A core genetic module : the Mixed Feedback Loop

The so-called Mixed Feedback Loop (MFL) is a small two-gene network where protein A regulates the transcription of protein B and the two proteins form a heterodimer. It has been found to be statistically over-represented in statistical analyses of gene and protein interaction databases and to lie at the core of several computer-generated genetic networks. Here, we propose and mathematically study a model of the MFL and show that, by itself, it can serve both as a bistable switch and as a clock (an oscillator) depending on kinetic parameters. The MFL phase diagram as well as a detailed description of the nonlinear oscillation regime are presented and some biological examples are discussed. The results emphasize the role of protein interactions in the function of genetic modules and the usefulness of modelling RNA dynamics explicitly.Comment: To be published in Physical Review

Static Rouse Modes and Related Quantities: Corrections to Chain Ideality in Polymer Melts

Following the Flory ideality hypothesis intrachain and interchain excluded volume interactions are supposed to compensate each other in dense polymer systems. Multi-chain effects should thus be neglected and polymer conformations may be understood from simple phantom chain models. Here we provide evidence against this phantom chain, mean-field picture. We analyze numerically and theoretically the static correlation function of the Rouse modes. Our numerical results are obtained from computer simulations of two coarse-grained polymer models for which the strength of the monomer repulsion can be varied, from full excluded volume (`hard monomers') to no excluded volume (`phantom chains'). For nonvanishing excluded volume we find the simulated correlation function of the Rouse modes to deviate markedly from the predictions of phantom chain models. This demonstrates that there are nonnegligible correlations along the chains in a melt. These correlations can be taken into account by perturbation theory. Our simulation results are in good agreement with these new theoretical predictions.Comment: 9 pages, 7 figures, accepted for publication in EPJ

Bound and resonance states of the nonlinear Schroedinger equation in simple model systems

The stationary nonlinear Schroedinger equation, or Gross-Pitaevskii equation, is studied for the cases of a single delta potential and a delta-shell potential. These model systems allow analytical solutions, and thus provide useful insight into the features of stationary bound, scattering and resonance states of the nonlinear Schroedinger equation. For the single delta potential, the influence of the potential strength and the nonlinearity is studied as well as the transition from bound to scattering states. Furthermore, the properties of resonance states for a repulsive delta-shell potential are discussed.Comment: 19 pages, 10 figure

Computed tomographic findings in incisors and canine teeth with equine odontoclastic tooth resorption and hypercementosis: a retrospective study in 115 Warmblood horses

Computed tomography (CT) has become a routine method to examine the equine skull. Its clinical use for the diagnosis of diseases of the incisors and canine teeth has not been reported so far. The goal of this study was to study the prevalence and relationship of single CT features and equine odontoclastic tooth resorption and hypercementosis (EOTRH) in equine incisors and canine teeth. In this descriptive retrospective study, helical CT studies of 115 warmblood horses of the age of 5 years or older examined between 2007 and 2020 for reasons unrelated to the incisors and canine teeth were included. Resorption in the crown or root, hypercementosis, widening of the periodontal space, clubbing of the root, lysis of the lamina dura, an abnormal pulp cavity and fracture of the root were recorded in all incisors and canine teeth. The length of the pulp cavity and the labial and lingual/palatal length of the enamel and root was measured in each incisor and canine tooth. Additionally, the angulation was assessed in each incisor. The variable EOTRH was defined based on the presence of resorptive lesions, hypercementosis and clubbing. In result median age of the included horses was 12 years (range, 5-29 years). With regard to the investigated population of horses, 44.3% of all horses had normal incisors whereas 55.7% of the horses had mild EOTRH changes in one incisor at least. Regarding the canine teeth, 54.7% of the horses had normal canine teeth whereas 43.3% horses had mild EOTRH in one canine tooth at least. With regard to all investigated teeth, 868 teeth (53.0%) were classified as normal, whereas 769 incisors and canine teeth (47.0%) showed at least one abnormal CT criterion. Clubbing of the root and hypercementosis were most common (37.1% and 22.7%, respectively) and EOTRH was present in 27.1% of all teeth. Mild changes were more common than moderate or severe abnormalities. In the lower jaw, hypercementosis and widening of the periodontal space at the anatomical root and apex of the root was significantly more frequent (p = 0.004 and 0.02), whereas clubbing of the root was more common in the upper jaw (p = 0.009). In canine teeth, resorption in the anatomical crown and anatomical root, widening of the periodontal space, clubbing and lysis of the lamina dura were significantly more common whereas hypercementosis was more common in incisors (p < 0.001). Frequency of certain CT changes significantly increased from central to middle and corner incisors. Severity of all single CT criteria as well as prevalence and severity of EOTRH significantly increased with age (r = 0.08-0.56). Linear forward and backward multivariate regression analysis confirmed a significant association between prevalence and severity of EOTRH and age, changes of the pulp cavity, widening of the periodontal space at the anatomical root and incisor group (central, middle, corner) (p = 0.01 - < 0.001). In conclusion computed tomographic changes of the incisors and canine teeth are common and age-related in warmblood horses. Therefore, treatment of EOTRH should not be based on diagnostic imaging alone, but always in combination with a thorough clinical examination

Modelling the Interactions of Soils, Climate, and Management for Grass Production in England and Wales

This study examines the effectiveness of a model called LINGRA-N-Plus to simulate the interaction of climate, soil and management on the green leaf and total dry matter yields of ryegrass in England and Wales. The LINGRA-N-Plus model includes modifications of the LINGRA-N model such as temperature- and moisture-dependent soil nitrogen mineralization and differential partitioning to leaves and stems with thermal time from the last harvest. The resulting model was calibrated against the green leaf and total grass yields from a harvest interval x nitrogen application experiment described by Wilman et al. (1976). When the LINGRA-N-Plus model was validated against total grass yields from nitrogen experiments at ten sites described by Morrison et al. (1980), its modelling efficiency improved greatly compared to the original LINGRA-N. High predicted yields, at zero nitrogen application, were related to soils with a high initial nitrogen content. The lowest predicted yields occurred at sites with low rainfall and shallow rooting depth; mitigating the effect of drought at such sites increased yields by up to 4 t ha−1. The results highlight the usefulness of grass models, such as LINGRA-N-Plus, to explore the combined effects of climate, soil, and management, like nitrogen application, and harvest intervals on grass productivity

Four Poynting Theorems

The Poynting vector is an invaluable tool for analysing electromagnetic problems. However, even a rigorous stress-energy tensor approach can still leave us with the question: is it best defined as \Vec{E} \cross \Vec{H} or as \Vec{D} \cross \Vec{B}? Typical electromagnetic treatments provide yet another perspective: they regard \Vec{E} \cross \Vec{B} as the appropriate definition, because \Vec{E} and \Vec{B} are taken to be the fundamental electromagnetic fields. The astute reader will even notice the fourth possible combination of fields: i.e. \Vec{D} \cross \Vec{H}. Faced with this diverse selection, we have decided to treat each possible flux vector on its merits, deriving its associated energy continuity equation but applying minimal restrictions to the allowed host media. We then discuss each form, and how it represents the response of the medium. Finally, we derive a propagation equation for each flux vector using a directional fields approach; a useful result which enables further interpretation of each flux and its interaction with the medium.Comment: 8 pages. Updated slightly from EJP versio

An analysis of fast photochemistry over high northern latitudes during spring and summer using in-situ observations from ARCTAS and TOPSE

Observations of chemical constituents and meteorological quantities obtained during the two Arctic phases of the airborne campaign ARCTAS (Arctic Research of the Composition of the Troposphere from Aircraft and Satellites) are analyzed using an observationally constrained steady state box model. Measurements of OH and HO2 from the Penn State ATHOS instrument are compared to model predictions. Forty percent of OH measurements below 2 km are at the limit of detection during the spring phase (ARCTAS-A). While the median observed-to-calculated ratio is near one, both the scatter of observations and the model uncertainty for OH are at the magnitude of ambient values. During the summer phase (ARCTAS-B), model predictions of OH are biased low relative to observations and demonstrate a high sensitivity to the level of uncertainty in NO observations. Predictions of HO2 using observed CH2O and H2O2 as model constraints are up to a factor of two larger than observed. A temperature-dependent terminal loss rate of HO2 to aerosol recently proposed in the literature is shown to be insufficient to reconcile these differences. A comparison of ARCTAS-A to the high latitude springtime portion of the 2000 TOPSE campaign (Tropospheric Ozone Production about the Spring Equinox) shows similar meteorological and chemical environments with the exception of peroxides; observations of H2O2 during ARCTAS-A were 2.5 to 3 times larger than those during TOPSE. The cause of this difference in peroxides remains unresolved and has important implications for the Arctic HOx budget. Unconstrained model predictions for both phases indicate photochemistry alone is unable to simultaneously sustain observed levels of CH2O and H2O2; however when the model is constrained with observed CH2O, H2O2 predictions from a range of rainout parameterizations bracket its observations. A mechanism suitable to explain observed concentrations of CH2O is uncertain. Free tropospheric observations of acetaldehyde (CH3CHO) are 2–3 times larger than its predictions, though constraint of the model to those observations is sufficient to account for less than half of the deficit in predicted CH2O. The box model calculates gross O3 formation during spring to maximize from 1–4 km at 0.8 ppbv d−1, in agreement with estimates from TOPSE, and a gross production of 2–4 ppbv d−1 in the boundary layer and upper troposphere during summer. Use of the lower observed levels of HO2 in place of model predictions decreases the gross production by 25–50%. Net O3 production is near zero throughout the ARCTAS-A troposphere, and is 1–2 ppbv in the boundary layer and upper altitudes during ARCTAS-B

T cell immune memory after covid-19 and vaccination

The T cell memory response is a crucial component of adaptive immunity responsible for limiting or preventing viral reinfection. T cell memory after infection with the SARS-CoV-2 virus or vaccination is broad, and spans multiple viral proteins and epitopes, about 20 in each individual. So far the T cell memory response is long lasting and provides a high level of cross reactivity and hence resistance to viral escape by variants of the SARS-CoV-2 virus, such as the omicron variant. All current vaccine regimens tested produce robust T cell memory responses, and heterologous regimens will probably enhance protective responses through increased breadth. T cell memory could have a major role in protecting against severe covid-19 disease through rapid viral clearance and early presentation of epitopes, and the presence of cross reactive T cells might enhance this protection. T cell memory is likely to provide ongoing protection against admission to hospital and death, and the development of a pan-coronovirus vaccine might future proof against new pandemic strains

Dynamical signatures of the vulcanization transition

Dynamical properties of vulcanized polymer networks are addressed via a Rouse-type model that incorporates the effect of permanent random crosslinks. The incoherent intermediate scattering function is computed in the sol and gel phases, and at the vulcanization transition between them. At any nonzero crosslink density within the sol phase Kohlrausch relaxation is found. The critical point is signalled by divergence of the longest time-scale, and at this point the scattering function decays algebraically, whereas within the gel phase it acquires a time-persistent part identified with the gel fraction.Comment: 4 page