in dense aqueous environments, have no synthetic equivalence and serve as a natural proof‐of‐concept as well as synthetic inspiration for thin scattering media. Here, we present the synthesis of core‐shell spherulites composed of guanine crystal platelets (Δn ∼ 25%) in a two‐step emulsification process in which we use a water/oil/water emulsion and induced pH changes to promote interfacial crystallization. Carboxylic acids neutralize the dissolved guanine salts to form spherulites composed of single, radially stacked, β‐guanine platelets, which are oriented tangentially to the spherulite surface. Using Mie theory calculations and forward scattering measurements from single spherulites, we find that due to the single‐crystal properties and orientation, the synthetic spherulites possess a high tangential refractive index, similarly to biogenic particles.This article is protected by copyright. All rights reserved

Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs

Glioblastoma multiforme (GBM) encompasses brain malignancies marked by phenotypic and transcriptional heterogeneity thought to render these tumors aggressive, resistant to therapy, and inevitably recurrent. However, little is known about how the spatial organization of GBM genomes underlies this heterogeneity and its effects. Here, we compile a cohort of 28 patient-derived glioblastoma stem cell-like lines (GSCs) known to reflect the properties of their tumor-of-origin; six of these were primary-relapse tumor pairs from the same patient. We generate and analyze 5 kbp-resolution chromosome conformation capture (Hi-C) data from all GSCs to systematically map thousands of standalone and complex structural variants (SVs) and the multitude of neoloops arising as a result. By combining Hi-C, histone modification, and gene expression data with chromatin folding simulations, we explain how the pervasive, uneven, and idiosyncratic occurrence of neoloops sustains tumor-specific transcriptional programs via the formation of new enhancer-promoter contacts. We also show how even moderately recurrent neoloops can relate to patient-specific vulnerabilities. Together, our data provide a resource for dissecting GBM biology and heterogeneity, as well as for informing therapeutic approaches.

Ecology and social behavior of the midday gerbil Meriones meridianus: Insights from long-term research in the wild and seminatural environments

The present review provides a compilation of the published data on the ecology and social behavior of midday gerbils. Both field studies and observations under semi-natural conditions provide evidence that the midday gerbil is a nocturnal, primarily granivorous rodent that lives in highly seasonal habitats. A typical feature of the midday gerbils’ spatial organization is formation of multi-male–multi-female associations (breeding colonies) in which male home ranges overlap each other and with female ranges to a great extent, while females tend to occupy exclusive home ranges. The mating system of this species can be defined as polygynandry or promiscuity; males appear to compete for access to receptive females. The social structure in the midday gerbil is primarily based on aggressive interactions between conspecifics resulting in a dominance hierarchy among males and site-dependent dominance among females, especially during the breeding season. After the cessation of reproduction, a tendency towards more pronounced gregariousness appears, and midday gerbils form wintering groups; gerbils, however, lead solitary lives within these groups. Overall, the data presented expand our understanding of socio-ecology of gerbils.

The Impact of Geographic Factors on Credit Risk: A Study of Chinese Commercial Banks

Abstract Controlling credit risk is crucial for maintaining financial stability, and the role of geographic factors in this regard is a significant concern for scholars and policymakers. Drawing on the concept of information asymmetry, we developed a theoretical model to analyze how geographic factors influence credit risk. Our theoretical proposition suggests that the spatial organization of banks affects the efficiency of collecting and processing soft information, ultimately impacting the credit risk. To test this proposition, we collected microdata from Chinese commercial banks spanning the period from 2011 to 2022. Employing a mediating effect model, we empirically examined the relationship between spatial organizational structure and credit risk. Our results indicate that the distance between bank operations and functional distance impedes the collection and processing of soft information, thereby exacerbating credit risk in banks. The study focuses on examining how the spatial organizational structure of Chinese commercial banks affects credit risk. By analyzing geographic factors and information asymmetry, the study aims to understand how the organization of banks influences the collection and processing of soft information, which in turn impacts the credit risk. Furthermore, our analysis of the sample reveals that the mediating role of soft information varies between state-owned banks and joint-stock banks due to their distinct customer profiles. On the basis of these findings, we propose several policy recommendations, including a focus on enhancing the collection and processing of soft information, promoting the growth of locally based small and medium-sized banks, and reducing information barriers within bank hierarchies.

Molecular pixelation: spatial proteomics of single cells by sequencing.

The spatial distribution of cell surface proteins governs vital processes of the immune system such as intercellular communication and mobility. However, fluorescence microscopy has limited scalability in the multiplexing and throughput needed to drive spatial proteomics discoveries at subcellular level. We present Molecular Pixelation (MPX), an optics-free, DNA sequence-based method for spatial proteomics of single cells using antibody-oligonucleotide conjugates (AOCs) and DNA-based, nanometer-sized molecular pixels. The relative locations of AOCs are inferred by sequentially associating them into local neighborhoods using the sequence-unique DNA pixels, forming >1,000 spatially connected zones per cell in 3D. For each single cell, DNA-sequencing reads are computationally arranged into spatial proteomics networks for 76 proteins. By studying immune cell dynamics using spatial statistics on graph representations of the data, we identify known and new patterns of spatial organization of proteins on chemokine-stimulated T cells, highlighting the potential of MPX in defining cell states by the spatial arrangement of proteins.

Spatial transcriptomics in health and disease.

The ability to localize hundreds of macromolecules to discrete locations, structures and cell types in a tissue is a powerful approach to understand the cellular and spatial organization of an organ. Spatially resolved transcriptomic technologies enable mapping of transcripts at single-cell or near single-cell resolution in a multiplex manner. The rapid development of spatial transcriptomic technologies has accelerated the pace of discovery in several fields, including nephrology. Its application to preclinical models and human samples has provided spatial information about new cell types discovered by single-cell sequencing and new insights into the cell-cell interactions within neighbourhoods, and has improved our understanding of the changes that occur in response to injury. Integration of spatial transcriptomic technologies with other omics methods, such as proteomics and spatial epigenetics, will further facilitate the generation of comprehensive molecular atlases, and provide insights into the dynamic relationships of molecular components in homeostasis and disease. This Review provides an overview of current and emerging spatial transcriptomic methods, their applications and remaining challenges for the field.

ХАРАКТЕРИСТИКА МАРШРУТНОЙ СЕТИ ОБЩЕСТВЕННОГО ТРАНСПОРТА ГОРОДА БАРНАУЛА

The development of a city is closely related to the state of its transport system and the spatial organization of urban public transport. In general, a number of transport problems can be noted for the city related to the waiting time for transport, the provision of various areas with urban public transport routes, etc. These problems have become particularly relevant in the 21st century and have become very actively discussed. The article is devoted to the analysis of the route network of the city of Barnaul, as well as the number of rolling stock on the routes. Particular attention is paid to routes where there is a shortage of rolling stock. The purpose of the work is to analyze the current state of the route network of the city of Barnaul and identify problems. The main methods were literature analysis, as well as monitoring public transport using the 2GIS service. In general, it can be noted that the city’s public transport runs stably and interruptions occur due to weather conditions (in particular freezing) or traffic situations (congestion in the morning and evening); there is also a dependence of preferential traffic to the city center and from the city center to depending on the time of day.

Genome organization around nuclear speckles drives mRNA splicing efficiency.

The nucleus is highly organized, such that factors involved in thetranscription and processing of distinct classes of RNA are confined within specific nuclear bodies1,2. One example is the nuclear speckle, which is defined by high concentrations of protein and noncoding RNA regulators of pre-mRNA splicing3. What functional role, if any, speckles might play in the process of mRNA splicing is unclear4,5. Here we show that genes localized near nuclear speckles display higher spliceosome concentrations, increased spliceosome binding to their pre-mRNAs and higher co-transcriptional splicing levels than genes that are located farther from nuclear speckles. Gene organization around nuclear speckles is dynamic between cell types, and changes in speckle proximity lead to differences in splicing efficiency. Finally, directed recruitment of a pre-mRNA to nuclear speckles is sufficient to increase mRNA splicing levels. Together, our results integrate the long-standing observations of nuclear speckles with the biochemistry of mRNA splicing and demonstrate a crucial role for dynamic three-dimensional spatial organization of genomic DNA in driving spliceosome concentrations and controlling the efficiency of mRNA splicing.

Potential roles of inter-chromosomal interactions in cell fate determination

Mammalian genomic DNA is packed in a small nucleus, and its folding and organization in the nucleus are critical for gene regulation and cell fate determination. In interphase, chromosomes are compartmentalized into certain nuclear spaces and territories that are considered incompatible with each other. The regulation of gene expression is influenced by the epigenetic characteristics of topologically associated domains and A/B compartments within chromosomes (intrachromosomal). Previously, interactions among chromosomes detected via chromosome conformation capture-based methods were considered noise or artificial errors. However, recent studies based on newly developed ligation-independent methods have shown that inter-chromosomal interactions play important roles in gene regulation. This review summarizes the recent understanding of spatial genomic organization in mammalian interphase nuclei and discusses the potential mechanisms that determine cell identity. In addition, this review highlights the potential role of inter-chromosomal interactions in early mouse development.

Sustainability of Historical Buildings Through Reuse Projects: A Case Study of the Kadıköy District in Istanbul

This research focuses on the preservation and adaptive reuse of historic structures. It emphasizes the importance of conserving cultural and historical heritage, suggesting that assigning new functions to these buildings contributes to sustainability. The study progresses through successful examples of adaptive reuse of historical buildings acquired by the Kadıköy Municipality, addressing spatial, cultural, and legal dimensions. It underscores the importance of preserving the architectural characteristics, spatial organizations, and surroundings of these buildings when assigning new functions. The research advocates for minimal intervention principles in adaptive reuse projects, ensuring the historical and cultural values of the buildings are considered. Furthermore, it highlights that these projects should not only focus on physical restoration but also faster social and cultural interaction. Adaptive reuse projects in the Kadıköy region have been developed in line with these principles, creating active and functional spaces that respond to community needs. These projects successfully demonstrate how the preservation and active use of historical buildings can contribute to regional and cultural sustainability. Finally, the research addresses the challenges encountered in the preservation and adaptive reuse of historical buildings in Turkey, discussing legal, economic, and technical issues, and offers suggestions for effective strategies in this field. The aim is to increase awareness and develop efficient strategies for the preservation of Turkey’s historical structures.

Turbulence-induced droplet grouping and augmented rain formation in cumulus clouds

This paper provides the first observational analysis of how droplet separation is impacted by the flinging action of microscale vortices in turbulent clouds over a select radii range and how they vary over cloud cores and along the peripheral edges. It is premised that this mechanism initiates droplet separation within a cloud volume soon after condensational growth, largely in the cloud core, and operates until the cloud droplet radii exceed 20–30 µm when this effect fades rapidly. New observations are presented showing how microscale vortices also impact the settling rates of droplets over a critical size range (6–18 µm) causing them to sediment faster than in still air affecting swept volumes and thereby impacting the rain initiation and formation. Large-scale atmospheric models ignore these microscale effects linked to rapid droplet growth during the early stages of cloud conversion. Previous studies on droplet spatial organization along the cloud edges and inside the deep core have shown that homogeneous Poisson statistics, indicative of the presence of a vigorous in-cloud mixing process at small scales obtained, in contrast to an inhomogeneous distribution along the edges. In this paper, it is established that this marked core region, homogeneity can be linked to microscale vortical activity which flings cloud droplets in the range of 6–18 µm outward. The typical radius of the droplet trajectories or the droplet flung radii around the vortices correlates with the interparticle distance strongly. The correlation starts to diminish as one proceeds from the central core to the cloud fringes because of the added entrainment of cloud-free air. These first results imply that droplet growth in the core is first augmented with this small-scale interaction prior to other more large-scale processes involving entrainment mixing. This first study, combining these amplified velocities are included in a Weather Research and Forecasting- LES case study. Not only are significant differences observed in the cloud morphology when compared to a baseline case, but the ‘enhanced’ case also shows early commencement of rainfall along with intense precipitation activity compared to the ‘standard’ baseline case. It is also shown that the modelled equilibrium raindrop spectrum agrees better with observations when the enhanced droplet sedimentation rates mediated by microscale vortices are included in the calculations compared to the case where only still-air terminal velocities are used.

Obedience to authority as a function of the physical proximity of the student, teacher, and experimenter

ABSTRACT The authors are proposing a theoretical model explaining the behavior of individuals tested through experiments on obedience toward authority conducted according to Milgram’s paradigm. Their assumption is that the participant faces typical avoidance-avoidance conflict conditions. Participant does not want to hurt the learner in the adjacent room but he or she also does not want to harm the experimenter. The solution to this conflict, entailing hurting on of the two, may be different depending on the spatial organization of the experiment. In the study, experimental conditions were modified, so that the participant was (vs. was not) in the same room as the experimenter and was (vs. was not) in the same room as the learner. Forty individuals (20 women and 20 men) were tested in each of the four experimental conditions. It turns out that the physical presence of the experimenter was conducive to obedience, while the physical presence of the learner reduced it.