Journal articles: 'Proximity Interaction'

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Setiyana, Rusma, Nyak Mutia Ismail, Endah Annisa Rahma, and Faizatul Husna. "An Investigation of Proxemic Behavior among Acehnese in Public Places." Celt: A Journal of Culture, English Language Teaching & Literature 18, no. 2 (December 29, 2018): 187. http://dx.doi.org/10.24167/celt.v18i2.1272.

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It is assumed that Acehnese do not make use of personal space during interactions. This study aims to investigate the proximity levels used by Acehnese people when communicating with other people. The observation approach was used to collect data with people who were in natural interaction in public places as the participant. The data were pictured and kept anonymous in regards of ethical codes maintained in research. The results show that there are three conditions obtained from this study. First, mostly, Acehnese people use intimate level of proximity, which is less than 0.46 meter eventhough when they are interacting with strangers. However, this condition only applies if the interactions taking place is male-male interactions or female-female interactions. Second, in a condition where the stranger interaction is male-female, the proximity employed by the people is in the level of personal—which is 1.2 meter. Lastly, men maintained farther distance compared to women. In conclusion, the farthest proximity level that Acehnese applied was social level (1.2 m to 3.7 m); yet, the main influencing factor is genders.

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Tang, Jeff K. T., Jacky C. P. Chan, Howard Leung, and Taku Komura. "Interaction Retrieval by Spacetime Proximity Graphs." Computer Graphics Forum 31, no. 2pt4 (May 2012): 745–54. http://dx.doi.org/10.1111/j.1467-8659.2012.03033.x.

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Teo, L. P. "Massive scalar Casimir interaction beyond proximity force approximation." International Journal of Modern Physics A 30, no. 27 (September 30, 2015): 1550167. http://dx.doi.org/10.1142/s0217751x15501675.

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Since massive scalar field plays an important role in theoretical physics, we consider the interaction between a sphere and a plate due to the vacuum fluctuation of a massive scalar field. We consider combinations of Dirichlet and Neumann boundary conditions. There is a simple prescription to obtain the functional formulas for the Casimir interaction energies, known as TGTG formula, for the massive interactions from the massless interactions. From the TGTG formulas, we discuss how to compute the small separation asymptotic expansions of the Casimir interaction energies up to the next-to-leading order terms. Unlike the massless case, the results could not be expressed as simple algebraic expressions, but instead could only be expressed as infinite sums over some integrals. Nonetheless, it is easy to show that one can obtain the massless limits which agree with previously established results. We also show that the leading terms agree with that derive using proximity force approximation. The dependence of the leading order terms and the next-to-leading order terms on the mass of the scalar field is studied both numerically and analytically. In particular, we derive the small mass asymptotic expansions of these terms. Surprisingly, the small mass asymptotic expansions are quite complicated as they contain terms that are of odd powers in mass as well as logarithms of mass terms.

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Levin, Iris I., David M. Zonana, Bailey K. Fosdick, Se Jin Song, Rob Knight, and Rebecca J. Safran. "Stress response, gut microbial diversity and sexual signals correlate with social interactions." Biology Letters 12, no. 6 (June 2016): 20160352. http://dx.doi.org/10.1098/rsbl.2016.0352.

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Theory predicts that social interactions are dynamically linked to phenotype. Yet because social interactions are difficult to quantify, little is known about the precise details on how interactivity is linked to phenotype. Here, we deployed proximity loggers on North American barn swallows ( Hirundo rustica erythrogaster ) to examine intercorrelations among social interactions, morphology and features of the phenotype that are sensitive to the social context: stress-induced corticosterone (CORT) and gut microbial diversity. We analysed relationships at two spatial scales of interaction: (i) body contact and (ii) social interactions occurring between 0.1 and 5 m. Network analysis revealed that relationships between social interactions, morphology, CORT and gut microbial diversity varied depending on the sexes of the individuals interacting and the spatial scale of interaction proximity. We found evidence that body contact interactions were related to diversity of socially transmitted microbes and that looser social interactions were related to signalling traits and CORT.

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Weissinger, Ronja, Lisa Heinold, Saira Akram, Ralf-Peter Jansen, and Orit Hermesh. "RNA Proximity Labeling: A New Detection Tool for RNA–Protein Interactions." Molecules 26, no. 8 (April 14, 2021): 2270. http://dx.doi.org/10.3390/molecules26082270.

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Multiple cellular functions are controlled by the interaction of RNAs and proteins. Together with the RNAs they control, RNA interacting proteins form RNA protein complexes, which are considered to serve as the true regulatory units for post-transcriptional gene expression. To understand how RNAs are modified, transported, and regulated therefore requires specific knowledge of their interaction partners. To this end, multiple techniques have been developed to characterize the interaction between RNAs and proteins. In this review, we briefly summarize the common methods to study RNA–protein interaction including crosslinking and immunoprecipitation (CLIP), and aptamer- or antisense oligonucleotide-based RNA affinity purification. Following this, we focus on in vivo proximity labeling to study RNA–protein interactions. In proximity labeling, a labeling enzyme like ascorbate peroxidase or biotin ligase is targeted to specific RNAs, RNA-binding proteins, or even cellular compartments and uses biotin to label the proteins and RNAs in its vicinity. The tagged molecules are then enriched and analyzed by mass spectrometry or RNA-Seq. We highlight the latest studies that exemplify the strength of this approach for the characterization of RNA protein complexes and distribution of RNAs in vivo.

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Do, Trinh Minh Tri, and Daniel Gatica-Perez. "Human interaction discovery in smartphone proximity networks." Personal and Ubiquitous Computing 17, no. 3 (December 14, 2011): 413–31. http://dx.doi.org/10.1007/s00779-011-0489-7.

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Wang, Kun, Mahashweta Basu, Justin Malin, and Sridhar Hannenhalli. "A transcription-centric model of SNP-age interaction." PLOS Genetics 17, no. 3 (March 26, 2021): e1009427. http://dx.doi.org/10.1371/journal.pgen.1009427.

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Complex age-associated phenotypes are caused, in part, by an interaction between an individual’s genotype and age. The mechanisms governing such interactions are however not entirely understood. Here, we provide a novel transcriptional mechanism-based framework–SNiPage, to investigate such interactions, whereby a transcription factor (TF) whose expression changes with age (age-associated TF), binds to a polymorphic regulatory element in an allele-dependent fashion, rendering the target gene’s expression dependent on both, the age and the genotype. Applying SNiPage to GTEx, we detected ~637 significant TF-SNP-Gene triplets on average across 25 tissues, where the TF binds to a regulatory SNP in the gene’s promoter or putative enhancer and potentially regulates its expression in an age- and allele-dependent fashion. The detected SNPs are enriched for epigenomic marks indicative of regulatory activity, exhibit allele-specific chromatin accessibility, and spatial proximity to their putative gene targets. Furthermore, the TF-SNP interaction-dependent target genes have established links to aging and to age-associated diseases. In six hypertension-implicated tissues, detected interactions significantly inform hypertension state of an individual. Lastly, the age-interacting SNPs exhibit a greater proximity to the reported phenotype/diseases-associated SNPs than eSNPs identified in an interaction-independent fashion. Overall, we present a novel mechanism-based model, and a novel framework SNiPage, to identify functionally relevant SNP-age interactions in transcriptional control and illustrate their potential utility in understanding complex age-associated phenotypes.

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Meyer, Christian, Srikanth Padmala, and Luiz Pessoa. "Dynamic Threat Processing." Journal of Cognitive Neuroscience 31, no. 4 (April 2019): 522–42. http://dx.doi.org/10.1162/jocn_a_01363.

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During real-life situations, multiple factors interact dynamically to determine threat level. In the current fMRI study involving healthy adult human volunteers, we investigated interactions between proximity, direction (approach vs. retreat), and speed during a dynamic threat-of-shock paradigm. As a measure of threat-evoked physiological arousal, skin conductance responses were recorded during fMRI scanning. Some brain regions tracked individual threat-related factors, and others were also sensitive to combinations of these variables. In particular, signals in the anterior insula tracked the interaction between proximity and direction where approach versus retreat responses were stronger when threat was closer compared with farther. A parallel proximity-by-direction interaction was also observed in physiological skin conductance responses. In the right amygdala, we observed a proximity by direction interaction, but intriguingly in the opposite direction as the anterior insula; retreat versus approach responses were stronger when threat was closer compared with farther. In the right bed nucleus of the stria terminalis, we observed an effect of threat proximity, whereas in the right periaqueductal gray/midbrain we observed an effect of threat direction and a proximity by direction by speed interaction (the latter was detected in exploratory analyses but not in a voxelwise fashion). Together, our study refines our understanding of the brain mechanisms involved during aversive anticipation in the human brain. Importantly, it emphasizes that threat processing should be understood in a manner that is both context-sensitive and dynamic.

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Davidson, Jacob D., and Deborah M. Gordon. "Spatial organization and interactions of harvester ants during foraging activity." Journal of The Royal Society Interface 14, no. 135 (October 2017): 20170413. http://dx.doi.org/10.1098/rsif.2017.0413.

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Local interactions, when individuals meet, can regulate collective behaviour. In a system without any central control, the rate of interaction may depend simply on how the individuals move around. But interactions could in turn influence movement; individuals might seek out interactions, or their movement in response to interaction could influence further interaction rates. We develop a general framework to address these questions, using collision theory to establish a baseline expected rate of interaction based on proximity. We test the models using data from harvester ant colonies. A colony uses feedback from interactions inside the nest to regulate foraging activity. Potential foragers leave the nest in response to interactions with returning foragers with food. The time series of interactions and local density of ants show how density hotspots lead to interactions that are clustered in time. A correlated random walk null model describes the mixing of potential and returning foragers. A model from collision theory relates walking speed and spatial proximity with the probability of interaction. The results demonstrate that although ants do not mix homogeneously, trends in interaction patterns can be explained simply by the walking speed and local density of surrounding ants.

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Hill, J. Brett, Matthew A. Peeples, Deborah L. Huntley, and H. Jane Carmack. "Spatializing Social Network Analysis in the Late Precontact U.S. Southwest." Advances in Archaeological Practice 3, no. 1 (February 2015): 63–77. http://dx.doi.org/10.7183/2326-3768.3.1.63.

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AbstractIn this article we explore the relationship between spatial proximity and indices of social connectivity during the A.D. 1200–1450 interval in the United States (U.S.) Southwest. Using geographic information systems (GIS), we develop indices of spatial proximity based on the terrain-adjusted cost distance between sites in a regional settlement and material cultural database focused on the western U.S. Southwest. We evaluate the hypothesis that social interaction is a function of proximity and that interactions will be most intense among near neighbors. We find that this hypothesis is supported in some instances but that the correlation between proximity and interaction is highly variable in the context of late precontact social upheaval. Furthermore, we show important discrepancies between the Puebloan north and the Hohokam south that help to explain differences in community sustainability in the two regions.

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Braun, Andreas, Sebastian Zander-Walz, Martin Majewski, and Arjan Kuijper. "Curved - free-form interaction using capacitive proximity sensors." Procedia Computer Science 109 (2017): 59–66. http://dx.doi.org/10.1016/j.procs.2017.05.295.

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Vasquez, John A. "Why Do Neighbors Fight? Proximity, Interaction, or Territoriality." Journal of Peace Research 32, no. 3 (August 1995): 277–93. http://dx.doi.org/10.1177/0022343395032003003.

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Brahimi, M., and Doan-Kim-Son. "Interaction between two turbulent plumes in close proximity." Mechanics Research Communications 12, no. 5 (September 1985): 249–55. http://dx.doi.org/10.1016/0093-6413(85)90040-0.

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Lynden-Bell, R. M. "The interaction of crystal surfaces in close proximity." Surface Science Letters 244, no. 1-2 (March 1991): A116. http://dx.doi.org/10.1016/0167-2584(91)90753-e.

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Douglas, John E., and Carol Kramer. "Interaction, social proximity, and distance: A special issue." Journal of Anthropological Archaeology 11, no. 2 (June 1992): 103–10. http://dx.doi.org/10.1016/0278-4165(92)90015-4.

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Antonicka, Hana, Zhen-Yuan Lin, Alexandre Janer, Mari J. Aaltonen, Woranontee Weraarpachai, Anne-Claude Gingras, and Eric A. Shoubridge. "A High-Density Human Mitochondrial Proximity Interaction Network." Cell Metabolism 32, no. 3 (September 2020): 479–97. http://dx.doi.org/10.1016/j.cmet.2020.07.017.

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Lynden-Bell, R. M. "The interaction of crystal surfaces in close proximity." Surface Science 244, no. 3 (March 1991): 266–76. http://dx.doi.org/10.1016/0039-6028(91)90500-r.

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Illerbrun, Kurt, and Jens Roland. "Treeline proximity alters an alpine plant–herbivore interaction." Oecologia 166, no. 1 (December 24, 2010): 151–59. http://dx.doi.org/10.1007/s00442-010-1822-y.

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Li, Tao, and Sheng Zhang. "Inkjet-printed proximity sensor for human–robot interaction." Microsystem Technologies 24, no. 12 (April 13, 2018): 4875–80. http://dx.doi.org/10.1007/s00542-018-3901-7.

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Andre, Anthony D., and Christopher D. Wickens. "The Interaction of Spatial and Color Proximity in Aircraft Stability Information Displays." Proceedings of the Human Factors Society Annual Meeting 32, no. 19 (October 1988): 1371–75. http://dx.doi.org/10.1177/154193128803201914.

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The objective of a complex display design is to provide information in a way that maximizes the user's ability to process that information. This paper explores the effects of manipulating the spatial and color proximity among information displays relevant to aircraft stability during both integration and focused attention tasks. The principle of compatibility of proximity (Wickens, 1987) suggests that tasks requiring the operator to integrate multiple sources of information are better served by close display proximity while tasks that require focused attention on specific sources of information are better served by more separate displays. Color proximity results clearly supported this principle and showed that using a common color (i.e. close proximity) to code different information sources facilitated integration performance while using separate colors to code different information sources facilitated focused attention performance. However, close spatial proximity did not foster integration. Instead, distant spatial proximity yielded superior performance for both focused attention and integration tasks.

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Kim, Jiyoung, Sunmee Choi, and Drew Martin. "The halo effect of C2C interaction quality in prolonged close-proximity service settings." Journal of Services Marketing 34, no. 4 (February 14, 2020): 459–72. http://dx.doi.org/10.1108/jsm-02-2019-0098.

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Purpose Applying social capital and the social exchange theories to customer-to-customer (C2C) interactions, this study aims to propose that interaction quality perceptions affect the customer-to-service provider’s interaction quality perceptions in a prolonged, close-proximity service setting. Examining this exogenous dimension, the study also tests socio-emotional support perception’s mediating effect and customer proactiveness’ moderating effect. Design/methodology/approach This study adopts and modifies existing general services of C2C interaction dimensions to fit the health-care context. An in-person survey of 192 neurosurgery inpatients and their care-giving companions (both considered health-care customers) provides data to validate the dimensions and test the model. Structural equation modeling and moderated regression test the hypotheses. Findings Results show that affirmative C2C interactions positively affect the customer’s perceived socio-emotional support, whereas negative C2C interactions show no significant impact. Greater socio-emotional support acuity improves customers’ assurance and empathy quality perceptions about the provider’s service. Customer proactiveness moderates C2C interaction dimensions. Research limitations/implications This study extends the research of the C2C interaction to include their effect on service quality perceptions in a prolonged close-proximity service setting. Study results validate C2C interaction’s dimensions specific to an inpatient setting. Finally, this study extends the application of social capital theory and social exchange theory to C2C settings. Practical implications Findings emphasize the importance of managing C2C interactions during prolonged, close-proximity service delivery processes to improve customer perceptions of service quality. Results suggest that managers should monitor customer proactiveness to maximize positive C2C interactions’ positive effects while minimizing negative C2C interactions. Originality/value Prior service quality studies tend to focus on managing internal resources (staff, processes or physical environment); however, this study examines how the interactions among external resources create a halo effect and impact customers’ service quality perceptions. Results inform methods to improve their quality perceptions by better managing exogenous factors. The study also responds to calls for research on how C2C interactions affect functional service contexts (vs hedonic service contexts).

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Goligorsky, Michael S., Hong Li, Sergey Brodsky, and Jun Chen. "Relationships between caveolae and eNOS: everything in proximity and the proximity of everything." American Journal of Physiology-Renal Physiology 283, no. 1 (July 1, 2002): F1—F10. http://dx.doi.org/10.1152/ajprenal.00377.2001.

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Caveolae, flask-shaped invaginations of the plasma membrane occupying up to 30% of cell surface in capillaries, represent a predominant location of endothelial nitric oxide synthase (eNOS) in endothelial cells. The caveolar coat protein caveolin forms high-molecular-weight, Triton-insoluble complexes through oligomerization mediated by interactions between NH2-terminal residues 61–101. eNOS is targeted to caveolae by cotranslational N-myristoylation and posttranslational palmitoylation. Caveolin-1 coimmunoprecipitates with eNOS; interaction with eNOS occurs via the caveolin-1 scaffolding domain and appears to result in the inhibition of NOS activity. The inhibitory conformation of eNOS is reversed by the addition of excess Ca2+/calmodulin and by Akt-induced phosphorylation of eNOS. Here, we shall dissect the system using the classic paradigm of a reflex loop: 1) the action of afferent elements, such as fluid shear stress and its putative caveolar sensor, on caveolae; 2) the ways in which afferent signals may affect the central element, the activation of the eNOS-nitric oxide system; and 3) several resultant well-established and novel physiologically important effector mechanisms, i.e., vasorelaxation, angiogenesis, membrane fluidity, endothelial permeability, deterrance of inflammatory cells, and prevention of platelet aggregation.

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Kerbler, Sandra M., Roberto Natale, Alisdair R. Fernie, and Youjun Zhang. "From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants." International Journal of Molecular Sciences 22, no. 13 (July 1, 2021): 7101. http://dx.doi.org/10.3390/ijms22137101.

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The study of protein–protein interactions (PPIs) is fundamental in understanding the unique role of proteins within cells and their contribution to complex biological systems. While the toolkit to study PPIs has grown immensely in mammalian and unicellular eukaryote systems over recent years, application of these techniques in plants remains under-utilized. Affinity purification coupled to mass spectrometry (AP-MS) and proximity labeling coupled to mass spectrometry (PL-MS) are two powerful techniques that have significantly enhanced our understanding of PPIs. Relying on the specific binding properties of a protein to an immobilized ligand, AP is a fast, sensitive and targeted approach used to detect interactions between bait (protein of interest) and prey (interacting partners) under near-physiological conditions. Similarly, PL, which utilizes the close proximity of proteins to identify potential interacting partners, has the ability to detect transient or hydrophobic interactions under native conditions. Combined, these techniques have the potential to reveal an unprecedented spatial and temporal protein interaction network that better understands biological processes relevant to many fields of interest. In this review, we summarize the advantages and disadvantages of two increasingly common PPI determination techniques: AP-MS and PL-MS and discuss their important application to plant systems.

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Han, Shuo, Boxuan Simen Zhao, Samuel A. Myers, Steven A. Carr, Chuan He, and Alice Y. Ting. "RNA–protein interaction mapping via MS2- or Cas13-based APEX targeting." Proceedings of the National Academy of Sciences 117, no. 36 (August 24, 2020): 22068–79. http://dx.doi.org/10.1073/pnas.2006617117.

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RNA–protein interactions underlie a wide range of cellular processes. Improved methods are needed to systematically map RNA–protein interactions in living cells in an unbiased manner. We used two approaches to target the engineered peroxidase APEX2 to specific cellular RNAs for RNA-centered proximity biotinylation of protein interaction partners. Both an MS2-MCP system and an engineered CRISPR-Cas13 system were used to deliver APEX2 to the human telomerase RNA hTR with high specificity. One-minute proximity biotinylation captured candidate binding partners for hTR, including more than a dozen proteins not previously linked to hTR. We validated the interaction between hTR and theN6-methyladenosine (m6A) demethylase ALKBH5 and showed that ALKBH5 is able to erase the m6A modification on endogenous hTR. ALKBH5 also modulates telomerase complex assembly and activity. MS2- and Cas13-targeted APEX2 may facilitate the discovery of novel RNA–protein interactions in living cells.

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Vander Wal, E., P. C. Paquet, F. Messier, and P. D. McLoughlin. "Effects of phenology and sex on social proximity in a gregarious ungulate." Canadian Journal of Zoology 91, no. 9 (September 2013): 601–9. http://dx.doi.org/10.1139/cjz-2012-0237.

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Structure in sociality is known to relate to intrinsic and extrinsic factors. Less understood are the mechanics of sociality expressed as fine-scale behaviours that maintain hierarchies, mediate competition, or transmit pathogens. A recent novel approach to quantifying fine-scale social behaviour has been to use proximity-logging biotelemetry collars. This technology continuously records data whenever collars are within a predefined distance of each other, at times of day, and in habitats where traditional ethological approaches to focal-individual sampling of behaviours are unfeasible. We tested a series of expectations on fine-scale (≤1.4 m) interaction rates and durations consistent with competing hypotheses of seasonal and sexual segregation for elk (Cervus canadensis Erxleben, 1777). Female–female dyads interacted 4 times more frequently than male–male dyads (mean interaction rate per year: female–female = 62 vs. male–male = 14; P < 0.001), and male–male interactions were 1.5 times longer in duration than female–female interactions (mean interaction length: female–female = 30 s vs. male–male = 45 s; P < 0.001). We propose that fine-scale interactions among members of a population can be modeled as a trade-off between the frequency (quantity) and the duration (quality) of interactions. Our results have implications for understanding sex-based differences in sociality in gregarious herbivores and for disease transmission, which may follow from social intercourse.

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Branon, Tess, Shuo Han, and Alice Ting. "Beyond Immunoprecipitation: Exploring New Interaction Spaces with Proximity Biotinylation." Biochemistry 56, no. 26 (June 2, 2017): 3297–98. http://dx.doi.org/10.1021/acs.biochem.7b00466.

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Capone, M., G. Sangiovanni, C. Castellani, and M. Grilli. "Electron–phonon interaction in proximity of a Mott transition." Physica B: Condensed Matter 359-361 (April 2005): 636–38. http://dx.doi.org/10.1016/j.physb.2005.01.183.

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Williams, Ryan K., and Gaurav S. Sukhatme. "Constrained Interaction and Coordination in Proximity-Limited Multiagent Systems." IEEE Transactions on Robotics 29, no. 4 (August 2013): 930–44. http://dx.doi.org/10.1109/tro.2013.2257578.

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Bayman, B. F. "Form factors for a proximity interaction between deformed nuclei." Physical Review C 34, no. 4 (October 1, 1986): 1346–52. http://dx.doi.org/10.1103/physrevc.34.1346.

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Muhanna, N., A. Horani, S. Doron, and R. Safadi. "Lymphocyte-hepatic stellate cell proximity suggests a direct interaction." Clinical & Experimental Immunology 148, no. 2 (May 2007): 338–47. http://dx.doi.org/10.1111/j.1365-2249.2007.03353.x.

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Kreipl, Maximilian Stephan, Werner Friedland, and Herwig G. Paretzke. "Interaction of ion tracks in spatial and temporal proximity." Radiation and Environmental Biophysics 48, no. 4 (July 12, 2009): 349–59. http://dx.doi.org/10.1007/s00411-009-0234-z.

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Islam, M. Rafiqul, and Motohiko Murai. "Dynamic interaction of parallel moving ships in close proximity." Journal of Marine Science and Application 12, no. 3 (August 7, 2013): 261–71. http://dx.doi.org/10.1007/s11804-013-1205-y.

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Ghosh, Pijush, Dinesh R. Katti, and Kalpana S. Katti. "Mineral and Protein-Bound Water and Latching Action Control Mechanical Behavior at Protein-Mineral Interfaces in Biological Nanocomposites." Journal of Nanomaterials 2008 (2008): 1–8. http://dx.doi.org/10.1155/2008/582973.

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The nacre structure consists of laminated interlocked mineral platelets separated by nanoscale organic layers. Here, the role of close proximity of mineral to the proteins on mechanical behavior of the protein is investigated through steered molecular dynamics simulations. Our simulations indicate that energy required for unfolding protein in the proximity of mineral aragonite is several times higher than that for isolated protein in the absence of the mineral. Here, we present details of specific mechanisms which result in higher energy for protein unfolding in the proximity of mineral. At the early stage of pulling, peaks in the load-displacement (LD) plot at mineral proximity are quantitatively correlated to the interaction energy between atoms involved in the latching phenomenon of amino acid side chain to aragonite surface. Water plays an important role during mineral and protein interaction and water molecules closer to the mineral surface are highly oriented and remain rigidly attached as the protein strand is pulled. Also, the high magnitude of load for a given displacement originates from attractive interactions between the protein, protein-bound water, and mineral. This study provides an insight into mineral-protein interactions that are predominant in biological nanocomposites and also provides guidelines towards design of biomimetic nanocomposites.

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Licoppe, Christian. "Merging mobile communication studies and urban research: Mobile locative media, “onscreen encounters” and the reshaping of the interaction order in public places." Mobile Media & Communication 1, no. 1 (January 2013): 122–28. http://dx.doi.org/10.1177/2050157912464488.

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This communication discusses how the use of locative media in urban public settings allows users to recognize one another’s proximity on screen. Such “on screen encounters” make simultaneously relevant the categories of passer-by and mobile user, thus creating a tension between an orientation towards civil inattention or engaging in focused, face-to-face interactions. Such a tension is characteristic of the interaction order of urban settings experienced as location- or proximity-aware “hybrid ecologies”.

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Cao, Xianzhong, Gang Zeng, Lan Lin, and Lin Zou. "Hierarchical Characteristics and Proximity Mechanism of Intercity Innovation Networks: A Case of 290 Cities in China." Complexity 2021 (May 25, 2021): 1–14. http://dx.doi.org/10.1155/2021/5538872.

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The formation mechanism of innovation networks is one of the core issues in the current research of innovation networks, and proximity plays an important role in the formation and development of innovation networks; however, which proximity is more important and how different proximities interact remain to be further researched. This study conducts a social network analysis and adopts a spatial interaction model to examine innovation networks among 290 Chinese cities. The results reveal that, first, the hierarchical characteristics of Chinese cities’ innovation networks reflect a core periphery structure and the spatial patterns of large dispersion and small agglomeration. Further, bound by the Hu line, the hierarchy is high in the east and low in the west. Second, geographical, institutional, and cognitive proximities positively affect Chinese cities’ innovation networking. Cognitive proximity, particularly, has the highest impact. Geographical proximity reinforces the effect of institutional proximity, and thus, their interactions are complementary.

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Iakovou, Georgios, Steven Hayward, and Stephen Laycock. "A real-time proximity querying algorithm for haptic-based molecular docking." Faraday Discuss. 169 (2014): 359–77. http://dx.doi.org/10.1039/c3fd00123g.

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Intermolecular binding underlies every metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to their binding pose. Moreover, it allows human perception, intuition and knowledge to assist and accelerate the docking process, and reduces incorrect binding poses. Crucial for interactive docking is the real-time calculation of interaction forces. For smooth and accurate haptic exploration and manipulation, force-feedback cues have to be updated at a rate of 1 kHz. Hence, force calculations must be performed within 1ms. To achieve this, modern haptic-based docking approaches often utilize pre-computed force grids and linear interpolation. However, such grids are time-consuming to pre-compute (especially for large molecules), memory hungry, can induce rough force transitions at cell boundaries and cannot be applied to flexible docking. Here we propose an efficient proximity querying method for computing intermolecular forces in real time. Our motivation is the eventual development of a haptic-based docking solution that can model molecular flexibility. Uniquely in a haptics application we use octrees to decompose the 3D search space in order to identify the set of interacting atoms within a cut-off distance. Force calculations are then performed on this set in real time. The implementation constructs the trees dynamically, and computes the interaction forces of large molecular structures (i.e. consisting of thousands of atoms) within haptic refresh rates. We have implemented this method in an immersive, haptic-based, rigid-body, molecular docking application called Haptimol_RD. The user can use the haptic device to orientate the molecules in space, sense the interaction forces on the device, and guide the molecules to their binding pose. Haptimol_RD is designed to run on consumer level hardware, i.e. there is no need for specialized/proprietary hardware.

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Voter, Andrew F., Kelly A. Manthei, and James L. Keck. "A High-Throughput Screening Strategy to Identify Protein-Protein Interaction Inhibitors That Block the Fanconi Anemia DNA Repair Pathway." Journal of Biomolecular Screening 21, no. 6 (March 8, 2016): 626–33. http://dx.doi.org/10.1177/1087057116635503.

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Induction of the Fanconi anemia (FA) DNA repair pathway is a common mechanism by which tumors evolve resistance to DNA crosslinking chemotherapies. Proper execution of the FA pathway requires interaction between the FA complementation group M protein (FANCM) and the RecQ-mediated genome instability protein (RMI) complex, and mutations that disrupt FANCM/RMI interactions sensitize cells to DNA crosslinking agents. Inhibitors that block FANCM/RMI complex formation could be useful therapeutics for resensitizing tumors that have acquired chemotherapeutic resistance. To identify such inhibitors, we have developed and validated high-throughput fluorescence polarization and proximity assays that are sensitive to inhibitors that disrupt interactions between the RMI complex and its binding site on FANCM (a peptide referred to as MM2). A pilot screen of 74,807 small molecules was performed using the fluorescence polarization assay. Hits from the primary screen were further tested using the proximity assay, and an orthogonal proximity assay was used to assess inhibitor selectivity. Direct physical interaction between the RMI complex and the most selective inhibitor identified through the screening process was measured by surface plasmon resonance and isothermal titration calorimetry. Observation of direct binding by this small molecule validates the screening protocol.

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Zwisler, Joshua James, and César Alejandro Cuellar Cedano. "Sociolinguistic proximity in animal-directed speech." Lenguaje 48, no. 2 (July 1, 2020): 354–68. http://dx.doi.org/10.25100/lenguaje.v48i2.7484.

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This article explores how sociolinguistic proximity i.e. different varieties of socially close relationships enacted through speech interaction, is formed with animals in Ibagué, Colombia. It is common to hear that people speak with pets using ‘baby-talk’ or as friends. However, there are a range of registers/stances available to construct different social relationships through speech. Data regarding talk with pets and non-pet domestic animals from a self-report survey with a sample of 500 in the regional Colombian city of Ibagué was analysed using an experimental scale of sociolinguistic proximity devised by the authors. The results show that a variety of different relationships are created in speech with both pets and non-pets and that these relationships range from socially close to distant. Factors such as gender, education and owning a pet all affect the sociolinguistic proximity enacted through linguistic interaction with animals, with gender being the most influential of the variables.

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Ismail, M., and I. A. M. Abdul-Magead. "Comparison between different proximity potentials and the double-folding model for spherical–deformed interacting nuclei." Canadian Journal of Physics 94, no. 1 (January 2016): 102–11. http://dx.doi.org/10.1139/cjp-2015-0280.

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The Coulomb barrier parameters have been calculated for a spherical–deformed interacting pair of nuclei using 14 different versions of the proximity approaches and a simple analytical formula for the Coulomb part of the heavy ion potential. The results of these proximity versions have been compared with more accurate results obtained from the double-folding model (DFM). We have considered the interacting pair 48Ca + 238Pu as an example and assumed the presence of the quadrupole, octupole, and hexadecapole deformation parameters for 238Pu. The orientation angle dependence of the Coulomb barrier parameters has been computed for different sets of deformation parameters. We found that the proximity types named Prox77, BW Prox91, AW Prox95, Bass Prox77, and Bass Prox80 are the best ones of the available 14 versions of the proximity approaches for calculating the nuclear part of the interaction potential for a spherical–deformed pair of nuclei.

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Schneider, J., and J. D. Levine. "Automated identification of social interaction criteria in Drosophila melanogaster." Biology Letters 10, no. 10 (October 2014): 20140749. http://dx.doi.org/10.1098/rsbl.2014.0749.

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The study of social behaviour within groups has relied on fixed definitions of an ‘interaction’. Criteria used in these definitions often involve a subjectively defined cut-off value for proximity, orientation and time (e.g. courtship, aggression and social interaction networks) and the same numerical values for these criteria are applied to all of the treatment groups within an experiment. One universal definition of an interaction could misidentify interactions within groups that differ in life histories, study treatments and/or genetic mutations. Here, we present an automated method for determining the values of interaction criteria using a pre-defined rule set rather than pre-defined values. We use this approach and show changing social behaviours in different manipulations of Drosophila melanogaster . We also show that chemosensory cues are an important modality of social spacing and interaction. This method will allow a more robust analysis of the properties of interacting groups, while helping us understand how specific groups regulate their social interaction space.

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Melo, Paulo, and Sérgio Maravilhas. "ARE INTERACTION LINKAGES BASED ON GEOGRAPHIC PROXIMITY FOCUSED ON DEVELOPMENT OF FIRM’S INNOVATION ACTIVITIES STILL RELEVANT? EMPIRICAL STUDY OF THE ICT FIRMS LOCATED IN THE CITY OF SALVADOR, BAHIA, BRAZIL." Journal on Innovation and Sustainability. RISUS ISSN 2179-3565 10, no. 1 (March 12, 2019): 12–19. http://dx.doi.org/10.24212/2179-3565.2019v10i1p12-19.

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The current paper investigates the role of interactions based on geographic proximity for the development of firm’s innovation activities. Many authors such as Porter (1998) argued that the formation of interactive linkages based on geographic proximity seem to facilitate the search for new knowledge, information and technologies able to impact the development of innovation activities inside the organization generating competitive advantages. To perform this research, the authors decided to investigate the interaction behavior of micro and small firms in the information, communication and technology (ICT) sector located inside and outside the technological park in the city of Salvador, State of Bahia, Brazil. The findings showed in general that firms which had innovation activities, also had some kind of interactions with other agents, confirming that innovation is not a solitaire phenomenon. However, the empirical evidences did not confirm that interactions based on geographic proximity were relevant for the development of firms’ innovative activities. The study showed that, nowadays, firms use to interact with others regardless of whether they are geographically close or not. This may happen due to the fact that with the facilitation and the intensive use of new communication technologies have helped firms to reach partners wherever they are located at. Also, the study may suggest that arguments such as the role of geographic proximity and business agglomerations based on spatial proximity may need to be revised

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Garcia, Victor, Eon Joo Park, Mauro Siragusa, Florian Frohlich, Mohammad Mahfuzul Haque, Jonathan V. Pascale, Katherine R. Heberlein, Brant E. Isakson, Dennis J. Stuehr, and William C. Sessa. "Unbiased proteomics identifies plasminogen activator inhibitor-1 as a negative regulator of endothelial nitric oxide synthase." Proceedings of the National Academy of Sciences 117, no. 17 (April 16, 2020): 9497–507. http://dx.doi.org/10.1073/pnas.1918761117.

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Nitric oxide (NO) produced by endothelial nitric oxide synthase (eNOS) is a critical mediator of vascular function. eNOS is tightly regulated at various levels, including transcription, co- and posttranslational modifications, and by various protein–protein interactions. Using stable isotope labeling with amino acids in cell culture (SILAC) and mass spectrometry (MS), we identified several eNOS interactors, including the protein plasminogen activator inhibitor-1 (PAI-1). In cultured human umbilical vein endothelial cells (HUVECs), PAI-1 and eNOS colocalize and proximity ligation assays demonstrate a protein–protein interaction between PAI-1 and eNOS. Knockdown of PAI-1 or eNOS eliminates the proximity ligation assay (PLA) signal in endothelial cells. Overexpression of eNOS and HA-tagged PAI-1 in COS7 cells confirmed the colocalization observations in HUVECs. Furthermore, the source of intracellular PAI-1 interacting with eNOS was shown to be endocytosis derived. The interaction between PAI-1 and eNOS is a direct interaction as supported in experiments with purified proteins. Moreover, PAI-1 directly inhibits eNOS activity, reducing NO synthesis, and the knockdown or antagonism of PAI-1 increases NO bioavailability. Taken together, these findings place PAI-1 as a negative regulator of eNOS and disruptions in eNOS–PAI-1 binding promote increases in NO production and enhance vasodilation in vivo.

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Chaichitwanidchakol, Pitsanu, and Witcha Feungchan. "Exploring Mobile Game Interactions." International Journal of Electrical and Computer Engineering (IJECE) 8, no. 5 (October 1, 2018): 3954. http://dx.doi.org/10.11591/ijece.v8i5.pp3954-3965.

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The mobile game industry has been growing rapidly in both the number of games and revenues. Choosing the right interactions for a game has become a major challenge for developers. Some developers use inappropriate interactions in their games which causes them to be less fun than they should be. This research focuses on gathering and defining possible mobile game interactions so as to guide and enable designers and developers to choose the right interactions for their games. The researchers have extensively reviewed and explored various mobile game interactions both through research studies and through existing mobile games. Subsequent to observations, mobile game interactions were then categorized as follows: 1) Touch interaction 2) Motion/Movement interaction 3) Video interaction 4) Sound interaction 5) Special purpose interaction 6) Location interaction 7) Electroencep-halography (EEG) interaction 8) Date/Time interaction 9) Weather interaction 10) Light interaction 11) Proximity interaction 12) Network interaction 13) Social interaction and 14) Bioinformatics interaction. These 14 interactions can be used to support gameplay, ideas, and innovation of mobile games.

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Verset, Laurine, Joke Tommelein, Christine Decaestecker, Elly De Vlieghere, Marc Bracke, Isabelle Salmon, Olivier De Wever, and Pieter Demetter. "ADAM-17/FHL2 colocalisation suggests interaction and role of these proteins in colorectal cancer." Tumor Biology 39, no. 3 (March 2017): 101042831769502. http://dx.doi.org/10.1177/1010428317695024.

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FHL2 is a multifunctional scaffolding protein; its expression is associated with poor prognosis in colorectal cancer. ADAM-17 is a metalloprotease implicated in ectodomain shedding. FHL2 regulates ADAM-17 plasma membrane localisation, and FHL2 deficiency leads to decreased activity of ADAM-17 in mouse macrophages. Presence and relationship of the ADAM-17/FHL2 complex with colorectal cancer progression is unknown. We studied FHL2 and ADAM-17 expression in several colon cancer cell lines by immunocytochemistry and western blot. To highlight the interaction between both molecules, we used the Duolink® kit for proximity ligation assay on SW480 cells. We also performed proximity ligation assay on biopsies and surgical specimens of colorectal adenocarcinoma and on matched normal mucosa. Furthermore, biopsies of colorectal adenoma with matched normal mucosa were selected. For quantification, pictures of the malignant, adenomatous and normal tissues were taken. Proximity ligation assay signals were quantified. Mean numbers of proximity ligation assay signals and of proximity ligation assay signals/nucleus were calculated. All cell lines showed FHL2 immunoreactivity; strongest positivity was observed in SW480 cells. ADAM-17 was expressed in all cell lines. Proximity ligation assay signals were present in SW480 cells. Quantitative analysis revealed that the interaction between FHL2 and ADAM-17 is more frequent in malignant than in normal tissue (p = 0.005). The mean number of ADAM-17/FHL2 proximity ligation assay signals was higher in colorectal adenocarcinoma than in adenoma with low-grade dysplasia (p = 0.0004). FHL2 interacts with ADAM-17 in normal, dysplastic and malignant colon epithelial cells. Colocalisation of these proteins is more frequent in malignant than in normal and dysplastic cells, suggesting a role for ADAM-17/FHL2 complex in the development of colorectal cancer.

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Morrison, Kathryn A., Dirk Seidel, Niall C. Strang, and Lyle S. Gray. "The interaction between size and accommodation cues in predicting proximity." Ophthalmic and Physiological Optics 28, no. 1 (January 14, 2008): 97. http://dx.doi.org/10.1111/j.1475-1313.2007.00530_6.x.

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De Fuentes, Claudia, and Gabriela Dutrénit. "Geographic proximity and university–industry interaction: the case of Mexico." Journal of Technology Transfer 41, no. 2 (August 15, 2014): 329–48. http://dx.doi.org/10.1007/s10961-014-9364-9.

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Zhou, Huiyuan, Vinicius Ferreira, Thamara Silva Alves, Bonnie MacKay, Kirstie Hawkey, and Derek Reilly. "Exploring Privacy Notification and Control Mechanisms for Proximity-Aware Tablets." International Journal of Mobile Human Computer Interaction 7, no. 3 (July 2015): 1–19. http://dx.doi.org/10.4018/ijmhci.2015070101.

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In hospitals, offices and other settings, professionals face the challenge of accessing and sharing sensitive content in public areas. As tablets become increasingly adopted in work environments, it is important to explore ways to support privacy that are appropriate for tablet use in dynamic, mobile workflows. In this research we consider how spatial information can be utilized to support both individual and collaborative work in a natural way while respecting data privacy. We present a proof-of-concept implementation of a proximity-aware tablet, and a range of privacy notification and control mechanisms designed for such a tablet. Results from a user study support the idea that interpersonal distance and orientation can be used to mediate privacy management for tablet interfaces. Selecting a specific design for privacy threat notification and response is highly context-dependent—for example, in health care the first priority is to not impede the fluid exchange of information.

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Zhang, Ziheng, Weiping Sun, Tiezhu Shi, Pengfei Lu, Min Zhuang, and Ji-Long Liu. "Capturing RNA–protein interaction via CRUIS." Nucleic Acids Research 48, no. 9 (March 6, 2020): e52-e52. http://dx.doi.org/10.1093/nar/gkaa143.

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Abstract No RNA is completely naked from birth to death. RNAs function with and are regulated by a range of proteins that bind to them. Therefore, the development of innovative methods for studying RNA–protein interactions is very important. Here, we developed a new tool, the CRISPR-based RNA-United Interacting System (CRUIS), which captures RNA–protein interactions in living cells by combining the power of CRISPR and PUP-IT, a novel proximity targeting system. In CRUIS, dCas13a is used as a tracker to target specific RNAs, while proximity enzyme PafA is fused to dCas13a to label the surrounding RNA-binding proteins, which are then identified by mass spectrometry. To identify the efficiency of CRUIS, we employed NORAD (Noncoding RNA activated by DNA damage) as a target, and the results show that a similar interactome profile of NORAD can be obtained as by using CLIP (crosslinking and immunoprecipitation)-based methods. Importantly, several novel NORAD RNA-binding proteins were also identified by CRUIS. The use of CRUIS facilitates the study of RNA–protein interactions in their natural environment, and provides new insights into RNA biology.

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J. NELSON, Thomas, Wei-Qin ZHAO, Shauna YUAN, Antonella FAVIT, Lucas POZZO-MILLER, and Daniel L. ALKON. "Calexcitin interaction with neuronal ryanodine receptors." Biochemical Journal 341, no. 2 (July 8, 1999): 423–33. http://dx.doi.org/10.1042/bj3410423.

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Calexcitin (CE), a Ca2+- and GTP-binding protein, which is phosphorylated during memory consolidation, is shown here to co-purify with ryanodine receptors (RyRs) and bind to RyRs in a calcium-dependent manner. Nanomolar concentrations of CE released up to 46% of the 45Ca label from microsomes preloaded with 45CaCl2. This release was Ca2+-dependent and was blocked by antibodies against the RyR or CE, by the RyR inhibitor dantrolene, and by a seven-amino-acid peptide fragment corresponding to positions 4689-4697 of the RyR, but not by heparin, an Ins(1,4,5)P3-receptor antagonist. Anti-CE antibodies, in the absence of added CE, also blocked Ca2+ release elicited by ryanodine, suggesting that the CE and ryanodine binding sites were in relative proximity. Calcium imaging with bis-fura-2 after loading CE into hippocampal CA1 pyramidal cells in hippocampal slices revealed slow, local calcium transients independent of membrane depolarization. Calexcitin also released Ca2+ from liposomes into which purified RyR had been incorporated, indicating that CE binding can be a proximate cause of Ca2+ release. These results indicated that CE bound to RyRs and suggest that CE may be an endogenous modulator of the neuronal RyR.

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Wilhelm, Mathias, Daniel Krakowczyk, and Sahin Albayrak. "PeriSense: Ring-Based Multi-Finger Gesture Interaction Utilizing Capacitive Proximity Sensing." Sensors 20, no. 14 (July 17, 2020): 3990. http://dx.doi.org/10.3390/s20143990.

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Rings are widely accepted wearables for gesture interaction. However, most rings can sense only the motion of one finger or the whole hand. We present PeriSense, a ring-shaped interaction device enabling multi-finger gesture interaction. Gestures of the finger wearing ring and its adjacent fingers are sensed by measuring capacitive proximity between electrodes and human skin. Our main contribution is the determination of PeriSense’s interaction space involving the evaluation of capabilities and limitations. We introduce a prototype named PeriSense, analyze the sensor resolution at different distances, and evaluate finger gestures and unistroke gestures based on gesture sets allowing the determination of the strengths and limitations. We show that PeriSense is able to sense the change of conductive objects reliably up to 2.5 cm. Furthermore, we show that this capability enables different interaction techniques such as multi-finger gesture recognition or two-handed unistroke input.

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Journal articles on the topic 'Proximity Interaction'

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