Threshold-like Behaviour Research Articles

Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems.

Bacteria have adaptive immunity against viruses (phages) in the form of CRISPR-Cas immune systems. Currently, 6 types of CRISPR-Cas systems are known and the molecular study of three of these has revealed important molecular differences. It is unknown if and how these molecular differences change the outcome of phage infection and the evolutionary pressure the CRISPR-Cas systems faces. To determine the importance of these molecular differences, we model a phage outbreak entering a population defending exclusively with a type I/II or a type III CRISPR-Cas system. We show that for type III CRISPR-Cas systems, rapid phage extinction is driven by the probability to acquire at least one resistance spacer. However, for type I/II CRISPR-Cas systems, rapid phage extinction is characterized by an a threshold-like behaviour: any acquisition probability below this threshold leads to phage survival whereas any acquisition probability above it, results in phage extinction. We also show that in the absence of autoimmunity, high acquisition rates evolve. However, when CRISPR-Cas systems are prone to autoimmunity, intermediate levels of acquisition are optimal during a phage outbreak. As we predict an optimal probability of spacer acquisition 2 factors of magnitude above the one that has been measured, we discuss the origin of such a discrepancy. Finally, we show that in a biologically relevant parameter range, a type III CRISPR-Cas system can outcompete a type I/II CRISPR-Cas system with a slightly higher probability of acquisition.

Diagnostics of hot electrons leaving the ECR plasma sustained by the high-power gyrotron

Energy distribution of electrons in the electron-cyclotron resonance (ECR) discharge has a complicated shape as a function of various parameters that still remains unknown. Meanwhile, it is an important plasma characteristic. There are some methods and approaches, which give the possibility to measure or estimate the properties of the distribution. One of them, similar to the ion mass spectrometry [1], was used in this work to obtain the energy distribution of electrons escaping the magnetic confinement in the non-classical continuous ECR ion source with high (up to 50–100 W/cm3) specific energy input along with bremsstrahlung spectra. A threshold-like behaviour was discovered, which comprised of the bursts of energetic electrons, bremsstrahlung and, supposedly, the development of kinetic instabilities, once the energy input exceeds a certain level.

Duration invariance and intensity dependence of the human circadian system phase shifting response to brief light flashes.

The melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs) are characterized by a delayed off-time following the cessation of light stimulation. Here, we exploited this unusual physiologic property to characterize the exquisite sensitivity of the human circadian system to flashed light. In a 34 h in-laboratory between-subjects design, we examined phase shifting in response to variable-intensity (3–9500 photopic lux) flashes at fixed duration (2 ms; n = 28 participants) and variable-duration (10 µs–10 s) flashes at fixed intensity (2000 photopic lux; n = 31 participants). Acute melatonin suppression, objective alertness and subjective sleepiness during the flash sequence were also assessed. We find a dose–response relationship between flash intensity and circadian phase shift, with an indication of a possible threshold-like behaviour. We find a slight parametric relationship between flash duration and circadian phase shift. Consistent with prior studies, we observe no dose–response relationship to either flash intensity or duration and the acute impact of light on melatonin suppression, objective alertness or subjective sleepiness. Our findings are consistent with circadian responses to a sequence of flashes being mediated by rod or cone photoreceptors via ipRGC integration.

Influence of swift heavy ion irradiation on the photoluminescence of Si-nanoparticles and defects in SiO2

The influence of swift heavy ion (SHI) irradiation on the photoluminescence (PL) of silicon nanoparticles (SiNPs) and defects in SiO2-film is investigated. SiNPs were formed by implantation of 70 keV Si+ and subsequent thermal annealing to produce optically active SiNPs and to remove implantation-induced defects. Seven different ion species with energy between 3–36 MeV and fluence from 1011–1014 cm−2 were employed for irradiation of the implanted samples prior to the thermal annealing. Induced changes in defect and SiNP PL were characterized and correlated with the specific energy loss of the employed SHIs. We find that SHI irradiation, performed before the thermal annealing process, affects both defect and SiNP PL. The change of defect and SiNP PL due to SHI irradiation is found to show a threshold-like behaviour with respect to the electronic stopping power, where a decrease in defect PL and an anticorrelated increase in SiNP PL after the subsequent thermal annealing are observed for electronic stopping exceeding 3–5 keV nm−1. PL intensities are also compared as a function of total energy deposition and nuclear energy loss. The observed effects can be explained by ion track formation as well as a different type of annealing mechanisms active for SHI irradiation compared to the thermal annealing.

Pesticides and bees: Ecological-economic modelling of bee populations on farmland

Production of insect-pollinated crops typically relies on both pesticide use and pollination, leading to a potential conflict between these two inputs. In this paper we combine ecological modelling with economic analysis to investigate the effects of pesticide use on wild and commercial bees, whilst allowing farmers to partly offset the negative effects of pesticides on bee populations by creating more on-farm bee habitat. Farmers have incentives to invest in creating wild bee habitat to increase pollination inputs due to the contribution this makes to yields. However, the optimal allocation of on-farm habitat strongly depends on the negative effects of pesticides, with a threshold-like behaviour at a critical level of the impairment. When this threshold is crossed, the population of wild bees becomes locally extinct and their availability to pollinate breaks down. We show that availability of commercial bees masks this decrease in pollination services which would otherwise incentivise farmers to conserve the wild pollinator population. Indeed, if commercial bees are available, optimum profit may be achieved by providing no habitat at all for wild bees, and allowing these wild pollinators to go extinct.

Race, religion and the city: twitter word frequency patterns reveal dominant demographic dimensions in the United States

AbstractRecently, numerous approaches have emerged in the social sciences to exploit the opportunities made possible by the vast amounts of data generated by online social networks (OSNs). Having access to information about users on such a scale opens up a range of possibilities—from predicting individuals’ demographics and health status to their beliefs and political opinions—all without the limitations associated with often slow and expensive paper-based polls. A question that remains to be satisfactorily addressed, however, is how demography is represented in OSN content—that is, what are the relevant aspects that constitute detectable large-scale patterns in language? Here, we study language use in the United States using a corpus of text compiled from over half a billion geotagged messages from the online microblogging platform Twitter. Our intention is to reveal the most important spatial patterns in language use in an unsupervised manner and relate them to demographics. Our approach is based on Latent Semantic Analysis augmented with the Robust Principal Component Analysis methodology, which permits identification of the data’s main sources of variation with an automatic filtering of noise and outliers without influencing results by a priori assumptions. We find spatially correlated patterns that can be interpreted based on the words associated with them. The main language features can be related to slang use, urbanization, travel, religion and ethnicity, the patterns of which are shown to correlate plausibly with traditional census data. Apart from the standard measure of linear correlation, some relations seem to be better explained by Boolean implications, suggesting a threshold-like behaviour where demographic variables influence the users’ word use. Our findings validate the concept of demography being represented in OSN language use and show that the traits observed are inherently present in the word frequencies without any previous assumptions about the dataset. They therefore could form the basis of further research focusing on the evaluation of demographic data estimation from other big data sources, or on the dynamical processes that result in the patterns identified here.

Dominant mechanisms for the delivery of fine sediment and phosphorus to fluvial networks draining grassland dominated headwater catchments

Recent advances in monitoring technology have enabled high frequency, in-situ measurements of total phosphorus and total reactive phosphorus to be undertaken with high precision, whilst turbidity can provide an excellent surrogate for suspended sediment. Despite these measurements being fundamental to understanding the mechanisms and flow paths that deliver these constituents to river networks, there is a paucity of such data for headwater agricultural catchments. The aim of this paper is to deduce the dominant mechanisms for the delivery of fine sediment and phosphorus to an upland river network in the UK through characterisation of the temporal variability of hydrological fluxes, and associated soluble and particulate concentrations for the period spanning March 2012–February 2013. An assessment of the factors producing constituent hysteresis is undertaken following factor analysis (FA) on a suite of measured environmental variables representing the fluvial and wider catchment conditions prior to, and during catchment-wide hydrological events. Analysis indicates that suspended sediment is delivered to the fluvial system predominantly via rapidly responding pathways driven by event hydrology. However, evidence of complex, figure-of-eight hysteresis is observed following periods of hydrological quiescence, highlighting the importance of preparatory processes. Sediment delivery via a slow moving, probably sub-surface pathway does occur, albeit infrequently and during low magnitude events at the catchment outlet. Phosphorus is revealed to have a distinct hysteretic response to that of suspended sediment, with sub-surface pathways dominating. However, high magnitude events were observed to exhibit threshold-like behaviour, whereby activation and connection of usually disconnected depositional zones to the fluvial networks results in the movement of vast phosphorus fluxes. Multiple pathways are observed for particulate and soluble constituents, highlighting the challenges faced in mitigating the delivery of contaminant fluxes to headwater river systems.

Transient photoinduced ‘hidden’ phase in a manganite

Photoinduced phase transitions are of special interest in condensed matter physics because they can be used to change complex macroscopic material properties on the ultrafast timescale. Cooperative interactions between microscopic degrees of freedom greatly enhance the number and nature of accessible states, making it possible to switch electronic, magnetic or structural properties in new ways. Photons with high energies, of the order of electron volts, in particular are able to access electronic states that may differ greatly from states produced with stimuli close to equilibrium. In this study we report the photoinduced change in the lattice structure of a charge and orbitally ordered Nd(0.5)Sr(0.5)MnO(3) thin film using picosecond time-resolved X-ray diffraction. The photoinduced state is structurally ordered, homogeneous, metastable and has crystallographic parameters different from any thermodynamically accessible state. A femtosecond time-resolved spectroscopic study shows the formation of an electronic gap in this state. In addition, the threshold-like behaviour and high efficiency in photo-generation yield of this gapped state highlight the important role of cooperative interactions in the formation process. These combined observations point towards a 'hidden insulating phase' distinct from that found in the hitherto known phase diagram.

Superflow of resonantly driven polaritons against a defect

In the linear response approximation, coherently driven microcavity polaritons in the pump-only configuration are expected to satisfy the Landau criterion for superfluidity at either strong enough pump powers or small flow velocities. Here, we solve non-perturbatively the time dependent Gross-Pitaevskii equation describing the resonantly-driven polariton system. We show that, even in the limit of asymptotically large densities, where in linear response approximation the system satisfies the Landau criterion, the fluid always experiences a residual drag force when flowing through the defect. We illustrate the result in terms of the polariton lifetime being finite, finding that the equilibrium limit of zero drag can only be recovered in the case of perfect microcavities. In general, both the drag force exerted by the defect on the fluid, as well as the height of Cerenkov radiation, and the percentage of particles scattered by the defect, show a smooth crossover rather than a sharp threshold-like behaviour typical of superfluids which obey the Landau criterion.

Modelling subsurface drainage pathways in an artificial catchment

The relationship between rainfall and runoff in catchments is a nonlinear function largely controlled by hydrologically connected hillslope elements. In this study, we investigate material and geometrical hillslope properties determining connection of hillslope elements to form subsurface drainage pathways in an artificial catchment (Chicken Creek) and we examine the impact of the drainage pathway connectivity on the catchment runoff. We developed a three-dimensional model based on percolation theory to simulate the drainage pathways in the catchment and to quantify the contribution from subsurface flow paths to total catchment outflow. The simulations show that the degree of drainage pathway connectivity depends on small-scale variability of soil depth, soil hydraulic properties and topography. Additionally, connectivity was very sensitive to changes of soil water content in the catchment with dramatic change of subsurface flow for small changes in soil water content. This threshold-like behaviour of flow paths connectivity accounted for the sudden availability of a large amount of drainable water, postulating a nonlinear rainfall–runoff relationship as confirmed by first observations in the Chicken Creek catchment. The model reproduced subsurface flow patterns, which were indicated by soil moisture measurements and visual observations in the catchment.

Energy spike effects in ion-bombarded GaN

We study structural disorder in GaN bombarded at room temperature with 1.3 keV amu−1 PFn (n = 0, 2 and 4) cluster ions. Results are compared with our previous studies of irradiation with atomic ions of different masses. An algorithm for cascade density calculations that take into account the formation of subcascades is presented. Quantitative analysis of both new and previous data shows that an increase in the cascade density above a certain critical value results in a rapid increase in the rate of planar amorphization and the rate of damage buildup in the crystal bulk. Both such rates increase with decreasing sample temperature. This threshold-like behaviour suggests an important role of nonlinear energy spikes in the formation of stable implantation disorder in GaN. We also discuss the striking difference between cascade density effects in damage buildup in different semiconductors, including GaN, ZnO and Si.

Shear-induced breaking of large internal solitary waves

The stability properties of 24 experimentally generated internal solitary waves (ISWs) of extremely large amplitude, all with minimum Richardson number less than 1/4, are investigated. The study is supplemented by fully nonlinear calculations in a three-layer fluid. The waves move along a linearly stratified pycnocline (depth h2) sandwiched between a thin upper layer (depth h1) and a deep lower layer (depth h3), both homogeneous. In particular, the wave-induced velocity profile through the pycnocline is measured by particle image velocimetry (PIV) and obtained in computation. Breaking ISWs were found to have amplitudes (a1) in the range $a_1\,{>}\,2.24\sqrt{h_1h_2}(1+h_2/h_1)$, while stable waves were on or below this limit. Breaking ISWs were investigated for 0.27 < h2/h1 < 1 and 4.14 < h3/(h1 + h2) < 7.14 and stable waves for 0.36 < h2/h1 < 3.67 and 3.22 < h3/(h1 + h2) < 7.25. Kelvin–Helmholtz-like billows were observed in the breaking cases. They had a length of 7.9h2 and a propagation speed 0.09 times the wave speed. These measured values compared well with predicted values from a stability analysis, assuming steady shear flow with U(z) and ρ(z) taken at the wave maximum (U(z) horizontal velocity profile, ρ(z) density along the vertical z). Only unstable modes in waves of sufficient strength have the chance to grow sufficiently fast to develop breaking: the waves that broke had an estimated growth (of unstable modes) more than 3.3–3.7 times than in the strongest stable case. Evaluation of the minimum Richardson number (Rimin, in the pycnocline), the horizontal length of a pocket of possible instability, with wave-induced Ri < 14, (Lx) and the wavelength (λ), showed that all measurements fall within the range Rimin = −0.23Lx/λ + 0.298 ± 0.016 in the (Lx/λ, Rimin)-plane. Breaking ISWs were found for Lx/λ > 0.86 and stable waves for Lx/λ < 0.86. The results show a sort of threshold-like behaviour in terms of Lx/λ. The results demonstrate that the breaking threshold of Lx/λ = 0.86 was sharper than one based on a minimum Richardson number and reveal that the Richardson number was found to become almost antisymmetric across relatively thick pycnoclines, with the minimum occurring towards the top part of the pycnocline.

Threshold behaviour of a SIR epidemic model with age structure and immigration

We consider a SIR age-structured model with immigration of infectives in all epidemiological compartments; the population is assumed to be in demographic equilibrium between below-replacement fertility and immigration; the spread of the infection occurs through a general age-dependent kernel. We analyse the equations for steady states; because of immigration of infectives a steady state with a positive density of infectives always exists; however, a quasi-threshold theorem is proved, in the sense that, below the threshold, the density of infectives is close to 0, while it is away from 0, above the threshold; furthermore, conditions that guarantee uniqueness of steady states are obtained. Finally, we present some numerical examples, inspired by the Italian demographic situation, that illustrate the threshold-like behaviour, and other features of the stationary solutions and of the transient.

Assessing nested hydrological and hydrochemical behaviour of a mesoscale catchment using continuous tracer data

Summary High resolution (15 min) continuous environmental tracer data (conductivity, pH and derived Gran alkalinity) were used to investigate the hydrological functioning of the 233 km 2 Feugh catchment in NE Scotland and two of its nested sub-catchments (42 km 2 and 1 km 2 ). Over the 2003–2004 hydrological year, a fine resolution Gran alkalinity time series was derived and indicated detailed and subtle changes in stream chemistry. Diurnal variation in alkalinity and flow were observed under low flow conditions, attributed to instream-respiration and riparian-evapotranspiration respectively. At high flows, abrupt threshold-like behaviour was evident during storm events as hydrological sources in the acidic surface horizons of the catchment soils replace groundwater as the dominant source of runoff. Using Gran alkalinity to define end-member compositions, chemically-based hydrograph separations revealed that as catchment scale increased, groundwater contributions to annual runoff increased from 52 ± 10%, to 67 ± 6%, to 70 ± 11%. This is consistent with previous mean residence times (MRT) estimated from weekly δ 18 O data which respectively increased from 1.3–4.7 months −1 to 2.4–10.6 months −1 to 2.5–11.1 months −1 . Linking continuous tracer data with GIS interpretation of landscape characteristics increased the sophistication of our conceptual model of catchment processes. Increasing dominance of responsive peaty soils leads to more saturation overland flow, increased flashiness of runoff, reduced groundwater recharge, reduced MRTs and more marked diurnal variations in flow, which drive concomitant difference in hydrochemistry. Conversely, increased cover of free-draining soils and aquifers in drift, reduced flashiness, increased groundwater contributions and increased MRTs. It is proposed that high resolution tracer data, in conjunction with other measurements defining catchment characteristics, represent a resource and challenge to modellers if models can be produced which use tracer data, as well as physical parameters as objective functions in model evaluation.

Rapid electron internal transport barrier formation during magnetic shear reversal in fully non-inductive TCV discharges

The rapid formation of an electron internal transport barrier (eITB) is observed during a slow evolution (≃200 ms) from a centrally peaked to a hollow current density profile, while all external actuators remain constant. The time constant for the barrier formation appears to be shorter than the electron energy confinement time. The improved confinement associated with the barrier formation occurs first in a localized region off-axis. Then the effects propagate to inner and outer flux surfaces on a confinement time scale. The temporal and spatial localizations of the barrier formation suggest a threshold in the magnetic shear profile that triggers the onset of the eITB. The threshold-like behaviour can be attributed to the sudden appearance of a minimum q (or zero-shear) flux surface in the safety factor profile. Based on modelling of the current profile evolution using the ASTRA transport code, the appearance of the zero-shear flux surface is correlated with the temporal and spatial formation of the barrier.

Disorder induced modification of reflection and transmission spectra of a two-dimensionalphotonic crystal with an incomplete band-gap

Transmission and reflection of light in disordered two-dimensional photonic crystals with anincomplete photonic band-gap have been modelled for various levels of disorder. It is foundthat ballistic and scattered light display different behaviours as a function ofthe disorder parameter. For ballistic light, the dependence of the transmissioncoefficient on the disorder parameter exhibits a threshold-like behaviour, whereas thetransmission of scattered light increases rapidly for small disorder. Unlike forphotonic crystals with a complete band-gap, the minimum of the transmissionfor scattered light does not coincide with the centre of the photonic band-gap,and Fabry–Perot-type oscillations can be seen within the photonic band-gap.

Disorder-induced modification of the transmission of light through two-dimensionalphotonic crystals

Disordered two-dimensional photonic crystals with a complete photonic band-gap havebeen investigated. Transmission and reflection spectra have been modelled for both ballisticand scattered light. The density of states and electromagnetic field profiles ofdisorder-induced localized states have also been calculated, for various levels of disorder. Itis found that there is a threshold-like behaviour in the amount of disorder. Below thethreshold, it is seen that there is a vanishing probability of disorder-induced localized statesbeing introduced into the centre of the photonic band-gap, but that edge-states narrow theband-gap. Above the threshold, there is a non-zero probability of disorder-induced localizedstates throughout the photonic band-gap, and the modification of the transmissionand reflection spectra due to disorder rapidly increases with increasing disorder.

Mesostructured dye-doped titanium dioxide for micro-optoelectronic applications.

Optically transparent, mesostructured titanium dioxide thin films were fabricated using an amphiphilic poly(alkylene oxide) block copolymer template in combination with retarded hydrolysis of a titanium isopropoxide precursor. Prior to calcination, the films displayed a stable hexagonal mesophase and high refractive indices (1.5 to 1.6) relative to mesostructured silica (1.43). After calcination, the hexagonal mesophase was retained with surface areas > 300 m2 g-1. The dye Rhodamine 6G (commonly used as a laser dye) was incorporated into the copolymer micelle during the templating process. In this way, novel dye-doped mesostructured titanium dioxide films were synthesised. The copolymer not only directs the film structure, but also provides a solubilizing environment suitable for sustaining a high monomer-to-aggregate ratio at elevated dye concentrations. The dye-doped films displayed optical thresholdlike behaviour characteristic of amplified spontaneous emission. Soft lithography was successfully applied to micropattern the dye-doped films. These results pave the way for the fabrication and demonstration of novel microlaser structures and other active optical structures. This new, high-refractive index, mesostructured, dye-doped material could also find applications in areas such as optical coatings, displays and integrated photonic devices.

An analysis of hot deformation of an Al–Cu–Mg alloy produced by powder metallurgy

The high-temperature plasticity of a 2014 aluminium alloy produced by powder metallurgy was investigated in a wide range of temperatures and strain rates. When the strain rate was plotted as a function of stress (either peak flow stress in torsion, or applied stress in tensile creep), the alloy exhibited the same threshold-like behaviour observed in similar materials. The microstructure of representative torsioned samples was analysed in a transmission electron microscope (TEM) and the characteristics of particles and precipitate distribution were estimated. The dependence on stress and temperature was analysed by means of the conventional constitutive equations used for describing the hot-working behaviour and by means of a modified form of the sinh-equation, where the stress was substituted by an effective stress i.e. by the difference between the actual stress and a threshold stress. This temperature-dependent threshold stress was found to be a constant fraction (15%) of the Orowan stress generated by the dispersion of alumina particles and of precipitated intermetallic phases.

Interpretation of creep behaviour of dispersion-strengthened Al–Fe–V–Si alloys in terms of detachment mechanisms: an overview

Creep data for different Al–Fe–V–Si alloys and composites were analysed using the detachment model. Between 673 and 723 K, the materials exhibited a typical threshold-like behaviour but the magnitude of the threshold stress was found to change from one material to another. The threshold stress was ascribed to the particle-dislocation interaction; in particular, the Rösler–Arzt model for athermal detachment of dislocations from interacting particles was considered. The different values of the threshold stress and its dependence on temperature were thus related to the magnitude of the k r parameter and to the initial size of the dispersoids. The disappearance of the threshold stress observed when testing a composite at temperatures above 723 K, as suggested in the literature, was explained in terms of transition from athermal to thermally activated detachment of dislocations from the particles; however, it was concluded that this mechanism becomes rate-controlling only for low applied stresses, i.e. when the applied stress is lower than the athermal-detachment stress, as originally postulated by Rösler and Arzt. When the applied stress exceeds the athermal-detachment stress, the latter becomes rate-controlling, irrespective of the testing temperature.