Correction to: 3D modelling of the impact of stellar activity on tidally locked terrestrial exoplanets: atmospheric composition and habitability

This is the final version. Available on open access from Oxford University Press via the DOI in this recordThe article for which this is the correction is available in ORE at http://hdl.handle.net/10871/131398This is a correction to: R. J. Ridgway, M. Zamyatina, N. J. Mayne, J. Manners, F. H. Lambert, M. Braam, B. Drummond, E. Hébrard, P. I. Palmer, K. Kohary, 3D modelling of the impact of stellar activity on tidally locked terrestrial exoplanets: atmospheric composition and habitability, Monthly Notices of the Royal Astronomical Society, Volume 518, Issue 2, January 2023, Pages 2472–2496, https://doi.org/10.1093/mnras/stac3105Science and Technology Facilities Council (STFC

A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation

Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization patterns of molecules in fluorescence microscopy images with simulation, we devised a visualization method that mimics the microphotography process by showing the trajectory of simulated molecules averaged according to the camera exposure time. In the rod-shaped bacterium _Escherichia coli_, the division site is suppressed at the cell poles by periodic pole-to-pole oscillations of the Min proteins (MinC, MinD and MinE) arising from carefully orchestrated RD in both cytoplasm and membrane compartments. Using Spatiocyte we could model and reproduce the _in vivo_ MinDE localization dynamics by accounting for the established properties of MinE. Our results suggest that the MinE ring, which is essential in preventing polar septation, is largely composed of MinE that is transiently attached to the membrane independently after recruited by MinD. Overall, Spatiocyte allows simulation and visualization of complex spatial and reaction-diffusion mediated cellular processes in volumes and surfaces. As we showed, it can potentially provide mechanistic insights otherwise difficult to obtain experimentally

Simulating biosignatures from pre-oxygen photosynthesising life on TRAPPIST-1e

This is the author accepted manuscript. The final version is available on open access from Oxford University Press via the DOI in this recordData availability: The model output used for this study will be made available following this work’s acceptance for publicationIn order to assess observational evidence for potential atmospheric biosignatures on exoplanets, it will be essential to test whether spectral fingerprints from multiple gases can be explained by abiotic or biotic-only processes. Here, we develop and apply a coupled 1D atmosphere-ocean-ecosystem model to understand how primitive biospheres, which exploit abiotic sources of H2 , CO and O2 , could influence the atmospheric composition of rocky terrestrial exoplanets. We apply this to the Earth at 3.8 Ga and to TRAPPIST-1e. We focus on metabolisms that evolved before the evolution of oxygenic photosynthesis, which consume H2 and CO and produce potentially detectable levels of CH4 . O2 -consuming metabolisms are also considered for TRAPPIST-1e, as abiotic O2 production is predicted on M-dwarf orbiting planets. We show that these biospheres can lead to high levels of surface O2 (approximately 1–5 %) as a result of CO consumption, which could allow high O2 scenarios, by removing the main loss mechanisms of atomic oxygen. Increasing stratospheric temperatures, which increases atmospheric OH can reduce the likelihood of such a state forming. O2 -consuming metabolisms could also lower O2 levels to around 10 ppm and support a productive biosphere at low reductant inputs. Using predicted transmission spectral features from CH4 , CO, O2 /O3 and CO2 across the hypothesis space for tectonic reductant input, we show that biotically-produced CH4 may only be detectable at high reductant inputs. CO is also likely to be a dominant feature in transmission spectra for planets orbiting M-dwarfs, which could reduce the confidence in any potential biosignature observations linked to these biospheres.Science and Technology Facilities Council (STFC)UK Research and InnovationJohn Templeton FoundationLeverhulme TrustHill Family ScholarshipInstitute of Physic

Accounting for Diffusion in Agent Based Models of Reaction-Diffusion Systems with Application to Cytoskeletal Diffusion

Diffusion plays a key role in many biochemical reaction systems seen in nature. Scenarios where diffusion behavior is critical can be seen in the cell and subcellular compartments where molecular crowding limits the interaction between particles. We investigate the application of a computational method for modeling the diffusion of molecules and macromolecules in three-dimensional solutions using agent based modeling. This method allows for realistic modeling of a system of particles with different properties such as size, diffusion coefficients, and affinity as well as the environment properties such as viscosity and geometry. Simulations using these movement probabilities yield behavior that mimics natural diffusion. Using this modeling framework, we simulate the effects of molecular crowding on effective diffusion and have validated the results of our model using Langevin dynamics simulations and note that they are in good agreement with previous experimental data. Furthermore, we investigate an extension of this framework where single discrete cells can contain multiple particles of varying size in an effort to highlight errors that can arise from discretization that lead to the unnatural behavior of particles undergoing diffusion. Subsequently, we explore various algorithms that differ in how they handle the movement of multiple particles per cell and suggest an algorithm that properly accommodates multiple particles of various sizes per cell that can replicate the natural behavior of these particles diffusing. Finally, we use the present modeling framework to investigate the effect of structural geometry on the directionality of diffusion in the cell cytoskeleton with the observation that parallel orientation in the structural geometry of actin filaments of filopodia and the branched structure of lamellipodia can give directionality to diffusion at the filopodia-lamellipodia interface

Cardiovascular magnetic resonance physics for clinicians: part I

There are many excellent specialised texts and articles that describe the physical principles of cardiovascular magnetic resonance (CMR) techniques. There are also many texts written with the clinician in mind that provide an understandable, more general introduction to the basic physical principles of magnetic resonance (MR) techniques and applications. There are however very few texts or articles that attempt to provide a basic MR physics introduction that is tailored for clinicians using CMR in their daily practice. This is the first of two reviews that are intended to cover the essential aspects of CMR physics in a way that is understandable and relevant to this group. It begins by explaining the basic physical principles of MR, including a description of the main components of an MR imaging system and the three types of magnetic field that they generate. The origin and method of production of the MR signal in biological systems are explained, focusing in particular on the two tissue magnetisation relaxation properties (T1 and T2) that give rise to signal differences from tissues, showing how they can be exploited to generate image contrast for tissue characterisation. The method most commonly used to localise and encode MR signal echoes to form a cross sectional image is described, introducing the concept of k-space and showing how the MR signal data stored within it relates to properties within the reconstructed image. Before describing the CMR acquisition methods in detail, the basic spin echo and gradient pulse sequences are introduced, identifying the key parameters that influence image contrast, including appearances in the presence of flowing blood, resolution and image acquisition time. The main derivatives of these two pulse sequences used for cardiac imaging are then described in more detail. Two of the key requirements for CMR are the need for data acquisition first to be to be synchronised with the subject's ECG and to be fast enough for the subject to be able to hold their breath. Methods of ECG synchronisation using both triggering and retrospective gating approaches, and accelerated data acquisition using turbo or fast spin echo and gradient echo pulse sequences are therefore outlined in some detail. It is shown how double inversion black blood preparation combined with turbo or fast spin echo pulse sequences acquisition is used to achieve high quality anatomical imaging. For functional cardiac imaging using cine gradient echo pulse sequences two derivatives of the gradient echo pulse sequence; spoiled gradient echo and balanced steady state free precession (bSSFP) are compared. In each case key relevant imaging parameters and vendor-specific terms are defined and explained

Visual Lateralization in Wild Striped Dolphins (Stenella coeruleoalba) in Response to Stimuli with Different Degrees of Familiarity

Background: Apart from findings on both functional and motor asymmetries in captive aquatic mammals, only few studies have focused on lateralized behaviour of these species in the wild. Methodology/Principal Findings: In this study we focused on lateralized visual behaviour by presenting wild striped dolphins with objects of different degrees of familiarity (fish, ball, toy). Surveys were conducted in the Gulf of Taranto, the northern Ionian Sea portion delimited by the Italian regions of Calabria, Basilicata and Apulia. After sighting striped dolphins from a research vessel, different stimuli were presented in a random order by a telescopic bar connected to the prow of the boat. The preferential use of the right/left monocular viewing during inspection of the stimuli was analysed. Conclusion: Results clearly showed a monocular viewing preference with respect to the type of the stimulus employed. Due to the complete decussation of the optical nerves in dolphin brain our results reflected a different specialization of brain hemispheres for visual scanning processes confirming that in this species different stimuli evoked different patterns of eye use. A preferential use of the right eye (left hemisphere) during visual inspection of unfamiliar targets was observed supporting the hypothesis that, in dolphins, the organization of the functional neural structures which reflected cerebral asymmetries for visual object recognition could have been subjected to a deviation from the evolutionary line of mos

Compulsive buying and branding phenomena

The purpose of this paper was to explore the impact of brand variables such as brand awareness, brand loyalty, brand attachment, and perceived brand quality on compulsive buying behavior. A self-administered questionnaire, containing demographic items and items related to compulsive buying, brand awareness, brand loyalty, brand attachment and perceived quality, was used to collect data. Participants were 269 US university students at a large mid-western university (138 men, 131 women; mean age = 21.96). Data were analyzed using descriptive statistics, t-test and MANOVA/ANOVA. Reliability of all scales was acceptable. In the current study, 18% of the participants were classified as compulsive buyers. Women showed higher compulsive buying tendency than men. Participants with greater compulsive buying tendency scored higher on brand attachment and brand loyalty and lower on brand awareness; there was no difference in scores on perceived brand quality. Results support that brand variables such as brand awareness, brand loyalty, and brand attachment are related to compulsive buying behavior. New perceptions and implications for both academicians and practitioners are provided

Diversification across an altitudinal gradient in the Tiny Greenbul (Phyllastrephus debilis) from the Eastern Arc Mountains of Africa

<p>Abstract</p> <p>Background</p> <p>The Eastern Arc Mountains of Africa have become one of the focal systems with which to explore the patterns and mechanisms of diversification among montane species and populations. One unresolved question is the extent to which populations inhabiting montane forest interact with those of adjacent lowland forest abutting the coast of eastern Africa. The Tiny Greenbul (<it>Phyllastephus debilis</it>) represents the only described bird species within the Eastern Arc/coastal forest mosaic, which is polytypic across an altitudinal gradient: the subspecies <it>albigula </it>(green head) is distributed in the montane Usambara and Nguru Mountains whereas the subspecies <it>rabai </it>(grey head) is found in Tanzanian lowland and foothill forest. Using a combination of morphological and genetic data, we aim to establish if the pattern of morphological differentiation in the Tiny Greenbul (<it>Phyllastrephus debilis</it>) is the result of disruptive selection along an altitudinal gradient or a consequence of secondary contact following population expansion of two differentiated lineages.</p> <p>Results</p> <p>We found significant biometric differences between the lowland (<it>rabai</it>) and montane (<it>albigula</it>) populations in Tanzania. The differences in shape are coupled with discrete differences in the coloration of the underparts. Using multi-locus data gathered from 124 individuals, we show that lowland and montane birds form two distinct genetic lineages. The divergence between the two forms occurred between 2.4 and 3.1 Myrs ago.</p> <p>Our coalescent analyses suggest that limited gene flow, mostly from the subspecies <it>rabai </it>to <it>albigula</it>, is taking place at three mid-altitude localities, where lowland and montane rainforest directly abut. The extent of this introgression appears to be limited and is likely a consequence of the recent expansion of <it>rabai </it>further inland.</p> <p>Conclusion</p> <p>The clear altitudinal segregation in morphology found within the Tiny Greenbul is the result of secondary contact of two highly differentiated lineages rather than disruptive selection in plumage pattern across an altitudinal gradient. Based on our results, we recommend <it>albigula </it>be elevated to species rank.</p