Epidemics in Networks of Spatially Correlated Three-dimensional Root Branching Structures

Using digitized images of the three-dimensional, branching structures for root systems of bean seedlings, together with analytical and numerical methods that map a common 'SIR' epidemiological model onto the bond percolation problem, we show how the spatially-correlated branching structures of plant roots affect transmission efficiencies, and hence the invasion criterion, for a soil-borne pathogen as it spreads through ensembles of morphologically complex hosts. We conclude that the inherent heterogeneities in transmissibilities arising from correlations in the degrees of overlap between neighbouring plants, render a population of root systems less susceptible to epidemic invasion than a corresponding homogeneous system. Several components of morphological complexity are analysed that contribute to disorder and heterogeneities in transmissibility of infection. Anisotropy in root shape is shown to increase resilience to epidemic invasion, while increasing the degree of branching enhances the spread of epidemics in the population of roots. Some extension of the methods for other epidemiological systems are discussed.Comment: 21 pages, 8 figure

Extracting the time-dependent transmission rate from infection data via solution of an inverse ODE problem

The transmission rate of many acute infectious diseases varies significantly in time, but the underlying mechanisms are usually uncertain. They may include seasonal changes in the environment, contact rate, immune system response, etc. The transmission rate has been thought difficult to measure directly. We present a new algorithm to compute the time-dependent transmission rate directly from prevalence data, which makes no assumptions about the number of susceptible or vital rates. The algorithm follows our complete and explicit solution of a mathematical inverse problem for SIR-type transmission models. We prove that almost any infection profile can be perfectly fitted by an SIR model with variable transmission rate. This clearly shows a serious danger of overfitting such transmission models. We illustrate the algorithm with historic UK measles data and our observations support the common belief that measles transmission was predominantly driven by school contacts

Functional significance may underlie the taxonomic utility of single amino acid substitutions in conserved proteins

We hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of ß-tubulin. Our analysis identified one amino acid substitution—ß-tubulin F224—which was highly lineage specific. Investigation of ß-tubulin for other phylogenetically restricted amino acids identified several with apparent specificity for well-defined phylogenetic groups. Intriguingly, none showed specificity for “supergroups” other than the unikonts. To understand why, we analysed the ß-tubulin Neighbor-Net and demonstrated a fundamental division between core ß-tubulins (plant-like) and divergent ß-tubulins (animal and fungal). F224 was almost completely restricted to the core ß-tubulins, while divergent ß-tubulins possessed Y224. Thus, our specific example offers insight into the restrictions associated with the co-evolution of ß-tubulin during the radiation of eukaryotes, underlining a fundamental dichotomy between F-type, core ß-tubulins and Y-type, divergent ß-tubulins. More broadly our study provides proof of principle for the taxonomic utility of critical amino acids in the active sites of conserved proteins

ENSO and the Carbon Cycle

This is the author accepted manuscript. The final version is available from the American Geophysical Union via the DOI in this recordObservational studies of atmospheric CO2, land ecosystems, and ocean processes show that variability in the carbon cycle is closely related with ENSO. Years with a warm anomaly in the tropical Pacific show a faster CO2 rise due to weaker land carbon sinks, particularly in the tropics, with a partial offset by stronger net uptake by oceans. The opposite happens in years with cool Pacific SST anomalies. This relationship holds for small ENSO SST anomalies as well as large ones and is robust enough for the annual CO2 growth rate anomaly to be highly predictable on the basis of SST observations and forecasts. Generally, variability in the land‐atmosphere carbon flux is mainly driven by physiological processes (photosynthesis and/or respiration), with a smaller contribution from fire. Fire was important in the 1997–1998 El Niño, making a major contribution to the CO2 rise, which can be viewed as anthropogenic in nature since the ignition was caused by humans. However, in the 2015–2016 El Niño event, the change in land carbon flux was mainly due to physiological processes, particularly reduced productivity. In the oceans, El Niño conditions involve decreased upwelling of carbon in the equatorial Pacific due to a weakening of the trade winds, causing this region to become a weaker sink of CO2, or near neutral if the El Niño event is strong. The year‐to‐year variations in the rate of CO2 rise can be successfully reconstructed and predicted on the basis of sea surface temperatures in the Pacific. ENSO‐CO2 relationships may also provide an emergent constraint on the strength of climate‐carbon cycle feedbacks on future anthropogenic climate change

Spin-glasses in optical cavity

Recent advances in nanofabrication and optical control have garnered tremendous interest in multi-qubit-cavity systems. Here we analyze a spin-glass version of such a nanostructure, solving analytically for the phase diagrams in both the matter and radiation subsystems in the replica symmetric regime. Interestingly, the resulting phase transitions turn out to be tunable simply by varying the matter-radiation coupling strength

The effects of CO2, climate and land-use on terrestrial carbon balance, 1920-1992: An analysis with four process-based ecosystem models

The concurrent effects of increasing atmospheric CO2 concentration, climate variability, and cropland establishment and abandonment on terrestrial carbon storage between 1920 and 1992 were assessed using a standard simulation protocol with four process-based terrestrial biosphere models. Over the long-term(1920–1992), the simulations yielded a time history of terrestrial uptake that is consistent (within the uncertainty) with a long-term analysis based on ice core and atmospheric CO2 data. Up to 1958, three of four analyses indicated a net release of carbon from terrestrial ecosystems to the atmosphere caused by cropland establishment. After 1958, all analyses indicate a net uptake of carbon by terrestrial ecosystems, primarily because of the physiological effects of rapidly rising atmospheric CO2. During the 1980s the simulations indicate that terrestrial ecosystems stored between 0.3 and 1.5 Pg C yr−1, which is within the uncertainty of analysis based on CO2 and O2 budgets. Three of the four models indicated (in accordance with O2 evidence) that the tropics were approximately neutral while a net sink existed in ecosystems north of the tropics. Although all of the models agree that the long-term effect of climate on carbon storage has been small relative to the effects of increasing atmospheric CO2 and land use, the models disagree as to whether climate variability and change in the twentieth century has promoted carbon storage or release. Simulated interannual variability from 1958 generally reproduced the El Niño/Southern Oscillation (ENSO)-scale variability in the atmospheric CO2 increase, but there were substantial differences in the magnitude of interannual variability simulated by the models. The analysis of the ability of the models to simulate the changing amplitude of the seasonal cycle of atmospheric CO2 suggested that the observed trend may be a consequence of CO2 effects, climate variability, land use changes, or a combination of these effects. The next steps for improving the process-based simulation of historical terrestrial carbon include (1) the transfer of insight gained from stand-level process studies to improve the sensitivity of simulated carbon storage responses to changes in CO2 and climate, (2) improvements in the data sets used to drive the models so that they incorporate the timing, extent, and types of major disturbances, (3) the enhancement of the models so that they consider major crop types and management schemes, (4) development of data sets that identify the spatial extent of major crop types and management schemes through time, and (5) the consideration of the effects of anthropogenic nitrogen deposition. The evaluation of the performance of the models in the context of a more complete consideration of the factors influencing historical terrestrial carbon dynamics is important for reducing uncertainties in representing the role of terrestrial ecosystems in future projections of the Earth system

The CRESST Experiment: Recent Results and Prospects

The CRESST experiment seeks hypothetical WIMP particles that could account for the bulk of dark matter in the Universe. The detectors are cryogenic calorimeters in which WIMPs would scatter elastically on nuclei, releasing phonons. The first phase of the experiment has successfully deployed several 262 g sapphire devices in the Gran Sasso underground laboratories. A main source of background has been identified as microscopic mechanical fracturing of the crystals, and has been eliminated, improving the background rate by up to three orders of magnitude at low energies, leaving a rate close to one count per day per kg and per keV above 10 keV recoil energy. This background now appears to be dominated by radioactivity, and future CRESST scintillating calorimeters which simultaneously measure light and phonons will allow rejection of a great part of it.Comment: To appear in the proceedings of the CAPP2000 Conference, Verbier, Switzerland, July, 2000 (eds J. Garcia-Bellido, R. Durrer, and M. Shaposhnikov

Assessment of the nano-mechanical properties of healthy and atherosclerotic coronary arteries by atomic force microscopy.

Nano-indentation techniques might be better equipped to assess the heterogeneous material properties of plaques than macroscopic methods but there are no bespoke protocols for this kind of material testing for coronary arteries. Therefore, we developed a measurement protocol to extract mechanical properties from healthy and atherosclerotic coronary artery tissue sections. Young's modulus was derived from force-indentation data. Metrics of collagen fibre density were extracted from the same tissue, and the local material properties were co-registered to the local collagen microstructure with a robust framework. The locations of the indentation were retrospectively classified by histological category (healthy, plaque, lipid-rich, fibrous cap) according to Picrosirius Red stain and adjacent Hematoxylin & Eosin and Oil-Red-O stains. Plaque tissue was softer (p < 0.001) than the healthy coronary wall. Areas rich in collagen within the plaque (fibrous cap) were significantly (p < 0.001) stiffer than areas poor in collagen/lipid-rich, but less than half as stiff as the healthy coronary media. Young's moduli correlated (Pearson's ρ = 0.53, p < 0.05) with collagen content. Atomic force microscopy (AFM) is capable of detecting tissue stiffness changes related to collagen density in healthy and diseased cardiovascular tissue. Mechanical characterization of atherosclerotic plaques with nano-indentation techniques could refine constitutive models for computational modelling

Stationary waves in a superfluid exciton gas in quantum Hall bilayers

Stationary waves in a superfluid magnetoexciton gas in nu = 1 quantum Hall bilayers are considered. The waves are induced by counter-propagating electrical currents that flow in a system with a point obstacle. It is shown that stationary waves can emerge only in imbalanced bilayers in a certain diapason of currents. It is found that the stationary wave pattern is modified qualitatively under a variation of the ratio of the interlayer distance to the magnetic length d/l. The advantages of use graphene-dielectric-graphene sandwiches for the observation of stationary waves are discussed. We determine the range of parameters (the dielectric constant of the layer that separates two graphene layers and the ratio d/l) for which the state with superfluid magnetoexcitons can be realized in such sandwiches. Typical stationary wave patterns are presented as density plotsComment: 17 pages, 8 figure

Two aspects of decadal ENSO variability modulating the long-term global carbon cycle

The El Niño–Southern Oscillation (ENSO) drives variations in terrestrial carbon fluxes by affecting the terrestrial ecosystem via atmospheric teleconnections and thus plays an important role in interannual variability of the global carbon cycle. However, we lack such knowledge on decadal time scales, that is, how the carbon cycle can be affected by decadal variations of ENSO characteristics. Here we examine how, and by how much, decadal ENSO variability affects decadal variability of the global carbon cycle by analyzing a 1,801‐year preindustrial control simulation. We identify two different aspects, together explaining ~36% of the decadal variations in the global carbon cycle. First, climate variations induced by decadal ENSO‐like variability regulate terrestrial carbon flux and hence atmospheric CO2 on decadal time scales. Second, decadal changes in the asymmetrical response of the terrestrial ecosystem, resulting from decadal modulation of ENSO amplitude and asymmetry, rectify the background mean state, thereby generating decadal variability of land carbon fluxes