Journal articles: 'Spatial pathways'

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Zandvoort, Mark, Nora Kooijmans, Paul Kirshen, and Adri van den Brink. "Designing with Pathways: A Spatial Design Approach for Adaptive and Sustainable Landscapes." Sustainability 11, no. 3 (January 22, 2019): 565. http://dx.doi.org/10.3390/su11030565.

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Despite rising attention to pathways thinking in multiple domains such as climate adaptation, energy supply planning, and flood risk management, their spatial translation is so far understudied. We set out to study how spatial design based on pathways thinking can help develop more adaptive and sustainable landscapes. Using landscape analysis, field research, and research-through-designing in a case study on climate resilience in Boston (USA), we argue for better understanding of the spatial and design consequences of pathways in general. Our results indicate that pathways can be spatially translated, demanding landscape-informed choices when sequencing different policy actions. We found that spatial designing makes the landscape consequences of pathways transparent and enables policy-makers to replace the input of policy actions with spatial interventions, select pathways according to different underlying design strategies, use the mapped pathways to initiate an iterative research-through-designing process to test and inform different designs, and spatially visualize the pathways and possible sequences of actions. We conclude that policy-makers should be cognizant about the spatial implications of pathways and offer directions to enrich applications of pathways thinking for achieving adaptive and sustainable landscapes.

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Krishnan, J., Lingjun Lu, and Aiman Alam Nazki. "The interplay of spatial organization and biochemistry in building blocks of cellular signalling pathways." Journal of The Royal Society Interface 17, no. 166 (May 2020): 20200251. http://dx.doi.org/10.1098/rsif.2020.0251.

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Biochemical pathways and networks are central to cellular information processing. While a broad range of studies have dissected multiple aspects of information processing in biochemical pathways, the effect of spatial organization remains much less understood. It is clear that space is central to intracellular organization, plays important roles in cellular information processing and has been exploited in evolution; additionally, it is being increasingly exploited in synthetic biology through the development of artificial compartments, in a variety of ways. In this paper, we dissect different aspects of the interplay between spatial organization and biochemical pathways, by focusing on basic building blocks of these pathways: covalent modification cycles and two-component systems, with enzymes which may be monofunctional or bifunctional. Our analysis of spatial organization is performed by examining a range of ‘spatial designs’: patterns of localization or non-localization of enzymes/substrates, theoretically and computationally. Using these well-characterized in silico systems, we analyse the following. (i) The effect of different types of spatial organization on the overall kinetics of modification, and the role of distinct modification mechanisms therein. (ii) How different information processing characteristics seen experimentally and studied from the viewpoint of kinetics are perturbed, or generated. (iii) How the activity of enzymes (bifunctional enzymes in particular) may be spatially manipulated, and the relationship between localization and activity. (iv) How transitions in spatial organization (encountered either through evolution or through the lifetime of cells, as seen in multiple model organisms) impacts the kinetic module (and pathway) behaviour, and how transitions in chemistry may be impacted by prior spatial organization. The basic insights which emerge are central to understanding the role of spatial organization in biochemical pathways in both bacteria and eukaryotes, and are of direct relevance to engineering spatial organization of pathways in bottom-up synthetic biology in cellular and cell-free systems.

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Von Gerhardt, K., A. Van Niekerk, M. Kidd, M. Samways, and J. Hanks. "The role of elephantLoxodonta africanapathways as a spatial variable in crop-raiding location." Oryx 48, no. 3 (February 13, 2014): 436–44. http://dx.doi.org/10.1017/s003060531200138x.

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AbstractShort-range elephantLoxodonta africanamovements were examined in a heterogeneous landscape mosaic of settlements, crop fields and remnant forest in the Caprivi Strip, Namibia. We explored the penetration of the landscape through the use of permanent pathways and determined the impact of pathway use on crop-raiding location. Pathways were linear, devoid of vegetation and maintained by repeated movement. Functional connectivity of pathways was not species-specific, and pathways were used by various species. Elephants travelled in single file at night and we recorded selective pathway use: females selected pathways away from settlements to access water, whereas males used pathways among settlements to launch crop raids. Proximity of raided fields to the nearest pathway was the only significant spatial variable explaining crop-raiding location. Bulls were responsible for all crop-raiding incidents. We conclude that (1) pathways were the most significant spatial variable influencing which fields were raided, (2) crop-raiding from pathways may maximize foraging efficiency by reducing time spent and distance travelled while foraging, (3) pathways may facilitate penetration of the matrix by connecting predictable resources (crops) with preferred shelter areas, crossing points at roads and preferred drinking spots, and (4) access to the Kwandu River is restricted by settlements, predictably resulting in human–elephant conflict. By highlighting the relevance of pathways for movement of elephants we show that an understanding of the use of pathways is important for land-use planning in conservation landscapes, specifically with regard to human–elephant conflict. We also argue for the need to more fully explore pathway occurrence and use at larger spatial scales.

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Beaudot, W. H. A. "Dynamics in Parvocellular and Magnocellular Pathways: Consequences for Luminance and Colour Processing Streams." Perception 25, no. 1_suppl (August 1996): 9. http://dx.doi.org/10.1068/v96l0710.

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An achromatic neuromorphic model of the vertebrate retina has already accounted for X and Y pathways (Beaudot and Hérault, 1994 Perception23 Supplement, 25) and has shown a temporal ‘coarse-to-fine’ processing of spatial information (Beaudot et al, 1995 Perception24 Supplement, 93). This model has been extended to colour vision. By taking into account the chromatic sensitivities of cones, functional properties of the parvocellular pathway are modelled. Approximating the responses of colour-opponent cells, the model provides a spatial multiplexing of luminance and chrominance information: sustained responses show spatial band-pass behaviour to luminance variations and low-pass behaviour to equiluminant colour changes. In addition the spatiotemporal inseparability for luminance in the parvocellular model leads to a temporal multiplexing of spatial luminance information: at higher temporal frequencies the spatial filtering is low-pass, conveying only luminance information. Demultiplexing this mixed information suggests interactions between retinal channels. By locally combining additive and subtractive mechanisms between opposite parvocellular pathways (eg G+/ R−± R+/ G−), and an inhibition from the magnocellular pathway, the existence of at least three functional subchannels is predicted: (i) a transient, spatially low-pass channel, (ii) a sustained, spatially band-pass channel, dedicated to the analysis of luminance information in a spatiotemporally separable way (eg moving shadows and static textures), and (iii) a spatiotemporally low-pass, colour-opponent channel leading to colour induction, which is little affected by the presence of shadows and is more representative of objects. This hypothesis of spatiotemporal demultiplexing of luminance and chrominance information, which should presumably occur at an early cortical level, is in accordance with the multiple-processing-streams organisation of the primate visual system.

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Findlay, John M., and Robin Walker. "A model of saccade generation based on parallel processing and competitive inhibition." Behavioral and Brain Sciences 22, no. 4 (August 1999): 661–74. http://dx.doi.org/10.1017/s0140525x99002150.

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During active vision, the eyes continually scan the visual environment using saccadic scanning movements. This target article presents an information processing model for the control of these movements, with some close parallels to established physiological processes in the oculomotor system. Two separate pathways are concerned with the spatial and the temporal programming of the movement. In the temporal pathway there is spatially distributed coding and the saccade target is selected from a “salience map.” Both pathways descend through a hierarchy of levels, the lower ones operating automatically. Visual onsets have automatic access to the eye control system via the lower levels. Various centres in each pathway are interconnected via reciprocal inhibition. The model accounts for a number of well-established phenomena in target-elicited saccades: the gap effect, express saccades, the remote distractor effect, and the global effect. High-level control of the pathways in tasks such as visual search and reading is discussed; it operates through spatial selection and search selection, which generally combine in an automated way. The model is examined in relation to data from patients with unilateral neglect.

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MADRID, M., and M. A. CROGNALE. "Long-term maturation of visual pathways." Visual Neuroscience 17, no. 6 (November 2000): 831–37. http://dx.doi.org/10.1017/s0952523800176023.

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Previous research in adults has demonstrated the utility of the visual evoked potential (VEP) to measure the integrity of the chromatic and achromatic visual pathways. The VEP has also been shown to be a valuable indicator of maturation of these pathways in infants up to 1 year of age. The present manuscript reports changes in the visual pathways from 2 years to adulthood as measured by the spatio-chromatic VEP. The responses to achromatic reversal stimuli designed to preferentially activate the low spatial-frequency achromatic (luminance) pathways appear adult-like by 1 year of age. The responses to low spatial-frequency isoluminant onset stimuli designed to preferentially activate the chromatic pathway do not appear as they do in the adult until after 12–13 years of age. The shapes of the chromatic VEP waveforms shift from a positive–negative complex to a negative–positive complex. These changes can be modeled by a decrease in the latency of a large negative component between the ages of 1 year and adulthood. The results suggest that for low spatial-frequency stimuli, there are long-term changes in the development of the chromatic pathways that are not observed in the low spatial-frequency achromatic pathways. The changes in the chromatic VEP waveforms with age may be a physiological correlate of reported behavioral changes.

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Atay, Oguzhan, and Jan M. Skotheim. "Spatial and temporal signal processing and decision making by MAPK pathways." Journal of Cell Biology 216, no. 2 (January 2, 2017): 317–30. http://dx.doi.org/10.1083/jcb.201609124.

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Mitogen-activated protein kinase (MAPK) pathways are conserved from yeast to man and regulate a variety of cellular processes, including proliferation and differentiation. Recent developments show how MAPK pathways perform exquisite spatial and temporal signal processing and underscores the importance of studying the dynamics of signaling pathways to understand their physiological response. The importance of dynamic mechanisms that process input signals into graded downstream responses has been demonstrated in the pheromone-induced and osmotic stress–induced MAPK pathways in yeast and in the mammalian extracellular signal-regulated kinase MAPK pathway. Particularly, recent studies in the yeast pheromone response have shown how positive feedback generates switches, negative feedback enables gradient detection, and coherent feedforward regulation underlies cellular memory. More generally, a new wave of quantitative single-cell studies has begun to elucidate how signaling dynamics determine cell physiology and represents a paradigm shift from descriptive to predictive biology.

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Nilsson, Thomy. "Spatial Multiplexing." International Journal of Adaptive, Resilient and Autonomic Systems 5, no. 4 (October 2014): 46–70. http://dx.doi.org/10.4018/ijaras.2014100104.

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Geometrical constraints limit how much information can be received and emitted along real pathways across the boundary of any processor. Applied to central nervous systems this imposes a seemingly impassable bottleneck to the evolution of large brains. A small brain could never access enough information to warrant a larger brain. A small brain could not send enough information to operate a large body. Larger bodies are needed to support larger brains. Thus, with a rare exception, there are no invertebrates with large brains or large bodies. It is proposed that a convergent-divergent scanning neural network developed which enabled vertebrates to squeeze more information through this bottleneck by “spatial multiplexing”. This reduces the number of pathways into, between and from processors by a factor of 16 while maintaining spatial and intensity accuracy. This paper describes spatial multiplexing using downloadable spreadsheet models and shows how the necessity of scanning likely introduced brain rhythms.

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Han, Zhixian, and Anne Sereno. "Modeling the Ventral and Dorsal Cortical Visual Pathways Using Artificial Neural Networks." Neural Computation 34, no. 1 (January 1, 2022): 138–71. http://dx.doi.org/10.1162/neco_a_01456.

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Abstract Although in conventional models of cortical processing, object recognition and spatial properties are processed separately in ventral and dorsal cortical visual pathways respectively, some recent studies have shown that representations associated with both objects' identity (of shape) and space are present in both visual pathways. However, it is still unclear whether the presence of identity and spatial properties in both pathways have functional roles. In our study, we have tried to answer this question through computational modeling. Our simulation results show that both a model ventral and dorsal pathway, separately trained to do object and spatial recognition, respectively, each actively retained information about both identity and space. In addition, we show that these networks retained different amounts and kinds of identity and spatial information. As a result, our modeling suggests that two separate cortical visual pathways for identity and space (1) actively retain information about both identity and space (2) retain information about identity and space differently and (3) that this differently retained information about identity and space in the two pathways may be necessary to accurately and optimally recognize and localize objects. Further, modeling results suggests these findings are robust and do not strongly depend on the specific structures of the neural networks.

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Housden, Benjamin E., and Norbert Perrimon. "Spatial and temporal organization of signaling pathways." Trends in Biochemical Sciences 39, no. 10 (October 2014): 457–64. http://dx.doi.org/10.1016/j.tibs.2014.07.008.

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Haegerstrom-Portnoy, G., and A. J. Adams. "Spatial sensitization of the B cone pathways." Vision Research 28, no. 5 (January 1988): 629–38. http://dx.doi.org/10.1016/0042-6989(88)90112-5.

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Shin, Jung Hwan, Min Song, Se-Bum Paik, and Min Whan Jung. "Spatial organization of functional clusters representing reward and movement information in the striatal direct and indirect pathways." Proceedings of the National Academy of Sciences 117, no. 43 (October 14, 2020): 27004–15. http://dx.doi.org/10.1073/pnas.2010361117.

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To obtain insights into striatal neural processes underlying reward-based learning and movement control, we examined spatial organizations of striatal neurons related to movement and reward-based learning. For this, we recorded the activity of direct- and indirect-pathway neurons (D1 and A2a receptor-expressing neurons, respectively) in mice engaged in probabilistic classical conditioning and open-field free exploration. We found broadly organized functional clusters of striatal neurons in the direct as well as indirect pathways for both movement- and reward-related variables. Functional clusters for different variables were partially overlapping in both pathways, but the overlap between outcome- and value-related functional clusters was greater in the indirect than direct pathway. Also, value-related spatial clusters were progressively refined during classical conditioning. Our study shows the broad and learning-dependent spatial organization of functional clusters of dorsal striatal neurons in the direct and indirect pathways. These findings further argue against the classic model of the basal ganglia and support the importance of spatiotemporal patterns of striatal neuronal ensemble activity in the control of behavior.

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Rivas, R. J., and H. P. Moore. "Spatial segregation of the regulated and constitutive secretory pathways." Journal of Cell Biology 109, no. 1 (July 1, 1989): 51–60. http://dx.doi.org/10.1083/jcb.109.1.51.

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Recent experiments using DNA transfection have shown that secretory proteins in AtT-20 cells are sorted into two biochemically distinct secretory pathways. These two pathways differ in the temporal regulation of exocytosis. Proteins secreted by the regulated pathway are stored in dense-core granules until release is stimulated by secretagogues. In contrast, proteins secreted by the constitutive pathway are exported continuously, without storage. It is not known whether there are mechanisms to segregate regulated and constitutive secretory vesicles spatially. In this study, we examined the site of insertion of constitutive vesicles and compared it with that of regulated secretory granules. Regulated granules accumulate at tips of processes in these cells. To determine whether constitutively externalized membrane proteins are inserted into plasma membrane at the cell body or at process tips, AtT-20 cells were infected with ts-O45, a temperature-sensitive mutant of vesicular stomatitis virus in which transport of the surface glycoprotein G is conditionally blocked in the ER. After switching to the permissive temperature, insertion of G protein was detected at the cell body, not at process tips. Targeting of constitutive and regulated secretory vesicles to distinct areas of the plasma membrane appears to be mediated by microtubules. We found that while disruption of microtubules by colchicine had no effect on constitutive secretion, it completely blocked the accumulation of regulated granules at special release sites. Colchicine also affected the proper packaging of regulated secretory proteins. We conclude that regulated and constitutive secretory vesicles are targeted to different areas of the plasma membrane, most probably by differential interactions with microtubules. These results imply that regulated secretory granules may have unique membrane receptors for selective attachment to microtubules.

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Pérez, María Lucía, and José Luis Peña. "Comparison of Midbrain and Thalamic Space-Specific Neurons in Barn Owls." Journal of Neurophysiology 95, no. 2 (February 2006): 783–90. http://dx.doi.org/10.1152/jn.00833.2005.

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Spatial receptive fields of neurons in the auditory pathway of the barn owl result from the sensitivity to combinations of interaural time (ITD) and level differences across stimulus frequency. Both the forebrain and tectum of the owl contain such neurons. The neural pathways, which lead to the forebrain and tectal representations of auditory space, separate before the midbrain map of auditory space is synthesized. The first nuclei that belong exclusively to either the forebrain or the tectal pathways are the nucleus ovoidalis (Ov) and the external nucleus of the inferior colliculus (ICx), respectively. Both receive projections from the lateral shell subdivision of the inferior colliculus but are not interconnected. Previous studies indicate that the owl's tectal representation of auditory space is different from those found in the owl's forebrain and the mammalian brain. We addressed the question of whether the computation of spatial cues in both pathways is the same by comparing the ITD tuning of Ov and ICx neurons. Unlike in ICx, the relationship between frequency and ITD tuning had not been studied in single Ov units. In contrast to the conspicuous frequency independent ITD tuning of space-specific neurons of ICx, ITD selectivity varied with frequency in Ov. We also observed that the spatially tuned neurons of Ov respond to lower frequencies and are more broadly tuned to ITD than in ICx. Thus there are differences in the integration of frequency and ITD in the two sound-localization pathways. Thalamic neurons integrate spatial information not only within a broader frequency band but also across ITD channels.

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Wu, Yinghao, Kalyani Dhusia, and Zhaoqian Su. "Mechanistic dissection of spatial organization in NF-κB signaling pathways by hybrid simulations." Integrative Biology 13, no. 5 (April 24, 2021): 109–20. http://dx.doi.org/10.1093/intbio/zyab006.

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Abstract The nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is one of the most important transcription factors involved in the regulation of inflammatory signaling pathways. Inappropriate activation of these pathways has been linked to autoimmunity and cancers. Emerging experimental evidences have been showing the existence of elaborate spatial organizations for various molecular components in the pathways. One example is the scaffold protein tumor necrosis factor receptor associated factor (TRAF). While most TRAF proteins form trimeric quaternary structure through their coiled-coil regions, the N-terminal region of some members in the family can further be dimerized. This dimerization of TRAF trimers can drive them into higher-order clusters as a response to receptor stimulation, which functions as a spatial platform to mediate the downstream poly-ubiquitination. However, the molecular mechanism underlying the TRAF protein clustering and its functional impacts are not well-understood. In this article, we developed a hybrid simulation method to tackle this problem. The assembly of TRAF-based signaling platform at the membrane-proximal region is modeled with spatial resolution, while the dynamics of downstream signaling network, including the negative feedbacks through various signaling inhibitors, is simulated as stochastic chemical reactions. These two algorithms are further synchronized under a multiscale simulation framework. Using this computational model, we illustrated that the formation of TRAF signaling platform can trigger an oscillatory NF-κB response. We further demonstrated that the temporal patterns of downstream signal oscillations are closely regulated by the spatial factors of TRAF clustering, such as the geometry and energy of dimerization between TRAF trimers. In general, our study sheds light on the basic mechanism of NF-κB signaling pathway and highlights the functional importance of spatial regulation within the pathway. The simulation framework also showcases its potential of application to other signaling pathways in cells.

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Piantoni, Giovanni, Eric Halgren, and Sydney S. Cash. "The Contribution of Thalamocortical Core and Matrix Pathways to Sleep Spindles." Neural Plasticity 2016 (2016): 1–10. http://dx.doi.org/10.1155/2016/3024342.

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Sleep spindles arise from the interaction of thalamic and cortical neurons. Neurons in the thalamic reticular nucleus (TRN) inhibit thalamocortical neurons, which in turn excite the TRN and cortical neurons. A fundamental principle of anatomical organization of the thalamocortical projections is the presence of two pathways: the diffuse matrix pathway and the spatially selective core pathway. Cortical layers are differentially targeted by these two pathways with matrix projections synapsing in superficial layers and core projections impinging on middle layers. Based on this anatomical observation, we propose that spindles can be classified into two classes, those arising from the core pathway and those arising from the matrix pathway, although this does not exclude the fact that some spindles might combine both pathways at the same time. We find evidence for this hypothesis in EEG/MEG studies, intracranial recordings, and computational models that incorporate this difference. This distinction will prove useful in accounting for the multiple functions attributed to spindles, in that spindles of different types might act on local and widespread spatial scales. Because spindle mechanisms are often hijacked in epilepsy and schizophrenia, the classification proposed in this review might provide valuable information in defining which pathways have gone awry in these neurological disorders.

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White, G., W. B. Levy, and O. Steward. "Spatial overlap between populations of synapses determines the extent of their associative interaction during the induction of long-term potentiation and depression." Journal of Neurophysiology 64, no. 4 (October 1, 1990): 1186–98. http://dx.doi.org/10.1152/jn.1990.64.4.1186.

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1. This study evaluates the associative interactions between inputs that lead to long-term potentiation (LTP) and long-term depression (LTD) in the dentate gyrus (DG). Previous studies have revealed that when two inputs are coconditioned, the extent of LTP is greater than when each input is conditioned alone. Moreover, for a weak input that does not show LTP when conditioned alone, LTP can be induced in that weak input if it is coconditioned with a strong input. LTD results when one input is silent when another is conditioned. In the present study, we evaluate whether these associative interactions depend on the extent of overlap of the terminal fields of the different inputs. 2. The experiment took advantage of the topographical organization of the temporodentate pathway from the entorhinal cortex (EC) to the DG. Four stimulating electrodes were placed so as to activate ipsilateral and crossed components of the projections from medial and lateral portions of the EC. Recording electrodes were positioned unilaterally in the DG so as to record field potentials. The localization of the synaptic field that was activated by each electrode was determined by current source density (CSD) analysis. The extent of overlap between the terminal fields of ipsi- and contralateral pathways was assessed, and the pathways were divided into groups where the overlap between current sinks was 0-50 or 51-100%. 3. Conditioning stimulation (400-Hz trains of 8 pulses delivered 8 times) was delivered to pathways alone or in combination with other pathways. The extent of LTP was evaluated after coactivation of pathways that overlapped substantially (51-100%) or minimally (0-50%). The extent of LTD was evaluated in pathways that were silent during conditioning of other overlapping or nonoverlapping pathways. 4. The extent of associative LTP or LTD depended on the extent of overlap between the terminal fields of pathways. Coactivation of two pathways that overlapped by 51-100% led to LTP; coactivation of pathways that overlapped by 0-50% did not. Moreover, LTD was induced in a crossed pathway when an ipsilateral pathway that overlapped by 51-100% was activated, but not when a nonoverlapping (0-50% overlap) ipsilateral pathway was activated. The degree of associative LTP or LTD that was induced in crossed pathways was correlated with the percent overlap with the terminal field of the active ipsilateral pathway. 5. Evaluation of whether LTD was induced when one division (medial or lateral) of the ipsilateral pathway was silent when the other division was conditioned revealed similar relationships.(ABSTRACT TRUNCATED AT 400 WORDS)

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Pidoux, Guillaume, and Kjetil Taskén. "Specificity and spatial dynamics of protein kinase A signaling organized by A-kinase-anchoring proteins." Journal of Molecular Endocrinology 44, no. 5 (February 11, 2010): 271–84. http://dx.doi.org/10.1677/jme-10-0010.

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Protein phosphorylation is the most common post-translational modification observed in cell signaling and is controlled by the balance between protein kinase and phosphatase activities. The cAMP–protein kinase A (PKA) pathway is one of the most studied and well-known signal pathways. To maintain a high level of specificity, the cAMP–PKA pathway is tightly regulated in space and time. A-kinase-anchoring proteins (AKAPs) target PKA to specific substrates and distinct subcellular compartments providing spatial and temporal specificity in the mediation of biological effects controlled by the cAMP–PKA pathway. AKAPs also serve as scaffolding proteins that assemble PKA together with signal terminators such as phosphoprotein phosphatases and cAMP-specific phosphodiesterases as well as components of other signaling pathways into multiprotein-signaling complexes.

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Zachou, Athena, and Adolfo Bronstein. "Vestibulo-spatial navigation: Pathways and sense of direction." Journal of the Neurological Sciences 429 (October 2021): 117729. http://dx.doi.org/10.1016/j.jns.2021.117729.

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Allen, E. A., and R. D. Freeman. "Dynamic Spatial Processing Originates in Early Visual Pathways." Journal of Neuroscience 26, no. 45 (November 8, 2006): 11763–74. http://dx.doi.org/10.1523/jneurosci.3297-06.2006.

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Chambers, Christopher D., Jonathan M. Payne, Mark G. Stokes, and Jason B. Mattingley. "Fast and slow parietal pathways mediate spatial attention." Nature Neuroscience 7, no. 3 (February 22, 2004): 217–18. http://dx.doi.org/10.1038/nn1203.

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Hrazdina, G., and R. A. Jensen. "Spatial Organization of Enzymes in Plant Metabolic Pathways." Annual Review of Plant Physiology and Plant Molecular Biology 43, no. 1 (June 1992): 241–67. http://dx.doi.org/10.1146/annurev.pp.43.060192.001325.

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METHA, ANDREW B., and PETER LENNIE. "Transmission of spatial information in S-cone pathways." Visual Neuroscience 18, no. 6 (November 2001): 961–72. http://dx.doi.org/10.1017/s095252380118613x.

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The mosaics of S-cones and the neurons to which they are connected are relatively well characterized, so the S-cone system is a good vehicle for exploring how the sampling of the retinal image controls visual performance. We used an interferometer to measure the grating acuity of the S-cone system in the fovea and at a range of eccentricities out to 20 deg. We also developed a simple model observer that, by assuming only that cone pathways are noisy and that signals are subject to eccentricity-dependent postreceptoral pooling, predicts the measured acuities from the sampling properties of the S-cone mosaic. The amount of pooling required to explain performance is consistent with that suggested by anatomical and physiological measurements.

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Alam-Nazki, Aiman, and J. Krishnan. "Spatial Control of Biochemical Modification Cascades and Pathways." Biophysical Journal 108, no. 12 (June 2015): 2912–24. http://dx.doi.org/10.1016/j.bpj.2015.05.012.

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Bowman, Shanna Lynn, Daniel John Shiwarski, and Manojkumar A. Puthenveedu. "Distinct G protein–coupled receptor recycling pathways allow spatial control of downstream G protein signaling." Journal of Cell Biology 214, no. 7 (September 19, 2016): 797–806. http://dx.doi.org/10.1083/jcb.201512068.

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G protein–coupled receptors (GPCRs) are recycled via a sequence-dependent pathway that is spatially and biochemically distinct from bulk recycling. Why there are two distinct recycling pathways from the endosome is a fundamental question in cell biology. In this study, we show that the separation of these two pathways is essential for normal spatial encoding of GPCR signaling. The prototypical β-2 adrenergic receptor (B2AR) activates Gα stimulatory protein (Gαs) on the endosome exclusively in sequence-dependent recycling tubules marked by actin/sorting nexin/retromer tubular (ASRT) microdomains. B2AR was detected in an active conformation in bulk recycling tubules, but was unable to activate Gαs. Protein kinase A phosphorylation of B2AR increases the fraction of receptors localized to ASRT domains and biases the downstream transcriptional effects of B2AR to genes controlled by endosomal signals. Our results identify the physiological relevance of separating GPCR recycling from bulk recycling and suggest a mechanism to tune downstream responses of GPCR signaling by manipulating the spatial origin of G protein signaling.

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Palathingal, Safvan, and G. K. Ananthasuresh. "Analytical modelling of spatial deformation pathways in planar and spatial shallow bistable arches." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 475, no. 2227 (July 2019): 20190164. http://dx.doi.org/10.1098/rspa.2019.0164.

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We analyse spatial bistable arches and present an analytical model incorporating axial, two transverse bending and torsion energy components. We extend the St. Venant and Michell relationship used in flexural-torsional buckling of planar arches and use it in modelling spatial arches. We study deformation pathways in spatial arches and their effect on critical characteristics of bistability such as back and forth switching forces, and the distance travelled by a point of the arch. We show that not considering spatial deformation leads to incorrect inferences concerning the bistability of planar arches too. Thus, this model serves as a generalized framework for the existing analysis on planar arches since they belong to a subset of spatial arches. Additionally, the effects of eccentric loading on spatial deformations are explored for arches with a range of as-fabricated shapes and boundary conditions, and the results are validated with finite-element analysis.

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Li, Xiang, Qinqin Zha, Brigitte Lovell, Jane Reed, Anna Juncker-Jensen, Tricia Peters, and Lakshmi Chandramohan. "Abstract 6778: Spatial analysis of genomic signatures on colorectal cancer pathogenesis using the GeoMx® Digital Spatial Profiler." Cancer Research 83, no. 7_Supplement (April 4, 2023): 6778. http://dx.doi.org/10.1158/1538-7445.am2023-6778.

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Abstract Background: The development of colorectal cancer (CRC) is a complex process, involving multiple sequential molecular aberrations that contribute to disease progression. Understanding the immunopathogenesis of CRC particularly within the spatial context of tumor microenvironment (TME) may elucidate the genomic and biological changes to improve patient prognosis for adjuvant therapies and identifying potential drug targets. However, this can be challenging, as genomic signatures from sub-cellular populations and varying levels of immune cell infiltration in TME may be lost in bulk sequencing. In this study, we used the NanoString GeoMx® Digital Spatial Profiler (DSP) to spatially select epithelial, proximal stromal and distal stromal regions of TMEs on a total of 10 FFPE samples (5 colon cancer patients and 5 healthy donor samples) and profiled up to 1,800 genes included in the Cancer Transcriptome Atlas (CTA) panel. Methods: Selection of regions of interest (ROI) were guided by pathology assessment of H&E images and fluorescent markers (CD45, PanCK, Syto13). Tumor and stroma (proximal and distal) regions were profiled through geometric ROI selection in PanCK+ (epithelial) and CD45+ (stromal/immune) enriched areas respectively, followed by collection of indexed oligonucleotides and sequencing on NextSeq 550 Illumina instrument. Differential expression and pathways enrichment analyses was performed using R BioConductor package DESeq2 and DSP GeoMx analysis suite. A subset of samples were tested for bulk RNA expression using PanCancer IO360 panel on NanoString nCounter Flex system and data analyzed using nSolver software 3.0 and TIS algorithm App. Results: The CTA panel is designed to profile the global immune response and all aspects of tumor microenvironment biology. From differential gene expression analysis of epithelial and distal/proximal stromal ROIs, we have identified biomarkers such as SOX9, IRAK2 and NLRP3 that are specifically upregulated in CRC samples compared to the healthy cohort. Comprehensive pathways analysis revealed an over activation of NF-kB signaling, extracellular matrix organization and interferon signaling pathways in the CRC cohort. Suppression of the NF-kB signaling pathway is a potential therapeutic approach in the treatment of colon cancer. Conclusion: With this spatial study using GeoMx CTA panel, we have highlighted key genes and pathways involved in CRC in order to provide a much-needed understanding of the underlying mechanisms as well as immune signatures in the development of colon cancer. Citation Format: Xiang Li, Qinqin Zha, Brigitte Lovell, Jane Reed, Anna Juncker-Jensen, Tricia Peters, Lakshmi Chandramohan. Spatial analysis of genomic signatures on colorectal cancer pathogenesis using the GeoMx® Digital Spatial Profiler. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6778.

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D’Souza, Jonathan, Felix Prasanna, Luna-Nefeli Valayannopoulos-Akrivou, Peter Sherman, Elise Penn, Shaojie Song, Alexander T. Archibald, and Michael B. McElroy. "Projected changes in seasonal and extreme summertime temperature and precipitation in India in response to COVID-19 recovery emissions scenarios." Environmental Research Letters 16, no. 11 (October 29, 2021): 114025. http://dx.doi.org/10.1088/1748-9326/ac2f1b.

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Abstract Fossil fuel and aerosol emissions have played important roles on climate over the Indian subcontinent over the last century. As the world transitions toward decarbonization in the next few decades, emissions pathways could have major impacts on India’s climate and people. Pathways for future emissions are highly uncertain, particularly at present as countries recover from COVID-19. This paper explores a multimodel ensemble of Earth system models leveraging potential global emissions pathways following COVID-19 and the consequences for India’s summertime (June–July–August–September) climate in the near- and long-term. We investigate specifically scenarios which envisage a fossil-based recovery, a strong renewable-based recovery and a moderate scenario in between the two. We find that near-term climate changes are dominated by natural climate variability, and thus likely independent of the emissions pathway. By 2050, pathway-induced spatial patterns in the seasonally-aggregated precipitation become clearer with a slight drying in the fossil-based scenario and wetting in the strong renewable scenario. Additionally, extreme temperature and precipitation events in India are expected to increase in magnitude and frequency regardless of the emissions scenario, though the spatial patterns of these changes as well as the extent of the change are pathway dependent. This study provides an important discussion on the impacts of emissions recover pathways following COVID-19 on India, a nation which is likely to be particularly susceptible to climate change over the coming decades.

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Ammeux, Noemie, Benjamin E. Housden, Andrew Georgiadis, Yanhui Hu, and Norbert Perrimon. "Mapping signaling pathway cross-talk in Drosophila cells." Proceedings of the National Academy of Sciences 113, no. 35 (August 15, 2016): 9940–45. http://dx.doi.org/10.1073/pnas.1610432113.

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During development and homeostasis, cells integrate multiple signals originating either from neighboring cells or systemically. In turn, responding cells can produce signals that act in an autocrine, paracrine, or endocrine manner. Although the nature of the signals and pathways used in cell–cell communication are well characterized, we lack, in most cases, an integrative view of signaling describing the spatial and temporal interactions between pathways (e.g., whether the signals are processed sequentially or concomitantly when two pathways are required for a specific outcome). To address the extent of cross-talk between the major metazoan signaling pathways, we characterized immediate transcriptional responses to either single- or multiple pathway stimulations in homogeneous Drosophila cell lines. Our study, focusing on seven core pathways, epidermal growth factor receptor (EGFR), bone morphogenetic protein (BMP), Jun kinase (JNK), JAK/STAT, Notch, Insulin, and Wnt, revealed that many ligands and receptors are primary targets of signaling pathways, highlighting that transcriptional regulation of genes encoding pathway components is a major level of signaling cross-talk. In addition, we found that ligands and receptors can integrate multiple pathway activities and adjust their transcriptional responses accordingly.

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Leonova, Anna, Joel Pokorny, and Vivianne C. Smith. "Spatial frequency processing in inferred PC- and MC-pathways." Vision Research 43, no. 20 (September 2003): 2133–39. http://dx.doi.org/10.1016/s0042-6989(03)00333-x.

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Bridgeman, Bruce. "Modeling separate processing pathways for spatial and object vision." Behavioral and Brain Sciences 12, no. 3 (September 1989): 398. http://dx.doi.org/10.1017/s0140525x00056818.

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Yamada, Tomoko, Yue Yang, and Azad Bonni. "Spatial organization of ubiquitin ligase pathways orchestrates neuronal connectivity." Trends in Neurosciences 36, no. 4 (April 2013): 218–26. http://dx.doi.org/10.1016/j.tins.2012.12.004.

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Sanchirico, James N., Heidi J. Albers, Carolyn Fischer, and Conrad Coleman. "Spatial Management of Invasive Species: Pathways and Policy Options." Environmental and Resource Economics 45, no. 4 (November 1, 2009): 517–35. http://dx.doi.org/10.1007/s10640-009-9326-0.

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Kieckbusch, Jan, Joachim Schrautzer, and Michael Trepel. "Spatial heterogeneity of water pathways in degenerated riverine peatlands." Basic and Applied Ecology 7, no. 5 (September 2006): 388–97. http://dx.doi.org/10.1016/j.baae.2006.05.004.

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Chen, Huishu, and Li Yang. "Spatio-Temporal Experience of Tour Routes in the Humble Administrator’s Garden Based on Isovist Analysis." Sustainability 15, no. 16 (August 18, 2023): 12570. http://dx.doi.org/10.3390/su151612570.

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Chinese classical gardens (CCGs), as a distinct spatial category within architectural, historical research, are renowned for creating intricate and ever-changing spatial experiences within confined areas. Despite the existing literature and theories that attempt to explain these rich experiential qualities, many of these explanations need concrete empirical evidence due to the complex nature of gardens, where visual characteristics transform with the movement of people. This study employs a computational analysis method known as isovist to measure the evolving visual features of visitors along four representative pathways within a large-scale garden, the Humble Administrator’s Garden. By analyzing and comparing the changing visual attributes of these four routes, the aim is to validate the relationship between the garden’s pathway system and its spatial structure and assess the influence of pathway selection on the overall garden spatial experience.

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Colbert, Leiam, Benjamin Patterson, Cheng Yi Chen, Nicolas Fernandez, and Jiang He. "Abstract 5885: A pathway-centric approach to characterising tumour heterogeneity and cell diversity across multiple cancer types." Cancer Research 83, no. 7_Supplement (April 4, 2023): 5885. http://dx.doi.org/10.1158/1538-7445.am2023-5885.

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Abstract Biological tissues are composed of heterogeneous populations intricately organized in 3D architectures, yet cell type composition and spatial organization remain largely unknown for most tissue types. Single-cell sequencing analysis provides a systematic and quantitative approach to identify cell types and determine their composition in tissues. However, the spatial organization of cells and cell-cell interactions that are critical for tissue function are lost when cells are dissociated from tissue. This is especially important when working with the complex microenvironment of a tumour where such information is needed to fully understand patient prognosis. Complex diseases such as cancer can be better understood from the perspective of dysregulated pathways, rather than as a disease resulting from alterations of individual genes. Recently, spatially resolved, single-cell imaging platforms have provided a necessary solution to bridge the spatial information gap evident in previous transcriptomic methodologies. Vizgen’s MERSCOPE platform, built on multiplexed error robust in situ hybridisation (MERFISH) technology, enables the direct profiling of the spatial organisation of intact tissue with subcellular resolution. Here, we present a Pan-Cancer approach to characterise various cancers in human clinical samples with MERSCOPE. Using a 500-gene panel that includes the canonical signalling pathways of cancer, cancer type-specific genes, key immune genes, proto-oncogenes, and tumour-suppressor genes we demonstrate MERSCOPE’s ability to spatially profile gene expression across multiple tumour samples, including breast, colon, prostate, ovarian, lung, and skin cancer. To confirm the specificity and sensitivity of our pathway-focused gene panel, we assessed how tumour cell clusters in each dataset expressed different cancer type-specific markers. As expected, we found specific cancer types enriched in corresponding marker genes. To further evaluate how individual cell types in each tumour are dysregulated by cancer, we compared non-tumour cell clusters to similarly annotated clusters derived from single-cell RNA-sequencing data of normal tissue. Notably, the non-tumour cells in these datasets exhibit higher expression of stress and inflammation pathways, while immune cell clusters demonstrate higher immune activity and higher immune exhaustion compared to those in normal tissue. These results demonstrate the power of the MERSCOPE platform to generate individualised, accurate cell atlases from patient-derived tumours and to enable further insights into the relationship between genomic profiles, dysregulated pathways, and disease phenotype. Such network-centric approaches are critical for identifying genotypic causes of diseases, classifying disease subtypes, and identifying drug targets. Citation Format: Leiam Colbert, Benjamin Patterson, Cheng Yi Chen, Nicolas Fernandez, Jiang He. A pathway-centric approach to characterising tumour heterogeneity and cell diversity across multiple cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5885.

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Gill, Kyle G., Anthony W. D’Amato, and Shawn Fraver. "Multiple developmental pathways for range-margin Pinus banksiana forests." Canadian Journal of Forest Research 46, no. 2 (February 2016): 200–214. http://dx.doi.org/10.1139/cjfr-2015-0321.

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Empirical knowledge of forest structure and development in early successional and range-margin populations is often lacking, limiting our ability to effectively model and manage these forests. Such is the case for jack pine (Pinus banksiana Lamb.) in central Minnesota, USA, where it reaches its southwestern range limit. Our objective was to quantify this population’s historical range of variability of structural conditions and developmental pathways. We collected structural, spatial, and dendrochronological data on 0.25 ha plots from 10 jack pine dominated sites that initiated and developed outside of active management. Our results revealed a broad range of structural characteristics and developmental pathways, including rapid and protracted recruitment windows (5–50 years), with subsequent even- and uneven-aged structures, and random and clumped stem spatial arrangements. As such, these mature, early successional forests often displayed a degree of complexity more typically associated with old-growth forests. Our findings suggest that this population, like other southern range-margin populations with mostly nonserotinous cones, historically followed a variety of stand development pathways and did not solely follow the rapid establishment, even-aged pathway often attributed to this forest type. We suggest that even- and uneven-aged silvicultural systems should be used to reflect this historical range of developmental pathways and to increase resilience and adaptability.

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Mao, Yao, Jian'an Ren, and Jieshou Li. "Regulated Spatial Distribution of Cyclooxygenases and Lipoxygenases in Crohn's Ulcer." Mediators of Inflammation 2006 (2006): 1–6. http://dx.doi.org/10.1155/mi/2006/89581.

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Background and Aims. Arachidonic acid metabolism actively participates in the initiation, climaxing, and resolution phases of inflammation, and its close connection with inflammatory bowel diseases has been only recently discovered. We aimed to clarify the role of different arachidonic pathways and the interrelationships between them in Crohn's disease.Methods. Seventeen specimens of Crohn's disease dated between 2003/1/1 and 2005/1/1 were collected and underwent immunohistochemical analyses with cylcooxygenase 1, cyclooxygenase 2, 5-lipoxygenase, and 15-lipoxygenase-1 antibodies.Results. (1) The spatial distribution of the three leading enzymes in arachidonic acid pathway—cyclooxygenase 2, 5-lipoxygenase, and 15-lipoxygenase-1—followed sequential arrangement in Crohn's ulcer: neutrophils highly expressing 5-lipoxygenase were in the utmost surface which bordered the band of cyclooxygenase-2 expression that is located just beneath it, and in the lower layers and below the granulation region were eosinophils carrying 15-lipoxygeanse-1. (2) Cyclooxygenase-2 and 15-Lipoxygenase-1-positive cells formed two barrier-like structures that possibly inhibited neutrophil infiltration.Conclusion. The regulated distribution indicated coordinated interplay between inflammatory cells and parenchymal cells, between arachidonic acid pathways, and between innate and adaptive immunity; and the barrier-like structures indicated protective roles for cyclooxygenase 2 and 15-Lipoxygenase-1 in Crohn's disease.

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Lehky, Sidney R., and Anne B. Sereno. "Comparison of Shape Encoding in Primate Dorsal and Ventral Visual Pathways." Journal of Neurophysiology 97, no. 1 (January 2007): 307–19. http://dx.doi.org/10.1152/jn.00168.2006.

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Ventral and dorsal visual pathways perform fundamentally different functions. The former is involved in object recognition, whereas the latter carries out spatial localization of stimuli and visual guidance of motor actions. Despite the association of the dorsal pathway with spatial vision, recent studies have reported shape selectivity in the dorsal stream. We compared shape encoding in anterior inferotemporal cortex (AIT), a high-level ventral area, with that in lateral intraparietal cortex (LIP), a high-level dorsal area, during a fixation task. We found shape selectivities of individual neurons to be greater in anterior inferotemporal cortex than in lateral intraparietal cortex. At the neural population level, responses to different shapes were more dissimilar in AIT than LIP. Both observations suggest a greater capacity in AIT for making finer shape distinctions. Multivariate analyses of AIT data grouped together similar shapes based on neural population responses, whereas such grouping was indistinct in LIP. Thus in a first comparison of shape response properties in late stages of the two visual pathways, we report that AIT exhibits greater capability than LIP for both object discrimination and generalization. These differences in the two visual pathways provide the first neurophysiological evidence that shape encoding in the dorsal pathway is distinct from and not a mere duplication of that formed in the ventral pathway. In addition to shape selectivity, we observed stimulus-driven cognitive effects in both areas. Stimulus repetition suppression in LIP was similar to the well-known repetition suppression in AIT and may be associated with the “inhibition of return” memory effect observed during reflexive attention.

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Benedek, K., J. Tajti, M. Janáky, L. Vécsei, and G. Benedek. "Spatial Contrast Sensitivity of Migraine Patients Without Aura." Cephalalgia 22, no. 2 (March 2002): 142–45. http://dx.doi.org/10.1046/j.1468-2982.2002.00351.x.

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Visual disturbances are frequent symptoms in migraine. Since there is a possibility of separate damage in the magno- or parvo-cellular visual pathway in migraine patients, we performed a study including the measurement of static and dynamic spatial contrast sensitivity on 15 patients suffering from migraine without aura under photopic and scotopic conditions. Fifteen healthy volunteers without primary headache served as controls. The results revealed a marked decrease in contrast sensitivity at low spatial frequencies in the migraine patients. Spatial contrast sensitivity demonstrated some lateralization, as the sensitivity to low spatial frequencies obtained through separate eyes showed significantly larger side-differences in migraine patients than in control subjects. These findings suggest that the mechanisms responsible for vision at low spatial frequencies are impaired in migraine patients. This might indicate impaired function of the magnocellular pathways in this condition.

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Arora, Rohit, Christian Cao, Mehul Kumar, Ayan Chanda, Divya Samuel, Wayne Matthews, Shamir Chandarana, et al. "Spatial transcriptomics unravels novel signaling patterns at the leading edge of oral squamous cell carcinoma." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): e18043-e18043. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e18043.

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e18043 Background: Head and neck cancer is the 6th most common cancer worldwide. Oral squamous cell carcinoma (OSCC) is the most prevalent head and neck cancer that is characterized by aggressive local invasion and metastasis. Despite the leading edge (invasive front) of the tumor being a driver of OSCC pathophysiology, its biology and clinical relevance have not been fully characterized. We used spatial transcriptomics to explore signaling patterns within the leading edge and tumor core. Methods: Fresh-frozen, surgically resected OSCC samples from three HPV-negative OSCC patients were profiled using the 10x Genomics Visium Spatial Gene Expression platform. Leading edge and tumor core regions were defined by pathologist annotations and expression of previously identified edge and core gene signatures from the literature. Spatial differential gene expression (DGE) analysis and pathway analysis was performed using the Seurat package and Ingenuity Pathway Analysis (IPA), respectively. Cell-cell interaction networks were reconstructed using the CellChat package. Results: The leading edge and tumor core displayed unique transcriptional and signaling profiles that were conserved across all three OSCC patient samples. DEG analysis revealed 31 genes enriched in the leading edge and 62 genes enriched in the tumor core with a log2FC > 0.58 and adjusted p-value < 0.01. The top genes upregulated in the leading edge were FN1, COL1A1, COL1A2, IFITM3, and SPARC. Top tumor-core genes included CRCT1, LCE3D, DEFB4A, SPRR2A, and CNFN. IPA analysis of upregulated DEGs in the leading edge and tumor core predicted the activation of wound healing and GP6 signaling pathways, and activation of intrinsic prothrombin activation and MSP-RON signaling pathways, respectively. Cell communication analysis revealed that the leading edge had higher intercellular signaling than the tumor core. Upregulated leading edge cell signaling modules included collagen, CD99, CSPG4, and non-canonical WNT pathways, which have been linked to tumor invasion, metastasis, and adhesion. COL1A1 and COL1A2 ligands and CD44 and SDC1 receptors were upregulated in leading edge signaling. The tumor core was enriched for ANGPTL and PERIOSTIN cell signaling modules. Conclusions: This is the first study to characterize the tumor core and leading edge of OSCC tumors using spatial transcriptomics. Further investigation of the therapeutic potential of identified signaling pathways may improve OSCC outcomes.

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Arora, Rohit, Christian Cao, Mehul Kumar, Ayan Chanda, Divya Samuel, Wayne Matthews, Shamir Chandarana, et al. "Spatial transcriptomics unravels novel signaling patterns at the leading edge of oral squamous cell carcinoma." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): e18043-e18043. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e18043.

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e18043 Background: Head and neck cancer is the 6th most common cancer worldwide. Oral squamous cell carcinoma (OSCC) is the most prevalent head and neck cancer that is characterized by aggressive local invasion and metastasis. Despite the leading edge (invasive front) of the tumor being a driver of OSCC pathophysiology, its biology and clinical relevance have not been fully characterized. We used spatial transcriptomics to explore signaling patterns within the leading edge and tumor core. Methods: Fresh-frozen, surgically resected OSCC samples from three HPV-negative OSCC patients were profiled using the 10x Genomics Visium Spatial Gene Expression platform. Leading edge and tumor core regions were defined by pathologist annotations and expression of previously identified edge and core gene signatures from the literature. Spatial differential gene expression (DGE) analysis and pathway analysis was performed using the Seurat package and Ingenuity Pathway Analysis (IPA), respectively. Cell-cell interaction networks were reconstructed using the CellChat package. Results: The leading edge and tumor core displayed unique transcriptional and signaling profiles that were conserved across all three OSCC patient samples. DEG analysis revealed 31 genes enriched in the leading edge and 62 genes enriched in the tumor core with a log2FC > 0.58 and adjusted p-value < 0.01. The top genes upregulated in the leading edge were FN1, COL1A1, COL1A2, IFITM3, and SPARC. Top tumor-core genes included CRCT1, LCE3D, DEFB4A, SPRR2A, and CNFN. IPA analysis of upregulated DEGs in the leading edge and tumor core predicted the activation of wound healing and GP6 signaling pathways, and activation of intrinsic prothrombin activation and MSP-RON signaling pathways, respectively. Cell communication analysis revealed that the leading edge had higher intercellular signaling than the tumor core. Upregulated leading edge cell signaling modules included collagen, CD99, CSPG4, and non-canonical WNT pathways, which have been linked to tumor invasion, metastasis, and adhesion. COL1A1 and COL1A2 ligands and CD44 and SDC1 receptors were upregulated in leading edge signaling. The tumor core was enriched for ANGPTL and PERIOSTIN cell signaling modules. Conclusions: This is the first study to characterize the tumor core and leading edge of OSCC tumors using spatial transcriptomics. Further investigation of the therapeutic potential of identified signaling pathways may improve OSCC outcomes.

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Richardson, Thomas O., and Thomas E. Gorochowski. "Beyond contact-based transmission networks: the role of spatial coincidence." Journal of The Royal Society Interface 12, no. 111 (October 2015): 20150705. http://dx.doi.org/10.1098/rsif.2015.0705.

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Animal societies rely on interactions between group members to effectively communicate and coordinate their actions. To date, the transmission properties of interaction networks formed by direct physical contacts have been extensively studied for many animal societies and in all cases found to inhibit spreading. Such direct interactions do not, however, represent the only viable pathways. When spreading agents can persist in the environment, indirect transmission via ‘same-place, different-time’ spatial coincidences becomes possible. Previous studies have neglected these indirect pathways and their role in transmission. Here, we use rock ant colonies, a model social species whose flat nest geometry, coupled with individually tagged workers, allowed us to build temporally and spatially explicit interaction networks in which edges represent either direct physical contacts or indirect spatial coincidences. We show how the addition of indirect pathways allows the network to enhance or inhibit the spreading of different types of agent. This dual-functionality arises from an interplay between the interaction-strength distribution generated by the ants' movement and environmental decay characteristics of the spreading agent. These findings offer a general mechanism for understanding how interaction patterns might be tuned in animal societies to control the simultaneous transmission of harmful and beneficial agents.

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Costa, Michelle N., Krishnan Radhakrishnan, Bridget S. Wilson, Dionisios G. Vlachos, and Jeremy S. Edwards. "Coupled Stochastic Spatial and Non-Spatial Simulations of ErbB1 Signaling Pathways Demonstrate the Importance of Spatial Organization in Signal Transduction." PLoS ONE 4, no. 7 (July 23, 2009): e6316. http://dx.doi.org/10.1371/journal.pone.0006316.

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Levitan, Bennett, and Gershon Buchsbaum. "Parallel cone bipolar to on-β ganglion cell pathways in the cat retina: spatial responses, spatial aliasing, and spatial variance." Journal of the Optical Society of America A 13, no. 6 (June 1, 1996): 1152. http://dx.doi.org/10.1364/josaa.13.001152.

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Battista, Josephine, David R. Badcock, and Allison M. McKendrick. "Spatial Summation Properties for Magnocellular and Parvocellular Pathways in Glaucoma." Investigative Opthalmology & Visual Science 50, no. 3 (March 1, 2009): 1221. http://dx.doi.org/10.1167/iovs.08-2517.

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Thomas, K. L., S. Laroche, M. L. Errington, T. V. P. Bliss, and S. P. Hunt. "Spatial and temporal changes in signal transduction pathways during LTP." Neuron 13, no. 3 (September 1994): 737–45. http://dx.doi.org/10.1016/0896-6273(94)90040-x.

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Nicodemi, Mario, and Antonella Prisco. "Thermodynamic Pathways to Genome Spatial Organization in the Cell Nucleus." Biophysical Journal 96, no. 6 (March 2009): 2168–77. http://dx.doi.org/10.1016/j.bpj.2008.12.3919.

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Wang, Chengjin, César Ducruet, and Wei Wang. "Port integration in China: Temporal pathways, spatial patterns and dynamics." Chinese Geographical Science 25, no. 5 (March 4, 2015): 612–28. http://dx.doi.org/10.1007/s11769-015-0752-3.

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Burgess, Harold A., Hannah Schoch, and Michael Granato. "Distinct Retinal Pathways Drive Spatial Orientation Behaviors in Zebrafish Navigation." Current Biology 20, no. 4 (February 2010): 381–86. http://dx.doi.org/10.1016/j.cub.2010.01.022.

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Journal articles on the topic 'Spatial pathways'

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