Journal articles: 'Biophysical transition'

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Van Dyke, Chris. "Boxing daze – using state-and-transition models to explore the evolution of socio-biophysical landscapes." Progress in Physical Geography: Earth and Environment 39, no. 5 (May 17, 2015): 594–621. http://dx.doi.org/10.1177/0309133315581700.

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Critical physical geography (CPG) proposes to bridge the lingering gap between human and physical geographers. To rejuvenate conversations among different corners of the discipline about the possibility of trans-disciplinary collaboration, CPG must provide unique epistemological, methodological, and conceptual frameworks that human and physical geographers alike will find appealing, relevant, and timely. These should help them perceptively characterize, narrate, and anticipate changes in socio-biophysical landscapes. This paper outlines a conceptual framework that can be harnessed in future CPG studies and reflects on what it means to be a critical geographer. To solve the epistemological dilemmas confronting CPG, this paper demonstrates that state-and-transition models (STMs) can provide a unifying framework to address questions about socio-biophysical landscape evolution. Originally developed to account for nonlinear dynamics in rangeland ecosystems, STMs have been used to analyze a variety of ecological, geomorphic, and hydrological transitions in complex biophysical landscapes. STMs have epistemological commonalities with explanatory frameworks pioneered by political ecologists, and while thus far they have been used to account for complex biophysical dynamics, they can be expanded to accommodate critical investigations of the social dynamics underpinning landscape change. By foregrounding the transitional dynamics of socio-biophysical landscape – a theme that has interested physical and critical human geographers – STMs establish a conceptual space in which to holistically interpret the interacting drivers that underwrite socio-biophysical landscape change.

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Larson, Ben T., Teresa Ruiz-Herrero, Stacey Lee, Sanjay Kumar, L. Mahadevan, and Nicole King. "Biophysical principles of choanoflagellate self-organization." Proceedings of the National Academy of Sciences 117, no. 3 (January 2, 2020): 1303–11. http://dx.doi.org/10.1073/pnas.1909447117.

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Inspired by the patterns of multicellularity in choanoflagellates, the closest living relatives of animals, we quantify the biophysical processes underlying the morphogenesis of rosette colonies in the choanoflagellate Salpingoeca rosetta. We find that rosettes reproducibly transition from an early stage of 2-dimensional (2D) growth to a later stage of 3D growth, despite the underlying variability of the cell lineages. Our perturbative experiments demonstrate the fundamental importance of a basally secreted extracellular matrix (ECM) for rosette morphogenesis and show that the interaction of the ECM with cells in the colony physically constrains the packing of proliferating cells and, thus, controls colony shape. Simulations of a biophysically inspired model that accounts for the size and shape of the individual cells, the fraction of ECM, and its stiffness relative to that of the cells suffices to explain our observations and yields a morphospace consistent with observations across a range of multicellular choanoflagellate colonies. Overall, our biophysical perspective on rosette development complements previous genetic perspectives and, thus, helps illuminate the interplay between cell biology and physics in regulating morphogenesis.

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UEMURA, Sotaro. "Importance of Research Field Transition with Biophysical Standpoint." Seibutsu Butsuri 52, no. 2 (2012): 096–97. http://dx.doi.org/10.2142/biophys.52.096.

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Oelschlaeger, Max. "Ecosemiotics and the sustainability transition." Sign Systems Studies 29, no. 1 (December 31, 2001): 219–36. http://dx.doi.org/10.12697/sss.2001.29.1.14.

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The emerging epistemic community of ecosemioticians and the multidisciplinary field of inquiry known as ecosemiotics offer a radical and relevant approach to so-called global environmental crisis. There are no environmental fixes within the dominant code, since that code overdetermines the future, thereby perpetuating ecologically untenable cultural forms. The possibility of a sustainability transition (the attempt to overcome destitution and avoid ecocatastrophe) becomes real when mediated by and through ecosemiotics. In short, reflexive awareness of humankind's linguisticality is a necessary condition for transforming ecologically maladaptive cultural forms. As a multidisciplinary, interdisciplinary research program integrating the human and natural sciences, ecosemiotic inquiry closes the gap between biophysical ecology and human ecology. A provisional outline of a pragmatic theory of ecoserniotics attempts to describe the processes by which adaptive cultural changes might be facilitated and points toward substantive content areas that constitute sites for further research. Ecosemiotic inquiry frames cultural codes as these shape and reproduce the ongoing stream of individual and societal choices that shape distinctively human existence in a larger context of biophysical realities that drive natural selection. However, while ecosemiotics is a necessary condition for the sustainability transition, it is not a sufficient condition.

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Olson, Donald B. "Biophysical dynamics of western transition zones: a preliminary synthesis." Fisheries Oceanography 10, no. 2 (June 2001): 133–50. http://dx.doi.org/10.1046/j.1365-2419.2001.00161.x.

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Fernandez, Fernando R., Jordan D. T. Engbers, and Ray W. Turner. "Firing Dynamics of Cerebellar Purkinje Cells." Journal of Neurophysiology 98, no. 1 (July 2007): 278–94. http://dx.doi.org/10.1152/jn.00306.2007.

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Knowledge of intrinsic neuronal firing dynamics is a critical first step to establishing an accurate biophysical model of any neuron. In this study we examined cerebellar Purkinje cells to determine the bifurcations likely to underlie firing dynamics within a biophysically realistic and experimentally supported model. We show that Purkinje cell dynamics are consistent with a system undergoing a saddle-node bifurcation of fixed points in the transition from rest to firing and a saddle homoclinic bifurcation from firing to rest. Our analyses account for numerous observed Purkinje cell firing properties that include bistability, plateau potentials, specific aspects of the frequency–current ( F– I) relationship, first spike latency, and the ability for climbing fiber input to induce state transitions in the bistable regime. We also experimentally confirm new properties predicted from our model and analysis that include the presence of a depolarizing afterpotential (DAP), the ability to fire at low frequencies (<50 Hz) and with a high gain in the F– I relationship, and a bistable region limited to low-frequency firing. Purkinje cell dynamics, including bistability, prove to arise from numerous biophysical factors that include the DAP, fast refractory dynamics, and a long membrane time constant. A hyperpolarizing activated cation current ( IH) is shown not to be directly involved in establishing bistable dynamics but rather reduces the range for bistability. A combined electrophysiological and modeling approach thus accounts for several properties of Purkinje cells, providing a firm basis from which to assess Purkinje cell output patterns.

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Singh, Simron Jit, and Clemens M. Grünbühel. "Environmental relations and biophysical transition: the case of trinket island." Geografiska Annaler: Series B, Human Geography 85, no. 4 (December 2003): 191–208. http://dx.doi.org/10.1111/j.0435-3684.2003.00142.x.

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Lu, Yi, Amdrea K. Brown, Juewen Liu, Jing Li, and Peter J. Bruesehoff. "Biochemical and biophysical study of transition metal ion-dependent DNAzymes." Journal of Inorganic Biochemistry 96, no. 1 (July 2003): 182. http://dx.doi.org/10.1016/s0162-0134(03)80695-5.

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Tesloianu, Nicolae Dan, Lucian Dobreci, Vlad Ghizdovat, Andrei Zala, Adrian Valentin Cotirlet, Alina Gavrilut, Maricel Agop, et al. "Multifractality through Non-Markovian Stochastic Processes in the Scale Relativity Theory. Acute Arterial Occlusions as Scale Transitions." Entropy 23, no. 4 (April 9, 2021): 444. http://dx.doi.org/10.3390/e23040444.

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By assimilating biological systems, both structural and functional, into multifractal objects, their behavior can be described in the framework of the scale relativity theory, in any of its forms (standard form in Nottale’s sense and/or the form of the multifractal theory of motion). By operating in the context of the multifractal theory of motion, based on multifractalization through non-Markovian stochastic processes, the main results of Nottale’s theory can be generalized (specific momentum conservation laws, both at differentiable and non-differentiable resolution scales, specific momentum conservation law associated with the differentiable–non-differentiable scale transition, etc.). In such a context, all results are explicated through analyzing biological processes, such as acute arterial occlusions as scale transitions. Thus, we show through a biophysical multifractal model that the blocking of the lumen of a healthy artery can happen as a result of the “stopping effect” associated with the differentiable-non-differentiable scale transition. We consider that blood entities move on continuous but non-differentiable (multifractal) curves. We determine the biophysical parameters that characterize the blood flow as a Bingham-type rheological fluid through a normal arterial structure assimilated with a horizontal “pipe” with circular symmetry. Our model has been validated based on experimental clinical data.

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Lima, Igor, Ambuja Navalkar, Samir K. Maji, Jerson L. Silva, Guilherme A. P. de Oliveira, and Elio A. Cino. "Biophysical characterization of p53 core domain aggregates." Biochemical Journal 477, no. 1 (January 8, 2020): 111–20. http://dx.doi.org/10.1042/bcj20190778.

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Aggregation is the cause of numerous protein conformation diseases. A common facet of these maladies is the transition of a protein from its functional native state into higher order forms, such as oligomers and amyloid fibrils. p53 is an essential tumor suppressor that is prone to such conformational transitions, resulting in its compromised ability to avert cancer. This work explores the biophysical properties of early-, mid-, and late-stage p53 core domain (p53C) aggregates. Atomistic and coarse-grained molecular dynamics (MD) simulations suggest that early- and mid-stage p53C aggregates have a polymorphic topology of antiparallel and parallel β-sheets that localize to the core amyloidogenic sequence. Both topologies involve similar extents of interstrand mainchain hydrogen bonding, while sidechain interactions could play a role in regulating strand orientation. The free energy difference between the antiparallel and parallel states was within statistical uncertainty. Negative stain electron microscopy of mature fibrils shows a wide distribution of fiber widths, indicating that polymorphism may extend to the quaternary structure level. Circular dichroism of the fibrils was indicative of β-sheet rich structures in atypical conformations. The Raman spectrum of aggregated p53C was consistent with a mixture of arranged β-sheets and heterogeneous structural elements, which is compatible with the MD findings of an ordered β-sheet nucleus flanked by disordered structure. Structural polymorphism is a common property of amyloids; however, because certain polymorphs of the same protein can be more harmful than others, going forward it will be pertinent to establish correlations between p53C aggregate structure and pathology.

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Seufferheld, Manfredo J., and Cecil Stushnoff. "SUCROSE AND DEHYDRATION INDUCE GLASS TRANSITIONS DURING CRYOPRESERVATION OF STRAWBERRY PLANTLETS." HortScience 28, no. 5 (May 1993): 584f—584. http://dx.doi.org/10.21273/hortsci.28.5.584f.

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Differential scanning calorimetry was used to study the effects of sucrose and dehydration on biophysical aspects during cryopreservation of strawberry plantlets, regenerated from leaf disks. Plantlets were encapsulated in alginate beads, soaked 24, 48, 72 and 96 hours in sucrose solutions (0 to 2.0 M) and dehydrated. Imbibition in 1.0 - 2.0 M sucrose and controlled desiccation influenced both ice nucleation and glass transitions during cryopreservation. A surprising discovery was the presence of an exotherm at -100C (sucrose 1.5 and 2.0 M samples imbibed for 48 hours and desiccated 4 hours). The exotherm disappeared and was replaced by a glass transition when imbibition time was increased to (72 hours). Phase diagrams from the DSC data, illustrate a sucrose concentration dependency in the range of 1.0 to 2.0 M, where exotherms occur. We conclude that imbibition with sucrose, coupled with desiccation treatments, may be used to manipulate the biophysical properties of freeze tender tissues to permit successful cryopreservation. Strawberry plantlets provide an ideal model to study this behavior.

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Amschler, Katharina, and Michael P. Schön. "Modulating Tumor Cell Functions by Tunable Nanopatterned Ligand Presentation." Nanomaterials 10, no. 2 (January 26, 2020): 212. http://dx.doi.org/10.3390/nano10020212.

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Cancer comprises a large group of complex diseases which arise from the misrouted interplay of mutated cells with other cells and the extracellular matrix. The extracellular matrix is a highly dynamic structure providing biochemical and biophysical cues that regulate tumor cell behavior. While the relevance of biochemical signals has been appreciated, the complex input of biophysical properties like the variation of ligand density and distribution is a relatively new field in cancer research. Nanotechnology has become a very promising tool to mimic the physiological dimension of biophysical signals and their positive (i.e., growth-promoting) and negative (i.e., anti-tumoral or cytotoxic) effects on cellular functions. Here, we review tumor-associated cellular functions such as proliferation, epithelial-mesenchymal transition (EMT), invasion, and phenotype switch that are regulated by biophysical parameters such as ligand density or substrate elasticity. We also address the question of how such factors exert inhibitory or even toxic effects upon tumor cells. We describe three principles of nanostructured model systems based on block copolymer nanolithography, electron beam lithography, and DNA origami that have contributed to our understanding of how biophysical signals direct cancer cell fate.

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Subbalakshmi, Ayalur Raghu, Bazella Ashraf, and Mohit Kumar Jolly. "Biophysical and biochemical attributes of hybrid epithelial/mesenchymal phenotypes." Physical Biology 19, no. 2 (February 7, 2022): 025001. http://dx.doi.org/10.1088/1478-3975/ac482c.

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Abstract The epithelial–mesenchymal transition (EMT) is a biological phenomenon associated with explicit phenotypic and molecular changes in cellular traits. Unlike the earlier-held popular belief of it being a binary process, EMT is now thought of as a landscape including diverse hybrid E/M phenotypes manifested by varying degrees of the transition. These hybrid cells can co-express both epithelial and mesenchymal markers and/or functional traits, and can possess the property of collective cell migration, enhanced tumor-initiating ability, and immune/targeted therapy-evasive features, all of which are often associated with worse patient outcomes. These characteristics of the hybrid E/M cells have led to a surge in studies that map their biophysical and biochemical hallmarks that can be helpful in exploiting their therapeutic vulnerabilities. This review discusses recent advances made in investigating hybrid E/M phenotype(s) from diverse biophysical and biochemical aspects by integrating live cell-imaging, cellular morphology quantification and mathematical modeling, and highlights a set of questions that remain unanswered about the dynamics of hybrid E/M states.

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Pages, Benjamin J., Dale L. Ang, Elisé P. Wright, and Janice R. Aldrich-Wright. "Metal complex interactions with DNA." Dalton Transactions 44, no. 8 (2015): 3505–26. http://dx.doi.org/10.1039/c4dt02700k.

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Increasing numbers of DNA structures are being revealed using a diverse range of transition metal complexes and biophysical spectroscopic techniques. Here we present a review of metal complex-DNA interactions in which several binding modes and DNA structural forms are explored.

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Chen, Jiabin, and Shaobo Wen. "Implications of Energy Intensity Ratio for Carbon Dioxide Emissions in China." Sustainability 12, no. 17 (August 26, 2020): 6925. http://dx.doi.org/10.3390/su12176925.

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Industrial carbon dioxide (CO2) emissions are mainly derived from fossil energy use, which is composed of procedures involving extraction of energy from the natural system as well as its exchange and consumption in the social system. However, recent research on low-carbon transitions considers the cost of energy commodities from a separate perspective—a biophysical or monetary perspective. We introduce the energy intensity ratio (EIR), which is a novelty perspective combining biophysical and monetary metrics to estimate the cost of energy commodities in the low-carbon energy transitions. This combination is essential, since the feedback of energy into the biophysical system will influence the performance of energy in the economic system and vice versa. Based on the Logarithmic Mean Divisia Index (LMDI), we developed the EIR-LMDI method to explain the changes in CO2 emissions. The changes in CO2 emissions caused by the EIR are the net energy effect. In China, the net energy effect kept CO2 emissions at a compound annual growth rate of 6.15% during 2007–2018. Especially after 2014, the net energy effect has been the largest driver of the increase in CO2 emissions. During the study period, high net energy usually indicated high CO2 emissions. Coal is the most important energy commodity and dominates the net energy effect; the least volatile component is the EIR of natural gas. The EIR affects CO2 emissions by the price crowding-out effect and the scale expansion effect, which make the process of low-carbon transition uncertain. The results illuminate that policymakers should monitor the net energy effect to prevent it from offsetting efforts to reduce energy intensity.

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Villers, Manon, Daniela C. A. Pigosso, Thomas J. Howard, and Tim C. McAloone. "Towards a unified absolute environmental sustainability decoupling indicator." Proceedings of the Design Society 4 (May 2024): 1507–16. http://dx.doi.org/10.1017/pds.2024.153.

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AbstractManufacturing firms are facing the critical need to manage their business growth while staying within the biophysical limits of the planet. Absolute environmental sustainability decoupling (AESD) combines these goals and is one of the keys for manufacturing firms to achieve their sustainable transition. This study offers an initial contribution to categorise decoupling at the firm level while incorporating absolute environmental sustainability goals. It also explores the role of design in achieving AESD and opens doors for further research on manufacturing firms' sustainability transition.

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Ciaccia, Corrado, Elena Testani, Angelo Fiore, Ileana Iocola, Marta Di Pierro, Giuseppe Mele, Filippo Ferlito, et al. "Organic Agroforestry Long-Term Field Experiment Designing Trough Actors’ Knowledge towards Food System Sustainability." Sustainability 13, no. 10 (May 15, 2021): 5532. http://dx.doi.org/10.3390/su13105532.

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The implementation of agroecology principles within organic farming research is a crux to redesign sustainable agri-food systems. To govern this transition, the local research demand should be addressed by direct engagement of all stakeholders in the research process. The first step is the involvement of farmers and technicians, with the aim of restoring their decision-making role, switching governance to local scale. The co-design/co-management of Long-Term Experiments (LTEs) can be crucial to govern the above-described transition through networking and participatory activities. In this study, we report the experience of co-designing a new LTE in Southern Italy by local actors and scientists. Through a participatory action research methodology, an LTE was considered as a biophysical component of an agroecological living lab, a public–private environment aimed to design a local food system. The setup of parallel field trials in satellite farms stands for the other biophysical component, whereas the stakeholder platform represents the social one. Through definition of common objectives, a step-by-step process is presented, which highlights the interest of local organic actors to share ideas and perspectives for the territory, pointing out the inclusion of end-users (the consumers) in the process to complete the transition to sustainable food systems.

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Korkut, Anil, and Wayne A. Hendrickson. "Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase." Proceedings of the National Academy of Sciences 106, no. 37 (August 25, 2009): 15673–78. http://dx.doi.org/10.1073/pnas.0907684106.

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Many proteins function through conformational transitions between structurally disparate states, and there is a need to explore transition pathways between experimentally accessible states by computation. The sizes of systems of interest and the scale of conformational changes are often beyond the scope of full atomic models, but appropriate coarse-grained approaches can capture significant features. We have designed a comprehensive knowledge-based potential function based on a Cα representation for proteins that we call the virtual atom molecular mechanics (VAMM) force field. Here, we describe an algorithm for using the VAMM potential to describe conformational transitions, and we validate this algorithm in application to a transition between open and closed states of adenylate kinase (ADK). The VAMM algorithm computes normal modes for each state and iteratively moves each structure toward the other through a series of intermediates. The move from each side at each step is taken along that normal mode showing greatest engagement with the other state. The process continues to convergence of terminal intermediates to within a defined limit—here, a root-mean-square deviation of 1 Å. Validations show that the VAMM algorithm is highly effective, and the transition pathways examined for ADK are compatible with other structural and biophysical information. We expect that the VAMM algorithm can address many biological systems.

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Ivo, Israel Oliveira, Marcelo Sacardi Biudes, Rayanna de Oliveira Costa, Nadja Gomes Machado, Luiz Octávio Fabrício Do Santos, and Altemar Lopes Pedreira Junior. "VARIAÇÃO TEMPORAL DE PARÂMETROS BIOFÍSICOS DA SUPERFÍCIE POR IMAGENS Landsat 5 EM DIFERENTES COBERTURAS DO SOLO EM UMA ÁREA DE TRANSIÇÃO DE CERRADO E PANTANAL EM MATO GROSSO." Nativa 8, no. 5 (September 25, 2020): 597–602. http://dx.doi.org/10.31413/nativa.v8i5.10064.

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A substituição da vegetação nativa e a sazonalidade climática modificam os parâmetros biofísicos da superfície. Como 50% do Cerrado tem sido convertido em lavouras e pastagens, o objetivo desse estudo foi avaliar a variação temporal de parâmetros biofísicos em áreas nativas e convertidas em uma área de transição entre Cerrado e Pantanal no Mato Grosso. O estudo foi conduzido na Fazenda Experimental da UFMT (15° 51’ 15.23’’ S e 56° 04’ 13.50’’ W) com imagens do sensor TM-Landsat 5 entre abril e setembro de 2011. O Índice de Vegetação da Diferença Normalizada (NDVI), o albedo da superfície (α) e a temperatura da superfície (Ts) foram estimados em áreas de Cerrado strito sensu (CER), pastagem de Brachiaria brizantha (PAS) e mangueiral (MAN). Os maiores valores de NDVI e menores valores de α e Ts foram observados nas áreas mais densamente vegetadas. O Cerrado apresentou menores valores de α e a MAN apresentou maiores valores de NDVI ao longo de todo experimento. A substituição da cobertura nativa da região de transição de Cerrado e Pantanal por vegetação exótica modificou significativamente os parâmetros biofísicos avaliados, com potencial de modificar os balanços de radiação, energia, carbono da superfície. Palavras-chave: desmatamento; sensoriamento remoto; aquecimento regional. TEMPORAL VARIATION OF BIOPHYSICAL PARAMETERS OF THE SURFACE BY LANDSAT 5 IMAGES IN DIFFERENT SOIL COVERS IN A TRANSITIONAL AREA OF CERRADO AND PANTANAL IN MATO GROSSO ABSTRACT: The substitution of native vegetation and climatic seasonality modify the surface biophysical parameters. As 50% of the Cerrado has been converted to crops and pastures, the objective of this study was to evaluate the temporal variation of biophysical parameters in native areas and converted into a transition area between Cerrado and Pantanal in Mato Grosso. The study was conducted at the UFMT Experimental Farm (15° 51’ 15.23’’ S e 56° 04’ 13.50’’ W) with TM Landsat 5 images between April and September 2011. The Normalized Difference Vegetation Index (NDVI), and the surface albedo (α) and surface temperature (Ts) were obtained from a Cerrado stricto sensu (CER), a pasture of Brachiaria brizantha (PAS) and a mangrove (MAN). The highest NDVI values and lowest α and Ts values were observed in the most densely vegetated areas. The replacement of the native cover of the Cerrado and Pantanal transition region with exotic vegetation significantly modified the biophysical parameters evaluated, with the potential to modify the radiation, energy and carbon balances of the surface. Keywords: deforestation; remote sensing; regional warming.

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Bezerra, Alan Cézar, Jhon Lennon Bezerra da Silva, Douglas Alberto de Oliveira Silva, Cristina Rodrigues Nascimento, Eberson Pessoa Ribeiro, Josiclêda Domiciano Galvincio, Marcos Vinícius da Silva, et al. "Seasonality of Biophysical Parameters in Extreme Years of Precipitation in Pernambuco: Relations, Regionalities, and Variability." Atmosphere 14, no. 12 (November 21, 2023): 1712. http://dx.doi.org/10.3390/atmos14121712.

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This study analyzed the seasonality of biophysical parameters in the extreme years of precipitation and the relationship with the monthly precipitation of the state of Pernambuco at the regional level (Pernambuco) and homogeneous precipitation zones: zone 1—semiarid, zone 2—transition and zone 3—coastal. For this, the biophysical parameters at the monthly level in the extreme years, 2004 (wet) and 2012 (dry) were related to precipitation data of 45 rainfall stations. Using the Google Earth Engine platform, we calculate the biophysical parameters with MODIS products: Albedo, Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI), Soil Adjusted Vegetation Index (SAVI), Normalized Difference Water Index (NDWI) and surface temperature (ST). Considering the most critical period, between September and December, of a wet year (2004) with a dry year (2012), there is an average reduction of 14% of vegetation indices (NDVI, EVI and SAVI), a 60% reduction in NDWI, an increase of 4% in albedo and 3% in surface temperature. For monitoring the water conditions of the state of Pernambuco, the most appropriate biophysical parameter is the NDWI index and surface temperature. In addition to NDWI, it is recommended to use EVI for semiarid areas (zone 1) and ST for coastal areas (Zones 2 and 3).

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Huang, Tze-Yun, Chung-ke Chang, Ya-Fen Kao, Chih-Hao Chin, Cheng-Wei Ni, Hao-Yi Hsu, Nien-Jen Hu, et al. "Parity-dependent hairpin configurations of repetitive DNA sequence promote slippage associated with DNA expansion." Proceedings of the National Academy of Sciences 114, no. 36 (August 21, 2017): 9535–40. http://dx.doi.org/10.1073/pnas.1708691114.

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Repetitive DNA sequences are ubiquitous in life, and changes in the number of repeats often have various physiological and pathological implications. DNA repeats are capable of interchanging between different noncanonical and canonical conformations in a dynamic fashion, causing configurational slippage that often leads to repeat expansion associated with neurological diseases. In this report, we used single-molecule spectroscopy together with biophysical analyses to demonstrate the parity-dependent hairpin structural polymorphism of TGGAA repeat DNA. We found that the DNA adopted two configurations depending on the repeat number parity (even or odd). Transitions between these two configurations were also observed for longer repeats. In addition, the ability to modulate this transition was found to be enhanced by divalent ions. Based on the atomic structure, we propose a local seeding model where the kinked GGA motifs in the stem region of TGGAA repeat DNA act as hot spots to facilitate the transition between the two configurations, which may give rise to disease-associated repeat expansion.

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Kazlauskaite, Jurate, and Teresa J. T. Pinheiro. "Aggregation and fibrillization of prions in lipid membranes." Biochemical Society Symposia 72 (January 1, 2005): 211–22. http://dx.doi.org/10.1042/bss0720211.

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A key molecular event in prion diseases is the conversion of PrP (prion protein) from its normal cellular form (PrPc) into the disease-specific form (PrPSc). The transition from PrPc to PrPSc involves a major conformational change, resulting in amorphous aggregates and/or fibrillar amyloid deposits. Here, we review several lines of evidence implicating membranes in the conversion of PrP, and summarize recent results from our own work on the role of lipid membranes in conformational transitions of prion proteins. By establishing new correlations between in vivo biological findings with in vitro biophysical results, we propose a role for lipid rafts in prion conversion, which takes into account the structural heterogeneity of PrP in different lipid environments.

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Su, Yapeng, Wei Wei, Lidia Robert, Min Xue, Jennifer Tsoi, Angel Garcia-Diaz, Blanca Homet Moreno, et al. "Single-cell analysis resolves the cell state transition and signaling dynamics associated with melanoma drug-induced resistance." Proceedings of the National Academy of Sciences 114, no. 52 (December 11, 2017): 13679–84. http://dx.doi.org/10.1073/pnas.1712064115.

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Continuous BRAF inhibition of BRAF mutant melanomas triggers a series of cell state changes that lead to therapy resistance and escape from immune control before establishing acquired resistance genetically. We used genome-wide transcriptomics and single-cell phenotyping to explore the response kinetics to BRAF inhibition for a panel of patient-derived BRAFV600-mutant melanoma cell lines. A subset of plastic cell lines, which followed a trajectory covering multiple known cell state transitions, provided models for more detailed biophysical investigations. Markov modeling revealed that the cell state transitions were reversible and mediated by both Lamarckian induction and nongenetic Darwinian selection of drug-tolerant states. Single-cell functional proteomics revealed activation of certain signaling networks shortly after BRAF inhibition, and before the appearance of drug-resistant phenotypes. Drug targeting those networks, in combination with BRAF inhibition, halted the adaptive transition and led to prolonged growth inhibition in multiple patient-derived cell lines.

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Arakawa, Christopher, Celina Gunnarsson, Caitlin Howard, Maria Bernabeu, Kiet Phong, Eric Yang, Cole A. DeForest, Joseph D. Smith, and Ying Zheng. "Biophysical and biomolecular interactions of malaria-infected erythrocytes in engineered human capillaries." Science Advances 6, no. 3 (January 2020): eaay7243. http://dx.doi.org/10.1126/sciadv.aay7243.

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Microcirculatory obstruction is a hallmark of severe malaria, but mechanisms of parasite sequestration are only partially understood. Here, we developed a robust three-dimensional microvessel model that mimics the arteriole-capillary-venule (ACV) transition consisting of a narrow 5- to 10-μm-diameter capillary region flanked by arteriole- or venule-sized vessels. Using this platform, we investigated red blood cell (RBC) transit at the single cell and at physiological hematocrits. We showed normal RBCs deformed via in vivo–like stretching and tumbling with negligible interactions with the vessel wall. By comparison, Plasmodium falciparum–infected RBCs exhibited virtually no deformation and rapidly accumulated in the capillary-sized region. Comparison of wild-type parasites to those lacking either cytoadhesion ligands or membrane-stiffening knobs showed highly distinctive spatial and temporal kinetics of accumulation, linked to velocity transition in ACVs. Our findings shed light on mechanisms of microcirculatory obstruction in malaria and establish a new platform to study hematologic and microvascular diseases.

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Plante, Samuel, Kyung-Mee Moon, Pascale Lemieux, Leonard J. Foster, and Christian R. Landry. "Breaking spore dormancy in budding yeast transforms the cytoplasm and the solubility of the proteome." PLOS Biology 21, no. 4 (April 20, 2023): e3002042. http://dx.doi.org/10.1371/journal.pbio.3002042.

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The biophysical properties of the cytoplasm are major determinants of key cellular processes and adaptation. Many yeasts produce dormant spores that can withstand extreme conditions. We show that spores of Saccharomyces cerevisiae exhibit extraordinary biophysical properties, including a highly viscous and acidic cytosol. These conditions alter the solubility of more than 100 proteins such as metabolic enzymes that become more soluble as spores transit to active cell proliferation upon nutrient repletion. A key regulator of this transition is the heat shock protein, Hsp42, which shows transient solubilization and phosphorylation, and is essential for the transformation of the cytoplasm during germination. Germinating spores therefore return to growth through the dissolution of protein assemblies, orchestrated in part by Hsp42 activity. The modulation of spores’ molecular properties are likely key adaptive features of their exceptional survival capacities.

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Arp, C. D., M. S. Whitman, B. M. Jones, G. Grosse, B. V. Gaglioti, and K. C. Heim. "Distribution and biophysical processes of beaded streams in Arctic permafrost landscapes." Biogeosciences 12, no. 1 (January 6, 2015): 29–47. http://dx.doi.org/10.5194/bg-12-29-2015.

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Abstract. Beaded streams are widespread in permafrost regions and are considered a common thermokarst landform. However, little is known about their distribution, how and under what conditions they form, and how their intriguing morphology translates to ecosystem functions and habitat. Here we report on a circum-Arctic survey of beaded streams and a watershed-scale analysis in northern Alaska using remote sensing and field studies. We mapped over 400 channel networks with beaded morphology throughout the continuous permafrost zone of northern Alaska, Canada, and Russia and found the highest abundance associated with medium to high ground-ice content permafrost in moderately sloping terrain. In one Arctic coastal plain watershed, beaded streams accounted for half of the drainage density, occurring primarily as low-order channels initiating from lakes and drained lake basins. Beaded streams predictably transition to alluvial channels with increasing drainage area and decreasing channel slope, although this transition is modified by local controls on water and sediment delivery. The comparisons of one beaded channel using repeat photography between 1948 and 2013 indicate a relatively stable landform, and 14C dating of basal sediments suggest channel formation may be as early as the Pleistocene–Holocene transition. Contemporary processes, such as deep snow accumulation in riparian zones, effectively insulate channel ice and allows for perennial liquid water below most beaded stream pools. Because of this, mean annual temperatures in pool beds are greater than 2 °C, leading to the development of perennial thaw bulbs or taliks underlying these thermokarst features that range from 0.7 to 1.6 m. In the summer, some pools thermally stratify, which reduces permafrost thaw and maintains cold-water habitats. Snowmelt-generated peak flows decrease rapidly by two or more orders of magnitude to summer low flows with slow reach-scale velocity distributions ranging from 0.01 to 0.1 m s−1, yet channel runs still move water rapidly between pools. The repeating spatial pattern associated with beaded stream morphology and hydrological dynamics may provide abundant and optimal foraging habitat for fish. Beaded streams may create important ecosystem functions and habitat in many permafrost landscapes and their distribution and dynamics are only beginning to be recognized in Arctic research.

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Klitgaard, Kent A. "The Failed Growth Economy, Stagnation, and Biophysical Limits to Growth." International Journal of Social Science Research 1, no. 1 (August 31, 2013): 140. http://dx.doi.org/10.5296/ijssr.v1i1.4032.

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There are many indications that the era of economic degrowth has already begun, despite conscious policy efforts to maintain it. This indicated by a secular decline in the rate of GDP growth for essentially all OECD countries and many developing ones over the second half of the twentieth century. I believe that this phenomenon has occurred because the mature economies of the world have confronted a set of internal, or social, limits driven by the internal dynamics of capital accumulation and by approaching biophysical limits. These patterns are likely to continue. The purpose of this paper is to synthesize the literature on internal limits to capital accumulation and economic growth with the emerging literature on biophysical limits. Growth-oriented mainstream economics is incapable of analyzing adequately the historical conjuncture of the internal and biophysical limits. A study of heterodox political economy and institutional economics is needed in order to understand the transition to sustainability. The paper surveys prior theories of the internal limits to economic growth and synthesizes them with future potential limits imposed by the decrease in availability and increase in cost of high-quality resources, climate change and peak oil.

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Burland, Anna, and Moritz von Cossel. "Towards Managing Biodiversity of European Marginal Agricultural Land for Biodiversity-Friendly Biomass Production." Agronomy 13, no. 6 (June 20, 2023): 1651. http://dx.doi.org/10.3390/agronomy13061651.

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The use of marginal land, especially that which has already been used for agricultural purposes in the past two decades, for biomass cultivation is seen as an important approach for the transition to a sustainable bioeconomy. Marginal land can provide many other important ecosystem services than biomass provisioning for bioenergy and biobased products such as erosion mitigation, groundwater protection and nursery services to promote biodiversity. However, marginal land is also often subject to dynamic processes, mostly soil degradation and climate change, which make its fauna and flora particularly vulnerable to land-use changes. This study provides insights into marginal land’s potential biodiversity characterization and critically discusses further steps towards applicable management approaches. Not all commonly used indicators apply to all types of marginal land, especially regarding the site-specific biophysical constraints and the landscape heterogeneity. This is because both the biodiversity and biophysical constraints are sensitive to disturbances. Therefore, when marginal lands are used for biomass production, all available measures should be taken to allow for predominantly positive impacts on local biodiversity, such as a survey of the status quo using camera traps, area mapping, or caterpillar mimics and a forecast of potential biophysical and agrobiological impacts of management.

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Jalilov, Muxiddin Xalimovich, Xudoykulova Shoira Narzullayevna, Ergashev Askar Jangoboyevich, Xusniddin Muxiddinovich Jalilov, and Xalikulova Amina Qamariddnovna. "Online Passage Of The Practical Lesson On The Topic" Fluid Flow And Biophysical Properties " In The Module System." American Journal of Medical Sciences and Pharmaceutical Research 03, no. 01 (January 25, 2021): 97–101. http://dx.doi.org/10.37547/tajmspr/volume03issue01-15.

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This article is devoted to the transition of "Fluid flow and biophysical properties" in a modular system. The importance of viscosity coefficient in medicine, its application in diagnosis and forensic medical examination is described. However, the Stokes method of finding the viscosity coefficient, the availability of viscometric methods, the application of Gess (VK-4) viscometer in medicine to find the viscosity coefficient are described.

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Marino, Davide, Antonio Barone, Angelo Marucci, Silvia Pili, and Margherita Palmieri. "Impact of Land Use Changes on Ecosystem Services Supply: A Meta Analysis of the Italian Context." Land 12, no. 12 (December 16, 2023): 2173. http://dx.doi.org/10.3390/land12122173.

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Changes in land use and land cover (LULC) are caused by several factors, including climate change, socio-demographic dynamics, human pressures and urban sprawl. These factors alter the structure and functionality of ecosystems and their capacity to provide ecosystem goods and services to society. The study of LULC changes is important for understanding the dynamics of relationships between environmental, social and economic components and for analyzing the factors affecting natural capital. Including ecosystem services (ES) in spatial planning tools and sectoral policies is useful for improving governance. In this paper, the impact of LULC changes on ES provision has been estimated. To this end, we carried out a literature review (Step 1) to select the biophysical and economic coefficients of ES supply by land cover classes and collect them in a database (Step 2). We subsequently aggregated the economic and biophysical coefficients by macro classes (Step 3) and, using the benefit transfer approach, we estimated the change in the supply of ESs concerning permanence and transition phenomena in Italy from 1990 to 2018 (Step 4). The transition phenomena analysis also allowed us to evaluate the consequences of urbanization and urban green space governance on ES supply. Indeed, these urban green spaces can help reduce risks to people’s health and safety and mitigate the effects induced by climate change. In total, approximately 800 coefficients (biophysical and economic) of ESs supplied by Corine Land Cover classes were acquired. The results show a reduction in the annual supply of ecosystem services of EUR 927 million (2022) caused by LULC changes between 1990 and 2018. This research proposes a methodology to improve knowledge of ESs concerning anthropogenic impacts and to support land-use planning policies regarding Agenda 2030 for Sustainable Development Goals.

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Warshel, Arieh, and William W. Parson. "Dynamics of biochemical and biophysical reactions: insight from computer simulations." Quarterly Reviews of Biophysics 34, no. 4 (November 2001): 563–679. http://dx.doi.org/10.1017/s0033583501003730.

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1. Introduction 5632. Obtaining rate constants from molecular-dynamics simulations 5642.1 General relationships between quantum electronic structures and reaction rates 5642.2 The transition-state theory (TST) 5692.3 The transmission coefficient 5723. Simulating biological electron-transfer reactions 5753.1 Semi-classical surface-hopping and the Marcus equation 5753.2 Treating quantum mechanical nuclear tunneling by the dispersed-polaron/spin-boson method 5803.3 Density-matrix treatments 5833.4 Charge separation in photosynthetic bacterial reaction centers 5844. Light-induced photoisomerizations in rhodopsin and bacteriorhodopsin 5965. Energetics and dynamics of enzyme reactions 6145.1 The empirical-valence-bond treatment and free-energy perturbation methods 6145.2 Activation energies are decreased in enzymes relative to solution, often by electrostatic effects that stabilize the transition state 6205.3 Entropic effects in enzyme catalysis 6275.4 What is meant by dynamical contributions to catalysis? 6345.5 Transmission coefficients are similar for corresponding reactions in enzymes and water 6365.6 Non-equilibrium solvation effects contribute to catalysis mainly through Δg[Dagger], not the transmission coefficient 6415.7 Vibrationally assisted nuclear tunneling in enzyme catalysis 6485.8 Diffusive processes in enzyme reactions and transmembrane channels 6516. Concluding remarks 6587. Acknowledgements 6588. References 658Obtaining a detailed understanding of the dynamics of a biochemical reaction is a formidable challenge. Indeed, it might appear at first sight that reactions in proteins are too complex to analyze microscopically. At room temperature, even a relatively small protein can have as many as 1034 accessible conformational states (Dill, 1985). In many cases, however, we have detailed structural information about the active site of an enzyme, whereas such information is missing for corresponding chemical systems in solution. The atomic coordinates of the chromophore in bacteriorhodopsin, for example, are known to a resolution of 1–2 Å. In addition, experimental studies of biological processes such as photoisomerization and electron transfer have provided a wealth of detailed information that eventually may make some of these processes classical problems in chemical physics as well as biology.

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Cocklin, Chris, and Meg Keen. "Urbanization in the Pacific: environmental change, vulnerability and human security." Environmental Conservation 27, no. 4 (December 2000): 392–403. http://dx.doi.org/10.1017/s0376892900000448.

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The world is in the midst of a substantial urban transition, but the impacts of this on the environment and human societies are not fully understood. Very little attention has been paid to urbanization processes in developing countries with smaller populations, despite the evident problems associated with urbanization. There are both biophysical and social vulnerabilities associated with urbanization in the South Pacific and these vulnerabilities affect human security. The biophysical vulnerabilities include the fragile environments of the island nations, limited land resources, shortages of basic resources, and the risks associated with global warming. The ability to respond to these problems is constrained by social vulnerabilities, notably weak economies, difficulties associated with land ownership, and institutional limitations. There is a need for institutional reform, improved planning, better urban resource management, and greater regional cooperation, if Pacific island nations are to respond effectively to rapid urbanization and global change.

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Flomenbom, Ophir. "Single File Dynamics Advances with a Focus on Biophysical Relevance." Biophysical Reviews and Letters 09, no. 04 (December 2014): 307–31. http://dx.doi.org/10.1142/s1793048014400013.

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In this review (appearing in the Special Issue on single file dynamics in biophysics and related extensions), three recently treated variants in file dynamics are presented: files with density that is not fixed, files with heterogeneous particles, and files with slow particles. The results in these files include:• In files with a density law that is not fixed, but decays as a power law with an exponent a the distance from the origin, the particle in the origin mean square displacement (MSD) scales like MSD ~ t[1+a]/2, with a Gaussian probability density function (PDF). This extends the scaling, MSD ~ t1/2, seen in a constant density file.• When, in addition, the particles' diffusion coefficients are distributed like a power law with an exponent γ (around the origin), the MSD follows MSD ~ t[1-γ]/[2/(1+a) - γ], with a Gaussian PDF.• In anomalous files that are renewal, namely, when all particles attempt a jump together, yet, with jump times taken from a PDF that decays as a power law with an exponent -1 - ε, ψ(t) ~ t-1-ε, the MSD scales like the MSD of the corresponding normal file, in the power ε.• In anomalous files of independent particles, the MSD is very slow and scales like MSD ~ log2(t). Even more exciting, the particles form clusters, defining a dynamical phase transition: depending on the anomaly power ε, the percentage of particles in clusters ξ follows [Formula: see text], yet when ε > 1, fluidity rather than clusters is seen.We talk about utilizing these results while focusing on biophysical processes and applications: dynamics in channels, membranes, biosensors, etc.[Formula: see text] Special Issue Comments: In this article, results about recently suggested variants in single file dynamics appear: heterogeneous files and slow files, yet also, the relevance with biophysical processes. It is related to the Special Issue articles about expansions in files,61files with force,62and the zig zag occurrences in files.63

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Afroz, Tariq, Manuela Pérez-Berlanga, and Magdalini Polymenidou. "Structural Transition, Function and Dysfunction of TDP-43 in Neurodegenerative Diseases." CHIMIA International Journal for Chemistry 73, no. 5 (May 29, 2019): 380–90. http://dx.doi.org/10.2533/chimia.2019.380.

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Altered cellular localization and pathologic aggregation of RNA binding proteins (RPBs) containing low complexity regions (LCRs) is a hallmark of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Given the importance of RBPs in maintaining a healthy RNA homeostasis, a common mechanism in disease progression is the loss of RNA-related cellular functions. In this review, we summarize and discuss the knowledge gained in the recent years on the molecular mechanisms of TDP-43 proteinopathies that comprise a set of neurodegenerative diseases characterized by the mislocalization and aggregation of the RNA-binding protein TDP-43. Based on biophysical, biochemical and in vivo data, we highlight pathways that are misregulated early in disease and contribute to its progression, thereby representing attractive therapeutic targets.

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Raju, Rekha, Theresa Merl, Madeleine K. Adam, Emiliyan Staykov, Robert N. Ben, Gary Bryant, and Brendan L. Wilkinson. "n-Octyl (Thio)glycosides as Potential Cryoprotectants: Glass Transition Behaviour, Membrane Permeability, and Ice Recrystallization Inhibition Studies." Australian Journal of Chemistry 72, no. 8 (2019): 637. http://dx.doi.org/10.1071/ch19159.

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A series of eight n-octyl (thio)glycosides (1α, β–4α, β) with d-glucose or d-galactose-configured head groups and varying anomeric configuration were synthesized and evaluated for glass transition behaviour, membrane permeability, and ice recrystallization inhibition (IRI) activity. Of these, n-octyl β-d-glucopyranoside (2β) exhibited a high glass transition temperatures (Tg), both as a neat sample and 20 wt-% aqueous solution. Membrane permeability studies of this compound revealed cellular uptake to concentrations relevant to the inhibition of intracellular ice formation, thus presenting a promising lead candidate for further biophysical and cryopreservation studies. Compounds were also evaluated as ice recrystallization inhibitors; however, no detectable activity was observed for the newly tested compounds.

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Coronel-Oliveros, Carlos, Rodrigo Cofré, and Patricio Orio. "Cholinergic neuromodulation of inhibitory interneurons facilitates functional integration in whole-brain models." PLOS Computational Biology 17, no. 2 (February 18, 2021): e1008737. http://dx.doi.org/10.1371/journal.pcbi.1008737.

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Segregation and integration are two fundamental principles of brain structural and functional organization. Neuroimaging studies have shown that the brain transits between different functionally segregated and integrated states, and neuromodulatory systems have been proposed as key to facilitate these transitions. Although whole-brain computational models have reproduced this neuromodulatory effect, the role of local inhibitory circuits and their cholinergic modulation has not been studied. In this article, we consider a Jansen & Rit whole-brain model in a network interconnected using a human connectome, and study the influence of the cholinergic and noradrenergic neuromodulatory systems on the segregation/integration balance. In our model, we introduce a local inhibitory feedback as a plausible biophysical mechanism that enables the integration of whole-brain activity, and that interacts with the other neuromodulatory influences to facilitate the transition between different functional segregation/integration regimes in the brain.

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Jalilov, Muhiddin Halimovich, Hudaykulova Shoira Narzullaevna, Hamroev Jobir, and Ahrorov Marufnasimovich. "Passing Lecture On The Topic" Fluid Flow And Biophysical Properties " In The Online System." American Journal of Interdisciplinary Innovations and Research 02, no. 11 (November 30, 2020): 150–53. http://dx.doi.org/10.37547/tajiir/volume02issue11-25.

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This article is devoted to the transition of"fluid flow and biophysical properties" in the module system. It is stated that it is possible to find the coefficient of viscosity in the Stox method, the coefficient of viscometric methods, to find the coefficient of viscosity in the axiom of Medicine, in diagnosis and in medical and forensic expertise. It is also described to find the coefficient of processes and surface tension on the surface of liquids by drip method.

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Keller, B. U., R. P. Hartshorne, J. A. Talvenheimo, W. A. Catterall, and M. Montal. "Sodium channels in planar lipid bilayers. Channel gating kinetics of purified sodium channels modified by batrachotoxin." Journal of General Physiology 88, no. 1 (July 1, 1986): 1–23. http://dx.doi.org/10.1085/jgp.88.1.1.

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Single channel currents of sodium channels purified from rat brain and reconstituted into planar lipid bilayers were recorded. The kinetics of channel gating were investigated in the presence of batrachotoxin to eliminate inactivation and an analysis was conducted on membranes with a single active channel at any given time. Channel opening is favored by depolarization and is strongly voltage dependent. Probability density analysis of dwell times in the closed and open states of the channel indicates the occurrence of one open state and several distinct closed states in the voltage (V) range-120 mV less than or equal to V less than or equal to +120 mV. For V less than or equal to 0, the transition rates between stages are exponentially dependent on the applied voltage, as described in mouse neuroblastoma cells (Huang, L. M., N. Moran, and G. Ehrenstein. 1984. Biophysical Journal. 45:313-322). In contrast, for V greater than or equal to 0, the transition rates are virtually voltage independent. Autocorrelation analysis (Labarca, P., J. Rice, D. Fredkin, and M. Montal. 1985. Biophysical Journal. 47:469-478) shows that there is no correlation in the durations of successive open or closing events. Several kinetic schemes that are consistent with the experimental data are considered. This approach may provide information about the mechanism underlying the voltage dependence of channel activation.

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Reddy, P. Madhusudhana, R. Umapathi, and P. Venkatesu. "Interactions of ionic liquids with hydration layer of poly(N-isopropylacrylamide): comprehensive analysis of biophysical techniques results." Phys. Chem. Chem. Phys. 16, no. 22 (2014): 10708–18. http://dx.doi.org/10.1039/c4cp00010b.

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Day, Thomas C., Pedro Márquez-Zacarías, Pablo Bravo, Aawaz R. Pokhrel, Kathryn A. MacGillivray, William C. Ratcliff, and Peter J. Yunker. "Varied solutions to multicellularity: The biophysical and evolutionary consequences of diverse intercellular bonds." Biophysics Reviews 3, no. 2 (June 2022): 021305. http://dx.doi.org/10.1063/5.0080845.

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The diversity of multicellular organisms is, in large part, due to the fact that multicellularity has independently evolved many times. Nonetheless, multicellular organisms all share a universal biophysical trait: cells are attached to each other. All mechanisms of cellular attachment belong to one of two broad classes; intercellular bonds are either reformable or they are not. Both classes of multicellular assembly are common in nature, having independently evolved dozens of times. In this review, we detail these varied mechanisms as they exist in multicellular organisms. We also discuss the evolutionary implications of different intercellular attachment mechanisms on nascent multicellular organisms. The type of intercellular bond present during early steps in the transition to multicellularity constrains future evolutionary and biophysical dynamics for the lineage, affecting the origin of multicellular life cycles, cell–cell communication, cellular differentiation, and multicellular morphogenesis. The types of intercellular bonds used by multicellular organisms may thus result in some of the most impactful historical constraints on the evolution of multicellularity.

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Wironen, Michael B., and Jon D. Erickson. "A critically modern ecological economics for the Anthropocene." Anthropocene Review 7, no. 1 (November 6, 2019): 62–76. http://dx.doi.org/10.1177/2053019619884485.

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Ecological economics recognizes economic activity as a biophysical process mediated by social systems and ultimately subject to the constraints of a finite earth system. The Anthropocene discourse appears as validation of the central concerns of ecological economics yet throws into relief its limits as a normative transdiscipline oriented toward social transformation. We review ecological economics in light of two overarching challenges: first, negotiating between biophysical reality and plural constructed social realities, so as to create legitimate grounds for a sustainability transition; second, accounting for multi-level, multi-scale social and political action, which demands a means for arbitrating among competing normative propositions. We argue that attempts to address these challenges within ecological economics have been inconsistent and relatively scarce, reflecting an unresolved tension regarding modern and postmodern social theory. We demonstrate that a critically modern ecological economics could draw on aligned social movements and build on deliberative theory as a foundation for social and political change fit for navigating the Anthropocene.

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Carvalho, Diogo Duarte, Susana Soares, Rodrigo Zacca, João Sousa, Daniel Almeida Marinho, António José Silva, João Paulo Vilas-Boas, and Ricardo J. Fernandes. "Anaerobic Threshold Biophysical Characterisation of the Four Swimming Techniques." International Journal of Sports Medicine 41, no. 05 (January 23, 2020): 318–27. http://dx.doi.org/10.1055/a-0975-9532.

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AbstractThe anaerobic threshold (AnT) seems to be not only a physiologic boundary but also a transition after which swimmers technique changes, modifying their biomechanical behaviour. We expanded the AnT concept to a biophysical construct in the four conventional swimming techniques. Seventy-two elite swimmers performed a 5×200 m incremental protocol in their preferred swimming technique (with a 0.05 m·s−1 increase and a 30 s interval between steps). A capillary blood samples were collected from the fingertip and stroke rate (SR) and length (SL) determined for the assessment of [La], SR and SL vs. velocity inflexion points (using the interception of a pair of linear and exponential regression curves). The [La] values at the AnT were 3.3±1.0, 3.9±1.1, 2.9±1 .34 and 4.5±1.4 mmol·l−1 (mean±SD) for front crawl, backstroke, breaststroke and butterfly, and its corresponding velocity correlated highly with those at SR and SL inflection points (r=0.91–0.99, p<0.001). The agreement analyses confirmed that AnT represents a biophysical boundary in the four competitive swimming techniques and can be determined individually using [La] and/or SR/SL. Blood lactate increase speed can help characterise swimmers’ anaerobic behaviour after AnT and between competitive swimming techniques.

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Duveiller, Gregory, Giovanni Forzieri, Eddy Robertson, Wei Li, Goran Georgievski, Peter Lawrence, Andy Wiltshire, et al. "Biophysics and vegetation cover change: a process-based evaluation framework for confronting land surface models with satellite observations." Earth System Science Data 10, no. 3 (July 13, 2018): 1265–79. http://dx.doi.org/10.5194/essd-10-1265-2018.

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Abstract. Land use and land cover change (LULCC) alter the biophysical properties of the Earth's surface. The associated changes in vegetation cover can perturb the local surface energy balance, which in turn can affect the local climate. The sign and magnitude of this change in climate depends on the specific vegetation transition, its timing and its location, as well as on the background climate. Land surface models (LSMs) can be used to simulate such land–climate interactions and study their impact in past and future climates, but their capacity to model biophysical effects accurately across the globe remain unclear due to the complexity of the phenomena. Here we present a framework to evaluate the performance of such models with respect to a dedicated dataset derived from satellite remote sensing observations. Idealized simulations from four LSMs (JULES, ORCHIDEE, JSBACH and CLM) are combined with satellite observations to analyse the changes in radiative and turbulent fluxes caused by 15 specific vegetation cover transitions across geographic, seasonal and climatic gradients. The seasonal variation in net radiation associated with land cover change is the process that models capture best, whereas LSMs perform poorly when simulating spatial and climatic gradients of variation in latent, sensible and ground heat fluxes induced by land cover transitions. We expect that this analysis will help identify model limitations and prioritize efforts in model development as well as inform where consensus between model and observations is already met, ultimately helping to improve the robustness and consistency of model simulations to better inform land-based mitigation and adaptation policies. The dataset consisting of both harmonized model simulation and remote sensing estimations is available at https://doi.org/10.5281/zenodo.1182145.

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FRANK, T. D. "COLLECTIVE BEHAVIOR OF BIOPHYSICAL SYSTEMS WITH THERMODYNAMIC FEEDBACK LOOPS: A CASE STUDY FOR A NONLINEAR MARKOV MODEL — THE TAKATSUJI SYSTEM." Modern Physics Letters B 25, no. 08 (March 30, 2011): 551–68. http://dx.doi.org/10.1142/s0217984911025845.

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We study order–disorder transitions and the emergence of collective behavior using a particular mean field model: the dynamic Takatsuji system. This model satisfies linear non-equilibrium thermodynamics and can be described in terms of a nonlinear Markov process defined by a nonlinear Fokker–Planck equation, that is, an evolution equation that is nonlinear with respect to its probability density. We discuss quantitatively the impact of a feedback loop that involves a macroscopic, thermodynamic variable. We demonstrate by means of semi-analytical methods and numerical simulations that the feedback loop increases the magnitude of order, increases the gap between the free energy of the ordered and disordered states, and increases the maximal rate of entropy production that can be observed during the order–disorder transition.

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Al Mutairi, Amal Abdullah, and Mohsen Mahmoud Mady. "Biophysical Characterization of (DOX-NPtm): FTIR and DSC Studies." JOURNAL OF ADVANCES IN PHYSICS 20 (March 3, 2022): 41–47. http://dx.doi.org/10.24297/jap.v20i.9194.

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Doxorubicin loaded into liposomes grafted with polyethylene glycol (PEG) has been demonstrated to have a longer circulation time and lower cardiotoxicity than doxorubicin (DOX). This study aims to investigate the biophysical characterization of a marketed formulation DOX-encapsulated liposome (DOX-NPTM). The interactions between doxorubicin and liposomal lipids can help in liposomal development. The liposome and DOX-NPTM were characterized in terms of differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopy (FTIR). The rheological properties of liposomal samples were also measured. Physical interactions may be occurred between the drug functional groups and liposomal lipids, probably by weak hydrogen bond formation or weak bond formation due to dipole-dipole interaction. There was no shift of existing peaks or appearance of new peaks was detected between the characteristic peaks of the liposomal lipids were present in the DOX-encapsulated liposome sample. This suggests that there were physical interactions that took place only between the drug and lipids and no chemical interaction between them. DSC information shows that the phase transition temperature shifts to lower temperature degrees after loading of DOX into the liposomes. The DSC curve has a small broadening. This may infer a little cooperativity decrease between acyl chains of liposomal membranes after DOX inclusion. The encapsulation of DOX into liposomes decreases the plastic viscosity of liposomes (from 1.64 to 1.48 cP), which shows that the membrane ﬂuidity was increased.

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Jawaid, Muhammad Zaki, Rosalie Sinclair, Vincent Bulone, Daniel L. Cox, and Georgia Drakakaki. "A biophysical model for plant cell plate maturation based on the contribution of a spreading force." Plant Physiology 188, no. 2 (November 27, 2021): 795–806. http://dx.doi.org/10.1093/plphys/kiab552.

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Abstract Plant cytokinesis, a fundamental process of plant life, involves de novo formation of a “cell plate” partitioning the cytoplasm of dividing cells. Cell plate formation is directed by orchestrated delivery, fusion of cytokinetic vesicles, and membrane maturation to form a nascent cell wall by timely deposition of polysaccharides. During cell plate maturation, the fragile membrane network transitions to a fenestrated sheet and finally a young cell wall. Here, we approximated cell plate sub-structures with testable shapes and adopted the Helfrich-free energy model for membranes, including a stabilizing and spreading force, to understand the transition from a vesicular network to a fenestrated sheet and mature cell plate. Regular cell plate development in the model was possible, with suitable bending modulus, for a two-dimensional late stage spreading force of 2–6 pN/nm, an osmotic pressure difference of 2–10 kPa, and spontaneous curvature between 0 and 0.04 nm−1. With these conditions, stable membrane conformation sizes and morphologies emerged in concordance with stages of cell plate development. To reach a mature cell plate, our model required the late-stage onset of a spreading/stabilizing force coupled with a concurrent loss of spontaneous curvature. Absence of a spreading/stabilizing force predicts failure of maturation. The proposed model provides a framework to interrogate different players in late cytokinesis and potentially other membrane networks that undergo such transitions. Callose, is a polysaccharide that accumulates transiently during cell plate maturation. Callose-related observations were consistent with the proposed model’s concept, suggesting that it is one of the factors involved in establishing the spreading force.

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McGrail, Daniel J., Roman Mezencev, Quang Minh N. Kieu, John F. McDonald, and Michelle R. Dawson. "SNAIL‐induced epithelial‐to‐mesenchymal transition produces concerted biophysical changes from altered cytoskeletal gene expression." FASEB Journal 29, no. 4 (December 9, 2014): 1280–89. http://dx.doi.org/10.1096/fj.14-257345.

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Brautigam, C. A., R. K. Deka, Z. Ouyang, M. Machius, G. Knutsen, D. R. Tomchick, and M. V. Norgard. "Biophysical and Bioinformatic Analyses Implicate the Treponema pallidum Tp34 Lipoprotein (Tp0971) in Transition Metal Homeostasis." Journal of Bacteriology 194, no. 24 (October 5, 2012): 6771–81. http://dx.doi.org/10.1128/jb.01494-12.

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Ahmed, Azaj, Anas Shamsi, and Bilqees Bano. "Oxadiargyl induced conformational transition of cystatin isolated from yellow mustard seeds: Biophysical and biochemical approach." International Journal of Biological Macromolecules 98 (May 2017): 802–9. http://dx.doi.org/10.1016/j.ijbiomac.2017.02.055.

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Bhanjadeo, Madhabi M., Bineeth Baral, and Umakanta Subudhi. "Sequence-specific B-to-Z transition in self-assembled DNA: A biophysical and thermodynamic study." International Journal of Biological Macromolecules 137 (September 2019): 337–45. http://dx.doi.org/10.1016/j.ijbiomac.2019.06.166.

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Journal articles on the topic 'Biophysical transition'

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