Search Results (67)

Diffusion basis spectrum imaging–derived restricted fraction (DBSI-RF) isolates the low apparent diffusion coefficient water signal attributed to cellular crowding. It is therefore proposed as a putative magnetic resonance imaging (MRI) marker of neuroinflammation. The purpose of this narrative review is to evaluate animal and human studies that compared DBSI-RF with histopathological benchmarks and clinical parameters. Across inflammatory demyelination, viral encephalitis, traumatic brain injury, and neurodegenerative disorders, DBSI-RF correlated moderately to strongly with immune cell density and distinguished inflammation from demyelinating or axonal pathology. In acute multiple sclerosis, combined isotropic fractions predicted lesion evolution, clinical subtypes, and deep-learning models that included DBSI-RF classified lesion subtypes with high accuracy. DBSI-RF might also be used to track putative neuroinflammation associated with psychosocial stress, mood disorders, and anxiety disorders. The strengths of the method include sensitivity to subclinical changes and the concurrent mapping of coexisting edema, demyelination, and axon loss. Limitations include non-specific etiology features, a demanding acquisition protocol, and limited large-scale human validation. Overall, DBSI-RF may demonstrate a promising diagnostic and prognostic accuracy, warranting standardized, multicenter, prospective trials and external validation. Full article

The assessment of a ligand’s activity is typically established by measuring its binding affinity in a biochemical assay, often expressed as K_a or K_d values. Further validation of its biological activity is achieved through cellular assays. There is frequently an inconsistency between the activity values obtained from those assays, which could delay research progress as well as drug development. Factors such as the permeability, solubility, specificity, and stability of active compounds are usually held responsible for this discrepancy. Even when these values are known, inconsistencies in activity measurements remain challenging to explain. This is not surprising since intracellular physicochemical conditions are undoubtedly different from the simplified conditions used in most in vitro biochemical assays. It is therefore reasonable to assume that these differences would be minimized if biochemical measurements were performed under conditions that more accurately mimic the intracellular environment. These physicochemical conditions can alter the K_d values. While the cellular environment has been extensively studied for decades, more recent efforts have focused on obtaining equilibrium and kinetic data directly from in-cell environments. Clarifying molecular crowding, salt composition, and lipophilic parameters inside the cell and thus their effect on molecular equilibrium is a crucial step toward replicating the intracellular environment. Full article

The growing participation of elderly individuals in cruise tourism introduces asymmetry in passenger mobility and perception, posing challenges for onboard emergency evacuation. To address this, an interactive cellular automata model that enables dynamic human–signage interaction, incorporating age-dependent variations in walking speed and visual field. The model simulates passenger behavior during evacuation by integrating a static potential field, signage attraction, and directional guidance mechanisms. A bi-objective optimization framework is proposed to determine the optimal signage layout for symmetrical cruise ship theaters, balancing evacuation effectiveness across age groups with design constraints such as economic considerations. The optimization uses a genetic algorithm through simulation experiments under varying age compositions and smoke concentration levels. Results indicate that age-sensitive and interactive signage design substantially enhances evacuation efficiency, particularly for elderly passengers and under limited visibility conditions. This study offers practical insights into signage layout strategies for enhancing shipboard evacuation safety in diverse demographic and environmentally complex scenarios. Full article

In order to investigate the influence of factors such as pheromones and avoidance behavior on the evacuation of heterogeneous crowds, a multi-speed cellular automata evacuation model based on asymmetric competitiveness is proposed for the evacuation of the complex groups in a single-exit room. By optimizing the crowd density and pedestrian speed equations, multi-speed heterogeneous crowds can be obtained in the model. In order to achieve the description of a multi-dimensional asymmetric competitiveness heterogeneous population, the evacuation competitiveness is considered in the pedestrians with different speed, age, gender, etc., and by considering the avoidance character existing among pedestrians, the avoidance behavior is also discussed in this model. It is well known that the information received by different pedestrians is different. In order to consider the asymmetry of information, the pheromones are introduced into the evacuation model to discuss the effect of information differences on evacuation. The evacuation results show that the asymmetry of information has a facilitating effect on the evacuation speed of pedestrians, and the best evacuation effect is obtained when the radius of the pheromone is about 3 m. Moreover, evacuation time is weakly correlated with pedestrians’ gender but strongly correlated with pedestrians’ age. The avoidance behavior plays a positive role in evacuation, and the evacuation time reaches the minimum value when the avoidance probability is about 0.5. The slope of the reduction in evacuation time is greatest when the avoidance threshold is 0.4 to 0.8. The findings can support evacuation capacity assessment, emergency planning, and decision making. Full article

Background: The diagnostic challenges presented by hyperchromatic crowded cell groups (HCGs) in cervical cytology often result in either overdiagnosis or underdiagnosis due to their densely packed, three-dimensional structures. The objective of this study is to characterize the structural differences among HSIL-HCGs, AGC-HCGs, and NILM-HCGs using quantitative texture analysis metrics, with the aim of facilitating the differentiation of benign from malignant cases. Methods: A total of 585 HCGs images were analyzed, with assessments conducted on 8-bit gray-scale value, thickness, skewness, and kurtosis across various groups. Results: HSIL-HCGs are distinctly classified based on 8-bit gray-scale value. Significant statistical differences were observed in all groups, with HSIL-HCGs exhibiting higher cellular density and cluster thickness compared to NILM and AGC groups. In the AGC group, HCGs shows statistically significant differences in 8-bit gray-scale value compared to NILM-HCGs, but the classification performance by 8-bit gray-scale value is not high because the cell density and thickness are almost similar. These variations reflect the characteristic cellular structures unique to each group and substantiate the potential of 8-bit gray-scale value as an objective diagnostic indicator, especially for HSIL-HCGs. Conclusion: Our findings indicate that the integration of gray-scale-based texture analysis has the potential to improve diagnostic accuracy in cervical cytology and break through current diagnostic limitations in the identification of high-risk lesions. Full article

The 1-anilino-8-naphthalenesulfonate (ANS) fluorescent dye is widely used in protein folding studies due to the significant increase in its fluorescence quantum yield upon binding to protein hydrophobic regions that become accessible during protein unfolding. However, when modeling cellular macromolecular crowding conditions in protein folding experiments in vitro using crowding agents with guanidine hydrochloride (GdnHCl) as the denaturant, the observed changes in ANS spectral characteristics require careful consideration. This study demonstrates that crowding agents can form clusters that interact differently with ANS. Furthermore, GdnHCl can disrupt these clusters and directly affect the ANS spectral characteristics. A model for the interaction between GdnHCl, crowders, and ANS is proposed. Using bovine serum albumin (BSA) as a model protein, the limitations of using ANS for studying conformational transitions induced by GdnHCl in the presence of crowding agents are demonstrated. Full article

Water exists in the beginning and hydrates all matter. Life emerged in water, requiring three essential components in compartmentalized spaces: (1) universal energy sources driving biochemical reactions and processes, (2) molecules that store, encode, and transmit information, and (3) functional players carrying out biological activities and structural organization. Phosphorus has been selected to create adenosine triphosphate (ATP) as the universal energy currency, nucleic acids for genetic information storage and transmission, and phospholipids for cellular compartmentalization. Meanwhile, proteins composed of 20 α-amino acids have evolved into extremely diverse three-dimensional forms, including folded domains, intrinsically disordered regions (IDRs), and membrane-bound forms, to fulfill functional and structural roles. This review examines several unique findings: (1) insoluble proteins, including membrane proteins, can become solubilized in unsalted water, while folded cytosolic proteins can acquire membrane-inserting capacity; (2) Hofmeister salts affect protein stability by targeting hydration; (3) ATP biphasically modulates liquid–liquid phase separation (LLPS) of IDRs; (4) ATP antagonizes crowding-induced protein destabilization; and (5) ATP and triphosphates have the highest efficiency in inducing protein folding. These findings imply the following: (1) hydration might be encoded in protein sequences, central to manifestation and modulation of protein structures, dynamics, and functionalities; (2) phosphate anions have a unique capacity in enhancing μs-ms protein dynamics, likely through ionic state exchanges in the hydration shell, underpinning ATP, polyphosphate, and nucleic acids as molecular chaperones for protein folding; and (3) ATP, by linking triphosphate with adenosine, has acquired the capacity to spacetime-specifically release energy and modulate protein hydration, thus possessing myriad energy-dependent and -independent functions. In light of the success of AlphaFolds in accurately predicting protein structures by neural networks that store information as distributed patterns across nodes, a fundamental question arises: Could cellular networks also handle information similarly but with more intricate coding, diverse topological architectures, and spacetime-specific ATP energy supply in membrane-compartmentalized aqueous environments? Full article

Despite the promising potential of cell-based therapies developed using tissue engineering techniques to treat a wide range of diseases, including limbal stem cell deficiency (LSCD), which leads to corneal blindness, their commercialization remains constrained. This is primarily attributable to the limited cell sources, the use of non-standardizable, unscalable, and unsustainable techniques, and the extended manufacturing processes required to produce transplantable tissue-like surrogates. Herein, we present the first demonstration of the potential of a novel approach combining collagen films (CF), hyaluronic acid (HA), human telomerase-immortalized limbal epithelial stem cells (T-LESCs), and macromolecular crowding (MMC) to develop innovative biomimetic substrates for limbal epithelial stem cells (LESCs). The initial step involved the fabrication and characterization of CF and CF enriched with HA (CF-HA). Subsequently, T-LESCs were seeded on CF, CF-HA, and tissue culture plastic (TCP). Thereafter, the effect of these matrices on basic cellular function and tissue-specific extracellular matrix (ECM) deposition with or without MMC was evaluated. The viability and metabolic activity of cells cultured on CF, CF-HA, and TCP were found to be similar, while CF-HA induced the highest (p < 0.05) cell proliferation. It is notable that CF and HA induced cell growth, whereas MMC increased (p < 0.05) the deposition of collagen IV, fibronectin, and laminin in the T-LESC culture. The data highlight the potential of, in particular, immortalized cells and MMC for the development of biomimetic cell culture substrates, which could be utilized in ocular surface reconstruction following further in vitro, in vivo, and clinical validation of the approach. Full article

The pathological process of prion diseases implicates that the normal physiological cellular prion protein (PrP^C) converts into misfolded abnormal scrapie prion (PrP^Sc) through post-translational modifications that increase β-sheet conformation. We recently demonstrated that HuPrP(90–231) thermal unfolding is partially irreversible and characterized by an intermediate state (β-PrPI), which has been revealed to be involved in the initial stages of PrP^C fibrillation, with a seeding activity comparable to that of human infectious prions. In this study, we report the thermal unfolding characterization, in cell-mimicking conditions, of the truncated (HuPrP(90–231)) and full-length (HuPrP(23–231)) human prion protein by means of CD and NMR spectroscopy, revealing that HuPrP(90–231) thermal unfolding is characterized by two successive transitions, as in buffer solution. The amyloidogenic propensity of HuPrP(90–231) under crowded conditions has also been investigated. Our findings show that although the prion intermediate, structurally very similar to β-PrPI, forms at a lower temperature compared to when it is dissolved in buffer solution, in cell-mimicking conditions, the formation of prion fibrils requires a longer incubation time, outlining how molecular crowding influences both the equilibrium states of PrP and its kinetic pathways of folding and aggregation. Full article

This study presents a novel approach to enhancing indoor navigation in crowded multi-terminal airports using visible light communication (VLC) technology. By leveraging existing luminaires as transmission points, encoded messages are conveyed through modulated light signals to provide location-specific guidance. The objectives are to facilitate navigation, optimize routes, and improve system performance through Edge/Fog integration. The methodology includes the use of tetrachromatic LED-equipped luminaires with On–Off Keying (OOK) modulation and a mesh cellular hybrid structure. Detailed airport modeling and user analysis (pedestrians and luggage/passenger carriers) equipped with PINPIN optical sensors are conducted. A VLC-specific communication protocol with coding and decoding techniques ensures reliable data transmission, while wayfinding algorithms offer real-time guidance. The results show effective data transmission and localization, enabling self-localization, travel direction inference, and route optimization. Agent-based simulations demonstrate improved traffic control, with analyses of user halting and average speed. This approach provides reliable indoor navigation independent of GPS signals, enhancing accessibility and convenience for airport users. The integration of VLC with Edge/Fog architecture ensures efficient movement through complex airport layouts. Full article

Understanding the spatial distribution (SD) of unicellular organisms is crucial for comprehending population dynamics and adaptive strategies at the microbial scale. These behaviors include the formation of ordered structures through intercellular interactions and the broader implications for ecosystem interactions. In this study, the spatial distribution of the motile unicellular alga Chlamydomonas reinhardtii was investigated, with a focus on high-density conditions approximated by an area fraction of φ = 10%. Cell counting was carried out by image analysis, which applies the quasi-two-dimensional observation technique developed in our previous studies to analyze cell interactions in microspaces with thicknesses of 80 µm and 200 µm using both variance-to-mean ratio (VMR) and Eberhardt statistics (ES). The study reveals that experimental results, when evaluated using both VMR and ES, confirmed a similar trend and a density-dependent transition in cellular interaction. This transition ranges from swarming at lower densities to dispersal at higher densities, with a critical boundary observed at approximately φ = 8%. The findings suggest that cell behavior in dense populations shifts due to limited space and resources, offering a new perspective on the adaptive strategies of cells. These insights could enhance understanding of the mechanisms governing cell behavior in crowded environments. Full article

With the development of civil engineering, lightweight and high-strength materials, as well as large-span, low-frequency structural systems, are increasingly used. However, its self-oscillation frequency is often close to the stride frequency of pedestrians, which is easily affected by human activities. To study the effect of human activities on the dynamic response of structures, it is crucial to choose an appropriate anthropogenic load model. Considering the inter-subject and intra-subject variability of pedestrian walking parameters and induced forces in a crowd, we introduce the interaction rules between pedestrians based on the floor field cellular automata (FFCA). A stochastic crowd-loading model coupling walking parameters, induced forces between pedestrians, and induced forces between pedestrians and structures is proposed for simulating crowd-walking loads. The feasibility of the model is verified by comparing the measured response of a space large-span structure with the predicted response of the proposed stochastic crowd-loading model. The comfort level of the structure under different crowd densities was also evaluated based on the model. It was found that both random combinations of walking parameters and dynamic behaviors of pedestrians can cause significant differences in the structural response. Therefore, the crowd-loading model should consider the influence of pedestrian behavioral factors on the structural response. Full article

Even though tissue-engineered medicines are under intense academic, clinical, and commercial investigation, only a handful of products have been commercialised, primarily due to the costs associated with their prolonged manufacturing. While macromolecular crowding has been shown to enhance and accelerate extracellular matrix deposition in eukaryotic cell culture, possibly offering a solution in this procrastinating tissue-engineered medicine development, there is still no widely accepted macromolecular crowding agent. With these in mind, we herein assessed the potential of gum Arabic, gum gellan, gum karaya, and gum xanthan as macromolecular crowding agents in WS1 skin fibroblast cultures (no macromolecular crowding and carrageenan were used as a control). Dynamic light scattering analysis revealed that all macromolecules had negative charge and were polydispersed. None of the macromolecules affected basic cellular function. At day 7 (the longest time point assessed), gel electrophoresis analysis revealed that all macromolecules significantly increased collagen type I deposition in comparison to the non-macromolecular crowding group. Also at day 7, immunofluorescence analysis revealed that carrageenan; the 50 µg/mL, 75 µg/mL, and 100 µg/mL gum gellan; and the 500 µg/mL and 1000 µg/mL gum xanthan significantly increased both collagen type I and collagen type III deposition and only carrageenan significantly increased collagen type V deposition, all in comparison to the non-macromolecular crowding group at the respective time point. This preliminary study demonstrates the potential of gums as macromolecular crowding agents, but more detailed biological studies are needed to fully exploit their potential in the development of tissue-engineered medicines. Full article

Proteins in the crowded environment of human cells have often been studied regarding nonspecific interactions, misfolding, and aggregation, which may cause cellular malfunction and disease. Specifically, proteins with high abundance are more susceptible to these issues due to the law of mass action. Therefore, the surfaces of highly abundant cytoplasmic (HAC) proteins directly exposed to the environment can exhibit specific physicochemical, structural, and geometrical characteristics that reduce nonspecific interactions and adapt to the environment. However, the quantitative relationships between the overall surface descriptors still need clarification. Here, we used machine learning to identify HAC proteins using hydrophobicity, charge, roughness, secondary structures, and B-factor from the protein surfaces and quantified the contribution of each descriptor. First, several supervised learning algorithms were compared to solve binary classification problems for the surfaces of HAC and extracellular proteins. Then, logistic regression was used for the feature importance analysis of descriptors considering model performance (80.2% accuracy and 87.6% AUC) and interpretability. The HAC proteins showed positive correlations with negatively and positively charged areas but negative correlations with hydrophobicity, the B-factor, the proportion of beta structures, roughness, and the proportion of disordered regions. Finally, the details of each descriptor could be explained concerning adaptative surface strategies of HAC proteins to regulate nonspecific interactions, protein folding, flexibility, stability, and adsorption. This study presented a novel approach using various surface descriptors to identify HAC proteins and provided quantitative design rules for the surfaces well-suited to human cellular crowded environments. Full article

The cellular environment is highly crowded, with up to 40% of the volume fraction of the cell occupied by various macromolecules. Most laboratory experiments take place in dilute buffer solutions; by adding various synthetic or organic macromolecules, researchers have begun to bridge the gap between in vitro and in vivo measurements. This is a review of the reported effects of macromolecular crowding on the compaction and extension of DNA, the effect of macromolecular crowding on DNA kinetics, and protein-DNA interactions. Theoretical models related to macromolecular crowding and DNA are briefly reviewed. Gaps in the literature, including the use of biologically relevant crowders, simultaneous use of multi-sized crowders, empirical connections between macromolecular crowding and liquid–liquid phase separation of nucleic materials are discussed. Full article