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Journal articles on the topic 'Complex Spatiotemporal Interplay of Biomolecules'

Author: Grafiati

Published: 7 September 2023

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1

Nguyen, Trung Duc, Yuan-I. Chen, Limin H. Chen, and Hsin-Chih Yeh. "Recent Advances in Single-Molecule Tracking and Imaging Techniques." Annual Review of Analytical Chemistry 16, no. 1 (2023): 253–84. http://dx.doi.org/10.1146/annurev-anchem-091922-073057.

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Since the early 1990s, single-molecule detection in solution at room temperature has enabled direct observation of single biomolecules at work in real time and under physiological conditions, providing insights into complex biological systems that the traditional ensemble methods cannot offer. In particular, recent advances in single-molecule tracking techniques allow researchers to follow individual biomolecules in their native environments for a timescale of seconds to minutes, revealing not only the distinct pathways these biomolecules take for downstream signaling but also their roles in s

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Kataria, Meghna, and Hiroyuki Yamano. "Interplay between Phosphatases and the Anaphase-Promoting Complex/Cyclosome in Mitosis." Cells 8, no. 8 (2019): 814. http://dx.doi.org/10.3390/cells8080814.

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Accurate division of cells into two daughters is a process that is vital to propagation of life. Protein phosphorylation and selective degradation have emerged as two important mechanisms safeguarding the delicate choreography of mitosis. Protein phosphatases catalyze dephosphorylation of thousands of sites on proteins, steering the cells through establishment of the mitotic phase and exit from it. A large E3 ubiquitin ligase, the anaphase-promoting complex/cyclosome (APC/C) becomes active during latter stages of mitosis through G1 and marks hundreds of proteins for destruction. Recent studies

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HILLENBRAND, ULRICH, and J. LEO van HEMMEN. "Spatiotemporal adaptation through corticothalamic loops: A hypothesis." Visual Neuroscience 17, no. 1 (2000): 107–18. http://dx.doi.org/10.1017/s0952523800171111.

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The thalamus is the major gate to the cortex and its control over cortical responses is well established. Cortical feedback to the thalamus is, in turn, the anatomically dominant input to relay cells, yet its influence on thalamic processing has been difficult to interpret. For an understanding of complex sensory processing, detailed concepts of the corticothalamic interplay need yet to be established. Drawing on various physiological and anatomical data, we elaborate the novel hypothesis that the visual cortex controls the spatiotemporal structure of cortical receptive fields via feedback to

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Miller, R. A., and B. E. Britigan. "Role of oxidants in microbial pathophysiology." Clinical Microbiology Reviews 10, no. 1 (1997): 1–18. http://dx.doi.org/10.1128/cmr.10.1.1.

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Reactive oxidant species (superoxide, hydrogen peroxide, hydroxyl radical, hypohalous acid, and nitric oxide) are involved in many of the complex interactions between the invading microorganism and its host. Regardless of the source of these compounds or whether they are produced under normal conditions or those of oxidative stress, these oxidants exhibit a broad range of toxic effects to biomolecules that are essential for cell survival. Production of these oxidants by microorganisms enables them to have a survival advantage in their environment. Host oxidant production, especially by phagocy

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Das, N. S., S. T. Dheen, E. A. Ling, B. H. Bay, and D. K. Srinivasan. "Therapeutic Prospects in Preeclampsia - A Mini-Review." Current Medicinal Chemistry 26, no. 25 (2019): 4786–98. http://dx.doi.org/10.2174/0929867326666190228115423.

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Background: Preeclapmsia (PE) is characterized by early onset symptoms such as elevated blood pressure, proteinuria and edema in the pregnant woman, and may result in seizures in the affected female. Currently, there are no therapeutic drugs available to treat this condition, but there are interventions to regulate the symptoms based on the gestational period of the fetus, although the largely favored option is delivery of the fetus and placenta. Objective: A search for biomolecules associated with PE was conducted so as to identify diagnostic markers and therapeutic leads. Results: The litera

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Zhang, Bing, Weijuan Huang, Sen Pei, et al. "Mechanisms for the circulation of influenza A(H3N2) in China: A spatiotemporal modelling study." PLOS Pathogens 18, no. 12 (2022): e1011046. http://dx.doi.org/10.1371/journal.ppat.1011046.

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Circulation of seasonal influenza is the product of complex interplay among multiple drivers, yet characterizing the underlying mechanism remains challenging. Leveraging the diverse seasonality of A(H3N2) virus and abundant climatic space across regions in China, we quantitatively investigated the relative importance of population susceptibility, climatic factors, and antigenic change on the dynamics of influenza A(H3N2) through an integrative modelling framework. Specifically, an absolute humidity driven multiscale transmission model was constructed for the 2013/2014, 2014/2015 and 2016/2017

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Abbasi, Omid, Nadine Steingräber, Nikos Chalas, Daniel S. Kluger, and Joachim Gross. "Spatiotemporal dynamics characterise spectral connectivity profiles of continuous speaking and listening." PLOS Biology 21, no. 7 (2023): e3002178. http://dx.doi.org/10.1371/journal.pbio.3002178.

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Speech production and perception are fundamental processes of human cognition that both rely on intricate processing mechanisms that are still poorly understood. Here, we study these processes by using magnetoencephalography (MEG) to comprehensively map connectivity of regional brain activity within the brain and to the speech envelope during continuous speaking and listening. Our results reveal not only a partly shared neural substrate for both processes but also a dissociation in space, delay, and frequency. Neural activity in motor and frontal areas is coupled to succeeding speech in delta

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Cowan, A. E., Y. Li, F. R. Morgan, et al. "Using the Virtual Cell Simulation Environment for Extracting Quantitative Parameters from Live Cell Fluorescence Imaging Data." Microscopy Today 17, no. 6 (2009): 36–39. http://dx.doi.org/10.1017/s1551929509991039.

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Rapid advances in fluorescence probe and imaging technologies now provide easily accessible tools for biologists to perform highly detailed analysis of molecular interactions in living cells. However it can be difficult to extract accurate parameters from these experiments because of the complex interplay of diffusion-reaction events with the morphology of the cell. As a result, only a small fraction of the available spatiotemporal information is utilized, and in many cases analysis remains at a qualitative level. The Virtual Cell (VCell, http://vcell.org) simulation environment is uniquely su

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Ruhl, C. J., R. E. Abercrombie, K. D. Smith, and I. Zaliapin. "Complex spatiotemporal evolution of the 2008 M w 4.9 Mogul earthquake swarm (Reno, Nevada): Interplay of fluid and faulting." Journal of Geophysical Research: Solid Earth 121, no. 11 (2016): 8196–216. http://dx.doi.org/10.1002/2016jb013399.

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Chen, Lijun, and Shangjing Jiang. "Spatiotemporal Polyrhythm Characteristics of Public Bicycle Mobility in Urban Chronotopes Context." ISPRS International Journal of Geo-Information 11, no. 1 (2021): 6. http://dx.doi.org/10.3390/ijgi11010006.

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Cycling rhythm performance is the result of a complex interplay between active travel demand and cycling network supply. Most studies focused on bicycle flow, but little attention has been paid to cycling rhythm changes for public bicycles. Full sample data of origin–destination enables an efficient description of network-wide cycling mobility efficiency in urban public bicycle systems. In this paper, we show how the spatiotemporal characteristics of cycling speed reveal the performance of cycling rhythms. The inference method of riding speed estimation is proposed with an unknown cycling path

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Wirth, Corina, and Hans-R. Lüscher. "Spatiotemporal Evolution of Excitation and Inhibition in the Rat Barrel Cortex Investigated With Multielectrode Arrays." Journal of Neurophysiology 91, no. 4 (2004): 1635–47. http://dx.doi.org/10.1152/jn.00950.2003.

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We investigated the spatiotemporal evolution of activity in the rat barrel cortex using multielectrode arrays (MEAs). In acute brain slices, field potentials were recorded simultaneously from 60 electrodes with high spatial and temporal resolution. This new technique allowed us to map functionally discrete barrels and to observe the interplay between the excitatory and inhibitory network. The local field potentials (LFPs) were elicited by focal electrical stimulation in layer 4 (L4). Excitation recorded in a single barrel was first confined to the stimulated barrel and subsequently spread in a

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Munaron, Luca. "A Tridimensional Model of Proangiogenic Calcium Signals in Endothelial Cells." Open Biology Journal 2, no. 1 (2009): 114–29. http://dx.doi.org/10.2174/1874196700902010114.

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Angiogenic factors, including bFGF and VEGF, induce cytosolic calcium (Cac) increases in endothelial cells, critically involved in angiogenesis progression. At low agonist concentrations, Cac elevation is mainly due to calcium entry controlled by a complex interplay between two intracellular messengers, arachidonic acid (AA) and nitric oxide (NO), released upon stimulation with proangiogenic factors: they trigger spatially localized calcium signals restricted to the cell periphery, and such a spatiotemporal pattern could contribute to the specificity of cellular responses. Based on experimenta

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Özturan, Doğancan, Tunç Morova, and Nathan A. Lack. "Androgen Receptor-Mediated Transcription in Prostate Cancer." Cells 11, no. 5 (2022): 898. http://dx.doi.org/10.3390/cells11050898.

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Androgen receptor (AR)-mediated transcription is critical in almost all stages of prostate cancer (PCa) growth and differentiation. This process involves a complex interplay of coregulatory proteins, chromatin remodeling complexes, and other transcription factors that work with AR at cis-regulatory enhancer regions to induce the spatiotemporal transcription of target genes. This enhancer-driven mechanism is remarkably dynamic and undergoes significant alterations during PCa progression. In this review, we discuss the AR mechanism of action in PCa with a focus on how cis-regulatory elements mod

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Li, Chao, Meng Cheng, Maoyan Zhu, and Timothy W. Lyons. "Heterogeneous and dynamic marine shelf oxygenation and coupled early animal evolution." Emerging Topics in Life Sciences 2, no. 2 (2018): 279–88. http://dx.doi.org/10.1042/etls20170157.

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It is generally agreed that early diversification of animals and significant rise of atmospheric and oceanic oxygen (O2) levels occurred in the Ediacaran (635–541 million years ago, Ma) and early Cambrian (ca. 541–509 Ma). The strength and nature of their relationship, however, remain unclear and debated. A recent wave of paleoredox research — with a particular focus on the fossiliferous sections in South China — demonstrates high spatial heterogeneity of oceanic O2 (redox) conditions and dynamic marine shelf oxygenation in a dominantly anoxic ocean during the Ediacaran and early Cambrian. Thi

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Frank, Lawrence R., Vitaly L. Galinsky, Leigh Orf, and Joshua Wurman. "Dynamic Multiscale Modes of Severe Storm Structure Detected in Mobile Doppler Radar Data by Entropy Field Decomposition." Journal of the Atmospheric Sciences 75, no. 3 (2018): 709–30. http://dx.doi.org/10.1175/jas-d-17-0117.1.

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Abstract The detection of complex spatially and temporally varying coherent structures in data from highly nonlinear and non-Gaussian systems is a challenging problem in a wide range of scientific disciplines. This is the case in the analysis of Doppler on Wheels (DOW) mobile Doppler radar (MDR) data where the goal is to detect rapidly evolving coherent storm structures that reflect the complex interplay of nonlinear dynamical processes. Estimating and quantifying such structures from the noisy and relatively sparsely sampled MDR data poses a difficult inverse problem for which traditional ana

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Litwin, Piotr, Beata Zybura, and Paweł Motyka. "Tactile information counteracts the attenuation of rubber hand illusion attributable to increased visuo-proprioceptive divergence." PLOS ONE 15, no. 12 (2020): e0244594. http://dx.doi.org/10.1371/journal.pone.0244594.

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Sense of body ownership is an immediate and distinct experience of one’s body as belonging to oneself. While it is well-recognized that ownership feelings emerge from the integration of visual and somatosensory signals, the principles upon which they are integrated are still intensely debated. Here, we used the rubber hand illusion (RHI) to examine how the interplay of visual, tactile, and proprioceptive signals is governed depending on their spatiotemporal properties. For this purpose, the RHI was elicited in different conditions varying with respect to the extent of visuo-proprioceptive dive

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Mentkowski, Kyle I., Lindsey M. Euscher, Akshar Patel, B. Rita Alevriadou, and Jennifer K. Lang. "Monocyte recruitment and fate specification after myocardial infarction." American Journal of Physiology-Cell Physiology 319, no. 5 (2020): C797—C806. http://dx.doi.org/10.1152/ajpcell.00330.2020.

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Monocytes are critical mediators of the inflammatory response following myocardial infarction (MI) and ischemia-reperfusion injury. They are involved in both initiation and resolution of inflammation and play an integral role in cardiac repair. The antagonistic nature of their function is dependent on their subset heterogeneity and biphasic response following injury. New advancements in single-cell transcriptomics and mass cytometry have allowed us to identify smaller, transcriptionally distinct clusters that may have functional relevance in disease and homeostasis. Additionally, recent insigh

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Dharmadana, Durga, Nicholas P. Reynolds, Charlotte E. Conn, and Céline Valéry. "Molecular interactions of amyloid nanofibrils with biological aggregation modifiers: implications for cytotoxicity mechanisms and biomaterial design." Interface Focus 7, no. 4 (2017): 20160160. http://dx.doi.org/10.1098/rsfs.2016.0160.

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Amyloid nanofibrils are ubiquitous biological protein fibrous aggregates, with a wide range of either toxic or beneficial activities that are relevant to human disease and normal biology. Protein amyloid fibrillization occurs via nucleated polymerization, through non-covalent interactions. As such, protein nanofibril formation is based on a complex interplay between kinetic and thermodynamic factors. The process entails metastable oligomeric species and a highly thermodynamically favoured end state. The kinetics, and the reaction pathway itself, can be influenced by third party moieties, eithe

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Gessner, Isabel, and Ines Neundorf. "Nanoparticles Modified with Cell-Penetrating Peptides: Conjugation Mechanisms, Physicochemical Properties, and Application in Cancer Diagnosis and Therapy." International Journal of Molecular Sciences 21, no. 7 (2020): 2536. http://dx.doi.org/10.3390/ijms21072536.

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Based on their tunable physicochemical properties and the possibility of producing cell-specific platforms through surface modification with functional biomolecules, nanoparticles (NPs) represent highly promising tools for biomedical applications. To improve their potential under physiological conditions and to enhance their cellular uptake, combinations with cell-penetrating peptides (CPPs) represent a valuable strategy. CPPs are often cationic peptide sequences that are able to translocate across biological membranes and to carry attached cargos inside cells and have thus been recognized as

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Becker, Alyssa L., and Arup K. Indra. "Oxidative Stress in Melanoma: Beneficial Antioxidant and Pro-Oxidant Therapeutic Strategies." Cancers 15, no. 11 (2023): 3038. http://dx.doi.org/10.3390/cancers15113038.

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Cutaneous melanoma ranks as the fifth most common cancer in the United States and represents one of the deadliest forms of skin cancer. While recent advances in systemic targeted therapies and immunotherapies have positively impacted melanoma survival, the survival rate of stage IV melanoma remains at a meager 32%. Unfortunately, tumor resistance can impede the effectiveness of these treatments. Oxidative stress is a pivotal player in all stages of melanoma progression, with a somewhat paradoxical function that promotes tumor initiation but hinders vertical growth and metastasis in later disea

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Guimarães, Paulo R. "The Structure of Ecological Networks Across Levels of Organization." Annual Review of Ecology, Evolution, and Systematics 51, no. 1 (2020): 433–60. http://dx.doi.org/10.1146/annurev-ecolsys-012220-120819.

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Interactions connect the units of ecological systems, forming networks. Individual-based networks characterize variation in niches among individuals within populations. These individual-based networks merge with each other, forming species-based networks and food webs that describe the architecture of ecological communities. Networks at broader spatiotemporal scales portray the structure of ecological interactions across landscapes and over macroevolutionary time. Here, I review the patterns observed in ecological networks across multiple levels of biological organization. A fundamental challe

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Gaire, Janak, Valentina Supper, Darrice Montgomery, and Chelsey S. Simmons. "Spiny mice (Acomys) cells fail to engraft in NOD scid gamma." PLOS ONE 18, no. 5 (2023): e0286000. http://dx.doi.org/10.1371/journal.pone.0286000.

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Immune cells and stromal cells regulate wound healing and regeneration through complex activation patterns with spatiotemporal variation. The scarless regeneration of Spiny mice (Acomys species) is no exception; differential activation of immune and stromal cell populations seems to play a role in its remarkable regenerative capacity. To elucidate the role and interplay of Acomys immune cells in mammalian regeneration, we sought to create Acomys-Mus chimeras by transplanting bone marrow (BM) from Acomys into NOD Scid Gamma (NSG), a severely immunodeficient mouse line often used in creating hum

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Wang, Weiqiang, and Rui Zhang. "Interplay of Active Stress and Driven Flow in Self-Assembled, Tumbling Active Nematics." Crystals 11, no. 9 (2021): 1071. http://dx.doi.org/10.3390/cryst11091071.

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Lyotropic chromonic liquid crystals (LCLCs) are a special type of hierarchical material in which self-assembled molecular aggregates are responsible for the formation of liquid crystal phases. Thanks to its unusual material properties and bio compatibility, it has found wide applications including the formation of active nematic liquid crystals. Recent experiments have uncovered tumbling character of certain LCLCs. However, how tumbling behavior modifies structure and flow in driven and active nematics is poorly understood. Here, we rely on continuum simulation to study the interplay of extens

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Kim, Kyra, and James Heiss. "Methods in Capturing the Spatiotemporal Dynamics of Flow and Biogeochemical Reactivity in Sandy Beach Aquifers: A Review." Water 13, no. 6 (2021): 782. http://dx.doi.org/10.3390/w13060782.

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Sandy beach aquifers are complex hydrological and biogeochemical systems where fresh groundwater and seawater mix. The extent of the intertidal mixing zone and the rates of circulating flows within beaches are a primary control on porewater chemistry and microbiology of the intertidal subsurface. Interplay between the hydrological and biogeochemical processes at these land-sea transition zones moderate fluxes of chemicals, particulates, heavy metals, and biota across the aquifer-ocean interface, affecting coastal water quality and nutrient loads to marine ecosystems. Thus, it is important to c

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Sajadimajd, Soraya, and Mozafar Khazaei. "Oxidative Stress and Cancer: The Role of Nrf2." Current Cancer Drug Targets 18, no. 6 (2018): 538–57. http://dx.doi.org/10.2174/1568009617666171002144228.

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Oxidative stress due to imbalance between ROS production and detoxification plays a pivotal role in determining cell fate. In response to the excessive ROS, apoptotic signaling pathway is activated to promote normal cell death. However, through deregulation of biomolecules, high amount of ROS promotes carcinogenesis in cells with defective signaling factors. In this line, NRF2 appears to be as a master regulator, which protects cells from oxidative and electrophilic stress. Nrf2 is an intracellular transcription factor that regulates the expression of a number of genes to encode anti-oxidative

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Perrella, Fulvio, Federico Coppola, Nadia Rega, and Alessio Petrone. "An Expedited Route to Optical and Electronic Properties at Finite Temperature via Unsupervised Learning." Molecules 28, no. 8 (2023): 3411. http://dx.doi.org/10.3390/molecules28083411.

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Electronic properties and absorption spectra are the grounds to investigate molecular electronic states and their interactions with the environment. Modeling and computations are required for the molecular understanding and design strategies of photo-active materials and sensors. However, the interpretation of such properties demands expensive computations and dealing with the interplay of electronic excited states with the conformational freedom of the chromophores in complex matrices (i.e., solvents, biomolecules, crystals) at finite temperature. Computational protocols combining time depend

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Fatoux-Ardore, Marie, Franck Peysselon, Anthony Weiss, Patrick Bastien, Francine Pratlong, and Sylvie Ricard-Blum. "Large-Scale Investigation of Leishmania Interaction Networks with Host Extracellular Matrix by Surface Plasmon Resonance Imaging." Infection and Immunity 82, no. 2 (2013): 594–606. http://dx.doi.org/10.1128/iai.01146-13.

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ABSTRACTWe have set up an assay to study the interactions of live pathogens with their hosts by using protein and glycosaminoglycan arrays probed by surface plasmon resonance imaging. We have used this assay to characterize the interactions ofLeishmaniapromastigotes with ∼70 mammalian host biomolecules (extracellular proteins, glycosaminoglycans, growth factors, cell surface receptors). We have identified, in total, 27 new partners (23 proteins, 4 glycosaminoglycans) of procyclic promastigotes of sixLeishmaniaspecies and 18 partners (15 proteins, 3 glycosaminoglycans) of three species of stati

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Cloete, Karen J., Žiga Šmit, and Alessandra Gianoncelli. "Multidimensional Profiling of Human Body Hairs Using Qualitative and Semi-Quantitative Approaches with SR-XRF, ATR-FTIR, DSC, and SEM-EDX." International Journal of Molecular Sciences 24, no. 4 (2023): 4166. http://dx.doi.org/10.3390/ijms24044166.

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This study aimed to assess the potential of a multidimensional approach to differentiate body hairs based on their physico-chemical properties and whether body hairs can replace the use of scalp hair in studies linked to forensic and systemic intoxication. This is the first case report controlling for confounding variables to explore the utility of multidimensional profiling of body hair using synchrotron synchrotron microbeam X-ray fluorescence (SR-XRF) for longitudinal and hair morphological region mapping) and benchtop methods, including attenuated total reflectance Fourier transform infrar

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Torok, Justin, Pedro D. Maia, Parul Verma, Christopher Mezias, and Ashish Raj. "Emergence of directional bias in tau deposition from axonal transport dynamics." PLOS Computational Biology 17, no. 7 (2021): e1009258. http://dx.doi.org/10.1371/journal.pcbi.1009258.

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Defects in axonal transport may partly underpin the differences between the observed pathophysiology of Alzheimer’s disease (AD) and that of other non-amyloidogenic tauopathies. Particularly, pathological tau variants may have molecular properties that dysregulate motor proteins responsible for the anterograde-directed transport of tau in a disease-specific fashion. Here we develop the first computational model of tau-modified axonal transport that produces directional biases in the spread of tau pathology. We simulated the spatiotemporal profiles of soluble and insoluble tau species in a mult

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Albert, Noémi. "“A Multitude of Drops.” David Mitchell’s Cloud Atlas and the Subject between Space and Time." Acta Universitatis Sapientiae, Philologica 11, no. 1 (2019): 49–63. http://dx.doi.org/10.2478/ausp-2019-0004.

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Abstract David Mitchell’s Cloud Atlas (2004) presents its readers with a “borderless world.” This borderlessness concerns space and time, with complex and interweaving spatiotemporal planes. In this fictional world, the subject will serve as an entity that brings together disparate spatialities and temporalities through an intricate symbolic web that connects the subject’s body to the world it inhabits. Numerous versions of past, present, and future run in parallel, the actual and the virtual coexist, and the text folds upon itself. The novel operates a constant state of liminality, a state th

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Fink, Charles C., Boris Slepchenko, Ion I. Moraru, James Schaff, James Watras, and Leslie M. Loew. "Morphological Control of Inositol-1,4,5-Trisphosphate–Dependent Signals." Journal of Cell Biology 147, no. 5 (1999): 929–36. http://dx.doi.org/10.1083/jcb.147.5.929.

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Inositol-1,4,5-trisphosphate (InsP3)-mediated calcium signals represent an important mechanism for transmitting external stimuli to the cell. However, information about intracellular spatial patterns of InsP3 itself is not generally available. In particular, it has not been determined how the interplay of InsP3 generation, diffusion, and degradation within complex cellular geometries can control the patterns of InsP3 signaling. Here, we explore the spatial and temporal characteristics of [InsP3]cyt during a bradykinin-induced calcium wave in a neuroblastoma cell. This is achieved by using a un

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Rathjens, Hendrik, Jens Kiesel, Michael Winchell, Jeffrey Arnold, and Robin Sur. "Technical note: Extending the SWAT model to transport chemicals through tile and groundwater flow." Hydrology and Earth System Sciences 27, no. 1 (2023): 159–67. http://dx.doi.org/10.5194/hess-27-159-2023.

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Abstract. The Soil and Water Assessment Tool (SWAT) is frequently used to simulate the transport of water-soluble chemicals in the environment such as pesticides and their metabolites originating from agricultural applications. However, the model does not simulate the transport of chemicals through subsurface tile drains and groundwater. This limitation is particularly significant in lowland regions and when simulating stable chemicals that can leach into and accumulate in groundwater. To fill this gap, the publicly available SWAT code was modified to complement the simulation of chemicals by

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Goddard, Erin, Samuel G. Solomon, and Thomas A. Carlson. "Dynamic population codes of multiplexed stimulus features in primate area MT." Journal of Neurophysiology 118, no. 1 (2017): 203–18. http://dx.doi.org/10.1152/jn.00954.2016.

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The middle-temporal area (MT) of primate visual cortex is critical in the analysis of visual motion. Single-unit studies suggest that the response dynamics of neurons within area MT depend on stimulus features, but how these dynamics emerge at the population level, and how feature representations interact, is not clear. Here, we used multivariate classification analysis to study how stimulus features are represented in the spiking activity of populations of neurons in area MT of marmoset monkey. Using representational similarity analysis we distinguished the emerging representations of moving

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Rosés, Raquel, Cristina Kadar, Charlotte Gerritsen, and Chris Rouly. "Simulating Offender Mobility: Modeling Activity Nodes from Large-Scale Human Activity Data." Journal of Artificial Intelligence Research 68 (July 9, 2020): 541–70. http://dx.doi.org/10.1613/jair.1.11831.

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In recent years, simulation techniques have been applied to investigate the spatiotemporal dynamics of crime. Researchers have instantiated mobile offenders in agent-based simulations for theory testing, experimenting with crime prevention strategies, and exploring crime prediction techniques, despite facing challenges due to the complex dynamics of crime and the lack of detailed information about offender mobility. This paper presents a simulation model to explore offender mobility, focusing on the interplay between the agent's awareness space and activity nodes. The simulation generates patt

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De Groef, Lies, Manuel Salinas-Navarro, Griet Van Imschoot, Claude Libert, Roosmarijn E. Vandenbroucke, and Lieve Moons. "Decreased TNF Levels and Improved Retinal Ganglion Cell Survival in MMP-2 Null Mice Suggest a Role for MMP-2 as TNF Sheddase." Mediators of Inflammation 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/108617.

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Matrix metalloproteinases (MMPs) have been designated as both friend and foe in the central nervous system (CNS): while being involved in many neurodegenerative and neuroinflammatory diseases, their actions appear to be indispensable to a healthy CNS. Pathological conditions in the CNS are therefore often related to imbalanced MMP activities and disturbances of the complex MMP-dependent protease network. Likewise, in the retina, various studies in animal models and human patients suggested MMPs to be involved in glaucoma. In this study, we sought to determine the spatiotemporal expression prof

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Willoughby, D., and D. M. F. Cooper. "Use of single-cell imaging techniques to assess the regulation of cAMP dynamics." Biochemical Society Transactions 34, no. 4 (2006): 468–71. http://dx.doi.org/10.1042/bst0340468.

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cAMP is a ubiquitous intracellular signalling molecule that can regulate a wide array of cellular processes. The diversity of action of this second messenger owes much to the localized generation, action and hydrolysis of cAMP within discrete subcellular regions. Further signalling specificity can be achieved by the ability of cells to modulate the frequency or incidence of such cAMP signals. Here, we discuss the use of two cAMP biosensors that measure real-time cAMP changes in the single cell, to address the mechanisms underlying the generation of dynamic cAMP signals. The first method monito

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Papanicolaou, Natali, and Alessandro Bonetti. "The New Frontier of Functional Genomics: From Chromatin Architecture and Noncoding RNAs to Therapeutic Targets." SLAS DISCOVERY: Advancing the Science of Drug Discovery 25, no. 6 (2020): 568–80. http://dx.doi.org/10.1177/2472555220926158.

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Common diseases are complex, multifactorial disorders whose pathogenesis is influenced by the interplay of genetic predisposition and environmental factors. Genome-wide association studies have interrogated genetic polymorphisms across genomes of individuals to test associations between genotype and susceptibility to specific disorders, providing insights into the genetic architecture of several complex disorders. However, genetic variants associated with the susceptibility to common diseases are often located in noncoding regions of the genome, such as tissue-specific enhancers or long noncod

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Kang, Byungho, and Orencio Duran Vinent. "The Application of CNN-Based Image Segmentation for Tracking Coastal Erosion and Post-Storm Recovery." Remote Sensing 15, no. 14 (2023): 3485. http://dx.doi.org/10.3390/rs15143485.

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Coastal erosion due to extreme events can cause significant damage to coastal communities and deplete beaches. Post-storm beach recovery is a crucial natural process that rebuilds coastal morphology and reintroduces eroded sediment to the subaerial beach. However, monitoring the beach recovery, which occurs at various spatiotemporal scales, presents a significant challenge. This is due to, firstly, the complex interplay between factors such as storm-induced erosion, sediment availability, local topography, and wave and wind-driven sand transport; secondly, the complex morphology of coastal are

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Canning, Anna Rose, Peer Fietzek, Gregor Rehder, and Arne Körtzinger. "Technical note: Seamless gas measurements across the land–ocean aquatic continuum – corrections and evaluation of sensor data for CO<sub>2</sub>, CH<sub>4</sub> and O<sub>2</sub> from field deployments in contrasting environments." Biogeosciences 18, no. 4 (2021): 1351–73. http://dx.doi.org/10.5194/bg-18-1351-2021.

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Abstract. The ocean and inland waters are two separate regimes, with concentrations in greenhouse gases differing on orders of magnitude between them. Together, they create the land–ocean aquatic continuum (LOAC), which comprises itself largely of areas with little to no data with regards to understanding the global carbon system. Reasons for this include remote and inaccessible sample locations, often tedious methods that require collection of water samples and subsequent analysis in the lab, and the complex interplay of biological, physical and chemical processes. This has led to large incon

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Mosconi, Enrico Maria, Andrea Colantoni, Filippo Gambella, Eva Cudlinová, Luca Salvati, and Jesús Rodrigo-Comino. "Revisiting the Environmental Kuznets Curve: The Spatial Interaction between Economy and Territory." Economies 8, no. 3 (2020): 74. http://dx.doi.org/10.3390/economies8030074.

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A complex interplay of socio-ecological drivers of change exists at the different spatiotemporal scales affecting environmental degradation. This is a key issue worldwide and needs to be understood to develop efficient management solutions. One of the most applied theories in the regional analysis is the U-shaped relationship between environmental degradation and the level of income in a given economic system or Environmental Kuznets Curve (EKC). Specifically, the EKC hypothesis underlines the (potentially positive) role of formal responses to environmental degradation grounded on government p

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Tlili, S., J. Yin, J. F. Rupprecht, et al. "Shaping the zebrafish myotome by intertissue friction and active stress." Proceedings of the National Academy of Sciences 116, no. 51 (2019): 25430–39. http://dx.doi.org/10.1073/pnas.1900819116.

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Organ formation is an inherently biophysical process, requiring large-scale tissue deformations. Yet, understanding how complex organ shape emerges during development remains a major challenge. During zebrafish embryogenesis, large muscle segments, called myotomes, acquire a characteristic chevron morphology, which is believed to aid swimming. Myotome shape can be altered by perturbing muscle cell differentiation or the interaction between myotomes and surrounding tissues during morphogenesis. To disentangle the mechanisms contributing to shape formation of the myotome, we combine single-cell

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Dentith, Jennifer E., Ruza F. Ivanovic, Lauren J. Gregoire, Julia C. Tindall, and Laura F. Robinson. "Simulating stable carbon isotopes in the ocean component of the FAMOUS general circulation model with MOSES1 (XOAVI)." Geoscientific Model Development 13, no. 8 (2020): 3529–52. http://dx.doi.org/10.5194/gmd-13-3529-2020.

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Abstract. Ocean circulation and the marine carbon cycle can be indirectly inferred from stable and radiogenic carbon isotope ratios (δ13C and Δ14C, respectively), measured directly in the water column, or recorded in geological archives such as sedimentary microfossils and corals. However, interpreting these records is non-trivial because they reflect a complex interplay between physical and biogeochemical processes. By directly simulating multiple isotopic tracer fields within numerical models, we can improve our understanding of the processes that control large-scale isotope distributions an

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Chakraborty, Trisha, Debashish Das, Rafiq Hamdi, Ansar Khan, and Dev Niyogi. "Large-Scale Urban Heating and Pollution Domes over the Indian Subcontinent." Remote Sensing 15, no. 10 (2023): 2681. http://dx.doi.org/10.3390/rs15102681.

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The unique geographical diversity and rapid urbanization across the Indian subcontinent give rise to large-scale spatiotemporal variations in urban heating and air emissions. The complex relationship between geophysical parameters and anthropogenic activity is vital in understanding the urban environment. This study analyses the characteristics of heating events using aerosol optical depth (AOD) level variability, across 43 urban agglomerations (UAs) with populations of a million or more, along with 13 industrial districts (IDs), and 14 biosphere reserves (BRs) in the Indian sub-continent. Pre

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Canepa, Federico, Massimiliano Burlando, Horia Hangan, and Djordje Romanic. "Experimental Investigation of the Near-Surface Flow Dynamics in Downburst-like Impinging Jets Immersed in ABL-like Winds." Atmosphere 13, no. 4 (2022): 621. http://dx.doi.org/10.3390/atmos13040621.

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Downburst winds are strong downdrafts of cold air that embed into the atmospheric boundary layer (ABL) and produce intense horizontal outflow upon impingement on the ground. They are highly transient and three-dimensional extreme wind phenomena with a limited spatiotemporal structure that often makes the anemometric measurements in nature inadequate for reconstructing their complex flow fields. In the framework of the project THUNDERR, an experimental campaign on downburst outflows has been carried out at the WindEEE Dome at Western University, Canada. The present study analyzes the three-dime

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Atasoy, Selen, Gustavo Deco, Morten L. Kringelbach, and Joel Pearson. "Harmonic Brain Modes: A Unifying Framework for Linking Space and Time in Brain Dynamics." Neuroscientist 24, no. 3 (2017): 277–93. http://dx.doi.org/10.1177/1073858417728032.

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A fundamental characteristic of spontaneous brain activity is coherent oscillations covering a wide range of frequencies. Interestingly, these temporal oscillations are highly correlated among spatially distributed cortical areas forming structured correlation patterns known as the resting state networks, although the brain is never truly at “rest.” Here, we introduce the concept of harmonic brain modes—fundamental building blocks of complex spatiotemporal patterns of neural activity. We define these elementary harmonic brain modes as harmonic modes of structural connectivity; that is, connect

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Costa, M., K. N. Dodds, L. Wiklendt, N. J. Spencer, S. J. H. Brookes, and P. G. Dinning. "Neurogenic and myogenic motor activity in the colon of the guinea pig, mouse, rabbit, and rat." American Journal of Physiology-Gastrointestinal and Liver Physiology 305, no. 10 (2013): G749—G759. http://dx.doi.org/10.1152/ajpgi.00227.2013.

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Gastrointestinal motility involves interactions between myogenic and neurogenic processes intrinsic to the gut wall. We have compared the presence of propagating myogenic contractions of the isolated colon in four experimental animals (guinea pig, mouse, rabbit, and rat), following blockade of enteric neural activity. Isolated colonic preparations were distended with fluid, with the anal end either closed or open. Spatiotemporal maps of changes in diameter were constructed from video recordings. Distension-induced peristaltic contractions were abolished by tetrodotoxin (TTX; 0.6 μM) in all ani

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Corniani, Giulia, Miguel A. Casal, Stefano Panzeri, and Hannes P. Saal. "Population coding strategies in human tactile afferents." PLOS Computational Biology 18, no. 12 (2022): e1010763. http://dx.doi.org/10.1371/journal.pcbi.1010763.

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Sensory information is conveyed by populations of neurons, and coding strategies cannot always be deduced when considering individual neurons. Moreover, information coding depends on the number of neurons available and on the composition of the population when multiple classes with different response properties are available. Here, we study population coding in human tactile afferents by employing a recently developed simulator of mechanoreceptor firing activity. First, we highlight the interplay of afferents within each class. We demonstrate that the optimal afferent density to convey maximal

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Joshi, Lalit Mohan, Lung-Chih Tsai, and Shin-Yi Su. "Wavenumber-4 Structure in COSMIC-2 Observations: Vertical Plane Perspective." Remote Sensing 15, no. 8 (2023): 2105. http://dx.doi.org/10.3390/rs15082105.

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High-rate radio occultation (RO) in COSMIC-2 (FORMOSAT7) enables us to investigate the finer details of the ionosphere owing to the measurements being made at a significantly high spatiotemporal resolution, which was unthinkable a decade ago. In the vertical plane, local-time ionospheric wavenumber-4 (WN4) structures display tilted phase-fronts over the equatorial ionization anomaly (EIA) belt. The longitudinal extent of a tilted WN4 phase-front approximates the zonal wavelength of nonmigrating DE3 tide in the local-time frame of reference, i.e., ~900. The WN4-filtered (residual) component ind

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Lombardi, Aniello, Peter Jedlicka, Heiko Luhmann, and Werner Kilb. "Interactions between Membrane Resistance, GABA-A Receptor Properties, Bicarbonate Dynamics and Cl−-Transport Shape Activity-Dependent Changes of Intracellular Cl− Concentration." International Journal of Molecular Sciences 20, no. 6 (2019): 1416. http://dx.doi.org/10.3390/ijms20061416.

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The effects of ionotropic γ-aminobutyric acid receptor (GABA-A, GABAA) activation depends critically on the Cl−-gradient across neuronal membranes. Previous studies demonstrated that the intracellular Cl−-concentration ([Cl−]i) is not stable but shows a considerable amount of activity-dependent plasticity. To characterize how membrane properties and different molecules that are directly or indirectly involved in GABAergic synaptic transmission affect GABA-induced [Cl−]i changes, we performed compartmental modeling in the NEURON environment. These simulations demonstrate that GABA-induced [Cl−]

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Mahul-Mellier, Anne-Laure, Johannes Burtscher, Niran Maharjan та ін. "The process of Lewy body formation, rather than simply α-synuclein fibrillization, is one of the major drivers of neurodegeneration". Proceedings of the National Academy of Sciences 117, № 9 (2020): 4971–82. http://dx.doi.org/10.1073/pnas.1913904117.

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Parkinson’s disease (PD) is characterized by the accumulation of misfolded and aggregated α-synuclein (α-syn) into intraneuronal inclusions named Lewy bodies (LBs). Although it is widely believed that α-syn plays a central role in the pathogenesis of PD, the processes that govern α-syn fibrillization and LB formation remain poorly understood. In this work, we sought to dissect the spatiotemporal events involved in the biogenesis of the LBs at the genetic, molecular, biochemical, structural, and cellular levels. Toward this goal, we further developed a seeding-based model of α-syn fibrillizatio

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